Histone deacetylase inhibitor
HDIs have a long history of use in psychiatry and neurology as mood stabilizers and anti-epileptics. More recently they are being investigated as possible treatments for cancers, parasitic and inflammatory diseases.
To carry out gene expression, a cell must control the coiling and uncoiling of DNA around histones. This is accomplished with the assistance of histone acetyl transferases (HAT), which acetylate the lysine residues in core histones leading to a less compact and more transcriptionally active chromatin, and, on the converse, the actions of histone deacetylases (HDAC), which remove the acetyl groups from the lysine residues leading to the formation of a condensed and transcriptionally silenced chromatin. Reversible modification of the terminal tails of core histones constitutes the major epigenetic mechanism for remodeling higher-order chromatin structure and controlling gene expression. HDAC inhibitors (HDI) block this action and can result in hyperacetylation of histones, thereby affecting gene expression.
The histone deacetylase inhibitors are a new class of cytostatic agents that inhibit the proliferation of tumor cells in culture and in vivo by inducing cell cycle arrest, differentiation and/or apoptosis. Histone deacetylase inhibitors exert their anti-tumour effects via the induction of expression changes of oncogenes or tumour suppressor, through modulating that the acetylation/deactylation of histones and/or non-histone proteins such as transcription factors. Histone acetylation and deacetylation play important roles in the modulation of chromatin topology and the regulation of gene transcription. Histone deacetylase inhibition induces the accumulation of hyperacetylated nucleosome core histones in most regions of chromatin but affects the expression of only a small subset of genes, leading to transcriptional activation of some genes, but repression of an equal or larger number of other genes. Non-histone proteins such as transcription factors are also targets for acetylation with varying functional effects. Acetylation enhances the activity of some transcription factors such as the tumor suppressor p53 and the erythroid differentiation factor GATA-1 but may repress transcriptional activity of others including T cell factor and the co-activator ACTR. Recent studies [...] have shown that the estrogen receptor alpha (ERalpha) can be hyperacetylated in response to histone deacetylase inhibition, suppressing ligand sensitivity and regulating transcriptional activation by histone deacetylase inhibitors. Conservation of the acetylated ER-alpha motif in other nuclear receptors suggests that acetylation may play an important regulatory role in diverse nuclear receptor signaling functions. A number of structurally diverse histone deacetylase inhibitors have shown potent antitumor efficacy with little toxicity in vivo in animal models. Several compounds are currently in early phase clinical development as potential treatments for solid and hematological cancers both as monotherapy and in combination with cytotoxics and differentiation agents."
- Class I, which includes HDAC1, -2, -3 and -8 are related to yeast RPD3 gene;
- Class II, which includes HDAC4, -5, -6, -7, -9 and -10 are related to yeast Hda1 gene;
- Class III, also known as the sirtuins are related to the Sir2 gene and include SIRT1-7
- Class IV, which contains only HDAC11 has features of both Class I and II.
The “classical” HDIs act exclusively on Class I, II and Class IV HDACs by binding to the zinc-containing catalytic domain of the HDACs. These classical HDIs can be classified into several groupings named according to the chemical moiety that binds to the zinc ion (except cyclic tetrapeptides which bind to the zinc ion with a thiol group). Some examples in decreasing order of the typical zinc binding affinity:
- hydroxamic acids (or hydroxamates), such as trichostatin A,
- cyclic tetrapeptides (such as trapoxin B), and the depsipeptides,
- electrophilic ketones, and
- the aliphatic acid compounds such as phenylbutyrate and valproic acid.
"Second-generation" HDIs include the hydroxamic acids vorinostat (SAHA), belinostat (PXD101), LAQ824, and panobinostat (LBH589); and the benzamides : entinostat (MS-275), CI994, and mocetinostat (MGCD0103).
HDIs should not be considered to act solely as enzyme inhibitors of HDACs. A large variety of nonhistone transcription factors and transcriptional co-regulators are known to be modified by acetylation. HDIs can alter the degree of acetylation nonhistone effector molecules and, therefore, increase or repress the transcription of genes by this mechanism. Examples include: ACTR, cMyb, E2F1, EKLF, FEN 1, GATA, HNF-4, HSP90, Ku70, NF-κB, PCNA, p53, RB, Runx, SF1 Sp3, STAT, TFIIE, TCF, YY1, etc.
