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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 et al., Computational Biology and Chemistry, doi:10.1016/j.compbiolchem.2022.107692
May 2022  
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Ivermectin for COVID-19
4th treatment shown to reduce risk in August 2020
 
*, now known with p < 0.00000000001 from 102 studies, recognized in 22 countries.
Lower risk for mortality, ventilation, ICU admission, hospitalization, recovery, cases, and viral clearance.
No treatment is 100% effective. Protocols combine complementary and synergistic treatments. * >10% efficacy in meta analysis with ≥3 clinical studies.
4,000+ studies for 60+ treatments. c19ivm.org
In Silico study comparing ivermectin and paxlovid Mpro interaction, showing similar interaction for paxlovid and the ivermectin B1a homologue, a different mechanism for ivermectin B1b, and interaction at different sites for paxlovid.
66 preclinical studies support the efficacy of ivermectin for COVID-19:
28 In Silico studies Alvarado, Aminpour, Bello, Chellasamy, Choudhury, Eweas, Francés-Monerris, Francés-Monerris (B), González-Paz, González-Paz (B), Kalhor, Kern, Lehrer, Maurya, Muthusamy, Oranu, Parvez, Parvez (B), Qureshi, Rana, Saha, Schöning, Suravajhala, Swargiary, Udofia, Umar, Vottero, Zhao
24 In Vitro studies Boschi, Caly, Croci, De Forni, Delandre, Fauquet, García-Aguilar, Jeffreys, Jitobaom, Jitobaom (B), Jitobaom (C), Li, Liu, Liu (B), Mody, Mountain Valley MD, Munson, Saha (B), Segatori, Shahin, Surnar, Yesilbag, Zhang, Zheng
14 In Vivo animal studies Abd-Elmawla, Albariqi, Arévalo, Chaccour, de Melo, Errecalde, Gao, Ma, Madrid, Mountain Valley MD, Uematsu, Yan, Zhang, Zheng
Ivermectin, better known for antiparasitic activity, is a broad spectrum antiviral with activity against many viruses including H7N7 Götz, Dengue Jitobaom, Tay, Wagstaff, HIV-1 Wagstaff, Simian virus 40 Wagstaff (B), Zika Barrows, Jitobaom, Yang, West Nile Yang, Yellow Fever Mastrangelo, Varghese, Japanese encephalitis Mastrangelo, Chikungunya Varghese, Semliki Forest virus Varghese, Human papillomavirus Li, Epstein-Barr Li, BK Polyomavirus Bennett, and Sindbis virus Varghese.
Ivermectin inhibits importin-α/β-dependent nuclear import of viral proteins Götz, Kosyna, Wagstaff, Wagstaff (B), shows spike-ACE2 disruption at 1nM with microfluidic diffusional sizing Fauquet, binds to glycan sites on the SARS-CoV-2 spike protein preventing interaction with blood and epithelial cells and inhibiting hemagglutination Boschi, Scheim, shows dose-dependent inhibition of wildtype and omicron variants Shahin, exhibits dose-dependent inhibition of lung injury Abd-Elmawla, Ma, may inhibit SARS-CoV-2 via IMPase inhibition Jitobaom, may inhibit SARS-CoV-2 induced formation of fibrin clots resistant to degradation Vottero, inhibits SARS-CoV-2 3CLpro Mody, may inhibit SARS-CoV-2 RdRp activity Parvez (B), may minimize viral myocarditis by inhibiting NF-κB/p65-mediated inflammation in macrophages Gao, may be beneficial for COVID-19 ARDS by blocking GSDMD and NET formation Liu (C), shows protection against inflammation, cytokine storm, and mortality in an LPS mouse model sharing key pathological features of severe COVID-19 DiNicolantonio, Zhang, may be beneficial in severe COVID-19 by binding IGF1 to inhibit the promotion of inflammation, fibrosis, and cell proliferation that leads to lung damage Zhao, may minimize SARS-CoV-2 induced cardiac damage Liu, Liu (B), increases Bifidobacteria which play a key role in the immune system Hazan, has immunomodulatory Munson and anti-inflammatory DiNicolantonio (B), Yan properties, and has an extensive and very positive safety profile Descotes.
Important missing comments or errors? Let us know.
Alvarado et al., 14 May 2022, peer-reviewed, 12 authors. Contact: alvaradoysaias@gmail.com, lgonzalezpaz@gmail.com.
