Review
Epi-drugs to fight cancer: From chemistry to cancer treatment, the road ahead

https://doi.org/10.1016/j.biocel.2008.08.020Get rights and content

Abstract

In addition to genetic events, a variety of epigenetic events have been widely reported to contribute to the onset of many diseases including cancer. DNA methylation and histone modifications (such as acetylation, methylation, sumoylation, and phosphorylation) involving chromatin remodelling are among the most studied epigenetic mechanisms for regulation of gene expression leading, when altered, to some diseases. Epigenetic therapy tries to reverse the aberrations followed to the disruption of the balance of the epigenetic signalling ways through the use of both natural compounds and synthetic molecules, active on specific epi-targets. Such epi-drugs are, for example, inhibitors of DNA methyltransferases, histone deacetylases, histone acetyltransferases, histone methyltransferases, and histone demethylases. In this review we will focus on the chemical aspects of such molecules, joined to their effective (or potential) application in cancer therapy.

Introduction

A great research interest has been focused on the pharmacological restoration of epigenetic regulation balance by using epi-drugs. At the present, pharmaco-epigenomics constitute the hope for a new strategy in cancer treatment.

Nucleosomes are the basal units that structure the eukaryotic chromatin. A typical nucleosome is composed of an octamer of the four pairs of core histones H2A, H2B, H3 and H4, and ∼146 base pairs of DNA wrapped around them (Luger et al., 1997). The core histone N-terminal domains are rich in positively charged basic amino acids, which can actively interact with DNA (Lenfant et al., 1996). The chromatin barrier formed by histone–DNA interaction blocks the binding of the basic transcription complex to gene promoters, and suppresses gene expression (Gregory et al., 2001). The dynamic process of histone acetylation has been linked to gene transcription, and histone deacetylation has been related to inactive chromatin (Grunstein, 1997). Under physiological conditions, chromatin acetylation is regulated by the balanced action of histone acetyltransferases (HATs) and deacetylases (HDACs). The HATs transfer acetyl groups from acetyl coenzyme A (acetyl-CoA) onto the ɛ-amino groups of conserved lysine residues within the core histones (Tanner et al., 1999). Acetylation can neutralize the positive charge of histones, loosening their interactions with the negatively charged DNA backbone, and leading to a more “open” active chromatin structure that favours the binding of transcription factors for active gene transcription (Gregory et al., 2001). Contrarily, the re-establishment of the positive charge in the amino-terminal tails of core histones catalyzed by HDACs is thought to tighten the interaction between histones and DNA, blocking the binding sites on promoter thus inhibiting gene transcription. Obviously, a subtly orchestrated balance between the actions of HATs and HDACs is essential to the maintenance of normal cellular functions, and shifts of this balance in both senses might have dramatic consequences on the cell phenotypes such as carcinogenesis (Altucci et al., 2005, Minucci and Pelicci, 2006).

Another major epigenetic modification is the methylation of cytosine residues in genomic DNA (Bird, 2002). About 4% of the cytosines are typically methylated in genomic DNA and this methylation is essential in development (Li et al., 1992). DNA methylation plays an essential role in epigenetic phenomena, including genomic imprinting (Li et al., 1993), X-chromosome inactivation (Panning and Jaenisch, 1996), and retroelement silencing (Walsh et al., 1998). CpG dinucleotides represent the consensus target sequences of DNA methylation in differentiated mammalian cells, but only a relatively small fraction of these sequences becomes methylated. CpG dinucleotides can be clustered in CpG islands which are often related with promoter regions and stay unmethylated for most genes. The signals that determine whether a particular CpG island becomes methylated have not been determined yet, but protein–protein interactions between DNA methyltransferases and chromatin-associated proteins might play an central role (Burgers et al., 2002). As a consequence, DNA methylation is not uniformly distributed over the genome. While the majority of repetitive elements are deeply methylated, gene-specific methylation appears to be restricted. DNA methylation patterns can be altered in human tumors (Ehrlich, 2002). Tumor cells are characterized by specific genetic and epigenetic changes that promote uncontrolled cellular proliferation (Jones and Baylin, 2002, Jones and Baylin, 2007). DNA methylation is catalyzed by DNA methyltransferases, a family of enzymes that comprises DNMT1, DNMT2, DNMT3A and DNMT3B in human cells (Goll and Bestor, 2005). DNA methyltransferase knockouts effects on DNA methylation patterns have been analyzed by both 24 differential methylation hybridization and amplification of inter-methylated sites (Paz et al., 2003). Based on the rationale that hypermethylation-induced gene silencing could be uncovered by gene demethylation and reactivation, many efforts have been put in the identification and characterization of inhibitors of DNA methylation as tools to treat cancer.

