MMFA-DTA: Multimodal Feature Attention Fusion Network for Drug-Target Affinity Prediction for Drug Repurposing Against SARS-CoV-2

Abstract

The continuous emergence of novel infectious diseases poses a significant threat to global public health security, necessitating the development of small-molecule inhibitors that directly target pathogens. The RNA-dependent RNA polymerase (RdRp) and main protease (Mpro) of SARS-CoV-2 have been validated as potential key antiviral drug targets for the treatment of COVID-19. However, the conventional new drug R&D cycle takes 10–15 years, failing to meet the urgent needs during epidemics. Here, we propose a general multimodal deep learning framework for drug repurposing, MMFA-DTA, to enable rapid virtual screening of known drugs and significantly improve discovery efficiency. By extracting graph topological and sequence features from both small molecules and proteins, we design attention mechanisms to achieve dynamic fusion across modalities. Results demonstrate the superior performance of MMFA-DTA in drug-target affinity prediction over several state-of-the-art baseline methods on Davis and KIBA data sets, validating the benefits of heterogeneous information integration for representation learning and interaction modeling. Further fine-tuning on COVID-19-relevant bioactivity data enhances model predictions for critical SARS-CoV-2 enzymes. Case studies screening the FDA-approved drug library successfully identify etacrynic acid as the potential lead compound against both RdRp and Mpro. Molecular dynamics simulations further confirm the stability and binding affinity of etacrynic acid to these targets. This study proves the great potential and advantages of deep learning and drug repurposing strategies in supporting antiviral drug discovery. The proposed general and rapid response computational framework holds significance for preparedness against future public health events.