Araştırma Makalesi
BibTex RIS Kaynak Göster

Comparison of The Molecular Docking Properties of Three Potentially Active Agents

Yıl 2023, Cilt: 9 Sayı: 2, 81 - 85, 30.06.2023

Güvenç Görgülü Bülent Dede

https://doi.org/10.22399/ijcesen.1147789

Öz

Antineoplastic agents are generally the drugs used to recess or prevent tumor growth which is promoted in many cases by certain factors like vascular endothelial growth factor-2 (VEGFR-2) and cyclooxygenase-2 (COX-2). These two factors seem important in angiogenesis and lymphangiogenesis in fetal, normal and neoplastic tissue. Prevention of VEGF family of proteins and cyclooxygenase-2 enzyme is a good strategy to inhibit the growth of tumor tissue eventually may give rise to recession.
In this study, three potentially active and an active ligand were tested for their binding properties to two target molecules mentioned above by molecular docking study. This research is aimed to compare three different molecules according to their binding affinities, binding energies and the nature of bonds formed between the ligand and the target molecules. Showing the 3D structures will localize the fitted ligands on proteins and the possible hydrogen bonds formed were defined. Among the three proposed ligands, Ligand 1 showed the closest results to the commercial product lenalidomide®. All three ligands showed similar ∆G values and fitness scores with lenalidomide® which is an indicator of good fit, proximity and orientation with the target molecule.

Anahtar Kelimeler

Molecular Docking VEGFR-2 COX-2 In-silico

Kaynakça

  • [1] Kenakin, T. (2018). A Pharmacology Primer: Techniques for More Effective and Strategic Drug Discovery, 4th ed. San Diego, CA, Academic Press.
  • [2] Strømgaard K, Krogsgaard-Larsen P, Madsen U, (2017). Eds. Textbook of Drug Design and Discovery. CRC Press.
  • [3] Gorgulu, G., Cicek, M. B., Dede, B. (2018). Novel Aminoketooxime Ligand and Its Cu(II) and Mn(II) Complexes: Synthesis, Characterization and Molecular Docking Studies. Acta Physica Polonica A, 133(2), 250–255. DOI: 10.12693/APhysPolA.133.250
  • [4] Sliwoski, G., Kothiwale, S., Meiler, J., Lowe, E. W. (2014). Computational methods in drug discovery. Pharmacological Reviews, 66(1), 334-395. DOI:10.1124/pr.112.007336
  • [5] Tammela, T., Enholm, B., Alitalo, K., Paavonen, K. (2005). The biology of vascular endothelial growth factors, Cardiovascular Research, 65(3), 550–563. DOI:10.1016/j.cardiores.2004.12.002
  • [6] Wilkinson-Berka, J. L. (2004). Vasoactive factors and diabetic retinopathy: vascular endothelial growth factor, cycoloxygenase-2 and nitric oxide. Current Pharmaceutical Design, 10(27), 3331-3348. DOI:10.2174/1381612043383142
  • [7] Tuccillo, C., Romano, M., Troiani, T., Martinelli, E., Morgillo, F., De Vita, F., Bianco, R., Gabriella, F., Bianco, R.A., Tortora, G., Ciardiello, F. (2005). Antitumor activity of ZD6474, a vascular endothelial growth factor-2 and epidermal growth factor receptor small molecule tyrosine kinase inhibitor, in combination with SC-236, a cyclooxygenase-2 inhibitor. Clinical Cancer Research, 11(3), 1268-1276. DOI: 10.1158/1078-0432.1268.11.3
  • [8] Ferrara, N., Gerber, H.P., LeCouter, J. (2003). The biology of VEGF and its receptors, Nature Medicine, 9(6), 669-676. DOI:10.1038/nm0603-669
  • [9] Karipcin, F., Arabali, F., Karatas, I. (2006). Synthesis and characterization of 4-(alkylaminoisonitrosoacetyl) biphenyls and their complexes. Russian Journal of Coordination Chemistry, 32(2), 109-115. DOI:10.1134/S1070328406020059
  • [10] Karipcin, F., Dede, B., Cengiz, M. (2010). Synthesis of (2-hydroxo-5-chlorophenylaminoisonitroso acetyl) phenyl ligands and their complexes: Spectral, thermal and solvent-extraction studies. Russian Journal of Inorganic Chemistry, 55(4), 530-540. DOI:10.1134/S0036023610040078
  • [11] Dede, B., Karipcin, F., Arabalı, F., Cengiz, M. (2010). Synthesis, structure, and solvent-extraction properties of tridentate oxime ligands and their cobalt (II), nickel (II), copper (II), zinc (II) complexes. Chemical Papers, 64(1), 25-33. DOI: 10.2478/s11696-009-0095-6
  • [12] Grosdidier, A., Vincent Z., Olivier M. (2011). Swissdock, A Protein-Small Molecule Docking Web Service Based on EADock DSS. Nucleic Acids Res, 39(2), 270-277. DOI: 10.1093/nar/gkr366
  • [13] GaussView, Revision 5.0.9, R. Dennington, T. A. Keith, J. M. Millam, Semichem Inc., Shawnee Mission, KS, 2009.
  • [14] 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

