Araştırma Makalesi
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(Z)-3-((1-(5-amino-1,3,4-tiadiazol-2-il)-2-feniletil)imino)-5-nitroindolin-2-on Schiff Bazının DFT Hesaplamaları ADME ve Moleküler Doking ile Antimikrobiyal ve Antitüberküloz Değerlendirmesi

Yıl 2024, Cilt: 14 Sayı: 4, 1694 - 1708, 15.12.2024
https://doi.org/10.31466/kfbd.1423367

Öz

(Z)-3-((1-(5-Amino-1,3,4-Thiadiazol-2-il)-2-Feniletil)İmino)-5-nitroindolin-2-one Schiff Bazı bileşiği (ATSB) son zamanlarda popülerlik kazandığından bu bileşiklerin araştırılması gerektiği kavramı ön plana çıkmıştır. Eşsiz bir Schiff bazı kompleksi olan ATSB molekülü, literatürde yayınlanmak üzere moleküler modelleme araştırması için seçildi. İlk olarak ATSB molekülü üzerinde yoğunluk fonksiyonel teorisi (DFT) hesaplamaları (geometri optimizasyonu, HOMOLUMO, MEPS haritaları, dipol moment hesaplamaları, NBO analizi ve Mulliken atom yükleri) yapıldı. Aynı zamanda ATSB molekülü için ADME analizleri yapılmış olup, renk bölgeleri ayrı ayrı verilmiştir. Schiff bazlarının antibakteriyel ve antitüberküloz ilaç hastalıkları ve ilaç onarımında önemli bir role sahip olduğu gösterilmiştir. Son olarak araştırmamızda ATSB molekülü için ayrı ayrı iki farklı enzim (5V3X and 5V3Y) ile moleküler kenetlenme analizleri yapıldı ve kenetlenme skorları ve reseptör modelleri verildi.

