Pracinostat | SB939 | CAS#929016-96-6 | HDAC inhibitor

MedKoo Cat#: 205626 | Name: Pracinostat

Description:

WARNING: This product is for research use only, not for human or veterinary use.

Pracinostat, also known as SB939, is an orally bioavailable, small-molecule histone deacetylase (HDAC) inhibitor with potential antineoplastic activity. 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. In March 2014, pracinostat has granted Orphan Drug for acute myelocytic leukemia (AML) and for the treatment of T-cell lymphoma by the Food and Drug Administration.

Chemical Structure

Pracinostat

CAS#929016-96-6

Theoretical Analysis

MedKoo Cat#: 205626

Name: Pracinostat

CAS#: 929016-96-6

Chemical Formula: C20H30N4O2

Exact Mass: 358.2369

Molecular Weight: 358.48

Elemental Analysis: C, 67.01; H, 8.44; N, 15.63; O, 8.93

Price and Availability

Size	Price	Availability
25mg	USD 150.00	2 weeks
50mg	USD 250.00	2 weeks
100mg	USD 450.00	2 weeks
200mg	USD 750.00	2 weeks
500mg	USD 1,650.00	2 weeks
1g	USD 2,950.00	2 weeks
2g	USD 5,250.00	2 weeks

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Related CAS #

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Synonym

SB939; SB 939; SC-939; Pracinostat.

IUPAC/Chemical Name

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

InChi Key

JHDKZFFAIZKUCU-ZRDIBKRKSA-N

InChi Code

InChI=1S/C20H30N4O2/c1-4-7-8-19-21-17-15-16(10-12-20(25)22-26)9-11-18(17)24(19)14-13-23(5-2)6-3/h9-12,15,26H,4-8,13-14H2,1-3H3,(H,22,25)/b12-10+

SMILES Code

O=C(NO)/C=C/C1=CC=C2N(CCN(CC)CC)C(CCCC)=NC2=C1

Appearance

white solid powder

Purity

>98% (or refer to the Certificate of Analysis)

Shipping Condition

Shipped under ambient temperature as non-hazardous chemical. This product is stable enough for a few weeks during ordinary shipping and time spent in Customs.

Storage Condition

Dry, dark and at 0 - 4 C for short term (days to weeks) or -20 C for long term (months to years).

Solubility

Soluble in DMSO, not in water

Shelf Life

>2 years if stored properly

Drug Formulation

This drug may be formulated in DMSO

Stock Solution Storage

0 - 4 C for short term (days to weeks), or -20 C for long term (months).

HS Tariff Code

2934.99.9001

More Info

Product Data

Product Data

Instruction

View handling instruction

Biological target:

Pracinostat is a potent histone deacetylase (HDAC) inhibitor, with IC50s of 40-140 nM.

In vitro activity:

SB939 (pracinostat) is a hydroxamic acid based HDAC inhibitor with favorable pharmacokinetic, physicochemical and pharmaceutical properties, and this study investigated if this drug could overcome BIM deletion polymorphism-induced TKI resistance. This study found that SB939 corrects BIM pre-mRNA splicing in CML cells with the BIM deletion polymorphism, and induces apoptotic cell death in CML cell lines and primary cells with the BIM deletion polymorphism. More importantly, SB939 both decreases the viability of CML cell lines and primary CML progenitors with the BIM deletion and restores TKI-sensitivity. Reference: PLoS One. 2017 Mar 16;12(3):e0174107. https://pubmed.ncbi.nlm.nih.gov/28301600/

In vivo activity:

Western blot, cellular immunofluorescence, and EMSA were used to explore the molecular mechanism of SB939 in suppressing breast cancer metastasis. MDA-MB-231 subcutaneous tumor-bearing model of nude mice and the spontaneous metastasis model of breast cancer were both applied to verify in vivo anti-tumor growth and anti-metastatic effects. Results demonstrated that SB939 at 0.5-1 μmol/L markedly impaired the chemotactic motility of breast cancer cells. SB939 reversed epithelial-mesenchymal transition (EMT) process, as evidenced by upregulation E-cadherin expression and downregulation expressions of N-cadherin and vimentin through increasing the levels of ac-histone H3 and H4 and drecreasing the expressiongs of HDAC 5 and 4. This cascade inhibition mediated by SB939 was well interpreted by inactivating phosphorylation of STAT3, blocking its DNA-binding activity, and decreasing the expressions of STAT3-dependent target genes, including MMP2 and MMP9. Furhtermore, this study found that SB939 significantly inhibited breast cancer metastasis and tumor growth in vivo and showed superior anti-tumor properties compared with SAHA in two breast cancer animal models. Reference: Life Sci. 2020 May 1;248:117469. https://pubmed.ncbi.nlm.nih.gov/32109485/

