Prediction of target proteins using compound-protein-phenotype multi-layer model

Abstract

Basic process of drug bioactivity that is pharmaceutical effects and side effects is as follows. Compound interacts with target proteins. The activated proteins transmit signals into the cell, that is called signaling pathways. The signaling pathway results in cellular phenotype changes such as cell death, proliferation, differentiation, and so on. Our motivation for rational drug design is to understand molecular mechanism from drugs to phenotypes, involving interactions between drugs, target proteins, pathways, and phenotypes. In this study, we constructed a multi-layer model for predicting target proteins using chemical and biological data such as drugs, proteins, and phenotypes. We proposed a machine learning method that predicted associations between drugs and phenotypes, and so target proteins involved in the phenotypic changes.