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Molecular Docking Analysis of Used Drugs for the Treatment of Cancer

Yıl 2021, Cilt: 25 Sayı: 3, 539 - 547, 30.12.2021

A. Demet Demirag Sefa Çelik , Sevim Akyüz , Ayşe Özel

https://doi.org/10.19113/sdufenbed.871423
Cited By: 2

Öz

In this study, the lowest energy molecular structures were determined by conformational analysis of six drugs commonly used in cancer treatment, in order to use as initial data for docking simulations. Using the AutoDock Vina software, the interaction mechanisms of the 6 FDA approved drugs (Pemetrexed, Irinotecan, Tamoxifen, Gemcitabine, Topotecan and Temozolomide) with DNA were investigated. In addition, MM/PB(GB)SA calculations for the drug-DNA structures under investigation have been performed. The calculated binding affinities and binding free energies of interactions were showed the stability of the structures. It has been found that the active site where these molecules interact with DNA is the same and that their various interactions, primarily hydrogen bond, play an important role in this stability of the structures. Furthermore, the pharmacophoric features of the investigated molecules were determined.The aim of the work is to deeply investigate the binding properties of the title drugs with DNA.

Anahtar Kelimeler

Cancer Drugs Molecular modeling Conformational analysis Molecular docking

Kaynakça

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Kanser Tedavisinde Kullanılan İlaçların Moleküler Kenetlenme Analizi

Yıl 2021, Cilt: 25 Sayı: 3, 539 - 547, 30.12.2021

A. Demet Demirag Sefa Çelik , Sevim Akyüz , Ayşe Özel

https://doi.org/10.19113/sdufenbed.871423
Cited By: 2

Öz

Bu çalışmada, kenetlenme simülasyonları için başlangıç verileri olarak kullanılmak üzere, kanser tedavisinde yaygın olarak kullanılan altı ilacın konformasyonel analizi ile en düşük enerjili moleküler yapıları belirlenmiştir. AutoDock Vina programı kullanılarak FDA onaylı 6 ilacın (Pemetrekset, Irinotekan, Tamoksifen, Gemsitabin, Topotekan ve Temozolomid) DNA ile etkileşim mekanizmaları araştırılmıştır. Ek olarak, araştırılan ilaç-DNA yapıları için MM/PB(GB)SA hesaplamaları yapılmıştır. Etkileşimlere ait hesaplanan bağlanma afiniteleri ve bağlanma serbest enerjileri yapıların kararlılığını göstermiştir. Bu moleküllerin DNA ile etkileştiği aktif bölgenin aynı olduğu ve başta hidrojen bağı olmak üzere yapmış oldukları çeşitli etkileşimlerin yapıların bu kararlılığında önemli bir rol oynadığı bulunmuştur. Ayrıca, incelenen moleküllerin farmokofor özellikleri belirlenmiştir. Bu çalışmanın amacı, başlıktaki ilaçların DNA ile bağlanma özelliklerini derinlemesine araştırmaktır.