Psychiatry and neurology
HDIs have a long history of use in psychiatry and neurology as mood stabilzers and anti-epileptics. The prime example of this is valproic acid, marketed as a drug under the trade names Depakene, Depakote, and Divalproex. In more recent times, HDIs are being studied as a mitigator for neurodegenerative diseases such as Alzheimer's disease and Huntington's disease. Enhancement of memory formation is increased in mice given the HDIs sodium butyrate or SAHA, or by genetic knockout of the HDAC2 gene in mice. While that may have relevance to Alzheimer's disease, it was shown that some cognitive deficits were restored in actual transgenic mice that have a model of Alzheimer's disease (3xTg-AD) by orally administered nicotinamide, a competitive HDI of Class III sirtuins.
Also in recent years, there has been an effort to develop HDIs as a cancer treatment or adjunct The exact mechanisms by which the compounds may work are unclear, but epigenetic pathways are proposed. HDAC inhibitors can induce p21 (WAF1) expression, a regulator of p53's tumor suppressor activity. HDACs are involved in the pathway by which the retinoblastoma protein (pRb) suppresses cell proliferation. The pRb protein is part of a complex that attracts HDACs to the chromatin so that it will deacetylate histones. HDAC1 negatively regulates the cardiovascular transcription factor Kruppel-like factor 5 through direct interaction. Estrogen is well-established as a mitogenic factor implicated in the tumorigenesis and progression of breast cancer via its binding to the estrogen receptor alpha (ERα). Recent data indicate that chromatin inactivation mediated by HDAC and DNA methylation is a critical component of ERα silencing in human breast cancer cells.
- Vorinostat was licenced by the U.S. FDA in October 2006 for the treatment of cutaneous T cell lymphoma (CTCL).
- Romidepsin (trade name Istodax) was licenced by the US FDA in Nov 2009 for cutaneous T-cell lymphoma (CTCL).
- Chidamide approved by China in 2015 for pancreatic cancer.
- Panobinostat (trade name Farydak) was licensed by the US FDA in Feb 2015 for the treatment of multiple myeloma.
Started phase III clinical trials
- Panobinostat (LBH589) is in clinical trials for various cancers including a phase III trial for cutaneous T cell lymphoma (CTCL).
- Valproic acid (as Mg valproate) in phase III trials for cervical cancer and ovarian cancer, has also been trialled in spinal muscular atrophy.
Started pivotal phase II clinical trials
- Belinostat (PXD101) has had a phase II trial for relapsed ovarian cancer, and reported good results for T cell lymphoma.
Started phase II clinical trials
- Mocetinostat (MGCD0103) is undergoing clinical trials for treatment of various cancers (including follicular lymphoma, Hodgkin lymphoma and acute myeloid leukemia).
- Abexinostat (PCI-24781) has started a phase II trial for sarcoma, and another for lymphoma
- Entinostat (MS-275) in phase II for Hodgkin lymphoma, lung cancer and breast cancer.
- SB939 starting a phase II trial for Recurrent or Metastatic Prostate Cancer (HRPC). (phase I results,)
- Resminostat (4SC-201) an oral pan-HDACi. Results re Hodgkin lymphoma Also in trials for hepatocellular carcinoma for which it has FDA Orphan Drug status, and met phase II primary endpoint.
- Givinostat (ITF2357) for refractory leukemias and myelomas.
- Quisinostat (JNJ-26481585)
Started phase I clinical trials
- Kevetrin, selective for HDAC2. Is past the 10th cohort in an Open-Label Dose-Escalation, Safety, Pharmacokinetic and Pharmacodynamic study in patients with advanced solid tumors. Early good results reported for Ovarian Cancer Spleen Metastasis Jan 20 2015
- CUDC-101 intended for cancer, has started clinical trials, it also inhibits EGFR and HER2. Early results reported in Nov 2010.
- AR-42 has started clinical trials in 2010 for various cancers (relapsed or treatment-resistant multiple myeloma, chronic lymphocytic leukemia or lymphoma). The trial should report in 2013 In 2012 AR-42 got 2 Orphan Drug designations from the FDA for two benign tumour types.
