Belinostat | HDAC Inhibitor | Orphan Drug | Treatment of Peripheral T-cell Lymphoma

Belinostat [(2E)-N-Hydroxy-3-[3-(phenylsulfamoyl)phenyl]prop-2-enamide] is a small-molecule hydroxamate-type inhibitor of class I, II and IV histone deacetylase (HDAC) enzymes [1, 2]. 

Belinostat was granted orphan drug status for the treatment of Peripheral T-cell lymphoma (PTCL) in the US in September 2009 and the EU in October 2012. In July 2015, an orphan drug designation has also been granted for malignant thymoma in the EU. 

Belinostat received its first global approval in the US-FDA on 3 July 2014 for the intravenous (IV) treatment of relapsed or refractory PTCL in adults.

Belinostat: 2D and 3D Structure

The IV formulation of Belinostat is currently in development around the world for a range of haematological and solid tumour malignancies; these include thymoma, acute myeloid leukaemia, non-small cell lung cancer (NSCLC), ovarian cancer, and hepatocellular carcinoma (HCC). An oral formulation of Belinostat is in early clinical development for the treatment of lymphoma and solid tumours, including NSCLC.

What is Peripheral T-cell lymphoma (PTCL)?

Peripheral T-cell lymphoma (PTCL) corresponds to a heterogeneous subgroup of relatively rare and aggressive extranodal forms of non-Hodgkin’s lymphoma (NHL). Traditionally, treatment for PTCL has been similar to that for B-cell lymphoma, with anthracycline-based chemotherapy being the most commonly used treatments, although patients with PTCL have poorer outcomes. Patients with relapsed or refractory PTCL have a particularly poor prognosis.

The prognosis for patients with PTCL varies between subtypes, with 5-year overall survival rates ranging from 14 % for patients with adult T-cell leukaemia/lymphoma to 70 % for ALK-+ anaplastic large cell lymphoma; the median 5-year survival rate for the most common form, PTCL not otherwise specified (NOS), is 32 % [1].

Belinostat Synthesis

Helv Chim Acta 2005, 88(7), 1630-1657: It is first reported synthesis for Belinostat and many other derivatives. The procedure uses oleum, thionyl chloride (SOCl₂) as well as oxalyl chloride (COCl)₂, no wonder better procedures were derived from it.

Synth Comm 2010, 40(17), 2520–2524: The synthesis avoids the use of the extremely corrosive oleum and thionyl chloride (SOCl₂) and therefore is possibly better for scaled-up production. Second, synthetic steps do not involve tedious separations and give a better overall yield.

Identifications:

1H NMR (Estimated) for Belinostat

Experimental: ¹H NMR (300 MHz, DMSO-d₆): δ 6.52 (d, J=15.9 Hz, 1H), 6.81–7.12 (m, 6H), 7.33 (d, J=15.9 Hz, 1H), 7.47–7.67 (m, 3 H), 7.87 (s, 1H), 9.00–11.20 (br, 3H).

Sideeffects:

The most common Adverse Events of any grade (AE) occurring in patients (greater than 20%) with belinostat monotherapy are in order nausea (42% of patients), fatigue (37%), pyrexia (35%), anaemia (32 %), vomiting (29%), constipation (23%), diarrhoea (23%), dyspnoea (22 %), rash (20%) and peripheral oedema (20%).

The most frequent NCI-CTC grade 3 or 4 adverse events were anaemia (11%), thrombocytopenia (7%), dyspnoea (6%), fatigue (5%), hypokalaemia (4 %), QT interval prolongation (4 %), hypotension (3 %) and pruritus (3 %).

A total of 61 patients (47.3 %) experienced serious adverse events during or within 30 days of treatment with Belinostat, with pneumonia, pyrexia, infection, anaemia, creatinine elevations, thrombocytopenia and multi-organ failure being the most frequent ([2 % of patients each). There was one treatment-related death due to hepatic failure during the trial. Adverse events led to treatment discontinuation in 25 patients (19.4 %), most commonly due to anaemia, febrile neutropenia, fatigue and multi-organ failure; 12 % of patients required dose modification due to adverse events.

Belinostat comes with boxed warnings and precautions regarding the risk of thrombocytopenia and leukopenia, serious infections, hepatotoxicity and tumour lysis syndrome, and the potential for foetal harm if used in pregnant women. Monitoring of blood counts and liver function is advised for patients receiving Belinostat, with dose modification recommended if toxicities occur.

References:
1. Poole, R. M. Belinostat: First Global Approval. Drugs 2014, 74, 1543-1554. (FMO only)
2. Plumb, J. A.; et. al. Pharmacodynamic response and inhibition of growth of human tumor xenografts by the novel histone deacetylase inhibitor PXD101. Mol Cancer Ther 2003, 2(8), 721-8. (free copy)

Drugs in Clinical Pipeline: Tefinostat

Tefinostat [Cyclopentyl (S)-2-cyclohexyl-2-((4-(8-(hydroxyamino)-8-oxooctanamido) benzyl) amino)acetate] is a novel monocyte/macrophage-targeted histone deacetylase inhibitor (HDACi) that is cleaved to an active acid, CHR-2847, by an intracellular esterase (human carboxylesterase-1, hCE-1), found only in cells of monocytoid lineage and hepatocytes. 

