Carbon nanotube prevents the secondary structure formation of amyloid-β trimers: an all-atom molecular dynamics study

Song, Menghua; Zhu, Yanyan; Wei, Guanghong; Li, Huiyu

doi:10.1080/08927022.2017.1321757

Cited by 13 publications

(13 citation statements)

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“…This finding might have important research value in the future in targeted therapy of organ fibrosis and in vivo protein fibrosis. By using molecule simulation, researchers reported that carbon nanotubes and fullerene prevented the secondary structure formation of amyloid-β peptide oligomers [ 76 , 77 , 78 ].…”

Section: Resultsmentioning

confidence: 99%

The Interplay between Whey Protein Fibrils with Carbon Nanotubes or Carbon Nano-Onions

Kang

Jiang²,

Gao

et al. 2021

Materials

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Whey protein isolate (WPI) fibrils were prepared using an acid hydrolysis induction process. Carbon nanotubes (CNTs) and carbon nano-onions (CNOs) were made via the catalytic chemical vapor deposition (CVD) of methane. WPI fibril–CNTs and WPI fibril–CNOs were prepared via hydrothermal synthesis at 80 °C. The composites were characterized by SEM, TEM, FTIR, XRD, Raman, and TG analyses. The interplay between WPI fibrils and CNTs and CNOs were studied. The WPI fibrils with CNTs and CNOs formed uniform gels and films. CNTs and CNOs were highly dispersed in the gels. Hydrogels of WPI fibrils with CNTs (or CNOs) could be new materials with applications in medicine or other fields. The CNTs and CNOs shortened the WPI fibrils, which might have important research value for curing fibrosis diseases such as Parkinson’s and Alzheimer’s diseases. The FTIR revealed that CNTs and CNOs both had interactions with WPI fibrils. The XRD analysis suggested that most of the CNTs were wrapped in WPI fibrils, while CNOs were partially wrapped. This helped to increase the biocompatibility and reduce the cytotoxicity of CNTs and CNOs. HR-TEM and Raman spectroscopy studies showed that the graphitization level of CNTs was higher than for CNOs. After hybridization with WPI fibrils, more defects were created in CNTs, but some original defects were dismissed in CNOs. The TG results indicated that a new phase of WPI fibril–CNTs or CNOs was formed.

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Section: Resultsmentioning

confidence: 99%

The Interplay between Whey Protein Fibrils with Carbon Nanotubes or Carbon Nano-Onions

Kang

Jiang²,

Gao

et al. 2021

Materials

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“…Numerous areas of science and technology have been significantly impacted by the fast-developing field of nanotechnology. Among these are previously-reported nanomaterials, such as fullerene [ 9 , 10 ], carbon nanotubes [ 11 , 12 ] and polymeric [ 13 ] and gold nanoparticles (AuNPs) [ 14 , 15 , 16 ]. Naturally, AuNPs have become one of the most outstanding candidates in different practical applications and fundamental research studies [ 15 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

Exploring the Mechanism of Inhibition of Au Nanoparticles on the Aggregation of Amyloid-β(16-22) Peptides at the Atom Level by All-Atom Molecular Dynamics

Song

Sun

Luo

et al. 2018

IJMS

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The abnormal self-assembly of the amyloid-β peptide into toxic β-rich aggregates can cause Alzheimer’s disease. Recently, it has been shown that small gold nanoparticles (AuNPs) inhibit Aβ aggregation and fibrillation by slowing down the nucleation process in experimental studies. However, the effects of AuNPs on Aβ oligomeric structures are still unclear. In this study, we investigate the conformation of Aβ(16-22) tetramers/octamers in the absence and presence of AuNPs using extensive all-atom molecular-dynamics simulations in explicit solvent. Our studies demonstrate that the addition of AuNPs into Aβ(16-22) solution prevents β-sheet formation, and the inhibition depends on the concentration of Aβ(16-22) peptides. A detailed analysis of the Aβ(16-22)/Aβ(16-22)/water/AuNPs interactions reveals that AuNPs inhibit the β-sheet formation resulting from the same physical forces: hydrophobic interactions. Overall, our computational study provides evidence that AuNPs are likely to inhibit Aβ(16-22) and full-length Aβ fibrillation. Thus, this work provides theoretical insights into the development of inorganic nanoparticles as drug candidates for treatment of AD.

