In silico design of novel proton-pump inhibitors with reduced adverse effects

Abstract

The development of new proton-pump inhibitors (PPIs) with less adverse effects by lowering the pKa values of nitrogen atoms in pyrimidine rings has been previously suggested by our group. In this work, we proposed that new PPIs should have the following features: (1) number of ring II = number of ring I+ 1; (2) preferably five, six, or seven-membered heteroatomic ring for stability; and (3) 1<pKa1<4. Six molecular scaffolds based on the aforementioned criteria were constructed, and R groups were extracted from compounds in extensive data sources. A virtual molecule dataset was established, and the pKa values of specific atoms on the molecules in the dataset were calculated to select the molecules with required pKa values. Drug-likeness screening was further conducted to obtain the candidates that significantly reduced the adverse effects of long-term PPI use. This study provided insights and tools for designing targeted molecules in silico that are suitable for practical applications.

Keywords

proton-pump inhibitor / adverse effect / pharmacological mechanism / toxicological mechanism / pKa calculation

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Acknowledgements

This work was supported by National Natural Science Foundation of China (Nos. 31200986 and 41530105) (to RZ), Natural Science Foundation, the Shanghai Committee of Science and Technology (No. 16ZR1449800) (to RZ), the Fundamental Research Funds for the Central Universities (Nos. 10247201546 and 2000219083) (to RZ), a departmental start-up fund (to LZ), the Peter and Tommy Fund, Inc., Buffalo, NY (to LZ), Funds from the University at Buffalo Community of Excellence in Genome, Environment and Microbiome (GEM) (to LZ) and UTHealth Innovation for Cancer Prevention Research Training Program Post-doctoral Fellowship (Cancer Prevention and Research Institute of Texas, grant #RP160015) (to HK). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Compliance with ethics guidelines

Xiaoyi Li, Hong Kang, Wensheng Liu, Sarita Singhal, Na Jiao, Yong Wang, Lixin Zhu, and Ruixin Zhu declare that they have no conflict of interest. This manuscript does not contain any studies with human or animal subjects.

Electronic Supplementary Material

Supplementary material is available in the online version of this article at https://doi.org/10.1007/s11684-018-0630-3 and is accessible for authorized users.

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