2. Academic Validation
  3. Stabilization of the Dimeric State of SARS-CoV-2 Main Protease by GC376 and Nirmatrelvir

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

  • Int J Mol Sci. 2023 Mar 23;24(7):6062. doi: 10.3390/ijms24076062.
Alessandro Paciaroni 1,  Valeria Libera 1 2,  Francesca Ripanti 1,  Andrea Orecchini 1,  Caterina Petrillo 1,  Daniela Francisci 3,  Elisabetta Schiaroli 3,  Samuele Sabbatini 4,  Anna Gidari 3,  Elisa Bianconi 5,  Antonio Macchiarulo 5,  Rohanah Hussain 6,  Lucia Silvestrini 7,  Paolo Moretti 7,  Norhan Belhaj 7,  Matteo Vercelli 7,  Yessica Roque 7,  Paolo Mariani 7,  Lucia Comez 2,  Francesco Spinozzi 7
Affiliations

Affiliations

  • 1 Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy.
  • 2 Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy.
  • 3 Department of Medicine and Surgery, Clinic of Infectious Diseases, University of Perugia, Piazzale Gambuli, 06129 Perugia, Italy.
  • 4 Department of Medicine and Surgery, Medical Microbiology Section, University of Perugia, Piazzale Gambuli, 06129 Perugia, Italy.
  • 5 Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo, 06123 Perugia, Italy.
  • 6 Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
  • 7 Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy.
PMID: 37047038 DOI: 10.3390/ijms24076062
Abstract

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.

Keywords

COVID-19; PF-07321332; Paxlovid; SARS-CoV-2; circular dichroism; dimerization; inhibitor; main protease; microscale thermophoresis; small angle X-ray scattering.

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