title: Computational determination of binding structures and free energies of glucose 6-phosphate dehydrogenase with novel steroid inhibitors.
abstract: Glucose 6-phosphate dehydrogenase (G6PD), the first and the rate-limiting enzyme in the pentose phosphate pathway (PPP), catalyzes the oxidation of G6P to 6-phosphogluconolactone and the reduction of NADP(+) to NADPH. Its key role in cancer promotes the development of a potent and selective inhibitor that might increase cancer cell death when combined with radiotherapy. In the present study, we investigated the detailed binding modes and binding free energies for G6PD interacting with a promising series of recently developed inhibitors, i.e., the steroid derivatives, by performing molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations. The docking indicates that the inhibitors occupy the binding sites of both G6P and NADP(+). The calculated binding free energies on the basis of the MD-simulated enzyme-inhibitor complexes are in good agreement with the experimental activity data for all of the examined inhibitors. The valuable insights into the detailed enzyme-inhibitor binding including the important intermolecular interactions, e.g., the hydrogen bond interaction and the hydrophobic interaction, have been provided. The computational results provide new insights into future rational design of more potent inhibitors of G6PD as a treatment for cancer.
authors.affiliation: State Key Laboratory of Urban Water Resource and Environment, Academy of Fundamental and Interdisciplinary Science, Harbin Institute of Technology, Harbin 150080, People's Republic of China.
authors.forename: Zhi-Bo
authors.initials: ZB
authors.lastname: Zhao
authors.affiliation: State Key Laboratory of Urban Water Resource and Environment, Academy of Fundamental and Interdisciplinary Science, Harbin Institute of Technology, Harbin 150080, People's Republic of China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Urban Water Resource and Environment, Academy of Fundamental and Interdisciplinary Science, Harbin Institute of Technology, Harbin 150080, People's Republic of China. Electronic address: yyuan@hit.edu.cn.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Yao
mesh_terms: D015068:17-Ketosteroids / Q000737:chemistry; D000970:Antineoplastic Agents / Q000737:chemistry*; D020134:Catalytic Domain; D015195:Drug Design; D004791:Enzyme Inhibitors / Q000737:chemistry*; D005954:Glucosephosphate Dehydrogenase / Q000037:antagonists & inhibitors* / Q000737:chemistry; D006801:Humans; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D058990:Molecular Targeted Therapy; D009369:Neoplasms / Q000188:drug therapy; D011485:Protein Binding; D013816:Thermodynamics
chemical_list: D015068:17-Ketosteroids; D000970:Antineoplastic Agents; D004791:Enzyme Inhibitors; D005954:Glucosephosphate Dehydrogenase
keywords: Binding free energy; Binding mode; Glucose 6-phosphate dehydrogenase; MM–PBSA; Molecular docking; Molecular dynamics simulation