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The European Research Network on Signal Transduction (ERNEST): Toward a Multidimensional Holistic Understanding of G Protein-Coupled Receptor Signaling
- Martha E. Sommer*Martha E. Sommer*Email: [email protected]Institute of Medical Physics and Biophysics, Charité−Universitätsmedizin Berlin, Berlin, 10117, GermanyMax Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, GermanyMore by Martha E. Sommer
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- Jana SelentJana SelentResearch Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM) - Pompeu Fabra University (UPF), Barcelona, 08003, SpainMore by Jana Selent
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- Jens CarlssonJens CarlssonScience for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 752 36, SwedenMore by Jens Carlsson
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- Chris De Graaf
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- David E. GloriamDavid E. GloriamDepartment of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, 1017, DenmarkMore by David E. Gloriam
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- Gyorgy M. KeseruGyorgy M. KeseruMedicinal Chemistry Research Group, Research Center for Natural Sciences (RCNS), Budapest, H-1117, HungaryMore by Gyorgy M. Keseru
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- Mickey KosloffMickey KosloffDepartment of Human Biology, University of Haifa, Haifa, 3498838, IsraelMore by Mickey Kosloff
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- Stefan MordalskiStefan MordalskiDepartment of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, 1017, DenmarkDepartment of Medicinal Chemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, Krakow, 31-343, PolandMore by Stefan Mordalski
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- Aurelien Rizk
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- Mette M. RosenkildeMette M. RosenkildeLaboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK 2200, DenmarkMore by Mette M. Rosenkilde
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- Eddy SoteloEddy SoteloCentro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS) and Facultade de Farmacia. Universidade de Santiago de Compostela, Santiago de compostela, 15782, SpainMore by Eddy Sotelo
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- Johanna K. S. TiemannJohanna K. S. TiemannInstitute for Medical Physics and Biophysics, Leipzig University, Leipzig, 04109, GermanyLinderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Kobenhavn, 2200, DenmarkMore by Johanna K. S. Tiemann
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- Andrew TobinAndrew TobinThe Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, U.K.More by Andrew Tobin
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- Nina VardjanNina VardjanLaboratory of Neuroendocrinology-Molecular Cell Physiology, Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Ljubljana, 1000, SloveniaLaboratory of Cell Engineering, Celica Biomedical, Ljubljana, 1000, SloveniaMore by Nina Vardjan
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- Maria Waldhoer
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- Peter Kolb*Peter Kolb*Email: [email protected]Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, 35039, GermanyMore by Peter Kolb
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Abstract
G protein-coupled receptors (GPCRs) are intensively studied due to their therapeutic potential as drug targets. Members of this large family of transmembrane receptor proteins mediate signal transduction in diverse cell types and play key roles in human physiology and health. In 2013 the research consortium GLISTEN (COST Action CM1207) was founded with the goal of harnessing the substantial growth in knowledge of GPCR structure and dynamics to push forward the development of molecular modulators of GPCR function. The success of GLISTEN, coupled with new findings and paradigm shifts in the field, led in 2019 to the creation of a related consortium called ERNEST (COST Action CA18133). ERNEST broadens focus to entire signaling cascades, based on emerging ideas of how complexity and specificity in signal transduction are not determined by receptor–ligand interactions alone. A holistic approach that unites the diverse data and perspectives of the research community into a single multidimensional map holds great promise for improved drug design and therapeutic targeting.
SPECIAL ISSUE
This article is part of the
The European Cooperation in Science and Technology (COST), founded in 1971, funds research networks (COST Actions) created by researchers themselves to address specific and significant challenges in their respective fields. COST supports networking activities, e.g. conferences, training schools, international exchange of investigators between research groups, dissemination, and communication activities. COST Actions are highly interdisciplinary, open to new participants throughout their lifetime of 4 years, and active in promoting early career investigators and investigators from less research-intensive countries. Hence, COST plays a key role in stimulating international cooperation that pushes scientific progress and benefits a diverse community of researchers. For more information, see: https://www.cost.eu.
The importance of research on G protein-coupled receptor (GPCR) signal transduction is known and appreciated by most in the biomedical field. Over one-third of all prescribed drugs target a GPCR, (1) which is not surprising considering the substantial number of GPCRs expressed in the human body and their prevalence in mediating signal transduction in nearly every cell. Since the first crystal structure of a GPCR (2) was published in the year 2000, there has been intense activity elucidating how these receptors work on the molecular level. The field has benefited immensely from a blossoming of structural data on different GPCRs in various states of activation, bound to different types of ligands and/or to intracellular binding partners. (3−5) Currently, the “resolution revolution” (6) in cryo-electron microscopy is rapidly producing unprecedented insights into the structures of GPCRs in native-like and functionally relevant states and complexes. (7,8)
Simultaneous to these advancements, strategies for structure-based GPCR drug design are moving in an exciting new direction, based on the discovery that different ligands can bind to the same receptor yet stimulate the association of different effector proteins to different extents. These concepts of biased agonism and the broadly more general functional selectivity (discussed more below) open significant possibilities for creating more effective drugs that have desired therapeutic effects while avoiding deleterious side-effects. Indeed, examples of such biased GPCR ligands for improved treatment of various diseases have already been identified and tested in clinical trials. (9) The potential of signaling pathway-specific drugs to improve human health worldwide cannot be understated. Despite this fact, as a field we still know very little about the mechanisms governing ligand bias and functional selectivity. To explain these phenomena, multiple approaches that encompass a wider perspective including information on where and when signaling events take place—while taking into account the unique environment inside different cell types—is required. Moreover, recent studies cast doubt on key established dogmas underlying ligand bias and functional selectivity. As a field, we stand at a critical turning point and must re-evaluate our assumptions and seek innovative and interdisciplinary approaches to understand the mechanisms governing GPCR signal transduction. Our efforts at designing better drugs and therapeutics will be severely hampered until we do so.
In this perspective piece, we introduce the recently launched COST (1) Action CA18133 “European Research Network on Signal Transduction” (ERNEST), the primary goal of which is to address these challenges faced by the research community. We describe the origins of ERNEST and how these roots led to a more holistic approach to understand GPCR signal transduction. We outline the specific objectives of ERNEST and how these will be met by the large and diverse community of researchers that compose the Network. We discuss the current state of knowledge in the field, the major unresolved questions, and our reasoning why our planned approach holds the best promise for untangling these issues. Finally, we provide an outlook of the anticipated long-lasting impacts of ERNEST on science and society.
GLISTEN and the Dawn of ERNEST
ARTICLE SECTIONS
Launched in 2013, the COST Action CM1207 GLISTEN (GPCR-Ligand Interactions, Structures, and Transmembrane Signaling: a European Research Network) was dedicated to deepening the understanding of GPCRs, especially with regard to the receptor activation mechanism, ligand binding, and effects of the membrane and other interaction partners on GPCR signaling. A central motivation of GLISTEN was to utilize this information to identify and design chemical modulators of GPCR signaling. In line with this focus, many pharmacologists, structure-based drug designers, and computational and medicinal chemists, joined the network early on. As the network grew, membership became more diverse as those with other perspectives in structural and cell biology, (patho)physiology, and translational medicine became aware of GLISTEN. Recruitment and diversification were made possible by decentralization of semiannual meeting organization. Local organizers were free to designate the thematic focus of their respective meetings according to their own research interests and perspectives. Hence, a wide variety of topics in the GPCR field was covered in the course of eight GLISTEN meetings. The trajectory went from a focus on computational methods at the inaugural meeting in Warsaw (2013), (10) followed by meetings with emphasis on biophysics, structural biology, and drug discovery in Barcelona (2014), (11) Budapest (2014), (12) and Allschwil (2015), (13) to meetings focused on medicinal chemistry and pharmacology in Amsterdam (2015), (14) Erlangen (2016), (15) and Prague (2016) (16) to more (patho)physiological aspects at the last meeting in Porto, Portugal (2017). (17) GLISTEN meetings were put together by enthusiastic local organizers representing different academic institutes and companies in Europe (see Acknowledgments). Notably, several industry partners were closely involved in scientific program development and hosting companies to stimulate and integrate academic and biotech/pharmaceutical drug discovery cooperation in GLISTEN. GPCR research training was further advanced by a series of workshops and training schools, including GPCR Computational Chemistry Workshops in Warsaw (2013) (Computer-Aided Drug Design, Molecular Dynamics, Protein Homology Modeling, Structural Chemogenomics and Chemoinformatics), GPCRdb Structural Bioinformatics tutorials at every GLISTEN meeting from 2013 to 2017, a training school on GPCR Fragment-Based Drug Discovery (FBDD), and Molecular Pharmacology in Budapest (2014), a GLISTEN-Lorentz Workshop in Leiden (2014) on in vitro to in vivo GPCR biology, a workshop on GPCR Research Valorization in Amsterdam (2015), and contributions of GLISTEN researchers at the Biophysics Training School in Croatia in 2016. (18)
The eventual composition of the network (more than 200 research groups from 31 countries) fulfilled the main purpose of GLISTEN to connect researchers and thereby enable cross-disciplinary cooperation. In addition, information exchange was promoted by cross-border exchanges of investigators between laboratories and training schools that connected experts and novices. The strategies employed by GLISTEN in its activities were highly successful at fostering collaborative research, in particular between experimental and theoretical groups, and ultimately provided valuable examples for similar consortia. Many leading experts of the GPCR field in Europe and worldwide, as well as the key pharmaceutical companies, were regular participants at GLISTEN events. One significant indicator of the importance of GLISTEN to the research community was the popularity of the semiannual meetings. Meetings were often oversubscribed within hours of the opening of online registration, most notably for the meeting in Erlangen that featured Nobel laureate Brian Kobilka as keynote speaker.
GLISTEN formally came to an end in 2017, yet its many successes are still being realized. First, more than 65 joint publications stemming from collaborations established within the network have been released. Notable GLISTEN publications are cited here. (19−24) In addition, a multitude of joint grants for research funding was acquired by network members, many of which will continue to produce significant scientific findings in the coming years (e.g., Oncornet 2.0 (25) and PSYBIAS (26,27)). Technology and know-how were spread by GLISTEN-sponsored exchanges of investigators between research groups in different countries and training schools, and the impact of this dissemination will continue to benefit diverse groups and individuals for a long time to come. Relatedly, GLISTEN positively influenced the careers of many early career investigators, which will serve to strengthen the future scientific output of the field. Last but certainly not least, GLISTEN pushed the development and use of GPCR-focused web-based databases and tools for the benefit of the international research community. GPCRdb, which was originally headed by Gert Vriend at the EMBL in Heidelberg, Germany, (28) relocated to the group of David Gloriam at the University of Copenhagen, Denmark in 2013. Several investigator-exchanges and the contributions of GLISTEN members helped this database to grow to contain GPCR reference data, visualization/analysis suites, and tools to design new experiments. (1,21,29−31−33) GLISTEN also spurred the creation of GPCRmd, an online repository and visualization platform for molecular dynamics (MD) simulation data and their analysis. This database arose from the need to organize and standardize this information including experimental setups/protocols and to provide intuitive analysis tools. By these means, GPCRmd promotes transparency, consistency, and reproducibility in the field of GPCR dynamics and also facilitates data exchange between GPCR scientists from different disciplines. (24)
Well before the official end of COST funding, the inclusiveness and influence of GLISTEN drove an intense community-wide desire to evolve a new COST Action. At the same time, developments in the field made clear that in order to meet current challenges, a wider perspective must be taken (explained in detail below). Hence, ERNEST came into existence, continuing the excellent tradition of GLISTEN and leading the field in an exciting new direction.
Unresolved Questions in Signal Transduction
ARTICLE SECTIONS
To survive and reproduce, all living cells must be able to sense their environments and respond in an appropriate way. Nature accomplishes this task by signal transduction, the process of passing external stimuli into and through the cell in order to induce cellular responses. Every signaling pathway essentially consists of a series of macromolecular interactions, and the signal is carried through the chain of interactions by biochemical events (e.g., changes in protein structure, association or dissociation of small molecules, or chemical modification of proteins). Most signaling pathways consist of a transmembrane receptor protein that binds an extracellular ligand (e.g., small molecule, peptide, or ion). This event triggers the binding of intracellular effector proteins that then produce second messengers, usually small molecules or protein modifications, which activate the next level of effector proteins. Each molecular interaction along a pathway can be considered a node at which the signal can be modulated and amplified, and different signaling cascades can consist of any number of nodes.
The spectrum of stimuli encountered by cells is both sizable and diverse, as is the number and type of cellular responses elicited by these stimuli. Yet, remarkably, signal transduction systems use a relatively limited repertoire of intracellular signaling components. This small number of effector proteins nevertheless enables a cellular signaling apparatus that is flexible and versatile. Versatility is achieved by modulation at the molecular, spatial, and temporal levels of the macromolecular interactions at each node in the pathway. In effect, a limited number of nodes, each with several alternative downstream pathways, can give rise to a vast number of distinct signaling pathways. Although versatile and complex, the biological role of signal transduction demands specificity and precision in signaling. This is, in part, achieved through a large number of receptors (about 1000 GPCRs (34)), each of which binds only one or a few endogenous ligands.
On the atomic level, the receptor is a dynamic structure that exists in different conformations or states, and ligand binding enhances the presence of some receptor states over others. States derived from experimental structural determination techniques are usually described as either active or inactive, depending on whether they can couple to effectors or not. Moreover, ligands can selectively stabilize receptor states that preferentially interact with certain primary effectors over others, a concept called biased agonism. Put another way, different biased ligands can stimulate distinct signaling pathways with different efficacies, a concept also referred to as functional selectivity. Biased agonists differentially influence the conformational dynamics of GPCRs, (35−38) yet it is not fully understood how these signals control interactions with effector proteins and their downstream cellular functions.
The influence of molecular, temporal, and spatial factors is widely appreciated in the field and actively discussed. (39−43) However, the underlying mechanisms by which these factors and the cellular environment modulate signal transduction remain unexplained. A few recent studies have approached this gap in knowledge by using experimental or computational systems. (44,45) However, in order to progress as a field toward molecular modulators that have predictable and reproducible effects in living cells (and eventually patients), the field requires a detailed map of signal transduction that takes into account all known factors that influence pathway selectivity. To build such a holistic multidimensional map, diverse types of data must be integrated in a way to allow mechanistic insight and formulation of general principles that govern signal transduction modulation in different cell types. This ambitious endeavor, which is out of reach for individual research groups and smaller research consortia, now forms a key objective of ERNEST. The network is in a unique position to harness the diverse data and expertise of hundreds of researchers in different disciplines.
There is an urgent need for a holistic mapping of signal transduction. Signal transduction plays a ubiquitous and critical role in normal physiology, and aberrations in pathways controlled by GPCRs lead to disease. Currently many research groups are unravelling signaling pathways that contribute to different disease states, and there is great excitement for the promise of biased ligands to treat these diseases more effectively and with fewer side effects. For example, ligands that promote sustained G protein signaling from β-adrenergic and angiotensin receptors lead to deleterious effects on the heart, while those that stimulate arrestin activity bring many cardioprotective effects. (46) In the case of the dopamine D2 receptor, drug candidates for the treatment of schizophrenia are being developed that selectively antagonize arrestin activity (leading to antipsychotic effects) while still promoting G protein signaling and thus avoiding motoric side effects. (47−49) For the opioid receptors, many academic research groups and companies have sought biased agonists, based on the belief that analgesic effects are supported by G protein-signaling, while unpleasant side-effects (e.g., respiratory depression and constipation) arise from arrestin-mediated effects. (50,51) A few such G protein-biased agonists have shown promise as potential drug candidates. (50,52) However, recent publications cast doubt on whether some of these drug candidates are actually biased, (53,54) and moreover, on whether arrestin activity at opioid receptors is responsible for side-effects. (55,56) The developing controversies in biased agonism at opioid receptors illustrate our significant gaps in knowledge in GPCR signal transduction, (57,53) often exacerbated by inconsistent or incorrectly applied quantitative pharmacology, (58,59) that undermine efforts to translate candidate drugs into the clinic. (60)
Objectives of ERNEST
ARTICLE SECTIONS
The main purpose of ERNEST is to establish and support a diverse network of signal transduction investigators through regular meetings, training schools, cross-border research group exchanges, and other dissemination activities. ERNEST promotes communication, knowledge exchange, and cooperation between scientists from different training levels, disciplines, institutions, and countries to address unresolved questions in signal transduction. Specific points to be addressed are described below.
Clarification of Biased Agonism and Functional Selectivity
The ability of certain ligands to elicit distinct cellular responses is broadly referred to as functional selectivity, the first determinate of which is the receptor–ligand interaction. Biased agonism, where certain GPCR conformations are preferentially stabilized that recruit certain effector proteins, can certainly influence the functional selectivity of a ligand. However, many other factors have significant influence over the signaling outcome, including allosteric modulation, membrane environment, crosstalk, intracellular location, and cell type, among others. (58) Biased agonism at GPCRs, and its specific influence on functional selectivity, is widely discussed in the field. (59,61−63) However, there is much confusion about the precise definition of biased agonism and how it relates to functional selectivity. The field requires community-wide accepted methods to assess and report ligand bias in GPCR signaling, and to distinguish signaling bias (i.e., functional selectivity) from bias in terms of preferential receptor coupling to intracellular proteins. For example, most studies report bias by comparing the relative abilities of different ligands to stimulate activation of different G proteins and/or arrestin recruitment. Since these events are measured experimentally in different ways, often using indirect readouts at different time points and in different cell types, clear conclusions and comparisons to other studies are neither possible nor sound. Another fundamental issue is the choice of reference ligands for each GPCR, and whether endogenous ligands should preferentially be used as reference, since they themselves might be biased. Moreover, the widely accepted paradigm of arrestin as a GPCR signal transducer in its own right is being re-evaluated in recent publications, (64−66) which complicates the interpretation of “arrestin-biased” ligands. ERNEST, in coordination with other authoritative organisations and groups, is addressing these issues by gathering leading experts to constructively dissect the root issues from their diverse perspectives and then publish collective strategies for resolving discrepancies by suggesting best practices. In addition, ERNEST will push the development of better methods, technologies, and database resources for evaluating biased agonism and, eventually, functional selectivity.
Multidimensional Signaling Map
As described above, future development of signaling pathway-specific molecular modulators is hindered by our incomplete understanding of the complexities of GPCR-mediated signaling. ERNEST is addressing this challenge by coordinating and supporting development of a holistic multidimensional map of signal transduction that will be comparable to previous and ongoing efforts to map interactomes and signaling pathways with respect to scale and level of detail, (67−75) yet will be distinctive in its focus on elucidating the mechanisms of biased agonism in GPCR signal transduction. ERNEST has clear advantages for accomplishing this ambitious task, namely a substantial membership of diverse researchers and the ability to bring the key players together to work in interdisciplinary cooperation. Development of the signaling map is at present ongoing and will proceed in three phases (Figure 1). First, the data and expertise of all Network members will be curated, catalogued, and (when possible) standardized with the help of experts in data integration and database development. A “blueprint” of all signaling pathways studied within the Network will be generated, thereby allowing the identification of the pathways containing a sufficient amount of validated data (as well as highlighting gaps in information that need to be addressed) for the development of a comprehensive map. ERNEST efforts will be guided by similar web-based resources for mapping biomolecule interactions and signaling pathways. (76,77) Next, a focused “Mapping Group” within ERNEST will facilitate communication between data contributors and the systems biologists who will eventually create the signaling map. Communication between these participants will be bidirectional. Systems biologists will receive and evaluate substantial data from Network members and then give feedback regarding the usefulness of the data and shortcomings that need to be resolved. Again, the size and interdisciplinarity of ERNEST affords the participating system biologists a rare opportunity to optimize the necessary parameters (e.g., binding affinities, rates and kinetics of interactions, cellular localization, cell type) for their computational modeling approaches. Since signaling responses differ between different organisms and also within different cell types (primary and cultured), all gathered data will be labeled with great detail according to their origin and environment. With enough data at hand, signaling map(s) could be visualized for different cell types and growth conditions. Comparison of signaling pathways in different cell types may provide further information on how signaling is modulated by cell-specific characteristics, as well as indicate gaps in understanding. Armed with this large and well-curated data set, the systems biologists will develop signaling map(s). Multiple approaches will be encouraged and supported by ERNEST by facilitating joint grant applications. The envisioned signaling maps will serve three main purposes: (1) Provide an overview of available GPCR knowledge and missing links; (2) Visualize and understand how molecular, spatiotemporal, and cell environment factors control signal transduction; (3) Allow prediction of which cellular responses are elicited by particular GPCR ligands (depending on cell type). The predictive capability of the signaling maps—of utmost importance for the improved development of pathway-specific drugs—will be verified and further optimized by collaborations between map developers, drug designers, and experimentalists within ERNEST.
Figure 1
Figure 1. Schematic overview of how ERNEST will develop a holistic multidimensional map of GPCR-mediated signal transduction. See text for full description.
Pathway-Specific Chemical Modulators of Signal Transduction
Biased ligands might provide improved efficacy and/or side effect and safety profiles. (78) A holistic signaling map will obviously greatly advance the development strategies of such ligands for therapeutically significant GPCR targets. We anticipate that participating computational drug designers will benefit from this map already in the early stages of development, and ERNEST invites such researchers to join the Network in order to stimulate progress. Besides drug discovery efforts, the field requires chemical probes to study signal transduction, that is, specific inhibitors to determine which pathways receptors signal through, or how different signaling networks are interconnected. Such tools will benefit the entire GPCR field, and their application will further assist development and refinement of the signaling map.
An advantage of the large ERNEST network will be to extend the characterization of developed molecular modulators into animal models, both to study pharmacology and test the treatment of disease states, and eventually to translate these findings to patients in clinical trials. Such work will be carried out by linking the drug developers to physiologists, clinicians and those in industry.
Advanced Methods, Technologies, and Database Resources
Over the last 10 years, research on signal transduction has been propelled forward by new methods and technologies spanning many disciplines. These include advancements in structural biology (e.g., nanobodies for stabilization of proteins and protein complexes, free-electron lasers for poorly diffracting crystals, atomic resolution improvements in cryo-electron microscopy), computational biology (longer molecular dynamics simulations of complex systems, advanced sampling methods, novel methodologies), cell biology (visualization of cellular structures and proteins, including super-resolution microscopy, biosensors, single-molecule fluorescence), chemical biology (ad-hoc chemical probes, for example, new radioligands and radiotracers, covalent ligands, affinity-based probes, fluorescent probes, allosteric and bitopic ligands) and systems biology (“omics” and bioinformatics methods, such as deep-mutational scanning, data mining, coevolution, and machine learning approaches). In addition, the field has benefited immensely from public web-based resources, such as GPCRdb and GPCRmd. In order to advance all aspects of signal transduction research, to promote international cooperation and to facilitate its scientific objectives, ERNEST will further develop and disseminate new methods and technologies. These goals will be accomplished by (1) cataloguing known expertise within the Network in an open platform for participants to find collaborators; (2) identifying new methods and technologies that are needed by the community through constructive discussions at Network meetings; (3) pushing the development of new methods and technologies by recruiting the right experts and supporting them in grant applications; (4) establishing “best practice” principles for new and existing approaches by recruiting experts and encouraging publication on this topic. ERNEST will foster further development of GPCRdb and GPCRmd by enabling communication between database users and developers regarding which features and tools are needed by the research community.
Cooperation between Academia and Industry
The potential of ERNEST to improve the design of signaling pathway-specific drugs naturally attracts many researchers from both academia and industry. On the basis of experience from GLISTEN, the close inclusion and involvement of participants from pharmaceutical and biotech companies will be valuable for ERNEST and its goals. Pathway-specific chemical modulators would be of interest due to the challenging target validation and target engagement efforts in early phase drug discovery programs. Advanced methods and technologies developed in ERNEST might attract significant attention in pharmaceutical and biotech settings. Cooperation between industry and academic researchers will be fostered at dedicated sessions on the topic at ERNEST meetings. Besides promoting collaboration between researchers in academia and industry, ERNEST will support cross-sectoral training of early career investigators by sponsoring exchange programs between academic groups and research-oriented companies.
Working Groups of ERNEST
ARTICLE SECTIONS
Network participants belong to one or more Working Groups (WG), whose task is to coordinate members and their expertise in order to achieve the objectives of the Network. The focus areas of ERNEST are designed to be inclusive of all researchers in the signal transduction field, from the molecular to the cellular to the physiological perspectives, as well as those focused on pushing forward new methods, technologies, and resources for the advancement of research (Figure 2).
Figure 2
Figure 2. Thematic synergism between the Working Groups (WG) of ERNEST. WGs 1, 2, and 3 form the core of scientific knowledge of the Action, and the overlaps represent shared focus and potential for interdisciplinary cooperation. WG4 will support the three core WGs with new methods and technologies and also establish best practice standards for their application. Output from the three core workgroups (arrows out) will be incorporated by WG5 into database resources for public dissemination, and WG5 will generate database tools that will feedback into the three core WGs (arrows in). Figure reprinted in part from COST Action CA18133 ERNEST Memorandum of Understanding with permission from the COST Association. (80)
WG1: Macromolecular Interactions in Signaling Pathways
Signal transduction is mediated and dependent on macromolecular interactions. The protein players in signal transduction cascades are molecular machines, the conformations and movements of which are modulated by interactions with small molecules and other biological macromolecules, resulting in different signaling states. The main objective of WG1 is elucidation of structural dynamics and molecular interactions at the atomic level that give rise to signal transduction, with emphasis on how the modulation of interactions generates specificity in transmembrane receptor-mediated signal transduction.
WG2: Biological Roles of Signal Transduction
The biological importance of macromolecular interactions can only be understood within the context of a living cell. The main objective of WG2 is to connect the molecular interactions and their subcellular localization to the cellular response and (patho)physiological states. Signaling pathways must be defined and characterized for different cell types and systems, involving experts in different physiological systems (e.g., neurobiology, cardiovascular system, cancer, and immunity) within the Network. This activity has the benefit that new biological model systems can be developed and new therapeutic targets can be identified. Signaling pathways must also be defined in order to understand how disease results from imbalances in signal transduction.
WG3: Molecular Modulators of Signal Transduction
WG3 will harness chemical space for modulation of protein interactions and signaling. The core objective is the design and optimization of molecules that interact with components of the signal transduction cascade. The design of functionally selective therapeutics will be possible through information about relevant receptor conformations or residues provided by WG1 and WG2. WG3 will also work closely with WG4 (advanced technologies and methods) and industry partners to develop chemical probes to investigate cell signaling mechanisms and to stabilize GPCR complexes with binding partners for high-resolution structural analysis and hit/lead compounds for drug discovery programs.
WG4: Advanced Methodologies and Technologies
The main objective of WG4 is to promote advanced methodologies and technologies within ERNEST, and to coordinate sharing through collaboration. Included are novel approaches that can help achieve the aims of the Network, as well as repurposing of existing methods and technologies from other fields of biomedical research. This WG will also establish best practice principles for the application of commonly used methodologies across groups within and beyond the Network. These advancements in experimental approach and technology will support the other WGs and overall objectives of ERNEST.
WG5: Public Web Resources
The key objective of WG5 is to structure, integrate, and make accessible different types of data emanating from ERNEST and its members and the global GPCR community. Online databases have greatly benefited the signal transduction research community in the past decade. WG5 will contribute key public online resources in this area for reference data and analysis tools. Experts from all WGs will design and use this resource and thus increase the dissemination of their scientific results.
Future Outlook and Anticipated Impacts to the Field and beyond
ARTICLE SECTIONS
ERNEST was created by a diverse group of researchers to directly address and collectively resolve the major challenges facing the field of GPCR-mediated signal transduction. The support of the COST Association in the endeavor will prove highly worthwhile, as several positive impacts of this Action are anticipated. The large membership of the Network, including most world-leading GPCR experts in Europe, united in close cooperation with a holistic concept of how to best understand signal transduction and harness this knowledge, is likely to achieve many successes. In the short term, ERNEST will stimulate collaborations between academic groups of quite disparate fields, which will be brought together because of the unprecedented holistic approach to understanding signal transduction. In particular, collaborations between academia and industry will be pushed by the new targeting possibilities offered by the signaling map. In the long term, ERNEST will advance this holistic view of signal transduction and establish new paradigms for modulation of signaling pathways. The detailed multidimensional map and database tools that will be developed during the lifetime of the Network will be valuable resources for the research community for many years to come. In addition, new chemical modulators developed through ERNEST activities will be invaluable for future research and as starting points for drug development. These therapeutic agents will have a significant and positive socio-economic impact by improving human health worldwide.
ERNEST will have further long-term impact through the cross-disciplinary training of early career investigators, as these individuals will drive signal transduction research into the future. ERNEST-sponsored cross-border exchanges will open up career perspectives and opportunities for many researchers. These exchanges will have further lasting benefits by spreading technologies and knowhow throughout Europe and beyond. Finally, ERNEST will promote diversity in the leadership ranks of European research by promoting target groups, especially women and scientists from less research-intensive countries. In summary, the future looks promising for signal transduction research, and time will tell the importance of being ERNEST. (79)
Author Information
ARTICLE SECTIONS
- Martha E. Sommer - Institute of Medical Physics and Biophysics, Charité−Universitätsmedizin Berlin, Berlin, 10117, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, Germany;
http://orcid.org/0000-0003-0493-8584;
- Peter Kolb - Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, 35039, Germany;http://orcid.org/0000-0003-4089-614X;
- Jana Selent - Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM) - Pompeu Fabra University (UPF), Barcelona, 08003, Spain;http://orcid.org/0000-0002-1844-4449
- Jens Carlsson - Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 752 36, Sweden;http://orcid.org/0000-0003-4623-2977
- Gyorgy M. Keseru - Medicinal Chemistry Research Group, Research Center for Natural Sciences (RCNS), Budapest, H-1117, Hungary;http://orcid.org/0000-0003-1039-7809
- Mette M. Rosenkilde - Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK 2200, Denmark;http://orcid.org/0000-0001-9600-3254
- Eddy Sotelo - Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS) and Facultade de Farmacia. Universidade de Santiago de Compostela, Santiago de compostela, 15782, Spain;http://orcid.org/0000-0001-5571-2812
- Johanna K. S. Tiemann - Institute for Medical Physics and Biophysics, Leipzig University, Leipzig, 04109, Germany; Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Kobenhavn, 2200, Denmark;http://orcid.org/0000-0001-7551-6245
- Andrew Tobin - The Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, U.K.;http://orcid.org/0000-0002-1807-3123
Acknowledgments
ARTICLE SECTIONS
The authors are grateful for the continued support of the European Cooperation in Science and Technology (COST) through Actions CM1207 GLISTEN and CA18133 ERNEST. On behalf of ERNEST, M.E.S. thanks the Max Delbrück Center for Molecular Medicine Berlin for support in managing the Action. M.E.S. is supported by the Deutsche Forschungsgemeinschaft (DFG) (SO1037/1-3) and the Berlin Institute of Health (Delbrück Fellowship BIH_PRO_314). J.S. acknowledges support from the Instituto de Salud Carlos III FEDER (PI18/00094) and the ERA-NET NEURON & Ministry of Economy, Industry and Competitiveness (AC18/00030). J.C. receives funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 715052). D.E.G. is supported by the Lundbeck Foundation (R313-2019-526) and Novo Nordisk Foundation (NNF17OC0031226). G.M.K. is funded by the National Brain Research Program (2017-1.2.1-NKP-2017-00002). M.K. acknowledges support from the Israel Science Foundation (Grants 1454/13 and 3512/19) and the DS Research Center at the University of Haifa. S.M. is supported by the Alfred Benzon Foundation (ABF-0-0-312) and Polish National Science Center (HARMONIA 2015/18/M/NZ2/00423). M.M.R. acknowledges support from the European Research Council: VIREX Grant agreement 682549, Call ERC-2105-CoG, the Independent Research Fund Denmark, the NovoNordisk Foundation (NNF17OC0029222:) and the Lundbeck Foundation (R268-2017-409). E.S. thanks the Xunta de Galicia (Centro singular de Investigación de Galicia acreditación 2019-2022, ED431G 2019/03 and GI-1597 2017-2019 ED431B2017/70) and the European Union (European Regional Development Fund - ERDF) for financial support. J.K.S.T. acknowledges support from the DFG (HI1502/1-2) and the Novo Nordisk Foundation (Challenge Grant PRISM). N.V. is funded by grants from the Slovenian Research Agency (P3-310, J3-7605, BI-DE/18-19-015). P.K. is supported by the DFG (KO4095/4-1 and Heisenberg professorship KO4095/5-1). All coauthors thank the stellar organizers of the eight GLISTEN meetings for their vital contributions and their associated institutes and companies for support, including the University of Warsaw (Poland), Pompeu Fabra University and Autonomous University of Barcelona (Spain), Research Centre for Natural Sciences of the Hungarian Academy of Sciences (Budapest, Hungary), Actelion Pharmaceuticals (Allschwil, Switerland), Vrije Universiteit (Amsterdam, The Netherlands), Friedrich Alexander University Erlangen and Philipps-University Marburg (Germany), University of Chemistry and Technology Prague (Czech Republic), the University of Porto (Portugal), and Sosei Heptares (Cambridge, UK). Parts of this paper are derived from the Memorandum of Understanding for the implementation of the COST Action “European Research Network on Signal Transduction” (ERNEST) CA18133. (80)
1
The European Cooperation in Science and Technology (COST), founded in 1971, funds research networks (COST Actions) created by researchers themselves to address specific and significant challenges in their respective fields. COST supports networking activities, e.g. conferences, training schools, international exchange of investigators between research groups, dissemination, and communication activities. COST Actions are highly interdisciplinary, open to new participants throughout their lifetime of 4 years, and active in promoting early career investigators and investigators from less research-intensive countries. Hence, COST plays a key role in stimulating international cooperation that pushes scientific progress and benefits a diverse community of researchers. For more information, see: https://www.cost.eu.
