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Molecular Docking Analysis Of Small Fullerene (C20, C22, C24) Nanoparticles With Lung (1X2J) And Breast (3HY3) Cancer Target Proteins

Yıl 2025, Cilt: 9 Sayı: 5, 77 - 85

Saadet Kaya

Öz

Nanotechnology-based therapeutic approaches play a crucial role in the development of next-generation drug carriers and therapeutic agents, particularly in cancer treatment. In this study, the molecular interactions of small fullerene nanoparticles—C20, C22, and C24—with target proteins associated with lung cancer (PDB ID: 1X2J) and breast cancer (PDB ID: 3HY3) were investigated through molecular docking analysis. Each fullerene nanoparticle was docked separately with the specific target protein of the corresponding cancer type, and their binding energies and molecular interaction profiles were compared. The results demonstrated that small fullerenes can form strong and specific interactions with both lung and breast cancer target proteins. These findings suggest that small fullerene nanoparticles hold potential as biological agents or carrier systems in cancer therapy, providing a foundation for future advanced experimental studies. Additionally, HOMO-LUMO contour analyses and Molecular Electrostatic Potential (MEP) maps were visualized and interpreted to evaluate the electronic properties and potential reactive sites of the C20, C22, and C24 complexes.

Anahtar Kelimeler

Nanotechnology Small fullerenes Molecular docking Nanoparticle

Kaynakça

  • [1] N. Alrushaid, F. A. Khan, E. A. Al-Suhaimi, & Elaissari, A. Nanotechnology in cancer diagnosis and treatment. Pharmaceutics, , 15(3), (2023) 1025.
  • [2] K. Elumalai, S. Srinivasan, & A. Shanmugam Review of the efficacy of nanoparticle-based drug delivery systems for cancer treatment. Biomedical Technology, 5, (2024) 109-122.
  • [3] D. Bobo, K. J. Robinson, J. Islam, K. J. Thurecht, & S. R. Corrie. Nanoparticle-based medicines: A review of FDA-approved materials and clinical trials to date. Pharmaceutical Research, 33(10), (2016) , 2373–2387.
  • [4] N. Kosar, H. Tahir, K. Ayub, & T. Mahmood. DFT studies of single and multiple alkali metals doped C24 fullerene for electronics and nonlinear optical applications. Journal of Molecular Graphics and Modelling 105, (2021), 107867.
  • [5] N. B. Fernandes, R. U. K. Shenoy, K M. K. ajampady, C. E. DCruz, R. K. Shirodkar, L. Kumar, & R. Verma. Fullerenes for the treatment of cancer: an emerging tool. Environmental Science and Pollution Research 29(39), (2022) 58607-58627.
  • [6] R. Bakry, R. M. Vallant, M. Najam-ul-Haq, M. Rainer, Z. Szabo, C. W. Huck, & G. K. Bonn. Medicinal applications of fullerenes. International Journal of Nanomedicine 2(4), (2007) 639–649.
  • [7] M. Krause, et al. Fullerene–biomolecule interactions: Understanding the potential for nanomedicine. ChemBioChem 19(1), (2018) 1–10.
  • [8] X. Zhao, et al. Fullerene nanomaterials inhibit cancer progression by regulating oxidative stress and apoptosis pathways. Nanomedicine 14(4), (2019) 451–464.
  • [9] G. V. Andrievsky, M. V. Kosevich, O. M. Vovk, V. S. Shelkovsky, & L. A. Vashchenko. Studies of aqueous colloidal solutions of fullerene C60 by electron microscopy. Chemical Physics Letters 364(1–2), (2002) 8–17.
