International Microbiology

, Volume 22, Issue 1, pp 69–80 | Cite as

Integration of virtual screening and susceptibility test to discover active-site subpocket-specific biogenic inhibitors of Helicobacter pylori shikimate dehydrogenase

  • Kuifeng Wang
  • Min Zhu
  • Yongzhi Tang
  • Junyan Liu
  • Fei Yan
  • Zhenjun Yu
  • Jiansheng ZhuEmail author
Original Article


Shikimate dehydrogenase (HpSDH) (EC is a key enzyme in the shikimate pathway of Helicobacter pylori (H. pylori), which catalyzes the NADPH-dependent reversible reduction of 3-dehydroshikimate to shikimate. Targeting HpSDH has been recognized as an attractive therapeutic strategy against H. pylori infection. Here, the catalytic active site in the crystal structure of HpSDH in complex with its substrate NADPH and product shikimate was examined in detail; the site can be divided into three spatially separated subpockets that separately correspond to the binding regions of shikimate, NADPH dihydronicotinamide moiety, and NADPH adenine moiety. Subsequently, a cascading protocol that integrated virtual screening and antibacterial test was performed against a biogenic compound library to identify biologically active, subpocket-specific inhibitors. Consequently, five, eight, and six promising compounds for, respectively, subpockets 1, 2, and 3 were selected from the top-100 docking-ranked hits, from which 11 compounds were determined to have high or moderate antibacterial potencies against two reference H. pylori strains, with MIC range between 8 and 93 μg/mL. It is found that the HpSDH active site prefers to accommodate amphipathic and polar inhibitors that consist of an aromatic core as well as a number of oxygen-rich polar/charged substituents such as hydroxyl, carbonyl, and carboxyl groups. Subpockets 1- and 2-specific inhibitors exhibit a generally higher activity than subpocket 3-specific inhibitors. Molecular dynamics simulations revealed an intense nonbonded network of hydrogen bonds, π-π stacking, and van der Waals contacts at the tightly packed complex interfaces of active-site subpockets with their cognate inhibitors, conferring strong stability and specificity to these complex systems. Binding energetic analysis demonstrated that the identified potent inhibitors can target their cognate subpockets with an effective selectivity over noncognate ones.


Helicobacter pylori Shikimate dehydrogenase Biogenic compound Subpocket Virtual screening Rational drug discovery 


Funding information

This work was supported by the Zhejiang Provincial Medical Science and Technology Project (No. 2016KYA187).


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Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  • Kuifeng Wang
    • 1
  • Min Zhu
    • 1
  • Yongzhi Tang
    • 1
  • Junyan Liu
    • 1
  • Fei Yan
    • 1
  • Zhenjun Yu
    • 1
  • Jiansheng Zhu
    • 1
    Email author
  1. 1.Department of Infectious DiseasesAffiliated Taizhou Hospital of Wenzhou Medical UniversityTaizhouChina

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