Integrative Peptide Drug Development: Chemical Engineering, AI-Driven Design, and Cell-Penetrating Peptides

Peptide therapeutics occupy a unique chemical space between small molecules and biologics, combining high target specificity with structural programmability and favorable safety profiles. Recent regulatory approvals and expanding clinical pipelines underscore the growing therapeutic and commercial relevance of peptide-based drugs. This review outlines chemical modification approaches and contemporary design strategies, and evaluates their impact on proteolytic stability, pharmacokinetics, membrane permeability, and target engagement. We then highlight recent advances in artificial intelligence (AI)-guided peptide drug design, including machine learning models, protein language models, and generative architectures that enable high-throughput activity prediction, property optimization, and de novo sequence generation. These approaches collectively accelerate the traditional discovery-design-validation cycle while reducing experimental attrition through data-driven, structure-informed modeling frameworks. Among these applications, AI also enables the rational design of cell-penetrating peptides (CPPs) to enhance intracellular delivery and biological activity. Building on these methodological advances, we further examine their application to peptide therapeutics, with particular emphasis on AI-based predictive models for CPPs as well as on therapeutic applications within the central nervous and pulmonary systems. We conclude by outlining future perspectives and emphasize that the systematic integration of AI-enabled sequence design with rational chemical engineering and advanced delivery technologies, supported by rigorous experimental validation, will be critical for developing robust and clinically durable peptide-based medicines.