4E92

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

DOI: 10.2210/pdb4E92/pdb

Classification: STRUCTURAL PROTEIN/INHIBITOR
Organism(s): Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-03-20 Released: 2012-04-25
Deposition Author(s): Lemke, C.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.264
R-Value Work: 0.220
R-Value Observed: 0.223

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

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

PubMed: 22496222 Search on PubMedSearch on PubMed Central
DOI: 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.

Related Citations:

A novel inhibitor-binding site on the HIV-1 capsid N-terminal domain leads to improved crystallization via compound-mediated dimerization.
Lemke, C.T., Titolo, S., Goudreau, N., Faucher, A.M., Mason, S.W., Bonneau, P.
(2013) Acta Crystallogr D Biol Crystallogr 69: 1115

Organizational Affiliation:

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag protein	A, B	146	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: gag EC: 3.4.23.16 (UniProt), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497 Go to UniProtKB: P12497
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0OG Query on 0OG Download Ideal Coordinates CCD File SDF format, chain D [A] SDF format, chain F [B] MOL2 format, chain D [A] MOL2 format, chain F [B]	A, 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 URCIOERTSWRWBE-UHFFFAOYSA-N		Ligand Interaction
0OE Query on 0OE Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain E [B] MOL2 format, chain C [A] MOL2 format, chain E [B]	A, 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 LGXPZODGTPYYBU-UHFFFAOYSA-N		Ligand Interaction