core site-moiety maps reveal inhibitors and binding mechanisms of orthologous proteins by screening compound libraries核心site-moiety地图揭示同源蛋白的抑制剂和绑定机制筛选化合物库.pdf

Core Site-Moiety Maps Reveal Inhibitors and Binding Mechanisms of Orthologous Proteins by Screening Compound Libraries 1. 2. 1 2 1 Kai-Cheng Hsu , Wen-Chi Cheng , Yen-Fu Chen , Hung-Jung Wang , Ling-Ting Li , Wen-Ching Wang2*, Jinn-Moon Yang1,3* 1 Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, 2 Department of Life Sciences, Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan, 3 Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan Abstract Members of protein families often share conserved structural subsites for interaction with chemically similar moieties despite low sequence identity. We propose a core site-moiety map of multiple proteins (called CoreSiMMap) to discover inhibitors and mechanisms by profiling subsite-moiety interactions of immense screening compounds. The consensus anchor, the subsite-moiety interactions with statistical significance, of a CoreSiMMap can be regarded as a ‘‘hot spot’’ that represents the conserved binding environments involved in biological functions. Here, we derive the CoreSiMMap with six consensus anchors and identify six inhibitors (IC50,8.0 m M) of shikimate kinases (SKs) of Mycobacterium tuberculosis and Helicobacter pylori from the NCI database (236,962 compounds). Studies of site-directed mutagenesis and analogues reveal that these conserved interacting residues and moieties contribute to pocket-moiety interaction spots and biological functions. These results reveal that our multi-target screening strategy and the CoreSiMMap can increase the accuracy of screening in the identification of novel inhibitors and su