Characterizing Interhelical Interactions of G-Protein Coupled Receptors with the Fragment Molecular Orbital Method

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This article references 66 other publications.

1. 1

   Hauser, A. S.; Attwood, M. M.; Rask-Andersen, M.; Schioth, H. B.; Gloriam, D. E. Trends in GPCR Drug Discovery: New Agents, Targets and Indications. Nat. Rev. Drug Discovery 2017, 16, 829– 842,  DOI: 10.1038/nrd.2017.178

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   Trends in GPCR drug discovery: new agents, targets and indications

   Hauser, 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.
2. 2

   Venkatakrishnan, A. J.; Deupi, X.; Lebon, G.; Heydenreich, F. M.; Flock, T.; Miljus, T.; Balaji, S.; Bouvier, M.; Veprintsev, D. B.; Tate, C. G.; Schertler, G. F.; Babu, M. M. Diverse Activation Pathways in Class A GPCRs Converge near the G-Protein-Coupling Region. Nature 2016, 536, 484– 7,  DOI: 10.1038/nature19107

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   Diverse activation pathways in class A GPCRs converge near the G-protein-coupling region

   Venkatakrishnan, A. J.; Deupi, Xavier; Lebon, Guillaume; Heydenreich, Franziska M.; Flock, Tilman; Miljus, Tamara; Balaji, Santhanam; Bouvier, Michel; Veprintsev, Dmitry B.; Tate, Christopher G.; Schertler, Gebhard F. X.; Babu, M. Madan

   Nature (London, United Kingdom) (2016), 536 (7617), 484-487CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)

   Class A G-protein-coupled receptors (GPCRs) are a large family of membrane proteins that mediate a wide variety of physiol. functions, including vision, neurotransmission and immune responses. They are the targets of nearly one-third of all prescribed medicinal drugs such as beta blockers and antipsychotics. GPCR activation is facilitated by extracellular ligands and leads to the recruitment of intracellular G proteins. Structural rearrangements of residue contacts in the transmembrane domain serve as 'activation pathways' that connect the ligand-binding pocket to the G-protein-coupling region within the receptor. In order to investigate the similarities in activation pathways across class A GPCRs, we analyzed 27 GPCRs from diverse subgroups for which structures of active, inactive or both states were available. Here we show that, despite the diversity in activation pathways between receptors, the pathways converge near the G-protein-coupling region. This convergence is mediated by a highly conserved structural rearrangement of residue contacts between transmembrane helixes 3, 6 and 7 that releases G-protein-contacting residues. The convergence of activation pathways may explain how the activation steps initiated by diverse ligands enable GPCRs to bind a common repertoire of G proteins.
3. 3

   Venkatakrishnan, A. J.; Deupi, X.; Lebon, G.; Tate, C. G.; Schertler, G. F.; Babu, M. M. Molecular Signatures of G-Protein-Coupled Receptors. Nature 2013, 494, 185– 94,  DOI: 10.1038/nature11896

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   Molecular signatures of G-protein-coupled receptors

   Venkatakrishnan, A. J.; Deupi, Xavier; Lebon, Guillaume; Tate, Christopher G.; Schertler, Gebhard F.; Babu, M. Madan

   Nature (London, United Kingdom) (2013), 494 (7436), 185-194CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)

   A review. G-protein-coupled receptors (GPCRs) are physiol. important membrane proteins that sense signaling mols. such as hormones and neurotransmitters, and are the targets of several prescribed drugs. Recent exciting developments are providing unprecedented insights into the structure and function of several medically important GPCRs. Here, through a systematic anal. of high-resoln. GPCR structures, we uncover a conserved network of non-covalent contacts that defines the GPCR fold. Furthermore, our comparative anal. reveals characteristic features of ligand binding and conformational changes during receptor activation. A holistic understanding that integrates mol. and systems biol. of GPCRs holds promise for new therapeutics and personalized medicine.
4. 4

   Popov, P.; Peng, Y.; Shen, L.; Stevens, R. C.; Cherezov, V.; Liu, Z. J.; Katritch, V. Computational Design of Thermostabilizing Point Mutations for G Protein-Coupled Receptors. eLife 2018, 7, e34729,  DOI: 10.7554/eLife.34729

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   Computational design of thermostabilizing point mutations for G protein-coupled receptors

   Popov, Petr; Peng, Yao; Shen, Ling; Stevens, Raymond C.; Cherezov, Vadim; Liu, Zhi-Jie; Katritch, Vsevolod

   eLife (2018), 7 (), e34729/1-e34729/22CODEN: ELIFA8; ISSN:2050-084X. (eLife Sciences Publications Ltd.)

   Engineering of GPCR constructs with improved thermostability is a key for successful structural and biochem. studies of this transmembrane protein family, targeted by 40% of all therapeutic drugs. Here we introduce a comprehensive computational approach to effective prediction of stabilizing mutations in GPCRs, named CompoMug, which employs sequence-based anal., structural information, and a derived machine learning predictor. Tested exptl. on the serotonin 5-HT2C receptor target, CompoMug predictions resulted in 10 new stabilizing mutations, with an apparent thermostability gain ∼8.8°C for the best single mutation and ∼13°C for a triple mutant. Binding of antagonists confers further stabilization for the triple mutant receptor, with total gains of ∼21°C as compared to wild type apo 5-HT2C. The predicted mutations enabled crystn. and structure detn. for the 5-HT2C receptor complexes in inactive and active-like states. While CompoMug already shows high 25% hit rate and utility in GPCR structural studies, further improvements are expected with accumulation of structural and mutation data.
5. 5

   Vaidehi, N.; Bhattacharya, S.; Larsen, A. B. Structure and Dynamics of G-Protein Coupled Receptors. Adv. Exp. Med. Biol. 2014, 796, 37– 54,  DOI: 10.1007/978-94-007-7423-0_3

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   Structure and Dynamics of G-Protein Coupled Receptors

   Vaidehi, Nagarajan; Bhattacharya, Supriyo; Larsen, Adrien B.

   Advances in Experimental Medicine and Biology (2014), 796 (G Protein-Coupled Receptors--Modeling and Simulation), 37-54CODEN: AEMBAP; ISSN:2214-8019. (Springer)

   G-protein coupled receptors (GPCRs) are seven helical transmembrane proteins that mediate cell-to-cell communication. They also form the largest superfamily of drug targets. Hence detailed studies of the three dimensional structure and dynamics are crit. to understanding the functional role of GPCRs in signal transduction pathways, and for drug design. In this chapter we compare the features of the crystal structures of various biogenic amine receptors, such as β1 and β2 adrenergic receptors, dopamine D3 receptor, M2 and M3 muscarinic acetylcholine receptors. This anal. revealed that conserved residues are located facing the inside of the transmembrane domain in these GPCRs improving the efficiency of packing of these structures. The NMR structure of the chemokine receptor CXCR1 without any ligand bound, shows significant dynamics of the transmembrane domain, esp. the helical kink angle on the transmembrane helix6. The activation mechanism of the β2 -adrenergic receptor has been studied using multiscale computational methods. The results of these studies showed that the receptor without any ligand bound, samples conformations that resemble some of the structural characteristics of the active state of the receptor. Ligand binding stabilizes some of the conformations already sampled by the apo receptor. This was later obsd. in the NMR study of the dynamics of human β2 -adrenergic receptor. The dynamic nature of GPCRs leads to a challenge in obtaining purified receptors for biophys. studies. Deriving thermostable mutants of GPCRs has been a successful strategy to reduce the conformational heterogeneity and stabilize the receptors. This has lead to several crystal structures of GPCRs. However, the cause of how these mutations lead to thermostability is not clear. Computational studies are beginning to shed some insight into the possible structural basis for the thermostability. Mol. Dynamics simulations studying the conformational ensemble of thermostable mutants have shown that the stability could arise from both enthalpic and entropic factors. There are regions of high stress in the wild type GPCR that gets relieved upon mutation conferring thermostability.
6. 6

   Magnani, F.; Serrano-Vega, M. J.; Shibata, Y.; Abdul-Hussein, S.; Lebon, G.; Miller-Gallacher, J.; Singhal, A.; Strege, A.; Thomas, J. A.; Tate, C. G. A Mutagenesis and Screening Strategy to Generate Optimally Thermostabilized Membrane Proteins for Structural Studies. Nat. Protoc. 2016, 11, 1554– 71,  DOI: 10.1038/nprot.2016.088

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   A mutagenesis and screening strategy to generate optimally thermostabilized membrane proteins for structural studies

   Magnani Francesca; Serrano-Vega Maria J; Shibata Yoko; Abdul-Hussein Saba; Lebon Guillaume; Miller-Gallacher Jennifer; Singhal Ankita; Strege Annette; Thomas Jennifer A; Tate Christopher G

   Nature protocols (2016), 11 (8), 1554-71 ISSN:.

   The thermostability of an integral membrane protein (MP) in detergent solution is a key parameter that dictates the likelihood of obtaining well-diffracting crystals that are suitable for structure determination. However, many mammalian MPs are too unstable for crystallization. We developed a thermostabilization strategy based on systematic mutagenesis coupled to a radioligand-binding thermostability assay that can be applied to receptors, ion channels and transporters. It takes ∼6-12 months to thermostabilize a G-protein-coupled receptor (GPCR) containing 300 amino acid (aa) residues. The resulting thermostabilized MPs are more easily crystallized and result in high-quality structures. This methodology has facilitated structure-based drug design applied to GPCRs because it is possible to determine multiple structures of the thermostabilized receptors bound to low-affinity ligands. Protocols and advice are given on how to develop thermostability assays for MPs and how to combine mutations to make an optimally stable mutant suitable for structural studies. The steps in the procedure include the generation of ∼300 site-directed mutants by Ala/Leu scanning mutagenesis, the expression of each mutant in mammalian cells by transient transfection and the identification of thermostable mutants using a thermostability assay that is based on binding of an (125)I-labeled radioligand to the unpurified, detergent-solubilized MP. Individual thermostabilizing point mutations are then combined to make an optimally stable MP that is suitable for structural biology and other biophysical studies.
7. 7

   Heydenreich, F. M.; Vuckovic, Z.; Matkovic, M.; Veprintsev, D. B. Stabilization of G Protein-Coupled Receptors by Point Mutations. Front. Pharmacol. 2015, 6, 82,  DOI: 10.3389/fphar.2015.00082

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   Stabilization of G protein-coupled receptors by point mutations

   Heydenreich Franziska M; Vuckovic Ziva; Matkovic Milos; Veprintsev Dmitry B

   Frontiers in pharmacology (2015), 6 (), 82 ISSN:1663-9812.

   G protein-coupled receptors (GPCRs) are flexible integral membrane proteins involved in transmembrane signaling. Their involvement in many physiological processes makes them interesting targets for drug development. Determination of the structure of these receptors will help to design more specific drugs, however, their structural characterization has so far been hampered by the low expression and their inherent instability in detergents which made protein engineering indispensable for structural and biophysical characterization. Several approaches to stabilize the receptors in a particular conformation have led to breakthroughs in GPCR structure determination. These include truncations of the flexible regions, stabilization by antibodies and nanobodies, fusion partners, high affinity and covalently bound ligands as well as conformational stabilization by mutagenesis. In this review we focus on stabilization of GPCRs by insertion of point mutations, which lead to increased conformational and thermal stability as well as improved expression levels. We summarize existing mutagenesis strategies with different coverage of GPCR sequence space and depth of information, design and transferability of mutations and the molecular basis for stabilization. We also discuss whether mutations alter the structure and pharmacological properties of GPCRs.
8. 8

   Heifetz, A.; Chudyk, E. I.; Gleave, L.; Aldeghi, M.; Cherezov, V.; Fedorov, D. G.; Biggin, P. C.; Bodkin, M. J. The Fragment Molecular Orbital Method Reveals New Insight into the Chemical Nature of GPCR-Ligand Interactions. J. Chem. Inf. Model. 2016, 56, 159– 72,  DOI: 10.1021/acs.jcim.5b00644

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   The Fragment Molecular Orbital Method Reveals New Insight into the Chemical Nature of GPCR-Ligand Interactions

   Heifetz, Alexander; Chudyk, Ewa I.; Gleave, Laura; Aldeghi, Matteo; Cherezov, Vadim; Fedorov, Dmitri G.; Biggin, Philip C.; Bodkin, Mike J.

   Journal of Chemical Information and Modeling (2016), 56 (1), 159-172CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)

   Our interpretation of ligand-protein interactions is often informed by high-resoln. structures, which represent the cornerstone of structure-based drug design. However, visual inspection and mol. mechanics approaches cannot explain the full complexity of mol. interactions. Quantum Mechanics approaches are often too computationally expensive, but one method, Fragment MO (FMO), offers an excellent compromise and has the potential to reveal key interactions that would otherwise be hard to detect. To illustrate this, we have applied the FMO method to 18 Class A GPCR-ligand crystal structures, representing different branches of the GPCR genome. Our work reveals key interactions that are often omitted from structure-based descriptions, including hydrophobic interactions, nonclassical hydrogen bonds, and the involvement of backbone atoms. This approach provides a more comprehensive picture of receptor-ligand interactions than is currently used and should prove useful for evaluation of the chem. nature of ligand binding and to support structure-based drug design.
9. 9

   Tautermann, C. S. GPCR Structures in Drug Design, Emerging Opportunities with New Structures. Bioorg. Med. Chem. Lett. 2014, 24, 4073– 9,  DOI: 10.1016/j.bmcl.2014.07.009

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   GPCR structures in drug design, emerging opportunities with new structures

   Tautermann, Christofer S.

