Identification of Potent Small Molecule Inhibitors of SARS-CoV-2 Entry

Mediouni, Sonia; Mou, Huihui; Otsuka, Yuka; Jablonski, Joseph Anthony; Adcock, Robert Scott; Batra, Lalit; Chung, Dong-Hoon; Rood, Christopher; de Vera, Ian Mitchelle S.; Rahaim, Ronald; Ullah, Sultan; Yu, Xuerong; Nguyen, Tu-Trinh; Hull, Mitchell; Chen, Emily; Bannister, Thomas D.; Baillargeon, Pierre; Scampavia, Louis; Farzan, Michael; Valente, Susana T.; Spicer, Timothy P.

The severe acute respiratory syndrome coronavirus 2 responsible for COVID-19 remains a persistent threat to mankind, especially for the immunocompromised and elderly for which the vaccine may have limited effectiveness. Entry of SARS-CoV-2 requires a high affinity interaction of the viral spike protein with the cellular receptor angiotensin-converting enzyme 2. Novel mutations on the spike protein correlate with the high transmissibility of new variants of SARS-CoV-2, highlighting the need for small molecule inhibitors of virus entry into target cells. We report the identification of such inhibitors through a robust high-throughput screen testing 15,000 small molecules from unique libraries. Several leads were validated in a suite of mechanistic assays, including whole cell SARS-CoV-2 infectivity assays. The main lead compound, Calpeptin, was further characterized using SARS-CoV-1 and the novel SARS-CoV-2 variant entry assays, SARS-CoV-2 protease assays and molecular docking. This study reveals Calpeptin as a potent and specific inhibitor of SARS-CoV-2 and some variants.