ACS Publications. Most Trusted. Most Cited. Most Read

OR SEARCH CITATIONS

My Activity
Publications
CONTENT TYPES

Figure 1Loading Img
Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Am. Chem. Soc. 2021, 143, 14, 5497-5507
RETURN TO ISSUEPREVArticleNEXT

Genetically Encoded Fragment-Based Discovery from Phage-Displayed Macrocyclic Libraries with Genetically Encoded Unnatural Pharmacophores

  • Arunika I. Ekanayake
    Arunika I. Ekanayake
    Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
    More by Arunika I. Ekanayake
  • , 
  • Lena Sobze
    Lena Sobze
    Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
    More by Lena Sobze
  • , 
  • Payam Kelich
    Payam Kelich
    Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas 79968, United States
    More by Payam Kelich
  • , 
  • Jihea Youk
    Jihea Youk
    Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
    More by Jihea Youk
  • , 
  • Nicholas J. Bennett
    Nicholas J. Bennett
    Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
    More by Nicholas J. Bennett
  • , 
  • Raja Mukherjee
    Raja Mukherjee
    Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
    More by Raja Mukherjee
  • , 
  • Atul Bhardwaj
    Atul Bhardwaj
    Cross Cancer Institute, University of Alberta, Edmonton, AB T6G 1Z2, Canada
    More by Atul Bhardwaj
  • , 
  • Frank Wuest
    Frank Wuest
    Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
    Cross Cancer Institute, University of Alberta, Edmonton, AB T6G 1Z2, Canada
    More by Frank Wuest
    Orcidhttp://orcid.org/0000-0002-6705-6450
  • , 
  • Lela Vukovic
    Lela Vukovic
    Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas 79968, United States
    More by Lela Vukovic
    Orcidhttp://orcid.org/0000-0002-9053-5708
  • , and 
  • Ratmir Derda*
    Ratmir Derda
    Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
    *Email: [email protected]
    More by Ratmir Derda
    Orcidhttp://orcid.org/0000-0003-1365-6570
Cite this: J. Am. Chem. Soc. 2021, 143, 14, 5497–5507
Publication Date (Web):March 30, 2021
https://doi.org/10.1021/jacs.1c01186
Copyright © 2021 American Chemical Society
Request reuse permissions

    Article Views

    6877

    Altmetric

    -

    Citations

    21
    LEARN ABOUT THESE METRICS
    Read OnlinePDF (5 MB)
    Get e-Alerts
    Supporting Info (3)»
    SUBJECTS:

    Abstract

    Abstract Image

    Genetically encoded macrocyclic peptide libraries with unnatural pharmacophores are valuable sources for the discovery of ligands for many targets of interest. Traditionally, generation of such libraries employs “early stage” incorporation of unnatural building blocks into the chemically or translationally produced macrocycles. Here, we describe a divergent late-stage approach to such libraries starting from readily available starting material: genetically encoded libraries of peptides. A diketone linchpin 1,5-dichloropentane-2,4-dione converts peptide libraries displayed on phage to 1,3-diketone bearing macrocyclic peptides (DKMP): shelf-stable precursors for Knorr pyrazole synthesis. Ligation of diverse hydrazine derivatives onto DKMP libraries displayed on phage that carries silent DNA-barcodes yields macrocyclic libraries in which the amino acid sequence and the pharmacophore are encoded by DNA. Selection of this library against carbonic anhydrase enriched macrocycles with benzenesulfonamide pharmacophore and nanomolar Kd. The methodology described in this manuscript can graft diverse pharmacophores into many existing genetically encoded phage libraries and significantly increase the value of such libraries in molecular discoveries.

    Supporting Information

    ARTICLE SECTIONS
    Jump To

    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/jacs.1c01186.

    • Detailed synthetic methods, biochemical methods describing the synthesis and selection of phage libraries, isothermal titration calorimetry (ITC) assay or protein–ligand binding, data processing methods describing the analysis of the DNA sequencing data, statistical methods, and computational calculations and predictions for bovine carbonic anhydrase (BCA)-macrocycle binding and solution conformations of the macrocycles (PDF)

    • LCMS monitoring of byproduct generation, NMR spectra of byproduct with peptide 3b, synthesis and characterization of diketone and extra products from EDT (PDF)

    • Source data: submitted as “data.zip” contain files describing “Kinetics Matlab” directory with raw data used to monitor the kinetics of reactions and MatLab scripts for curve fit; “Sequence files” directory with *.txt files describing the raw deep-sequencing data, *.xlsx tables describing the silent barcoding, *.xlsx tables describing the differential enrichment (DE) analysis; Supplementary Files S1 and S2 describing the output of differential enrichment analysis and clustering; Titers.xlsx describing the phage titers (PFU) for all experiments described in this manuscript; .gif file showing the binding pose of sa-SFCDTYC:BCA (ZIP)

    Accession Codes

    CCDC 2001271 contains the supplementary crystallographic data for this paper. These data can be obtained free of charge via www.ccdc.cam.ac.uk/data_request/cif, or by emailing [email protected], or by contacting The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK; fax: +44 1223 336033.

