AI-guided design of candidate BMPR1A-binding peptides for cartilage regeneration: a multi-tool computational benchmarking study

Abstract

Bone morphogenetic protein receptor type IA (BMPR1A) is a key mediator of chondrogenesis and a validated therapeutic target for cartilage repair, yet existing BMP mimetic peptides suffer from low potency and the full-length protein (rhBMP-2) carries significant safety risks. Generative AI tools for protein design can now produce de novo peptide binders, but none have been applied to cartilage regeneration targets. Here, we benchmarked four architecturally distinct AI tools--RFdiffusion, BindCraft, PepMLM, and RFpeptides--to design candidate BMPR1A-binding peptides. We generated 192 candidates alongside 98 negative controls (290 total) and evaluated all complexes using AlphaFold 3 structure prediction, dual physics-based energy scoring (PyRosetta and FoldX), and contact recapitulation against the crystallographic BMP-2:BMPR1A interface (PDB: 1REW). A four-metric composite ranking identified a 15-residue PepMLM design (pepmlm_L15_0026) as the top candidate, combining favorable binding energy (PyRosetta dGseparated = -45.9 REU; FoldX {Delta}G = -19.4 kcal/mol) with the highest contact recapitulation among top-ranked peptides (11/30 gold-standard interface residues). Designed candidates significantly outperformed controls on ipTM (p = 0.002) and FoldX {Delta}G (p < 0.001). BindCraft candidates achieved the highest structural confidence (ipTM up to 0.81) but exhibited moderate contact recapitulation (mean 0.224), consistent with the computational hypothesis that they may engage alternative BMPR1A binding surfaces rather than the native BMP-2 interface. Physicochemical filtering yielded a shortlist of 54 candidates across all four tools. These results establish a reproducible computational framework for AI-guided peptide design targeting cartilage regeneration and identify specific candidates for future experimental validation via binding assays and chondrocyte differentiation studies. Author summaryDamaged cartilage has limited capacity to heal, and current biological therapies based on bone morphogenetic protein 2 (BMP-2) carry serious safety concerns including ectopic bone formation and inflammation. Short peptides that mimic BMP-2s interaction with its receptor BMPR1A could offer a safer, more targeted alternative, but designing such peptides from scratch is challenging. We used four different artificial intelligence tools--each employing a distinct computational strategy--to generate 192 candidate peptides designed to bind BMPR1A. We then evaluated all candidates using multiple independent computational methods to assess binding quality, energy favorability, and whether each peptide targets the correct site on the receptor. Our analysis identified a shortlist of 54 promising candidates, with a 15-residue peptide from the language model-based tool PepMLM emerging as the top-ranked design. We also found evidence that one tool (BindCraft) may produce peptides that bind BMPR1A at sites different from the natural BMP-2 interface, highlighting the importance of validating not just whether a peptide binds, but where it binds. Our computational framework and candidate peptides provide a foundation for future laboratory testing toward cartilage repair therapies.