In Silico studies are an important part of preclinical research, however results may be very different in vivo.
This PaperIvermectinAll
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
Ysaias José Alvarado, Yosmari Olivarez, Carla Lossada, Joan Vera-Villalobos, José Luis Paz, Eddy Vera, Marcos Loroño, Alejandro Vivas, Fernando Javier Torres, María Laura N Jeffreys, María Laura Hurtado-León, Lenin González-Paz
Computational Biology and Chemistry, doi:10.1016/j.compbiolchem.2022.107692
This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Under this same study strategy, it was found that PF-07321332 can also covalently bind to another region of the monomer (a drug multi-site for M pro ), but both complexes have similar structural flexibility and volumetric properties. Finally, we consider that this type of study can help to understand the mechanism by which a ligand can block the homodimerization of this important monomer to form the dimeric protease dM pro and in turn help in studies of activity-structure relationships for the design of new drugs. Declaration of competing interest. The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Highlights
References
Adhikari, Park, Kwon, Hydrogen-bond dynamics and energetics of biological water, Chempluschem, doi:10.1002/cplu.202000744
Aggarwal, Biswas, Interaction volume is a measure of the aggregation propensity of amyloid-β, J. Phys. Chem. Lett, doi:10.1021/acs.jpclett.0c00922
Aghdam, Habibi, Taheri, Using informative features in machine learning based method for COVID-19 drug repurposing, J. Cheminform, doi:10.1186/s13321-021-00553-9
Agrawal, Singh, Srivastava, Singh, Kishore et al., Benchmarking of different molecular docking methods for protein-peptide docking, BMC bioinformatics, doi:10.1186/s12859-018-2449-y
Ahmad, Batool, Ain, Kim, Choi, Exploring the binding mechanism of PF-07321332 SARS-CoV-2 protease inhibitor through molecular dynamics and binding free energy simulations, Int. J. Mol. Sci, doi:10.33263/briac112.95669586
Alvarado, Ballestas-Barrientos, Restrepo, Vera-Villalobos, Ferrer-Amado et al., Volume-related properties of thiophene and furan-2-carboxaldehyde phenylhydrazone derivatives in DMSO: A discussion about non-intrinsic contribution, J. Chem. Thermodyn, doi:10.1016/j.jct.2015.01.016
Alvarado, Ferrebuz, Paz, Rodriguez-Lugo, Restrepo et al., Surface behavior of BSA/water/carbohydrate systems from molecular polarizability measurements, J. Phys. Chem. B, doi:10.1021/acs.jpcb.7b11998
Alvarado, Rodríguez-Lugo, Vera-Villalobos, Ferrer-Amado, Ferrebuz et al., Non-intrinsic contribution to the limiting partial molar volume of globular proteins in water: a study comparative between a new refractometric strategy and densitometric classical approach, Biointerface Res. Appl. Chem
Alvarado, Vera-Parra, Méndez, Romero, González-Paz et al., Conformational change of ovalbumin induced by Surface cavity binding of N-phthaloyl gamma-aminobutyric acid derivative: A study theoretical and experimental, Bioint. Res. Appl. Chem, doi:10.33263/briac112.95669586
Antonopoulou, Sapountzaki, Rova, Christakopoulos, Inhibition of the main protease of SARS-CoV-2 (Mpro) by repurposing/designing drug-like substances and J o u r n a l P r e -p r o o f utilizing nature's toolbox of bioactive compounds, Computational and Structural Biotechnology Journal, doi:10.1016/j.csbj.2022.03.009
Awoonor-Williams, Abu-Saleh, Covalent and non-covalent binding free energy calculations for peptidomimetic inhibitors of SARS-CoV-2 main protease, Physical Chemistry Chemical Physics, doi:10.1039/D1CP00266J
Azam, Eid, Almutairi, Targeting SARS-CoV-2 main protease by teicoplanin: A mechanistic insight by docking, MM/GBSA and molecular dynamics simulation, Journal of molecular structure, doi:10.1016/j.molstruc.2021.131124
Azam, Taban, Eid, Iqbal, Alam et al., An in-silico analysis of ivermectin interaction with potential SARS-CoV-2 targets and host nuclear importin α, J. Biomol. Struct. Dyn, doi:10.1080/07391102.2020.1841028
