Structural Studies of the HIV-1 Integrase Protein: Compound Screening and Characterization of a DNA-Binding Inhibitor.

Peter K Quashie,Thibault Mesplède,Said Hassounah,Mark A Wainberg,Ying-Shan Han,David Harrich

doi:10.1371/journal.pone.0128310

Peter K Quashie, Thibault Mesplède + Show 4 more

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https://doi.org/10.1371/journal.pone.0128310

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Journal: PloS one	Publication Date: Jun 5, 2015
Citations: 15	License type: CC BY 4.0

Affiliation: Jewish General Hospital, McGill University

Abstract

Understanding the HIV integrase protein and mechanisms of resistance to HIV integrase inhibitors is complicated by the lack of a full length HIV integrase crystal structure. Moreover, a lentiviral integrase structure with co-crystallised DNA has not been described. For these reasons, we have developed a structural method that utilizes free software to create quaternary HIV integrase homology models, based partially on available full-length prototype foamy virus integrase structures as well as several structures of truncated HIV integrase. We have tested the utility of these models in screening of small anti-integrase compounds using randomly selected molecules from the ZINC database as well as a well characterized IN:DNA binding inhibitor, FZ41, and a putative IN:DNA binding inhibitor, HDS1. Docking studies showed that the ZINC compounds that had the best binding energies bound at the IN:IN dimer interface and that the FZ41 and HDS1 compounds docked at approximately the same location in integrase, i.e. behind the DNA binding domain, although there is some overlap with the IN:IN dimer interface to which the ZINC compounds bind. Thus, we have revealed two possible locations in integrase that could potentially be targeted by allosteric integrase inhibitors, that are distinct from the binding sites of other allosteric molecules such as LEDGF inhibitors. Virological and biochemical studies confirmed that HDS1 and FZ41 share a similar activity profile and that both can inhibit each of integrase and reverse transcriptase activities. The inhibitory mechanism of HDS1 for HIV integrase seems to be at the DNA binding step and not at either of the strand transfer or 3' processing steps of the integrase reaction. Furthermore, HDS1 does not directly interact with DNA. The modeling and docking methodology described here will be useful for future screening of integrase inhibitors as well as for the generation of models for the study of integrase drug resistance.

Highlights

HIV-1 integrase (IN) is a multi-domain protein that is activated after cleavage from the HIV Gag-Pol poly-protein by HIV protease during viral maturation
We have presented a comprehensive method for creation of viable HIV IN models based on the partial HIV crystal structures as well as full-length prototype foamy virus (PFV) IN structures
These models were in good agreement with the PFV crystal structures as well as two published HIV integrase models [19, 20]

Summary

Introduction

HIV-1 integrase (IN) is a multi-domain protein that is activated after cleavage from the HIV Gag-Pol poly-protein by HIV protease during viral maturation. HIV IN has three well characterised domains (Fig 1A); an N-terminal dimerization domain (NTD) that has a conserved HCCH Zn2+-binding motif, a central RNAse H-like catalytic core domain (CCD), and a C-terminal domain (CTD) that plays a role in IN DNA binding [1,2,3] Each of these domains has been purified, crystallised and characterized, either individually, in complex with other proteins, or as double-domain partial structures [1,2,3,4]. Additional structural knowledge was gained through the elucidation of drug resistance mutations for RAL and EVG in tissue culture [11, 12] and clinical trials [13] It was really the successful crystallization of the prototype foamy virus (PFV) IN protein [14,15,16,17] that provided an understanding of the correct binding mode of INSTIs and resistance to them(4,18–25)

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Results

Conclusion