In Silico Design of a Multimodal Trimeric Peptide Candidate Predicted to Simultaneously Target Glycemic Control, Autoimmunity, and Pancreatic β-Cell Regeneration in Type 1 Diabetes

Introduction: Type 1 diabetes mellitus (T1DM) currently affects 9.5 million individuals worldwide, with incidence rising through 2040. Clinical management remains anchored to exogenous insulin replacement, which neither arrests autoreactive CD8⁺ T-cell–mediated insulitis, nor blocks IL-1β–driven β-cell apoptosis, nor restores PDX-1/NGN3-dependent endocrine identity. No approved agent addresses these three pathological axes concurrently. Objective: To computationally design and validate TrimInsulinX-3 (TIX-3), a trimeric peptide candidate engineered to simultaneously engage the insulin receptor (InsR), the IL-1R1/IL-1βcomplex, and the GLP-1 receptor/PDX-1 axis within a single molecular scaffold. Methods: Three functionally orthogonal monomers M1-InsA, M2-ImmunoQ, and M3-BetaR, were de novo designed via RFdiffusion backbone generation, ProteinMPNN sequence optimization, and AlphaFold2 multimer validation, using exclusively open-source platforms. The trimeric construct was assembled with disulfide-stabilized PEG₄ linkers and subjected to 200 ns molecular dynamics (GROMACS 2023.3/AMBER ff19SB). Docking was performed with AutoDock Vina 1.2.7 and cross-validated with HADDOCK 2.4; binding free energies were computed via gmx_MMPBSA. ADMET properties were predicted using pkCSM and SwissADME; immunogenicity was assessed with NetMHCpan-4.1/NetMHCIIpan-4.3. Results: All monomers adopted stable helix–loop–helix folds (pLDDT > 85; iBSA > 850 Ų). Backbone RMSD stabilized below 2.3 Å over 200 ns simulations. Docking convergence was high across platforms (Cα RMSD < 1.6 Å), with predicted ΔGbind of −11.2, −10.6, and −11.9 kcal·mol⁻¹ for InsR, IL-1R1, and GLP-1R, respectively. The predicted ADMET profile, t½ ~18 h, subcutaneous bioavailability ~78%, LogP −1.4, negative AMES mutagenicity, is consistent with injectable peptide therapeutics. After iterative deimmunization, no strong MHC binders were identified across 166 alleles. Conclusion: TIX-3 is the first in silico –conceived trimeric peptide designed to address the metabolic, immunological, and regenerative axes of T1DM within a unified molecular architecture, and its predicted pharmacological profile supports advancement to experimental validation.