Small Molecule Inhibitors of the LEDGF Site of Human Immunodeficiency Virus Integrase Identified by Fragment Screening and Structure Based Design

Abstract

A fragment-based screen against human immunodeficiency virus type 1 (HIV) integrase led to a number of compounds that bound to the lens epithelium derived growth factor (LEDGF) binding site of the integrase catalytic core domain. We determined the crystallographic structures of complexes of the HIV integrase catalytic core domain for 10 of these compounds and quantitated the binding by surface plasmon resonance. We demonstrate that the compounds inhibit the interaction of LEDGF with HIV integrase in a proximity AlphaScreen assay, an assay for the LEDGF enhancement of HIV integrase strand transfer and in a cell based assay. The compounds identified represent a potential framework for the development of a new series of HIV integrase inhibitors that do not bind to the catalytic site of the enzyme.

Fragment-based drug discovery and protein–protein interactions

“…This is not an exhaustive list, and other notable examples, such as the use of X-ray techniques with FBDD in the discovery of HIV-1/LEDGF inhibitors 55 are not described in detail in the interests of brevity.…”

The discovery of allyltyrosine based tripeptides as selective inhibitors of the HIV-1 integrase strand-transfer reaction

“…This compound inhibited HIV-1 replication with an EC50 value of ~38 nM. Given our ongoing interest in the development of HIV inhibitors 23,24,[27][28][29] and the renewed vigour for the development of next generation IN inhibitors, we conducted a screening program utilising a number of 'in-house' compound libraries from which an O-allyltyrosine-based tripeptide (Compound 6, Figure 3) was identified to inhibit IN with an IC50 value of 17.5 µM. This tripeptide, which emerged from our ongoing antibacterial drug design program,30-32 presented as an appealing scaffold for drug development endeavours since: a) analogues could be rapidly accessed via standard peptide coupling approaches, b) the scaffold is amenable to diverse structural and functional group alterations and c) the tripeptide bears no significant structural similarity to any currently reported peptide-based integrase inhibitors.…”

“…[22][23][24] These molecules disrupt the protein-protein interaction between transcriptional co-activator lens epithelium derived growth factor (LEDGF) and the IN catalytic core. [22][23][24][25][26] LEDGF has been shown to be a dominant factor to promote localisation of the PIC to the host chromatin as well as enhancing strand transfer in isolated protein assays. Full-length LEDGF was also shown to promote tetramerisation of full-length HIV-IN, which is essential for the integration of both viral DNA ends into the chromosomal DNA.…”

“…Full-length LEDGF was also shown to promote tetramerisation of full-length HIV-IN, which is essential for the integration of both viral DNA ends into the chromosomal DNA. [22][23][24][25][26] Of these analogues the most recently reported GSK1264 (5) has been cocrystallised within the LEDGF binding pocket of IN catalytic core (Figure 2). This compound inhibited HIV-1 replication with an EC50 value of ~38 nM.…”

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.…”