Biological activities and DNA interactions of aqueous extract of Phlomis linearis (Boiss. & Bal.)

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Phlomis linearis, Biological activity, Cytotoxicity, DNA interaction, Molecular docking


Phlomis linearis Boiss. & Bal. of the Lamiaceae family is one of the endemic species in Turkey, i.e., growing in the east, central, and southeast parts of Anatolia and used for herbal tea. This study was designed to identify the biochemical and bioactivity properties of this endemic species by DPPH scavenging activity, metal chelating activity, total phenolic content, HPLC-DAD analysis, and MTT assay. Furthermore, the plant extract was evaluated for its antimicrobial activity against bacteria and fungi by using the microdilution method. The interactions between extract and plasmid DNA and their restriction endonuclease reactions were investigated by agarose gel electrophoresis. To support our hypothesis, we performed a molecular docking analysis. The DPPH scavenging activity of the plant extract was 53.86 ± 0.50 µg/ml in terms of IC50 value. The IC50 value of the plant extract was determined as 14.71 ± 4.01 mg/ml for metal chelating assay. The phenolic content of the extract was 231.55 ± 2.11 mg/g dry weight expressed as gallic acid equivalents (GAE). HPLC-DAD results revealed that the phenolic compounds were mainly derivatives of rosmarinic acid, chlorogenic acid, luteolin, luteolin-7-glycoside, luteolin derivatives, rutin derivatives, and apigenin derivatives. Besides, the cytotoxic activity of the plant extract against L929 fibroblast, H1299 non-small-cell lung carcinoma, and Caco-2 colorectal adenocarcinoma cell lines was determined by MTT assay. Phenolic content and molecular docking results correlated with each other.


Afolabi, O. B., & Oloyede, O. I. (2014). Antioxidant properties of the extracts of Talinum triangulare and its effect on antioxidant enzymes in tissue homogenate of Swiss albino rat. Toxicology International, 21(3), 307-313.

Alizadeh, R., Yousuf, I., Afzal, M., Srivastav, S., Srikrishna, S., & Arjmand, F. (2015). Enantiomeric fluoro-substituted benzothiazole Schiff base-valine Cu (II)/Zn (II) complexes as chemotherapeutic agents: DNA binding profile, cleavage activity, MTT assay and cell imaging studies. Journal of Photochemistry and Photobiology B: Biology, 143, 61-73.

Arteel, G. E. (2003). Oxidants and antioxidants in alcohol-induced liver disease. Gastroenterology, 124(3), 778-790.

Ayubi, Z., Jafari, A., Ayatollahi-Mousavi, S., Jafari, H., & Panddeh, M. (2021). Using Comet assay for genotoxic evaluation of Zataria multiflora Boiss., an Iranian endemic plant. Journal of Food Quality and Hazards Control, 8, 45-49.

Binici, A., Elmas, G., Okumuş, A., Erden Tayhan, S., Hökelek, T., Şeker, B. N., Açık, L., & Kılıç, Z. (2023). Phosphorus–nitrogen compounds. Part 58. Syntheses, structural characterizations and biological activities of 4-fluorobenzyl-spiro (N/O) cyclotriphosphazene derivatives. Journal of Biomolecular Structure and Dynamics, 41(1), 298-318.

Braca, A., De Tommasi, N., Di Bari, L., Pizza, C., Politi, M., & Morelli, I. (2001). Antioxidant principles from Bauhinia tarapotensis. Journal of Natural Products, 64(7), 892-895.

Cao, H., Pauff, J. M., & Hille, R. (2010). Substrate orientation and catalytic specificity in the action of xanthine oxidase: the sequential hydroxylation of hypoxanthine to uric acid. Journal of Biological Chemistry, 285(36), 28044-28053.

Chen, X., Li, H., Tian, L., Li, Q., Luo, J., & Zhang, Y. (2020). Analysis of the physicochemical properties of acaricides based on Lipinski's rule of five. Journal of Computational Biology, 27(9), 1397-1406.