   Bioorganic & Medicinal Chemistry Letters (2014), 24 (17), 4073-4079CODEN: BMCLE8; ISSN:0960-894X. (Elsevier B.V.)

   A review. In recent years, GPCR targets from diverse regions of phylogenetic space have been detd. This effort has culminated this year in the detn. of representatives of all major classes of GPCRs (A, B, C, and F). Although much of the now well established knowledge on GPCR structures has been known for some years, the new high-resoln. structures allow structural insight into the causes of ligand efficacy, biased signaling, and allosteric modulation. In this digest the structural basis for GPCR signaling in the light of the new structures is reviewed and the use of the new non-class A GPCRs for drug design is discussed.
10. 10

    Shonberg, J.; Kling, R. C.; Gmeiner, P.; Lober, S. GPCR Crystal Structures: Medicinal Chemistry in the Pocket. Bioorg. Med. Chem. 2015, 23, 3880– 906,  DOI: 10.1016/j.bmc.2014.12.034

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    GPCR crystal structures: Medicinal chemistry in the pocket

    Shonberg, Jeremy; Kling, Ralf C.; Gmeiner, Peter; Loeber, Stefan

    Bioorganic & Medicinal Chemistry (2015), 23 (14), 3880-3906CODEN: BMECEP; ISSN:0968-0896. (Elsevier B.V.)

    A review. Recent breakthroughs in G protein-coupled receptor (GPCR) structural biol. have significantly increased the understanding of drug action at these therapeutically relevant receptors, and this will undoubtedly lead to the design of better therapeutics. In recent years, crystal structures of GPCRs from classes A, B, C, and F have been solved, unveiling a precise snapshot of ligand-receptor interactions. Furthermore, some receptors have been crystd. in different functional states in complex with antagonists, partial agonists, full agonists, biased agonists, and allosteric modulators, providing further insight into the mechanisms of ligand-induced GPCR activation. It is now obvious that there is enormous diversity in the size, shape and position of the ligand-binding pockets in GPCRs. Here, the authors summarize the current state of solved GPCR structures, with a particular focus on ligand-receptor interactions in the binding pocket, and how this can contribute to the design of GPCR ligands with better affinity, subtype selectivity, or efficacy.
11. 11

    Jazayeri, A.; Dias, J. M.; Marshall, F. H. From G Protein-Coupled Receptor Structure Resolution to Rational Drug Design. J. Biol. Chem. 2015, 290, 19489– 95,  DOI: 10.1074/jbc.R115.668251

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    From G Protein-coupled Receptor Structure Resolution to Rational Drug Design

    Jazayeri, Ali; Dias, Joao M.; Marshall, Fiona H.

    Journal of Biological Chemistry (2015), 290 (32), 19489-19495CODEN: JBCHA3; ISSN:0021-9258. (American Society for Biochemistry and Molecular Biology)

    A review. A no. of recent tech. solns. have led to significant advances in G protein-coupled receptor (GPCR) structural biol. Apart from a detailed mechanistic view of receptor activation, the new structures have revealed novel ligand binding sites. Together, these insights provide avenues for rational drug design to modulate the activities of these important drug targets. The application of structural data to GPCR drug discovery ushers in an exciting era with the potential to improve existing drugs and discover new ones. In this review, we focus on tech. solns. that have accelerated GPCR crystallog. as well as some of the salient findings from structures that are relevant to drug discovery. Finally, we outline some of the approaches used in GPCR structure based drug design.
12. 12

    Bissantz, C.; Kuhn, B.; Stahl, M. A Medicinal Chemist’s Guide to Molecular Interactions. J. Med. Chem. 2010, 53, 5061– 84,  DOI: 10.1021/jm100112j

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    A Medicinal Chemist's Guide to Molecular Interactions

    Bissantz, Caterina; Kuhn, Bernd; Stahl, Martin

    Journal of Medicinal Chemistry (2010), 53 (14), 5061-5084CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)

    A review.
13. 13

    Tong, Y.; Mei, Y.; Li, Y. L.; Ji, C. G.; Zhang, J. Z. Electrostatic Polarization Makes a Substantial Contribution to the Free Energy of Avidin-Biotin Binding. J. Am. Chem. Soc. 2010, 132, 5137– 42,  DOI: 10.1021/ja909575j

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    Electrostatic Polarization Makes a Substantial Contribution to the Free Energy of Avidin-Biotin Binding

    Tong, Yan; Mei, Ye; Li, Yong L.; Ji, Chang G.; Zhang, John Z. H.

    Journal of the American Chemical Society (2010), 132 (14), 5137-5142CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)

    Avidin-biotin is one of the strongest protein-ligand binding systems, with broad applications in biomedical science. Here we report a quantum-based computational study to help elucidate the mechanism of binding avidin to biotin (BTN1) and its close analog, 2'-iminobiotin (BTN2). Our study reveals that electronic polarization of protein plays a crit. role in stabilizing the β sheet (Thr113-Arg122) at the binding site and makes a substantial contribution to the free energy of avidin-biotin binding. The current finding is in contradiction to the previous notion that electrostatic interaction has no effect on or makes an unfavorable contribution to the free energy of avidin-biotin binding. Our calcns. also show that the difference in binding free energy of avidin to BTN1 and BTN2 is almost entirely due to the contribution of electrostatic interaction resulting from polarization-induced stabilization of a hydrogen bond between avidin and BTN1. The current result provides strong evidence that protein polarization accounts for the electrostatic contribution to binding free energy that was missing in previous studies of avidin-biotin binding.
14. 14

    Raha, K.; Peters, M. B.; Wang, B.; Yu, N.; Wollacott, A. M.; Westerhoff, L. M.; Merz, K. M., Jr. The Role of Quantum Mechanics in Structure-Based Drug Design. Drug Discovery Today 2007, 12, 725– 31,  DOI: 10.1016/j.drudis.2007.07.006

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    The role of quantum mechanics in structure-based drug design

    Raha, Kaushik; Peters, Martin B.; Wang, Bing; Yu, Ning; Wollacott, Andrew M.; Westerhoff, Lance M.; Merz, Kenneth M., Jr.

    Drug Discovery Today (2007), 12 (17&18), 725-731CODEN: DDTOFS; ISSN:1359-6446. (Elsevier B.V.)

    A review. Herein we will focus on the use of quantum mechanics (QM) in drug design (DD) to solve disparate problems from scoring protein-ligand poses to building QM QSAR models. Through the variational principle of QM we know that we can obtain a more accurate representation of mol. systems than classical models, and while this is not a matter of debate, it still has not been shown that the expense of QM approaches is offset by improved accuracy in DD applications. Objectively validating the improved applicability and performance of QM over classical-based models in DD will be the focus of research in the coming years along with research on the conformational sampling problem as it relates to protein-ligand complexes.
15. 15

    Beratan, D. N.; Liu, C.; Migliore, A.; Polizzi, N. F.; Skourtis, S. S.; Zhang, P.; Zhang, Y. Charge Transfer in Dynamical Biosystems, or the Treachery of (Static) Images. Acc. Chem. Res. 2015, 48, 474– 81,  DOI: 10.1021/ar500271d

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    Charge Transfer in Dynamical Biosystems, or The Treachery of (Static) Images.

    Beratan, David N.; Liu, Chaoren; Migliore, Agostino; Polizzi, Nicholas F.; Skourtis, Spiros S.; Zhang, Peng; Zhang, Yuqi

    Accounts of Chemical Research (2015), 48 (2), 474-481CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)

    A review. The image is not the thing. Just as a pipe rendered in an oil painting cannot be smoked, quantum mech. coupling pathways rendered on LCDs do not convey electrons. The aim of this Account is to examine some of the authors' recent discoveries regarding biol. electron transfer (ET) and transport mechanisms that emerge when one moves beyond treacherous static views to dynamical frameworks. Studies over the last two decades introduced both atomistic detail and macromol. dynamics to the description of biol. ET. The first model to move beyond the structureless square-barrier tunneling description is the Pathway model, which predicts how protein secondary motifs and folding-induced through-bond and through-space tunneling gaps influence kinetics. Explicit electronic structure theory is applied routinely now to elucidate ET mechanisms, to capture pathway interferences, and to treat redox cofactor electronic structure effects. Importantly, structural sampling of proteins provides an understanding of how dynamics may change the mechanisms of biol. ET, as ET rates are exponentially sensitive to structure. Does protein motion av. out tunneling pathways. Do conformational fluctuations gate biol. ET. Are transient multistate resonances produced by energy gap fluctuations. These questions are becoming accessible as the static view of biol. ET recedes and dynamical viewpoints take center stage. This Account introduces ET reactions at the core of bioenergetics, summarizes the authors' team's progress toward arriving at an atomistic-level description, examines how thermal fluctuations influence ET, presents metrics that characterize dynamical effects on ET, and discusses applications in very long (micrometer scale) bacterial nanowires. The persistence of structural effects on the ET rates in the face of thermal fluctuations is considered. Finally, the flickering resonance (FR) view of charge transfer is presented to examine how fluctuations control low-barrier transport among multiple groups in van der Waals contact. FR produces exponential distance dependence in the absence of tunneling; the exponential character emerges from the probability of matching multiple vibronically broadened electronic energies within a tolerance defined by the root-mean-square coupling among interacting groups. FR thus produces band like coherent transport on the nanometer length scale, enabled by conformational fluctuations. Taken as a whole, the emerging context for ET in dynamical biomols. provides a robust framework to design and interpret the inner workings of bioenergetics from the mol. to the cellular scale and beyond, with applications in biomedicine, biocatalysis, and energy science.
16. 16

    Ozawa, T.; Okazaki, K.; Kitaura, K. CH/π Hydrogen Bonds Play a Role in Ligand Recognition and Equilibrium between Active and Inactive States of the Beta2 Adrenergic Receptor: An Ab Initio Fragment Molecular Orbital (FMO) Study. Bioorg. Med. Chem. 2011, 19, 5231– 7,  DOI: 10.1016/j.bmc.2011.07.004

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    CH/π hydrogen bonds play a role in ligand recognition and equilibrium between active and inactive states of the β2 adrenergic receptor: An ab initio fragment molecular orbital (FMO) study

    Ozawa, Tomonaga; Okazaki, Kosuke; Kitaura, Kazuo

    Bioorganic & Medicinal Chemistry (2011), 19 (17), 5231-5237CODEN: BMECEP; ISSN:0968-0896. (Elsevier B.V.)

    We examd. CH/π hydrogen bonds using an ab initio fragment MO (FMO) method, combined with the CHPI program, to evaluate complexes of active (bound with agonist 1) and inactive (bound with inverse agonist 2) β2 adrenergic receptor (β2AR) states. In both states, we found that CH/π hydrogen bonds were present. Subtle changes in the binding pocket between the active and inactive states of β2AR were obsd. Comparison of the CH/π networks in both states suggests that the networks differ at the β2AR core. Recombination of the CH/π hydrogen bonds occurred during conversion between the two states. We suggest that CH/π hydrogen bonds play a key role in ligand recognition and conversion between the active and inactive states.
17. 17

    Fedorov, D. G.; Nagata, T.; Kitaura, K. Exploring Chemistry with the Fragment Molecular Orbital Method. Phys. Chem. Chem. Phys. 2012, 14, 7562– 77,  DOI: 10.1039/c2cp23784a

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    Exploring chemistry with the fragment molecular orbital method

    Fedorov, Dmitri G.; Nagata, Takeshi; Kitaura, Kazuo

    Physical Chemistry Chemical Physics (2012), 14 (21), 7562-7577CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)

    The fragment MO (FMO) method makes possible nearly linear scaling calcns. of large mol. systems, such as water clusters, proteins and DNA. In particular, FMO has been widely used in biochem. applications involving protein-ligand binding and drug design. The method has been efficiently parallelized suitable for petascale computing. Many commonly used wave functions and solvent models have been interfaced with FMO. We review the historical background of FMO, and summarize its method development and applications.
18. 18

    Lu, Y.-X.; Zou, J.-W.; Wang, Y.-H.; Yu, Q.-S. Substituent Effects on Noncovalent Halogen/Π Interactions: Theoretical Study. Int. J. Quantum Chem. 2007, 107, 1479– 1486,  DOI: 10.1002/qua.21279

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    Substituent effects on noncovalent halogen/π interactions: theoretical study

    Lu, Yun-Xiang; Zou, Jian-Wei; Wang, Yan-Hua; Yu, Qing-Sen

    International Journal of Quantum Chemistry (2007), 107 (6), 1479-1486CODEN: IJQCB2; ISSN:0020-7608. (John Wiley & Sons, Inc.)

