Research Article
BibTex RIS Cite

Molecular Docking Analysis of Used Drugs for the Treatment of Cancer

Year 2021, , 539 - 547, 30.12.2021

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

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

Abstract

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.

Keywords

Cancer Drugs Molecular modeling Conformational analysis Molecular docking

References

  • [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.
  • [14] Taylor, E.C., Patel, H.H. 1992. Synthesis of pyrazolo(3,4,-d)pyrimidine analogues of the potent antitumor agent n-{4-(2-(2-amino-4(3h)- oxo-7h-pyrrolo(2,3- d)pyrimidin-5-yl)ethyl) benzoyl}-l-glutamic acid (LY231514). Tetrahedron Lett., 48, 8089-8100.
  • [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.
  • [32] Pharmacia and Upjohn. Camptosar product monograph. Mississauga, Ontario; 26 August 1999.
  • [33] Ferlay, J., H. R. Shin, F. Bray, D. Forman, C. Mathers, and D. M. Parkin. 2010. Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int. J. Cancer, 127, 2893–2917.
  • [34] Jemal, A., F. Bray, M. M. Center, J. Ferlay, E. Ward, and D. Forman. 2011. Global cancer statistics. CA Cancer J. Clin., 61, 69–90.
  • [35] Van Cutsem, E., Köhne, C. H., Hitre, E., Zaluski, J., Chang Chien, C. R., Makhson, A., ... & Rougier, P. 2009. Cetuximab and chemotherapy as initial treatment for metastatic colorectal cancer. New England Journal of Medicine, 360(14), 1408-1417.
  • [36] Schmoll, H. J., E. Van Cutsem, A. Stein, V. Valentini, B. Glimelius, K. Haustermans, et al. 2012. ESMO Consensus Guidelines for management of patients with colon and rectal cancer. A personalized approach to clinical decision making. Ann. Oncol., 23, 2479–2516.
  • [37] Seymour, M. T., Maughan, T. S., Ledermann, J. A., Topham, C., James, R., Gwyther, S. J. Et al. 2007. Different strategies of sequential and combination chemotherapy for patients with poor prognosis advanced colorectal cancer (MRC FOCUS): a randomised controlled trial. The Lancet, 370(9582), 143-152.
  • [38] Rothenberg, M.L., Kuhn, J.G., Schaaf, L.J. et al. 1998. Alternative dosing schedules for irinotecan. Oncology (Huntington), 12, 68-71.
  • [39] McDaniel, R. E., Maximov, P. Y., Jordan, V. C. 2013. Estrogen-mediated mechanisms to control the growth and apoptosis of breast cancer cells: a translational research success story. Vitamins & Hormones, 93, 1-49.
  • [40] Maximov, P.Y., Lee, T.M., Jordan, V.C. 2013. The discovery and development of selective estrogen receptor modulators (SERMs) for clinical practice. Curr. Clin. Pharmacol., 8, 135–155.
  • [41] Ruddy, K.J., Desantis, S.D., Gelman, R.S., Wu, A.H., Punglia, R.S., Mayer, E.L., Tolaney, S.M., Winer, E.P., Partridge, A.H., Burstein, H.J. 2013. Personalized medicine in breast cancer: tamoxifen, endoxifen, and CYP2D6 in clinical practice. Breast Cancer Res. Treat., 141,421–427.
  • [42] Ariazi, E. A., Ariazi, J. L., Cordera, F., & Jordan, V. C. 2006. Estrogen receptors as therapeutic targets in breast cancer. Current topics in medicinal chemistry, 6(3), 181-202.
  • [43] MacGregor, J.I, Jordan, V.C. 1998. Basic guide to the mechanisms of antiestrogen action. Pharmacol Rev., 50, 151-196.
  • [44] Shiau, A.K., Barstad, D., Loria, P.M. et al. 1998. The structural basis of estrogen receptor coactivator recognition and the antagonism of this interaction by tamoxifen. Cell, 95, 927-937.
  • [45] Wong, A., Soo, R.A., Yong, W.P., Innocenti, F. 2009. Clinical pharmacology and pharmacogenetics of gemcitabine. Drug Metab Rev., 41,77–88.
  • [46] Montano, R., Khan, N., Hou, H., Seigne, J., Ernstoff, M. S., Lewis, L. D., & Eastman, A. 2017. Cell cycle perturbation induced by gemcitabine in human tumor cells in cell culture, xenografts and bladder cancer patients: implications for clinical trial designs combining gemcitabine with a Chk1 inhibitor. Oncotarget, 8(40), 67754.
  • [47] Alvarellos, M. L., Lamba, J., Sangkuhl, K., Thorn, C. F., Wang, L., Klein, D. J., ... & Klein, T. E. 2014. PharmGKB summary: gemcitabine pathway. Pharmacogenetics and genomics, 24(11), 564.
  • [48] Congur, G., Erdem, A., & Mese, F. 2015. Electrochemical investigation of the interaction between topotecan and DNA at disposable graphite electrodes. Bioelectrochemistry, 102, 21-28.
