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Bazı Sülfonamid Bileşiklerinin Moleküler Yerleştirme Yöntemiyle Antibakteriyel Özelliklerinin Belirlenmesi

Yıl 2021, Cilt: 16 Sayı: 2, 458 - 467, 25.11.2021
https://doi.org/10.29233/sdufeffd.996484

Öz

Antibakteriyel çağı başlatan sülfonamid bileşiği olan Prontosil, ticari olarak temin edilebilen ilk antibakteriyel ajandır. Sülfonamid fonksiyonel grupları, antibakteriyel ilaçların ilk duyurulmasından bu yana tıbbi kimyada önem kazanmıştır. Sentetik sülfonamidler genel olarak biyolojik sistemlerdeki bakteriyel enfeksiyonların tedavisinde kullanıldığı gibi mantar önleyici, iltihap önleyici antioksidan, diüretikler, karbonik anhidrazlar, antitümör vb olarakta kullanılmaktadırlar. Çok çeşitli biyolojik uygulamaları nedeniyle biyoloji ve tıpta yüksek merak uyandırmıştır.
Bu çalışmada, daha önceki bir çalışmada sentezlenen sülfonamid türevi bileşiklerin potansiyel antibakteriyel özelliklerini araştırmak için moleküler yerleştirme çalışmaları uygulanmıştır. Kenetlenme olasılığı, moleküler yerleştirmeyi de gerçekleştiren Autodock 4.2 kodu ile analiz edildi. E. coli β-ketoasil-asil taşıyıcı protein sentaz III'ün (KAS III, PDB ID: 1HNJ) aktif bölgesindeki sülfonamid bileşiklerinin yerleştirme simülasyonları, olası bağlanma modellerini ve engelleyici etkileri belirlemek için gerçekleştirilmiştir. Yerleştirme sonuçları, ticari bir antibakteriyel madde olarak kullanılan triklosan ile de karşılaştırıldı. Moleküler yerleştirme sonuçlarını analiz etmek için Biovia Discovery Studio Visualizer 2020 ve Autodock 4.2 yazılımı kullanıldı.
Çalışmada kullanılan 3, 4, 5 ve 6 isimli sülfanamidlerin KAS III enzimine bağlanma enerjileri sırasıyla -6,94, -7,22, -7,76, -8,13 bulunmuştur. Moleküler docking çalışmasının sonucu bu sülfonamid türevlerinin potansiyel antibakteriyel özelliğe sahip olabileceğini göstermiştir.

