Investigation of Antiviral Activities of Nickel and Copper Complexes with Macrocyclic Ligands against Crimean-Congo Hemorrhagic Fever by In Silico Calculations

erkan, sultan; BULUT, NİYAZİ; Karakaş, Duran

doi:10.17776/csj.1375105

Investigation of Antiviral Activities of Nickel and Copper Complexes with Macrocyclic Ligands against Crimean-Congo Hemorrhagic Fever by In Silico Calculations

Sultan ERKAN, (Sivas Cumhuriyet Üniversitesi, Fen Fakültesi, Kimya Bölümü, Sivas, Türkiye)

Niyazi BULUT, (Fırat Üniversitesi, Fen Fakültesi, Fizik Bölümü, Elazığ, Türkiye)

Duran KARAKAŞ (Sivas Cumhuriyet Üniversitesi, Fen Fakültesi, Kimya Bölümü, Sivas, Türkiye)

Cumhuriyet Science Journal

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Yıl: 2023 Cilt: 44 Sayı: 4 Sayfa Aralığı: 723 - 732 Metin Dili: İngilizce DOI: 10.17776/csj.1375105 İndeks Tarihi: 03-01-2024

Investigation of Antiviral Activities of Nickel and Copper Complexes with Macrocyclic Ligands against Crimean-Congo Hemorrhagic Fever by In Silico Calculations

Öz:

For the first time, electronic characteristics of potential drug candidates and their inhibitory activities have been linked thanks to this work. Synthesized copper and nickel complexes with trans-N1,N8-bis(2-cyanoethyl)-2,4,4,9,11,11-hexamethyl-1,5,8,12-tetraazacyclotetradecane (tet-bx) ligand, as well as the proposed hypothetical complexes, were properly examined by the appropriate calculation method in atomic and molecular dimensions. The appropriate calculation level was achieved by using the IR spectroscopic data of the tet-bx ligand. The experimental and calculated bond stretching frequencies were compared for synthesized complexes [Ni(tet-bx)](ClO4)2 (1), [Cu(tet-bx)](ClO4)2 (2), [Ni(tet-bx)(NCS)2] (3), and [Ni(tet-bx)(ClO4)Cl] (5). Some bond stretching frequencies of hypothetical complexes [Cu(tet-bx)(NCS)2] (4) and [Cu(tet-bx)(ClO4)Cl] (6) have also been proposed and their molecular structure were determined. To analyze the electronic behavior of the examined complexes at the atomic level, Fukui function indices (nucleophilic f+ and electrophilic f- populations) were determined. Furthermore, antibacterial and antiviral inhibition efficiency of the complexes against Crimean-Congo hemorrhagic fever has been investigated by docking studies

