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Computational Chemistry Methods for Molecular Analysis and In Silico Investigation of Platinum (IV) Complexes

Yıl 2025, Cilt: 9 Sayı: 5, 110 - 124

Saadet Kaya , Sultan Erkan

Öz

Computational chemistry methods were used to investigate the six-coordinated Pt1, Pt2 and Pt3 complexes at the molecular level and to determine their advantages over the four-coordinated complexes. The most suitable calculation level was determined by benchmark analysis using experimental bond lengths and the WB97XD/6-31G(d,p)/SDD method was selected. IR, 1H- and 13C-NMR spectroscopic data were calculated for the structural analysis of Pt1-Pt3 complexes and compared with experimental findings. HOMO and LUMO contour diagrams and molecular electrostatic potential (MEP) maps were created to understand the electron transfer potential of the complexes. This information provides important clues in predicting their interactions with biological receptors. Molecular docking studies were performed to evaluate the comparative biological activities of the studied platinum (IV) complexes (Pt1-Pt3) with platinum (II) complexes, one of the current chemotherapy agents. Pt1-Pt3 complexes were docked with breast cancer (PDB ID: 1JNX), lung cancer (PDB ID: 1X2J) and colon cancer (PDB ID: 2HQ6) proteins. As a result of the investigations, it was determined that these complexes were superior in terms of anticancer activity compared to the reference complex (cis-Pt).

Anahtar Kelimeler

Platinum (IV) Complexes anticancer docking

Kaynakça

  • [1] Zheng, Y. R., Suntharalingam, K., Johnstone, T. C., & Lippard, S. J. (2015). Encapsulation of Pt (IV) prodrugs within a Pt (II) cage for drug delivery. Chemical science, 6(2), 1189-1193.
  • [2] Sánchez-Camacho, J., Infante-Tadeo, S., Carrasco, A. C., Scoditti, S., Martínez, Á., Barroso- Bujans, F., ... & Salassa, L. (2023). Flavin-conjugated Pt (IV) anticancer agents. Inorganic Chemistry, 62(14), 5644-5651.
  • [3] Barth, M. C., Häfner, N., Runnebaum, I. B., & Weigand, W. (2023). Synthesis, Characterization and Biological Investigation of the Platinum (IV) Tolfenamato Prodrug–Resolving Cisplatin-Resistance in Ovarian Carcinoma Cell Lines. International Journal of Molecular Sciences, 24(6), 5718.
  • [4] Kenny, R. G., Chuah, S. W., Crawford, A., & Marmion, C. J. (2017). Platinum (IV) prodrugs–a step closer to Ehrlich's vision?. European Journal of Inorganic Chemistry, 2017(12), 1596-1612.
  • [5] Zhou, Z., Shi, P., Wang, C., Sun, Y., & Gao, C. (2024). Recent updates in nanoscale delivery systems of platinum (IV) antitumor prodrugs. Coordination Chemistry Reviews, 508, 215774.
  • [6] Dikova, Y. M., Yufit, D. S., & Williams, J. G. (2023). Platinum (IV) Complexes with Tridentate, NNC-Coordinating Ligands: Synthesis, Structures, and Luminescence. Inorganic Chemistry, 62(4), 1306-1322.
  • [7] Farrer, N. J., Woods, J. A., Salassa, L., Zhao, Y., Robinson, K. S., Clarkson, G., ... & Sadler, P. J. (2010). A potent trans‐diimine platinum anticancer complex photoactivated by visible light. Angewandte Chemie, 47(122), 9089-9092.
  • [8] Novohradsky, V., Pracharova, J., Kasparkova, J., Imberti, C., Bridgewater, H. E., Sadler, P. J., & Brabec, V. (2020). Induction of immunogenic cell death in cancer cells by a photoactivated platinum (IV) prodrug. Inorganic chemistry frontiers, 7(21), 4150-4159.
  • [9] Yanai, T., Tew, D. P., & Handy, N. C. (2004). A new hybrid exchange–correlation functional using the Coulomb-attenuating method (CAM-B3LYP). Chemical Physics Letters, 393(1-3), 51-57.
  • [10] Ditchfield, R., Hehre, W. J., & Pople, J. A. (1971). Self-consistent molecular orbital methods. IX. An extended Gaussian‐type basis for molecular‐orbital studies of organic molecules. Journal of Chemical Physics, 54(2), 724-728.
  • [11] Andrae, D., Häußermann, U., Dolg, M., Stoll, H., & Preuß, H. (1990). Energy‐adjusted ab initio pseudopotentials for the second and third row transition elements. Theoretical Chemistry Accounts, 77(2), 123-141.
  • [12] Ohtomo, Y., Ishiwata, K., Hashimoto, S., Kuroiwa, T., & Tahara, K. (2021). Revisiting Dehydrothiopheno [12] annulenes: Synthesis, Electronic Properties, and Aromaticity. The Journal of Organic Chemistry, 86(19), 13198-13211.
  • [13] Khalid, H. H., Erkan, S., & Bulut, N. (2021). Halogens effect on spectroscopy, anticancer and molecular docking studies for platinum complexes. Optik, 244, 166324.
  • [14] Kaya, S., Erkan, S., & Karakaş, D. (2021). Computational investigation of molecular structures, spectroscopic properties and antitumor-antibacterial activities of some Schiff bases. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 244, 118829.
  • [15] Padmanabhan, B., Tong, K. I., Ohta, T., Nakamura, Y., Scharlock, M., Ohtsuji, M., ... & Yamamoto, M. (2006). Structural basis for defects of Keap1 activity provoked by its point mutations in lung cancer. Molecular cell, 21(5), 689-700.
  • [16] Davis, T. L., Walker, J. R., Campagna-Slater, V., Finerty Jr, P. J., Paramanathan, R., Bernstein, G., ... & Dhe-Paganon, S. (2010). Structural and biochemical characterization of the human cyclophilin family of peptidyl-prolyl isomerases. PLoS biology, 8(7), e1000439.

