Crystal Structure of the N-Terminal Domain of HIV-1 Capsid in Complex With Inhibitor BM4

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

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Distinct Effects of Two HIV-1 Capsid Assembly Inhibitor Families That Bind the Same Site within the N-Terminal Domain of the Viral CA Protein.

Lemke, C.T.Titolo, S.von Schwedler, U.Goudreau, N.Mercier, J.F.Wardrop, E.Faucher, A.M.Coulombe, R.Banik, S.S.Fader, L.Gagnon, A.Kawai, S.H.Rancourt, J.Tremblay, M.Yoakim, C.Simoneau, B.Archambault, J.Sundquist, W.I.Mason, S.W.

(2012) J Virol 86: 6643-6655

  • DOI: https://doi.org/10.1128/JVI.00493-12
  • Primary Citation of Related Structures:  
    4E91, 4E92

  • PubMed Abstract: 

    The emergence of resistance to existing classes of antiretroviral drugs necessitates finding new HIV-1 targets for drug discovery. The viral capsid (CA) protein represents one such potential new target. CA is sufficient to form mature HIV-1 capsids in vitro, and extensive structure-function and mutational analyses of CA have shown that the proper assembly, morphology, and stability of the mature capsid core are essential for the infectivity of HIV-1 virions. Here we describe the development of an in vitro capsid assembly assay based on the association of CA-NC subunits on immobilized oligonucleotides. This assay was used to screen a compound library, yielding several different families of compounds that inhibited capsid assembly. Optimization of two chemical series, termed the benzodiazepines (BD) and the benzimidazoles (BM), resulted in compounds with potent antiviral activity against wild-type and drug-resistant HIV-1. Nuclear magnetic resonance (NMR) spectroscopic and X-ray crystallographic analyses showed that both series of inhibitors bound to the N-terminal domain of CA. These inhibitors induce the formation of a pocket that overlaps with the binding site for the previously reported CAP inhibitors but is expanded significantly by these new, more potent CA inhibitors. Virus release and electron microscopic (EM) studies showed that the BD compounds prevented virion release, whereas the BM compounds inhibited the formation of the mature capsid. Passage of virus in the presence of the inhibitors selected for resistance mutations that mapped to highly conserved residues surrounding the inhibitor binding pocket, but also to the C-terminal domain of CA. The resistance mutations selected by the two series differed, consistent with differences in their interactions within the pocket, and most also impaired virus replicative capacity. Resistance mutations had two modes of action, either directly impacting inhibitor binding affinity or apparently increasing the overall stability of the viral capsid without affecting inhibitor binding. These studies demonstrate that CA is a viable antiviral target and demonstrate that inhibitors that bind within the same site on CA can have distinct binding modes and mechanisms of action.

  • Organizational Affiliation

    Department of Chemistry, Research & Development, Laval, Quebec, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gag protein
A, B
146Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: gag
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12497
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0OG

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
3-{5-[3-ethyl-5-(5-methylfuran-2-yl)-1H-pyrazol-1-yl]-1-[(6-oxo-1,6-dihydropyridin-3-yl)methyl]-1H-benzimidazol-2-yl}-4-hydroxybenzoic acid
C30 H25 N5 O5
Query on 0OE

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
4-{2-[5-(3-chlorophenyl)-1H-pyrazol-4-yl]-1-[3-(1H-imidazol-1-yl)propyl]-1H-benzimidazol-5-yl}benzoic acid
C29 H23 Cl N6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.709α = 90
b = 81.709β = 90
c = 90.15γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHENIXmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2012-04-25 
  • Deposition Author(s): Lemke, C.T.

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2012-06-06
    Changes: Database references
  • Version 1.2: 2013-06-12
    Changes: Database references