Cirilli, M., Bachechi, F., Ughetto, G., Colonna, F. P., & Capobianco, M. L. (1993). Interactions between morpholinyl anthracyclines and DNA: the crystal structure of a morpholino doxorubicin bound to d (CGTACG). Journal of Molecular Biology, 230(3), 878-889.

CLSI (2008). Reference method for broth dilution antifungal susceptibility testing of yeasts; approved standard-third edition. In CLSI document M27-A3, Clinical and Laboratory Standards Institute Wayne, PA.

CLSI (2018). Methods for dilution antimicrobial susceptibility tests for bacteria that grow aerobically-11th edition. In CLSI standard M07, Clinical and Laboratory Standards Institute: Wayne, PA.

da Silva Dantas, F. G., de Castilho, P. F., de Almeida-Apolonio, A. A., de Araujo, R. P., & de Oliveira, K. M. P. (2020). Mutagenic potential of medicinal plants evaluated by the Ames Salmonella/microsome assay: A systematic review. Mutation Research/Reviews in Mutation Research, 786, 108338.

Dadandı, M. (2012). Phlomis. In A. Guner, S. Aslan, T. Ekim, M. Vural, & M. Babac (Eds.), List of Plants of Turkey (Veinous Plants): Nezahat Gökyiğit Botanical Garden and Flora Research Association Publication, İstanbul.

Davis, P. (2019). Flora of Turkey, Volume 1: Edinburgh University Press, Edinburgh.

Demirci, B., Dadandı, M. Y., Franz, G., & Başer, K. H. C. (2003). Chemical composition of the essential oil of Phlomis linearis Boiss. & Bal., and biological effects on the CAM-assay: a safety evaluation. Zeitschrift für Naturforschung C, 58(11-12), 826-829.

Deqnah, N., Yu, J. Q., Beale, P., Fisher, K., & Huq, F. (2012). Synthesis of trans-bis-(2-hydroxypyridine) dichloroplatinum (II) and its Activity in Human Ovarian Tumour Models. Anticancer Research, 32(1), 135-140.

Drew, H. R., Wing, R. M., Takano, T., Broka, C., Tanaka, S., Itakura, K., & Dickerson, R. E. (1981). Structure of a B-DNA dodecamer: conformation and dynamics. Proceedings of the National Academy of Sciences, 78(4), 2179-2183.

Duffy, E. M., & Jorgensen, W. L. (2000). Prediction of properties from simulations: free energies of solvation in hexadecane, octanol, and water. Journal of the American Chemical Society, 122(12), 2878-2888.

El-Medani, S. M., Makhlouf, A. A., Moustafa, H., Afifi, M. A., Haukka, M., & Ramadan, R. M. (2020). Spectroscopic, crystal structural, theoretical and biological studies of phenylacetohydrazide Schiff base derivatives and their copper complexes. Journal of Molecular Structure, 1208, 127860.

Formagio, A., Vieira, M., Volobuff, C., Silva, M., Matos, A., Cardoso, C., Foglio, M., & Carvalho, J. (2015). In vitro biological screening of the anticholinesterase and antiproliferative activities of medicinal plants belonging to Annonaceae. Brazilian Journal of Medical and Biological Research, 48, 308-315.

Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., Repasky, M. P., Knoll, E. H., Shelley, M., et al. (2004). Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry, 47(7), 1739-1749.

Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., Sanschagrin, P. C., & Mainz, D. T. (2006). Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein− ligand complexes. Journal of Medicinal Chemistry, 49(21), 6177-6196.

Ghosh, S. (2019). Cisplatin: The first metal based anticancer drug. Bioorganic Chemistry, 88, 102925.

Göger, G., Türkyolu, Ü., Gürşen, E. N., Yur, S., Karaduman, A. B., Göger, F., Tekin, M., & Özek, G. (2021). Phytochemical characterisation of Phlomis linearis Boiss. & Bal and screening foranticholinesterase, antiamylase, antimicrobial, and cytotoxic properties. Turkish Journal of Chemistry, 45(2), 387-399.

Greenwood, J. R., Calkins, D., Sullivan, A. P., & Shelley, J. C. (2010). Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution. Journal of Computer-Aided Molecular Design, 24(6-7), 591-604.

