Current trends in clinical trials and the development of small molecule epigenetic inhibitors as cancer therapeutics

Abstract

Epigenetic mechanisms control and regulate normal chromatin structure and gene expression patterns, with epigenetic dysregulation observed in many different cancer types. Importantly, epigenetic modifications are reversible, offering the potential to silence oncogenes and reactivate tumor suppressors. Small molecule drugs manipulating these epigenetic mechanisms are at the leading edge of new therapeutic options for cancer treatment. The clinical use of histone deacetyltransferases inhibitors (HDACi) demonstrates the effectiveness of targeting epigenetic mechanisms for cancer treatment. Notably, the development of new classes of inhibitors, including lysine acetyltransferase inhibitors (KATi), are the future of epigenetic-based therapeutics. We outline the progress of current classes of small molecule epigenetic drugs for use against cancer (preclinical and clinical) and highlight the potential market growth in epigenetic-based therapeutics.

Plain language summary

Cancer affects a lot of people worldwide – about one in every two individuals will face it in their lifetime. Although cancer rates are going up, survival rates have also improved in many cases, largely thanks to better and more specific drugs. These new drugs target specific changes in tumors, which are identified using molecular testing. These changes can be in the deoxyribonucleic acid (DNA) sequence, or in the ‘epigenetics’, which does not change the DNA sequence. Importantly epigenetic changes can be reversed, unlike DNA changes. This opens up the possibility of targeting these epigenetic changes to treat cancer, potentially turning back on anti-cancer processes that were turned off. Scientists are now working on developing new drugs that target these epigenetic changes. These drugs, called small molecule epigenetic inhibitors, have shown promise in improving the effectiveness of cancer treatment. They're opening up new options for treating various diseases, including cancer. Lots of new epigenetic drugs are being developed and tested, with some already moving into clinical trials with a few already in use to treat cancer patients. In this summary, we'll discuss the progress of these drugs, how they are being used against cancer, and the growing interest in epigenetic-based therapies.

Tweetable abstract

We review development of small molecule epigenetic anti-cancer therapeutics and outline the progress of epigenetic drug development, preclinical and clinical trials, highlighting market growth in epigenetic-based therapeutics.

Graphical abstract

Plain language summary

Executive summary.

The challenge

• Worldwide the incidence of cancer is now almost 1 in 2.

• Increasing rates of cancer requires new targeted therapeutic options to improve patient survival.

• The common dysregulation of epigenetics observed in many tumors offers a promising new opportunity for the development of new specific and targeted treatments.

• New classes of drugs offer new development and investment opportunities for pharma.

Small molecule epigenetic inhibitors

• Epigenetic inhibitors are an exciting new class of therapeutics.

• New classes of epigenetic drugs are undergoing clinical trials, with the recent approval of one drug for the treatment of a solid tumor type (breast cancer).

• The epigenetic market is growing substantially.

Conclusion

• The development of new epigenetic inhibitors will lead to new clinical approvals for cancer treatment.

• The expanding clinical use of small molecule epigenetic inhibitors will lead to a significant expansion of the market, with increasing returns for patients, and pharma.

Precision medicine led next generation cancer therapeutics

Cancer ranks as the second most prevalent cause of global mortality, after heart disease [1]. Cancer is a multifaceted disease with treatment and progression influenced by factors including tumor genetic heterogeneity, dysregulated molecular signaling and environmental and socioeconomic factors. The traditional non-precision approach to cancer treatment (including surgery, non-targeted chemotherapy and radiotherapy) is effective. However, these treatment strategies damage non-cancer cells, which is not optimal [2].