References
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This article references 80 other publications.
- 1Hauser, A. S., Attwood, M. M., Rask-Andersen, M., Schioth, H. B., and Gloriam, D. E. (2017) Trends in GPCR drug discovery: new agents, targets and indications. Nat. Rev. Drug Discovery 16 (12), 829– 842, DOI: 10.1038/nrd.2017.178Google Scholar1https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhslansbzF&md5=560893258493bd96c0af24d3bef08b6fTrends in GPCR drug discovery: new agents, targets and indicationsHauser, Alexander S.; Attwood, Misty M.; Rask-Andersen, Mathias; Schioth, Helgi B.; Gloriam, David E.Nature Reviews Drug Discovery (2017), 16 (12), 829-842CODEN: NRDDAG; ISSN:1474-1776. (Nature Research)G protein-coupled receptors (GPCRs) are the most intensively studied drug targets, mostly due to their substantial involvement in human pathophysiol. and their pharmacol. tractability. Here, we report an up-to-date anal. of all GPCR drugs and agents in clin. trials, which reveals current trends across mol. types, drug targets and therapeutic indications, including showing that 475 drugs (∼34% of all drugs approved by the US Food and Drug Administration (FDA)) act at 108 unique GPCRs. Approx. 321 agents are currently in clin. trials, of which ∼20% target 66 potentially novel GPCR targets without an approved drug, and the no. of biol. drugs, allosteric modulators and biased agonists has increased. The major disease indications for GPCR modulators show a shift towards diabetes, obesity and Alzheimer disease, although several central nervous system disorders are also highly represented. The 224 (56%) non-olfactory GPCRs that have not yet been explored in clin. trials have broad untapped therapeutic potential, particularly in genetic and immune system disorders. Finally, we provide an interactive online resource to analyze and infer trends in GPCR drug discovery.
- 2Palczewski, K., Kumasaka, T., Hori, T., Behnke, C. A., Motoshima, H., Fox, B. A., Le Trong, I., Teller, D. C., Okada, T., Stenkamp, R. E., Yamamoto, M., and Miyano, M. (2000) Crystal structure of rhodopsin: A G protein-coupled receptor. Science 289 (5480), 739– 45, DOI: 10.1126/science.289.5480.739Google Scholar2https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXlslOqs78%253D&md5=b3d229fc696247ec0f4a6efa10490922Crystal structure of rhodopsin: A G protein-coupled receptorPalczewski, Krzysztof; Kumasaka, Takashi; Hori, Tetsuya; Behnke, Craig A.; Motoshima, Hiroyuki; Fox, Brian A.; Le Trong, Isolde; Teller, David C.; Okada, Tetsuji; Stenkamp, Ronald E.; Yamamoto, Masaki; Miyano, MasashiScience (Washington, D. C.) (2000), 289 (5480), 739-745CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)Heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) respond to a variety of different external stimuli and activate G proteins. GPCRs share many structural features, including a bundle of seven transmembrane α-helixes connected by six loops of varying lengths. We detd. the structure of rhodopsin from diffraction data extending to 2.8 angstroms resoln. The highly organized structure in the extracellular region, including a conserved disulfide bridge, forms a basis for the arrangement of the seven-helix transmembrane motif. The ground-state chromophore, 11-cis-retinal, holds the transmembrane region of the protein in the inactive conformation. Interactions of the chromophore with a cluster of key residues det. the wavelength of the max. absorption. Changes in these interactions among rhodopsins facilitate color discrimination. Identification of a set of residues that mediate interactions between the transmembrane helixes and the cytoplasmic surface, where G-protein activation occurs, also suggests a possible structural change upon photoactivation.
- 3Wacker, D., Stevens, R. C., and Roth, B. L. (2017) How Ligands Illuminate GPCR Molecular Pharmacology. Cell 170 (3), 414– 427, DOI: 10.1016/j.cell.2017.07.009Google Scholar3https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXht1GisLvF&md5=d4f7f48d757cf3d13a980d2f7f1be138How ligands illuminate GPCR molecular pharmacologyWacker, Daniel; Stevens, Raymond C.; Roth, Bryan L.Cell (Cambridge, MA, United States) (2017), 170 (3), 414-427CODEN: CELLB5; ISSN:0092-8674. (Cell Press)A review. G protein-coupled receptors (GPCRs), which are modulated by a variety of endogenous and synthetic ligands, represent the largest family of druggable targets in the human genome. Recent structural and mol. studies have both transformed and expanded classical concepts of receptor pharmacol. and have begun to illuminate the distinct mechanisms by which structurally, chem., and functionally diverse ligands modulate GPCR function. These mol. insights into ligand engagement and action have enabled new computational methods and accelerated the discovery of novel ligands and tool compds., esp. for understudied and orphan GPCRs. These advances promise to streamline the development of GPCR-targeted medications.
- 4Zhou, X. E., Melcher, K., and Xu, H. E. (2017) Understanding the GPCR biased signalling through G protein and arrestin complex structures. Curr. Opin. Struct. Biol. 45, 150– 159, DOI: 10.1016/j.sbi.2017.05.004Google Scholar4https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXotFyns74%253D&md5=7b36ce15a853972b9abbe895852fc794Understanding the GPCR biased signaling through G protein and arrestin complex structuresZhou, X. Edward; Melcher, Karsten; Xu, H. EricCurrent Opinion in Structural Biology (2017), 45 (), 150-159CODEN: COSBEF; ISSN:0959-440X. (Elsevier Ltd.)G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors and are important drug targets for many human diseases. The detn. of the 3-D structure of GPCRs and their signaling complexes has promoted our understanding of GPCR biol. and provided templates for structure-based drug discovery. In this review, we focus on the recent structure work on GPCR signaling complexes, the β2-adrenoreceptor-Gs and the rhodopsin-arrestin complexes in particular, and highlight the structural features of GPCR complexes involved in G protein- and arrestin-mediated signal transduction. The crystal structures reveal distinct structural mechanisms by which GPCRs recruit a G protein and an arrestin. A comparison of the two complex structures provides insight into the mol. mechanism of functionally selective GPCR signaling, and a structural basis for the discovery of G protein- and arrestin-biased treatments of human diseases related to GPCR signal transduction.
- 5Hilger, D., Masureel, M., and Kobilka, B. K. (2018) Structure and dynamics of GPCR signalling complexes. Nat. Struct. Mol. Biol. 25 (1), 4– 12, DOI: 10.1038/s41594-017-0011-7Google Scholar5https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhtlCqu7jM&md5=6af99d3ea2b5422d377575815a867458Structure and dynamics of GPCR signaling complexesHilger, Daniel; Masureel, Matthieu; Kobilka, Brian K.Nature Structural & Molecular Biology (2018), 25 (1), 4-12CODEN: NSMBCU; ISSN:1545-9993. (Nature Research)A review. G-protein-coupled receptors (GPCRs) relay numerous extracellular signals by triggering intracellular signaling through coupling with G proteins and arrestins. Recent breakthroughs in the structural detn. of GPCRs and GPCR-transducer complexes represent important steps toward deciphering GPCR signal transduction at a mol. level. A full understanding of the mol. basis of GPCR-mediated signaling requires elucidation of the dynamics of receptors and their transducer complexes as well as their energy landscapes and conformational transition rates. Here, we summarize current insights into the structural plasticity of GPCR-G-protein and GPCR-arrestin complexes that underlies the regulation of the receptor's intracellular signaling profile.
- 6Callaway, E. (2015) The revolution will not be crystallized: a new method sweeps through structural biology. Nature 525 (7568), 172– 4, DOI: 10.1038/525172aGoogle Scholar6https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsVyrtLfN&md5=9806c5cc42ee81de65b2c4037909c6b8The revolution will not be crystallized: a new method sweeps through structural biologyCallaway, EwenNature (London, United Kingdom) (2015), 525 (7568), 172-174CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)Move over X-ray crystallog. Cryo-electron microscopy is kicking up a storm by revealing the hidden machinery of the cell.
- 7Safdari, H. A., Pandey, S., Shukla, A. K., and Dutta, S. (2018) Illuminating GPCR Signalling by Cryo-EM. Trends Cell Biol. 28 (8), 591– 594, DOI: 10.1016/j.tcb.2018.06.002Google Scholar7https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhtF2jt7vJ&md5=57be67178fff2cd78d337fd050865df6Illuminating GPCR Signaling by Cryo-EMSafdari, Haaris Ahsan; Pandey, Shubhi; Shukla, Arun K.; Dutta, SomnathTrends in Cell Biology (2018), 28 (8), 591-594CODEN: TCBIEK; ISSN:0962-8924. (Elsevier Ltd.)A review. The wave of resoln. revolution in cryo-EM has touched, and made a significant impact on, the structural biol. of GPCRs. High-resoln. structures of several GPCR-G-protein complexes are now detd. by cryo-EM and they illuminate fine structural details of this central macromol. complex involved in cellular signaling.
- 8Garcia-Nafria, J. and Tate, C. G. (2020) Cryo-Electron Microscopy: Moving Beyond X-Ray Crystal Structures for Drug Receptors and Drug Development. Annu. Rev. Pharmacol. Toxicol. 60, 51– 71, DOI: 10.1146/annurev-pharmtox-010919-023545Google Scholar8https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhsVGru77M&md5=035f2b8d1c64fc8c4ce85255df233c84Cryo-Electron Microscopy: Moving Beyond X-Ray Crystal Structures for Drug Receptors and Drug DevelopmentGarcia-Nafria, Javier; Tate, Christopher G.Annual Review of Pharmacology and Toxicology (2020), 60 (), 51-71CODEN: ARPTDI; ISSN:0362-1642. (Annual Reviews)Electron cryo-microscopy (cryo-EM) has revolutionized structure detn. of membrane proteins and holds great potential for structure-based drug discovery. Here we discuss the potential of cryo-EM in the rational design of therapeutics for membrane proteins compared to X-ray crystallog. We also detail recent progress in the field of drug receptors, focusing on cryo-EM of two protein families with established therapeutic value, the γ-aminobutyric acid A receptors (GABAARs) and G protein-coupled receptors (GPCRs). GABAARs are pentameric ion channels, and cryo-EM structures of physiol. heteromeric receptors in a lipid environment have uncovered the mol. basis of receptor modulation by drugs such as diazepam. The structures of ten GPCR-G protein complexes from three different classes of GPCRs have now been detd. by cryo-EM. These structures give detailed insights into mol. interactions with drugs, GPCR-G protein selectivity, how accessory membrane proteins alter receptor-ligand pharmacol., and the mechanism by which HIV uses GPCRs to enter host cells.
- 9Schrage, R. and Kostenis, E. (2017) Functional selectivity and dualsteric/bitopic GPCR targeting. Curr. Opin. Pharmacol. 32, 85– 90, DOI: 10.1016/j.coph.2016.12.001Google Scholar9https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XitFWlsLrE&md5=851d67a8acaa8e260726eca996628a01Functional selectivity and dualsteric/bitopic GPCR targetingSchrage, Ramona; Kostenis, EviCurrent Opinion in Pharmacology (2017), 32 (), 85-90CODEN: COPUBK; ISSN:1471-4892. (Elsevier Ltd.)Functional selectivity provides a new avenue to selectively engage particular pathways of the pleiotropic signaling repertoire of a G protein-coupled receptor. First examples for signaling biased compds. at the angiotensin II receptor and the μ opioid receptor have progressed to clin. trials and are promising in regard to selective activation of signaling pathways that can be linked to beneficial clin. outcomes. Dualsteric/bitopic hybrid compds. which consist of at least two pharmacophores combined in one single ligand are more recent examples for functionally selective ligands. Their binding topog. makes them ideally suited to disrupt receptor flexibility and rationally induce signaling bias. Therefore, the dualsteric/bitopic design principle is most promising to facilitate generation of structurally diverse biased agonists at G protein-coupled receptors.
- 10www.biomodellab.eu/1glisten (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 11http://eventia.upf.edu/Barcelona-GPCR-Conference-2014 (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 12http://glisten.ttk.hu/ (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 13https://sites.google.com/site/glisten2015/home (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 14http://www.medchemsymposium.org/Home.html (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 15http://grk1910.de/glisten-2016.html (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 16www.glisten2016.cz (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 17https://glistensymposium.wordpress.com (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 18http://school.ifs.hr/2016 (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 19Rodriguez, D., Brea, J., Loza, M. I., and Carlsson, J. (2014) Structure-based discovery of selective serotonin 5-HT(1B) receptor ligands. Structure 22 (8), 1140– 1151, DOI: 10.1016/j.str.2014.05.017Google Scholar19https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtFyjt7fE&md5=bf293d7c1bb6f4465ed0574ae298e81fStructure-Based Discovery of Selective Serotonin 5-HT1B Receptor LigandsRodriguez, David; Brea, Jose; Loza, Maria Isabel; Carlsson, JensStructure (Oxford, United Kingdom) (2014), 22 (8), 1140-1151CODEN: STRUE6; ISSN:0969-2126. (Elsevier Ltd.)The development of safe and effective drugs relies on the discovery of selective ligands. Serotonin (5-hydroxytryptamine [5-HT]) G protein-coupled receptors are therapeutic targets for CNS disorders but are also assocd. with adverse drug effects. The detn. of crystal structures for the 5-HT1B and 5-HT2B receptors provided an opportunity to identify subtype selective ligands using structure-based methods. From docking screens of 1.3 million compds., 22 mols. were predicted to be selective for the 5-HT1B receptor over the 5-HT2B subtype, a requirement for safe serotonergic drugs. Nine compds. were exptl. verified as 5-HT1B-selective ligands, with up to 300-fold higher affinities for this subtype. Three of the ligands were agonists of the G protein pathway. Anal. of state-of-the-art homol. models of the two 5-HT receptors revealed that the crystal structures were crit. for predicting selective ligands. Our results demonstrate that structure-based screening can guide the discovery of ligands with specific selectivity profiles.
- 20Piscitelli, C. L., Kean, J., de Graaf, C., and Deupi, X. (2015) A Molecular Pharmacologist’s Guide to G Protein-Coupled Receptor Crystallography. Mol. Pharmacol. 88 (3), 536– 51, DOI: 10.1124/mol.115.099663Google Scholar20https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsVCgs77M&md5=544b3458352b57e776055fbc65f97cbdA molecular pharmacologist's guide to G protein-coupled receptor crystallographyPiscitelli, Chayne L.; Kean, James; de Graaf, Chris; Deupi, XavierMolecular Pharmacology (2015), 88 (3), 536-551CODEN: MOPMA3; ISSN:1521-0111. (American Society for Pharmacology and Experimental Therapeutics)G protein-coupled receptor (GPCR) structural biol. has progressed dramatically in the last decade. There are now over 120 GPCR crystal structures deposited in the Protein Data Bank of 32 different receptors from families scattered across the phylogenetic tree, including class B, C, and Frizzled GPCRs. These structures have been obtained in combination with a wide variety of ligands and captured in a range of conformational states. This surge in structural knowledge has enlightened research into the mol. recognition of biol. active mols., the mechanisms of receptor activation, the dynamics of functional selectivity, and fueled structure-based drug design efforts for GPCRs. Here we summarize the innovations in both protein engineering/mol. biol. and crystallog. techniques that have led to these advances in GPCR structural biol. and discuss how they may influence the resulting structural models. We also provide a brief mol. pharmacologist's guide to GPCR X-ray crystallog., outlining some key aspects in the process of structure detn., with the goal to encourage noncrystallographers to interrogate structures at the mol. level. Finally, we show how chemogenomics approaches can be used to marry the wealth of existing receptor pharmacol. data with the expanding repertoire of structures, providing a deeper understanding of the mechanistic details of GPCR function.
- 21Munk, C., Isberg, V., Mordalski, S., Harpsoe, K., Rataj, K., Hauser, A. S., Kolb, P., Bojarski, A. J., Vriend, G., and Gloriam, D. E. (2016) GPCRdb: the G protein-coupled receptor database - an introduction. Br. J. Pharmacol. 173 (14), 2195– 207, DOI: 10.1111/bph.13509Google Scholar21https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XptFWgtbc%253D&md5=ca467fd4423d55d52c896c55d6aad964GPCRdb: the G protein-coupled receptor database - an introductionMunk, C.; Isberg, V.; Mordalski, S.; Harpsoe, K.; Rataj, K.; Hauser, A. S.; Kolb, P.; Bojarski, A. J.; Vriend, G.; Gloriam, D. E.British Journal of Pharmacology (2016), 173 (14), 2195-2207CODEN: BJPCBM; ISSN:1476-5381. (Wiley-Blackwell)GPCRs make up the largest family of human membrane proteins and of drug targets. Recent advances in GPCR pharmacol. and crystallog. have shed new light on signal transduction, allosteric modulation and biased signalling, translating into new mechanisms and principles for drug design. The GPCR database, GPCRdb, has served the community for over 20 years and has recently been extended to include a more multidisciplinary audience. This review is intended to introduce new users to the services in GPCRdb, which meets three overall purposes: firstly, to provide ref. data in an integrated, annotated and structured fashion, with a focus on sequences, structures, single-point mutations and ligand interactions. Secondly, to equip the community with a suite of web tools for swift anal. of structures, sequence similarities, receptor relationships, and ligand target profiles. Thirdly, to facilitate dissemination through interactive diagrams of, for example, receptor residue topologies, phylogenetic relationships and crystal structure statistics. Herein, these services are described for the first time; visitors and guides are provided with good practices for their utilization. Finally, we describe complementary databases cross-referenced by GPCRdb and web servers with corresponding functionality.
- 22Lally, C. C., Bauer, B., Selent, J., and Sommer, M. E. (2017) C-edge loops of arrestin function as a membrane anchor. Nat. Commun. 8, 14258, DOI: 10.1038/ncomms14258Google Scholar22https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXjtlyisLg%253D&md5=fb282d62caf23b0d520aff5c1342a7e9C-edge loops of arrestin function as a membrane anchorLally, Ciara C. M.; Bauer, Brian; Selent, Jana; Sommer, Martha E.Nature Communications (2017), 8 (), 14258CODEN: NCAOBW; ISSN:2041-1723. (Nature Publishing Group)G-protein-coupled receptors are membrane proteins that are regulated by a small family of arrestin proteins. During formation of the arrestin-receptor complex, arrestin first interacts with the phosphorylated receptor C terminus in a pre-complex, which activates arrestin for tight receptor binding. Currently, little is known about the structure of the pre-complex and its transition to a high-affinity complex. Here we present mol. dynamics simulations and site-directed fluorescence expts. on arrestin-1 interactions with rhodopsin, showing that loops within the C-edge of arrestin function as a membrane anchor. Activation of arrestin by receptor-attached phosphates is necessary for C-edge engagement of the membrane, and we show that these interactions are distinct in the pre-complex and high-affinity complex in regard to their conformation and orientation. Our results expand current knowledge of C-edge structure and further illuminate the conformational transitions that occur in arrestin along the pathway to tight receptor binding.
- 23Chevillard, F., Stotani, S., Karawajczyk, A., Hristeva, S., Pardon, E., Steyaert, J., Tzalis, D., and Kolb, P. (2019) Interrogating dense ligand chemical space with a forward-synthetic library. Proc. Natl. Acad. Sci. U. S. A. 116 (23), 11496– 11501, DOI: 10.1073/pnas.1818718116Google Scholar23https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhtV2itL%252FO&md5=22fa702bc6a87b1c1a62228538775a8fInterrogating dense ligand chemical space with a forward-synthetic libraryChevillard, Florent; Stotani, Silvia; Karawajczyk, Anna; Hristeva, Stanimira; Pardon, Els; Steyaert, Jan; Tzalis, Dimitrios; Kolb, PeterProceedings of the National Academy of Sciences of the United States of America (2019), 116 (23), 11496-11501CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Forward-synthetic databases are an efficient way to enumerate chem. space. The authors explored here whether these databases are good sources of novel protein ligands and how many mols. are obtainable and in which time frame. Based on docking calcns., series of mols. were selected to gain insights into the ligand structur-activity relation. To evaluate the novelty of compds. in a challenging way, the authors chose the β2-adrenergic receptor, for which a large no. of ligands is already known. Finding dissimilar ligands is thus the exception rather than the rule. Here the authors report on the results, the successful synthesis of 127/240 mols. in just 2 wk, the discovery of previously unreported dissimilar ligands of the β2-adrenergic receptor, and the optimization of one series to a KD of 519 nM in only one round. Moreover, the finding that only 3 of 240 mols. had ever been synthesized before indicates that large parts of chem. space are unexplored.
- 24Rodríguez-Espigares, I., Torrens-Fontanals, M., Tiemann, J. K. S., Aranda-García, D., Ramírez-Anguita, J. M., Stepniewski, T. M., Worp, N., Varela-Rial, A., Morales-Pastor, A., Lacruz, B. M., Pándy-Szekeres, G., Mayol, E., Giorgino, T., Carlsson, J., Deupi, X., Filipek, S., Filizola, M., Gómez-Tamayo, J. C., Gonzalez, A., Gutierrez-de-Teran, H., Jimenez, M., Jespers, W., Kapla, J., Khelashvili, G., Kolb, P., Latek, D., Marti-Solano, M., Matricon, P., Matsoukas, M.-T., Miszta, P., Olivella, M., Perez-Benito, L., Provasi, D., Ríos, S., Rodríguez-Torrecillas, I., Sallander, J., Sztyler, A., Vaidehi, N., Vasile, S., Weinstein, H., Zachariae, U., Hildebrand, P. W., Fabritiis, G. D., Sanz, F., Gloriam, D. E., Cordomi, A., Guixà-González, R., and Selent, J. (2019) GPCRmd uncovers the dynamics of the 3D-GPCRome. bioRxiv 839597Google ScholarThere is no corresponding record for this reference.
- 25http://www.oncornet.eu/ (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 26https://www.era-learn.eu/network-information/networks/neuron-cofund/call-for-proposals-for-transnational-research-projects-on-mental-disorders/a-novel-paradigm-for-effective-and-safer-treatment-of-schizophrenia-biased-ant-agonists-with-a-characterized-polypharmacological-profile (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 27https://www.neuron-eranet.eu/_media/PSYBIAS_summary.pdf (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 28Horn, F., Weare, J., Beukers, M. W., Horsch, S., Bairoch, A., Chen, W., Edvardsen, O., Campagne, F., and Vriend, G. (1998) GPCRDB: an information system for G protein-coupled receptors. Nucleic Acids Res. 26 (1), 275– 9, DOI: 10.1093/nar/26.1.275Google Scholar28https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1cXovVehsw%253D%253D&md5=c32036731939e950081c6cfbdad00002GPCRDB: an information system for G protein-coupled receptorsHorn, F.; Weare, J.; Beukers, M. W.; Horsch, S.; Bairoch, A.; Chen, W.; Edvardsen, O.; Campagne, F.; Vriend, G.Nucleic Acids Research (1998), 26 (1), 275-279CODEN: NARHAD; ISSN:0305-1048. (Oxford University Press)The GPCRDB is a G protein-coupled receptor (GPCR) database system aimed at the collection and dissemination of GPCR related data. It holds sequences, mutant data and ligand binding consts. as primary (exptl.) data. Computationally derived, data such as multiple sequence alignments, three dimensional models, phylogenetic trees and two dimensional visualization tools are added to enhance the database's usefulness. The GPCRDB is an EU sponsored project aimed at building a generic mol. class specific database capable of dealing with highly heterogeneous data. GPCRs were chosen as test mols. because of their enormous importance for medical sciences and due to the availability of so much highly heterogeneous data. The GPCRDB is available via the WWW at http://www.gpcr.org/7tm.
- 29Isberg, V., Mordalski, S., Munk, C., Rataj, K., Harpsoe, K., Hauser, A. S., Vroling, B., Bojarski, A. J., Vriend, G., and Gloriam, D. E. (2016) GPCRdb: an information system for G protein-coupled receptors. Nucleic Acids Res. 44 (D1), D356– 64, DOI: 10.1093/nar/gkv1178Google Scholar29https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhtV2gu7bJ&md5=ee7db0ef81d65cf6e5ab8750b990bb78GPCRdb: an information system for G protein-coupled receptorsIsberg, Vignir; Mordalski, Stefan; Munk, Christian; Rataj, Krzysztof; Harpsoee, Kasper; Hauser, Alexander S.; Vroling, Bas; Bojarski, Andrzej J.; Vriend, Gert; Gloriam, David E.Nucleic Acids Research (2016), 44 (D1), D356-D364CODEN: NARHAD; ISSN:0305-1048. (Oxford University Press)A review. Recent developments in G protein-coupled receptor (GPCR) structural biol. and pharmacol. have greatly enhanced our knowledge of receptor structure-function relations, and have helped improve the scientific foundation for drug design studies. The GPCR database, GPCRdb, serves a dual role in disseminating and enabling new scientific developments by providing ref. data, anal. tools and interactive diagrams. This paper highlights new features in the fifth major GPCRdb release: (i) GPCR crystal structure browsing, superposition and display of ligand interactions; (ii) direct deposition by users of point mutations and their effects on ligand binding; (iii) refined snake and helix box residue diagram looks; and (iv) phylogenetic trees with receptor classification color schemes. Under the hood, the entire GPCRdb front- and back-ends have been recoded within one infrastructure, ensuring a smooth browsing experience and development. GPCRdb is available at http://www.gpcrdb.org/ and it's open source code at https://bitbucket.org/gpcr/protwis.
- 30Flock, T., Hauser, A. S., Lund, N., Gloriam, D. E., Balaji, S., and Babu, M. M. (2017) Selectivity determinants of GPCR-G-protein binding. Nature 545 (7654), 317– 322, DOI: 10.1038/nature22070Google Scholar30https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXnsVeis74%253D&md5=947db386e0e0f74b09465a99d880c518Selectivity determinants of GPCR-G-protein bindingFlock, Tilman; Hauser, Alexander S.; Lund, Nadia; Gloriam, David E.; Balaji, Santhanam; Babu, M. MadanNature (London, United Kingdom) (2017), 545 (7654), 317-322CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)The selective coupling of G-protein-coupled receptors (GPCRs) to specific G proteins is crit. to trigger the appropriate physiol. response. However, the determinants of selective binding have remained elusive. Here, we reveal the existence of a selectivity barcode (i.e., patterns of amino acids) on each of the 16 human G proteins that is recognized by distinct regions on the ∼800 human receptors. Although universally conserved positions in the barcode allow the receptors to bind and activate G proteins in a similar manner, different receptors recognize the unique positions of the G-protein barcode through distinct residues, like multiple keys (receptors) opening the same lock (G protein) using nonidentical cuts. Considering the evolutionary history of GPCRs allows the identification of these selectivity-detg. residues. These findings lay the foundation for understanding the mol. basis of coupling selectivity within individual receptors and G proteins.
- 31Hauser, A. S., Chavali, S., Masuho, I., Jahn, L. J., Martemyanov, K. A., Gloriam, D. E., and Babu, M. M. (2018) Pharmacogenomics of GPCR Drug Targets. Cell 172 (1–2), 41– 54 e19, DOI: 10.1016/j.cell.2017.11.033Google Scholar31https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhvF2js7rE&md5=aea194a723f8704cdcf4f05773c4880ePharmacogenomics of GPCR Drug TargetsHauser, Alexander S.; Chavali, Sreenivas; Masuho, Ikuo; Jahn, Leonie J.; Martemyanov, Kirill A.; Gloriam, David E.; Babu, M. MadanCell (Cambridge, MA, United States) (2018), 172 (1-2), 41-54.e19CODEN: CELLB5; ISSN:0092-8674. (Cell Press)Natural genetic variation in the human genome is a cause of individual differences in responses to medications and is an underappreciated burden on public health. Although 108 G-protein-coupled receptors (GPCRs) are the targets of 475 (∼34%) Food and Drug Administration (FDA)-approved drugs and account for a global sales vol. of over 180 billion US dollars annually, the prevalence of genetic variation among GPCRs targeted by drugs is unknown. By analyzing data from 68,496 individuals, we find that GPCRs targeted by drugs show genetic variation within functional regions such as drug- and effector-binding sites in the human population. We exptl. show that certain variants of μ-opioid and Cholecystokinin-A receptors could lead to altered or adverse drug response. By analyzing UK National Health Service drug prescription and sales data, we suggest that characterizing GPCR variants could increase prescription precision, improving patients' quality of life, and relieve the economic and societal burden due to variable drug responsiveness.
- 32Pandy-Szekeres, G., Munk, C., Tsonkov, T. M., Mordalski, S., Harpsoe, K., Hauser, A. S., Bojarski, A. J., and Gloriam, D. E. (2018) GPCRdb in 2018: adding GPCR structure models and ligands. Nucleic Acids Res. 46 (D1), D440– D446, DOI: 10.1093/nar/gkx1109Google Scholar32https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXitlGisLbE&md5=0cf77dd5ea934548a2d3a0ca69991f60GPCRdb in 2018: adding GPCR structure models and ligandsPandy-Szekeres, Gaspar; Munk, Christian; Tsonkov, Tsonko M.; Mordalski, Stefan; Harpsoee, Kasper; Hauser, Alexander S.; Bojarski, Andrzej J.; Gloriam, David E.Nucleic Acids Research (2018), 46 (D1), D440-D446CODEN: NARHAD; ISSN:1362-4962. (Oxford University Press)G protein-coupled receptors are the most abundant mediators of both human signaling processes and therapeutic effects. Herein, we report GPCRomewide homol. models of unprecedented quality, and roughly 150 000 GPCR ligands with data on biol. activities and com. availability. Based on the strategy of 'Less model - more Xtal', each model exploits both a main template and alternative local templates. This achieved higher similarity to new structures than any of the existing resources, and refined crystal structures with missing or distorted regions. Models are provided for inactive, intermediate and active states-except for classes C and F that so far only have inactive templates. The ligand database has sep. browsers for: (i) target selection by receptor, family or class, (ii) ligand filtering based on cross-expt. activities (min, max and mean) or chem. properties, (iii) ligand source data and (iv) com. availability. SMILES structures and activity spreadsheets can be downloaded for further processing. Furthermore, three recent landmark publications on GPCR drugs, G protein selectivity and genetic variants have been accompanied with resources that now let readers view and analyze the findings themselves in GPCRdb. Altogether, this update will enable scientific investigation for the wider GPCR community.
