Dendritic polymers in glycobiology

Approaches to the synthesis of glycodendrimers, monodisperse and polyvalent models used to study molecular recognition processes, and their biological properties are considered. Dedicated to Academician Nikolai Konstantinovich Kochetkov, the founder of the Russian school of carbohydrates on the occasion of his 90th birthday. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 1037–1055, May, 2005.     

基于网络药理学探究黄酮对2型糖尿病的作用机制

应用网络药理学的方法探究了已分离得到的6个黄酮与2型糖尿病相互作用的机制.通过相关数据库的筛选与预测,获得了化合物与疾病的靶基因,进一步得到了两者的交集基因;通过Cytoscape 3.8.0软件构建了这些化合物与2型糖尿病相关的PPI网络与成分-疾病-靶点网络图;通过R语言半编程程序对交集基因进行生物功能富集和通路富...     

Dendrimer building toolkit: Model building and characterization of various dendrimer architectures

We have developed a graphical user interface based dendrimer builder toolkit (DBT) which can be used to generate the dendrimer configuration of desired generation for various dendrimer architectures. The validation of structures generated by this tool was carried out by studying the structural properties of two well known classes of dendrimers: ethylenediamine cored poly(amidoamine) (PAMAM) dendrimer, diaminobutyl cored poly(propylene imine) (PPI) dendrimer. Using full atomistic molecular dynamics (MD) simulation we have calculated the radius of gyration, shape tensor and monomer density distribution for PAMAM and PPI dendrimer at neutral and high pH. A good agreement between the available simulation and experimental (small angle X‐ray and neutron scattering; SAXS, SANS) results and calculated radius of gyration was observed. With this validation we have used DBT to build another new class of nitrogen cored poly(propyl ether imine) dendrimer and study it's structural features using all atomistic MD simulation. DBT is a versatile tool and can be easily used to generate other dendrimer structures with different chemistry and topology. The use of general amber force field to describe the intra‐molecular interactions allows us to integrate this tool easily with the widely used molecular dynamics software AMBER. This makes our tool a very useful utility which can help to facilitate the study of dendrimer interaction with nucleic acids, protein and lipid bilayer for various biological applications. © 2012 Wiley Periodicals, Inc.     

基于网络药理学的五苓散多成分-多靶点-多通路作用机制研究

通过中药系统药理学数据库与分析平台（traditional Chinese medicine system pharmacology datebase and analysis platform,TCMSP)筛选五苓散组分白术、茯苓、猪苓、泽泻、桂枝的潜在活性成分,PharmMapper服务器预测潜在靶点,构建化合物-靶点网络、蛋白互作( protein-protein interaction,PPI) 网络,进行基因本体( gene ontology,GO) 富集分析、基于KEGG( Kyoto encyclopedia of genes and enomes) 的生物通路富集分析。结果表明,筛选得到五苓散中50种活性成分,构建化合物 靶点网络共459个节点,关键靶点包括CSDE1、PRPS1、HSD17B4、CLPP、ACBD7、AZGP1等。构建五苓散靶点的PPI互作网络包含155个节点和527条相互作用关系,关键节点包括CSDE1、CITED2、RANBP2、HSD17B4、TAF13、SOD2等。GO富集分析途径相关条目主要涉及细胞溶质、细胞对有机物质和化学刺激的反应,含氮物质代谢,有机物循环代谢进程,蛋白、小分子和离子结合及转运活性等。KEGG代谢通路分析包括膀胱癌、前列腺癌、内分泌抵抗、癌症中的蛋白聚糖、流体剪切应力和动脉粥样硬化等途径。研究结果初步验证了五苓散药理作用的分子机制,为进一步深入揭示其分子作用机制奠定了基础,预测五苓散的潜在作用靶点如PRPS1、HSD17B4等,可为五苓散的深入研究提供新思路。