    Terms & Conditions

    Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.

    Cited By

    This article is cited by 21 publications.

    1. Rafael Alcala-Torano, Mariha Islam, Jaclyn Cika, Kwok Ho Lam, Rongsheng Jin, Konstantin Ichtchenko, Charles B. Shoemaker, James A. Van Deventer. Yeast Display Enables Identification of Covalent Single-Domain Antibodies against Botulinum Neurotoxin Light Chain A. ACS Chemical Biology 2022, 17 (12) , 3435-3449. https://doi.org/10.1021/acschembio.2c00574
    2. Guilherme M. Lima, Alexey Atrazhev, Susmita Sarkar, Mirat Sojitra, Revathi Reddy, Karin Torres-Obreque, Carlota de Oliveira Rangel-Yagui, Matthew S. Macauley, Gisele Monteiro, Ratmir Derda. DNA-Encoded Multivalent Display of Chemically Modified Protein Tetramers on Phage: Synthesis and in Vivo Applications. ACS Chemical Biology 2022, 17 (11) , 3024-3035. https://doi.org/10.1021/acschembio.1c00835
    3. Xinting Li, Timothy W. Craven, Paul M. Levine. Cyclic Peptide Screening Methods for Preclinical Drug Discovery. Journal of Medicinal Chemistry 2022, 65 (18) , 11913-11926. https://doi.org/10.1021/acs.jmedchem.2c01077
    4. Andrei A. Golosov Alec N. Flyer Lauren G. Monovich . Design and Discovery of Orally Bioavailable Macrocycles: Toward Orally Bioavailable Peptide Therapeutics. , 199-222. https://doi.org/10.1021/bk-2022-1417.ch008
    5. Rajeshwer Vanjari, Deepanjan Panda, Shaswati Mandal, Ganga B. Vamisetti, Ashraf Brik. Gold(I)-Mediated Rapid Cyclization of Propargylated Peptides via Imine Formation. Journal of the American Chemical Society 2022, 144 (11) , 4966-4976. https://doi.org/10.1021/jacs.1c12906
    6. Titia Rixt Oppewal, Ivar D. Jansen, Johan Hekelaar, Clemens Mayer. A Strategy to Select Macrocyclic Peptides Featuring Asymmetric Molecular Scaffolds as Cyclization Units by Phage Display. Journal of the American Chemical Society 2022, 144 (8) , 3644-3652. https://doi.org/10.1021/jacs.1c12822
    7. Xin Chu, Linhua Shen, Bo Li, Peng Yang, Chengzhuo Du, Xiaoye Wang, Gang He, Samir Messaoudi, Gong Chen. Construction of Peptide Macrocycles via Palladium-Catalyzed Multiple S-Arylation: An Effective Strategy to Expand the Structural Diversity of Cross-Linkers. Organic Letters 2021, 23 (20) , 8001-8006. https://doi.org/10.1021/acs.orglett.1c03003
    8. Jeffrey Y. K. Wong, Arunika I. Ekanayake, Serhii Kharchenko, Steven E. Kirberger, Ryan Qiu, Payam Kelich, Susmita Sarkar, Jianqian Li, Kleinberg X. Fernandez, Edgar R. Alvizo-Paez, Jiayuan Miao, Shiva Kalhor-Monfared, J. Dwyer John, Hongsuk Kang, Hwanho Choi, John M. Nuss, John C. Vederas, Yu-Shan Lin, Matthew S. Macauley, Lela Vukovic, William C. K. Pomerantz, Ratmir Derda. Genetically encoded discovery of perfluoroaryl macrocycles that bind to albumin and exhibit extended circulation in vivo. Nature Communications 2023, 14 (1) https://doi.org/10.1038/s41467-023-41427-y
    9. Payam Kelich, Huanhuan Zhao, Jose R. Orona, Lela Vuković. BinderSpace : A package for sequence space analyses for datasets of affinity‐selected oligonucleotides and peptide‐based molecules. Journal of Computational Chemistry 2023, 44 (22) , 1836-1844. https://doi.org/10.1002/jcc.27130
    10. Joshua Trae Hampton, Chia-Chuan Dean Cho, Demonta D Coleman, Zhi Zachary Geng, Peng-Hsun Chase Chen, Gopal K Dubey, Lauralee D Sylvain, Shiqing Xu, Wenshe Ray Liu. An amber-encoding helper phage for more efficient phage display of noncanonical amino acids. Nucleic Acids Research 2023, 51 (13) , 6566-6577. https://doi.org/10.1093/nar/gkad488
