Agentic Discovery of Non-Canonical Antimicrobial Peptides with AMPGAN v3

Authors:Jay Jung, Xiaohan Zhang, Shenghan Song, Mahmoud Sayedahmed, Chijian Xiang, Yunong Xu, Ahmed AbdelKhalek, Severin T. Schneebeli, Matthew J. Wargo, Jianing Li, Safwan Wshah

Abstract:Antimicrobial resistance causes to over a million deaths annually. Antimicrobial peptides (AMPs) are a promising solution, but generative AMP models are not yet ready to design peptides with non-natural amino acids and/or chemical modifications, which are essential for real-world peptide drugs. We present AMPGAN v3, a multi-objective conditional GAN that expands the generative vocabulary to D-amino acids and N/C-terminus modifications such as amidation. By separating adversarial and activity-aware supervision across two specialized discriminators, AMPGAN v3 substantially improves training stability and outperforms prior generative AMP models on external classifiers. We validated five candidates spanning three structural classes in vitro; two showed activity against Gram-positive strains, with the best candidate reaching MIC 8 {\mu}g/mL against B. subtilis. To support downstream curation, we further present PepCraft, a multi-agent framework for end-to-end AMP discovery in which a Planning Agent orchestrates specialized executors for generation, filtering, and verification. Its prioritization recommendations align with our in vitro outcomes. Together, these contributions let us examine, on a small but real scale, how generative and agentic AI compose in therapeutic peptide discovery. Code: this https URL

Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)

arXiv:2606.17127 [q-bio.QM]

(or arXiv:2606.17127v1 [q-bio.QM] for this version)