- 33Munk, C., Mutt, E., Isberg, V., Nikolajsen, L. F., Bibbe, J. M., Flock, T., Hanson, M. A., Stevens, R. C., Deupi, X., and Gloriam, D. E. (2019) An online resource for GPCR structure determination and analysis. Nat. Methods 16 (2), 151– 162, DOI: 10.1038/s41592-018-0302-xGoogle Scholar33https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXmtFGru74%253D&md5=a0e1ffb48671b58a63764ed4cff86901An online resource for GPCR structure determination and analysisMunk, Christian; Mutt, Eshita; Isberg, Vignir; Nikolajsen, Louise F.; Bibbe, Janne M.; Flock, Tilman; Hanson, Michael A.; Stevens, Raymond C.; Deupi, Xavier; Gloriam, David E.Nature Methods (2019), 16 (2), 151-162CODEN: NMAEA3; ISSN:1548-7091. (Nature Research)G-protein-coupled receptors (GPCRs) transduce physiol. and sensory stimuli into appropriate cellular responses and mediate the actions of one-third of drugs. GPCR structural studies have revealed the general bases of receptor activation, signaling, drug action and allosteric modulation, but so far cover only 13% of nonolfactory receptors. We broadly surveyed the receptor modifications/engineering and methods used to produce all available GPCR crystal and cryo-electron microscopy (cryo-EM) structures, and present an interactive resource integrated in GPCRdb (http://www.gpcrdb.org) to assist users in designing constructs and browsing appropriate exptl. conditions for structure studies.
- 34Takeda, S., Kadowaki, S., Haga, T., Takaesu, H., and Mitaku, S. (2002) Identification of G protein-coupled receptor genes from the human genome sequence. FEBS Lett. 520 (1–3), 97– 101, DOI: 10.1016/S0014-5793(02)02775-8Google Scholar34https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XktFOgt7s%253D&md5=d327417400f31b9fbcc7d01239494d0bIdentification of G protein-coupled receptor genes from the human genome sequenceTakeda, Shigeki; Kadowaki, Shiro; Haga, Tatsuya; Takaesu, Hirotomo; Mitaku, ShigekiFEBS Letters (2002), 520 (1-3), 97-101CODEN: FEBLAL; ISSN:0014-5793. (Elsevier Science B.V.)We have identified novel G protein-coupled receptors (GPCRs) with no introns in the coding region from the human genome sequence: 322 olfactory receptors; 22 taste receptors; 128 registered GPCRs for endogenous ligands; 50 novel GPCR candidates homologous to registered GPCRs for endogenous ligands; and 59 novel GPCR candidates not homologous to registered GPCRs. The total no. of GPCRs with and without introns in the human genome was estd. to be approx. 950, of which 500 are odorant or taste receptors and 450 are receptors for endogenous ligands.
- 35Rahmeh, R., Damian, M., Cottet, M., Orcel, H., Mendre, C., Durroux, T., Sharma, K. S., Durand, G., Pucci, B., Trinquet, E., Zwier, J. M., Deupi, X., Bron, P., Baneres, J. L., Mouillac, B., and Granier, S. (2012) Structural insights into biased G protein-coupled receptor signalling revealed by fluorescence spectroscopy. Proc. Natl. Acad. Sci. U. S. A. 109 (17), 6733– 8, DOI: 10.1073/pnas.1201093109Google Scholar35https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XmslGhtLk%253D&md5=62d24b44641a2ead4a8b83df84639606Structural insights into biased G protein-coupled receptor signaling revealed by fluorescence spectroscopyRahmeh, Rita; Damian, Marjorie; Cottet, Martin; Orcel, Helene; Mendre, Christiane; Durroux, Thierry; Sharma, K. Shivaji; Durand, Gregory; Pucci, Bernard; Trinquet, Eric; Zwier, Jurriaan M.; Deupi, Xavier; Bron, Patrick; Baneres, Jean-Louis; Mouillac, Bernard; Granier, SebastienProceedings of the National Academy of Sciences of the United States of America (2012), 109 (17), 6733-6738, S6733/1-S6733/11CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)G protein-coupled receptors (GPCRs) are seven-transmembrane proteins that mediate most cellular responses to hormones and neurotransmitters, representing the largest group of therapeutic targets. Recent studies show that some GPCRs signal through both G protein and arrestin pathways in a ligand-specific manner. Ligands that direct signaling through a specific pathway are known as biased ligands. The arginine-vasopressin type 2 receptor (V2R), a prototypical peptide-activated GPCR, is an ideal model system to investigate the structural basis of biased signaling. Although the native hormone arginine-vasopressin leads to activation of both the stimulatory G protein (Gs) for the adenylyl cyclase and arrestin pathways, synthetic ligands exhibit highly biased signaling through either Gs alone or arrestin alone. We used purified V2R stabilized in neutral amphipols and developed fluorescence-based assays to investigate the structural basis of biased signaling for the V2R. Our studies demonstrate that the Gs-biased agonist stabilizes a conformation that is distinct from that stabilized by the arrestin-biased agonists. This study provides unique insights into the structural mechanisms of GPCR activation by biased ligands that may be relevant to the design of pathway-biased drugs.
- 36Wacker, D., Wang, C., Katritch, V., Han, G. W., Huang, X. P., Vardy, E., McCorvy, J. D., Jiang, Y., Chu, M., Siu, F. Y., Liu, W., Xu, H. E., Cherezov, V., Roth, B. L., and Stevens, R. C. (2013) Structural features for functional selectivity at serotonin receptors. Science 340 (6132), 615– 9, DOI: 10.1126/science.1232808Google Scholar36https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXmslWksb0%253D&md5=16e96d0255be3ac367aeda7187aa4c15Structural Features for Functional Selectivity at Serotonin ReceptorsWacker, Daniel; Wang, Chong; Katritch, Vsevolod; Han, Gye Won; Huang, Xi-Ping; Vardy, Eyal; McCorvy, John D.; Jiang, Yi; Chu, Meihua; Siu, Fai Yiu; Liu, Wei; Xu, H. Eric; Cherezov, Vadim; Roth, Bryan L.; Stevens, Raymond C.Science (Washington, DC, United States) (2013), 340 (6132), 615-619CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)Drugs active at G protein-coupled receptors (GPCRs) can differentially modulate either canonical or noncanonical signaling pathways via a phenomenon known as functional selectivity or biased signaling. The authors report biochem. studies showing that the hallucinogen lysergic acid diethylamide, its precursor ergotamine (ERG), and related ergolines display strong functional selectivity for β-arrestin signaling at the 5-HT2B 5-hydroxytryptamine (5-HT) receptor, whereas they are relatively unbiased at the 5-HT1B receptor. To investigate the structural basis for biased signaling, the authors detd. the crystal structure of the human 5-HT2B receptor bound to ERG and compared it with the 5-HT1B/ERG structure. Given the relatively poor understanding of GPCR structure and function to date, insight into different GPCR signaling pathways is important to better understand both adverse and favorable therapeutic activities.
- 37Wingler, L. M., Elgeti, M., Hilger, D., Latorraca, N. R., Lerch, M. T., Staus, D. P., Dror, R. O., Kobilka, B. K., Hubbell, W. L., and Lefkowitz, R. J. (2019) Angiotensin Analogs with Divergent Bias Stabilize Distinct Receptor Conformations. Cell 176 (3), 468– 478 e11, DOI: 10.1016/j.cell.2018.12.005Google Scholar37https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXovFKktA%253D%253D&md5=2fe46c9f2061ac849b52bb2b372cd048Angiotensin Analogs with Divergent Bias Stabilize Distinct Receptor ConformationsWingler, Laura M.; Elgeti, Matthias; Hilger, Daniel; Latorraca, Naomi R.; Lerch, Michael T.; Staus, Dean P.; Dror, Ron O.; Kobilka, Brian K.; Hubbell, Wayne L.; Lefkowitz, Robert J.Cell (Cambridge, MA, United States) (2019), 176 (3), 468-478.e11CODEN: CELLB5; ISSN:0092-8674. (Cell Press)"Biased" G protein-coupled receptor (GPCR) agonists preferentially activate pathways mediated by G proteins or β-arrestins. Here, we use double electron-electron resonance spectroscopy to probe the changes that ligands induce in the conformational distribution of the angiotensin II type I receptor. Monitoring distances between 10 pairs of nitroxide labels distributed across the intracellular regions enabled mapping of four underlying sets of conformations. Ligands from different functional classes have distinct, characteristic effects on the conformational heterogeneity of the receptor. Compared to angiotensin II, the endogenous agonist, agonists with enhanced Gq coupling more strongly stabilize an "open" conformation with an accessible transducer-binding site. β-Arrestin-biased agonists deficient in Gq coupling do not stabilize this open conformation but instead favor two more occluded conformations. These data suggest a structural mechanism for biased ligand action at the angiotensin receptor that can be exploited to rationally design GPCR-targeting drugs with greater specificity of action.
- 38Lamichhane, R., Liu, J. J., White, K. L., Katritch, V., Stevens, R. C., Wuthrich, K., and Millar, D. P. (2020) Biased Signalling of the G-Protein-Coupled Receptor beta2AR Is Governed by Conformational Exchange Kinetics. Structure 28, 371, DOI: 10.1016/j.str.2020.01.001Google Scholar38https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhsFyitr8%253D&md5=222f483356ddbd8e67adae49f9e9126eBiased Signaling of the G-Protein-Coupled Receptor β2AR Is Governed by Conformational Exchange KineticsLamichhane, Rajan; Liu, Jeffrey J.; White, Kate L.; Katritch, Vsevolod; Stevens, Raymond C.; Wuthrich, Kurt; Millar, David P.Structure (Oxford, United Kingdom) (2020), 28 (3), 371-377.e3CODEN: STRUE6; ISSN:0969-2126. (Elsevier Ltd.)G-protein-coupled receptors (GPCRs) mediate a wide range of human physiol. functions by transducing extracellular ligand binding events into intracellular responses. GPCRs can activate parallel, independent signaling pathways mediated by G proteins or β-arrestins. Whereas "balanced" agonists activate both pathways equally, "biased" agonists dominantly activate one pathway, which is of interest for designing GPCR-targeting drugs because it may mitigate undesirable side effects. Previous studies demonstrated that β-arrestin activation is assocd. with transmembrane helix VII (TM VII) of GPCRs. Here, single-mol. fluorescence spectroscopy with the β2-adrenergic receptor (β2AR) in the ligand-free state showed that TM VII spontaneously fluctuates between one inactive and one active-like conformation. The presence of the β-arrestin-biased agonist isoetharine prolongs the dwell time of TM VII in the active-like conformation compared with the balanced agonist formoterol, suggesting that ligands can induce signaling bias by modulating the kinetics of receptor conformational exchange.
- 39Steen, A., Larsen, O., Thiele, S., and Rosenkilde, M. M. (2014) Biased and g protein-independent signalling of chemokine receptors. Front. Immunol. 5, 277, DOI: 10.3389/fimmu.2014.00277Google Scholar39https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC2cbgt1OisQ%253D%253D&md5=814b5ab6c48f59e2543803e516b35bbfBiased and g protein-independent signaling of chemokine receptorsSteen Anne; Larsen Olav; Thiele Stefanie; Rosenkilde Mette MFrontiers in immunology (2014), 5 (), 277 ISSN:1664-3224.Biased signaling or functional selectivity occurs when a 7TM-receptor preferentially activates one of several available pathways. It can be divided into three distinct forms: ligand bias, receptor bias, and tissue or cell bias, where it is mediated by different ligands (on the same receptor), different receptors (with the same ligand), or different tissues or cells (for the same ligand-receptor pair). Most often biased signaling is differentiated into G protein-dependent and β-arrestin-dependent signaling. Yet, it may also cover signaling differences within these groups. Moreover, it may not be absolute, i.e., full versus no activation. Here we discuss biased signaling in the chemokine system, including the structural basis for biased signaling in chemokine receptors, as well as in class A 7TM receptors in general. This includes overall helical movements and the contributions of micro-switches based on recently published 7TM crystals and molecular dynamics studies. All three forms of biased signaling are abundant in the chemokine system. This challenges our understanding of "classic" redundancy inevitably ascribed to this system, where multiple chemokines bind to the same receptor and where a single chemokine may bind to several receptors - in both cases with the same functional outcome. The ubiquitous biased signaling confers a hitherto unknown specificity to the chemokine system with a complex interaction pattern that is better described as promiscuous with context-defined roles and different functional outcomes in a ligand-, receptor-, or cell/tissue-defined manner. As the low number of successful drug development plans implies, there are great difficulties in targeting chemokine receptors; in particular with regard to receptor antagonists as anti-inflammatory drugs. Un-defined and putative non-selective targeting of the complete cellular signaling system could be the underlying cause of lack of success. Therefore, biased ligands could be the solution.
- 40Roth, S., Kholodenko, B. N., Smit, M. J., and Bruggeman, F. J. (2015) G Protein-Coupled Receptor Signalling Networks from a Systems Perspective. Mol. Pharmacol. 88 (3), 604– 16, DOI: 10.1124/mol.115.100057Google Scholar40https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsVCgsrfJ&md5=80924202aa2be037de8739f99bdd7f03G protein-coupled receptor signaling networks from a systems perspectiveRoth, S.; Kholodenko, B. N.; Smit, M. J.; Bruggeman, F. J.Molecular Pharmacology (2015), 88 (3), 604-616CODEN: MOPMA3; ISSN:1521-0111. (American Society for Pharmacology and Experimental Therapeutics)The signal-transduction network of a mammalian cell integrates internal and external cues to initiate adaptive responses. Among the cell-surface receptors are the G protein-coupled receptors (GPCRs), which have remarkable signal-integrating capabilities. Binding of extracellular signals stabilizes intracellular-domain conformations that selectively activate intracellular proteins. Hereby, multiple signaling routes are activated simultaneously to degrees that are signal-combination dependent. Systems-biol. studies indicate that signaling networks have emergent processing capabilities that go far beyond those of single proteins. Such networks are spatiotemporally organized and capable of gradual, oscillatory, all-or-none, and subpopulation-generating responses. Protein-protein interactions, generating feedback and feedforward circuitry, are generally required for these spatiotemporal phenomena. Understanding of information processing by signaling networks therefore requires network theories in addn. to biochem. and biophys. concepts. Here we review some of the key signaling systems behaviors that have been discovered recurrently across signaling networks. We emphasize the role of GPCRs, so far underappreciated receptors in systems-biol. research.
- 41Grundmann, M. and Kostenis, E. (2017) Temporal Bias: Time-Encoded Dynamic GPCR Signalling. Trends Pharmacol. Sci. 38 (12), 1110– 1124, DOI: 10.1016/j.tips.2017.09.004Google Scholar41https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhs1elsbbK&md5=8ea88ba1c0028bc1ac67b64375d09824Temporal Bias: Time-Encoded Dynamic GPCR SignalingGrundmann, Manuel; Kostenis, EviTrends in Pharmacological Sciences (2017), 38 (12), 1110-1124CODEN: TPHSDY; ISSN:0165-6147. (Elsevier Ltd.)A review. Evidence suggests that cells can time-encode signals for secure transport and perception of information, and it appears that this dynamic signaling is a common principle of nature to code information in time. G-protein-coupled receptor (GPCR) signaling networks are no exception as their compn. and signal transduction appear temporally flexible. In this review, we discuss the potential mechanisms by which GPCRs code biol. information in time to create 'temporal bias'. We highlight dynamic signaling patterns from the second messenger to the receptor-ligand level and shed light on the dynamics of G-protein cycles, the kinetics of ligand-receptor interaction, and the occurrence of distinct signaling waves within the cell. A dynamic feature such as temporal bias adds to the complexity of GPCR signaling bias and gives rise to the question whether this trait could be exploited to gain control over time-encoded cell physiol.
- 42Irannejad, R., Pessino, V., Mika, D., Huang, B., Wedegaertner, P. B., Conti, M., and von Zastrow, M. (2017) Functional selectivity of GPCR-directed drug action through location bias. Nat. Chem. Biol. 13 (7), 799– 806, DOI: 10.1038/nchembio.2389Google Scholar42https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXosFSrurg%253D&md5=49bff4da00d6c7a2d975aef416ff55dbFunctional selectivity of GPCR-directed drug action through location biasIrannejad, Roshanak; Pessino, Veronica; Mika, Delphine; Huang, Bo; Wedegaertner, Philip B.; Conti, Marco; von Zastrow, MarkNature Chemical Biology (2017), 13 (7), 799-806CODEN: NCBABT; ISSN:1552-4450. (Nature Publishing Group)G-protein-coupled receptors (GPCRs) are increasingly recognized to operate from intracellular membranes as well as the plasma membrane. The β2-adrenergic GPCR can activate Gs-linked cAMP (Gs-cAMP) signaling from endosomes. We show here that the homologous human β1-adrenergic receptor initiates an internal Gs-cAMP signal from the Golgi app. By developing a chem. method to acutely squelch G-protein coupling at defined membrane locations, we demonstrate that Golgi activation contributes significantly to the overall cellular cAMP response. Golgi signaling utilizes a preexisting receptor pool rather than receptors delivered from the cell surface, requiring sep. access of extracellular ligands. Epinephrine, a hydrophilic endogenous ligand, accesses the Golgi-localized receptor pool by facilitated transport requiring the org. cation transporter 3 (OCT3), whereas drugs can access the Golgi pool by passive diffusion according to hydrophobicity. We demonstrate marked differences, among both agonist and antagonist drugs, in Golgi-localized receptor access and show that β-blocker drugs currently used in the clinic differ markedly in ability to antagonize the Golgi signal. We propose 'location bias' as a new principle for achieving functional selectivity of GPCR-directed drug action.
- 43Eichel, K. and von Zastrow, M. (2018) Subcellular Organization of GPCR Signalling. Trends Pharmacol. Sci. 39 (2), 200– 208, DOI: 10.1016/j.tips.2017.11.009Google Scholar43https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXitVCmsbjL&md5=6c5222b28cb227d8367283aff2befa4cSubcellular Organization of GPCR SignalingEichel, Kelsie; von Zastrow, MarkTrends in Pharmacological Sciences (2018), 39 (2), 200-208CODEN: TPHSDY; ISSN:0165-6147. (Elsevier Ltd.)A review. G protein-coupled receptors (GPCRs) comprise a large and diverse class of signal-transducing receptors that undergo dynamic and isoform-specific membrane trafficking. GPCRs thus have an inherent potential to initiate or regulate signaling reactions from multiple membrane locations. This review discusses emerging insights into the subcellular organization of GPCR function in mammalian cells, focusing on signaling transduced by heterotrimeric G proteins and β-arrestins. We summarize recent evidence indicating that GPCR-mediated activation of G proteins occurs not only from the plasma membrane (PM) but also from endosomes and Golgi membranes and that β-arrestin-dependent signaling can be transduced from the PM by β-arrestin trafficking to clathrin-coated pits (CCPs) after dissocn. from a ligand-activated GPCR.
- 44Shaw, W. M., Yamauchi, H., Mead, J., Gowers, G. F., Bell, D. J., Oling, D., Larsson, N., Wigglesworth, M., Ladds, G., and Ellis, T. (2019) Engineering a Model Cell for Rational Tuning of GPCR Signalling. Cell 177 (3), 782– 796 e27, DOI: 10.1016/j.cell.2019.02.023Google Scholar44https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXmvFShtbc%253D&md5=2c7072e6cde1759d9d3e41968c137dd3Engineering a Model Cell for Rational Tuning of GPCR SignalingShaw, William M.; Yamauchi, Hitoshi; Mead, Jack; Gowers, Glen-Oliver F.; Bell, David J.; Oling, David; Larsson, Niklas; Wigglesworth, Mark; Ladds, Graham; Ellis, TomCell (Cambridge, MA, United States) (2019), 177 (3), 782-796.e27CODEN: CELLB5; ISSN:0092-8674. (Cell Press)G protein-coupled receptor (GPCR) signaling is the primary method eukaryotes use to respond to specific cues in their environment. However, the relation between stimulus and response for each GPCR is difficult to predict due to diversity in natural signal transduction architecture and expression. Using genome engineering in yeast, the authors constructed an insulated, modular GPCR signal transduction system to study how the response to stimuli can be predictably tuned using synthetic tools. The authors delineated the contributions of a minimal set of key components via computational and exptl. refactoring, identifying simple design principles for rationally tuning the dose response. Using five different GPCRs, this enables cells and consortia to be engineered to respond to desired concns. of peptides, metabolites, and hormones relevant to human health. This work enables rational tuning of cell sensing while providing a framework to guide reprogramming of GPCR-based signaling in other systems.
- 45Apostolakou, A. E., Baltoumas, F. A., Stravopodis, D. J., and Iconomidou, V. A. (2020) Extended Human G-Protein Coupled Receptor Network: Cell-Type-Specific Analysis of G-Protein Coupled Receptor Signalling Pathways. J. Proteome Res. 19 (1), 511– 524, DOI: 10.1021/acs.jproteome.9b00754Google Scholar45https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXit1CrsrjP&md5=66ad9ec99da475e6be98a6ca3efcbc9aExtended Human G-Protein Coupled Receptor Network: Cell-Type-Specific Analysis of G-Protein Coupled Receptor Signaling PathwaysApostolakou, Avgi E.; Baltoumas, Fotis A.; Stravopodis, Dimitrios J.; Iconomidou, Vassiliki A.Journal of Proteome Research (2020), 19 (1), 511-524CODEN: JPROBS; ISSN:1535-3893. (American Chemical Society)G-protein coupled receptors (GPCRs) mediate crucial physiol. functions in humans, have been implicated in an array of diseases, and are therefore prime drug targets. GPCRs signal via a multitude of pathways, mainly through G-proteins and β-arrestins, to regulate effectors responsible for cellular responses. The limited no. of transducers results in different GPCRs exerting control on the same pathway, while the availability of signaling proteins in a cell defines the result of GPCR activation. The aim of this study was to construct the extended human GPCR network (hGPCRnet) and examine the effect that cell-type specificity has on GPCR signaling pathways. To achieve this, protein-protein interaction data between GPCRs, G-protein coupled receptor kinases (GRKs), Gα subunits, β-arrestins, and effectors were combined with protein expression data in cell types. This resulted in the hGPCRnet, a very large interconnected network, and similar cell-type-specific networks in which, distinct GPCR signaling pathways were formed. Finally, a user friendly web application, hGPCRnet (http://bioinformatics.biol.uoa.gr/hGPCRnet), was created to allow for the visualization and exploration of these networks and of GPCR signaling pathways. This work, and the resulting application, can be useful in further studies of GPCR function and pharmacol.
- 46Wang, J., Gareri, C., and Rockman, H. A. (2018) G-Protein-Coupled Receptors in Heart Disease. Circ. Res. 123 (6), 716– 735, DOI: 10.1161/CIRCRESAHA.118.311403Google Scholar46https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhs1WitLnP&md5=0af28f631cfaea6d08c1154806229dbaG-Protein-Coupled Receptors in Heart DiseaseWang, Jialu; Gareri, Clarice; Rockman, Howard A.Circulation Research (2018), 123 (6), 716-735CODEN: CIRUAL; ISSN:0009-7330. (Lippincott Williams & Wilkins)GPCRs (G-protein [guanine nucleotide-binding protein]-coupled receptors) play a central physiol. role in the regulation of cardiac function in both health and disease and thus represent one of the largest class of surface receptors targeted by drugs. Several antagonists of GPCRs, such as βARs (β-adrenergic receptors) and Ang II (angiotensin II) receptors, are now considered std. of therapy for a wide range of cardiovascular disease, such as hypertension, coronary artery disease, and heart failure. Although the mechanism of action for GPCRs was thought to be largely worked out in the 80s and 90s, recent discoveries have brought to the fore new and previously unappreciated mechanisms for GPCR activation and subsequent downstream signaling. In this review, we focus on GPCRs most relevant to the cardiovascular system and discuss traditional components of GPCR signaling and highlight evolving concepts in the field, such as ligand bias, β-arrestin-mediated signaling, and conformational heterogeneity.
- 47Allen, J. A., Yost, J. M., Setola, V., Chen, X., Sassano, M. F., Chen, M., Peterson, S., Yadav, P. N., Huang, X. P., Feng, B., Jensen, N. H., Che, X., Bai, X., Frye, S. V., Wetsel, W. C., Caron, M. G., Javitch, J. A., Roth, B. L., and Jin, J. (2011) Discovery of beta-arrestin-biased dopamine D2 ligands for probing signal transduction pathways essential for antipsychotic efficacy. Proc. Natl. Acad. Sci. U. S. A. 108 (45), 18488– 93, DOI: 10.1073/pnas.1104807108Google Scholar47https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhsFymtLzK&md5=d5b06e4ac4d2cc4cd04fd1de760ec628Discovery of β-arrestin-biased dopamine D2 ligands for probing signal transduction pathways essential for antipsychotic efficacyAllen, John A.; Yost, Julianne M.; Setola, Vincent; Chen, Xin; Sassano, Maria F.; Chen, Meng; Peterson, Sean; Yadav, Prem N.; Huang, Xi-Ping; Feng, Bo; Jensen, Niels H.; Che, Xin; Bai, Xu; Frye, Stephen V.; Wetsel, William C.; Caron, Marc G.; Javitch, Jonathan A.; Roth, Bryan L.; Jin, JianProceedings of the National Academy of Sciences of the United States of America (2011), 108 (45), 18488-18493, S18488/1-S18488/15CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Elucidating the key signal transduction pathways essential for both antipsychotic efficacy and side-effect profiles is essential for developing safer and more effective therapies. Recent work has highlighted noncanonical modes of dopamine D2 receptor (D2R) signaling via β-arrestins as being important for the therapeutic actions of both antipsychotic and antimanic agents. We thus sought to create unique D2R agonists that display signaling bias via β-arrestinergic signaling. Through a robust diversity-oriented modification of the scaffold represented by aripiprazole (1), we discovered UNC9975 (2), UNC0006 (3); and UNC9994 (4) as unprecedented β-arrestin-biased D2R ligands. These compds. also represent unprecedented β-arrestin-biased ligands for a Gi-coupled G protein-coupled receptor (GPCR). Significantly, UNC9975, UNC0006, and UNC9994 are simultaneously antagonists of Gi-regulated cAMP prodn. and partial agonists for D2R/β-arrestin-2 interactions. Importantly, VNC9975 displayed potent antipsychotic-like activity without inducing motoric side effects in inbred C57BL/6 mice in vivo. Genetic deletion of β-arrestin-2 simultaneously attenuated the antipsychotic actions of UNC9975 and transformed it into a typical antipsychotic .drug with a high propensity to induce catalepsy. Similarly, the antipsychotic-like activity displayed by UNC9994, an extremely β-arrestin-biased D2R agonist, in wild-type mice was completely abolished in β-arrestin-2 knockout mice. Taken together, our results suggest that β-arrestin signaling and recruitment can be simultaneously a significant contributor to antipsychotic efficacy and protective against motoric side effects. These functionally selective, β-arrestin-biased D2R ligands represent valuable chem. probes for further investigations of D2R signaling in health and disease.
- 48Moller, D., Kling, R. C., Skultety, M., Leuner, K., Hubner, H., and Gmeiner, P. (2014) Functionally selective dopamine D(2), D(3) receptor partial agonists. J. Med. Chem. 57 (11), 4861– 75, DOI: 10.1021/jm5004039Google Scholar48https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC2cjjtFCquw%253D%253D&md5=ddab57825968f481f733b766ce2bec64Functionally selective dopamine D2, D3 receptor partial agonistsMoller Dorothee; Kling Ralf C; Skultety Marika; Leuner Kristina; Hubner Harald; Gmeiner PeterJournal of medicinal chemistry (2014), 57 (11), 4861-75 ISSN:.Dopamine D2 receptor-promoted activation of Gα(o) over Gα(i) may increase synaptic plasticity and thereby might improve negative symptoms of schizophrenia. Heterocyclic dopamine surrogates comprising a pyrazolo[1,5-a]pyridine moiety were synthesized and investigated for their binding properties when low- to subnanomolar K(i) values were determined for D(2L), D(2S), and D3 receptors. Measurement of [(35)S]GTPγS incorporation at D(2S) coexpressed with G-protein subunits indicated significant bias for promotion of Gα(o1) over Gα(i2) coupling for several test compounds. Functionally selective D(2S) activation was most striking for the carbaldoxime 8b (Gα(o1), pEC50 = 8.87, E(max) = 65%; Gα(i2), pEC50 = 6.63, E(max) = 27%). In contrast, the investigated 1,4-disubstituted aromatic piperazines (1,4-DAPs) behaved as antagonists for β-arrestin-2 recruitment, implying significant ligand bias for G-protein activation over β-arrestin-2 recruitment at D(2S) receptors. Ligand efficacy and selectivity between D(2S) and D3 activation were strongly influenced by regiochemistry and the nature of functional groups attached to the pyrazolo[1,5-a]pyridine moiety.
- 49Weiwer, M., Xu, Q., Gale, J. P., Lewis, M., Campbell, A. J., Schroeder, F. A., Van de Bittner, G. C., Walk, M., Amaya, A., Su, P., L, D. O., Sacher, J. R., Skepner, A., Fei, D., Dennehy, K., Nguyen, S., Faloon, P. W., Perez, J., Cottrell, J. R., Liu, F., Palmer, M., Pan, J. Q., Hooker, J. M., Zhang, Y. L., Scolnick, E., Wagner, F. F., and Holson, E. B. (2018) Functionally Biased D2R Antagonists: Targeting the beta-Arrestin Pathway to Improve Antipsychotic Treatment. ACS Chem. Biol. 13 (4), 1038– 1047, DOI: 10.1021/acschembio.8b00168Google Scholar49https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXjtlOrtbw%253D&md5=51d636dd2a0ebfc83d58a6158a1da40eFunctionally Biased D2R Antagonists: Targeting the β-Arrestin Pathway to Improve Antipsychotic TreatmentWeiwer, Michel; Xu, Qihong; Gale, Jennifer P.; Lewis, Michael; Campbell, Arthur J.; Schroeder, Frederick A.; Van de Bittner, Genevieve C.; Walk, Michelle; Amaya, Aldo; Su, Ping; Dordevic, Luka; Sacher, Joshua R.; Skepner, Adam; Fei, David; Dennehy, Kelly; Nguyen, Shannon; Faloon, Patrick W.; Perez, Jose; Cottrell, Jeffrey R.; Liu, Fang; Palmer, Michelle; Pan, Jen Q.; Hooker, Jacob M.; Zhang, Yan-Ling; Scolnick, Edward; Wagner, Florence F.; Holson, Edward B.ACS Chemical Biology (2018), 13 (4), 1038-1047CODEN: ACBCCT; ISSN:1554-8929. (American Chemical Society)Schizophrenia is a severe neuropsychiatric disease that lacks completely effective and safe therapies. As a polygenic disorder, genetic studies have only started to shed light on its complex etiol. To date, the pos. symptoms of schizophrenia are well-managed by antipsychotic drugs, which primarily target the dopamine D2 receptor (D2R). However, these antipsychotics are often accompanied by severe side effects, including motoric symptoms. At D2R, antipsychotic drugs antagonize both G-protein dependent (Gαi/o) signaling and G-protein independent (β-arrestin) signaling. However, the relevant contributions of the distinct D2R signaling pathways to antipsychotic efficacy and on-target side effects (motoric) are still incompletely understood. Recent evidence from mouse genetic and pharmacol. studies point to β-arrestin signaling as the major driver of antipsychotic efficacy and suggest that a β-arrestin biased D2R antagonist could achieve an addnl. level of selectivity at D2R, increasing the therapeutic index of next generation antipsychotics. Here, we characterize BRD5814, a highly brain penetrant β-arrestin biased D2R antagonist. BRD5814 demonstrated good target engagement via PET imaging, achieving efficacy in an amphetamine-induced hyperlocomotion mouse model with strongly reduced motoric side effects in a rotarod performance test. This proof of concept study opens the possibility for the development of a new generation of pathway selective antipsychotics at D2R with reduced side effect profiles for the treatment of schizophrenia.
