Computational study on Polydatin with the Human Alpha-Defensins and the Human Beta Defensins evaluated by Blind Molecular Docking method

Ivan Vito Ferrari¹ , Giampietro Ravagnan²

1. Institute of clinical physiology of CNR, Massa, Italy.
2. Institute of Translational Pharmacology, Consiglio Nazionale delle Ricerche, Rome, Italy.

Section:Research Paper, Product Type: Journal-Paper
Vol.10 , Issue.6 , pp.1-6, Dec-2023

Online published on Dec 31, 2023

Copyright © Ivan Vito Ferrari, Giampietro Ravagnan . This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
 

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Abstract :
In a comprehensive Molecular Docking investigation using Autodock Vina with the Pyrx program, six Human Defensins (Alpha Defensin-1, Alpha Defensin-3, Alpha Defensin-4, Beta-Defensin-1, Beta-Defensin-2, Beta Defensin-3) were studied alongside various natural compounds. Notably, all investigated compounds exhibited similar binding energy scores with Human Alpha Defensin-1 and Alpha Defensin-3, around -6.0 kcal/mol. However, with Human Defensin-4, Astringin, and Rhapontin, greater energetic affinities were observed, approximately -7.5 kcal/mol, compared to Polydatin and Eleutheroside-B. In the case of Beta-defensins, the natural compounds demonstrated higher binding capacities compared to Alpha defensins. Specifically, Polydatin exhibited a noteworthy binding affinity with Human Beta-Defensin-2, with a Vina Score of approximately -9.2 kcal/mol. Astringins and Rhapontis also showed significant binding energies with Human Beta-Defensin-2, with Vina scores of -8.8 kcal/mol and -8.6 kcal/mol, respectively. While these computational findings are preliminary and rely on a Blind Docking approach, they suggest that Polydatin and its derivatives may have a higher binding affinity for Beta-Defensins, particularly Beta-Defensin-2, providing a theoretical basis for further biological and molecular studies.

Key-Words / Index Term :
Polydatin, Autodock Vina, Pyrx , Human Defensins, Piceid, Human Beta-Defesin-2

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