In Silico Designing of APR-Derived Pentapeptides as Inhibitors of Human Insulin Amyloidogenesis

Abstract

An important therapeutic approach for the treatment of amyloidosis is the rational design of sequence-oriented short peptides, which can prevent the highly ordered cross-β-sheet aggregates formed by misfolded amyloidogenic proteins. In this chapter, we have emphasized human insulin that is a much-studied model protein for amyloidogenesis, because of its well-studied fibrillation pathways. We were able to examine the three delineated aggregation-prone regions (APRs) for targeting insulin aggregation: ICSLYQLENYCN [-9, -9] in the A-chain, HLVEALYL-at [-7] substitution in the B-chain; and RGFFYT [-6] which is the central hexapeptide motif of B-chain, and is important for nucleation and elongation of the fibril. We targeted these regions, as they greatly favor the formation of β-sheets and lead to aggregation. The designed short peptide inhibitors were deliberative to complement the amyloidogenic stretches, or impede their assembly ability. Each designed peptide was structurally optimized and energy minimized to achieve similar conformations and subsequent molecular docking simulations against all three APRs to analyze inhibition potential. Docking results provided substantial information regarding peptide-APR interactions, with primary peptide-APR binding scores, hydrogen-bonds, and residue-level contacts leading to candidates with high inhibition potential, overall. Comparison of three amyloidogenic hotspots showed that some designed peptides consistently had desirable affinity and stabilizing interactions that provided evidence of inhibition potential. Also, the highest represented homologs were the five ligands with the highest binding affinities out of all configured candidates; the five ligands with highest binding affinities being to YGKPN with a docking score of -8.7, YRLTK with -8.6, NRGYE with -8.5, YNPGK with -8.4, and YTIRD with -8.3; wherein all would interact with multiple APRs in stable interactions. These results provide a useful in-silico baseline for moving forward with these peptide inhibitors in in-vitro applications, which will provide further evaluation toward new peptide-based therapeutic approaches to regulate the formation of insulin-derived amyloid fibrils.