  • [49] Gai, X.J., Wei, Y.M., Tao, H.M., An, D.Z., Sun, J.T., Li, B.S. 2016. Comparison of long-term survival between temozolomide-based chemoradio therapy and radiotherapy alone for patients with low‐grade gliomas after surgical resection. Onco. Targets Ther., 9, 5117-5121.
  • [50] Ashby, L.S., Smith, K.A.,Stea, B. 2016. Gliadel wafer implantation combined with standard radiotherapy and concurrent followed by adjuvant temozolomide for treatment of newly diagnosed high-grade glioma: A systematic literature review. World J. Surg. Oncol., 14, 225.
  • [51] Коbylinska, L.I., Klyuchivska, O.Y., Grytsyna, I.I., Finiuk, N., Panchuk, R.R., Starykovych, M.O., Lehka, L., Lesyk, R.B., Zіmenkovsky, B.S., Stoika, R.S. 2017. Differential pro‐apoptotic effects of synthetic 4-thiazolidinone derivative Les-3288, doxo- rubicin and temozolomide in human glioma U251 cells. Croat. Med. J., 58, 150‐159.
  • [52] Chen, T.C., Cho, H.Y., Wang, W., Wetzel, S.J., Singh, A., Nguyen, J., Hofman, F.M., Schönthal, A.H. 2015. Chemotherapeutic effect of a novel temozolomide analog on nasopharyngeal carcinoma in vitro and in vivo. J. Biomed. Sci., 22, 71.
  • [53] Davis, M.E. 2016. HHS public access. Clin. J. Oncol. Nurs., 20, S2–S8.
  • [54] Quan, R., Zhang, H., Li, Z., Li, X. 2020. Survival analysis of patients with glioblastoma treated by long-term administration of temozolomide. Medicine, 99, e18591.
  • [55] Jiapaer, S., Furuta, T., Tanaka, S., Kitabayashi, T., Nakada, M. 2018. Potential strategies overcoming the temozolomide resistance for glioblastoma. Neurol. Med. Chir., 58, 405–421.
  • [56] Lopes, I.C., De Oliveira, S.C.B., Oliveira-Brett, A.M. 2013. Temozolomide chemical degradation to 5-aminoimidazole-4-carboxamide-Electrochemical study. J. Electroanal. Chem., 704, 183–189.
  • [57] Wei, J.H., Zhou, R.H., Peng, Y., Liu, Y.C. 2013. Studies on the Binding Properties of Temozolomide with DNA. Asian J. Chem., 25, 2597–2600.
  • [58] Gurova, K. 2009. New hopes from old drugs: revisiting DNA-binding small molecules as anticancer agents. Future oncology, 5(10), 1685-1704.
  • [59] Shao, Y., Molnar, L.F., Jung, Y., Kussmann, J., Ochsenfeld, C. et al. Advances in methods and algorithms in a modern quantum chemistry program package. Physical Chemistry Chemical Physics 2006, 8(27), 3172-3191.
  • [60] Stewart, J.J.P. 1989. Optimization of parameters for semiempirical methods I. Method. J. Comput. Chem., 10(2), 209–220.
  • [61] Stewart, J.J.P. 1989. Optimization of parameters for semiempirical methods II. Applications. J. Comput. Chem., 10 (2): 221–264.
  • [62] Stewart, J.J.P. 1991. Optimization of parameters for semiempirical methods. III Extension of PM3 to Be, Mg, Zn, Ga, Ge, As, Se, Cd, In, Sn, Sb, Te, Hg, Tl, Pb, and Bi. Journal of Computational Chemistry. 12 (3), 320–341.
  • [63] Stewart, J.J.P. 2004. Optimization of parameters for semiempirical methods IV: Extension of MNDO, AM1, and PM3 to more main group elements. Journal of Molecular Modeling, 10 (2), 155–64.
  • [64] Trott, O., Olson, A.J. 2010. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of computational chemistry, 31(2), 455-461.
  • [65] 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. [66] Wang, Z., Wang, X., Li, Y., Lei, T., Wang, E., Li, D., Kang, Y., Zhu, F., Hou, T. 2019. farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB (GB) SA methods. Bioinformatics, 35(10), 1777-1779.
  • [67] Inbar Y, Schneidman-Duhovny D, Dror O, Nussinov R, Wolfson HJ. Deterministic Pharmacophore Detection via Multiple Flexible Alignment of Drug-Like Molecules. In Proc. of RECOMB 2007, vol. 3692 of Lecture Notes in Computer Science, pp. 423-434. Springer Verlag.
  • [68] Schneidman-Duhovny D, Dror O, Inbar Y, Nussinov R, Wolfson HJ. PharmaGist: a webserver for ligand-based pharmacophore detection. Nucleic Acids Research 2008.
  • [69] Dror O, Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. Novel approach for efficient pharmacophore-based virtual screening: method and applications. J Chem Inf Model. 2009 Oct;49(10):2333-43.
  • [70] Chinnathambi, R., Santhanam, V., Vadivelu, M., Ramachandran, U. P., & Hopper, W. (2017). Synthesis, crystal studies and pharmacological role prediction of 3-iodo-2- methyl-1 phenyl sulfonyl-1h indole. Asian Journal of Pharmaceutical and Clinical Research, 10(3), 341-346.

