Structure-based virtual screening and molecular dynamics elucidate novel inhibitors of HIV-1 TAR RNA from enamine library.

The HIV-1 trans-activation response (TAR) RNA is a key regulatory element necessary for viral replication, presenting a high-value target for anti-HIV therapeutics. Recent advances in RNA-targeted drug discovery have leveraged large, diverse compound libraries, such as the Enamine collection, using structure-based virtual screening to uncover novel modulators of RNA structure and function. In this study, we employed an integrative in silico approach combining high-throughput virtual screening of the Enamine library against the central bulge region of HIV-1 TAR RNA with molecular dynamics (MD) simulations to assess binding stability and conformational adaptability of lead molecules. Virtual screening pinpointed multiple candidate ligands predicted to disrupt the critical Tat-TAR interaction interface, with subsequent MD simulations over 500-nanosecond timescales revealing ligand-induced stabilization of druggable RNA conformations and dynamic remodelling of key binding pockets. Notably, some top-scoring compounds featured strong and persistent contacts within the U23-C25 bulge and the adjacent major groove, recapitulating pharmacologically relevant mechanistic disruption. These findings reinforce the synergy of structure-based screening and MD for identifying and validating RNA-targeted small molecules and provide promising new scaffolds for further experimental testing as selective HIV-1 replication inhibitors.