VEGFR-2 与抑制剂Sunitinib 的分子对接及分子动力学研究

用分子对接方法研究了VEGFR-2 和抑制剂Sunitinib 的相互作用模式, 并对其复合物进行了10 ns 的分子动力学(Molecular Dynamics, MD)模拟. 结果表明, 抑制剂Sunitinib 能与VEGFR-2 中位于活性空腔的Glu885, Ile888, His1026,Asp1028, Asp1046 五个氨基酸残基形成疏水作用; 另外, VEGFR-2 中His1026, Cys1024, Asp1046 三个氨基酸残基能与Sunitinib 形成三个作用强度不同的氢键. 这些基团之间的相互作用是Sunitinib 抑制VEGFR-2 活性的关键因素. 研究结果可为VEGFR-2 抑制剂的结构改良、分子设计、合成提供理论参考, 并有助于寻找活性更高、效果更好的抗肿瘤药物.     

新型哌啶-查尔酮类衍生物的设计、合成及抗宫颈癌和逆转顺铂耐药活性

本文采用活性亚结构拼接原理,设计并合成了15个新型含哌啶的查尔酮类衍生物,利用¹H NMR、¹³C NMR和HR-MS对结构进行表征,并初步评价了其抗宫颈癌和抗顺铂耐药宫颈癌活性作用。结果表明,化合物6g具有一定的抗肿瘤活性和逆转顺铂耐药作用;并采用Elisa法、联合顺铂用药、Western Blot和分子对接对化合物6g与VEGFR-2和P-gp靶点进行了初步的研究。本研究为基于VEGFR-2和P-gp双靶点新型分子靶向查尔酮类衍生物的设计提供了一条思路。     

含吡唑酮基团的喹唑啉衍生物的合成及其作为EGFR/VEGFR-2双靶标酪氨酸激酶抑制剂

双靶标酪氨酸激酶抑制剂在克服药物抗性和减少药物毒副作用方面具有重要作用,本文设计并合成了含有吡唑酮基团的喹唑啉衍生物作为EGFR/VEGFR-2双靶标酪氨酸激酶抑制剂。目标化合物由喹唑啉中间体和吡唑酮中间体通过亲核取代反应合成。喹唑啉中间体以2,3,4-三羟基苯甲酸为原料,通过酯化、硝化、还原、氯化和环化等反应合成;吡唑酮中间体以4-取代苯基肼盐酸盐为原料,通过甲基化和氧化等反应合成。目标化合物通过¹H NMR、¹³C NMR和HR-MS进行结构鉴定。分别采用ADP-Glo激酶活性检测方法和CCK-8法测定了目标化合物对EGFR和VEGFR-2的抑制活性以及对Hela细胞、A549细胞、HUVEC细胞的抗增殖活性,其对EGFR和VEGFR-2抑制活性IC₅₀值为10～899 nM, 15～712 nM;对部分在分子水平测定表现出较高活性的化合物进行了抗增殖活性测定,所选定的化合物对人肺癌A549细胞的半抑制浓度IC₅₀值为10～267 nM,对人脐静脉内皮细胞HUVEC的半抑制浓度IC_50...     

蛋白酪氨酸激酶小分子抑制剂的研究新进展

酪氨酸激酶在细胞的恶性生长和增殖中起着非常重要的作用,发展选择性的蛋白激酶抑制剂来阻断或调控由于这些信号通路异常产生的疾病已被广泛认为是抗肿瘤药物开发的一个富有前景和有效的研究策略.近年来科学家在蛋白酪氨酸激酶抑制剂这一领域进行了大量的工作,合成了数百个受体型或者非受体型酪氨酸激酶抑制剂,其中8个小分子抑制剂被美国食品药品管理局(FDA)批准作为抗肿瘤药物进入临床使用.随着肿瘤多重耐药性的出现,新机理的小分子酪氨酸激酶抑制剂被不断探索.以小分子抑制剂与酪氨酸激酶小同的作用模式来进行分类,系统地阐述了小分子酪氨酸激酶抑制剂的研究进展和发展趋势,并对代表性化合物的合成进行了介绍.     