Guidi, I., Galimberti, D., Lonati, S., Novembrino, C., Bamonti, F., Tiriticco, M., Fenoglio, C., Venturelli, E., Baron, P., et al. (2006). Oxidative imbalance in patients with mild cognitive impairment and Alzheimer's disease. Neurobiology of Aging, 27(2), 262-269.

Halgren, T. (2007). New method for fast and accurate binding‐site identification and analysis. Chemical Biology & Drug Design, 69(2), 146-148.

Halgren, T. A. (2009). Identifying and characterizing binding sites and assessing druggability. Journal of Chemical Information and Modeling, 49(2), 377-389.

Heiblig, M., Sobh, M., & Nicolini, F. (2014). Subcutaneous omacetaxine mepesuccinate in patients with chronic myeloid leukemia in tyrosine kinase inhibitor-resistant patients: Review and perspectives. Leukemia Research, 38(10), 1145-1153.

Hyun, D. H., Hernandez, J. O., Mattson, M. P., & de Cabo, R. (2006). The plasma membrane redox system in aging. Ageing Research Reviews, 5(2), 209-220.

Iqbal, J., Abbasi, B. A., Mahmood, T., Kanwal, S., Ali, B., Shah, S. A., & Khalil, A. T. (2017). Plant-derived anticancer agents: A green anticancer approach. Asian Pacific Journal of Tropical Biomedicine, 7(12), 1129-1150.

Irwin, J. J., & Shoichet, B. K. (2005). ZINC− a free database of commercially available compounds for virtual screening. Journal of Chemical Information and Modeling, 45(1), 177-182.

Irwin, J. J., Sterling, T., Mysinger, M. M., Bolstad, E. S., & Coleman, R. G. (2012). ZINC: a free tool to discover chemistry for biology. Journal of Chemical Information and Modeling, 52(7), 1757-1768.

ISO 10993-5 (2009). Biological evaluation of medical devices-Part 5: Tests for in vitro cytotoxicity: ISO Geneva.

Jacobson, M. P., Friesner, R. A., Xiang, Z., & Honig, B. (2002). On the role of the crystal environment in determining protein side-chain conformations. Journal of Molecular Biology, 320(3), 597-608.

Jacobson, M. P., Pincus, D. L., Rapp, C. S., Day, T. J., Honig, B., Shaw, D. E., & Friesner, R. A. (2004). A hierarchical approach to all‐atom protein loop prediction. Proteins: Structure, Function, and Bioinformatics, 55(2), 351-367.

Kim, I. S., Yang, M. R., Lee, O. H., & Kang, S. N. (2011). Antioxidant activities of hot water extracts from various spices. International Journal of Molecular Sciences, 12(6), 4120-4131.

Kim, J. E., Kwon, J. Y., Seo, S. K., Son, J. E., Jung, S. K., Min, S. Y., Hwang, M. K., Heo, Y. S., Lee, K. W., et al. (2010). Cyanidin suppresses ultraviolet B-induced COX-2 expression in epidermal cells by targeting MKK4, MEK1, and Raf-1. Biochemical Pharmacology, 79(10), 1473-1482.

Kinnula, V. L., & Crapo, J. D. (2004). Superoxide dismutases in malignant cells and human tumors. Free Radical Biology and Medicine, 36(6), 718-744.

Koutsoukis, C., Roukos, C., Demertzis, P. G., Kandrelis, S., & Akrida‐Demertzi, K. (2019). The variation of the chemical composition of the main plant species in a subalpine grassland in northwestern Greece. Legume Science, 1(1), e23.

Kuruppu, A. I., Paranagama, P., & Goonasekara, C. L. (2019). Medicinal plants commonly used against cancer in traditional medicine formulae in Sri Lanka. Saudi Pharmaceutical Journal, 27(4), 565-573.

Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2012). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 64, 4-17.

Madhavi Sastry, G., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design, 27, 221-234.

