Colonization of human stomach by the bacterium Helicobacter pylori is a major causative factor for
gastrointestinal illnesses and gastric cancer. However, the discovery of anti-H. pylori agents is a difficult
task due to lack of mature protein targets. Therefore, identifying new molecular targets for developing
new drugs against H. pylori is obviously necessary. In this study, the in-house potential drug target database
(PDTD, http://www.dddc.ac.cn/tarfisdock/) was searched by the reverse docking approach using an active
natural product (compound 1) discovered by anti-H. pylori screening as a probe. Homology search revealed
that, among the 15 candidates discovered by reverse docking, only diaminopimelate decarboxylase (DC)
and peptide deformylase (PDF) have homologous proteins in the genome of H. pylori. Enzymatic assay
demonstrated compound 1 and its derivative compound 2 are the potent inhibitors against H. pylori PDF
(HpPDF) with IC50 values of 10.8 and 1.25 mM, respectively. X-ray crystal structures of HpPDF and the
complexes of HpPDF with 1 and 2 were determined for the first time, indicating that these two inhibitors
bind well with HpPDF binding pocket. All these results indicate that HpPDF is a potential target for
screening new anti-H. pylori agents. In addition, compounds 1 and 2 were predicted to bind to HpPDF with
relatively high selectivity, suggesting they can be used as leads for developing new anti-H. pylori agents.
The results demonstrated that our strategy, reverse docking in conjunction with bioassay and structural
biology, is effective and can be used as a complementary approach of functional genomics and chemical
biology in target identification.