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A new possible antibacterial compound isolated from Prangos aricakensis, Daucosterol: Antibacterial activity and molecular docking approaches via DD-peptidase and gyrase

Year 2026, Volume: 29 Issue: 1, 40 - 50

Serbay Şafak Gökçimen , Yaşar İpek , Tevfik Ozen , İbrahim Demirtas , Lütfi Behçet

https://doi.org/10.18016/ksutarimdoga.vi.1683529

Abstract

Prangos species have been used for years to treat various ailments due to their chemical components. Eastern Türkiye is home to the locally endemic species Prangos aricakensis. This work is the first to isolate the daucosterol molecule from P. aricakensis stems. Daucosterol's structure was ascertained by 1D and 2D NMR analysis. Daucosterol has been studied to have many effects in many areas, such as antibacterial, immune system strengthening, and anti-cancer. Studies have been conducted on the molecule's antibacterial activity in vitro and its predicted molecular docking with antibiotic target proteins in silico. Compared to standard antibiotics, daucosterol had better effects against Bacillus cereus (512 μg/mL) and Listeria monocytogenes (1024 μg/mL). Additionally, daucosterol (512 μg/mL) and amoxicillin (512 μg/mL) demonstrated comparable efficacy against Enterococcus faecalis and Klebsiella pneumoniae. To predict the antibacterial effect of daucosterol in a computer environment, molecular docking interactions of daucosterol with DD-peptidase and gyrase (antibiotic target proteins) were studied and compared with tetracycline as a control antibiotic. Daucosterol and DD-peptidase showed perfect binding affinity, as -9.00, and daucosterol and gyrase had -8.90 kcal/mol. Results showed that the daucosterol molecule interacted with antibiotic target proteins and can be used as an in vitro antibacterial agent.

Keywords

Prangos aricakensis Isolation Daucosterol Antibacterial activity Molecular docking

Project Number

221Z330

References

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Prangos aricakensis'ten izole edilen yeni olası antibakteriyel molekül, Daukosterol: Antibakteriyel aktivite ve DD-peptidaz ve giraz üzerinden moleküler yerleştirme yaklaşımları

Year 2026, Volume: 29 Issue: 1, 40 - 50

Serbay Şafak Gökçimen , Yaşar İpek , Tevfik Ozen , İbrahim Demirtas , Lütfi Behçet

https://doi.org/10.18016/ksutarimdoga.vi.1683529

Abstract

Prangos türleri kimyasal bileşenlerinden dolayı yıllardır çeşitli rahatsızlıkların tedavisinde kullanılmıştır. Türkiye’nin doğusu, yerel olarak endemik tür olan Prangos aricakensis'e ev sahipliği yapmaktadır. Bu çalışma, daukosterol molekülünün P. aricakensis gövde kısmından izole edildiği ilk çalışmadır. Daukosterol'ün yapısı 1D ve 2D NMR analiziyle belirlenmiştir. Daukosterol’ün antibakteriyel, immün sistemi güçlendirici ve anti-kanser gibi birçok alanda etkisinin araştırıldığı bilinmektedir. Molekülün in vitro antibakteriyel aktivitesi ve in silico antibiyotik hedef proteinlerle öngörülen moleküler yerleşimi üzerine çalışmalar yürütülmüştür. Standart antibiyotiklerle karşılaştırıldığında, daukosterol Bacillus cereus'a (512 μg/mL) ve Listeria monocytogenes'e (1024 μg/mL) karşı iyi etkilere sahip çıkmıştır. Ayrıca, daukosterol (512 μg/mL) ve amoksisilin (512 μg/mL), Enterococcus faecalis ve Klebsiella pneumoniae'ye karşı karşılaştırılabilir etkinlik göstermiştir. Bilgisayar ortamında Daukosterol’ün antibakteriyel etkisini tahmin etmek için daukosterol’ün DD-peptidaz ve giraz (antibiyotik hedef proteinleri) ile moleküler yerleştirme etkileşimleri incelendi ve kontrol antibiyotik olarak tetrasiklinin bu hedef proteinlerle olan etkileşimleri ile karşılaştırıldı. Daukosterol ve DD-peptidaz -9.00 kcal/mol ile çok iyi bağlanma afinitesi gösterirken daukosterol ve giraz ise -8.90 kcal/mol ile iyi bir etkileşime sahip görünmektedir. Sonuçlar daukosterol molekülünün antibiyotik hedef proteinlerle etkileyici etkileşimlere sahip olduğunu ve in vitro antibakteriyel reaktif olarak kullanılabileceğini gösterdi.

Keywords

Prangos aricakensis Daucosterol İzolasyon Moleküler yerleştirme Antibakteriyel aktivite

Ethical Statement

Gerek yoktur.

