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Antikanser Aktivite için Metallil Sübstitüe N-Heterosiklik Karben Tuzlarının Moleküler Doking ve DFT Analizi

Yıl 2021, Cilt 11, Sayı 2, 186 - 192, 31.12.2021
https://doi.org/10.54370/ordubtd.977478

Öz

Çalışmalar büyüme hormonlarının, birçok kanser türündeki kötü huylu hücre oluşumunu ve metastazı etkilediğini göstermektedir. Vasküler endotelyal büyüme hormonunun salınımı, vasküler endotelyal büyüme hormonu reseptörü tarafından düzenlenir. Bu nedenle, vasküler endotelyal büyüme hormonu reseptörünün inhibisyonu, kanserli hücrelerin ve metastaz oluşumunun engellenmesinde önemlidir. Kansere karşı savaşmak için çok sayıda yeni molekül sentezlenmektedir ve bunların antikanser aktiviteleri araştırılmaktadır. N-heterosiklik karben moleküllerinin ilk sentezinden bu yana birçok biyoaktivite çalışması yapılmış ve bir kısmı tedavi prosedürlerinde kullanılan ilaç haline gelmiştir. Moleküllerin biyoaktivitelerini incelemek için kullanılan yöntemlerin zorluğu ve maliyeti nedeniyle, olası aktif moleküllerin aktivitelerine ilişkin öngörüler değerlidir. Bu ön değerlendirmeleri in-siliko yöntemlerle yapmakta fayda vardır. Deneysel analiz sonuçlarının in-silico sonuçlarla karşılaştırılması, hesaplama yöntemlerinin geçerliliği hakkında bilgi sahibi olmak açısından önemlidir. Bu çalışmada, N-heterosiklik karben tip benzimidazolyum katyonları, vasküler endotelyal büyüme faktörü reseptörü-2, DFT / TDDFT hesaplama yöntemleri ve moleküler doking ile analiz edildi.

