In silico design of a novel more stable metal binding MESD-derived peptide for targeting the second functional domains of LRP6

The Wnt/β-catenin signalling is one of the most conserved pathways with a crucial role in embryonic development, tissue homeostasis, and cancers. LRP6, a co-receptor with two large functional domains (E1E2 and E3E4), binds Wnt ligands alongside Frizzled receptors, making it a therapeutic target in cancers. The LRP6 has an essential chaperone called MESD, which proved to be a competitive inhibitor of Wnt molecules, with its inhibitory activity residing in the carboxyl-terminal escort domain. The carboxyl-terminal, composed of two helices linked by a short loop, resembles the EF-hand domain of calmodulin, showing lower efficacy than the full-length protein, compared with full-length MESD. Here, considering the structural similarity of the MESD C-terminal domain to EF-hand and its helix-loop-helix (HLH) stabilization potential, using molecular modelling, molecular docking, and all-atom molecular dynamics simulation, we designed a chimeric peptide derived from MESD and the EF-hand, which is not only more stable, showing higher number of intramolecular hydrogen bond and helicity, but also displays comparable potential of Wnt inhibitory function as gained by full-length MESD and its C-terminal derived peptide. Moreover, MM/PBSA analysis and free energy landscape plot, along with PCA and correlation analysis, revealed that the chimeric peptide has a distinguishably better potential for inhibiting Wnt proteins which bound to the E3E4-LRP6 functional domain. This study paves the way for designing novel chimer-metal bound peptides with similar structures with stable nature-designed motifs with optimal efficacy and stability, targeting pivotal cancer-relevant signalling pathways such as Wnt/β-catenin. • Inspired by the calmodulin EF-hand we designed a metal-binding MESD peptide variant with enhanced structural stability gains. • The study used validated full-length MESD and its C-terminal peptide to compare baseline states with the Ca-bound variant. • The designed peptide shows greater stability, with increased helicity and improved hydrogen bonding for resilience. • MMPBSA analysis shows significantly stronger binding affinity to the second functional domain of LRP6 target site.