Access the full text.
Sign up today, get DeepDyve free for 14 days.
Loading next page...
/lp/springer-journals/target-sars-cov-2-computation-of-binding-energies-with-drugs-of-VPz0eIHIqN
References (60)
-
(2003)
Molecular dynamics simulation of protein folding by essential dynamics sampling: folding landscape of horse heart cytochrome cBiophys J, 85
-
(2000)
Protein dynamics from NMRNat Struct Biol, 7
-
(2000)
Theory and applications of the generalized born solvation model in macromolecular simulationsBiopolym Orig Res Biomol, 56
-
(2020)
Dexamethasone in the era of COVID-19: friend or foe? An essay on the effects of dexamethasone and the potential risks of its inadvertent use in patients with diabetesDiabetol Metab Syndr, 12
-
(Tachoua W, Kabrine M. Molecular docking study of COVID-19 main protease with clinically approved drugs. ChemRxiv. 2020. 10.26434/chemrxiv.12318689.v1.)
Tachoua W, Kabrine M. Molecular docking study of COVID-19 main protease with clinically approved drugs. ChemRxiv. 2020. 10.26434/chemrxiv.12318689.v1.Tachoua W, Kabrine M. Molecular docking study of COVID-19 main protease with clinically approved drugs. ChemRxiv. 2020. 10.26434/chemrxiv.12318689.v1., Tachoua W, Kabrine M. Molecular docking study of COVID-19 main protease with clinically approved drugs. ChemRxiv. 2020. 10.26434/chemrxiv.12318689.v1.
-
(2000)
A human homolog of angiotensin-converting enzyme cloning and functional expression as a captopril-insensitive carboxypeptidaseJ Biol Chem, 275
-
(Moradi SZ , Nowroozi A , Sadrjavadi K , Moradi S , Mansouri K , Hosseinzadeh L, Shahlaei M (2018), Int. J. Biol. Macromol.114 , 40 —53.)
Moradi SZ , Nowroozi A , Sadrjavadi K , Moradi S , Mansouri K , Hosseinzadeh L, Shahlaei M (2018), Int. J. Biol. Macromol.114 , 40 —53.Moradi SZ , Nowroozi A , Sadrjavadi K , Moradi S , Mansouri K , Hosseinzadeh L, Shahlaei M (2018), Int. J. Biol. Macromol.114 , 40 —53., Moradi SZ , Nowroozi A , Sadrjavadi K , Moradi S , Mansouri K , Hosseinzadeh L, Shahlaei M (2018), Int. J. Biol. Macromol.114 , 40 —53.
-
(2020)
SARS-CoV-2: recent reports on antiviral therapies based on lopinavir/ritonavir, darunavir/umifenovir, hydroxychloroquine, remdesivir, favipiravir and other drugs for the treatment of the new coronavirusCurr Med Chem, 27
-
(2016)
Novel binding patterns between ganoderic acids and neuraminidase: insights from docking, molecular dynamics and MM/PBSA studiesJ Mol Graph Model, 65
-
(2015)
Improved peptide and protein torsional energetics with the OPLS-AA force fieldJ. Chem. Theory Comput, 11
-
(2014)
Thermoacoustic, volumetric, and viscometric investigations in binary liquid system of cyclohexanone with methyl benzoate at T = 30815, 31315, and 31815 KJ Thermodyn, 2014
-
(2012)
VMD DisRg: new user-friendly implement for calculation distance and radius of gyration in VMD programBioinformation, 8
-
(2011)
LigPlot+: multiple ligand-protein interaction diagrams for drug discoveryJ Chem Inf Model, 51
-
(Atkins PW, De Paula J, Keeler J (2018) Atkins’ physical chemistry. Oxford university press.)
Atkins PW, De Paula J, Keeler J (2018) Atkins’ physical chemistry. Oxford university press.Atkins PW, De Paula J, Keeler J (2018) Atkins’ physical chemistry. Oxford university press., Atkins PW, De Paula J, Keeler J (2018) Atkins’ physical chemistry. Oxford university press.
