Lycopene destabilizes preformed Aβ fibrils: Mechanistic insights from all-atom molecular dynamics simulation

Shivani Gupta; Ashok Kumar Dasmahapatra

doi:10.1016/j.compbiolchem.2023.107903

Lycopene destabilizes preformed Aβ fibrils: Mechanistic insights from all-atom molecular dynamics simulation

Comput Biol Chem. 2023 Aug:105:107903. doi: 10.1016/j.compbiolchem.2023.107903. Epub 2023 Jun 10.

Authors

Shivani Gupta¹, Ashok Kumar Dasmahapatra²

Affiliations

¹ Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
² Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India; Center for Nanotechnology, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India. Electronic address: akdm@iitg.ac.in.

PMID: 37320982
DOI: 10.1016/j.compbiolchem.2023.107903

Abstract

The therapeutic strategy employing destabilization of the preformed Aβ fibril by various natural compounds, as studied by experimental and computational methods, has been reported significant in curing Alzheimer's disease (AD). However, lycopene (a carotenoid), from terpenes family, needs investigation for its destabilization potential of Aβ fibril. The highest antioxidant potential and ability to cross blood brain barrier makes lycopene a preferred choice as drug lead for treating AD. The current study focuses on investigating the destabilization potential and underpinning mechanism of lycopene on different polymorphic forms of Aβ fibril via Molecular Dynamics (MD) simulation. The key findings highlight binding of lycopene to the outer surface of the chain F of the fibril (2NAO). Herein G9, K16 and V18 residues were found to be involved in van der Waals with the methyl groups of the lycopene. Additionally, Y10 and F20 residues were observed to interact via π-π interactions with CC bonds of the lycopene. The surface mediated binding of lycopene to the fibril is attributed to the large size and structural rigidity of lycopene along with the bulky size of 2NAO and narrow space of fibrillar cavity. The destabilization of the fibril is evident by breakage of inherent H-bonds and hydrophobic interactions in the presence of one lycopene molecule. The lesser β-sheet content explains disorganization of the fibril and bars the higher order aggregation curbing neurotoxicity of the fibril. The higher concentration of the lycopene is not found to be linearly correlated with the extent of destabilization of the fibril. Lycopene is also observed to destabilize the other polymorphic form of Aβ fibril (2BEG), by accessing the fibrillar cavity and lowering the β-sheet content. The destabilization observed by lycopene on two major polymorphs of Aβ fibril explains its potency towards developing an effective therapeutic approach in treating AD.

Keywords: Alzheimer’ Disease; Aβ fibril; Destabilization; Lycopene; Molecular Dynamic Simulations.

MeSH terms

Amyloid beta-Peptides* / chemistry
Lycopene
Molecular Dynamics Simulation*
Peptide Fragments / chemistry
Protein Conformation, beta-Strand

Substances

Amyloid beta-Peptides
Lycopene
Peptide Fragments