IN SILICO TRIAL APPROACHES BETWEEN PHYTOCHEMICAL COMPOSITION OF VERBENA OFFICINALIS AND LIVER CANCER TARGETS

Hatice Akkaya; Aydın Özmaldar

doi:10.33483/jfpau.1417289

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IN SILICO TRIAL APPROACHES BETWEEN PHYTOCHEMICAL COMPOSITION OF VERBENA OFFICINALIS AND LIVER CANCER TARGETS

Year 2024, Volume: 48 Issue: 3, 975 - 992, 10.09.2024

Hatice Akkaya , Aydın Özmaldar

https://doi.org/10.33483/jfpau.1417289

Abstract

Objective: The abundance of bioactive metabolites in Verbena officinalis explains the biological benefits and folkloric use of the plant. Liver cancer is an extremely heterogeneous malignant disease compared to other defined tumors. To explore the potential therapeutic value of bioactive metabolites in Verbena officinalis, this study aimed to filter secondary metabolites, conduct ADME-Tox assessments, perform drug similarity tests, and analyze with molecular dynamic simulations. The objective was to evaluate how potential drug candidates derived from Verbena officinalis behave in biological systems and assess their potential toxicity risks.
Material and Method: Ligands selected from the ADME assay were utilized in in silico molecular docking studies against Glucose-6-phosphate dehydrogenase enzyme in the oxidative part of the pentose phosphate pathway, which is crucial for liver diseases. These studies were conducted using Autodock Vina embedded in Chimera 1.16. Molecular dynamics simulations were performed with the AMBER16.
Result and Discussion: When the ADME test results were evaluated, 88 secondary metabolites were identified as ligands. Among all the ligands evaluated against Glucose-6-phosphate dehydrogenase enzyme, which is the key enzyme of the pentose phosphate pathway, quercetin flavonoid was determined to be the most active ligand with a docking score of -8.1 kcal/mol and binding energy of -118.51 kcal/mol. A molecular dynamics simulation performed for 300 nanoseconds confirmed that quercetin can remain stable in its microenvironment. The activity of this metabolite is worthy of further testing in vitro and in vivo as it may highlight a therapeutic modality within the pentose phosphate pathway.

Keywords

In silico, liver cancer, pentose phosphate pathway, toxicitiy, Verbena officinalis

References

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VERBENA OFFICINALIS'İN FİTOKİMYASAL BİLEŞİMİ İLE KARACİĞER KANSERİ HEDEFLERİ ARASINDAKİ İN SİLİKO DENEME YAKLAŞIMLARI

Year 2024, Volume: 48 Issue: 3, 975 - 992, 10.09.2024

Hatice Akkaya , Aydın Özmaldar

https://doi.org/10.33483/jfpau.1417289

Abstract

Amaç: Verbena officinalis bitkisinde bulunan biyoaktif metabolitlerin bolluğu, bitkinin biyolojik faydalarını ve halk arasındaki kullanımını açıklar. Karaciğer kanseri, diğer tanımlanmış tümörlere kıyasla son derece heterojen kötü huylu bir hastalıktır. Verbena officinalis'teki biyoaktif metabolitlerin potansiyel terapötik değerini keşfetmek için, bu çalışma ikincil metabolitleri filtrelemeyi, ADME-Tox değerlendirmeleri yapmayı, ilaç benzerlik testleri gerçekleştirmeyi ve moleküler dinamik simülasyonları ile analiz etmeyi amaçlamıştır. Hedef, Verbena officinalis'ten elde edilen potansiyel ilaç adaylarının biyolojik sistemlerde nasıl davrandığını değerlendirmek, potansiyel toksisite risklerini değerlendirmekti.
Gereç ve Yöntem: ADME testinden seçilen ligandlar, karaciğer hastalıkları için önemli olan pentoz fosfat yolunun oksidatif kısmındaki Glukoz-6-fosfat dehidrogenaz enzimi için in siliko moleküler bağlanma çalışmalarında kullanıldı. Bu çalışmalar Chimera 1.16'ya gömülü Autodock Vina kullanılarak gerçekleştirildi. Moleküler dinamik simülasyonları AMBER16 programı ile gerçekleştirildi.
Sonuç ve Tartışma: ADME test sonuçları değerlendirildiğinde, 88 sekonder metabolit ligand olarak belirlendi. Pentoz fosfat yolunun anahtar enzimi olan Glukoz-6-fosfat dehidrogenaz enzimine karşı değerlendirilen tüm ligandlar arasında, kuersetin flavonoidi, -8.1 kcal/mol bağlanma skoru ve -118.51 kcal/mol bağlanma enerjisi ile en etkin ligand olarak belirlendi. 300 nanosaniye boyunca yapılan moleküler dinamik simülasyonu ise quercetinin bulunduğu mikroçevrede stabil olarak kalabildiğini doğruladı. Bu metabolitin aktivitesi, pentoz fosfat yolu içinde terapötik bir modaliteyi ortaya koyabileceği için in vitro ve in vivo testlerle daha ileri incelenmeye değerdir.

