Araştırma Makalesi
BibTex RIS Kaynak Göster

Moleküler Modelleme ile Kolorektal Kanser Tedavisinde Doğal Ajanların Potansiyelinin Araştırılması

Yıl 2025, Cilt: 15 Sayı: 2, 787 - 806, 15.06.2025

Eda Arabacı , Nil Sazlı , Deniz Karataş

https://doi.org/10.31466/kfbd.1624597

Öz

Kolorektal kanser, kalın bağırsağın iç kısmındaki hücrelerin kontrolsüz büyümesiyle oluşur. Kolorektal kanser gelişiminde rol oynayan en önemli faktör adenomatöz polipozis koli (APC) genindeki mutasyonlardır. Kolorektal kanserin kemoterapi tedavisinde kullanılan kimyasal ilaçlardan olan irinotekan ve folinik asit insan vücudu üzerinde birçok yan etkiye sahiptir. Bu nedenle kimyasal ilaçlara alternatif olarak doğal ajanlarla, her geçen gün daha az maliyetli ve daha hızlı ilaç tasarımı yapılabilen in silico ortamlarda çözümler aranmaktadır. Bahsedilen ilaçlara ek olarak, bu çalışmada withaferin A, epigallocatechin gallate (EGCG) ve ganoderiol A'nın APC ile etkileşimi moleküler yerleştirme ve dinamik simülasyonlar kullanılarak modellenmiştir. Yerleştirme çalışmalarında withaferin A, (EGCG) ve ganoderiol A'nın etkileşim enerjisi sonuçları sırasıyla -8,5, -7,8 ve -7,9 kcal/mol'dür. MD simülasyonlarında, bu üç ajanın ortalama RMSD değerleri withaferin A ve ganoderiol A için 0,5 nm ve daha dallanmış, hacimli EGCG için 1,5 nm'dir. Modelleme sonuçları, doğal ajanların kolorektal kanserle ilişkili APC geni üzerindeki terapötik ilaç potansiyelini ortaya koyabileceği ve diğer çalışmalar için bir temel sağlayacağı düşünülmektedir.