Ball, Water is an active matrix of life for cell and molecular biology, Proc. Natl. Acad. Sci, doi:10.1073/pnas.1703781114
Barletta, Fernández-Alberti, Protein fluctuations and cavity changes relationship, J. Chem. Theory Comput, doi:10.1021/acs.jctc.7b00744
Barletta, Franchini, Corsico, Fernández-Alberti, Fatty acid and retinolbinding protein: Unusual protein conformational and cavity changes dictated by ligand fluctuations, J. Chem. Inf. Model, doi:10.1021/acs.jcim.9b00364
Blake, Soliman, Identification of irreversible protein splicing inhibitors as potential anti-TB drugs: insight from hybrid non-covalent/covalent docking virtual screening and molecular dynamics simulations, Medicinal Chemistry Research, doi:10.1007/s00044-013-0822-y
Brovchenko, Andrews, Oleinikova, Volumetric properties of human islet amyloid polypeptide in liquid water, Phys. Chem. Chem. Phys, doi:10.1039/B918706E
Carvallo, Hirsch, Ivermectin, aspirin, dexametasone and enoxaparin as treatment for COVID 19, J Am Med Assoc
Chalikian, Breslauer, On volume changes accompanying conformational transitions of biopolymers, Biopolymers, doi:10.1002/(SICI)1097-0282(199611)39:5%3c619::AID-BIP1%3e3.0.CO;2-Z
Chalikian, Does the release of hydration water come with a Gibbs energy contribution?, J. Chem. Thermodyn, doi:10.1016/j.jct.2021.106409
Chalikian, Excluded volume contribution to cosolvent-mediated modulation of macromolecular folding and binding reactions, Biophys. Chem, doi:10.1016/j.bpc.2015.11.001
Chalikian, Filfil, How large are the volume changes accompanying protein transitions and binding?, Biophys. Chem, doi:10.1016/s0301-4622(03)00037-1
Chalikian, Macgregor, On empirical decomposition of volumetric data, Biophys. Chem, doi:10.1016/j.bpc.2018.12.005
Chalikian, Totrov, Abagyan, Breslauer, The hydration of globular proteins as derived from volume and compressibility measurements, cross correlating thermodynamic and structural data, J. Mol. Biol, doi:10.1006/jmbi.1996.0423
Chhetri, Chettri, Rai, Sinha, Brahman, Exploration of inhibitory action of Azo imidazole derivatives against COVID-19 main protease (M pro ): A computational study, J. Mol. Struct, doi:10.1016/j.molstruc.2020.129178
Choudhury, Das, Patra, Bhattacharya, Ghosh et al., Exploring the binding efficacy of ivermectin against the key proteins of SARS-CoV-2 pathogenesis: and in silico approach, Future Virol, doi:10.2217/fvl-2020-0342
Cooper, Protein fluctuations and the thermodynamic uncertainty principle, Prog. Biophys. Mol. Biol, doi:10.1016/0079-6107(84)90008-7
Dadarlat, Post, Insights into protein compressibility from molecular dynamics simulations, J. Phys. Chem. B, doi:10.1021/jp0024118
Delandre, Gendrot, Jardot, Bideau, Boxberger et al., Antiviral Activity of Repurposing Ivermectin against a Panel of 30 Clinical SARS-CoV-2 Strains Belonging to 14 Variants, Pharmaceuticals, doi:10.3390/ph15040445
Delre, Caporuscio, Saviano, Mangiatordi, Repurposing known drugs as covalent and non-covalent inhibitors of the SARS-CoV-2 papain-like protease, Frontiers in Chemistry, doi:10.3389/fchem.2020.594009
Durojaye, Mushiana, Uzoeto, Cosmas, Udowo et al., Potential therapeutic target identification in the novel 2019 coronavirus: insight from homology modeling and blind docking study, Egyptian Journal of Medical Human Genetics, doi:10.1186/s43042-020-00081-5
Emekli, Schneidman-Duhovny, Wolfson, Nussinov, Haliloglu, Hinge Prot: automated prediction of hinges in protein structures, Proteins Struct. Funct. Bioinf, doi:10.1002/prot.21613
Ferraz, Gomes, Novaes, Trossini, Ligand and structure-based virtual screening applied to the SARS-CoV-2 main protease: an in silico repurposing study, Future Medicinal Chemistry, doi:10.4155/fmc-2020-0165
Filfil, Ratavosi, Chalikian, Binding of bovine pancreatic trypsin inhibitor to trypsinogen: Spectroscopic and volumetric studies, Biochemistry, doi:10.1021/bi030188
