Structure-based Design of Small Molecule Inhibitors of HIV-1 Entry
type: CreativeWork
description: HIV infection begins when gp120 envelope protein on the viral surface binds to the CD4 receptor on the host cell. This initial protein-protein interaction starts the rest of the HIV lifecycle of coreceptor binding, fusion and replication. One of the targets of HIV entry inhibitors is the interaction between CD4 and gp120. A large percentage of CD4-gp120 contacts revolved around a cavity in gp120 in which the PHE43 residue of CD4 caps. We were able to design and synthesize a progression of small molecule compounds targeting the PHE43CD4 cavity in gp120 based on a previous CD4-mimetic, NBD-556. By either soaking or co-crystallizing the newly designed compounds bound to gp120, we were able to solve four x-ray crystal structures in order to observe the interactions with the binding cavity on the atomic level. Using x-ray crystal structure, isothermal calorimetry and viral binding assay to guide design, we were able to improve the binding affinity more than 30 fold compared to the original NBD-556. Our most potent compound DMJ-II-121-R,R is able to bind to gp120 at a Kd of 0.11 micromolar and specifically block HIV-1 entry at an IC50 of 2.3 micromolar. Along with improved potency, the new design alleviated the agonistic properties of the original NBD-556, which was inducing gp120 to bind to the coreceptors on the host cell instead of blocking the progression of the HIV lifecycle. In parallel, we also utilized the soakable gp120 crystal system to screen a library of 352 fragments of various shapes using x-ray crystallography to detect and identify two positive hits, benzimidazole and 3-hydroxyphenylacetic acid. The possible leads from the two identified fragments along with our improved potency of NBD-556 based derivatives offer valuable insight to guide us on the development toward a subnanomolar small molecular antagonist of gp120-CD4 binding.
abstract: HIV infection begins when gp120 envelope protein on the viral surface binds to the CD4 receptor on the host cell. This initial protein-protein interaction starts the rest of the HIV lifecycle of coreceptor binding, fusion and replication. One of the targets of HIV entry inhibitors is the interaction between CD4 and gp120. A large percentage of CD4-gp120 contacts revolved around a cavity in gp120 in which the PHE43 residue of CD4 caps. We were able to design and synthesize a progression of small molecule compounds targeting the PHE43CD4 cavity in gp120 based on a previous CD4-mimetic, NBD-556. By either soaking or co-crystallizing the newly designed compounds bound to gp120, we were able to solve four x-ray crystal structures in order to observe the interactions with the binding cavity on the atomic level. Using x-ray crystal structure, isothermal calorimetry and viral binding assay to guide design, we were able to improve the binding affinity more than 30 fold compared to the original NBD-556. Our most potent compound DMJ-II-121-R,R is able to bind to gp120 at a Kd of 0.11 micromolar and specifically block HIV-1 entry at an IC50 of 2.3 micromolar. Along with improved potency, the new design alleviated the agonistic properties of the original NBD-556, which was inducing gp120 to bind to the coreceptors on the host cell instead of blocking the progression of the HIV lifecycle. In parallel, we also utilized the soakable gp120 crystal system to screen a library of 352 fragments of various shapes using x-ray crystallography to detect and identify two positive hits, benzimidazole and 3-hydroxyphenylacetic acid. The possible leads from the two identified fragments along with our improved potency of NBD-556 based derivatives offer valuable insight to guide us on the development toward a subnanomolar small molecular antagonist of gp120-CD4 binding.
author: Le-Khac, Matthew
language: English
keywords: Biochemistry, Pharmacology
date published: 2013
date modified: 2026-07-24T01:44:31Z
provider: Columbia University
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: Columbia University

PropertyValue
property ID: DOI
value: 10.7916/D8W09D5Q