Kanser Tedavisinde Kullanılan İlaçların Moleküler Kenetlenme Analizi

Year 2021, , 539 - 547, 30.12.2021

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

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

Abstract

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.

Keywords

Kanser İlaçlar Moleküler modelleme Konformasyon analizi Moleküler kenetlenme

References

  • [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.
  • [14] Taylor, E.C., Patel, H.H. 1992. Synthesis of pyrazolo(3,4,-d)pyrimidine analogues of the potent antitumor agent n-{4-(2-(2-amino-4(3h)- oxo-7h-pyrrolo(2,3- d)pyrimidin-5-yl)ethyl) benzoyl}-l-glutamic acid (LY231514). Tetrahedron Lett., 48, 8089-8100.
  • [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.
  • [32] Pharmacia and Upjohn. Camptosar product monograph. Mississauga, Ontario; 26 August 1999.
  • [33] Ferlay, J., H. R. Shin, F. Bray, D. Forman, C. Mathers, and D. M. Parkin. 2010. Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int. J. Cancer, 127, 2893–2917.
  • [34] Jemal, A., F. Bray, M. M. Center, J. Ferlay, E. Ward, and D. Forman. 2011. Global cancer statistics. CA Cancer J. Clin., 61, 69–90.
  • [35] Van Cutsem, E., Köhne, C. H., Hitre, E., Zaluski, J., Chang Chien, C. R., Makhson, A., ... & Rougier, P. 2009. Cetuximab and chemotherapy as initial treatment for metastatic colorectal cancer. New England Journal of Medicine, 360(14), 1408-1417.
  • [36] Schmoll, H. J., E. Van Cutsem, A. Stein, V. Valentini, B. Glimelius, K. Haustermans, et al. 2012. ESMO Consensus Guidelines for management of patients with colon and rectal cancer. A personalized approach to clinical decision making. Ann. Oncol., 23, 2479–2516.
  • [37] Seymour, M. T., Maughan, T. S., Ledermann, J. A., Topham, C., James, R., Gwyther, S. J. Et al. 2007. Different strategies of sequential and combination chemotherapy for patients with poor prognosis advanced colorectal cancer (MRC FOCUS): a randomised controlled trial. The Lancet, 370(9582), 143-152.
  • [38] Rothenberg, M.L., Kuhn, J.G., Schaaf, L.J. et al. 1998. Alternative dosing schedules for irinotecan. Oncology (Huntington), 12, 68-71.
  • [39] McDaniel, R. E., Maximov, P. Y., Jordan, V. C. 2013. Estrogen-mediated mechanisms to control the growth and apoptosis of breast cancer cells: a translational research success story. Vitamins & Hormones, 93, 1-49.
  • [40] Maximov, P.Y., Lee, T.M., Jordan, V.C. 2013. The discovery and development of selective estrogen receptor modulators (SERMs) for clinical practice. Curr. Clin. Pharmacol., 8, 135–155.
  • [41] Ruddy, K.J., Desantis, S.D., Gelman, R.S., Wu, A.H., Punglia, R.S., Mayer, E.L., Tolaney, S.M., Winer, E.P., Partridge, A.H., Burstein, H.J. 2013. Personalized medicine in breast cancer: tamoxifen, endoxifen, and CYP2D6 in clinical practice. Breast Cancer Res. Treat., 141,421–427.