Fleming, Fleming, HullRad: Fast calculations of folded and disordered protein and nucleic acid hydrodynamic properties, Biophys. J, doi:10.1016/j.bpj.2018.01.002
Fornés, Electrical fluctuations on the surfaces of proteins from hydrodynamic data, J. Colloid Interface Sci, doi:10.1016/j.jcis.2008.04.036
Gautam, Chong, Chin, Zain, Rahman et al., Loop dynamics behind the affinity of DARPins towards ERK2: Molecular dynamics simulations (MDs) and elastic network model (ENM), Journal of Molecular Liquids, doi:10.1016/j.molliq.2018.10.157
Gekko, Hasegawa, Compressibility-structure relationship of globular proteins, Biochemistry, doi:10.1021/bi00369a034
González-Paz, Alvarado, Hurtado-León, Lossada, Vera-Villalobos et al., Comparative study of SARS-CoV-2 infection in different cell types: Biophysical-computational approach to the role of potential receptors, Computers in Biology and Medicine, doi:10.1016/j.compbiomed.2022.105245
González-Paz, Hurtado-León, Lossada, Fernández-Materán, Vera-Villalobos et al., Comparative study of the interaction of ivermectin with proteins of interest associates with SARS-CoV-2: A computational and biophysical approach, Biophys. Chem, doi:10.1016/j.bpc.2021.106677
González-Paz, Hurtado-León, Lossada, Fernández-Materán, Vera-Villalobos et al., Structural deformability induced in proteins of potential interest associated with COVID-19 by binding of J o u r n a l P r e -p r o o f 55 homologues present in ivermectin: Comparative study based in elastic networks models, J. Mol. Liq, doi:10.1016/j.molliq.2021.117284
González-Paz, Lossada, Fernández-Materán, Paz, Vera-Villalobos et al., Can non-steroidal anti-inflammatory drugs affect the interaction between receptor binding domain of SARS-COV-2 spike and the human ACE2 receptor? A computational biophysical study, Front. Phys, doi:10.3389/fphy.2020.587606
González-Paz, Lossada, Moncayo, Romero, Paz et al., A bioinformatics study of structural perturbation of 3CL-protease and the J o u r n a l P r e -p r o o f HR2-domain of SARS-CoV-2 induced by synergistic interaction with ivermectins, Biointerface Research in Applied Chemistry, doi:10.33263/BRIAC112.98139826
Goyal, Goyal, Targeting the dimerization of the main protease of coronaviruses: A potential broad-spectrum therapeutic strategy, ACS Comb. Sci, doi:10.1021/acscombsci.0c00058
Grahl, Alcará, Perin, Moro, Pinto et al., Evaluation of drug repositioning by molecular docking of pharmaceutical resources available in the Brazilian healthcare system against SARS-CoV-2, Informatics in medicine unlocked, doi:10.1016/j.imu.2021.100539
Grau-Expósito, Perea, Suppi, Massana, Vergara et al., Evaluation of SARS-CoV-2 entry, inflammation and new therapeutics in human lung tissue cells, PLoS pathogens, doi:10.1371/journal.ppat.1010171
Graziano, Energetics of the contact minimum configuration of two hard spheres in water, Chem. Phys. Lett, doi:10.1016/j.cplett.2017.07.030
Graziano, Non-intrinsic contribution to the partial molar volume of cavities in water, Chem. Phys. Lett, doi:10.1016/j.cplett.2006.08.065
Graziano, On the magnitude of border thickness in the partial molar volume of cavities in water, Chem. Phys. Lett, doi:10.1016/j.cplett.2013.03.052
Graziano, Partial molar volumen of n-alcohols at infinite dilution in water calculated by means of scaled particle theory, J. Chem. Phys, doi:10.1063/1.2186319
Graziano, Temperature dependence of the pairwise association of hard spheres in water, J. Phys. Soc. Jpn, doi:10.7566/JPSJ.85.024801
Guedes, Costa, Santos, Karl, Rocha et al., Drug design and repurposing with DockThor-VS web server focusing on SARS-CoV-2 therapeutic targets and their non-synonym variants, Sci. Rep, doi:10.1038/s41598-021-84700-0
Gupta, Jadaun, Kumar, Raj, Varadwaj et al., Exploration of new druglike inhibitors for serine/threonine protein phosphatase 5 of Plasmodium falciparum: a docking and simulation study, Journal of Biomolecular Structure and Dynamics, doi:10.1080/07391102.2015.1051114
