Monitoring binding of HIV-1 capsid assembly inhibitors using (19)F ligand-and (15)N protein-based NMR and X-ray crystallography: early hit validation of a benzodiazepine series

The emergence of resistance to existing classes of antiretroviral drugs underlines the need to find novel human immunodeficiency virus (HIV)-1 targets for drug discovery. The viral capsid protein (CA) represents one such potential target. Recently, a series of benzodiazepine inhibitors was identifie...

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Bibliographic Details
Published in:ChemMedChem 2013-03, Vol.8 (3), p.405-414
Main Authors: Goudreau, Nathalie, Coulombe, René, Faucher, Anne-Marie, Grand-Maître, Chantal, Lacoste, Jean-Eric, Lemke, Christopher T, Malenfant, Eric, Bousquet, Yves, Fader, Lee, Simoneau, Bruno, Mercier, Jean-François, Titolo, Steve, Mason, Stephen W
Format: Article
Language:English
Subjects:
Benzodiazepines - chemistry
Benzodiazepines - metabolism
Binding Sites
Capsid Proteins - chemistry
Capsid Proteins - metabolism
Crystallography, X-Ray
Fluorine - chemistry
HIV-1 - metabolism
Humans
Ligands
Magnetic Resonance Spectroscopy
Nitrogen Isotopes - chemistry
Protein Binding
Protein Structure, Tertiary
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Summary:The emergence of resistance to existing classes of antiretroviral drugs underlines the need to find novel human immunodeficiency virus (HIV)-1 targets for drug discovery. The viral capsid protein (CA) represents one such potential target. Recently, a series of benzodiazepine inhibitors was identified via high-throughput screening using an in vitro capsid assembly assay (CAA). Here, we demonstrate how a combination of NMR and X-ray co-crystallography allowed for the rapid characterization of the early hits from this inhibitor series. Ligand-based (19)F NMR was used to confirm inhibitor binding specificity and reversibility as well as to identify the N-terminal domain of the capsid (CA(NTD)) as its molecular target. Protein-based NMR ((1)H and (15)N chemical shift perturbation analysis) identified key residues within the CA(NTD) involved in inhibitor binding, while X-ray co-crystallography confirmed the inhibitor binding site and its binding mode. Based on these results, two conformationally restricted cyclic inhibitors were designed to further validate the possible binding modes. These studies were crucial to early hit confirmation and subsequent lead optimization.
ISSN:1860-7187
DOI:10.1002/cmdc.201200580