3D-QSAR of Benzothiazole Derivatives as Potent Anticancer Agents

Comparative molecular field analysis (CoMFA) method was applied to study three-dimensional quantitative structure activity relationship (3D-QSAR) of a series of benzothiazole derivatives as potent anticancer agents. The CoMFA model of cross-validation and the partial-least-square (PLS) model of non cross-validation have been well established. The best CoMFA model gives a good cross-validation coe±cient of 0.642 and a conventional correlation coe±cient of 0.976. Moreover, the estimated standard error is 0.161 and the statistical square deviation ratio F(3;20) is 111.4. The statistical parameters of the best CoMFA model show this model is reasonable and has predictive ability. The CoMFA results suggest that an electron-withdrawing group or atom (e.g. F atom) linking to the first atom (C19) of substituent R can increase the positive charges of C19 and its fi-site atoms, which lie in the blue-colored regions in the electrostatic field contour map of CoMFA, and thus can improve the activity of the compound. Meanwhile, selecting an R with an appropriatevolume is also advantageous for improving the activity.     

3D-QSAR Studies on 3-Substituted N-Benzhydryl-nortropane Analogs as Nociception Receptor Agonists

The nociceptin receptor(NOP) has been involved in multiple biological functions, including pain, anxiety, cough, substance abuse, cardiovascular control, and immunity. Thus, selective NOP agonists might have clinical potential for the treatment of related diseases. In the present work, three-dimensional quantitative structure-activity relationship(3D-QSAR) studies were performed on a series of 3-substituted N-benzhydryl-nortropane analogs as NOP agonists using comparative molecular field analysis(Co MFA) and comparative molecular similarity indices analysis(CoM SIA) techniques. The statistically significant models were obtained with 54 compounds in training set by ligand-based atom-by-atom matching alignment. The CoM FA model gave cross-validated coefficient(q2) value of 0.530 using 6 components, non-cross-validated(r2) value of 0.921 with estimated F value of 93.668, and standard error of estimate(SEE) of 0.185. The best Co MSIA model resulted in q2 = 0.592, r2 = 0.945, N = 10, SEE = 0.162, and F = 75.654, based on steric, electrostatic, hydrophobic and hydrogen bond acceptor fields. The predictive ability of the Co MFA and CoM SIA models was further validated using a test set of 18 molecules that were not included in the training set, which resulted in predictive correlation coefficients(r2pred) of 0.551 and 0.637, respectively. Moreover, the CoM FA and CoM SIA contour maps identified the features important for exhibiting potent binding affinities on NOP, and can thus serve as a useful guide for the design of potential NOP agonists.     

雪花胺类化合物的三维构效关系研究

雪花胺是一类重要的乙酰胆碱脂酶抑制剂，有可能发展成治疗阿尔茨海默病的药物. 利用分子力学计算得到了这类化合物的优势构象，并对这些化合物进行了CoMFA研究．发现，对于雪花胺类化合物，影响其药效的主要因素是空间结构，电荷作用力的影响较小．对空间因素的进一步分析发现，对于该类分子，不宜用空阻较大的基团进行取代．由电荷影响的分析得到了在不同位置上取代基所应有的电荷性质．三维定量构效关系研究为基于雪花胺的抑制剂设计提供了方案．     

3D-QSAR Studies of the Pteridine Analogues as iNOS Inhibitors

Inducible nitric oxide synthase(iNOS), which can produce nitric oxide(NO) in the induction of cytokines and other factors, has an important impact onthe physiological functions of the body for the transmission of information. However,continuous generation of NOwill produce a lot of great damages to organisms. Therefore, iNOS inhibitors with good inhibitory activity and selectivity have beenimportant means of treating a variety of diseases. Based on the public-alignment of pteridine, 3D-QSAR(Three-Dimensional Quantitative Structure-Activity Relationship) models of pteridine analogues as iNOS inhibitors were established by the 3D-QSAR protocol of Discovery Studio 3.0. Pteridine molecules divided in different groups obtained four approximate models, indicating good stability of such models, in which A3 is preferable(q~2 = 0.672, r~2 = 0.996, r_(pred)~2 . = 0.888, q~2 denotes the cross-validation coefficient, r~2 denotes the non-cross-validation coefficient). This study should be significant for the future structure design and modification of pteridine analogues as iNOS inhibitors.     

