Suravajhala, R and Parashar, A and Choudhir, G and Kumar, A and Malik, B and Nagaraj, VA and Padmanaban, G and Polavarapu, R and Suravajhala, P and Kishor, PBK (2021) Molecular docking and dynamics studies of curcumin with COVID-19 proteins. In: Network Modeling Analysis in Health Informatics and Bioinformatics, 10 (1).
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Abstract
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. © 2021, The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.
| Item Type: | Journal Article |
|---|---|
| Publication: | Network Modeling Analysis in Health Informatics and Bioinformatics |
| Publisher: | Springer |
| Additional Information: | The copyright for this article belongs to Authors |
| Keywords: | Binding energy; Complexation; Molecular dynamics; Proteins; RNA; Viruses, Antiviral mechanisms; Bioactive molecules; Mechanistic studies; Molecular dynamics simulations; RNA-dependent RNA polymerase; Severe acute respiratory syndrome coronavirus; Simulation studies; Therapeutic potentials, Diseases |
| Department/Centre: | Division of Biological Sciences > Biochemistry |
| Date Deposited: | 01 Sep 2021 09:58 |
| Last Modified: | 01 Sep 2021 09:58 |
| URI: | http://eprints.iisc.ac.in/id/eprint/69445 |
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