    Noncovalent halogen/π interactions of FCl with substituted benzenes were studied using ab initio calcns. The predicted max. interaction energy gap between the substituted and unsubstituted systems amts. to 1.14 kcal/mol, and therefore substituents on benzene have a pronounced effect on the strength of halogen/π interactions. While the presence of electron-donating groups (NH2, CH3, and OH) on benzene enhances the interaction energy appreciably, an opposite effect is obsd. for electron-accepting groups (NO2, CN, Br, Cl, and F). The large gain of the attraction by electron correlation illustrates that the stabilities of the systems considered arise primarily from the dispersion interaction. Beside the dispersion interaction, the charge-transfer interaction also plays an important role in halogen/π interactions, as a charge d. anal. suggested. To provide more insight into the nature of halogen/π interactions, topol. anal. of the electron d. distribution and properties of bond crit. points were detd. in terms of the atoms in mols. (AIM) theory.
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    Gallivan, J. P.; Dougherty, D. A. Cation-Pi Interactions in Structural Biology. Proc. Natl. Acad. Sci. U. S. A. 1999, 96, 9459– 64,  DOI: 10.1073/pnas.96.17.9459

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    Cation-π interactions in structural biology

    Gallivan, Justin P.; Dougherty, Dennis A.

    Proceedings of the National Academy of Sciences of the United States of America (1999), 96 (17), 9459-9464CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)

    Cation-π interactions in protein structures are identified and evaluated by using an energy-based criterion for selecting significant side-chain pairs. Cation-π interactions are found to be common among structures in the Protein Data Bank, and it is clearly demonstrated that, when a cationic side-chain (Lys or Arg) is near an arom. side-chain (Phe, Tyr, or Trp), the geometry is biased toward one that would experience a favorable cation-π interaction. The side-chain of Arg is more likely than that of Lys to be in a cation-π interaction. Among the aroms., a strong bias toward Trp is clear, such that over one-fourth of all tryptophans in the data bank experience an energetically significant cation-π interaction.
20. 20

    Johnston, R. C.; Cheong, P. H. C-H···O Non-Classical Hydrogen Bonding in the Stereomechanics of Organic Transformations: Theory and Recognition. Org. Biomol. Chem. 2013, 11, 5057– 64,  DOI: 10.1039/c3ob40828k

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    C-H···O non-classical hydrogen bonding in the stereomechanics of organic transformations: theory and recognition

    Johnston, Ryne C.; Cheong, Paul Ha-Yeon

    Organic & Biomolecular Chemistry (2013), 11 (31), 5057-5064CODEN: OBCRAK; ISSN:1477-0520. (Royal Society of Chemistry)

    A review. This manuscript describes the role of non-classical hydrogen bonds (NCHBs), specifically C-H···O interactions, in modern synthetic org. transformations. Our goal is to point out the seminal examples where C-H···O interactions have been invoked as a key stereocontrolling element and to provide predictive value in recognizing future and/or potential C-H···O interactions in modern transformations.
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    Pace, C. N.; Fu, H.; Fryar, K. L.; Landua, J.; Trevino, S. R.; Shirley, B. A.; Hendricks, M. M.; Iimura, S.; Gajiwala, K.; Scholtz, J. M.; Grimsley, G. R. Contribution of Hydrophobic Interactions to Protein Stability. J. Mol. Biol. 2011, 408, 514– 528,  DOI: 10.1016/j.jmb.2011.02.053

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    Contribution of hydrophobic interactions to protein stability

    Pace, C. Nick; Fu, Hailong; Fryar, Katrina Lee; Landua, John; Trevino, Saul R.; Shirley, Bret A.; McNutt Hendricks, Marsha; Iimura, Satoshi; Gajiwala, Ketan; Scholtz, J. Martin; Grimsley, Gerald R.

    Journal of Molecular Biology (2011), 408 (3), 514-528CODEN: JMOBAK; ISSN:0022-2836. (Elsevier Ltd.)

    The authors' goal was to gain a better understanding of the contribution of hydrophobic interactions to protein stability. The authors measured the change in conformational stability, Δ(ΔG), for hydrophobic mutants of 4 proteins: (1) villin headpiece subdomain (VHP) with 36 residues; (2) surface protein VlsE of Borrelia burgdorferi with 341 residues; and 2 proteins previously studied in the authors' lab., (3) RNase Sa and (4) RNase T1. The authors compared their results with those of previous studies and reached the following conclusions: (1) hydrophobic interactions contribute less to the stability of a small protein, VHP (0.6 kcal/mol per -CH2- group), than to the stability of a large protein, VlsE (1.6 kcal/mol per -CH2- group); (2) hydrophobic interactions make the major contribution to the stability of VHP (40 kcal/mol) and the major contributors are (in kcal/mol) Phe-18 (3.9), Met-13 (3.1), Phe-7 (2.9), Phe-11 (2.7), and Leu-21 (2.7); (3) based on Δ(ΔG) values for 148 hydrophobic mutants in 13 proteins, burying a -CH2- group on folding contributes, on av., 1.1 kcal/mol to protein stability; (4) the exptl. Δ(ΔG) values for aliph. side-chains (Ala, Val, Ile, and Leu) are in good agreement with their ΔGtr values from water to cyclohexane; (5) for 22 proteins with 36 to 534 residues, hydrophobic interactions contribute 60% and H-bonds contribute 40% to protein stability; (6) conformational entropy contributes ∼2.4 kcal/mol per residue to protein instability. The globular conformation of proteins was stabilized predominantly by hydrophobic interactions.
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    Yu, N.; Li, X.; Cui, G.; Hayik, S. A.; Merz, K. M., 2nd Critical Assessment of Quantum Mechanics Based Energy Restraints in Protein Crystal Structure Refinement. Protein Sci. 2006, 15, 2773– 84,  DOI: 10.1110/ps.062343206

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    Critical assessment of quantum mechanics based energy restraints in protein crystal structure refinement

    Yu, Ning; Li, Xue; Cui, Guanglei; Hayik, Seth A.; Merz, Kenneth M., Jr.

    Protein Science (2006), 15 (12), 2773-2784CODEN: PRCIEI; ISSN:0961-8368. (Cold Spring Harbor Laboratory Press)

    A crit. evaluation of the performance of x-ray refinement protocols using various energy functions is presented using the bovine pancreatic trypsin inhibitor (BPTI) protein. The four potential energy functions the authors explored include: (1) fully quantum mech. calcns.; (2) one based on an incomplete mol. mechanics (MM) energy function employed in the Crystallog. and NMR System (CNS) with empirical parameters developed by R. A. Engh and R. Huber (1991, EH), which lacks electrostatic and attractive van der Waals terms; (3) one based on a complete MM energy function (AMBER ff99 parameter set); and (4) the same as 3, with the addn. of a Generalized Born (GB) implicit solvation term. The R, Rfree, real space R values of the refined structures and deviations from the original exptl. structure were used to assess the relative performance. It was found that at 1 Å resoln. the phys. based energy functions 1, 3, and 4 performed better than energy function 2, which the authors attribute to the better representation of key interactions, particularly electrostatics. The obsd. departures from the exptl. structure were similar for the refinements with phys. based energy functions and were smaller than the structure refined with EH. A test refinement was also performed with the reflections truncated at a high-resoln. cutoff of 2.5 Å and with random perturbations introduced into the initial coordinates, which showed that low-resoln. refinements with phys. based energy functions held the structure closer to the exptl. structure solved at 1 Å resoln. than the EH-based refinements.
23. 23

    Fedorov, D. G.; Kitaura, K. Extending the Power of Quantum Chemistry to Large Systems with the Fragment Molecular Orbital Method. J. Phys. Chem. A 2007, 111, 6904– 14,  DOI: 10.1021/jp0716740

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    Extending the Power of Quantum Chemistry to Large Systems with the Fragment Molecular Orbital Method

    Fedorov, Dmitri G.; Kitaura, Kazuo

    Journal of Physical Chemistry A (2007), 111 (30), 6904-6914CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)

    A review. Following the brief review of the modern fragment-based methods and other approaches to perform quantum-mech. calcns. of large systems, the theor. development of the fragment MO method (FMO) is covered in detail, with the emphasis on the phys. properties, which can be computed with FMO. The FMO-based polarizable continuum model (PCM) for treating the solvent effects in large systems and the pair interaction energy decompn. anal. (PIEDA) are described in some detail, and a range of applications of FMO to biol. studies is introduced. The factors detg. the relative stability of polypeptide conformers (α-helix, β-turn, and extended form) are elucidated using FMO/PCM and PIEDA, and the interactions in the Trp-cage miniprotein construct (PDB: 1L2Y) are analyzed using PIEDA.
24. 24

    Phipps, M. J.; Fox, T.; Tautermann, C. S.; Skylaris, C. K. Energy Decomposition Analysis Approaches and Their Evaluation on Prototypical Protein-Drug Interaction Patterns. Chem. Soc. Rev. 2015, 44, 3177– 211,  DOI: 10.1039/C4CS00375F

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    24

    Energy decomposition analysis approaches and their evaluation on prototypical protein-drug interaction patterns

    Phipps, Maximillian J. S.; Fox, Thomas; Tautermann, Christofer S.; Skylaris, Chris-Kriton

    Chemical Society Reviews (2015), 44 (10), 3177-3211CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)

    The partitioning of the energy in ab initio quantum mech. calcns. into its chem. origins (e.g., electrostatics, exchange-repulsion, polarization, and charge transfer) is a relatively recent development; such concepts of isolating chem. meaningful energy components from the interaction energy have been demonstrated by variational and perturbation based energy decompn. anal. approaches. The variational methods are typically derived from the early energy decompn. anal. of Morokuma [Morokuma, J. Chem. Phys., 1971, 55, 1236], and the perturbation approaches from the popular symmetry-adapted perturbation theory scheme [Jeziorski et al., Methods and Techniques in Computational Chem.: METECC-94, 1993, ch. 13, p. 79]. Since these early works, many developments have taken place aiming to overcome limitations of the original schemes and provide more chem. significance to the energy components, which are not uniquely defined. In this review, after a brief overview of the origins of these methods we examine the theory behind the currently popular variational and perturbation based methods from the point of view of biochem. applications. We also compare and discuss the chem. relevance of energy components produced by these methods on six test sets that comprise model systems that display interactions typical of biomols. (such as hydrogen bonding and π-π stacking interactions) including various treatments of the dispersion energy.
25. 25

    Kitaura, K.; Ikeo, E.; Asada, T.; Nakano, T.; Uebayasi, M. Fragment Molecular Orbital Method: An Approximate Computational Method for Large Molecules. Chem. Phys. Lett. 1999, 313, 701– 706,  DOI: 10.1016/S0009-2614(99)00874-X

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    25

    Fragment molecular orbital method: an approximate computational method for large molecules

    Kitaura, K.; Ikeo, E.; Asada, T.; Nakano, T.; Uebayasi, M.

    Chemical Physics Letters (1999), 313 (3,4), 701-706CODEN: CHPLBC; ISSN:0009-2614. (Elsevier Science B.V.)

    An approx. MO method was proposed for calcg. large mols. such as proteins. This method assigns the electrons of the mols. to fragments, and the MOs of fragments and fragment pairs are calcd. to obtain the total energy of the mol. The method avoids the MO calcn. of the whole mol., and is expected to reduce the computational time drastically for large mols. Numerical calcns. were performed on C3H8, PrOH and AcNHMe to show the accuracy of the method. The optimized geometries and total energies were in good agreement with those from the ab initio MO calcns.
26. 26

    Alexeev, Y.; Mazanetz, M. P.; Ichihara, O.; Fedorov, D. G. GAMESS as a Free Quantum-Mechanical Platform for Drug Research. Curr. Top. Med. Chem. 2012, 12, 2013– 2033,  DOI: 10.2174/156802612804910269

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    26

    GAMESS as a free quantum-mechanical platform for drug research

    Alexeev, Yuri; Mazanetz, Michael P.; Ichihara, Osamu; Fedorov, Dmitri G.

    Current Topics in Medicinal Chemistry (Sharjah, United Arab Emirates) (2012), 12 (18), 2013-2033CODEN: CTMCCL; ISSN:1568-0266. (Bentham Science Publishers Ltd.)