人类蛋白激酶组的多靶点分子对接系统

蛋白激酶在信号转导、基因转录和蛋白翻译等生物过程起关键性作用,因而与大量人类疾病密切相关。所以,蛋白激酶的抑制剂筛选是抗肿瘤药物开发的热点,正在向基于全激酶组的高通量多靶点筛选模式发展。为了降低大规模实验筛选的成本,提高成功率,本文构建人类蛋白激酶组的多靶点分子对接系统,对抑制剂-激酶组的相互作用进行预测。我们首先利用同源模建方法,对人类激酶组约500个激酶变异体的催化域进行结构建模;接着以催化域结构模型为受体,用已知激酶抑制剂进行分子对接,对抑制剂与各激酶变异体的结合亲和力进行了定量计算。结果显示,本文所建立的多靶点分子对接系统可以准确预测抑制剂与激酶变异体的相互作用,结合自由能的计算值与实验值有很强的相关性。所以,该分子对接系统可用于多靶点激酶抑制剂的计算筛选,为激酶抑制剂开发与抗肿瘤药物设计提供理论依据。     

基于计算机模拟技术对JAK2抑制剂的定量构效关系、分子设计和分子动力学研究

本文选取了52个对Janus激酶2(JAK2)有抑制作用的小分子化合物,分别使用3D-QSAR中的CoMFA和CoMSIA方法构建了两个可靠的、具有预测能力的模型,并利用分子对接分析数据集化合物与JAK2蛋白的相互作用,表明化合物主要通过氢键和范德华作用与JAK2靶蛋白结合。根据3D-QSAR模型的分析结果,设计了40个化合物,利用构建的模型预测其抑制活性;使用软件预测了化合物的药代动力学(ADME)参数,开展分子对接模拟,最终选择化合物D01和D22与JAK2靶蛋白进行了分子动力学模拟研究,结果显示两个复合物结合构象稳定,与分子对接结果趋势一致。本研究的结果可以为JAK2抑制剂的研发提供一些新的思路,为临床开发此类药物提供理论支撑。     

含脲砌块的4-氨基喹唑啉衍生物的设计、合成及抗肿瘤活性研究（英文）

为了寻找新的具有靶向治疗作用的抗肿瘤药物,设计并合成了一系列新型的含脲砌块的4-氨基喹唑啉类衍生物,并采用噻唑蓝(MTT)法测定目标化合物对MCF-7(人乳腺癌细胞)、MGC-803(人胃癌细胞)、SW620(人结肠癌细胞)、A549(人肺癌细胞)四种肿瘤细胞的抗肿瘤活性.结果显示大部分化合物具有较好的抗肿瘤活性,其中2-((4-((3,4,5-三甲氧基苯基)-氨基)喹唑啉-2-基)-硫代)-N-((3,4,5-三甲氧基苯基)氨基甲酰基)乙酰胺(10p)对MGC-803、SW620和A549三种细胞显示出最好的抗肿瘤活性, IC_(50)值分别为(7.02±0.46)、(6.00±0.78)和(7.04±1.11)μmol·L~(-1),其抗肿瘤活性和阳性对照品吉非替尼相当.分子对接结果显示,化合物10p能与EGFR很好地结合,有可能成为潜在的抗肿瘤药物.     

基于分子对接的苯丙素甙（PPGs）类化合物的虚拟筛选和合理设计

采用虚拟化合物生成法对抗肿瘤的苯丙素甙(PPGs)类化合物进行了配体受体对 接研究。以三种不同的骨架结构为基础分别生成了五十个虚拟苯丙素甙(PPGs)类化 合物，并将它们与端粒DNA受体进行分子对接，分析已知结构的对接结果，通过虚 拟筛选的方法得到了一批与受体相互作用能较高并且复合物能量较低的新的有潜力 的活性化合物。该方法可以弥补分子对接研究中，只能计算药物与受体的相互作用 ，无法有效设计新化合物的不足。这种方法在基于结构的药物分子设计中具有重要 的意义。     

