喜树碱类抗肿瘤药物作用模式的柔性分子对接研究

研究采用柔性分子对接技术，将15个喜树碱类化合物对接到拓扑异构酶I (Topo I)-DNA切割复合物中，从原子水平和分子力场角度阐明了喜树碱类抗肿瘤药 物与DNA，Topo I的相互作用机制。研究发现，喜树碱分子插入Topp I-DNA复合物 的切割位点，并与Asn722，Asp533，Lys532和Lys720形成氢键作用网络。定量构效 关系研究进一步表明喜树碱分子可以与Topo I-DNA切割复合物形成电荷迁移作用。 该对接模型系统解释了喜树碱类化合物的构效关系、定点突变等诸多实验事实，为 下一步设计、合成新型高效的喜树碱类衍生物打下了坚实基础。     

Synthesis,cytotoxicity, topoisomerase I inhibition and molecular docking of novel phosphoramide mustard sophoridinic acid analogues

A series of novel phosphoramide mustard sophoridinic acid analogues, consisting of nitrogen mustard group and sophoridinic acid scaffold, have been designed, synthesized and evaluated for their topoisomerase inhibitory activity as well as cytotoxicity against six tumor cell lines (SMMC‐7721, LoVo, MCF‐7, K562, S180 and H22) and a normal cell line (L929). Among the compounds tested, five were found to be potent inhibitors and exhibited potent cytotoxicity against S180 and H22 cell lines with IC₅₀ values of 1–4 μM. Further mechanistic studies showed that this class of compounds acted as novel topoisomerase I (Topo I) catalytic inhibitors by preventing the binding of Topo I to DNA and inhibiting the cleavage of DNA, and molecular docking studies revealed that the binding energy for these compounds was comparable to that for classic Topo I inhibitors CPT and HCPT, indicating that the compounds have an interaction with DNA and Topo I.     

Design and synthesis of novel 7-[(N-substituted-thioureidopiperazinyl)-methyl]-camptothecin derivatives as potential cytotoxic agents

Abstract

As part of continuing our research on diverse C-7 derivatives of camptothecin (CPT), 16 CPT derivatives bearing piperazinyl-thiourea chemical scaffold and different substituent groups have been designed, synthesized and evaluated in vitro for cytotoxicity against five tumor cell lines (A-549, MDA-MB-231, MCF-7, KB and KBvin). As a result, all the synthesized compounds showed promising in vitro cytotoxic activity against the five tumor cell lines tested, and were more potent than irinotecan. Importantly, compounds 13?g (IC₅₀ = 0.514?μM) and 13o (IC₅₀ = 0.275?μM) possessed similar or better antiproliferative activity against the multidrug-resistant (MDR) KBvin subline than that of topotecan (IC₅₀ = 0.511?μM) and merit further development as anticancer candidates for clinical trail. With these results in hand, we have a reason to conclude that incorporating piperazinyl-thiourea motifs into position-7 of camptothecin confers well cytotoxic activity against cancer cell lines, probably resulting in new anticancer drugs.     

Preparation of a Camptothecin Prodrug with Glutathione‐Responsive Disulfide Linker for Anticancer Drug Delivery

We present here a novel camptothecin (CPT) prodrug based on polyethylene glycol monomethyl ether‐block‐poly(2‐methacryl ester hydroxyethyl disulfide‐graft‐CPT) (MPEG‐SS‐PCPT). It formed biocompatible nanoparticles (NPs) with diameters of approximately 122 nm with a CPT loading content as high as approximately 25 wt % in aqueous solution. In in vitro release studies, these MPEG‐SS‐PCPT NPs could undergo triggered disassembly and much faster release of CPT under glutathione (GSH) stimulus than in the absence of GSH. The CPT prodrug had high antitumor activity, and another anticancer drug, doxorubicin hydrochloride (DOX ? HCl), could also be introduced into the prodrug with a high loading amount. The DOX ? HCl‐loaded CPT prodrug could deliver two anticancer drugs at the same time to produce a collaborative cytotoxicity toward cancer cells, which suggested that this GSH‐responsive NP system might become a promising carrier to improve drug‐delivery efficacy.     

Synthesis of 7‐Triazole‐substituted Camptothecin via Click Chemistry and Evaluation of in vitro Antitumor Activity

Camptothecin (CPT) is a natural topoisomerase I inhibitor with powerful antineoplastic activity against colorectal, breast, lung and ovarian cancers. To discover more potent antitumor agents, a series of new CPT derivatives were synthesized utilizing click chemistry. All compounds were assessed for cytotoxicity against A549, HCT‐116, HT‐29, LoVo, MDA‐MB‐231 cell lines, and some compounds exhibited good in vitro potency. Furthermore, all compounds kept or enhanced Topo I inhibition.     

