Pseudo-Dipeptide Bearing α,α-Difluoromethyl Ketone Moiety as Electrophilic Warhead with Activity against Coronaviruses

The synthesis of alpha-fluorinated methyl ketones has always been challenging. New methods based on the homologation chemistry via nucleophilic halocarbenoid transfer, carried out recently in our labs, allowed us to design and synthesize a target-directed dipeptidyl alpha,alpha-difluoromethyl ketone (DFMK) 8 as a potential antiviral agent with activity against human coronaviruses. The ability of the newly synthesized compound to inhibit viral replication was evaluated by a viral cytopathic effect (CPE)-based assay performed on MCR5 cells infected with one of the four human coronaviruses associated with respiratory distress, i.e., hCoV-229E, showing antiproliferative activity in the micromolar range (EC50 = 12.9 +/- 1.22 mu M), with a very low cytotoxicity profile (CC50 = 170 +/- 3.79 mu M, 307 +/- 11.63 mu M, and 174 +/- 7.6 mu M for A549, human embryonic lung fibroblasts (HELFs), and MRC5 cells, respectively). Docking and molecular dynamics simulations studies indicated that 8 efficaciously binds to the intended target hCoV-229E main protease (M-pro). Moreover, due to the high similarity between hCoV-229E M-pro and SARS-CoV-2 M-pro, we also performed the in silico analysis towards the second target, which showed results comparable to those obtained for hCoV-229E M-pro and promising in terms of energy of binding and docking pose.

Automated summary

A new method successfully synthesized a potential antiviral agent against coronaviruses, inhibiting viral replication with low cytotoxicity. The compound showed promising antiproliferative activity in cells and effectively bound to the target proteinase, with potential for activity against SARS-CoV-2.