Pharmacophore‐Based Discovery of Small‐Molecule Inhibitors of Protein–Protein Interactions between HIV‐1 Integrase and Cellular Cofactor LEDGF/p75

Abstract

The cellular protein lens epithelium‐derived growth factor, or transcriptional coactivator p75 (LEDGF/p75), plays a crucial role in HIV integration. The protein–protein interactions (PPIs) between HIV‐1 integrase (IN) and its cellular cofactor LEDGF/p75 may therefore serve as targets for the development of new anti‐HIV drugs. In this work, a structure‐based pharmacophore model for potential small‐molecule inhibitors of HIV‐1 IN–LEDGF/p75 interaction was developed using the LigandScout software. The 3D model obtained was used for virtual screening of our in‐house chemical database, CHIME, leading to the identification of compound CHIBA‐3002 as an interesting hit for further optimization. The rational design, synthesis and biological evaluation of four derivatives were then carried out. Our studies resulted in the discovery of a new and more potent small molecule (7, CHIBA‐3003) that is able to interfere with the HIV‐1 IN–LEDGF/p75 interaction at micromolar concentration, representing one of the first compounds to show activity against these specific PPIs. Docking simulations were subsequently performed in order to investigate the possible binding mode of our new lead compound to HIV‐1 IN. This study is a valid starting point for the identification of anti‐HIV agents with a different mechanism of action from currently available antiviral drugs.

Preclinical Profile of BI 224436, a Novel HIV-1 Non-Catalytic-Site Integrase Inhibitor

“…The binding of BI 224436 to the integrase LEDGF binding pocket has been confirmed by crystallography studies with the integrase core domain (data not shown). Similar findings have been reported for this chemical series by our group (18), researchers at Gilead Sciences (45,50), and for an analogous chemical series referred to as LEDGINs (23). %) are described at the following levels: Ͼ100, strong synergy; 50 to 100, moderate synergy; 25 to 50, minor amount of synergy; 25 to Ϫ25, additive; Ϫ25 to Ϫ50, minor amount of antagonism; Ϫ50 to Ϫ100, moderate antagonism; and ϽϪ100, strong antagonism.…”

“…A virtual screen of the LEDGF binding pocket on integrase with follow-up profiling using an integrase-LEDGF interaction assay identified a chemical series analogous to the NCINIs, termed LEDGINs, that were optimized to exhibit low M antiviral potency (23).…”

Synthesis and biological evaluation of novel antiviral agents as protein–protein interaction inhibitors

“…In previous research from our laboratory, it was found that N-benzyl-indoles, bearing diketo acid moiety, were able to exert a specific blockade of the IN/LEDGF interaction [14][15][16][17][18] and among them we found CHI-1043, CHIBA-3000 and some methylbenzyl derivatives such as CHIBA-3017 and CHIBA-3053 ( Figure 1) as interesting PPI inhibitors 14,19 . Encouraged by these promising results, which could represent an interesting starting point for the development of novel dual drugs, and with the aim of achieving further information about the IN/LEDGF protein interaction, we focused our efforts to synthesize new indole analogues.…”

“…Synthesis of 3-acetyl-4-methoxy-1H-indole (2a) and 3-acetyl-4-hydroxy-1H-indole (2b) was carried out following the previously reported procedure 14,15,25 . Phosphoryl chloride (0.92 mL, 10 mmol) was added to ice cold dimethylacetamide (2.79 mL, 30 mmol) under stirring and cooling in ice.…”

A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core Domain

“…The emergence of fragment-based drug discovery, which entails screening of libraries of small molecule compounds (typically Ͻ250 Da) using either biophysical techniques or enzymatic assays, has opened a novel avenue for the identification of new inhibitors that bind at the IN-LEDGF/p75 interface (31). Several new chemical classes of IN-LEDGF/p75 inhibitors, including benzylindoles (32,33), benzodioxole-4-carboxylic acid (34), and 8-hydroxyquinoline (35), have been identified using in silico methods coupled with fragment-based approaches using surface plasmon resonance or nuclear magnetic resonance (NMR) spectroscopy as primary screening methods. However, further development of these initial fragment hits was hindered by the lack of structural data.…”