DFT‐based QSAR study and molecular design of AHMA derivatives as potent anticancer agents

A quantitative structure–activity relationship (QSAR) of 3‐(9‐acridinylamino)‐5‐hydroxymethylaniline (AHMA) derivatives and their alkylcarbamates as potent anticancer agents has been studied using density functional theory (DFT), molecular mechanics (MM+), and statistical methods. In the best established QSAR equation, the energy (E_NL) of the next lowest unoccupied molecular orbital (NLUMO) and the net charges (Q_FR) of the first atom of the substituent R, as well as the steric parameter (MR₂) of subsituent R₂ are the main independent factors contributing to the anticancer activity of the compounds. A new scheme determining outliers by “leave‐one‐out” (LOO) cross‐validation coefficient (q) was suggested and successfully used. The fitting correlation coefficient (R²) and the “LOO” cross‐validation coefficient (q²) values for the training set of 25 compounds are 0.881 and 0.829, respectively. The predicted activities of 5 compounds in the test set using this QSAR model are in good agreement with their experimental values, indicating that this model has excellent predictive ability. Based on the established QSAR equation, 10 new compounds with rather high anticancer activity much greater than that of 34 compounds have been designed and await experimental verification. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

pH‐responsive near‐infrared emitting conjugated polymer nanoparticles for cellular imaging and controlled‐drug delivery

In this article, pH‐responsive near‐infrared emitting conjugated polymer nanoparticles (CPNs) are prepared, characterized, and their stabilities are investigated under various conditions. These nanoparticles have capacity to be loaded with water insoluble, anticancer drug, camptothecin (CPT), with around 10% drug loading efficiency. The in vitro release studies demonstrate that the release of CPTs from CPNs is pH‐dependent such that significantly faster drug release at mildly acidic pH of 5.0 compared with physiological pH 7.4 is observed. Time and dose‐dependent in vitro cytotoxicity tests of blank and CPT‐loaded nanoparticles are performed by real‐time cell electronic sensing (RT‐CES) assay with hepatocellular carcinoma cells (Huh7). The results indicate that CPNs can be effectively utilized as vehicles for pH‐triggered release of anticancer drugs. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 114–122     

取代苯丙酮肟衍生物的合成、QSAR研究以及优化

本文介绍了用结合化学、生物实验以及计算机辅助分子设计方法优化对瓜类白粉病毒有抑制作用的先导化合物的研究。用3－取代氨基－1－芳基丙酮－1－肟以及卤代烃合成了44个取代苯丙酮肟衍生物。生物测试的结果表示这些化合物大部分对瓜类白粉病毒有抑制作用。基于这些生物测试,对这44个化合物做了QSAR研究。根据所得CoMFA (rcv2, S 以及 r2 分别为0.577, 0.258, 0.962) 和 CoMSIA (rcv2, S 以及 r2 分别为0.583, 0.343, 0.932) 模型,设计了3个新化合物,而且预测结果显示,它们无致癌和致突变毒性。测试结果显示预测活性与实验活性相对应,说明这两个模型具有较高的预测准确率。     

A Quantitative Structure–Activity Relationship Study of Calpeptin (Calpain Inhibitor) as an Anticancer Agent

Calpeptin analogs show anticancer properties with inhibition of calpain. In this work, we applied a quantitative structure–activity relationship (QSAR) model on 34 calpeptin derivatives to select the most appropriate compound. QSAR was employed to generate the models and predict the more significant compounds through a series of calpeptin derivatives. The HyperChem, Gaussian 09, and Dragon software programs were used for geometry optimization of the molecules. The 2D and 3D molecular structures were drawn by ChemDraw (Ultra 16.0) and Chem3D (Pro16.0) software. The Unscrambler program was used for the analysis of data. Multiple linear regression (MLR‐MLR), partial least‐squares (MLR‐PLS1), principal component regression (MLR‐PCR), a genetic algorithm‐artificial neural networks (GA‐ANN), and a novel similarity analysis‐artificial neural network (SA‐ANN) method were used to create QSAR models. Among the three MLR models, MLR‐MLR provided better statistical parameters. The R² and RMSE of the prediction were estimated as 0.8248 and 0.26, respectively. Nevertheless, the constructed model using GA‐ANN revealed the best statistical parameters among the studied methods (R² test = 0.9643, RMSE test = 0.0155, R² train = 0.9644, RMSE train = 0.0139). The GA‐ANN model is found to be the most favorable method among the statistical methods and can be employed for designing new calpeptin analogs as potent calpain inhibitors in cancer treatment.     

