多维定量构效关系及药物分子设计研究进展

本文介绍并综述超分子化学，多维定量构效关系及药物分子设计的发展概况与研究进展，为新药创制和医药工业提供了有用信息。     

3C-like蛋白酶抑制剂的构效关系、分子对接和分子动力学

3C-like蛋白酶是中东呼吸综合征冠状病毒（MERS-CoV）等其它冠状病毒的繁殖过程中极为重要的蛋白酶。它已成为人类在抗冠状病毒领域中的研究热点。本文基于计算生物学方法对与MERS-CoV同属的蝙蝠冠状病毒HKU4（HKU4-CoV）的43个肽类3C-like蛋白酶抑制剂分子,建立三维定量构效关系（3D-QSAR）模型。在基于配体叠合的基础上,发现比较分子相似性指数分析法（CoMSIA）中的四个场组合（位阻场、静电场、氢键供体场与氢键受体场）为最优的模型（Q²=0.522,R_ncv²=0.996,R_pre²=0.904;Q²：交叉验证相关系数,R_ncv²：非交叉验证相关系数,R_pre²：验证集分子的预测值相关系数）,并借助该模型通过分子对接（docking）与分子动力学（MD）方法阐明了配受体结合作用。实验结果表明：（1）基于最优的CoMSIA模型基础上的三维等势图形象地说明了分子基团的位阻作用、静电作用、氢键供体与氢键受体作用对分子生物活性的影响;（2）分子对接研究结果显示了疏水性以及结晶水、氨基酸His166和Glu169在配体和受体结合过程中产生重要作用;（3）分子动力学模拟进一步验证了分子对接模型的可靠性,并发现了两个新的关键氨基酸Ser24与Gln192,它们与配体产生了两个较强的氢键。此外,根据这些结果,一些新的具有潜在抑制活性的肽类化合物作为3C-like蛋白酶抑制剂被获得。以上结果能够帮助深入了解3C-like蛋白酶与肽类抑制剂的作用机理,并且能够为今后的抗MERS-CoV药物设计提供有价值的参考。     

磷酸二酯酶4b抑制剂定量构效关系及分子对接研究

磷酸二酯酶4(PDE4)是第二信使环磷酸腺苷(cAMP)选择性高亲和力的水解酶,影响气道平滑肌、炎性细胞和免疫细胞的功能,选择性PDE4b抑制剂作为抗炎药治疗哮喘和慢性阻塞性肺病(COPD)因为不会引起恶心呕吐等副反应而受到极大的关注。本文使用比较分子场(CoMFA)方法,对系列嘧啶二芳基取代的PDE4b抑制剂构建了合理的三维定量构效关系(3D-QSAR)模型,使用分子对接方法研究了抑制剂与酶的相互作用,发现该系列化合物的嘧啶环2位引入带有较大电负性基团取代的五元环状烃基可提升活性;嘧啶环4位、5位两个碳原子上建议保留小体积取代基;嘧啶环6位引入带有氢键给体或氢键受体取代的芳烃基可增加化合物活性。本研究可为后续合理设计高效的PDE4b抑制剂提供理论指导。     

分子距边矢量研究链烃与醛酮的定量构效关系

按碳原子及键合特性分类定义并计算了链烃包括烷、烯,炔,双烯,烯炔烃的分子距离－边数矢量（ＭＤＥ）,将１５３个链烃的ＭＤＥ矢量与相应的沸点相关联,得到良好的线性模型,复相关系数Ｒ＝０．９９７６,均方根误差０．９９７５、ＲＭＳ＝４．７２Ｋ和Ｒ＝０．９９７２、ＲＭＳ＝５．１３Ｋ。结果表明模型具有良好的稳定性和预测能力。进一步对杂原用染色因子进行标识,提出了一种适用于含杂原子体系分子结构描述的ＭＤＥ矢量,     

ALS抑制剂合理分子设计的研究进展

以乙酰乳酸合成酶为靶标合理设计开发新型超高效除草剂是当前除草剂化学研究中的重要领域。结合本课题组的研究工作,从ALS抑制剂的结构特征、分子力学与量子化学研究、定量构效关系(QSAR)与三维定量构效关系(3D-QSAR)研究、非线性QSAR研究以及新型除草剂的分子设计等几个方面对该领域的研究现状进行了总结报道,并对该领域的发展前景及存在的问题进行了展望。     

咪唑啉衍生物缓蚀剂的定量构效关系及分子设计

采用量子化学密度泛函理论(DFT)及线性回归分析方法, 对十一烷基咪唑啉衍生物缓蚀剂抗H2S、CO2腐蚀性能进行了定量构效关系(QSAR)研究. 通过回归分析, 筛选出了影响缓蚀剂缓蚀性能的主要因素, 建立了QSAR模型, 并使用留一法交叉验证对模型的稳定性及预测能力进行了分析. 结果表明, 电子转移参数△N、咪唑环上非氢原子静电荷之和∑Qring及分子极化率α对咪唑啉类缓蚀剂的缓蚀性能有很大的贡献, 所得模型的拟合相关系数(R2)和交叉验证相关系数(q2)分别为0.924 和0.917, 模型对此类缓蚀剂抗H2S、CO2腐蚀性能具有较好的预测效果. 应用QSAR研究结果进行了分子设计, 在理论上提出了一些具有较高抗H2S、CO2腐蚀性能的新型咪唑啉衍生物, 为实验工作者合成新型缓蚀剂提供理论参考.     