	Solvent	mg/mL	mM
Solubility
	DMF	30.0	83.69
	DMSO	117.3	327.30
	Ethanol	16.0	44.63
	Ethanol:PBS (pH 7.2) (1:1)	0.5	1.40

Note: There can be variations in solubility for the same chemical from different vendors or different batches from the same vendor. The following factors can affect the solubility of the same chemical: solvent used for crystallization, residual solvent content, polymorphism, salt versus free form, degree of hydration, solvent temperature. Please use the solubility data as a reference only. Warming and sonication will facilitate dissolving. Still have questions? Please contact our Technical Support scientists.

Preparing Stock Solutions

The following data is based on the product molecular weight 358.48 Batch specific molecular weights may vary from batch to batch due to the degree of hydration, which will affect the solvent volumes required to prepare stock solutions.

Concentration / Solvent Volume / Mass	1 mg	5 mg	10 mg
1 mM	1.15 mL	5.76 mL	11.51 mL
5 mM	0.23 mL	1.15 mL	2.3 mL
10 mM	0.12 mL	0.58 mL	1.15 mL
50 mM	0.02 mL	0.12 mL	0.23 mL

Formulation protocol:

1. Rauzan M, Chuah CT, Ko TK, Ong ST. The HDAC inhibitor SB939 overcomes resistance to BCR-ABL kinase Inhibitors conferred by the BIM deletion polymorphism in chronic myeloid leukemia. PLoS One. 2017 Mar 16;12(3):e0174107. doi: 10.1371/journal.pone.0174107. PMID: 28301600; PMCID: PMC5354438. 2. Wang H, Yu N, Chen D, Lee KC, Lye PL, Chang JW, Deng W, Ng MC, Lu T, Khoo ML, Poulsen A, Sangthongpitag K, Wu X, Hu C, Goh KC, Wang X, Fang L, Goh KL, Khng HH, Goh SK, Yeo P, Liu X, Bonday Z, Wood JM, Dymock BW, Kantharaj E, Sun ET. Discovery of (2E)-3-{2-butyl-1-[2-(diethylamino)ethyl]-1H-benzimidazol-5-yl}-N-hydroxyacrylamide (SB939), an orally active histone deacetylase inhibitor with a superior preclinical profile. J Med Chem. 2011 Jul 14;54(13):4694-720. doi: 10.1021/jm2003552. Epub 2011 Jun 16. PMID: 21634430. 3. Chen J, Li N, Liu B, Ling J, Yang W, Pang X, Li T. Pracinostat (SB939), a histone deacetylase inhibitor, suppresses breast cancer metastasis and growth by inactivating the IL-6/STAT3 signalling pathways. Life Sci. 2020 May 1;248:117469. doi: 10.1016/j.lfs.2020.117469. Epub 2020 Feb 25. PMID: 32109485. 4. Novotny-Diermayr V, Sangthongpitag K, Hu CY, Wu X, Sausgruber N, Yeo P, Greicius G, Pettersson S, Liang AL, Loh YK, Bonday Z, Goh KC, Hentze H, Hart S, Wang H, Ethirajulu K, Wood JM. 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 Mar;9(3):642-52. doi: 10.1158/1535-7163.MCT-09-0689. Epub 2010 Mar 2. PMID: 20197387.

In vitro protocol:

In vivo protocol:

1. Chen J, Li N, Liu B, Ling J, Yang W, Pang X, Li T. Pracinostat (SB939), a histone deacetylase inhibitor, suppresses breast cancer metastasis and growth by inactivating the IL-6/STAT3 signalling pathways. Life Sci. 2020 May 1;248:117469. doi: 10.1016/j.lfs.2020.117469. Epub 2020 Feb 25. PMID: 32109485. 2. Novotny-Diermayr V, Sangthongpitag K, Hu CY, Wu X, Sausgruber N, Yeo P, Greicius G, Pettersson S, Liang AL, Loh YK, Bonday Z, Goh KC, Hentze H, Hart S, Wang H, Ethirajulu K, Wood JM. 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 Mar;9(3):642-52. doi: 10.1158/1535-7163.MCT-09-0689. Epub 2010 Mar 2. PMID: 20197387.