Hariyanto, Halim, Rosalind, Gunawan, Kurniawan, Ivermectin and outcomes from Covid-19 pneumonia: a systematic review and meta-analysis of randomized clinical trial studies, Reviews in Medical Virology, doi:10.1002/rmv.2265
Hub, Validating solution ensembles from molecular dynamics simulation by wide-angle X-ray scattering data, Biophysical journal, doi:10.1016/j.bpj.2014.06.006
J O U R N A L P R E, -p r o o f, doi:10.1002/jcc.21256
J O U R N A L P R E, -p r o o f, doi:10.1016/j.bpj.2014.06.006
J O U R N A L P R E, -p r o o f, doi:10.1016/j.molliq.2018.10.157
Jeffreys, Pennington, Duggan, Caygill, Lopeman et al., Remdesivir-ivermectin combination displays synergistic interaction with improved in vitro activity against SARS-CoV-2, International journal of antimicrobial agents, doi:10.1016/j.ijantimicag.2022.106542
Jiang, Kirmizialtin, Sanchez, Dynamic void distribution in myoglobin and five mutants, Sci. Rep, doi:10.1038/srep04011
Jofily, Pascutti, Torres, Improving blind docking in DOCK6 through an automated preliminary fragment probing strategy, Molecules, doi:10.3390/molecules26051224
Kamerzell, Middaugh, The complex inter-relationships between protein flexibility and stability, J. Pharm. Sci, doi:10.1002/jps.21269
Kapoor, Winter, Pressure perturbation: A prime tool to study conformational substates and volume fluctuations of biomolecular assemblies, doi:10.1007/978-4-431-55840-8_2
Kasahara, Terazawa, Itaya, Goto, Nakamura et al., myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling, Biophys. Physicobiol, doi:10.2142/biophysico.BSJ-2020013
Kaur, Kaur, Banipal, Banipal, Investigations on the pH-dependent binding of sodium valproate with bovine serum albumin: A calorimetric, spectroscopic and volumetric approach, J. Chem. Thermodyn, doi:10.1016/j.jct.2020.106269
Kaur, Sharma, Banipal, Banipal, Probing the binding ability of vitamin B 1 with bovine serum albumin: Calorimetric, light scattering, spectroscopic and volumetric studies, J. Chem. Thermodyn, doi:10.1016/j.jct.2018.07.009
Kharakoz, Partial molar volumes of molecules of arbitrary shape and the effect of hydrogen bonding with water, J. Solution Chem, doi:10.1007/BF00649565
Kharakoz, Sarvazyan, Hydrational and intrinsic compressibilities of globular proteins, Biopolymers, doi:10.1002/bip.360330103
Khoury, Bashir, Tokajian, Nemer, Merhi et al., In silico evidence of beauvericin antiviral activity against SARS-CoV-2, Computers in biology and medicine, doi:10.1016/j.compbiomed.2021.105171
Khoury, Jing, Cuzzolin, Deplano, Loco et al., Computationally driven discovery of SARS-CoV-2 M pro inhibitors: from design to experimental validation, Chemical Science, doi:10.48550/arXiv.2110.05427
Kneller, Li, Phillips, Weiss, Zhang et al., Covalent narlaprevir-and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease: room-temperature X-ray and neutron crystallography, binding thermodynamics, and antiviral activity, doi:10.21203/rs.3.rs-1318037/v1
Knight, Hub, WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics, Nucleic acids research, doi:10.1093/nar/gkv309
Koulgi, Jani, Uppuladinne, Sonavane, Nath et al., Drug repurposing studies targeting SARS-CoV-2: an ensemble docking approach on drug target 3C-like protease (3CL pro ), J. Biomol. Struct. Dyn, doi:10.1080/07391102.2020.1792344
Kumar, Ter Ellen, Bouma, Troost, Van De Pol et al., Moxidectin and ivermectin inhibit SARS-CoV-2 replication in Vero E6 cells but not in human primary airway epithelium cells, Antimicrobial Agents and Chemotherapy, doi:10.1128/AAC.01543-21
Laage, Elsaesser, Hynes, Water dynamics in the hydration shells of biomolecules, Chem. Rev, doi:10.1021/acs.chemrev.6b00765
Lee, Partial molar volumen from the hard-sphere mixture model, J. Phys. Chem, doi:10.1021/j100224a026