    A review. Driven by a steady improvement of computational hardware and significant progress in ab initio method development, quantum-mech. approaches can now be applied to large biochem. systems and drug design. We review the methods implemented in GAMESS, which are suitable to calc. large biochem. systems. An emphasis is put on the fragment MO method (FMO) and quantum mechanics interfaced with mol. mechanics (QM/MM). The use of FMO in the protein-ligand binding, structure-activity relationship (SAR) studies, fragment- and structure-based drug design (FBDD/SBDD) is discussed in detail.
27. 27

    Heifetz, A.; James, T.; Southey, M.; Morao, I.; Aldeghi, M.; Sarrat, L.; Fedorov, D. G.; Bodkin, M. J.; Townsend-Nicholson, A. Characterising GPCR-Ligand Interactions Using a Fragment Molecular Orbital-Based Approach. Curr. Opin. Struct. Biol. 2019, 55, 85– 92,  DOI: 10.1016/j.sbi.2019.03.021

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    27

    Characterising GPCR-ligand interactions using a fragment molecular orbital-based approach

    Heifetz, Alexander; James, Tim; Southey, Michelle; Morao, Inaki; Aldeghi, Matteo; Sarrat, Laurie; Fedorov, Dmitri G.; Bodkin, Mike J.; Townsend-Nicholson, Andrea

    Current Opinion in Structural Biology (2019), 55 (), 85-92CODEN: COSBEF; ISSN:0959-440X. (Elsevier Ltd.)

    A review. There has been fantastic progress in solving GPCR crystal structures. However, the ability of X-ray crystallog. to guide the drug discovery process for GPCR targets is limited by the availability of accurate tools to explore receptor-ligand interactions. Visual inspection and mol. mechanics approaches cannot explain the full complexity of mol. interactions. Quantum mech. approaches (QM) are often too computationally expensive, but the fragment MO (FMO) method offers an excellent soln. that combines accuracy, speed and the ability to reveal key interactions that would otherwise be hard to detect. Integration of GPCR crystallog. or homol. modeling with FMO reveals atomistic details of the individual contributions of each residue and water mol. towards ligand binding, including an anal. of their chem. nature.
28. 28

    Chudyk, E. I.; Sarrat, L.; Aldeghi, M.; Fedorov, D. G.; Bodkin, M. J.; James, T.; Southey, M.; Robinson, R.; Morao, I.; Heifetz, A.; Exploring GPCR-ligand interactions with the fragment molecular orbital (FMO) Method. In Computational Methods for GPCR Drug Discovery; Heifetz, A., Ed.; Humana Press: New York, 2018, Vol. 1705, pp 179− 195.

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29. 29

    Fedorov, D. G.; Kitaura, K. Pair Interaction Energy Decomposition Analysis. J. Comput. Chem. 2007, 28, 222– 37,  DOI: 10.1002/jcc.20496

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    29

    Pair interaction energy decomposition analysis

    Fedorov, Dmitri G.; Kitaura, Kazuo

    Journal of Computational Chemistry (2007), 28 (1), 222-237CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)

    The energy decompn. anal. (EDA) by Kitaura and Morokuma was redeveloped in the framework of the fragment MO method (FMO). The proposed pair interaction energy decompn. anal. (PIEDA) can treat large mol. clusters and the systems in which fragments are connected by covalent bonds, such as proteins. The interaction energy in PIEDA is divided into the same contributions as in EDA: the electrostatic, exchange-repulsion, and charge transfer energies, to which the correlation (dispersion) term was added. The careful comparison to the ab initio EDA interaction energies for water clusters with 2-16 mols. revealed that PIEDA has the error of at most 1.2 kcal/mol (or about 1%). The anal. was applied to (H2O)1024, the α helix, β turn, and β strand of polyalanine (ALA)10, as well as to the synthetic protein (PDB code 1L2Y) with 20 residues. The comparative aspects of the polypeptide isomer stability are discussed in detail.
30. 30

    Heifetz, A.; Aldeghi, M.; Chudyk, E. I.; Fedorov, D. G.; Bodkin, M. J.; Biggin, P. C. Using the Fragment Molecular Orbital Method to Investigate Agonist-Orexin-2 Receptor Interactions. Biochem. Soc. Trans. 2016, 44, 574– 81,  DOI: 10.1042/BST20150250

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    30

    Using the fragment molecular orbital method to investigate agonist-orexin-2 receptor interactions

    Heifetz, Alexander; Aldeghi, Matteo; Chudyk, Ewa I.; Fedorov, Dmitri G.; Bodkin, Mike J.; Biggin, Philip C.

    Biochemical Society Transactions (2016), 44 (2), 574-581CODEN: BCSTB5; ISSN:0300-5127. (Portland Press Ltd.)

    The understanding of binding interactions between any protein and a small mol. plays a key role in the rationalization of affinity and selectivity and is essential for an efficient structure-based drug discovery (SBDD) process. Clearly, to begin SBDD, a structure is needed, and although there has been fantastic progress in solving G-protein-coupled receptor (GPCR) crystal structures, the process remains quite slow and is not currently feasible for every GPCR or GPCR-ligand complex. This situation significantly limits the ability of X-ray crystallog. to impact the drug discovery process for GPCR targets in 'real-time' and hence there is still a need for other practical and cost-efficient alternatives. We present here an approach that integrates our previously described hierarchical GPCR modeling protocol (HGMP) and the fragment MO (FMO) quantum mechanics (QM) method to explore the interactions and selectivity of the human orexin-2 receptor (OX2R) and its recently discovered nonpeptidic agonists. HGMP generates a 3D model of GPCR structures and its complexes with small mols. by applying a set of computational methods. FMO allows ab initio approaches to be applied to systems that conventional QM methods would find challenging. The key advantage of FMO is that it can reveal information on the individual contribution and chem. nature of each residue and water mol. to the ligand binding that normally would be difficult to detect without QM. We illustrate how the combination of both techniques provides a practical and efficient approach that can be used to analyze the existing structure-function relationships (SAR) and to drive forward SBDD in a real-world example for which there is no crystal structure of the complex available.
31. 31

    Heifetz, A.; Trani, G.; Aldeghi, M.; MacKinnon, C. H.; McEwan, P. A.; Brookfield, F. A.; Chudyk, E. I.; Bodkin, M.; Pei, Z.; Burch, J. D.; Ortwine, D. F. Fragment Molecular Orbital Method Applied to Lead Optimization of Novel Interleukin-2 Inducible T-Cell Kinase (Itk) Inhibitors. J. Med. Chem. 2016, 59, 4352– 63,  DOI: 10.1021/acs.jmedchem.6b00045

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    Fragment Molecular Orbital Method Applied to Lead Optimization of Novel Interleukin-2 Inducible T-Cell Kinase (ITK) Inhibitors

    Heifetz, Alexander; Trani, Giancarlo; Aldeghi, Matteo; MacKinnon, Colin H.; McEwan, Paul A.; Brookfield, Frederick A.; Chudyk, Ewa I.; Bodkin, Mike; Pei, Zhonghua; Burch, Jason D.; Ortwine, Daniel F.

    Journal of Medicinal Chemistry (2016), 59 (9), 4352-4363CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)

    Inhibition of inducible T-cell kinase (ITK), a nonreceptor tyrosine kinase, may represent a novel treatment for allergic asthma. In our previous reports, we described the discovery of sulfonylpyridine (SAP), benzothiazole (BZT), indazole (IND), and tetrahydroindazole (THI) series as novel ITK inhibitors and how computational tools such as dihedral scans and docking were used to support this process. X-ray crystallog. and modeling were applied to provide essential insight into ITK-ligand interactions. However, "visual inspection" traditionally used for the rationalization of protein-ligand affinity cannot always explain the full complexity of the mol. interactions. The fragment MO (FMO) quantum-mech. (QM) method provides a complete list of the interactions formed between the ligand and protein that are often omitted from traditional structure-based descriptions. FMO methodol. was successfully used as part of a rational structure-based drug design effort to improve the ITK potency of high-throughput screening hits, ultimately delivering ligands with potency in the subnanomolar range.
32. 32

    Morao, I.; Fedorov, D. G.; Robinson, R.; Southey, M.; Townsend-Nicholson, A.; Bodkin, M. J.; Heifetz, A. Rapid and Accurate Assessment of GPCR-Ligand Interactions Using the Fragment Molecular Orbital-Based Density-Functional Tight-Binding Method. J. Comput. Chem. 2017, 38, 1987– 1990,  DOI: 10.1002/jcc.24850

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    32

    Rapid and accurate assessment of GPCR-ligand interactions Using the fragment molecular orbital-based density-functional tight-binding method

    Morao, Inaki; Fedorov, Dmitri G.; Robinson, Roger; Southey, Michelle; Townsend-Nicholson, Andrea; Bodkin, Mike J.; Heifetz, Alexander

    Journal of Computational Chemistry (2017), 38 (23), 1987-1990CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)

    The reliable and precise evaluation of receptor-ligand interactions and pair-interaction energy is an essential element of rational drug design. While quantum mech. (QM) methods have been a promising means by which to achieve this, traditional QM is not applicable for large biol. systems due to its high computational cost. Here, the fragment MO (FMO) method has been used to accelerate QM calcns., and by combining FMO with the d.-functional tight-binding (DFTB) method we are able to decrease computational cost 1000 times, achieving results in seconds, instead of hours. We have applied FMO-DFTB to three different GPCR-ligand systems. Our results correlate well with site directed mutagenesis data and findings presented in the published literature, demonstrating that FMO-DFTB is a rapid and accurate means of GPCR-ligand interactions. © 2017 Authors Journal of Computational Chem. Published by Wiley Periodicals, Inc.
33. 33

    Fedorov, D. G. Solvent Screening in Zwitterions Analyzed with the Fragment Molecular Orbital Method. J. Chem. Theory Comput. 2019, 15, 5404– 5416,  DOI: 10.1021/acs.jctc.9b00715

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    33

    Solvent Screening in Zwitterions Analyzed with the Fragment Molecular Orbital Method

    Fedorov, Dmitri G.

    Journal of Chemical Theory and Computation (2019), 15 (10), 5404-5416CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)

    Based on induced solvent charges, a new model of solvent screening is developed in the framework of the fragment MO combined with the polarizable continuum model. The developed model is applied to analyze interactions in a prototypical zwitterionic system, sodium chloride in water, and it is shown that the large underestimation of the interaction in the original solvent screening based on local charges is successfully cor. The model is also applied to a complex of the Trp-cage (PDB: 1 L2Y) miniprotein with an anionic ligand, and the phys. factors detd. protein-ligand binding in soln. are unraveled.
34. 34

    Mazanetz, M. P.; Ichihara, O.; Law, R. J.; Whittaker, M. Prediction of Cyclin-Dependent Kinase 2 Inhibitor Potency Using the Fragment Molecular Orbital Method. J. Cheminf. 2011, 3, 2,  DOI: 10.1186/1758-2946-3-2

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    Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method

    Mazanetz, Michael P.; Ichihara, Osamu; Law, Richard J.; Whittaker, Mark

    Journal of Cheminformatics (2011), 3 (), 2CODEN: JCOHB3; ISSN:1758-2946. (Chemistry Central Ltd.)

    The reliable and robust estn. of ligand binding affinity continues to be a challenge in drug design. Many current methods rely on mol. mechanics (MM) calcns. which do not fully explain complex mol. interactions. Full quantum mech. (QM) computation of the electronic state of protein-ligand complexes has recently become possible by the latest advances in the development of linear-scaling QM methods such as the ab initio fragment MO (FMO) method. This approx. MO method is sufficiently fast that it can be incorporated into the development cycle during structure-based drug design for the reliable estn. of ligand binding affinity. Addnl., the FMO method can be combined with approxns. for entropy and solvation to make it applicable for binding affinity prediction for a broad range of target and chemotypes. We applied this method to examine the binding affinity for a series of published cyclin-dependent kinase 2 (CDK2) inhibitors. We calcd. the binding affinity for 28 CDK2 inhibitors using the ab initio FMO method based on a no. of X-ray crystal structures. The sum of the pair interaction energies (PIE) was calcd. and used to explain the gas-phase enthalpic contribution to binding. The correlation of the ligand potencies to the protein-ligand interaction energies gained from FMO was examd. and was seen to give a good correlation which outperformed three MM force field based scoring functions used to appoximate the free energy of binding. Although the FMO calcn. allows for the enthalpic component of binding interactions to be understood at the quantum level, as it is an in vacuo single point calcn., the entropic component and solvation terms are neglected. For this reason a more accurate and predictive est. for binding free energy was desired. Therefore, addnl. terms used to describe the protein-ligand interactions were then calcd. to improve the correlation of the FMO derived values to exptl. free energies of binding. These terms were used to account for the polar and non-polar solvation of the mol. estd. by the Poisson-Boltzmann equation and the solvent accessible surface area (SASA), resp., as well as a correction term for ligand entropy. A quant. structure-activity relationship (QSAR) model obtained by Partial Least Squares projection to latent structures (PLS) anal. of the ligand potencies and the calcd. terms showed a strong correlation (r2 = 0.939, q2 = 0.896) for the 14 mol. test set which had a Pearson rank order correlation of 0.97. A training set of a further 14 mols. was well predicted (r2 = 0.842), and could be used to obtain meaningful estns. of the binding free energy. Our results show that binding energies calcd. with the FMO method correlate well with published data. Anal. of the terms used to derive the FMO energies adds greater understanding to the binding interactions than can be gained by MM methods. Combining this information with addnl. terms and creating a scaled model to describe the data results in more accurate predictions of ligand potencies than the abs. values obtained by FMO alone.
35. 35

    Sheng, Y.; Watanabe, H.; Maruyama, K.; Watanabe, C.; Okiyama, Y.; Honma, T.; Fukuzawa, K.; Tanaka, S. Towards Good Correlation between Fragment Molecular Orbital Interaction Energies and Experimental IC₅₀ for Ligand Binding: A Case Study of P38 Map Kinase. Comput. Struct. Biotechnol. J. 2018, 16, 421– 434,  DOI: 10.1016/j.csbj.2018.10.003

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    35

    Towards good correlation between fragment molecular orbital interaction energies and experimental IC50 for ligand binding: A case study of p38 MAP kinase

    Sheng, Yinglei; Watanabe, Hirofumi; Maruyama, Keiya; Watanabe, Chiduru; Okiyama, Yoshio; Honma, Teruki; Fukuzawa, Kaori; Tanaka, Shigenori

    Computational and Structural Biotechnology Journal (2018), 16 (), 421-434CODEN: CSBJAC; ISSN:2001-0370. (Elsevier B.V.)

