Binding and inhibitory effect of ravidasvir on 3CLpro of
SARS-CoV-2: a molecular docking, molecular dynamics and MM/PBSA
approach

J 2022

Binding and inhibitory effect of ravidasvir on 3CLpro of SARS-CoV-2: a molecular docking, molecular dynamics and MM/PBSA approach

BERA, Krishnendu

Základní údaje

Originální název

Binding and inhibitory effect of ravidasvir on 3CLpro of SARS-CoV-2: a molecular docking, molecular dynamics and MM/PBSA approach

Autoři

BERA, Krishnendu (356 Indie, garant, domácí)

Vydání

Journal of Biomolecular Structure and Dynamics, Taylor & Francis, 2022, 0739-1102

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 4.400

Kód RIV

RIV/00216224:14740/22:00124912

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1080/07391102.2021.1896388

UT WoS

000626418500001

Klíčová slova anglicky

3CLpro; MM/PBSA; SARS-CoV-2; molecular docking; molecular dynamics simulation; principal component analysis

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 6. 2. 2023 19:28, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

Drug repurposing requires a limited resource, cost-effective and faster method to combat severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Therefore, this in silico studies attempts to identify the drug-likeness properties of ravidasvir, an II/III phase clinical trial chronic hepatitis C drug against 3-Chymotrypsin-like protease (3CLpro) of SARS-CoV-2 to combat the ongoing coronavirus disease 2019 (COVID-19) pandemic. This protease is predominantly involved in virus replication cycle; hence it is considered as a potent drug target. The molecular docking results showed that ravidasvir was found to be potent inhibitors of 3CLpro with scoring function based binding energy is -26.7kJ/mol. Further dynamic behaviour of apo form and complex form of ravidasvir with 3CLpro were studied using molecular dynamics (MD) simulations over 500ns each, total 2s time scale. The motion of the protein was studied using principal component analysis of the MD simulation trajectories. The binding free energy calculated using MM/PBSA method from the MD simulation trajectory was -190.3±70.2kJ/mol and -106.0±26.7kJ/mol for GROMOS96 54A7 and AMBER99SB-ILDN force field, respectively. This in silico studies suggesting ravidasvir might be a potential lead molecule against SARS-CoV-2 for further optimization and drug development to combat the life-threatening COVID-19 pandemic.Communicated by Ramaswamy H. Sarma.

Návaznosti

LM2018140, projekt VaV

Název: e-Infrastruktura CZ (Akronym: e-INFRA CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, e-Infrastruktura CZ

LTAUSA18168, projekt VaV

Název: Selektivní NMR značení jako nástroj pro charakterizaci proteinových komplexů zapojených do neurodegenerativních onemocnění

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Selektivní NMR značení jako nástroj pro charakterizaci proteinových komplexů zapojených do neurodegenerativních onemocnění, INTER-ACTION

Citovat

BERA, Krishnendu. Binding and inhibitory effect of ravidasvir on 3CLpro of SARS-CoV-2: a molecular docking, molecular dynamics and MM/PBSA approach. Journal of Biomolecular Structure and Dynamics. Taylor & Francis, 2022, roč. 40, č. 16, s. 7303-7310. ISSN 0739-1102. Dostupné z: https://dx.doi.org/10.1080/07391102.2021.1896388.

@article{1751017,
   author = {Bera, Krishnendu},
   article_number = {16},
   doi = {http://dx.doi.org/10.1080/07391102.2021.1896388},
   keywords = {3CLpro; MM/PBSA; SARS-CoV-2; molecular docking; molecular dynamics simulation; principal component analysis},
   language = {eng},
   issn = {0739-1102},
   journal = {Journal of Biomolecular Structure and Dynamics},
   title = {Binding and inhibitory effect of ravidasvir on 3CLpro of SARS-CoV-2: a molecular docking, molecular dynamics and MM/PBSA approach},
   url = {https://www.tandfonline.com/doi/full/10.1080/07391102.2021.1896388},
   volume = {40},
   year = {2022}
}

TY  - JOUR
ID  - 1751017
AU  - Bera, Krishnendu
PY  - 2022
TI  - Binding and inhibitory effect of ravidasvir on 3CLpro of SARS-CoV-2: a molecular docking, molecular dynamics and MM/PBSA approach
JF  - Journal of Biomolecular Structure and Dynamics
VL  - 40
IS  - 16
SP  - 7303-7310
EP  - 7303-7310
PB  - Taylor & Francis
SN  - 07391102
KW  - 3CLpro
KW  - MM/PBSA
KW  - SARS-CoV-2
KW  - molecular docking
KW  - molecular dynamics simulation
KW  - principal component analysis
UR  - https://www.tandfonline.com/doi/full/10.1080/07391102.2021.1896388
N2  - Drug repurposing requires a limited resource, cost-effective and faster method to combat severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Therefore, this in silico studies attempts to identify the drug-likeness properties of ravidasvir, an II/III phase clinical trial chronic hepatitis C drug against 3-Chymotrypsin-like protease (3CLpro) of SARS-CoV-2 to combat the ongoing coronavirus disease 2019 (COVID-19) pandemic. This protease is predominantly involved in virus replication cycle; hence it is considered as a potent drug target. The molecular docking results showed that ravidasvir was found to be potent inhibitors of 3CLpro with scoring function based binding energy is -26.7kJ/mol. Further dynamic behaviour of apo form and complex form of ravidasvir with 3CLpro were studied using molecular dynamics (MD) simulations over 500ns each, total 2s time scale. The motion of the protein was studied using principal component analysis of the MD simulation trajectories. The binding free energy calculated using MM/PBSA method from the MD simulation trajectory was -190.3±70.2kJ/mol and -106.0±26.7kJ/mol for GROMOS96 54A7 and AMBER99SB-ILDN force field, respectively. This in silico studies suggesting ravidasvir might be a potential lead molecule against SARS-CoV-2 for further optimization and drug development to combat the life-threatening COVID-19 pandemic.Communicated by Ramaswamy H. Sarma.
ER  -

BERA, Krishnendu. Binding and inhibitory effect of ravidasvir on 3CLpro of SARS-CoV-2: a molecular docking, molecular dynamics and MM/PBSA approach. \textit{Journal of Biomolecular Structure and Dynamics}. Taylor \&{} Francis, 2022, roč.~40, č.~16, s.~7303-7310. ISSN~0739-1102. Dostupné z: https://dx.doi.org/10.1080/07391102.2021.1896388.

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