Grid potential analysis,virtual screening studies and ADME/T profiling on N‐arylsulfonylindoles as anti‐HIV‐1 agents

A grid potential analysis employing a novel approach of 3D quantitative structure–activity relationships (QSAR) as AutoGPA module in MOE2009.10 was performed on a dataset of 42 compounds of N‐arylsulfonylindoles as anti‐HIV‐1 agents. The uniqueness of AutoGPA module is that it automatically builds the 3D‐QSAR model on the pharmacophore‐based molecular alignment. The AutoGPA‐based 3D‐QSAR model obtained in the present study gave the cross‐validated Q² value of 0.588, r²_pred value of 0.701, r²_m statistics of 0.732 and Fisher value of 94.264. The results of 3D‐QSAR analysis indicated that hydrophobic groups at R₁ and R₂ positions and electron releasing groups at R₃ position are favourable for good activity. To find similar analogues, virtual screening on ZINC database was carried out using generated AutoGPA‐based 3D‐QSAR model and showed good prediction. In addition to those mentioned earlier, in‐silico ADME absorption, distribution, metabolism and excretion profiling and toxicity risk assessment test was performed, and results showed that majority of compounds from current dataset and newly virtually screened hits generated were within their standard limit. Copyright © 2013 John Wiley & Sons, Ltd.     

QSAR and docking studies on chalcone derivatives for antitubercular activity against M. tuberculosis H37Rv

In our prior studies, we reported some known antitubercular drugs (rifampicin and streptomycin) and newly synthesized chalcone derivatives (16–26) tested in vitro against Mycobacterium tuberculosis H₃₇Rv strain. Most of the tested compounds were efficient antimycobacterial agents showing minimum inhibitory concentration values ranging from 3.5 to 30 µg mL⁻¹. In the present work, a quantitative structure–activity relationship (QSAR) study has been performed on these active chalcone derivatives to correlate their chemical structures with their observed inhibiting activity against M. tuberculosis. A QSAR model that is able to correlate well the antitubercular activity with the chemical structures of active chalcone derivatives 16, 24, 25a, 25c, and 26 has been developed, which is potentially helpful in the design of novel and more potent antitubercular agents. The r² and rCV² of a newly derived QSAR model were 0.89 and 0.84, respectively. The QSAR study indicates that chemical properties, viz. heat of formation (kcal mol⁻¹), lowest unoccupied molecular orbital energy (eV), and amine, hydroxyl, and methyl groups counts, correlate well with the activity. In silico screening results for oral bioavailability and absorption, distribution, metabolism, excretion, and toxicity compliance showed that compounds 25a, 25c, and 24 were found active similar to rifampicin and streptomycin. The docking study for the exploration of mechanism of action showed high binding affinity of active derivatives. Copyright © 2014 John Wiley & Sons, Ltd.     

Structural investigations of anthranilimide derivatives by CoMFA and CoMSIA 3D-QSAR studies reveal novel insight into their structures toward glycogen phosphorylase inhibition

In the present work, three-dimensional quantitative structure–activity relationship (3-D QSAR) studies on a set of 70 anthranilimide compounds has been performed using docking-based as well as substructure-based molecular alignments. This resulted in the selection of more statistically relevant substructure-based alignment for further studies. Further, molecular models with good predictive power were derived using CoMFA (r ^2?=?0.997; Q ^2?=?0.578) and CoMSIA (r ^2?=?0.976; Q ^2?=?0.506), for predicting the biological activity of new compounds. The so-developed contour plots identified several key features of the compounds explaining wide activity ranges. Based on the information derived from the CoMFA contour maps, novel leads were proposed which showed better predicted activity with respect to the already reported systems. Thus, the present study not only offers a highly significant predictive QSAR model for anthranilimide derivatives as glycogen phosphorylase (GP) inhibitors which can eventually assist and complement the rational drug-design attempts, but also proposes a highly predictive pharmacophore model as a guide for further development of selective and more potent GP inhibitors as anti-diabetic agents.     

Drug discovery studies on quinoline-based derivatives as potential antimalarial agents

Molecular modelling studies were performed to identify the essential structural requirements of quinoline-based derivatives for improving their antimalarial activity. The developed CoMFA, CoMSIA and HQSAR models for a training set comprising 37 derivatives showed good statistical significance in terms of internal cross validation (q²) 0.70, 0.69 and 0.80 and non-cross validation (r²) 0.80, 0.79 and 0.80. Also, the predicted r² values (r²_pred) of 0.63, 0.61 and 0.72 for a test set consisting of 12 compounds suggested significant predicting ability of the models. Structural features were correlated in terms of steric, electrostatic, hydrophobic, hydrogen bond donor and hydrogen bond acceptor interactions. Furthermore, the bioactive conformation was explored and explained by docking compounds #28, 32 and 40 into the active binding site of lactate dehydrogenase of Plasmodium falciparum. The QSAR models, contour map and docking binding affinity obtained could be successfully utilized as a guiding tool for the design and discovery of novel quinoline-based derivatives with potent antimalarial activity.     