3-氨磺酰苯甲酸类AKR1C3抑制剂的3D-QSAR和分子对接研究

醛酮还原酶1C3(AKR1C3)作为治疗前列腺癌的新靶点已成为研究热点,3-氨磺酰苯甲酸衍生物对其具有高效的选择性和抑制活性。本文采用比较分子场分析(COMFA)和比较分子相似性指数分析(COMSIA)方法,将经分子对接后的34个优势构象组成训练集和11个优势构象组成测试集,构建三维定量构效关系(3D-QSAR)模型。COMFA模型的交叉验证系数(q2),非交叉验证系数(R2),标准偏差(SEE)和F值分别为0.761,0.973,0.122,185.963;自举法回归系数为R2bs=0.98。最佳组合COMSIA模型的q2,R2,SEE,F和R2bs分别为0.734,0.984,0.097,147.850,0.994。COMFA和COMSIA模型的系统外部测试R2pred分别为0.864和0.756,r2m分别为0.8127和0.5377。这些结果表明,所建立的QSAR模型具有较高的可靠性和较强预测能力。经三维等势图分析可知,在2、5或6位适当增加取代基体积,或在5位引入氢键受体,或在7位引入负电性取代基则能提高化合物的生物活性。该模型为进一步设计具有更优选择性和活性的化合物提供了理论依据。     

3-(Methoxycarbonyl)thiophene Thiourea Derivatives as Potential Potent Bacterial Acetyl-CoA Carboxylase Inhibitors

Russian Journal of Organic Chemistry - Novel thiourea derivatives containing a 3-(methoxycarbonyl)thiophene pharmacophore were synthesized and tested for activity against Gram-positive (Salmonella...     

二芳基三嗪类HIV-1逆转录酶抑制剂的分子对接及3D-QSAR研究

对40个二芳基三嗪类HIV-1逆转录酶抑制剂进行了分子对接研究,结果表明,2个疏水性芳香取代基团与结合口袋底部形成的疏水和范德华相互作用、三嗪环母核及其R4取代基与结合位点产生的氢键和静电作用以及R4取代基与袋口形成的空间位阻效应是影响该系列化合物活性的重要因素.根据对接优势构象进行分子叠合和比较分子相似性指数分析(C...     

含萘三氮唑甲烷骨架的硫代乙酸类尿酸转运体1(URAT1)抑制剂的合成及其构效关系

分别以1-溴萘和酮或1-萘甲醛及有机金属试剂为原料,经12步反应合成了8个含萘三氮唑甲烷骨架的硫代乙酸类尿酸转运体1(URAT1)抑制剂(1h~1o),其结构经¹H NMR, ¹³C NMR和MS（ESI）表征。体外活性测试结果显示：对URAT1的抑制活性最强的是1k,是阳性对照药lesinurad的133倍［IC₅₀=0.054 μmol·L^-1(1k), 7.18 μmol·L^-1(lesinurad)］。     

Mucin-Inspired Single-Chain Polymer (MIP) Fibers as Potent SARS-CoV-2 Inhibitors

Mucins are the key component of the defensive mucus barrier. They are extended fibers of very high molecular weight with diverse biological functions depending strongly on their specific structural parameters. Here, we present a mucin-inspired nanostructure, produced via a synthetic methodology to prepare methacrylate-based dendronized polysulfates ( MIP-1 ) on a multi gram-scale with high molecular weight (MW=450 kDa) and thiol end-functionalized mucin-inspired polymer ( MIP ) via RAFT polymerization. Cryo-electron tomography (Cryo-ET) analysis of MIP-1 confirmed a mucin-mimetic wormlike single-chain fiber structure (length=144±59 nm) in aqueous solution. This biocompatible fiber showed promising activity against SARS-CoV-2 and its mutant strain, with a remarkable low half maximal (IC₅₀) inhibitory concentration (IC₅₀=10.0 nM). Additionally, we investigate the impact of fiber length on SARS-CoV-2 inhibition by testing other functional polymers ( MIPs ) of varying fiber lengths.     

