Effect of naturally occurring polymorphisms on HIV-1 integrase structure and dolutegravir binding in subtypes A1 and D

Abstract Background Dolutegravir (DTG), a second-generation integrase strand transfer inhibitor (INSTI), is recommended for first-line antiretroviral therapy due to its high potency and genetic barrier to resistance. However, emerging evidence of reduced DTG efficacy in absence of major DTG resistance mutations among non-subtype B populations requires investigation into alternative resistance mechanisms. This study investigated the impact of naturally occurring polymorphisms (NOPs) on integrase stability and DTG binding in HIV-1 subtypes A1 and D, which are predominant in East Africa. Methods We analyzed sequences from ART-naïve individuals derived from the Los Alamos HIV sequence database for subtypes A1 and D. Consensus integrase sequences for subtypes A1 and D were generated and 3D structures of HIV-1 A1 and D integrase were predicted using SWISS-MODEL. Molecular docking of HIV-1 integrase and DTG was performed with AutoDock Vina, and interaction profiles were analyzed using Protein-Ligand Interaction Profile (PLIP). Stability effects of major INSTI resistance mutations on HIV-1 integrase-vDNA-Mg²⁺-DTG complexes were assessed using the mutation scanning matrix (mCSM). Binding energy of DTG was predicted using PRODIGY-LIG. Results We identified a total of 16 NOPs in subtype A1 and D consensus sequences relative to the subtype B sequence. The predicted 3D structures of subtype A1 and D integrase contained a short helical segment in the C-terminal domain, spanning residues 229–235 that was unresolved in the template structure (PDB ID: 8W34). Molecular docking of the predicted 3D structures reproduced the established INSTI mechanism of action across subtypes. DTG chelated the active site Mg²⁺ ions, which are coordinated by the residues of DDE motif (D64, D116, and E152), and DTG interacted with the terminal adenine of the viral DNA. Stability analysis showed that major INSTI resistance mutations at E138 and G140 destabilize the HIV-1 integrase-vDNA-Mg²⁺-DTG complex, whereas those at Y143 and Q148 stabilize it. These predicted stability changes provide structural insights into the effects of resistance-associated mutations rather than direct evidence of drug resistance. Conclusion Naturally occurring polymorphisms in HIV-1 subtypes A1 and D did not substantially alter integrase structure or DTG binding mechanism; major INSTI resistance mutations induced similar effects across all subtypes. These findings indicate that the core determinants of HIV-1 integrase-DTG interactions are highly conserved, supporting DTG-based regimens in populations where subtypes A1 and D are dominant.