不同电荷场优化咪唑并吡啶类VEGFR-2抑制剂的三维定量构效关系研究

运用不同电荷场优化咪唑并吡啶类VEGFR-2抑制剂,挑选出最优电荷场Gasteiger-Marsili,用COMFA和CoMSIA两种方法建立3D-QSAR模型,以分析化合物结构与分子活性之间的关系。COMFA和CoMSIA模型的交叉验证系数分别为q2=0.673和q2=0.612,拟合验证系数分别为r~2=0.891和r~2=0.973,外部验证复相关系数分别为r2 pred=0.669和r2 pred=0.658,结果表明两种模型都有良好的可信度和预测能力。COMFA和CoMSIA模型在三维等视图上相互对照和验证,得到的结论与分子对接结果一致,确立了分子结构对抑制剂活性影响的具体作用方式,对指导药物的设计与改造,新VEGFR-2抑制剂的合成提供参考。     

螺环吲哚类MDM2抑制剂的分子对接、定量构效关系和分子动力学模拟

采用分子对接、三维定量构效关系(3D-QSAR)和分子动力学方法研究了21个螺环吲哚类化合物与MDM2蛋白的相互作用, 并建立了相关预测模型. 比较分子场分析法(CoMFA)和比较分子相似性指数分析法(CoMSIA)模型的交互验证相关系数q²分别为0.573 和0.651, 非交互验证相关系数r²分别为0.948和0.980. 分子对接得到的结合模式与分子动力学模拟得到的结果一致, 结合模式表明该类螺环吲哚化合物主要通过疏水相互作用和氢键与MDM2结合. 基于上述相互作用模型设计并合成了6个新结构螺环吲哚化合物, 并在MDM2高表达的前列腺癌LNCaP细胞株上测定其活性, 结果表明化合物5, 6的半数抑制浓度均低于1μg·mL^-1, 可作为新的抗肿瘤药物先导化合物进一步深入研究. 本研究对以MDM2为靶点的新结构螺环吲哚类抑制剂的开发提供了理论和实验依据.     

de novo design and synthesis of N-benzylanilines as new candidates for VEGFR tyrosine kinase inhibitors

N-Benzylanilines were designed and synthesized as vascular endothelial growth factor (VEGF)-2 inhibitors using de novo drug design systems based on the X-ray structure of VEGFR-2 kinase domain. Among compounds synthesized, compound showed the most potent inhibitory activity toward VEGFR-2 (KDR) tyrosine kinase and its IC(50) value was 0.57 microM.     

Molecular Modeling Studies of Vascular Endothelial Growth Factor Receptor Tyrosine Kinase Inhibitors Combining Molecular Docking and 3D-QSAR Methods

The vascular endothelial growth factor (VEGF) and its receptor tyrosine kinases VEGFR-2 or kinase insertdomain receptor (KDR) have emerged as attractive targets for the design of novel anticancer agents. In the present work, molecular docking method combined with three dimensional quantitative structure-activity relationships (comparative molecular field analysis (CoMFA) and comparative molecular similarity indice analysis (CoMSIA)) to analyze the possible interactions between KDR and those derivatives which acted as selective inhibitors. The CoMFA and CoMSIA models gave a cross-validated coefficient Q2 of 0.713 and 0.549, non-cross-validated R2 values of 0.974 and 0.878, and predicted R2 values of 0.966 and 0.823, respectively. The 3D contour maps generated by the CoMFA and CoMSIA models were used to identify the key structural requirements responsible for the biological activity. The information obtained from 3D-QSAR and docking studies were very helpful to design novel selective inhibitors of KDR with desired activity and good chemical property.     

Facile Synthesis of Novel Perfluorocarbon‐Modulated 4‐Anilinoquinazoline Analogues

4‐Anilinoquinazoline analogues stand out among many kinds of small molecules that inhibit the tyrosine kinase activities of epidermal growth factor receptor (EGFR ), thus serving as significant molecular targets for anticancer drug design. Herein, a series of novel perfluorocarbon (PFC ) modulated 4‐anilinoquinazolines were designed and prepared straightforwardly by nucleophilic substitution reaction of various anilinoquinazolines and PFC ‐derived methanesulfonate. In the presence of base, the reaction proceeded smoothly to afford a wide range of 4‐anilinoquinazolines with different substituents on aniline moiety in good to high yields. Furthermore, the PFC ‐modified analogues of gefitinib and erlotinib were also obtained in 93% and 90% respectively, which may have potential for developing new inhibitors of the epidermal growth factor receptor (EGFR ) tyrosine kinase and fluorinated contrast agents (CA ) for ¹⁹F MRI .     

