F01(Univ. Lille)

Coronaviruses have caused 3 pandemics in the past 2 decades. The SARS-CoV-2, the causative agent of the COVID-19 already led to more than 7 million deaths worldwide. The 3CL protease (3CL^pro, M^pro) plays a key role in the replication of the SARS-CoV-2 and has been validated as promising therapeutic target as evidenced by the recent clinical use of anti-coronavirus drugs inhibitors of this protease. In addition, its high conservation among coronaviruses gives an opportunity to identify broad-spectrum anti-coronavirus compounds to combat not only SARS-CoV-2 but also emerging coronaviruses. Here we report our efforts to optimize a small non-covalent inhibitor (F01) identified by an NMR-based screening, which resulted in a 40-fold potency improvement in 3CL^pro inhibition with the low micromolar inhibitor 55. This compound displayed a promising antiviral activity in cells without cytotoxicity. In addition, it was shown to inhibit the 3CL^pro of SARS-CoV-1 and displayed high selectivity towards host cysteine proteases such as cathepsins L and K and calpain. The binding mode of a closed analog (57) was elucidated by X-ray structure with the protease and revealed the compound opens and fills a new pocket (S2∗) untargeted by others inhibitors. This original structural feature along with the promising preliminary results obtained for this new chemotype deserve future optimization to further improve potency and pharmacokinetics properties of this series.