    We describe several procedures for the preprocessing of fragment MO (FMO) calcns. on p38 mitogen-activated protein (MAP) kinase and discuss the influence of the procedures on the protein-ligand interaction energies represented by inter-fragment interaction energies (IFIEs). The correlation between the summation of IFIEs for a ligand and amino acid residues of protein (IFIE-sum) and exptl. affinity values (IC50) was poor when considered for the whole set of protein-ligand complexes. To improve the correlation for prediction of ligand binding affinity, we carefully classified data set by the ligand charge, the DFG-loop state (DFG-in/out loop), which is characteristic of kinase, and the scaffold of ligand. The correlation between IFIE-sums and the activity values was examd. using the classified data set. As a result, it was confirmed that there was a selected data set that showed good correlation between IFIE-sum and activity value by appropriate classification. In addn., we found that the differences in protonation and hydrogen orientation caused by subtle differences in preprocessing led to a relatively large difference in IFIE values. Further, we also examd. the effect of structure optimization with different force fields. It was confirmed that the difference in the force field had no significant effect on IFIE-sum. From the viewpoint of drug design using FMO calcns., various investigations on IFIE-sum in this research, such as those regarding several classifications of data set and the different procedures of structural prepn., would be expected to provide useful knowledge for improvement of prediction ability about the ligand binding affinity.
36. 36

    Okiyama, Y.; Watanabe, C.; Fukuzawa, K.; Mochizuki, Y.; Nakano, T.; Tanaka, S. Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson-Boltzmann Equation: Ii. Protein and Its Ligand-Binding System Studies. J. Phys. Chem. B 2019, 123, 957– 973,  DOI: 10.1021/acs.jpcb.8b09326

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    Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson-Boltzmann Equation: II. Protein and Its Ligand-Binding System Studies

    Okiyama, Yoshio; Watanabe, Chiduru; Fukuzawa, Kaori; Mochizuki, Yuji; Nakano, Tatsuya; Tanaka, Shigenori

    Journal of Physical Chemistry B (2019), 123 (5), 957-973CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)

    In this study, the electronic properties of bioactive proteins were analyzed using an ab initio fragment MO (FMO) methodol. in soln.: coupling with an implicit solvent model based on the Poisson-Boltzmann surface area called as FMO-PBSA. We investigated the solvent effects on practical and heterogeneous targets with uneven exposure to solvents unlike DNA analyzed in our recent study. Interfragment interaction energy (IFIE) and its decompn. analyses by FMO-PBSA revealed solvent-screening mechanisms that affect local stability inside ubiquitin protein: the screening suppresses excessiveness in bare charge-charge interactions and enables an intuitive IFIE anal. The electrostatic character and assocd. solvation free energy also give consistent results as a whole to previous studies on the explicit solvent model. Moreover, by using the estrogen receptor alpha (ERα) protein bound to ligands, we elucidated the importance of specific interactions that depend on the elec. charge and activatability as agonism/antagonism of the ligand while estg. the influences of the implicit solvent on the ligand and helix-12 bindings. The predicted ligand-binding affinities of bioactive compds. to ERα also show a good correlation with their in vitro activities. The FMO-PBSA approach would thus be a promising tool both for biol. and pharmaceutical research targeting proteins.
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    Iwasaki, S.; Iwasaki, W.; Takahashi, M.; Sakamoto, A.; Watanabe, C.; Shichino, Y.; Floor, S. N.; Fujiwara, K.; Mito, M.; Dodo, K.; Sodeoka, M.; Imataka, H.; Honma, T.; Fukuzawa, K.; Ito, T.; Ingolia, N. T. The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA. Mol. Cell 2019, 73, 738,  DOI: 10.1016/j.molcel.2018.11.026

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    The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA

    Iwasaki, Shintaro; Iwasaki, Wakana; Takahashi, Mari; Sakamoto, Ayako; Watanabe, Chiduru; Shichino, Yuichi; Floor, Stephen N.; Fujiwara, Koichi; Mito, Mari; Dodo, Kosuke; Sodeoka, Mikiko; Imataka, Hiroaki; Honma, Teruki; Fukuzawa, Kaori; Ito, Takuhiro; Ingolia, Nicholas T.

    Molecular Cell (2019), 73 (4), 738-748.e9CODEN: MOCEFL; ISSN:1097-2765. (Elsevier Inc.)

    A class of translation inhibitors, exemplified by the natural product rocaglamide A (RocA), isolated from Aglaia genus plants, exhibits antitumor activity by clamping eukaryotic translation initiation factor 4A (eIF4A) onto polypurine sequences in mRNAs. This unusual inhibitory mechanism raises the question of how the drug imposes sequence selectivity onto a general translation factor. Here, we detd. the crystal structure of the human eIF4A1·ATP analog·RocA·polypurine RNA complex. RocA targets the "bi-mol. cavity" formed characteristically by eIF4A1 and a sharply bent pair of consecutive purines in the RNA. Natural amino acid substitutions found in Aglaia eIF4As changed the cavity shape, leading to RocA resistance. This study provides an example of an RNA-sequence-selective interfacial inhibitor fitting into the space shaped cooperatively by protein and RNA with specific sequences.
38. 38

    Barker, J. J.; Barker, O.; Courtney, S. M.; Gardiner, M.; Hesterkamp, T.; Ichihara, O.; Mather, O.; Montalbetti, C. A.; Muller, A.; Varasi, M.; Whittaker, M.; Yarnold, C. J. Discovery of a Novel Hsp90 Inhibitor by Fragment Linking. ChemMedChem 2010, 5, 1697– 700,  DOI: 10.1002/cmdc.201000219

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    Discovery of a novel Hsp90 inhibitor by fragment linking

    Barker, John J.; Barker, Oliver; Courtney, Stephen M.; Gardiner, Mihaly; Hesterkamp, Thomas; Ichihara, Osamu; Mather, Owen; Montalbetti, Christian A. G. N.; Muller, Annett; Varasi, Mario; Whittaker, Mark; Yarnold, Christopher J.

    ChemMedChem (2010), 5 (10), 1697-1700CODEN: CHEMGX; ISSN:1860-7179. (Wiley-VCH Verlag GmbH & Co. KGaA)

    Following a high-throughput biochem. fragment screen, we have identified novel fragment inhibitors of Hsp90. Two fragment hits were combined to give a dual-fragment Hsp90 complex. The compd., I, with the lowest strain energy was synthesized, and a 1000-fold improvement in activity was achieved.
39. 39

    Ichihara, O.; Barker, J.; Law, R. J.; Whittaker, M. Compound Design by Fragment-Linking. Mol. Inf. 2011, 30, 298– 306,  DOI: 10.1002/minf.201000174

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    Compound Design by Fragment-Linking

    Ichihara, Osamu; Barker, John; Law, Richard J.; Whittaker, Mark

    Molecular Informatics (2011), 30 (4), 298-306CODEN: MIONBS; ISSN:1868-1743. (Wiley-VCH Verlag GmbH & Co. KGaA)

    The linking together of two fragment compds. that bind to distinct protein sub-sites can lead to a superadditivity of binding affinities, in which the binding free energy of the linked fragments exceeds the simple sum of the binding energies of individual fragments (linking coeff. E<1). However, a review of the literature shows that such events are relatively rare and, in the majority of the cases, linking coeffs. are far from optimal being much greater than 1. It is crit. to design a linker that does not disturb the original binding poses of each fragment in order to achieve successful linking. However, such an ideal linker is often difficult to design and even more difficult to actually synthesize. We suggest that the chance of achieving successful fragment linking can be significantly improved by choosing a fragment pair that consists of one fragment that binds by strong H-bonds (or non-classical equiv.) and a second fragment that is more tolerant of changes in binding mode (hydrophobic or vdW binders). We also propose that the fragment MO (FMO) calcns. can be used to analyze the nature of the binding interactions of the fragment hits for the selection of fragments for evolution, merging and linking in order to optimize the chance of success.
40. 40

    Barker, J. J.; Barker, O.; Boggio, R.; Chauhan, V.; Cheng, R. K.; Corden, V.; Courtney, S. M.; Edwards, N.; Falque, V. M.; Fusar, F.; Gardiner, M.; Hamelin, E. M.; Hesterkamp, T.; Ichihara, O.; Jones, R. S.; Mather, O.; Mercurio, C.; Minucci, S.; Montalbetti, C. A.; Muller, A.; Patel, D.; Phillips, B. G.; Varasi, M.; Whittaker, M.; Winkler, D.; Yarnold, C. J. Fragment-Based Identification of Hsp90 Inhibitors. ChemMedChem 2009, 4, 963– 6,  DOI: 10.1002/cmdc.200900011

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    Fragment-based Identification of Hsp90 Inhibitors

    Barker, John J.; Barker, Oliver; Boggio, Roberto; Chauhan, Viddhata; Cheng, Robert K. Y.; Corden, Vincent; Courtney, Stephen M.; Edwards, Neil; Falque, Virginie M.; Fusar, Fulvia; Gardiner, Mihaly; Hamelin, Estelle M. N.; Hesterkamp, Thomas; Ichihara, Osamu; Jones, Richard S.; Mather, Owen; Mercurio, Ciro; Minucci, Saverio; Montalbetti, Christian A. G. N.; Muller, Annett; Patel, Deepti; Phillips, Banu G.; Varasi, Mario; Whittaker, Mark; Winkler, Dirk; Yarnold, Christopher J.

    ChemMedChem (2009), 4 (6), 963-966CODEN: CHEMGX; ISSN:1860-7179. (Wiley-VCH Verlag GmbH & Co. KGaA)

    Heat shock protein 90 (Hsp90) plays a key role in stress response and protection of the cell against the effects of mutation. Herein we report the identification of an Hsp90 inhibitor identified by fragment screening using a high-concn. biochem. assay, as well as its optimization by in silico searching coupled with a structure-based drug design (SBDD) approach.
41. 41

    Choi, J.; Kim, H.-J.; Jin, X.; Lim, H.; Kim, S.; Roh, I.-S.; Kang, H.-E.; No, K. T.; Sohn, H.-J. Application of the Fragment Molecular Orbital Method to Discover Novel Natural Products for Prion Disease. Sci. Rep. 2018, 8, 13063,  DOI: 10.1038/s41598-018-31080-7

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    Application of the fragment molecular orbital method to discover novel natural products for prion disease

    Choi Jiwon; Kim Songmi; No Kyoung Tai; Kim Hyo-Jin; Roh In-Soon; Kang Hae-Eun; Sohn Hyun-Joo; Jin Xuemei; Lim Hocheol; No Kyoung Tai

    Scientific reports (2018), 8 (1), 13063 ISSN:.