Mendonça, E. D., da Silva, J., Dos Santos, M. S., Carvalho, P., Papke, D. K. M., Ortmann, C. F., Picada, J. N., Reginatto, F. H., & Ferraz, A. D. B. F. (2016). Genotoxic, mutagenic and antigenotoxic effects of Cecropia pachystachya Trécul aqueous extract using in vivo and in vitro assays. Journal of Ethnopharmacology, 193, 214-220.

Morsy, N. M., Hassan, A. S., Hafez, T. S., Mahran, M. R., Sadawe, I. A., & Gbaj, A. M. (2021). Synthesis, antitumor activity, enzyme assay, DNA binding and molecular docking of Bis-Schiff bases of pyrazoles. Journal of the Iranian Chemical Society, 18, 47-59.

OECD (1997). Guidelines for the testing of chemicals, section 4 health effects, Test Guideline No. 471, Bacterial Reverse Mutation Test.

Okumuş, A., Akbaş, H., Kılıç, Z., Yasemin Koç, L., Açık, L., Aydın, B., Türk, M., Hökelek, T., & Dal, H. (2016). Phosphorus–nitrogen compounds part 33: in vitro cytotoxic and antimicrobial activities, DNA interactions, syntheses, and structural investigations of new mono (4-nitrobenzyl) spirocyclotriphosphazenes. Research on Chemical Intermediates, 42, 4221-4251.

Orlando, B. J., & Malkowski, M. G. (2016). Substrate-selective inhibition of cyclooxygeanse-2 by fenamic acid derivatives is dependent on peroxide tone. Journal of Biological Chemistry, 291(29), 15069-15081.

Ozkan, S. C., Aksakal, F., & Yilmaz, A. (2020). Synthesis of novel calix [4] arene p-benzazole derivatives and investigation of their DNA binding and cleavage activities with molecular docking and experimental studies. RSC Advances, 10(63), 38695-38708.

Patel, K. R., Brown, V. A., Jones, D. J., Britton, R. G., Hemingway, D., Miller, A. S., West, K. P., Booth, T. D., Perloff, M., et al. (2010). Clinical pharmacology of resveratrol and its metabolites in colorectal cancer patients resveratrol in colorectal cancer patients. Cancer Research, 70(19), 7392-7399.

Rahier, N., Thomas, C., & Hecht, S. (2005). Camptothecin and its analogs. In G. Cragg, D. Kinston, & D. New (Eds.), Anticancer agents from natural products (pp. 5-22): Boca Raton, FL: Taylor and Francis.

Sas, K., Robotka, H., Toldi, J., & Vécsei, L. (2007). Mitochondria, metabolic disturbances, oxidative stress and the kynurenine system, with focus on neurodegenerative disorders. Journal of the Neurological Sciences, 257(1-2), 221-239.

Schrödinger Release. (2020-3a). Epik: Schrödinger, LLC, New York.

Schrödinger Release. (2020-3b). Glide: Schrödinger, LLC, New York.

Schrödinger Release. (2020-3c). LigPrep: Schrödinger, LLC, New York.

Schrödinger Release. (2020-3d). MacroModel: Schrödinger, LLC, New York.

Schrödinger Release. (2020-3e). Maestro: Schrödinger, LLC, New York.

Schrödinger Release. (2020-3f). Prime: Schrödinger, LLC, New York.

Schrödinger Release. (2020-3g). Protein Preparation Wizard: Schrödinger, LLC, New York.

Schrödinger Release. (2020-3h). QikProp: Schrödinger, LLC, New York.

Schrödinger Release. (2020-3i). SiteMap: Schrödinger, LLC, New York.

Seo, H., Jo, J., Ku, J., Choi, H., Choi, Y., & Woo, J. (2015). Induction of caspase-dependent extrinsic apoptosis by apigenin through inhibition of signal transducer and activator of transcription 3 (STAT3) signalling in HER2-overexpressing BT-474 breast cancer cells. Bioscience Reports, 35(6), e00276.

Singh, U., & Jialal, I. (2006). Oxidative stress and atherosclerosis. Pathophysiology, 13(3), 129-142.