Novel pyrrolo[2,3-d]pyrimidine derivatives as multi-kinase inhibitors with VEGFR-2 selectivity

Since the discovery of imatinib, the first tyrosine kinase inhibitor, in 2001, targeted therapy has become mainstream of cancer therapeutics. Despite the advantages in efficacy and low side effects compared with conventional chemotherapy, the success of the targeted anticancer drugs is still limited by the drug resistance which happens due to the fact that the development of cancer is stimulated by several stimuli and therefore, defeating cancer may occur upon the inhibition of several targets. However, coadministration of multiple drugs always lead to many disadvantages including increased toxicity and less patient compliance. Therefore, the aim of research is to develop anticancer agents with multi-target action based on the modification of the chemical structure of sunitinib, a well-known multi-kinase inhibitor. A series of fifteen compounds comprising pyrrolo[2,3-d]pyrimidine and hydrazone have been designed and successfully synthesized. Among the synthesized compounds, compounds 6f, 6l and 6n inhibited the enzymatic activity of EGFR, Her2, VEGFR-2 and CDK2 kinase enzymes similar to sunitinib and the reference protein kinase inhibitors. Interestingly, remarkable results were revealed by compounds 6j and 6c that demonstrated selective VEGFR-2 inhibition activities and compound 6i that exhibited selective dual inhibition of Her2/VEGFR-2 enzymes. Further analysis revealed that compounds 6f and 6n suppressed cell cycle progression of HepG2 cells and induced early and late apoptosis. Moreover, those two compounds triggered a significant elevation in caspase 3 and Bax proapoptotic proteins and a notable reduction in Bcl-2 anti-apoptotic protein. Finally, molecular docking studies were conducted to predict the possible binding interactions of 6f and 6n with CDK2 and 6f, 6n, 6j and 6c with VEGFR-2.     

Molecular simulation studies to reveal the binding mechanisms of shikonin derivatives inhibiting VEGFR-2 kinase

Traditional vascular endothelial growth factor receptor 2 (VEGFR-2) inhibitors can manage angiogenesis; however, severe toxicity and resistance limit their long-term applications in clinical therapy. Shikonin (SHK) and its derivatives could be promising to inhibit the VEGFR-2 mediated angiogenesis, as they are reported to bind in the catalytic kinase domain with low affinity. However, the detailed molecular insights and binding dynamics of these natural inhibitors are unknown, which is crucial for potential SHK based lead design. Therefore, the present study employed molecular modeling and simulations techniques to get insight into the binding behaviors of SHK and its two derivates, β-hydroxyisovalerylshikonin (β-HIVS) and acetylshikonin (ACS). Here the intermolecular interactions between protein and ligands were studied by induced fit docking approach, which were further evaluated by treating QM/MM (quantum mechanics/molecular mechanics) and molecular dynamics (MD) simulation. The result showed that the naphthazarin ring of the SHK derivates is vital for strong binding to the catalytic domain; however, the binding stability can be modulated by the side chain modification. Because of having electrostatic potential, this ring makes essential interactions with the DFG (Asp1046 and Phe1047) motif and also allows interacting with the allosteric binding site. Taken together, the studies will advance our knowledge and scope for the development of new selective VEGFR-2 inhibitors based on SHK and its analogs.     

Polyphyllin D Shows Anticancer Effect through a Selective Inhibition of Src Homology Region 2-Containing Protein Tyrosine Phosphatase-2 (SHP2)

Natural products have continued to offer tremendous opportunities for drug development, as they have long been used in traditional medicinal systems. SHP2 has served as an anticancer target. To identify novel SHP2 inhibitors with potential anticancer activity, we screened a library containing 658 natural products. Polyphyllin D was found to selectively inhibit SHP2 over SHP1, whereas two other identified compounds (echinocystic acid and oleanolic acid) demonstrated dual SHP1 and SHP2 inhibition. In a cell-based assay, polyphyllin D exhibited cytotoxicity in Jurkat cells, an acute lymphoma leukemia cell line, whereas the other two compounds were ineffective. Polyphyllin D also decreased the level of phosphorylated extracellular signal-regulated kinase (p-ERK), a proliferation marker in Jurkat cells. Furthermore, knockdown of protein tyrosine phosphatase (PTP)N6 (SHP1) or PTPN11 (SHP2) decreased p-ERK levels. However, concurrent knockdown of PTPN6 and PTPN11 in Jurkat cells recovered p-ERK levels. These results demonstrated that polyphyllin D has potential anticancer activity, which can be attributed to its selective inhibition of SHP2 over SHP1.     