Anahtar Kelimeler

Kanser İlaçlar Moleküler modelleme Konformasyon analizi Moleküler kenetlenme

Kaynakça

  • [1] Robson, M., Storm, C., Weitzel, J., Wollins, D., Offit, K. 2010. American society of clinical oncology policy statement update: genetic and genomic testing for cancer susceptibility. Journal of Clinical Oncology, 25(8), 893- 901.
  • [2] Demirelli, F. 2003. Kanserin moleküler temelleri. Güncel Klinik Onkoloji, 9-15.
  • [3] Rieger, P. 2006. Cancer biology and implications for practice. Clinical Journal of Oncology Nurisng, 10(4), 457-460.
  • [4] Hahn, W., Weinberg, R. 2002. Mechanisms of disease: rules for making human tumor cells. New England Journal of Medicine, 347, 1593-1603.
  • [5] Lewin, B. 1997. Genes VI. Oxford University Press, New York, USA, 1089-129.
  • [6] Schilsky, R.L. 1992. Antimetabolites. In: Perry MC, ed. The Chemotherapy Source Book. Baltimore, MD: Williams & Wilkin, 301-315.
  • [7] Baykara, O. 2015. Current Therapies and Latest Developments in Cancer Treatment. Horizons in Cancer Research, 57, 105-156.
  • [8] Mian, M., Tinelli, M., De March, E., Turri, G., Meneghini, V., Pescosta, N., ... & Pizzolo, G. 2016. Bortezomib, thalidomide and lenalidomide: Have they really changed the outcome of multiple myeloma?. Anticancer Research, 36(3), 1059-1065.
  • [9] Yang, I. A., Shaw, J. G., Goddard, J. R., Clarke, M. S., & Reid, D. W. 2016. Use of inhaled corticosteroids in COPD: improving efficacy. Expert Review of Respiratory Medicine, 10(3), 339-350.
  • [10] Lee, C. H., Hyun, M. K., Jang, E. J., Lee, N. R., Kim, K., & Yim, J. J. 2013. Inhaled corticosteroid use and risks of lung cancer and laryngeal cancer. Respiratory medicine, 107(8), 1222-1233.
  • [11] Patil, Y., Amitay, Y., Ohana, P., Shmeeda, H., & Gabizon, A. 2016. Targeting of pegylated liposomal mitomycin-C prodrug to the folate receptor of cancer cells: Intracellular activation and enhanced cytotoxicity. Journal of Controlled Release, 225, 87-95.
  • [12] Michalska, M., Schultze-Seemann, S., Bogatyreva, L., Hauschke, D., Wetterauer, U., & Wolf, P. 2016. In vitro and in vivo effects of a recombinant anti-PSMA immunotoxin in combination with docetaxel against prostate cancer. Oncotarget, 7(16), 22531.
  • [13] Olsen, I. H., Knigge, U., Federspiel, B., Hansen, C. P., Skov, A., Kjær, A., & Langer, S. W. 2014. Topotecan monotherapy in heavily pretreated patients with progressive advanced stage neuroendocrine carcinomas. Journal of Cancer, 5(8), 628.
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  • [15] Clarke, S., Millward, M., Findlay, M. et al. 1998. Activity of the multi-targeted antifolate MTA (LY231514) in advanced non-small cell lung cancer (NSCLC). Ann. Oncol., 9, 86.
  • [16] Rusthoven, J., Eisenhauer, E., Butts, C. et al. 1999. Multitargeted antifolate, LY231514, as first-line chemotherapy for patients with advanced non-small-cell lung cancer: a phase II study. J. Clin. Oncol., 17,1194-1199.
  • [17] Lind, M.J.,Smith,I.E.,Coleman, R.E. 1998. Phase II study of MTA (LY231514) in patients (pts) with locally recurrent or metastatic breast cancer (LR/MBC). Proc. Am. Soc. Clin. Oncol., 17, 433a.
  • [18] Spielmann, M., Martin, M., Hamer, M. et al. 1999. Activity of MTA (Multitargeted Antifolate, LY231514) in metastatic breast can- cer (MBC) patients previously treated with an anthracycline and a taxane. Breast Cancer Res Treat., 57,123.
  • [19] Cripps, C., Burnell, M., Jolivet, J. 1999. Phase II study of first-line LY231514 (multitargeted antifolate) in patients with locally advanced or metastatic colorectal cancer: an NCIC clinical trials group study. Ann. Oncol., 10, 1175-1179.
  • [20] John, W., Picus, J., Blanke, C. 2000. Multi targeted antifolate(peme- trexed disodium, LY231514) activity in patients with advanced colorectal cancer results from a phase II study. Cancer, 88,1807-1813.
  • [21] Pivot, X., Raymond, E., Gedouin, D. et al. 1999. Phase II trial of MTA (LY231514, a multitargeted antifolate) in advanced or recur- rent squamous cell carcinoma of the head and neck. Proc. Am. Soc. Clin. Oncol., 18, 397a.
  • [22] Celio, L., Bajetta, E., Toffolatti, L. 2000. PhaseII trialofpemetrexed disodium administered every 21 days in patients (pts) with gas- tric cancer: efficacy and toxicity without and with folic acid. Ann. Oncol., 11, 65.
  • [23] Pazares, L., Tabernero, J., Moyano A. 1998. Significant activity of the multi-targeted antifolate MTA (LY231514) in advanced transitional cell carcinoma (TCC) of the bladder: results of a phase II trial. Ann. Oncol., 9, 292.
  • [24] Goedhals, L., van Wijk A.L. 1998. MTA (LY231514) in advanced carcinoma of the cervix. Ann. Oncol., 9, 339a.
  • [25] Miller, K.D., Loehrer, P.J., Picus, J. et al. 2000. Phase II study of the multi-targeted antifolate LY231514 (ALIMTA(tm), MTA, pemetrexed disodium) in patients with advanced pancreatic cancer. Ann. Oncol., 11,101-103.
  • [26] Grindey, G.B., Shih, C., Barnett, C.J. et al. 1992. LY231514, A novel pyrrolopyrimidine antifolate that inhibits thymidylate synthase (TS). Proc. Am. Assoc. Cancer Res., 33,411.
  • [27] Shih, C., Chen, V.J., Gossett, L.S. et al. 1997. LY231514, a pyrrolo (2,3-d) pyrimidine-based antifolate that inhibits multiple folate-requiring enzymes. Cancer Res., 57,1116-1123.
  • [28] Grem, J.L. 1990. Fluorinated pyrimidines. In: Chabner BA, Collins JM, eds. Cancer Chemotherapy: Principles and Practice. Philadelphia, Lippincott, 180-224.
  • [29] Schilsky, R.L. 1992. Antimetabolites. In: Perry MC, ed. The Chemotherapy Source Book. Baltimore: Williams & Wilkins, 301-315.
  • [30] Shih, C., Chen, V.J., Gossetti, L.S., Gates, S.B., MacKellar, W.C., Habeck, L.L. et al. 1997. LY231514, a pirrolo[2,3-d]pyrimidine-based antifolate that inhibits multiple folate requiring enzymes. Cancer Res., 57, 1116–23.
  • [31] Schultz, R.M., Chen, V.J., Bewley, J.R., Roberts, E.F., Shih, C., Dempsey, J.A. 1999. Biological activity of the multitargeted antifolate, MTA (LY231514), in human cell lines with different resistance mechanisms to antifolate drugs. Sem Oncol., 26, 68–73.
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Toplam 69 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Konular Mühendislik
Bölüm Makaleler
Yazarlar