Sirajuddin, M., Ali, S., & Badshah, A. (2013). Drug–DNA interactions and their study by UV–Visible, fluorescence spectroscopies and cyclic voltametry. Journal of Photochemistry and Photobiology B: Biology, 124, 1-19.

Sponchiado, G., Adam, M. L., Silva, C. D., Soley, B. S., de Mello-Sampayo, C., Cabrini, D. A., Correr, C. J., & Otuki, M. F. (2016). Quantitative genotoxicity assays for analysis of medicinal plants: A systematic review. Journal of Ethnopharmacology, 178, 289-296.

Stagos, D. (2019). Antioxidant activity of polyphenolic plant extracts. Antioxidants, 9(1), 19.

Stamos, J., Sliwkowski, M. X., & Eigenbrot, C. (2002). Structure of the epidermal growth factor receptor kinase domain alone and in complex with a 4-anilinoquinazoline inhibitor. Journal of Biological Chemistry, 277(48), 46265-46272.

Thakore, P., Mani, R. K., & Kavitha, S. J. (2012). A brief review of plants having anti-cancer property. International Journal of Pharmaceutical Research Development, 3, 129-136.

Turumtay, E. A., İslamoğlu, F., Çavuş, D., Şahin, H., Turumtay, H., & Vanholme, B. (2014). Correlation between phenolic compounds and antioxidant activity of Anzer tea (Thymus praecox Opiz subsp. caucasicus var. caucasicus). Industrial Crops and Products, 52, 687-694.

Upadrasta, L., Mukhopadhyay, M., & Banerjee, R. (2011). Tannins: Chemistry, biological properties and biodegradation. In A. Sabu, S. Roussos, & C. Aguilar (Eds.), Chemistry and Biotechnology of Polyphenols (pp. 5-32): Cibet Publishers; Thiruvananthapuram, India.

Uritu, C. M., Mihai, C. T., Stanciu, G. D., Dodi, G., Alexa-Stratulat, T., Luca, A., Leon-Constantin, M. M., Stefanescu, R., Bild, V., et al. (2018). Medicinal plants of the family Lamiaceae in pain therapy: A review. Pain Research and Management, 2018, 801543.

Wallace, R. J. (2004). Antimicrobial properties of plant secondary metabolites. Proceedings of the Nutrition Society, 63(4), 621-629.

WHO (2015). Global Action Plan on Antimicrobial Resistance: The WHO Document Production Services, Geneva, Switzerland.

Williams, P. A., Cosme, J., Ward, A., Angove, H. C., Matak Vinković, D., & Jhoti, H. (2003). Crystal structure of human cytochrome P450 2C9 with bound warfarin. Nature, 424(6947), 464-468.

Wood, E. R., Truesdale, A. T., McDonald, O. B., Yuan, D., Hassell, A., Dickerson, S. H., Ellis, B., Pennisi, C., Horne, E., et al. (2004). A unique structure for epidermal growth factor receptor bound to GW572016 (Lapatinib) relationships among protein conformation, inhibitor off-rate, and receptor activity in tumor cells. Cancer Research, 64(18), 6652-6659.

Zhou, J., Yang, Q., Zhu, X., Lin, T., Hao, D., & Xu, J. (2020). Antioxidant activities of Clerodendrum cyrtophyllum Turcz leaf extracts and their major components. PLoS One, 15(6), e0234435.

Zhou, Y., Jiang, Z., Lu, H., Xu, Z., Tong, R., Shi, J., & Jia, G. (2019). Recent advances of natural polyphenols activators for Keap1‐Nrf2 signaling pathway. Chemistry & Biodiversity, 16(11), e1900400.




How to Cite

Aydın, B., Gönder, L. Y., Çerçi, N. A., Ateş, Y. C., Yalçınkaya, İlayda S., Canbolat, N., Açık, L., Karacan, N., Akyüz Turumtay, E., & Turumtay, H. (2023). Biological activities and DNA interactions of aqueous extract of Phlomis linearis (Boiss. & Bal.). International Journal of Plant Based Pharmaceuticals, 3(1), 73–85.



Research Articles
Received 2022-11-29
Accepted 2023-03-01
Published 2023-03-03