Keywords

İn siliko, karaciğer kanseri, pentoz fosfat yolu, toksisite, Verbena officinalis

References

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2. López-López, E., Bajorath, J., Medina-Franco, J.L. (2021). Informatics for chemistry, biology, and biomedical sciences. Journal of Chemical Infori Modeling, 61 (1), 26-35. [CrossRef]
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5. Ghazanfar, S.A. (1994). Handbook of Arabian Medicinal Plants, CRC Press, Boca Raton, Florida, p. 176. [CrossRef]
6. Kubica, P., Szopa, A., Dominiak, J., Luczkiewicz, M., Ekiert, H. (2020). Verbena officinalis (Common Vervain)-A Review on the investigations of this medicinally important plant species. Planta Medica, 86(17). [CrossRef]
7. Rehecho, S., Hidalgo, O., de Cirano, M. G.I., Navarro, I., Astiasarán, I., Ansorena, D., Cavero, R.Y., Calvo, M.I. (2011). Chemical composition, mineral content and antioxidant activity of Verbena officinalis L. LWT-Food Science and Technology, 44 (4), 875-882. [CrossRef]
8. Liu, Z., Xu, Z., Zhou, H., Cao, G., Cong, X.D., Zhang, Y., Cai, B.C. (2012). Simultaneous determination of four bioactive compounds in Verbena officinalis L. by using high-performance liquid chromatography. Pharmacognosy Magazine, 8(30), 162-165. [CrossRef]
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10. Akour, A., Kasabri, V., Afifi, F.U., Bulatova, N. (2016). The use of medicinal herbs in gynecological and pregnancy-related disorders by Jordanian women: A review of folkloric practice vs. evidence-based pharmacology. Pharmaceutical Biology, 54(9), 1901-1918. [CrossRef]
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12. Lai, S.W., Yu, M.S., Yuen, W.H., Chang, R.C. (2006). Novel neuroprotective effects of the aqueous extracts from Verbena officinalis Linn. Neuropharmacology, 50(6), 641-650. [CrossRef]
13. Ashok Kumar, B.S., Lakshman, K., Velmurugan, C., Sridhar, S.M., Gopisetty, S. (2014). Antidepressant activity of methanolic extract of amaranthus spinosus. Basic and Clinical Neuroscience, 5(1), 11-17.
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15. Speroni, E., Cervellati, R., Costa, S., Guerra, M.C., Utan, A., Govoni, P., Berger, A., Müller, A., Stuppner, H. (2007). Effects of differential extraction of Verbena officinalis on rat models of inflammation, cicatrization and gastric damage. Planta Medica, 73(3), 227-235. [CrossRef]
16. Calvo M.I. (2006). Anti-inflammatory and analgesic activity of the topical preparation of Verbena officinalis L. Journal of Ethnopharmacology, 107(3), 380-382. [CrossRef]
17. Casanova, E., García-Mina, J.M., Calvo, M.I. (2008). Antioxidant and antifungal activity of Verbena officinalis L. leaves. Plant Foods for Human Nutrition (Dordrecht, Netherlands), 63(3), 93-97. [CrossRef]
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Details

