8TPG

Synthesis, X-Ray Crystallographic and Biological Activities of Covalent, Non-Peptidic Inhibitors of SARS-CoV-2 Main Protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Design, Synthesis, X-ray Crystallography, and Biological Activities of Covalent, Non-Peptidic Inhibitors of SARS-CoV-2 Main Protease.

Ashraf-Uz-Zaman, M.Chua, T.K.Li, X.Yao, Y.Moku, B.K.Mishra, C.B.Avadhanula, V.Piedra, P.A.Song, Y.

(2024) ACS Infect Dis 10: 715-731

  • DOI: https://doi.org/10.1021/acsinfecdis.3c00565
  • Primary Citation of Related Structures:  
    8TPB, 8TPC, 8TPD, 8TPE, 8TPF, 8TPG, 8TPH, 8TPI

  • PubMed Abstract: 

    Highly contagious SARS-CoV-2 coronavirus has infected billions of people worldwide with flu-like symptoms since its emergence in 2019. It has caused deaths of several million people. The viral main protease (Mpro) is essential for SARS-CoV-2 replication and therefore a drug target. Several series of covalent inhibitors of Mpro were designed and synthesized. Structure-activity relationship studies show that (1) several chloroacetamide- and epoxide-based compounds targeting Cys145 are potent inhibitors with IC 50 values as low as 0.49 μM and (2) Cys44 of Mpro is not nucleophilic for covalent inhibitor design. High-resolution X-ray studies revealed the protein-inhibitor interactions and mechanisms of inhibition. It is of interest that Cys145 preferably attacks the more hindered C α atom of several epoxide inhibitors. Chloroacetamide inhibitor 13 and epoxide inhibitor 30 were found to inhibit cellular SARS-CoV-2 replication with an EC 68 (half-log reduction of virus titer) of 3 and 5 μM. These compounds represent new pharmacological leads for anti-SARS-CoV-2 drug development.


  • Organizational Affiliation

    Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural protein 7305Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
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
JKL (Subject of Investigation/LOI)
Query on JKL

Download Ideal Coordinates CCD File 
B [auth A](3R)-N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-3-hydroxybutanamide
C27 H37 N3 O3
FQCVOMNESMUUJL-KBMIEXCESA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.268α = 90
b = 53.304β = 102.13
c = 44.967γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
pointlessdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21AI159323
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA266057
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP220232

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-24
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Database references