Abstract
Resistance associated mutations (RAMs) threaten the long-term success of combination antiretroviral therapy (cART) outcomes for HIV-1 treatment. HIV-1 Integrase (IN) strand transfer inhibitors (INSTIs) have proven to be a viable option for highly specific HIV-1 therapy. The INSTI, Dolutegravir is recommended by the World Health Organization for use as first-line cART. This study aims to understand how RAMs affect the stability of IN, as well as the binding of the drug Dolutegravir to the catalytic pocket of the protein. A homology model of HIV-1 subtype C IN was successfully constructed and validated. The site directed mutator webserver was used to predict destabilizing and/or stabilizing effects of known RAMs while FoldX confirmed any changes in protein energy upon introduction of mutation. Also, interaction analysis was performed between neighbouring residues. Three mutations known to be associated with Raltegravir, Elvitegravir and Dolutegravir resistance were selected; E92Q, G140S and Y143R, for molecular dynamics simulations. The structural quality assessment indicated high reliability of the HIV-1C IN tetrameric structure, with more than 90% confidence in modelled regions. Change in free energy for the three mutants indicated different effects, while simulation analysis showed G140S to have the largest affect on protein stability and flexibility. This was further supported by weaker non-bonded pairwise interaction energy and binding free energy values between the drug DTG and E92Q, Y143R and G140S mutants suggesting reduced binding affinity, as indicated by interaction analysis in comparison to the WT. Our findings suggest the G140S mutant has the strongest effect on the HIV-1C IN protein structure and Dolutegravir binding. To the best of our knowledge, this is the first study that uses the consensus wild type HIV-1C IN sequence to build an accurate 3D model to understand the effect of three known mutations on DTG drug binding in a South Africa context.
Highlights
The Integrase (IN) enzyme plays an important role in the Human Immunodeficiency Virus type 1 (HIV-1) replication cycle by catalysing two distinct reactions termed: 3’-end processing and strand transfer
The tetrameric protein structure built for HIV-1 subtype C (HIV-1C) IN had a Global mean quality estimate score of 0.59 and 60% sequence similarity to 5U1C (S2 Fig)
We selected three known mutations E92Q, G140S and Y143R associated with RAL, EVG and DTG resistance to investigate their effect on the protein structure of HIV-1C IN and DTG drug binding
Summary
The Integrase (IN) enzyme plays an important role in the Human Immunodeficiency Virus type 1 (HIV-1) replication cycle by catalysing two distinct reactions termed: 3’-end processing and strand transfer. The subsequent step involves strand transfer whereby, IN attacks the phosphodiester backbone of the host DNA and links the exposed 3’-end to the 5’ hydroxyl end of the host DNA [1]. This makes HIV-1 IN an important target for combination antiretroviral therapy (cART). HIV-1 IN is a 32 kilo Dalton (kDa) protein, and consist of three structural and functional domains; the N-terminal domain (NTD, residues 1–49), the catalytic core domain (CCD, residues 50– 212), and C-terminal domain (CTD, residues 213–288) It contains a conserved DDE motif consisting of residues Asp, Asp116 and Glu152 in the CCD, important for drug binding and enzyme activity [2]. All first-generation INSTIs have been reported to have relatively low genetic barrier to resistance while second-generation INSTIs including DTG (a coplanar and linear molecule) are associated with a higher genetic barrier against resistance associated mutations (RAMs), and are rendered safe and tolerable, showing little to none drug-drug interactions resistance [7]
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