Anahtar Kelimeler

APC geni Kolorektal kanser Moleküler modelleme Doğal ajan

Kaynakça

  • Akash, S., Islam, M. R., Bhuiyan, A. A., Islam, M. N., Bayil, I., Saleem, R. M., . . . Abdel-Daim, M. M. (2024). In silico evaluation of anti-colorectal cancer inhibitors by Resveratrol derivatives targeting Armadillo repeats domain of APC: molecular docking and molecular dynamics simulation. Front Oncol, 14, 1360745. doi: 10.3389/fonc.2024.1360745
  • Bharadwaj, S., Lee, K. E., Dwivedi, V. D., Yadava, U., Nees, M., & Kang, S. G. (2020). Density functional theory and molecular dynamics simulation support Ganoderma lucidum triterpenoids as broad range antagonist of matrix metalloproteinases. Journal of Molecular Liquids, 311. doi: 10.1016/j.molliq.2020.113322
  • Bontempo, P., De Masi, L., & Rigano, D. (2023). Functional Properties of Natural Products and Human Health. Nutrients, 15(13). doi: 10.3390/nu15132961
  • Chaachouay, N., & Zidane, L. (2024). Plant-Derived Natural Products: A Source for Drug Discovery and Development. Drugs and Drug Candidates, 3(1), 184-207. doi: 10.3390/ddc3010011
  • Chen, D., Chen, Y., Huang, F., Zhang, X., Zhou, Y., & Xu, L. (2023). The underlying regulatory mechanisms of colorectal carcinoma by combining Vitexin and Aspirin: based on systems biology, molecular docking, molecular dynamics simulation, and in vitro study. Front Endocrinol (Lausanne), 14, 1147132. doi: 10.3389/fendo.2023.1147132
  • Chicurel, M. (2002). Putting a name on it. Nature, 419(6908), 755, 757. doi: 10.1038/419755a
  • Choi, B. Y., & Kim, B. W. (2015). Withaferin-A Inhibits Colon Cancer Cell Growth by Blocking STAT3 Transcriptional Activity. J Cancer Prev, 20(3), 185-192. doi: 10.15430/JCP.2015.20.3.185
  • Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep, 7, 42717. doi: 10.1038/srep42717
  • Dar, R. A., Shahnawaz, M., Ahanger, M. A., & Majid, I. u. (2023). Exploring the Diverse Bioactive Compounds from Medicinal Plants: A Review. The Journal of Phytopharmacology, 12(3), 189-195. doi: 10.31254/phyto.2023.12307
  • El-Mernissi, R., Khaldan, A., Bouamrane, S., Rehman, H. M., Alaqarbeh, M., Ajana, M. A., . . . Bouachrine, M. (2024). 3D-QSAR, molecular docking, simulation dynamic and ADMET studies on new quinolines derivatives against colorectal carcinoma activity. J Biomol Struct Dyn, 42(7), 3682-3699. doi: 10.1080/07391102.2023.2214233
  • El Fadili, M., Er-Rajy, M., Kara, M., Assouguem, A., Belhassan, A., Alotaibi, A., . . . Elhallaoui, M. (2022). QSAR, ADMET In Silico Pharmacokinetics, Molecular Docking and Molecular Dynamics Studies of Novel Bicyclo (Aryl Methyl) Benzamides as Potent GlyT1 Inhibitors for the Treatment of Schizophrenia. Pharmaceuticals (Basel), 15(6). doi: 10.3390/ph15060670
  • Gao, J. J., Hirakawa, A., Min, B. S., Nakamura, N., & Hattori, M. (2005). In vivo antitumor effects of bitter principles from the antlered form of fruiting bodies of Ganoderma lucidum. Journal of Natural Medicines, 60(1), 42-48. doi: 10.1007/s11418-005-0003-5
  • Gmeiner, W. H. (2024). Recent Advances in Therapeutic Strategies to Improve Colorectal Cancer Treatment. Cancers (Basel), 16(5). doi: 10.3390/cancers16051029
  • Guru, P. R., Kar, R. K., Nayak, A. K., & Mohapatra, S. (2023). A comprehensive review on pharmaceutical uses of plant-derived biopolysaccharides. Int J Biol Macromol, 233, 123454. doi: 10.1016/j.ijbiomac.2023.123454