Kaynakça

  • Arduengo III, A. J., Harlow, R. L., & Kline, M. (1991). A stable crystalline carbene [Erratum to document cited in CA114 (7): 62009r]. Journal of the American Chemical Society, 113(7), 2801-2801. https://doi.org/10.1021/ja00007a092
  • Becke, A. D. (2014). Perspective: Fifty years of density-functional theory in chemical physics. The Journal of Chemical Physics, 140(18), 18A301. https://doi.org/10.1063/1.4869598
  • Bikadi, Z., & Hazai, E. (2009). Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock. Journal of Cheminformatics, 1(1), 1-16. https://doi.org/10.1186/1758-2946-1-15
  • Bisht, M., Dhasmana, D. C., & Bist, S. S. (2010). Angiogenesis: Future of pharmacological modulation. Indian Journal of Pharmacology, 42(1), 2. https://doi.org/10.4103/0253-7613.62395
  • Carmeliet, P. (2003). Angiogenesis in health and disease. Nature Medicine, 9(6), 653-660. https://doi.org/10.1038/nm0603-653
  • Choudhary, V., Bhatt, A., Dash, D., & Sharma, N. (2019). DFT calculations on molecular structures, HOMO–LUMO study, reactivity descriptors and spectral analyses of newly synthesized diorganotin (IV) 2‐chloridophenylacetohydroxamate complexes. Journal of Computational Chemistry, 40(27), 2354-2363. https://doi.org/10.1002/jcc.26012
  • De Ruyck, J., Brysbaert, G., Blossey, R., & Lensink, M. F. (2016). Molecular docking as a popular tool in drug design, an in-silico travel. Advances And Applications in Bioinformatics and Chemistry: AABC, 9, 1. https://doi.org/10.2147/AABC.S105289
  • Dewar, M. J. (1989). A critique of frontier orbital theory. Journal of Molecular Structure: THEOCHEM, 200, 301-323. https://doi.org/10.1016/0166-1280(89)85062-6
  • Ferreira, L. G., Dos Santos, R. N., Oliva, G., & Andricopulo, A. D. (2015). Molecular docking and structure-based drug design strategies. Molecules, 20(7), 13384-13421. https://doi.org/10.3390/molecules200713384
  • Gürbüz, N., Kaloğlu, N., Kızrak, Ü., Özdemir, İ., Türkmen, N. B., Çiftçi, O., ... Naceur, H. (2020). Silver (I) N-heterocyclic carbene complexes: Synthesis, characterization and cytotoxic properties. Journal of Organometallic Chemistry, 923, 121434. https://doi.org/10.1016/j.jorganchem.2020.121434
  • Haque, R. A., Choo, S. Y., Budagumpi, S., Iqbal, M. A., & Abdullah, A. A. A. (2015). Silver (I) complexes of mono-and bidentate N-heterocyclic carbene ligands: synthesis, crystal structures, and in vitro antibacterial and anticancer studies. European Journal of Medicinal Chemistry, 90, 82-92. https://doi.org/10.1016/j.ejmech.2014.11.005
  • Jahnke, M. C., & Hahn, F. E. (2016). Introduction to N-heterocyclic carbenes: Synthesis and stereoelectronic parameters. In Silvia Diez-Gonzalez (ed.), Laboratory Curiosities to Efficient Synthetic Tools (pp. 1-45). https://doi.org/10.1039/9781782626817-00001
  • Jaque, P., & Toro-Labbé, A. (2002). Characterization of copper clusters through the use of density functional theory reactivity descriptors. The Journal of Chemical Physics, 117(7), 3208-3218. https://doi.org/10.1063/1.1493178
  • Karkkainen, M. J., & Petrova, T. V. (2000). Vascular endothelial growth factor receptors in the regulation of angiogenesis and lymphangiogenesis. Oncogene, 19(49), 5598-5605. https://doi.org/10.1038/sj.onc.1203855
  • Kohn, W., Becke, A. D., & Parr, R. G. (1996). Density functional theory of electronic structure. The Journal of Physical Chemistry, 100(31), 12974-12980. https://doi.org/10.1021/jp960669l
  • Mayor, S. (2015). Side-effects of cancer drugs are under-reported in trials. The Lancet Oncology, 16(3), 107. https://doi.org/10.1016/S1470-2045(15)70023-9
  • Morell, C., Grand, A., & Toro-Labbe, A. (2005). New dual descriptor for chemical reactivity. The Journal of Physical Chemistry A, 109(1), 205-212. https://doi.org/10.1021/jp046577a
  • Morris, G. M., & Lim-Wilby, M. (2008). Molecular docking. In Molecular modeling of proteins (pp. 365-382). Humana Press. https://doi.org/10.1007/978-1-59745-177-2_19