Kaynakça

  • Bagayoko, D. (2014). Understanding density functional theory (DFT) and completing it in practice. AIP Advances, 4(12).
  • Bağlan, M., Gören, K., & Çakmak, İ. (2022). Theoretical Investigation of 1H and 13C NMR Spectra of Diethanol Amine Dithiocarbamate RAFT Agent [Dietanol Amin Ditiyokarbamat RAFT Ajanının 1H ve 13C NMR Spektrumlarının Teorik İncelenmesi]. Journal of the Institute of Science and Technology, 12(3), 1677-1689.
  • Bağlan, M., Gören, K., & Yildiko, Ü. (2023a). DFT Computations and Molecular Docking Studies of 3-(6-(3-aminophenyl)thiazolo[1,2,4]triazol-2-yl)-2H-chromen-2-one(ATTC) Molecule. Hittite Journal of Science and Engineering, 10(1), 11-19.
  • Bağlan, M., Gören, K., & Yildiko, Ü. (2023b). HOMO–LUMO, NBO, NLO, MEP analysis and molecular docking using DFT calculations in DFPA molecule. International Journal of Chemistry and Technology, 7(1), 38-47.
  • Bağlan, M., Yildiko, Ü., & Gören, K. (2022). Computational Investigation of trihydroxy-3,7-dimethoxy;-O-biflavone from Flavonoids Using DFT Calculations and Molecular Docking. Adıyaman University Journal of Science, 12(2), 283-298.
  • Bağlan, M., Yildiko, Ü., & Gören, K. (2023). DFT Calculatıons and Molecular Dockıng Study in 6-(2”-Pyrrolıdınone-5”-Yl)-(-) Epıcatechın Molecule from Flavonoıds [Flavonoİdlerden 6-(2”-pyrolİdİnone-5”-yl)-(-)epİcatechİn molekÜlÜnde dft hesaplamalari ve molekÜler yerleŞtİrme ÇaliŞmasi]. Eskişehir Teknik Üniversitesi Bilim ve Teknoloji Dergisi B - Teorik Bilimler, 11(1), 43-55.
  • Bhuiyan, M. D. H., Ashraf, M., Teshome, A., Gainsford, G. J., Kay, A. J., Asselberghs, I., & Clays, K. (2011). Synthesis, linear & non linear optical (NLO) properties of some indoline based chromophores. Dyes and Pigments, 89(2), 177-187.
  • Cordes, E. H., & Jencks, W. P. (1962). On the Mechanism of Schiff Base Formation and Hydrolysis. Journal of the American Chemical Society, 84(5), 832-837.
  • da Silva, C. M., da Silva, D. L., Modolo, L. V., Alves, R. B., de Resende, M. A., Martins, C. V. B., & de Fátima, Â. (2011). Schiff bases: A short review of their antimicrobial activities. Journal of Advanced Research, 2(1), 1-8.
  • Demir, P., & Akman, F. (2017). Molecular structure, spectroscopic characterization, HOMO and LUMO analysis of PU and PCL grafted onto PEMA-co-PHEMA with DFT quantum chemical calculations. Journal of Molecular Structure, 1134, 404-415.
  • Ekins, S., Bugrim, A., Brovold, L., Kirillov, E., Nikolsky, Y., Rakhmatulin, E., Sorokina, S., Ryabov, A., Serebryiskaya, T., Melnikov, A., Metz, J., & Nikolskaya, T. (2006). Algorithms for network analysis in systems-ADME/Tox using the MetaCore and MetaDrug platforms. Xenobiotica, 36(10-11), 877-901.
  • Glendening, E. D., Landis, C. R., & Weinhold, F. (2013). NBO 6.0: Natural bond orbital analysis program. Journal of Computational Chemistry, 34(16), 1429-1437.
  • Hodnett, E. M., & Dunn, W. J. (1970). Structure-antitumor activity correlation of some Schiff bases. Journal of Medicinal Chemistry, 13(4), 768-770.
  • Jakhar, R., Dangi, M., Khichi, A., & Chhillar, A. K. (2020). Relevance of Molecular Docking Studies in Drug Designing. Current Bioinformatics, 15(4), 270-278.
  • Kassel, D. B. (2004). Applications of high-throughput ADME in drug discovery. Current Opinion in Chemical Biology, 8(3), 339-345.
  • Kurt, M., Babu, P. C., Sundaraganesan, N., Cinar, M., & Karabacak, M. (2011). Molecular structure, vibrational, UV and NBO analysis of 4-chloro-7-nitrobenzofurazan by DFT calculations. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 79(5), 1162-1170.
  • Lakshminarayanan, S., Jeyasingh, V., Murugesan, K., Selvapalam, N., & Dass, G. (2021). Molecular electrostatic potential (MEP) surface analysis of chemo sensors: An extra supporting hand for strength, selectivity & non-traditional interactions. Journal of Photochemistry and Photobiology, 6, 100022.
  • Metzler, C. M., Cahill, A., & Metzler, D. E. (1980). Equilibriums and absorption spectra of Schiff bases. Journal of the American Chemical Society, 102(19), 6075-6082.
  • Michael J. Frisch, T., G.W, Bernhard Schlegel, Gustavo Scuseria. (2016). (Version In Revision E.01 ) Morris, G. M., & Lim-Wilby, M. (2008). Molecular Docking. In A. Kukol (Ed.), Molecular Modeling of Proteins (pp. 365-382). Humana Press. https://doi.org/10.1007/978-1-59745-177-2_19
  • Prasad, S. R., Satyanarayan, N. D., Shetty, A. S. K., & Thippeswamy, B. (2022). Synthesis, antimicrobial, and antitubercular evaluation of new Schiff bases with in silico ADME and molecular docking studies. European Journal of Chemistry, 13(1), 109-116.
  • Rodney, D., Ventelon, L., Clouet, E., Pizzagalli, L., & Willaime, F. (2017). Ab initio modeling of dislocation core properties in metals and semiconductors. Acta Materialia, 124, 633-659.
  • Suhasini, M., Sailatha, E., Gunasekaran, S., & Ramkumaar, G. R. (2015). Vibrational and electronic investigations, thermodynamic parameters, HOMO and LUMO analysis on Lornoxicam by density functional theory. Journal of Molecular Structure, 1100, 116-128.
  • Taylor, J., Guo, H., & Wang, J. (2001). Ab initio modeling of open systems: Charge transfer, electron conduction, and molecular switching of a ${\mathrm{C}}_{60}$ device. Physical Review B, 63(12), 121104.
  • Wang, Z., Zhang, W., & Liu, B. (2021). Computational Analysis of Synthetic Planning: Past and Future. Chinese Journal of Chemistry, 39(11), 3127-3143.
  • Weinhold, F., Landis, C. R., & Glendening, E. D. (2016). What is NBO analysis and how is it useful? International Reviews in Physical Chemistry, 35(3), 399-440.
  • Yildiko, Ü., Türkan, F., Tanriverdi, A. A., Ata, A. C., Atalar, M. N., & Cakmak, İ. (2021). Synthesis, enzymes inhibitory properties and characterization of 2- (bis (4-aminophenyl) methyl) butan-1-ol compound: Quantum simulations, and in-silico molecular docking studies. Journal of the Indian Chemical Society, 98(11), 100206.