  • Han, B., Zhai, Y., Li, X., Zhao, H., Sun, C., Zeng, Y., . . . Kai, G. (2023). Total flavonoids of Tetrastigma hemsleyanum Diels et Gilg inhibits colorectal tumor growth by modulating gut microbiota and metabolites. Food Chem, 410, 135361. doi: 10.1016/j.foodchem.2022.135361
  • Hephzibah Cathryn, R., & George Priya Doss, C. (2023). Comparative molecular dynamics simulation of apo and holo forms of the P53 mutant C176F: a structural perspective. Journal of Taibah University for Science, 18(1). doi: 10.1080/16583655.2023.2297457
  • Justino, G. C., Nascimento, C. P., & Justino, M. C. (2021). Molecular dynamics simulations and analysis for bioinformatics undergraduate students. Biochem Mol Biol Educ, 49(4), 570-582. doi: 10.1002/bmb.21512
  • Kinzler, K. W., & Vogelstein, B. (1996). Lessons from hereditary colorectal cancer. Cell, 87(2), 159-170. doi: 10.1016/s0092-8674(00)81333-1
  • Li, B., Zhang, G., & Xu, X. (2023). APC mutation correlated with poor response of immunotherapy in colon cancer. BMC Gastroenterol, 23(1), 95. doi: 10.1186/s12876-023-02725-3
  • Macharia, J. M., Kaposztas, Z., & Bence, R. L. (2023). Medicinal Characteristics of Withania somnifera L. in Colorectal Cancer Management. Pharmaceuticals (Basel), 16(7). doi: 10.3390/ph16070915
  • Morris, C. J., & Corte, D. D. (2021). Using molecular docking and molecular dynamics to investigate protein-ligand interactions. Modern Physics Letters B, 35(08). doi: 10.1142/s0217984921300027
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785-2791. doi: 10.1002/jcc.21256
  • Moshawih, S., Lim, A. F., Ardianto, C., Goh, K. W., Kifli, N., Goh, H. P., . . . Ming, L. C. (2022). Target-Based Small Molecule Drug Discovery for Colorectal Cancer: A Review of Molecular Pathways and In Silico Studies. Biomolecules, 12(7). doi: 10.3390/biom12070878
  • Nasir, A., Bullo, M. M. H., Ahmed, Z., Imtiaz, A., Yaqoob, E., Jadoon, M., . . . Yaqoob, S. (2020). Nutrigenomics: Epigenetics and cancer prevention: A comprehensive review. Crit Rev Food Sci Nutr, 60(8), 1375-1387. doi: 10.1080/10408398.2019.1571480
  • Olkinuora, A. P., Peltomaki, P. T., Aaltonen, L. A., & Rajamaki, K. (2021). From APC to the genetics of hereditary and familial colon cancer syndromes. Hum Mol Genet, 30(R2), R206-R224. doi: 10.1093/hmg/ddab208
  • Peng, H., Ying, J., Zang, J., Lu, H., Zhao, X., Yang, P., . . . Wang, Z. (2023). Specific Mutations in APC, with Prognostic Implications in Metastatic Colorectal Cancer. Cancer Res Treat, 55(4), 1270-1280. doi: 10.4143/crt.2023.415
  • 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. doi: 10.1002/jcc.20084
  • Polakis, P. (2007). The many ways of Wnt in cancer. Curr Opin Genet Dev, 17(1), 45-51. doi: 10.1016/j.gde.2006.12.007
  • Qawoogha, S. S., & Shahiwala, A. (2020). Identification of potential anticancer phytochemicals against colorectal cancer by structure-based docking studies. J Recept Signal Transduct Res, 40(1), 67-76. doi: 10.1080/10799893.2020.1715431
  • Rampogu, S., Lee, G., Park, J. S., Lee, K. W., & Kim, M. O. (2022). Molecular Docking and Molecular Dynamics Simulations Discover Curcumin Analogue as a Plausible Dual Inhibitor for SARS-CoV-2. Int J Mol Sci, 23(3). doi: 10.3390/ijms23031771
  • Saha, P., Hegde, M., Chakraborty, K., Singha, A., Mukerjee, N., Ghosh, D., . . . Sil, S. K. (2024). Targeted inhibition of colorectal cancer proliferation: The dual-modulatory role of 2,4-DTBP on anti-apoptotic Bcl-2 and Survivin proteins. J Cell Mol Med, 28(7), e18150. doi: 10.1111/jcmm.18150
  • Shailes, H., Tse, W. Y., Freitas, M. O., Silver, A., & Martin, S. A. (2022). Statin Treatment as a Targeted Therapy for APC-Mutated Colorectal Cancer. Front Oncol, 12, 880552. doi: 10.3389/fonc.2022.880552
