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Energetic factors determining the binding of type I inhibitors to c-Met kinase: experimental studies and quantum mechanical calculations

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Yu Zhe 1   Ma Yuchi 1   Ai Jing 1   Chen Danqi 1   Zhao Dongmei 2 *   Wang Xin 1   Chen Yuelei 1   Geng Meiyu 1   Xiong Bing 1 *   Cheng Maosheng 2   Shen Jingkang 1 *  
文摘 Aim To decipher the molecular interactions between c-Met and its type I inhibitors and to facilitate the design of novel c-Met inhibitors. Methods: Based on the prototype model inhibitor 1, four ligands with subtle differences in the fused aromatic rings were synthesized. Quantum chemistry was employed to calculate the binding free energy for each ligand. Symmetry-adapted perturbation theory (SAPT) was used to decompose the binding energy into several fundamental forces to elucidate the determinant factors. Results: Binding free energies calculated from quantum chemistry were correlated well with experimental data. SAPT calculations showed that the predominant driving force for binding was derived from a sandwich π–π interaction with Tyr-1230. Arg-1208 was the differentiating factor, interacting with the 6-position of the fused aromatic ring system through the backbone carbonyl with a force pattern similar to hydrogen bonding. Therefore, a hydrogen atom must be attached at the 6-position, and changing the carbon atom to nitrogen caused unfavorable electrostatic interactions. Conclusion: The theoretical studies have elucidated the determinant factors involved in the binding of type I inhibitors to c-Met.
来源 Acta Pharmacologica Sinica ,2013,34(11):1475-1483 【核心库】
DOI 10.1038/aps.2013.85
关键词 receptor tyrosine kinase ; type I c-Met inhibitor ; cancer ; quantum chemistry ; protein-ligand interaction ; symmetry-adapted perturbation theory (SAPT)
地址

1. Shanghai Institute of Materia Medica, Chinese Academy of Sciences, State Key Laboratory of Drug Research, Shanghai, 201203  

2. Shenyang Pharmaceutical University, School of Pharmaceutical Engineering, Shenyang, 110016

语种 英文
文献类型 研究性论文
ISSN 1671-4083
学科 药学
基金 support from the Program of Excellent Young Scientists of the Chinese Academy of Sciences to Bing XIONG ;  the National Natural Science Foundation of China to Bing XIONG ;  the “Interdisciplinary Cooperation Team” Program for Science and Technology Innovation of the Chinese Academy of Sciences
文献收藏号 CSCD:4966502

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引证文献 2 篇

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