Stabilization of the Dimeric State of SARS-CoV-2 Main Protease by GC376 and Nirmatrelvir

• Published in: International journal of molecular sciences Vol. 24; no. 7; p. 6062
• Main Authors: Paciaroni, Alessandro, Libera, Valeria, Ripanti, Francesca, Orecchini, Andrea, Petrillo, Caterina, Francisci, Daniela, Schiaroli, Elisabetta, Sabbatini, Samuele, Gidari, Anna, Bianconi, Elisa, Macchiarulo, Antonio, Hussain, Rohanah, Silvestrini, Lucia, Moretti, Paolo, Belhaj, Norhan, Vercelli, Matteo, Roque, Yessica, Mariani, Paolo, Comez, Lucia, Spinozzi, Francesco
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 23.03.2023; MDPI
• Subjects: Antiviral activity; Antiviral agents; Antiviral Agents - chemistry; Antiviral Agents - pharmacology; Binding; Binding sites; Bioavailability; Catalytic activity; Coronaviridae; Coronaviruses; COVID-19; COVID-19 vaccines; Cysteine Endopeptidases - metabolism; Dimerization; Drug development; Drugs; Enzymes; Equilibrium; Feline infectious peritonitis; Health aspects; Humans; Hydrogen; Hydrogen bonding; Hydrogen bonds; Infections; inhibitor; Inhibitors; Ligands; main protease; Middle East respiratory syndrome; Molecular Docking Simulation; Paxlovid; Peritonitis; Polyproteins; Protease; Protease Inhibitors - chemistry; Protease Inhibitors - pharmacology; Proteases; Proteinase; Proteinase inhibitors; Proteins; Respiratory diseases; SARS-CoV-2; SARS-CoV-2 - metabolism; Severe acute respiratory syndrome coronavirus 2; Germany; Middle East; COVID-19; Paxlovid; SARS-CoV-2; inhibitor; main protease; dimerization; microscale thermophoresis; circular dichroism; PF-07321332; small angle X-ray scattering
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms24076062

The main protease (Mpro or 3CLpro) is an enzyme that is evolutionarily conserved among different genera of coronaviruses. As it is essential for processing and maturing viral polyproteins, Mpro has been identified as a promising target for the development of broad-spectrum drugs against coronaviruses. Like SARS-CoV and MERS-CoV, the mature and active form of SARS-CoV-2 Mpro is a dimer composed of identical subunits, each with a single active site. Individual monomers, however, have very low or no catalytic activity. As such, inhibition of Mpro can be achieved by molecules that target the substrate binding pocket to block catalytic activity or target the dimerization process. In this study, we investigated GC376, a transition-state analog inhibitor of the main protease of feline infectious peritonitis coronavirus, and Nirmatrelvir (NMV), an oral, bioavailable SARS-CoV-2 Mpro inhibitor with pan-human coronavirus antiviral activity. Our results show that both GC376 and NMV are capable of strongly binding to SARS-CoV-2 Mpro and altering the monomer-dimer equilibrium by stabilizing the dimeric state. This behavior is proposed to be related to a structured hydrogen-bond network established at the Mpro active site, where hydrogen bonds between Ser1' and Glu166/Phe140 are formed in addition to those achieved by the latter residues with GC376 or NMV.