  • Shariatinia, Z., & Mazloom-Jalali, A. (2020). Molecular dynamics simulations on chitosan/graphene nanocomposites as anticancer drug delivery using systems. Chinese Journal of Physics, 66, 362-382. doi: 10.1016/j.cjph.2020.04.012
  • Siegel, R. L., Miller, K. D., & Jemal, A. (2020). Cancer statistics, 2020. CA Cancer J Clin, 70(1), 7-30. doi: 10.3322/caac.21590
  • Skariyachan, S., Gopal, D., Chakrabarti, S., Kempanna, P., Uttarkar, A., Muddebihalkar, A. G., & Niranjan, V. (2020). Structural and molecular basis of the interaction mechanism of selected drugs towards multiple targets of SARS-CoV-2 by molecular docking and dynamic simulation studies- deciphering the scope of repurposed drugs. Comput Biol Med, 126, 104054. doi: 10.1016/j.compbiomed.2020.104054
  • Surya Ulhas, R., & Malaviya, A. (2023). In-silico validation of novel therapeutic activities of withaferin a using molecular docking and dynamics studies. J Biomol Struct Dyn, 41(11), 5045-5056. doi: 10.1080/07391102.2022.2078410
  • Vallikondaperumal, M., N, B., T. V, A. K., & V, P. (2023). In Silico Molecular Screening and Docking Approaches on Antineoplastic Agent-Irinotecan Towards the Marker Proteins of Colon Cancer. International Journal of Applied Pharmaceutics, 84-92. doi: 10.22159/ijap.2023v15i5.48523
  • Wahnou, H., Liagre, B., Sol, V., El Attar, H., Attar, R., Oudghiri, M., . . . Limami, Y. (2023). Polyphenol-Based Nanoparticles: A Promising Frontier for Enhanced Colorectal Cancer Treatment. Cancers (Basel), 15(15). doi: 10.3390/cancers15153826
  • Wankowicz, S. A., de Oliveira, S. H., Hogan, D. W., van den Bedem, H., & Fraser, J. S. (2022). Ligand binding remodels protein side-chain conformational heterogeneity. Elife, 11. doi: 10.7554/eLife.74114
  • Yadav, M., Abdalla, M., Madhavi, M., Chopra, I., Bhrdwaj, A., Soni, L., . . . Singh, S. K. (2022). Structure-Based Virtual Screening, Molecular Docking, Molecular Dynamics Simulation and Pharmacokinetic modelling of Cyclooxygenase-2 (COX-2) inhibitor for the clinical treatment of Colorectal Cancer. Molecular Simulation, 48(12), 1081-1101. doi: 10.1080/08927022.2022.2068799
  • Yalcin, S. (2020). Molecular Docking, Drug Likeness, and ADMET Analyses of Passiflora Compounds as P-Glycoprotein (P-gp) Inhibitor for the Treatment of Cancer. Current Pharmacology Reports, 6(6), 429-440. doi: 10.1007/s40495-020-00241-6
  • Yang, J., He, K., Zhang, M., Wu, L., Qin, S., Luo, M., & Xia, X. (2024). Unveiling the therapeutic potential of epigallocatechin gallate in liver cancer: insights from network pharmacology and in vitro assays. Nat Prod Res, 1-5. doi: 10.1080/14786419.2024.2384083
  • Ye, T., Ge, Y., Jiang, X., Song, H., Peng, C., & Liu, B. (2023). A review of anti-tumour effects of Ganoderma lucidum in gastrointestinal cancer. Chin Med, 18(1), 107. doi: 10.1186/s13020-023-00811-y
  • Zhang, M., Cheng, S., Jin, Y., Zhao, Y., & Wang, Y. (2021). Roles of CA125 in diagnosis, prediction, and oncogenesis of ovarian cancer. Biochim Biophys Acta Rev Cancer, 1875(2), 188503. doi: 10.1016/j.bbcan.2021.188503
  • Zrinej, J., Elmchichi, L., Alaqarbeh, M., Lakhlifi, T., & Bouachrine, M. (2023). Computational approach: 3D-QSAR, molecular docking, ADMET, molecular dynamics simulation investigations, and retrosynthesis of some curcumin analogues as PARP-1 inhibitors targeting colon cancer. New Journal of Chemistry, 47(45), 20987-21009. doi: 10.1039/d3nj03981a