A facile synthesis of novel 5‐substituted pyridine 2 carboxamide derivatives and their biological evaluation and 3D QSAR studies

A variety of novel 5‐substituted pyridine 2 carboxamides were designed and synthesized using both normal and solvent‐free microwave (MW) irradiation techniques. The results revealed that MW protocol proceeded smoothly under mild reaction conditions in short reaction times, thus avoiding the use of toxic organic solvents. Structural elucidation of the synthesized compounds was carried out on the basis of various spectroscopic methods, such as ¹H NMR, ¹³C NMR, LCMS, and IR. The synthesized compounds were evaluated for their in vitro antimicrobial activity (MIC) using the agar disk diffusion method. Among the various synthetic compounds, compound 3b showed higher potential activity against Escherichia coli than the other compounds. The order of activity against E. coli of the studied compounds is 3b > 3e > 3g > 3h > 3d > 3c > 3a > 3f . Additionally, 2D and 3D structural features of the synthesized derivatives were recognized by the 3D‐QSAR model. This validated model exhibited good internal (r², 0.924) and external prediction (r²pred, 0.851) correlation. The results of QSAR studies concluded that Alog P, the number of hydrogen bond acceptors, and the number of rotatable bonds were necessary features for the activity of the pyridine carboxamide derivatives.     

Cucurbit[n]urils (n=7, 8) binding of camptothecin and the effects on solubility and reactivity of the anticancer drug

The interaction between cucurbit[n]uril (n = 7, 8)(Q[n]) with two forms namely lactone modality and carboxylate modality of anticancer drug camptothecin (CPT) was studied. The results revealed that the combination of Q[n] with the lactone form of CPT was observed by electronic absorption spectroscopy, fluorescence spectroscopy and ¹H NMR technique in the acid solution (pH 2) and the total stability constants β were also obtained by Job plot with a host:guest ratio of 2:1; while in the phosphate buffer solution (pH 7.4), only Q[8] bound the carboxylate form of CPT in ratio 1:1, but no obvious interaction between Q[7] and the carboxylate form of CPT was observed. The solubility of CPT was enhanced up to about 70 and 8 times at pH 2 due to the formation of interaction complexes with Q[7] and Q[8], respectively, by using phase solubility method. The cytotoxicity tests revealed that compared with the free CPT, the complexes of Q[n] and CPT had the same cytotoxic activity on the human lung cancer cell line A549 and murine macrophage cell line P388D1 and the moderate depressed activity on human leukaemia cell line K562.     

Synthesis,Characterization, and Molecular Docking of Novel bis‐thiazolyl Thienothiophene Derivatives as Promising Cytotoxic Antitumor Drug

A novel, facile reaction for the synthesis of series of bis‐thiazole derivatives has been developed from the reaction of the appropriate thiosemicarbazone derivatives and bis‐2‐bromoacetylthieno[2,3‐b ]thiophene derivatives in ethanol under reflux. The structures of the newly synthesized products were established on the basis of spectral data (mass, IR, and ¹H and ¹³C NMR) and elemental analyses. Fifteen compounds of the synthesized compounds were evaluated for their anticancer activity against human liver hepatocellular carcinoma cell line (HepG2). All compounds showed anticancer activity but differs in potency comparable with the reference drug Cisplatin. Moreover, molecular docking study using MOE software predicted the best binding mode between the most active compound 5o into the active site of human heat‐shock protein 90. The computational studies are confirming the results in biological activity.     

Synthesis of an esterase‐sensitive degradable polyester as facile drug carrier for cancer therapy

Polyethylene glycol (PEG) is widely used as a carrier to improve the pharmaceutical properties of drugs with low molecular weight. However, PEG has few functional groups (usually two) for drug conjugation and the resulting low drug content (1–2%) has hampered its clinical applications. For this study, we synthesized biodegradable poly(ethylene glycol‐co‐anhydride). This polyester‐based polymer possesses multiple carboxylic acid groups that can be used as facile drug carriers. Two anticancer drugs, camptothecin (CPT) and doxorubicin (DOX) were loaded into the carrier and their releasing properties and in vitro anticancer activities were studied. The polymer–drug conjugates exhibited esterase‐promoted degradation and drug release. Their cytotoxicity against the human ovarian cancer cell line SKOV‐3 was comparable to unconjugated drugs. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 507–515