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Molecular docking and dynamics studies of curcumin with COVID-19 proteins

Coronavirus disease 2019 (COVID-19) is caused by a Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2), which is a positive-strand RNA virus. The SARS-CoV-2 genome and its association to SAR-CoV-1 vary from ca. 66 to 96% depending on the type of betacoronavirideae family members. With sever...

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Autores principales: Suravajhala, Renuka, Parashar, Abhinav, Choudhir, Gourav, Kumar, Anuj, Malik, Babita, Nagaraj, Viswanathan Arun, Padmanaban, Govindarajan, Polavarapu, Rathnagiri, Suravajhala, Prashanth, Kishor, P. B. Kavi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Vienna 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8192041/
https://www.ncbi.nlm.nih.gov/pubmed/34131556
http://dx.doi.org/10.1007/s13721-021-00312-8
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author Suravajhala, Renuka
Parashar, Abhinav
Choudhir, Gourav
Kumar, Anuj
Malik, Babita
Nagaraj, Viswanathan Arun
Padmanaban, Govindarajan
Polavarapu, Rathnagiri
Suravajhala, Prashanth
Kishor, P. B. Kavi
author_facet Suravajhala, Renuka
Parashar, Abhinav
Choudhir, Gourav
Kumar, Anuj
Malik, Babita
Nagaraj, Viswanathan Arun
Padmanaban, Govindarajan
Polavarapu, Rathnagiri
Suravajhala, Prashanth
Kishor, P. B. Kavi
author_sort Suravajhala, Renuka
collection PubMed
description Coronavirus disease 2019 (COVID-19) is caused by a Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2), which is a positive-strand RNA virus. The SARS-CoV-2 genome and its association to SAR-CoV-1 vary from ca. 66 to 96% depending on the type of betacoronavirideae family members. With several drugs, viz. chloroquine, hydroxychloroquine, ivermectin, artemisinin, remdesivir, azithromycin considered for clinical trials, there has been an inherent need to find distinctive antiviral mechanisms of these drugs. Curcumin, a natural bioactive molecule has been shown to have therapeutic potential for various diseases, and its effect on COVID-19 is also currently being explored. In this study, we show the binding potential of curcumin targeted to a variety of SARS-CoV-2 proteins, viz. spike glycoproteins (PDB ID: 6VYB), nucleocapsid phosphoprotein (PDB ID: 6VYO), spike protein-ACE2 (PDB ID: 6M17) along with nsp10 (PDB ID: 6W4H) and RNA dependent RNA polymerase (PDB ID: 6M71) structures. Furthermore, representative docking complexes were validated using molecular dynamics simulations and mechanistic studies at 100 ns was carried on nucleocapsid and nsp10 proteins with curcumin complexes which resulted in stable and efficient binding energies and correlated with that of docked binding energies of the complexes. Both the docking and simulation studies indicate that curcumin has the potential as an antiviral against COVID-19.
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spelling pubmed-81920412021-06-11 Molecular docking and dynamics studies of curcumin with COVID-19 proteins Suravajhala, Renuka Parashar, Abhinav Choudhir, Gourav Kumar, Anuj Malik, Babita Nagaraj, Viswanathan Arun Padmanaban, Govindarajan Polavarapu, Rathnagiri Suravajhala, Prashanth Kishor, P. B. Kavi Netw Model Anal Health Inform Bioinform Original Article Coronavirus disease 2019 (COVID-19) is caused by a Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2), which is a positive-strand RNA virus. The SARS-CoV-2 genome and its association to SAR-CoV-1 vary from ca. 66 to 96% depending on the type of betacoronavirideae family members. With several drugs, viz. chloroquine, hydroxychloroquine, ivermectin, artemisinin, remdesivir, azithromycin considered for clinical trials, there has been an inherent need to find distinctive antiviral mechanisms of these drugs. Curcumin, a natural bioactive molecule has been shown to have therapeutic potential for various diseases, and its effect on COVID-19 is also currently being explored. In this study, we show the binding potential of curcumin targeted to a variety of SARS-CoV-2 proteins, viz. spike glycoproteins (PDB ID: 6VYB), nucleocapsid phosphoprotein (PDB ID: 6VYO), spike protein-ACE2 (PDB ID: 6M17) along with nsp10 (PDB ID: 6W4H) and RNA dependent RNA polymerase (PDB ID: 6M71) structures. Furthermore, representative docking complexes were validated using molecular dynamics simulations and mechanistic studies at 100 ns was carried on nucleocapsid and nsp10 proteins with curcumin complexes which resulted in stable and efficient binding energies and correlated with that of docked binding energies of the complexes. Both the docking and simulation studies indicate that curcumin has the potential as an antiviral against COVID-19. Springer Vienna 2021-06-10 2021 /pmc/articles/PMC8192041/ /pubmed/34131556 http://dx.doi.org/10.1007/s13721-021-00312-8 Text en © The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature 2021 This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.
spellingShingle Original Article
Suravajhala, Renuka
Parashar, Abhinav
Choudhir, Gourav
Kumar, Anuj
Malik, Babita
Nagaraj, Viswanathan Arun
Padmanaban, Govindarajan
Polavarapu, Rathnagiri
Suravajhala, Prashanth
Kishor, P. B. Kavi
Molecular docking and dynamics studies of curcumin with COVID-19 proteins
title Molecular docking and dynamics studies of curcumin with COVID-19 proteins
title_full Molecular docking and dynamics studies of curcumin with COVID-19 proteins
title_fullStr Molecular docking and dynamics studies of curcumin with COVID-19 proteins
title_full_unstemmed Molecular docking and dynamics studies of curcumin with COVID-19 proteins
title_short Molecular docking and dynamics studies of curcumin with COVID-19 proteins
title_sort molecular docking and dynamics studies of curcumin with covid-19 proteins
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8192041/
https://www.ncbi.nlm.nih.gov/pubmed/34131556
http://dx.doi.org/10.1007/s13721-021-00312-8
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