目的:研究赤芍抗流感病毒的作用机制与分子基础,为利用中药赤芍开发出安全有效的抗流感药物提供理论依据。方法:基于计算机虚拟筛选的方法,以单味中药赤芍的119个化学成分为对象,选取5个目前与流感治疗密切相关的靶点蛋白作为受体,采用S...目的:研究赤芍抗流感病毒的作用机制与分子基础,为利用中药赤芍开发出安全有效的抗流感药物提供理论依据。方法:基于计算机虚拟筛选的方法,以单味中药赤芍的119个化学成分为对象,选取5个目前与流感治疗密切相关的靶点蛋白作为受体,采用SYBYL分子对接的方法,以Total Score结合打分为标准筛选出得分最高的分子并观察其MOLCAD展示的与5个流感病毒靶蛋白的表面疏水性和氢键供体与受体区域,借助Discovery Studio 2016软件对其进行相互作用的分析,预测其结合模式及亲和力。结果:通过SYBYL分子对接的方法,观察到赤芍119个成分与流感相关受体分子结合Total Score打分普遍较高,并均超过其与自身配体结合打分,且发现小分子与受体分子结合,可产生多种分子间作用力,使小分子牢固地结合在活性位点。结论:基于计算机虚拟筛选方法中的分子对接技术,发现赤芍具有很好地发挥多靶点抗流感病毒的优势,是一种具有开发潜能的抗流感中药。展开更多
Alkaline phosphatases(APs) include the placental AP(PLAP), germ cell AP(GCAP), intestinal AP(IAP) and tissue nonspecific AP(TNAP). Over expression of TNAP in smooth muscle cells of kidney and vessels provokes the prog...Alkaline phosphatases(APs) include the placental AP(PLAP), germ cell AP(GCAP), intestinal AP(IAP) and tissue nonspecific AP(TNAP). Over expression of TNAP in smooth muscle cells of kidney and vessels provokes the progress of such serious diseases as end-stage renal disease, idiopathic infantile arterial calcification, ankylosis, osteoarthritis and diabetes. In order to design and optimize the potent TNAP inhibitors, comparative molecular field analysis(CoMFA) and comparative molecular similarity indices analysis(CoMSIA) were used to analyze 3D structure-activity relationships(3D-QSAR) of TNAP inhibitors. The 3D-QSAR model(CoMFA with q^2 = 0.521, r^2 = 0.930; CoMSIA with q^2 = 0.529, r^2 = 0.933) had a good predictability. Surflex-dock was used to reveal the binding mode between the inhibitors and TNAP protein. CoMFA, CoMSIA and docking results provide guidance for the discovery of TNAP inhibitors. Finally, eight new compounds as potential TNAP inhibitors were designed.展开更多
Tyrosine protein kinase JAK3 has a very important significance on organ transplantation and the treatment of autoimmune diseases, which has been a potential therapeutic target. In recent years, a large number of JAK3 ...Tyrosine protein kinase JAK3 has a very important significance on organ transplantation and the treatment of autoimmune diseases, which has been a potential therapeutic target. In recent years, a large number of JAK3 inhibitors have been reported. However, the poor selectivity and side effects have limited their widespread use in clinical practice. In order to solve this problem, 52 potential small-molecule inhibitors were combined with JAK1, JAK2 and JAK3 respectively to obtain the optimal conformation of small molecules. On the basis of that we established 3D quantitative structure-activity relationships（3D-QSAR） model. Comparative molecular field analysis（Co MFA） and molecular similarity analysis（Co MSIA） were used to evaluate the model. We took advantage of reverse docking to explore the underlying toxicity and side effects. Combining 3D quantitative structure-activity relationships, surflex-dock and reverse docking results, ten 5 H-pyrrolo[2,3-b]pyrazine-2-phenyl ether derivatives based on the most optimal selectivity and activity compound 39 were designed. It can be seen from Co MFA and Co MSIA predicted active values of designed molecules that the selectivity of designed small molecules was improved obviously. Among them, compounds 61 and 62 could become the potential small molecule compounds.展开更多
