Understanding the co-evolutionary molecular mechanisms of resistance in the HIV-1 Gag and protease

Abstract

Due to high human immunodeficiency virus type 1 (HIV-1) subtype C infections coupled with increasing antiretroviral treatment failure, the elucidation of complex drug resistance mutational patterns arising through protein co-evolution is required. Despite the inclusion of potent protease inhibitors Lopinavir (LPV) and Darunavir (DRV) in second- and third-line therapies, many patients still fail treatment due to the accumulation of mutations in protease (PR) and recently, Gag. To understand the co-evolutionary molecular mechanisms of resistance in the HIV-1 PR and Gag, we performed 100 ns molecular dynamic simulations on multidrug resistant PR’s when bound to LPV, DRV or a mutated A431V NC|p1 Gag cleavage site (CS). Here we showed that distinct changes in PR’s active site, flap and elbow regions due to several PR resistance mutations (L10F, M46I, I54V, L76V, V82A) were found to alter LPV and DRV drug binding. However, binding was significantly exacerbated when the mutant PRs were bound to the NC|p1 Gag CS. Although A431V was shown to coordinate several residues in PR, the L76V PR mutation was found to have a significant role in substrate recognition. Consequently, a greater binding affinity was observed when the mutated substrate was bound to an L76V-inclusive PR mutant (G_bind: −62.46 ± 5.75 kcal/mol) than without (Gbind: −50.34 ± 6.28 kcal/mol). These data showed that the co-selection of resistance mutations in the enzyme and substrate can simultaneously constrict regions in PR’s active site whilst flexing the flaps to allow flexible movement of the substrate and multiple, complex mechanisms of resistance to occur.

Communicated by Ramaswamy H. Sarma

Keywords:

• Antiretroviral drug resistance
• co-evolution
• HIV-1 Gag and protease
• molecular dynamic simulations
• protease inhibitors

Acknowledgements

The authors would like to thank the National Research Foundation, South Africa and the HIV Pathogenesis Programme for providing the PhD scholarship.

Disclosure statement

The authors declare they have no competing interests.

Notes

1 In nature, the HIV-1 PR enzyme consists of two identical chains that comprise 99 AAs and runs anti-parallel to one another. While chain A is numbered from 1–99, chain B is numbered from 100–198. In practice, chain B residues may also be referred to as prime, for example, residue ALA 82 (V82A) in chain A is represented as ALA 181 (V82A') in chain B.

Additional information

Funding

This work was supported by the South African Medical Research Council (SIR grant), Poliomyelitis Research Foundation (grant # 16/67) and the University of KwaZulu-Natal’s College of Health Sciences PhD grant.