  • [42] Ariazi, E. A., Ariazi, J. L., Cordera, F., & Jordan, V. C. 2006. Estrogen receptors as therapeutic targets in breast cancer. Current topics in medicinal chemistry, 6(3), 181-202.
  • [43] MacGregor, J.I, Jordan, V.C. 1998. Basic guide to the mechanisms of antiestrogen action. Pharmacol Rev., 50, 151-196.
  • [44] Shiau, A.K., Barstad, D., Loria, P.M. et al. 1998. The structural basis of estrogen receptor coactivator recognition and the antagonism of this interaction by tamoxifen. Cell, 95, 927-937.
  • [45] Wong, A., Soo, R.A., Yong, W.P., Innocenti, F. 2009. Clinical pharmacology and pharmacogenetics of gemcitabine. Drug Metab Rev., 41,77–88.
  • [46] Montano, R., Khan, N., Hou, H., Seigne, J., Ernstoff, M. S., Lewis, L. D., & Eastman, A. 2017. Cell cycle perturbation induced by gemcitabine in human tumor cells in cell culture, xenografts and bladder cancer patients: implications for clinical trial designs combining gemcitabine with a Chk1 inhibitor. Oncotarget, 8(40), 67754.
  • [47] Alvarellos, M. L., Lamba, J., Sangkuhl, K., Thorn, C. F., Wang, L., Klein, D. J., ... & Klein, T. E. 2014. PharmGKB summary: gemcitabine pathway. Pharmacogenetics and genomics, 24(11), 564.
  • [48] Congur, G., Erdem, A., & Mese, F. 2015. Electrochemical investigation of the interaction between topotecan and DNA at disposable graphite electrodes. Bioelectrochemistry, 102, 21-28.
  • [49] Gai, X.J., Wei, Y.M., Tao, H.M., An, D.Z., Sun, J.T., Li, B.S. 2016. Comparison of long-term survival between temozolomide-based chemoradio therapy and radiotherapy alone for patients with low‐grade gliomas after surgical resection. Onco. Targets Ther., 9, 5117-5121.
  • [50] Ashby, L.S., Smith, K.A.,Stea, B. 2016. Gliadel wafer implantation combined with standard radiotherapy and concurrent followed by adjuvant temozolomide for treatment of newly diagnosed high-grade glioma: A systematic literature review. World J. Surg. Oncol., 14, 225.
  • [51] Коbylinska, L.I., Klyuchivska, O.Y., Grytsyna, I.I., Finiuk, N., Panchuk, R.R., Starykovych, M.O., Lehka, L., Lesyk, R.B., Zіmenkovsky, B.S., Stoika, R.S. 2017. Differential pro‐apoptotic effects of synthetic 4-thiazolidinone derivative Les-3288, doxo- rubicin and temozolomide in human glioma U251 cells. Croat. Med. J., 58, 150‐159.
  • [52] Chen, T.C., Cho, H.Y., Wang, W., Wetzel, S.J., Singh, A., Nguyen, J., Hofman, F.M., Schönthal, A.H. 2015. Chemotherapeutic effect of a novel temozolomide analog on nasopharyngeal carcinoma in vitro and in vivo. J. Biomed. Sci., 22, 71.
  • [53] Davis, M.E. 2016. HHS public access. Clin. J. Oncol. Nurs., 20, S2–S8.
  • [54] Quan, R., Zhang, H., Li, Z., Li, X. 2020. Survival analysis of patients with glioblastoma treated by long-term administration of temozolomide. Medicine, 99, e18591.
