FIG 2.

Molecular models of BIC (A, gray), DTG (B, yellow), and overlap (C) bound to the HIV-1 IN active site. HIV-1 IN and vDNA are shown in blue-red-white and rainbow electrostatic surface representation, respectively. The two Mg²⁺ ions are shown in magenta spheres. The bicyclic A-ring of BIC makes van der Waals contacts with the IN β4-α2 loop (G118 shown for reference) and 3′-dA of the vDNA, filling up this region of the binding pocket efficiently and acting as additional anchoring points. DTG with its monocyclic ring and flipped stereochemistry makes partial contact with this region. Compound 2 (C, green) is a stereoisomer of BIC (gray) where the bicyclic ring points away from the 3′-dA vDNA. The optimal contacts of BIC with IN β4-α2 loop and vDNA may be major contributors to anchoring the inhibitor in the pocket. Methodologies for the models are as follows. The INSTIs were docked to a homology model of WT and G140S+Q148H mutant HIV-1 IN based on cryo-EM structures (SIVrcm IN) (2) using Prime in Schrodinger Suite 2019-2 (Schrödinger, LLC, New York, NY) and a knowledge-based approach (23). The sequence alignment between SIVrcm IN (template) and HIV-1 IN (query) was optimized using ClustalW (24), yielding a sequence identity of 73%, a sequence similarity of 83%. The residues that were similar between the two sequences were retained while building the model. The side chains of the residues that were not part of the template were iteratively sampled using a coarse library of rotamers derived from known PDB structures until no clashes remained. The coordinates of all atoms not derived directly from the template itself were then minimized, producing the final refined model. BIC, DTG, and compound 2 were prepared with LigPrep with the metal binding states option using Schrodinger Suite 2019 (Schrödinger). INSTIs were docked using Glide XP docking protocol with expanded sampling method (25). Solvent molecules that coordinate to active site Mg²⁺ ions were kept in place during docking. Top three docked poses for both the INSTIs were saved as an output.