Kekik (Thymus eigii M. Zohary Et P.H. Davis) Jalas Türünün Uçucu Yağının Karakterizasyonu ve in silico Modelleme Perspektifi

Abstract

Son yıllarda, aromatik bitkilerin ve tedavi edici özellikleri için kullanılan bitkilerin kullanımını içeren bitkisel ilaçların kullanımında bir artış olmuştur. Her geçen gün artan bu talebi karşılayabilmek için tıbbi bitkilerden elde edilen aktif bileşiklerin miktarının belirlenmesine önemli bir ihtiyaç duyulmaktadır. Bu araştırma için Hatay ili Amanos Dağı'ndan kekik (Thymus eigii M. Zohary et P.H. Davis) bitki örnekleri toplanmıştır. Bitkinin yer üstü kısmından uçucu yağı çıkarmak için hidrodistilasyon yöntemi kullanıldı ve uçucu yağın bileşenlerini analiz etmek için bir Gaz kromatografisi-kütle spektrometresi (GC-MS) kullanılmıştır. Yapılan analizler sonucunda 21 adet uçucu yağ bileşeni tespit edilmiştir. En yüksekler arasından ana bileşenler olarak Gamma-terpinene (%27.49), Carvacrol (%27.38) ve P-cymene (%14.40) belirlenmiştir. Fusarium oxysporum kütinaz yapısı ile H-bağlı etkileşimleri ortaya çıkaran başlıca monoterpenlerin etki mekanizması moleküler modelleme teknikleri kullanılarak araştırılmış ve bu yöntemler kullanılarak da en düşük bağlanma enerjileri hesaplanmıştır. Verilen bulguların, yaygın kekik bitkilerinden fitoterapötik bileşikler oluşturmaya yönelik gelecekteki araştırmaların yolunu açması olasıdır.

Keywords

• uçucu yağ bileşeni
• tıbbi bitki
• moleküler modelleme
• moleüler bağlanma
• patojen

Characterization of essential oil and in silico modelling perspectives of thyme (Thymus eigii M. Zohary et P.H. Davis) jalas species

Abstract

In recent years, the use of herbal medicines has increased, including the use of aromatic plants and plants used for their therapeutic properties. To meet this ever-increasing demand, the quantity of active compounds extracted from medicinal plants must be significantly determined. For this study, plant samples of thyme (Thymus eigii M. Zohary et P.H. Davis) were collected from Amanos Mountain in the province of Hatay. Hydrodistillation was utilized to extract the essential oil from the aboveground portion of the plant, and Gas chromatography-mass spectrometry (GC-MS) was utilized to analyze the essential oil's constituents. As a consequence of the analysis, twenty-one components of essential oils were identified. The principal components were determined as Gamma-terpinene (27.49%), Carvacrol (27.38%), and P-cymene (14.40%). The mechanism of action of the major monoterpenes that reveal H-bonded interactions with the structure of Fusarium oxysporum cutinase was investigated using molecular modeling techniques, and the lowest binding energies were calculated using these techniques. The presented findings are likely to pave the way for future research on phytotherapeutic compounds derived from common thyme plants.

Keywords

• essential oil component
• medicinal plant
• molecular modelling
• molecular docking
• pathogen

References

1. Altundağ Ş, Aslım B, 2005. Kekiğin Bazı Bitki Patojeni Bakteriler Üzerine Antimikrobiyal Etkisi. Orlab On-Line Mikrobiyoloji Dergisi, 3 (7): 12-14.
2. Barrera-Necha LL, Garduno-Pizana C, Garcia-Barrera LJ, 2009. In vitro Antifungal Activity Of Essential Oils And Their Compounds On Mycelial Growth of Fusarium oxysporum f. sp. gladioli (Massey) Snyder and Hansen. Plant Pathology Journal (Faisalabad), 8 (1): 17-21.
3. Barut M, Tansı S, Karaman Ş, 2021. Yield and Essential Oil Composition of Thymus eigii (M. Zohary & PH Davis) Jalas Leaves and Flowers at Various Growth Stages in the Mediterranean Region. Avrupa Bilim ve Teknoloji Dergisi, (31): 523-530.
4. Baser KHC, Kürkçüoglu M, Tümen G, Sezik E, 1996. Composition of the Essential oil of Thymus eigii (M. Zohary et PH Davis) Jalas from Turkey. Journal of Essential Oil Research, 8 (1): 85-86.
5. Başer KHC, 2001. Her Derde Deva Bir Bitki Kekik. Bilim ve Teknik Dergisi, 402 (26): 74-77.
6. Butt SS, Badshah Y, Shabbir M, Rafiq M, 2020. Molecular Docking Using Chimera And Autodock Vina Software For Nonbioinformaticians. JMIR Bioinformatics and Biotechnology, 1 (1): e14232.
7. Cairns TC, Studholme DJ, Talbot NJ, Haynes K, 2016. New and Improved Techniques for the Study of Pathogenic Fungi. Trends in Microbiology, 24 (1): 35-50.
8. Can Baser KH, 2008. Biological and Pharmacological Activities of Carvacrol and Carvacrol Bearing Essential Oils. Current Pharmaceutical Design, 14 (29): 3106-3119.