  • Neese, F. (2006). A critical evaluation of DFT, including time-dependent DFT, applied to bioinorganic chemistry. JBIC Journal of Biological Inorganic Chemistry, 11(6), 702-711. https://doi.org/10.1007/s00775-006-0138-1
  • Neese, F. (2009). Prediction of molecular properties and molecular spectroscopy with density functional theory: From fundamental theory to exchange-coupling. Coordination Chemistry Reviews, 253(5-6), 526-563. https://doi.org/10.1016/j.ccr.2008.05.014
  • Neese, F. (2012). The ORCA program system. WIREs Comput Mol Sci, 2, 73–78. https://doi.org/10.1002/wcms.81
  • Öfele, K. (1968). 1, 3-Dimethyl-4-imidazolinyliden-(2)-pentacarbonylchrom ein neuer Übergangsmetall-carben-komplex. Journal of Organometallic Chemistry, 12(3), 42-43.
  • Şahin, N., Şahin-Bölükbaşı, S., & Marşan, H. (2019). Synthesis and antitumor activity of new silver (I)-N-heterocyclic carbene complexes. Journal of Coordination Chemistry, 72(22-24), 3602-3613. https://doi.org/10.1080/00958972.2019.1697808
  • Sajjadi, M., Nasrollahzadeh, M., & Tahsili, M. R. (2019). Catalytic and antimicrobial activities of magnetic nanoparticles supported N-heterocyclic palladium (II) complex: A magnetically recyclable catalyst for the treatment of environmental contaminants in aqueous media. Separation and Purification Technology, 227, 115716. https://doi.org/10.1016/j.seppur.2019.115716
  • Sayin, K., Karakaş, D., Karakuş, N., Sayin, T. A., Zaim, Z., & Kariper, S. E. (2015). Spectroscopic investigation, FMOs and NLO analyses of Zn (II) and Ni (II) phenanthroline complexes: A DFT approach. Polyhedron, 90, 139-146. https://doi.org/10.1016/j.poly.2015.01.047
  • Shah, A. A., Kamal, M. A., & Akhtar, S. (2021). Tumor angiogenesis and VEGFR-2: Mechanism, pathways and current biological therapeutic interventions. Current Drug Metabolism, 22(1), 50-59. https://doi.org/10.2174/1389200221666201019143252
  • Sharif Siam, M. K., Sarker, A., & Sayeem, M. M. S. (2020). In silico drug design and molecular docking studies targeting Akt1 (RAC-alpha serine/threonine-protein kinase) and Akt2 (RAC-beta serine/threonine-protein kinase) proteins and investigation of CYP (cytochrome P450) inhibitors against MAOB (monoamine oxidase B) for OSCC (oral squamous cell carcinoma) treatment. Journal of Biomolecular Structure and Dynamics, 1-13. https://doi.org/10.1080/07391102.2020.1802335
  • Slimani, I., Mansour, L., Özdemir, I., Gürbüz, N., & Hamdi, N. (2021). Synthesis, characterization and catalytic activity of PEPPSI-type palladium–NHC complexes. Inorganica Chimica Acta, 515, 120043. https://doi.org/10.1016/j.ica.2020.120043
  • Suter, T. M., & Ewer, M. S. (2013). Cancer drugs and the heart: importance and management. European Heart Journal, 34(15), 1102-1111. https://doi.org/10.1093/eurheartj/ehs181
  • Tezer, N., & Karakus, N. (2009). Theoretical study on the ground state intramolecular proton transfer (IPT) and solvation effect in two Schiff bases formed by 2-aminopyridine with 2-hydroxy-1-naphthaldehyde and 2-hydroxy salicylaldehyde. Journal of Molecular Modeling, 15(3), 223-232. https://doi.org/10.1007/s00894-008-0397-6
  • Vijayan, V., Purushothaman, E., Arjunan, V., & Mohan, S. (2019). Quantum Chemical Investigations on the Structure, Bonding Orbitals, Frontier Molecular Orbitals and Reactivity Properties of Diphenylguanidine–Vulcanizing Accelerator. Chemical Science, 8(3), 318-330. https://doi.org/10.7598/cst2019.1575
  • Wanzlick, H. W., & Schönherr, H. J. (1968). Direct synthesis of a mercury salt‐carbene complex. Angewandte Chemie International Edition in English, 7(2), 141-142.
  • Wei, B. Q., Baase, W. A., Weaver, L. H., Matthews, B. W., & Shoichet, B. K. (2002). A model binding site for testing scoring functions in molecular docking. Journal of Molecular Biology, 322(2), 339-355. https://doi.org/10.1016/S0022-2836(02)00777-5

