Interactions between carbon nanotubes and external structures of SARS-CoV-2 using molecular docking and molecular dynamics

Lobato, Júlio Cesar Mendes; Arouche, Tiago da Silva; Nero, Jordan Del; Filho, Tarciso Andrade; Borges, Rosivaldo dos Santos; Neto, Antonio Maia de Jesus Chaves

doi:10.1016/j.molstruc.2023.135604

Cited by 4 publications

(2 citation statements)

References 93 publications

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“…MOFs exhibit exceptionally high surface area and porosity, making them versatile in biomedical research for applications such as drug delivery, disease diagnosis, and treatment . Notably, MOFs feature a specific anisotropy among pores, , and the dominant forces arise from coordination bonds formed by metal centers and ligands, alongside additional interactions like hydrogen bonds, van der Waals forces, and π–π stacking. − …”

Section: Resultsmentioning

confidence: 99%

Disordered Convolution Region of P(VDF-TrFE) Piezoelectric Nanoparticles: The Core of Sono–Piezo Dynamic Therapy

Chen,

Yang,

Yang

et al. 2023

ACS Appl. Mater. Interfaces

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The recent focus on P(VDF-TrFE) material in biomedical engineering stems from its outstanding mechanical properties and biocompatibility. However, its application in sono−piezo dynamic therapy (SPDT) has been relatively unexplored. In this study, we developed composite piezoelectric nanoparticles (rPGd NPs@RGD) based on recrystallized P(VDF-TrFE) particles, which offer dual capabilities of MRI imaging and targeted treatment for brain gliomas. SEM observations of P(VDF-TrFE) particles in the disordered convolution region (DCR) revealed recrystallization, representing the polymer chain structure and particle polarity. In comparison to nonrecrystallized nanoparticles, rPGd NPs@RGD exhibited remarkable stability and biocompatibility. Under ultrasound excitation, they generated significantly higher levels of reactive oxygen species, effectively inhibiting tumor cell proliferation, invasion, and migration. rPGd NPs@RGD demonstrated excellent MRI imaging capabilities and antitumor activity in U87 tumor-bearing mice. This study highlights the remarkable SPDT abilities of the developed nanoparticles, attributed to the microscopic morphological changes in the DCR that increase the nanoparticle's polarity and thus boost its potential for SPDT. This research opens new possibilities for utilizing P(VDF-TrFE) materials in advanced biomedical applications.

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Section: Resultsmentioning

confidence: 99%

Disordered Convolution Region of P(VDF-TrFE) Piezoelectric Nanoparticles: The Core of Sono–Piezo Dynamic Therapy

Chen,

Yang,

Yang

et al. 2023

ACS Appl. Mater. Interfaces

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show abstract

“…Additionally, π−π stacking interactions, noncovalent attractive forces between two aromatic rings, have been identified as contributing factors to the binding of carbon nanotubes with proteins. 71,72,70 Notably, the Hep25 peptides tend to be predominantly enveloped by the hydrophobic tails of the AAP molecule. This outcome aligns with the observation of fewer atoms being adsorbed and a reduced contact area in an aqueous solution.…”

Section: Analysis Of Binding Free Energymentioning

confidence: 99%

Molecular Insights into the Binding and Conformational Changes of Hepcidin25 Blood Peptide with 4-Aminoantipyrine and Their Sorption Mechanism by Carboxylic-Functionalized Multiwalled Carbon Nanotubes: A Comprehensive Spectral Analysis and Molecular Dynamics Simulation Study

Rasoolzadeh,

Baptista,

Vajedi

et al. 2024

ACS Omega

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In this work, the main purpose is to analyze and understand the mechanism and thermodynamic interactions of carboxylic acid-functionalized multiwalled carbon nanotubes (cf-MWCNTs) and 4-aminoantipyrine (AAP) with human hepcidine25 (Hep25) using multispectroscopic and molecular docking modeling methods, binding free energy calculations, and molecular dynamics (MD) simulations under physiological conditions. AAP belongs to a class of persistent environmental contaminants, and its residue is a potential hazard to human health, exhibiting a high binding affinity with blood peptides. Hepcidin is a 25-residue peptide hormone with four disulfide bonds that regulates the iron balance in vertebrates and contributes to host immunity as a cysteine-rich antimicrobial peptide. Due to their diverse properties and pollutant absorption capabilities, CNTs demonstrate important biological effects in biological applications, particularly in the noncovalent interactions with blood peptides. A comprehensive molecular dynamics simulation integrated with molecular docking methodologies was employed to explore the binding free energy between AAP and Hep25, identify binding sites, elucidate thermodynamic characteristics, and evaluate the binding forces governing their interaction. The investigation delved into elucidating the precise binding site of AAP within the Hep25 protein and thoroughly analyzed the impact of AAP on the microenvironment and conformational dynamics of Hep25. The circular dichroism (CD) experimental results highlight a reduction in β-sheet composition following the introduction of AAP and cf-MWCNT. In addition, outcomes from fluorescence spectroscopy demonstrate that both cf-MWCNT and AAP significantly attenuated Hep-25 fluorescence via a static quenching mechanism. According to the MD simulations, the presence of AAP induces changes in the secondary structure of Hep25 and enhances its hydrophobicity. Additionally, our findings demonstrated that alongside the alteration in protein structure and functionality induced by contaminants, cf-MWCNTs possess the capability to mitigate the contaminant-induced effects on Hep25 activity while preserving the overarching structural integrity of Hep25. Based on the distance and RDF data, we found that during the simulation the presence of the cf-MWCNT causes the AAP to move away from the Hep25, and as a result fewer and weaker interactions of the AAP with the Hep25 will be observed. Likewise, free energy calculations indicate that the binding of Hep25 to AAP and cf-MWCNT involves electrostatic, π-cationic, and π−π stacking interactions. The research findings offer invaluable insights into the intricate influence of pollutants and carbon nanotubes on protein functionality within the circulatory system and their toxicity in vivo for prospective investigations.

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Molecular interactions of the Omicron, Kappa, and Delta SARS-CoV-2 spike proteins with quantum dots of graphene oxide

da Silva Arouche,

Lobato,

dos Santos Borges

et al. 2024

J Mol Model

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Interactions between carbon nanotubes and external structures of SARS-CoV-2 using molecular docking and molecular dynamics

Cited by 4 publications

References 93 publications

Disordered Convolution Region of P(VDF-TrFE) Piezoelectric Nanoparticles: The Core of Sono–Piezo Dynamic Therapy

Disordered Convolution Region of P(VDF-TrFE) Piezoelectric Nanoparticles: The Core of Sono–Piezo Dynamic Therapy

Molecular Insights into the Binding and Conformational Changes of Hepcidin25 Blood Peptide with 4-Aminoantipyrine and Their Sorption Mechanism by Carboxylic-Functionalized Multiwalled Carbon Nanotubes: A Comprehensive Spectral Analysis and Molecular Dynamics Simulation Study

Molecular interactions of the Omicron, Kappa, and Delta SARS-CoV-2 spike proteins with quantum dots of graphene oxide

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