Synergistic Data Mining Methods Between Functional Genomics And Chemoinformatics In Drug Development

Drug development is an integrated process involving mathematics,chemistry, biology, computer science and so on. The key points in thedrug development process is to find drug targets and the mechanism ofaction. After the completion of the Human Genome Project, peoplegenerally believed that along with the large-scale high-throughputgenomics and bio-informatics technology, the discovery of new drugtarget will presents a geometric growth. But in fact, the speed of drugdevelopment all these years did not have much improvement. Thereason mainly lies in the lag of high-throughput data analysis means.The traditional method for the analysis of gene expression data is toseek drug targets within a lot of difference expressed genes. Thispractice is tantamount to fish for a needle in the ocean.To solve this problem, a large-scale cross-species data miningmethod, CGEMining, is developed in this paper to dig information ofdrug mechanism, drug repositioning, side effects, and combination ofmedication. By combining various transcriptome data of disease ordrug experiments on animals, CGEMining could dig out drugrepositioning, side effects and drug mechanisms from the drug-diseaseor drug-drug relationships. For some small molecule drugs withunknown mechanism, CGEMining methods could help find thepotential targets by comparative analysis, and then docking will be used to confirm the results. This process is illustrated by a case ofanalyzing the target of diabetes drugs. For some herbal compound thatcontains a variety of ingredients, CGEMining method could not onlydig out its complex mechanism, but also discover its new features. Inaddition to the CGEMining method, another method, VIScreen, willalso be introduced in this paper, which combines viral protein sequencedata and chemical informatics. VIScreen takes chemoinformaticsstructure information as an intermediary for creating linkages betweenviral protein sequences and drug small molecules and then mine thepotential combination of viral drugs and protein targets. Finally, thispaper also introduced a causal co-expression network analysis methodto study the difference between two drugs in network pharmacology.