Kaynakça

  • [1] J.E. Cronan Jr, C.O. “Rock, biosynthesis of membrane lipids, E. coli and Salmonella, Cellular and Molecular Biology,” ASM Press, Washington, DC, pp. 612-638, 1996.
  • [2] J.L. Garwin, A.L. Klages, J.E. Cronan Jr, “Structural, enzymatic, and genetic studies of β-ketoacyl-acyl carrier protein synthases I and II of Escherichia coli,” J. Biol. Chem., 255, pp. 11949-11956, 1980.
  • [3] Q. Meng, H. Liang, H. Gao. “Roles of multiple KAS III homologues of Shewanella oneidensis in initiation of fatty acid synthesis and in cerulenin resistance,” Biochimica et Biophysica Acta (BBA)-Molecular and Cell Biology of Lipids, 2018, 1863 (10), 1153-1163, 2018.
  • [4] J.Y. Lee, K.W. Jeong, J.U. Lee, D.I. Kang, Y. Kim, "Novel E. coli beta-ketoacyl-acyl carrier protein synthase III inhibitors as targeted antibiotic," Bioorg Med Chem., 17 (4), 1506-13, 2009.
  • [5] P. C. Lv, K.R. Wang, Y. Yang, W.J. Mao, J. Chen, J. Xiong, H.L. Zhu, "Design, synthesis and biological evaluation of novel thiazole derivatives as potent FabH inhibitors," Bioorg Med Chem Lett., 19 (23), 6750-4, 2009.
  • [6] P. C. Lv, J. Sun, Y. Luo, Y. Yang, H.L. Zhu, "Design, synthesis, and structure-activity relationships of pyrazole derivatives as potential FabH inhibitors." Bioorg Med Chem Lett., 20 (15), 4657-60, 2010.
  • [7] L. Shi, R.Q. Fang, Z.W. Zhu, Y. Yang, K. Cheng, W.Q. Zhong, H.L. Zhu, "Design and synthesis of potent inhibitors of beta-ketoacyl-acyl carrier protein synthase III (FabH) as potential antibacterial agents," Eur J Med Chem., 45 (9), 4358-64, 2010.
  • [8] H.Q. Li, Y. Luo, H.L. Zhu, "Discovery of vinylogous carbamates as a novel class of β-ketoacyl-acyl carrier protein synthase III (FabH) inhibitors," Bioorg Med Chem., 19 (15), 4454-9, 2011.
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  • [21] M. Durgun, H. Turkmen, M. Ceruso, C. T. Supuran, “Synthesis of 4-sulfamoylphenyl-benzylamine derivatives with inhibitory activity against human carbonic anhydrase isoforms I, II, IX and XII,” Bioorganic and Medicinal Chemistry, 24 (5), 982-988, 2016.
  • [22] M. Durgun, H. Turkmen, G. Zengin, H. Zengin, M. Koyunsever, I. Koyuncu, “Synthesis, characterization, in vitro cytotoxicity and antimicrobial investigation and evaluation of physicochemical properties of novel 4-(2-methylacetamite) benzenesulfonamite derivatives,” Bioorganic chemistry, 70, 163-172, 2017.
  • [23] M. Durgun, C. Türkeş, M. Işik, Y. Demir, A. Sakli, A. Kuru, A. Güzel, Ş. Beydemir, S. Akocak, S. M. Osman, Z. Alothman, C. T. Supuran, “Synthesis, characterisation, biological evaluation and in silico studies of sulphonamide Schiff base,” Journal of enzyme inhibition and medicinal chemistry, 35 (1), 950-962, 2020.
  • [24] I. Koyuncu, A. Gonel, M. Durgun, A. Kocyigit, O. Yuksekdag, C. T. Supuran, “Assessment of the antiproliferative and apoptotic roles of sulfonamite carbonic anhydrase IX inhibitors in HeLa cancer cell line,” Journal of enzyme inhibition and medicinal chemistry, 34 (1), 75-86, 2019.
  • [25] I. Koyuncu, A. Gonel, A. Kocyigit, E. Temiz, M. Durgun, C. T. Supuran, “Selective inhibition of carbonic anhydrase-IX by sulphonamite derivatives induces pH and reactive oxygen species-mediated apoptosis in cervical cancer HeLa cells,” Journal of enzyme inhibition and medicinal chemistry, 33 (1), 1137-1149, 2018.
  • [26] A. Kołaczek, I. Fusiarz, J. Ławecka, D. Branowska, “Biological activity and synthesis of sulfonamide derivatives: a brief review,” Chemik, 68 (7), 620-628, 2014.
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Determination of Antibacterial Properties of Some Sulfonamide Compounds by Molecular Docking

Yıl 2021, Cilt: 16 Sayı: 2, 458 - 467, 25.11.2021
https://doi.org/10.29233/sdufeffd.996484

Öz

Prontosil, the sulfonamide compound that started the antibacterial era, was the first commercially available antibacterial agent. Sulfonamide functional groups have gained importance in medicinal chemistry since the first announcement of antibacterial drugs. Synthetic sulfonamides are generally used for the treatment of bacterial infections in biological systems, as well as antifungal, anti-inflammatory antioxidant, diuretics, carbonic anhydrases, antitumor and so on. It has aroused high curiosity in biology and medicine due to its wide range of biological applications.
In this study, molecular docking studies were applied to investigate the potential antibacterial properties of sulfonamide derivative compounds synthesized in previous study. The binding energies was anaylzed by Autodock 4.2 code which also performed molecular docking. Docking simulations of sulfonamide compounds at the active site of E. coli β-ketoacyl-acyl carrier protein synthase III (KAS III, PDB ID: 1HNJ) were performed to determine possible binding patterns and inhibitory effects. Docking results were also compared with triclosan used as a commercial antibacterial agent. Biovia Discovery Studio Visualizer 2020 and Autodock 4.2 software were used to analyze results of molecular docking.
The binding energies of 3, 4, 5 and 6 sulfonamides used in the study to KAS III enzyme were found to be -6.94, -7.22, -7.76, -8.13, respectively. As a result of molecular docking study, these sulfonamide derivatives may have potential antibacterial properties.