Supporting Institution

TÜBİTAK

Project Number

221Z330

Thanks

Türkiye Bilimsel ve Teknolojik Araştırma Kurumunun çalışmalarımıza desteğine teşekkürler

References

  • Abdollahnezhad, H., Bahadori, M. B., Pourjafar, H., & Movahhedin, N. (2021). Purification, characterization, and antioxidant activity of daucosterol and stigmasterol from Prangos ferulacea. Lett. Appl. Biosci, 10, 2174-2180. https://doi.org/10.33263/lianbs102.21742180
  • Abdullah, S. A., Mohammed, M. J., Marah, S., & Ozen, T. (2024). Metal ion complexes of 2-thioxoimidazolidine-4-one derivatives mixed ligand synthesis, characterization, in-vitro biological activities and in-silico studies. Journal of the Indian Chemical Society, 101(10), 101344. https://doi.org/10.1016/ j.jics.2024.101344
  • Andrews, J. M. (2001). Determination of minimum inhibitory concentrations. Journal of antimicrobial Chemotherapy, 48(suppl_1), 5-16. https://doi.org/10.1093/jac/48.suppl_1.5
  • Bandow, J. E., Brötz, H., Leichert, L. I. O., Labischinski, H., & Hecker, M. (2003). Proteomic approach to understanding antibiotic action. Antimicrobial agents and chemotherapy, 47(3), 948-955. https://doi.org/10.1128/aac.47.3.948-955.2003
  • Behçet, L., Yapar, Y., & Olgun, Ş. (2019). Prangos aricakensis (Apiaceae), a new species from eastern Turkey. Phytotaxa, 401(1), 55-63. https://doi.org/10.11646/phytotaxa.401.1.5
  • Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The protein data bank. Nucleic acids research, 28(1), 235-242. https://doi.org/10.1107/ 97809553602060000722
  • BIOVIA, D. S. (2019). BIOVIA Discovery Studio Visualize 2019, version 2019. Dassault Systèmes BIOVIA: San Diego, CA, USA. https://doi.org/10.1016/b978-0-12-816954-4.00002-4
  • Bruno, M., Ilardi, V., Lupidi, G., Quassinti, L., Bramucci, M., Fiorini, D., Venditti, A., & Maggi, F. (2019). The nonvolatile and volatile metabolites of Prangos ferulacea and their biological properties. Planta medica, 85(11/12), 815-824. https://doi.org/10.1055/a-0873-8622
  • Cho, E. J., Choi, J. Y., Lee, K. H., & Lee, S. (2012). Isolation of antibacterial compounds from Parasenecio pseudotaimingasa. Horticulture, Environment, and Biotechnology, 53, 561-564. https://doi.org/10.1007/s13580-012-0040-4
  • Delnavazi, M.-R., Hadjiakhoondi, A., Delazar, A., Ajani, Y., Tavakoli, S., & Yassa, N. (2015). Phytochemical and Antioxidant Investigation of the Aerial Parts of Dorema glabrum Fisch. & CA Mey. Iranian journal of pharmaceutical research: IJPR, 14(3), 925. https://doi.org/10.1007/s00044-014-1138-2
  • Dhamodiran, M., Chinnaperumal, K., Venkatesan, G., Alshiekheid, M. A., & Suseem, S. (2024). Isolation, structural elucidation of bioactive compounds and their wound-healing ability, antibacterial and in silico molecular docking applications. Environmental Research, 252, 119023. https://doi.org/10.1016/ j.envres.2024.119023
  • El Omari, N., Jaouadi, I., Lahyaoui, M., Benali, T., Taha, D., Bakrim, S., El Menyiy, N., El Kamari, F., Zengin, G., & Bangar, S. P. (2022). Natural Sources, Pharmacological Properties, and Health Benefits of Daucosterol: Versatility of Actions. Applied Sciences, 12(12), 5779. https://doi.org/10.3390/app12125779
  • Esmaeili, M. A., & Farimani, M. M. (2014). Inactivation of PI3K/Akt pathway and upregulation of PTEN gene are involved in daucosterol, isolated from Salvia sahendica, induced apoptosis in human breast adenocarcinoma cells. South African Journal of Botany, 93, 37-47. https://doi.org/10.1016/j.sajb.2014.03.010
  • Gao, C.-y., Lu, Y.-h., Tian, C.-r., Xu, J.-g., Guo, X.-p., Zhou, R., & Hao, G. (2011). Main nutrients, phenolics, antioxidant activity, DNA damage protective effect and microstructure of Sphallerocarpus gracilis root at different harvest time. Food chemistry, 127(2), 615-622. https://doi.org/10.1016/j.foodchem.2011.01.053
  • Gao, P., Huang, X., Liao, T., Li, G., Yu, X., You, Y., & Huang, Y. (2019). Daucosterol induces autophagic-dependent apoptosis in prostate cancer via JNK activation. Bioscience Trends, 13(2), 160-167. https://doi.org/10.5582/bst.2018.01293