This review will discuss the latest ‘epi-drug’ discoveries focusing on the chemical characterization and use of epigenetic modulators in pre-clinical and clinical settings against cancer.

Section snippets

Chemistry of HDAC inhibitors (HDACi) and anticancer applications

Over-expression or malfunction of HDACs may be a cause of carcinogenesis. Sequentially, deregulation of gene expression may induce cancer. HDAC inhibitors (HDACi) are thought to be able to interact with the catalytic domain of histone deacetylases to block the substrate recognition ability of these enzymes, thus resulting in restoration of relevant genes expression (Finnin et al., 1999, Finnin et al., 2001). The main biological effects of HDACi are cell cycle arrest, induction of

Chemistry of SIRT inhibitors and their applications against cancer

In contrast to class I/II/IV HDACi, the inhibitors of class III HDACs (sirtuins) are much less validated as anticancer agents and in general less developed on the pharmacological side. Sirtuins play an important role in many cellular processes such as gene silencing, regulation of transcription factors [i.e., the tumor suppressor and sequence-specific DNA-binding transcription factor p53, the p53-related p73, p300 histone acetyltransferase (HAT), E2F1, NF-κB, and others], fatty acid metabolism,

DNA methylation inhibition for the treatment of cancer

DNA methylation at the C5 position of cytosine in CpG nucleotides, catalyzed by DNMTs with the involvement of S-adenosyl-l-methionine as the methyl donor, is a physiological mechanism of epigenetic regulation of gene expression. However, hypermethylation of CpG islands leads to gene silencing and is known to be a common marker of cancer cells (Esteller, 2002). The first reported DNMT inhibitors (DNMTi) were two cytidine analogues, 5-aza- and 5-aza-2′-deoxycytidine (5-aza-CR and 5-aza-CdR) (

Inhibitors of acetyltransferases (HATs) against cancer

A large group of transcriptional regulators, mainly co-activators, exhibit intrinsic HAT activity. Among them, the p300/cAMP response element binding protein (CREB)-binding protein (CBP) family is involved in several cellular processes such as proliferation, differentiation, and apoptosis (Chan and La Thangue, 2001). Chromosomal translocation of the genes that encode p300 or CBP with those for other HAT proteins (such as monocytic leukemia zinc finger (MOZ) and MOZ-related factor (MORF)

Inhibitors of histone methylation

In addition to histone and non-histone protein acetylation, histone methylation has also been shown to be important in epigenetic regulation of gene expression through the establishment of stable gene-expression patterns. Differently from acetylation, histone methylation does not alter the overall charge of histone tails, but has an influence on basicity, hydrophobicity, and on the affinity for anionic molecules such as DNA. Histone methylation can occur on both Lys (K) or Arg (R) residues.

Inhibitors of demethylases

Two classes of histone demethylases have been described up to now, different in their reaction chemistry, coenzyme use, and reaction products. Lysine-specific histone demethylase 1 (LSD1) is a FAD-dependent enzyme that catalyzes the oxidative removal of one or two methyl groups from H3K4 or, when in complex with the androgen receptor, H3K9, releasing formaldehyde and hydrogen peroxide (Shi et al., 2004, Metzger et al., 2005). LSD1 takes part to a transcriptional repressor complex, with the

Perspectives, remarks and conclusions

The pharmacoepigenomic field is highly improved in the last years. Old drugs have been rediscovered for new functions and new molecules have been developed to target epigenetic enzymes and their alterations in cancer. We are just at the beginning of the understanding of the cross-talk between genetic information and epigenetic regulation. Whereas HDACi have entered the anticancer field with the application of SAHA to CTCL, all the other epi-drugs are still at the molecular or preclinical

Acknowledgements

Lucia Altucci dedicates this work to the memory of Lucia Latela, died fighting cancer and alive in the memory of those who love her.

Work in the author’s laboratories is supported by EU EPITRON LSHC-CT2005-518417; CANCERDIP 200620; APO-SYS 200767 (LA), PRIN 2006 (LA; AM), La Regione Campania L5 annualità 2005 (LA), AIRC 2007 (AM), FIRB RBIP067F9E and RETI FIRB RBPR05NWWC_006 (AM).

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