Interactions of 2,6-substituted purines with purine nucleoside phosphorylase from Helicobacter pylori in solution and in the crystal, and the effects of these compounds on cell cultures of this bacterium

Abstract

Helicobacter pylori represents a global health threat with around 50% of the world population infected. Due to the increasing number of antibiotic-resistant strains, new strategies for eradication of H. pylori are needed. In this study, we suggest purine nucleoside phosphorylase (PNP) as a possible new drug target, by characterising its interactions with 2- and/or 6-substituted purines as well as the effect of these compounds on bacterial growth. Inhibition constants are in the micromolar range, the lowest being that of 6-benzylthio-2-chloropurine. This compound also inhibits H. pylori 26695 growth at the lowest concentration. X-ray structures of the complexes of PNP with the investigated compounds allowed the identification of interactions of inhibitors in the enzyme’s base-binding site and the suggestion of structures that could bind to the enzyme more tightly. Our findings prove the potential of PNP inhibitors in the design of drugs against H. pylori.

Keywords:

• Helicobacter pylori
• purine nucleoside phosphorylase
• substituted purines
• minimal inhibitory concentration
• X-ray structure

Acknowledgements

The authors are indebted to the late prof. Zygmunt Kazimierczuk from Warsaw University of Life Sciences for the kind gift of 6BnS-2Cl-Pu-9dr, to Dr. Katarzyna Bocian-Ostrzycka and Dr. Magdalena Grzeszczuk from Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, for assistance in developing conditions for H. pylori growth in the liquid medium. The authors are also grateful to MSc. Alicja Dyzma and MSc. Natasza Gajda from the Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, for the invaluable help in the first stages of this project, and for the excellent technical assistance in the determination of inhibition constants; to MSc. Alicja Dyzma also for the help in the checkerboard assay experiments. The authors are also grateful to Dr. Nicola Demitri for the assistance during synchrotron measurements at Elettra.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

Supported from the project Harmonia 2015/18/M/NZ1/00776 granted by the National Science Centre of Poland, partially also from the project 2018/29/B/NZ1/00140, from the Polish Ministry for Science and Higher Education 501-D111-01-1110102, and from the University of Warsaw project IDUB PSP-501-D111-20-0004316. Experiments conducted in Ruđer Bošković Institute in Zagreb were supported by the Croatian Science Foundation [under the project numbers IP-2013-11-7423 and IP-2019-04-6764]. Some experiments were performed in the Laboratory of Biopolymers, ERDF Project POIG.02.01.00-14-122/09.