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Alvarado YJ, Olivarez Y, Lossada C, Vera-Villalobos J, Paz JL, Vera E, Loroño M, Vivas A, Torres FJ, Jeffreys LN, Hurtado-León ML, González-Paz L. 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. Comput Biol Chem 2022; 99:107692. [PMID: 35640480 PMCID: PMC9107165 DOI: 10.1016/j.compbiolchem.2022.107692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/28/2022] [Accepted: 05/02/2022] [Indexed: 02/04/2023]
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 Mpro. Theoretical developments of catalytic site-directed docking support thermodynamically feasible non-covalent binding to Mpro. 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 mMpro 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 mMpro shows that the mMpro-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 mMpro 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.
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Affiliation(s)
- Ysaias José Alvarado
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Bolivarian Republic of Venezuela.
| | - Yosmari Olivarez
- Universidad del Zulia (LUZ). Facultad Experimental de Ciencias (FEC), Departamento de Quimica, Laboratorio de Electronica Molecular, 4001 Maracaibo, Bolivarian Republic of Venezuela
| | - Carla Lossada
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Bolivarian Republic of Venezuela
| | - Joan Vera-Villalobos
- Facultad de Ciencias Naturales y Matemáticas, Departamento de Química y Ciencias Ambientales, Laboratorio de Análisis Químico Instrumental (LAQUINS), Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - José Luis Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Eddy Vera
- Universidad del Zulia (LUZ). Facultad Experimental de Ciencias (FEC), Departamento de Quimica, Laboratorio de Electronica Molecular, 4001 Maracaibo, Bolivarian Republic of Venezuela
| | - Marcos Loroño
- Departamento Académico de Química Analítica e Instrumental, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Alejandro Vivas
- Universidad del Zulia (LUZ). Facultad Experimental de Ciencias (FEC), Departamento de Quimica, Laboratorio de Electronica Molecular, 4001 Maracaibo, Bolivarian Republic of Venezuela
| | - Fernando Javier Torres
- Grupo de Química Computacional y Teórica (QCT-UR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Grupo de Química Computacional y Teórica (QCT-USFQ), Instituto de Simulación Computacional (ISC-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Laura N Jeffreys
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - María Laura Hurtado-León
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio de Genética y Biología Molecular (LGBM), Maracaibo 4001, Zulia, Bolivarian Republic of Venezuela
| | - Lenin González-Paz
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio de Genética y Biología Molecular (LGBM), Maracaibo 4001, Zulia, Bolivarian Republic of Venezuela; Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Estudios Botanicos y Agroforestales, (CEBA), Laboratorio de Proteccion Vegetal, 4001 Maracaibo, Bolivarian Republic of Venezuela.
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Li C, Lin D, Zhao W. Electric Field Induced Dewetting of Hydrophobic Nanocavities at Ambient Temperature. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E736. [PMID: 32290614 PMCID: PMC7221969 DOI: 10.3390/nano10040736] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/09/2020] [Accepted: 04/09/2020] [Indexed: 11/26/2022]
Abstract
The understanding of water dewetting in nanoporous materials is of great importance in various fields of science and technology. Herein, we report molecular dynamics simulation results of dewetting of water droplet in hydrophobic nanocavities between graphene walls under the influence of electric field. At ambient temperature, the rate of dewetting induced by electric field is significantly large. Whereas, it is a very low rate of dewetting induced by high temperature (423 K) due to the strong interaction of the hydrogen-bonding networks of water droplets in nanocavities. In addition, the electric filed induced formation of a water column has been found in a vacuum chamber. When the electric field is turned off, the water column will transform into a water droplet. Importantly, the results demonstrate that the rate of electric field-induced dewetting increases with growth of the electric field. Overall, our results suggest that electric field may have a great potential application for nanomaterial dewetting.
