Predict potential drug targets from the ion channel proteins based on SVM.
The identification of molecular targets is a critical step in the drug discovery and development process. Ion channel proteins represent highly attractive drug targets implicated in a diverse range of disorders, in particular in the cardiovascular and central nervous systems. Due to the limits of experimental technique and low-throughput nature of patch-clamp electrophysiology, they remain a target class waiting to be exploited. In our study, we combined three types of protein features, primary sequence, secondary structure and subcellular localization to predict potential drug targets from ion channel proteins applying classical support vector machine (SVM) method. In addition, our prediction comprised two stages. In stage 1, we predicted ion channel target proteins based on whole-genome target protein characteristics. Firstly, we performed feature selection by Mann-Whitney U test, then made predictions to identify potential ion channel targets by SVM and designed a new evaluating indicator Q to prioritize results. In stage 2, we made a prediction based on known ion channel target protein characteristics. Genetic algorithm was used to select features and SVM was used to predict ion channel targets. Then, we integrated results of two stages, and found that five ion channel proteins appeared in both prediction results including CGMP-gated cation channel beta subunit and Gamma-aminobutyric acid receptor subunit alpha-5, etc., and four of which were relative to some nerve diseases. It suggests that these five proteins are potential targets for drug discovery and our prediction strategies are effective.
Huang
Chen
C
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China.
Zhang
Ruijie
R
Chen
Zhiqiang
Z
Jiang
Yongshuai
Y
Shang
Zhenwei
Z
Sun
Peng
P
Zhang
Xuehong
X
Li
Xia
X
D000465:Algorithms; D000595:Amino Acid Sequence; D002626:Chemistry, Pharmaceutical / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D015195:Drug Design; D016678:Genome; D006801:Humans; D007473:Ion Channels / Q000737:chemistry; D010363:Pattern Recognition, Automated / Q000379:methods; D004364:Pharmaceutical Preparations; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry; D020539:Sequence Analysis, Protein / Q000379:methods*
D007473:Ion Channels; D004364:Pharmaceutical Preparations; D011506:Proteins