Tefinostat and its acid CHR-2845 had similar 50% inhibitory concentrations (IC₅₀) when tested against the HDAC activity of HeLa cell nuclear extracts that contain multiple HDAC isoforms (113 nM for Tefinostat, 160 nM for CHR-2847, respectively).

CHR-2847, being a charged molecule, cannot readily leave cells and, hence, selectively accumulates and is active within hCE1- expressing cells, resulting in a 20- to 100-fold increase in the anti-proliferative potency of Tefinostat for monocytic, over non-monocytic, tumour cells. The Esterase Sensitive Motif (ESM) technology used to design Tefinostat is widely applicable and an increase in potency against monocytic tumour cell lines has been demonstrated with a variety of targets [1, 2].

Tefinostat is a much better substrate for hCE1 than for the related, and ubiquitously expressed, hCE2, as evidenced by the rate of production of CHR-2847 when hydrolysed by the two enzymes: thus hCE1 produces CHR-2847 at 4400 pg/ml/ min whereas hCE2 hydrolyses tefinostat much more slowly with a rate less than 200 pg/ml/min.                                

The activity of Tefinostat is as follows:

IC₅₀ (HDAC HeLa cell nuclear extract assay) = 113 nM

Common Name: Tefinostat

Synonyms: CHR-2845; CHR 2845; CHR2845

IUPAC Name: Cyclopentyl (S)-2-cyclohexyl-2-((4-(8-(hydroxyamino)-8-oxooctanamido) benzyl)amino)acetate

CAS Number: 914605-76-8

Mechanism of Action: HDAC Inhibitor; Histone Deacetylase Inhibitor

Indication: Various Cancers

Development Stage: Phase I/II

Company: Chroma Therapeutics

Phase I Study  [3]

In a first-in-human, standard 3 + 3 dose escalating trial of oral, once daily Tefinostat was conducted to determine the safety, tolerability, pharmacokinetic and pharmacodynamic profile of tefinostat in relapsed/refractory haematological diseases. 

Eighteen patients were enrolled at doses of 20-640 mg. Plasma concentrations of Tefinostat exceeded those demonstrated to give in vitro anti-proliferative activity. Flow cytometric pharmacodynamic assays demonstrated monocyte-targeted increases in protein acetylation, without corresponding changes in lymphocytes. 

Dose-limiting toxicities (DLTs) were not observed and dose escalation was halted at 640 mg without identification of the maximum tolerated dose (MTD). Drug-related toxicities were largely Common Toxicity Criteria for Adverse Events grade 1/2 and included nausea, anorexia, fatigue, constipation, rash and increased blood creatinine. 

a: A patient with chronic monomyelocytic leukaemia achieved a bone marrow response, with no change in peripheral monocytes. 

b: An acute myeloid leukaemia type M2 patient showed a more than 50% decrease in bone marrow blasts and clearance of peripheral blasts. 

In conclusion, Tefinostat produces monocyte-targeted HDACi activity and is well tolerated, without the DLTs, e.g. fatigue, diarrhoea, thrombocytopenia, commonly seen with non-targeted HDACi. The early signs of efficacy and absence of significant toxicity warrant further evaluation of Tefinostat in larger studies.

References:

1. Ossenkoppele, G. J.; et. al. A phase I first-in-human study with tefinostat-a monocyte/macrophage targeted histone deacetylase inhibitor-in patients with advanced haematological malignancies. Br J Haematol 2013, 162(2), 191-201.

2. Needham, L.A.; et. al.  Drug targeting to monocytes and macrophages using esterase-sensitive chemical motifs. J Pharmacol Exp Ther 2011, 339, 132-142. 
3. Ossenkoppele, G. J.; et. al. A phase I first-in-human study with tefinostat - a monocyte/macrophage targeted histone deacetylase inhibitor-in patients with advanced haematological malignancies. Br J Haematol 2013, 162(2), 191-201.
4. ClinicalTrials.gov Safety and Tolerability of CHR-2845 to Treat Haematological Diseases or Lymphoid Malignancies (CHR-2845-001). NCT00820508 (retrieved 28-09-2015)

Drugs in Clinical Pipeline: MC1568

MC1568 [(E)-3-(5-((E)-3-(3-fluorophenyl)-3-oxoprop-1-en-1-yl)-1-methyl-1H-pyrrol-2-yl)-N-hydroxyacrylamide], one of the only known selective inhibitors of class IIa histone deacetylase (HDAC) enzymes to be documented in the literature till date. It was identified from a series of novel (aryloxopropenyl)-pyrrolyl hydroxyamides which are structurally related to aroyl-pyrrolyl-hydroxy-amides (APHAs) and were highly selective against the class II (class IIa) histone deacetylase homologue HD1-A. The compound has also been the starting point for a number of structure-activity relationship and molecular modelling studies.

