Virtual Screening and Molecular Design of Potential SARS-COV-2 Inhibitors

Tinkov, O. V.; Grigorev, V. Yu.; Grigoreva, L. D.

According to recent studies, the main M(pro) protease of the SARS-CoV-2 virus, which is the most important target in the development of promising drugs for the treatment of COVID-19, is evolutionarily conservative and has not undergone significant changes compared with the main M(pro) protease of the SARS-CoV virus. Many researchers note the similarity between the binding sites of the main M(pro) protease of SARS-CoV and SARS-CoV-2 viruses; thus, with the spreading epidemic, further studies on inhibitors of the main M(pro) protease of the SARS-CoV virus to fight COVID-19 seems logical. In the course of the study, satisfactory QSAR models are built using simplex, fractal, and HYBOT descriptors; the Partial Least Squares (PLS), Random Forest (RF), Support Vectors, Gradient Boosting (GBM) methods; and the OCHEM Internet platform (https://ochem.eu), in which different types of molecular descriptors and machine learning methods are implemented. The structural interpretation, which allowed us to identify molecular fragments that increase and decrease the activity of SARS-CoV inhibitors, is performed for the obtained models. The results of the structural interpretation are used for the rational molecular design of potential SARS-CoV-2 inhibitors. The resulting QSAR models are used for the virtual screening of 2087 FDA-approved drugs.