Investigating the Potential of Natural Agents for Colorectal Cancer Treatment with Molecular Modeling

Yıl 2025, Cilt: 15 Sayı: 2, 787 - 806, 15.06.2025

Eda Arabacı , Nil Sazlı , Deniz Karataş

https://doi.org/10.31466/kfbd.1624597

Öz

Colorectal cancer occurs with the uncontrolled growth of cells in the inner part of the large intestine. The most important factor playing a role in the development of colorectal cancer is mutations in the adenomatous polyposis coli (APC) gene. Irinotecan and folinic acid, which are chemical drugs used in the chemotherapy treatment of colorectal cancer, have many side effects on the human body. For this reason, solutions are being sought with natural agents as alternatives to chemical drugs, using in silico environments where less costly and faster drug design can be done day by day. In addition to the drugs mentioned, this study modeled the interaction of withaferin A, epigallocatechin gallate (EGCG), and ganoderiol A with APC using molecular docking and dynamic simulations. In docking studies, the interaction energy results of withaferin A, (EGCG), and ganoderiol A are -8.5, -7.8, and -7.9 kcal/mol, respectively. In MD simulations, the average RMSD values of these three agents are 0.5 nm for withaferin A and ganoderiol A and 1.5 nm for the more branched, bulky EGCG. The modeling results reveal the therapeutic drug potential of natural agents on the APC gene associated with colorectal cancer and provide a basis for other studies.