MC1568 was tested against maize HD1-B and HD1-A two mammalian class I and class II (IIa) HDAC homologues. It inhibited HD1-B and HD1-A with IC₅₀ value 38.8 ± 1.16 and 0.22 ± 0.01 uM, respectively. The selectivity index was 176.4 in favour of class IIa. Moreover, its maize HD2 50% inhibitory activity (IC₅₀) was found to be 22.0 ± 1.32 uM.

Being the most selective compound in the maize HD1-B/ HD1-A system, MC1568 was evaluated against human HDAC1 and HDAC4 in comparison with SAHA as reference drug. Human breast cancer ZR-75.1 cell lysates were immunoprecipitated with antibodies against HDAC1 and HDAC4, and inhibitory assays were performed on such immunoprecipitates (IPs) with MC1568 (5 µM) and SAHA (5 µM). Data reported clearly show that MC1568 lacked any inhibitory activity against human HDAC1 (% inhibition of 5 uM = 0%) but was effective in inhibiting human HDAC4 enzyme (% inhibition of 5 uM = 54.9 %) [1].

The activity of MC1568 is as follows:

% Inhibition of HDAC1 @ 5 uM = 0 %

% Inhibition of HDAC4 @ 5 uM = 54.9 %

Common Name: MC1568

Synonyms: MC1568; MC 1568; MC-1568

IUPAC Name: (E)-3-(5-((E)-3-(3-fluorophenyl)-3-oxoprop-1-en-1-yl)-1-methyl-1H-pyrrol-2-yl)-N-hydroxyacrylamide

CAS Number: 852475-26-4

Mechanism of Action: HDAC Inhibitor; Histone Deacetylase Inhibitor; HDAC4 Inhibitor

Indication: Various Cancers

Development Stage: Investigational

Company: Italian University

References:

1. Mai, M.; et. al. Class II (IIa)-selective histone deacetylase inhibitors. 1. Synthesis and biological evaluation of novel (aryloxopropenyl)pyrrolyl hydroxyamides. J Med Chem 2005, 48(9), 3344-3353.

Drugs in Clinical Pipeline: Compound 7

Compound 7 [tert-butyl (4-(3-((7-(hydroxyamino)-7-oxoheptyl)carbamoyl)isoxazol-5-yl)phenyl)carbamate] a picomolar inhibitor of Histone Deacetylases 6 (HDAC6 IC₅₀ ~ 2 pM) was identified in a series of hydroxamate based HDAC inhibitors. The series of inhibitors contain a phenylisoxazole as the CAP group that has been synthesized using nitrile oxide cycloaddition chemistry.

The activity of Compound 7 is as follows:

IC₅₀ (HDAC1 enzyme assay) = 271 ± 23 nM

IC₅₀ (HDAC2 enzyme assay) = 252 ± 10 nM

IC₅₀ (HDAC3 enzyme assay) = 0.42 ± 0.08 nM

IC₅₀ (HDAC8 enzyme assay) = 6851 ± 707 nM

IC₅₀ (HDAC6 enzyme assay) = 0.002 nM

IC₅₀ (HDAC10 enzyme assay) = 90.7 ± 12 nM

Common Name: Compound 7

Synonyms:  -

IUPAC Name: tert-butyl (4-(3-((7-(hydroxyamino)-7-oxoheptyl)carbamoyl)isoxazol-5-yl) phenyl)carbamate

CAS Number: 1045792-66-2

SMILES: O=C(OC(C)(C)C)NC1=CC=C(C2=CC(C(NCCCCCCC(NO)=O)=O)=NO2)C=C1

Mechanism of Action: HDAC Inhibitor; HDAC6 Inhibitor; Histone Deacetylases 6 Inhibitor

Indication: Various Cancers; Anti-tumor Therapy

Development Stage: Investigational

Company: University of Illinois and Mayo Clinic

The design of HDAC inhibitors as novel therapeutics for the treatment of a wide range of disorders, including cancers, neurodegenerative diseases, and even malaria has generated a lot of interest. These compounds owe their action to their ability to reactivate silenced genes by modulating the condensation status of DNA. The post-translational acetylation status of chromatin is determined by the competing activities of two classes of enzymes, histone acetyltransferases (HATs) and histone deacetylases (HDACs), which control the acetylation of lysine residues making up the histones. In general, HATs function to acetylate lysine groups in nuclear histones, resulting in neutralization of the charges on the histones and a more open, transcriptionally active chromatin structure, while the HDACs function to deacetylate and suppress transcription (the positively charged lysine amine group interacts with the negatively charge DNA organophosphate groups to cause compaction of the chromatin structure). A shift in the balance of acetylation on chromatin may result in changes in the regulation of patterns of gene expression. Many cancers are associated with aberrant transcriptional activity and HDACs and HATs associate with transcription activators and repressors, these enzymes have been identified as attractive targets for cancer therapy. Indeed, inhibitors of the HDACs have been shown to block tumor cell growth and induce differentiation and cell death [1].