Yıl 2025, Cilt: 9 Sayı: 5, 110 - 124

Saadet Kaya , Sultan Erkan

Öz

Kaynakça

  • [1] Zheng, Y. R., Suntharalingam, K., Johnstone, T. C., & Lippard, S. J. (2015). Encapsulation of Pt (IV) prodrugs within a Pt (II) cage for drug delivery. Chemical science, 6(2), 1189-1193.
  • [2] Sánchez-Camacho, J., Infante-Tadeo, S., Carrasco, A. C., Scoditti, S., Martínez, Á., Barroso- Bujans, F., ... & Salassa, L. (2023). Flavin-conjugated Pt (IV) anticancer agents. Inorganic Chemistry, 62(14), 5644-5651.
  • [3] Barth, M. C., Häfner, N., Runnebaum, I. B., & Weigand, W. (2023). Synthesis, Characterization and Biological Investigation of the Platinum (IV) Tolfenamato Prodrug–Resolving Cisplatin-Resistance in Ovarian Carcinoma Cell Lines. International Journal of Molecular Sciences, 24(6), 5718.
  • [4] Kenny, R. G., Chuah, S. W., Crawford, A., & Marmion, C. J. (2017). Platinum (IV) prodrugs–a step closer to Ehrlich's vision?. European Journal of Inorganic Chemistry, 2017(12), 1596-1612.
  • [5] Zhou, Z., Shi, P., Wang, C., Sun, Y., & Gao, C. (2024). Recent updates in nanoscale delivery systems of platinum (IV) antitumor prodrugs. Coordination Chemistry Reviews, 508, 215774.
  • [6] Dikova, Y. M., Yufit, D. S., & Williams, J. G. (2023). Platinum (IV) Complexes with Tridentate, NNC-Coordinating Ligands: Synthesis, Structures, and Luminescence. Inorganic Chemistry, 62(4), 1306-1322.
  • [7] Farrer, N. J., Woods, J. A., Salassa, L., Zhao, Y., Robinson, K. S., Clarkson, G., ... & Sadler, P. J. (2010). A potent trans‐diimine platinum anticancer complex photoactivated by visible light. Angewandte Chemie, 47(122), 9089-9092.
  • [8] Novohradsky, V., Pracharova, J., Kasparkova, J., Imberti, C., Bridgewater, H. E., Sadler, P. J., & Brabec, V. (2020). Induction of immunogenic cell death in cancer cells by a photoactivated platinum (IV) prodrug. Inorganic chemistry frontiers, 7(21), 4150-4159.
  • [9] Yanai, T., Tew, D. P., & Handy, N. C. (2004). A new hybrid exchange–correlation functional using the Coulomb-attenuating method (CAM-B3LYP). Chemical Physics Letters, 393(1-3), 51-57.
  • [10] Ditchfield, R., Hehre, W. J., & Pople, J. A. (1971). Self-consistent molecular orbital methods. IX. An extended Gaussian‐type basis for molecular‐orbital studies of organic molecules. Journal of Chemical Physics, 54(2), 724-728.
  • [11] Andrae, D., Häußermann, U., Dolg, M., Stoll, H., & Preuß, H. (1990). Energy‐adjusted ab initio pseudopotentials for the second and third row transition elements. Theoretical Chemistry Accounts, 77(2), 123-141.
  • [12] Ohtomo, Y., Ishiwata, K., Hashimoto, S., Kuroiwa, T., & Tahara, K. (2021). Revisiting Dehydrothiopheno [12] annulenes: Synthesis, Electronic Properties, and Aromaticity. The Journal of Organic Chemistry, 86(19), 13198-13211.
  • [13] Khalid, H. H., Erkan, S., & Bulut, N. (2021). Halogens effect on spectroscopy, anticancer and molecular docking studies for platinum complexes. Optik, 244, 166324.
  • [14] Kaya, S., Erkan, S., & Karakaş, D. (2021). Computational investigation of molecular structures, spectroscopic properties and antitumor-antibacterial activities of some Schiff bases. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 244, 118829.
  • [15] Padmanabhan, B., Tong, K. I., Ohta, T., Nakamura, Y., Scharlock, M., Ohtsuji, M., ... & Yamamoto, M. (2006). Structural basis for defects of Keap1 activity provoked by its point mutations in lung cancer. Molecular cell, 21(5), 689-700.
  • [16] Davis, T. L., Walker, J. R., Campagna-Slater, V., Finerty Jr, P. J., Paramanathan, R., Bernstein, G., ... & Dhe-Paganon, S. (2010). Structural and biochemical characterization of the human cyclophilin family of peptidyl-prolyl isomerases. PLoS biology, 8(7), e1000439.
Toplam 16 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Konular Fiziksel Kimya (Diğer)
Bölüm Research Article
Yazarlar

