6W0T

Co-crystal structures of CHIKV nsP3 macrodomain with pyrimidone fragments


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

Starting Model: experimental
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Literature

Pyrimidone inhibitors targeting Chikungunya Virus nsP3 macrodomain by fragment-based drug design.

Zhang, S.Garzan, A.Haese, N.Bostwick, R.Martinez-Gzegozewska, Y.Rasmussen, L.Streblow, D.N.Haise, M.T.Pathak, A.K.Augelli-Szafran, C.E.Wu, M.

(2021) PLoS One 16: e0245013-e0245013

  • DOI: https://doi.org/10.1371/journal.pone.0245013
  • Primary Citation of Related Structures:  
    6VUQ, 6W0T, 6W7H, 6W8K, 6W8M, 6W8Q, 6W8Y, 6W8Z, 6W91

  • PubMed Abstract: 

    The macrodomain of nsP3 (nsP3MD) is highly conserved among the alphaviruses and ADP-ribosylhydrolase activity of Chikungunya Virus (CHIKV) nsP3MD is critical for CHIKV viral replication and virulence. No small molecule drugs targeting CHIKV nsP3 have been identified to date. Here we report small fragments that bind to nsP3MD which were discovered by virtually screening a fragment library and X-ray crystallography. These identified fragments share a similar scaffold, 2-pyrimidone-4-carboxylic acid, and are specifically bound to the ADP-ribose binding site of nsP3MD. Among the fragments, 2-oxo-5,6-benzopyrimidine-4-carboxylic acid showed anti-CHIKV activity with an IC50 of 23 μM. Our fragment-based drug discovery approach provides valuable information to further develop a specific and potent nsP3 inhibitor of CHIKV viral replication based on the 2-pyrimidone-4-carboxylic acid scaffold. In silico studies suggest this pyrimidone scaffold could also bind to the macrodomains of other alphaviruses and coronaviruses and thus, have potential pan-antiviral activity.


  • Organizational Affiliation

    Drug Discovery Division, Chemistry Department, Southern Research, Birmingham, Alabama, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural protein 3
A, B, C, D
168Chikungunya virus strain Senegal 37997Mutation(s): 0 
EC: 3.1.3.84
UniProt
Find proteins for Q8JUX6 (Chikungunya virus (strain S27-African prototype))
Explore Q8JUX6 
Go to UniProtKB:  Q8JUX6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8JUX6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.774α = 90
b = 87.774β = 90
c = 83.105γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1U19AI142759-01

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-02-03
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Advisory, Data collection, Database references, Refinement description