Building And Analysing Of Chinese Medici Ne Monomers Virtual PDB Library

This study aims to provide convenience for virtual screening of traditional C hinese medicine minomers as drug lead compounds and informations query of rel evant proteins, meanwhile offer method and idea about mechanism of drug actio n from molecular level. Datebase is an important tool in drug research, there is less database about ligands interact with macromolecular, so we intend to build a virtual protein data bank of traditional Chinese medicine(traditional Chinese med icine monomers virtual PDB library for short). This paper introduced Chinese me dcine databases and Bioinformatics databases first. Many Chinese medicine datab ases have been built today and mainly included monomer compound library, Chi nese medicine components library, Chinese medicine chemical component databas e, Chinese medicine chemical information database; Bioinformatics datebase can be divided into four classes:Genome database, Nucleic acid and protein primary structure sequence database, biological macromolecular three-dimensional space s tructure database and the second literature database on the basis of the above thr ee kinds, the three-dimensional space structure of PDB is the main biological ma cromolecular database. It has been obtained wide attention to research pathologic al mechanism from protein molecular, but protein informations about diseases tha t threat to human health is lack of arrangement, for example, tumor, diseases of nervous system, and so on. It is need to build an integrated protein database tha t relate to diseases in order to summarize informations of proteins associate with common diseases and research mechanism of drug from molecular level, meanw hile promote development of medical biology and facilitate drug research.Traditional Chinese medicine has a long history in China and is still widely used. With fierce competition of western medicine development and a trend of return to natural, Chinese medicine has also been widely attention all over the w orld. In recent years, many pharmaceutical companies and researchers have turne d their attention to traditional Chinese medicine. Because components of traditio nal Chinese medicine are complicated, it is difficult to study active ingredients a nd mechanism, as a means for drug research, computer aided drug design has be en widely concerned. Virtual screening technology can accurately simulate interac tions between receptors and ligands, diminish scope of compounds screening. It will provide convenience for lead compounds screening from traditional Chinese medicine if we combined virtual screening with traditional experiment method to gether.The research based on RCSB PDB database and virtual screening platform of iScreen to build traditional Chinese medicine monomers virtual PDB library, t he main contents are as follows:1. Built traditional Chinese medicine monomers virtual PDB library. We buil t the library by using RCSB PDB database, iScreen online services, website of BLAST, Chimera software, Discovery Studio 3.5 (DS 3.5 for short) software. Th ere are about 3200 protein complexes in the library and mainly contains protein informations with original ligands and reference ligands, which will provide conv ience for protein informations query.2. Analysed proteins of PDB library. We combined Chimera software, DS 3. 5 software and Molsoft ICM-Browser software together to analyse proteins. By c omparing conformation match and key amino acid residues interactions between i nhibitors and traditional Chinese medicine monomers with proteins respectively, we can offer convenience for screen drug lead compounds on the one hand, on the other hand, it will supply idea and method for analysing mechanism about d rug action. We classified proteins to six kinds that includes virus, pathogens, turn ours, inflammatory, nervous systems, others to introduce.3. Researched bacteriostatic test of traditional Chinese medicine monomers an d analysed mechanisms. We used Candida albicans, Yeast and Hactobacillus acid ophilus as experimental strains to study. Results showed that baicalin, squalene a nd methyl behenate have no obvious effect on Candida albicans and Yeast; resul ts of squalene, methyl behenat and octacosane are not ideal on Hactobacillus aci dophilus. We concluded that conformation match between inhibitor and protein a nd interaction between inhibitor and key amino acid residue is required to gener ate inhibition effect.