-
(2010)
Ligand docking and binding site analysis with PyMOL and Autodock/VinaJ Comput Aided Mol Des, 24
-
(2016)
Approved antiviral drugs over the past 50 yearsClin Microbiol Rev, 29
-
(2020)
After 62 years of regulating immunity, dexamethasone meets COVID-19Nat Rev Immunol, 20
-
(2017)
Structural basis of influenza virus fusion inhibition by the antiviral drug ArbidolProc Natl Acad Sci U S A, 114
-
(https://www.who.int/news-room/detail/16-06-2020-who-welcomes-preliminary-results-aboutdexamethasone-use-in-treating-critically-ill-covid-19-patients, WHO welcomes preliminary results about dexamethasone use in treating critically ill COVID-19 patients. 2020.)
https://www.who.int/news-room/detail/16-06-2020-who-welcomes-preliminary-results-aboutdexamethasone-use-in-treating-critically-ill-covid-19-patients, WHO welcomes preliminary results about dexamethasone use in treating critically ill COVID-19 patients. 2020.https://www.who.int/news-room/detail/16-06-2020-who-welcomes-preliminary-results-aboutdexamethasone-use-in-treating-critically-ill-covid-19-patients, WHO welcomes preliminary results about dexamethasone use in treating critically ill COVID-19 patients. 2020., https://www.who.int/news-room/detail/16-06-2020-who-welcomes-preliminary-results-aboutdexamethasone-use-in-treating-critically-ill-covid-19-patients, WHO welcomes preliminary results about dexamethasone use in treating critically ill COVID-19 patients. 2020.
-
(2020)
Potential inhibitors against 2019-nCoV coronavirus M protease from clinically approved medicinesJ Genet Genomics, 47
-
(1990)
Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equationJ Phys Chem, 94
-
(2018)
From proteins to perturbed Hamiltonians: a suite of tutorials for the GROMACS-2018 molecular simulation package [article v1. 0]Living J Comput Mol Sci, 1
-
(2020)
Dexamethasone nanomedicines for COVID-19Nat Nanotechnol, 15
-
(2017)
LigParGen web server: an automatic OPLS-AA parameter generator for organic ligandsNucleic Acids Res, 45
-
(Li, G. and E. De Clercq, Therapeutic options for the 2019 novel coronavirus (2019-nCoV). 2020, Nat Publ Group.)
Li, G. and E. De Clercq, Therapeutic options for the 2019 novel coronavirus (2019-nCoV). 2020, Nat Publ Group.Li, G. and E. De Clercq, Therapeutic options for the 2019 novel coronavirus (2019-nCoV). 2020, Nat Publ Group., Li, G. and E. De Clercq, Therapeutic options for the 2019 novel coronavirus (2019-nCoV). 2020, Nat Publ Group.
-
(2014)
C. Open source drug discovery and A. LynnJ Chem Inf Model, 54
-
(Biovia DS (2017) Discovery studio visualizer. San Diego.)
Biovia DS (2017) Discovery studio visualizer. San Diego.Biovia DS (2017) Discovery studio visualizer. San Diego., Biovia DS (2017) Discovery studio visualizer. San Diego.
-
(2020)
COVID-19 and dexamethasone: a potential strategy to avoid steroid-related strongyloides hyperinfectionJAMA., 324
-
(2020)
Therapeutic and triage strategies for 2019 novel coronavirus disease in fever clinicsLancet Respir Med, 8
-
(2020)
Pathogenicity and transmissibility of 2019-nCoV—a quick overview and comparison with other emerging virusesMicrobes Infect, 22
-
(2014)
Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoringPhys Chem Chem Phys, 16
-
(Mittal, L., et al., Identification of potential molecules against COVID-19 main protease through structure-guided virtual screening approach. Journal of Biomolecular Structure and Dynamics, 2020(just-accepted): p. 1–26.)