- CHR-2845, CHR-3996
- 4SC-202 selective, for advanced hematological indications
- CG200745 for solid tumors.
- ACY-1215, selective for HDAC6, in two clinical trials for multiple myeloma in combination with bortezomib (Velcade, Takeda Millennium) and with lenalidomide (Revlimid, Celgene).
- ME-344, for solid refractory tumors
- Also sulforaphane
After the successful initial round of in vitro research in January 2013, the Danish Research Council awarded the research team lead by Dr. Ole Søgaard from the Danish Aarhus University Hospital the amount of $2 million to proceed with clinical trials on 15 humans. The HDAC inhibitors flush HIV from the reservoirs it builds within the DNA of infected cells. After that a separate vaccination to eliminate HIV allows the immune system to neutralize the virus.
- Givinostat (ITF2357) is also under investigation for treatment of polycythemia vera (PV), essential thrombocythemia (ET) and myelofibrosis (MF).
- Miller, Thomas A.; Witter, David J.; Belvedere, Sandro (2003). "Histone Deacetylase Inhibitors". Journal of Medicinal Chemistry 46 (24): 5097–116. doi:10.1021/jm0303094. PMID 14613312.
- c. Mwakwari, Sandra; Patil, Vishal; Guerrant, William; Oyelere, Adegboyega (2010). "Macrocyclic Histone Deacetylase Inhibitors". Current Topics in Medicinal Chemistry 10 (14): 1423–40. doi:10.2174/156802610792232079. PMC 3144151. PMID 20536416.
- Patil, Vishal; Guerrant, William; Chen, Po C.; Gryder, Berkley; Benicewicz, Derek B.; Khan, Shabana I.; Tekwani, Babu L.; Oyelere, Adegboyega K. (2010). "Antimalarial and antileishmanial activities of histone deacetylase inhibitors with triazole-linked cap group". Bioorganic & Medicinal Chemistry 18: 415–425. doi:10.1016/j.bmc.2009.10.042.
- Blanchard, Frédéric; Chipoy, Céline (2005). "Histone deacetylase inhibitors: New drugs for the treatment of inflammatory diseases?". Drug Discovery Today 10 (3): 197–204. doi:10.1016/S1359-6446(04)03309-4. PMID 15708534.
- Thiagalingam, SAM; Cheng, Kuang-Hung; Lee, Hyunjoo J.; Mineva, Nora; Thiagalingam, Arunthathi; Ponte, Jose F. (2003). "Histone Deacetylases: Unique Players in Shaping the Epigenetic Histone Code". Annals of the New York Academy of Sciences 983: 84–100. doi:10.1111/j.1749-6632.2003.tb05964.x. PMID 12724214.
- Marks, P. A.; Richon, V. M.; Rifkind, R. A. (2000). "Histone Deacetylase Inhibitors: Inducers of Differentiation or Apoptosis of Transformed Cells". JNCI Journal of the National Cancer Institute 92 (15): 1210–6. doi:10.1093/jnci/92.15.1210. PMID 10922406.
- Dokmanovic, M.; Clarke, C.; Marks, P. A. (2007). "Histone Deacetylase Inhibitors: Overview and Perspectives". Molecular Cancer Research 5 (10): 981–9. doi:10.1158/1541-7786.MCR-07-0324. PMID 17951399.
- Chueh, Anderly (2014). "Mechanisms of Histone Deacetylase Inhibitor-Regulated Gene Expression in Cancer Cells". Antioxidants & Redox Signaling: 150127063122000. doi:10.1089/ars.2014.5863. PMID 24512308.
- Gryder, Berkley E.; Rood, Michael K.; Johnson, Kenyetta A.; Patil, Vishal; Raftery, Eric D.; Yao, Li-Pan D.; Rice, Marcie; Azizi, Bahareh; Doyle, Donald F.; Oyelere, Adegboyega K. (2013). "Histone Deacetylase Inhibitors Equipped with Estrogen Receptor Modulation Activity". Journal of Medicinal Chemistry 56 (14): 5782–5796. doi:10.1021/jm400467w.
