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Wu Y, Qian R, Yang Y, Sheng Y, Li W, Wang W. Activation Pathways and Free Energy Landscapes of the SARS-CoV-2 Spike Protein. ACS OMEGA 2021; 6:23432-23441. [PMID: 34514271 PMCID: PMC8424691 DOI: 10.1021/acsomega.1c03384] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/24/2021] [Indexed: 05/09/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses a spike protein (S-protein) to recognize the receptor protein ACE2 of human cells and initiate infection, during which the conformational transition of the S-protein from inactive (down) state to active (up) state is one of the key molecular events determining the infectivity but the underlying mechanism remains poorly understood. In this work, we investigated the activation pathways and free energy landscape of the S-protein of SARS-CoV-2 and compared with those of the closely related counterpart SARS-CoV using molecular dynamics simulations. Our results revealed a large difference between the activation pathways of the two S-proteins. The transition from inactive to an active state for the S-protein of SARS-CoV-2 is more cooperative, involving simultaneous disruptions of several key interfacial hydrogen bonds, and the transition encounters a much higher free energy barrier. In addition, the conformational equilibrium of the SARS-CoV-2 S-protein is more biased to the inactive state compared to that of the SARS-CoV S-protein, suggesting the transient feature of the active state before binding to the receptor protein of the host cell. The key interactions contributing to the difference of the activation pathways and free energy landscapes were discussed. The results provide insights into the molecular mechanism involved in the initial stage of the SARS-CoV-2 infection.
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Affiliation(s)
- Yichao Wu
- Department of Physics, National
Laboratory of Solid State Microstructure, Nanjing University, Nanjing 210093, China
| | - Ruixin Qian
- Department of Physics, National
Laboratory of Solid State Microstructure, Nanjing University, Nanjing 210093, China
| | - Yan Yang
- Department of Physics, National
Laboratory of Solid State Microstructure, Nanjing University, Nanjing 210093, China
| | - Yuebiao Sheng
- Department of Physics, National
Laboratory of Solid State Microstructure, Nanjing University, Nanjing 210093, China
| | - Wenfei Li
- Department of Physics, National
Laboratory of Solid State Microstructure, Nanjing University, Nanjing 210093, China
| | - Wei Wang
- Department of Physics, National
Laboratory of Solid State Microstructure, Nanjing University, Nanjing 210093, China
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Muratov EN, Amaro R, Andrade CH, Brown N, Ekins S, Fourches D, Isayev O, Kozakov D, Medina-Franco JL, Merz KM, Oprea TI, Poroikov V, Schneider G, Todd MH, Varnek A, Winkler DA, Zakharov AV, Cherkasov A, Tropsha A. A critical overview of computational approaches employed for COVID-19 drug discovery. Chem Soc Rev 2021; 50:9121-9151. [PMID: 34212944 PMCID: PMC8371861 DOI: 10.1039/d0cs01065k] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Indexed: 01/18/2023]
Abstract
COVID-19 has resulted in huge numbers of infections and deaths worldwide and brought the most severe disruptions to societies and economies since the Great Depression. Massive experimental and computational research effort to understand and characterize the disease and rapidly develop diagnostics, vaccines, and drugs has emerged in response to this devastating pandemic and more than 130 000 COVID-19-related research papers have been published in peer-reviewed journals or deposited in preprint servers. Much of the research effort has focused on the discovery of novel drug candidates or repurposing of existing drugs against COVID-19, and many such projects have been either exclusively computational or computer-aided experimental studies. Herein, we provide an expert overview of the key computational methods and their applications for the discovery of COVID-19 small-molecule therapeutics that have been reported in the research literature. We further outline that, after the first year the COVID-19 pandemic, it appears that drug repurposing has not produced rapid and global solutions. However, several known drugs have been used in the clinic to cure COVID-19 patients, and a few repurposed drugs continue to be considered in clinical trials, along with several novel clinical candidates. We posit that truly impactful computational tools must deliver actionable, experimentally testable hypotheses enabling the discovery of novel drugs and drug combinations, and that open science and rapid sharing of research results are critical to accelerate the development of novel, much needed therapeutics for COVID-19.