Mittal, L., et al., Identification of potential molecules against COVID-19 main protease through structure-guided virtual screening approach. Journal of Biomolecular Structure and Dynamics, 2020(just-accepted): p. 1–26.Mittal, L., et al., Identification of potential molecules against COVID-19 main protease through structure-guided virtual screening approach. Journal of Biomolecular Structure and Dynamics, 2020(just-accepted): p. 1–26., Mittal, L., et al., Identification of potential molecules against COVID-19 main protease through structure-guided virtual screening approach. Journal of Biomolecular Structure and Dynamics, 2020(just-accepted): p. 1–26.
-
(2006)
Molecular dynamics: survey of methods for simulating the activity of proteinsChem Rev, 106
-
(2020)
Umifenovir treatment is not associated with improved outcomes in patients with coronavirus disease 2019: a retrospective studyClin Microbiol Infect, 26
-
(2020)
Candidate drugs against SARS-CoV-2 and COVID-19Pharmacol Res, 157
-
(2020)
Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive studyLancet, 395
-
(2008)
Interaction of anthracycline disaccharide with human serum albumin: investigation by fluorescence spectroscopic technique and modeling studiesJ Pharm Biomed Anal, 48
-
(Coronavirus disease 2019 https://www.who.int/emergencies/diseases/novel-coronavirus-2019)
Coronavirus disease 2019 https://www.who.int/emergencies/diseases/novel-coronavirus-2019Coronavirus disease 2019 https://www.who.int/emergencies/diseases/novel-coronavirus-2019, Coronavirus disease 2019 https://www.who.int/emergencies/diseases/novel-coronavirus-2019
-
(2017)
The role of ACE2, angiotensin-(1–7) and Mas1 receptor axis in glucocorticoid-induced intrauterine growth restrictionReprod Biol Endocrinol, 15
-
(Chang R (2005) Physical chemistry for the biosciences. University Science Books.)
Chang R (2005) Physical chemistry for the biosciences. University Science Books.Chang R (2005) Physical chemistry for the biosciences. University Science Books., Chang R (2005) Physical chemistry for the biosciences. University Science Books.
-
(Low-cost dexamethasone reduces death by up to one third in hospitalised patients with severe respiratory complications of COVID-19. http://www.ox.ac.uk/news/2020-06-16-low-cost-dexamethasone-reduces-death-one-third-hospitalised-patients-severe, 2020.)
Low-cost dexamethasone reduces death by up to one third in hospitalised patients with severe respiratory complications of COVID-19. http://www.ox.ac.uk/news/2020-06-16-low-cost-dexamethasone-reduces-death-one-third-hospitalised-patients-severe, 2020.Low-cost dexamethasone reduces death by up to one third in hospitalised patients with severe respiratory complications of COVID-19. http://www.ox.ac.uk/news/2020-06-16-low-cost-dexamethasone-reduces-death-one-third-hospitalised-patients-severe, 2020., Low-cost dexamethasone reduces death by up to one third in hospitalised patients with severe respiratory complications of COVID-19. http://www.ox.ac.uk/news/2020-06-16-low-cost-dexamethasone-reduces-death-one-third-hospitalised-patients-severe, 2020.
-
(Ledford, H., Coronavirus breakthrough: dexamethasone is first drug shown to save lives. 2020.)
Ledford, H., Coronavirus breakthrough: dexamethasone is first drug shown to save lives. 2020.Ledford, H., Coronavirus breakthrough: dexamethasone is first drug shown to save lives. 2020., Ledford, H., Coronavirus breakthrough: dexamethasone is first drug shown to save lives. 2020.
