1. The dimer-monomer equilibrium of SARS-CoV-2 main protease is affected by small molecule inhibitors
- Author
-
Antonino Lauria, Lucia Comez, Lucrezia Savini, Yuri Gerelli, Francesco Spinozzi, Antonio Palumbo Piccionello, Paola Marzullo, Lucia Silvestrini, Norhan Belhaj, Alessandro Paciaroni, Caterina Petrillo, Paolo Mariani, Valeria Libera, Maria Grazia Ortore, Silvestrini L., Belhaj N., Comez L., Gerelli Y., Lauria A., Libera V., Mariani P., Marzullo P., Ortore M.G., Palumbo Piccionello A., Petrillo C., Savini L., Paciaroni A., and Spinozzi F.
- Subjects
0301 basic medicine ,Molecular biology ,Protein Conformation ,Science ,medicine.medical_treatment ,Dimer ,Biophysics ,Plasma protein binding ,010402 general chemistry ,Antiviral Agents ,01 natural sciences ,Article ,Dissociation (chemistry) ,03 medical and health sciences ,chemistry.chemical_compound ,Protein structure ,X-Ray Diffraction ,Drug Discovery ,medicine ,Humans ,Protease Inhibitors ,Coronavirus 3C Proteases ,Virtual screening ,Multidisciplinary ,Protease ,SARS-CoV-2 ,Chemistry ,SARS-CoV-2, main protease Mpro, enzymatic activity inhibition, Small Angle X-ray Scattering, small inhibitors, virtual screening ,COVID-19 ,Computational Biology ,Small molecule ,Computational biology and bioinformatics ,0104 chemical sciences ,Molecular Docking Simulation ,Dissociation constant ,030104 developmental biology ,Medicine ,Thermodynamics ,Dimerization ,Protein Binding - Abstract
The maturation of coronavirus SARS-CoV-2, which is the etiological agent at the origin of the COVID-19 pandemic, requires a main protease Mpro to cleave the virus-encoded polyproteins. Despite a wealth of experimental information already available, there is wide disagreement about the Mpro monomer-dimer equilibrium dissociation constant. Since the functional unit of Mpro is a homodimer, the detailed knowledge of the thermodynamics of this equilibrium is a key piece of information for possible therapeutic intervention, with small molecules interfering with dimerization being potential broad-spectrum antiviral drug leads. In the present study, we exploit Small Angle X-ray Scattering (SAXS) to investigate the structural features of SARS-CoV-2 Mpro in solution as a function of protein concentration and temperature. A detailed thermodynamic picture of the monomer-dimer equilibrium is derived, together with the temperature-dependent value of the dissociation constant. SAXS is also used to study how the Mpro dissociation process is affected by small inhibitors selected by virtual screening. We find that these inhibitors affect dimerization and enzymatic activity to a different extent and sometimes in an opposite way, likely due to the different molecular mechanisms underlying the two processes. The Mpro residues that emerge as key to optimize both dissociation and enzymatic activity inhibition are discussed.
- Published
- 2021