  • [10] H. Yamawaki, & Y. Imai. Potential toxicity of engineered nanoparticles in the lung. Advanced Drug Delivery Reviews, 58 (14) (2006) 1436–1441.
  • [11] S. Erkan & D Karakaş. DFT investigation and molecular docking studies on dinuclear metal carbonyls containing pyridyl ligands with alkyne unit. Chemical Papers 73, (2019) 2387-2398.
  • [12] Z. Bikadi & E. Hazai. Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock. Journal of cheminformatics 1, (2009) 1-16.
  • [13] R. Huey, G. M. Morris, A. J. Olson, & D. S. Goodsell. semiempirical free energy force field with charge‐based desolvation. Journal of computational chemistry 28(6), (2007) 1145-1152.
  • [14] J. J. Stewart Stewart computational chemistry. (2007) http://openmopac. net/
  • [15] Frisch, M. J. E. A. gaussian 09, Revision d. 01, Gaussian. Inc, Wallingford CT (2009) 201.
  • [16] P. Politzer & J. S. Murray. The fundamental nature and role of the electrostatic potential in atoms and molecules. Theoretical Chemistry Accounts 108(3), (2002) 134-142.
  • [17] A. M. Bayoumy, M. Ibrahim & A.Omar. Mapping molecular electrostatic potential (MESP) for fulleropyrrolidine and its derivatives. Optical and Quantum Electronics 52, (2020) 1-13.
  • [18] Z. Akbari, C. Stagno, N. Iraci, T. Efferth, E. A. Omer, A. Piperno,... & N. Micale Biological evaluation, DFT, MEP, HOMO-LUMO analysis and ensemble docking studies of Zn (II) complexes of bidentate and tetradentate Schiff base ligands as antileukemia agents. Journal of Molecular Structure 1301, (2024) 137400.
  • [19] S. Zinatloo-Ajabshir, S. Rakhshani, Z. Mehrabadi, M. Farsadrooh, M. Feizi-Dehnayebi, S. Rakhshani,... & T. M. Aminabhavi. Novel rod-like [Cu (phen) 2 (OAc)]· PF6 complex for high-performance visible-light-driven photocatalytic degradation of hazardous organic dyes: DFT approach, Hirshfeld and fingerprint plot analysis. Journal of Environmental Management 350, (2024) 119545.
  • [20] R. G. Parr Density functional theory of atoms and molecules. In Horizons of Quantum Chemistry: Proceedings of the Third International Congress of Quantum Chemistry Held at Kyoto, Japan, October 29-November 3, 1979 , (1989) (pp. 5-15).
  • [21] R. G. Pearson. Absolute electronegativity and hardness: application to organic chemistry. Journal of Organic Chemistry 54(6), (1986) 1423–1430
  • [22] X. Y. Meng, H. X. Zhang, M. Mezei, & M. Cui. Molecular docking: a powerful approach for structure-based drug discovery. Current computer-aided drug design 7(2), (2011) 146-157.
  • [23] G. M. Morris, R. Huey, W. Lindstrom, M. F. Sanner, R. K. Belew, D. S. Goodsell, & A. J. Olson. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of computational chemistry 30(16), (2009) 2785-2791.
  • [24] D. B. Kitchen, H. Decornez, J. R. Furr & J. Bajorath. Docking and scoring in virtual screening for drug discovery: methods and applications. Nature Reviews Drug Discovery 3(11), (2004) 935–949.
  • [25] S. Y. Huang, S. Z. Grinter, & X. Zou. Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions. Physical Chemistry Chemical Physics 12(40), (2010) 12899–12908.
  • [26] N. S. Pagadala, K. Syed, & J. Tuszynski. Software for molecular docking: a review. Biophysical Reviews 9(2), (2017) 91–102.

