Mechanism of non-competitive inhibition of the SARS-CoV-2 3CL protease dimerization: Therapeutic and clinical promise of the lichen secondary metabolite perlatolinic acid

In response to the COVID-19 pandemic, identifying effective treatments against SARS-CoV-2 has become of utmost importance. This study elucidates the mechanism by which perlatolinic acid, a lichen-derived secondary metabolite, non-competitively inhibits the dimerization of the SARS-CoV-2 3CL protease, a pivotal enzyme in the virus lifecycle. Utilising a combination of kinetic parameter determination, inhibition assays, and molecular docking studies, we demonstrate that perlatolinic acid effectively disrupts the enzymatic function by binding at the dimer interface with a measured <i>K</i> _<i>i</i> value of 0.67 μM, thereby impeding the protease catalytic activity essential for viral replication. Molecular docking studies further corroborate the binding specificity of perlatolinic acid to the dimer interface, which is attributed to the loss of key interactions essential for dimerization, consequently impairing catalytic activity, highlighting its potential as a scaffold for developing broad-spectrum antiviral drugs. Despite a dose-dependent cytotoxicity of perlatolinic acid, its <i>TC</i> _<i>50</i> is approximately 43 times higher than the <i>K</i> _<i>i</i> value. Our findings suggest that perlatolinic acid holds significant promise as a lead compound for the development of new therapeutics against COVID-19, warranting further investigation and clinical evaluation. In conclusion, the study sheds light on the therapeutic potential of natural compounds in combating SARS-CoV-2, paving the way for the exploration of lichen secondary metabolites as a reservoir of potential antiviral agents.