靛玉红类CDK1抑制剂的同源模建、分子对接及3D-QSAR研究

细胞周期蛋白依赖性激酶1的异常表达会导致G2期的停滞及多种肿瘤的发生,故CDK1近年来已成为一个理想的治疗靶点. 本文以细胞分裂调控蛋白2的同源体为模板,同源模建了CDK1的结构,并与靛玉红类小分子抑制剂进行分子对接. 分别运用三种叠合方法进行分子叠合,并在此基础上采用Sybyl 7.1中的比较分子场分析(CoMFA)模块及Discovery Studio 3.0中的三维定量构效关系(3D-QSAR)模块(以下简称为DS)分别建立了3D-QSAR模型. 其中,将分子对接叠合与公共骨架叠合联合运用的叠合方法所得3D-QSAR模型的评价参数是最佳的(CoMFA：q²=0.681,r²=0.909,r_pred.²=0.836; DS：q²=0.579,r²=0.971,r_pred.²=0.795,其中q²为交叉验证系数,r²为非交叉验证系数). 本文的研究结果在对靛玉红类小分子进行结构修饰设计出新的CDK1抑制剂方面,可提供重要的理论基础.     

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.     

Pharmacophore and Docking-based 3D-QSAR Studies on HIV-1 Integrase Inhibitors

Integrase（IN） plays an essential role in the process of HIV-1 replication.IN inhibitors of diketo acid derivatives（DKAs） were analysed by the Comparative Molecular Field Analysis（CoMFA） and Comparative Molecular Similarity Induces Analysis（CoMSIA） methods.A set of 42 compounds were randomly selected as the training set（35） and test set（7）.Firstly,a good pharmacophore（goodness of hit=0.787） was obtained and used to align ligands.Then,predictive models were constructed with the CoMFA and CoMSIA methods based on the pharmacophore alignment.As a result,the CoMS1A method yielded the best model with an r2 of 0.955 and a q2 of 0.665,which can predict the activities of the tested DKAs very well（r2=0.559）.Finally,DKAs were docked into IN,and the predicit modes were superimposed on the contour maps obtained from the best CoMSIA model.The superimposed maps gave a visualized and meaningful insight into the inhibitory behaviors,providing significantly useful information for the rational drug design of anti-IN agents.     

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.     

Bioactive Phytoconstituents as Potent Inhibitors of Tyrosine-Protein Kinase Yes (YES1): Implications in Anticancer Therapeutics

Tyrosine-protein kinase Yes (YES1) belongs to the Tyrosine-protein kinase family and is involved in several biological activities, including cell survival, cell–cell adhesion, cell differentiation, and cytoskeleton remodeling. It is highly expressed in esophageal, lung, and bladder cancers, and thus considered as an attractive drug target for cancer therapy. In this study, we performed a virtual screening of phytoconstituents from the IMPPAT database to identify potential inhibitors of YES1. Initially, the molecules were retrieved on their physicochemical properties following the Lipinski rule of five. Then binding affinities calculation, PAINS filter, ADMET, and PASS analyses followed by an interaction analysis to select safe and clinically better hits. Finally, two compounds, Glabrene and Lupinisoflavone C (LIC), with appreciable affinities and a specific interaction towards the AlphaFold predicted structure of YES1, were identified. Their time-evolution analyses were carried out using an all-atom molecular dynamics (MD) simulation, principal component analysis, and free energy landscapes. Altogether, we propose that Glabrene and LIC can be further explored in clinical settings to develop anticancer therapeutics targeting YES1 kinase.     

3D-QSAR and Docking Studies of Pyrido[2,3-d]pyrimidine Derivatives as Wee1 Inhibitors

In order to investigate the inhibiting mechanism and obtain some helpful information for de-signing functional inhibitors against Wee1, three-dimensional quantitative structure-activity relationship (3D-QSAR) and docking studies have been performed on 45 pyrido[2,3-d] pyrim-idine derivatives acting as Wee1 inhibitors. Two optimal 3D-QSAR models with significant statistical quality and satisfactory predictive ability were established, including the CoMFA model (q²=0.707, R²=0.964) and CoMSIA model (q²=0.645, R²=0.972). The external val-idation indicated that both CoMFA and CoMSIA models were quite robust and had high predictive power with the predictive correlation coefficient values of 0.707 and 0.794, essen-tial parameter r²_m values of 0.792 and 0.826, the leave-one-out r²_m(LOO) values of 0.781 and 0.809, r²_m(overall) values of 0.787 and 0.810, respectively. Moreover, the appropriate binding orientations and conformations of these compounds interacting with Wee1 were revealed by the docking studies. Based on the CoMFA and CoMSIA contour maps and docking analyses, several key structural requirements of these compounds responsible for inhibitory activity were identified as follows: simultaneously introducing high electropositive groups to the sub-stituents R1 and R5 may increase the activity, the substituent R2 should be smaller bulky and higher electronegative, moderate-size and strong electron-withdrawing groups for the substituent R3 is advantageous to the activity, but the substituent X should be medium-size and hydrophilic. These theoretical results help to understand the action mechanism and design novel potential Wee1 inhibitors.     