    Conformational conversion of the normal cellular isoform of the prion protein PrP(C) into an infectious isoform PrP(Sc) causes pathogenesis in prion diseases. To date, numerous antiprion compounds have been developed to block this conversion and to detect the molecular mechanisms of prion inhibition using several computational studies. Thus far, no suitable drug has been identified for clinical use. For these reasons, more accurate and predictive approaches to identify novel compounds with antiprion effects are required. Here, we have applied an in silico approach that integrates our previously described pharmacophore model and fragment molecular orbital (FMO) calculations, enabling the ab initio calculation of protein-ligand complexes. The FMO-based virtual screening suggested that two natural products with antiprion activity exhibited good binding interactions, with hotspot residues within the PrP(C) binding site, and effectively reduced PrP(Sc) levels in a standard scrapie cell assay. Overall, the outcome of this study will be used as a promising strategy to discover antiprion compounds. Furthermore, the SAR-by-FMO approach can provide extremely powerful tools in quickly establishing virtual SAR to prioritise compounds for synthesis in further studies.
42. 42

    Ishikawa, T. [Applications of the Fragment Molecular Orbital Method in Drug Discovery]. Yakugaku Zasshi 2016, 136, 121– 30,  DOI: 10.1248/yakushi.15-00230-5

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    Applications of the fragment molecular orbital method in drug discovery

    Ishikawa, Takeshi

    Yakugaku Zasshi (2016), 136 (1), 121-130CODEN: YKKZAJ; ISSN:0031-6903. (Pharmaceutical Society of Japan)

    Recently, ab initio quantum mech. calcns. have been applied to large mols., including biomol. systems. The fragment MO (FMO) method is one of the most efficient approaches for the quantum mech. investigation of such mols. In the FMO method, dividing a target mol. into small fragments reduces computational effort. The clear definition of inter-fragment interaction energy (IFIE) as an expression of total energy is another valuable feature of the FMO method because it provides the ability to analyze interactions in biomols. Thus, the FMO method is expected to be useful for drug discovery. This study demonstrates applications of the FMO method related to drug discovery. First, 1FIE, according to FMO calcns., was used in the optimization of drug candidates for the development of anti-prion compds. The second example involved interaction anal. of the human immunodeficiency virus type 1 (HIV-I) protease and a drug compd. that used a novel anal. method for dispersion interaction, i.e., fragment interaction anal. based on LMP2 (FILM).
43. 43

    Kolovskaya, O. S.; Zamay, T. N.; Zamay, G. S.; Babkin, V. A.; Medvedeva, E. N.; Neverova, N. A.; Kirichenko, A. K.; Zamay, S. S.; Lapin, I. N.; Morozov, E. V.; Sokolov, A. E.; Narodov, A. A.; Fedorov, D. G.; Tomilin, F. N.; Zabluda, V. N.; Alekhina, Y.; Lukyanenko, K. A.; Glazyrin, Y. E.; Svetlichnyi, V. A.; Berezovski, M. V.; Kichkailo, A. S. Aptamer-Conjugated Superparamagnetic Ferroarabinogalactan Nanoparticles for Targeted Magnetodynamic Therapy of Cancer. Cancers 2020, 12, 216,  DOI: 10.3390/cancers12010216

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    Aptamer-conjugated superparamagnetic ferroarabinogalactan nanoparticles for targeted magnetodynamic therapy of cancer

    Kolovskaya, Olga S.; Zamay, Tatiana N.; Zamay, Galina S.; Babkin, Vasily A.; Medvedeva, Elena N.; Neverova, Nadezhda A.; Kirichenko, Andrey K.; Zamay, Sergey S.; Lapin, Ivan N.; Morozov, Evgeny V.; Sokolov, Alexey E.; Narodov, Andrey A.; Fedorov, Dmitri G.; Tomilin, Felix N.; Zabluda, Vladimir N.; Alekhina, Yulia; Lukyanenko, Kirill A.; Glazyrin, Yury E.; Svetlichnyi, Valery A.; Berezovski, Maxim V.; Kichkailo, Anna S.

    Cancers (2020), 12 (1), 216CODEN: CANCCT; ISSN:2072-6694. (MDPI AG)

    Nanotechnologies involving phys. methods of tumor destruction using functional oligonucleotides are promising for targeted cancer therapy. Our study presents magnetodynamic therapy for selective elimination of tumor cells in vivo using DNA aptamer-functionalized magnetic nanoparticles exposed to a low frequency alternating magnetic field. We developed an enhanced targeting approach of cancer cells with aptamers and arabinogalactan. Aptamers to fibronectin (AS-14) and heat shock cognate 71 kDa protein (AS-42) facilitated the delivery of the nanoparticles to Ehrlich carcinoma cells, and arabinogalactan (AG) promoted internalization through asialoglycoprotein receptors. Specific delivery of the aptamer-modified FeAG nanoparticles to the tumor site was confirmed by magnetic resonance imaging (MRI). After the following treatment with a low frequency alternating magnetic field, AS-FeAG caused cancer cell death in vitro and tumor redn. in vivo. Histol. analyses showed mech. disruption of tumor tissues, total necrosis, cell lysis, and disruption of the extracellular matrix. The enhanced targeted magnetic theranostics with the aptamer conjugated superparamagnetic ferroarabinogalactans opens up a new venue for making biocompatible contrasting agents for MRI imaging and performing non-invasive anti-cancer therapies with a deep penetrated magnetic field.
44. 44

    Fedorov, D. G.; Kitaura, K. Energy Decomposition Analysis in Solution Based on the Fragment Molecular Orbital Method. J. Phys. Chem. A 2012, 116, 704– 19,  DOI: 10.1021/jp209579w

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    Energy Decomposition Analysis in Solution Based on the Fragment Molecular Orbital Method

    Fedorov, Dmitri G.; Kitaura, Kazuo

    Journal of Physical Chemistry A (2012), 116 (1), 704-719CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)

    We develop the pair interaction energy decompn. anal. (PIEDA) in soln. by combining the fragment MO (FMO) method with the polarizable continuum model (PCM). The solvent screening of the electrostatic interaction and the desolvation penalty in complex formation are described by this approach from ab initio calcns. of fragments and their pairs. The applications to the complex of solvated sodium and chlorine ions, as well as to lysine and aspartic acid, show how the anal. helps reveal the phys. picture. The PIEDA/PCM method is also applied to a small protein chignolin (PDB: 1UAO), and the solvent screening of the pair interactions is discussed.
45. 45

    El Kerdawy, A.; Murray, J. S.; Politzer, P.; Bleiziffer, P.; Hesselmann, A.; Gorling, A.; Clark, T. Directional Noncovalent Interactions: Repulsion and Dispersion. J. Chem. Theory Comput. 2013, 9, 2264– 75,  DOI: 10.1021/ct400185f

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    Directional Noncovalent Interactions: Repulsion and Dispersion

    El Kerdawy, Ahmed; Murray, Jane S.; Politzer, Peter; Bleiziffer, Patrick; Hesselmann, Andreas; Goerling, Andreas; Clark, Timothy

    Journal of Chemical Theory and Computation (2013), 9 (5), 2264-2275CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)

    The interaction energies between an argon atom and the dihalogens Br2, BrCl, and BrF have been investigated using frozen core CCSD(T)(fc)/aug-cc-pVQZ calcns. as ref. values for other levels of theory. The potential-energy hypersurfaces show two types of min.: (1) collinear with the dihalogen bond and (2) in a bridging position. The former represent the most stable min. for these systems, and their binding energies decrease in the order Br > Cl > F. Isotropic atom-atom potentials cannot reproduce this binding pattern. Of the other levels of theory, CCSD(T)(fc)/aug-cc-pVTZ reproduces the ref. data very well, as does MP2(fc)/aug-cc-pVDZ, which performs better than MP2 with the larger basis sets (aug-cc-pVQZ and aug-cc-pvTZ). B3LYP-D3 and M06-2X reproduce the binding patterns moderately well despite the former using an isotropic dispersion potential correction. B3LYP-D3(bj) performs even better. The success of the B3LYP-D3 methods is because polar flattening of the halogens allows the argon atom to approach more closely in the direction collinear with the bond, so that the sum of dispersion potential and repulsion is still neg. at shorter distances than normally possible and the min. is deeper at the van der Waals distance. Core polarization functions in the basis set and including the core orbitals in the CCSD(T)(full) calcns. lead to a uniform decrease of approx. 20% in the magnitudes of the calcd. interaction energies. The EXXRPA + @EXX (exact exchange RPA) orbital-dependent d. functional also gives interaction energies that correlate well with the highest level of theory but are approx. 10% low. The newly developed EXXRPA + @dRPA functional represents a systematic improvement on EXXRPA + @EXX.
46. 46

    Ballesteros, J. A.; Weinstein, H. Integrated Methods for the Construction of Three-Dimensional Models and Computational Probing of Structure-Function Relations in G Protein-Coupled Receptors. Methods Neurosci. 1995, 25, 366– 428,  DOI: 10.1016/S1043-9471(05)80049-7

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    Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors

    Ballesteros, Juan A.; Weinstein, Harel

    Methods in Neurosciences (1995), 25 (), 366-428CODEN: MENEE5; ISSN:1043-9471.

    A review, with 135 refs., on approaches that can be used to resolve the apparent ambiguities that burden the pharmacol. testing of G protein-coupled receptor (GPCR) models, based on the integration of structural information about the receptor, about mutants, and about the changes induced by ligand binding.
47. 47

    Prioleau, C.; Visiers, I.; Ebersole, B. J.; Weinstein, H.; Sealfon, S. C. Conserved Helix 7 Tyrosine Acts as a Multistate Conformational Switch in the 5HT2C Receptor. Identification of a Novel ″Locked-on″ Phenotype and Double Revertant Mutations. J. Biol. Chem. 2002, 277, 36577– 36584,  DOI: 10.1074/jbc.M206223200

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    Conserved Helix 7 Tyrosine Acts as a Multistate Conformational Switch in the 5HT2C Receptor. Identification of a Novel "Locked-On" Phenotype and Double Revertant Mutations

    Prioleau, Cassandra; Visiers, Irache; Ebersole, Barbara J.; Weinstein, Harel; Sealfon, Stuart C.

    Journal of Biological Chemistry (2002), 277 (39), 36577-36584CODEN: JBCHA3; ISSN:0021-9258. (American Society for Biochemistry and Molecular Biology)

    Studies in many rhodopsin-like G-protein-coupled receptors are providing a general scheme of the structural processes underlying receptor activation. Microdomains in several receptors have been identified that appear to function as activation switches. However, evidence is emerging that these receptor proteins exist in multiple conformational states. To study the mol. control of this switching process, we investigated the function of a microdomain involving the conserved helix 7 tyrosine in the serotonin 5HT2C receptor. This tyrosine of the NPXXY motif was substituted for all naturally occurring amino acids. Three distinct constitutively active receptor phenotypes were found: moderate, high, and "locked-on" constitutive activity. In contrast to the activity of the other receptor mutants, the high basal signaling of the locked-on Y7.53N mutant was neither increased by agonists nor decreased by inverse agonists. The Y7.53F mutant was uncoupled. Computational modeling based on the rhodopsin crystal structure suggested that Y7.53 interacts with the conserved arom. ring at position 7.60 in the recently identified helix 8 domain. This provided a basis for seeking revertant mutations to correct the defective function of the Y7.53F receptor. When the Y7.53F receptor was mutated at position 7.60, the wild-type phenotype was restored. These results suggest that Y7.53 and Y7.60 contribute to a common functional microdomain connecting helixes 7 and 8 that influences the switching of the 5HT2C receptor among multiple active and inactive conformations.
48. 48

    Isberg, V.; Vroling, B.; van der Kant, R.; Li, K.; Vriend, G.; Gloriam, D. GPCRDB: An Information System for G Protein-Coupled Receptors. Nucleic Acids Res. 2014, 42, D422– 5,  DOI: 10.1093/nar/gkt1255

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    GPCRDB: an information system for G protein-coupled receptors

    Isberg, Vignir; Vroling, Bas; van der Kant, Rob; Li, Kang; Vriend, Gert; Gloriam, David

    Nucleic Acids Research (2014), 42 (D1), D422-D425CODEN: NARHAD; ISSN:0305-1048. (Oxford University Press)

    For the past 20 years, the GPCRDB (G protein-coupled receptors database; http://www.gpcr.org/7tm/) has been a one-stop shop' for G protein-coupled receptor (GPCR)-related data. The GPCRDB contains exptl. data on sequences, ligand-binding consts., mutations and oligomers, as well as many different types of computationally derived data, such as multiple sequence alignments and homol. models. The GPCRDB also provides visualization and anal. tools, plus a no. of query systems. In the latest GPCRDB release, all multiple sequence alignments, and >65 000 homol. models, have been significantly improved, thanks to a recent flurry of GPCR X-ray structure data. Tools were introduced to browse X-ray structures, compare binding sites, profile similar receptors and generate amino acid conservation statistics. Snake plots and helix box diagrams can now be custom colored (e.g. by chem. properties or mutation data) and saved as figures. A series of sequence alignment visualization tools has been added, and sequence alignments can now be created for subsets of sequences and sequence positions, and alignment statistics can be produced for any of these subsets.
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    Labute, P. Protonate3D: Assignment of Ionization States and Hydrogen Coordinates to Macromolecular Structures. Proteins: Struct., Funct., Genet. 2009, 75, 187– 205,  DOI: 10.1002/prot.22234

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    Protonate3D: assignment of ionization states and hydrogen coordinates to macromolecular structures

    Labute, Paul

    Proteins: Structure, Function, and Bioinformatics (2009), 75 (1), 187-205CODEN: PSFBAF ISSN:. (Wiley-Liss, Inc.)

