A unified framework for potency-oriented AMP discovery via multi-modal learning and guided sequence synthesis

The rapid emergence of drug-resistant pathogens poses a critical threat to global health. With traditional antibiotics losing efficacy, antimicrobial peptides (AMPs) have gained attention for their unique mechanisms and lower resistance potential. We aimed to accelerate AMP discovery by proposing a closed-loop framework that combines AMP-Hunter (a shared-architecture discriminator for AMP classification and MIC prediction that integrates convolutional neural networks with graph neural networks), and AMP-Forge (a generator integrating multiple sequence alignment to select original candidates) and is guided by minimum inhibitory concentration (MIC)for latent space optimization and candidate selection. AMP-Hunter outperformed baseline models in both AMP classification and MIC prediction, achieving 95.82% accuracy and a 95.80% F1 score on the test set for classification, and an R2 of 0.9245 with an MAE of 0.2305 for MIC prediction. Guided by its predictions, AMP-Forge generated peptide sequences with lower MIC values and improved physicochemical properties associated with antimicrobial activity. Molecular dynamics simulations further provided in silico evidence supporting the antimicrobial potential of selected sequences by identifying stable membrane disruption and insertion behaviors consistent with membrane-targeting activity. Thus, the generation-screening-validation workflow enables reliable discovery of potent AMPs, and provides a practical strategy for rational peptide design, rapid prediction, and translational applications.