4E91

Crystal Structure of the N-Terminal Domain of HIV-1 Capsid in Complex With Inhibitor BD3

Summary for 4E91

• Entry DOI: 10.2210/pdb4e91/pdb
• Related: 4E92
• Descriptor: Gag protein, 4-{2-[5-(3-chlorophenyl)-1H-pyrazol-4-yl]-1-[3-(1H-imidazol-1-yl)propyl]-1H-benzimidazol-5-yl}benzoic acid, (3S)-1-ethyl-3-[3-hydroxy-5-(pyridin-3-yl)phenyl]-5-phenyl-7-(trifluoromethyl)-1H-1,5-benzodiazepine-2,4(3H,5H)-dione, ... (5 entities in total)
• Functional Keywords: structural protein capsid, structural protein, structural protein-inhibitor complex, structural protein/inhibitor
• Biological source: Human immunodeficiency virus 1
• Cellular location: Capsid protein p24: Virion (By similarity). Matrix protein p17: Virion (By similarity). Nucleocapsid protein p7: Virion (By similarity): Q79791
• Total number of polymer chains: 2
• Total formula weight: 34480.23

Authors

Lemke, C.T. (deposition date: 2012-03-20, release date: 2012-04-25, Last modification date: 2024-02-28)

Primary citation

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.
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.
J.Virol., 86:6643-6655, 2012

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.

PubMed: 22496222
DOI: 10.1128/JVI.00493-12

Experimental method

X-RAY DIFFRACTION (1.7 Å)