Delineating the structural distortions in hIAPP protofibrils by rationally designed hexapeptides using computer...

Disease-associated fibrillation of human islet amyloid polypeptide (hIAPP), also referred to as human amylin, plays a pivotal role in the etiology of type 2 diabetes (T2D). The hIAPP fibrillation leads to the generation of cytotoxic β-sheet-rich oligomers and protofibrils that contribute to the apoptosis of pancreatic β-cells. Potter et al. reported hIAPP fragment peptide ANFLVH (residues 13-18, designated as AF6) as a potent inhibitor of hIAPP fibrillation. Notably, AF6 blocked IAPP fibrillation in vitro and in human islet cell cultures, which noticeably enhanced the viability of islet cells. In this work, a structure-based virtual screening approach was employed to screen a library of hexapeptides generated through systematic mutations in AF6, and the potential of the top hit peptides for the conformational destabilization of full-length ζ-shaped hIAPP protofibrils (PDB: 7YKW) has been assessed using molecular docking, MM-PBSA, and molecular dynamics (MD) simulations. Notably, AQYPVH (AY6) and PQWPPH (PW6) displayed high-affinity binding to hIAPP protofibrils, mainly governed by van der Waals interactions, with binding free energies of -30.17 ± 5.92 and -27.19 ± 4.25 kcal mol^-1, respectively, as compared to -21.42 ± 3.63 kcal mol^-1 for AF6. Importantly, MD simulations revealed progressive destabilization of hIAPP protofibrils upon the incorporation of AY6 and PW6, characterized by enhanced structural fluctuations and reduced interchain hydrogen bonds in hIAPP protofibrils. Interestingly, a decline in the β-sheet with an associated rise in coil content in hIAPP protofibrils was noticed upon the incorporation of AF6 and top hit peptides (AY6 and PW6), with the most pronounced modulation in the secondary structure noticed in the presence of PW6, depicting structural destabilization and deformation in the ζ-shaped hIAPP protofibril. Notably, conformational snapshots corroborated PW6-induced structural changes in the protofibril, illustrating disruption of the ζ-shaped hIAPP protofibril by progressive strand loosening and structural deformation. Furthermore, the in silico ADMET analysis depicted favourable solubility and low toxicity, suggesting drug-likeness of the top hit peptides. The present study, for the first time, illuminated the binding interactions of AF6 with hIAPP protofibrils as well as AF6-mediated structural distortions in hIAPP protofibrils. Importantly, computation-driven rational design, followed by structure-based virtual screening and MD validation in this work, identified a novel hexapeptide, PW6, with noteworthy potential to destabilize the hIAPP protofibril.