8CZ7

Crystal structure of SARS-CoV-2 Mpro with compound C2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

A novel class of broad-spectrum active-site-directed 3C-like protease inhibitors with nanomolar antiviral activity against highly immune-evasive SARS-CoV-2 Omicron subvariants.

Perez-Vargas, J.Worrall, L.J.Olmstead, A.D.Ton, A.T.Lee, J.Villanueva, I.Thompson, C.A.H.Dudek, S.Ennis, S.Smith, J.R.Shapira, T.De Guzman, J.Gang, S.Ban, F.Vuckovic, M.Bielecki, M.Kovacic, S.Kenward, C.Hong, C.Y.Gordon, D.G.Levett, P.N.Krajden, M.Leduc, R.Boudreault, P.L.Niikura, M.Paetzel, M.Young, R.N.Cherkasov, A.Strynadka, N.C.J.Jean, F.

(2023) Emerg Microbes Infect 12: 2246594-2246594

  • DOI: https://doi.org/10.1080/22221751.2023.2246594
  • Primary Citation of Related Structures:  
    8CYU, 8CYZ, 8CZ4, 8CZ7, 8SXR

  • PubMed Abstract: 

    Antivirals with broad coronavirus activity are important for treating high-risk individuals exposed to the constantly evolving SARS-CoV-2 variants of concern (VOCs) as well as emerging drug-resistant variants. We developed and characterized a novel class of active-site-directed 3-chymotrypsin-like protease (3CLpro) inhibitors ( C2-C5a ). Our lead direct-acting antiviral (DAA), C5a , is a non-covalent, non-peptide with a dissociation constant of 170 nM against recombinant SARS-CoV-2 3CLpro. The compounds C2-C5a exhibit broad-spectrum activity against Omicron subvariants (BA.5, BQ.1.1, and XBB.1.5) and seasonal human coronavirus-229E infection in human cells. Notably, C5a has median effective concentrations of 30-50 nM against BQ.1.1 and XBB.1.5 in two different human cell lines. X-ray crystallography has confirmed the unique binding modes of C2-C5a to the 3CLpro, which can limit virus cross-resistance to emerging Paxlovid-resistant variants. We tested the effect of C5a with two of our newly discovered host-directed antivirals (HDAs): N-0385, a TMPRSS2 inhibitor, and bafilomycin D (BafD), a human vacuolar H + -ATPase [V-ATPase] inhibitor. We demonstrated a synergistic action of C5a in combination with N-0385 and BafD against Omicron BA.5 infection in human Calu-3 lung cells. Our findings underscore that a SARS-CoV-2 multi-targeted treatment for circulating Omicron subvariants based on DAAs ( C5a ) and HDAs (N-0385 or BafD) can lead to therapeutic benefits by enhancing treatment efficacy. Furthermore, the high-resolution structures of SARS-CoV-2 3CLpro in complex with C2-C5a will facilitate future rational optimization of our novel broad-spectrum active-site-directed 3C-like protease inhibitors.


  • Organizational Affiliation

    Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase
A, B, C, D
306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.574α = 74.95
b = 67.47β = 80.03
c = 93.099γ = 66.73
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release