  • Gökçimen, S. Ş., İpek, Y., Behçet, L., Demirtaş, İ., & Özen, T. (2024). Isolation, characterization and evaluation of oxypeucedanin and osthol from local endemic Prangos aricakensis Behçet and Yapar root as antioxidant, enzyme inhibitory, antibacterial and DNA protection: molecular docking and DFT approaches. Journal of Biomolecular Structure and Dynamics, 1-18. https://doi.org/10.1080/07391102.2024.2303387
  • Gu, Y., Yang, X., Shang, C., Thao, T. T. P., & Koyama, T. (2021a). Inhibition and interactions of alpha-amylase by daucosterol from the peel of Chinese water chestnut (Eleocharis dulcis). Food & Function, 12(18), 8411-8424. https://doi.org/10.1039/d1fo00887k
  • Gu, Y., Yang, X., Shang, C., Thao, T. T. P., & Koyama, T. (2021b). Inhibitory properties of saponin from Eleocharis dulcis peel against α-glucosidase. RSC advances, 11(25), 15400-15409. https://doi.org/10.1039/d1ra02198b
  • Jang, J., Kim, S.-M., Yee, S.-M., Kim, E.-M., Lee, E.-H., Choi, H.-R., Lee, Y.-S., Yang, W.-K., Kim, H.-Y., & Kim, K.-H. (2019). Daucosterol suppresses dextran sulfate sodium (DSS)-induced colitis in mice. International Immunopharmacology, 72, 124-130. https://doi.org/10.1016/j.intimp.2019.03.062
  • Lai, G. F., Wang, Y. F., Lu, C. H., Cao, J. X., Xu, Y. L., & Luo, S. D. (2003). Three novel triterpenoids from the aerial part of Helwingia chinensis. Helvetica Chimica Acta, 86(6), 2136-2141. https://doi.org/10.1002/hlca.200390170
  • Landgren, M., Oden, H., Kühn, I., Österlund, A., & Kahlmeter, G. (2005). Diversity among 2481 Escherichia coli from women with community-acquired lower urinary tract infections in 17 countries. Journal of antimicrobial Chemotherapy, 55(6), 928-937. https://doi.org/10.1093/jac/dki122
  • Lee, J.-H., Lee, J. Y., Park, J. H., Jung, H. S., Kim, J. S., Kang, S. S., Kim, Y. S., & Han, Y. (2007). Immunoregulatory activity by daucosterol, a β-sitosterol glycoside, induces protective Th1 immune response against disseminated Candidiasis in mice. Vaccine, 25(19), 3834-3840. https://doi.org/10.1016/ j.vaccine.2007.01.108
  • Li, T., Yin, X., Pan, W., Yang, J., & Liang, G. (2010). Chemical constituents of Humulus scandens. Zhong yao cai= Zhongyaocai= Journal of Chinese medicinal materials, 33, 55-57.
  • Marah, S., İpek, Y., Ozen, T., Demirtas, İ., & Behçet, L. (2025). Bioactivity-guided isolation of inositol as acetylcholinesterase inhibitory from endemic Campanula baskilensis Behcet: In vitro bioactivity, PCA analysis, and silico supporting studies. Kahramanmaraş Sütçü İmam Üniversitesi Tarım ve Doğa Dergisi, 28(3), 717-735. https://doi.org/10.18016/ksutarimdoga.vi.1632935
  • Mozaffarian, V. (1996). A dictionary of Iranian plant names. Tehran: Farhang Moaser, 396.
  • Nayel, N., Marah, S., Ozen, T., Yıldız, I., Erenler, R., & Behcet, L. (2024). Characterization and Comparative Investigation of In Vitro Bioactivities for Lactuca anatolica Root Aqueous Extract and Their Green-Chemical Synthesized Nanoparticles; Molecular Docking Studies. BioNanoScience, 14(3), 2854-2871. https://doi.org/10.1007/s12668-024-01353-9
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There are 42 citations in total.

Details

Primary Language Turkish
Subjects Pharmaceutical Botany
Journal Section RESEARCH ARTICLE
Authors

Serbay Şafak Gökçimen 0000-0002-3147-7042

Yaşar İpek 0000-0002-1041-267X

Tevfik Ozen 0000-0003-0133-5630

İbrahim Demirtas 0000-0001-8946-647X

Lütfi Behçet 0000-0001-8334-7816

Project Number 221Z330
Early Pub Date October 18, 2025
Publication Date October 19, 2025
Submission Date April 26, 2025
Acceptance Date August 22, 2025
Published in Issue Year 2026 Volume: 29 Issue: 1

Cite

APA Gökçimen, S. Ş., İpek, Y., Ozen, T., … Demirtas, İ. (2025). Prangos aricakensis’ten izole edilen yeni olası antibakteriyel molekül, Daukosterol: Antibakteriyel aktivite ve DD-peptidaz ve giraz üzerinden moleküler yerleştirme yaklaşımları. Kahramanmaraş Sütçü İmam Üniversitesi Tarım Ve Doğa Dergisi, 29(1), 40-50. https://doi.org/10.18016/ksutarimdoga.vi.1683529
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