Recent advances in the widespread accessibility of genomics (and other ‘omics’) have facilitated the molecular profiling of tumors, allowing the use of personalized/precise treatment regimens (based on tumours cells specific molecular and phenotypic profile) [2]. The genomic profiling of a patient/tumor provides data on key diagnostic and prognostic markers (e.g., breast cancer gene [BRCA] 1/2 mutation status), guiding clinical decision making on the selection of new targeted complimentary therapeutic options (e.g., poly-ADP ribose polymerase [PARP] inhibitors) [3]. This approach induces synthetic lethality specifically in the cancer cells, underpinning the effectiveness of these new targeted therapeutics. Reflecting the importance of this new molecular profiling led approach, 90% of the top pharmaceutical companies in the world are currently investing in developing new targeted drugs [2].

An exciting new avenue of therapeutic research is the potential of using epigenetic inhibitors in tumors lacking actionable genetic alterations [4,5]. Epigenetics is the heritable change in gene expression (switching genes on/off) which does not alter the underlying genetic sequence. Epigenetic inhibitors can reprogram gene expression, reactivating tumor suppressors or silencing oncogenes, to induce targeted death in cancer cells [6–8].

Epigenetics

Key epigenetic marks include DNA methylation and histone modifications (primarily acetylation) (Table 1). Several significant enzyme classes have been identified as responsible for regulating these epigenetic marks, including DNA methyltransferases (DNMT), lysine acetyltransferases (KAT), and histone deacetylases (HDAC). Disruptions in the function of these enzymes and any subsequent epigenetic dysregulation ultimately promote and/or support tumorigenesis [9–11].

Table 1.

Epigenetic modifications.

Epigenetic mechanism	Modification
Histone post-translational modifications	Acetylation
	Methylation
	Phosphorylation
	ADP-ribosylation
	Ubiquitination
	SUMOylation
	Crotonylation
	Carbonylation
	Glycosylation
	Guanylation
	Succinylation
	Lactylation
	β-hydroxybutyrylation
	Citrullination
	Propionylation
	Deamination
	Formylation
	O-GlcNAcylation
	Proline isomerization
DNA methylation	Genome-wide hypomethylation
	Site-specific hypermethylation

In many cancers, tumor suppressors are silenced by hypermethylation while oncogenes can be activated by demethylation, supporting tumor growth [9]. Resetting this dysregulated epigenetic profile by selective targeting of key epigenetic enzymes can facilitate restoring normal epigenomic regulation of key anti-tumor genes which inhibits tumor growth or progression [12–15].

Targeting epigenetic modifiers as cancer therapeutics

The creation of DNA methylation reversing agents allowed breakthroughs which advanced our understanding of epigenetic regulatory mechanisms, and the applications of epigenetic inhibitors [1]. The clinical utility of epigenetic targeting drugs has been established by DNMT, HDAC, HMT (which include histone lysine methyltransferases (KMTs]) and enhancer of zeste homolog 2 (EZ2H) inhibitors, all of which are currently approved for clinical use against multiple non-solid cancer types, while recently one HDACi has gained approval for [se against some solid breast tumors (Table 2) [7,16]. While these epigenetic drugs complement current treatment options, new epigenetic drugs are emerging [9]. Importantly, some epigenetically relevant post-translational modifications (PTM), including phosphorylation and ubiquitination, are multifaceted and predominantly exert their effects by regulating key non-epigenetic cellular processes (including cell cycle control, fundamental cell signalling pathways or DNA repair) which make epigenetic-specific targeting of these process/PTMs difficult as their primary anti-cancer mechanism of action is related to non-epigenetic effects [13,17,18].

Table 2.

Clinically approved epigenetic inhibitors.

