<p>Graphene-Based Nanoparticles as Potential Treatment Options for Parkinson’s Disease: A Molecular Dynamics Study</p>

Abstract

Introduction The study of abnormal aggregation of proteins in different tissues of the body has recently earned great attention from researchers in various fields of science. Concerning neurological diseases, for instance, the accumulation of amyloid fibrils can contribute to Parkinson’s disease, a progressively severe neurodegenerative disorder. The most prominent features of this disease are the degeneration of neurons in the substantia nigra and accumulation of α-synuclein aggregates, especially in the brainstem, spinal cord, and cortical areas. Dopamine replacement therapies and other medications have reduced motor impairment and had positive consequences on patients’ quality of life. However, if these medications are stopped, symptoms of the disease will recur even more severely. Therefore, the improvement of therapies targeting more basic mechanisms like prevention of amyloid formation seems to be critical. It has been shown that the interactions between monolayers like graphene and amyloids could prevent their fibrillation. Methods For the first time, the impact of four types of last-generation graphene-based nanostructures on the prevention of α-synuclein amyloid fibrillation was investigated in this study by using molecular dynamics simulation tools. Results Although all monolayers were shown to prevent amyloid fibrillation, nitrogen-doped graphene (N-Graphene) caused the most instability in the secondary structure of α-synuclein amyloids. Moreover, among the four monolayers, N-Graphene was shown to present the highest absolute value of interaction energy, the lowest contact level of amyloid particles, the highest number of hydrogen bonds between water and amyloid molecules, the highest instability caused in α-synuclein particles, and the most significant decrease in the compactness of α-synuclein protein. Discussion Ultimately, it was concluded that N-Graphene could be the most effective monolayer to disrupt amyloid fibrillation, and consequently, prevent the progression of Parkinson’s disease.

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“…To assess the contact area of protein, solvent‐accessible surface area analysis, or SASA can be used [54–56] . Herein, SASA analysis was used for investigating the contact area of Aβ in the presence of COFs.…”

“…To assess the contact area of protein, solvent‐accessible surface area analysis, or SASA can be used. [ 54 , 55 , 56 ] Herein, SASA analysis was used for investigating the contact area of Aβ in the presence of COFs. The lowest average contact areas were seen in the presence of JUC‐510‐COF and TPA‐COF, closely followed by CH 3 −Li−ImCOF (Table 1 ).…”

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“…All the particles were placed inside the box, and the TIP3P water model was used as the solvent [ 60 ]. In the next step, the system temperature gradually increased from 0 to 310 K for 100 picoseconds in constant volume, using the Nose–Hoover algorithm [ 61 , 62 ].…”

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“…At NVT and NPT stages, the temperature and pressure of boxes reached equilibrium at 300K and 1 bar, using v-rescale and Parrinello_Rahman algorithms. Finally, the simulations were performed using the LINCS algorithm, with the cut-off radius of 1.5 nm, and the H-bonds were considered in 100 ns with steps of 2 fs [75]. It should be noted, DSSP analyses are provided from All Atom simulations.…”