  • [55] Jiapaer, S., Furuta, T., Tanaka, S., Kitabayashi, T., Nakada, M. 2018. Potential strategies overcoming the temozolomide resistance for glioblastoma. Neurol. Med. Chir., 58, 405–421.
  • [56] Lopes, I.C., De Oliveira, S.C.B., Oliveira-Brett, A.M. 2013. Temozolomide chemical degradation to 5-aminoimidazole-4-carboxamide-Electrochemical study. J. Electroanal. Chem., 704, 183–189.
  • [57] Wei, J.H., Zhou, R.H., Peng, Y., Liu, Y.C. 2013. Studies on the Binding Properties of Temozolomide with DNA. Asian J. Chem., 25, 2597–2600.
  • [58] Gurova, K. 2009. New hopes from old drugs: revisiting DNA-binding small molecules as anticancer agents. Future oncology, 5(10), 1685-1704.
  • [59] Shao, Y., Molnar, L.F., Jung, Y., Kussmann, J., Ochsenfeld, C. et al. Advances in methods and algorithms in a modern quantum chemistry program package. Physical Chemistry Chemical Physics 2006, 8(27), 3172-3191.
  • [60] Stewart, J.J.P. 1989. Optimization of parameters for semiempirical methods I. Method. J. Comput. Chem., 10(2), 209–220.
  • [61] Stewart, J.J.P. 1989. Optimization of parameters for semiempirical methods II. Applications. J. Comput. Chem., 10 (2): 221–264.
  • [62] Stewart, J.J.P. 1991. Optimization of parameters for semiempirical methods. III Extension of PM3 to Be, Mg, Zn, Ga, Ge, As, Se, Cd, In, Sn, Sb, Te, Hg, Tl, Pb, and Bi. Journal of Computational Chemistry. 12 (3), 320–341.
  • [63] Stewart, J.J.P. 2004. Optimization of parameters for semiempirical methods IV: Extension of MNDO, AM1, and PM3 to more main group elements. Journal of Molecular Modeling, 10 (2), 155–64.
  • [64] Trott, O., Olson, A.J. 2010. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of computational chemistry, 31(2), 455-461.
  • [65] 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. [66] Wang, Z., Wang, X., Li, Y., Lei, T., Wang, E., Li, D., Kang, Y., Zhu, F., Hou, T. 2019. farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB (GB) SA methods. Bioinformatics, 35(10), 1777-1779.
  • [67] Inbar Y, Schneidman-Duhovny D, Dror O, Nussinov R, Wolfson HJ. Deterministic Pharmacophore Detection via Multiple Flexible Alignment of Drug-Like Molecules. In Proc. of RECOMB 2007, vol. 3692 of Lecture Notes in Computer Science, pp. 423-434. Springer Verlag.
  • [68] Schneidman-Duhovny D, Dror O, Inbar Y, Nussinov R, Wolfson HJ. PharmaGist: a webserver for ligand-based pharmacophore detection. Nucleic Acids Research 2008.
  • [69] Dror O, Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. Novel approach for efficient pharmacophore-based virtual screening: method and applications. J Chem Inf Model. 2009 Oct;49(10):2333-43.
  • [70] Chinnathambi, R., Santhanam, V., Vadivelu, M., Ramachandran, U. P., & Hopper, W. (2017). Synthesis, crystal studies and pharmacological role prediction of 3-iodo-2- methyl-1 phenyl sulfonyl-1h indole. Asian Journal of Pharmaceutical and Clinical Research, 10(3), 341-346.
There are 69 citations in total.

