Development of 2-chloroquinoline based heterocyclic frameworks as dual inhibitors of SARS-CoV-2 M(Pro) and PL(Pro)

Evolution of new variants of SARS-CoV-2 warrant the need for the continued efforts in identifying target-oriented new drugs. Dual targeting agents against M(Pro) and PL(Pro) not only overcome the incomplete efficacy but also the drug resistance, which is common problem. Since both these are cysteine proteases, we designed 2-chloroquinoline based molecules with additional imine moiety in the middle as possible nucleophilic warheads. In the first round of design and synthesis, three molecules (C3, C4 and C5) inhibited (Ki < 2 μM) only M(Pro) by binding covalently to C145 and one molecule (C10) inhibited both the proteases non-covalently (Ki < 2 μM) with negligible cytotoxicity. Further conversion of the imine in C10 to azetidinone (C11) improved the potency against both the enzymes in the nanomolar range (820 nM against M(Pro) and 350 nM against PL(Pro)) with no cytotoxicity. Conversion of imine to thiazolidinone (C12), reduced the inhibition by 3–5 folds against both the enzymes. Biochemical and computational studies suggest that C10–C12 bind in the substrate binding pocket of M(Pro) and in the BL2 loop of the PL(Pro). Since these dual inhibitors have least cytotoxicity, they could be further explored as therapeutics against the SARS-CoV-2 and other analogous viruses.