9. Davis PH, 1970. Flora of Turkey and the East Aegean Islands. Vol. 3. Flora of Turkey and the East Aegean Islands. University Press: Edinburgh, Scotland, Vol. 7, 349-382.
10. Dean R, Van Kan JA, Pretorius ZA, Hammond‐Kosack KE, Di Pietro A, Spanu PD, Foster GD, 2012. The Top 10 Fungal Pathogens in Molecular Plant Pathology. Molecular Plant Pathology, 13 (4): 414-430.
11. Dimarogona M, Nikolaivits E, Kanelli M, Christakopoulos P, Sandgren M, Topakas E, 2015. Structural and Functional Studies of a Fusarium oxysporum Cutinase with Polyethylene Terephthalate Modification Potential. Biochimica et Biophysica Acta (BBA)-General Subjects, 1850 (11): 2308-2317.
12. Fourie G, Steenkamp ET, Ploetz RC, Gordon TR, Viljoen A, 2011. Current Status of the Taxonomic Position of Fusarium oxysporum Formae Specialis Cubense Within the Fusarium oxysporum Complex. Infection, Genetics and Evolution, 11 (3): 533-542.
13. Gill AO, Holley RA, 2006. Inhibition of Membrane Bound ATPases of Escherichia coli and Listeria monocytogenes by Plant Oil Aromatics. International journal of food microbiology, 111 (2): 170-174.
14. Gordon TR, Martyn RD, 1997. The Evolutionary Biology of Fusarium oxysporum. Annual review of phytopathology, 35 (1): 111-128.
15. Goze I, Alim A, Cetinus SA, Durmus N, Vural N, Goze HM, 2009. Chemical Composition and Antioxidant, Antimicrobial, Antispasmodic Activities of the Essential oil of Thymus fallax Fisch, Mey. J Med Plants Res, 3 (3): 174-178.
16. Halpern HC, Bell AA, Wagner TA, Liu J, Nichols RL, Olvey J, Brewer MT, 2018. First Report of Fusarium wilt of Cotton Caused by Fusarium oxysporum f. sp. vasinfectum race 4 in Texas, USA. Plant disease, 102 (2): 446-446.
17. Jianu C, Stoin D, Cocan I, David I, Pop G, Lukinich-Gruia AT, Horhat DI, 2021. In silico and in vitro Evaluation of the Antimicrobial and Antioxidant Potential of Mentha× smithiana R. GRAHAM Essential Oil from Western Romania. Foods, 10 (4): 815.
18. Kocabas YZ, Karaman S, 2001. Essential Oils of Lamiaceae Family From South East Mediterranean Region (Turkey). Pakistan Journal of Biological Sciences, 4 (10): 1221-1223.
19. Koçak R, Boyraz N, 2006. Bazı Bitki Uçucu Yağlarının Fungisidal ve Fungistatik Etkileri. Selcuk Journal of Agriculture and Food Sciences, 20 (38): 76-81.
20. Korkmaz G, Usta M, Demirel S, 2022. Potato virus S (PVS)-Bitlis İzolatının Kılıf Proteinin in silico Karakterizasyonu ve Konak Proteini ile Docking analizi. Journal of Agriculture 5 (1): 57-67.
21. Könemann B, 1999. The İllustrated AZ of Over 10,000 Garden Plants and How to Cultivate Them. Hong Kong: Gordon Cheers Publication, 51-3.
22. Kundu A, Dutta A, Mandal A, Negi L, Malik M, Puramchatwad R, Singh PK, 2021. A Comprehensive in vitro and in silico Analysis of Nematicidal Action of Essential Oils. Frontiers in Plant Science, 11: 614143.
23. Küçükbay FZ, Kuyumcu E, Çelen S, Azaz AD, Arabaci T, Yildiz B, 2013. Chemical Composition and Antimicrobial and Antioxidant Activities of Three Turkish Thyme Essential Oils. Journal of Essential Oil Bearing Plants, 16 (5): 661-671.