1: Kim CE, Lee SM, Yoon EH, Won HJ, Jung YJ, Jegal Y, Kim DH, Kwon B, Seo SK. Induction of indoleamine 2,3-dioxygenase 1 expression in neurons of the central nervous system through inhibition of histone deacetylases blocks the progression of experimental autoimmune encephalomyelitis. Int Immunopharmacol. 2024 Jun 15;134:112246. doi: 10.1016/j.intimp.2024.112246. Epub 2024 May 17. PMID: 38759372. 2: Garcia-Manero G, Kazmierczak M, Wierzbowska A, Fong CY, Keng MK, Ballinari G, Scarci F, Adès L. Pracinostat combined with azacitidine in newly diagnosed adult acute myeloid leukemia (AML) patients unfit for standard induction chemotherapy: PRIMULA phase III study. Leuk Res. 2024 May;140:107480. doi: 10.1016/j.leukres.2024.107480. Epub 2024 Mar 12. PMID: 38499457. 3: Wang KL, Yeh TY, Hsu PC, Wong TH, Liu JR, Chern JW, Lin MH, Yu CW. Discovery of novel anaplastic lymphoma kinase (ALK) and histone deacetylase (HDAC) dual inhibitors exhibiting antiproliferative activity against non-small cell lung cancer. J Enzyme Inhib Med Chem. 2024 Dec;39(1):2318645. doi: 10.1080/14756366.2024.2318645. Epub 2024 Mar 11. PMID: 38465731; PMCID: PMC10930102. 4: Huang J, Tang Y, Li Y, Wei W, Kang F, Tan S, Lin L, Lu X, Wei H, Wang N. ALDH1A3 contributes to tumorigenesis in high-grade serous ovarian cancer by epigenetic modification. Cell Signal. 2024 Apr;116:111044. doi: 10.1016/j.cellsig.2024.111044. Epub 2024 Jan 9. PMID: 38211842. 5: Liang XL, Ouyang L, Yu NN, Sun ZH, Gui ZK, Niu YL, He QY, Zhang J, Wang Y. Histone deacetylase inhibitor pracinostat suppresses colorectal cancer by inducing CDK5-Drp1 signaling-mediated peripheral mitofission. J Pharm Anal. 2023 Oct;13(10):1168-1182. doi: 10.1016/j.jpha.2023.06.005. Epub 2023 Jun 10. PMID: 38024857; PMCID: PMC10657975. 6: Zheng H, Zhao Y, Zhou H, Tang Y, Xie Z. The Comprehensive Analysis of m6A-Associated Anoikis Genes in Low-Grade Gliomas. Brain Sci. 2023 Sep 12;13(9):1311. doi: 10.3390/brainsci13091311. PMID: 37759912; PMCID: PMC10527396. 7: Lian B, Chen X, Shen K. Inhibition of histone deacetylases attenuates tumor progression and improves immunotherapy in breast cancer. Front Immunol. 2023 Mar 9;14:1164514. doi: 10.3389/fimmu.2023.1164514. PMID: 36969235; PMCID: PMC10034161. 8: Abedin SM, Badar T, Gauger K, Michaelis LC, Runaas L, Carlson KS, Murthy GG, Atallah E. Safety and efficacy of pracinostat in combination with gemtuzumab ozogamicin (PraGO) in patients with relapsed/refractory acute myeloid leukemia. Leuk Res. 2022 Dec;123:106984. doi: 10.1016/j.leukres.2022.106984. Epub 2022 Nov 2. PMID: 36401944. 9: Dinakar YH, Kumar H, Mudavath SL, Jain R, Ajmeer R, Jain V. Role of STAT3 in the initiation, progression, proliferation and metastasis of breast cancer and strategies to deliver JAK and STAT3 inhibitors. Life Sci. 2022 Nov 15;309:120996. doi: 10.1016/j.lfs.2022.120996. Epub 2022 Sep 25. PMID: 36170890. 10: Chen M, Zhang L, Zhan R, Zheng X. The novel histone deacetylase inhibitor pracinostat suppresses the malignant phenotype in human glioma. Mol Biol Rep. 2022 Aug;49(8):7507-7519. doi: 10.1007/s11033-022-07559-y. Epub 2022 May 27. PMID: 35622308. 