同源模建和分子对接研究HDAC1/HDAC8的选择性

组蛋白去乙酰化酶(HDACs)是近年来治疗肿瘤的重要靶标之一.由于HDACs包含多种亚型,且各亚型的生理功能存在一定的差异,其选择性抑制剂的开发已成为当前的研发热点.我们通过同源模建的HDAC1结构,与已有的HDAC8晶体结构的活性位点进行比较分析,探讨了对两者选择性有重要影响的残基,为基于受体的选择性抑制剂研究提供重要信息.同时选择了52个HDAC抑制剂,分别建立了HDAC1、HDAC8的活性值与对接打分值的线性回归模型.所建的HDAC1和HDAC8的线性构效关系模型的非交叉验证系数R2分别为0.82和0.80,表明具有一定的统计学意义.利用所建模型对已设计合成的化合物进行了预测,预测结果对HDAC1、HDAC8选择性抑制剂的优化改造提供了一定的指导意义.     

Conformal prediction of HDAC inhibitors

The growing interest in epigenetic probes and drug discovery, as revealed by several epigenetic drugs in clinical use or in the lineup of the drug development pipeline, is boosting the generation of screening data. In order to maximize the use of structure–activity relationships there is a clear need to develop robust and accurate models to understand the underlying structure–activity relationship. Similarly, accurate models should be able to guide the rational screening of compound libraries. Herein we introduce a novel approach for epigenetic quantitative structure–activity relationship (QSAR) modelling using conformal prediction. As a case study, we discuss the development of models for 11 sets of inhibitors of histone deacetylases (HDACs), which are one of the major epigenetic target families that have been screened. It was found that all derived models, for every HDAC endpoint and all three significance levels, are valid with respect to predictions for the external test sets as well as the internal validation of the corresponding training sets. Furthermore, the efficiencies for the predictions are above 80% for most data sets and above 90% for four data sets at different significant levels. The findings of this work encourage prospective applications of conformal prediction for other epigenetic target data sets.     

氧肟酸类组蛋白去乙酰化酶抑制剂的药效团模型研究

基于24个目前已知的氧肟酸类组蛋白去乙酰化酶抑制剂,我们运用Catalyst软件建立了一个三维药效团模型。其中,最好的药效团模型1,包含了四个化学特征（一个氢键供体,一个芳环和两个疏水基）,相关系数达到0.946,并由另外20个化合物进行了测试验证。我们第一次特征性描述了组蛋白去乙酰化酶的帽子（CAP）部分。我们的研究结果对于设计全新组蛋白去乙酰化酶抑制剂具有很好的指导作用。     

Exploring the Potential binding Sites of Some Known HDAC Inhibitors on Some HDAC8 Conformers by Docking Studies

We describe the conformational behavior of histone deacetylase 8 (HDAC8) using molecular dynamics (MD) simulations. HDAC8 conformers were used for the docking studies using some known HDAC inhibitors (HDACi) suberoylanilide hydroxamic acid (SAHA), valproic acid (VPA), aroyl-pyrrole-hydroxy-amide (APHA-8) and tubacin to explore their interactions, binding modes, free energy values. The MD simulation show that HDAC8 make important surface changes at the catalytic site (CS) entrance as well as at two entrances locations in the 14-Å tunnel. In addition, we identify an alternate entrance to the 14-Å tunnel named adjacent to the catalytic site pocket (ACSP). By using docking studies, it was possible to elucidate the importance of hydrophobic and π–π interactions that are the most important for the ligand–HDAC8 complex structural stabilization. In conclusion, the ligand flexibility, molecular weight and chemical moieties (hydroxamic acid, aryl and aliphatic moieties) are the principal properties required to increase the binding affinity on HDAC8.     

磺胺基羟肟酸类HDAC抑制剂三维定量构效关系

组蛋白去乙酰化酶(HDAC)对染色质分布和基因调节起着重要的作用,也是治疗癌症和其它疾病的新靶点.羟肟酸类抑制剂是目前研究最多的组蛋白去乙酰化酶抑制剂.应用比较分子力场(CoMFA)法对一系列磺胺基羟肟酸类HDAC抑制剂进行了结构活性关系研究,得到的模型具有较高的交叉验证系数(q²=0.704).并在此基础上,建立了非交叉验证的偏最小二乘分析(PLS)模型.用该模型对随机选择的6个化合物组成的测试集进行了预测,得到了令人满意的结果,所建模型具有良好的预测能力.本研究对于设计高活性的HDAC抑制剂及抗癌药物都有指导意义.     

