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Allisin ve Diallil Disülfitin Moleküler Yerleştirme ve Reaktif Bölgelerinin Tanımlanması (Homo–Lumo, Mep): Potansiyel Antikanser İnhibitörü

Year 2023, Volume: 13 Issue: 4, 1523 - 1539, 15.12.2023

Sevtap Çağlar Yavuz

https://doi.org/10.31466/kfbd.1307190

Abstract

Doğal ürünler tarihsel olarak, özellikle kanser hastalıkları için farmakoterapiye önemli bir katkı sağlamıştır. Sarımsak, allisin ve diallil disülfit dahil olmak üzere antikanser etkileri olan çeşitli biyoaktif moleküller içerir. Bu çalışmada, allisin ve diallil disülfit için fonksiyonel B3LYP yöntemi/6-31++G(d,p) temel seti ile DFT kullanılarak Gaussian 09 W'da optimizasyon hesaplamaları yapılmıştır. İlaca benzerlik ve absorpsiyon, dağılım, metabolizma, atılım ve toksisite (ADMET) özellikleri incelendi. Allisin ve diallil disülfitin biyolojik bilgisini araştırmak için moleküler yerleştirme gerçekleştirildi. Bu hesaplamalarda tercih edilen protein, 5XGN, EGFR mutantları T790M/C797S kompleksinin kristal yapısıdır. Allisin ve diallil disülfit molekülleri-EGFR mutantları T790M/C797S kompleksi için bağlanma enerjileri sırasıyla -8.3 kcal/mol ve -8.2 kcal/mol olarak hesaplandı. Bu iki bileşik için anlamlı sonuçlar elde edildi.

Keywords

Allisin Diallil disülfit DFT HOMO-LUMO Moleküler yerleştirme Sarımsak

References

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Molecular Docking and Reactive Sites Identification (Homo–Lumo, Mep) of Allicin and Diallyl Disulfide: Potential Anticancer Inhibitor

Year 2023, Volume: 13 Issue: 4, 1523 - 1539, 15.12.2023

Sevtap Çağlar Yavuz

https://doi.org/10.31466/kfbd.1307190

Abstract

Natural products have historically made a significant contribution to pharmacotherapy, especially for cancer diseases. Garlic contains a variety of bioactive molecules with anticancer effects, including allicin and diallyl disulfide. In this study, optimization computations were performed in the Gaussian 09 W utilizing the DFT with functional B3LYP method/6-31++G(d,p) basis set for allicin and diallyl disulfide. Drug-likeness and ADME-Tox properties were examined. Molecular docking was achieved to research the biological knowledge of allicin and diallyl disulfide. The protein preferred in these computations is the crystal structure of the 5XGN, EGFR mutants T790M/C797S complex. The binding energies for the allicin and diallyl disulfide molecules-EGFR mutants T790M/C797S complex were computed as -8.3 kcal/mol and -8.2 kcal/mol respectively. Meaningful results were achieved for these two compounds.