11: Erkin ÖC, Cömertpay B, Göv E. Integrative Analysis for Identification of Therapeutic Targets and Prognostic Signatures in Non-Small Cell Lung Cancer. Bioinform Biol Insights. 2022 Apr 6;16:11779322221088796. doi: 10.1177/11779322221088796. PMID: 35422618; PMCID: PMC9003654. 12: Decourtye-Espiard L, Bougen-Zhukov N, Godwin T, Brew T, Schulpen E, Black MA, Guilford P. E-Cadherin-Deficient Epithelial Cells Are Sensitive to HDAC Inhibitors. Cancers (Basel). 2021 Dec 30;14(1):175. doi: 10.3390/cancers14010175. PMID: 35008338; PMCID: PMC8749989. 13: Sunami Y, Yokoyama T, Yoshino S, Takahara T, Yamazaki Y, Harada H, Nakamura T. BCL11A promotes myeloid leukemogenesis by repressing PU.1 target genes. Blood Adv. 2022 Mar 22;6(6):1827-1843. doi: 10.1182/bloodadvances.2021004558. PMID: 34714913; PMCID: PMC8941473. 14: Mensah AA, Spriano F, Sartori G, Priebe V, Cascione L, Gaudio E, Tarantelli C, Civanelli E, Aresu L, Rinaldi A, Damia G, Lovati E, Zucca E, Stathis A, Pietra C, Bertoni F. Study of the antilymphoma activity of pracinostat reveals different sensitivities of DLBCL cells to HDAC inhibitors. Blood Adv. 2021 May 25;5(10):2467-2480. doi: 10.1182/bloodadvances.2020003566. PMID: 33999145; PMCID: PMC8152508. 15: Badar T, Atallah E. Do histone deacytelase inhibitors and azacitidine combination hold potential as an effective treatment for high/very-high risk myelodysplastic syndromes? Expert Opin Investig Drugs. 2021 Jun;30(6):665-673. doi: 10.1080/13543784.2021.1915986. Epub 2021 Apr 19. PMID: 33836635. 16: Ganai SA. Characterizing binding intensity and energetic features of histone deacetylase inhibitor pracinostat towards class I HDAC isozymes through futuristic drug designing strategy. In Silico Pharmacol. 2021 Feb 9;9(1):18. doi: 10.1007/s40203-021-00077-y. PMID: 33628709; PMCID: PMC7873132. 17: Pulya S, Amin SA, Adhikari N, Biswas S, Jha T, Ghosh B. HDAC6 as privileged target in drug discovery: A perspective. Pharmacol Res. 2021 Jan;163:105274. doi: 10.1016/j.phrs.2020.105274. Epub 2020 Nov 7. PMID: 33171304. 18: Dushanan R, Weerasinghe S, Dissanayake DP, Senthilinithy R. Cracking a cancer code histone deacetylation in epigenetic: the implication from molecular dynamics simulations on efficacy assessment of histone deacetylase inhibitors. J Biomol Struct Dyn. 2022 Mar;40(5):2352-2368. doi: 10.1080/07391102.2020.1838328. Epub 2020 Nov 2. PMID: 33131428. 19: Rice CA, Colon BL, Chen E, Hull MV, Kyle DE. Discovery of repurposing drug candidates for the treatment of diseases caused by pathogenic free-living amoebae. PLoS Negl Trop Dis. 2020 Sep 24;14(9):e0008353. doi: 10.1371/journal.pntd.0008353. PMID: 32970675; PMCID: PMC7546510. 20: Li Y, Zhu S, Liu W, Ming J, Wang X, Hu X. Ruxolitinib-based combinations in the treatment of myelofibrosis: worth looking forward to. Ann Hematol. 2020 Jun;99(6):1161-1176. doi: 10.1007/s00277-020-04028-z. Epub 2020 Apr 24. PMID: 32333155; PMCID: PMC7237512.