Elucidating the multi-targeted anti-amyloid activity and enhanced islet amyloid polypeptide binding of β-wrapins

Abstract

β-wrapins are engineered binding proteins stabilizing the β-hairpin conformations of amyloidogenic proteins islet amyloid polypeptide (IAPP), amyloid-β, and α-synuclein, thus inhibiting their amyloid propensity. Here, we use computational and experimental methods to investigate the molecular recognition of IAPP by β-wrapins. We show that the multi-targeted, IAPP, amyloid-β, and α-synuclein, binding properties of β-wrapins originate mainly from optimized interactions between β-wrapin residues and sets of residues in the three amyloidogenic proteins with similar physicochemical properties. Our results suggest that IAPP is a comparatively promiscuous β-wrapin target, probably due to the low number of charged residues in the IAPP β-hairpin motif. The sub-micromolar affinity of β-wrapin HI18, specifically selected against IAPP, is achieved in part by salt-bridge formation between HI18 residue Glu10 and the IAPP N-terminal residue Lys1, both located in the flexible N-termini of the interacting proteins. Our findings provide insights towards developing novel protein-based single- or multi-targeted therapeutics.

Interactions between Curcumin Derivatives and Amyloid-β Fibrils: Insights from Molecular Dynamics Simulations

“…Computational methods have been used to provide insights into molecular docking, 22 , 23 , 52 , 102 , 103 drug discovery, 16 − 20 , 94 and amyloid formation 104 − 130 and inhibition. 27 , 36 , 37 , 86 , 82 , 131 − 149 The thermodynamics of Aβ fibril elongation and dissociation was also investigated in the absence of any molecules, providing outstanding insights into the atomistic origins of the Arrhenius barriers. 150 , 151 Such computational methods have enhanced the understanding of Aβ fibril formation as well as curcumin’s interactions with Aβ peptides, primarily monomers.…”

“… 90 − 92 Due to the use of the MM-GBSA one-trajectory approximation, the association energy values are systemically large in magnitude due to the combination of the omission of the entropic effect due to structural relaxation and the approximations of the continuum solvation model. 37 , 90 The MM-GBSA one-trajectory approximation was preferred over more computationally demanding methods, as they are computationally efficient, 93 which is important when investigating a large number of simulated complexes and has proven successful in assessing the relative affinities of different binding modes of a given molecule in a number of studies. 77 , 86 , 94 Due to the use of the one-trajectory approximation, the calculated energies are referred to as association energies and were used to compare and rank the relative energetic favorability of the binding conformations per molecule in complex with the Aβ 1–42 fibril rather than to compare the energetic favorability across different molecules; the above energy calculations were performed in CHARMM.…”

“… 8 , 13 − 28 In addition, larger molecules have been suggested as amyloid inhibitors, including human monoclonal antibodies (e.g., aducanumab that selectively reacts with Aβ aggregates, including soluble oligomers and insoluble fibrils crossing the blood–brain barrier, engaging its target, and clearing Aβ from plaque-bearing transgenic mouse brains 4 ), or β-wrapin proteins, engineered to bind and sequester amyloid monomeric proteins, including Αβ, and thereby reduce their toxicity. 29 − 37 …”

Activation of COUP-TFI by a Novel Diindolylmethane Derivative

“…To refine the initial structure and to allow the COUP-TFII binding pocket to potentially expand, and thus facilitate the initial, independent placement of the two compounds, we introduced a short 10 ns constrained explicit-solvent molecular dynamics (MD) simulation in which binding pocket residues (207–223, 245–300, 370–396) and the modeled loop residues (194–206, 269–285) were unconstrained and the remaining residues were lightly constrained with 1.0 kcal/mol on heavy backbone atoms and 0.5 kcal/mol on heavy side chain atoms. The MD simulation was performed in a 109 Å cubic water box with the N- and C-terminal ends of the modeled protein acetylated and amidated to eliminate artificially placed positive and negative charges at the backbone termini analogously to References [41,42,43,44,45,46,47].…”

Cell Responses to Extracellular α-Synuclein

“…One approach is to modify synuclein’s secondary and tertiary structure by interaction with β-wrapins—genetically engineered binding proteins. β-wrapins are artificial proteins which stabilize the β-hairpin conformations of α-synuclein and other amyloidogenic proteins and inhibit their aggregation and toxicity [33,40]. The exact design of β-wrapins may be optimized for specific pathology by computational methods, molecular dynamics simulations, and free energy calculations.…”