Artificial Intelligence as a Catalyst for Antimicrobial Discovery: From Predictive Models to De Novo Design
Romaisaa Boudza, Salim Bounou, Jaume Segura-García, Ismaïl Moukadiri, Sergi Maicas
Abstract
Antimicrobial resistance represents one of the most critical global health challenges of the 21st century, urgently demanding innovative strategies for antimicrobial discovery. Traditional antibiotic development pipelines are slow, costly, and increasingly ineffective against multidrug-resistant pathogens. In this context, recent advances in artificial intelligence have emerged as transformative tools capable of accelerating antimicrobial discovery and expanding accessible chemical and biological space. This comprehensive review critically synthesizes recent progress in AI-driven approaches applied to the discovery and design of both small-molecule antibiotics and antimicrobial peptides. We examine how machine learning, deep learning, and generative models are being leveraged for virtual screening, activity prediction, mechanism-informed prioritization, and de novo antimicrobial design. Particular emphasis is placed on graph-based neural networks, attention-based and transformer architectures, and generative frameworks such as variational autoencoders and large language model-based generators. Across these approaches, AI has enabled the identification of structurally novel compounds, facilitated narrow-spectrum antimicrobial strategies, and improved interpretability in peptide prediction. However, significant challenges remain, including data scarcity and imbalance, limited experimental validation, and barriers to clinical translation. By integrating methodological advances with a critical analysis of the current limitations, this review highlights emerging trends and outlines future directions aimed at bridging the gap between in silico discovery and real-world therapeutic development.