Yıl 2025, Cilt: 9 Sayı: 5, 77 - 85

Saadet Kaya

Öz

Kaynakça

  • [1] N. Alrushaid, F. A. Khan, E. A. Al-Suhaimi, & Elaissari, A. Nanotechnology in cancer diagnosis and treatment. Pharmaceutics, , 15(3), (2023) 1025.
  • [2] K. Elumalai, S. Srinivasan, & A. Shanmugam Review of the efficacy of nanoparticle-based drug delivery systems for cancer treatment. Biomedical Technology, 5, (2024) 109-122.
  • [3] D. Bobo, K. J. Robinson, J. Islam, K. J. Thurecht, & S. R. Corrie. Nanoparticle-based medicines: A review of FDA-approved materials and clinical trials to date. Pharmaceutical Research, 33(10), (2016) , 2373–2387.
  • [4] N. Kosar, H. Tahir, K. Ayub, & T. Mahmood. DFT studies of single and multiple alkali metals doped C24 fullerene for electronics and nonlinear optical applications. Journal of Molecular Graphics and Modelling 105, (2021), 107867.
  • [5] N. B. Fernandes, R. U. K. Shenoy, K M. K. ajampady, C. E. DCruz, R. K. Shirodkar, L. Kumar, & R. Verma. Fullerenes for the treatment of cancer: an emerging tool. Environmental Science and Pollution Research 29(39), (2022) 58607-58627.
  • [6] R. Bakry, R. M. Vallant, M. Najam-ul-Haq, M. Rainer, Z. Szabo, C. W. Huck, & G. K. Bonn. Medicinal applications of fullerenes. International Journal of Nanomedicine 2(4), (2007) 639–649.
  • [7] M. Krause, et al. Fullerene–biomolecule interactions: Understanding the potential for nanomedicine. ChemBioChem 19(1), (2018) 1–10.
  • [8] X. Zhao, et al. Fullerene nanomaterials inhibit cancer progression by regulating oxidative stress and apoptosis pathways. Nanomedicine 14(4), (2019) 451–464.
  • [9] G. V. Andrievsky, M. V. Kosevich, O. M. Vovk, V. S. Shelkovsky, & L. A. Vashchenko. Studies of aqueous colloidal solutions of fullerene C60 by electron microscopy. Chemical Physics Letters 364(1–2), (2002) 8–17.
  • [10] H. Yamawaki, & Y. Imai. Potential toxicity of engineered nanoparticles in the lung. Advanced Drug Delivery Reviews, 58 (14) (2006) 1436–1441.
  • [11] S. Erkan & D Karakaş. DFT investigation and molecular docking studies on dinuclear metal carbonyls containing pyridyl ligands with alkyne unit. Chemical Papers 73, (2019) 2387-2398.
  • [12] Z. Bikadi & E. Hazai. Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock. Journal of cheminformatics 1, (2009) 1-16.
  • [13] R. Huey, G. M. Morris, A. J. Olson, & D. S. Goodsell. semiempirical free energy force field with charge‐based desolvation. Journal of computational chemistry 28(6), (2007) 1145-1152.
  • [14] J. J. Stewart Stewart computational chemistry. (2007) http://openmopac. net/
  • [15] Frisch, M. J. E. A. gaussian 09, Revision d. 01, Gaussian. Inc, Wallingford CT (2009) 201.
  • [16] P. Politzer & J. S. Murray. The fundamental nature and role of the electrostatic potential in atoms and molecules. Theoretical Chemistry Accounts 108(3), (2002) 134-142.
  • [17] A. M. Bayoumy, M. Ibrahim & A.Omar. Mapping molecular electrostatic potential (MESP) for fulleropyrrolidine and its derivatives. Optical and Quantum Electronics 52, (2020) 1-13.
  • [18] Z. Akbari, C. Stagno, N. Iraci, T. Efferth, E. A. Omer, A. Piperno,... & N. Micale Biological evaluation, DFT, MEP, HOMO-LUMO analysis and ensemble docking studies of Zn (II) complexes of bidentate and tetradentate Schiff base ligands as antileukemia agents. Journal of Molecular Structure 1301, (2024) 137400.
  • [19] S. Zinatloo-Ajabshir, S. Rakhshani, Z. Mehrabadi, M. Farsadrooh, M. Feizi-Dehnayebi, S. Rakhshani,... & T. M. Aminabhavi. Novel rod-like [Cu (phen) 2 (OAc)]· PF6 complex for high-performance visible-light-driven photocatalytic degradation of hazardous organic dyes: DFT approach, Hirshfeld and fingerprint plot analysis. Journal of Environmental Management 350, (2024) 119545.
  • [20] R. G. Parr Density functional theory of atoms and molecules. In Horizons of Quantum Chemistry: Proceedings of the Third International Congress of Quantum Chemistry Held at Kyoto, Japan, October 29-November 3, 1979 , (1989) (pp. 5-15).
  • [21] R. G. Pearson. Absolute electronegativity and hardness: application to organic chemistry. Journal of Organic Chemistry 54(6), (1986) 1423–1430
  • [22] X. Y. Meng, H. X. Zhang, M. Mezei, & M. Cui. Molecular docking: a powerful approach for structure-based drug discovery. Current computer-aided drug design 7(2), (2011) 146-157.
  • [23] G. M. Morris, R. Huey, W. Lindstrom, M. F. Sanner, R. K. Belew, D. S. Goodsell, & A. J. Olson. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of computational chemistry 30(16), (2009) 2785-2791.
  • [24] D. B. Kitchen, H. Decornez, J. R. Furr & J. Bajorath. Docking and scoring in virtual screening for drug discovery: methods and applications. Nature Reviews Drug Discovery 3(11), (2004) 935–949.
  • [25] S. Y. Huang, S. Z. Grinter, & X. Zou. Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions. Physical Chemistry Chemical Physics 12(40), (2010) 12899–12908.
  • [26] N. S. Pagadala, K. Syed, & J. Tuszynski. Software for molecular docking: a review. Biophysical Reviews 9(2), (2017) 91–102.
Toplam 26 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Konular Moleküler Görüntüleme
Bölüm Research Article
Yazarlar

