Stabilization of the dimeric state of SARS-CoV-2 main protease by GC376 and Nirmatrelvir

DOI: 10.3390/ijms24076062

Authors: Alessandro Paciaroni (University of Perugia) , Valeria Libera (University of Perugia; National Research Council-CNR) , Francesca Ripanti (University of Perugia) , Andrea Orecchini (University of Perugia) , Caterina Petrillo (University of Perugia) , Daniela Francisci (University of Perugia) , Elisabetta Schiaroli (University of Perugia) , Samuele Sabbatini (University of Perugia) , Anna Gidari (University of Perugia) , Elisa Bianconi (University of Perugia) , Antonio Macchiarulo (University of Perugia) , Rohanah Hussain (Diamond Light Source) , Lucia Silvestrini (Polytechnic University of Marche) , Paolo Moretti (Polytechnic University of Marche) , Norhan Belhaj (Polytechnic University of Marche) , Matteo Vercelli (Polytechnic University of Marche) , Yessica Roque (Polytechnic University of Marche) , Paolo Mariani (Polytechnic University of Marche) , Lucia Comez (National Research Council-CNR) , Francesco Spinozzi (Polytechnic University of Marche)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: International Journal Of Molecular Sciences , VOL 24

State: Published (Approved)
Published: March 2023
Diamond Proposal Number(s): 29982 , 32331

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.

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

Diamond Keywords: COVID-19; Viruses; Enzymes

Subject Areas: Biology and Bio-materials, Medicine


Instruments: B21-High Throughput SAXS , B23-Circular Dichroism

Added On: 29/03/2023 15:00

Discipline Tags:

Pathogens Infectious Diseases Health & Wellbeing Structural biology Biophysics Drug Discovery Life Sciences & Biotech

Technical Tags:

Scattering Spectroscopy Small Angle X-ray Scattering (SAXS) Circular Dichroism (CD)