Anahtar Kelime: Fukui function indices Molecular Docking Crimean-Congo

Belge Türü: Makale Makale Türü: Araştırma Makalesi Erişim Türü: Erişime Açık

[1] Martell, A. E., Smith, R. M., Critical stability constants, vol 3 Plenum Press. New York, NY, (1977).
[2] Hassan, M. M., Kinetics and mechanism of complex formation of a pendant arm macrocycle reacting with copper (II) and mercury (II), J. Saudi Chem. Soc., 13(2) (2009) 185-190.
[3] Shankarwar, S. G., Nagolkar, B. B., Shelke, V. A., Chondhekar, T. K., Synthesis, spectral, thermal and antimicrobial studies of transition metal complexes of 14-membered tetraaza [N4] macrocyclic ligand, Spectrochim. Acta, Part A, 145 (2015) 188-193.
[4] Bernhardt, P. V., Sharpe, P. C., C-substituted macrocycles as candidates for radioimmunotherapy, Inorg. Chem, 39 (18) (2000) 4123-4129.
[5] Hughes, J. P., Rees, S., Kalindjian, S. B., Philpott, K. L., Principles of early drug discovery, Br. J. Pharmacol., 162 (6) (2011) 1239-1249.
[6] Lipinski, C. A., Lombardo, F., Dominy, B. W., Feeney, P. J., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings, Adv. Drug Delivery Rev., 23(1-3) (1997) 3-25.
[7] Erkan, S., Activity of the rocuronium molecule and its derivatives: A theoretical calculation, J. Mol. Struct., 1189 (2019) 257-264.
[8] Kaya, S., Erkan, S., Karakaş, D., Computational investigation of molecular structures, spectroscopic properties and antitumor-antibacterial activities of some Schiff bases, Spectrochim, Acta, Part A, 244 (2021) 118829.
[9] Zivcec, M., Scholte, F. E., Spiropoulou, C. F., Spengler, J. R., Bergeron, É., Molecular insights into Crimean-Congo hemorrhagic fever virus, Viruses, 8(4) (2016) 106.
[10] Guo, Y., Wang, W., Ji, W., Deng, M., Sun, Y., Zhou, H., ... Rao, Z., Crimean–Congo hemorrhagic fever virus nucleoprotein reveals endonuclease activity in bunyaviruses, Proc. Natl. Acad. Sci. U.S.A., 109(13) (2012) 5046-5051.
[11] Sharifi, A., Amanlou, A., Moosavi-Movahedi, F., Golestanian, S., Amanlou, M., Tetracyclines as a potential antiviral therapy against Crimean Congo hemorrhagic fever virus: Docking and molecular dynamic studies, Comput. Biol. Chem., 70 (2017) 1-6.
[12] R.D. Dennington, T.A. Keith, J.M. Millam, GaussView 6.0. 16, Semichem. Inc., Shawnee Mission KS, 2016.
[13] Becke, A. D. Perspective: Fifty years of density-functional theory in chemical physics, J. Chem. Phys., 140(18) (2014) 18A301.
[14] Lee, C., Yang, W., Parr, R. G., Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Phys. Rev. B, 37(2) (1988) 785.
[15] Zhao, Y., Truhlar, D. G., The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals, Theor. Chem. Acc., 120(1-3) (2008) 215-241.
[16] Check, C. E., Faust, T. O., Bailey, J. M., Wright, B. J., Gilbert, T. M., Sunderlin, L. S., Addition of polarization and diffuse functions to the LANL2DZ basis set for p-block elements, J. Phys. Chem. A, 105(34) (2001) 8111-8116.
[17] Rassolov, V.A., Ratner, M.A., Pople, J.A., Redfern, P.C., Curtiss, L.A., 6-31G* basis set for third-row atoms, J. Comput. Chem., 22 (9) (2001) 976–984.
[18] Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman,J.R., ... Nakatsuji, H., Gaussian09 Revision D. 01, Gaussian Inc.,Wallingford CT, 2009. http://www.gaussian.com.
[19] Bikadi, Z., Hazai, E., Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock, J. Cheminform, 1(1) (2009) 1-16. https://www.dockingserver.com/web
[20] Güzel, E., Koçyiğit, Ü. M., Taslimi, P., Erkan, S., Taskin, O. S., Biologically active phthalocyanine metal complexes: Preparation, evaluation of α glycosidase and anticholinesterase enzyme inhibition activities, and molecular docking studies, J. Biochem. Mol. Toxicol., (2021) e22765.
[21] Zapata Trujillo, Juan C.; Mckemmish, Laura K. Meta analysis of uniform scaling factors for harmonic frequency calculations, Wiley Interdiscip. Rev., Comput. Mol. Sci., 12 (2022) 1584.
[22] Ünal, Y., Nassif, W., Özaydin, B. C., Sayin, K. Scale factor database for the vibration frequencies calculated in M06-2X, one of the DFT methods, Vib. Spectrosc., 112 (2021) 103189.
[23] Dey, L., Rabi, S., Hazari, S. K. S., Roy, T. G., Buchholz, A., Plass, W. Copper (II) and nickel (II) complexes of an N-pendent bis-(cyanoethyl) derivative of an isomeric hexamethyl tetraazamarocyclic ligand: Synthesis, characterization, electrolytic behavior and antimicrobial studies, Inorg. Chim. Acta, 517 (2021) 120172.
[24] R.B. Woodward and R. Hoffmann, J. Amer. Chem. Soc., 87 395 (1965)
[25] Sychantha, D., Little, D. J., Chapman, R. N., Boons, G. J., Robinson, H., Howell, P. L., Clarke, A. J. PatB1 is an O-acetyltransferase that decorates secondary cell wall polysaccharides, Nat. Chem. Biol., 14(1) (2018) 79.
[26] Song, L., Zhang, Y., Chen, W., Gu, T., Zhang, S. Y., Ji, Q., Mechanistic insights into staphylopine-mediated metal acquisition, Proc. Natl. Acad. Sci. U.S.A., 115(15) (2018) 3942-3947.
[27] Madsen, A., Dai, Y. N., McMahon, M., Schmitz, A. J., Turner, J. S., Tan, J., ... Ellebedy, A. H., Human antibodies targeting influenza B virus neuraminidase active site are broadly protective, Immunity, 53(4) (2020) 852-863.
[28] Song, W. S., Yoon, S. I., Crystal structure of FliC flagellin from Pseudomonas aeruginosa and its implication in TLR5 binding and formation of the flagellar filament, Biochem. Biophys. Res. Commun., 444(2) (2014) 109-115.
[29] Estrada, D. F., De Guzman, R. N., Structural characterization of the Crimean-Congo hemorrhagic fever virus Gn tail provides insight into virus assembly, J. Biol. Chem., 286(24) (2011) 21678-21686.
[30] Capodagli, G. C., McKercher, M. A., Baker, E. A., Masters, E. M., Brunzelle, J. S., Pegan, S. D., Structural analysis of a viral ovarian tumor domain protease from the Crimean-Congo hemorrhagic fever virus in complex with covalently bonded ubiquitin, J. Virol., 85(7) (2011) 3621-3630.
[31] Rey, F. A., Heinz, F. X., Mandl, C., Kunz, C., Harrison, S. C., The envelope glycoprotein from tick-borne encephalitis virus at 2 Å resolution, Nature, 375(6529) (1995) 291-298.
[32] Guo, Y., Wang, W., Ji, W., Deng, M., Sun, Y., Zhou, H., ... Rao, Z., Crimean–Congo hemorrhagic fever virus nucleoprotein reveals endonuclease activity in bunyaviruses, Proc. Natl. Acad. Sci. U.S.A., 109(13) (2012) 5046-5051.
[33] Füzik, T., Formanová, P., Růžek, D., Yoshii, K., Niedrig, M., Plevka, P., Structure of tick-borne encephalitis virus and its neutralization by a monoclonal antibody, Nat. Commun., 9(1) (2018) 1-11.
[34] Huey, R., Morris, G. M., Olson, A. J., Goodsell, D. S., A semiempirical free energy force field with charge based desolvation, J. Comput. Chem., 28(6) (2007) 1145-1152.

