Biogenic synthesis, molecular docking, biomedical and environmental applications of multifunctional CuO nanoparticles mediated Phragmites australis

Kocabas, Buket Bulut; Attar, Azade; Yuka, Selcen Ari; Yapaöz, Melda Altıkatoğlu

doi:10.1016/j.bioorg.2023.106414

Cited by 6 publications

(3 citation statements)

References 52 publications

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“…The binding site of chitin deacetylase was found using AutoSite (v1.1) of AutoGridFR (AGFR v1.2) tool [14]. The monoclinic crystal structure of CuONPs was compiled using Avogadro molecular editor software (v1.2) as reported in our previous work [15,16]. Molecular docking analysis and file prepocessing were performed in AutoDock Vina (v1.2.3) [17].…”

Section: In Silico Molecular Docking Of Cuonpsmentioning

confidence: 99%

“…The low tendency of agglomeration distinguished in the figures may be attributed to the phenolic content of the K. arvensis flower extract. The phenolic compounds acting as capping and stabilizing organic agent that causes dispersion may be adsorbed on the surface of the CuONPs or the CuONPs may be coated with a layer of phenolic compounds [16,24]. The smooth surface morphology can be seen in SEM microstructure, which can be explained by biochemical constituents of the K. arvensis.…”

Section: Sem Analysesmentioning

confidence: 99%

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Bio-capped multifunctional CuO nanoparticles via Knautia arvensis for dye removal, antibacterial and antifungal efficiency, and molecular docking

Sazak,

Attar,

Ari Yuka

et al. 2024

Mater. Res. Express

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Copper oxide nanoparticles (CuONPs) synthesized using Knautia arvensis flower extract in an environmentally friendly and one-step procedure were characterized by UV–vis, FT-IR, SEM and DLS. The in vitro antibacterial and antifungal activities of CuONPs were determined using E. coli, S. aureus and A. niger. In silico antibacterial and antifungal evaluation of CuONPs were performed by molecular docking analysis using chitin deacetylase of A. niger, topoisomerase IV of E. coli and tyrosyl-tRNA synthetase of S. aureus. The best binding energy was determined using these microbial targets in molecular docking analyses and the antimicrobial mechanisms between the microorganism and the CuONP were elucidated. The degradation potential of Remazol brilliant blue R (RBBR) and Napthol blue black (NBB) dyes in the presence of CuONPs were investigated. The peak obtained at 289 nm as a result of UV–vis analysis revealed the presence of CuONPs. The spherical morphology of CuONPs and the particle size varying between 88–289 nm were visualized by SEM. DLS analysis pointed out the mean diameter of CuONPs was 189 nm along with the PDI value of 0.324. The 600 and 595 cm−1 vibrations attained in the FT-IR spectroscopy showed the presence of CuONPs. In addition, the presence of phenolic compounds found in the plant extract responsible for bio-capping of copper ions into CuONPs were enlightened by the FT-IR analysis. Dye degradation activity of CuONPs was found as 69% and 71% using NBB and RBBR at 50 °C in 90 min, respectively. Antifungal and antibacterial interactions of CuONPs with chitin deacetylase of A. niger, topoisomerase IV of E. coli and tyrosyl-tRNA synthetase of S. aureus were analyzed in order to reveal the antimicrobial mechanisms of CuONPs and it was found that CuONPs demonstrate significant interactions with those proteins with binding energies −7.25, −7.14 and −7.89 kcal mol−1, respectively.

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Section: In Silico Molecular Docking Of Cuonpsmentioning

confidence: 99%

Section: Sem Analysesmentioning

confidence: 99%

Bio-capped multifunctional CuO nanoparticles via Knautia arvensis for dye removal, antibacterial and antifungal efficiency, and molecular docking

Sazak,

Attar,

Ari Yuka

et al. 2024

Mater. Res. Express

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“…Kocabas and colleagues used Phragmites australis leaf extract for the synthesis of copper oxide nanoparticles. They carried out in silico molecular docking against the active binding sites of dihydropteroate synthase, thymidylate kinase, and Staphylococcus aureus FtsZ, with docking scores of −9.067, −8.048, and −7.349 kcal/mol, respectively [ 143 ]. In contrast to the binding of TiO 2 to HSA into subdomain IIA, the expected binding position of CuO NPs in the same protein was subdomain IIIA, aided by the interaction with Arg472 [ 144 ].…”

Section: Analysis Of Biomacromolecule–np Interactions Using Molecular...mentioning

confidence: 99%

Molecular Docking Approach for Biological Interaction of Green Synthesized Nanoparticles

Kar,

Oriola,

Oyedeji

2024

Molecules

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In recent years, significant progress has been made in the subject of nanotechnology, with a range of methods developed to synthesize precise-sized and shaped nanoparticles according to particular requirements. Often, the nanoparticles are created by employing dangerous reducing chemicals to reduce metal ions into uncharged nanoparticles. Green synthesis or biological approaches have been used recently to circumvent this issue because biological techniques are simple, inexpensive, safe, clean, and extremely productive. Nowadays, much research is being conducted on how different kinds of nanoparticles connect to proteins and nucleic acids using molecular docking models. Therefore, this review discusses the most recent advancements in molecular docking capacity to predict the interactions between various nanoparticles (NPs), such as ZnO, CuO, Ag, Au, and Fe3O4, and biological macromolecules.

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Biogenically synthesized copper oxide, titanium oxide, and silver oxide nanoparticles: characterization and biological effects

Omran,

Rabbee,

Abdel-Salam

et al. 2024

Clean Techn Environ Policy

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Biogenic synthesis, molecular docking, biomedical and environmental applications of multifunctional CuO nanoparticles mediated Phragmites australis

Cited by 6 publications

References 52 publications

Bio-capped multifunctional CuO nanoparticles via Knautia arvensis for dye removal, antibacterial and antifungal efficiency, and molecular docking

Bio-capped multifunctional CuO nanoparticles via Knautia arvensis for dye removal, antibacterial and antifungal efficiency, and molecular docking

Molecular Docking Approach for Biological Interaction of Green Synthesized Nanoparticles

Biogenically synthesized copper oxide, titanium oxide, and silver oxide nanoparticles: characterization and biological effects

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