Synthesis of Novel Tacrine Analogs as Acetylcholinesterase Inhibitors

In this work, a wide range of novel pyrazolo[4′,3′:5,6]pyrano[2,3‐b ]quinolin‐5‐amines were synthesized as tacrine analogs. At first, reaction of 3‐methyl‐1‐phenyl‐1H‐pyrazol‐5(4H )‐one, aromatic aldehydes, and malononitrile gave 6‐amino‐4‐aryl‐3‐methyl‐1‐phenyl‐1,4‐dihydropyrano[2,3‐c ]pyrazole‐5‐carbonitriles. Then, reaction of the latter compounds with cyclohexanone led to the formation of the title compounds. Also, they were evaluated for their in vitro acetylcholinesterase and butyrylcholinesterase inhibitory activities. Interestingly, most of them showed good inhibitory activity comparing with rivastigmine as the reference drug.     

New Triazinoindole Bearing Benzimidazole/Benzoxazole Hybrids Analogs as Potent Inhibitors of Urease: Synthesis,In Vitro Analysis and Molecular Docking Studies

Twenty-four analogs based on triazinoindole bearing benzimidazole/benzoxazole moieties (1–25) were synthesized. Utilizing a variety of spectroscopic methods, including ¹H-, ¹³C-NMR, and HREI-MS, the newly afforded compounds (1–25) were analyzed. The synthesized analogs were tested against urease enzyme (in vitro) as compared to the standard thiourea drug. All triazinoindole-based benzimidazole/benzoxazole analogs (1–25) exhibited moderate to excellent inhibition profiles, having IC₅₀ values of 0.20 ± 0.01 to 36.20 ± 0.70 μM when evaluated under the positive control of thiourea as a standard drug. To better understand the structure–activity relationship, the synthesized compounds were split into two groups, “A” and “B.” Among category “A” analogs, analogs 8 (bearing tri-hydroxy substitutions at the 2,4,6-position of aryl ring C) and 5 (bearing di-hydroxy substitutions at the 3,4-position of aryl ring C) emerged as the most potent inhibitors of urease enzyme and displayed many times more potency than a standard thiourea drug. Besides that, analog 22 (which holds di-hydroxy substitutions at the 2,3-position of the aryl ring) and analog 23 (bearing ortho-fluoro substitution) showed ten-fold-enhanced inhibitory potential compared to standard thiourea among category “B” analogs. Molecular docking studies on the active analogs of each category were performed; the results obtained revealed that the presence of hydroxy and fluoro-substitutions on different positions of aryl ring C play a pivotal role in binding interactions with the active site of the targeted urease enzyme.     

2,4-二氨基嘧啶类FAK抑制剂的3D-QSAR研究

摘要 本文选取42个2,4-二氨基嘧啶类FAK小分子抑制剂,分别以比较分子场分析法（CoMFA）与相似性指数分析法（CoMSIA）构建3D-QSAR模型,评价模板分子、公共骨架点、最小能量优化参数、分子构象等因素对模型优化的影响。分析最优模型中立体场、静电场以及氢键等因素对抑制剂活性的影响,并应用分子对接分析该类抑制剂与FAK蛋白的相互作用。结果表明选择16号化合物作为模板分子,骨架A作为公共骨架点,最小能量优化参数中电荷、最大迭代系数、最低能量限定值分别为MMFF94、1000、0.01 Kcal/mol时所构建的模型最优。以CoMFA和CoMSIA构建的3D-QSAR模型的交叉验证系数（q2）分别为0.666和0.736,非交叉验证系数（R2）分别为0.990和0.989,表明此模型具有良好的预测能力。分子对接分析显示,其与FAK的氨基酸残基CYS502、ASP564形成了重要的氢键作用,并与周围残基形成了较强的疏水作用。通过3D-QSAR的构建与分子对接分析,可指导2,4-二氨基嘧啶类FAK小分子抑制剂的进一步结构优化设计。