HDAC6 plays an important role in deacetylation of tubulin, hence is a huge interest in the researcher and pharma community [2]. Using X-ray crystal structure of HDAC7 (2PQP) template a HDAC6 homology model was built. Preliminary investigations of other class I and class II HDAC homology models indicate that the loop areas surrounding the CAP residues show significant differences among the various HDACs and may eventually account for the enzyme selectivity that has been observed [1].

The enzyme selectivity of compound 7 was explained on the basis of the following drug-target interactions:

1. The ZBG (zinc-binding group) hydroxamic acid group and the six methylene groups bind deep inside the narrow binding pocket.

2. The CAP region of the bound ligand appears to interact with only one side of the protein.

3. The carbonyl group of the Boc group might interact with His499, which may be important in positioning the CAP residue on the surface of the HDAC protein. Such interactions are absent with the other inhibitors included in this study and may thus explain the higher potency observed for this compound.

Compound 7 was tested against five transformed cell lines as well as against two normal cell lines. Compounds 7 is active against both the Mia Paca-2 and Panc04.03 cell lines at the 100 nM level and at the 200-300 nM level against HupT3 [1].

References:

1. Kozikowski, A. P.; et. al. Use of the nitrile oxide cycloaddition (NOC) reaction for molecular probe generation: a new class of enzyme selective histone deacetylase inhibitors (HDACIs) showing picomolar activity at HDAC6. J Med Chem 2008, 51(15), 4370-4373.

2. Bulinski, J. C.; et. al. HDAC6 deacetylation of tubulin modulates dynamics of cellular adhesions. Journal of Cell Science 2007, 120, 1469-1479.

Drugs in Clinical Pipeline: Quisinostat

Quisinostat [N-hydroxy-2-(4-((((1-methyl-1H-indol-3-yl)methyl)amino)methyl)piperidin-1-yl)pyrimidine-5-carboxamide] is an orally bioavailable, second-generation, HDAC ( histone deacetylase) inhibitor based on hydroxamic acid. Quisinostat inhibits HDACs, which may result in the accumulation of highly acetylated histones, followed by the induction of chromatin remodeling; the selective transcription of tumor suppressor genes; the tumor suppressor protein-mediated inhibition of tumor cell division; and, finally, the induction of tumor cell apoptosis. It has the potential antineoplastic activity. Compared to some first generation HDAC inhibitors, JNJ-26481585 may induce superior HSP70 upregulation and bcl-2 downregulation.

Quisinostat is a novel second-generation HDAC inhibitor with highest potency for HDAC1 with IC₅₀ of 0.11 nM in a cell-free assay. The compound exhibits greater than 30-fold selectivity against HDACs 3, 5, 8 and 9, with lowest potency for HDACs 6 and 7. It also displays broad spectrum antiproliferative activity in solid and hematologic cancer cell lines, such as all lung, breast, colon, prostate, brain, and ovarian tumor cell lines, with IC₅₀ ranging from 3.1-246 nM, which is more potent than vorinostat, R306465, panobinostat, CRA-24781, or mocetinostat in various human cancer cell lines tested [1]. 

The activity of Quisinostat is as follows:

IC₅₀ (HDAC1 cell-free assay) = 0.11 nM

IC₅₀ (HDAC2 cell-free assay) = 0.33 nM

IC₅₀ (HDAC11 cell-free assay) = 0.37 nM

IC₅₀ (HDAC10 cell-free assay) = 0.46 nM

IC₅₀ (HDAC4 cell-free assay) = 0.64 nM

IC₅₀ (HDAC5 cell-free assay) = 3.69 nM

IC₅₀ (HDAC8 cell-free assay) = 4.26 nM

IC₅₀ (HDAC3 cell-free assay) = 4.86 nM

IC₅₀ (HDAC9 cell-free assay) = 32.1 nM

IC₅₀ (HDAC6 cell-free assay) = 76.8 nM

IC₅₀ (HDAC7 cell-free assay) = 119 nM

Common Name: Quisinostat

Synonyms:  JNJ-26481585; JNJ26481585; JNJ 26481585

IUPAC Name: N-hydroxy-2-(4-((((1-methyl-1H-indol-3-yl)methyl)amino)methyl)piperidin-1-yl)pyrimidine-5-carboxamide

CAS Number: 875320-29-9

SMILES: CN1C=C(C2=CC=CC=C21)CNCC3CCN(CC3)C4=NC=C(C=N4)C(=O)NO

Mechanism of Action: Second generation, HDAC Inhibitor

Indication: Lymphoma, T-cell, Cutaneous

Development Stage: Phase II

Company: Janssen Research and Development, LLC

HDACs are a class of enzymes that remove acetyl group (O=C-CH3) from an e-N-acetyl lysine amino acid on a histone. This allows the histone to wrap the DNA more tightly. It’s important because DNA is wrapped around histones, and DNA expression is regulated by acetylation and de-acetylation. HDAC proteins are also called lysine deacetylases (KDAC), to describe their function rather than their target, which also included non-histone proteins. Altered expression and mutations of genes that encode HDACs have been linked to tumor development since they both induce the aberrant transcription of key genes regulating important cellular functions such as cell proliferation, cell-cycle regulation and apoptosis. Thus, HDACs are among the most promising therapeutic targets for cancer treatment, and they have inspired researchers to study and develop HDAC inhibitors. HDACs (except class III) contain Zinc and are also known as Zn-dependent histone deacetylases.