Kaynakça

  • [1] J.E. Cronan Jr, C.O. “Rock, biosynthesis of membrane lipids, E. coli and Salmonella, Cellular and Molecular Biology,” ASM Press, Washington, DC, pp. 612-638, 1996.
  • [2] J.L. Garwin, A.L. Klages, J.E. Cronan Jr, “Structural, enzymatic, and genetic studies of β-ketoacyl-acyl carrier protein synthases I and II of Escherichia coli,” J. Biol. Chem., 255, pp. 11949-11956, 1980.
  • [3] Q. Meng, H. Liang, H. Gao. “Roles of multiple KAS III homologues of Shewanella oneidensis in initiation of fatty acid synthesis and in cerulenin resistance,” Biochimica et Biophysica Acta (BBA)-Molecular and Cell Biology of Lipids, 2018, 1863 (10), 1153-1163, 2018.
  • [4] J.Y. Lee, K.W. Jeong, J.U. Lee, D.I. Kang, Y. Kim, "Novel E. coli beta-ketoacyl-acyl carrier protein synthase III inhibitors as targeted antibiotic," Bioorg Med Chem., 17 (4), 1506-13, 2009.
  • [5] P. C. Lv, K.R. Wang, Y. Yang, W.J. Mao, J. Chen, J. Xiong, H.L. Zhu, "Design, synthesis and biological evaluation of novel thiazole derivatives as potent FabH inhibitors," Bioorg Med Chem Lett., 19 (23), 6750-4, 2009.
  • [6] P. C. Lv, J. Sun, Y. Luo, Y. Yang, H.L. Zhu, "Design, synthesis, and structure-activity relationships of pyrazole derivatives as potential FabH inhibitors." Bioorg Med Chem Lett., 20 (15), 4657-60, 2010.
  • [7] L. Shi, R.Q. Fang, Z.W. Zhu, Y. Yang, K. Cheng, W.Q. Zhong, H.L. Zhu, "Design and synthesis of potent inhibitors of beta-ketoacyl-acyl carrier protein synthase III (FabH) as potential antibacterial agents," Eur J Med Chem., 45 (9), 4358-64, 2010.
  • [8] H.Q. Li, Y. Luo, H.L. Zhu, "Discovery of vinylogous carbamates as a novel class of β-ketoacyl-acyl carrier protein synthase III (FabH) inhibitors," Bioorg Med Chem., 19 (15), 4454-9, 2011.
  • [9] H.J. Zhang, D.D. Zhu, Z.L. Li, J. Sun, H.L. Zhu, "Synthesis, molecular modeling and biological evaluation of β-ketoacyl-acyl carrier protein synthase III (FabH) as novel antibacterial agents," Bioorg Med Chem., 19 (15), 4513-9, 2011.
  • [10] K.S. Gajiwala, S. Margosiak, J. Lu, J. Cortez, Y. Su, Z. Nie, K. Appelt, "Crystal structures of bacterial FabH suggest a molecular basis for the substrate specificity of the enzyme, " FEBS Lett., 583 (17), 2939-46, 2009.
  • [11] M.M. Alhamadsheh, F. Musayev, A.A. Komissarov, S. Sachdeva, H.T. Wright, N. Scarsdale, G. Florova, K. A. Reynolds, "Alkyl-CoA disulfides as inhibitors and mechanistic probes for FabH enzymes," Chem Biol., 14 (5), 513-24, 2007.
  • [12] R.A. Daines, I. Pendrak, K. Sham, G.S. Van Aller, A.K. Konstantinidis, J.T. Lonsdale, C.A. Janson, X. Qiu, M. Brandt, S. S. Khandekar, C. Silverman, M.S. Head, "First X-ray cocrystal structure of a bacterial FabH condensing enzyme and a small molecule inhibitor achieved using rational design and homology modeling," J Med Chem., 46 (1), 5-8, 2003.
  • [13] C. Davies, R. J. Heath, S. W. White, C. O. Rock, "The 1.8 A crystal structure and active-site architecture of beta-ketoacyl-acyl carrier protein synthase III (FabH) from escherichia coli," Structure, 8 (2), 185-95, 2000.
  • [14] Y. Perez-Castillo, M. Froeyen, M.A. Cabrera-Perez, A. Nowe, "Molecular dynamics and docking simulations as a proof of high flexibility in E. coli FabH and its relevance for accurate inhibitor modeling," J Comput Aided Mol Des., 25 (4), 371-93, 2011.
  • [15] E. K. Schroeder, N. de Souza, D. S. Santos, J. S. Blanchard, L. A. Basso, "Drugs that inhibit mycolic acid biosynthesis in Mycobacterium tuberculosis," Curr Pharm Biotechnol., 3 (3), 197–225, 2002.
