布洛芬衍生物的合成及抗炎镇痛活性

基于环氧合酶-2(COX-2)与COX-1结构上的差异, 设计了在布洛芬苯环3位引入取代苯甲酰胺基的系列化合物, 以期利用COX-2的侧面口袋, 增加对COX-2的结合作用. 以布洛芬为原料经五步反应合成12个目标化合物, 其结构经核磁共振氢谱、质谱和元素分析(或高分辨质谱)确证. 体外筛选结果表明, 化合物有一定的COX-2抑制活性; 对化合物7g和7h进行了体内实验, 结果表明抗炎活性弱, 但镇痛活性比较强.     

HIV-1蛋白酶与抑制剂作用的结合自由能计算

HIV-1蛋白酶是治疗艾滋病的重要靶标酶之一. 采用分子动力学模拟, 运用MM-PBSA方法计算了HIV-1蛋白酶与三个抑制剂BE4, BE5和BE6的结合自由能, 结果表明抑制剂P₁/ 位置的苄基上双氟原子的不同位置对结合自由能产生不同的影响. 通过能量分解的方法考察了HIV-1蛋白酶的主要残基与三个抑制剂间的相互作用与识别, 结果表明三个抑制剂以相同的作用模式与HIV-1蛋白酶结合, 计算结果与实验结果基本吻合.     

Hydroxamate类抑制剂与MMP-3的结合自由能的计算

用自由能微扰方法(FEP)计算了两种hydroxamate类的抑制剂和MMP-3的相对结合自由能。在计算中,对于催化区的锌离子与其共价结合的配体(包括抑制和组氨酸)采用了键合的模型,抑制剂和周围配体的部分电荷的计算采用两步静电势收敛方法。自由能计算采用了慢增长(Slowgrowth)和固定窗口增长(Fixedwidthwindowgrowth)两种方法,并且在每次计算中都采用了双向采样(Double-widesampling)的策略。两种方法计算得到的相对结合自由能都能和实验值很好的符合。同时从动力学模拟的得到的分子轨迹得到了抑制剂和受体之间相互作用模式,抑制剂的P1部分可以和受体的S1'口袋形成很强范德华和疏水相互作用,P1上的苯环可以和Tyr223上的苯环形成较好的π键堆积相互作用。     

萘普生噻唑衍生物的设计和合成及其环氧合酶-2抑制活性的体外评价

基于环氧合酶-2 (COX-2)与COX-1结构上的差异, 设计了萘普生的噻唑衍生物, 以期利用COX-2的侧面口袋, 增加对COX-2的结合作用. 以萘普生为原料经四步反应合成7个目标化合物, 其结构经核磁共振氢谱、质谱和元素分析(或高分辨质谱)确证. 体外筛选结果表明, 化合物有一定的COX-2抑制活性.     

机器学习方法用于选择性环氧化酶-2抑制剂活性预测模型的建立

与传统的非甾体类消炎药相比,选择性环氧化酶-2抑制剂具有无胃肠道粘膜损伤,溃疡和肾功能障碍等严重的副作用,设计选择性环氧化酶-2抑制剂具有重要意义。本文用支持矢量学习机和神经网络两种机器学习方法建立选择性环氧化酶-2抑制剂的活性预测模型,以期为选择性环氧化酶-2抑制剂药物的合成提供先导化合物。我们将467个环氧化酶-2抑制剂用Kennard-Stone方法分为训练集,验证集和独立测试集,对每一抑制剂分子我们计算了463个包含组成描述符和拓扑描述符的分子描述符来表征其分子结构,并通过F-Score方法选取最重要的分子描述符用于分类模型的建立。结果表明,SVM方法通过变量筛选后具有很好的预测能力,其预测正确率达到93.30%。     

CDK2-抑制剂结合自由能计算

细胞周期蛋白依赖性激酶Ⅱ(cyclin-dependent kinase 2,CDK2)是一种重要的治疗癌症的靶标.本文中采用分子动力学取样,运用MM-PBSA/GBSA两种方法计算了CDK2-NU6102复合物的绝对结合自由能.通过能量分解的方法考察了CDK2大分子主要残基与配体NU6102之间的相互作用和识别.     