In vivo pharmacodynamics analysis of potent pyrimidyl-hydroxamic acid analogues resulted in the identification of Quisinostat. Once daily oral administration of the compound induced continuous histone H3 acetylation. Quisinostat, was found to induce the HDAC1-suppressed p21^waf1,cip1 promoter in vivo, and a continuous pharmacodynamics response (histone H3 acetylation) in tumor tissue. The compound completely inhibited the growth of Ras mutant pre-established HCT116 colon xenografts, 5-FU (5-fluorouracil) and Vorinostat displayed only modest activity under same settings. It was noted that, although Quisinostat strongly inhibited tumor growth in vivo of Ras mutant NSCLC xenografts, no efficacy in vivo was observed in Ras wild-type NCI-H1703 NSCLC xenografts. In human colon cancer cell lines, in vitro, Quisinostat induced potent apoptosis at 3 to 30 nM/L, both in APC wild-type (HCT116) and in APC mutant (HT-29) backgrounds [1].

Quisinostat also potently upregulated the HDAC1-suppressed expression of E-cadherin (at 30 nM conc.), which resulted in sensitization to epidermal growth factor receptor inhibitors in NSCLCs [2].

A recent study shows that Quisinostat promotes myeloma cell death at low nanomolar concentrations by resulting in Mcl-1 depletion and Hsp72 induction [3].

References:

1. Arts, J.; et. al. JNJ-26481585, a novel “second-generation” oral histone deacetylase inhibitor, shows broad-spectrum preclinical antitumoral activity. Clin Cancer Res 2009, 15(22), 6841-6851.

2. Witta, S. E.; et. al. Restoring E-cadherin expression increases sensitivity to epidermal growth factor receptor inhibitors in lung cancer cell lines. Cancer Res. 2006, 66(2), 944-950.

3. Stuhmer, T.; et al. Preclinical anti-myeloma activity of the novel HDAC-inhibitor JNJ-26481585. Br J Haematol 2010, 149(4), 529-536.

4. Tong, W. G.; et. al. Preclinical antileukemia activity of JNJ-26481585, a potent second-generation histone deacetylase inhibitor. Leuk Res 2010, 34(2), 221-228.

5. Venugopal, B.; et. al. A phase I study of quisinostat (JNJ-26481585), an oral hydroxamate histone deacetylase inhibitor with evidence of target modulation and antitumor activity, in patients with advanced solid tumors. Clin Cancer Res 2013, 19(15), 4262-4272.

6. Carol, H.; et. al. Initial testing (stage 1) of the histone deacetylase inhibitor, quisinostat (JNJ-26481585), by the pediatric preclinical testing program. Pediatr. Blood Cancer 2014, 61(2), 245-252.

Drugs in Clinical Pipeline: Pracinostat

Pracinostat [(E)-3-(2-butyl-1-(2-(diethylamino)ethyl)-1H-benzo[d]imidazol-5-yl)-N-hydroxyacrylamide] is an orally bioavailable, small-molecule pan-HDAC (histone deacetylase inhibitor) based on hydroxamic acid. Pracinostat inhibits HDACs, which may result in the accumulation of highly acetylated histones, followed by the induction of chromatin remodeling; the selective transcription of tumor suppressor genes; the tumor suppressor protein-mediated inhibition of tumor cell division; and, finally, the induction of tumor cell apoptosis [1]. It is potent in its activity, having K_i values of 16-48 nM [with the exception of HDAC6 (247 nM)], and it is also selective. In particular, it does not inhibit [3H]-dofetilide binding to the human Ether-à-go-go Related Gene potassium channel.

Pracinostat possess favourable metabolic, pharmacokinetic and pharmacological properties compared to other HDAC inhibitors [2].

Pracinostat has shown evidence of single-agent activity in multiple clinical trials, including advanced hematologic malignancies such as MDS, acute myeloid leukemia and myelofibrosis. Pracinostat has also demonstrated pre-clinical activity in hematologic disorders and solid tumors when used alone or in combination with a wide range of therapies in laboratory studies [3].

In March 2014, Pracinostat was approved for rare disease (orphan disease) acute myelocytic leukemia (AML) and for the treatment of T-cell lymphoma by the Food and Drug Administration. Acute myeloid leukemia (also known as acute myelogenous leukemia or acute nonlymphocytic leukemia (ANLL), is a cancer of the myeloid line of blood cells, characterized by the rapid growth of abnormal white blood cells that accumulate in the bone marrow and interfere with the production of normal blood cells. AML is the most common acute leukemia affecting adults, and its incidence is expected to increase as the population ages.

