Evolutionary Structure Optimization of Ensitrelvir as Non-Covalent Inhibitor of SARS-CoV-2 Main Protease Mpro

Ensitrelvir is a non-covalent, non-peptide inhibitor of the SARS-CoV-2 main protease, Mpro. It has demonstrated effective antiviral activity against various coronavirus variants in vitro, along with favorable drug metabolism and pharmacokinetic profiles suitable for oral treatment. Thus, developing novel analogues of ensitrelvir is of great importance. In this study, we conducted in silico design of its analogues by employing evolutionary structure optimization of the parent ensitrelvir scaffold. In the first stage, we generated a virtual evolutionary library consisting of 6334 new analogues based on a series of fitness criteria, including molecular weight (Mw), cLogP, polar surface area, structural and conformational similarity, flexibility, and molecular shape. Next, we filtered the evolutionary library using a 3D pharmacophore model created from the available X-ray structure of the co-crystallized complex of ensitrelvir and Mpro. We then performed molecular docking calculations to rank the selected candidates according to their binding affinity and selectivity for the Mpro receptor. This binding score ranking allowed us to identify ten analogues of ensitrelvir that exhibit superior binding affinity to the protease Mpro compared to the original ensitrelvir inhibitor. Our evolutionary structure optimization indicates that the primary structural modifications that enhance the overall antiviral effect of ensitrelvir are found in the 1-methyl-1H-1,2,4-triazole and 6-chloro-2-methyl-2H-indazole fragments.