Chemical arsenal for helicase Hunters: Striking the toughest targets in antiviral research

Abstract

Helicases have emerged as promising targets in antiviral drug development but remain largely undrugged. To support the focused development of viral helicase inhibitors we identified, collected, and integrated all chemogenomics data for all helicases annotated in the ChEMBL database. After thoroughly curating and enriching the data with accurate annotations we have created a derivative database of helicase inhibitors which we dubbed Heli-SMACC (Helicase-targeting SMAll Molecule Compound Collection). Heli-SMACC contains 13,597 molecules, 29 proteins, and 20,431 bioactivity entries for viral, human, and bacterial helicases. We selected 30 compounds with promising viral helicase activity and tested them in a SARS-CoV-2 NSP13 ATPase assay. Twelve compounds demonstrated ATPase inhibition and a consistent dose-response curve. While Heli-SMACC provides a rich resource for identifying candidate inhibitors, cross-species compound transferability remains a significant challenge. In particular, inhibitory activity observed against viral helicases often does not translate well to human or bacterial homologs and vice versa due to differences in binding site composition, helicase structure, and cofactor dependencies. Despite these limitations, Heli-SMACC offers a valuable starting point for structure-based optimization and target-specific inhibitor design. The Heli-SMACC database may serve as a reference for virologists and medicinal chemists working on the development of novel helicase inhibitors. Heli-SMACC is publicly available at https://smacc.mml.unc.edu.