Category of epigenetic drugs	Number of approved drugs	Name of approved drug	Cancers targeted	Approved By	Ref.
DNMTi	4	5-azacitidine	Myelodysplastic syndromes	FDA (USA)	[1]
		Decitabine (5-aza-2′-deoxycytidine)	Myelodysplastic syndromes	FDA (USA)	[2]
		Clofarabine	Acute myeloid leukemia	FDA (USA)	[3]
		Arsenic trioxide	Acute promyelocytic leukemia	FDA (USA)	[4]
IDHi	2	Ivosidenib	Acute myeloid leukemia	FDA (USA)
		Enasidenib	Acute myeloid leukemia	FDA (USA)
HDACi	5	Vorinostat	Cutaneous T-cell lymphoma	FDA (USA)	[5]
		Romidepsin	Cutaneous T-cell lymphoma	FDA (USA)	[6]
		Panobinostat	Multiple myeloma	FDA (USA)	[7]
		Belinostat	Peripheral T-cell lymphoma	FDA (USA)	[8]
		Tucidinostat (Chidamide)	Advanced breast cancer, adult T-cell leukemia	FCDA (China), MHLW (Japan)	[9]
KMTi (EZH2 inhibitor)	1	Tazemetostat	Follicular lymphoma	FDA (USA)	[10]

Developing epigenetic therapeutics

Supporting the growth of epigenetic inhibitors as clinical tools, the next generation of epigenetic therapies (some impacting on multiple cellular process, in addition to epigenetic ones, often improving their efficacy) are undergoing development and preclinical evaluation in a range of tumor types and models (Table 3). Building on the clinical success of HDACi, recent in vivo studies have demonstrated the ability of small molecule lysine acetyltransferase inhibitors (KATi, also referred to as histone acetyltransferase inhibitors HATi) to treat cancer [19,20]. The KAT family includes five subfamilies and 17 enzymes. Highlighting the importance of the MYST group, many members have had inhibitors developed targeting them [8,21–25]. Within the MYST sub-family, Tip60 (Tat interactive protein 60 kDa) is a particularly intriguing target as it is essential for cellular survival, is involved in multiple cellular process (regulating the DNA double strand break response, transcriptional regulation and immune responses) and is dysregulated in many cancers [8,26]. A large number of studies have demonstrated that Tip60 has multiple roles in tumor progression (including metastasis) in various cancers. These multi-process features of Tip60 make it an attractive drug target, as a drug targeting Tip60 will target multiple features associated with tumor progression or survival, increasing Tip60-targeting drug's potential anti-cancer efficacy [25]. Among Tip60 inhibitors (including NU9056, MG149 and TH1834), TH1834 has shown significant in vivo activity against breast cancer [8,19,27,28].

Table 3.

Epigenetic inhibitors in preclinical studies.

Class of epigenetic drug	Drug in preclinical study	Research stage	Application
DNMTi	CP-4200 (elaidic acid)	In vivo/in vitro	Acute myeloid leukemia
	SGI-1027	In vitro	Solid tumors
	Fazarabine	In vivo/in vitro	Lymphoblastic leukemia
	Caffeic acid phenethyl ester	In vitro	Hepatocarcinoma
	Zebularine	In vivo/in vitro	Cholangiocarcinoma
	NPEOC-DAC	In vitro	Liver cancer
Histone demethylase inhibitor (lysine specific demethylase 1 [LSD1])	DDP38003	In vitro	Acute myeloid leukemia
	MC_2580	In vitro	Acute myeloid leukemia
HMTi	EPZ004777	In vitro	Mixed lineage leukemia
	EPZ005687	In vivo/in vitro	Lymphoma
	DZNeP	In vitro	Colon cancer, breast cancer
	AZ505	In vitro	Glioma
	LLY-507	In vitro	Ovarian clear cell carcinoma
	A-893	In vitro	Lung cancer
	BIX-01294	In vivo/in vitro	Colon cancer
	UNC0638	In vivo/in vitro	Renal cancer
	Dimethoxycurcumin	In vitro	Leukemia
KATi (or HATi)	TH1834	In vivo/in vitro	Breast cancer, prostate cancer, lung cancer, liver cancer
	Anacardic acid	In vitro	Breast cancer
	NU9056 disulfide	In vitro	Prostate cancer
	A-485	In vitro	Haematological cancers, androgen receptor-positive prostate cancer
	SR3029 + MG149	In vitro	Colon cancer
	WM-3835	In vivo/in vitro	Castration-resistant prostate cancer
	Garcinol	In vivo/in vitro	Breast cancer, esophageal cancer
	C646/C146/C375	In vivo/in vitro	Cervical cancer, pancreatic cancer
	ICG-001	In vivo/in vitro	Nasopharyngeal carcinoma, lung cancer
KDMi (Lysine demethylase inhibitor)	Pargyline	In vivo/in vitro	Prostate cancer
	Polyamine analogues	In vitro	Breast cancer
	Namoline	In vivo/in vitro	Prostate cancer
	HCI-2509	In vivo/in vitro	Prostate cancer
	C646	In vivo/in vitro	Acute myeloid leukemia
	6-alkyl salicylates	In vivo/in vitro	Cancer
	PU139	In vivo/in vitro	Neuroblastoma
	PU141	In vivo/in vitro	Neuroblastoma
BETi (bromodomain and extra-terminal motif inhibitor)	JQ1	In vivo/in vitro	Multiple myeloma
	GSK778 (iBET-BD1)	In vivo	Breast cancer, acute myeloid leukemia
	GSK046 (iBET-BD2)	In vivo	Breast cancer, acute myeloid leukemia
TETi (ten-eleven translocation inhibitor)	TETi76	In vitro	Myeloid neoplasia
	Ascorbate	In vivo/in vitro	Leukemia
	Bobcat339	In vitro	Breast cancer
Histone ubiquitylation inhibitors	CC0651	In vitro	Prostate cancer