- 50DeWire, S. M., Yamashita, D. S., Rominger, D. H., Liu, G., Cowan, C. L., Graczyk, T. M., Chen, X. T., Pitis, P. M., Gotchev, D., Yuan, C., Koblish, M., Lark, M. W., and Violin, J. D. (2013) A G protein-biased ligand at the mu-opioid receptor is potently analgesic with reduced gastrointestinal and respiratory dysfunction compared with morphine. J. Pharmacol. Exp. Ther. 344 (3), 708– 17, DOI: 10.1124/jpet.112.201616Google Scholar50https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXjvVaisro%253D&md5=33a685cd1952dd9cb1fb82afe78452afA G protein-biased ligand at the μ-opioid receptor is potently analgesic with reduced gastrointestinal and respiratory dysfunction compared with morphineDeWire, Scott M.; Yamashita, Dennis S.; Rominger, David H.; Liu, Guodong; Cowan, Conrad L.; Graczyk, Thomas M.; Chen, Xiao-Tao; Pitis, Philip M.; Gotchev, Dimitar; Yuan, Catherine; Koblish, Michael; Lark, Michael W.; Violin, Jonathan D.Journal of Pharmacology and Experimental Therapeutics (2013), 344 (3), 708-717CODEN: JPETAB; ISSN:1521-0103. (American Society for Pharmacology and Experimental Therapeutics)The concept of ligand bias at G protein-coupled receptors broadens the possibilities for agonist activities and provides the opportunity to develop safer, more selective therapeutics. Morphine pharmacol. in β-arrestin-2 knockout mice suggested that a ligand that promotes coupling of the μ-opioid receptor (MOR) to G proteins, but not β-arrestins, would result in higher analgesic efficacy, less gastrointestinal dysfunction, and less respiratory suppression than morphine. Here we report the discovery of TRV130 ([(3-methoxythiophen-2-yl)methyl]({2-[(9R)-9-(pyridin-2-yl)-6-oxaspiro[4.5]decan-9-yl]ethyl})amine), a novel MOR G protein-biased ligand. In cell-based assays, TRV130 elicits robust G protein signaling, with potency and efficacy similar to morphine, but with far less β-arrestin recruitment and receptor internalization. In mice and rats, TRV130 is potently analgesic while causing less gastrointestinal dysfunction and respiratory suppression than morphine at equianalgesic doses. TRV130 successfully translates evidence that analgesic and adverse MOR signaling pathways are distinct into a biased ligand with differentiated pharmacol. These preclin. data suggest that TRV130 may be a safer and more tolerable therapeutic for treating severe pain.
- 51Schmid, C. L., Kennedy, N. M., Ross, N. C., Lovell, K. M., Yue, Z., Morgenweck, J., Cameron, M. D., Bannister, T. D., and Bohn, L. M. (2017) Bias Factor and Therapeutic Window Correlate to Predict Safer Opioid Analgesics. Cell 171 (5), 1165– 1175 e13, DOI: 10.1016/j.cell.2017.10.035Google Scholar51https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhvFOhs7vE&md5=6d3f21c03fb40bc83adbe62c3ea331fcBias Factor and Therapeutic Window Correlate to Predict Safer Opioid AnalgesicsSchmid, Cullen L.; Kennedy, Nicole M.; Ross, Nicolette C.; Lovell, Kimberly M.; Yue, Zhizhou; Morgenweck, Jenny; Cameron, Michael D.; Bannister, Thomas D.; Bohn, Laura M.Cell (Cambridge, MA, United States) (2017), 171 (5), 1165-1175.e13CODEN: CELLB5; ISSN:0092-8674. (Cell Press)Biased agonism has been proposed as a means to sep. desirable and adverse drug responses downstream of G protein-coupled receptor (GPCR) targets. Herein, we describe structural features of a series of mu-opioid-receptor (MOR)-selective agonists that preferentially activate receptors to couple to G proteins or to recruit βarrestin proteins. By comparing relative bias for MOR-mediated signaling in each pathway, we demonstrate a strong correlation between the respiratory suppression/antinociception therapeutic window in a series of compds. spanning a wide range of signaling bias. We find that β-arrestin-biased compds., such as fentanyl, are more likely to induce respiratory suppression at weak analgesic doses, while G protein signaling bias broadens the therapeutic window, allowing for antinociception in the absence of respiratory suppression.
- 52James, I. E., Skobieranda, F., Soergel, D. G., Ramos, K. A., Ruff, D., and Fossler, M. J. (2020) A First-in-Human Clinical Study With TRV734, an Orally Bioavailable G-Protein-Biased Ligand at the mu-Opioid Receptor. Clin. Pharmacol. Drug Dev. 9 (2), 256– 266, DOI: 10.1002/cpdd.721Google Scholar52https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXisFajs7w%253D&md5=46faef25a0959ddbd0f95623c186e674A First-in-Human Clinical Study With TRV734, an Orally Bioavailable G-Protein-Biased Ligand at the μ-Opioid ReceptorJames, Ian E.; Skobieranda, Franck; Soergel, David G.; Ramos, Kimberly A.; Ruff, Dennis; Fossler, Michael J.Clinical Pharmacology in Drug Development (2020), 9 (2), 256-266CODEN: CPDDAH; ISSN:2160-7648. (John Wiley & Sons, Inc.)TRV734 is an orally bioavailable G-protein-biased ligand at the μ-opioid receptor. In nonclin. studies it was potently analgesic while causing less gastrointestinal dysfunction than morphine, suggesting unique benefits in acute pain management. A 2-part, first-in-human study was conducted with ascending doses of TRV734 to explore its tolerability, pharmacokinetics, and pharmacodynamics in healthy volunteers. TRV734 was well tolerated over the dose range 2 to 250 mg when administered orally. Plasma TRV734 max. concn. and area under the plasma concn.-time curve generally increased with dose, while time to max. concn. was similar across doses (0.5-1.3 h). The half-life increased with dose from 10 mg through 150 mg (0.75-2.28 h) but was similar from 150 mg through 250 mg. Pupil constriction, confirming central nervous system μ-opioid receptor engagement, correlated with higher plasma TRV734 concns.; the greatest redns. in pupil diam. occurring between 0 and 4 h after dosing (-2.9 mm/h, with redn. peaking at 1 h, and returning to baseline by 8 h). Following administration of TRV734 125 mg under fasted or fed conditions, there was no significant difference in bioavailability when given as a soln. or drug in capsule to fasted subjects. When drug in capsule was given to subjects following a high-fat meal, absorption was slowed, resulting in decreased peak concns., but area under the plasma concn.-time curve was not affected.
- 53Conibear, A. E. and Kelly, E. (2019) A Biased View of mu-Opioid Receptors?. Mol. Pharmacol. 96 (5), 542– 549, DOI: 10.1124/mol.119.115956Google Scholar53https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXitlams7zK&md5=2bdf67af51575f7abfd1514345086cd8A biased view of μ-opioid receptors?Conibear, Alexandra E.; Kelly, EamonnMolecular Pharmacology (2019), 96 (5), 542-549CODEN: MOPMA3; ISSN:1521-0111. (American Society for Pharmacology and Experimental Therapeutics)A review. The field of biased agonism has grown substantially in recent years and the μ-opioid receptor has been one of the most intensively studied receptor targets for developing biased agonists. Yet, despite extensive research efforts, the development of analgesics with reduced adverse effects remains a significant challenge. In this review we discuss the evidence to support the prevailing hypothesis that a G protein-biased agonist at the μ-opioid receptor would be an effective analgesic without the accompanying adverse effects assocd. with conventional μ-opioid agonists. We also assess the current status of established and novel μ-opioid-receptor ligands that are proposed to be biased ligands.
- 54Pedersen, M. F., Wrobel, T. M., Marcher-Rorsted, E., Pedersen, D. S., Moller, T. C., Gabriele, F., Pedersen, H., Matosiuk, D., Foster, S. R., Bouvier, M., and Brauner-Osborne, H. (2020) Biased agonism of clinically approved mu-opioid receptor agonists and TRV130 is not controlled by binding and signalling kinetics. Neuropharmacology 166, 107718, DOI: 10.1016/j.neuropharm.2019.107718Google Scholar54https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXit12ktrbI&md5=a63ba99f8beb16f92aa793dcc1e0a0f7Biased agonism of clinically approved μ-opioid receptor agonists and TRV130 is not controlled by binding and signaling kineticsPedersen, Mie Fabricius; Wrobel, Tomasz Marcin; Marcher-Roersted, Emil; Pedersen, Daniel Sejer; Moeller, Thor Christian; Gabriele, Federica; Pedersen, Henrik; Matosiuk, Dariusz; Foster, Simon Richard; Bouvier, Michel; Brauner-Osborne, HansNeuropharmacology (2020), 166 (), 107718CODEN: NEPHBW; ISSN:0028-3908. (Elsevier B.V.)Here we provide a comprehensive kinetic pharmacol. comparison of clin. relevant μ-opioid receptor agonists, including the novel biased agonist oliceridine (TRV130) which is in clin. trial for pain management. We demonstrate that the bias profile obsd. for the selected agonists is not time-dependent and that agonists with dramatic differences in their binding kinetic properties can display the same degree of bias. Binding kinetics analyses demonstrate that buprenorphine has 18-fold higher receptor residence time than oliceridine. This is thus the largest pharmacodynamic difference between the clin. approved drug buprenorphine and the clin. candidate oliceridine, since their bias profiles are similar. Further, we provide the first pharmacol. characterization of (S)-TRV130 demonstrating that it has a similar pharmacol. profile as the (R)-form, oliceridine, but displays 90-fold lower potency than the (R)-form. This difference is driven by a significantly slower assocn. rate. GRK2 and GRK5 overexpression greatly increased μ-opioid receptor internalization induced by morphine, but only had modest effects on buprenorphine and oliceridine-induced internalization. Overall, our data reveal that the clin. available drug buprenorphine displays a similar pharmacol. bias profile in vitro compared to the clin. candidate drug oliceridine and that this bias is independent of binding kinetics suggesting a mechanism driven by receptor-conformations.
- 55Kliewer, A., Schmiedel, F., Sianati, S., Bailey, A., Bateman, J. T., Levitt, E. S., Williams, J. T., Christie, M. J., and Schulz, S. (2019) Phosphorylation-deficient G-protein-biased mu-opioid receptors improve analgesia and diminish tolerance but worsen opioid side effects. Nat. Commun. 10 (1), 367, DOI: 10.1038/s41467-018-08162-1Google Scholar55https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXntFeks7k%253D&md5=19fa2354d75d29b28503d21f63754d45Phosphorylation-deficient G-protein-biased mu-opioid receptors improve analgesia and diminish tolerance but worsen opioid side effectsKliewer, A.; Schmiedel, F.; Sianati, S.; Bailey, A.; Bateman, J. T.; Levitt, E. S.; Williams, J. T.; Christie, M. J.; Schulz, S.Nature Communications (2019), 10 (1), 367CODEN: NCAOBW; ISSN:2041-1723. (Nature Research)Opioid analgesics are powerful pain relievers; however, over time, pain control diminishes as analgesic tolerance develops. The mol. mechanisms initiating tolerance have remained unresolved to date. We have previously shown that desensitization of the mu-opioid receptor and interaction with beta-arrestins is controlled by carboxyl-terminal phosphorylation. Here we created knockin mice with a series of serine- and threonine-to-alanine mutations that render the receptor increasingly unable to recruit beta-arrestins. Desensitization is inhibited in locus coeruleus neurons of mutant mice. Opioid-induced analgesia is strongly enhanced and analgesic tolerance is greatly diminished. Surprisingly, respiratory depression, constipation, and opioid withdrawal signs are unchanged or exacerbated, indicating that beta-arrestin recruitment does not contribute to the severity of opioid side effects and, hence, predicting that G-protein-biased mu-agonists are still likely to elicit severe adverse effects. In conclusion, our findings identify carboxyl-terminal multisite phosphorylation as key step that drives acute mu-opioid receptor desensitization and long-term tolerance.
- 56Kliewer, A., Gillis, A., Hill, R., Schmidel, F., Bailey, C., Kelly, E., Henderson, G., Christie, M. J., and Schulz, S. (2020) Morphine-induced respiratory depression is independent of beta-arrestin2 signalling. Br. J. Pharmacol. DOI: 10.1111/bph.15004Google ScholarThere is no corresponding record for this reference.
- 57Michel, M. C. and Charlton, S. J. (2018) Biased Agonism in Drug Discovery-Is It Too Soon to Choose a Path?. Mol. Pharmacol. 93 (4), 259– 265, DOI: 10.1124/mol.117.110890Google Scholar57https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhs12qsr3K&md5=a975e0fedbb29ba2059fe14c5be5d434Biased agonism in drug discovery-is it too soon to choose a path?Michel, Martin C.; Charlton, Steven J.Molecular Pharmacology (2018), 93 (4), 259-265CODEN: MOPMA3; ISSN:1521-0111. (American Society for Pharmacology and Experimental Therapeutics)A single receptor can activate multiple signaling pathways that have distinct or even opposite effects on cell function. Biased agonists stabilize receptor conformations preferentially stimulating one of these pathways, and therefore allow a more targeted modulation of cell function and treatment of disease. Dedicated development of biased agonists has led to promising drug candidates in clin. development, such as the G proteinbiased μ opioid receptor agonist oliceridine. However, leveraging the theor. potential of biased agonism for drug discovery faces several challenges. Some of these challenges are tech., such as techniques for quant. anal. of bias and development of suitable screening assays; others are more fundamental, such as the need to robustly identify in a very early phase which cell type harbors the cellular target of the drug candidate, which signaling pathway leads to the desired therapeutic effect, and how these pathways may be modulated in the disease to be treated. We conclude that biased agonism has potential mainly in the treatment of conditions with a wellunderstood pathophysiol.; in contrast, it may increase effort and com. risk under circumstances where the pathophysiol. has been less well defined, as is the case with many highly innovative treatments.
- 58Wootten, D., Christopoulos, A., Marti-Solano, M., Babu, M. M., and Sexton, P. M. (2018) Mechanisms of signalling and biased agonism in G protein-coupled receptors. Nat. Rev. Mol. Cell Biol. 19 (10), 638– 653, DOI: 10.1038/s41580-018-0049-3Google Scholar58https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhsFSqtbzO&md5=61ffa3780b7da6df8a8ccee2365354aeMechanisms of signalling and biased agonism in G protein-coupled receptorsWootten, Denise; Christopoulos, Arthur; Marti-Solano, Maria; Babu, M. Madan; Sexton, Patrick M.Nature Reviews Molecular Cell Biology (2018), 19 (10), 638-653CODEN: NRMCBP; ISSN:1471-0072. (Nature Research)A review. G protein-coupled receptors (GPCRs) are the largest group of cell surface receptors in humans that signal in response to diverse inputs and regulate a plethora of cellular processes. Hence, they constitute one of the primary drug target classes. Progress in our understanding of GPCR dynamics, activation and signalling has opened new possibilities for selective drug development. A key advancement has been provided by the concept of biased agonism, which describes the ability of ligands acting at the same GPCR to elicit distinct cellular signalling profiles by preferentially stabilizing different active conformational states of the receptor. Application of this concept raises the prospect of 'designer' biased agonists as optimized therapeutics with improved efficacy and/or reduced side-effect profiles. However, this application will require a detailed understanding of the spectrum of drug actions and a structural understanding of the drug-receptor interactions that drive distinct pharmacologies. The recent revolution in GPCR structural biol. provides unprecedented insights into ligand binding, conformational dynamics and the control of signalling outcomes. These insights, together with new approaches to multi-dimensional anal. of drug action, are allowing refined classification of drugs according to their pharmacodynamic profiles, which can be linked to receptor structure and predictions of preclin. drug efficacy.
- 59Kenakin, T. (2019) Biased Receptor Signalling in Drug Discovery. Pharmacol. Rev. 71 (2), 267– 315, DOI: 10.1124/pr.118.016790Google Scholar59https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhvV2gtL3E&md5=ddf8cb5adb1dc14783bfc82a308fc70dBiased receptor signaling in drug discoveryKenakin, TerryPharmacological Reviews (2019), 71 (2), 267-315CODEN: PAREAQ; ISSN:1521-0081. (American Society for Pharmacology and Experimental Therapeutics)A review. A great deal of exptl. evidence suggests that ligands can stabilize different receptor active states that go on to interact with cellular signaling proteins to form a range of different complexes in varying quantities. In pleiotropically linked receptor systems, this leads to selective activation of some signaling pathways at the expense of others (biased signaling). This article summarizes the current knowledge about the complex components of receptor systems, the evidence that biased signaling is used in natural physiol. to fine-tune signaling, and the current thoughts on how this mechanism may be applied to the design of better drugs. Although this is a fairly newly discovered phenomenon, theor. and exptl. data suggest that it is a ubiquitous behavior of ligands and receptors and to be expected. Biased signaling is simple to detect in vitro and there are numerous methods to quantify the effect with scales that can be used to optimize this activity in structure-activity medicinal chem. studies. At present, the major hurdle in the application of this mechanism to therapeutics is the translation of in vitro bias to in vivo effect; this is because of the numerous factors that can modify measures of bias in natural physiol. systems. In spite of this, biased signaling still has the potential to justify revisiting of receptor targets previously thought to be intractable and also furnishes the means to pursue targets previously thought to be forbidden due to deleterious physiol. (as these may be eliminated through biased signaling).
- 60Pang, P. S., Butler, J., Collins, S. P., Cotter, G., Davison, B. A., Ezekowitz, J. A., Filippatos, G., Levy, P. D., Metra, M., Ponikowski, P., Teerlink, J. R., Voors, A. A., Bharucha, D., Goin, K., Soergel, D. G., and Felker, G. M. (2017) Biased ligand of the angiotensin II type 1 receptor in patients with acute heart failure: a randomized, double-blind, placebo-controlled, phase IIB, dose ranging trial (BLAST-AHF). Eur. Heart J. 38 (30), 2364– 2373, DOI: 10.1093/eurheartj/ehx196Google Scholar60https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXitFGksbvO&md5=62e28c6fa244809d87e52d8f979ce629Biased ligand of the angiotensin II type 1 receptor in patients with acute heart failure: a randomized, double-blind, placebo-controlled, phase IIB, dose ranging trial (BLAST-AHF)Pang, Peter S.; Butler, Javed; Collins, Sean P.; Cotter, Gad; Davison, Beth A.; Ezekowitz, Justin A.; Filippatos, Gerasimos; Levy, Phillip D.; Metra, Marco; Ponikowski, Piotr; Teerlink, John R.; Voors, Adriaan A.; Bharucha, David; Goin, Kathleen; Soergel, David G.; Michael Felker, G.European Heart Journal (2017), 38 (30), 2364-2373CODEN: EHJODF; ISSN:1522-9645. (Oxford University Press)Aims: Currently, no acute heart failure (AHF) therapy definitively improves outcomes. Reducing morbidity and mortality from acute heart failure (AHF) remains an unmet need. TRV027 is a novel 'biased' ligand of the angiotensin II type 1 receptor (AT1R), selectively antagonizing the neg. effects of angiotensin II, while preserving the potential procontractility effects of AT1R stimulation. BLAST-AHF was designed to det. the safety, efficacy, and opti- mal dose of TRV027 to advance into future studies. Methods and results: BLAST-AHF was a multi-center, international, randomized, double-blind, placebo-controlled, parallel group, phase IIb dose-ranging study, enrolling patients with AHF into 4 groups: placebo, 1, 5, or 25 mg/h of TRV027. Treatment was by IV infusion for 48-96 h. The primary composite endpoint was comprised of the following: (i) time from baseline to death through day 30, (ii) time from baseline to heart failure re-hospitalization through day 30, (iii) the first assessment time point following worsening heart failure through day 5, (iv) change in dyspnea visual analog scale (VAS) score calcd. as the area under the curve (AUC) representing the change from baseline over time from baseline through day 5, and (v) length of initial hospital stay (in days) from baseline. Analyses were by modified intention-to-treat. Overall, 621 patients were enrolled. After 254 patients, a pre-specified interim anal. resulted in several protocol changes, including a lower blood pressure inclusion criterion as well as a new allocation scheme of 2:1:2:1, overweighting both placebo, and the 5 mg/h dose. TRV027 did not confer any benefit over placebo at any dose with regards to the primary composite endpoint or any of the individual components. There were no significant safety issues with TRV027. Conclusion: In this phase IIb dose-ranging AHF study, TRV027 did not improve clin. status through 30-day follow-up compared with placebo.
- 61Violin, J. D., Crombie, A. L., Soergel, D. G., and Lark, M. W. (2014) Biased ligands at G-protein-coupled receptors: promise and progress. Trends Pharmacol. Sci. 35 (7), 308– 16, DOI: 10.1016/j.tips.2014.04.007Google Scholar61https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXosl2htr4%253D&md5=768953e7aa5726d1a47ecbdb068469d8Biased ligands at G-protein-coupled receptors: promise and progressViolin, Jonathan D.; Crombie, Aimee L.; Soergel, David G.; Lark, Michael W.Trends in Pharmacological Sciences (2014), 35 (7), 308-316CODEN: TPHSDY; ISSN:0165-6147. (Elsevier Ltd.)A review. Drug discovery targeting G protein-coupled receptors (GPCRs) is no longer limited to seeking agonists or antagonists to stimulate or block cellular responses assocd. with a particular receptor. GPCRs are now known to support a diversity of pharmacol. profiles, a concept broadly referred to as functional selectivity. In particular, the concept of ligand bias, whereby a ligand stabilizes subsets of receptor conformations to engender novel pharmacol. profiles, has recently gained increasing prominence. This review discusses how biased ligands may deliver safer, better tolerated, and more efficacious drugs, and highlights several biased ligands that are in clin. development. Biased ligands targeting the angiotensin II type 1 receptor and the μ opioid receptor illustrate the translation of the biased ligand concept from basic biol. to clin. drug development.
- 62Costa-Neto, C. M., Parreiras, E. S. L. T., and Bouvier, M. (2016) A Pluridimensional View of Biased Agonism. Mol. Pharmacol. 90 (5), 587– 595, DOI: 10.1124/mol.116.105940Google Scholar62https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXitVaktbc%253D&md5=959701333007f859e11126cc6629336eA pluridimensional view of biased agonismCosta-Neto, Claudio M.; Parreiras-e-Silva, Lucas T.; Bouvier, MichelMolecular Pharmacology (2016), 90 (5), 587-595CODEN: MOPMA3; ISSN:1521-0111. (American Society for Pharmacology and Experimental Therapeutics)A review. When studying G protein-coupled receptor (GPCR) signaling and ligand-biased agonism, at least three dimensional spaces must be considered, as follows: (1) the distinct conformations that can be stabilized by different ligands promoting the engagement of different signaling effectors and accessory regulators; (2) the distinct subcellular trafficking that can be conferred by different ligands, which results in spatially distinct signals; and (3) the differential binding kinetics that maintain the receptor in specific conformation and/or subcellular localization for different periods of time, allowing for the engagement of distinct signaling effector subsets. These three pluridimensional aspects of signaling contribute to different faces of functional selectivity and provide a complex, interconnected way to define the signaling profile of each individual ligand acting at GPCRs. In this review, we discuss how each of these aspects may contribute to the diversity of signaling, but also how they shed light on the complexity of data analyses and interpretation. The impact of phenotype variability as a source of signaling diversity, and the influence of novel and more sensitive assays in the detection and anal. of signaling pluridimensionality, is also discussed. Finally, we discuss perspectives for the use of the concept of pluridimensional signaling in drug discovery, in which we highlight future predictive tools that may facilitate the identification of compds. with optimal therapeutic and safety properties based on the signaling signatures of drug candidates.
- 63Smith, J. S., Lefkowitz, R. J., and Rajagopal, S. (2018) Biased signalling: from simple switches to allosteric microprocessors. Nat. Rev. Drug Discovery 17 (4), 243– 260, DOI: 10.1038/nrd.2017.229Google Scholar63https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXjvFentw%253D%253D&md5=fb7d2f27109d412abd53c031575455deBiased signalling: from simple switches to allosteric microprocessorsSmith, Jeffrey S.; Lefkowitz, Robert J.; Rajagopal, SudarshanNature Reviews Drug Discovery (2018), 17 (4), 243-260CODEN: NRDDAG; ISSN:1474-1776. (Nature Research)A review. G protein-coupled receptors (GPCRs) are the largest class of receptors in the human genome and some of the most common drug targets. It is now well established that GPCRs can signal through multiple transducers, including heterotrimeric G proteins, GPCR kinases and β-arrestins. While these signaling pathways can be activated or blocked by 'balanced' agonists or antagonists, they can also be selectively activated in a 'biased' response. Biased responses can be induced by biased ligands, biased receptors or system bias, any of which can result in preferential signaling through G proteins or β-arrestins. At many GPCRs, signaling events mediated by G proteins and β-arrestins have been shown to have distinct biochem. and physiol. actions from one another, and an accurate evaluation of biased signaling from pharmacol. through physiol. is crucial for preclin. drug development. Recent structural studies have provided snapshots of GPCR-transducer complexes, which should aid in the structure-based design of novel biased therapies. Our understanding of GPCRs has evolved from that of two-state, on-and-off switches to that of multistate allosteric microprocessors, in which biased ligands transmit distinct structural information that is processed into distinct biol. outputs. The development of biased ligands as therapeutics heralds an era of increased drug efficacy with reduced drug side effects.
- 64O’Hayre, M., Eichel, K., Avino, S., Zhao, X., Steffen, D. J., Feng, X., Kawakami, K., Aoki, J., Messer, K., Sunahara, R., Inoue, A., von Zastrow, M., and Gutkind, J. S. (2017) Genetic evidence that beta-arrestins are dispensable for the initiation of beta2-adrenergic receptor signalling to ERK. Sci. Signaling 10 (484), eaal3395, DOI: 10.1126/scisignal.aal3395Google ScholarThere is no corresponding record for this reference.
- 65Grundmann, M., Merten, N., Malfacini, D., Inoue, A., Preis, P., Simon, K., Ruttiger, N., Ziegler, N., Benkel, T., Schmitt, N. K., Ishida, S., Muller, I., Reher, R., Kawakami, K., Inoue, A., Rick, U., Kuhl, T., Imhof, D., Aoki, J., Konig, G. M., Hoffmann, C., Gomeza, J., Wess, J., and Kostenis, E. (2018) Lack of beta-arrestin signalling in the absence of active G proteins. Nat. Commun. 9 (1), 341, DOI: 10.1038/s41467-017-02661-3Google Scholar65https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC1MvjsFKiug%253D%253D&md5=4afaac8e9bb4a87bd9d02ea469024efcLack of beta-arrestin signaling in the absence of active G proteinsGrundmann Manuel; Merten Nicole; Malfacini Davide; Preis Philip; Simon Katharina; Benkel Tobias; Schmitt Nina Katharina; Muller Ines; Rick Ulrike; Gomeza Jesus; Kostenis Evi; Inoue Asuka; Ishida Satoru; Kawakami Kouki; Inoue Ayumi; Aoki Junken; Inoue Asuka; Ruttiger Nelly; Hoffmann Carsten; Ziegler Nicole; Reher Raphael; Konig Gabriele M; Kuhl Toni; Imhof Diana; Aoki Junken; Wess JurgenNature communications (2018), 9 (1), 341 ISSN:.G protein-independent, arrestin-dependent signaling is a paradigm that broadens the signaling scope of G protein-coupled receptors (GPCRs) beyond G proteins for numerous biological processes. However, arrestin signaling in the collective absence of functional G proteins has never been demonstrated. Here we achieve a state of "zero functional G" at the cellular level using HEK293 cells depleted by CRISPR/Cas9 technology of the Gs/q/12 families of Gα proteins, along with pertussis toxin-mediated inactivation of Gi/o. Together with HEK293 cells lacking β-arrestins ("zero arrestin"), we systematically dissect G protein- from arrestin-driven signaling outcomes for a broad set of GPCRs. We use biochemical, biophysical, label-free whole-cell biosensing and ERK phosphorylation to identify four salient features for all receptors at "zero functional G": arrestin recruitment and internalization, but-unexpectedly-complete failure to activate ERK and whole-cell responses. These findings change our understanding of how GPCRs function and in particular of how they activate ERK1/2.
- 66Luttrell, L. M., Wang, J., Plouffe, B., Smith, J. S., Yamani, L., Kaur, S., Jean-Charles, P. Y., Gauthier, C., Lee, M. H., Pani, B., Kim, J., Ahn, S., Rajagopal, S., Reiter, E., Bouvier, M., Shenoy, S. K., Laporte, S. A., Rockman, H. A., and Lefkowitz, R. J. (2018) Manifold roles of beta-arrestins in GPCR signalling elucidated with siRNA and CRISPR/Cas9. Sci. Signaling 11 (549), eaat7650, DOI: 10.1126/scisignal.aat7650Google ScholarThere is no corresponding record for this reference.
- 67Abbott, A. (1999) Alliance of US labs plans to build map of cell signalling pathways. Nature 402 (6759), 219– 20, DOI: 10.1038/46111Google Scholar67https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1MXnvVynsL8%253D&md5=2cb4092b5f97204c6f4b1b61539dfe2fAlliance of US labs plans to build map of cell signalling pathwaysAbbott, AlisonNature (London) (1999), 402 (6759), 219-220CODEN: NATUAS; ISSN:0028-0836. (Macmillan Magazines)There is no expanded citation for this reference.
- 68Rual, J. F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G. F., Gibbons, F. D., Dreze, M., Ayivi-Guedehoussou, N., Klitgord, N., Simon, C., Boxem, M., Milstein, S., Rosenberg, J., Goldberg, D. S., Zhang, L. V., Wong, S. L., Franklin, G., Li, S., Albala, J. S., Lim, J., Fraughton, C., Llamosas, E., Cevik, S., Bex, C., Lamesch, P., Sikorski, R. S., Vandenhaute, J., Zoghbi, H. Y., Smolyar, A., Bosak, S., Sequerra, R., Doucette-Stamm, L., Cusick, M. E., Hill, D. E., Roth, F. P., and Vidal, M. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437 (7062), 1173– 8, DOI: 10.1038/nature04209Google Scholar68https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXhtFahtLzP&md5=5485dfc7a711b2c7f649402475f1046dTowards a proteome-scale map of the human protein-protein interaction networkRual, Jean-Francois; Venkatesan, Kavitha; Hao, Tong; Hirozane-Kishikawa, Tomoko; Dricot, Amelie; Li, Ning; Berriz, Gabriel F.; Gibbons, Francis D.; Dreze, Matija; Ayivi-Guedehoussou, Nono; Klitgord, Niels; Simon, Christophe; Boxem, Mike; Milstein, Stuart; Rosenberg, Jennifer; Goldberg, Debra S.; Zhang, Lan V.; Wong, Sharyl L.; Franklin, Giovanni; Li, Siming; Albala, Joanna S.; Lim, Janghoo; Fraughton, Carlene; Llamosas, Estelle; Cevik, Sebiha; Bex, Camille; Lamesch, Philippe; Sikorski, Robert S.; Vandenhaute, Jean; Zoghbi, Huda Y.; Smolyar, Alex; Bosak, Stephanie; Sequerra, Reynaldo; Doucette-Stamm, Lynn; Cusick, Michael E.; Hill, David E.; Roth, Frederick P.; Vidal, MarcNature (London, United Kingdom) (2005), 437 (7062), 1173-1178CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)Systematic mapping of protein-protein interactions, or interactome mapping, was initiated in model organisms, starting with defined biol. processes and then expanding to the scale of the proteome. Although far from complete, such maps have revealed global topol. and dynamic features of interactome networks that relate to known biol. properties, suggesting that a human interactome map will provide insight into development and disease mechanisms at a systems level. Here we describe an initial version of a proteome-scale map of human binary protein-protein interactions. Using a stringent, high-throughput yeast two-hybrid system, we tested pairwise interactions among the products of ∼8,100 currently available Gateway-cloned open reading frames and detected ∼2,800 interactions. This data set, called CCSB-HI1, has a verification rate of ∼78% as revealed by an independent co-affinity purifn. assay, and correlates significantly with other biol. attributes. The CCSB-HI1 data set increases by ∼70% the set of available binary interactions within the tested space and reveals more than 300 new connections to over 100 disease-assocd. proteins. This work represents an important step toward a systematic and comprehensive human interactome project.