- Vigushin, D.; Coombes, R. (2004). "Targeted Histone Deacetylase Inhibition for Cancer Therapy". Current Cancer Drug Targets 4 (2): 205–18. doi:10.2174/1568009043481560. PMID 15032670.
- HDAC Inhibitors Database
- Drummond, Daryl C.; Noble, Charles O.; Kirpotin, Dmitri B.; Guo, Zexiong; Scott, Gary K.; Benz, Christopher C. (2005). "Clinical Development of Histone Deacetylase Inhibitors As Anticancer Agents". Annual Review of Pharmacology and Toxicology 45: 495–528. doi:10.1146/annurev.pharmtox.45.120403.095825. PMID 15822187.
- Beckers, Thomas; Burkhardt, Carmen; Wieland, Heike; Gimmnich, Petra; Ciossek, Thomas; Maier, Thomas; Sanders, Karl (2007). "Distinct pharmacological properties of second generation HDAC inhibitors with the benzamide or hydroxamate head group". International Journal of Cancer 121 (5): 1138–48. doi:10.1002/ijc.22751. PMID 17455259.
- Acharya, M. R.; Sparreboom, A; Venitz, J; Figg, WD (2005). "Rational Development of Histone Deacetylase Inhibitors as Anticancer Agents: A Review". Molecular Pharmacology 68 (4): 917–32. doi:10.1124/mol.105.014167. PMID 15955865.
- Porcu, Marco; Chiarugi, Alberto (2005). "The emerging therapeutic potential of sirtuin-interacting drugs: From cell death to lifespan extension". Trends in Pharmacological Sciences 26 (2): 94–103. doi:10.1016/j.tips.2004.12.009. PMID 15681027.
- Yang, X-J; Seto, E (2007). "HATs and HDACs: From structure, function and regulation to novel strategies for therapy and prevention". Oncogene 26 (37): 5310–8. doi:10.1038/sj.onc.1210599. PMID 17694074.
- Hahnen, Eric; Hauke, Jan; Tränkle, Christian; Eyüpoglu, Ilker Y; Wirth, Brunhilde; Blümcke, Ingmar (2008). "Histone deacetylase inhibitors: Possible implications for neurodegenerative disorders". Expert Opinion on Investigational Drugs 17 (2): 169–84. doi:10.1517/135437188.8.131.52. PMID 18230051.
- Guan, Ji-Song; Haggarty, Stephen J.; Giacometti, Emanuela; Dannenberg, Jan-Hermen; Joseph, Nadine; Gao, Jun; Nieland, Thomas J. F.; Zhou, Ying; Wang, Xinyu; Mazitschek, Ralph; Bradner, James E.; Depinho, Ronald A.; Jaenisch, Rudolf; Tsai, Li-Huei (2009). "HDAC2 negatively regulates memory formation and synaptic plasticity". Nature 459 (7243): 55–60. doi:10.1038/nature07925. PMC 3498958. PMID 19424149.
- Green, K. N.; Steffan, J. S.; Martinez-Coria, H.; Sun, X.; Schreiber, S. S.; Thompson, L. M.; Laferla, F. M. (2008). "Nicotinamide Restores Cognition in Alzheimer's Disease Transgenic Mice via a Mechanism Involving Sirtuin Inhibition and Selective Reduction of Thr231-Phosphotau". Journal of Neuroscience 28 (45): 11500–10. doi:10.1523/JNEUROSCI.3203-08.2008. PMC 2617713. PMID 18987186.
- Marks, Paul A; Dokmanovic, Milos (2005). "Histone deacetylase inhibitors: Discovery and development as anticancer agents". Expert Opinion on Investigational Drugs 14 (12): 1497–511. doi:10.1517/135437184.108.40.2067. PMID 16307490.
- Richon, Victoria M.; O'Brien, James P. (2002). "Histone Deacetylase Inhibitors: A New Class of Potential Therapeutic Agents for Cancer Treatment". Clinical Cancer Research 8 (3): 662–4. PMID 11895892.
- Monneret, Claude (2007). "Histone deacetylase inhibitors for epigenetic therapy of cancer". Anti-Cancer Drugs 18 (4): 363–70. doi:10.1097/CAD.0b013e328012a5db. PMID 17351388.