Liang, Karagiannis, Pitsillou, Darmawan, Ng et al., Site mapping and small molecule blind docking reveal a possible target site on the SARS-CoV-2 main protease dimer interface, Computational biology and chemistry, doi:10.1016/j.compbiolchem.2020.107372
Lim, Hor, Tay, Jelani, Tan et al., Efficacy of ivermectin treatment on disease progression among adults with mild to moderate COVID-19 and comorbidities: The I-TECH randomized clinical trial, JAMA Internal Medicine, doi:10.1001/jamainternmed.2022.0189
Lindow, Baum, Bondar, Hege, Exploring cavity dynamics in biomolecular systems, BMC Bioinformatics, doi:10.1186/1471-2105-14-S19-S5
Lockbaum, Reyes, Lee, Tilvawala, Nalivaika et al., Crystal structure of SARS-CoV-2 main protease in complex with the non-covalent inhibitor ML188, Viruses, doi:10.3390/v13020174
Low, Yip, Repositioning Ivermectin for Covid-19 treatment: Molecular mechanisms of action against SARS-CoV-2 replication, Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease, doi:10.1016/j.bbadis.2021.166294
Luong, Kapoor, Winter, Pressure-A gateway to fundamental insights into protein solvation, dynamics, and function, Chemphyschem, doi:10.1002/cphc.201500669
Macchiagodena, Pagliai, Procacci, Characterization of the non-covalent interaction between the PF-07321332 inhibitor and the SARS-CoV-2 main protease, Journal of Molecular Graphics and Modelling, doi:10.1016/j.jmgm.2021.108042
Madhavi, Weerasinghe, Momot, Reorientational dynamics of molecules in liquid methane: A molecular dynamics simulation study, Journal of Molecular Liquids, doi:10.1016/j.molliq.2020.114727
Mahdian, Zarrabi, Panahi, Dabbagh, Repurposing FDA-approved drugs to fight COVID-19 using in silico methods: targeting SARS-CoV-2 RdRp enzyme and host cell receptors (ACE2, CD147) through virtual screening and molecular dynamic simulations, Informatics in medicine unlocked, doi:10.1016/j.imu.2021.100541
Marchi, Compressibility of cavities and biological water from Voronoi volumes in hydrated proteins, J. Phys. Chem. B, doi:10.1021/jp0342935
Mejía-Tamayo, Nigen, Apolinar-Valiente, Doco, Williams et al., Flexibility and hydration of amphiphilic hyperbranched arabinogalactan-protein from plant exudate: A volumetric perspective, Colloids Interfaces, doi:10.3390/colloids2010011
Monkos, A viscometric approach of pH effect on hydrodynamic properties of human serum albumin in the normal form, Gen. Physiol. Biophys, doi:10.4149/gpb_2013011
Monkos, On the hydrodynamics and temperature dependence of the solution conformation of human serum albumin from viscometry approach, Biochim. Biophys. Acta, doi:10.1016/j.bbapap.2004.03.006
Mori, Seki, Yamada, Matsumoto, Soda, Evaluation of intrinsic compressibility of proteins by molecular dynamics simulation, J. Chem. Phys, doi:10.1063/1.2219741
Morris, Huey, Lindstrom, Sanner, Belew et al., AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility, Journal of computational chemistry, doi:10.1002/jcc.21256
O'boyle, Banck, James, Morley, Vandermeersch et al., Open Babel: An open chemical toolbox, J. Cheminform, doi:10.1186/1758-2946-3-33
Osipiuk, Azizi, Dvorkin, Endres, Jedrzejczak et al., Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors, Nature communications, doi:10.1038/s41467-021-21060-3
Panikar, Shoba, Arun, Sahayarayan, Nanthini et al., Essential oils as an effective alternative for the treatment of COVID-19: Molecular interaction analysis of protease (M pro ) with pharmacokinetics and toxicological properties, J. Infect. Publ. Health, doi:10.1016/j.jiph.2020.12.037
Patel, Dubins, Pomès, Chalikian, Size dependence of cavity volume: A molecular dynamics study, Biophys. Chem, doi:10.1016/j.bpc.2011.10.001
Patil, Verma, Masand, Prospective mode of action of Ivermectin: SARS-CoV-2, European Journal of Medicinal Chemistry Reports, doi:10.1016/j.ejmcr.2021.100018
Paul, Sapienza, Zhang, Zuo, Petit, Native state volume fluctuations in proteins as a mechanism for dynamic allostery, J. Am. Chem. Soc, doi:10.1021/jacs.6b12058