- 69Hein, M. Y., Hubner, N. C., Poser, I., Cox, J., Nagaraj, N., Toyoda, Y., Gak, I. A., Weisswange, I., Mansfeld, J., Buchholz, F., Hyman, A. A., and Mann, M. (2015) A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 163 (3), 712– 23, DOI: 10.1016/j.cell.2015.09.053Google Scholar69https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhslWrsLnK&md5=599f46801c2006cbc7b26d6ff8a00d6dA Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and AbundancesHein, Marco Y.; Hubner, Nina C.; Poser, Ina; Cox, Juergen; Nagaraj, Nagarjuna; Toyoda, Yusuke; Gak, Igor A.; Weisswange, Ina; Mansfeld, Joerg; Buchholz, Frank; Hyman, Anthony A.; Mann, MatthiasCell (Cambridge, MA, United States) (2015), 163 (3), 712-723CODEN: CELLB5; ISSN:0092-8674. (Cell Press)The organization of a cell emerges from the interactions in protein networks. The interactome is critically dependent on the strengths of interactions and the cellular abundances of the connected proteins, both of which span orders of magnitude. However, these aspects have not yet been analyzed globally. Here, the authors have generated a library of HeLa cell lines expressing 1125 GFP-tagged proteins under near-endogenous control, which the authors used as input for a next-generation interaction survey. Using quant. proteomics, the authors detect specific interactions, est. interaction stoichiometries, and measure cellular abundances of interacting proteins. These three quant. dimensions reveal that the protein network is dominated by weak, substoichiometric interactions that play a pivotal role in defining network topol. The minority of stable complexes can be identified by their unique stoichiometry signature. This study provides a rich interaction dataset connecting thousands of proteins and introduces a framework for quant. network anal.
- 70Huttlin, E. L., Ting, L., Bruckner, R. J., Gebreab, F., Gygi, M. P., Szpyt, J., Tam, S., Zarraga, G., Colby, G., Baltier, K., Dong, R., Guarani, V., Vaites, L. P., Ordureau, A., Rad, R., Erickson, B. K., Wuhr, M., Chick, J., Zhai, B., Kolippakkam, D., Mintseris, J., Obar, R. A., Harris, T., Artavanis-Tsakonas, S., Sowa, M. E., De Camilli, P., Paulo, J. A., Harper, J. W., and Gygi, S. P. (2015) The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell 162 (2), 425– 440, DOI: 10.1016/j.cell.2015.06.043Google Scholar70https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXht1KgtL3I&md5=79b8d96037646f6679baab3b966b9d47The BioPlex Network: A Systematic Exploration of the Human InteractomeHuttlin, Edward L.; Ting, Lily; Bruckner, Raphael J.; Gebreab, Fana; Gygi, Melanie P.; Szpyt, John; Tam, Stanley; Zarraga, Gabriela; Colby, Greg; Baltier, Kurt; Dong, Rui; Guarani, Virginia; Vaites, Laura Pontano; Ordureau, Alban; Rad, Ramin; Erickson, Brian K.; Wuhr, Martin; Chick, Joel; Zhai, Bo; Kolippakkam, Deepak; Mintseris, Julian; Obar, Robert A.; Harris, Tim; Artavanis-Tsakonas, Spyros; Sowa, Mathew E.; De Camilli, Pietro; Paulo, Joao A.; Harper, J. Wade; Gygi, Steven P.Cell (Cambridge, MA, United States) (2015), 162 (2), 425-440CODEN: CELLB5; ISSN:0092-8674. (Cell Press)Protein interactions form a network whose structure drives cellular function and whose organization informs biol. inquiry. Using high-throughput affinity-purifn. mass spectrometry, the authors identify interacting partners for 2594 human proteins in HEK293T cells. The resulting network (BioPlex) contains 23,744 interactions among 7668 proteins with 86% previously undocumented. BioPlex accurately depicts known complexes, attaining 80%-100% coverage for most CORUM complexes. The network readily subdivides into communities that correspond to complexes or clusters of functionally related proteins. More generally, network architecture reflects cellular localization, biol. process, and mol. function, enabling functional characterization of thousands of proteins. Network structure also reveals assocns. among thousands of protein domains, suggesting a basis for examg. structurally related proteins. Finally, BioPlex, in combination with other approaches, can be used to reveal interactions of biol. or clin. significance. For example, mutations in the membrane protein VAPB implicated in familial amyotrophic lateral sclerosis perturb a defined community of interactors.
- 71Uhlen, M., Fagerberg, L., Hallstrom, B. M., Lindskog, C., Oksvold, P., Mardinoglu, A., Sivertsson, A., Kampf, C., Sjostedt, E., Asplund, A., Olsson, I., Edlund, K., Lundberg, E., Navani, S., Szigyarto, C. A., Odeberg, J., Djureinovic, D., Takanen, J. O., Hober, S., Alm, T., Edqvist, P. H., Berling, H., Tegel, H., Mulder, J., Rockberg, J., Nilsson, P., Schwenk, J. M., Hamsten, M., von Feilitzen, K., Forsberg, M., Persson, L., Johansson, F., Zwahlen, M., von Heijne, G., Nielsen, J., and Ponten, F. (2015) Proteomics. Tissue-based map of the human proteome. Science 347 (6220), 1260419, DOI: 10.1126/science.1260419Google Scholar71https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC2MvptFakug%253D%253D&md5=95510888806e5feb6b8024ee2a417d1cProteomics. Tissue-based map of the human proteomeUhlen Mathias; Fagerberg Linn; Oksvold Per; Sivertsson ¡ÑÜAsa; Lundberg Emma; Odeberg Jacob; Alm Tove; Nilsson Peter; Schwenk Jochen M; von Feilitzen Kalle; Forsberg Mattias; Persson Lukas; Johansson Fredric; Zwahlen Martin; Hallstrom Bjorn M; Lindskog Cecilia; Kampf Caroline; Asplund Anna; Olsson IngMarie; Djureinovic Dijana; Edqvist Per-Henrik; Ponten Fredrik; Mardinoglu Adil; Sjostedt Evelina; Edlund Karolina; Navani Sanjay; Szigyarto Cristina Al-Khalili; Takanen Jenny Ottosson; Hober Sophia; Berling Holger; Tegel Hanna; Rockberg Johan; Hamsten Marica; Mulder Jan; von Heijne Gunnar; Nielsen JensScience (New York, N.Y.) (2015), 347 (6220), 1260419 ISSN:.Resolving the molecular details of proteome variation in the different tissues and organs of the human body will greatly increase our knowledge of human biology and disease. Here, we present a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray-based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level. Our tissue-based analysis detected more than 90% of the putative protein-coding genes. We used this approach to explore the human secretome, the membrane proteome, the druggable proteome, the cancer proteome, and the metabolic functions in 32 different tissues and organs. All the data are integrated in an interactive Web-based database that allows exploration of individual proteins, as well as navigation of global expression patterns, in all major tissues and organs in the human body.
- 72Huttlin, E. L., Bruckner, R. J., Paulo, J. A., Cannon, J. R., Ting, L., Baltier, K., Colby, G., Gebreab, F., Gygi, M. P., Parzen, H., Szpyt, J., Tam, S., Zarraga, G., Pontano-Vaites, L., Swarup, S., White, A. E., Schweppe, D. K., Rad, R., Erickson, B. K., Obar, R. A., Guruharsha, K. G., Li, K., Artavanis-Tsakonas, S., Gygi, S. P., and Harper, J. W. (2017) Architecture of the human interactome defines protein communities and disease networks. Nature 545 (7655), 505– 509, DOI: 10.1038/nature22366Google Scholar72https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXnvVCrsro%253D&md5=be9c296f38f01ac4d177e3e97e4882e7Architecture of the human interactome defines protein communities and disease networksHuttlin, Edward L.; Bruckner, Raphael J.; Paulo, Joao A.; Cannon, Joe R.; Ting, Lily; Baltier, Kurt; Colby, Greg; Gebreab, Fana; Gygi, Melanie P.; Parzen, Hannah; Szpyt, John; Tam, Stanley; Zarraga, Gabriela; Pontano-Vaites, Laura; Swarup, Sharan; White, Anne E.; Schweppe, Devin K.; Rad, Ramin; Erickson, Brian K.; Obar, Robert A.; Guruharsha, K. G.; Li, Kejie; Artavanis-Tsakonas, Spyros; Gygi, Steven P.; Harper, J. WadeNature (London, United Kingdom) (2017), 545 (7655), 505-509CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)The physiol. of a cell can be viewed as the product of thousands of proteins acting in concert to shape the cellular response. Coordination is achieved in part through networks of protein-protein interactions that assemble functionally related proteins into complexes, organelles, and signal transduction pathways. Understanding the architecture of the human proteome has the potential to inform cellular, structural, and evolutionary mechanisms and is crit. to elucidating how genome variation contributes to disease. Here we present BioPlex 2.0 (Biophys. Interactions of ORFeome-derived complexes), which uses robust affinity purifn.-mass spectrometry methodol. to elucidate protein interaction networks and co-complexes nucleated by more than 25% of protein-coding genes from the human genome, and constitutes, to our knowledge, the largest such network so far. With more than 56,000 candidate interactions, BioPlex 2.0 contains more than 29,000 previously unknown co-assocns. and provides functional insights into hundreds of poorly characterized proteins while enhancing network-based analyses of domain assocns., subcellular localization, and co-complex formation. Unsupervised Markov clustering of interacting proteins identified more than 1,300 protein communities representing diverse cellular activities. Genes essential for cell fitness are enriched within 53 communities representing central cellular functions. Moreover, we identified 442 communities assocd. with more than 2,000 disease annotations, placing numerous candidate disease genes into a cellular framework. BioPlex 2.0 exceeds previous exptl. derived interaction networks in depth and breadth, and will be a valuable resource for exploring the biol. of incompletely characterized proteins and for elucidating larger-scale patterns of proteome organization.
- 73Rozenblatt-Rosen, O., Stubbington, M. J. T., Regev, A., and Teichmann, S. A. (2017) The Human Cell Atlas: from vision to reality. Nature 550 (7677), 451– 453, DOI: 10.1038/550451aGoogle Scholar73https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhslajtr7M&md5=0653d7120f724c2950136e535ed95892The Human Cell Atlas: from vision to realityRozenblatt-Rosen, Orit; Stubbington, Michael J. T.; Regev, Aviv; Teichmann, Sarah A.Nature (London, United Kingdom) (2017), 550 (7677), 451-453CODEN: NATUAS; ISSN:0028-0836. (Nature Research)As an ambitious project to map all the cells in the human body gets officially under way, Aviv Regev, Sarah Teichmann and colleagues outline some key challenges.
- 74Fabregat, A., Jupe, S., Matthews, L., Sidiropoulos, K., Gillespie, M., Garapati, P., Haw, R., Jassal, B., Korninger, F., May, B., Milacic, M., Roca, C. D., Rothfels, K., Sevilla, C., Shamovsky, V., Shorser, S., Varusai, T., Viteri, G., Weiser, J., Wu, G., Stein, L., Hermjakob, H., and D’Eustachio, P. (2018) The Reactome Pathway Knowledgebase. Nucleic Acids Res. 46 (D1), D649– D655, DOI: 10.1093/nar/gkx1132Google Scholar74https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXitlGis7bM&md5=691a9b4fb2ab28dd06b9d012a3e936b7The reactome pathway knowledgebaseFabregat, Antonio; Jupe, Steven; Matthews, Lisa; Sidiropoulos, Konstantinos; Gillespie, Marc; Garapati, Phani; Haw, Robin; Jassal, Bijay; Korninger, Florian; May, Bruce; Milacic, Marija; Roca, Corina Duenas; Rothfels, Karen; Sevilla, Cristoffer; Shamovsky, Veronica; Shorser, Solomon; Varusai, Thawfeek; Viteri, Guilherme; Weiser, Joel; Wu, Guanming; Stein, Lincoln; Hermjakob, Henning; D'eustachio, PeterNucleic Acids Research (2018), 46 (D1), D649-D655CODEN: NARHAD; ISSN:1362-4962. (Oxford University Press)A review. The Reactome Knowledgebase provides mol. details of signal transduction, transport, DNA replication, metab., and other cellular processes as an ordered network of mol. transformations-an extended version of a classic metabolic map, in a single consistent data model. Reactome functions both as an archive of biol. processes and as a tool for discovering unexpected functional relationships in data such as gene expression profiles or somatic mutation catalogs from tumor cells. To support the continued brisk growth in the size and complexity of Reactome, we have implemented a graph database, improved performance of data anal. tools, and designed new data structures and strategies to boost diagram viewer performance. To make our website more accessible to human users, we have improved pathway display and navigation by implementing interactive Enhanced High Level Diagrams (EHLDs) with an assocd. icon library, and subpathway highlighting and zooming, in a simplified and reorganized web site with adaptive design. To encourage re-use of our content, we have enabled export of pathway diagrams as 'PowerPoint' files.
- 75Singla, J., McClary, K. M., White, K. L., Alber, F., Sali, A., and Stevens, R. C. (2018) Opportunities and Challenges in Building a Spatiotemporal Multi-scale Model of the Human Pancreatic beta Cell. Cell 173 (1), 11– 19, DOI: 10.1016/j.cell.2018.03.014Google Scholar75https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXlvVOqsbY%253D&md5=b5eeeb7a09d17372ee28aa409f45134cOpportunities and Challenges in Building a Spatiotemporal Multi-scale Model of the Human Pancreatic β CellSingla, Jitin; McClary, Kyle M.; White, Kate L.; Alber, Frank; Sali, Andrej; Stevens, Raymond C.Cell (Cambridge, MA, United States) (2018), 173 (1), 11-19CODEN: CELLB5; ISSN:0092-8674. (Cell Press)A review. The construction of a predictive model of an entire eukaryotic cell that describes its dynamic structure from at. to cellular scales is a grand challenge at the intersection of biol., chem., physics, and computer science. Having such a model will open new dimensions in biol. research and accelerate healthcare advancements. Developing the necessary exptl. and modeling methods presents abundant opportunities for a community effort to realize this goal. Here, we present a vision for creation of a spatiotemporal multi-scale model of the pancreatic β-cell, a relevant target for understanding and modulating the pathogenesis of diabetes.
- 76https://reactome.org/ (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 77https://string-db.org/ (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 78Tan, L., Yan, W., McCorvy, J. D., and Cheng, J. (2018) Biased Ligands of G Protein-Coupled Receptors (GPCRs): Structure-Functional Selectivity Relationships (SFSRs) and Therapeutic Potential. J. Med. Chem. 61 (22), 9841– 9878, DOI: 10.1021/acs.jmedchem.8b00435Google Scholar78https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXht1Snu73N&md5=a7bd605b82666357f5a0a209002225e5Biased Ligands of G Protein-Coupled Receptors (GPCRs): Structure-Functional Selectivity Relationships (SFSRs) and Therapeutic PotentialTan, Liang; Yan, Wenzhong; McCorvy, John D.; Cheng, JianjunJournal of Medicinal Chemistry (2018), 61 (22), 9841-9878CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)A review. G protein-coupled receptors (GPCRs) signal through both G-protein-dependent and G-protein-independent pathways, and β-arrestin recruitment is the most recognized one of the latter. Biased ligands selective for either pathway are expected to regulate biol. functions of GPCRs in a more precise way, therefore providing new drug mols. with superior efficacy and/or reduced side effects. During the past decade, biased ligands have been discovered and developed for many GPCRs, such as the μ opioid receptor, the angiotensin II receptor type 1, the dopamine D2 receptor, and many others. In this Perspective, recent advances in this field are reviewed by discussing the structure-functional selectivity relationships (SFSRs) of GPCR biased ligands and the therapeutic potential of these mols. Further understanding of the biol. functions assocd. with each signaling pathway and structural basis for biased signaling will facilitate future drug design in this field.
- 79Wilde, O. The Importance of Being Earnest: a Trivial Comedy for Serious People; Leonard Smithers and Co.: London, 1898.Google ScholarThere is no corresponding record for this reference.
- 80https://www.cost.eu/actions/CA18133/ (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
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Abstract
Figure 1
Figure 1. Schematic overview of how ERNEST will develop a holistic multidimensional map of GPCR-mediated signal transduction. See text for full description.
Figure 2
Figure 2. Thematic synergism between the Working Groups (WG) of ERNEST. WGs 1, 2, and 3 form the core of scientific knowledge of the Action, and the overlaps represent shared focus and potential for interdisciplinary cooperation. WG4 will support the three core WGs with new methods and technologies and also establish best practice standards for their application. Output from the three core workgroups (arrows out) will be incorporated by WG5 into database resources for public dissemination, and WG5 will generate database tools that will feedback into the three core WGs (arrows in). Figure reprinted in part from COST Action CA18133 ERNEST Memorandum of Understanding with permission from the COST Association. (80)
References
ARTICLE SECTIONSThis article references 80 other publications.
- 1Hauser, A. S., Attwood, M. M., Rask-Andersen, M., Schioth, H. B., and Gloriam, D. E. (2017) Trends in GPCR drug discovery: new agents, targets and indications. Nat. Rev. Drug Discovery 16 (12), 829– 842, DOI: 10.1038/nrd.2017.178Google Scholar1https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhslansbzF&md5=560893258493bd96c0af24d3bef08b6fTrends in GPCR drug discovery: new agents, targets and indicationsHauser, Alexander S.; Attwood, Misty M.; Rask-Andersen, Mathias; Schioth, Helgi B.; Gloriam, David E.Nature Reviews Drug Discovery (2017), 16 (12), 829-842CODEN: NRDDAG; ISSN:1474-1776. (Nature Research)G protein-coupled receptors (GPCRs) are the most intensively studied drug targets, mostly due to their substantial involvement in human pathophysiol. and their pharmacol. tractability. Here, we report an up-to-date anal. of all GPCR drugs and agents in clin. trials, which reveals current trends across mol. types, drug targets and therapeutic indications, including showing that 475 drugs (∼34% of all drugs approved by the US Food and Drug Administration (FDA)) act at 108 unique GPCRs. Approx. 321 agents are currently in clin. trials, of which ∼20% target 66 potentially novel GPCR targets without an approved drug, and the no. of biol. drugs, allosteric modulators and biased agonists has increased. The major disease indications for GPCR modulators show a shift towards diabetes, obesity and Alzheimer disease, although several central nervous system disorders are also highly represented. The 224 (56%) non-olfactory GPCRs that have not yet been explored in clin. trials have broad untapped therapeutic potential, particularly in genetic and immune system disorders. Finally, we provide an interactive online resource to analyze and infer trends in GPCR drug discovery.
- 2Palczewski, K., Kumasaka, T., Hori, T., Behnke, C. A., Motoshima, H., Fox, B. A., Le Trong, I., Teller, D. C., Okada, T., Stenkamp, R. E., Yamamoto, M., and Miyano, M. (2000) Crystal structure of rhodopsin: A G protein-coupled receptor. Science 289 (5480), 739– 45, DOI: 10.1126/science.289.5480.739Google Scholar2https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXlslOqs78%253D&md5=b3d229fc696247ec0f4a6efa10490922Crystal structure of rhodopsin: A G protein-coupled receptorPalczewski, Krzysztof; Kumasaka, Takashi; Hori, Tetsuya; Behnke, Craig A.; Motoshima, Hiroyuki; Fox, Brian A.; Le Trong, Isolde; Teller, David C.; Okada, Tetsuji; Stenkamp, Ronald E.; Yamamoto, Masaki; Miyano, MasashiScience (Washington, D. C.) (2000), 289 (5480), 739-745CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)Heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) respond to a variety of different external stimuli and activate G proteins. GPCRs share many structural features, including a bundle of seven transmembrane α-helixes connected by six loops of varying lengths. We detd. the structure of rhodopsin from diffraction data extending to 2.8 angstroms resoln. The highly organized structure in the extracellular region, including a conserved disulfide bridge, forms a basis for the arrangement of the seven-helix transmembrane motif. The ground-state chromophore, 11-cis-retinal, holds the transmembrane region of the protein in the inactive conformation. Interactions of the chromophore with a cluster of key residues det. the wavelength of the max. absorption. Changes in these interactions among rhodopsins facilitate color discrimination. Identification of a set of residues that mediate interactions between the transmembrane helixes and the cytoplasmic surface, where G-protein activation occurs, also suggests a possible structural change upon photoactivation.
- 3Wacker, D., Stevens, R. C., and Roth, B. L. (2017) How Ligands Illuminate GPCR Molecular Pharmacology. Cell 170 (3), 414– 427, DOI: 10.1016/j.cell.2017.07.009Google Scholar3https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXht1GisLvF&md5=d4f7f48d757cf3d13a980d2f7f1be138How ligands illuminate GPCR molecular pharmacologyWacker, Daniel; Stevens, Raymond C.; Roth, Bryan L.Cell (Cambridge, MA, United States) (2017), 170 (3), 414-427CODEN: CELLB5; ISSN:0092-8674. (Cell Press)A review. G protein-coupled receptors (GPCRs), which are modulated by a variety of endogenous and synthetic ligands, represent the largest family of druggable targets in the human genome. Recent structural and mol. studies have both transformed and expanded classical concepts of receptor pharmacol. and have begun to illuminate the distinct mechanisms by which structurally, chem., and functionally diverse ligands modulate GPCR function. These mol. insights into ligand engagement and action have enabled new computational methods and accelerated the discovery of novel ligands and tool compds., esp. for understudied and orphan GPCRs. These advances promise to streamline the development of GPCR-targeted medications.
- 4Zhou, X. E., Melcher, K., and Xu, H. E. (2017) Understanding the GPCR biased signalling through G protein and arrestin complex structures. Curr. Opin. Struct. Biol. 45, 150– 159, DOI: 10.1016/j.sbi.2017.05.004Google Scholar4https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXotFyns74%253D&md5=7b36ce15a853972b9abbe895852fc794Understanding the GPCR biased signaling through G protein and arrestin complex structuresZhou, X. Edward; Melcher, Karsten; Xu, H. EricCurrent Opinion in Structural Biology (2017), 45 (), 150-159CODEN: COSBEF; ISSN:0959-440X. (Elsevier Ltd.)G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors and are important drug targets for many human diseases. The detn. of the 3-D structure of GPCRs and their signaling complexes has promoted our understanding of GPCR biol. and provided templates for structure-based drug discovery. In this review, we focus on the recent structure work on GPCR signaling complexes, the β2-adrenoreceptor-Gs and the rhodopsin-arrestin complexes in particular, and highlight the structural features of GPCR complexes involved in G protein- and arrestin-mediated signal transduction. The crystal structures reveal distinct structural mechanisms by which GPCRs recruit a G protein and an arrestin. A comparison of the two complex structures provides insight into the mol. mechanism of functionally selective GPCR signaling, and a structural basis for the discovery of G protein- and arrestin-biased treatments of human diseases related to GPCR signal transduction.
- 5Hilger, D., Masureel, M., and Kobilka, B. K. (2018) Structure and dynamics of GPCR signalling complexes. Nat. Struct. Mol. Biol. 25 (1), 4– 12, DOI: 10.1038/s41594-017-0011-7Google Scholar5https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhtlCqu7jM&md5=6af99d3ea2b5422d377575815a867458Structure and dynamics of GPCR signaling complexesHilger, Daniel; Masureel, Matthieu; Kobilka, Brian K.Nature Structural & Molecular Biology (2018), 25 (1), 4-12CODEN: NSMBCU; ISSN:1545-9993. (Nature Research)A review. G-protein-coupled receptors (GPCRs) relay numerous extracellular signals by triggering intracellular signaling through coupling with G proteins and arrestins. Recent breakthroughs in the structural detn. of GPCRs and GPCR-transducer complexes represent important steps toward deciphering GPCR signal transduction at a mol. level. A full understanding of the mol. basis of GPCR-mediated signaling requires elucidation of the dynamics of receptors and their transducer complexes as well as their energy landscapes and conformational transition rates. Here, we summarize current insights into the structural plasticity of GPCR-G-protein and GPCR-arrestin complexes that underlies the regulation of the receptor's intracellular signaling profile.
- 6Callaway, E. (2015) The revolution will not be crystallized: a new method sweeps through structural biology. Nature 525 (7568), 172– 4, DOI: 10.1038/525172aGoogle Scholar6https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsVyrtLfN&md5=9806c5cc42ee81de65b2c4037909c6b8The revolution will not be crystallized: a new method sweeps through structural biologyCallaway, EwenNature (London, United Kingdom) (2015), 525 (7568), 172-174CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)Move over X-ray crystallog. Cryo-electron microscopy is kicking up a storm by revealing the hidden machinery of the cell.
- 7Safdari, H. A., Pandey, S., Shukla, A. K., and Dutta, S. (2018) Illuminating GPCR Signalling by Cryo-EM. Trends Cell Biol. 28 (8), 591– 594, DOI: 10.1016/j.tcb.2018.06.002Google Scholar7https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhtF2jt7vJ&md5=57be67178fff2cd78d337fd050865df6Illuminating GPCR Signaling by Cryo-EMSafdari, Haaris Ahsan; Pandey, Shubhi; Shukla, Arun K.; Dutta, SomnathTrends in Cell Biology (2018), 28 (8), 591-594CODEN: TCBIEK; ISSN:0962-8924. (Elsevier Ltd.)A review. The wave of resoln. revolution in cryo-EM has touched, and made a significant impact on, the structural biol. of GPCRs. High-resoln. structures of several GPCR-G-protein complexes are now detd. by cryo-EM and they illuminate fine structural details of this central macromol. complex involved in cellular signaling.
- 8Garcia-Nafria, J. and Tate, C. G. (2020) Cryo-Electron Microscopy: Moving Beyond X-Ray Crystal Structures for Drug Receptors and Drug Development. Annu. Rev. Pharmacol. Toxicol. 60, 51– 71, DOI: 10.1146/annurev-pharmtox-010919-023545Google Scholar8https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhsVGru77M&md5=035f2b8d1c64fc8c4ce85255df233c84Cryo-Electron Microscopy: Moving Beyond X-Ray Crystal Structures for Drug Receptors and Drug DevelopmentGarcia-Nafria, Javier; Tate, Christopher G.Annual Review of Pharmacology and Toxicology (2020), 60 (), 51-71CODEN: ARPTDI; ISSN:0362-1642. (Annual Reviews)Electron cryo-microscopy (cryo-EM) has revolutionized structure detn. of membrane proteins and holds great potential for structure-based drug discovery. Here we discuss the potential of cryo-EM in the rational design of therapeutics for membrane proteins compared to X-ray crystallog. We also detail recent progress in the field of drug receptors, focusing on cryo-EM of two protein families with established therapeutic value, the γ-aminobutyric acid A receptors (GABAARs) and G protein-coupled receptors (GPCRs). GABAARs are pentameric ion channels, and cryo-EM structures of physiol. heteromeric receptors in a lipid environment have uncovered the mol. basis of receptor modulation by drugs such as diazepam. The structures of ten GPCR-G protein complexes from three different classes of GPCRs have now been detd. by cryo-EM. These structures give detailed insights into mol. interactions with drugs, GPCR-G protein selectivity, how accessory membrane proteins alter receptor-ligand pharmacol., and the mechanism by which HIV uses GPCRs to enter host cells.
- 9Schrage, R. and Kostenis, E. (2017) Functional selectivity and dualsteric/bitopic GPCR targeting. Curr. Opin. Pharmacol. 32, 85– 90, DOI: 10.1016/j.coph.2016.12.001Google Scholar9https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XitFWlsLrE&md5=851d67a8acaa8e260726eca996628a01Functional selectivity and dualsteric/bitopic GPCR targetingSchrage, Ramona; Kostenis, EviCurrent Opinion in Pharmacology (2017), 32 (), 85-90CODEN: COPUBK; ISSN:1471-4892. (Elsevier Ltd.)Functional selectivity provides a new avenue to selectively engage particular pathways of the pleiotropic signaling repertoire of a G protein-coupled receptor. First examples for signaling biased compds. at the angiotensin II receptor and the μ opioid receptor have progressed to clin. trials and are promising in regard to selective activation of signaling pathways that can be linked to beneficial clin. outcomes. Dualsteric/bitopic hybrid compds. which consist of at least two pharmacophores combined in one single ligand are more recent examples for functionally selective ligands. Their binding topog. makes them ideally suited to disrupt receptor flexibility and rationally induce signaling bias. Therefore, the dualsteric/bitopic design principle is most promising to facilitate generation of structurally diverse biased agonists at G protein-coupled receptors.
- 10www.biomodellab.eu/1glisten (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 11http://eventia.upf.edu/Barcelona-GPCR-Conference-2014 (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 12http://glisten.ttk.hu/ (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 13https://sites.google.com/site/glisten2015/home (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 14http://www.medchemsymposium.org/Home.html (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 15http://grk1910.de/glisten-2016.html (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 16www.glisten2016.cz (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 17https://glistensymposium.wordpress.com (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 18http://school.ifs.hr/2016 (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 19Rodriguez, D., Brea, J., Loza, M. I., and Carlsson, J. (2014) Structure-based discovery of selective serotonin 5-HT(1B) receptor ligands. Structure 22 (8), 1140– 1151, DOI: 10.1016/j.str.2014.05.017Google Scholar19https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtFyjt7fE&md5=bf293d7c1bb6f4465ed0574ae298e81fStructure-Based Discovery of Selective Serotonin 5-HT1B Receptor LigandsRodriguez, David; Brea, Jose; Loza, Maria Isabel; Carlsson, JensStructure (Oxford, United Kingdom) (2014), 22 (8), 1140-1151CODEN: STRUE6; ISSN:0969-2126. (Elsevier Ltd.)The development of safe and effective drugs relies on the discovery of selective ligands. Serotonin (5-hydroxytryptamine [5-HT]) G protein-coupled receptors are therapeutic targets for CNS disorders but are also assocd. with adverse drug effects. The detn. of crystal structures for the 5-HT1B and 5-HT2B receptors provided an opportunity to identify subtype selective ligands using structure-based methods. From docking screens of 1.3 million compds., 22 mols. were predicted to be selective for the 5-HT1B receptor over the 5-HT2B subtype, a requirement for safe serotonergic drugs. Nine compds. were exptl. verified as 5-HT1B-selective ligands, with up to 300-fold higher affinities for this subtype. Three of the ligands were agonists of the G protein pathway. Anal. of state-of-the-art homol. models of the two 5-HT receptors revealed that the crystal structures were crit. for predicting selective ligands. Our results demonstrate that structure-based screening can guide the discovery of ligands with specific selectivity profiles.
- 20Piscitelli, C. L., Kean, J., de Graaf, C., and Deupi, X. (2015) A Molecular Pharmacologist’s Guide to G Protein-Coupled Receptor Crystallography. Mol. Pharmacol. 88 (3), 536– 51, DOI: 10.1124/mol.115.099663Google Scholar20https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsVCgs77M&md5=544b3458352b57e776055fbc65f97cbdA molecular pharmacologist's guide to G protein-coupled receptor crystallographyPiscitelli, Chayne L.; Kean, James; de Graaf, Chris; Deupi, XavierMolecular Pharmacology (2015), 88 (3), 536-551CODEN: MOPMA3; ISSN:1521-0111. (American Society for Pharmacology and Experimental Therapeutics)G protein-coupled receptor (GPCR) structural biol. has progressed dramatically in the last decade. There are now over 120 GPCR crystal structures deposited in the Protein Data Bank of 32 different receptors from families scattered across the phylogenetic tree, including class B, C, and Frizzled GPCRs. These structures have been obtained in combination with a wide variety of ligands and captured in a range of conformational states. This surge in structural knowledge has enlightened research into the mol. recognition of biol. active mols., the mechanisms of receptor activation, the dynamics of functional selectivity, and fueled structure-based drug design efforts for GPCRs. Here we summarize the innovations in both protein engineering/mol. biol. and crystallog. techniques that have led to these advances in GPCR structural biol. and discuss how they may influence the resulting structural models. We also provide a brief mol. pharmacologist's guide to GPCR X-ray crystallog., outlining some key aspects in the process of structure detn., with the goal to encourage noncrystallographers to interrogate structures at the mol. level. Finally, we show how chemogenomics approaches can be used to marry the wealth of existing receptor pharmacol. data with the expanding repertoire of structures, providing a deeper understanding of the mechanistic details of GPCR function.