    A new method, called Protonate3D, is presented for the automated prediction of hydrogen coordinates given the 3D coordinates of the heavy atoms of a macromol. structure. Protonate3D considers side-chain "flip," rotamer, tautomer, and ionization states of all chem. groups, ligands, and solvent, provided suitable templates are available in a parameter file. The energy model includes van der Waals, Coulomb, solvation, rotamer, tautomer, and titrn. effects. The results of computational validation expts. suggest that Protonate3D can accurately predict the location of hydrogen atoms in macromol. structures.
50. 50

    Gerber, P. R.; Muller, K. Mab, a Generally Applicable Molecular Force Field for Structure Modelling in Medicinal Chemistry. J. Comput.-Aided Mol. Des. 1995, 9, 251– 68,  DOI: 10.1007/BF00124456

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    MAB, a generally applicable molecular force field for structure modeling in medicinal chemistry

    Gerber, Paul R.; Mueller, Klaus

    Journal of Computer-Aided Molecular Design (1995), 9 (3), 251-68CODEN: JCADEQ; ISSN:0920-654X. (ESCOM)

    The math. formulation, parametrization scheme, and structural results of a new, generally applicable mol. force field are presented. The central features are a scheme for automatic parameter assignments, the consistent united-atom approxn., the absence of atom types other than elements, the replacement of electrostatic terms by geometrical hydrogen-bonding terms, the concomitant lack of a need for partial at. charge assignment and the strict adherence to a finite-range design. As a consequence of omitting all hydrogen atoms, optimal hydrogen-bond patterns are computed dynamically by appropriate network analyses. For a test set of 1589 structures, selected from the Cambridge Structural Database solely on the grounds of a given element list and criteria for high structure refinement, the agreements are on av. 2 pm for bonds, 2° for valence angles and 10 to 20 pm for the root-mean-square deviation of atom positions, depending somewhat on size and flexibility of the structures. More qual. testing of large-scale structural properties of the force field on proteins and DNA oligomers revealed satisfactory performance.
51. 51

    Cerutti, D. S.; Swope, W. C.; Rice, J. E.; Case, D. A. ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins. J. Chem. Theory Comput. 2014, 10, 4515– 4534,  DOI: 10.1021/ct500643c

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    ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins

    Cerutti, David S.; Swope, William C.; Rice, Julia E.; Case, David A.

    Journal of Chemical Theory and Computation (2014), 10 (10), 4515-4534CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)

    The authors present the ff14ipq force field, implementing the previously published IPolQ charge set for simulations of complete proteins. Minor modifications to the charge derivation scheme and van der Waals interactions between polar atoms are introduced. Torsion parameters are developed through a generational learning approach, based on gas-phase MP2/cc-pVTZ single-point energies computed of structures optimized by the force field itself rather than the quantum benchmark. In this manner, the authors sacrifice information about the true quantum min. to ensure that the force field maintains optimal agreement with the MP2/cc-pVTZ benchmark for the ensembles it will actually produce in simulations. A means of making the gas-phase torsion parameters compatible with soln.-phase IPolQ charges is presented. The ff14ipq model is an alternative to ff99SB and other Amber force fields for protein simulations in programs that accommodate pair-specific Lennard-Jones combining rules. The force field gives strong performance on α-helical and β-sheet oligopeptides as well as globular proteins over microsecond time scale simulations, although it has not yet been tested in conjunction with lipid and nucleic acid models. The authors' choices in parameter development influence the resulting force field and other choices that may have appeared reasonable would actually led to poorer results. The tools the authors developed may also aid in the development of future fixed-charge and even polarizable biomol. force fields.
52. 52

    Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S.; Windus, T. L.; Dupuis, M.; Montgomery, J. A. General Atomic and Molecular Electronic Structure System. J. Comput. Chem. 1993, 14, 1347– 1363,  DOI: 10.1002/jcc.540141112

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    General atomic and molecular electronic structure system

    Schmidt, Michael W.; Baldridge, Kim K.; Boatz, Jerry A.; Elbert, Steven T.; Gordon, Mark S.; Jensen, Jan H.; Koseki, Shiro; Matsunaga, Nikita; Nguyen, Kiet A.; et al.

    Journal of Computational Chemistry (1993), 14 (11), 1347-63CODEN: JCCHDD; ISSN:0192-8651.

    A description of the ab initio quantum chem. package GAMESS is presented. Chem. systems contg. atoms through Rn can be treated with wave functions ranging from the simplest closed-shell case up to a general MCSCF case, permitting calcns. at the necessary level of sophistication. Emphasis is given to novel features of the program. The parallelization strategy used in the RHF, ROHF, UHF, and GVB sections of the program is described, and detailed speedup results are given. Parallel calcns. can be run on ordinary workstations as well as dedicated parallel machines.
53. 53

    Yoshino, R.; Yasuo, N.; Inaoka, D. K.; Hagiwara, Y.; Ohno, K.; Orita, M.; Inoue, M.; Shiba, T.; Harada, S.; Honma, T.; Balogun, E. O.; da Rocha, J. R.; Montanari, C. A.; Kita, K.; Sekijima, M. Pharmacophore Modeling for Anti-Chagas Drug Design Using the Fragment Molecular Orbital Method. PLoS One 2015, 10, e0125829,  DOI: 10.1371/journal.pone.0125829

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    Pharmacophore modeling for anti-chagas drug design using the fragment molecular orbital method

    Yoshino, Ryunosuke; Yasuo, Nobuaki; Inaoka, Daniel Ken; Hagiwara, Yohsuke; Ohno, Kazuki; Orita, Masaya; Inoue, Masayuki; Shiba, Tomoo; Harada, Shigeharu; Honma, Teruki; Balogun, Emmanuel Oluwadare; Rocha, Josmar Rodrigues da; Montanari, Carlos Alberto; Kita, Kiyoshi; Sekijima, Masakazu

    PLoS One (2015), 10 (5), e0125829/1-e0125829/15CODEN: POLNCL; ISSN:1932-6203. (Public Library of Science)

    Background Chagas disease, caused by the parasite Trypanosoma cruzi, is a neglected tropical disease that causes severe human health problems. To develop a new chemotherapeutic agent for the treatment of Chagas disease, we predicted a pharmacophore model for T. cruzi dihydroorotate dehydrogenase (TcDHODH) by fragment MO (FMO) calcn. for orotate, oxonate, and 43 orotate derivs. Methodol./Principal Findings Intermol. interactions in the complexes of TcDHODH with orotate, oxonate, and 43 orotate derivs. were analyzed by FMO calcn. at the MP2/6-31G level. The results indicated that the orotate moiety, which is the base fragment of these compds., interacts with the Lys43, Asn67, and Asn194 residues of TcDHODH and the cofactor FMN (FMN), whereas functional groups introduced at the orotate 5-position strongly interact with the Lys214 residue. Conclusions/Significance FMO-based interaction energy analyses revealed a pharmacophore model for TcDHODH inhibitor. Hydrogen bond acceptor pharmacophores correspond to Lys43 and Lys214, hydrogen bond donor and acceptor pharmacophores correspond to Asn67 and Asn194, andthe arom. ring pharmacophore corresponds to FMN, which shows important characteristics of compds. that inhibit TcDHODH. In addn., the Lys214 residue is not conserved between TcDHODH and human DHODH. Our anal. suggests that these orotate derivs. should preferentially bind to TcDHODH, increasing their selectivity. Our results obtained by pharmacophore modeling provides insight into the structural requirements for the design of TcDHODH inhibitors and their development as new anti-Chagas drugs.
54. 54

    Hitaoka, S.; Chuman, H.; Yoshizawa, K. A Qsar Study on the Inhibition Mechanism of Matrix Metalloproteinase-12 by Arylsulfone Analogs Based on Molecular Orbital Calculations. Org. Biomol. Chem. 2015, 13, 793– 806,  DOI: 10.1039/C4OB01843E

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    A QSAR study on the inhibition mechanism of matrix metalloproteinase-12 by arylsulfone analogs based on molecular orbital calculations

    Hitaoka, Seiji; Chuman, Hiroshi; Yoshizawa, Kazunari

    Organic & Biomolecular Chemistry (2015), 13 (3), 793-806CODEN: OBCRAK; ISSN:1477-0520. (Royal Society of Chemistry)

    A binding mechanism between human matrix metalloproteinase-12 (MMP-12) and eight arylsulfone analogs having two types of carboxylic and hydroxamic acids as the most representative zinc binding group is investigated using a quant. structure-activity relationship (QSAR) anal. based on a linear expression by representative energy terms (LERE). The LERE-QSAR anal. quant. reveals that the variation in the obsd. (exptl.) inhibitory potency among the arylsulfone analogs is decisively governed by those in the intrinsic binding and dispersion interaction energies. The results show that the LERE-QSAR anal. not only can excellently reproduce the obsd. overall free-energy change but also can det. the contributions of representative free-energy changes. An inter-fragment interaction energy difference (IFIED) anal. based on the fragment MO (FMO) method (FMO-IFIED) leads to the identification of key residues governing the variation in the inhibitory potency as well as to the understanding of the difference between the interactions of the carboxylic and hydroxamic acid zinc binding groups. The current results that have led to the optimization of the inhibitory potency of arylsulfone analogs toward MMP-12 to be used in the treatment of chronic obstructive pulmonary disease may be useful for the development of a new potent MMP-12 inhibitor.
55. 55

    Fedorov, D. G.; Kitaura, K. Second Order Møller-Plesset Perturbation Theory Based Upon the Fragment Molecular Orbital Method. J. Chem. Phys. 2004, 121, 2483– 90,  DOI: 10.1063/1.1769362

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    Second order Moller-Plesset perturbation theory based upon the fragment molecular orbital method

    Fedorov, Dmitri G.; Kitaura, Kazuo

    Journal of Chemical Physics (2004), 121 (6), 2483-2490CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)

    The fragment MO (FMO) method was combined with the second order Moller-Plesset (MP2) perturbation theory. The accuracy of the method using the 6-31G* basis set was tested on (H2O)n, n = 16,32,64; α-helixes and β-strands of alanine n-mers, n = 10,20,40; as well as on (H2O)n, n = 16,32,64 using the 6-31++G** basis set. Relative to the regular MP2 results that could be afforded, the FMO2-MP2 error in the correlation energy did not exceed 0.003 a.u., the error in the correlation energy gradient did not exceed 0.000 05 a.u./bohr and the error in the correlation contribution to dipole moment did not exceed 0.03 debye. An approxn. reducing computational load based on fragment sepn. was introduced and tested. The FMO2-MP2 method demonstrated nearly linear scaling and drastically reduced the memory requirements of the regular MP2, making possible calcns. with several thousands basis functions using small Pentium clusters. As an example, (H2O)64 with the 6-31++G** basis set (1920 basis functions) can be run in 1 Gbyte RAM and it took 136 s on a 40-node Pentium4 cluster.
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    Isberg, V.; Mordalski, S.; Munk, C.; Rataj, K.; Harpsøe, K.; Hauser, A. S.; Vroling, B.; Bojarski, A. J.; Vriend, G.; Gloriam, D. E. GPCRDB: An Information System for G Protein-Coupled Receptors. Nucleic Acids Res. 2016, 44, D356– D364,  DOI: 10.1093/nar/gkv1178

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    56

    GPCRdb: an information system for G protein-coupled receptors

    Isberg, 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.
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    Munk, C.; Isberg, V.; Mordalski, S.; Harpsøe, K.; Rataj, K.; Hauser, A. S.; Kolb, P.; Bojarski, A. J.; Vriend, G.; Gloriam, D. E. GPCRdb: The G Protein-Coupled Receptor Database - an Introduction. Br. J. Pharmacol. 2016, 173, 2195– 2207,  DOI: 10.1111/bph.13509

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    GPCRdb: the G protein-coupled receptor database - an introduction

    Munk, 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.
58. 58

    Kobilka, B. K. G Protein Coupled Receptor Structure and Activation. Biochim. Biophys. Acta, Biomembr. 2007, 1768, 794– 807,  DOI: 10.1016/j.bbamem.2006.10.021

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    G protein coupled receptor structure and activation

    Kobilka, Brian K.

    Biochimica et Biophysica Acta, Biomembranes (2007), 1768 (4), 794-807CODEN: BBBMBS; ISSN:0005-2736. (Elsevier Ltd.)

    A review. G protein coupled receptors (GPCRs) are remarkably versatile signaling mols. The members of this large family of membrane proteins are activated by a spectrum of structurally diverse ligands, and have been shown to modulate the activity of different signaling pathways in a ligand specific manner. In this manuscript I will review what is known about the structure and mechanism of activation of GPCRs focusing primarily on two model systems, rhodopsin and the β2 adrenoceptor.
59. 59

    Latorraca, N. R.; Venkatakrishnan, A. J.; Dror, R. O. GPCR Dynamics: Structures in Motion. Chem. Rev. 2017, 117, 139– 155,  DOI: 10.1021/acs.chemrev.6b00177

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    GPCR Dynamics: Structures in Motion

    Latorraca, Naomi R.; Venkatakrishnan, A. J.; Dror, Ron O.

