title: Core site-moiety maps reveal inhibitors and binding mechanisms of orthologous proteins by screening compound libraries.
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 (IC(50)<8.0 µM) 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 subsite-moiety environments for elucidating the binding mechanisms of targets.
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.
authors.forename: Kai-Cheng
authors.initials: KC
authors.lastname: Hsu
authors.forename: Wen-Chi
authors.initials: WC
authors.lastname: Cheng
authors.forename: Yen-Fu
authors.initials: YF
authors.lastname: Chen
authors.forename: Hung-Jung
authors.initials: HJ
authors.lastname: Wang
authors.forename: Ling-Ting
authors.initials: LT
authors.lastname: Li
authors.forename: Wen-Ching
authors.initials: WC
authors.lastname: Wang
authors.forename: Jinn-Moon
authors.initials: JM
authors.lastname: Yang
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D002942:Circular Dichroism; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D015195:Drug Design; D004791:Enzyme Inhibitors / Q000494:pharmacology; D015723:Gene Library; D016480:Helicobacter pylori / Q000378:metabolism; D020128:Inhibitory Concentration 50; D008826:Microbial Sensitivity Tests; D016297:Mutagenesis, Site-Directed; D009169:Mycobacterium tuberculosis / Q000378:metabolism; D017853:Phosphotransferases (Alcohol Group Acceptor) / Q000037:antagonists & inhibitors; D011485:Protein Binding; D015203:Reproducibility of Results
chemical_list: D004791:Enzyme Inhibitors; D017853:Phosphotransferases (Alcohol Group Acceptor); C022642:shikimate kinase