a5b3021f9256ebde9f2fb567bfc96757 biomolecules-16-01445.pdf 9efd3fc23555f499875e390945f1a226114e7d2b biomolecules-16-01445.pdf bed9565471876f668b64448c4102d4569f4aa980a0c6e72edf53db8d4fe5022f biomolecules-16-01445.pdf Title: Artificial Intelligence for Therapeutic Peptide Discovery and Development Subject: Therapeutic peptides combine biological specificity with chemical versatility, and artificial intelligence (AI) now contributes to their identification, design, and optimisation. Peptide discovery, however, cannot be reduced to generating amino-acid sequences: therapeutic performance also depends on chemistry, conformation, assay context, stability, delivery, safety, manufacturability, and in vivo exposure. This critical review examines AI use across the major peptide classes: receptor agonists, protein–protein interaction inhibitors, oncology and tumour-targeting peptides, antimicrobial and phenotype-driven peptides, delivery peptides, vaccine epitopes, self-assembling materials, and chemically constrained macrocycles. It compares sequence-based, chemical, graph, structure-aware, and multimodal representations across predictive, generative, and experimentally integrated workflows. Coverage spans recent general protein foundation, prediction, and design systems (ProtGPT2, ESM-2/ESM3, ProGen/ProGen2, ProteinMPNN, RFdiffusion, and AlphaFold 3) and peptide-focused methods (RFpeptides, PepFlow, and PepGLAD). Particular attention is given to benchmark integrity, the limits of structure prediction for short and non-canonical molecules, and the gap between retrospective and prospective evidence. To make claims comparable, the review adapts established reporting, validation, and readiness concepts into a peptide-specific, two-dimensional Peptide–AI Evidence Grid that separates methodological rigour (M0–M3) from translational depth (T0–T3), applies it to representative studies, and provides a checklist extending DOME, TRIPOD + AI, and FAIR guidance with the chemistry- and assay-specific items peptide work requires. Keywords: therapeutic peptides; artificial intelligence; peptide design; protein language models; generative models; molecular representation; non-canonical amino acids; active learning; benchmark integrity; translational validation Author: Salvador Ventura Creator: LaTeX with hyperref Producer: pdfTeX-1.40.29; modified using OpenPDF 1.4.2 CreationDate: Sat Oct 3 11:41:51 2026 CEST ModDate: Sat Oct 3 11:49:22 2026 CEST Custom Metadata: yes Metadata Stream: no Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 45 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 514078 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- UXUPMC+URWPalladioL-Ital Type 1 Custom yes yes yes 247 0 PPLOHK+URWPalladioL-Bold Type 1 Custom yes yes yes 248 0 QKZKVH+VnURWPalladioL Type 1 Custom yes yes yes 249 0 PVMPEW+URWPalladioL-Roma Type 1 Custom yes yes yes 250 0 ASZHDD+CMSY10 Type 1 Builtin yes yes yes 400 0 GUQMNN+EURM10 Type 1 Builtin yes yes yes 401 0 SIFNRY+URWPalladioL-BoldItal Type 1 Custom yes yes yes 462 0 Jhove (Rel. 1.28.0, 2023-05-18) Date: 2026-10-20 03:56:39 CEST RepresentationInformation: biomolecules-16-01445.pdf ReportingModule: PDF-hul, Rel. 1.12.4 (2023-03-16) LastModified: 2026-10-19 12:57:49 CEST Size: 514078 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 1137 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: ViewerPreferences: HideToolbar: false HideMenubar: false HideWindowUI: false FitWindow: true CenterWindow: false DisplayDocTitle: false NonFullScreenPageMode: UseNone Direction: L2R ViewArea: CropBox ViewClip: CropBox PrintArea: CropBox PageClip: CropBox PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Item: Title: The Design Space Children: Item: Title: Endocrine and Metabolic Peptides Item: Title: Target-Specific PPI and Intracellular Inhibitors Item: Title: Oncology, Tumour-Targeting, and Peptide Conjugates Item: Title: Phenotype-Driven Antimicrobial and Related Peptides Item: Title: Cell-Penetrating, Oral-Delivery, and Auxiliary Functional Peptides Item: Title: Vaccine, Epitope, and Immunomodulatory Peptides Item: Title: