Drug repurposing for ligand-induced rearrangement of Sirt2 active site-based inhibitors via molecular modeling and quantum mechanics calculations

• Published in: Scientific reports Vol. 11; no. 1; p. 10169
• Main Authors: Bharadwaj, Shiv, Dubey, Amit, Kamboj, Nitin Kumar, Sahoo, Amaresh Kumar, Kang, Sang Gu, Yadava, Umesh
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 13-05-2021; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114; 631/114/2397; 631/154; 692/4017; Acetamides - chemistry; Acetamides - pharmacology; Adenine; Aging; Catalytic Domain - drug effects; Crystallography, X-Ray; Drug development; Drug Repositioning - methods; Drugs; Enzyme Inhibitors - chemistry; Enzyme Inhibitors - pharmacology; FDA approval; Fluphenazine; Humanities and Social Sciences; Humans; Inhibitors; Ligands; Molecular Docking Simulation; Molecular dynamics; Molecular Dynamics Simulation; Molecular modelling; multidisciplinary; NAD; Neurodegenerative diseases; Neuromodulation; Pharmaceutical Preparations - chemistry; Protein Binding; Quantitative Structure-Activity Relationship; Science; Science (multidisciplinary); Simulation analysis; Sirtuin 2 - antagonists & inhibitors; Sirtuin 2 - chemistry; Structure-activity relationships; Therapeutic targets; Thiazoles - chemistry; Thiazoles - pharmacology
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-021-89627-0

Sirtuin 2 (Sirt2) nicotinamide adenine dinucleotide-dependent deacetylase enzyme has been reported to alter diverse biological functions in the cells and onset of diseases, including cancer, aging, and neurodegenerative diseases, which implicate the regulation of Sirt2 function as a potential drug target. Available Sirt2 inhibitors or modulators exhibit insufficient specificity and potency, and even partially contradictory Sirt2 effects were described for the available inhibitors. Herein, we applied computational screening and evaluation of FDA-approved drugs for highly selective modulation of Sirt2 activity via a unique inhibitory mechanism as reported earlier for SirReal2 inhibitor. Application of stringent molecular docking results in the identification of 48 FDA-approved drugs as selective putative inhibitors of Sirt2, but only top 10 drugs with docking scores > − 11 kcal/mol were considered in reference to SirReal2 inhibitor for computational analysis. The molecular dynamics simulations and post-simulation analysis of Sirt2-drug complexes revealed substantial stability for Fluphenazine and Nintedanib with Sirt2. Additionally, developed 3D-QSAR-models also support the inhibitory potential of drugs, which exclusively revealed highest activities for Nintedanib (pIC50 ≥ 5.90 µM). Conclusively, screened FDA-approved drugs were advocated as promising agents for Sirt2 inhibition and required in vitro investigation for Sirt2 targeted drug development.