环肽类组蛋白去乙酰化酶抑制剂

组蛋白去乙酰化酶抑制剂是一类以组蛋白去乙酰化酶为靶点的新型靶向抗肿瘤药物,在抗增殖、促凋亡、促分化、阻滞细胞生长周期、抗血管生成等方面有很好的作用。组蛋白去乙酰化酶抑制剂以其独特的抗肿瘤作用机理,在研发肿瘤治疗药物中占有重要地位。在组蛋白去乙酰化酶抑制剂分类中,环肽类抑制剂结构最为复杂,对多种类型的实体瘤及血液学癌细胞均具有良好的对抗作用。本文针对天然和化学合成的环肽类组蛋白去乙酰化酶抑制剂中金属结合区、表面识别区以及连接区的结构特点进行了综述,并描述了各类抑制剂对酶的抑制活性和抗肿瘤增殖活性。对抑制剂不同结构区的修饰、改造可以使抑制剂对不同肿瘤细胞具有高效性和特异性作用,通过构效关系研究寻找具有高效低毒、靶向性环肽类抑制剂的结构规律,可为研究开发抗肿瘤药物提供帮助。     

基于Chlamydocin骨架设计合成环肽类HDACi及其抗肿瘤活性

组蛋白去乙酰化酶(HDACs)通过催化各种底物蛋白包括组蛋白、转录因子、α-微管蛋白和核输入蛋白等的ε-赖氨酸残基乙酰化侧链的去乙酰化来影响细胞功能,抑制HDAC活性可以治疗表观遗传异常引起的癌症和其他慢性疾病.以HDAC抑制剂(HDACi) Chlamydocin为骨架设计合成一类新型抑制剂,将HDACi的结合区设计为二硫键结构、在环肽中苯丙氨酸的苯环不同位点引入甲基,合成4种不同序列的环肽类HDACi.考察HDACi体外抗肿瘤细胞(MCF-7,Hela和7721)活性,结果表明HDACi对三种肿瘤细胞系均显示良好的生长抑制作用,细胞形态都发生明显变化,其中对Hela细胞的毒性最高,IC50达到0.1 μmol/L.     

基于组蛋白去乙酰化酶靶点的羟肟酸类化合物及其抗肿瘤活性研究进展

组蛋白去乙酰化酶（histone deacetylase, HDACs）是肿瘤治疗的靶点之一,组蛋白去乙酰化酶抑制剂（histone deacetylase inhibitor, HDACi）可通过多种机制发挥抗肿瘤作用,包括抑制肿瘤细胞活力、迁移、侵袭、血管生成、增殖、DNA修复和诱导细胞凋亡。本文对近年来以HDACs为单靶点和多靶点的羟肟酸类衍生物的合成及其抗肿瘤活性进行综述,并对此方面的发展趋势、应用前景进行展望。     

新型苯甲酰胺类HDAC抑制剂的合成及其抗肿瘤活性

以MS-275为先导化合物,设计并合成了7个新型苯甲酰胺类化合物（6a~6c, 14a, 14b, 15a和18）,其结构经¹H NMR和ESI-MS表征。采用MTT法测定了6a~6c, 14a, 14b, 15a和18对人急性白血病细胞(HL60)和人乳腺癌细胞(MCF-7)的体外抗肿瘤细胞增殖活性。结果表明：N-(2-氨基苯)-3-［4-(吡啶-3-基)嘧啶-2-氨基］己酰胺（6a）, N-(2-氨基苯)-4-【3-{4-［(二乙胺基)甲基］苯基}丙烯酰】苯甲酰胺（14a）和N-(2-氨基苯)-4-［3-(吡啶-3-基)丙烯酰］丙酰胺(18）的抑制活性较好,其GI₅₀依次为5.72 μmol·L^-1, 6.91 μmol·L^-1, 7.11 μmol·L^-1和3.46 μmol·L^-1, 4.12 μmol·L^-1, 3.97 μmol·L^-1,优于MS-275(7.88 μmol·L^-1和4.49 μmol·L^-1)。     

HDAC对接研究:苯甲酰胺类抑制剂结合方式推测

通过计算机模拟的对接过程研究，发现了MS-275— 一种苯甲酰胺类的组蛋白去乙酰酶（HDAC）抑制剂与酶的可能的全新结合方式.这种结合方式与已经阐明的组蛋白去乙酰酶类似蛋白（HDLP）与曲古柳菌素A(trichostatin A, TSA)和suberoylanilide hydroxamic acid(SAHA)形成的复合物晶体结构中配体与酶的作用方式完全不同.从对接结果看，MS-275的作用靶点在酶活性口袋的最狭窄部位，而不是直接作用于锌离子.这似乎能够解释MS-275的低毒性特点，并且为设计和筛选全新的HDAC抑制剂提供了新思路.     

