Potency Prediction of Covalent Inhibitors against SARS-CoV-2 3CL-like Protease and Multiple Mutants by Multiscale...

Area of Science:

• Biochemistry
• Computational Chemistry
• Drug Discovery

Background:

• 3-Chymotrypsin-like protease (3CLpro) is a critical target for antiviral therapies against coronaviruses.
• Covalent inhibitors targeting 3CLpro require detailed mechanistic understanding for predicting efficacy against viral variants.

Purpose of the Study:

• To explore covalent inhibition mechanisms of five inhibitors against SARS-CoV-2 3CLpro and its mutants using molecular dynamics simulations.
• To evaluate the accuracy of computational methods in predicting inhibitor binding affinity, reactivity, and drug resistance.

Main Methods:

• Classical and hybrid QM/MM molecular dynamics simulations were employed.
• Binding affinity and reactivity of inhibitors were calculated and compared with experimental data.
• Inhibitory potency against wild-type and mutant 3CLpro was predicted and validated with enzymatic assays.

Main Results:

• Simulation results showed high consistency with experimental data for binding affinity and reactivity.
• Predicted inhibitory potencies against 3CLpro mutants (L167F, E166V, T21I/E166V) matched experimental IC50 values.
• Mutagenesis impacts structural dynamics, affecting noncovalent binding and covalent reaction free energy in an inhibitor-dependent manner, leading to varied drug resistance.

Conclusions:

• The simulation protocol effectively evaluates the reactivity and potency of covalent inhibitors.
• Elucidated molecular mechanisms provide insights into drug resistance and guide structure-based drug design against emerging coronaviruses.
• The compound '11a' demonstrated no resistance against the tested 3CLpro mutants, highlighting its potential therapeutic value.