CDKN2 In silico diosmetin molecular docking molecular simulation

Journal

Journal of biomolecular structure & dynamics
ISSN: 1538-0254
Titre abrégé: J Biomol Struct Dyn
Pays: England
ID NLM: 8404176

Informations de publication

Date de publication:
24 Aug 2023
Historique:
medline: 24 8 2023
pubmed: 24 8 2023
entrez: 24 8 2023
Statut: aheadofprint

Résumé

Prostate cancer is the second most dangerous cancer type worldwide. While various treatment options are present i.e. agonists and antagonists, their utilization leads to adverse effects and due to this resistance developing, ultimately the outcome is remission. So, to overcome this issue, we have undertaken an in-silico investigation to identify promising and unique flavonoid candidates for combating prostate cancer. Using GOLD software, the study assessed the effectiveness of 560 natural secondary polyphenols against CDKN2. Protein Data Bank was used to retrieve the 3D crystal structure of CDKN2 (PDB Id: 4EK3) and we retrieved the structure of selected secondary polyphenols from the PubChem database. The compound Diosmetin shows the highest GOLD score with the selected Protein i.e. CDKN2 which is 58.72. To better understand the 2-dimensional and 3-dimensional interactions, the interacting amino acid residues were visualised using Discovery Studio 3.5 and Maestro 13.5. Using Schrodinger-Glide, the Diosmetin and CDKN2 were re-docked, and decoy ligands were docked to CDKN2, which was used to further ascertain the study. The ligands with the highest Gold score were forecasted for pharmacokinetics characteristics, and the results were tabulated and analysed. Utilising the Gromacs software and Desmond packages, 100 ns of Diosmetin molecular dynamics simulations were run to evaluate the structural persistence and variations of protein-ligand complexes. Additionally, our investigation revealed that Diosmetin had a better binding affinity with CDKN2 measuring 58.72, and it also showed remarkable stability across a 100-ns simulation. Thus, following

Identifiants

pubmed: 37615411
doi: 10.1080/07391102.2023.2250451
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

1-13

Auteurs

Sumit Sheoran (S)

School of Bioengineering & Biosciences, Lovely Professional University, Jalandhar, India.

Swati Arora (S)

School of Bioengineering & Biosciences, Lovely Professional University, Jalandhar, India.

Tanmayee Basu (T)

Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India.

Swati Negi (S)

Department of Chemistry, Delhi University, New Delhi, India.

Naidu Subbarao (N)

School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.

Anupam Kumar (A)

School of Bioengineering & Biosciences, Lovely Professional University, Jalandhar, India.

Himanshu Singh (H)

School of Bioengineering & Biosciences, Lovely Professional University, Jalandhar, India.

Dhamodharan Prabhu (D)

Centre for Drug Discovery, Department of Biotechnology, Karpagam Academy of Higher Education, Coimbatore, India.

Atul Kumar Upadhyay (AK)

Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India.

Neeraj Kumar (N)

Geetanjali Institute of Pharmacy, Udaipur, India.

Sugunakar Vuree (S)

School of Bioengineering & Biosciences, Lovely Professional University, Jalandhar, India.
MNR Foundation for Research and Innovation (MNR-FRI), MNR Medical College and Hospital, Fasalwadi Village, Hyderabad, India.

Classifications MeSH