Apicidin选择性抑制ClassⅠ HDACs分子动力学研究

采用模拟方法研究组蛋白脱乙酰酶抑制剂(Apicidin)选择性抑制组蛋白去乙酰化酶(Histone deacetylases, HDACs)中的HDAC1和HDAC8. 通过HDAC8晶体结构同源模建HDAC1三维结构模型, 将Apicidin分别与HDAC1和HDAC8对接并进行分子动力学模拟, 结果表明, HDAC1活性口袋入口处的Arg270是Apicidin-HDAC1形成稳定结构的重要因素; HDAC1中Tyr303及His178与Apicidin形成2个持续存在的氢键, 而在HDAC8中未发现, 这是Apicidin选择性抑制HDAC1高于HDAC8的另一重要原因.     

基于配体的组蛋白去乙酰化酶抑制剂的分子设计

本文采用Topomer Co MFA方法对39个组蛋白去乙酰化酶抑制剂进行了3D-QSAR研究,得到q~2=0. 877,r~2=0. 987的可靠模型。运用基于R基团搜索的Topomer Search技术对ZINC2015数据库进行了虚拟筛选,筛选出一批具有潜在活性的目标化合物,模型预测结果表明,筛选出的化合物活性比最初合成的化合物大幅度提高,其中筛选出的最高活性化合物S2-7(IC_(50)=0. 0235μmol·L~(-1))活性达到了最初合成的高活性化合物21(IC_(50)=0. 103μmol·L~(-1))的4倍。分子对接技术揭示了化合物结构和靶酶之间的联系,为更新型HDACIs的设计以及结构优化提供了重要信息和理论指导。     

太子参环肽B(Heterophyllin B, HB)的酶环化反应

利用从Pseudostellaria heterophylla提取分离的粗酶PH-1, 以链八肽NH₂-Gly¹-Gly²-Leu-Pro-Pro-Pro-Ile-Phe-COOH (4)为底物成功地进行了太子参环肽B(heterophyllin B (HB))的环化反应, 并利用TLC, HPLC, M, NMR以及同位素标记等手段对反应产物进行了分析和确证.     

亲电酮类HDAC抑制剂的3D-QSAR和分子对接研究

组蛋白去乙酰化酶抑制剂(histone deacetylase inhibitor,HDACi)是近年来治疗癌症的重要靶向药物,其中羟氨酸类,苯甲酰胺类多种药物已进入临床试验阶段,但对于亲电酮类HDACi还有待于进一步研究,本研究应用比较分子力场分析法(comparative molecular field analy...     

Non-Hydroxamate Zinc-Binding Groups as Warheads for Histone Deacetylases

Histone deacetylases (HDACs) remove acetyl groups from acetylated lysine residues and have a large variety of substrates and interaction partners. Therefore, it is not surprising that HDACs are involved in many diseases. Most inhibitors of zinc-dependent HDACs (HDACis) including approved drugs contain a hydroxamate as a zinc-binding group (ZBG), which is by far the biggest contributor to affinity, while chemical variation of the residual molecule is exploited to create more or less selectivity against HDAC isozymes or other metalloproteins. Hydroxamates have a propensity for nonspecificity and have recently come under considerable suspicion because of potential mutagenicity. Therefore, there are significant concerns when applying hydroxamate-containing compounds as therapeutics in chronic diseases beyond oncology due to unwanted toxic side effects. In the last years, several alternative ZBGs have been developed, which can replace the critical hydroxamate group in HDACis, while preserving high potency. Moreover, these compounds can be developed into highly selective inhibitors. This review aims at providing an overview of the progress in the field of non-hydroxamic HDACis in the time period from 2015 to present. Formally, ZBGs are clustered according to their binding mode and structural similarity to provide qualitative assessments and predictions based on available structural information.     

A Photoactivatable Platinum(IV) Complex Targeting Genomic DNA and Histone Deacetylases

We report toxic effects of a photoactivatable platinum(IV) complex conjugated with suberoyl‐bis‐hydroxamic acid in tumor cells. The conjugate exerts, after photoactivation, two functions: activity as both a platinum(II) anticancer drug and histone deacetylase (HDAC) inhibitor in cancer cells. This approach relies on the use of a Pt^IV pro‐drug, acting by two independent mechanisms of biological action in a cooperative manner, which can be selectively photoactivated to a cytotoxic species in and around a tumor, thereby increasing selectivity towards cancer cells. These results suggest that this strategy is a valuable route to design new platinum agents with higher efficacy for photodynamic anticancer chemotherapy.     