Pavan, Bolcato, Bassani, Sturlese, Moro, Supervised Molecular Dynamics (SuMD) Insights into the mechanism of action of SARS-CoV-2 main protease inhibitor PF-07321332, Journal of Enzyme Inhibition and Medicinal Chemistry, doi:10.1080/14756366.2021.1954919
Peralta-Garcia, Torrens-Fontanals, Stepniewski, Grau-Expósito, Perea et al., Entrectinib-A SARS-CoV-2 Inhibitor in Human Lung Tissue (HLT) Cells, International journal of molecular sciences, doi:10.3390/ijms222413592
Pereira, Jain, Garde, Quantifying the protein core flexibility through analysis of cavity formation, J. Chem. Phys, doi:10.1063/1.2149848
Persson, Halle, Compressibility of the protein-water interface, J. Chem. Phys, doi:10.1063/1.5026774
Petřek, Košinová, Koča, Otyepka, MOLE: A Voronoi diagram-based explorer of molecular channels, pores, and tunnels, Structure, doi:10.1016/j.str.2007.10.007
Pfeiffer, Heremans, Wevers, The influence of correlated protein-water volume fluctuations on the apparent compressibility of proteins determined by ultrasonic velocimetry, Biochimica et Biophysica Acta, doi:10.1016/j.bbapap.2008.08.002
Rabie, Two antioxidant 2, 5-disubstituted-1, 3, 4-oxadiazoles (CoViTris2020 and ChloViD2020): successful repurposing against COVID-19 as the first potent multitarget anti-SARS-CoV-2 drugs, New Journal of Chemistry, doi:10.1039/D0NJ03708G
Reardon, Flawed ivermectin preprint highlights challenges of COVID drug studies, Nature, doi:10.1038/d41586-021-02081-w
Reid, Yu, Leitner, Change in vibrational entropy with change in protein volume estimated with mode Grüneisen parameters, J. Chem. Pysh, doi:10.1063/5.0039175
Remsing, Xi, Patel, Protein hydration thermodynamics: The influence of flexibility and salt on hydrophobin II hydration, J. Phys. Chem. B, doi:10.1021/acs.jpcb.7b12060
Richards, Viscosity and the shapes of macromolecules: A physical chemistry experiment using molecular-level models in the interpretation of macroscopic data obtained from simple measurements, J. Chem. Educ, doi:10.1021/ed070p685
Rother, Preissner, Goede, Frömmel, Inhomogeneous molecular density: Reference packing densities and distribution of cavities within proteins, Bioinformatics, doi:10.1093/bioinformatics/btg292
Saikia, Jha, Deka, Molecular dynamics study on graphene-mediated pyrazinamide drug delivery onto the pncA protein, Rsc Advances, doi:10.1039/C4RA01486C
Seyedi, Matyushov, Dipolar susceptibility of protein hydration shells, Chem. Phys. Lett, doi:10.1016/j.cplett.2018.10.045
Shek, Chalikian, Interactions of glycine betaine with proteins: Insights from volume and compressibility measurements, Biochemistry, doi:10.1021/bi301554h
Sirotkin, Komissarov, Khadiullina, Hydration of proteins: Excess partial volumes of water and proteins, J. Phys. Chem. B, doi:10.1021/jp300726p
Son, Chalikian, Volumetrically derived thermodynamic profile of interactions of urea with a native protein, Biochemistry, doi:10.1021/acs.biochem.6b00805
Son, Shek, Dubins, Chalikian, Volumetric characterization of tri-Nacetylglucosamine binding to lysozyme, Biochemistry, doi:10.1021/bi3006994
Son, Shek, Tikhomirova, Baltasar, Chalikian, Interactions of urea with native and unfolded proteins: A volumetric study, J. Phys. Chem B, doi:10.1021/jp509356k
Stank, Kokh, Fuller, Wade, Protein binding pocket dynamics, Acc. Chem. Res, doi:10.1021/acs.accounts.5b00516
Sulimov, Kutov, Taschilova, Ilin, Stolpovskaya et al., In search of non-covalent inhibitors of SARS-CoV-2 main protease: Computer aided drug design using docking and quantum chemistry, Supercomputing Frontiers and Innovations, doi:10.14529/jsfi200305
Surampudi, Ashbaugh, Direct evaluation of polypeptide partial molar volumes in water using molecular dynamics simulations, Journal of Chemical & Engineering Data, doi:10.1021/je5001999
Tang, Dill, Native protein fluctuations: The conformational-motion temperature and the inverse correlation of protein flexibility with protein stability, J. Biomol. Struct. Dyn, doi:10.1080/07391102.1998.10508256