多肽定量构效关系与分子设计

综述了多肽定量构效关系和计算机辅助多肽分子设计方法的最新进展,重点介绍了多肽定量构效关系研究中的化学结构定量描述符和建立数学模型的统计方法,并对模拟肽学和虚拟组合多肽库在多肽分子设计中的应用进行了简要的论述.     

基于药效团模型的DHODH抑制剂构效关系研究

利用药效团模型研究二氢乳清酸脱氢酶(Dihydroorotate dehydrogenase,DHODH)抑制剂的构效关系,为DHODH抑制剂的虚拟筛选提供新的方法.以31个具有DHODH抑制活性的化合物为训练集化合物,半数抑制浓度(IC50)范围为7~63000 nmol/L,利用Catalyst/HypoGen算法构建DHODH抑制剂药效团模型,通过对训练集化合物多个构象进行叠合,提取药效团特征及三维空间限制构建药效团模型.利用基于CatScramble的交叉验证方法及评价模型对已知活性化合物的活性预测能力,确定较优药效团模型.模型包含1个氢键受体、3个疏水中心,表征了受体配体相互作用时可能发生的氢键相互作用、疏水相互作用和π-π相互作用,4个药效特征在三维空间的排列概括了DHODH抑制剂产生活性的结构特点.所得较优模型对训练集化合物及测试集化合物的计算活性值与实验活性值的相关系数分别为0.8405和0.8788.利用药效团模型对来源于微生物的系列化合物进行虚拟筛选,筛选出59个预测活性较好的化合物,可作为进一步药物研发的候选化合物.     

α-芋螺毒素构效关系与分子设计

α-芋螺毒素(α-conotoxins)是从芋螺毒液中提取到的一类活性多肽. 与其它家族的芋螺毒素相比, 它们含二硫键少, 结构相对简单, 由于作用于神经肌肉接头的N-乙酰胆碱受体(nAChRs)的不同亚型, 拮抗乙酰胆碱, 可作为鉴定nAChRs亚型及其亚基的有效工具, 已成为芋螺毒素结构改造的最佳先导化合物. 利用HyperChem软件包的量子化学半经验方法AM1对8个具有代表性的α-芋螺毒素进行了量子化学计算, 研究了它们的电子结构及构效关系. 结果表明, 空间结构的相似性使它们作用于同一受体, 局部结构差异而导致的电子结构的较大差别是它们能作用于不同受体亚型的重要原因. 在此基础上, 以α-芋螺毒素GI为模型设计了7个类似物并进行了量子化学计算, 比较了类似物与GI在空间结构及电子结构方面的特征.     

Structure-activity relationships of dopamine- and norepinephrine-uptake inhibitors

Quantitative structure-activity relationship (QSAR) analysis of 3-phenyl-1-indanamines, 1-amino-4-aryltetralins, and 6-phenylpyrrolo[2,1-a] isoquinolines has been performed for catecholamine-uptake inhibition activities. Similar equations were obtained for these series of congeners indicating a common tendency that the increase in hydrophobicity of the substituents on the primary phenyl ring (ring C) enhances the activity, and the important aromatic ring which interacts with the receptor is this ring C. It was also indicated that the effect of the introduction of the second N-methyl group differs depending on the series of congeners. These results were used to characterize a binding model for a pharmacophore, which comprised a phenyl ring and a basic nitrogen. This model defined the necessary three-dimensional features leading to the uptake inhibition, and degree of fitness with this model predicted the strength of the activity. Furthermore, it appeared likely that a substituent existing in a specific region of the inhibitor molecule causes a steric hindrance with the receptor site and reduces the activity.     

Discovery of Novel Epoxyketone Peptides as Lipase Inhibitors

Obesity is the most common nutritional disorder in the developed world and is associated with important comorbidities. Pancreatic lipase (PL) inhibitors play a key role in the metabolism of human fat. A series of novel epoxyketones peptide derivatives were investigated for their pancreatic lipase inhibitory activity. The epoxyketone moiety is a well-known reactive electrophile group that has been used as part of proteasome inhibitors in cancer therapy, and it is widely believed that these are very selective for targeting the proteasome active site. Here we investigated various peptide derivatives with an epoxide warhead for their anti-lipase activity. The assessment of these novel epoxyketones was performed by an in-house method that we developed for rapid screening and identification of lipase inhibitors using GC-FID. Herein, we present a novel anti-lipase pharmacophore based on epoxyketone peptide derivatives that showed potent anti-lipase activity. Many of these derivatives had comparable or more potent activity than the clinically used lipase inhibitors such as orlistat. In addition, the lipase appears to be inhibited by a wide range of epoxyketone analogues regardless of the configuration of the epoxide in the epoxyketone moiety. The presented data in this study shows the first example of the use of epoxyketone peptides as novel lipase inhibitors.     