Cyclic Peptides as Inhibitors of Amyloid Fibrillation

Many neurodegenerative diseases, like Parkinson’s, Alzheimer’s, or Huntington’s disease, occur as a result of amyloid protein fibril formation and cell death induced by this process. Cyclic peptides (CPs) and their derivatives form a new class of powerful inhibitors that prevent amyloid fibrillation and decrease the cytotoxicity of aggregates. The strategies for designing CPs are described, with respect to their amino acid sequence and/or conformational similarity to amyloid fibrils. The implications of CPs for the study and possible treatment of amyloid‐related diseases are discussed.     

Target Design of Novel Histone Deacetylase 6 Selective Inhibitors with 2-Mercaptoquinazolinone as the Cap Moiety

Epigenetic alterations found in all human cancers are promising targets for anticancer therapy. In this sense, histone deacetylase inhibitors (HDACIs) are interesting anticancer agents that play an important role in the epigenetic regulation of cancer cells. Here, we report 15 novel hydroxamic acid-based histone deacetylase inhibitors with quinazolinone core structures. Five compounds exhibited antiproliferative activity with IC₅₀ values of 3.4–37.8 µM. Compound 8 with a 2-mercaptoquinazolinone cap moiety displayed the highest antiproliferative efficacy against MCF-7 cells. For the HDAC6 target selectivity study, compound 8 displayed an IC₅₀ value of 2.3 µM, which is 29.3 times higher than those of HDAC3, HDAC4, HDAC8, and HDAC11. Western blot assay proved that compound 8 strongly inhibited tubulin acetylation, a substrate of HDAC6. Compound 8 also displayed stronger inhibition activity against HDAC11 than the control drug Belinostat. The inhibitory mechanism of action of compound 8 on HDAC enzymes was then explored using molecular docking study. The data revealed a high binding affinity (−7.92 kcal/mol) of compound 8 toward HDAC6. In addition, dock pose analysis also proved that compound 8 might serve as a potent inhibitor of HDAC11.     

一种香豆素荧光标记多肽的合成及应用

Sirtuin蛋白是一类称为依赖烟酰胺腺嘌呤二核苷酸（NAD）的组蛋白去乙酰化酶,共有7个成员,均是潜在的疾病治疗靶点。 然而,目前的荧光筛选方法,只适用于SIRT1~SIRT3。 因此,根据SIRT5的新酶活,设计、合成了针对SIRT5的荧光标记多肽（ISGASE(SuK) AMC）,并通过LC-MS和荧光检测证明了该荧光标记多肽能应用于SIRT5的活性筛选。     

3D-QSAR Study on Apicidin Inhibit Histone Deacetylase

For Histone Deacetylase (HDAC) Inhibitor, four 3D-QSAR models for four types of different activities, were constructed.The cross-valldated q^2 value of CoMFA Model 1 is 0.624 and the noncross-validated r2 value is 0.939. The cross-validated q^2 value of Model 2 for training set is 0.652 and the noncross-validated r^2 value is 0.963. The cross-validated q^2 value for Model 3 is 0.713, with noncross-validated r^2 value 0.947. The crossvalidated q2 value for Model 4 is 0.566 with noncross-validated r^2 value 0.959. Their predicted abilities were validated by different test sets which did not include in training set. Then the relationship between substituents and activities was analyzed by using these models and the main influence elements in different positions (positions 8 and 14) were found. The polar donor electron group of position 8 could increase the activity of inhibition of HDAC, because it could form chelation with the catalytic Zn. Suitable bulk and positive groups at position 14 are favorable to anti-HDAC activity. These models could web interpret the relationship between inhibition activity and apicidin structure affording us important information for structurebased drug design.     

Binding Free Energy (BFE) Calculations and Quantitative Structure–Activity Relationship (QSAR) Analysis of Schistosoma mansoni Histone Deacetylase 8 (smHDAC8) Inhibitors

Histone-modifying proteins have been identified as promising targets to treat several diseases including cancer and parasitic ailments. In silico methods have been incorporated within a variety of drug discovery programs to facilitate the identification and development of novel lead compounds. In this study, we explore the binding modes of a series of benzhydroxamates derivatives developed as histone deacetylase inhibitors of Schistosoma mansoni histone deacetylase (smHDAC) using molecular docking and binding free energy (BFE) calculations. The developed docking protocol was able to correctly reproduce the experimentally established binding modes of resolved smHDAC8–inhibitor complexes. However, as has been reported in former studies, the obtained docking scores weakly correlate with the experimentally determined activity of the studied inhibitors. Thus, the obtained docking poses were refined and rescored using the Amber software. From the computed protein–inhibitor BFE, different quantitative structure–activity relationship (QSAR) models could be developed and validated using several cross-validation techniques. Some of the generated QSAR models with good correlation could explain up to ~73% variance in activity within the studied training set molecules. The best performing models were subsequently tested on an external test set of newly designed and synthesized analogs. In vitro testing showed a good correlation between the predicted and experimentally observed IC₅₀ values. Thus, the generated models can be considered as interesting tools for the identification of novel smHDAC8 inhibitors.