Self-Assembling Peptides and Peptide Materials Item: Title: Data Foundations and Benchmark Integrity Children: Item: Title: Split Design and External Validation Item: Title: Leakage, Reproducibility, and Negative Data Item: Title: Molecular Representation: What Must a Peptide Model Encode? Children: Item: Title: Sequence and Protein-Language Representations Item: Title: Chemical Languages, Graphs, and Atom-Level Models Item: Title: Topology and Specific Chemical Modifications Item: Title: Three-Dimensional Ensembles and Multimodal Representations Item: Title: Predictive Modelling: Activity, Developability, and Safety Children: Item: Title: Target Activity, Peptide-Protein Interactions, and Model Reliability Item: Title: Solubility, Aggregation, Stability, and Permeability Item: Title: Manufacturability and Regulatory Constraints Item: Title: Toxicity, Immunogenicity, and Off-Target Liabilities Item: Title: Generative Design Across Therapeutic Peptide Classes Children: Item: Title: Sequence Generation and Foundation-Model Conditioning Item: Title: Multi-Objective Optimisation and Pareto Reporting Item: Title: Cyclic, Stapled, and Chemically Constrained Generation Item: Title: Generative Design for CPPs, Oncology, Vaccines, and Self-Assembly Item: Title: How to Interpret a Generative Peptide Study Item: Title: Structure-Aware Peptide Design Children: Item: Title: Why Peptide-Protein Complexes Remain Difficult Item: Title: Non-Canonical Chemistry and Model Mismatch Item: Title: A Defensible Structural Workflow Item: Title: Integrating Models with Experiments Children: Item: Title: Prospective Candidate Selection and Matched Comparators Item: Title: Active Learning and Experimental Information Gain Item: Title: Autonomous Agents, Reinforcement Learning, and Human Oversight Item: Title: From Computational Score to Therapeutic Evidence Children: Item: Title: Reading the Grid Item: Title: Minimum Versus Ideal Evidence Item: Title: Reporting Standards for Peptide AI Children: Item: Title: Relation to Existing Reporting Frameworks Item: Title: Benchmark Standards and Thresholds Item: Title: Outlook: Testable Priorities for the Next Generation of Peptide AI Item: Title: Conclusions Item: Title: References Info: Title: Artificial Intelligence for Therapeutic Peptide Discovery and Development Author: Salvador Ventura Subject: Therapeutic peptides combine biological specificity with chemical versatility, and artificial intelligence (AI) now contributes to their identification, design, and optimisation. Peptide discovery, however, cannot be reduced to generating amino-acid sequences: therapeutic performance also depends on chemistry, conformation, assay context, stability, delivery, safety, manufacturability, and in vivo exposure. This critical review examines AI use across the major peptide classes: receptor agonists, protein–protein interaction inhibitors, oncology and tumour-targeting peptides, antimicrobial and phenotype-driven peptides, delivery peptides, vaccine epitopes, self-assembling materials, and chemically constrained macrocycles. It compares sequence-based, chemical, graph, structure-aware, and multimodal representations across predictive, generative, and experimentally integrated workflows. Coverage spans recent general protein foundation, prediction, and design systems (ProtGPT2, ESM-2/ESM3, ProGen/ProGen2, ProteinMPNN, RFdiffusion, and AlphaFold 3) and peptide-focused methods (RFpeptides, PepFlow, and PepGLAD). Particular attention is given to benchmark integrity, the limits of structure prediction for short and non-canonical molecules, and the gap between retrospective and prospective evidence. To make claims comparable, the review adapts established reporting, validation, and readiness concepts into a peptide-specific, two-dimensional Peptide–AI Evidence Grid that separates methodological rigour (M0–M3) from translational depth (T0–T3), applies it to representative studies, and provides a checklist extending DOME, TRIPOD + AI, and FAIR guidance with the chemistry- and assay-specific items peptide work requires. 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