- Mack, George S (2010). "To selectivity and beyond". Nature Biotechnology 28 (12): 1259–66. doi:10.1038/nbt.1724. PMID 21139608.
- Richon, V. M.; Sandhoff, T. W.; Rifkind, R. A.; Marks, P. A. (2000). "Histone deacetylase inhibitor selectively induces p21WAF1 expression and gene-associated histone acetylation". Proceedings of the National Academy of Sciences 97 (18): 10014–9. Bibcode:2000PNAS...9710014R. doi:10.1073/pnas.180316197. JSTOR 123305. PMC 27656. PMID 10954755.
- Kouzarides, Tony; Miska, Alexander; McCance, Eric A.; Reid, Dennis J.; Bannister, Juliet L.; Kouzarides, Andrew J. (1998). "Retinoblastoma protein recruits histone deacetylase to repress transcription". Nature 391 (6667): 597–601. doi:10.1038/35404. PMID 9468139.
- Matsumura, T.; Suzuki, T; Aizawa, K; Munemasa, Y; Muto, S; Horikoshi, M; Nagai, R (2004). "The Deacetylase HDAC1 Negatively Regulates the Cardiovascular Transcription Factor Kruppel-like Factor 5 through Direct Interaction". Journal of Biological Chemistry 280 (13): 12123–9. doi:10.1074/jbc.M410578200. PMID 15668237.
- Zhang, Zhenhuan; Yamashita, Hiroko; Toyama, Tatsuya; Sugiura, Hiroshi; Ando, Yoshiaki; Mita, Keiko; Hamaguchi, Maho; Hara, Yasuo; Kobayashi, Shunzo; Iwase, Hirotaka (2005). "Quantitation of HDAC1 mRNA Expression in Invasive Carcinoma of the Breast*". Breast Cancer Research and Treatment 94 (1): 11–6. doi:10.1007/s10549-005-6001-1. PMID 16172792.
- Clinical trial number NCT01027910 for "PCI-24781 in Combination With Doxorubicin to Treat Sarcoma" at ClinicalTrials.gov
- Clinical trial number NCT00724984 for "Study of the Safety and Tolerability of PCI-24781 in Patients With Lymphoma (PCYC-0403)" at ClinicalTrials.gov
- Tan, Jiahuai; Cang, Shundong; Ma, Yuehua; Petrillo, Richard L; Liu, Delong (February 2010). "Novel histone deacetylase inhibitors in clinical trials as anti-cancer agents". Journal of Hematology & Oncology 3: 5. doi:10.1186/1756-8722-3-5. PMC 2827364. PMID 20132536.
- "S*BIO Initiates Canadian Phase 2 Clinical Trial of Oral Histone Deacetylase (HDAC) Inhibitor SB939 for the Treatment of Recurrent or Metastatic Prostate Cancer (HRPC)" (Press release). S*BIO. September 27, 2008. Retrieved September 12, 2013.
- "S*BIO's Oral Histone Deacetylase (HDAC) Inhibitor SB939 Shows Tolerability and Safety in Phase 1 Clinical Trial in Patients with Advanced Hematologic Malignancies" (Press release). S*BIO. December 7, 2010. Retrieved September 12, 2013.
- "52nd ASH Annual Meeting Presentation of Initial Phase II Data from the Saphire Hodgkin's Lymphoma Trial with Resminostat" (Press release). 4SC. December 1, 2010. Retrieved September 12, 2013.
- "Yakult Pays 4SC €6M Up Front for Japanese Rights to Phase II Anticancer Drug". Genetic Engineering & Biotechnology News. April 14, 2011. Retrieved September 12, 2013.
- "FDA Grants Orphan Drug Designation to 4SC's Oral Pan-HDAC Inhibitor Resminostat for the Treatment of Hepatocellular Carcinoma" (Press release). 4SC. July 12, 2011. Retrieved September 12, 2013.
- Sheridan, Cormac (January 20, 2012). "Strong Phase II Resminostat Data Send 4SC Shooting Up". BioWorld Today.