Molecular Docking and DFT Analysis of Methallyl Substituted N-Heterocyclic Carbene Salts for Potential Anticancer Activity

Yıl 2021, Cilt 11, Sayı 2, 186 - 192, 31.12.2021
https://doi.org/10.54370/ordubtd.977478

Öz

The research recorded that growth hormones are effective in malignant cell formation and metastasis in many types of cancer. The release of vascular endothelial growth hormone has regulated by vascular endothelial growth hormone receptors. Therefore, inhibition of the vascular endothelial growth hormone receptor is important in hindering the formation of cancerous cells and metastasis. Many new molecules have been synthesized for fighting against cancer and their anticancer activity has been investigated. Since the first synthesis of N-heterocyclic carbene molecules, much bioactivities research has been performed and some of them have become drugs that are used in treatment procedures. Due to the difficulty and cost of the methods used to examine the bioactivities of molecules, foresight regarding the activities of possible active molecules is valuable. It is useful to make these preliminary evaluations in-silico methods. Comparing the results of the experimental analysis with the in-silico results is important in terms of having information about the validity of computational methods. In this study, N-heterocyclic carbene type benzimidazolium cations were analyzed with DFT/TDDFT computational methods and molecular docking for vascular endothelial growth factor receptor-2.

Kaynakça

  • Arduengo III, A. J., Harlow, R. L., & Kline, M. (1991). A stable crystalline carbene [Erratum to document cited in CA114 (7): 62009r]. Journal of the American Chemical Society, 113(7), 2801-2801. https://doi.org/10.1021/ja00007a092
  • Becke, A. D. (2014). Perspective: Fifty years of density-functional theory in chemical physics. The Journal of Chemical Physics, 140(18), 18A301. https://doi.org/10.1063/1.4869598
  • Bikadi, Z., & Hazai, E. (2009). Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock. Journal of Cheminformatics, 1(1), 1-16. https://doi.org/10.1186/1758-2946-1-15
  • Bisht, M., Dhasmana, D. C., & Bist, S. S. (2010). Angiogenesis: Future of pharmacological modulation. Indian Journal of Pharmacology, 42(1), 2. https://doi.org/10.4103/0253-7613.62395
  • Carmeliet, P. (2003). Angiogenesis in health and disease. Nature Medicine, 9(6), 653-660. https://doi.org/10.1038/nm0603-653
  • Choudhary, V., Bhatt, A., Dash, D., & Sharma, N. (2019). DFT calculations on molecular structures, HOMO–LUMO study, reactivity descriptors and spectral analyses of newly synthesized diorganotin (IV) 2‐chloridophenylacetohydroxamate complexes. Journal of Computational Chemistry, 40(27), 2354-2363. https://doi.org/10.1002/jcc.26012
  • De Ruyck, J., Brysbaert, G., Blossey, R., & Lensink, M. F. (2016). Molecular docking as a popular tool in drug design, an in-silico travel. Advances And Applications in Bioinformatics and Chemistry: AABC, 9, 1. https://doi.org/10.2147/AABC.S105289
  • Dewar, M. J. (1989). A critique of frontier orbital theory. Journal of Molecular Structure: THEOCHEM, 200, 301-323. https://doi.org/10.1016/0166-1280(89)85062-6
  • Ferreira, L. G., Dos Santos, R. N., Oliva, G., & Andricopulo, A. D. (2015). Molecular docking and structure-based drug design strategies. Molecules, 20(7), 13384-13421. https://doi.org/10.3390/molecules200713384
  • Gürbüz, N., Kaloğlu, N., Kızrak, Ü., Özdemir, İ., Türkmen, N. B., Çiftçi, O., ... Naceur, H. (2020). Silver (I) N-heterocyclic carbene complexes: Synthesis, characterization and cytotoxic properties. Journal of Organometallic Chemistry, 923, 121434. https://doi.org/10.1016/j.jorganchem.2020.121434
  • Haque, R. A., Choo, S. Y., Budagumpi, S., Iqbal, M. A., & Abdullah, A. A. A. (2015). Silver (I) complexes of mono-and bidentate N-heterocyclic carbene ligands: synthesis, crystal structures, and in vitro antibacterial and anticancer studies. European Journal of Medicinal Chemistry, 90, 82-92. https://doi.org/10.1016/j.ejmech.2014.11.005
  • Jahnke, M. C., & Hahn, F. E. (2016). Introduction to N-heterocyclic carbenes: Synthesis and stereoelectronic parameters. In Silvia Diez-Gonzalez (ed.), Laboratory Curiosities to Efficient Synthetic Tools (pp. 1-45). https://doi.org/10.1039/9781782626817-00001
  • Jaque, P., & Toro-Labbé, A. (2002). Characterization of copper clusters through the use of density functional theory reactivity descriptors. The Journal of Chemical Physics, 117(7), 3208-3218. https://doi.org/10.1063/1.1493178
  • Karkkainen, M. J., & Petrova, T. V. (2000). Vascular endothelial growth factor receptors in the regulation of angiogenesis and lymphangiogenesis. Oncogene, 19(49), 5598-5605. https://doi.org/10.1038/sj.onc.1203855
  • Kohn, W., Becke, A. D., & Parr, R. G. (1996). Density functional theory of electronic structure. The Journal of Physical Chemistry, 100(31), 12974-12980. https://doi.org/10.1021/jp960669l