Anahtar Kelimeler

APC gene Colorectal cancer Molecular modeling Natural agent

Kaynakça

  • Akash, S., Islam, M. R., Bhuiyan, A. A., Islam, M. N., Bayil, I., Saleem, R. M., . . . Abdel-Daim, M. M. (2024). In silico evaluation of anti-colorectal cancer inhibitors by Resveratrol derivatives targeting Armadillo repeats domain of APC: molecular docking and molecular dynamics simulation. Front Oncol, 14, 1360745. doi: 10.3389/fonc.2024.1360745
  • Bharadwaj, S., Lee, K. E., Dwivedi, V. D., Yadava, U., Nees, M., & Kang, S. G. (2020). Density functional theory and molecular dynamics simulation support Ganoderma lucidum triterpenoids as broad range antagonist of matrix metalloproteinases. Journal of Molecular Liquids, 311. doi: 10.1016/j.molliq.2020.113322
  • Bontempo, P., De Masi, L., & Rigano, D. (2023). Functional Properties of Natural Products and Human Health. Nutrients, 15(13). doi: 10.3390/nu15132961
  • Chaachouay, N., & Zidane, L. (2024). Plant-Derived Natural Products: A Source for Drug Discovery and Development. Drugs and Drug Candidates, 3(1), 184-207. doi: 10.3390/ddc3010011
  • Chen, D., Chen, Y., Huang, F., Zhang, X., Zhou, Y., & Xu, L. (2023). The underlying regulatory mechanisms of colorectal carcinoma by combining Vitexin and Aspirin: based on systems biology, molecular docking, molecular dynamics simulation, and in vitro study. Front Endocrinol (Lausanne), 14, 1147132. doi: 10.3389/fendo.2023.1147132
  • Chicurel, M. (2002). Putting a name on it. Nature, 419(6908), 755, 757. doi: 10.1038/419755a
  • Choi, B. Y., & Kim, B. W. (2015). Withaferin-A Inhibits Colon Cancer Cell Growth by Blocking STAT3 Transcriptional Activity. J Cancer Prev, 20(3), 185-192. doi: 10.15430/JCP.2015.20.3.185
  • Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep, 7, 42717. doi: 10.1038/srep42717
  • Dar, R. A., Shahnawaz, M., Ahanger, M. A., & Majid, I. u. (2023). Exploring the Diverse Bioactive Compounds from Medicinal Plants: A Review. The Journal of Phytopharmacology, 12(3), 189-195. doi: 10.31254/phyto.2023.12307
  • El-Mernissi, R., Khaldan, A., Bouamrane, S., Rehman, H. M., Alaqarbeh, M., Ajana, M. A., . . . Bouachrine, M. (2024). 3D-QSAR, molecular docking, simulation dynamic and ADMET studies on new quinolines derivatives against colorectal carcinoma activity. J Biomol Struct Dyn, 42(7), 3682-3699. doi: 10.1080/07391102.2023.2214233
  • El Fadili, M., Er-Rajy, M., Kara, M., Assouguem, A., Belhassan, A., Alotaibi, A., . . . Elhallaoui, M. (2022). QSAR, ADMET In Silico Pharmacokinetics, Molecular Docking and Molecular Dynamics Studies of Novel Bicyclo (Aryl Methyl) Benzamides as Potent GlyT1 Inhibitors for the Treatment of Schizophrenia. Pharmaceuticals (Basel), 15(6). doi: 10.3390/ph15060670
  • Gao, J. J., Hirakawa, A., Min, B. S., Nakamura, N., & Hattori, M. (2005). In vivo antitumor effects of bitter principles from the antlered form of fruiting bodies of Ganoderma lucidum. Journal of Natural Medicines, 60(1), 42-48. doi: 10.1007/s11418-005-0003-5
  • Gmeiner, W. H. (2024). Recent Advances in Therapeutic Strategies to Improve Colorectal Cancer Treatment. Cancers (Basel), 16(5). doi: 10.3390/cancers16051029
  • Guru, P. R., Kar, R. K., Nayak, A. K., & Mohapatra, S. (2023). A comprehensive review on pharmaceutical uses of plant-derived biopolysaccharides. Int J Biol Macromol, 233, 123454. doi: 10.1016/j.ijbiomac.2023.123454
  • Han, B., Zhai, Y., Li, X., Zhao, H., Sun, C., Zeng, Y., . . . Kai, G. (2023). Total flavonoids of Tetrastigma hemsleyanum Diels et Gilg inhibits colorectal tumor growth by modulating gut microbiota and metabolites. Food Chem, 410, 135361. doi: 10.1016/j.foodchem.2022.135361