-
(2020)
Hydroxychloroquine and dexamethasone in COVID-19: who won and who lost?Clin Mol Allergy, 18
-
(Ren J, Yuan X, Li J, et al (2019) Assessing the performance of the g_mmpbsa tools to simulate the inhibition of oseltamivir to influenza virus neuraminidase by molecular mechanics Poisson–Boltzmann surface area methods. J Chinese Chem Soc.)
Ren J, Yuan X, Li J, et al (2019) Assessing the performance of the g_mmpbsa tools to simulate the inhibition of oseltamivir to influenza virus neuraminidase by molecular mechanics Poisson–Boltzmann surface area methods. J Chinese Chem Soc.Ren J, Yuan X, Li J, et al (2019) Assessing the performance of the g_mmpbsa tools to simulate the inhibition of oseltamivir to influenza virus neuraminidase by molecular mechanics Poisson–Boltzmann surface area methods. J Chinese Chem Soc., Ren J, Yuan X, Li J, et al (2019) Assessing the performance of the g_mmpbsa tools to simulate the inhibition of oseltamivir to influenza virus neuraminidase by molecular mechanics Poisson–Boltzmann surface area methods. J Chinese Chem Soc.
-
(Coralie Valle, Baptiste Martin, Franck Touret, Ashleigh Shannon, Bruno Canard, Jean-Claude Guillemot, Bruno Coutard, Etienne Decroly; Drugs against SARS-CoV-2: what do we know about their mode of action? Rev Med Virol. 2020;e2143. 10.1002/rmv.2143)
Coralie Valle, Baptiste Martin, Franck Touret, Ashleigh Shannon, Bruno Canard, Jean-Claude Guillemot, Bruno Coutard, Etienne Decroly; Drugs against SARS-CoV-2: what do we know about their mode of action? Rev Med Virol. 2020;e2143. 10.1002/rmv.2143Coralie Valle, Baptiste Martin, Franck Touret, Ashleigh Shannon, Bruno Canard, Jean-Claude Guillemot, Bruno Coutard, Etienne Decroly; Drugs against SARS-CoV-2: what do we know about their mode of action? Rev Med Virol. 2020;e2143. 10.1002/rmv.2143, Coralie Valle, Baptiste Martin, Franck Touret, Ashleigh Shannon, Bruno Canard, Jean-Claude Guillemot, Bruno Coutard, Etienne Decroly; Drugs against SARS-CoV-2: what do we know about their mode of action? Rev Med Virol. 2020;e2143. 10.1002/rmv.2143
-
(2004)
Thermodynamics of protein–ligand interactions: history, presence, and future aspectsJ Recept Signal Transduct, 24
-
(2020)
Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination eventInfect Genet Evol, 79
-
(Liu X, Zhang B, Jin Z, et al (2020) The crystal structure of COVID-19 main protease in complex with an inhibitor N3. Protein DataBank)
Liu X, Zhang B, Jin Z, et al (2020) The crystal structure of COVID-19 main protease in complex with an inhibitor N3. Protein DataBankLiu X, Zhang B, Jin Z, et al (2020) The crystal structure of COVID-19 main protease in complex with an inhibitor N3. Protein DataBank, Liu X, Zhang B, Jin Z, et al (2020) The crystal structure of COVID-19 main protease in complex with an inhibitor N3. Protein DataBank
-
(1995)
A smooth particle mesh Ewald potentialJ Chem Phys, 103
-
(2020)
Return of the coronavirus: 2019-nCoVViruses, 12
-
(2013)
Mutation effects of neuraminidases and their docking with ligands: a molecular dynamics and free energy calculation studyJ Comput Aided Mol Des, 27
-
(2016)
Enthalpic and entropic contributions to hydrophobicityJ Chem Theory Comput, 12
-
(2017)
Effect of force fields and water models on egfrviii-MR1 (scfv) complex by molecular dynamics simulation, MM-PBSA calculation, and ITC experimentChem J Chin Univ, 38
-
(2012)
Angiotensin-converting enzyme 2 (ACE2) is a key modulator of the renin angiotensin system in health and diseaseInt J Pept, 2012
-
(2015)
Chemical basis for the recognition of trimethyllysine by epigenetic reader proteinsNat Commun, 6
-