Currently, 5 of 36 patented KATi are in clinical trial for the treatment of cancers including, hematological and solid tumors (Table 4) [29]. This is expected to increase in the future as more molecules targeting epigenetics (including KATi and BETi) move to in vivo studies and clinical trials [28].

Table 4.

Epigenetic drugs in selected clinical trials.

Epigenetic drug class	Name of drug	Targeted cancer	Trial/s status	Trial identifiers
DNMTi	RX-3117	Metastatic pancreatic cancer, solid tumor, metastatic bladder cancer	Completed	NCT03189914 NCT02030067
	aza-TdC	Neoplasms, solid tumors	Phase I	NCT03366116
	SGI-110	Germ cell tumor, testis cancer, myeloproliferative neoplasms, acute myeloid leukemia, myelodysplastic syndromes, chronic myelomonocytic leukemia, hepatocellular carcinoma	Completed	NCT02429466 NCT03075826 NCT01261312 NCT01752933
	FdCyd + THU (Tetrahydrouridine)	Neoplasms, acute myeloid leukemia, myelodysplastic syndromes	Completed	NCT01534598
	Disulfiram	Breast cancer, metastatic breast cancer	Phase II	NCT03323346
	Disulfiram	Prostate cancer, germ cell tumor, melanoma	Completed	NCT03950830 NCT01118741 NCT00256230
	Curcumin	Pancreatic neoplasms, adenocarcinoma, colorectal cancer, uterine cervical dysplasia	Completed	NCT00094445 NCT00027495 NCT01035580
	Genistein	Colon, rectal, endometrial, breast, colorectal cancer	Completed	NCT01985763 NCT00099008
	Hydralazine	Breast cancer, rectal cancer	Withdrawn	NCT00575978 NCT00575640
HDACi	Phenylbutyrate	Brain neoplasms, neuroblastoma, brain tumor	Completed	NCT00006450 NCT00001565
	CHR-3996	Solid tumor	Phase I	NCT00697879
	Mocetinostat	Urothelial carcinoma	Phase II	NCT02236195
	Valproic acid	Hematuria, bladder cancer, brain tumor, childhood solid tumor, head and neck, oral cavity and oropharyngeal cancer, sarcoma, chronic lymphocytic leukemia	Completed	NCT01738815 NCT00107458 NCT01695122 NCT00075777 NCT02144623
	Valproic acid	Pancreatic cancer, non-small lung cancer	Unknown	NCT01333631 NCT01203735
	Resveratrol	Neuroendocrine tumor, colon, solid tumors	Completed	NCT01476592 NCT00256334
	[14C]-resminostat	Cutaneous T-cell lymphoma	Phase I	NCT04955340
KATi (HATi)	PF-07248144	Advanced/metastatic breast cancer	Phase I	NCT04606446
	Curcumin	Solid tumors, including breast cancer	Phase I, II and III	NCT03980509 NCT00094445 NCT05768919 NCT00295035
	EGCG	Colorectal cancer, prostate cancer	Phase I, II	NCT02891538 NCT05758571 NCT00676780
	EP31670	Castrate resistant prostate cancer, advanced solid tumors	Phase I	NCT05488548
	CCS1477	Prostate cancer, breast cancer, non-small-cell lung cancer, advanced solid tumors, acute myeloid leukemia, peripheral T cell lymphoma, multiple myeloma	Phase I, II	NCT03568656 NCT04068597
BETi	CC-90010	Lymphoma, non-Hodgkin's neoplasms	Phase I	NCT03220347
	ZEN003694	Squamous cell lung cancer	Phase II	NCT05607108
IDHi	AG881	Acute myeloid leukemia, myelodysplastic syndromes	Completed	NCT02492737
		Glioma	Phase I	NCT02481154
	Safusidenib	Glioma	Phase II	NCT05303519
	IDH305	Advanced malignancies	Phase I	NCT02381886
	BAY1436032	Advanced solid tumors	Phase I	NCT02746081
		Acute myeloid leukemia	Completed	NCT03127735
Histone phosphorylation inhibitors†	Enzastaurin	Lymphoma/solid tumors	Completed	NCT01432951
	AZD1152	Lymphoma	Completed	NCT01354392
	AZD1480	Myeloproliferative diseases	Completed	NCT00910728
Histone ubiquitination inhibitors	PTC596	Advanced solid tumors	Completed	NCT02404480
	MLN7243	Advanced solid tumors	Phase I	NCT02045095

