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Autoprocessing and oxyanion loop reorganization upon GC373 and nirmatrelvir binding of monomeric SARS-CoV-2 main protease catalytic domain

Journal Article · · Communications Biology
 [1];  [2];  [2];  [1];  [1];  [2];  [1]
  1. National Institutes of Health (NIH), Bethesda, MD (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
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The monomeric catalytic domain (residues 1–199) of SARS-CoV-2 main protease (MPro1-199) fused to 25 amino acids of its flanking nsp4 region mediates its autoprocessing at the nsp4-MPro1-199 junction. We report the catalytic activity and the dissociation constants of MPro1-199 and its analogs with the covalent inhibitors GC373 and nirmatrelvir (NMV), and the estimated monomer-dimer equilibrium constants of these complexes. Mass spectrometry indicates the presence of the accumulated adduct of NMV bound to MProWT and MPro1-199 and not of GC373. A room temperature crystal structure reveals a native-like fold of the catalytic domain with an unwound oxyanion loop (E state). In contrast, the structure of a covalent complex of the catalytic domain-GC373 or NMV shows an oxyanion loop conformation (E* state) resembling the full-length mature dimer. These results suggest that the E-E* equilibrium modulates autoprocessing of the main protease when converting from a monomeric polyprotein precursor to the mature dimer.
Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC05-00OR22725
OSTI ID:
1890334
Journal Information:
Communications Biology, Journal Name: Communications Biology Journal Issue: 1 Vol. 5; ISSN 2399-3642
Publisher:
Springer NatureCopyright Statement
Country of Publication:
United States
Language:
English

References (57)

