Design, synthesis and biological evaluation of thienopyrimidine hydroxamic acid based derivatives as structurally novel histone deacetylase (HDAC) inhibitors

doi:10.1016/j.ejmech.2017.01.035

European Journal of Medicinal Chemistry

Volume 128, 10 March 2017, Pages 293-299

https://doi.org/10.1016/j.ejmech.2017.01.035 Get rights and content

Highlights

•
Novel thienopyrimidine hydroxamic acid based derivatives were designed and synthesized.
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Most of these compounds displayed good to excellent inhibitory activity against HDACs with the IC₅₀ values below 50 nM.
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Some compounds significantly up-regulated the levels of Histone H3 acetylation and α-tubulin acetylation as well as exhibited powerful anti-proliferative activities against cancer cell lines in vitro.

Abstract

New thienopyrimidine hydroxamic acid derivatives as HDACs inhibitors were designed, synthesized and evaluated. All compounds were evaluated for their ability to inhibit recombinant human HDAC1, HDAC3, and HDAC6 isoforms and in vitro anti-proliferative activity on tumor cell lines RMPI 8226 and HCT 116. Most of these compounds displayed good to excellent inhibitory activities against HDACs. The IC₅₀ values of compound 9m against HDAC1, HDAC3, and HDAC6 was 29.81 ± 0.52 nM, 24.71 ± 1.16 nM, and 21.29 ± 0.32 nM. Most of these compounds showed strong anti-proliferative activity against human cancer cell lines including RMPI 8226 and HCT 116. The IC₅₀ values of compound 9m against RPMI 8226 and HCT 116 proliferation were 0.97 ± 0.072 μM and 1.01 ± 0.033 μM, respectively. In addition, compound 9m noticeably up-regulated the level of histone H3 acetylation at the low concentration of 0.3 μM.

Graphical abstract

By rational design and modification, compound 9m showed excellent HDACs inhibitory activity, strong anti-proliferative activity against human cancer cell lines including RMPI 8226 and HCT 116. Moreover, compound 9m noticeably up-regulated the level of histone H3 acetylation at the low concentration of 0.3 μM.

Introduction

Histone acetylation and deacetylation, catalyzed by multisubunit complexes, play a key role in the regulation of eukaryotic gene expression [1]. The acetylation status of histones is determined by two sets of enzymes: histone acetyltransferases (HATs) and histone deacetylases (HDACs) [2]. HDACs also interact with retinoblastoma tumor-suppressor protein and this complex is a key element in the control of cell proliferation and differentiation. Together with metastasis-associated protein-2 (MAT2), HDACs deacetylates p53 and modulates its effect on cell growth and apoptosis. HDAC inhibitors demonstrated prominent antitumor efficacy on broad spectrum neoplasms in preclinical and clinical studies [3], [4], [5]. This concept has been well validated by the approval of HDAC inhibitors vorinostat (suberoylanilide hydroxamic acid, SAHA) [6] and romidepsin (depsipeptide) [7] for the treatment of cutaneous T-cell lymphoma.

The thienopyrimidine fragment is widely present in antitumor agents [8], anti-inflammatory agents [9], and anti-diabetic agents [10]. In our previous studies, we reported 4-anilinothieno[2,3-d]pyrimidine derivatives as irreversible EGFR inhibitors that displayed excellent inhibitory activities against wild type and mutant EGFR (Fig. 1) [11]. CUDC-101 has been reported as a multi inhibitors against HDAC, EGFR, and HER2 for the treatment of cancer, which contains a quinazoline moiety within its structure [12]. On the basis of these observations, we attempted using substituted 4-anilinothieno[3,2-d]pyrimidine moiety as a cap group (CAP) for protein surface interactions, fixed carbon chain as a linker region, and hydroxamic acid group as a zinc binding group (ZBG) (Fig. 1). Herein, we presented the design, synthesis and biological evaluation of thienopyrimidine hydroxamic acid based derivatives as novel HDACs inhibitors. Most of these compounds showed excellent potencies against HDACs and displayed powerful anti-proliferative activities against cancer cell lines in vitro.

Section snippets

Chemistry

The synthetic route to obtain the desired thienopyrimidine-based hydroxamic acid derivatives 9a-r are shown in Scheme 1. Heated by the microwave, the thieno[3,2-d]pyrimidin-4(3H)-one 3 was obtained via the cyclization of methyl 3-aminothiophene-2-carboxylate with formamidine acetate. Then, the nitration of intermediate 3, followed by chlorination to afford 5. Coupling with various substituted anilines and then reduction of nitro group using iron/NH₄Cl afforded the key intermediate 7. Treatment

Conclusion

In conclusion, based on the previous work in our laboratory, a series of thienopyrimidine-based hydroxamic acid derivatives 9a-r were designed, synthesized and evaluated as novel HDAC inhibitors. The in vitro biological evaluations indicated that most compounds exhibited excellent inhibition against recombinant HDAC enzyme activities and multiple cancer cells lines proliferation. Especially, the compounds 9e, 9m, and 9o could significantly inhibit the proliferation of RPMI 8226 and HCT 116

Chemistry

The reagents (chemicals) were commercially available and used without further purification. Analytical thin-layer chromatography (TLC) was performed on HSGF 254 (0.15–0.2 mm thickness). Column chromatography was performed on silica gel 300–400 mesh to purify the compounds. Nuclear magnetic resonance (NMR) spectra were performed on a Brucker AMX-400 (TMS as IS). Chemical shifts were reported in parts per million (ppm, δ) downfield from tetramethylsilane. Proton coupling patterns were described

Acknowledgements

We gratefully acknowledge financial support from the National Natural Science Foundation of China (81620108027, 21632008, 91229204, 21472209 and 81220108025) the Major Project of Chinese National Programs for Fundamental Research and Development (2015CB910304), and National S&T Major Projects (2014ZX09507002-001 and 2014ZX09507-002-005).

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¹: These authors contributed equally to this work.

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Research paperDesign, synthesis and biological evaluation of thienopyrimidine hydroxamic acid based derivatives as structurally novel histone deacetylase (HDAC) inhibitors

Highlights

Abstract

Graphical abstract

Introduction

Section snippets

Chemistry

Conclusion

Chemistry

Acknowledgements

Eur. J. Med. Chem.

Eur. J. Pharm. Sci.

Eur. J. Med. Chem.

Eur. J. Med. Chem.

Bioorg. Med. Chem. Lett.

Bioorg. Med. Chem.

J. Med. Chem.

Histone modifications as molecular targets in nasopharyngeal cancer

Curr. Med. Chem.

Impact of epigenetic dietary components on cancer through histone modifications

Curr. Med. Chem.

Recent advances in computer-assisted structure-based identification and design of histone deacetylases inhibitors

Curr. Top. Med. Chem.

Research paper
Design, synthesis and biological evaluation of thienopyrimidine hydroxamic acid based derivatives as structurally novel histone deacetylase (HDAC) inhibitors