Insights into the conformational switching mechanism of the human vascular endothelial growth factor receptor type 2 kinase domain

Human vascular endothelial growth factor receptor type 2 (h-VEFGR2) is a receptor tyrosine kinase involved in the angiogenesis process and regarded as an interesting target for the design of anticancer drugs. Its activation/inactivation mechanism is related to conformational changes in its cytoplasmatic kinase domain, involving first among all the αC-helix in N-lobe and the A-loop in C-lobe. Affinity of inhibitors for the active or inactive kinase form could dictate the open or closed conformation of the A-loop, thus making the different conformations of the kinase domain receptor (KDR) domain different drug targets in drug discovery. In this view, a detailed knowledge of the conformational landscape of KDR domain is of central relevance to rationalize the efficiency and selectivity of kinase inhibitors. Here, molecular dynamics simulations were used to gain insight into the conformational switching activity of the KDR domain and to identify intermediate conformations between the two limiting active and inactive conformations. Specific energy barriers have been selectively removed to induce, and hence highlight at the atomistic level, the regulation mechanism of the A-loop opening. The proposed strategy allowed to repeatedly observe the escape of the KDR domain from the DFG-out free energy basin and to identify rare intermediate conformations between the DFG-out and the DFG-in structures to be employed in a structure-based drug discovery process.     

In silico model for P-glycoprotein substrate prediction: insights from molecular dynamics and in vitro studies

P-glycoprotein (P-gp) is a plasma membrane efflux transporter belonging to ATP-binding cassette superfamily, responsible for multidrug resistance in tumor cells. Over-expression of P-gp in cancer cells limits the efficacy of many anticancer drugs. A clear understanding of P-gp substrate binding will be advantageous in early drug discovery process. However, substrate poly-specificity of P-gp is a limiting factor in rational drug design. In this investigation, we report a dynamic trans-membrane model of P-gp that accurately identified the substrate binding residues of known anticancer agents. The study included homology modeling of human P-gp based on the crystal structure of C. elegans P-gp, molecular docking, molecular dynamics analyses and binding free energy calculations. The model was further utilized to speculate substrate propensity of in-house anticancer compounds. The model demonstrated promising results with one anticancer compound (NSC745689). As per our observations, the molecule could be a potential lead for anticancer agents devoid of P-gp mediated multiple drug resistance. The in silico results were further validated experimentally using Caco-2 cell lines studies, where NSC745689 exhibited poor permeability (P _app 1.03 ± 0.16 × 10^?6 cm/s) and low efflux ratio of 0.26.     

Novel diphenylamine 2,4'-dicarboxamide based azoles as potential epidermal growth factor receptor inhibitors: synthesis and biological activity

Several hybrid molecules of diphenylamine-2,4'-dicarboxamide with various azolidinones and related heterocyclic rings have been synthesized and explored as epidermal growth factor receptor (EGFR) kinase inhibitors. Most of them displayed promising in vitro tyrosine kinase inhibition as well as potent cellular antiproliferative activity in the EGFR over-expressing breast cancer cell line (MCF-7). Compounds 12b and 13b that exhibited the highest inhibition in the kinase assay (89, 81% inhibition at 10 μM, respectively), showed potent antiproliferative effect against MCF-7 tumor cell line (IC(50) 1.04, 0.91 μM respectively). Molecular docking studies revealed that these compounds can bind to ATP binding site of the EGFR kinase domain and were involved in H-bonding with Met 793, in analogy to the known EGFR tyrosine kinase inhibitors. Moreover, compounds 15a-c possessed profound antitumor activity (IC(50) 0.59-0.73 μM) and significant EGFR-TK inhibition, making them of particular interest. In summary, the newly synthesized compounds provide promising new lead for the future design and development of anticancer agents of potential EGFR-TK inhibitory activity.