title: Drug repositioning by applying 'expression profiles' generated by integrating chemical structure similarity and gene semantic similarity.
abstract: Drug repositioning, also known as drug repurposing or reprofiling, is the process of finding new indications for established drugs. Because drug repositioning can reduce costs and enhance the efficiency of drug development, it is of paramount importance in medical research. Here, we present a systematic computational method to identify potential novel indications for a given drug. This method utilizes some prior knowledge such as 3D drug chemical structure information, drug-target interactions and gene semantic similarity information. Its prediction is based on another form of 'expression profile', which contains scores ranging from -1 to 1, reflecting the consensus response scores (CRSs) between each drug of 965 and 1560 proteins. The CRS integrates chemical structure similarity and gene semantic similarity information. We define the degree of similarity between two drugs as the absolute value of their correlation coefficients. Finally, we establish a drug similarity network (DSN) and obtain 33 modules of drugs with similar modes of action, determining their common indications. Using these modules, we predict new indications for 143 drugs and identify previously unknown indications for 42 drugs without ATC codes. This method overcomes the instability of gene expression profiling derived from experiments due to experimental conditions, and predicts indications for a new compound feasibly, requiring only the 3D structure of the compound. In addition, the high literature validation rate of 71.8% also suggests that our method has the potential to discover novel drug indications for existing drugs.
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin, Heilongjiang 150081, PR China. chenxiujie@ems.hrbmu.edu.cn.
authors.forename: Fujian
authors.initials: F
authors.lastname: Tan
authors.forename: Ruizhi
authors.initials: R
authors.lastname: Yang
authors.forename: Xiaoxue
authors.initials: X
authors.lastname: Xu
authors.forename: Xiujie
authors.initials: X
authors.lastname: Chen
authors.forename: Yunfeng
authors.initials: Y
authors.lastname: Wang
authors.forename: Hongzhe
authors.initials: H
authors.lastname: Ma
authors.forename: Xiangqiong
authors.initials: X
authors.lastname: Liu
authors.forename: Xin
authors.initials: X
authors.lastname: Wu
authors.forename: Yuelong
authors.initials: Y
authors.lastname: Chen
authors.forename: Lei
authors.initials: L
authors.lastname: Liu
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Jia
mesh_terms: D016000:Cluster Analysis; D058492:Drug Repositioning; D020869:Gene Expression Profiling; D063990:Gene Ontology; D005796:Genes; D058977:Molecular Sequence Annotation; D004364:Pharmaceutical Preparations / Q000737:chemistry* / Q000378:metabolism*; D011506:Proteins / Q000235:genetics / Q000378:metabolism; D012660:Semantics; D012984:Software
chemical_list: D004364:Pharmaceutical Preparations; D011506:Proteins