^†Currently non-specific epigenetic inhibitors, impacting many other cellular processes.

As our understanding of epigenetic mechanisms continues to advance and transform our understanding of disease process, this provides opportunities to develop new treatments for hard-to-treat diseases, including many cancer types, cardiovascular and neurological diseases [5,8,30–33]. Recently, key roles of these KAT enzymes in other diseases have been described [including amyotrophic lateral sclerosis, chronic obstructive pulmonary disease (COPD), Type-2 diabetes, obesity, heart failure, bipolar disorder, autism spectrum disorder, autoimmune disorders and neurodegenerative disorders], which recognizes the very real potential to use KATi as therapeutic options for these diseases [34–36].

Additionally, several DNMTi and acetylation targeting inhibitors have progressed to clinical trials, many against multiple cancer types (Table 4) [7,16,37]. Recently, there has been a clear effort to expand clinical trials exploring the use of inhibitors that target histone epigenetics (Table 5).

Table 5.

Clinical trials for US FDA approved and non-approved epigenetic drug classes.

Class of epigenetic drug	Number of trials for solid tumors		Number of trials for lymphoma/leukemia/myeloma		Number of trials for sarcomas		Number of trials for other diseases		Total
	Active	Complete	Active	Complete	Active	Complete	Active	Complete
DNMTi	4	3	12	3	–	–	–	–	22
Histone epigenetic inhibitors	54	199	63	216	3	11	12	46	604

Combined with paired biomarkers, this current generation of small molecule epigenetic drugs (including DNMTi and HDACi) are important tools in combinational targeted treatment regimes, working in synergy (often by sensitization of tumor cells) with current anticancer therapies (including reversing acquired drug resistance), while building evidence for their potential use as monotherapies [38–41]. It is worth noting that while small molecule epigenetic combinational therapies are predominantly approved for clinical use in hematological malignancies, recent work is demonstrating some small molecule inhibitors will be useful in targeting solid tumors (aided by enhanced understanding of their mechanisms in solid tumors, and improved biomarkers) [42–45].

