Identification of PPA1 inhibitor candidates for potential repurposing in cancer medicine

Abstract

Inorganic pyrophosphatase 1 (PPA1) is pivotal to cellular metabolism as it facilitates the hydrolysis of PPi—a by‐product of various metabolic processes that influence cell growth and differentiation. Overexpression of PPA1 enzyme has been linked to diminished patient survival and was shown to influence tumor cell dynamics, thereby positioning it as a potential therapy target for a variety of cancers including colorectal cancer, diffuse large B‐cell lymphoma, and lung adenocarcinoma. Despite this therapeutic promise, there are no known inhibitors of PPA1 as of today. In this study, we searched for potential PPA1 inhibitors using a molecular docking screen of 30 470 compounds with a history of clinical trials and/or US Food and Drug Administration approval. We specifically targeted the active pocket that coincides with the established catalytic domain. Our screen identified promising hits, which we further subjected to ADMET (absorption, distribution, metabolism, excretion, and toxicity) filtering. Subsequent molecular dynamics (MD) analyses were conducted on devazepide, quinotolast, and tarazepide—the three substances that successfully navigated all filters. MD analyses reinforced the stability of the protein‐ligand complexes and confirmed ligand binding, as substantiated by our root mean square deviation, radius of gyration and secondary structures of proteins analyses. Furthermore, Molecular Mechanics Poisson‐Boltzmann Surface Area calculations post‐MD identified devazepide and quinotolast as showing higher binding affinities; being supported by principal component analysis, free energy landscape, and dynamic cross‐correlation matrix results. Overall, our study reveals devazepide and quinotolast as potential candidates for PPA1 inhibition which could be considered for repurposing studies that need further experimental validation. These results not only reveal a potential for clinical repurposing for PPA1 inhibition but they also offer valuable insights into the development of future compounds for targeting the crucial PPA1 enzyme.

The inorganic pyrophosphatases of microorganisms: a structural and functional review

“…Evidence suggests that it is an essential housekeeping enzyme that is overexpressed in tumors and is a key player in cell signaling, both in the regulation of its activation and in the role of tumor cell metabolism ( Wang et al, 2022 ). The overexpression of c-PPase in tumors can potentially be targeted by anticancer drugs ( Niu et al, 2021 ; Menteş & Yandım, 2023 ). One example of the role of c-PPase is the heightened expression of PPA1, the housekeeping isoform of c-PPase in humans, in colorectal tumors ( Niu et al, 2023 ).…”