Details

Primary Language English
Subjects Engineering
Journal Section Articles
Authors

A. Demet Demirag This is me 0000-0002-9609-9150

Sefa Çelik 0000-0001-6216-1297

Sevim Akyüz 0000-0003-3313-6927

Ayşe Özel 0000-0002-8680-8830

Publication Date December 30, 2021
Published in Issue Year 2021

Cite

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. December 2021;25(3):539-547. doi:10.19113/sdufenbed.871423
Chicago Demirag, A. Demet, Sefa Çelik, Sevim Akyüz, and Ayşe Özel. “Molecular Docking Analysis of Used Drugs for the Treatment of Cancer”. Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi 25, no. 3 (December 2021): 539-47. https://doi.org/10.19113/sdufenbed.871423.
EndNote Demirag AD, Çelik S, Akyüz S, Özel A (December 1, 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, and A. Özel, “Molecular Docking Analysis of Used Drugs for the Treatment of Cancer”, Süleyman Demirel Üniv. Fen Bilim. Enst. Derg., vol. 25, no. 3, pp. 539–547, 2021, doi: 10.19113/sdufenbed.871423.
ISNAD Demirag, A. Demet et al. “Molecular Docking Analysis of Used Drugs for the Treatment of Cancer”. Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi 25/3 (December 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 et al. “Molecular Docking Analysis of Used Drugs for the Treatment of Cancer”. Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi, vol. 25, no. 3, 2021, pp. 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.

Cited By

Structural investigation, DNA/Mpox/COVID-19 molecular docking, and biological assays of two novel Co(II) and Cu(II) complexes derived from tri- and bi-dentate pyridyl-functionalized phosphoramide ligand [Ph]P(O)[NH-2Py]2
Inorganic Chemistry Communications
https://doi.org/10.1016/j.inoche.2024.113318
Novel Co2+ and Cd2+ Complexes Derived From a New N‐Donor Pyridyl‐Functionalized Thiophosphoric Triamide Ligand: Structural Investigation, DNA/COVID‐19/Monkeypox Molecular Docking, and Biological Assays
Applied Organometallic Chemistry
https://doi.org/10.1002/aoc.7750

e-ISSN :1308-6529
Linking ISSN (ISSN-L): 1300-7688

Dergide yayımlanan tüm makalelere ücretiz olarak erişilebilinir ve Creative Commons CC BY-NC Atıf-GayriTicari lisansı ile açık erişime sunulur. Tüm yazarlar ve diğer dergi kullanıcıları bu durumu kabul etmiş sayılırlar. CC BY-NC lisansı hakkında detaylı bilgiye erişmek için tıklayınız.