  • [16] S. J. Senior, P. A. Illarionov, S. S. Gurcha, I. B. Campbell, M. L. Schaeffer, D. E. Minnikin, G. S. Besra, “Biphenyl-based analogues of thiolactomycin, active against Mycobacterium tuberculosis mtFabH fatty acid condensing enzyme,” Bioorg. Med. Chem. Lett., 13 (21), 3685–8, 2003.
  • [17] X. He, A. M. Reeve, U. R. Desai, G. E. Kellogg, K. A. Reynolds, "1,2-Dithiole-3-Ones as Potent Inhibitors of the Bacterial 3-Ketoacyl Acyl Carrier Protein Synthase III (FabH)," Antimicrob. Agents Chemother, 48 (8), 3093–102, 2004.
  • [18] Q. Al-Balas, N. G. Anthony, B. Al-Jaidi, A. Alnimr, G. Abbott, A. K. Brown, R. C. Taylor, G. S. Besra, T. D. McHugh, S. H. Gillespie, B. F. Johnston, S. P. Mackay, G. D. Coxon, “Identification of 2-Aminothiazole-4-Carboxylate Derivatives Active against Mycobacterium tuberculosis H37Rv and the β-Ketoacyl-ACP Synthase mtFabH,”. Plos One, 4 (5), e5617, 2005.
  • [19] G. Domagk, "Ein Beitrag zur Chemotherapie der bakteriellen Infektionen," Deutsch. Med. WSCHR., 61 (7), 250, 1935.
  • [20] M. Durgun, H. Turkmen, M. Ceruso, C. T. Supuran, “Synthesis of Schiff base derivatives of 4-(2-aminoethyl)-benzenesulfonamite with inhibitory activity against carbonic anhydrase isoforms I, II, IX and XII,” Bioorganic and Medicinal Chemistry Letters, 25 (11), 2377-2381, 2015.
  • [21] M. Durgun, H. Turkmen, M. Ceruso, C. T. Supuran, “Synthesis of 4-sulfamoylphenyl-benzylamine derivatives with inhibitory activity against human carbonic anhydrase isoforms I, II, IX and XII,” Bioorganic and Medicinal Chemistry, 24 (5), 982-988, 2016.
  • [22] M. Durgun, H. Turkmen, G. Zengin, H. Zengin, M. Koyunsever, I. Koyuncu, “Synthesis, characterization, in vitro cytotoxicity and antimicrobial investigation and evaluation of physicochemical properties of novel 4-(2-methylacetamite) benzenesulfonamite derivatives,” Bioorganic chemistry, 70, 163-172, 2017.
  • [23] M. Durgun, C. Türkeş, M. Işik, Y. Demir, A. Sakli, A. Kuru, A. Güzel, Ş. Beydemir, S. Akocak, S. M. Osman, Z. Alothman, C. T. Supuran, “Synthesis, characterisation, biological evaluation and in silico studies of sulphonamide Schiff base,” Journal of enzyme inhibition and medicinal chemistry, 35 (1), 950-962, 2020.
  • [24] I. Koyuncu, A. Gonel, M. Durgun, A. Kocyigit, O. Yuksekdag, C. T. Supuran, “Assessment of the antiproliferative and apoptotic roles of sulfonamite carbonic anhydrase IX inhibitors in HeLa cancer cell line,” Journal of enzyme inhibition and medicinal chemistry, 34 (1), 75-86, 2019.
  • [25] I. Koyuncu, A. Gonel, A. Kocyigit, E. Temiz, M. Durgun, C. T. Supuran, “Selective inhibition of carbonic anhydrase-IX by sulphonamite derivatives induces pH and reactive oxygen species-mediated apoptosis in cervical cancer HeLa cells,” Journal of enzyme inhibition and medicinal chemistry, 33 (1), 1137-1149, 2018.
  • [26] A. Kołaczek, I. Fusiarz, J. Ławecka, D. Branowska, “Biological activity and synthesis of sulfonamide derivatives: a brief review,” Chemik, 68 (7), 620-628, 2014.
  • [27] D. A. Fedorovna, S. E. Georgievna, R. E. Nikolaevna, L.T. Mikhailovna, G. I. Urievna, “Supply Chain Of Promotion: From A New Substance To A Drug,” Methods and problems of practical application, 150, 2019.
  • [28] J. A. Read, V. J. Winter, C. M. Eszes, R. B. Sessions, R. L. Brady, "Structural basis for altered activity of M-and H-isozyme forms of human lactate dehydrogenase," Proteins: Structure, Function, and Bioinformatics, 43 (2), 175-185, 2011.
  • [29] E. Büyükfırat, M. Durgun, N. Yorulmaz, İ. Koyuncu, M. A. Karahan, A. Gonel, V. F. Pehlivan, “Interactions Between Sedative, Analgesic and Anaesthetic Drugs with SARS-CoV-2, ACE-2 and SARS-CoV-2- ACE-2 Complex," J Turk Soc Intens Care, DOI:10.4274/tybd.galenos.2021.69885