- 21Munk, C., Isberg, V., Mordalski, S., Harpsoe, K., Rataj, K., Hauser, A. S., Kolb, P., Bojarski, A. J., Vriend, G., and Gloriam, D. E. (2016) GPCRdb: the G protein-coupled receptor database - an introduction. Br. J. Pharmacol. 173 (14), 2195– 207, DOI: 10.1111/bph.13509Google Scholar21https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XptFWgtbc%253D&md5=ca467fd4423d55d52c896c55d6aad964GPCRdb: the G protein-coupled receptor database - an introductionMunk, C.; Isberg, V.; Mordalski, S.; Harpsoe, K.; Rataj, K.; Hauser, A. S.; Kolb, P.; Bojarski, A. J.; Vriend, G.; Gloriam, D. E.British Journal of Pharmacology (2016), 173 (14), 2195-2207CODEN: BJPCBM; ISSN:1476-5381. (Wiley-Blackwell)GPCRs make up the largest family of human membrane proteins and of drug targets. Recent advances in GPCR pharmacol. and crystallog. have shed new light on signal transduction, allosteric modulation and biased signalling, translating into new mechanisms and principles for drug design. The GPCR database, GPCRdb, has served the community for over 20 years and has recently been extended to include a more multidisciplinary audience. This review is intended to introduce new users to the services in GPCRdb, which meets three overall purposes: firstly, to provide ref. data in an integrated, annotated and structured fashion, with a focus on sequences, structures, single-point mutations and ligand interactions. Secondly, to equip the community with a suite of web tools for swift anal. of structures, sequence similarities, receptor relationships, and ligand target profiles. Thirdly, to facilitate dissemination through interactive diagrams of, for example, receptor residue topologies, phylogenetic relationships and crystal structure statistics. Herein, these services are described for the first time; visitors and guides are provided with good practices for their utilization. Finally, we describe complementary databases cross-referenced by GPCRdb and web servers with corresponding functionality.
- 22Lally, C. C., Bauer, B., Selent, J., and Sommer, M. E. (2017) C-edge loops of arrestin function as a membrane anchor. Nat. Commun. 8, 14258, DOI: 10.1038/ncomms14258Google Scholar22https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXjtlyisLg%253D&md5=fb282d62caf23b0d520aff5c1342a7e9C-edge loops of arrestin function as a membrane anchorLally, Ciara C. M.; Bauer, Brian; Selent, Jana; Sommer, Martha E.Nature Communications (2017), 8 (), 14258CODEN: NCAOBW; ISSN:2041-1723. (Nature Publishing Group)G-protein-coupled receptors are membrane proteins that are regulated by a small family of arrestin proteins. During formation of the arrestin-receptor complex, arrestin first interacts with the phosphorylated receptor C terminus in a pre-complex, which activates arrestin for tight receptor binding. Currently, little is known about the structure of the pre-complex and its transition to a high-affinity complex. Here we present mol. dynamics simulations and site-directed fluorescence expts. on arrestin-1 interactions with rhodopsin, showing that loops within the C-edge of arrestin function as a membrane anchor. Activation of arrestin by receptor-attached phosphates is necessary for C-edge engagement of the membrane, and we show that these interactions are distinct in the pre-complex and high-affinity complex in regard to their conformation and orientation. Our results expand current knowledge of C-edge structure and further illuminate the conformational transitions that occur in arrestin along the pathway to tight receptor binding.
- 23Chevillard, F., Stotani, S., Karawajczyk, A., Hristeva, S., Pardon, E., Steyaert, J., Tzalis, D., and Kolb, P. (2019) Interrogating dense ligand chemical space with a forward-synthetic library. Proc. Natl. Acad. Sci. U. S. A. 116 (23), 11496– 11501, DOI: 10.1073/pnas.1818718116Google Scholar23https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhtV2itL%252FO&md5=22fa702bc6a87b1c1a62228538775a8fInterrogating dense ligand chemical space with a forward-synthetic libraryChevillard, Florent; Stotani, Silvia; Karawajczyk, Anna; Hristeva, Stanimira; Pardon, Els; Steyaert, Jan; Tzalis, Dimitrios; Kolb, PeterProceedings of the National Academy of Sciences of the United States of America (2019), 116 (23), 11496-11501CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Forward-synthetic databases are an efficient way to enumerate chem. space. The authors explored here whether these databases are good sources of novel protein ligands and how many mols. are obtainable and in which time frame. Based on docking calcns., series of mols. were selected to gain insights into the ligand structur-activity relation. To evaluate the novelty of compds. in a challenging way, the authors chose the β2-adrenergic receptor, for which a large no. of ligands is already known. Finding dissimilar ligands is thus the exception rather than the rule. Here the authors report on the results, the successful synthesis of 127/240 mols. in just 2 wk, the discovery of previously unreported dissimilar ligands of the β2-adrenergic receptor, and the optimization of one series to a KD of 519 nM in only one round. Moreover, the finding that only 3 of 240 mols. had ever been synthesized before indicates that large parts of chem. space are unexplored.
- 24Rodríguez-Espigares, I., Torrens-Fontanals, M., Tiemann, J. K. S., Aranda-García, D., Ramírez-Anguita, J. M., Stepniewski, T. M., Worp, N., Varela-Rial, A., Morales-Pastor, A., Lacruz, B. M., Pándy-Szekeres, G., Mayol, E., Giorgino, T., Carlsson, J., Deupi, X., Filipek, S., Filizola, M., Gómez-Tamayo, J. C., Gonzalez, A., Gutierrez-de-Teran, H., Jimenez, M., Jespers, W., Kapla, J., Khelashvili, G., Kolb, P., Latek, D., Marti-Solano, M., Matricon, P., Matsoukas, M.-T., Miszta, P., Olivella, M., Perez-Benito, L., Provasi, D., Ríos, S., Rodríguez-Torrecillas, I., Sallander, J., Sztyler, A., Vaidehi, N., Vasile, S., Weinstein, H., Zachariae, U., Hildebrand, P. W., Fabritiis, G. D., Sanz, F., Gloriam, D. E., Cordomi, A., Guixà-González, R., and Selent, J. (2019) GPCRmd uncovers the dynamics of the 3D-GPCRome. bioRxiv 839597Google ScholarThere is no corresponding record for this reference.
- 25http://www.oncornet.eu/ (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 26https://www.era-learn.eu/network-information/networks/neuron-cofund/call-for-proposals-for-transnational-research-projects-on-mental-disorders/a-novel-paradigm-for-effective-and-safer-treatment-of-schizophrenia-biased-ant-agonists-with-a-characterized-polypharmacological-profile (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 27https://www.neuron-eranet.eu/_media/PSYBIAS_summary.pdf (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 28Horn, F., Weare, J., Beukers, M. W., Horsch, S., Bairoch, A., Chen, W., Edvardsen, O., Campagne, F., and Vriend, G. (1998) GPCRDB: an information system for G protein-coupled receptors. Nucleic Acids Res. 26 (1), 275– 9, DOI: 10.1093/nar/26.1.275Google Scholar28https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1cXovVehsw%253D%253D&md5=c32036731939e950081c6cfbdad00002GPCRDB: an information system for G protein-coupled receptorsHorn, F.; Weare, J.; Beukers, M. W.; Horsch, S.; Bairoch, A.; Chen, W.; Edvardsen, O.; Campagne, F.; Vriend, G.Nucleic Acids Research (1998), 26 (1), 275-279CODEN: NARHAD; ISSN:0305-1048. (Oxford University Press)The GPCRDB is a G protein-coupled receptor (GPCR) database system aimed at the collection and dissemination of GPCR related data. It holds sequences, mutant data and ligand binding consts. as primary (exptl.) data. Computationally derived, data such as multiple sequence alignments, three dimensional models, phylogenetic trees and two dimensional visualization tools are added to enhance the database's usefulness. The GPCRDB is an EU sponsored project aimed at building a generic mol. class specific database capable of dealing with highly heterogeneous data. GPCRs were chosen as test mols. because of their enormous importance for medical sciences and due to the availability of so much highly heterogeneous data. The GPCRDB is available via the WWW at http://www.gpcr.org/7tm.
- 29Isberg, V., Mordalski, S., Munk, C., Rataj, K., Harpsoe, K., Hauser, A. S., Vroling, B., Bojarski, A. J., Vriend, G., and Gloriam, D. E. (2016) GPCRdb: an information system for G protein-coupled receptors. Nucleic Acids Res. 44 (D1), D356– 64, DOI: 10.1093/nar/gkv1178Google Scholar29https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhtV2gu7bJ&md5=ee7db0ef81d65cf6e5ab8750b990bb78GPCRdb: an information system for G protein-coupled receptorsIsberg, Vignir; Mordalski, Stefan; Munk, Christian; Rataj, Krzysztof; Harpsoee, Kasper; Hauser, Alexander S.; Vroling, Bas; Bojarski, Andrzej J.; Vriend, Gert; Gloriam, David E.Nucleic Acids Research (2016), 44 (D1), D356-D364CODEN: NARHAD; ISSN:0305-1048. (Oxford University Press)A review. Recent developments in G protein-coupled receptor (GPCR) structural biol. and pharmacol. have greatly enhanced our knowledge of receptor structure-function relations, and have helped improve the scientific foundation for drug design studies. The GPCR database, GPCRdb, serves a dual role in disseminating and enabling new scientific developments by providing ref. data, anal. tools and interactive diagrams. This paper highlights new features in the fifth major GPCRdb release: (i) GPCR crystal structure browsing, superposition and display of ligand interactions; (ii) direct deposition by users of point mutations and their effects on ligand binding; (iii) refined snake and helix box residue diagram looks; and (iv) phylogenetic trees with receptor classification color schemes. Under the hood, the entire GPCRdb front- and back-ends have been recoded within one infrastructure, ensuring a smooth browsing experience and development. GPCRdb is available at http://www.gpcrdb.org/ and it's open source code at https://bitbucket.org/gpcr/protwis.
- 30Flock, T., Hauser, A. S., Lund, N., Gloriam, D. E., Balaji, S., and Babu, M. M. (2017) Selectivity determinants of GPCR-G-protein binding. Nature 545 (7654), 317– 322, DOI: 10.1038/nature22070Google Scholar30https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXnsVeis74%253D&md5=947db386e0e0f74b09465a99d880c518Selectivity determinants of GPCR-G-protein bindingFlock, Tilman; Hauser, Alexander S.; Lund, Nadia; Gloriam, David E.; Balaji, Santhanam; Babu, M. MadanNature (London, United Kingdom) (2017), 545 (7654), 317-322CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)The selective coupling of G-protein-coupled receptors (GPCRs) to specific G proteins is crit. to trigger the appropriate physiol. response. However, the determinants of selective binding have remained elusive. Here, we reveal the existence of a selectivity barcode (i.e., patterns of amino acids) on each of the 16 human G proteins that is recognized by distinct regions on the ∼800 human receptors. Although universally conserved positions in the barcode allow the receptors to bind and activate G proteins in a similar manner, different receptors recognize the unique positions of the G-protein barcode through distinct residues, like multiple keys (receptors) opening the same lock (G protein) using nonidentical cuts. Considering the evolutionary history of GPCRs allows the identification of these selectivity-detg. residues. These findings lay the foundation for understanding the mol. basis of coupling selectivity within individual receptors and G proteins.
- 31Hauser, A. S., Chavali, S., Masuho, I., Jahn, L. J., Martemyanov, K. A., Gloriam, D. E., and Babu, M. M. (2018) Pharmacogenomics of GPCR Drug Targets. Cell 172 (1–2), 41– 54 e19, DOI: 10.1016/j.cell.2017.11.033Google Scholar31https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhvF2js7rE&md5=aea194a723f8704cdcf4f05773c4880ePharmacogenomics of GPCR Drug TargetsHauser, Alexander S.; Chavali, Sreenivas; Masuho, Ikuo; Jahn, Leonie J.; Martemyanov, Kirill A.; Gloriam, David E.; Babu, M. MadanCell (Cambridge, MA, United States) (2018), 172 (1-2), 41-54.e19CODEN: CELLB5; ISSN:0092-8674. (Cell Press)Natural genetic variation in the human genome is a cause of individual differences in responses to medications and is an underappreciated burden on public health. Although 108 G-protein-coupled receptors (GPCRs) are the targets of 475 (∼34%) Food and Drug Administration (FDA)-approved drugs and account for a global sales vol. of over 180 billion US dollars annually, the prevalence of genetic variation among GPCRs targeted by drugs is unknown. By analyzing data from 68,496 individuals, we find that GPCRs targeted by drugs show genetic variation within functional regions such as drug- and effector-binding sites in the human population. We exptl. show that certain variants of μ-opioid and Cholecystokinin-A receptors could lead to altered or adverse drug response. By analyzing UK National Health Service drug prescription and sales data, we suggest that characterizing GPCR variants could increase prescription precision, improving patients' quality of life, and relieve the economic and societal burden due to variable drug responsiveness.
- 32Pandy-Szekeres, G., Munk, C., Tsonkov, T. M., Mordalski, S., Harpsoe, K., Hauser, A. S., Bojarski, A. J., and Gloriam, D. E. (2018) GPCRdb in 2018: adding GPCR structure models and ligands. Nucleic Acids Res. 46 (D1), D440– D446, DOI: 10.1093/nar/gkx1109Google Scholar32https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXitlGisLbE&md5=0cf77dd5ea934548a2d3a0ca69991f60GPCRdb in 2018: adding GPCR structure models and ligandsPandy-Szekeres, Gaspar; Munk, Christian; Tsonkov, Tsonko M.; Mordalski, Stefan; Harpsoee, Kasper; Hauser, Alexander S.; Bojarski, Andrzej J.; Gloriam, David E.Nucleic Acids Research (2018), 46 (D1), D440-D446CODEN: NARHAD; ISSN:1362-4962. (Oxford University Press)G protein-coupled receptors are the most abundant mediators of both human signaling processes and therapeutic effects. Herein, we report GPCRomewide homol. models of unprecedented quality, and roughly 150 000 GPCR ligands with data on biol. activities and com. availability. Based on the strategy of 'Less model - more Xtal', each model exploits both a main template and alternative local templates. This achieved higher similarity to new structures than any of the existing resources, and refined crystal structures with missing or distorted regions. Models are provided for inactive, intermediate and active states-except for classes C and F that so far only have inactive templates. The ligand database has sep. browsers for: (i) target selection by receptor, family or class, (ii) ligand filtering based on cross-expt. activities (min, max and mean) or chem. properties, (iii) ligand source data and (iv) com. availability. SMILES structures and activity spreadsheets can be downloaded for further processing. Furthermore, three recent landmark publications on GPCR drugs, G protein selectivity and genetic variants have been accompanied with resources that now let readers view and analyze the findings themselves in GPCRdb. Altogether, this update will enable scientific investigation for the wider GPCR community.
- 33Munk, C., Mutt, E., Isberg, V., Nikolajsen, L. F., Bibbe, J. M., Flock, T., Hanson, M. A., Stevens, R. C., Deupi, X., and Gloriam, D. E. (2019) An online resource for GPCR structure determination and analysis. Nat. Methods 16 (2), 151– 162, DOI: 10.1038/s41592-018-0302-xGoogle Scholar33https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXmtFGru74%253D&md5=a0e1ffb48671b58a63764ed4cff86901An online resource for GPCR structure determination and analysisMunk, Christian; Mutt, Eshita; Isberg, Vignir; Nikolajsen, Louise F.; Bibbe, Janne M.; Flock, Tilman; Hanson, Michael A.; Stevens, Raymond C.; Deupi, Xavier; Gloriam, David E.Nature Methods (2019), 16 (2), 151-162CODEN: NMAEA3; ISSN:1548-7091. (Nature Research)G-protein-coupled receptors (GPCRs) transduce physiol. and sensory stimuli into appropriate cellular responses and mediate the actions of one-third of drugs. GPCR structural studies have revealed the general bases of receptor activation, signaling, drug action and allosteric modulation, but so far cover only 13% of nonolfactory receptors. We broadly surveyed the receptor modifications/engineering and methods used to produce all available GPCR crystal and cryo-electron microscopy (cryo-EM) structures, and present an interactive resource integrated in GPCRdb (http://www.gpcrdb.org) to assist users in designing constructs and browsing appropriate exptl. conditions for structure studies.
- 34Takeda, S., Kadowaki, S., Haga, T., Takaesu, H., and Mitaku, S. (2002) Identification of G protein-coupled receptor genes from the human genome sequence. FEBS Lett. 520 (1–3), 97– 101, DOI: 10.1016/S0014-5793(02)02775-8Google Scholar34https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XktFOgt7s%253D&md5=d327417400f31b9fbcc7d01239494d0bIdentification of G protein-coupled receptor genes from the human genome sequenceTakeda, Shigeki; Kadowaki, Shiro; Haga, Tatsuya; Takaesu, Hirotomo; Mitaku, ShigekiFEBS Letters (2002), 520 (1-3), 97-101CODEN: FEBLAL; ISSN:0014-5793. (Elsevier Science B.V.)We have identified novel G protein-coupled receptors (GPCRs) with no introns in the coding region from the human genome sequence: 322 olfactory receptors; 22 taste receptors; 128 registered GPCRs for endogenous ligands; 50 novel GPCR candidates homologous to registered GPCRs for endogenous ligands; and 59 novel GPCR candidates not homologous to registered GPCRs. The total no. of GPCRs with and without introns in the human genome was estd. to be approx. 950, of which 500 are odorant or taste receptors and 450 are receptors for endogenous ligands.
- 35Rahmeh, R., Damian, M., Cottet, M., Orcel, H., Mendre, C., Durroux, T., Sharma, K. S., Durand, G., Pucci, B., Trinquet, E., Zwier, J. M., Deupi, X., Bron, P., Baneres, J. L., Mouillac, B., and Granier, S. (2012) Structural insights into biased G protein-coupled receptor signalling revealed by fluorescence spectroscopy. Proc. Natl. Acad. Sci. U. S. A. 109 (17), 6733– 8, DOI: 10.1073/pnas.1201093109Google Scholar35https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XmslGhtLk%253D&md5=62d24b44641a2ead4a8b83df84639606Structural insights into biased G protein-coupled receptor signaling revealed by fluorescence spectroscopyRahmeh, Rita; Damian, Marjorie; Cottet, Martin; Orcel, Helene; Mendre, Christiane; Durroux, Thierry; Sharma, K. Shivaji; Durand, Gregory; Pucci, Bernard; Trinquet, Eric; Zwier, Jurriaan M.; Deupi, Xavier; Bron, Patrick; Baneres, Jean-Louis; Mouillac, Bernard; Granier, SebastienProceedings of the National Academy of Sciences of the United States of America (2012), 109 (17), 6733-6738, S6733/1-S6733/11CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)G protein-coupled receptors (GPCRs) are seven-transmembrane proteins that mediate most cellular responses to hormones and neurotransmitters, representing the largest group of therapeutic targets. Recent studies show that some GPCRs signal through both G protein and arrestin pathways in a ligand-specific manner. Ligands that direct signaling through a specific pathway are known as biased ligands. The arginine-vasopressin type 2 receptor (V2R), a prototypical peptide-activated GPCR, is an ideal model system to investigate the structural basis of biased signaling. Although the native hormone arginine-vasopressin leads to activation of both the stimulatory G protein (Gs) for the adenylyl cyclase and arrestin pathways, synthetic ligands exhibit highly biased signaling through either Gs alone or arrestin alone. We used purified V2R stabilized in neutral amphipols and developed fluorescence-based assays to investigate the structural basis of biased signaling for the V2R. Our studies demonstrate that the Gs-biased agonist stabilizes a conformation that is distinct from that stabilized by the arrestin-biased agonists. This study provides unique insights into the structural mechanisms of GPCR activation by biased ligands that may be relevant to the design of pathway-biased drugs.
- 36Wacker, D., Wang, C., Katritch, V., Han, G. W., Huang, X. P., Vardy, E., McCorvy, J. D., Jiang, Y., Chu, M., Siu, F. Y., Liu, W., Xu, H. E., Cherezov, V., Roth, B. L., and Stevens, R. C. (2013) Structural features for functional selectivity at serotonin receptors. Science 340 (6132), 615– 9, DOI: 10.1126/science.1232808Google Scholar36https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXmslWksb0%253D&md5=16e96d0255be3ac367aeda7187aa4c15Structural Features for Functional Selectivity at Serotonin ReceptorsWacker, Daniel; Wang, Chong; Katritch, Vsevolod; Han, Gye Won; Huang, Xi-Ping; Vardy, Eyal; McCorvy, John D.; Jiang, Yi; Chu, Meihua; Siu, Fai Yiu; Liu, Wei; Xu, H. Eric; Cherezov, Vadim; Roth, Bryan L.; Stevens, Raymond C.Science (Washington, DC, United States) (2013), 340 (6132), 615-619CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)Drugs active at G protein-coupled receptors (GPCRs) can differentially modulate either canonical or noncanonical signaling pathways via a phenomenon known as functional selectivity or biased signaling. The authors report biochem. studies showing that the hallucinogen lysergic acid diethylamide, its precursor ergotamine (ERG), and related ergolines display strong functional selectivity for β-arrestin signaling at the 5-HT2B 5-hydroxytryptamine (5-HT) receptor, whereas they are relatively unbiased at the 5-HT1B receptor. To investigate the structural basis for biased signaling, the authors detd. the crystal structure of the human 5-HT2B receptor bound to ERG and compared it with the 5-HT1B/ERG structure. Given the relatively poor understanding of GPCR structure and function to date, insight into different GPCR signaling pathways is important to better understand both adverse and favorable therapeutic activities.
- 37Wingler, L. M., Elgeti, M., Hilger, D., Latorraca, N. R., Lerch, M. T., Staus, D. P., Dror, R. O., Kobilka, B. K., Hubbell, W. L., and Lefkowitz, R. J. (2019) Angiotensin Analogs with Divergent Bias Stabilize Distinct Receptor Conformations. Cell 176 (3), 468– 478 e11, DOI: 10.1016/j.cell.2018.12.005Google Scholar37https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXovFKktA%253D%253D&md5=2fe46c9f2061ac849b52bb2b372cd048Angiotensin Analogs with Divergent Bias Stabilize Distinct Receptor ConformationsWingler, Laura M.; Elgeti, Matthias; Hilger, Daniel; Latorraca, Naomi R.; Lerch, Michael T.; Staus, Dean P.; Dror, Ron O.; Kobilka, Brian K.; Hubbell, Wayne L.; Lefkowitz, Robert J.Cell (Cambridge, MA, United States) (2019), 176 (3), 468-478.e11CODEN: CELLB5; ISSN:0092-8674. (Cell Press)"Biased" G protein-coupled receptor (GPCR) agonists preferentially activate pathways mediated by G proteins or β-arrestins. Here, we use double electron-electron resonance spectroscopy to probe the changes that ligands induce in the conformational distribution of the angiotensin II type I receptor. Monitoring distances between 10 pairs of nitroxide labels distributed across the intracellular regions enabled mapping of four underlying sets of conformations. Ligands from different functional classes have distinct, characteristic effects on the conformational heterogeneity of the receptor. Compared to angiotensin II, the endogenous agonist, agonists with enhanced Gq coupling more strongly stabilize an "open" conformation with an accessible transducer-binding site. β-Arrestin-biased agonists deficient in Gq coupling do not stabilize this open conformation but instead favor two more occluded conformations. These data suggest a structural mechanism for biased ligand action at the angiotensin receptor that can be exploited to rationally design GPCR-targeting drugs with greater specificity of action.
- 38Lamichhane, R., Liu, J. J., White, K. L., Katritch, V., Stevens, R. C., Wuthrich, K., and Millar, D. P. (2020) Biased Signalling of the G-Protein-Coupled Receptor beta2AR Is Governed by Conformational Exchange Kinetics. Structure 28, 371, DOI: 10.1016/j.str.2020.01.001Google Scholar38https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhsFyitr8%253D&md5=222f483356ddbd8e67adae49f9e9126eBiased Signaling of the G-Protein-Coupled Receptor β2AR Is Governed by Conformational Exchange KineticsLamichhane, Rajan; Liu, Jeffrey J.; White, Kate L.; Katritch, Vsevolod; Stevens, Raymond C.; Wuthrich, Kurt; Millar, David P.Structure (Oxford, United Kingdom) (2020), 28 (3), 371-377.e3CODEN: STRUE6; ISSN:0969-2126. (Elsevier Ltd.)G-protein-coupled receptors (GPCRs) mediate a wide range of human physiol. functions by transducing extracellular ligand binding events into intracellular responses. GPCRs can activate parallel, independent signaling pathways mediated by G proteins or β-arrestins. Whereas "balanced" agonists activate both pathways equally, "biased" agonists dominantly activate one pathway, which is of interest for designing GPCR-targeting drugs because it may mitigate undesirable side effects. Previous studies demonstrated that β-arrestin activation is assocd. with transmembrane helix VII (TM VII) of GPCRs. Here, single-mol. fluorescence spectroscopy with the β2-adrenergic receptor (β2AR) in the ligand-free state showed that TM VII spontaneously fluctuates between one inactive and one active-like conformation. The presence of the β-arrestin-biased agonist isoetharine prolongs the dwell time of TM VII in the active-like conformation compared with the balanced agonist formoterol, suggesting that ligands can induce signaling bias by modulating the kinetics of receptor conformational exchange.
- 39Steen, A., Larsen, O., Thiele, S., and Rosenkilde, M. M. (2014) Biased and g protein-independent signalling of chemokine receptors. Front. Immunol. 5, 277, DOI: 10.3389/fimmu.2014.00277Google Scholar39https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC2cbgt1OisQ%253D%253D&md5=814b5ab6c48f59e2543803e516b35bbfBiased and g protein-independent signaling of chemokine receptorsSteen Anne; Larsen Olav; Thiele Stefanie; Rosenkilde Mette MFrontiers in immunology (2014), 5 (), 277 ISSN:1664-3224.Biased signaling or functional selectivity occurs when a 7TM-receptor preferentially activates one of several available pathways. It can be divided into three distinct forms: ligand bias, receptor bias, and tissue or cell bias, where it is mediated by different ligands (on the same receptor), different receptors (with the same ligand), or different tissues or cells (for the same ligand-receptor pair). Most often biased signaling is differentiated into G protein-dependent and β-arrestin-dependent signaling. Yet, it may also cover signaling differences within these groups. Moreover, it may not be absolute, i.e., full versus no activation. Here we discuss biased signaling in the chemokine system, including the structural basis for biased signaling in chemokine receptors, as well as in class A 7TM receptors in general. This includes overall helical movements and the contributions of micro-switches based on recently published 7TM crystals and molecular dynamics studies. All three forms of biased signaling are abundant in the chemokine system. This challenges our understanding of "classic" redundancy inevitably ascribed to this system, where multiple chemokines bind to the same receptor and where a single chemokine may bind to several receptors - in both cases with the same functional outcome. The ubiquitous biased signaling confers a hitherto unknown specificity to the chemokine system with a complex interaction pattern that is better described as promiscuous with context-defined roles and different functional outcomes in a ligand-, receptor-, or cell/tissue-defined manner. As the low number of successful drug development plans implies, there are great difficulties in targeting chemokine receptors; in particular with regard to receptor antagonists as anti-inflammatory drugs. Un-defined and putative non-selective targeting of the complete cellular signaling system could be the underlying cause of lack of success. Therefore, biased ligands could be the solution.
- 40Roth, S., Kholodenko, B. N., Smit, M. J., and Bruggeman, F. J. (2015) G Protein-Coupled Receptor Signalling Networks from a Systems Perspective. Mol. Pharmacol. 88 (3), 604– 16, DOI: 10.1124/mol.115.100057Google Scholar40https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsVCgsrfJ&md5=80924202aa2be037de8739f99bdd7f03G protein-coupled receptor signaling networks from a systems perspectiveRoth, S.; Kholodenko, B. N.; Smit, M. J.; Bruggeman, F. J.Molecular Pharmacology (2015), 88 (3), 604-616CODEN: MOPMA3; ISSN:1521-0111. (American Society for Pharmacology and Experimental Therapeutics)The signal-transduction network of a mammalian cell integrates internal and external cues to initiate adaptive responses. Among the cell-surface receptors are the G protein-coupled receptors (GPCRs), which have remarkable signal-integrating capabilities. Binding of extracellular signals stabilizes intracellular-domain conformations that selectively activate intracellular proteins. Hereby, multiple signaling routes are activated simultaneously to degrees that are signal-combination dependent. Systems-biol. studies indicate that signaling networks have emergent processing capabilities that go far beyond those of single proteins. Such networks are spatiotemporally organized and capable of gradual, oscillatory, all-or-none, and subpopulation-generating responses. Protein-protein interactions, generating feedback and feedforward circuitry, are generally required for these spatiotemporal phenomena. Understanding of information processing by signaling networks therefore requires network theories in addn. to biochem. and biophys. concepts. Here we review some of the key signaling systems behaviors that have been discovered recurrently across signaling networks. We emphasize the role of GPCRs, so far underappreciated receptors in systems-biol. research.
- 41Grundmann, M. and Kostenis, E. (2017) Temporal Bias: Time-Encoded Dynamic GPCR Signalling. Trends Pharmacol. Sci. 38 (12), 1110– 1124, DOI: 10.1016/j.tips.2017.09.004Google Scholar41https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhs1elsbbK&md5=8ea88ba1c0028bc1ac67b64375d09824Temporal Bias: Time-Encoded Dynamic GPCR SignalingGrundmann, Manuel; Kostenis, EviTrends in Pharmacological Sciences (2017), 38 (12), 1110-1124CODEN: TPHSDY; ISSN:0165-6147. (Elsevier Ltd.)A review. Evidence suggests that cells can time-encode signals for secure transport and perception of information, and it appears that this dynamic signaling is a common principle of nature to code information in time. G-protein-coupled receptor (GPCR) signaling networks are no exception as their compn. and signal transduction appear temporally flexible. In this review, we discuss the potential mechanisms by which GPCRs code biol. information in time to create 'temporal bias'. We highlight dynamic signaling patterns from the second messenger to the receptor-ligand level and shed light on the dynamics of G-protein cycles, the kinetics of ligand-receptor interaction, and the occurrence of distinct signaling waves within the cell. A dynamic feature such as temporal bias adds to the complexity of GPCR signaling bias and gives rise to the question whether this trait could be exploited to gain control over time-encoded cell physiol.