The activity of Pracinostat is as follows:

IC₅₀ (HDAC1 enzyme assay) = 49 nM

IC₅₀ (HDAC2 enzyme assay) = 96 nM

IC₅₀ (HDAC3 enzyme assay) = 43 nM

IC₅₀ (HDAC8 enzyme assay) = 140 nM

IC₅₀ (HDAC4 enzyme assay) = 56 nM

IC₅₀ (HDAC5 enzyme assay) = 47 nM

IC₅₀ (HDAC7 enzyme assay) = 137 nM

IC₅₀ (HDAC9 enzyme assay) = 70 nM

IC₅₀ (HDAC10 enzyme assay) = 40 nM

IC₅₀ (HDAC11 enzyme assay) = 93 nM

Common Name: Pracinostat

Synonyms:  SB939; SB 939; SC-939

IUPAC Name: (E)-3-(2-butyl-1-(2-(diethylamino)ethyl)-1H-benzo[d]imidazol-5-yl)-N-hydroxyacrylamide

CAS Number: 929016-96-6

SMILES: CCCCC1=NC2=C(N1CCN(CC)CC)C=CC(=C2)/C=C/C(=O)NO

Mechanism of Action: HDAC Inhibitor; pan-HDAC Inhibitor

Indication: Elderly Acute Myeloid Leukemia (AML)

Development Stage: Phase III

Company: MEI Pharma Inc (MEIP)

HDAC are a class of enzymes that remove acetyl group (O=C-CH3) from an e-N-acetyl lysine amino acid on a histone. This allows the histone to wrap the DNA more tightly. It’s important because DNA is wrapped around histones, and DNA expression is regulated by acetylation and de-acetylation. HDAC proteins are also called lysine deacetylases (KDAC), to describe their function rather than their target, which also included non-histone proteins. Altered expression and mutations of genes that encode HDACs have been linked to tumor development since they both induce the aberrant transcription of key genes regulating important cellular functions such as cell proliferation, cell-cycle regulation and apoptosis. Thus, HDACs are among the most promising therapeutic targets for cancer treatment, and they have inspired researchers to study and develop HDAC inhibitors. HDACs (except class III) contain Zinc and are also known as Zn-dependent histone deacetylases.

Pracinostat has a 100-fold greater selectivity for HDACs than for Zn-binding non-HDAC enzymes, receptors and ion channels. It selectively inhibits HDAC class I, II, IV without class III and HDAC6 in class IV [2]. It shows significant antiproliferative activity against a wide variety of tumor cell lines, especially Leukemia cells and cutaneous T-cell Lymphoma cells with IC₅₀ values ranging from 50 nM (H9 cells) to 170 nM (HEL92.1.7 cells) [2].

In preclinical in vivo studies, orally administered SB939 demonstrated dose-dependent antitumor activity against a variety of experimental solid tumor models and was found to selectively accumulate in tumor tissue, as evidenced by concentrations that were 10-fold higher than those in plasma, liver, kidney, and lung tissue. Repeated oral dosing studies showed it had a good safety profile in animals. The favorable pharmacological properties of SB939 including high aqueous solubility, tissue permeability, and no major interaction with cytochrome P-450 isoenzymes, which indicate best-in-class potential [4].

In a Phase I study to assess the safety, maximum tolerated dose (MTD), pharmacokinetics, pharmacodynamics, and preliminary efficacy of SB939, dose-escalating cohorts of three to six patients (36 patients) received SB939 orally thrice weekly for 3 weeks in a 4-week cycle. Acetylated histone H3 (acH3) was measured in peripheral blood mononuclear cells (PBMCs). The MTD of SB939 was 80 mg/day. The mean elimination half-life and oral clearance of SB939 were 7.2 ± 0.6 h and 53.0 ± 8.5 l/h, respectively, with no substantial accumulation on day 15. An increase in acH3 was observed at hour 3 and correlated with dose and Peak plasma concentration (Cmax). Stable disease was seen in several tumor types treated at = 40 mg. HDAC inhibition was consistently observed at 60 mg, the recommended dose. Dose-limiting toxic effects were fatigue, hypokalemia, troponin T elevation, and QTc prolongation [4].

Pracinostat failed phase 2 trials when tested in combination with another cancer drug Azacitidine (hypomethylation agent) for Myelodysplastic syndrome (MDS) [5]. Data from the phase 2 trial illustrated that the combination treatment was no more effective in inducing complete responses than Azacitidine alone [6].

References:

1.    Novotny-Diermayr, V.; et. al. The oral HDAC inhibitor pracinostat (SB939) is efficacious and synergistic with the JAK2 inhibitor pacritinib (SB1518) in preclinical models of AML. Blood Cancer J 2012, 2(5), e69.

2.    Novotny-Diermayr, V. et. al. SB939, a Novel Potent and Orally Active Histone Deacetylase Inhibitor with High Tumor Exposure and Efficacy in Mouse Models of Colorectal Cancer. Mol Cancer Ther 2010, 9(3), 642-652.

3. Sangthongpitag, K.; et. al. SB939: A Potent and Orally Active HDAC Inhibitor for the Treatment of Hematological Malignancies. Blood 2007, 110.

