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

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 stability effects of identified NOPs were assessed using the mutation scanning matrix (mCSM). Three-dimensional 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). Results We identified 15 NOPs in subtype A1 and 14 NOPs in subtype D consensus sequences relative to the HIV reference genome (HXB2). All NOPs showed destabilizing effects (ΔΔG: -1.617 to -0.011 kcal/mol), with I151V and S17N having the highest destabilization effect. Docking analyses showed preserved DTG coordination with the D64 and E152 residues across subtypes. However, subtype A1 showed an altered hydrophobic contact (Y143 vs P145) while subtype D lacked interaction with D116 and showed additional polar contacts with H67, K156, N155, and T66. Conclusion The NOPs identified in subtypes A1 and D do not completely disrupt DTG binding but induce thermodynamic destabilization, structural and interaction changes that may influence integrase stability and consequently drug susceptibility. These findings highlight the importance of subtype-specific structural analyses in exploring alternative drug resistance mechanisms.