Mutations in the Aβ 42 Recognition Sequence KLVFF Afford New Pentapeptide Inhibitors of Aβ 42 Fibrillation: Computation-Driven Rational Design and Experimental Validation

Alzheimer’s disease (AD) is the most prevalent neurodegenerative disorder, marked by the accumulation of amyloid-β (Aβ) plaques in the brain, excessive tau protein phosphorylation, and cholinergic neuron degeneration. In this work, a library of computationally designed peptides based on the Aβ 42 recognition sequence KLVFF has been generated, which is further evaluated for its ability to effectively attenuate Aβ 42 fibrillation. Notably, molecular mechanics Poisson–Boltzmann surface area analysis identified three new peptides, RPPWF (Δ G binding = −58.08 ± 9.02 kcal/mol), RPPWY (Δ G binding = −46.13 ± 3.62 kcal/mol), and KPPWW (Δ G binding = −44.27 ± 4.08 kcal/mol), displaying significantly higher binding affinity to the Aβ 42 monomer (Aβ 42 m) compared to KLVFF (Δ G binding = −38.70 ± 17.17 kcal/mol). Importantly, among the designed peptides, RPPWF induces the helix conformation in Aβ 42 m to the maximum extent and prevents the conformational transitions in Aβ 42 m to aggregation-competent β-sheet structures. Furthermore, the thioflavin T (ThT) fluorescence assay depicted no self-fibrillation of RPPWF and a maximum inhibitory effect among the synthesized peptides (IC 50 = 8.90 ± 0.98 μM) against Aβ 42 fibrillation, consistent with the computational results. Notably, DLS and TEM analyses confirmed the RPPWF-induced modulation in Aβ 42 fibrillation. RPPWF efficiently rescued PC12 cells from Aβ 42 aggregate-induced neurotoxicity by notably enhancing cell viability to 89.6% as compared to 42.2% (Aβ 42 alone). Remarkably, this study highlights the synergistic effect of multiple substitutions (K → R, L → P, V → P, and F → W) in the amyloidogenic KLVFF sequence of Aβ 42 and depicts the importance of arginine, proline, and tryptophan residues in the RPPWF sequence in affording an efficient new potent inhibitor, RPPWF, of Aβ 42 fibrillation. Furthermore, RPPWF has the potential for conjugation or further modifications to afford more effective and clinically relevant multifunctional agents against Aβ 42 fibrillation in AD.