4.    Goh, B. B.; et. al. Phase I and pharmacodynamic study of an orally administered novel inhibitor of histone deacetylases, SB939, in patients with refractory solid malignancies. Ann Oncol 2011, 22(11), 2516-2522.

5.    Montalban-Bravo, G.; et. al. Novel drugs for older patients with acute myeloid leukemia. Leukemia 2015, 29(4), 760-769.

6. Bose, P.; et. al. Orphan drug designation for pracinostat, volasertib and alvocidib in AML. Leuk Res 2014, 38(8), 862-865.

Drugs in Clinical Pipeline: TMP269

TMP269 [N-((4-(4-phenylthiazol-2-yl)tetrahydro-2H-pyran-4-yl)methyl)-3-(5-(trifluoromethyl)-1,2,4-oxadiazol-3-yl)benzamide] is a potent, selective class IIa histone deacetylases (HDACs) inhibitor. Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5, HDAC7, and HDAC9, are thought to regulate gene expression by interacting with various transcription factors to repress their transcriptional activity, but the precise mechanism of action of these proteins in signal transduction remains incompletely understood. TMP269 has an inhibitory profile  with IC₅₀ of 157 nM, 97 nM, 43 nM and 23 nM for HDAC4, HDAC5, HDAC7 and HDAC9, respectively.

Normally HDAC inhibition chemistry is ruled by hydroxamates, but with TMP269 the researchers have claimed introduction of unprecedented metal-binding group, trifluoromethyloxadiazole (TFMO), which circumvents the selectivity and pharmacologic liabilities of hydroxamates. Direct metal binding of the TFMO through crystallographic approaches and application of  chemoproteomics demonstarted the superior selectivity of the TFMO series relative to a hydroxamate-substituted analog.

The activity of TMP269 is as follows:

IC₅₀ (HDAC4 enzyme assay) = 157 nM

IC₅₀ (HDAC5 enzyme assay) = 97 nM

IC₅₀ (HDAC7 enzyme assay) = 43 nM

IC₅₀ (HDAC9 enzyme assay) = 23 nM

Common Name: TMP269

Synonyms:  TMP269; TMP 269; TMP-269

IUPAC Name: N-((4-(4-phenylthiazol-2-yl)tetrahydro-2H-pyran-4-yl)methyl)-3-(5-(trifluoromethyl)-1,2,4-oxadiazol-3-yl)benzamide

CAS Number: 1314890-29-3

SMILES: O=C(NCC1(C2=NC(C3=CC=CC=C3)=CS2)CCOCC1)C4=CC=CC(C5=NOC(C(F)(F)F)=N5)=C4

Mechanism of Action: HDAC Inhibitor; Class IIa HDAC Inhibitor; Histone Deacetylases Inhibitor

Indication: Various Cancers; Anti-tumor Therapy

Development Stage: Investigational

Company: Tempero Pharma/GlaxoSmithKline

Eidogen Sertanty Inc Provides Oncology Knowledge Base (OKB): a Collection of Various Cancer Targets and Their Inhibitors.

References:

1. Lobera, M.; et. al. Selective class IIa histone deacetylase inhibition via a nonchelating zinc-binding group. Nat Chem Biol 2013, 9(5), 319-325.

Drugs in Clinical Pipeline: Rocilinostat

Rocilinostat [2-(diphenylamino)-N-(7-(hydroxyamino)-7-oxoheptyl)pyrimidine-5-carboxamide] is novel, orally bioavailable, selective and specific inhibitor of histone deacetylase 6 (HDAC6) with potential antineoplastic activity. 

Rocilinostat, a hydroxamic acid derivative demonstrated potent and selective inhibitory activity against HDAC6, with an enzymatic IC₅₀ value of ~ 5 nM. Rocilinostat is 12-, 10-, and 11-fold less active against HDAC1, HDAC2, and HDAC3 (class I HDACs, IC₅₀ = 58, 48 and 51 nM), respectively. Rocilinostat has minimal activity (IC₅₀ greater than 1 µM) against HDAC4, HDAC5, HDAC7, HDAC9, HDAC11, Sirtuin1, and Sirtuin2, and has slight activity against HDAC8 (IC₅₀ = 0.1 µM) [1].

Acetylon Pharmaceuticals is developing Rocilinostat and it is evaluating Ricolinostat in several clinical studies for the treatment of multiple myeloma and lymphoma. Rocilinostat was chosen from several lead candidates because of its properties that favor drug development. These criteria included at least 10-fold selectivity against HDAC6 compared with class 1 HDACs, minimal activity against other HDAC enzymes, and a lack of significant activity against an extensive panel of receptors, transporters, and enzymes, including kinases. Additional criteria included suitable oral bioavailability in rodents and nonrodents, cellular permeability, metabolic stability, and an appropriate in vitro safety profile with minimal drug-drug interaction, minimal potential for QTc prolongation (hERG channel), and no significant genotoxic signal in mammalian cells. Further, experimental data show that Rocilinostat was less toxic against PBMCs and T cells isolated from healthy volunteers compared with SAHA.