Primary Language	English
Subjects	Pharmaceutical Biochemistry, Pharmacology and Pharmaceutical Sciences (Other)
Journal Section	Research Article
Authors	Hatice Akkaya 0000-0001-7276-6919 Aydın Özmaldar 0000-0002-0664-0100
Early Pub Date	July 24, 2024
Publication Date	September 10, 2024
Submission Date	January 9, 2024
Acceptance Date	July 11, 2024
Published in Issue	Year 2024 Volume: 48 Issue: 3

Cite

APA	Akkaya, H., & Özmaldar, A. (2024). IN SILICO TRIAL APPROACHES BETWEEN PHYTOCHEMICAL COMPOSITION OF VERBENA OFFICINALIS AND LIVER CANCER TARGETS. Journal of Faculty of Pharmacy of Ankara University, 48(3), 975-992. https://doi.org/10.33483/jfpau.1417289
AMA	Akkaya H, Özmaldar A. IN SILICO TRIAL APPROACHES BETWEEN PHYTOCHEMICAL COMPOSITION OF VERBENA OFFICINALIS AND LIVER CANCER TARGETS. J. Fac. Pharm. Ankara. September 2024;48(3):975-992. doi:10.33483/jfpau.1417289
Chicago	Akkaya, Hatice, and Aydın Özmaldar. “IN SILICO TRIAL APPROACHES BETWEEN PHYTOCHEMICAL COMPOSITION OF VERBENA OFFICINALIS AND LIVER CANCER TARGETS”. Journal of Faculty of Pharmacy of Ankara University 48, no. 3 (September 2024): 975-92. https://doi.org/10.33483/jfpau.1417289.
EndNote	Akkaya H, Özmaldar A (September 1, 2024) IN SILICO TRIAL APPROACHES BETWEEN PHYTOCHEMICAL COMPOSITION OF VERBENA OFFICINALIS AND LIVER CANCER TARGETS. Journal of Faculty of Pharmacy of Ankara University 48 3 975–992.
IEEE	H. Akkaya and A. Özmaldar, “IN SILICO TRIAL APPROACHES BETWEEN PHYTOCHEMICAL COMPOSITION OF VERBENA OFFICINALIS AND LIVER CANCER TARGETS”, J. Fac. Pharm. Ankara, vol. 48, no. 3, pp. 975–992, 2024, doi: 10.33483/jfpau.1417289.
ISNAD	Akkaya, Hatice - Özmaldar, Aydın. “IN SILICO TRIAL APPROACHES BETWEEN PHYTOCHEMICAL COMPOSITION OF VERBENA OFFICINALIS AND LIVER CANCER TARGETS”. Journal of Faculty of Pharmacy of Ankara University 48/3 (September 2024), 975-992. https://doi.org/10.33483/jfpau.1417289.
JAMA	Akkaya H, Özmaldar A. IN SILICO TRIAL APPROACHES BETWEEN PHYTOCHEMICAL COMPOSITION OF VERBENA OFFICINALIS AND LIVER CANCER TARGETS. J. Fac. Pharm. Ankara. 2024;48:975–992.
MLA	Akkaya, Hatice and Aydın Özmaldar. “IN SILICO TRIAL APPROACHES BETWEEN PHYTOCHEMICAL COMPOSITION OF VERBENA OFFICINALIS AND LIVER CANCER TARGETS”. Journal of Faculty of Pharmacy of Ankara University, vol. 48, no. 3, 2024, pp. 975-92, doi:10.33483/jfpau.1417289.
Vancouver	Akkaya H, Özmaldar A. IN SILICO TRIAL APPROACHES BETWEEN PHYTOCHEMICAL COMPOSITION OF VERBENA OFFICINALIS AND LIVER CANCER TARGETS. J. Fac. Pharm. Ankara. 2024;48(3):975-92.

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The Journal of Faculty of Pharmacy of Ankara University is an international medium, an open access, peer-reviewed journal for the publication of original research reports, reviews and short communications in English or Turkish on relevant developments in pharmaceutical sciences., Proceeding of scientific meetings may be published as special issues of supplements to the journal. Additionally, it contains previous and forthcoming national and international scientific meetings with social activities in pharmaceutical areas.