Quinazoline Based HDAC Dual Inhibitors as Potential Anti-Cancer Agents

Cancer is the most devastating disease and second leading cause of death around the world. Despite scientific advancements in the diagnosis and treatment of cancer which can include targeted therapy, chemotherapy, endocrine therapy, immunotherapy, radiotherapy and surgery in some cases, cancer cells appear to outsmart and evade almost any method of treatment by developing drug resistance. Quinazolines are the most versatile, ubiquitous and privileged nitrogen bearing heterocyclic compounds with a wide array of biological and pharmacological applications. Most of the anti-cancer agents featuring quinazoline pharmacophore have shown promising therapeutic activity. Therefore, extensive research is underway to explore the potential of these privileged scaffolds. In this context, a molecular hybridization approach to develop hybrid drugs has become a popular tool in the field of drug discovery, especially after witnessing the successful results during the past decade. Histone deacetylases (HDACs) have emerged as an important anti-cancer target in the recent years given its role in cellular growth, gene regulation, and metabolism. Dual inhibitors, especially based on HDAC in particular, have become the center stage of current cancer drug development. Given the growing significance of dual HDAC inhibitors, in this review, we intend to compile the development of quinazoline based HDAC dual inhibitors as anti-cancer agents.     

Zinc binding in HDAC inhibitors: a DFT study

Histone deacetylases (HDACs) are attractive targets for the treatment of cancers and a variety of other diseases. Most currently studied HDAC inhibitors contain hydroxamic acids, which are potentially problematic in the development of practical drugs. DFT calculations of the binding modes and free energies of binding for a variety of other functionalities in a model active site of HDAC are described. The protonation state of hydroxamic acids in the active site and the origin of the high affinity are discussed. These results emphasize the importance of a carefully chosen pKa for zinc binding and provide guidance for the design of novel, non-hydroxamic acid HDAC inhibitors.     

Synthesis of 2-quinolinecarboxamide derivatives as potential HDAC inhibitors

Inhibition of histone deacetylase activity appears as an original and effective approach for the treatment of cancer. A series of novel quinoline-containing derivatives has been synthesized and found that some of these compounds possess nanomolar histone deacetylase inhibitory activity.     

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.     

Switching the Switch: Ligand Induced Disulfide Formation in HDAC8

Human histone deacetylase 8 is a well-recognized target for T-cell lymphoma and particularly childhood neuroblastoma. PD-404,182 was shown to be a selective covalent inhibitor of HDAC8 that forms mixed disulfides with several cysteine residues and is also able to transform thiol groups to thiocyanates. Moreover, HDAC8 was shown to be regulated by a redox switch based on the reversible formation of a disulfide bond between cysteines Cys₁₀₂ and Cys₁₅₃. This study on the distinct effects of PD-404,182 on HDAC8 reveals that this compound induces the dose-dependent formation of intramolecular disulfide bridges. Therefore, the inhibition mechanism of HDAC8 by PD-404,182 involves both, covalent modification of thiols as well as ligand mediated disulfide formation. Moreover, this study provides a deep molecular insight into the regulation mechanism of HDAC8 involving several cysteines with graduated capability to form reversible disulfide bridges.     

HDAC6选择性抑制剂WT161的合成工艺优化

本文报道了一条新的合成HDAC6选择性抑制剂WT161的路线。以辛二酸单甲酯为起始原料,经缩合、取代、还原、脱水共四步反应得到HDAC6选择性抑制剂WT161,总收率64.8%,目标产物结构均经过~1HNMR、~(13)CNMR和HRMS等确证。优化后的工艺路线原料成本低、反应条件温和、反应后处理更简单、产物收率更高,比较适合较大规模制备。     

Polysaccharide Nanoparticles Bearing HDAC Inhibitor as Nontoxic Nanocarrier for Drug Delivery