- 42Irannejad, R., Pessino, V., Mika, D., Huang, B., Wedegaertner, P. B., Conti, M., and von Zastrow, M. (2017) Functional selectivity of GPCR-directed drug action through location bias. Nat. Chem. Biol. 13 (7), 799– 806, DOI: 10.1038/nchembio.2389Google Scholar42https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXosFSrurg%253D&md5=49bff4da00d6c7a2d975aef416ff55dbFunctional selectivity of GPCR-directed drug action through location biasIrannejad, Roshanak; Pessino, Veronica; Mika, Delphine; Huang, Bo; Wedegaertner, Philip B.; Conti, Marco; von Zastrow, MarkNature Chemical Biology (2017), 13 (7), 799-806CODEN: NCBABT; ISSN:1552-4450. (Nature Publishing Group)G-protein-coupled receptors (GPCRs) are increasingly recognized to operate from intracellular membranes as well as the plasma membrane. The β2-adrenergic GPCR can activate Gs-linked cAMP (Gs-cAMP) signaling from endosomes. We show here that the homologous human β1-adrenergic receptor initiates an internal Gs-cAMP signal from the Golgi app. By developing a chem. method to acutely squelch G-protein coupling at defined membrane locations, we demonstrate that Golgi activation contributes significantly to the overall cellular cAMP response. Golgi signaling utilizes a preexisting receptor pool rather than receptors delivered from the cell surface, requiring sep. access of extracellular ligands. Epinephrine, a hydrophilic endogenous ligand, accesses the Golgi-localized receptor pool by facilitated transport requiring the org. cation transporter 3 (OCT3), whereas drugs can access the Golgi pool by passive diffusion according to hydrophobicity. We demonstrate marked differences, among both agonist and antagonist drugs, in Golgi-localized receptor access and show that β-blocker drugs currently used in the clinic differ markedly in ability to antagonize the Golgi signal. We propose 'location bias' as a new principle for achieving functional selectivity of GPCR-directed drug action.
- 43Eichel, K. and von Zastrow, M. (2018) Subcellular Organization of GPCR Signalling. Trends Pharmacol. Sci. 39 (2), 200– 208, DOI: 10.1016/j.tips.2017.11.009Google Scholar43https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXitVCmsbjL&md5=6c5222b28cb227d8367283aff2befa4cSubcellular Organization of GPCR SignalingEichel, Kelsie; von Zastrow, MarkTrends in Pharmacological Sciences (2018), 39 (2), 200-208CODEN: TPHSDY; ISSN:0165-6147. (Elsevier Ltd.)A review. G protein-coupled receptors (GPCRs) comprise a large and diverse class of signal-transducing receptors that undergo dynamic and isoform-specific membrane trafficking. GPCRs thus have an inherent potential to initiate or regulate signaling reactions from multiple membrane locations. This review discusses emerging insights into the subcellular organization of GPCR function in mammalian cells, focusing on signaling transduced by heterotrimeric G proteins and β-arrestins. We summarize recent evidence indicating that GPCR-mediated activation of G proteins occurs not only from the plasma membrane (PM) but also from endosomes and Golgi membranes and that β-arrestin-dependent signaling can be transduced from the PM by β-arrestin trafficking to clathrin-coated pits (CCPs) after dissocn. from a ligand-activated GPCR.
- 44Shaw, W. M., Yamauchi, H., Mead, J., Gowers, G. F., Bell, D. J., Oling, D., Larsson, N., Wigglesworth, M., Ladds, G., and Ellis, T. (2019) Engineering a Model Cell for Rational Tuning of GPCR Signalling. Cell 177 (3), 782– 796 e27, DOI: 10.1016/j.cell.2019.02.023Google Scholar44https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXmvFShtbc%253D&md5=2c7072e6cde1759d9d3e41968c137dd3Engineering a Model Cell for Rational Tuning of GPCR SignalingShaw, William M.; Yamauchi, Hitoshi; Mead, Jack; Gowers, Glen-Oliver F.; Bell, David J.; Oling, David; Larsson, Niklas; Wigglesworth, Mark; Ladds, Graham; Ellis, TomCell (Cambridge, MA, United States) (2019), 177 (3), 782-796.e27CODEN: CELLB5; ISSN:0092-8674. (Cell Press)G protein-coupled receptor (GPCR) signaling is the primary method eukaryotes use to respond to specific cues in their environment. However, the relation between stimulus and response for each GPCR is difficult to predict due to diversity in natural signal transduction architecture and expression. Using genome engineering in yeast, the authors constructed an insulated, modular GPCR signal transduction system to study how the response to stimuli can be predictably tuned using synthetic tools. The authors delineated the contributions of a minimal set of key components via computational and exptl. refactoring, identifying simple design principles for rationally tuning the dose response. Using five different GPCRs, this enables cells and consortia to be engineered to respond to desired concns. of peptides, metabolites, and hormones relevant to human health. This work enables rational tuning of cell sensing while providing a framework to guide reprogramming of GPCR-based signaling in other systems.
- 45Apostolakou, A. E., Baltoumas, F. A., Stravopodis, D. J., and Iconomidou, V. A. (2020) Extended Human G-Protein Coupled Receptor Network: Cell-Type-Specific Analysis of G-Protein Coupled Receptor Signalling Pathways. J. Proteome Res. 19 (1), 511– 524, DOI: 10.1021/acs.jproteome.9b00754Google Scholar45https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXit1CrsrjP&md5=66ad9ec99da475e6be98a6ca3efcbc9aExtended Human G-Protein Coupled Receptor Network: Cell-Type-Specific Analysis of G-Protein Coupled Receptor Signaling PathwaysApostolakou, Avgi E.; Baltoumas, Fotis A.; Stravopodis, Dimitrios J.; Iconomidou, Vassiliki A.Journal of Proteome Research (2020), 19 (1), 511-524CODEN: JPROBS; ISSN:1535-3893. (American Chemical Society)G-protein coupled receptors (GPCRs) mediate crucial physiol. functions in humans, have been implicated in an array of diseases, and are therefore prime drug targets. GPCRs signal via a multitude of pathways, mainly through G-proteins and β-arrestins, to regulate effectors responsible for cellular responses. The limited no. of transducers results in different GPCRs exerting control on the same pathway, while the availability of signaling proteins in a cell defines the result of GPCR activation. The aim of this study was to construct the extended human GPCR network (hGPCRnet) and examine the effect that cell-type specificity has on GPCR signaling pathways. To achieve this, protein-protein interaction data between GPCRs, G-protein coupled receptor kinases (GRKs), Gα subunits, β-arrestins, and effectors were combined with protein expression data in cell types. This resulted in the hGPCRnet, a very large interconnected network, and similar cell-type-specific networks in which, distinct GPCR signaling pathways were formed. Finally, a user friendly web application, hGPCRnet (http://bioinformatics.biol.uoa.gr/hGPCRnet), was created to allow for the visualization and exploration of these networks and of GPCR signaling pathways. This work, and the resulting application, can be useful in further studies of GPCR function and pharmacol.
- 46Wang, J., Gareri, C., and Rockman, H. A. (2018) G-Protein-Coupled Receptors in Heart Disease. Circ. Res. 123 (6), 716– 735, DOI: 10.1161/CIRCRESAHA.118.311403Google Scholar46https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhs1WitLnP&md5=0af28f631cfaea6d08c1154806229dbaG-Protein-Coupled Receptors in Heart DiseaseWang, Jialu; Gareri, Clarice; Rockman, Howard A.Circulation Research (2018), 123 (6), 716-735CODEN: CIRUAL; ISSN:0009-7330. (Lippincott Williams & Wilkins)GPCRs (G-protein [guanine nucleotide-binding protein]-coupled receptors) play a central physiol. role in the regulation of cardiac function in both health and disease and thus represent one of the largest class of surface receptors targeted by drugs. Several antagonists of GPCRs, such as βARs (β-adrenergic receptors) and Ang II (angiotensin II) receptors, are now considered std. of therapy for a wide range of cardiovascular disease, such as hypertension, coronary artery disease, and heart failure. Although the mechanism of action for GPCRs was thought to be largely worked out in the 80s and 90s, recent discoveries have brought to the fore new and previously unappreciated mechanisms for GPCR activation and subsequent downstream signaling. In this review, we focus on GPCRs most relevant to the cardiovascular system and discuss traditional components of GPCR signaling and highlight evolving concepts in the field, such as ligand bias, β-arrestin-mediated signaling, and conformational heterogeneity.
- 47Allen, J. A., Yost, J. M., Setola, V., Chen, X., Sassano, M. F., Chen, M., Peterson, S., Yadav, P. N., Huang, X. P., Feng, B., Jensen, N. H., Che, X., Bai, X., Frye, S. V., Wetsel, W. C., Caron, M. G., Javitch, J. A., Roth, B. L., and Jin, J. (2011) Discovery of beta-arrestin-biased dopamine D2 ligands for probing signal transduction pathways essential for antipsychotic efficacy. Proc. Natl. Acad. Sci. U. S. A. 108 (45), 18488– 93, DOI: 10.1073/pnas.1104807108Google Scholar47https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhsFymtLzK&md5=d5b06e4ac4d2cc4cd04fd1de760ec628Discovery of β-arrestin-biased dopamine D2 ligands for probing signal transduction pathways essential for antipsychotic efficacyAllen, John A.; Yost, Julianne M.; Setola, Vincent; Chen, Xin; Sassano, Maria F.; Chen, Meng; Peterson, Sean; Yadav, Prem N.; Huang, Xi-Ping; Feng, Bo; Jensen, Niels H.; Che, Xin; Bai, Xu; Frye, Stephen V.; Wetsel, William C.; Caron, Marc G.; Javitch, Jonathan A.; Roth, Bryan L.; Jin, JianProceedings of the National Academy of Sciences of the United States of America (2011), 108 (45), 18488-18493, S18488/1-S18488/15CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Elucidating the key signal transduction pathways essential for both antipsychotic efficacy and side-effect profiles is essential for developing safer and more effective therapies. Recent work has highlighted noncanonical modes of dopamine D2 receptor (D2R) signaling via β-arrestins as being important for the therapeutic actions of both antipsychotic and antimanic agents. We thus sought to create unique D2R agonists that display signaling bias via β-arrestinergic signaling. Through a robust diversity-oriented modification of the scaffold represented by aripiprazole (1), we discovered UNC9975 (2), UNC0006 (3); and UNC9994 (4) as unprecedented β-arrestin-biased D2R ligands. These compds. also represent unprecedented β-arrestin-biased ligands for a Gi-coupled G protein-coupled receptor (GPCR). Significantly, UNC9975, UNC0006, and UNC9994 are simultaneously antagonists of Gi-regulated cAMP prodn. and partial agonists for D2R/β-arrestin-2 interactions. Importantly, VNC9975 displayed potent antipsychotic-like activity without inducing motoric side effects in inbred C57BL/6 mice in vivo. Genetic deletion of β-arrestin-2 simultaneously attenuated the antipsychotic actions of UNC9975 and transformed it into a typical antipsychotic .drug with a high propensity to induce catalepsy. Similarly, the antipsychotic-like activity displayed by UNC9994, an extremely β-arrestin-biased D2R agonist, in wild-type mice was completely abolished in β-arrestin-2 knockout mice. Taken together, our results suggest that β-arrestin signaling and recruitment can be simultaneously a significant contributor to antipsychotic efficacy and protective against motoric side effects. These functionally selective, β-arrestin-biased D2R ligands represent valuable chem. probes for further investigations of D2R signaling in health and disease.
- 48Moller, D., Kling, R. C., Skultety, M., Leuner, K., Hubner, H., and Gmeiner, P. (2014) Functionally selective dopamine D(2), D(3) receptor partial agonists. J. Med. Chem. 57 (11), 4861– 75, DOI: 10.1021/jm5004039Google Scholar48https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC2cjjtFCquw%253D%253D&md5=ddab57825968f481f733b766ce2bec64Functionally selective dopamine D2, D3 receptor partial agonistsMoller Dorothee; Kling Ralf C; Skultety Marika; Leuner Kristina; Hubner Harald; Gmeiner PeterJournal of medicinal chemistry (2014), 57 (11), 4861-75 ISSN:.Dopamine D2 receptor-promoted activation of Gα(o) over Gα(i) may increase synaptic plasticity and thereby might improve negative symptoms of schizophrenia. Heterocyclic dopamine surrogates comprising a pyrazolo[1,5-a]pyridine moiety were synthesized and investigated for their binding properties when low- to subnanomolar K(i) values were determined for D(2L), D(2S), and D3 receptors. Measurement of [(35)S]GTPγS incorporation at D(2S) coexpressed with G-protein subunits indicated significant bias for promotion of Gα(o1) over Gα(i2) coupling for several test compounds. Functionally selective D(2S) activation was most striking for the carbaldoxime 8b (Gα(o1), pEC50 = 8.87, E(max) = 65%; Gα(i2), pEC50 = 6.63, E(max) = 27%). In contrast, the investigated 1,4-disubstituted aromatic piperazines (1,4-DAPs) behaved as antagonists for β-arrestin-2 recruitment, implying significant ligand bias for G-protein activation over β-arrestin-2 recruitment at D(2S) receptors. Ligand efficacy and selectivity between D(2S) and D3 activation were strongly influenced by regiochemistry and the nature of functional groups attached to the pyrazolo[1,5-a]pyridine moiety.
- 49Weiwer, M., Xu, Q., Gale, J. P., Lewis, M., Campbell, A. J., Schroeder, F. A., Van de Bittner, G. C., Walk, M., Amaya, A., Su, P., L, D. O., Sacher, J. R., Skepner, A., Fei, D., Dennehy, K., Nguyen, S., Faloon, P. W., Perez, J., Cottrell, J. R., Liu, F., Palmer, M., Pan, J. Q., Hooker, J. M., Zhang, Y. L., Scolnick, E., Wagner, F. F., and Holson, E. B. (2018) Functionally Biased D2R Antagonists: Targeting the beta-Arrestin Pathway to Improve Antipsychotic Treatment. ACS Chem. Biol. 13 (4), 1038– 1047, DOI: 10.1021/acschembio.8b00168Google Scholar49https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXjtlOrtbw%253D&md5=51d636dd2a0ebfc83d58a6158a1da40eFunctionally Biased D2R Antagonists: Targeting the β-Arrestin Pathway to Improve Antipsychotic TreatmentWeiwer, Michel; Xu, Qihong; Gale, Jennifer P.; Lewis, Michael; Campbell, Arthur J.; Schroeder, Frederick A.; Van de Bittner, Genevieve C.; Walk, Michelle; Amaya, Aldo; Su, Ping; Dordevic, Luka; Sacher, Joshua R.; Skepner, Adam; Fei, David; Dennehy, Kelly; Nguyen, Shannon; Faloon, Patrick W.; Perez, Jose; Cottrell, Jeffrey R.; Liu, Fang; Palmer, Michelle; Pan, Jen Q.; Hooker, Jacob M.; Zhang, Yan-Ling; Scolnick, Edward; Wagner, Florence F.; Holson, Edward B.ACS Chemical Biology (2018), 13 (4), 1038-1047CODEN: ACBCCT; ISSN:1554-8929. (American Chemical Society)Schizophrenia is a severe neuropsychiatric disease that lacks completely effective and safe therapies. As a polygenic disorder, genetic studies have only started to shed light on its complex etiol. To date, the pos. symptoms of schizophrenia are well-managed by antipsychotic drugs, which primarily target the dopamine D2 receptor (D2R). However, these antipsychotics are often accompanied by severe side effects, including motoric symptoms. At D2R, antipsychotic drugs antagonize both G-protein dependent (Gαi/o) signaling and G-protein independent (β-arrestin) signaling. However, the relevant contributions of the distinct D2R signaling pathways to antipsychotic efficacy and on-target side effects (motoric) are still incompletely understood. Recent evidence from mouse genetic and pharmacol. studies point to β-arrestin signaling as the major driver of antipsychotic efficacy and suggest that a β-arrestin biased D2R antagonist could achieve an addnl. level of selectivity at D2R, increasing the therapeutic index of next generation antipsychotics. Here, we characterize BRD5814, a highly brain penetrant β-arrestin biased D2R antagonist. BRD5814 demonstrated good target engagement via PET imaging, achieving efficacy in an amphetamine-induced hyperlocomotion mouse model with strongly reduced motoric side effects in a rotarod performance test. This proof of concept study opens the possibility for the development of a new generation of pathway selective antipsychotics at D2R with reduced side effect profiles for the treatment of schizophrenia.
- 50DeWire, S. M., Yamashita, D. S., Rominger, D. H., Liu, G., Cowan, C. L., Graczyk, T. M., Chen, X. T., Pitis, P. M., Gotchev, D., Yuan, C., Koblish, M., Lark, M. W., and Violin, J. D. (2013) A G protein-biased ligand at the mu-opioid receptor is potently analgesic with reduced gastrointestinal and respiratory dysfunction compared with morphine. J. Pharmacol. Exp. Ther. 344 (3), 708– 17, DOI: 10.1124/jpet.112.201616Google Scholar50https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXjvVaisro%253D&md5=33a685cd1952dd9cb1fb82afe78452afA G protein-biased ligand at the μ-opioid receptor is potently analgesic with reduced gastrointestinal and respiratory dysfunction compared with morphineDeWire, Scott M.; Yamashita, Dennis S.; Rominger, David H.; Liu, Guodong; Cowan, Conrad L.; Graczyk, Thomas M.; Chen, Xiao-Tao; Pitis, Philip M.; Gotchev, Dimitar; Yuan, Catherine; Koblish, Michael; Lark, Michael W.; Violin, Jonathan D.Journal of Pharmacology and Experimental Therapeutics (2013), 344 (3), 708-717CODEN: JPETAB; ISSN:1521-0103. (American Society for Pharmacology and Experimental Therapeutics)The concept of ligand bias at G protein-coupled receptors broadens the possibilities for agonist activities and provides the opportunity to develop safer, more selective therapeutics. Morphine pharmacol. in β-arrestin-2 knockout mice suggested that a ligand that promotes coupling of the μ-opioid receptor (MOR) to G proteins, but not β-arrestins, would result in higher analgesic efficacy, less gastrointestinal dysfunction, and less respiratory suppression than morphine. Here we report the discovery of TRV130 ([(3-methoxythiophen-2-yl)methyl]({2-[(9R)-9-(pyridin-2-yl)-6-oxaspiro[4.5]decan-9-yl]ethyl})amine), a novel MOR G protein-biased ligand. In cell-based assays, TRV130 elicits robust G protein signaling, with potency and efficacy similar to morphine, but with far less β-arrestin recruitment and receptor internalization. In mice and rats, TRV130 is potently analgesic while causing less gastrointestinal dysfunction and respiratory suppression than morphine at equianalgesic doses. TRV130 successfully translates evidence that analgesic and adverse MOR signaling pathways are distinct into a biased ligand with differentiated pharmacol. These preclin. data suggest that TRV130 may be a safer and more tolerable therapeutic for treating severe pain.
- 51Schmid, C. L., Kennedy, N. M., Ross, N. C., Lovell, K. M., Yue, Z., Morgenweck, J., Cameron, M. D., Bannister, T. D., and Bohn, L. M. (2017) Bias Factor and Therapeutic Window Correlate to Predict Safer Opioid Analgesics. Cell 171 (5), 1165– 1175 e13, DOI: 10.1016/j.cell.2017.10.035Google Scholar51https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhvFOhs7vE&md5=6d3f21c03fb40bc83adbe62c3ea331fcBias Factor and Therapeutic Window Correlate to Predict Safer Opioid AnalgesicsSchmid, Cullen L.; Kennedy, Nicole M.; Ross, Nicolette C.; Lovell, Kimberly M.; Yue, Zhizhou; Morgenweck, Jenny; Cameron, Michael D.; Bannister, Thomas D.; Bohn, Laura M.Cell (Cambridge, MA, United States) (2017), 171 (5), 1165-1175.e13CODEN: CELLB5; ISSN:0092-8674. (Cell Press)Biased agonism has been proposed as a means to sep. desirable and adverse drug responses downstream of G protein-coupled receptor (GPCR) targets. Herein, we describe structural features of a series of mu-opioid-receptor (MOR)-selective agonists that preferentially activate receptors to couple to G proteins or to recruit βarrestin proteins. By comparing relative bias for MOR-mediated signaling in each pathway, we demonstrate a strong correlation between the respiratory suppression/antinociception therapeutic window in a series of compds. spanning a wide range of signaling bias. We find that β-arrestin-biased compds., such as fentanyl, are more likely to induce respiratory suppression at weak analgesic doses, while G protein signaling bias broadens the therapeutic window, allowing for antinociception in the absence of respiratory suppression.
- 52James, I. E., Skobieranda, F., Soergel, D. G., Ramos, K. A., Ruff, D., and Fossler, M. J. (2020) A First-in-Human Clinical Study With TRV734, an Orally Bioavailable G-Protein-Biased Ligand at the mu-Opioid Receptor. Clin. Pharmacol. Drug Dev. 9 (2), 256– 266, DOI: 10.1002/cpdd.721Google Scholar52https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXisFajs7w%253D&md5=46faef25a0959ddbd0f95623c186e674A First-in-Human Clinical Study With TRV734, an Orally Bioavailable G-Protein-Biased Ligand at the μ-Opioid ReceptorJames, Ian E.; Skobieranda, Franck; Soergel, David G.; Ramos, Kimberly A.; Ruff, Dennis; Fossler, Michael J.Clinical Pharmacology in Drug Development (2020), 9 (2), 256-266CODEN: CPDDAH; ISSN:2160-7648. (John Wiley & Sons, Inc.)TRV734 is an orally bioavailable G-protein-biased ligand at the μ-opioid receptor. In nonclin. studies it was potently analgesic while causing less gastrointestinal dysfunction than morphine, suggesting unique benefits in acute pain management. A 2-part, first-in-human study was conducted with ascending doses of TRV734 to explore its tolerability, pharmacokinetics, and pharmacodynamics in healthy volunteers. TRV734 was well tolerated over the dose range 2 to 250 mg when administered orally. Plasma TRV734 max. concn. and area under the plasma concn.-time curve generally increased with dose, while time to max. concn. was similar across doses (0.5-1.3 h). The half-life increased with dose from 10 mg through 150 mg (0.75-2.28 h) but was similar from 150 mg through 250 mg. Pupil constriction, confirming central nervous system μ-opioid receptor engagement, correlated with higher plasma TRV734 concns.; the greatest redns. in pupil diam. occurring between 0 and 4 h after dosing (-2.9 mm/h, with redn. peaking at 1 h, and returning to baseline by 8 h). Following administration of TRV734 125 mg under fasted or fed conditions, there was no significant difference in bioavailability when given as a soln. or drug in capsule to fasted subjects. When drug in capsule was given to subjects following a high-fat meal, absorption was slowed, resulting in decreased peak concns., but area under the plasma concn.-time curve was not affected.
- 53Conibear, A. E. and Kelly, E. (2019) A Biased View of mu-Opioid Receptors?. Mol. Pharmacol. 96 (5), 542– 549, DOI: 10.1124/mol.119.115956Google Scholar53https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXitlams7zK&md5=2bdf67af51575f7abfd1514345086cd8A biased view of μ-opioid receptors?Conibear, Alexandra E.; Kelly, EamonnMolecular Pharmacology (2019), 96 (5), 542-549CODEN: MOPMA3; ISSN:1521-0111. (American Society for Pharmacology and Experimental Therapeutics)A review. The field of biased agonism has grown substantially in recent years and the μ-opioid receptor has been one of the most intensively studied receptor targets for developing biased agonists. Yet, despite extensive research efforts, the development of analgesics with reduced adverse effects remains a significant challenge. In this review we discuss the evidence to support the prevailing hypothesis that a G protein-biased agonist at the μ-opioid receptor would be an effective analgesic without the accompanying adverse effects assocd. with conventional μ-opioid agonists. We also assess the current status of established and novel μ-opioid-receptor ligands that are proposed to be biased ligands.
- 54Pedersen, M. F., Wrobel, T. M., Marcher-Rorsted, E., Pedersen, D. S., Moller, T. C., Gabriele, F., Pedersen, H., Matosiuk, D., Foster, S. R., Bouvier, M., and Brauner-Osborne, H. (2020) Biased agonism of clinically approved mu-opioid receptor agonists and TRV130 is not controlled by binding and signalling kinetics. Neuropharmacology 166, 107718, DOI: 10.1016/j.neuropharm.2019.107718Google Scholar54https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXit12ktrbI&md5=a63ba99f8beb16f92aa793dcc1e0a0f7Biased agonism of clinically approved μ-opioid receptor agonists and TRV130 is not controlled by binding and signaling kineticsPedersen, Mie Fabricius; Wrobel, Tomasz Marcin; Marcher-Roersted, Emil; Pedersen, Daniel Sejer; Moeller, Thor Christian; Gabriele, Federica; Pedersen, Henrik; Matosiuk, Dariusz; Foster, Simon Richard; Bouvier, Michel; Brauner-Osborne, HansNeuropharmacology (2020), 166 (), 107718CODEN: NEPHBW; ISSN:0028-3908. (Elsevier B.V.)Here we provide a comprehensive kinetic pharmacol. comparison of clin. relevant μ-opioid receptor agonists, including the novel biased agonist oliceridine (TRV130) which is in clin. trial for pain management. We demonstrate that the bias profile obsd. for the selected agonists is not time-dependent and that agonists with dramatic differences in their binding kinetic properties can display the same degree of bias. Binding kinetics analyses demonstrate that buprenorphine has 18-fold higher receptor residence time than oliceridine. This is thus the largest pharmacodynamic difference between the clin. approved drug buprenorphine and the clin. candidate oliceridine, since their bias profiles are similar. Further, we provide the first pharmacol. characterization of (S)-TRV130 demonstrating that it has a similar pharmacol. profile as the (R)-form, oliceridine, but displays 90-fold lower potency than the (R)-form. This difference is driven by a significantly slower assocn. rate. GRK2 and GRK5 overexpression greatly increased μ-opioid receptor internalization induced by morphine, but only had modest effects on buprenorphine and oliceridine-induced internalization. Overall, our data reveal that the clin. available drug buprenorphine displays a similar pharmacol. bias profile in vitro compared to the clin. candidate drug oliceridine and that this bias is independent of binding kinetics suggesting a mechanism driven by receptor-conformations.
- 55Kliewer, A., Schmiedel, F., Sianati, S., Bailey, A., Bateman, J. T., Levitt, E. S., Williams, J. T., Christie, M. J., and Schulz, S. (2019) Phosphorylation-deficient G-protein-biased mu-opioid receptors improve analgesia and diminish tolerance but worsen opioid side effects. Nat. Commun. 10 (1), 367, DOI: 10.1038/s41467-018-08162-1Google Scholar55https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXntFeks7k%253D&md5=19fa2354d75d29b28503d21f63754d45Phosphorylation-deficient G-protein-biased mu-opioid receptors improve analgesia and diminish tolerance but worsen opioid side effectsKliewer, A.; Schmiedel, F.; Sianati, S.; Bailey, A.; Bateman, J. T.; Levitt, E. S.; Williams, J. T.; Christie, M. J.; Schulz, S.Nature Communications (2019), 10 (1), 367CODEN: NCAOBW; ISSN:2041-1723. (Nature Research)Opioid analgesics are powerful pain relievers; however, over time, pain control diminishes as analgesic tolerance develops. The mol. mechanisms initiating tolerance have remained unresolved to date. We have previously shown that desensitization of the mu-opioid receptor and interaction with beta-arrestins is controlled by carboxyl-terminal phosphorylation. Here we created knockin mice with a series of serine- and threonine-to-alanine mutations that render the receptor increasingly unable to recruit beta-arrestins. Desensitization is inhibited in locus coeruleus neurons of mutant mice. Opioid-induced analgesia is strongly enhanced and analgesic tolerance is greatly diminished. Surprisingly, respiratory depression, constipation, and opioid withdrawal signs are unchanged or exacerbated, indicating that beta-arrestin recruitment does not contribute to the severity of opioid side effects and, hence, predicting that G-protein-biased mu-agonists are still likely to elicit severe adverse effects. In conclusion, our findings identify carboxyl-terminal multisite phosphorylation as key step that drives acute mu-opioid receptor desensitization and long-term tolerance.
- 56Kliewer, A., Gillis, A., Hill, R., Schmidel, F., Bailey, C., Kelly, E., Henderson, G., Christie, M. J., and Schulz, S. (2020) Morphine-induced respiratory depression is independent of beta-arrestin2 signalling. Br. J. Pharmacol. DOI: 10.1111/bph.15004Google ScholarThere is no corresponding record for this reference.
- 57Michel, M. C. and Charlton, S. J. (2018) Biased Agonism in Drug Discovery-Is It Too Soon to Choose a Path?. Mol. Pharmacol. 93 (4), 259– 265, DOI: 10.1124/mol.117.110890Google Scholar57https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhs12qsr3K&md5=a975e0fedbb29ba2059fe14c5be5d434Biased agonism in drug discovery-is it too soon to choose a path?Michel, Martin C.; Charlton, Steven J.Molecular Pharmacology (2018), 93 (4), 259-265CODEN: MOPMA3; ISSN:1521-0111. (American Society for Pharmacology and Experimental Therapeutics)A single receptor can activate multiple signaling pathways that have distinct or even opposite effects on cell function. Biased agonists stabilize receptor conformations preferentially stimulating one of these pathways, and therefore allow a more targeted modulation of cell function and treatment of disease. Dedicated development of biased agonists has led to promising drug candidates in clin. development, such as the G proteinbiased μ opioid receptor agonist oliceridine. However, leveraging the theor. potential of biased agonism for drug discovery faces several challenges. Some of these challenges are tech., such as techniques for quant. anal. of bias and development of suitable screening assays; others are more fundamental, such as the need to robustly identify in a very early phase which cell type harbors the cellular target of the drug candidate, which signaling pathway leads to the desired therapeutic effect, and how these pathways may be modulated in the disease to be treated. We conclude that biased agonism has potential mainly in the treatment of conditions with a wellunderstood pathophysiol.; in contrast, it may increase effort and com. risk under circumstances where the pathophysiol. has been less well defined, as is the case with many highly innovative treatments.
- 58Wootten, D., Christopoulos, A., Marti-Solano, M., Babu, M. M., and Sexton, P. M. (2018) Mechanisms of signalling and biased agonism in G protein-coupled receptors. Nat. Rev. Mol. Cell Biol. 19 (10), 638– 653, DOI: 10.1038/s41580-018-0049-3Google Scholar58https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhsFSqtbzO&md5=61ffa3780b7da6df8a8ccee2365354aeMechanisms of signalling and biased agonism in G protein-coupled receptorsWootten, Denise; Christopoulos, Arthur; Marti-Solano, Maria; Babu, M. Madan; Sexton, Patrick M.Nature Reviews Molecular Cell Biology (2018), 19 (10), 638-653CODEN: NRMCBP; ISSN:1471-0072. (Nature Research)A review. G protein-coupled receptors (GPCRs) are the largest group of cell surface receptors in humans that signal in response to diverse inputs and regulate a plethora of cellular processes. Hence, they constitute one of the primary drug target classes. Progress in our understanding of GPCR dynamics, activation and signalling has opened new possibilities for selective drug development. A key advancement has been provided by the concept of biased agonism, which describes the ability of ligands acting at the same GPCR to elicit distinct cellular signalling profiles by preferentially stabilizing different active conformational states of the receptor. Application of this concept raises the prospect of 'designer' biased agonists as optimized therapeutics with improved efficacy and/or reduced side-effect profiles. However, this application will require a detailed understanding of the spectrum of drug actions and a structural understanding of the drug-receptor interactions that drive distinct pharmacologies. The recent revolution in GPCR structural biol. provides unprecedented insights into ligand binding, conformational dynamics and the control of signalling outcomes. These insights, together with new approaches to multi-dimensional anal. of drug action, are allowing refined classification of drugs according to their pharmacodynamic profiles, which can be linked to receptor structure and predictions of preclin. drug efficacy.