Yıl 2023, Cilt: 9 Sayı: 2, 81 - 85, 30.06.2023

Güvenç Görgülü Bülent Dede

https://doi.org/10.22399/ijcesen.1147789

Öz

Kaynakça

  • [1] Kenakin, T. (2018). A Pharmacology Primer: Techniques for More Effective and Strategic Drug Discovery, 4th ed. San Diego, CA, Academic Press.
  • [2] Strømgaard K, Krogsgaard-Larsen P, Madsen U, (2017). Eds. Textbook of Drug Design and Discovery. CRC Press.
  • [3] Gorgulu, G., Cicek, M. B., Dede, B. (2018). Novel Aminoketooxime Ligand and Its Cu(II) and Mn(II) Complexes: Synthesis, Characterization and Molecular Docking Studies. Acta Physica Polonica A, 133(2), 250–255. DOI: 10.12693/APhysPolA.133.250
  • [4] Sliwoski, G., Kothiwale, S., Meiler, J., Lowe, E. W. (2014). Computational methods in drug discovery. Pharmacological Reviews, 66(1), 334-395. DOI:10.1124/pr.112.007336
  • [5] Tammela, T., Enholm, B., Alitalo, K., Paavonen, K. (2005). The biology of vascular endothelial growth factors, Cardiovascular Research, 65(3), 550–563. DOI:10.1016/j.cardiores.2004.12.002
  • [6] Wilkinson-Berka, J. L. (2004). Vasoactive factors and diabetic retinopathy: vascular endothelial growth factor, cycoloxygenase-2 and nitric oxide. Current Pharmaceutical Design, 10(27), 3331-3348. DOI:10.2174/1381612043383142
  • [7] Tuccillo, C., Romano, M., Troiani, T., Martinelli, E., Morgillo, F., De Vita, F., Bianco, R., Gabriella, F., Bianco, R.A., Tortora, G., Ciardiello, F. (2005). Antitumor activity of ZD6474, a vascular endothelial growth factor-2 and epidermal growth factor receptor small molecule tyrosine kinase inhibitor, in combination with SC-236, a cyclooxygenase-2 inhibitor. Clinical Cancer Research, 11(3), 1268-1276. DOI: 10.1158/1078-0432.1268.11.3
  • [8] Ferrara, N., Gerber, H.P., LeCouter, J. (2003). The biology of VEGF and its receptors, Nature Medicine, 9(6), 669-676. DOI:10.1038/nm0603-669
  • [9] Karipcin, F., Arabali, F., Karatas, I. (2006). Synthesis and characterization of 4-(alkylaminoisonitrosoacetyl) biphenyls and their complexes. Russian Journal of Coordination Chemistry, 32(2), 109-115. DOI:10.1134/S1070328406020059
  • [10] Karipcin, F., Dede, B., Cengiz, M. (2010). Synthesis of (2-hydroxo-5-chlorophenylaminoisonitroso acetyl) phenyl ligands and their complexes: Spectral, thermal and solvent-extraction studies. Russian Journal of Inorganic Chemistry, 55(4), 530-540. DOI:10.1134/S0036023610040078
  • [11] Dede, B., Karipcin, F., Arabalı, F., Cengiz, M. (2010). Synthesis, structure, and solvent-extraction properties of tridentate oxime ligands and their cobalt (II), nickel (II), copper (II), zinc (II) complexes. Chemical Papers, 64(1), 25-33. DOI: 10.2478/s11696-009-0095-6
  • [12] Grosdidier, A., Vincent Z., Olivier M. (2011). Swissdock, A Protein-Small Molecule Docking Web Service Based on EADock DSS. Nucleic Acids Res, 39(2), 270-277. DOI: 10.1093/nar/gkr366
  • [13] GaussView, Revision 5.0.9, R. Dennington, T. A. Keith, J. M. Millam, Semichem Inc., Shawnee Mission, KS, 2009.
  • [14] 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
Toplam 14 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Bölüm Araştırma Makalesi
Yazarlar

Güvenç Görgülü 0000-0003-4740-7265

Bülent Dede 0000-0003-1416-7373

Yayımlanma Tarihi 30 Haziran 2023
Gönderilme Tarihi 23 Temmuz 2022
Kabul Tarihi 7 Haziran 2023
Yayımlandığı Sayı Yıl 2023 Cilt: 9 Sayı: 2

Kaynak Göster

APA Görgülü, G., & Dede, B. (2023). Comparison of The Molecular Docking Properties of Three Potentially Active Agents. International Journal of Computational and Experimental Science and Engineering, 9(2), 81-85. https://doi.org/10.22399/ijcesen.1147789
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