    Chemical Reviews (Washington, DC, United States) (2017), 117 (1), 139-155CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)

    A review. The function of G protein-coupled receptors (GPCRs), which represent the largest class of both human membrane proteins and drug targets, depends critically on their ability to change shape, transitioning among distinct conformations. Detg. the structural dynamics of GPCRs is thus essential both for understanding the physiol. of these receptors and for the rational design of GPCR-targeted drugs. Here, the authors review what is currently known about the flexibility and dynamics of GPCRs, as detd. through crystallog., spectroscopy, and computer simulations. The authors 1st provide an overview of the types of motion exhibited by a GPCR and then discuss GPCR dynamics in the context of ligand binding, activation, allosteric modulation, and biased signaling. Finally, the authors discuss the implications of GPCR conformational plasticity for drug design.
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    Dore, A. S.; Robertson, N.; Errey, J. C.; Ng, I.; Hollenstein, K.; Tehan, B.; Hurrell, E.; Bennett, K.; Congreve, M.; Magnani, F.; Tate, C. G.; Weir, M.; Marshall, F. H. Structure of the Adenosine A(2A) Receptor in Complex with ZM241385 and the Xanthines XAC and Caffeine. Structure 2011, 19, 1283– 93,  DOI: 10.1016/j.str.2011.06.014

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    Structure of the Adenosine A2A Receptor in Complex with ZM241385 and the Xanthines XAC and Caffeine

    Dore, Andrew S.; Robertson, Nathan; Errey, James C.; Ng, Irene; Hollenstein, Kaspar; Tehan, Ben; Hurrell, Edward; Bennett, Kirstie; Congreve, Miles; Magnani, Francesca; Tate, Christopher G.; Weir, Malcolm; Marshall, Fiona H.

    Structure (Cambridge, MA, United States) (2011), 19 (9), 1283-1293CODEN: STRUE6; ISSN:0969-2126. (Cell Press)

    Methylxanthines, including caffeine and theophylline, are among the most widely consumed stimulant drugs in the world. These effects are mediated primarily via blockade of adenosine receptors. Xanthine analogs with improved properties have been developed as potential treatments for diseases such as Parkinson's disease. Here we report the structures of a thermostabilized adenosine A2A receptor in complex with the xanthines xanthine amine congener and caffeine, as well as the A2A selective inverse agonist ZM241385. The receptor is crystd. in the inactive state conformation as defined by the presence of a salt bridge known as the ionic lock. The complete third intracellular loop, responsible for G protein coupling, is visible consisting of extended helixes 5 and 6. The structures provide new insight into the features that define the ligand binding pocket of the adenosine receptor for ligands of diverse chemotypes as well as the cytoplasmic regions that interact with signal transduction proteins.
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    Sloop, K. W.; Emmerson, P. J.; Statnick, M. A.; Willard, F. S. The Current State of GPCR-Based Drug Discovery to Treat Metabolic Disease. Br. J. Pharmacol. 2018, 175, 4060– 4071,  DOI: 10.1111/bph.14157

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    The current state of GPCR-based drug discovery to treat metabolic disease

    Sloop, Kyle W.; Emmerson, Paul J.; Statnick, Michael A.; Willard, Francis S.

    British Journal of Pharmacology (2018), 175 (21), 4060-4071CODEN: BJPCBM; ISSN:1476-5381. (Wiley-Blackwell)

    One approach of modern drug discovery is to identify agents that enhance or diminish signal transduction cascades in various cell types and tissues by modulating the activity of GPCRs. This strategy has resulted in the development of new medicines to treat many conditions, including cardiovascular disease, psychiatric disorders, HIV/AIDS, certain forms of cancer and Type 2 diabetes mellitus (T2DM). These successes justify further pursuit of GPCRs as disease targets and provide key learning that should help guide identifying future therapeutic agents. This report reviews the current landscape of GPCR drug discovery with emphasis on efforts aimed at developing new mols. for treating T2DM and obesity. We analyze historical efforts to generate GPCR-based drugs to treat metabolic disease in terms of causal factors leading to success and failure in this endeavour.
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    Venkatakrishnan, A. J.; Ma, A. K.; Fonseca, R.; Latorraca, N. R.; Kelly, B.; Betz, R. M.; Asawa, C.; Kobilka, B. K.; Dror, R. O. Diverse GPCRs Exhibit Conserved Water Networks for Stabilization and Activation. Proc. Natl. Acad. Sci. U. S. A. 2019, 116, 3288– 3293,  DOI: 10.1073/pnas.1809251116

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    62

    Diverse GPCRs exhibit conserved water networks for stabilization and activation

    Venkatakrishnan, A. J.; Ma, Anthony K.; Fonseca, Rasmus; Latorraca, Naomi R.; Kelly, Brendan; Betz, Robin M.; Asawa, Chaitanya; Kobilka, Brian K.; Dror, Ron O.

    Proceedings of the National Academy of Sciences of the United States of America (2019), 116 (8), 3288-3293CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)

    G protein-coupled receptors (GPCRs) have evolved to recognize incredibly diverse extracellular ligands while sharing a common architecture and structurally conserved intracellular signaling partners. It remains unclear how binding of diverse ligands brings about GPCR activation, the common structural change that enables intracellular signaling. Here, we identify highly conserved networks of water-mediated interactions that play a central role in activation. Using at.-level simulations of diverse GPCRs, we show that most of the water mols. in GPCR crystal structures are highly mobile. Several water mols. near the G protein-coupling interface, however, are stable. These water mols. form two kinds of polar networks that are conserved across diverse GPCRs: (i) a network that is maintained across the inactive and the active states and (ii) a network that rearranges upon activation. Comparative anal. of GPCR crystal structures independently confirms the striking conservation of water-mediated interaction networks. These conserved water-mediated interactions near the G protein-coupling region, along with diverse water-mediated interactions with extracellular ligands, have direct implications for structure-based drug design and GPCR engineering.
63. 63

    Rovati, G. E.; Capra, V.; Neubig, R. R. The Highly Conserved DRY Motif of Class a G Protein-Coupled Receptors: Beyond the Ground State. Mol. Pharmacol. 2007, 71, 959– 64,  DOI: 10.1124/mol.106.029470

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    63

    The highly conserved DRY motif of class A G protein-coupled receptors: beyond the ground state

    Rovati, G. Enrico; Capra, Valerie; Neubig, Richard R.

    Molecular Pharmacology (2007), 71 (4), 959-964CODEN: MOPMA3; ISSN:0026-895X. (American Society for Pharmacology and Experimental Therapeutics)

    A review. Despite extensive study of heptahelical G protein-coupled receptors (GPCRs), the precise mechanism of G protein activation is unknown. The role of one highly conserved stretch of residues, the amino acids glutamic acid/aspartic acid-arginine-tyrosine (i.e., the E/DRY motif), has received considerable attention with respect to regulating GPCR conformational states. In the consensus view, glutamic acid/aspartic acid maintains the receptor in its ground state, because mutations frequently induce constitutive activity (CA). This hypothesis has been confirmed by the rhodopsin ground-state crystal structure and by computational modeling approaches. However, some class A GPCRs are resistant to CA, suggesting alternative roles for the glutamic acid/aspartic acid residue and the E/DRY motif. Here, we propose two different subgroups of receptors within class A GPCRs that make different use of the E/DRY motif, independent of the G protein type (Gs, Gi, or Gq) to which the receptor couples. In phenotype 1 receptors, nonconservative mutations of the glutamic acid/aspartic acid-arginine residues, besides inducing CA, increase affinity for agonist binding, retain G protein coupling, and retain an agonist-induced response. In contrast, in second phenotype receptors, the E/DRY motif is more directly involved in governing receptor conformation and G protein coupling/recognition. Hence, mutations of the glutamic acid/aspartic acid residues do not induce CA. Conversely, nonconservative mutations of the arginine of the E/DRY motif always impair agonist-induced receptor responses and, generally, reduce agonist binding affinity. Thus, it is essential to look beyond the rhodopsin ground-state model of conformational activation to clarify the role of this highly conserved triplet in GPCR activation and function.
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    Zarzycka, B.; Zaidi, S. A.; Roth, B. L.; Katritch, V. Harnessing Ion-Binding Sites for GPCR Pharmacology. Pharmacol. Rev. 2019, 71, 571– 595,  DOI: 10.1124/pr.119.017863

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    Harnessing ion-binding sites for GPCR pharmacology

    Zarzycka, Barbara; Zaidi, Saheem A.; Roth, Bryan L.; Katritch, Vsevolod

    Pharmacological Reviews (2019), 71 (4), 571-595CODEN: PAREAQ; ISSN:1521-0081. (American Society for Pharmacology and Experimental Therapeutics)

    A review. Endogenous ions play important roles in the function and pharmacol. of G-protein coupled receptors (GPCRs). Since then, numerous studies documenting the effects of mono- and divalent ions on GPCR function have been published. While ions can act selectively and nonselectively at many sites in different receptors, the discovery of the conserved sodium ion site in class A GPCR structures in 2012 revealed the unique nature of Na1 site, which has emerged as a near-universal site for allosteric modulation of class A GPCR structure and function. In this review, we synthesize and highlight recent advances in the functional, biophys., and structural characterization of ions bound to GPCRs. Taken together, these findings provide a mol. understanding of the unique roles of Na1 and other ions as GPCR allosteric modulators. Wewill also discuss how this knowledge can be applied to the redesign of receptors and ligand probes for desired functional and pharmacol. profiles. Significance Statement--The function and pharmacol. of GPCRs strongly depend on the presence of mono and divalent ions in exptl. assays and in living organisms. Recent insights into the mol. mechanism of this ion-dependent allosterism from structural, biophys., biochem., and computational studies provide quant. understandings of the pharmacol. effects of drugs in vitro and in vivo and open new avenues for the rational design of chem. probes and drug candidates with improved properties.
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    Katritch, V.; Fenalti, G.; Abola, E. E.; Roth, B. L.; Cherezov, V.; Stevens, R. C. Allosteric Sodium in Class A GPCR Signaling. Trends Biochem. Sci. 2014, 39, 233– 44,  DOI: 10.1016/j.tibs.2014.03.002

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    65

    Allosteric sodium in class A GPCR signaling

    Katritch, Vsevolod; Fenalti, Gustavo; Abola, Enrique E.; Roth, Bryan L.; Cherezov, Vadim; Stevens, Raymond C.

    Trends in Biochemical Sciences (2014), 39 (5), 233-244CODEN: TBSCDB; ISSN:0968-0004. (Elsevier Ltd.)

    A review. Despite their functional and structural diversity, G-protein-coupled receptors (GPCRs) share a common mechanism of signal transduction via conformational changes in the seven-transmembrane (7TM) helical domain. New major insights into this mechanism come from the recent crystallog. discoveries of a partially hydrated sodium ion that is specifically bound in the middle of the 7TM bundle of multiple class A GPCRs. This review discusses the remarkable structural conservation and distinct features of the Na+ pocket in this most populous GPCR class, as well as the conformational collapse of the pocket upon receptor activation. New insights help to explain allosteric effects of sodium on GPCR agonist binding and activation, and sodium's role as a potential co-factor in class A GPCR function.
66. 66

    Massink, A.; Gutierrez-de-Teran, H.; Lenselink, E. B.; Ortiz Zacarias, N. V.; Xia, L.; Heitman, L. H.; Katritch, V.; Stevens, R. C.; Ijzerman, A. P. Sodium Ion Binding Pocket Mutations and Adenosine A2A Receptor Function. Mol. Pharmacol. 2015, 87, 305– 13,  DOI: 10.1124/mol.114.095737

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    Sodium ion binding pocket mutations and adenosine A2A receptor function

    Massink, Arnault; Gutierrez-de-Teran, Hugo; Lenselink, Eelke B.; Zacarias, Natalia V.; Xia, Lizi; Heitman, Laura H.; Katritch, Vsevolod; Stevens, Raymond C.; Ijzerman, Adriaan P.

    Molecular Pharmacology (2015), 87 (2), 305-313, 9 pp.CODEN: MOPMA3; ISSN:1521-0111. (American Society for Pharmacology and Experimental Therapeutics)

    Recently we identified a sodium ion binding pocket in a high-resoln. structure of the human adenosine A2A receptor. In the present study we explored this binding site through site-directed mutagenesis and mol. dynamics simulations. Amino acids in the pocket were mutated to alanine, and their influence on agonist and antagonist affinity, allosterism by sodium ions and amilorides, and receptor functionality was explored. Mutation of the polar residues in the Na+ pocket were shown to either abrogate (D52A2.50 and N284A7.49) or reduce (S91A3.39, W246A6.48, and N280A7.45) the neg. allosteric effect of sodium ions on agonist binding. Mutations D52A2.50 and N284A7.49 completely abolished receptor signaling, whereas mutations S91A3.39 and N280A7.45 elevated basal activity and mutations S91A3.39, W246A6.48, and N280A7.45 decreased agonist-stimulated receptor signaling. In mol. dynamics simulations D52A2.50 directly affected the mobility of sodium ions, which readily migrated to another pocket formed by Glu131.39 and His2787.43. The D52A2.50 mutation also decreased the potency of amiloride with respect to ligand displacement but did not change orthosteric ligand affinity. In contrast, W246A6.48 increased some of the allosteric effects of sodium ions and amiloride, whereas orthosteric ligand binding was decreased. These new findings suggest that the sodium ion in the allosteric binding pocket not only impacts ligand affinity but also plays a vital role in receptor signaling. Because the sodium ion binding pocket is highly conserved in other class A G protein-coupled receptors, our findings may have a general relevance for these receptors and may guide the design of novel synthetic allosteric modulators or bitopic ligands.