- 59Kenakin, T. (2019) Biased Receptor Signalling in Drug Discovery. Pharmacol. Rev. 71 (2), 267– 315, DOI: 10.1124/pr.118.016790Google Scholar59https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhvV2gtL3E&md5=ddf8cb5adb1dc14783bfc82a308fc70dBiased receptor signaling in drug discoveryKenakin, TerryPharmacological Reviews (2019), 71 (2), 267-315CODEN: PAREAQ; ISSN:1521-0081. (American Society for Pharmacology and Experimental Therapeutics)A review. A great deal of exptl. evidence suggests that ligands can stabilize different receptor active states that go on to interact with cellular signaling proteins to form a range of different complexes in varying quantities. In pleiotropically linked receptor systems, this leads to selective activation of some signaling pathways at the expense of others (biased signaling). This article summarizes the current knowledge about the complex components of receptor systems, the evidence that biased signaling is used in natural physiol. to fine-tune signaling, and the current thoughts on how this mechanism may be applied to the design of better drugs. Although this is a fairly newly discovered phenomenon, theor. and exptl. data suggest that it is a ubiquitous behavior of ligands and receptors and to be expected. Biased signaling is simple to detect in vitro and there are numerous methods to quantify the effect with scales that can be used to optimize this activity in structure-activity medicinal chem. studies. At present, the major hurdle in the application of this mechanism to therapeutics is the translation of in vitro bias to in vivo effect; this is because of the numerous factors that can modify measures of bias in natural physiol. systems. In spite of this, biased signaling still has the potential to justify revisiting of receptor targets previously thought to be intractable and also furnishes the means to pursue targets previously thought to be forbidden due to deleterious physiol. (as these may be eliminated through biased signaling).
- 60Pang, P. S., Butler, J., Collins, S. P., Cotter, G., Davison, B. A., Ezekowitz, J. A., Filippatos, G., Levy, P. D., Metra, M., Ponikowski, P., Teerlink, J. R., Voors, A. A., Bharucha, D., Goin, K., Soergel, D. G., and Felker, G. M. (2017) Biased ligand of the angiotensin II type 1 receptor in patients with acute heart failure: a randomized, double-blind, placebo-controlled, phase IIB, dose ranging trial (BLAST-AHF). Eur. Heart J. 38 (30), 2364– 2373, DOI: 10.1093/eurheartj/ehx196Google Scholar60https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXitFGksbvO&md5=62e28c6fa244809d87e52d8f979ce629Biased ligand of the angiotensin II type 1 receptor in patients with acute heart failure: a randomized, double-blind, placebo-controlled, phase IIB, dose ranging trial (BLAST-AHF)Pang, Peter S.; Butler, Javed; Collins, Sean P.; Cotter, Gad; Davison, Beth A.; Ezekowitz, Justin A.; Filippatos, Gerasimos; Levy, Phillip D.; Metra, Marco; Ponikowski, Piotr; Teerlink, John R.; Voors, Adriaan A.; Bharucha, David; Goin, Kathleen; Soergel, David G.; Michael Felker, G.European Heart Journal (2017), 38 (30), 2364-2373CODEN: EHJODF; ISSN:1522-9645. (Oxford University Press)Aims: Currently, no acute heart failure (AHF) therapy definitively improves outcomes. Reducing morbidity and mortality from acute heart failure (AHF) remains an unmet need. TRV027 is a novel 'biased' ligand of the angiotensin II type 1 receptor (AT1R), selectively antagonizing the neg. effects of angiotensin II, while preserving the potential procontractility effects of AT1R stimulation. BLAST-AHF was designed to det. the safety, efficacy, and opti- mal dose of TRV027 to advance into future studies. Methods and results: BLAST-AHF was a multi-center, international, randomized, double-blind, placebo-controlled, parallel group, phase IIb dose-ranging study, enrolling patients with AHF into 4 groups: placebo, 1, 5, or 25 mg/h of TRV027. Treatment was by IV infusion for 48-96 h. The primary composite endpoint was comprised of the following: (i) time from baseline to death through day 30, (ii) time from baseline to heart failure re-hospitalization through day 30, (iii) the first assessment time point following worsening heart failure through day 5, (iv) change in dyspnea visual analog scale (VAS) score calcd. as the area under the curve (AUC) representing the change from baseline over time from baseline through day 5, and (v) length of initial hospital stay (in days) from baseline. Analyses were by modified intention-to-treat. Overall, 621 patients were enrolled. After 254 patients, a pre-specified interim anal. resulted in several protocol changes, including a lower blood pressure inclusion criterion as well as a new allocation scheme of 2:1:2:1, overweighting both placebo, and the 5 mg/h dose. TRV027 did not confer any benefit over placebo at any dose with regards to the primary composite endpoint or any of the individual components. There were no significant safety issues with TRV027. Conclusion: In this phase IIb dose-ranging AHF study, TRV027 did not improve clin. status through 30-day follow-up compared with placebo.
- 61Violin, J. D., Crombie, A. L., Soergel, D. G., and Lark, M. W. (2014) Biased ligands at G-protein-coupled receptors: promise and progress. Trends Pharmacol. Sci. 35 (7), 308– 16, DOI: 10.1016/j.tips.2014.04.007Google Scholar61https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXosl2htr4%253D&md5=768953e7aa5726d1a47ecbdb068469d8Biased ligands at G-protein-coupled receptors: promise and progressViolin, Jonathan D.; Crombie, Aimee L.; Soergel, David G.; Lark, Michael W.Trends in Pharmacological Sciences (2014), 35 (7), 308-316CODEN: TPHSDY; ISSN:0165-6147. (Elsevier Ltd.)A review. Drug discovery targeting G protein-coupled receptors (GPCRs) is no longer limited to seeking agonists or antagonists to stimulate or block cellular responses assocd. with a particular receptor. GPCRs are now known to support a diversity of pharmacol. profiles, a concept broadly referred to as functional selectivity. In particular, the concept of ligand bias, whereby a ligand stabilizes subsets of receptor conformations to engender novel pharmacol. profiles, has recently gained increasing prominence. This review discusses how biased ligands may deliver safer, better tolerated, and more efficacious drugs, and highlights several biased ligands that are in clin. development. Biased ligands targeting the angiotensin II type 1 receptor and the μ opioid receptor illustrate the translation of the biased ligand concept from basic biol. to clin. drug development.
- 62Costa-Neto, C. M., Parreiras, E. S. L. T., and Bouvier, M. (2016) A Pluridimensional View of Biased Agonism. Mol. Pharmacol. 90 (5), 587– 595, DOI: 10.1124/mol.116.105940Google Scholar62https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXitVaktbc%253D&md5=959701333007f859e11126cc6629336eA pluridimensional view of biased agonismCosta-Neto, Claudio M.; Parreiras-e-Silva, Lucas T.; Bouvier, MichelMolecular Pharmacology (2016), 90 (5), 587-595CODEN: MOPMA3; ISSN:1521-0111. (American Society for Pharmacology and Experimental Therapeutics)A review. When studying G protein-coupled receptor (GPCR) signaling and ligand-biased agonism, at least three dimensional spaces must be considered, as follows: (1) the distinct conformations that can be stabilized by different ligands promoting the engagement of different signaling effectors and accessory regulators; (2) the distinct subcellular trafficking that can be conferred by different ligands, which results in spatially distinct signals; and (3) the differential binding kinetics that maintain the receptor in specific conformation and/or subcellular localization for different periods of time, allowing for the engagement of distinct signaling effector subsets. These three pluridimensional aspects of signaling contribute to different faces of functional selectivity and provide a complex, interconnected way to define the signaling profile of each individual ligand acting at GPCRs. In this review, we discuss how each of these aspects may contribute to the diversity of signaling, but also how they shed light on the complexity of data analyses and interpretation. The impact of phenotype variability as a source of signaling diversity, and the influence of novel and more sensitive assays in the detection and anal. of signaling pluridimensionality, is also discussed. Finally, we discuss perspectives for the use of the concept of pluridimensional signaling in drug discovery, in which we highlight future predictive tools that may facilitate the identification of compds. with optimal therapeutic and safety properties based on the signaling signatures of drug candidates.
- 63Smith, J. S., Lefkowitz, R. J., and Rajagopal, S. (2018) Biased signalling: from simple switches to allosteric microprocessors. Nat. Rev. Drug Discovery 17 (4), 243– 260, DOI: 10.1038/nrd.2017.229Google Scholar63https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXjvFentw%253D%253D&md5=fb7d2f27109d412abd53c031575455deBiased signalling: from simple switches to allosteric microprocessorsSmith, Jeffrey S.; Lefkowitz, Robert J.; Rajagopal, SudarshanNature Reviews Drug Discovery (2018), 17 (4), 243-260CODEN: NRDDAG; ISSN:1474-1776. (Nature Research)A review. G protein-coupled receptors (GPCRs) are the largest class of receptors in the human genome and some of the most common drug targets. It is now well established that GPCRs can signal through multiple transducers, including heterotrimeric G proteins, GPCR kinases and β-arrestins. While these signaling pathways can be activated or blocked by 'balanced' agonists or antagonists, they can also be selectively activated in a 'biased' response. Biased responses can be induced by biased ligands, biased receptors or system bias, any of which can result in preferential signaling through G proteins or β-arrestins. At many GPCRs, signaling events mediated by G proteins and β-arrestins have been shown to have distinct biochem. and physiol. actions from one another, and an accurate evaluation of biased signaling from pharmacol. through physiol. is crucial for preclin. drug development. Recent structural studies have provided snapshots of GPCR-transducer complexes, which should aid in the structure-based design of novel biased therapies. Our understanding of GPCRs has evolved from that of two-state, on-and-off switches to that of multistate allosteric microprocessors, in which biased ligands transmit distinct structural information that is processed into distinct biol. outputs. The development of biased ligands as therapeutics heralds an era of increased drug efficacy with reduced drug side effects.
- 64O’Hayre, M., Eichel, K., Avino, S., Zhao, X., Steffen, D. J., Feng, X., Kawakami, K., Aoki, J., Messer, K., Sunahara, R., Inoue, A., von Zastrow, M., and Gutkind, J. S. (2017) Genetic evidence that beta-arrestins are dispensable for the initiation of beta2-adrenergic receptor signalling to ERK. Sci. Signaling 10 (484), eaal3395, DOI: 10.1126/scisignal.aal3395Google ScholarThere is no corresponding record for this reference.
- 65Grundmann, M., Merten, N., Malfacini, D., Inoue, A., Preis, P., Simon, K., Ruttiger, N., Ziegler, N., Benkel, T., Schmitt, N. K., Ishida, S., Muller, I., Reher, R., Kawakami, K., Inoue, A., Rick, U., Kuhl, T., Imhof, D., Aoki, J., Konig, G. M., Hoffmann, C., Gomeza, J., Wess, J., and Kostenis, E. (2018) Lack of beta-arrestin signalling in the absence of active G proteins. Nat. Commun. 9 (1), 341, DOI: 10.1038/s41467-017-02661-3Google Scholar65https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC1MvjsFKiug%253D%253D&md5=4afaac8e9bb4a87bd9d02ea469024efcLack of beta-arrestin signaling in the absence of active G proteinsGrundmann Manuel; Merten Nicole; Malfacini Davide; Preis Philip; Simon Katharina; Benkel Tobias; Schmitt Nina Katharina; Muller Ines; Rick Ulrike; Gomeza Jesus; Kostenis Evi; Inoue Asuka; Ishida Satoru; Kawakami Kouki; Inoue Ayumi; Aoki Junken; Inoue Asuka; Ruttiger Nelly; Hoffmann Carsten; Ziegler Nicole; Reher Raphael; Konig Gabriele M; Kuhl Toni; Imhof Diana; Aoki Junken; Wess JurgenNature communications (2018), 9 (1), 341 ISSN:.G protein-independent, arrestin-dependent signaling is a paradigm that broadens the signaling scope of G protein-coupled receptors (GPCRs) beyond G proteins for numerous biological processes. However, arrestin signaling in the collective absence of functional G proteins has never been demonstrated. Here we achieve a state of "zero functional G" at the cellular level using HEK293 cells depleted by CRISPR/Cas9 technology of the Gs/q/12 families of Gα proteins, along with pertussis toxin-mediated inactivation of Gi/o. Together with HEK293 cells lacking β-arrestins ("zero arrestin"), we systematically dissect G protein- from arrestin-driven signaling outcomes for a broad set of GPCRs. We use biochemical, biophysical, label-free whole-cell biosensing and ERK phosphorylation to identify four salient features for all receptors at "zero functional G": arrestin recruitment and internalization, but-unexpectedly-complete failure to activate ERK and whole-cell responses. These findings change our understanding of how GPCRs function and in particular of how they activate ERK1/2.
- 66Luttrell, L. M., Wang, J., Plouffe, B., Smith, J. S., Yamani, L., Kaur, S., Jean-Charles, P. Y., Gauthier, C., Lee, M. H., Pani, B., Kim, J., Ahn, S., Rajagopal, S., Reiter, E., Bouvier, M., Shenoy, S. K., Laporte, S. A., Rockman, H. A., and Lefkowitz, R. J. (2018) Manifold roles of beta-arrestins in GPCR signalling elucidated with siRNA and CRISPR/Cas9. Sci. Signaling 11 (549), eaat7650, DOI: 10.1126/scisignal.aat7650Google ScholarThere is no corresponding record for this reference.
- 67Abbott, A. (1999) Alliance of US labs plans to build map of cell signalling pathways. Nature 402 (6759), 219– 20, DOI: 10.1038/46111Google Scholar67https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1MXnvVynsL8%253D&md5=2cb4092b5f97204c6f4b1b61539dfe2fAlliance of US labs plans to build map of cell signalling pathwaysAbbott, AlisonNature (London) (1999), 402 (6759), 219-220CODEN: NATUAS; ISSN:0028-0836. (Macmillan Magazines)There is no expanded citation for this reference.
- 68Rual, J. F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G. F., Gibbons, F. D., Dreze, M., Ayivi-Guedehoussou, N., Klitgord, N., Simon, C., Boxem, M., Milstein, S., Rosenberg, J., Goldberg, D. S., Zhang, L. V., Wong, S. L., Franklin, G., Li, S., Albala, J. S., Lim, J., Fraughton, C., Llamosas, E., Cevik, S., Bex, C., Lamesch, P., Sikorski, R. S., Vandenhaute, J., Zoghbi, H. Y., Smolyar, A., Bosak, S., Sequerra, R., Doucette-Stamm, L., Cusick, M. E., Hill, D. E., Roth, F. P., and Vidal, M. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437 (7062), 1173– 8, DOI: 10.1038/nature04209Google Scholar68https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXhtFahtLzP&md5=5485dfc7a711b2c7f649402475f1046dTowards a proteome-scale map of the human protein-protein interaction networkRual, Jean-Francois; Venkatesan, Kavitha; Hao, Tong; Hirozane-Kishikawa, Tomoko; Dricot, Amelie; Li, Ning; Berriz, Gabriel F.; Gibbons, Francis D.; Dreze, Matija; Ayivi-Guedehoussou, Nono; Klitgord, Niels; Simon, Christophe; Boxem, Mike; Milstein, Stuart; Rosenberg, Jennifer; Goldberg, Debra S.; Zhang, Lan V.; Wong, Sharyl L.; Franklin, Giovanni; Li, Siming; Albala, Joanna S.; Lim, Janghoo; Fraughton, Carlene; Llamosas, Estelle; Cevik, Sebiha; Bex, Camille; Lamesch, Philippe; Sikorski, Robert S.; Vandenhaute, Jean; Zoghbi, Huda Y.; Smolyar, Alex; Bosak, Stephanie; Sequerra, Reynaldo; Doucette-Stamm, Lynn; Cusick, Michael E.; Hill, David E.; Roth, Frederick P.; Vidal, MarcNature (London, United Kingdom) (2005), 437 (7062), 1173-1178CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)Systematic mapping of protein-protein interactions, or interactome mapping, was initiated in model organisms, starting with defined biol. processes and then expanding to the scale of the proteome. Although far from complete, such maps have revealed global topol. and dynamic features of interactome networks that relate to known biol. properties, suggesting that a human interactome map will provide insight into development and disease mechanisms at a systems level. Here we describe an initial version of a proteome-scale map of human binary protein-protein interactions. Using a stringent, high-throughput yeast two-hybrid system, we tested pairwise interactions among the products of ∼8,100 currently available Gateway-cloned open reading frames and detected ∼2,800 interactions. This data set, called CCSB-HI1, has a verification rate of ∼78% as revealed by an independent co-affinity purifn. assay, and correlates significantly with other biol. attributes. The CCSB-HI1 data set increases by ∼70% the set of available binary interactions within the tested space and reveals more than 300 new connections to over 100 disease-assocd. proteins. This work represents an important step toward a systematic and comprehensive human interactome project.
- 69Hein, M. Y., Hubner, N. C., Poser, I., Cox, J., Nagaraj, N., Toyoda, Y., Gak, I. A., Weisswange, I., Mansfeld, J., Buchholz, F., Hyman, A. A., and Mann, M. (2015) A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 163 (3), 712– 23, DOI: 10.1016/j.cell.2015.09.053Google Scholar69https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhslWrsLnK&md5=599f46801c2006cbc7b26d6ff8a00d6dA Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and AbundancesHein, Marco Y.; Hubner, Nina C.; Poser, Ina; Cox, Juergen; Nagaraj, Nagarjuna; Toyoda, Yusuke; Gak, Igor A.; Weisswange, Ina; Mansfeld, Joerg; Buchholz, Frank; Hyman, Anthony A.; Mann, MatthiasCell (Cambridge, MA, United States) (2015), 163 (3), 712-723CODEN: CELLB5; ISSN:0092-8674. (Cell Press)The organization of a cell emerges from the interactions in protein networks. The interactome is critically dependent on the strengths of interactions and the cellular abundances of the connected proteins, both of which span orders of magnitude. However, these aspects have not yet been analyzed globally. Here, the authors have generated a library of HeLa cell lines expressing 1125 GFP-tagged proteins under near-endogenous control, which the authors used as input for a next-generation interaction survey. Using quant. proteomics, the authors detect specific interactions, est. interaction stoichiometries, and measure cellular abundances of interacting proteins. These three quant. dimensions reveal that the protein network is dominated by weak, substoichiometric interactions that play a pivotal role in defining network topol. The minority of stable complexes can be identified by their unique stoichiometry signature. This study provides a rich interaction dataset connecting thousands of proteins and introduces a framework for quant. network anal.
- 70Huttlin, E. L., Ting, L., Bruckner, R. J., Gebreab, F., Gygi, M. P., Szpyt, J., Tam, S., Zarraga, G., Colby, G., Baltier, K., Dong, R., Guarani, V., Vaites, L. P., Ordureau, A., Rad, R., Erickson, B. K., Wuhr, M., Chick, J., Zhai, B., Kolippakkam, D., Mintseris, J., Obar, R. A., Harris, T., Artavanis-Tsakonas, S., Sowa, M. E., De Camilli, P., Paulo, J. A., Harper, J. W., and Gygi, S. P. (2015) The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell 162 (2), 425– 440, DOI: 10.1016/j.cell.2015.06.043Google Scholar70https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXht1KgtL3I&md5=79b8d96037646f6679baab3b966b9d47The BioPlex Network: A Systematic Exploration of the Human InteractomeHuttlin, Edward L.; Ting, Lily; Bruckner, Raphael J.; Gebreab, Fana; Gygi, Melanie P.; Szpyt, John; Tam, Stanley; Zarraga, Gabriela; Colby, Greg; Baltier, Kurt; Dong, Rui; Guarani, Virginia; Vaites, Laura Pontano; Ordureau, Alban; Rad, Ramin; Erickson, Brian K.; Wuhr, Martin; Chick, Joel; Zhai, Bo; Kolippakkam, Deepak; Mintseris, Julian; Obar, Robert A.; Harris, Tim; Artavanis-Tsakonas, Spyros; Sowa, Mathew E.; De Camilli, Pietro; Paulo, Joao A.; Harper, J. Wade; Gygi, Steven P.Cell (Cambridge, MA, United States) (2015), 162 (2), 425-440CODEN: CELLB5; ISSN:0092-8674. (Cell Press)Protein interactions form a network whose structure drives cellular function and whose organization informs biol. inquiry. Using high-throughput affinity-purifn. mass spectrometry, the authors identify interacting partners for 2594 human proteins in HEK293T cells. The resulting network (BioPlex) contains 23,744 interactions among 7668 proteins with 86% previously undocumented. BioPlex accurately depicts known complexes, attaining 80%-100% coverage for most CORUM complexes. The network readily subdivides into communities that correspond to complexes or clusters of functionally related proteins. More generally, network architecture reflects cellular localization, biol. process, and mol. function, enabling functional characterization of thousands of proteins. Network structure also reveals assocns. among thousands of protein domains, suggesting a basis for examg. structurally related proteins. Finally, BioPlex, in combination with other approaches, can be used to reveal interactions of biol. or clin. significance. For example, mutations in the membrane protein VAPB implicated in familial amyotrophic lateral sclerosis perturb a defined community of interactors.
- 71Uhlen, M., Fagerberg, L., Hallstrom, B. M., Lindskog, C., Oksvold, P., Mardinoglu, A., Sivertsson, A., Kampf, C., Sjostedt, E., Asplund, A., Olsson, I., Edlund, K., Lundberg, E., Navani, S., Szigyarto, C. A., Odeberg, J., Djureinovic, D., Takanen, J. O., Hober, S., Alm, T., Edqvist, P. H., Berling, H., Tegel, H., Mulder, J., Rockberg, J., Nilsson, P., Schwenk, J. M., Hamsten, M., von Feilitzen, K., Forsberg, M., Persson, L., Johansson, F., Zwahlen, M., von Heijne, G., Nielsen, J., and Ponten, F. (2015) Proteomics. Tissue-based map of the human proteome. Science 347 (6220), 1260419, DOI: 10.1126/science.1260419Google Scholar71https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC2MvptFakug%253D%253D&md5=95510888806e5feb6b8024ee2a417d1cProteomics. Tissue-based map of the human proteomeUhlen Mathias; Fagerberg Linn; Oksvold Per; Sivertsson ¡ÑÜAsa; Lundberg Emma; Odeberg Jacob; Alm Tove; Nilsson Peter; Schwenk Jochen M; von Feilitzen Kalle; Forsberg Mattias; Persson Lukas; Johansson Fredric; Zwahlen Martin; Hallstrom Bjorn M; Lindskog Cecilia; Kampf Caroline; Asplund Anna; Olsson IngMarie; Djureinovic Dijana; Edqvist Per-Henrik; Ponten Fredrik; Mardinoglu Adil; Sjostedt Evelina; Edlund Karolina; Navani Sanjay; Szigyarto Cristina Al-Khalili; Takanen Jenny Ottosson; Hober Sophia; Berling Holger; Tegel Hanna; Rockberg Johan; Hamsten Marica; Mulder Jan; von Heijne Gunnar; Nielsen JensScience (New York, N.Y.) (2015), 347 (6220), 1260419 ISSN:.Resolving the molecular details of proteome variation in the different tissues and organs of the human body will greatly increase our knowledge of human biology and disease. Here, we present a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray-based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level. Our tissue-based analysis detected more than 90% of the putative protein-coding genes. We used this approach to explore the human secretome, the membrane proteome, the druggable proteome, the cancer proteome, and the metabolic functions in 32 different tissues and organs. All the data are integrated in an interactive Web-based database that allows exploration of individual proteins, as well as navigation of global expression patterns, in all major tissues and organs in the human body.
- 72Huttlin, E. L., Bruckner, R. J., Paulo, J. A., Cannon, J. R., Ting, L., Baltier, K., Colby, G., Gebreab, F., Gygi, M. P., Parzen, H., Szpyt, J., Tam, S., Zarraga, G., Pontano-Vaites, L., Swarup, S., White, A. E., Schweppe, D. K., Rad, R., Erickson, B. K., Obar, R. A., Guruharsha, K. G., Li, K., Artavanis-Tsakonas, S., Gygi, S. P., and Harper, J. W. (2017) Architecture of the human interactome defines protein communities and disease networks. Nature 545 (7655), 505– 509, DOI: 10.1038/nature22366Google Scholar72https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXnvVCrsro%253D&md5=be9c296f38f01ac4d177e3e97e4882e7Architecture of the human interactome defines protein communities and disease networksHuttlin, Edward L.; Bruckner, Raphael J.; Paulo, Joao A.; Cannon, Joe R.; Ting, Lily; Baltier, Kurt; Colby, Greg; Gebreab, Fana; Gygi, Melanie P.; Parzen, Hannah; Szpyt, John; Tam, Stanley; Zarraga, Gabriela; Pontano-Vaites, Laura; Swarup, Sharan; White, Anne E.; Schweppe, Devin K.; Rad, Ramin; Erickson, Brian K.; Obar, Robert A.; Guruharsha, K. G.; Li, Kejie; Artavanis-Tsakonas, Spyros; Gygi, Steven P.; Harper, J. WadeNature (London, United Kingdom) (2017), 545 (7655), 505-509CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)The physiol. of a cell can be viewed as the product of thousands of proteins acting in concert to shape the cellular response. Coordination is achieved in part through networks of protein-protein interactions that assemble functionally related proteins into complexes, organelles, and signal transduction pathways. Understanding the architecture of the human proteome has the potential to inform cellular, structural, and evolutionary mechanisms and is crit. to elucidating how genome variation contributes to disease. Here we present BioPlex 2.0 (Biophys. Interactions of ORFeome-derived complexes), which uses robust affinity purifn.-mass spectrometry methodol. to elucidate protein interaction networks and co-complexes nucleated by more than 25% of protein-coding genes from the human genome, and constitutes, to our knowledge, the largest such network so far. With more than 56,000 candidate interactions, BioPlex 2.0 contains more than 29,000 previously unknown co-assocns. and provides functional insights into hundreds of poorly characterized proteins while enhancing network-based analyses of domain assocns., subcellular localization, and co-complex formation. Unsupervised Markov clustering of interacting proteins identified more than 1,300 protein communities representing diverse cellular activities. Genes essential for cell fitness are enriched within 53 communities representing central cellular functions. Moreover, we identified 442 communities assocd. with more than 2,000 disease annotations, placing numerous candidate disease genes into a cellular framework. BioPlex 2.0 exceeds previous exptl. derived interaction networks in depth and breadth, and will be a valuable resource for exploring the biol. of incompletely characterized proteins and for elucidating larger-scale patterns of proteome organization.
- 73Rozenblatt-Rosen, O., Stubbington, M. J. T., Regev, A., and Teichmann, S. A. (2017) The Human Cell Atlas: from vision to reality. Nature 550 (7677), 451– 453, DOI: 10.1038/550451aGoogle Scholar73https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhslajtr7M&md5=0653d7120f724c2950136e535ed95892The Human Cell Atlas: from vision to realityRozenblatt-Rosen, Orit; Stubbington, Michael J. T.; Regev, Aviv; Teichmann, Sarah A.Nature (London, United Kingdom) (2017), 550 (7677), 451-453CODEN: NATUAS; ISSN:0028-0836. (Nature Research)As an ambitious project to map all the cells in the human body gets officially under way, Aviv Regev, Sarah Teichmann and colleagues outline some key challenges.
- 74Fabregat, A., Jupe, S., Matthews, L., Sidiropoulos, K., Gillespie, M., Garapati, P., Haw, R., Jassal, B., Korninger, F., May, B., Milacic, M., Roca, C. D., Rothfels, K., Sevilla, C., Shamovsky, V., Shorser, S., Varusai, T., Viteri, G., Weiser, J., Wu, G., Stein, L., Hermjakob, H., and D’Eustachio, P. (2018) The Reactome Pathway Knowledgebase. Nucleic Acids Res. 46 (D1), D649– D655, DOI: 10.1093/nar/gkx1132Google Scholar74https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXitlGis7bM&md5=691a9b4fb2ab28dd06b9d012a3e936b7The reactome pathway knowledgebaseFabregat, Antonio; Jupe, Steven; Matthews, Lisa; Sidiropoulos, Konstantinos; Gillespie, Marc; Garapati, Phani; Haw, Robin; Jassal, Bijay; Korninger, Florian; May, Bruce; Milacic, Marija; Roca, Corina Duenas; Rothfels, Karen; Sevilla, Cristoffer; Shamovsky, Veronica; Shorser, Solomon; Varusai, Thawfeek; Viteri, Guilherme; Weiser, Joel; Wu, Guanming; Stein, Lincoln; Hermjakob, Henning; D'eustachio, PeterNucleic Acids Research (2018), 46 (D1), D649-D655CODEN: NARHAD; ISSN:1362-4962. (Oxford University Press)A review. The Reactome Knowledgebase provides mol. details of signal transduction, transport, DNA replication, metab., and other cellular processes as an ordered network of mol. transformations-an extended version of a classic metabolic map, in a single consistent data model. Reactome functions both as an archive of biol. processes and as a tool for discovering unexpected functional relationships in data such as gene expression profiles or somatic mutation catalogs from tumor cells. To support the continued brisk growth in the size and complexity of Reactome, we have implemented a graph database, improved performance of data anal. tools, and designed new data structures and strategies to boost diagram viewer performance. To make our website more accessible to human users, we have improved pathway display and navigation by implementing interactive Enhanced High Level Diagrams (EHLDs) with an assocd. icon library, and subpathway highlighting and zooming, in a simplified and reorganized web site with adaptive design. To encourage re-use of our content, we have enabled export of pathway diagrams as 'PowerPoint' files.
- 75Singla, J., McClary, K. M., White, K. L., Alber, F., Sali, A., and Stevens, R. C. (2018) Opportunities and Challenges in Building a Spatiotemporal Multi-scale Model of the Human Pancreatic beta Cell. Cell 173 (1), 11– 19, DOI: 10.1016/j.cell.2018.03.014Google Scholar75https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXlvVOqsbY%253D&md5=b5eeeb7a09d17372ee28aa409f45134cOpportunities and Challenges in Building a Spatiotemporal Multi-scale Model of the Human Pancreatic β CellSingla, Jitin; McClary, Kyle M.; White, Kate L.; Alber, Frank; Sali, Andrej; Stevens, Raymond C.Cell (Cambridge, MA, United States) (2018), 173 (1), 11-19CODEN: CELLB5; ISSN:0092-8674. (Cell Press)A review. The construction of a predictive model of an entire eukaryotic cell that describes its dynamic structure from at. to cellular scales is a grand challenge at the intersection of biol., chem., physics, and computer science. Having such a model will open new dimensions in biol. research and accelerate healthcare advancements. Developing the necessary exptl. and modeling methods presents abundant opportunities for a community effort to realize this goal. Here, we present a vision for creation of a spatiotemporal multi-scale model of the pancreatic β-cell, a relevant target for understanding and modulating the pathogenesis of diabetes.
- 76https://reactome.org/ (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 77https://string-db.org/ (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.
- 78Tan, L., Yan, W., McCorvy, J. D., and Cheng, J. (2018) Biased Ligands of G Protein-Coupled Receptors (GPCRs): Structure-Functional Selectivity Relationships (SFSRs) and Therapeutic Potential. J. Med. Chem. 61 (22), 9841– 9878, DOI: 10.1021/acs.jmedchem.8b00435Google Scholar78https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXht1Snu73N&md5=a7bd605b82666357f5a0a209002225e5Biased Ligands of G Protein-Coupled Receptors (GPCRs): Structure-Functional Selectivity Relationships (SFSRs) and Therapeutic PotentialTan, Liang; Yan, Wenzhong; McCorvy, John D.; Cheng, JianjunJournal of Medicinal Chemistry (2018), 61 (22), 9841-9878CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)A review. G protein-coupled receptors (GPCRs) signal through both G-protein-dependent and G-protein-independent pathways, and β-arrestin recruitment is the most recognized one of the latter. Biased ligands selective for either pathway are expected to regulate biol. functions of GPCRs in a more precise way, therefore providing new drug mols. with superior efficacy and/or reduced side effects. During the past decade, biased ligands have been discovered and developed for many GPCRs, such as the μ opioid receptor, the angiotensin II receptor type 1, the dopamine D2 receptor, and many others. In this Perspective, recent advances in this field are reviewed by discussing the structure-functional selectivity relationships (SFSRs) of GPCR biased ligands and the therapeutic potential of these mols. Further understanding of the biol. functions assocd. with each signaling pathway and structural basis for biased signaling will facilitate future drug design in this field.
- 79Wilde, O. The Importance of Being Earnest: a Trivial Comedy for Serious People; Leonard Smithers and Co.: London, 1898.Google ScholarThere is no corresponding record for this reference.
- 80https://www.cost.eu/actions/CA18133/ (accessed 2020/03/02).Google ScholarThere is no corresponding record for this reference.