Antimicrobial, and Antitubercular Evaluation with ADME and Molecular Docking Studies and DFT Calculatıons of (Z)-3-((1-(5-amino-1,3,4-thiadiazol-2-yl)-2-Phenylethyl)imino)-5-nitroindolin-2-one Schiff Base

Yıl 2024, Cilt: 14 Sayı: 4, 1694 - 1708, 15.12.2024
https://doi.org/10.31466/kfbd.1423367

Öz

(Z)-3-((1-(5-Amino-1,3,4-Thiadiazol-2-yl)-2-Phenylethyl)İmino)-5-nitroindolin-2-one Schiff Base compound (ATSB) have lately gained popularity, so the concept that these compounds should be researched has been highlighted. ATSB molecule, a unique Schiff base complex, was selected for molecular modeling research for publication in the literature. Initially, dependent density functional theory (DFT) computations were performed on ATSB molecule (geometry optimization, HOMO-LUMO, MEPS maps, dipole moment calculations, NBO analysis, and Mulliken Atomic Charges). Additionally, ADME analyzes have been carried out for the ATSB molecule and the color regions are given separately. Schiff bases have been shown to have an important role in antibacterial and antituberculosis medication illness and drug repair. Finally, in our investigation, molecular docking analysis ments were performed individually for ATSB molecule with two distinct enzymes (5V3X and 5V3Y), docking scores and receptor models have been given.