24. Lecomte C, Alabouvette C, Edel-Hermann V, Robert F, Steinberg C, 2016. Biological Control of Ornamental Plant Diseases Caused by Fusarium oxysporum: a Review. Biological control, 101: 17-30.
25. Maharramov S, Hüseynova A, 2017. Bazı Kekik Türlerinin (Thymus kotschyanus ve Thymus collinus) Gastrointestinal Parazitlere Karşı Antelmentik Etkisinin Araştırılması. 2018 24 1 January-February, 961.
26. Peters RD, MacLeod C, Seifert KA, Martin RA, Hale LR, Grau CR, MacInnis S, 2008. Pathogenicity to Potato Tubers of Fusarium spp. Isolated From Potato, Cereal and Forage Crops. American Journal of Potato Research, 85: 367-374.
27. Purdy RE, Kolattukudy PE, 1975. Hydrolysis of Plant Cuticle by Plant Pathogens. Properties of cutinase I, cutinase II, and a nonspecific esterase isolated from Fusarium solani pisi. Biochemistry, 14 (13): 2832-2840. Santana de Oliveira M, Pereira da Silva VM, Cantao Freitas L, Gomes Silva S, Nevez Cruz J, de Aguiar Andrade EH, 2021. Extraction Yield, Chemical Composition, Preliminary Toxicity of Bignonia Nocturna (bignoniaceae) Essential Oil and in silico Evaluation of the Interaction. Chemistry & Biodiversity, 18 (4): e2000982.
28. Sharifi‐Rad M, Varoni EM, Iriti M, Martorell M, Setzer WN, del Mar Contreras M, Sharifi‐Rad J, 2018. Carvacrol and Human Health: A Comprehensive Re view. Phytotherapy Research, 32 (9): 1675-1687.
29. Sharma A, Rajendran S, Srivastava A, Sharma S, Kundu B, 2017. Antifungal Activities of Selected Essential Oils Against Fusarium oxysporum f. sp. lycopersici 1322, with Emphasis on Syzygium aromaticum Essential Oil. Journal of Bioscience and Bioengineering, 123 (3): 308-313.
30. Silva SG, da Costa RA, de Oliveira MS, da Cruz JN, Figueiredo PLB, Brasil DDSB, Andrade EHDA, 2019. Chemical Profile of Lippia thymoides, Evaluation of the Acetylcholinesterase Inhibitory Activity of its Essential Oil, and Molecular Docking and Molecular Dynamics Simulations. PLoS One, 14 (3): e0213393.
31. Smith SN, 2007. An Overview of Ecological and Habitat Aspects in the Genus Fusarium with Special Emphasis on the Soil-borne Pathogenic Forms. Plant Pathol Bull, 16: 97-120.
32. Tepe B, Daferera D, Sökmen M, Polissiou M, Sökmen A, 2004. In vitro Antimicrobial and Antioxidant Activities of the Essential Oils and Various Extracts of Thymus eigii M. Zohary et PH Davis. Journal of Agricultural and Food Chemistry, 52 (5): 1132-1137.
33. Tharanathan RN, Kittur FS, 2003. Chitin—the Undisputed Biomolecule of Great Potential. Crit. Rev. Food Sci. Nutr., 43: 63-86.
34. Tümen GN, Kırımer KHC, Başer C, 1995. Composition of the Essential Oils of Thymus species Growing in Turkey. Chemistry of Natural Compounds, 3 (1): 42-45.
35. Usta M, Guller A, Demirel S, Korkmaz G, Kurt Z, 2023. New insights into tomato spotted wilt orthotospovirus (TSWV) infections in Türkiye: Molecular detection, phylogenetic analysis, and in silico docking study. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 51 (3):13245.
36. Yildirim B, Kumlay AM, Rezaeieh KAP, 2016. Chemical Composition of Bioactive Volatile Oils from Silene vulgaris L. International Scientific Researches Journal, 72: 213.