FKBP12蛋白与其抑制剂结合的分子动力学模拟和结合自由能计算

FKBP12 (FK506-binding protein-12)是一种具有神经保护和促神经再生作用的蛋白. 采用分子动力学模拟取样, 运用MM-GBSA方法计算了FKBP12和3个抑制剂(GPI-1046, 308和107)的绝对结合自由能, GPI-1046的结合能最小, 308小于107的结合能. 通过能量分解的方法考察了FKBP12蛋白的主要残基与抑制剂之间的相互作用和识别, 计算结果表明: 3个抑制剂具有相似的结合模式, Ile56和Tyr82主要表现为氢键作用, Tyr26, Phe46, Val55, Ile56, Trp59, Tyr82, Tyr87和Phe99形成疏水作用区. 计算结果和实验结果吻合.     

环氧合酶－2抑制剂的三维定量构效关系研究

建立三环系COX－1和COX－2抑制剂结构与活性的三维定量构效关系模型，为设 计新型的具有选择性的COX－2抑制剂提供线索。通过与酶的对接并优化，确定化合 物在受体结合腔中的构象，利用比较分子力场分析方法建立三维定量构效关系模型 。模型1R_(cv)~2=0.685，最佳主成分数为6，传统相关系数为R~2=0.988, F-726. 2，标准偏差S = 0.080；模型2 R_(cv)~2 = 0.573，最佳主成分数为6，传统相关 系数为R~2=0.996, F = 1147.6，标准偏差S = 0.034。所得的模型不仅解释了化合 物的构效关系，而且对预测集中的化合物有很好的预测能力；比较不同模型的系数 相关图，分析了结构与活性、结构与选择性的关系，得到的结果可以指导新化合物 的设计与合成。     

激酶ABL与肉豆蔻酰位点小分子作用机理的分子动力学模拟及自由能计算

采用分子动力学方法研究激酶ABL 与ATP 位点小分子imatinib、P16 及变构位点小分子STJ、MS7、MS9、3YY、MYR等的结合, 并用GBSA (generalized Born surface area)方法将结合自由能分解到各残基. 自由能计算结果表明, 小分子STJ、MS7、MS9 有利于imatinib 与ABL 结合; 小分子STJ、MS7、MS9 与激酶ABL的结合自由能接近, 绝对值均大于ABL 与3YY、MYR 的结合自由能. 能量分解表明, ABL 残基ILE502、VAL506、LEU510与STJ和MYR的相互作用是αI 螺旋处于弯曲状态的重要原因. 模拟过程中ABL肉豆蔻酰口袋残基均方根偏差(RMSD)变化值表明, STJ等小分子抑制剂与ABL结合后降低了肉豆蔻酰口袋残基的柔性.     

抑制剂对大肠杆菌作用的透射电镜及微量热法研究

用透射电镜对大肠杆菌以及大肠杆菌受到３种不同抑制剂抑制时的形态进行了观察，结果发现不同的抑制剂对大肠杆菌的不同抑制作用表现在大肠杆菌的微观形态发生了不同的变化，同时结合微量热的方法，测试了３种不同抑制剂作用下大肠杆菌的生长代谢热谱，热谱曲线的分析结果与透射电镜观察结果吻合。     

Activity-Guided Characterization of COX-2 Inhibitory Compounds in Waltheria indica L. Extracts

