9ART

Crystal structure of SARS-CoV-2 main protease A191T mutant in complex with an inhibitor 5h


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural and virologic mechanism of the emergence of resistance to M pro inhibitors in SARS-CoV-2.

Hattori, S.I.Bulut, H.Hayashi, H.Kishimoto, N.Takamune, N.Hasegawa, K.Furusawa, Y.Yamayoshi, S.Murayama, K.Tamamura, H.Li, M.Wlodawer, A.Kawaoka, Y.Misumi, S.Mitsuya, H.

(2024) Proc Natl Acad Sci U S A 121: e2404175121-e2404175121

  • DOI: https://doi.org/10.1073/pnas.2404175121
  • Primary Citation of Related Structures:  
    9ARQ, 9ARS, 9ART, 9AVQ

  • PubMed Abstract: 

    We generated SARS-CoV-2 variants resistant to three SARS-CoV-2 main protease (M pro ) inhibitors (nirmatrelvir, TKB245, and 5h), by propagating the ancestral SARS-CoV-2 WK521 WT in VeroE6 TMPRSS2 cells with increasing concentrations of each inhibitor and examined their structural and virologic profiles. A predominant E166V-carrying variant (SARS-CoV-2 WK521 E166V ), which emerged when passaged with nirmatrelvir and TKB245, proved to be resistant to the two inhibitors. A recombinant SARS-CoV-2 E166V was resistant to nirmatrelvir and TKB245, but sensitive to 5h. X-ray structural study showed that the dimerization of M pro was severely hindered by E166V substitution due to the disruption of the presumed dimerization-initiating Ser1'-Glu166 interactions. TKB245 stayed bound to M pro E166V , whereas nirmatrelvir failed. Native mass spectrometry confirmed that nirmatrelvir and TKB245 promoted the dimerization of M pro , and compromised the enzymatic activity; the Ki values of recombinant M pro E166V for nirmatrelvir and TKB245 were 117±3 and 17.1±1.9 µM, respectively, indicating that TKB245 has a greater (by a factor of 6.8) binding affinity to M pro E166V than nirmatrelvir. SARS-CoV-2 WK521 WT selected with 5h acquired A191T substitution in M pro (SARS-CoV-2 WK521 A191T ) and better replicated in the presence of 5h, than SARS-CoV-2 WK521 WT . However, no significant enzymatic or structural changes in M pro A191T were observed. The replicability of SARS-CoV-2 WK521 E166V proved to be compromised compared to SARS-CoV-2 WK521 WT but predominated over SARS-CoV-2 WK521 WT in the presence of nirmatrelvir. The replicability of SARS-CoV-2 WK521 A191T surpassed that of SARS-CoV-2 WK521 WT in the absence of 5h, confirming that A191T confers enhanced viral fitness. The present data should shed light on the understanding of the mechanism of SARS-CoV-2's drug resistance acquisition and the development of resistance-repellant COVID-19 therapeutics.


  • Organizational Affiliation

    Department of Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5A,
B [auth D]
305Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
Gene Names: rep1a-1b
EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V7G (Subject of Investigation/LOI)
Query on V7G

Download Ideal Coordinates CCD File 
C [auth A],
D
N-[(2S)-1-({(1S,2S)-1-(1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
C30 H35 N5 O5 S
DHQWCSDZTRDSRP-XIBGDNMGSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.111α = 114.79
b = 53.54β = 97.99
c = 63.86γ = 89.99
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
DIALSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Database references, Structure summary