Keywords

Allicin Diallyl disulfide DFT HOMO-LUMO Molecular docking Garlic

References

  • Akan, S. (2014). Health Promoting Properties of Garlic (Allium sativum L.) Consumption. Akademik Gıda, 12(2), 95-100.
  • Ali Abdalla, Y. O., Subramaniam, B., Nyamathulla, S., Shamsuddin, N., Arshad, N. M., Mun, K. S., Awang, K., Nagoor, N. H. (2022). Natural products for cancer therapy: a review of their mechanism of actions and toxicity in the past decade. Journal of Tropical Medicine, 2022.
  • Bailly, C. (2019). Irinotecan: 25 years of cancer treatment. Pharmacological research, 148, 104398.
  • Baldwin, E. L., and Osheroff, N. (2005). Etoposide, topoisomerase II and cancer. Current Medicinal Chemistry-Anti-Cancer Agents, 5(4), 363-372.
  • Banerjee, P., and Ulker, O. C. (2022). Combinative ex vivo studies and in silico models ProTox-II for investigating the toxicity of chemicals used mainly in cosmetic products. Toxicology mechanisms and methods, 32(7), 542-548.
  • Bayoumy, A. M., Ibrahim, M., Omar, A. (2020). Mapping molecular electrostatic potential (MESP) for fulleropyrrolidine and its derivatives. Optical and Quantum Electronics, 52, 1-13.
  • Bazaraliyeva, A., Moldashov, D., Turgumbayeva, A., Kartbayeva, E., Kalykova, A., Sarsenova, L., & Issayeva, R. (2022). Chemical and biological properties of bio-active compounds from garlic (Allium sativum). Pharmacia, 69(4), 955-964.
  • Bray, F., Ferlay, J., Soerjomataram, I., Siegel, R. L., Torre, L. A., Jemal, A. (2018). Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA: a cancer journal for clinicians, 68(6), 394-424.
  • Bulat, F. A., Toro-Labbé, A., Brinck, T., Murray, J. S., Politzer, P. (2010). Quantitative analysis of molecular surfaces: areas, volumes, electrostatic potentials and average local ionization energies. Journal of molecular modeling, 16, 1679-1691.
  • Butt, S. S., Badshah, Y., Shabbir, M., Rafiq, M. (2020). Molecular docking using chimera and autodock vina software for nonbioinformaticians. JMIR Bioinformatics and Biotechnology, 1(1), e14232.
  • Chakraborty, S., Rahman, T. (2012). The difficulties in cancer treatment. Ecancermedicalscience, 6.
  • Choudhari, A. S., Mandave, P. C., Deshpande, M., Ranjekar, P., Prakash, O. (2020). Phytochemicals in cancer treatment: From preclinical studies to clinical practice. Frontiers in pharmacology, 10, 1614.
  • D.S.J.S.D. Biovia, CA, USA, Discovery Studio Visualizer, 2017, 936.
  • Daina, A., Michielin, O., Zoete, V. (2017). SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific reports, 7(1), 42717.
  • Dehelean, C. A., Marcovici, I., Soica, C., Mioc, M., Coricovac, D., Iurciuc, S., Cretu O. M., Pinzaru, I. (2021). Plant-derived anticancer compounds as new perspectives in drug discovery and alternative therapy. Molecules, 26(4), 1109.
  • Desale, V. J., Mali, S. N., Thorat, B. R., Yamgar, R. S. (2021). Synthesis, admetSAR predictions, DPPH radical scavenging activity, and potent anti-mycobacterial studies of hydrazones of substituted 4-(anilino methyl) benzohydrazides (Part 2). Current Computer-Aided Drug Design, 17(4), 493-503.
  • Di, L., Kerns, E. H., Carter, G. T. (2009). Drug-like property concepts in pharmaceutical design. Current pharmaceutical design, 15(19), 2184-2194.
  • Diretto, G., Rubio-Moraga, A., Argandoña, J., Castillo, P., Gómez-Gómez, L., Ahrazem, O. (2017). Tissue-specific accumulation of sulfur compounds and saponins in different parts of garlic cloves from purple and white ecotypes. Molecules, 22(8), 1359.
  • El-Saber Batiha, G., Magdy Beshbishy, A., G. Wasef, L., Elewa, Y. H., A. Al-Sagan, A., Abd El-Hack, M. E., Taha, A. E., Abd-Elhakim, Y. M., Prasad Devkota, H. (2020). Chemical constituents and pharmacological activities of garlic (Allium sativum L.): A review. Nutrients, 12(3), 872.
  • Gaussian 09, Revision A. 1; Gaussian, Inc: Wallingford, CT, 2009
  • Gfeller, D., Grosdidier, A., Wirth, M., Daina, A., Michielin, O., Zoete, V. (2014). SwissTargetPrediction: a web server for target prediction of bioactive small molecules. Nucleic acids research, 42(W1), W32-W38.
  • Giaccone, G., Donadio, M., Bonardi, G., Testore, F., Calciati, A. (1988). Teniposide in the treatment of small-cell lung cancer: the influence of prior chemotherapy. Journal of Clinical Oncology, 6(8), 1264-1270.
  • Goktas, F., Karatas, M., Tuncer, S. C., Karacaer, N. T. (2023). Investigation of the Effect of Natural Bioactive Components on iNOS Activity in-Slico. Aksaray Üniversitesi Tıp Bilimleri Dergisi, 4(1), 12-17.
  • Guéniche, N., Huguet, A., Bruyere, A., Habauzit, D., Le Hégarat, L., Fardel, O. (2021). Comparative in silico prediction of P‐glycoprotein‐mediated transport for 2010–2020 US FDA‐approved drugs using six Web‐tools. Biopharmaceutics & Drug Disposition, 42(8), 393-398.
  • Gundogdu, Ö. (2023). Molecular docking studies and ADME predictions on synthesized chalcone compounds targeting EGFR. Hittite Journal of Science and Engineering, 10(2), 167-175.
  • Housman, G., Byler, S., Heerboth, S., Lapinska, K., Longacre, M., Snyder, N., Sarkar, S. (2014). Drug resistance in cancer: an overview. Cancers, 6(3), 1769-1792.
