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

• Published in: International journal of molecular sciences 2021-01, Vol.22 (3), p.1398
• Main Authors: Citarella, Andrea, Gentile, Davide, Rescifina, Antonio, Piperno, Anna, Mognetti, Barbara, Gribaudo, Giorgio, Sciortino, Maria Teresa, Holzer, Wolfgang, Pace, Vittorio, Micale, Nicola
• Format: Article
• Language: English
• Subjects: A549 Cells; Antiviral Agents - chemistry; Antiviral Agents - pharmacology; Binding Sites; Cell Line; Chemistry; Coronaviridae; coronavirus; Coronavirus 229E, Human - metabolism; Coronavirus M Proteins - chemistry; Coronavirus M Proteins - metabolism; Coronaviruses; COVID-19; COVID-19 - pathology; COVID-19 - virology; cysteine proteases; Cytotoxicity; difluoromethyl ketone; Dipeptides - chemistry; Embryo fibroblasts; Embryos; Fibroblasts; hCoV-229E; Hepatitis; HIV; Homology; Human immunodeficiency virus; Humans; Infections; Ketones; Ketones - chemistry; Molecular docking; Molecular Docking Simulation; Molecular dynamics; Molecular Dynamics Simulation; Potassium; RNA polymerase; SARS-CoV-2 - isolation & purification; SARS-CoV-2 - metabolism; SARS-CoV-2 Mpro; Severe acute respiratory syndrome coronavirus 2; Thermodynamics; Viral infections; Viral Matrix Proteins - chemistry; Viral Matrix Proteins - metabolism; Virus Replication - drug effects; Viruses
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms22031398

The synthesis of α-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 α,α-difluoromethyl ketone (DFMK) 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 (EC = 12.9 ± 1.22 µM), with a very low cytotoxicity profile (CC = 170 ± 3.79 µM, 307 ± 11.63 µM, and 174 ± 7.6 µM for A549, human embryonic lung fibroblasts (HELFs), and MRC5 cells, respectively). Docking and molecular dynamics simulations studies indicated that efficaciously binds to the intended target hCoV-229E main protease (M ). Moreover, due to the high similarity between hCoV-229E M and SARS-CoV-2 M , we also performed the in silico analysis towards the second target, which showed results comparable to those obtained for hCoV-229E M and promising in terms of energy of binding and docking pose.