A New Family of Jumonji C Domain-Containing KDM Inhibitors Inspired by Natural Product Purpurogallin.

José A Souto,Rosana Álvarez,Ángel R De Lera,Angela Nebbioso,Jessica Lombino,Alessandro Padova,Lucia Altucci,Chiara Papulino,Ugo Perricone,Federica Sarno

doi:10.3389/fchem.2020.00312

José A Souto, Rosana Álvarez + Show 8 more

Open Access

https://doi.org/10.3389/fchem.2020.00312

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Abstract

Aberrant epigenetic modifications are involved in cancer development. Jumonji C domain-containing histone lysine demethylases (KDMs) are found mainly up-regulated in breast, prostate, and colon cancer. Currently, growing interest is focusing on the identification and development of new inhibitors able to block the activity of KDMs and thus reduce tumor progression. KDM4A is known to play a role in several cellular physiological processes, and was recently found overexpressed in a number of pathological states, including cancer. In this work, starting from the structure of purpurogallin 9aa, previously identified as a natural KDM4A inhibitor, we synthesized two main sets of compound derivatives in order to improve their inhibitory activity against KDM4A in vitro and in cells, as well as their antitumor action. Based on the hypothetical biogenesis of the 5-oxo-5H-benzo[7]annulene skeleton of the natural product purpurogallin (Salfeld, 1960; Horner et al., 1961; Dürckheimer and Paulus, 1985; Tanaka et al., 2002; Yanase et al., 2005) the pyrogallol and catechol units were first combined with structural modifications at different positions of the aryl ring using enzyme-mediated oxidative conditions, generating a series of benzotropolone analogs. Two of the synthetic analogs of purpurogallin, 9ac and 9bc, showed an efficient inhibition (50 and 80%) of KDM4A in enzymatic assays and in cells by increasing levels of its specific targets, H3K9me3/2 and H3K36me3. However, these two compounds/derivatives did not induce cell death. We then synthesized a further set of analogs of these two compounds with greater structural diversification. The most potent of these analogs, 9bf, displayed the highest KDM4A inhibitory enzymatic activity in vitro (IC50 of 10.1 and 24.37 μM) in colon cancer cells, and the strongest antitumor action in several solid and hematological human cancer cell lines with no toxic effect in normal cells. Our findings suggest that further development of this compound and its derivatives may lead to the identification of new therapeutic antitumor agents acting through inhibition of KDM4A.

Highlights

Epigenetic modifications, in other words changes occurring in the phenotype without altering the genotype, are known to be responsible for a myriad of biological processes that can result in the development of fatal diseases such as cancer (Esteller, 2008; DeWoskin and Million, 2013)
The histone lysine demethylase (KDM) 4 (Jmj-D2) subfamily of KDMs (Kooistra and Helin, 2012; Black et al, 2013), which are upregulated in many cancer cell types (Franci et al, 2014), show a preference for demethylation of tri- and di-Nε-methylated H3K9 substrates, with KDM4A-C acting on H3K36 (Berry and Janknecht, 2013)
KDM4A is known to be involved in several cellular functions, including embryonic development, cell cycle regulation, and DNA damage response (Guerra-Calderas et al, 2015)

Summary

Introduction

Epigenetic modifications, in other words changes occurring in the phenotype without altering the genotype, are known to be responsible for a myriad of biological processes that can result in the development of fatal diseases such as cancer (Esteller, 2008; DeWoskin and Million, 2013). Jumonji C (Jmj-C) enzymes, a class of ∼60 proteins in humans (Loenarz and Schofield, 2011), are non-heme iron [Fe(II)]- and 2-oxoglutarate (2-OG)-dependent oxygenases that catalyze the demethylation of Nε-methylated lysine residues on histone tails, in particular the N-terminal tail of histone H3. This epigenetic modification was shown to induce dramatic effects on cell proliferation, causing, among other undesired activities, endocrine deregulation, and cancer development (Loenarz and Schofield, 2008; Handy et al, 2011). The histone lysine demethylase (KDM) 4 (Jmj-D2) subfamily of KDMs (Kooistra and Helin, 2012; Black et al, 2013), which are upregulated in many cancer cell types (Franci et al, 2014), show a preference for demethylation of tri- and di-Nε-methylated H3K9 substrates, with KDM4A-C acting on H3K36 (Berry and Janknecht, 2013)

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