Effects of a plant cyclotide on conformational dynamics and destabilization of β-amyloid fibrils through molecular dynamics simulations

Abstract

Aggregation of β-amyloid (Aβ) peptide is one of the hallmarks of Alzheimer’s disease (AD) which results in chronic and progressive neurodegeneration of the brain. A recent study by our group have shown the ability of cyclic disulfide-rich peptides (“cyclotides”) isolated from a medicinal plant, Clitoria ternatea, to inhibit the aggregation of Aβ peptides and reduce oxidative stress caused by reactive oxygen species using in vivo models of transgenic Caenorhabditis elegans. In the present study, through extensive computational docking and multi-ns molecular dynamics (MD) simulation, we evaluated if cyclotides can stably bind to Aβ molecules and/or destabilize the Aβ fibril by preventing conformational changes from α-helical to β-sheet rich structures. We demonstrate that cyclotides bind effectively and stably to different forms of Aβ structures via hydrogen bonding and hydrophobic interactions. One of the conserved hydrophobic interface residues, Tyr10 was mutated to Ala and the impact of this virtual mutation was estimated by additional MD simulations for the wild-type (WT) and mutant protein-peptide complexes. A detailed MD simulation analyses revealed that cyclotides form hydrogen bonds with the toxic amyloid assemblies thereby weakening the inter-strand hydrogen bonds between the Aβ peptide. The φ-ѱ distribution map of residues in the cyclotide binding pocket that ideally adopt β-sheet conformation show deviation towards right-handed ɑ-helical (ɑR) conformation. This effect was similar to that observed for the Tyr10Ala mutant and doubly so, for the cyclotide bound form. It is therefore possible to hypothesise that the opening up of amyloid β-sheet is due to an unfolding process occurring in the Aβ caused by cyclotide binding and inhibition. Our current findings provide novel structural insights on the mode of interaction between cyclotides and Aβ fibrils and describe their anti-amyloid aggregation potential. This sheds light on the future of cyclotide-based drug design against protein aggregation, a hallmark event in many neurodegenerative diseases.

Unlocking novel therapies: cyclic peptide design for amyloidogenic targets through synergies of experiments, simulations, and machine learning

“…139 The peptide was subsequently docked onto 3D structures of Ab 42 fibrils and subjected to molecular dynamics simulations. 140 The results explained experimental observations to reveal that the Cter-M cyclotide from C. ternatea (GLPTCGETCTLGTCYVPDCSCSW-PICMKN) binds the Ab 42 fibril via hydrogen bonding, hydrophobic, electrostatic and p-p interactions, thereby inhibiting aggregation. 140 Particularly, the peptide disrupts intermolecular hydrogen bonds and salt bridges in the Ab 42 fibril, which are crucial for its structural integrity.…”

“…140 The results explained experimental observations to reveal that the Cter-M cyclotide from C. ternatea (GLPTCGETCTLGTCYVPDCSCSW-PICMKN) binds the Ab 42 fibril via hydrogen bonding, hydrophobic, electrostatic and p-p interactions, thereby inhibiting aggregation. 140 Particularly, the peptide disrupts intermolecular hydrogen bonds and salt bridges in the Ab 42 fibril, which are crucial for its structural integrity. The effects occur within the first 50 ns of the simulations with disruptions in the fibril secondary structure at residues 2-7 and 38-41, resulting in the loss of extended b-sheet conformations.…”

Nutritional and Pharmaceutical Applications of Under-Explored Knottin Peptide-Rich Phytomedicines

“…The documented inhibition of prolyl oligopeptidase by knottin-like cyclotides [ 13 , 130 ] should trigger scientific investigation of the potential of knottin-like peptides, to inhibit the enzymes involved in a cascade of reactions leading to the extracellular plaques of beta-amyloid peptide (Aβ) deposits in the brain observed in Alzheimer’s disease [ 131 ]. As a first step, Kalmankar and colleagues [ 132 ] showed that cyclotides from Clitoria ternatea can inhibit the aggregation of amyloid β peptide (Aβ). This computational study showed that cyclotides can prevent Alzheimer’s progression by binding to peptide structures and inhibiting their aggregation.…”