Kaynakça

  • Bagayoko, D. (2014). Understanding density functional theory (DFT) and completing it in practice. AIP Advances, 4(12).
  • Bağlan, M., Gören, K., & Çakmak, İ. (2022). Theoretical Investigation of 1H and 13C NMR Spectra of Diethanol Amine Dithiocarbamate RAFT Agent [Dietanol Amin Ditiyokarbamat RAFT Ajanının 1H ve 13C NMR Spektrumlarının Teorik İncelenmesi]. Journal of the Institute of Science and Technology, 12(3), 1677-1689.
  • Bağlan, M., Gören, K., & Yildiko, Ü. (2023a). DFT Computations and Molecular Docking Studies of 3-(6-(3-aminophenyl)thiazolo[1,2,4]triazol-2-yl)-2H-chromen-2-one(ATTC) Molecule. Hittite Journal of Science and Engineering, 10(1), 11-19.
  • Bağlan, M., Gören, K., & Yildiko, Ü. (2023b). HOMO–LUMO, NBO, NLO, MEP analysis and molecular docking using DFT calculations in DFPA molecule. International Journal of Chemistry and Technology, 7(1), 38-47.
  • Bağlan, M., Yildiko, Ü., & Gören, K. (2022). Computational Investigation of trihydroxy-3,7-dimethoxy;-O-biflavone from Flavonoids Using DFT Calculations and Molecular Docking. Adıyaman University Journal of Science, 12(2), 283-298.
  • Bağlan, M., Yildiko, Ü., & Gören, K. (2023). DFT Calculatıons and Molecular Dockıng Study in 6-(2”-Pyrrolıdınone-5”-Yl)-(-) Epıcatechın Molecule from Flavonoıds [Flavonoİdlerden 6-(2”-pyrolİdİnone-5”-yl)-(-)epİcatechİn molekÜlÜnde dft hesaplamalari ve molekÜler yerleŞtİrme ÇaliŞmasi]. Eskişehir Teknik Üniversitesi Bilim ve Teknoloji Dergisi B - Teorik Bilimler, 11(1), 43-55.
  • Bhuiyan, M. D. H., Ashraf, M., Teshome, A., Gainsford, G. J., Kay, A. J., Asselberghs, I., & Clays, K. (2011). Synthesis, linear & non linear optical (NLO) properties of some indoline based chromophores. Dyes and Pigments, 89(2), 177-187.
  • Cordes, E. H., & Jencks, W. P. (1962). On the Mechanism of Schiff Base Formation and Hydrolysis. Journal of the American Chemical Society, 84(5), 832-837.
  • da Silva, C. M., da Silva, D. L., Modolo, L. V., Alves, R. B., de Resende, M. A., Martins, C. V. B., & de Fátima, Â. (2011). Schiff bases: A short review of their antimicrobial activities. Journal of Advanced Research, 2(1), 1-8.
  • Demir, P., & Akman, F. (2017). Molecular structure, spectroscopic characterization, HOMO and LUMO analysis of PU and PCL grafted onto PEMA-co-PHEMA with DFT quantum chemical calculations. Journal of Molecular Structure, 1134, 404-415.
  • Ekins, S., Bugrim, A., Brovold, L., Kirillov, E., Nikolsky, Y., Rakhmatulin, E., Sorokina, S., Ryabov, A., Serebryiskaya, T., Melnikov, A., Metz, J., & Nikolskaya, T. (2006). Algorithms for network analysis in systems-ADME/Tox using the MetaCore and MetaDrug platforms. Xenobiotica, 36(10-11), 877-901.
  • Glendening, E. D., Landis, C. R., & Weinhold, F. (2013). NBO 6.0: Natural bond orbital analysis program. Journal of Computational Chemistry, 34(16), 1429-1437.
  • Hodnett, E. M., & Dunn, W. J. (1970). Structure-antitumor activity correlation of some Schiff bases. Journal of Medicinal Chemistry, 13(4), 768-770.
  • Jakhar, R., Dangi, M., Khichi, A., & Chhillar, A. K. (2020). Relevance of Molecular Docking Studies in Drug Designing. Current Bioinformatics, 15(4), 270-278.
  • Kassel, D. B. (2004). Applications of high-throughput ADME in drug discovery. Current Opinion in Chemical Biology, 8(3), 339-345.
  • Kurt, M., Babu, P. C., Sundaraganesan, N., Cinar, M., & Karabacak, M. (2011). Molecular structure, vibrational, UV and NBO analysis of 4-chloro-7-nitrobenzofurazan by DFT calculations. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 79(5), 1162-1170.
  • Lakshminarayanan, S., Jeyasingh, V., Murugesan, K., Selvapalam, N., & Dass, G. (2021). Molecular electrostatic potential (MEP) surface analysis of chemo sensors: An extra supporting hand for strength, selectivity & non-traditional interactions. Journal of Photochemistry and Photobiology, 6, 100022.
  • Metzler, C. M., Cahill, A., & Metzler, D. E. (1980). Equilibriums and absorption spectra of Schiff bases. Journal of the American Chemical Society, 102(19), 6075-6082.
  • Michael J. Frisch, T., G.W, Bernhard Schlegel, Gustavo Scuseria. (2016). (Version In Revision E.01 ) Morris, G. M., & Lim-Wilby, M. (2008). Molecular Docking. In A. Kukol (Ed.), Molecular Modeling of Proteins (pp. 365-382). Humana Press. https://doi.org/10.1007/978-1-59745-177-2_19
  • Prasad, S. R., Satyanarayan, N. D., Shetty, A. S. K., & Thippeswamy, B. (2022). Synthesis, antimicrobial, and antitubercular evaluation of new Schiff bases with in silico ADME and molecular docking studies. European Journal of Chemistry, 13(1), 109-116.
  • Rodney, D., Ventelon, L., Clouet, E., Pizzagalli, L., & Willaime, F. (2017). Ab initio modeling of dislocation core properties in metals and semiconductors. Acta Materialia, 124, 633-659.
  • Suhasini, M., Sailatha, E., Gunasekaran, S., & Ramkumaar, G. R. (2015). Vibrational and electronic investigations, thermodynamic parameters, HOMO and LUMO analysis on Lornoxicam by density functional theory. Journal of Molecular Structure, 1100, 116-128.
  • Taylor, J., Guo, H., & Wang, J. (2001). Ab initio modeling of open systems: Charge transfer, electron conduction, and molecular switching of a ${\mathrm{C}}_{60}$ device. Physical Review B, 63(12), 121104.
  • Wang, Z., Zhang, W., & Liu, B. (2021). Computational Analysis of Synthetic Planning: Past and Future. Chinese Journal of Chemistry, 39(11), 3127-3143.
  • Weinhold, F., Landis, C. R., & Glendening, E. D. (2016). What is NBO analysis and how is it useful? International Reviews in Physical Chemistry, 35(3), 399-440.
  • Yildiko, Ü., Türkan, F., Tanriverdi, A. A., Ata, A. C., Atalar, M. N., & Cakmak, İ. (2021). Synthesis, enzymes inhibitory properties and characterization of 2- (bis (4-aminophenyl) methyl) butan-1-ol compound: Quantum simulations, and in-silico molecular docking studies. Journal of the Indian Chemical Society, 98(11), 100206.
Toplam 26 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Konular Fiziksel Kimya (Diğer)
Bölüm Makaleler
Yazarlar

Kenan Gören 0000-0001-5068-1762

Mehmet Bağlan 0000-0002-7089-7111

Ümit Yıldıko 0000-0001-8627-9038

Yayımlanma Tarihi 15 Aralık 2024
Gönderilme Tarihi 21 Ocak 2024
Kabul Tarihi 19 Ekim 2024
Yayımlandığı Sayı Yıl 2024 Cilt: 14 Sayı: 4

Kaynak Göster

APA Gören, K., Bağlan, M., & Yıldıko, Ü. (2024). Antimicrobial, and Antitubercular Evaluation with ADME and Molecular Docking Studies and DFT Calculatıons of (Z)-3-((1-(5-amino-1,3,4-thiadiazol-2-yl)-2-Phenylethyl)imino)-5-nitroindolin-2-one Schiff Base. Karadeniz Fen Bilimleri Dergisi, 14(4), 1694-1708. https://doi.org/10.31466/kfbd.1423367