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Journals / Anatolian Journal of Botany / 2025 / Cilt: 9 Sayı: 2

Extracts and silver nanoparticles from different parts of Rheum ribes: Characterization, in vitro antibacterial, and antioxidant activities, and in silico molecular dynamics studies

Rheum ribes'in farklı kısımlarından ekstrakt ve gümüş nanopartiküller: Karakterizasyonu, in vitro antibakteriyel ve antioksidan aktiviteleri ve in silico moleküler dinamik çalışmaları

Aybek Yiğit(Igdir University)0000-0001-8279-5908
Yunus Başar(IGDIR UNIVERSITY, APPLICATION LABORATORY APPLICATION AND RESEARCH CENTER)0000-0002-7785-3242
Semiha Yenigün(ONDOKUZ MAYIS UNIVERSITY, SAMSUN VOCATIONAL SCHOOL, DEPARTMENT OF CHEMISTRY AND CHEMICAL PROCESSING TECHNOLOGY)0000-0002-1979-5427
Mehmet Hakkı Alma(IGDIR UNIVERSITY, APPLICATION LABORATORY APPLICATION AND RESEARCH CENTER)0000-0001-6323-7230
Ayşe Karacalı Tunç(IGDIR UNIVERSITY, IĞDIR HEALTH SERVICES VOCATIONAL SCHOOL)0000-0002-6453-9887
Ahmet Zafer Tel(IGDIR UNIVERSITY, IĞDIR FACULTY OF AGRICULTURE, AGRICULTURAL BIOTECHNOLOGY, AGRICULTURAL BIOTECHNOLOGY)0000-0002-1204-3839
Pages
114–126
Publication Date
2025-11-15
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AI Summary & Key Takeaways

AI Insight
⚡ TL;DR(Too Long; Didn't Read)

In the 100-ns MD simulation, the RMSD values were constant at 10 nm and the MM/PBSA calculation resulted in a binding energy of -16.15 kcal/mol for hesperidin.

📌 3 Key Takeaways

🎯
Objective & Hypothesis:Rheum ribes is a medicinal plant with antioxidant, antibacterial effects, which have been demonstrated in various studies.
📊
Key Findings & Data:The MolDock scores of hesperidin and possible hesperidin-AgNP were calculated to be -111.83 and -171.08, respectively.
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Conclusion & Impact:In the 100-ns MD simulation, the RMSD values were constant at 10 nm and the MM/PBSA calculation resulted in a binding energy of -16.15 kcal/mol for hesperidin.
🔬Design:Araştırma Makalesi
📍Scope:Comprehensive Sample
⚙️Variables:Rheum ribes · Potansiyometrik biyosensör · AgNP

Abstract

Rheum ribes is a medicinal plant with antioxidant, antibacterial effects, which have been demonstrated in various studies. In this study, the biological activities (antioxidant and antimicrobial) and phytochemical contents (total phenolic content and phenolic substances content by LC-ESI-MS/MS) of the fruit and peel extracts obtained from R. ribes were determined. The antioxidant content (DPPH˙ and FRAP) and total phenolic content (FCR) of R. ribes were analyzed for the first time using a new potentiometric biosensor method. In addition, the characteristic properties (XRD, FT-IR, FE-SEM, FESEM-EDX, TEM, and UV-Vis) and antibacterial properties of silver nanoparticles (AgNPs) prepared by an environmentally friendly green synthesis method were investigated. In addition, the interactions of the main component (hesperidin) in the LC-ESI-MS/MS content analyses with the topoisomerase IV were calculated theoretically. While the antioxidant activity of the R. ribes peel extract was comparable to that of the fruit extract, it was higher for FRAP and DPPH˙ scavenging activity. R. ribes (fruit)-AgNPs were found to have high activity against the microorganisms. The MolDock scores of hesperidin and possible hesperidin-AgNP were calculated to be -111.83 and -171.08, respectively. Thus, hesperidin-AgNP complex was found to have higher inhibitory properties than hesperidin. In the 100-ns MD simulation, the RMSD values were constant at 10 nm and the MM/PBSA calculation resulted in a binding energy of -16.15 kcal/mol for hesperidin.

Özet

Rheum ribes, çeşitli çalışmalarla doğrulanmış antioksidan ve antibakteriyel etkilere sahip tıbbi bir bitkidir. Bu çalışmada, R. ribes'ten elde edilen meyve ve kabuk özütlerinin biyolojik aktiviteleri (antioksidan ve antimikrobiyal) ve fitokimyasal içerikleri (toplam fenolik içerik ve LC-ESI-MS/MS ile fenolik madde içeriği) belirlenmiştir. R. ribes'in antioksidan içeriği (DPPH˙ ve FRAP) ve toplam fenolik içeriği (FCR) ilk kez yeni bir potansiyometrik biyosensör yöntemi kullanılarak analiz edilmiştir. Ayrıca, çevre dostu yeşil sentez yöntemi ile elde edilen gümüş nanopartiküllerin (AgNP) karakteristik özellikleri (XRD, FT-IR, FE-SEM, FESEM-EDX, TEM ve UV-Vis) ve antibakteriyel özellikleri incelenmiştir. Ayrıca, LC-ESI-MS/MS içerik analizlerinde ana bileşenin (hesperidin) topoizomeraz IV ile etkileşimleri teorik olarak moleküler yerleştirme ile hesaplandı. R. ribes kabuk özütünün antioksidan aktivitesi meyve özütüne benzerken, FRAP ve DPPH˙ süpürücü aktivitesi için daha yüksekti. R. ribes meyve-AgNP'lerinin mikroorganizmalara karşı yüksek aktiviteye sahip olduğu görüldü. Hesperidin ve hesperidin-AgNP MolDock skorları sırasıyla; -111.83 ve -171.08 olarak hesaplndı. Dolayısıyla hesperidin-AgNP kompleksinin, hesperidin’den daha yüksek inhibitor özelliğine sahip olduğu gözlendi. 100 ns MD simülasyonunda, RMSD değerlerinin 10 nm'de sabit olduğu ve MM/PBSA hesaplaması hesperidin için -16.15 kcal/mol'lük bir bağlanma enerjisi hesaplandı.

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Cite This Article

Yiğit, A., Başar, Y., Yenigün, S., Alma, M. H., Tunç, A. K., Tel, A. Z. (2025). Extracts and silver nanoparticles from different parts of Rheum ribes: Characterization, in vitro antibacterial, and antioxidant activities, and in silico molecular dynamics studies. Anatolian Journal of Botany, Cilt: 9 Sayı: 2, 114–126. https://doi.org/10.30616/ajb.1654542

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