  • Hephzibah Cathryn, R., & George Priya Doss, C. (2023). Comparative molecular dynamics simulation of apo and holo forms of the P53 mutant C176F: a structural perspective. Journal of Taibah University for Science, 18(1). doi: 10.1080/16583655.2023.2297457
  • Justino, G. C., Nascimento, C. P., & Justino, M. C. (2021). Molecular dynamics simulations and analysis for bioinformatics undergraduate students. Biochem Mol Biol Educ, 49(4), 570-582. doi: 10.1002/bmb.21512
  • Kinzler, K. W., & Vogelstein, B. (1996). Lessons from hereditary colorectal cancer. Cell, 87(2), 159-170. doi: 10.1016/s0092-8674(00)81333-1
  • Li, B., Zhang, G., & Xu, X. (2023). APC mutation correlated with poor response of immunotherapy in colon cancer. BMC Gastroenterol, 23(1), 95. doi: 10.1186/s12876-023-02725-3
  • Macharia, J. M., Kaposztas, Z., & Bence, R. L. (2023). Medicinal Characteristics of Withania somnifera L. in Colorectal Cancer Management. Pharmaceuticals (Basel), 16(7). doi: 10.3390/ph16070915
  • Morris, C. J., & Corte, D. D. (2021). Using molecular docking and molecular dynamics to investigate protein-ligand interactions. Modern Physics Letters B, 35(08). doi: 10.1142/s0217984921300027
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785-2791. doi: 10.1002/jcc.21256
  • Moshawih, S., Lim, A. F., Ardianto, C., Goh, K. W., Kifli, N., Goh, H. P., . . . Ming, L. C. (2022). Target-Based Small Molecule Drug Discovery for Colorectal Cancer: A Review of Molecular Pathways and In Silico Studies. Biomolecules, 12(7). doi: 10.3390/biom12070878
  • Nasir, A., Bullo, M. M. H., Ahmed, Z., Imtiaz, A., Yaqoob, E., Jadoon, M., . . . Yaqoob, S. (2020). Nutrigenomics: Epigenetics and cancer prevention: A comprehensive review. Crit Rev Food Sci Nutr, 60(8), 1375-1387. doi: 10.1080/10408398.2019.1571480
  • Olkinuora, A. P., Peltomaki, P. T., Aaltonen, L. A., & Rajamaki, K. (2021). From APC to the genetics of hereditary and familial colon cancer syndromes. Hum Mol Genet, 30(R2), R206-R224. doi: 10.1093/hmg/ddab208
  • Peng, H., Ying, J., Zang, J., Lu, H., Zhao, X., Yang, P., . . . Wang, Z. (2023). Specific Mutations in APC, with Prognostic Implications in Metastatic Colorectal Cancer. Cancer Res Treat, 55(4), 1270-1280. doi: 10.4143/crt.2023.415
  • 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. doi: 10.1002/jcc.20084
  • Polakis, P. (2007). The many ways of Wnt in cancer. Curr Opin Genet Dev, 17(1), 45-51. doi: 10.1016/j.gde.2006.12.007
  • Qawoogha, S. S., & Shahiwala, A. (2020). Identification of potential anticancer phytochemicals against colorectal cancer by structure-based docking studies. J Recept Signal Transduct Res, 40(1), 67-76. doi: 10.1080/10799893.2020.1715431
  • Rampogu, S., Lee, G., Park, J. S., Lee, K. W., & Kim, M. O. (2022). Molecular Docking and Molecular Dynamics Simulations Discover Curcumin Analogue as a Plausible Dual Inhibitor for SARS-CoV-2. Int J Mol Sci, 23(3). doi: 10.3390/ijms23031771
  • Saha, P., Hegde, M., Chakraborty, K., Singha, A., Mukerjee, N., Ghosh, D., . . . Sil, S. K. (2024). Targeted inhibition of colorectal cancer proliferation: The dual-modulatory role of 2,4-DTBP on anti-apoptotic Bcl-2 and Survivin proteins. J Cell Mol Med, 28(7), e18150. doi: 10.1111/jcmm.18150
  • Shailes, H., Tse, W. Y., Freitas, M. O., Silver, A., & Martin, S. A. (2022). Statin Treatment as a Targeted Therapy for APC-Mutated Colorectal Cancer. Front Oncol, 12, 880552. doi: 10.3389/fonc.2022.880552
  • Shariatinia, Z., & Mazloom-Jalali, A. (2020). Molecular dynamics simulations on chitosan/graphene nanocomposites as anticancer drug delivery using systems. Chinese Journal of Physics, 66, 362-382. doi: 10.1016/j.cjph.2020.04.012
  • Siegel, R. L., Miller, K. D., & Jemal, A. (2020). Cancer statistics, 2020. CA Cancer J Clin, 70(1), 7-30. doi: 10.3322/caac.21590