  • Huizing, M. T., Misser, V. H. S., Pieters, R. C., ten Bokkel Huinink, W. W., Veenhof, C. H. N., Vermorken, J. B., Pinedo, H. M., Beijnen, J. H. (1995). Taxanes: a new class of antitumor agents. Cancer investigation, 13(4), 381-404
  • 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.
  • Kasmi, R., El Ouardi, Y., Bouachrine, M., Ouammou, A. (2022). Modeling study, 3D-QSAR and molecular docking of 9H-purine derivatives as EGFR inhibitors. Materials Today: Proceedings, 62, 6312-6323.
  • Kerns, E. H., Di, L. (2003). Pharmaceutical profiling in drug discovery. Drug discovery today, 8(7), 316-323.
  • Kuete, V. (2017). Allium sativum. In Medicinal Spices and Vegetables from Africa, 363-377.
  • Liu, Y. P., Zheng, C. C., Huang, Y. N., He, M. L., Xu, W. W., Li, B. (2021). Molecular mechanisms of chemo‐and radiotherapy resistance and the potential implications for cancer treatment. MedComm, 2(3), 315-340.
  • Martino, E., Casamassima, G., Castiglione, S., Cellupica, E., Pantalone, S., Papagni, F., Rui, M., Siciliano, A. M., Collina, S. (2018). Vinca alkaloids and analogues as anti-cancer agents: Looking back, peering ahead. Bioorganic & medicinal chemistry letters, 28(17), 2816-2826.
  • Martins, N., Petropoulos, S., Ferreira, I. C. (2016). Chemical composition and bioactive compounds of garlic (Allium sativum L.) as affected by pre-and post-harvest conditions: A review. Food Chemistr, 211, 41-50.
  • Mary, Y. S., Varghese, H. T., Panicker, C. Y., Thiemann, T., Al-Saadi, A. A., Popoola, S. A., Alsenoy, C.V., Al Jasem, Y. (2015). Molecular conformational analysis, vibrational spectra, NBO, NLO, HOMO–LUMO and molecular docking studies of ethyl 3-(E)-(anthracen-9-yl) prop-2-enoate based on density functional theory calculations. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 150, 533-542.
  • Miller, K. D., Siegel, R. L., Lin, C. C., Mariotto, A. B., Kramer, J. L., Rowland, J. H., Stein, K. D., Alteri, R., Jemal, A. (2016). Cancer treatment and survivorship statistics, 2016. CA: a cancer journal for clinicians, 66(4), 271-289.
  • Mitra, S., Das, R., Emran, T. B., Labib, R. K., Tabassum, N. E., Islam, F., Sharma, R., Ahmad, I., Nainu, F., Chidambaram, K., Alhumaydhi, F. A., Chandran, D., Capasso, R., Wilairatana, P. (2022). Diallyl disulfide: A bioactive garlic compound with anticancer potential. Frontiers in Pharmacology, 13.
  • Mitsudomi, T., Yatabe, Y. (2010). Epidermal growth factor receptor in relation to tumor development: EGFR gene and cancer. The FEBS journal, 277(2), 301-308.
  • Mohammed, H. A., Emwas, A. H., Khan, R. A. (2023). Salt-Tolerant Plants, Halophytes, as Renewable Natural Resources for Cancer Prevention and Treatment: Roles of Phenolics and Flavonoids in Immunomodulation and Suppression of Oxidative Stress towards Cancer Management. International Journal of Molecular Sciences, 24(6), 5171.
  • Pantaleão, S. Q., Fernandes, P. O., Gonçalves, J. E., Maltarollo, V. G., Honorio, K. M. (2022). Recent advances in the prediction of pharmacokinetics properties in drug design studies: a review. ChemMedChem, 17(1), e202100542.
  • Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., Ferrin, T. E. (2004). UCSF Chimera—a visualization system for exploratory research and analysis. Journal of computational chemistry, 25(13), 1605-1612.
  • Pulte, D., and Brenner, H. (2010). Changes in survival in head and neck cancers in the late 20th and early 21st century: a period analysis. The oncologist, 15(9), 994-1001.
  • Rayan, A., Raiyn, J., Falah, M. (2017). Nature is the best source of anticancer drugs: Indexing natural products for their anticancer bioactivity. PloS one, 12(11), e0187925.
  • Rekowska, E., and Skupień, K. (2009). The influence of selected agronomic practices on the yield and chemical composition of winter garlic. Journal of Fruit and Ornamental Plant Research, 70(1), 173-182.
  • Rouf, R., Uddin, S. J., Sarker, D. K., Islam, M. T., Ali, E. S., Shilpi, J. A., Nahar, L., Tiralongo, E., Sarker, S. D. (2020). Antiviral potential of garlic (Allium sativum) and its organosulfur compounds: A systematic update of pre-clinical and clinical data. Trends in food science & technology, 104, 219-234.
  • Shaker, B., Ahmad, S., Lee, J., Jung, C., Na, D. (2021). In silico methods and tools for drug discovery. Computers in biology and medicine, 137, 104851.
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Details

Primary Language English
Subjects Chemical Engineering (Other)
Journal Section Articles
Authors

Sevtap Çağlar Yavuz 0000-0001-6497-2907

Early Pub Date December 18, 2023
Publication Date December 15, 2023
Published in Issue Year 2023 Volume: 13 Issue: 4

Cite

APA Çağlar Yavuz, S. (2023). Molecular Docking and Reactive Sites Identification (Homo–Lumo, Mep) of Allicin and Diallyl Disulfide: Potential Anticancer Inhibitor. Karadeniz Fen Bilimleri Dergisi, 13(4), 1523-1539. https://doi.org/10.31466/kfbd.1307190
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