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Affiliation(s)
| | - Dongdong Lin
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China;
| | - Wenhui Zhao
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China;
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Rozenbaum VM, Dekhtyar ML, Lin SH, Trakhtenberg LI. Photoinduced diffusion molecular transport. J Chem Phys 2016. [DOI: 10.1063/1.4960622] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Viktor M. Rozenbaum
- Chuiko Institute of Surface Chemistry, National Academy of Sciences of Ukraine, Generala Naumova St. 17, Kiev 03164, Ukraine
| | - Marina L. Dekhtyar
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanskaya St. 5, Kiev 02094, Ukraine
| | - Sheng Hsien Lin
- Department of Applied Chemistry, National Chiao Tung University, 1001 Ta Hsuen Road, Hsinchu 300, Taiwan
| | - Leonid I. Trakhtenberg
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, Kosygin Street 4, Moscow 119991, Russia and Moscow Institute of Physics and Technology (State University), Institutskii Per. 9, Dolgoprudnyi, Moscow Region 141700, Russia
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4
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Zhao WH, Bai J, Yuan LF, Yang J, Zeng XC. Ferroelectric hexagonal and rhombic monolayer ice phases. Chem Sci 2014. [DOI: 10.1039/c3sc53368a] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Two new monolayer ice phases are predicted from molecular dynamics simulations, both proven to be ferroelectric.
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Affiliation(s)
- Wen-Hui Zhao
- Department of Chemical Physics
- Hefei National Laboratory for Physical Sciences at Microscale
- University of Science and Technology of China
- Hefei, China
| | - Jaeil Bai
- Department of Chemistry and Nebraska Center for Materials and Nanoscience
- University of Nebraska-Lincoln
- Lincoln, USA
| | - Lan-Feng Yuan
- Department of Chemical Physics
- Hefei National Laboratory for Physical Sciences at Microscale
- University of Science and Technology of China
- Hefei, China
| | - Jinlong Yang
- Department of Chemical Physics
- Hefei National Laboratory for Physical Sciences at Microscale
- University of Science and Technology of China
- Hefei, China
| | - Xiao Cheng Zeng
- Department of Chemistry and Nebraska Center for Materials and Nanoscience
- University of Nebraska-Lincoln
- Lincoln, USA
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Dekhtyar ML, Rozenbaum VM. Symmetry interplay in Brownian photomotors: From a single-molecule device to ensemble transport. J Chem Phys 2012; 137:124306. [PMID: 23020330 DOI: 10.1063/1.4754274] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Unlike most of Brownian motor models in which the state of a point particle is described by a single scalar fluctuating parameter, we consider light-induced dichotomic fluctuations of electron density distributions in an extended molecule moving in the electrostatic periodic potential of a polar substrate. This model implies that the potential energy profiles of two motor states differ substantially and their symmetry is dictated by the interplay between the symmetries of the substrate potential and of molecular electronic states. As shown, a necessary condition for the occurrence of directed motion, the asymmetry of the potential energy profiles, is satisfied for (i) symmetric electron density distributions in molecules on asymmetric substrates and (ii) asymmetric electron density distributions in molecules on symmetric substrates. In the former case, the average velocity of directed motion is independent of molecular orientations and the ensemble of molecules moves as a whole, whereas in the latter case, oppositely oriented molecules move counterdirectionally thus causing the ensemble to diffuse. Using quantum chemical data for a specific organic-based photomotor as an example, we demonstrate that the behavior of molecular ensembles is controllable by switching on/off resonance laser radiation: they can be transported as a whole or separated into differently oriented molecules depending on the ratio of symmetric and antisymmetric contributions to the substrate electrostatic potential and to the molecular electron density distributions.
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Affiliation(s)
- Marina L Dekhtyar
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanskaya str. 5, Kiev 02094, Ukraine.
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Hu X, Elghobashi-Meinhardt N, Gembris D, Smith JC. Response of water to electric fields at temperatures below the glass transition: A molecular dynamics analysis. J Chem Phys 2011; 135:134507. [DOI: 10.1063/1.3643077] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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