Molecular docking study of Lens culinaris L. phytochemicals to NS3-NS2B protease of dengue virus serotype 2

Authors: Tohmina Afroze Bondhon, Anamul Hasan, Khoshnur Jannat, Alok Paul, Rownak Jahan, Tooba Mahboob, Veeranoot Nissapatorn, Karma G Dolma, Maria L. Pereira, Christophe Wiart and Mohammed Rahmatullah

Ger. J. Microbiol. 2021. vol. 1, Iss. 1 pp:26-37
Doi: https://doi.org/10.51585/gjm.2021.0005

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Abstract:

Forty-three phytochemicals present in Lens culinaris were evaluated through in silico molecular docking studies for their binding affinities to the NS2B-NS3 activator-protease complex of dengue virus serotype 2 (DENV-2). Among the various compounds tested, flavonoids (flavanols, flavonols, proanthocyanidins, flavanones, flavones, and anthocyanins) demonstrated high binding affinities for the protease complex. Eriodictyol-7-O-rutinoside showed the least predicted binding energy at -9.1 kcal/mol followed by luteolin-7-O-glucoside at -8.8 kcal/mol. Glycosidic linkages appeared to enhance the binding affinities of flavonoids, aldohexoses being more potent than aldopentoses. Besides flavonoids, other classes of compounds demonstrating high binding affinities for the protease were carotenoids, phytosterols, and polyphenolic compounds like resveratrol and trans-resveratrol 3-O-b-glucoside (piceid), the latter showing predicted binding energy of -8.5 kcal/mol versus predicted binding energy of -7.2 kcal/mol for resveratrol. 2D interactions of four high binding affinity compounds like eriodictyol, eriodictyol-7-O-rutinoside, catechin gallate, and luteolin-7-O-glucoside showed that all four compounds bound to the active site of the NS3 protease and not to the activator NS2B. Lys74 of NS3 was the common amino acid interacting with all four phytochemicals. Analysis of physicochemical properties of the compounds (Lipinski’s Rule of 5) showed that the high binding affinity compounds all have less than two violations, indicating that they can serve as useful lead compounds or as dengue virus serotype 2 therapeutics.

Keywords:

Dengue, Flaviviridae, Lens culinaris, Phytochemical, Flavonoids

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