Tang, Kaneko, Long-range correlation in protein dynamics: Confirmation by structural data and normal mode analysis, Comput. Biol, doi:10.1371/journal.pcbi.1007670
Tarus, Chevalier, Richard, Delmas, Di Primo et al., Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding, PloS one, doi:10.1371/journal.pone.0030038
Tekpinar, Yildirim, Impact of dimerization and N3 binding on molecular dynamics of SARS-CoV and SARS-CoV-2 main proteases, Journal of Biomolecular Structure and Dynamics, doi:10.1080/07391102.2021.1880481
Timasheff, Protein-solvent preferential interactions, protein hydration, and the modulation of biochemical reactions by solvent components, Proc. Natl. Acad. Sci, doi:10.1073/pnas.122225399
Toleikis, Sirotkin, Skvarnavičius, Smirnoviené, Roumestand et al., Volume of Hsp90 protein-ligand binding determined by fluorescent pressure shift assay, densitometry, and NMR, J. Phys. Chem. B, doi:10.1021/acs.jpcb.6b06863
Unoh, Uehara, Nakahara, Nobori, Yamatsu et al., Discovery of S-217622, a Noncovalent Oral SARS-CoV-2 3CL Protease Inhibitor Clinical Candidate for Treating COVID-19, Journal of Medicinal Chemistry, doi:10.1021/acs.jmedchem.2c00117
Uversky, Intrinsically Disordered Proteins: Targets for the Future?, doi:ttps://doi.org/10.1002/9781118681121.ch25
Vandyck, Deval, Considerations for the discovery and development of 3-chymotrypsin-like cysteine protease inhibitors targeting SARS-CoV-2 infection, Curr. Opin. Virol, doi:10.1016/j.coviro.2021.04.006
Voloshin, Medvedev, Smolin, Geiger, Winter, Disentangling volumetric and hydrational properties of proteins, J. Phys. Chem, doi:10.1021/jp510891b
Voloshin, Medvedev, Smolin, Geiger, Winter, Exploring volume, compressibility and hydration changes of folded proteins upon compression, Phys. Chem. Chem. Phys, doi:10.1039/C5CP00251F
Voss, Gerstein, 3V: Cavity, channel and cleft volume calculator and extractor, Nucleic Acids Res, doi:10.1093/nar/gkq395
Whitten, García-Moreno, Hilser, Local conformational fluctuations can modulate the coupling between proton binding and global structural transitions in proteins, Proc. Natl. Acad. Sci, doi:10.1073/pnas.0407499102
Xavier Senra, Fonseca, New tyrosinases with putative action against contaminants of emerging concern, Proteins: Structure, Function, and Bioinformatics, doi:10.1002/prot.26139
Yonezawa, Electrostatic properties of water models evaluated by a long-range potential based solely on the Wolf charge-neutral condition, Chemical Physics Letters, doi:10.1016/j.cplett.2012.12.028
Yuce, Cicek, Inan, Dag, Kurkcuoglu et al., Repurposing of FDA-approved drugs against active site and potential allosteric drug-binding sites of COVID-19 main protease, Proteins Struct. Funct. Bioinforma, doi:10.1002/prot.26164
Zhang, Desdier, Scanlon, Ergometric studies of proteins: New insights into protein functionality in food systems, Trends Food Sci. Technol, doi:10.1016/j.tifs.2015.06.006
Zhao, Fang, Zhang, Zhang, Zhao et al., Crystal structure of SARS-CoV-2 main protease in complex with protease inhibitor PF-07321332, Protein Cell, doi:10.1007/s13238-021-00883-2
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Please send us corrections, updates, or comments. c19early involves the extraction of 100,000+ datapoints from thousands of papers. Community updates help ensure high accuracy. Treatments and other interventions are complementary. All practical, effective, and safe means should be used based on risk/benefit analysis. No treatment or intervention is 100% available and effective for all current and future variants. We do not provide medical advice. Before taking any medication, consult a qualified physician who can provide personalized advice and details of risks and benefits based on your medical history and situation. FLCCC and WCH provide treatment protocols.
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