马来酰亚胺类GSK-3β抑制剂的QSAR研究及分子设计

为了研究马来酰亚胺类化合物抑制活性与分子结构的定量构效关系,在分子理论的基础上计算了67个马来酰亚胺类化合物的电性距离矢量,通过最佳变量子集回归的方法,建立了抑制活性的五元线性回归模型,模型的传统相关系数(R2)和交叉验证相关系数(RCV2)分别为0.864和0.825.该模型经过Jackknife法检验、交叉验证、F检验及外部检验法证明具有良好的稳健性和预测能力.根据进入模型的5个变量分析,影响马来酰亚胺类GSK-3β抑制剂抑制活性的主要结构基团是-NH-,=O(或-OH),≡CH,Cl-及-O-(或-S-).同时基于QSAR模型设计了6个抑制活性显著提高的马来酰亚胺类分子,并预测了它们的抑制活性.     

5,6-二氢-(9H)-吡唑[3,4-c]-1,2,4-三唑[4,3-a]吡啶类抑制剂的HQSAR研究

应用分子全息定量构效关系(HQSAR)分析方法,以5,6-二氢-(9H)-吡唑[3,4-c]-1,2,4-三唑[4,3-a]吡啶类抑制剂为研究对象,建立了一组对磷酸二酯酶4有抑制活性的化合物HQSAR模型,分析化合物活性与分子结构之间的关系.探讨了分子全息长度、分子碎片大小以及碎片区分参数对模型质量的影响.最优模型的交叉验证相关系数q2=0.628,非交叉验证相关系数r2=0.930,标准偏差SE=0.277.该模型具有较好的预测能力,对该类化合物性质的预测及进一步合成工作有指导意义.     

Expanding molecular modeling and design tools to non‐natural sidechains

Protein–protein interactions encode the wiring diagram of cellular signaling pathways and their deregulations underlie a variety of diseases, such as cancer. Inhibiting protein–protein interactions with peptide derivatives is a promising way to develop new biological and therapeutic tools. Here, we develop a general framework to computationally handle hundreds of non‐natural amino acid sidechains and predict the effect of inserting them into peptides or proteins. We first generate all structural files (pdb and mol2), as well as parameters and topologies for standard molecular mechanics software (CHARMM and Gromacs). Accurate predictions of rotamer probabilities are provided using a novel combined knowledge and physics based strategy. Non‐natural sidechains are useful to increase peptide ligand binding affinity. Our results obtained on non‐natural mutants of a BCL9 peptide targeting beta‐catenin show very good correlation between predicted and experimental binding free‐energies, indicating that such predictions can be used to design new inhibitors. Data generated in this work, as well as PyMOL and UCSF Chimera plug‐ins for user‐friendly visualization of non‐natural sidechains, are all available at http://www.swisssidechain.ch . Our results enable researchers to rapidly and efficiently work with hundreds of non‐natural sidechains. © 2012 Wiley Periodicals, Inc.     

In silico study directed towards identification of the key structural features of GyrB inhibitors targeting MTB DNA gyrase: HQSAR,CoMSIA and molecular dynamics simulations

ABSTRACT

Mycobacterium tuberculosis DNA gyrase subunit B (GyrB) has been identified as a promising target for rational drug design against fluoroquinolone drug-resistant tuberculosis. In this study, we attempted to identify the key structural feature for highly potent GyrB inhibitors through 2D-QSAR using HQSAR, 3D-QSAR using CoMSIA and molecular dynamics (MD) simulations approaches on a series of thiazole urea core derivatives. The best HQSAR and CoMSIA models based on IC₅₀ and MIC displayed the structural basis required for good activity against both GyrB enzyme and mycobacterial cell. MD simulations and binding free energy analysis using MM-GBSA and waterswap calculations revealed that the urea core of inhibitors has the strongest interaction with Asp79 via hydrogen bond interactions. In addition, cation-pi interaction and hydrophobic interactions of the R₂ substituent with Arg82 and Arg141 help to enhance the binding affinity in the GyrB ATPase binding site. Thus, the present study provides crucial structural features and a structural concept for rational design of novel DNA gyrase inhibitors with improved biological activities against both enzyme and mycobacterial cell, and with good pharmacokinetic properties and drug safety profiles.     

双光子吸收材料的分子设计研究

介绍了双光子吸收材料分子设计原理.为了设计有大的双光子吸收响应的材料,对多种分子进行了系统的理论研究.用量子化学密度泛函理论和AM1方法进行分子几何构型优化.在优化结构的基础上,用ZINDO和自编程序求得分子的单、双光子吸收性质.设计了一些未知化合物,以期为合成新的具有大的双光子吸收截面的材料提供理论根据.以双层二聚二甲苯邻甲酸衍生物、铂乙炔化物、卟啉衍生物、C60、C70、八极矩分子为例,报道了我们在这方面的研究结果.