(Roberts A, Deming D, Paddock CD, et al (2007) A mouse-adapted SARS-coronavirus causes disease and mortality in BALB/c mice PLoS Pathog 3:)
Roberts A, Deming D, Paddock CD, et al (2007) A mouse-adapted SARS-coronavirus causes disease and mortality in BALB/c mice PLoS Pathog 3:Roberts A, Deming D, Paddock CD, et al (2007) A mouse-adapted SARS-coronavirus causes disease and mortality in BALB/c mice PLoS Pathog 3:, Roberts A, Deming D, Paddock CD, et al (2007) A mouse-adapted SARS-coronavirus causes disease and mortality in BALB/c mice PLoS Pathog 3:
-
(2020)
Scaffold morphing of arbidol (umifenovir) in search of multi-targeting therapy halting the interaction of SARS-CoV-2 with ACE2 and other proteases involved in COVID-19Virus Res, 289
-
(2020)
Arbidol: a potential antiviral drug for the treatment of SARS-CoV-2 by blocking trimerization of the spike glycoproteinInt J Antimicrob Agents, 56
-
(Bronowska AK (2011) Thermodynamics of ligand-protein interactions: implications for molecular design. In: Thermodynamics interaction studies-solids, liquids and gases. IntechOpen.)
Bronowska AK (2011) Thermodynamics of ligand-protein interactions: implications for molecular design. In: Thermodynamics interaction studies-solids, liquids and gases. IntechOpen.Bronowska AK (2011) Thermodynamics of ligand-protein interactions: implications for molecular design. In: Thermodynamics interaction studies-solids, liquids and gases. IntechOpen., Bronowska AK (2011) Thermodynamics of ligand-protein interactions: implications for molecular design. In: Thermodynamics interaction studies-solids, liquids and gases. IntechOpen.
-
(2020)
Clinical features of patients infected with 2019 novel coronavirus in Wuhan, ChinaLancet, 395
- Publisher
- Springer Journals
- Copyright
- Copyright © Sociedade Brasileira de Engenharia Biomedica 2021
- ISSN
- 2446-4732
- eISSN
- 2446-4740
- DOI
- 10.1007/s42600-020-00119-y
- Publisher site
- See Article on Publisher Site
Abstract
IntroductionIn recent times, myriads of public have been infected with a novel SARS-CoV-2, and the fatality toll has reached thousands and been mounting step by step, which is a major crisis in the world. The challenge for this burning issue pertinent to repurposed medicines which prevent novel coronavirus is of immense concern for all scientists around the globe until the arrival of the vaccine.MethodsBecause of the global high priority rating on the search for the repurposed drugs which outfits clinical suitability to SARS-CoV-2, a unique theoretical methodology is proposed. The approach is based on explorations of biothermodynamics computed via molecular dynamics, root-mean-square deviation (RMSD), radius of gyration (Rg) and interactions. This unique methodology is tested for umifenovir/dexamethasone drugs on (SARS-CoV-2) main protease.ResultsThis theoretical exploration not only suggested the presence of strong interactions between (SARS-CoV-2 + umifenovir/dexamethasone) but also emphasized the clinical suitability of dexamethasone over umifenovir to treat SARS-CoV-2. This supremacy of dexamethasone is well supported by the results of global clinical trials and COVID-19 therapeutic approved management guidelines of countries.ConclusionsThus, this work will pave a way for incremental advancement towards future design and development of more specific inhibitors for the treatment of SARS-CoV-2 infection in humans.
Journal
Research on Biomedical Engineering – Springer Journals
Published: Mar 1, 2022
Keywords: SARS-CoV-2 protein; Dexamethasone; Umifenovir; Molecular dynamics; Gromacs; Gibb’s free energy; Interactions