Interaction of the new inhibitor paxlovid (PF-07321332) and ivermectin with the monomer of the main protease SARS-CoV-2: A volumetric study based on molecular dynamics, elastic networks, classical thermodynamics and SPT.

Alvarado, Ysaias José, Olivarez, Yosmari, Lossada, Carla, Vera-Villalobos, Joan, Paz, José Luis, Vera, Eddy, Loroño, Marcos, Vivas, Alejandro, Torres, Fernando Javier, Jeffreys, Laura ORCID: https://orcid.org/0000-0002-0607-6116, Hurtado-León, María Laura and González-Paz, Lenin (2022) 'Interaction of the new inhibitor paxlovid (PF-07321332) and ivermectin with the monomer of the main protease SARS-CoV-2: A volumetric study based on molecular dynamics, elastic networks, classical thermodynamics and SPT.'. Computational Biology and Chemistry, Vol 99, p. 107692.

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Abstract

The COVID-19 pandemic has accelerated the study of drugs, most notably ivermectin and more recently Paxlovid (PF-07321332) which is in phase III clinical trials with experimental data showing covalent binding to the viral protease M . Theoretical developments of catalytic site-directed docking support thermodynamically feasible non-covalent binding to M . Here we show that Paxlovid binds non-covalently at regions other than the catalytic sites with energies stronger than reported and at the same binding site as the ivermectin B1a homologue, all through theoretical methodologies, including blind docking. We volumetrically characterize the non-covalent interaction of the ivermectin homologues (avermectins B1a and B1b) and Paxlovid with the mM monomer, through molecular dynamics and scaled particle theory (SPT). Using the fluctuation-dissipation theorem (FDT), we estimated the electric dipole moment fluctuations at the surface of each of complex involved in this study, with similar trends to that observed in the interaction volume. Using fluctuations of the intrinsic volume and the number of flexible fragments of proteins using anisotropic and Gaussian elastic networks (ANM+GNM) suggests the complexes with ivermectin are more dynamic and flexible than the unbound monomer. In contrast, the binding of Paxlovid to mM shows that the mM -PF complex is the least structurally dynamic of all the species measured in this investigation. The results support a differential molecular mechanism of the ivermectin and PF homologues in the mM monomer. Finally, the results showed that Paxlovid despite beingbound in different sites through covalent or non-covalent forms behaves similarly in terms of its structural flexibility and volumetric behaviour.

Item Type:	Article
Subjects:	QV Pharmacology > QV 4 General works WC Communicable Diseases > WC 20 Research (General) WC Communicable Diseases > Virus Diseases > Viral Respiratory Tract Infections. Respirovirus Infections > WC 506 COVID-19
Faculty: Department:	Biological Sciences > Department of Tropical Disease Biology
Digital Object Identifer (DOI):	https://doi.org/10.1016/j.compbiolchem.2022.107692
SWORD Depositor:	JISC Pubrouter
Depositing User:	JISC Pubrouter
Date Deposited:	07 Sep 2022 15:39
Last Modified:	13 Jun 2023 15:17
URI:	https://archive.lstmed.ac.uk/id/eprint/20582

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