The histone deacetylase inhibitors (HDACi) are potent drugs in the treatment of inflammatory diseases and defined cancer types. However, major drawbacks of HDACi, such as valproic acid (VPA), are limited serum half‐life, side effects and the short circulation time. Thus, the immobilization of VPA in a polysaccharide matrix is used to circumvent these problems and to design a suitable nanocarrier system. Therefore, VPA is covalently attached to cellulose and dextran via esterification with degree of substitution (DS) values of up to 2.20. The resulting hydrophobic polymers are shaped to spherical nanoparticles (NPs) with hydrodynamic diameter between 138 to 221 nm and polydispersity indices from 0.064 to 0.094 by nanoprecipitation and emulsification technique. Lipase treatment of the NPs leads to in vitro release of VPA and hence to an inhibition of HDAC2 activity in a HDAC2 assay. NPs are rapidly taken up by HeLa cells and mainly localize in the cytoplasm. The NPs are hemocompatible and nontoxic as revealed by the shell‐less hen’s egg model.     

Discovery of ErbB/HDAC inhibitors by combining the core pharmacophores of HDAC inhibitor vorinostat and kinase inhibitors vandetanib,BMS-690514, neratinib,and TAK-285

By combining the core pharmacophores of HDAC inhibitor vorinostat and kinase inhibitors vandetanib, BMS-690514, neratinib, and TAK-285 with 1,2,3-triazole as linker, eight novel 6-substituted-4- aminoquinazolin derivatives were synthesized and characterized by ¹H NMR, ¹³C NMR, and high resolution mass spectrometry. Their inhibitory activities against five enzymes (VEGFR2, HER2, EGFR, HDAC1, and HDAC6) and five cancer cell lines (A549, BT-474, A431, SK-BR-3, and NCI-H1975) were evaluated. The bioassay results show that the introduction of triazole linked vorinostat-like segment dramatically changed the selectivity profiles of newly synthetic compounds relative to vandetanib, BMS- 690514, neratinib, and TAK-285. Among them, compound 6b exerted outstanding enzymatic and cellular activities through its simultaneous and synergistic inhibitions on multiple pathways, which might have the great potential to confer the better benefits than single-targeted inhibitors in cancer therapy.     

Prediction of pH-dependent aqueous solubility of Histone Deacetylase (HDAC) inhibitors

Recently we developed a model for prediction of pH-dependent aqueous solubility of drugs and drug like molecules. In the present work, the model was applied on a series of novel Histone Deacetylases (HDAC) inhibitors discovered at TopoTarget. The applicability of our model was evaluated on the series of HDAC inhibitors by use of Self-Organizing Maps (SOM) and 2D-projection of the HDAC inhibitors on the chemical space of the training data set of the artificial neural network (ANN) module. The model was refined for the particular chemical space of interest, which led to two modifications in the training data set of the ANN. The performance of the original and the two modified versions of the model were evaluated against the commercial software from Simulations-plus and pH-dependent solubility measurements for representative compounds of the series. The results of the evaluation indicate that one can develop models that are more accurate in predicting differences in the solubility of structurally very similar compounds than models that have been trained on structurally unbiased, diverse data sets. Such 'tailor-made' models have the potential to become trustworthy enough to replace time-consuming and expensive medium- and high-throughput solubility experiments by providing results of similar or even better quality.     

A solid-phase total synthesis of the cyclic depsipeptide HDAC inhibitor spiruchostatin A

Spiruchostatin A, a potent histone deacetylase inhibitor, was efficiently synthesized from (3S,4R)-4-amino-3-hydroxy-5-methylhexanoic acid utilizing solid-phase peptide elongation with d-cysteine, d-alanine, and (E)-3-hydroxy-7-thio-4-heptenoic acid and solution-phase macrolactonization, followed by intramolecular disulfide formation.     

Syntheses of amamistatin fragments and determination of their HDAC and antitumor activity

[reaction: see text] Amamistatins A and B are natural products found to have anti-proliferative effects against MCF-7, A549, and MKN45 human tumor cell lines (IC50 0.24-0.56 microM). It was proposed that their activity was due to histone deacetylase (HDAC) inhibition mediated by the N-formyl-N-hydroxy lysine moiety. Amamistatin B fragment analogs were synthesized and screened for biological activity. These compounds were modest HDAC inhibitors and showed antitumor activity against MCF-7 and PC-3 human tumor cells.