  • [30] İ. Koyuncu, M. Durgun, N. Yorulmaz, S. Toprak, A. Gonel, N. Bayraktar, M. Caglayan, “Molecular Docking Demonstration of the Liquorice Chemical Molecules on the Protease and ACE2 of COVID-19 Virus”, Current Enzyme Inhibition, 17 (2), 98-110, 2021.
  • [31] M. Işık, S. Akocak, N. Lolak, P. Taslimi, C. Türkeş, İ. Gülçin, M. Durgun, Ş. Beydemir, Ş, “Synthesis, characterization, biological evaluation, and in silico studies of novel 1,3-diaryltriazene-substituted sulfathiazole derivatives,” Archiv Der Pharmazie, 353 (9), p.2000102, 2020.
  • [32] S. Akocak, P. Taslimi, N. Lolak, M. Işık, M. Durgun, Y. Budak, C. Türkeş, İ. Gülçin, Ş. Beydemir, “Synthesis, Characterization, and Inhibition Study of Novel Substituted Phenylureido Sulfaguanidine Derivatives as α-Glycosidase and Cholinesterase Inhibitors,” Chemistry & Biodiversity, 18 (4), p.e2000958, 2021.
  • [33] M. Işık, Ş. Beydemir, Y. Demir, M. Durgun, C. Türkeş, A. Nasır, A. Necip, M. Akkuş, “Benzenesulfonamide derivatives containing imine and amine groups: Inhibition on human paraoxonase and molecular docking studies,” International journal of biological macromolecules, 146, 1111-1123, 2020.
  • [34] N. Yorulmaz, O. Oltulu, E. Eroğlu, “Development of selective QSAR models and molecular docking study for inhibitory activity of sulfonamide derivatives against carbonic anhydrase isoforms II and IX,” Journal of Molecular Structure, 1163, 270-9, 2018.
  • [35] M. D. Hanwell, D. E. Curtis, D. C. Lonie, T. Vandermeersch, E. Zurek, G. R. Hutchison, “Avogadro: an advanced semantic chemical editor, visualization, and analysis platform,” Journal of cheminformatics, 4 (1), 1-17, 2012.
  • [36] G. M. Morris, R. Huey, W. Lindstrom, M. F. Sanner, R. K. Belew, D. S. Goodsell, A. Olson, “AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility,” J Journal of Computational Chemistry, 30 (16), 2785-91, 2009.
  • [37] R. Huey, G. M. Morris, S. Forli, “Using AutoDock 4 and AutoDock Vina with AutoDockTools: A Tutorial,” The Scripps Research Institute Molecular Graphics Laboratory, 2012.
  • [38] K. Cheng, Q. Z. Zheng, Y. Qian, L. Shi, J. Zhao, H. L. Zhu, “Synthesis, antibacterial activities and molecular docking studies of peptide and Schiff bases as targeted antibiotics,” Bioorganic & medicinal chemistry, 17 (23), 7861-7871, 2009.
  • [39] Ç. K. Atay, T. Tilki, D. E. Bülent, "Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method,” Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi, 14 (1), 150-154, 2019.
  • [40] P. Ramesh, V. Srinivasa Rao, Y. A. Hong, P. M. Reddy, A. Hu, “Molecular design, synthesis, and biological evaluation of 2-hydroxy-3-chrysino dithiocarbamate derivatives,” Molecules, 24 (17), 3038, 2019.
Toplam 40 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Konular Metroloji,Uygulamalı ve Endüstriyel Fizik, Kimya Mühendisliği
Bölüm Makaleler
Yazarlar

Hilal Öztürk 0000-0003-0079-5184

Nuri Yorulmaz 0000-0003-4959-2302

Mustafa Durgun 0000-0003-3012-7582

Zeynep Turhan İrak 0000-0002-3587-2576

İsmail Hakkı Sarpün 0000-0002-9788-699X

Yayımlanma Tarihi 25 Kasım 2021
Yayımlandığı Sayı Yıl 2021 Cilt: 16 Sayı: 2

Kaynak Göster

IEEE H. Öztürk, N. Yorulmaz, M. Durgun, Z. Turhan İrak, ve İ. H. Sarpün, “Determination of Antibacterial Properties of Some Sulfonamide Compounds by Molecular Docking”, Süleyman Demirel University Faculty of Arts and Science Journal of Science, c. 16, sy. 2, ss. 458–467, 2021, doi: 10.29233/sdufeffd.996484.