OptNCMiner: a deep learning approach for the discovery of natural compounds modulating disease-specific multi-targets

BACKGROUND: Due to their diverse bioactivity, natural product (NP)s have been developed as commercial products in the pharmaceutical, food and cosmetic sectors as natural compound (NC)s and in the form of extracts. Following administration, NCs typically interact with multiple target proteins to elicit their effects. Various machine learning models have been developed to predict multi-target modulating NCs with desired physiological effects. However, due to deficiencies with existing chemical-protein interaction datasets, which are mostly single-labeled and limited, the existing models struggle to predict new chemical-protein interactions. New techniques are needed to overcome these limitations. RESULTS: We propose a novel NC discovery model called OptNCMiner that offers various advantages. The model is trained via end-to-end learning with a feature extraction step implemented, and it predicts multi-target modulating NCs through multi-label learning. In addition, it offers a few-shot learning approach to predict NC-protein interactions using a small training dataset. OptNCMiner achieved better prediction performance in terms of recall than conventional classification models. It was tested for the prediction of NC-protein interactions using small datasets and for a use case scenario to identify multi-target modulating NCs for type 2 diabetes mellitus complications. CONCLUSIONS: OptNCMiner identifies NCs that modulate multiple target proteins, which facilitates the discovery and the understanding of biological activity of novel NCs with desirable health benefits. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-022-04752-5.