  • Skariyachan, S., Gopal, D., Chakrabarti, S., Kempanna, P., Uttarkar, A., Muddebihalkar, A. G., & Niranjan, V. (2020). Structural and molecular basis of the interaction mechanism of selected drugs towards multiple targets of SARS-CoV-2 by molecular docking and dynamic simulation studies- deciphering the scope of repurposed drugs. Comput Biol Med, 126, 104054. doi: 10.1016/j.compbiomed.2020.104054
  • Surya Ulhas, R., & Malaviya, A. (2023). In-silico validation of novel therapeutic activities of withaferin a using molecular docking and dynamics studies. J Biomol Struct Dyn, 41(11), 5045-5056. doi: 10.1080/07391102.2022.2078410
  • Vallikondaperumal, M., N, B., T. V, A. K., & V, P. (2023). In Silico Molecular Screening and Docking Approaches on Antineoplastic Agent-Irinotecan Towards the Marker Proteins of Colon Cancer. International Journal of Applied Pharmaceutics, 84-92. doi: 10.22159/ijap.2023v15i5.48523
  • Wahnou, H., Liagre, B., Sol, V., El Attar, H., Attar, R., Oudghiri, M., . . . Limami, Y. (2023). Polyphenol-Based Nanoparticles: A Promising Frontier for Enhanced Colorectal Cancer Treatment. Cancers (Basel), 15(15). doi: 10.3390/cancers15153826
  • Wankowicz, S. A., de Oliveira, S. H., Hogan, D. W., van den Bedem, H., & Fraser, J. S. (2022). Ligand binding remodels protein side-chain conformational heterogeneity. Elife, 11. doi: 10.7554/eLife.74114
  • Yadav, M., Abdalla, M., Madhavi, M., Chopra, I., Bhrdwaj, A., Soni, L., . . . Singh, S. K. (2022). Structure-Based Virtual Screening, Molecular Docking, Molecular Dynamics Simulation and Pharmacokinetic modelling of Cyclooxygenase-2 (COX-2) inhibitor for the clinical treatment of Colorectal Cancer. Molecular Simulation, 48(12), 1081-1101. doi: 10.1080/08927022.2022.2068799
  • Yalcin, S. (2020). Molecular Docking, Drug Likeness, and ADMET Analyses of Passiflora Compounds as P-Glycoprotein (P-gp) Inhibitor for the Treatment of Cancer. Current Pharmacology Reports, 6(6), 429-440. doi: 10.1007/s40495-020-00241-6
  • Yang, J., He, K., Zhang, M., Wu, L., Qin, S., Luo, M., & Xia, X. (2024). Unveiling the therapeutic potential of epigallocatechin gallate in liver cancer: insights from network pharmacology and in vitro assays. Nat Prod Res, 1-5. doi: 10.1080/14786419.2024.2384083
  • Ye, T., Ge, Y., Jiang, X., Song, H., Peng, C., & Liu, B. (2023). A review of anti-tumour effects of Ganoderma lucidum in gastrointestinal cancer. Chin Med, 18(1), 107. doi: 10.1186/s13020-023-00811-y
  • Zhang, M., Cheng, S., Jin, Y., Zhao, Y., & Wang, Y. (2021). Roles of CA125 in diagnosis, prediction, and oncogenesis of ovarian cancer. Biochim Biophys Acta Rev Cancer, 1875(2), 188503. doi: 10.1016/j.bbcan.2021.188503
  • Zrinej, J., Elmchichi, L., Alaqarbeh, M., Lakhlifi, T., & Bouachrine, M. (2023). Computational approach: 3D-QSAR, molecular docking, ADMET, molecular dynamics simulation investigations, and retrosynthesis of some curcumin analogues as PARP-1 inhibitors targeting colon cancer. New Journal of Chemistry, 47(45), 20987-21009. doi: 10.1039/d3nj03981a
Toplam 45 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Konular Biyomühendislik (Diğer)
Bölüm Makaleler
Yazarlar

Eda Arabacı 0009-0006-6780-6801

Nil Sazlı 0009-0006-6740-1169

Deniz Karataş 0000-0002-8176-4883

Yayımlanma Tarihi 15 Haziran 2025
Gönderilme Tarihi 21 Ocak 2025
Kabul Tarihi 6 Mayıs 2025
Yayımlandığı Sayı Yıl 2025 Cilt: 15 Sayı: 2

Kaynak Göster

APA Arabacı, E., Sazlı, N., & Karataş, D. (2025). Investigating the Potential of Natural Agents for Colorectal Cancer Treatment with Molecular Modeling. Karadeniz Fen Bilimleri Dergisi, 15(2), 787-806. https://doi.org/10.31466/kfbd.1624597
 Kapak Resmi İndir

by-nc-sa.pngThis work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.