Identification of fragments targeting an alternative pocket on HIV-1 gp41 by NMR screening and similarity searching.
The HIV-1 envelope glycoprotein gp41 fusion intermediate is a promising drug target for inhibiting viral entry. However, drug development has been impeded by challenges inherent in mediating the underlying protein-protein interaction. Here we report on the identification of fragments that bind to a C-terminal sub-pocket adjacent to the well-known hydrophobic pocket on the NHR coiled coil. Using a specifically designed assay and ligand-based NMR screening of a fragment library, we identified a thioenylaminopyrazole compound with a dissociation constant of ~500 μM. Interaction with the C-terminal sub-pocket was confirmed by paramagnetic relaxation enhancement NMR experiments, which also yielded the binding mode. Shape-based similarity searching detected additional phenylpyrazole and phenyltriazole fragments within the library, enriching the hit rate over random screening, and revealing molecular features required for activity. Discovery of the novel scaffolds and binding mechanism suggests avenues for extending the interaction surface and improving the potency of a hydrophobic pocket binding inhibitor.
Department of Basic Sciences, College of Osteopathic Medicine, Touro University California, Mare Island, Vallejo, CA 94592, USA.
Shidong
S
Chu
Miriam
M
Gochin
D004305:Dose-Response Relationship, Drug; D015700:HIV Envelope Protein gp41 / Q000037:antagonists & inhibitors* / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy / Q000592:standards; D008958:Models, Molecular; D015394:Molecular Structure; D011720:Pyrazoles / Q000737:chemistry / Q000494:pharmacology*; D012015:Reference Standards; D013329:Structure-Activity Relationship
D015700:HIV Envelope Protein gp41; D011720:Pyrazoles; C514787:gp41 protein, Human immunodeficiency virus 1; C587366:thioenylaminopyrazole
Fragment library; HIV-1; NMR; PRE; ROCS; ROCS similarity searching; Rapid Overlay of Chemical Structures; Water-Ligand Observed via Gradient Spectroscopy; WaterLOGSY; glycoprotein-41; gp41; paramagnetic relaxation enhancement