Identification of unique and potent inhibitors of SARS-CoV-2 main protease from DNA-encoded chemical libraries

In vitro screening of large libraries of compounds with automated High-throughput screening is expensive, time consuming and requires dedicated infrastructures. Conversely, the screening of DNA-encoded chemical libraries can be rapidly performed with basic equipment available in most laboratories. In this study we identified novel inhibitors of SARS-CoV-2 main protease (Mpro) through the affinity screening of the commercially available ″DELopen″ library, containing 4.2 billion compounds. The identified inhibitors were peptidomimetics compounds containing a C-terminal electrophilic group able to covalently bind to Mpro reactive Cys145 (confirmed by x-ray crystallography). Compound SLL11 had IC50 = 30nM and was found to be well optimized, proving that the rapid exploration of large chemical spaces, enabled by DECL technology, allows the direct identification of potent inhibitors avoiding several rounds of iterative medicinal chemistry. Compound MP6, a close analogue of SLL11, showed antiviral activity against SARS-CoV-2 in the low micromolar range when tested in Caco-2 and Calu-3 (EC50 = 2.3 μM) cell lines. As peptidomimetics compounds can suffer from low cell permeability and metabolic stability, the cyclization of the compounds as well as the substitution of selected residues with D-enantiomers will be explored in the future to improve the antiviral activity of these novel compounds. ### Competing Interest Statement The authors have declared no competing interest.