Saadet Kaya 0009-0006-3477-2115

Erken Görünüm Tarihi 2 Temmuz 2025
Yayımlanma Tarihi
Gönderilme Tarihi 14 Haziran 2025
Kabul Tarihi 24 Haziran 2025
Yayımlandığı Sayı Yıl 2025 Cilt: 9 Sayı: 5

Kaynak Göster

APA Kaya, S. (2025). Molecular Docking Analysis Of Small Fullerene (C20, C22, C24) Nanoparticles With Lung (1X2J) And Breast (3HY3) Cancer Target Proteins. Turkish Computational and Theoretical Chemistry, 9(5), 77-85.
AMA Kaya S. Molecular Docking Analysis Of Small Fullerene (C20, C22, C24) Nanoparticles With Lung (1X2J) And Breast (3HY3) Cancer Target Proteins. Turkish Comp Theo Chem (TC&TC). Temmuz 2025;9(5):77-85.
Chicago Kaya, Saadet. “Molecular Docking Analysis Of Small Fullerene (C20, C22, C24) Nanoparticles With Lung (1X2J) And Breast (3HY3) Cancer Target Proteins”. Turkish Computational and Theoretical Chemistry 9, sy. 5 (Temmuz 2025): 77-85.
EndNote Kaya S (01 Temmuz 2025) Molecular Docking Analysis Of Small Fullerene (C20, C22, C24) Nanoparticles With Lung (1X2J) And Breast (3HY3) Cancer Target Proteins. Turkish Computational and Theoretical Chemistry 9 5 77–85.
IEEE S. Kaya, “Molecular Docking Analysis Of Small Fullerene (C20, C22, C24) Nanoparticles With Lung (1X2J) And Breast (3HY3) Cancer Target Proteins”, Turkish Comp Theo Chem (TC&TC), c. 9, sy. 5, ss. 77–85, 2025.
ISNAD Kaya, Saadet. “Molecular Docking Analysis Of Small Fullerene (C20, C22, C24) Nanoparticles With Lung (1X2J) And Breast (3HY3) Cancer Target Proteins”. Turkish Computational and Theoretical Chemistry 9/5 (Temmuz 2025), 77-85.
JAMA Kaya S. Molecular Docking Analysis Of Small Fullerene (C20, C22, C24) Nanoparticles With Lung (1X2J) And Breast (3HY3) Cancer Target Proteins. Turkish Comp Theo Chem (TC&TC). 2025;9:77–85.
MLA Kaya, Saadet. “Molecular Docking Analysis Of Small Fullerene (C20, C22, C24) Nanoparticles With Lung (1X2J) And Breast (3HY3) Cancer Target Proteins”. Turkish Computational and Theoretical Chemistry, c. 9, sy. 5, 2025, ss. 77-85.
Vancouver Kaya S. Molecular Docking Analysis Of Small Fullerene (C20, C22, C24) Nanoparticles With Lung (1X2J) And Breast (3HY3) Cancer Target Proteins. Turkish Comp Theo Chem (TC&TC). 2025;9(5):77-85.

Journal Full Title: Turkish Computational and Theoretical Chemistry


Journal Abbreviated Title: Turkish Comp Theo Chem (TC&TC)