Venezuelan Equine Encephalitis Virus (VEEV) Nonstructural Protein 2 (nsP2) Cysteine Protease Inhibited with CA074

Experimental Data Snapshot

  • Resolution: 2.32 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.190 

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In Silico Screening of Inhibitors of the Venezuelan Equine Encephalitis Virus Nonstructural Protein 2 Cysteine Protease.

Hu, X.Morazzani, E.Compton, J.R.Harmon, M.Soloveva, V.Glass, P.J.Garcia, A.D.Marugan, J.J.Legler, P.M.

(2023) Viruses 15

  • DOI: https://doi.org/10.3390/v15071503
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The Venezuelan equine encephalitis virus (VEEV) nonstructural protein 2 (nsP2) cysteine protease (EC 3.4.22.B79) is essential for viral replication. High throughput in silico/in vitro screening using a focused set of known cysteine protease inhibitors identified two epoxysuccinyl prodrugs, E64d and CA074 methyl ester (CA074me) and a reversible oxindole inhibitor. Here, we determined the X-ray crystal structure of the CA074-inhibited nsP2 protease and compared it with our E64d-inhibited structure. We found that the two inhibitors occupy different locations in the protease. We designed hybrid inhibitors with improved potency. Virus yield reduction assays confirmed that the viral titer was reduced by >5 logs with CA074me. Cell-based assays showed reductions in viral replication for CHIKV, VEEV, and WEEV, and weaker inhibition of EEEV by the hybrid inhibitors. The most potent was NCGC00488909-01 which had an EC 50 of 1.76 µM in VEEV-Trd-infected cells; the second most potent was NCGC00484087 with an EC 50 = 7.90 µM. Other compounds from the NCATS libraries such as the H1 antihistamine oxatomide (>5-log reduction), emetine, amsacrine an intercalator (NCGC0015113), MLS003116111-01, NCGC00247785-13, and MLS00699295-01 were found to effectively reduce VEEV viral replication in plaque assays. Kinetic methods demonstrated time-dependent inhibition by the hybrid inhibitors of the protease with NCGC00488909-01 (K i = 3 µM) and NCGC00484087 (K i = 5 µM). Rates of inactivation by CA074 in the presence of 6 mM CaCl 2 , MnCl 2 , or MgCl 2 were measured with varying concentrations of inhibitor, Mg 2+ and Mn 2+ slightly enhanced inhibitor binding (3 to 6-fold). CA074 inhibited not only the VEEV nsP2 protease but also that of CHIKV and WEEV.

  • Organizational Affiliation

    National Center for Advancing Translational Sciences (NCATS), Rockville, MD 20850, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protease nsP2338Venezuelan equine encephalitis virusMutation(s): 0 
EC: 3.4.22 (PDB Primary Data), (PDB Primary Data), (PDB Primary Data), (PDB Primary Data)
Find proteins for P27282 (Venezuelan equine encephalitis virus (strain Trinidad donkey))
Explore P27282 
Go to UniProtKB:  P27282
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27282
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
074 (Subject of Investigation/LOI)
Query on 074

Download Ideal Coordinates CCD File 
C18 H31 N3 O6
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 2.32 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.762α = 90
b = 63.582β = 90
c = 86.283γ = 90
Software Package:
Software NamePurpose
SAINTdata reduction
SADABSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Defense Threat Reduction Agency (DTRA)United StatesJ9CBM CB4051

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-09
    Type: Initial release