Epigenetic therapeutics market

Pharma has recognized the potential for the clinical applications of small molecule epigenetic inhibitors, and in 2020 the global epigenetics market was valued at $1.0 billion (United States Dollar [USD]), with this expected to rise to over $4 billion by 2030 [with a compound annual growth rate (CAGR) of >14% (Figure 1) [30]. Summarising market predictions for epigenetic therapies (Table 6), it is clear there will be substantial growth, further increasing as the applications for epigenetic therapeutics continues to grow into new (non-oncology) diseases.

Figure 1.

Global epigenetics drugs market growth.

Values collated from [46,47].

Table 6.

Epigenetic therapeutic market analysis^†.

Past (2010–2019)	Present (2020–2023)	Future
$2.4 billion in 2020	–	$14 billion in 203111
$0.7 billion in 2016	$6.8 billion by 2025	$9.8 billion by 202812
–	$1.51 billion in 2022	$3.09 billion by 202813
–	–	$14.1 billion by 202914
–	$1.56 billion in 2021	$6.45 billion in 203015
–	$11.2 billion in 202316	–
–	$1.7 billion in 2022	$3.9 billion in 202717
–	$0.99 billion in 2022	$2.8 billion in 203218

^†These figures include valuations for both epigenetic drugs and kits.

Studying epigenetic drug classes, DNMTi are currently estimated to represent the largest share (approximately 71%) of the total epigenetic market due to their early development and clinical adoption. Focusing on the oncology market, the DNMTi azacitidine is believed to be the most commonly used epigenetic drug (>60%) and is currently approved for treating AML, CMML and MDS [48]. In contrast, HDACi are expected to have the fastest growth rate (6.8% compound annual growth rate: CAGR), driven by a pipeline of new HDACi's, and their increasing clinical utility. Vorinostat is believed to be the most commonly used HDACi (54.0%) driven by oral administration, its use against T-cell lymphoma, and its expanding efficacy against multiple cancers including hematological malignancies (including AML and non-Hodgkin lymphoma [NHL]) and solid tumors (including non-small-cell lung cancer [NSCLC] and breast cancer) [49].

Exploring the development of new classes of epigenetic inhibitors targeting the opposite process to the clinically approved HDACi, several KATi are currently in preclinical evaluation (Table 3), and importantly are being explored as treatments for other non-oncology diseases (including immune related disorders and neurological conditions) [28].

Conclusion

Combining next generation of small molecule epigenetic inhibitors with clinically relevant epigenetic biomarkers will facilitate the more precise selection of sensitive tumours for treatment, which will lead to further improvements in patient survival (Figure 2) [50]. The recent approval of Tucidinostat for clinical use against solid breast cancer tumors (Table 3) emphasizes the truly global efforts in further advancing clinical approvals and widening uses for these epigenetic drugs for cancer treatment worldwide.

Figure 2.

Epigenetic targets, classes of epigenetic small molecule inhibitors and drug-development pipeline.

Future perspective

Ultimately, the importance of using epigenetic regulatory machinery as targets for new small molecule inhibitors lies in their ability to restore a ‘normal’ epigenetic profile, resulting in targeted death in cancer cells or the sensitization of cancer cells to current therapeutics, without inducing significant off target effects. This is highlighted by the increasing number of epigenetic-targeting small molecule inhibitors undergoing clinical trials. Approved combinatorial therapies using epigenetic inhibitors to sensitize tumors to standard treatments (including chemotherapy and radiotherapy) have demonstrated their clinical effectiveness for the treatment of some cancers and other complex diseases, and new small molecule inhibitors will only further reinforce this effectiveness and utility [51,52].

Author contributions

JAL Brown: manuscript writing, final approval of manuscript. N Zohourian: manuscript draft and writing, data collection.

Financial disclosure

The authors have no financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Competing interests disclosure

The authors have no competing interests or relevant affiliations with any organization or entity with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Writing disclosure

No writing assistance was utilized in the production of this manuscript.