1. DergiPark
  2. Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi
  3. Arşiv
  4. Cilt 14, Sayı 1
Yıl 2019, Cilt 14 , Sayı 1, Sayfalar 150 - 154 2019-05-31

Moleküler Docking Yöntemi ile Bazı Azo Bileşiklerinin Potansiyel Antibakteriyel Özelliklerinin İncelenmesi
Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method

Çiğdem KARABACAK ATAY [1] , Tahir TİLKİ [2] , Bülent DEDE [3]

Öz

Bu çalışmada, önceki çalışmalarımızda sentezlediğimiz  üç azo boyarmaddenin, 2 - [(3,5-diamino-1H-pirazol-4-il)diazenil]-5-nitrobenzoik asit (A), 2-[(3,5)-dimetil-1H-pirazol-4-il) diazenil]-5-nitrobenzoik asit (B) ve 2-[(5-amino-3-metil-1H-pirazol-4-il) diazenil]-5-nitrobenzoik asit (C), potansiyel antibakteriyel özelliklerini araştırmak için moleküler doking çalışmaları yapıldı. Modelleme, SwissDock web sunucusunda EADock DSS algoritması kullanılarak gerçekleştirildi. Olası bağlanma konformasyonları ve inhibe edici etkileri belirlemek için E. coli beta-ketoaçil-açil taşıyıcı protein sentaz III (KAS III) aktif bölgesine ligandların (A, B ve C) bağlanma simülasyonları yapıldı. Doking sonuçları ayrıca ticari bir antibakteriyel madde olarak kullanılan triklosan ile karşılaştırıldı ve B bileşiğinin en iyi antibakteriyel özelliğe sahip olduğu bulundu.

In this study, molecular docking studies were applied to three azo dyes, 2-[(3,5-diamino-1H-pyrazol-4-yl)diazenyl]-5-nitrobenzoic acid (A), 2-[(3,5-dimethyl-1H-pyrazol-4-yl)diazenyl]-5-nitrobenzoic acid (B) and 2-[(5-amino-3-methyl-1H-pyrazol-4-yl)diazenyl]-5-nitrobenzoic acid (C), which synthesized in our previous studies, to investigate their potential antibacterial properties. Modelling was performed on SwissDock web server using EADock DSS algorithm. Docking simulations of ligands (A, B and C) were performed into the E. coli beta-ketoacyl-acyl carrier protein synthase III (KAS III) active site to determine the probable binding conformations and inhibitory effects. Docking results were also compared with triclosan used as a commercial antibacterial agent and it was found that compound B had the best antibacterial property.

Kaynakça

  • J. Lee, S. Kim, J. Sim, D. Lee, H. H. Kim, J. S. Hwang, D. G. Lee, Z. Y. Park, and J. I. Kim, “A potent antibacterial activity of new short D-enantiomeric lipopeptide against multi drug resistant bacteria,” Biochim Biophys Acta Biomembr., 1861, 34-42, 2019.
  • S. Tahir, T. Mahmood, F. Dastgir, I. Haq, A. Waseem, and U. Rashid, “Design, synthesis and anti-bacterial studies of piperazine derivatives against drug resistant bacteria,” Eur J Med Chem., 166, 224-231, 2019.
  • M. Caniçaa, V. Manageiro, H. Abriouel, J. Moran-Giladd, and C.M.A.P. Franzg, “Antibiotic resistance in foodborne bacteria,” Trends Food Sci. Technol., 84, 41-44, 2019.
  • I.J. Schalk, “Siderophoreeantibiotic conjugates: exploiting iron uptake to deliver drugs into bacteria,” Clin. Microbiol. Infect., 24, 801-802, 2018.
  • F. R. Fields, S. W. Lee, and M. J. McConnell, “Using bacterial genomes and essential genes for the development of new antibiotics,” Biochem. Pharmacol., 134, 74–86, 2017.
  • Ç. Karabacak Atay, T. Tilki, and B. Dede, “Design and synthesis of novel ribofuranose nucleoside analogues as antiproliferative agents: A molecular docking and DFT study,” J. Mol. Liq., 269, 315–326, 2018.
  • P. Sledz, and A. Caflisch, “Protein structure-based drug design: from docking to molecular Dynamics,” Curr. Opin. Struc. Biol., 48, 93–102, 2018.
  • S. Kumar, and S. Kumar, “Chapter 6: Molecular Docking: A Structure-Based Approach for Drug Repurposing,” In Silico Drug Design, 161-189, 2019.
  • K. A. Ramsbottoma, D. F. Carrb, A. R. Jonesa, and D. J. Rigdena, “Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with adverse drug reactions,” Mol. Immunol., 101, 488-499, 2018.
  • Ç. Karabacak Atay, M. Gokalp, S. Ozdemir Kart, and T. Tilki, “Mono azo dyes derived from 5-nitroanthranilic acid: Synthesis, absorption properties and DFT calculations,” J. Mol. Struct., 1141, 237-244, 2017.
  • A. Grosdidier, V. Zoete, and O. Michielin, “SwissDock, a protein-small molecule docking web service based on EADock DSS,” Nucleic Acids Res., 39, 270-277, 2011.
  • Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E., (2000). The Protein Data Bank. Nucleic Acids Res., 28(1), 235–242.
  • Gaussian 09, Revision E.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, G. A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. Marenich, J. Bloino, B. G. Janesko, R. Gomperts, B. Mennucci, H. P. Hratchian, J. V. Ortiz, A. F. Izmaylov, J. L. Sonnenberg, D. Williams-Young, F. Ding, F. Lipparini, F. Egidi, J. Goings, B. Peng, A. Petrone, T. Henderson, D. Ranasinghe, V. G. Zakrzewski, J. Gao, N. Rega, G. Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, K. Throssell, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, J. M. Millam, M. Klene, C. Adamo, R. Cammi, J. W. Ochterski, R. L. Martin, K. Morokuma, O. Farkas, J. B. Foresman, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2016.
  • E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, and T.E. Ferrin, “UCSF Chimera--a visualization system for exploratory research and analysis,” J. Comput. Chem., 13, 1605-1612, 2004.
  • A.D. Becke, “Density-functional exchange-energy approximation with correct asymptotic behavior,” Phys. Rev. A, 38, 3098-3100, 1988.
  • C. Lee, W. Yang, and R.G. Parr, “Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density,” Phys. Rev. B, 37, 785-789, 1988.

