title: Molecular docking and dynamics simulation, receptor-based hypothesis: application to identify novel sirtuin 2 inhibitors.
abstract: Sirtuin, NAD(+)-dependent histone deacetylase enzyme, emerged as a potential therapeutic target, and modulations by small molecules could be effective drugs for various diseases. Owing to the absence of complex structure of sirtuin 2 (SIRT2), sirtinol was docked in the NAD(+) binding site and subjected to 5-nseconds molecular dynamics (MD) simulation. LigandScout was used to develop hypotheses based on 3-representative SIRT2 complex structures from MD. Three structure-based hypotheses are generated and merged to form dynamics hypothesis. The dynamics hypothesis was validated using test and decoy sets. The results showed that dynamic hypothesis represents the complementary features of SIRT2 active site. Dynamic hypothesis was used to screen ChemDiv database, and hits were filtered through ADMET, rule of five, and two different molecular docking studies. Finally, 21 molecules were selected as potent leads based on consensus score from LigandFit, Gold fitness score, binding affinity from VINA as well as based on the important interactions with critical residues in SIRT2 active site. Hence, we suggest that the dynamic hypothesis will be reliable in the identification of SIRT2 new lead as well as to reduce time and cost in the drug discovery process.
authors.affiliation: Division of Applied Life Science (BK21 Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Gazha-dong, Jinju 660-701, Korea.
authors.forename: Sugunadevi
authors.initials: S
authors.lastname: Sakkiah
authors.forename: Sundarapandian
authors.initials: S
authors.lastname: Thangapandian
authors.forename: Chanin
authors.initials: C
authors.lastname: Park
authors.forename: Minky
authors.initials: M
authors.lastname: Son
authors.forename: Keun W
authors.initials: KW
authors.lastname: Lee
mesh_terms: D001665:Binding Sites; D015195:Drug Design; D004791:Enzyme Inhibitors / Q000737:chemistry* / Q000494:pharmacology*; D006801:Humans; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D056565:Sirtuin 2 / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism*; D013329:Structure-Activity Relationship
chemical_list: D004791:Enzyme Inhibitors; D056565:Sirtuin 2