Saadet Kaya 0009-0006-3477-2115

Sultan Erkan 0000-0001-6744-929X

Erken Görünüm Tarihi 2 Temmuz 2025
Yayımlanma Tarihi
Gönderilme Tarihi 28 Şubat 2025
Kabul Tarihi 13 Nisan 2025
Yayımlandığı Sayı Yıl 2025 Cilt: 9 Sayı: 5

Kaynak Göster

APA Kaya, S., & Erkan, S. (2025). Computational Chemistry Methods for Molecular Analysis and In Silico Investigation of Platinum (IV) Complexes. Turkish Computational and Theoretical Chemistry, 9(5), 110-124.
AMA Kaya S, Erkan S. Computational Chemistry Methods for Molecular Analysis and In Silico Investigation of Platinum (IV) Complexes. Turkish Comp Theo Chem (TC&TC). Temmuz 2025;9(5):110-124.
Chicago Kaya, Saadet, ve Sultan Erkan. “Computational Chemistry Methods for Molecular Analysis and In Silico Investigation of Platinum (IV) Complexes”. Turkish Computational and Theoretical Chemistry 9, sy. 5 (Temmuz 2025): 110-24.
EndNote Kaya S, Erkan S (01 Temmuz 2025) Computational Chemistry Methods for Molecular Analysis and In Silico Investigation of Platinum (IV) Complexes. Turkish Computational and Theoretical Chemistry 9 5 110–124.
IEEE S. Kaya ve S. Erkan, “Computational Chemistry Methods for Molecular Analysis and In Silico Investigation of Platinum (IV) Complexes”, Turkish Comp Theo Chem (TC&TC), c. 9, sy. 5, ss. 110–124, 2025.
ISNAD Kaya, Saadet - Erkan, Sultan. “Computational Chemistry Methods for Molecular Analysis and In Silico Investigation of Platinum (IV) Complexes”. Turkish Computational and Theoretical Chemistry 9/5 (Temmuz 2025), 110-124.
JAMA Kaya S, Erkan S. Computational Chemistry Methods for Molecular Analysis and In Silico Investigation of Platinum (IV) Complexes. Turkish Comp Theo Chem (TC&TC). 2025;9:110–124.
MLA Kaya, Saadet ve Sultan Erkan. “Computational Chemistry Methods for Molecular Analysis and In Silico Investigation of Platinum (IV) Complexes”. Turkish Computational and Theoretical Chemistry, c. 9, sy. 5, 2025, ss. 110-24.
Vancouver Kaya S, Erkan S. Computational Chemistry Methods for Molecular Analysis and In Silico Investigation of Platinum (IV) Complexes. Turkish Comp Theo Chem (TC&TC). 2025;9(5):110-24.

Journal Full Title: Turkish Computational and Theoretical Chemistry


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