血管内皮生长因子VEGF及其受体VEGFR2对于肿瘤血管生成起至关重要的作用。本文旨在研究VEGFR2的咪唑并哒嗪类抑制剂的三维定量构效关系及新抑制剂分子与VEGFR2的作用机制。构建的Topomer Co MFA模型具有较强的预测能力和拟合能力(q^2=0....血管内皮生长因子VEGF及其受体VEGFR2对于肿瘤血管生成起至关重要的作用。本文旨在研究VEGFR2的咪唑并哒嗪类抑制剂的三维定量构效关系及新抑制剂分子与VEGFR2的作用机制。构建的Topomer Co MFA模型具有较强的预测能力和拟合能力(q^2=0.809,r^2=0.968)以及外部预测能力(r_(pred)~2=0.571)。应用Topomer Search技术在含1304868个分子的ZINC数据库中进行了虚拟筛选,采用基于片段的药物设计方法设计了68个高活性的新VEGFR2抑制剂。最后借助Surflex-dock技术研究了新分子与VEFGR2的作用机制,发现新抑制剂与残基Glu885、Cys919、Asn923、Asp1046等作用显著。本研究为VEGFR2抑制剂分子的结构修饰、设计与合成提供了重要的理论指导。展开更多
利用surflex-dock模块对59个苯酰胺类抑制剂和组蛋白去乙酰化酶进行了对接研究,分析了配体和受体的相互作用模式,所得结论与文献报道的实验结果符合。并利用比较分子力场分析方法(comparative molecular field anal-ysis,CoMFA)对此类...利用surflex-dock模块对59个苯酰胺类抑制剂和组蛋白去乙酰化酶进行了对接研究,分析了配体和受体的相互作用模式,所得结论与文献报道的实验结果符合。并利用比较分子力场分析方法(comparative molecular field anal-ysis,CoMFA)对此类抑制剂分子进行了三维定量构效关系研究,所建模型交叉验证相关系数q^2=0.640,非交叉验证相关系数r^2=0.932,有较好的预测能力。CoMFA得到的立体场和静电场的等值线图可用于指导新型药物的设计与合成。展开更多
目的:评估QM/MM方法和Surflex-Dock分子对接程序对DNA-配体复合物模拟的准确性。方法:从蛋白质数据库(Protein Data Bank)下载DNA-配体复合物的三维结构,利用计算机辅助药物设计的分子对接程序Surflex-Dock模拟出147个诱饵化合物(decoys...目的:评估QM/MM方法和Surflex-Dock分子对接程序对DNA-配体复合物模拟的准确性。方法:从蛋白质数据库(Protein Data Bank)下载DNA-配体复合物的三维结构,利用计算机辅助药物设计的分子对接程序Surflex-Dock模拟出147个诱饵化合物(decoys)并计算其结合分数(binding score)。然后将得出的分数与从QM/MM计算的结合能力以Z-score和辨别力(DP)作比较。从而评估Surflex-Dock和QM/MM的准确性。结果:Surflex-Dock的DPi值比QM/MM高,显示Surflex-Dock的辨别力较低。结论:因QM/MM计算速度慢,本研究认为Surflex-Dock可用作快速虚拟筛选,而较准确的QM/MM则适合用于对拥有较高结合分数的化合物进行再评分(rescoring)。展开更多
文摘目的:研究赤芍抗流感病毒的作用机制与分子基础,为利用中药赤芍开发出安全有效的抗流感药物提供理论依据。方法:基于计算机虚拟筛选的方法,以单味中药赤芍的119个化学成分为对象,选取5个目前与流感治疗密切相关的靶点蛋白作为受体,采用SYBYL分子对接的方法,以Total Score结合打分为标准筛选出得分最高的分子并观察其MOLCAD展示的与5个流感病毒靶蛋白的表面疏水性和氢键供体与受体区域,借助Discovery Studio 2016软件对其进行相互作用的分析,预测其结合模式及亲和力。结果:通过SYBYL分子对接的方法,观察到赤芍119个成分与流感相关受体分子结合Total Score打分普遍较高,并均超过其与自身配体结合打分,且发现小分子与受体分子结合,可产生多种分子间作用力,使小分子牢固地结合在活性位点。结论:基于计算机虚拟筛选方法中的分子对接技术,发现赤芍具有很好地发挥多靶点抗流感病毒的优势,是一种具有开发潜能的抗流感中药。
基金supported by the Key Project of Natural Science Foundation of Chongqing(No.cstc2015jcyjBX0080)Science and Technology project of Chongqing Education Commission(KJ1600907)
文摘Alkaline phosphatases(APs) include the placental AP(PLAP), germ cell AP(GCAP), intestinal AP(IAP) and tissue nonspecific AP(TNAP). Over expression of TNAP in smooth muscle cells of kidney and vessels provokes the progress of such serious diseases as end-stage renal disease, idiopathic infantile arterial calcification, ankylosis, osteoarthritis and diabetes. In order to design and optimize the potent TNAP inhibitors, comparative molecular field analysis(CoMFA) and comparative molecular similarity indices analysis(CoMSIA) were used to analyze 3D structure-activity relationships(3D-QSAR) of TNAP inhibitors. The 3D-QSAR model(CoMFA with q^2 = 0.521, r^2 = 0.930; CoMSIA with q^2 = 0.529, r^2 = 0.933) had a good predictability. Surflex-dock was used to reveal the binding mode between the inhibitors and TNAP protein. CoMFA, CoMSIA and docking results provide guidance for the discovery of TNAP inhibitors. Finally, eight new compounds as potential TNAP inhibitors were designed.