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“…Hydrophobic interactions play important roles between the inhibitors and the residues of SIRT6. In previous computer simulation studies, hydrophobic interactions between small molecules and proteins have also been reported [44][45][46][47][48].…”

Section: Resultsmentioning

confidence: 88%

“…We performed the analysis using our in-house developed codes and the GROMACS facilities [46]. The MD trajectories were analysed using several parameters.…”

Section: Analysis Methodsmentioning

confidence: 99%

“…∆G polar is calculated by the GB model [64] and ∆G suf is estimated by the solvent accessible surface area (SASA). As the binding energy (∆G binding ) reported here is the relative binding free energy, the contribution of conformational entropy of the small molecule was ignored in accordance with a number of previous computational studies [45,46,66,67]. Therefore, in this study, we use the formula ∆G binding = ∆E MM + ∆G solv [61] to calculate the binding free energy.…”

Section: Analysis Methodsmentioning

confidence: 99%

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Structural Insight into the Interactions between Structurally Similar Inhibitors and SIRT6

Zhao

Zhu

Wang

et al. 2020

IJMS

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Sirtuin 6 (SIRT6) is an NAD+-dependent deacetylase with a significant role in 20% of all cancers, such as colon cancers and rectal adenocarcinoma. However, there is currently no effective drug for cancers related to SIRT6. To explore potential inhibitors of SIRT6, it is essential to reveal details of the interaction mechanisms between inhibitors and SIRT6 at the atomic level. The nature of small molecules from herbs have many advantages as inhibitors. Based on the conformational characteristics of the inhibitor Compound 9 (Asinex ID: BAS13555470), we explored the natural molecule Scutellarin, one compound of Huang Qin, which is an effective herb for curing cancer that has been described in the Traditional Chinese Medicine (TCMS) library. We investigated the interactions between SIRT6 and the inhibitors using molecular dynamics (MD) simulations. We illustrated that the structurally similar inhibitors have a similar binding mode to SIRT6 with residues-Leu9, Phe64, Val115, His133 and Trp188. Hydrophobic and π-stacking interactions play important roles in the interactions between SIRT6 and inhibitors. In summary, our results reveal the interactive mechanism of SIRT6 and the inhibitors and we also provide Scutellarin as a new potential inhibitor of SIRT6.Our study provides a new potential way to explore potential inhibitors from TCMS.Int. J. Mol. Sci. 2020, 21, 2601 2 of 15 cancers and rectal adenocarcinoma, according to the Cancer Genome Atlas database [17]. Crystal structure of SIRT6 (PDB code 3K35) [23,24] includes the hydrophobic channel, the Rossman fold and the small domain shown in Figure S1A [25]. The Rossman fold is one of the most common and widely distributed super-secondary structures. The dinucleotide such as FAD, NAD and NADP can bind in the domain [26]. There is a long hydrophobic-channel pocket that binds the small molecules [27].Probing potential inhibitors has become essential for the development of cancer drug design [4,28,29]. Several potential inhibitors of SIRT6 have been reported, such as Compound 9 [3,30], trichostatin A [23] and inhibitors with a salicylate-linked structure [31]. Parenti et al. synthesized three (SYN17739303, BAS13555470 or Compound 9 and BAS00417531) potential inhibitors for SIRT6 [30]. Interestingly we found that the three inhibitors have similar chemical structure. The structures of these inhibitors can give insight into the direction of the design of improved inhibitors. However, the mechanism of interactions between the inhibitors and SIRT6 is still elusive. The relationship between the interactions and the bioactivity of SIRT6 is also not clear.Small molecules from herbs have many advantages as inhibitors. For example, herbal medicine has low toxicity and can be easily absorbed and easily expelled from the body. In this investigation, we therefore sought to probe structure-based inhibitors similar to Compound 9 [30] from Traditional Chinese Medicines (TCMS). Scutellarin is one compound of Scutellaria baicalensis Georgi, named Huang Qin in TCMS. It has been reported that ...

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Carbon nanotube prevents the secondary structure formation of amyloid-β trimers: an all-atom molecular dynamics study

Cited by 13 publications

References 29 publications

The Interplay between Whey Protein Fibrils with Carbon Nanotubes or Carbon Nano-Onions

The Interplay between Whey Protein Fibrils with Carbon Nanotubes or Carbon Nano-Onions

Exploring the Mechanism of Inhibition of Au Nanoparticles on the Aggregation of Amyloid-β(16-22) Peptides at the Atom Level by All-Atom Molecular Dynamics

Structural Insight into the Interactions between Structurally Similar Inhibitors and SIRT6

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