Ayrıntılar

Birincil Dil en
Konular Mühendislik, Kimya
Bölüm Makaleler
Yazarlar

Orcid: 0000-0001-7226-9971
Yazar: Çiğdem KARABACAK ATAY
Kurum: BURDUR MEHMET AKİF ERSOY ÜNİVERSİTESİ
Ülke: Turkey

Orcid: 0000-0002-1040-2375
Yazar: Tahir TİLKİ (Sorumlu Yazar)
Kurum: SÜLEYMAN DEMİREL ÜNİVERSİTESİ
Ülke: Turkey

Orcid: 0000-0003-1416-7373
Yazar: Bülent DEDE
Kurum: SÜLEYMAN DEMİREL ÜNİVERSİTESİ
Ülke: Turkey
Tarihler

Yayımlanma Tarihi : 31 Mayıs 2019

Kaynak Göster

Bibtex @araştırma makalesi { sdufeffd544174, journal = {Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi}, issn = {}, eissn = {1306-7575}, address = {}, publisher = {Süleyman Demirel Üniversitesi}, year = {2019}, volume = {14}, pages = {150 - 154}, doi = {10.29233/sdufeffd.544174}, title = {Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method}, key = {cite}, author = {KARABACAK ATAY, Çiğdem and TİLKİ, Tahir and DEDE, Bülent} }
APA KARABACAK ATAY, Ç , TİLKİ, T , DEDE, B . (2019). 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 . DOI: 10.29233/sdufeffd.544174
MLA KARABACAK ATAY, Ç , TİLKİ, T , DEDE, B . "Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method". Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi 14 (2019 ): 150-154 <https://dergipark.org.tr/tr/pub/sdufeffd/issue/45380/544174>
Chicago KARABACAK ATAY, Ç , TİLKİ, T , DEDE, B . "Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method". Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi 14 (2019 ): 150-154
RIS TY - JOUR T1 - Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method AU - Çiğdem KARABACAK ATAY , Tahir TİLKİ , Bülent DEDE Y1 - 2019 PY - 2019 N1 - doi: 10.29233/sdufeffd.544174 DO - 10.29233/sdufeffd.544174 T2 - Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi JF - Journal JO - JOR SP - 150 EP - 154 VL - 14 IS - 1 SN - -1306-7575 M3 - doi: 10.29233/sdufeffd.544174 UR - https://doi.org/10.29233/sdufeffd.544174 Y2 - 2019 ER -
EndNote %0 Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method %A Çiğdem KARABACAK ATAY , Tahir TİLKİ , Bülent DEDE %T Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method %D 2019 %J Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi %P -1306-7575 %V 14 %N 1 %R doi: 10.29233/sdufeffd.544174 %U 10.29233/sdufeffd.544174
ISNAD KARABACAK ATAY, Çiğdem , TİLKİ, Tahir , DEDE, Bülent . "Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method". Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi 14 / 1 (Mayıs 2019): 150-154 . https://doi.org/10.29233/sdufeffd.544174
AMA KARABACAK ATAY Ç , TİLKİ T , DEDE B . Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method. SDÜFEFFD. 2019; 14(1): 150-154.
Vancouver KARABACAK ATAY Ç , TİLKİ T , DEDE B . Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method. Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi. 2019; 14(1): 154-150.
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