文摘组蛋白去乙酰化酶抑制剂(histone deacetylase inhibitor,HDACi)是近年来治疗癌症的重要靶向药物,其中羟氨酸类,苯甲酰胺类多种药物已进入临床试验阶段,但对于亲电酮类HDACi还有待于进一步研究,本研究应用比较分子力场分析法(comparative molecular field analysis,CoMFA),比较分子相似性指数法(compara-tive similarity indices analysis,CoMSIA)对29个亲电酮类HDAC抑制剂分子进行了定量构效关系分析,CoMFA模型的q2=0.668,r2=0.999;CoMSIA模型的q2=0.686,r2=0.995,所建模型预测能力较好。分子对接(sur-flex-dock)研究也进一步揭示出抑制剂分子与蛋白酶的作用模式,结合其作用模式比较合理地探讨了这类抑制剂的活性原因,为设计新型高效的亲电酮类HDACi提供了理论依据。
基金supported by the Natural Science Foundation of Chongqing(cstc2015jcyjBX0080)Chongqing Research Program of Basic Research and Frontier Technology(cstc2013jcyjA10019)
文摘Tyrosine protein kinase JAK3 has a very important significance on organ transplantation and the treatment of autoimmune diseases, which has been a potential therapeutic target. In recent years, a large number of JAK3 inhibitors have been reported. However, the poor selectivity and side effects have limited their widespread use in clinical practice. In order to solve this problem, 52 potential small-molecule inhibitors were combined with JAK1, JAK2 and JAK3 respectively to obtain the optimal conformation of small molecules. On the basis of that we established 3D quantitative structure-activity relationships（3D-QSAR） model. Comparative molecular field analysis（Co MFA） and molecular similarity analysis（Co MSIA） were used to evaluate the model. We took advantage of reverse docking to explore the underlying toxicity and side effects. Combining 3D quantitative structure-activity relationships, surflex-dock and reverse docking results, ten 5 H-pyrrolo[2,3-b]pyrazine-2-phenyl ether derivatives based on the most optimal selectivity and activity compound 39 were designed. It can be seen from Co MFA and Co MSIA predicted active values of designed molecules that the selectivity of designed small molecules was improved obviously. Among them, compounds 61 and 62 could become the potential small molecule compounds.
文摘血管内皮生长因子VEGF及其受体VEGFR2对于肿瘤血管生成起至关重要的作用。本文旨在研究VEGFR2的咪唑并哒嗪类抑制剂的三维定量构效关系及新抑制剂分子与VEGFR2的作用机制。构建的Topomer Co MFA模型具有较强的预测能力和拟合能力(q^2=0.809,r^2=0.968)以及外部预测能力(r_(pred)~2=0.571)。应用Topomer Search技术在含1304868个分子的ZINC数据库中进行了虚拟筛选,采用基于片段的药物设计方法设计了68个高活性的新VEGFR2抑制剂。最后借助Surflex-dock技术研究了新分子与VEFGR2的作用机制,发现新抑制剂与残基Glu885、Cys919、Asn923、Asp1046等作用显著。本研究为VEGFR2抑制剂分子的结构修饰、设计与合成提供了重要的理论指导。
文摘利用surflex-dock模块对59个苯酰胺类抑制剂和组蛋白去乙酰化酶进行了对接研究,分析了配体和受体的相互作用模式,所得结论与文献报道的实验结果符合。并利用比较分子力场分析方法(comparative molecular field anal-ysis,CoMFA)对此类抑制剂分子进行了三维定量构效关系研究,所建模型交叉验证相关系数q^2=0.640,非交叉验证相关系数r^2=0.932,有较好的预测能力。CoMFA得到的立体场和静电场的等值线图可用于指导新型药物的设计与合成。
文摘目的:评估QM/MM方法和Surflex-Dock分子对接程序对DNA-配体复合物模拟的准确性。方法:从蛋白质数据库(Protein Data Bank)下载DNA-配体复合物的三维结构,利用计算机辅助药物设计的分子对接程序Surflex-Dock模拟出147个诱饵化合物(decoys)并计算其结合分数(binding score)。然后将得出的分数与从QM/MM计算的结合能力以Z-score和辨别力(DP)作比较。从而评估Surflex-Dock和QM/MM的准确性。结果:Surflex-Dock的DPi值比QM/MM高,显示Surflex-Dock的辨别力较低。结论:因QM/MM计算速度慢,本研究认为Surflex-Dock可用作快速虚拟筛选,而较准确的QM/MM则适合用于对拥有较高结合分数的化合物进行再评分(rescoring)。
