# In Silico Optimization of Inhibitors of the 3-Chymotrypsin-like Protease of SARS-CoV-2

## TL;DR

This study uses computer modeling to design better inhibitors for a key SARS-CoV-2 enzyme, potentially leading to more effective treatments for COVID-19.

## Contribution

The study introduces a novel QSAR pharmacophore model and identifies new IPCL analogues with improved predicted potency against SARS-CoV-2 3CLpro.

## Key findings

- A QSAR model explained 92% of the variation in 3CLpro inhibition data using free energy calculations.
- 39 promising IPCL analogues were identified from a virtual library of over 567,000 compounds.
- The best inhibitor candidate IPCL 80-27-74-4 has a predicted IC50 of 0.8 nM, significantly better than known IPCLs.

## Abstract

In this study, new improved inhibitors of the viral enzyme 3-chymotrypsin-like protease (3CLpro) were designed using structure-based drug design techniques in an effort to discover more effective treatment of coronavirus disease 2019 (COVID-19). Three-dimensional models of 3CLpro–inhibitor complexes were prepared by in situ modification of the crystal structure of the submicromolar covalent inhibitor IPCL6 for a set of 25 known inhibitors with published inhibitory potencies (IC50exp). The QSAR model was prepared with a reasonable correlation between the calculated free energies of formation of the 3CLpro-IPCL complex (∆∆Gcom) and the experimentally determined activities
IC50exp, which explained approximately 92% of the variation in the 3CLpro inhibition data. A similar agreement was achieved for the QSAR pharmacophore model (PH4) built on the basis of the active conformations of the IPCL inhibitors bound at the active site of the 3CLpro. The virtual combinatorial library of more than 567,000 IPCL analogues was screened in silico using the PH4 model and resulted in the identification of 39 promising analogues. The best inhibitors designed in this study show high predicted affinity for the 3CLpro protease, as well as favourable predicted ADME properties. For the best new virtual inhibitor candidate IPCL 80-27-74-4, the inhibitory concentration
IC50pre was predicted equal to 0.8 nM, which represents a significant improvement in the inhibitory potency of known IPCLs. Ultimately, molecular dynamics simulations of the 12 newly designed top-scoring IPCL inhibitors demonstrated that the 3CLpro–inhibitor complexes exhibited good structural stability, confirming the potential for further development of the designed IPCL analogues.