Comparative Study of the Crystal Structure and Simulated 3D Structure of the Hsp90N‐Inhibitor Complex

Author:

Qin Wei1,Li Jie2,Wang Ming‐Chan2,Li Xin‐Yu1,Li Peng‐Quan1,Zhao Dong1,Chu Hai‐Qing1,Fu Jia1,He Chun‐Xia1,Li Hui‐Jin1,Xing Lu1,Zhou Xin1,Zhang Ye1,Sun Fang‐Yun2,Cao Hui‐Ling1ORCID

Affiliation:

1. Shaanxi Key Laboratory of Ischemic Cardiovascular Disease Shaanxi Key Laboratory of Brain disorders Institute of Basic and Translational Medicine Xi'an Medical University Xi'an 710021 China

2. Engineering Research Center of Tibetan Medicine Detection Technology Ministry of Education School of Medicine Xizang Minzu University Xianyang 712082 China

Abstract

AbstractThe crystal structure of a target‐ligand plays an indispensable role in rational drug design, structural optimization, and understanding the molecular interaction mechanism. For drug targets without crystal structures, the simulated 3D structure will provide an alternative important reference. However, the credibility of the simulated structure and its difference from the real crystal structure deserve deep consideration. The complex crystal structures of the target Hsp90N and its four small molecular inhibitors has previously been successfully determined. Herein, computer‐aided molecular docking technology is applied to predict complex 3D structures, and the comparison between the simulated 3D structures and crystal structures is analyzed. Compared with the complex crystal structures, the simulated 3D structures of the four groups have higher consistency with the main chains, whereas the branch chains, binding modes of inhibitors, and molecular interactions are different in detail. Thus, the simulated 3D complex structure can provide useful information to guide drug design and structural optimization of inhibitors when the crystal structure is missing, but it cannot replace the crystal structure and should be used with caution.

Funder

Xi'an Medical University

Shaanxi Provincial Science and Technology Department

National Natural Science Foundation of China

Publisher

Wiley

Subject

Condensed Matter Physics,General Materials Science,General Chemistry

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1. A Systematic Review of Isogeometric Contact Analysis and Its Applications;Archives of Computational Methods in Engineering;2024-04-29

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