Identifying unexpected drug interactions is an essential step in drug development. Most studies focus on predicting whether a drug pair interacts or is effective on a certain disease without considering the mechanism of action (MoA). Here, we introduce a novel method to infer effects and interactions of drug pairs with MoA based on the profiling of systemic effects of drugs. By investigating propagated drug effects from the molecular and phenotypic networks, we constructed profiles of 5,441 approved and investigational drugs for 3,833 phenotypes. Our analysis indicates that highly connected phenotypes between drug profiles represent the potential effects of drug pairs and the drug pairs with strong potential effects are more likely to interact. When applied to drug interactions with verified effects, both therapeutic and adverse effects have been successfully identified with high specificity and sensitivity. Finally, tracing drug interactions in molecular and phenotypic networks allows us to understand the MoA.

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BackgroundNatural products have been widely investigated in the drug development field. Their traditional use cases as medicinal agents and their resemblance of our endogenous compounds show the possibility of new drug development. Many researchers have focused on identifying therapeutic effects of natural products, yet the resemblance of natural products and human metabolites has been rarely touched.MethodsWe propose a novel method which predicts therapeutic effects of natural products based on their similarity with human metabolites. In this study, we compare the structure, target and phenotype similarities between natural products and human metabolites to capture molecular and phenotypic properties of both compounds. With the generated similarity features, we train support vector machine model to identify similar natural product and human metabolite pairs. The known functions of human metabolites are then mapped to the paired natural products to predict their therapeutic effects.ResultsWith our selected three feature sets, structure, target and phenotype similarities, our trained model successfully paired similar natural products and human metabolites. When applied to the natural product derived drugs, we could successfully identify their indications with high specificity and sensitivity. We further validated the found therapeutic effects of natural products with the literature evidence.ConclusionsThese results suggest that our model can match natural products to similar human metabolites and provide possible therapeutic effects of natural products. By utilizing the similar human metabolite information, we expect to find new indications of natural products which could not be covered by previous in silico methods.

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