Inflammation is the body’s response to infection or tissue injury in order to restore and maintain homeostasis. Prostaglandin E2 (PGE-2) derived from arachidonic acid (AA), via up-regulation of cyclooxygenase-2 (COX-2), is a key mediator of inflammation and can also be induced by several other factors including stress, chromosomal aberration, or environmental factors. Targeting prostaglandin production by inhibiting COX-2 is hence relevant for the successful resolution of inflammation. Waltheria indica L. is a traditional medicinal plant whose extracts have demonstrated COX-2 inhibitory properties. However, the compounds responsible for the activity remained unknown. For the preparation of extracts with effective anti-inflammatory properties, characterization of these substances is vital. In this work, we aimed to address this issue by characterizing the substances responsible for the COX-2 inhibitory activity in the extracts and generating prediction models to quantify the COX-2 inhibitory activity without biological testing. For this purpose, an extract was separated into fractions by means of centrifugal partition chromatography (CPC). The inhibitory potential of the fractions and extracts against the COX-2 enzyme was determined using a fluorometric COX-2 inhibition assay. The characterizations of compounds in the fractions with the highest COX-2 inhibitory activity were conducted by high resolution mass spectrometry (HPLC-MS/MS). It was found that these fractions contain alpha-linolenic acid, linoleic acid and oleic acid, identified and reported for the first time in Waltheria indica leaf extracts. After analyzing their contents in different Waltheria indica extracts, it could be demonstrated that these fatty acids are responsible for up to 41% of the COX-2 inhibition observed with Waltheria indica extract. Additional quantification of secondary metabolites in the extract fractions revealed that substances from the group of steroidal saponins and triterpenoid saponins also contribute to the COX-2 inhibitory activity. Based on the content of compounds contributing to COX-2 inhibition, two mathematical models were successfully developed, both of which had a root mean square error (RMSE) = 1.6% COX-2 inhibitory activity, demonstrating a high correspondence between predicted versus observed values. The results of the predictive models further suggested that the compounds contribute to COX-2 inhibition in the order linoleic acid > alpha linolenic acid > steroidal saponins > triterpenoid saponins. The characterization of substances contributing to COX-2 inhibition in this study enables a more targeted development of extraction processes to obtain Waltheria indica extracts with superior anti-inflammatory properties.     

Flavonoids: Antiplatelet Effect as Inhibitors of COX-1

Flavonoids are compounds with a benzopyranic structure that exhibits multiple pharmacological activities. They are known for their venotonic activity, but their mechanism of action remains unclear. It is thought that, as this mechanism is mediated by prostaglandins, these compounds may interfere with the arachidonic acid (AA) cascade. These assays are designed to measure the antiplatelet aggregation capacity of quercetin, rutin, diosmetin, diosmin, and hidrosmin, as well as to evaluate a potential structure−activity ratio. In this paper, several studies on platelet aggregation at different concentrations (from 0.33 mM to 1.5 mM) of different flavone compounds are conducted, measuring platelet aggregation by impedance aggregometry, and the cyclooxygenase (COX) activity by metabolites generated, including the activity of the pure recombinant enzyme in the presence of these polyphenols. The results obtained showed that quercetin and diosmetin aglycones have a greater antiplatelet effect and inhibit the COX enzyme activity to a greater extent than their heterosides; however, the fact that greater inhibition of the pure recombinant enzyme was achieved by heterosides suggests that these compounds may have difficulty in crossing biological membranes. In any case, in view of the results obtained, it can be concluded that flavonoids could be useful as coadjuvants in the treatment of cardiovascular pathologies.     

