7Q5E

Crystal structure of F2F-2020209-00X bound to the main protease (3CLpro/Mpro) of SARS-CoV-2.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Easy access to alpha-ketoamides as SARS-CoV-2 and MERS M pro inhibitors via the PADAM oxidation route.

Pelliccia, S.Cerchia, C.Esposito, F.Cannalire, R.Corona, A.Costanzi, E.Kuzikov, M.Gribbon, P.Zaliani, A.Brindisi, M.Storici, P.Tramontano, E.Summa, V.

(2022) Eur J Med Chem 244: 114853-114853

  • DOI: https://doi.org/10.1016/j.ejmech.2022.114853
  • Primary Citation of Related Structures:  
    7Q5E, 7Q5F

  • PubMed Abstract: 

    SARS-CoV-2 caused worldwide the current outbreak called COVID-19. Despite multiple countermeasures implemented, there is an urgent global need for new potent and efficient antiviral drugs against this pathogen. In this context, the main protease (M pro ) of SARS-CoV-2 is an essential viral enzyme and plays a pivotal role in viral replication and transcription. Its specific cleavage of polypeptides after a glutamine residue has been considered as a key element to design novel antiviral drugs. Herein, we reported the design, synthesis and structure-activity relationships of novel α-ketoamides as covalent reversible inhibitors of M pro , exploiting the PADAM oxidation route. The reported compounds showed μM to nM activities in enzymatic and in the antiviral cell-based assays against SARS-CoV-2 M pro . In order to assess inhibitors' binding mode, two co-crystal structures of SARS-CoV-2 M pro in complex with our inhibitors were solved, which confirmed the covalent binding of the keto amide moiety to the catalytic Cys145 residue of M pro . Finally, in order to interrogate potential broad-spectrum properties, we assessed a selection of compounds against MERS M pro where they showed nM inhibitory potency, thus highlighting their potential as broad-spectrum coronavirus inhibitors.


  • Organizational Affiliation

    Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy. Electronic address: sveva.pelliccia@unina.it.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase
A, B
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: 1.67 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.978α = 90
b = 101.017β = 90
c = 103.437γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionEuropean Union101003551

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description