- "Cellceutix Anti-Cancer Drug Shown to Regulate HDAC2, a Major Therapeutic Target for Treatment of a Broad Range of Cancers" (Press release). Cellceutix. January 17, 2012. Retrieved September 12, 2013.
- "Clinical Trials NCT01664000".
- "Cellceutix Reports Spleen Lesion ‘Disappears’ in Patient with Metastatic Stage 4 Ovarian Cancer in Clinical Trial of Anti-Cancer Drug Kevetrin" (Press release). Cellceutix. January 20, 2015. Retrieved January 20, 2015.
- http://www.themarketfinancial.com/stock-alert-for-curis-inc-cris/4078[full citation needed][dead link]
- "Curis Presents CUDC-101 Phase I Clinical Data and CU-201 Preclinical Data at 22nd EORTC-NCI-AACR Symposium" (Press release). Curis. November 18, 2010. Retrieved September 12, 2013.
- Huang, Po-Hsien (2010). Novel Small Molecules Regulating The Histone Marking, AR Signaling, And AKT Inhibition In Prostate Cancer (PhD Thesis). Ohio State University.[page needed]
- "Second Ohio State cancer drug begins clinical trials testing" (Press release). Ohio State University Medical Center. June 18, 2010. Retrieved September 12, 2013.
- Clinical trial number NCT01129193 for "AR-42 in Treating Patients With Advanced or Relapsed Multiple Myeloma, Chronic Lymphocytic Leukemia, or Lymphoma" at ClinicalTrials.gov
- "Arno Therapeutics Receives Two Orphan-Drug Designations for AR-42 in Treatment of Central-Nervous-System Tumors" (Press release). Arno Therapeutics. February 21, 2012. Retrieved September 12, 2013.
- "Cell Therapeutics Pays Chroma $5M Up Front for Rights to Late-Stage Cancer Drug". Genetic Engineering & Biotechnology News. March 14, 2011.
- Oh, Eun-Taex; Park, Moon-Taek; Choi, Bo-Hwa; Ro, Seonggu; Choi, Eun-Kyung; Jeong, Seong-Yun; Park, Heon Joo (2010). "Novel histone deacetylase inhibitor CG200745 induces clonogenic cell death by modulating acetylation of p53 in cancer cells". Investigational New Drugs 30 (2): 435–42. doi:10.1007/s10637-010-9568-2. PMID 20978925.
- "Celgene Invests $15M in Acetylon to Support HDAC Inhibitor Development". Genetic Engineering & Biotechnology News. February 9, 2012.
- "MEI Pharma's Mitochondrial Inhibitor Drug Candidate ME-344 Named One of Top 10 Oncology Products for 2012" (Press release). MEI Pharma. November 19, 2012. Retrieved September 12, 2013.
- Adcock, I M (2007). "HDAC inhibitors as anti-inflammatory agents". British Journal of Pharmacology 150 (7): 829–31. doi:10.1038/sj.bjp.0707166. PMC 2013887. PMID 17325655.
- Gayomali, Chris (April 29, 2013). "Breakthrough: Is an HIV cure just a few months away?". The Week (The Week Publications). Retrieved September 12, 2013.
- Granger, A.; Abdullah, I.; Huebner, F.; Stout, A.; Wang, T.; Huebner, T.; Epstein, J. A.; Gruber, P. J. (2008). "Histone deacetylase inhibition reduces myocardial ischemia-reperfusion injury in mice". The FASEB Journal 22 (10): 3549–60. doi:10.1096/fj.08-108548. PMC 2537432. PMID 18606865.
- HK application 1124320, Maier, Thomas; Beckers, Thomas; Hummel, Rolf-Peter; Feth, Martin; Müller, Matthias; Bär, Thomas; Volz, Jürgen, "Novel Sulphonylpyrroles as Inhibitors of Hdac S Novel Sulphonylpyrroles", published October 22, 2009
- HDAC inhibitors base information about molecules that block HDACs.
- Tambunan, Usman; Wulandari, Evi (2010). "Identification of a better Homo sapiens Class II HDAC inhibitor through binding energy calculations and descriptor analysis". BMC Bioinformatics 11: S16. doi:10.1186/1471-2105-11-S7-S16. PMC 2957684. PMID 21106123.