Crystallography,Molecular Modeling,and COX-2 Inhibition Studies on Indolizine Derivatives

The cyclooxygenase-2 (COX-2) enzyme is an important target for drug discovery and development of novel anti-inflammatory agents. Selective COX-2 inhibitors have the advantage of reduced side-effects, which result from COX-1 inhibition that is usually observed with nonselective COX inhibitors. In this study, the design and synthesis of a new series of 7-methoxy indolizines as bioisostere indomethacin analogues (5a–e) were carried out and evaluated for COX-2 enzyme inhibition. All the compounds showed activity in micromolar ranges, and the compound diethyl 3-(4-cyanobenzoyl)-7-methoxyindolizine-1,2-dicarboxylate (5a) emerged as a promising COX-2 inhibitor with an IC₅₀ of 5.84 µM, as compared to indomethacin (IC₅₀ = 6.84 µM). The molecular modeling study of indolizines indicated that hydrophobic interactions were the major contribution to COX-2 inhibition. The title compound diethyl 3-(4-bromobenzoyl)-7-methoxyindolizine-1,2-dicarboxylate (5c) was subjected for single-crystal X-ray studies, Hirshfeld surface analysis, and energy framework calculations. The X-ray diffraction analysis showed that the molecule (5c) crystallizes in the monoclinic crystal system with space group P 2₁/n with a = 12.0497(6)Å, b = 17.8324(10)Å, c = 19.6052(11)Å, α = 90.000°, β = 100.372(1)°, γ = 90.000°, and V = 4143.8(4)ų. In addition, with the help of Crystal Explorer software program using the B3LYP/6-31G(d, p) basis set, the theoretical calculation of the interaction and graphical representation of energy value was measured in the form of the energy framework in terms of coulombic, dispersion, and total energy.     

A comparative study of the COX-1 and COX-2 isozymes bound to lipid membranes

The monotopic proteins COX-1 and -2 in dimeric form bound to lipid bilayer membranes are studied using molecular dynamics simulations within an aqueous environment. The 25-ns simulations are performed for both isozymes with arachidonic acid bound in the cyclooxygenase sites. The interactions between the enzymes and the lipids are analyzed, providing insight into the attachment mechanism of monotopic proteins to membranes. Our study reveals some key differences between the two isozymes that include the orientations at which they sit on the surface of the membranes and the depths to which they embed within the membranes. The differences in membrane association of the isozymes indicate that they may integrate distinctively with the same membrane, and/or with different membranes or their lipid components. Our results indicate that arachidonic acid can be bound in the cyclooxygenase active site in distinct catalytically competent conformations that lead to certain hydroperoxy acids; and the arachidonic acid and/or cyclooxygenase sites undergo a conformational change which makes only one subunit of each homodimer catalytically active.     

苯并咪唑类缓蚀剂的3D-QSAR研究及分子设计

采用比较分子场分析法(CoMFA)和比较分子相似性指数分析法(CoMSIA), 对苯并咪唑衍生物抗盐酸腐蚀的缓蚀性能进行了三维定量构效关系研究, 并使用留一法交叉验证手段对3D-QSAR模型的稳定性及预测能力进行了分析. 结果表明, 立体场、静电场和氢键供体场(电子给体)是影响苯并咪唑缓蚀剂缓蚀性能的主要因素; 所构建的CoMFA模型(q2=0.541, R2=0.996)和CoMSIA模型(q2=0.581, R2=0.987)均具有较好的统计学稳定性和预测能力. 基于3D-QSAR等势图设计出了几种具有较好缓蚀性能的苯并咪唑化合物, 为油气田新型缓蚀剂的研发提供了一种新思路.     

有机化合物血卟啉及其衍生物被物理因素--超声激活机理研究

利用1,3-二苯基异苯并呋喃(DPBF)作为单线态氧捕获剂,研究了超声激活血卟啉的机理,通过用紫外-可见分光光度计测量了超声辐照配制好的血卟啉和DPBF溶液后的DPBF相对消耗量,表明了单线态氧的存在量．实验结果显示了DPBF的消耗量随超声照射时间和强度的增加而增加．从而支持了超声激活血卟啉产生单线态氧的说法．并提出了采用各向同性集光球把声致发光和声场分开的方法,进一步研究了是超声空化产生的荧光,还是高温热点激活血卟啉产生单线态氧．与白光对比结果表明,声致发光虽能使照相底版感光,但不足以激活血卟啉产生单线态氧．