Overview of Current Methods in Sedimentation Velocity and Sedimentation Equilibrium Analytical Ultracentrifugation journal February 2013
The establishment of reference sequence for SARS‐CoV‐2 and variation analysis journal March 2020
Depletion of amyloid-β peptides from solution by sequestration within fibril-seeded hydrogels journal March 2018
Current developments in Coot for macromolecular model building of Electron Cryo‐microscopy and Crystallographic Data journal March 2020
Use of a Fluorescence Plate Reader for Measuring Kinetic Parameters with Inner Filter Effect Correction journal February 1999
Liberation of SARS-CoV main protease from the viral polyprotein: N-terminal autocleavage does not depend on the mature dimerization mode journal January 2010
Activation and maturation of SARS-CoV main protease journal April 2011
On the analysis of protein self-association by sedimentation velocity analytical ultracentrifugation journal September 2003
Size-Distribution Analysis of Macromolecules by Sedimentation Velocity Ultracentrifugation and Lamm Equation Modeling journal March 2000
Thionesters as a probe for electrophilic catalysis in the serine protease mechanism. journal January 1983
Analytical Ultracentrifugation: Sedimentation Velocity and Sedimentation Equilibrium book January 2008
Calculations and Publication-Quality Illustrations for Analytical Ultracentrifugation Data book January 2015
Mutation of Glu-166 Blocks the Substrate-Induced Dimerization of SARS Coronavirus Main Protease journal April 2010
A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process journal September 2021
Malleability of the SARS-CoV-2 3CL Mpro Active-Site Cavity Facilitates Binding of Clinical Antivirals journal December 2020
Two adjacent mutations on the dimer interface of SARS coronavirus 3C-like protease cause different conformational changes in crystal structure journal June 2009
Evaluating the 3C-like protease activity of SARS-Coronavirus: Recommendations for standardized assays for drug discovery journal April 2008
Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease journal October 2021
Comprehensive Insights into the Catalytic Mechanism of Middle East Respiratory Syndrome 3C-Like Protease and Severe Acute Respiratory Syndrome 3C-Like Protease journal April 2020
Targeting the Dimerization of the Main Protease of Coronaviruses: A Potential Broad-Spectrum Therapeutic Strategy journal May 2020
Quaternary Structure of the Severe Acute Respiratory Syndrome (SARS) Coronavirus Main Protease † journal November 2004
Reversible covalent inhibition of papain by a peptide nitrile. Carbon-13 NMR evidence for a thioimidate ester adduct journal March 1986
Carboxypeptidase A catalyzed hydrolysis of thiopeptide and thioester analogs of specific substrates. An effect on kcat for peptide, but not ester, substrates journal September 1982
Hydrolysis of thioimidate esters. Tetrahedral intermediates and general acid catalysis journal December 1967
Picornaviral 3C cysteine proteinases have a fold similar to chymotrypsin-like serine proteinases journal May 1994
Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication journal August 2020
Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease journal April 2022
Coronavirus biology and replication: implications for SARS-CoV-2 journal October 2020
A new coronavirus associated with human respiratory disease in China journal February 2020
The dimer-monomer equilibrium of SARS-CoV-2 main protease is affected by small molecule inhibitors journal April 2021
Modulation of the monomer-dimer equilibrium and catalytic activity of SARS-CoV-2 main protease by a transition-state analog inhibitor journal March 2022
SARS-CoV 3CL protease cleaves its C-terminal autoprocessing site by novel subsite cooperativity journal October 2016
Unusual zwitterionic catalytic site of SARS–CoV-2 main protease revealed by neutron crystallography journal October 2020
Biosynthesis, Purification, and Substrate Specificity of Severe Acute Respiratory Syndrome Coronavirus 3C-like Proteinase journal October 2003
Dissection Study on the Severe Acute Respiratory Syndrome 3C-like Protease Reveals the Critical Role of the Extra Domain in Dimerization of the Enzyme: DEFINING THE EXTRA DOMAIN AS A NEW TARGET FOR DESIGN OF HIGHLY SPECIFIC PROTEASE INHIBITORS journal March 2004
Mechanism of the Maturation Process of SARS-CoV 3CL Protease journal March 2005
Mutation of Gly-11 on the Dimer Interface Results in the Complete Crystallographic Dimer Dissociation of Severe Acute Respiratory Syndrome Coronavirus 3C-like Protease journal January 2008
Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain journal July 2002
Virus-encoded proteinases and proteolytic processing in the Nidovirales journal April 2000
Phaser crystallographic software journal July 2007
electronic Ligand Builder and Optimization Workbench ( eLBOW ): a tool for ligand coordinate and restraint generation journal September 2009
MolProbity : all-atom structure validation for macromolecular crystallography journal December 2009
Overview of the CCP 4 suite and current developments journal March 2011
How good are my data and what is the resolution? journal June 2013
Mechanism for controlling the monomer–dimer conversion of SARS coronavirus main protease journal April 2013
Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography journal October 2021
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix journal October 2019
Autoprocessing mechanism of severe acute respiratory syndrome coronavirus 3C-like protease (SARS-CoV 3CL pro ) from its polyproteins journal March 2013
The catalysis of the SARS 3C-like protease is under extensive regulation by its extra domain journal March 2006
Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors journal March 2020
Without Its N-Finger, the Main Protease of Severe Acute Respiratory Syndrome Coronavirus Can Form a Novel Dimer through Its C-Terminal Domain journal May 2008
Mechanism for Controlling the Dimer-Monomer Switch and Coupling Dimerization to Catalysis of the Severe Acute Respiratory Syndrome Coronavirus 3C-Like Protease journal February 2008
Inhibition of papain by peptide nitriles: conversion of the nitrile group into other functionalities via the papain:nitrile thioimidate ester adduct journal August 1991
Molecular mechanisms of severe acute respiratory syndrome (SARS) journal January 2005
Large-Scale Purification of a Stable Form of Recombinant Tobacco Etch Virus Protease journal March 2001
Dipeptide-derived nitriles containing additional electrophilic sites: Potentially irreversible inhibitors of cysteine proteases journal November 2009
Structural Characterization of SARS-CoV-2: Where We Are, and Where We Need to Be journal December 2020

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