A. Demet Demirag Bu kişi benim 0000-0002-9609-9150

Sefa Çelik 0000-0001-6216-1297

Sevim Akyüz 0000-0003-3313-6927

Ayşe Özel 0000-0002-8680-8830

Yayımlanma Tarihi 30 Aralık 2021
Yayımlandığı Sayı Yıl 2021 Cilt: 25 Sayı: 3

Kaynak Göster

APA Demirag, A. D., Çelik, S., Akyüz, S., Özel, A. (2021). Molecular Docking Analysis of Used Drugs for the Treatment of Cancer. Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 25(3), 539-547. https://doi.org/10.19113/sdufenbed.871423
AMA Demirag AD, Çelik S, Akyüz S, Özel A. Molecular Docking Analysis of Used Drugs for the Treatment of Cancer. Süleyman Demirel Üniv. Fen Bilim. Enst. Derg. Aralık 2021;25(3):539-547. doi:10.19113/sdufenbed.871423
Chicago Demirag, A. Demet, Sefa Çelik, Sevim Akyüz, ve Ayşe Özel. “Molecular Docking Analysis of Used Drugs for the Treatment of Cancer”. Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi 25, sy. 3 (Aralık 2021): 539-47. https://doi.org/10.19113/sdufenbed.871423.
EndNote Demirag AD, Çelik S, Akyüz S, Özel A (01 Aralık 2021) Molecular Docking Analysis of Used Drugs for the Treatment of Cancer. Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi 25 3 539–547.
IEEE A. D. Demirag, S. Çelik, S. Akyüz, ve A. Özel, “Molecular Docking Analysis of Used Drugs for the Treatment of Cancer”, Süleyman Demirel Üniv. Fen Bilim. Enst. Derg., c. 25, sy. 3, ss. 539–547, 2021, doi: 10.19113/sdufenbed.871423.
ISNAD Demirag, A. Demet vd. “Molecular Docking Analysis of Used Drugs for the Treatment of Cancer”. Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi 25/3 (Aralık 2021), 539-547. https://doi.org/10.19113/sdufenbed.871423.
JAMA Demirag AD, Çelik S, Akyüz S, Özel A. Molecular Docking Analysis of Used Drugs for the Treatment of Cancer. Süleyman Demirel Üniv. Fen Bilim. Enst. Derg. 2021;25:539–547.
MLA Demirag, A. Demet vd. “Molecular Docking Analysis of Used Drugs for the Treatment of Cancer”. Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi, c. 25, sy. 3, 2021, ss. 539-47, doi:10.19113/sdufenbed.871423.
Vancouver Demirag AD, Çelik S, Akyüz S, Özel A. Molecular Docking Analysis of Used Drugs for the Treatment of Cancer. Süleyman Demirel Üniv. Fen Bilim. Enst. Derg. 2021;25(3):539-47.

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