    11. Millicent Dockerill, Nicolas Winssinger. DNA‐Encoded Libraries: Towards Harnessing their Full Power with Darwinian Evolution. Angewandte Chemie 2023, 135 (9) https://doi.org/10.1002/ange.202215542
    12. Millicent Dockerill, Nicolas Winssinger. DNA‐Encoded Libraries: Towards Harnessing their Full Power with Darwinian Evolution. Angewandte Chemie International Edition 2023, 62 (9) https://doi.org/10.1002/anie.202215542
    13. Michael Kugler, Martin Hadzima, Rastislav Dzijak, Robert Rampmaier, Pavel Srb, Lukáš Vrzal, Zdeněk Voburka, Pavel Majer, Pavlína Řezáčová, Milan Vrabel. Identification of specific carbonic anhydrase inhibitors via in situ click chemistry, phage-display and synthetic peptide libraries: comparison of the methods and structural study. RSC Medicinal Chemistry 2023, 14 (1) , 144-153. https://doi.org/10.1039/D2MD00330A
    14. Arlinda Rezhdo, Catherine T Lessard, Mariha Islam, James A Van Deventer. Strategies for enriching and characterizing proteins with inhibitory properties on the yeast surface. Protein Engineering, Design and Selection 2023, 36 https://doi.org/10.1093/protein/gzac017
    15. Simon Hansen, Yingnan Zhang, Sunhee Hwang, Ahmad Nabhan, Wanqing Li, Jakob Fuhrmann, Yvonne Kschonsak, Lijuan Zhou, Aaron H. Nile, Xinxin Gao, Robert Piskol, Felipe de Sousa e Melo, Frederic J. de Sauvage, Rami N. Hannoush. Directed evolution identifies high-affinity cystine-knot peptide agonists and antagonists of Wnt/β-catenin signaling. Proceedings of the National Academy of Sciences 2022, 119 (46) https://doi.org/10.1073/pnas.2207327119
    16. Grace L. Allen, Ashley K. Grahn, Katerina Kourentzi, Richard C. Willson, Sean Waldrop, Jiantao Guo, Brian K. Kay. Expanding the chemical diversity of M13 bacteriophage. Frontiers in Microbiology 2022, 13 https://doi.org/10.3389/fmicb.2022.961093
    17. Paddy R. A. Melsen, Ryoji Yoshisada, Seino A. K. Jongkees. Opportunities for Expanding Encoded Chemical Diversification and Improving Hit Enrichment in mRNA‐Displayed Peptide Libraries. ChemBioChem 2022, 23 (12) https://doi.org/10.1002/cbic.202100685
    18. Ming Gao, Bao-Bao Yu, Chen Jia, Zhu-Jun Yao. Cytotoxic analogues of marine diterpenoid plumisclerin A by shifting the lipophilic branch on the characteristic tricyclic core. Organic & Biomolecular Chemistry 2022, 20 (22) , 4553-4558. https://doi.org/10.1039/D2OB00539E
    19. Louise Plais, Jörg Scheuermann. Macrocyclic DNA-encoded chemical libraries: a historical perspective. RSC Chemical Biology 2022, 3 (1) , 7-17. https://doi.org/10.1039/D1CB00161B
    20. Kristina Hetherington, Som Dutt, Amaurys A. Ibarra, Emma E. Cawood, Fruzsina Hobor, Derek N. Woolfson, Thomas A. Edwards, Adam Nelson, Richard B. Sessions, Andrew J. Wilson. Towards optimizing peptide-based inhibitors of protein–protein interactions: predictive saturation variation scanning (PreSaVS). RSC Chemical Biology 2021, 2 (5) , 1474-1478. https://doi.org/10.1039/D1CB00137J
    21. Christian Heinis. Combining biological and chemical diversity. Nature Chemistry 2021, 13 (6) , 512-513. https://doi.org/10.1038/s41557-021-00722-1
    Download PDF

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    You’ve supercharged your research process with ACS and Mendeley!

    STEP 1:
    Click to create an ACS ID

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    MENDELEY PAIRING EXPIRED
    Your Mendeley pairing has expired. Please reconnect