Discovery of novel anticancer flavonoids as potential HDAC2 inhibitors: virtual screening approach based on molecular docking, DFT and molecular dynamics simulations studies

• Published in: 3 Biotech 2024-03, Vol.14 (3), p.83-83, Article 83
• Main Authors: Shah, Ashish, Choudhary, Aarti, Jain, Manav, Perumal, Sathiaseelan, Patel, Vaishali, Parmar, Ghanshyam, Patel, Ashish
• Format: Article
• Language: English
• Subjects: Agriculture; Amino acids; Binding; Bioinformatics; Biological activity; Biomaterials; Biotechnology; Cancer Research; Chemistry; Chemistry and Materials Science; Electrostatic properties; Flavonoids; HDAC2 protein; Histone deacetylase; Hydroxyl groups; Inhibitors; Isocyanates; Ligands; Molecular docking; Molecular dynamics; Molecular interactions; Molecular orbitals; Original Article; Screening; Stem Cells; Zinc
• ISSN: 2190-572X; 2190-5738
• DOI: 10.1007/s13205-023-03912-5

Virtual screening of a library of 329 flavonoids obtained from the NPACT database was performed to find out potential novel HDAC2 inhibitors. Eleven out of 329 selected flavonoids were screened based on molecular docking studies, as they have higher binding affinities than the standard drugs vorinostat and panobinostat. All screened compounds occupying the catalytic site of HDAC2 showed important molecular interaction with Zn 2+ and other important amino acids in the binding pocket. The screened compounds were validated using ADMET filtration and bioactivity prediction from which we obtained six compounds, NPACT00270, NPACT00676, NPACT00700, NPACT001008, NPACT001054, and NPACT001407, which were analyzed using DFT studies. DFT studies were performed for all six screened flavonoids. In DFT studies, three flavonoids, NPACT00700, NPACT001008, and NPACT001407, were found to be better based on HOMO–LUMO and molecular electrostatic potential (MEP) analyses. Furthermore, MD simulations were performed for 100 ns for the three compounds. In the MD analysis, NPACT001407 was found to be more stable in the active site of HDAC2 as zinc formed a coordination bond with ASP181, HIS183, ASP269, and GLY305, along with two hydroxyl groups of the ligand. Our findings reveal that these flavonoids can interact as ligands with the active site of HDAC2. Because of the absence of a hydroxamate group in flavonoids, there are no possibilities for the formation of isocyanate. This suggests that the major drawback of current HDACs inhibitors may be solved. Further experimental validation is needed to understand the selectivity of flavonoids as HDAC2 inhibitors.