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Affiliation(s)
- Eugene N. Muratov
- UNC Eshelman School of Pharmacy, University of North CarolinaChapel HillNCUSA
| | - Rommie Amaro
- University of California in San DiegoSan DiegoCAUSA
| | | | | | - Sean Ekins
- Collaborations PharmaceuticalsRaleighNCUSA
| | - Denis Fourches
- Department of Chemistry, North Carolina State UniversityRaleighNCUSA
| | - Olexandr Isayev
- Department of Chemistry, Carnegie Melon UniversityPittsburghPAUSA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook UniversityStony BrookNYUSA
| | | | - Kenneth M. Merz
- Department of Chemistry, Michigan State UniversityEast LansingMIUSA
| | - Tudor I. Oprea
- Department of Internal Medicine and UNM Comprehensive Cancer Center, University of New Mexico, AlbuquerqueNMUSA
- Department of Rheumatology and Inflammation Research, Gothenburg UniversitySweden
- Novo Nordisk Foundation Center for Protein Research, University of CopenhagenDenmark
| | | | - Gisbert Schneider
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of TechnologyZurichSwitzerland
| | | | - Alexandre Varnek
- Department of Chemistry, University of StrasbourgStrasbourgFrance
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido UniversitySapporoJapan
| | - David A. Winkler
- Monash Institute of Pharmaceutical Sciences, Monash UniversityMelbourneVICAustralia
- School of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe UniversityBundooraAustralia
- School of Pharmacy, University of NottinghamNottinghamUK
| | | | - Artem Cherkasov
- Vancouver Prostate Centre, University of British ColumbiaVancouverBCCanada
| | - Alexander Tropsha
- UNC Eshelman School of Pharmacy, University of North CarolinaChapel HillNCUSA
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Sztain T, Ahn SH, Bogetti AT, Casalino L, Goldsmith JA, Seitz E, McCool RS, Kearns FL, Acosta-Reyes F, Maji S, Mashayekhi G, McCammon JA, Ourmazd A, Frank J, McLellan JS, Chong LT, Amaro RE. A glycan gate controls opening of the SARS-CoV-2 spike protein. Nat Chem 2021; 13:963-968. [PMID: 34413500 PMCID: PMC8488004 DOI: 10.1038/s41557-021-00758-3] [Citation(s) in RCA: 202] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/21/2021] [Indexed: 12/18/2022]
Abstract
SARS-CoV-2 infection is controlled by the opening of the spike protein receptor binding domain (RBD), which transitions from a glycan-shielded 'down' to an exposed 'up' state to bind the human angiotensin-converting enzyme 2 receptor and infect cells. While snapshots of the 'up' and 'down' states have been obtained by cryo-electron microscopy and cryo-electron tomagraphy, details of the RBD-opening transition evade experimental characterization. Here over 130 µs of weighted ensemble simulations of the fully glycosylated spike ectodomain allow us to characterize more than 300 continuous, kinetically unbiased RBD-opening pathways. Together with ManifoldEM analysis of cryo-electron microscopy data and biolayer interferometry experiments, we reveal a gating role for the N-glycan at position N343, which facilitates RBD opening. Residues D405, R408 and D427 also participate. The atomic-level characterization of the glycosylated spike activation mechanism provided herein represents a landmark study for ensemble pathway simulations and offers a foundation for understanding the fundamental mechanisms of SARS-CoV-2 viral entry and infection.
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Affiliation(s)
- Terra Sztain
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, USA
| | - Surl-Hee Ahn
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, USA
| | - Anthony T Bogetti
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, USA
| | - Jory A Goldsmith
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Evan Seitz
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Ryan S McCool
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Fiona L Kearns
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, USA
| | - Francisco Acosta-Reyes
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA
| | - Suvrajit Maji
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA
| | - Ghoncheh Mashayekhi
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, USA.,Department of Pharmacology, University of California-San Diego, La Jolla, CA, USA
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Joachim Frank
- Department of Biological Sciences, Columbia University, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Lillian T Chong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, USA.
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Sztain T, Ahn SH, Bogetti AT, Casalino L, Goldsmith JA, Seitz E, McCool RS, Kearns FL, Acosta-Reyes F, Maji S, Mashayekhi G, McCammon JA, Ourmazd A, Frank J, McLellan JS, Chong LT, Amaro RE. A glycan gate controls opening of the SARS-CoV-2 spike protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.15.431212. [PMID: 33619492 PMCID: PMC7899456 DOI: 10.1101/2021.02.15.431212] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2 infection is controlled by the opening of the spike protein receptor binding domain (RBD), which transitions from a glycan-shielded "down" to an exposed "up" state in order to bind the human ACE2 receptor and infect cells. While snapshots of the "up" and "down" states have been obtained by cryoEM and cryoET, details of the RBD opening transition evade experimental characterization. Here, over 130 μs of weighted ensemble (WE) simulations of the fully glycosylated spike ectodomain allow us to characterize more than 300 continuous, kinetically unbiased RBD opening pathways. Together with ManifoldEM analysis of cryo-EM data and biolayer interferometry experiments, we reveal a gating role for the N-glycan at position N343, which facilitates RBD opening. Residues D405, R408, and D427 also participate. The atomic-level characterization of the glycosylated spike activation mechanism provided herein achieves a new high-water mark for ensemble pathway simulations and offers a foundation for understanding the fundamental mechanisms of SARS-CoV-2 viral entry and infection.
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Affiliation(s)
- Terra Sztain
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA 92093
| | - Surl-Hee Ahn
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA 92093
| | | | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA 92093
| | - Jory A. Goldsmith
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Evan Seitz
- Department of Biological Sciences, Columbia University, New York, NY, 10032, USA
| | - Ryan S. McCool
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Fiona L. Kearns
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA 92093
| | - Francisco Acosta-Reyes
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Suvrajit Maji
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Ghoncheh Mashayekhi
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI 53211, USA
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA 92093
- Department of Pharmacology, UC San Diego, La Jolla, CA 92093
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI 53211, USA
| | - Joachim Frank
- Department of Biological Sciences, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Lillian T. Chong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA 92093
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