HIV-1 integrase inhibitor mutations: analysis of structural and biochemical effects.

Abstract

Introduction. Combination antiretroviral therapy (cART), composed of drugs from different drug classes, is an effective HIV-1 treatment strategy. As part of cART, integrase strand transfer inhibitors (INSTIs) have become essential drugs and are now recommended for use in first-line, second-line, and subsequent HIV-1 treatment regimens. Though highly potent, the use of first-generation INSTIs Raltegravir and Elvitegravir still resulted in the development of integrase drug resistance mutations. Second-generation INSTIs Dolutegravir, Bictegravir, and Cabotegravir were developed to combat the emerging resistant virus strains to first-generation INSTIs and are considered some of the best antiretroviral drugs in HIV-1 treatment. Despite the fundamental changes and improved performance in second-generation INSTIs, they are not immune to drug resistance. This highlights the need to understand the molecular mechanisms of resistance to INSTIs. This thesis, through a combination of structural and biochemical methods, seeks to understand resistance development in South African HIV-1 subtype C (HIV-1C) viruses and the effect of resistance mutations on enzyme-substrate binding, DNA binding, and 3’ processing. Methods. A total of 48 HIV-1C sequences were analyzed in this study, of which 7 had a virologic failure (i.e. plasma viral loads >1000 copies/mL) and 41 were INSTI naïve isolates (32 treatment-naïve South African HIV-1C integrase sequences downloaded from GenBank and 9 INSTI-naïve isolates amplified in our laboratory). Virologic failures were receiving at least 6 months of INSTI-based cART and presented at the King Edward VIII hospital, a 3rd line regimen referral hospital in Durban, South Africa. Viral RNA was extracted, and the integrase region was amplified and sequenced using Sanger sequencing. To investigate the effect of mutations on the integrase structure, wild-type and representative mutant isolates were modeled on the SWISS model online server and visualized in Chimera v1.13.1. Raltegravir, Elvitegravir, and Dolutegravir were docked into each of the structures using the AutoDock-Vina Plugin available on Chimera, and molecular dynamics simulations were conducted using the AMBER 18 package. Integrase biochemical assays were carried out using a wild-type protein and the 3 mutant recombinant proteins that were expressed and purified. Integrase - LTR binding and 3’ processing assays were then performed. Results. Only one of the 7 (14,28%) INSTI-treated isolates had major mutations (i.e., G140A and Q148R). In addition, this isolate harboured the E157Q minor mutation and previously identified polymorphisms. Interestingly, S119T & V151I, located near the integrase active site, were only found in INSTI failures. Structural analysis results showed a reduced binding affinity for the mutants, which was supported by their weaker hydrogen-bond interaction compared to the wild-type. Our findings showed that the G140A+Q148R double mutant had the strongest effect on the HIV-1C protein structure and binding of EVG and RAL with binding free energies of -12.49 and -11.45 kcal/mol for EVG and RAL, respectively, which are approximately three times lower than the wild-type binding energy. Biochemical assays performed with purified integrase showed a decrease in integrase-LTR binding for all mutants. The 3’ processing activity was slightly decreased in the mutants compared to the wild-type protein; however, no appreciable differences were observed across the mutant isolates. Conclusions Changes near the highly conserved active site residues in HIV-1C integrase core domain and mutations in the 140’s loop have a negative effect on in vitro integrase activity, suggesting that these changes impact viral integration. While they are still few reports of INSTI resistance-associated mutations (RAMs) in South Africa , identification of the G140A+Q148R double mutant for the first time in South African HIV-1 clinical samples, and the identification of S119T and V151I in INSTI-treated patients warrants further investigation. This data broadens the understanding of HIV-1C resistance against INSTIs and adds to the available knowledge of drug resistance mutations that guide therapeutic decisions.