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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.
  • Suravajhala R; Department of Chemistry, Manipal University Jaipur, Jaipur, 303 007 Rajasthan India.
  • Parashar A; Bioclues.org, Hyderabad, India.
  • Choudhir G; Department of Biotechnology, Vignan's Foundation for Science, Technology and Research (Deemed To Be University), Vadlamudi, Guntur, 522 213 Andhra Pradesh India.
  • Kumar A; Centre for Rural Development and Technology, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, 110 016 India.
  • Malik B; Bioinformatics Laboratory, Uttarakhand Council for Biotechnology (UCB), Biotech Bhawan, Haldi, U.S. Nagar, Pantnagar, 263 145 Uttarakhand India.
  • Nagaraj VA; Department of Chemistry, Manipal University Jaipur, Jaipur, 303 007 Rajasthan India.
  • Padmanaban G; Institute of Life Sciences, Nalco Square, Chandrasekharpur, Bhubaneswar, 751 023 Odisha India.
  • Polavarapu R; Indian Institute of Science, Bengaluru, 560 012 India.
  • Suravajhala P; Genomix CARL Pvt. Ltd., Pulivendula, Kadapa, 516 390 Andhra Pradesh India.
  • Kishor PBK; Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, 320 001 Rajasthan India.
Netw Model Anal Health Inform Bioinform ; 10(1): 44, 2021.
Article in English | MEDLINE | ID: covidwho-1265590
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.
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Full text: Available Collection: International databases Database: MEDLINE Type of study: Prognostic study Language: English Journal: Netw Model Anal Health Inform Bioinform Year: 2021 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Type of study: Prognostic study Language: English Journal: Netw Model Anal Health Inform Bioinform Year: 2021 Document Type: Article