The activity of Rocilinostat is as follows:

IC₅₀ (HDAC6 enzyme assay) = 4.7 nM

IC₅₀ (HDAC2 enzyme assay) = 48 nM

IC₅₀ (HDAC3 enzyme assay) = 51 nM

IC₅₀ (HDAC1 enzyme assay) = 58 nM

IC₅₀ (HDAC8 enzyme assay) = 100 nM

IC₅₀ (HDAC7 enzyme assay) = 1400 nM

IC₅₀ (HDAC4 enzyme assay) = 7000 nM

IC₅₀ (HDAC5 enzyme assay) = 5000 nM

IC₅₀ (HDAC9 enzyme assay) = greater than 10 uM

IC₅₀ (HDAC11 enzyme assay) = greater than 10 uM

IC₅₀ (Sirtuin 1 enzyme assay) = greater than 10 uM

IC₅₀ (Sirtuin 2 enzyme assay) = greater than 10 uM

Common Name: Rocilinostat

Synonyms: ACY-1215; ACY-1215; ACY-1215

IUPAC Name: 2-(diphenylamino)-N-(7-(hydroxyamino)-7-oxoheptyl)pyrimidine-5-carboxamide

CAS Number: 1316214-52-4

Mechanism of Action: HDAC Inhibitor; HDAC6 Inhibitor; Histone Deacetylase 6 Inhibitor

Indication: Multiple Myeloma and Lymphoma

Development Stage: Phase I/II

Company: Acetylon Pharmaceuticals

Pre-Clinical Characterisation

Unlike all other HDACs, HDAC6 has substrate specificity for α-tubulin because of its α-tubulin deacetylase domain. Rocilinostat induces potent acetylation of α-tubulin at very low doses and triggers acetylation of lysine on histone H3 and histone H4 only at higher doses, confirming its specific inhibitory effect on HDAC6 activity. This specific inhibition was also observed in patient multiple myeloma (MM) cells, in which Rocilinostat increased acetylated a-tubulin after 4 hours of treatment. However, after prolonged exposure or with significantly higher concentrations of Rocilinostat, it is possible that the low level of class 1 HDACs (HDAC1, HDAC2, and HDAC3) inhibition by Rocilinostat may also contribute to MM cell cytotoxicity and to potent inhibition of HDAC6.

References:

1. Santo, L.; et. al. Preclinical activity, pharmacodynamic, and pharmacokinetic properties of a selective HDAC6 inhibitor, ACY-1215, in combination with bortezomib in multiple myeloma. Blood 2012, 119(11), 2579-2589.

Drugs in Clinical Pipeline: Abexinostat

Abexinostat [3-(dimethylaminomethyl)-N-[2-[4-(hydroxycarbamoyl)phenoxy]ethyl]-1-benzofuran-2-carboxamide] is a novel, second-generation phenyl hydroxamic acid-based, orally bioavailable HDAC inhibitor that has shown to have in vitro and in vivo activity  against a broad array of cancers, including hematopoietic malignancies and bone and soft-tissue sarcomas. Abexinostat inhibited pure recombinant HDAC1 with a Ki of 0.007 micromol/L, and also inhibited the other HDAC isozymes HDAC2, HDAC3/SMRT, HDAC6, HDAC8, and HDAC10 in the nanomolar range. Treatment of cultured tumor cell lines grown in vitro with Abexinostat resulted in the accumulation of acetylated histone and acetylated tubulin, resulting in an inhibition of tumor cell growth and the induction of apoptosis [1]. Abexinostat is being developed by Pharmacyclics Inc.

Common Name: Abexinostat

Synonyms: CRA-024781; CRA 024781; CRA024781; PCI-24781; PCI24781; PCI 24781

IUPAC Name: 3-(dimethylaminomethyl)-N-[2-[4-(hydroxycarbamoyl)phenoxy]ethyl]-1-benzofuran-2-carboxamide

CAS Number: 783355-60-2; 783356-67-2 (hydrochloride)

Mechanism of Action: HDAC Inhibitor; Histone Deacetylase Inhibitor

Indication: Various Cancers

Development Stage: Phase II

Company: Pharmacyclics Inc

It has also shown good tolerability and activity in Phase I and II clinical trials against lymphoma, as well as against solid tumors in Phase-I trials. Additionally, it acts as a potent radiosensitizing agent and is synergistic with cytotoxic chemotherapy, such as doxorubicin in preclinical models [2].

References:

1. Buggy, J. J.; et. al. CRA-024781: a novel synthetic inhibitor of histone deacetylase enzymes with antitumor activity in vitro and in vivo. Mol Cancer Ther 2006, 5(5), 1309-1317.

2. Sholler, G. S.; et. al. PCI-24781 (abexinostat), a novel histone deacetylase inhibitor, induces reactive oxygen species-dependent apoptosis and is synergistic with bortezomib in neuroblastoma. J Cancer Ther Res 2013, 2, 21.