MCPI: Integrating Multimodal Data for Enhanced Prediction of Compound Protein Interactions

TL;DR

This paper introduces MCPI, a novel model that integrates multiple data sources like networks and structural features to improve compound-protein interaction prediction, aiding drug discovery and repurposing.

Contribution

The study presents MCPI, a new integrative model that combines diverse data types to enhance CPI prediction accuracy over existing methods.

Findings

MCPI outperforms existing CPI prediction models on public datasets.

MCPI successfully identified potential SARS-CoV-2 inhibitors among FDA-approved drugs.

Predictions validated through literature support MCPI's practical utility.

Abstract

The identification of compound-protein interactions (CPI) plays a critical role in drug screening, drug repurposing, and combination therapy studies. The effectiveness of CPI prediction relies heavily on the features extracted from both compounds and target proteins. While various prediction methods employ different feature combinations, both molecular-based and network-based models encounter the common obstacle of incomplete feature representations. Thus, a promising solution to this issue is to fully integrate all relevant CPI features. This study proposed a novel model named MCPI, which is designed to improve the prediction performance of CPI by integrating multiple sources of information, including the PPI network, CCI network, and structural features of CPI. The results of the study indicate that the MCPI model outperformed other existing methods for predicting CPI on public datasets. Furthermore, the study has practical implications for drug development, as the model was applied to search for potential inhibitors among FDA-approved drugs in response to the SARS-CoV-2 pandemic. The prediction results were then validated through the literature, suggesting that the MCPI model could be a useful tool for identifying potential drug candidates. Overall, this study has the potential to advance our understanding of CPI and guide drug development efforts.