  • Mayor, S. (2015). Side-effects of cancer drugs are under-reported in trials. The Lancet Oncology, 16(3), 107. https://doi.org/10.1016/S1470-2045(15)70023-9
  • Morell, C., Grand, A., & Toro-Labbe, A. (2005). New dual descriptor for chemical reactivity. The Journal of Physical Chemistry A, 109(1), 205-212. https://doi.org/10.1021/jp046577a
  • Morris, G. M., & Lim-Wilby, M. (2008). Molecular docking. In Molecular modeling of proteins (pp. 365-382). Humana Press. https://doi.org/10.1007/978-1-59745-177-2_19
  • Neese, F. (2006). A critical evaluation of DFT, including time-dependent DFT, applied to bioinorganic chemistry. JBIC Journal of Biological Inorganic Chemistry, 11(6), 702-711. https://doi.org/10.1007/s00775-006-0138-1
  • Neese, F. (2009). Prediction of molecular properties and molecular spectroscopy with density functional theory: From fundamental theory to exchange-coupling. Coordination Chemistry Reviews, 253(5-6), 526-563. https://doi.org/10.1016/j.ccr.2008.05.014
  • Neese, F. (2012). The ORCA program system. WIREs Comput Mol Sci, 2, 73–78. https://doi.org/10.1002/wcms.81
  • Öfele, K. (1968). 1, 3-Dimethyl-4-imidazolinyliden-(2)-pentacarbonylchrom ein neuer Übergangsmetall-carben-komplex. Journal of Organometallic Chemistry, 12(3), 42-43.
  • Şahin, N., Şahin-Bölükbaşı, S., & Marşan, H. (2019). Synthesis and antitumor activity of new silver (I)-N-heterocyclic carbene complexes. Journal of Coordination Chemistry, 72(22-24), 3602-3613. https://doi.org/10.1080/00958972.2019.1697808
  • Sajjadi, M., Nasrollahzadeh, M., & Tahsili, M. R. (2019). Catalytic and antimicrobial activities of magnetic nanoparticles supported N-heterocyclic palladium (II) complex: A magnetically recyclable catalyst for the treatment of environmental contaminants in aqueous media. Separation and Purification Technology, 227, 115716. https://doi.org/10.1016/j.seppur.2019.115716
  • Sayin, K., Karakaş, D., Karakuş, N., Sayin, T. A., Zaim, Z., & Kariper, S. E. (2015). Spectroscopic investigation, FMOs and NLO analyses of Zn (II) and Ni (II) phenanthroline complexes: A DFT approach. Polyhedron, 90, 139-146. https://doi.org/10.1016/j.poly.2015.01.047
  • Shah, A. A., Kamal, M. A., & Akhtar, S. (2021). Tumor angiogenesis and VEGFR-2: Mechanism, pathways and current biological therapeutic interventions. Current Drug Metabolism, 22(1), 50-59. https://doi.org/10.2174/1389200221666201019143252
  • Sharif Siam, M. K., Sarker, A., & Sayeem, M. M. S. (2020). In silico drug design and molecular docking studies targeting Akt1 (RAC-alpha serine/threonine-protein kinase) and Akt2 (RAC-beta serine/threonine-protein kinase) proteins and investigation of CYP (cytochrome P450) inhibitors against MAOB (monoamine oxidase B) for OSCC (oral squamous cell carcinoma) treatment. Journal of Biomolecular Structure and Dynamics, 1-13. https://doi.org/10.1080/07391102.2020.1802335
  • Slimani, I., Mansour, L., Özdemir, I., Gürbüz, N., & Hamdi, N. (2021). Synthesis, characterization and catalytic activity of PEPPSI-type palladium–NHC complexes. Inorganica Chimica Acta, 515, 120043. https://doi.org/10.1016/j.ica.2020.120043
  • Suter, T. M., & Ewer, M. S. (2013). Cancer drugs and the heart: importance and management. European Heart Journal, 34(15), 1102-1111. https://doi.org/10.1093/eurheartj/ehs181
  • Tezer, N., & Karakus, N. (2009). Theoretical study on the ground state intramolecular proton transfer (IPT) and solvation effect in two Schiff bases formed by 2-aminopyridine with 2-hydroxy-1-naphthaldehyde and 2-hydroxy salicylaldehyde. Journal of Molecular Modeling, 15(3), 223-232. https://doi.org/10.1007/s00894-008-0397-6
  • Vijayan, V., Purushothaman, E., Arjunan, V., & Mohan, S. (2019). Quantum Chemical Investigations on the Structure, Bonding Orbitals, Frontier Molecular Orbitals and Reactivity Properties of Diphenylguanidine–Vulcanizing Accelerator. Chemical Science, 8(3), 318-330. https://doi.org/10.7598/cst2019.1575
  • Wanzlick, H. W., & Schönherr, H. J. (1968). Direct synthesis of a mercury salt‐carbene complex. Angewandte Chemie International Edition in English, 7(2), 141-142.
  • Wei, B. Q., Baase, W. A., Weaver, L. H., Matthews, B. W., & Shoichet, B. K. (2002). A model binding site for testing scoring functions in molecular docking. Journal of Molecular Biology, 322(2), 339-355. https://doi.org/10.1016/S0022-2836(02)00777-5

Ayrıntılar

Birincil Dil İngilizce
Konular Mühendislik
Bölüm Araştırma Makaleleri
Yazarlar

Elvan ÜSTÜN
ORDU UNIVERSITY
0000-0002-0587-7261
Türkiye


Neslihan ŞAHİN (Sorumlu Yazar)
Cumhuriyet Üniversitesi
0000-0003-1498-4170
Türkiye

Yayımlanma Tarihi 31 Aralık 2021
Yayınlandığı Sayı Yıl 2021, Cilt 11, Sayı 2

Kaynak Göster

APA Üstün, E. & Şahin, N. (2021). Molecular Docking and DFT Analysis of Methallyl Substituted N-Heterocyclic Carbene Salts for Potential Anticancer Activity . Ordu Üniversitesi Bilim ve Teknoloji Dergisi , 11 (2) , 186-192 . DOI: 10.54370/ordubtd.977478