APA	erkan s, BULUT N, Karakaş D (2023). Investigation of Antiviral Activities of Nickel and Copper Complexes with Macrocyclic Ligands against Crimean-Congo Hemorrhagic Fever by In Silico Calculations. , 723 - 732. 10.17776/csj.1375105
Chicago	erkan sultan,BULUT NİYAZİ,Karakaş Duran Investigation of Antiviral Activities of Nickel and Copper Complexes with Macrocyclic Ligands against Crimean-Congo Hemorrhagic Fever by In Silico Calculations. (2023): 723 - 732. 10.17776/csj.1375105
MLA	erkan sultan,BULUT NİYAZİ,Karakaş Duran Investigation of Antiviral Activities of Nickel and Copper Complexes with Macrocyclic Ligands against Crimean-Congo Hemorrhagic Fever by In Silico Calculations. , 2023, ss.723 - 732. 10.17776/csj.1375105
AMA	erkan s,BULUT N,Karakaş D Investigation of Antiviral Activities of Nickel and Copper Complexes with Macrocyclic Ligands against Crimean-Congo Hemorrhagic Fever by In Silico Calculations. . 2023; 723 - 732. 10.17776/csj.1375105
Vancouver	erkan s,BULUT N,Karakaş D Investigation of Antiviral Activities of Nickel and Copper Complexes with Macrocyclic Ligands against Crimean-Congo Hemorrhagic Fever by In Silico Calculations. . 2023; 723 - 732. 10.17776/csj.1375105
IEEE	erkan s,BULUT N,Karakaş D "Investigation of Antiviral Activities of Nickel and Copper Complexes with Macrocyclic Ligands against Crimean-Congo Hemorrhagic Fever by In Silico Calculations." , ss.723 - 732, 2023. 10.17776/csj.1375105
ISNAD	erkan, sultan vd. "Investigation of Antiviral Activities of Nickel and Copper Complexes with Macrocyclic Ligands against Crimean-Congo Hemorrhagic Fever by In Silico Calculations". (2023), 723-732. https://doi.org/10.17776/csj.1375105

APA	erkan s, BULUT N, Karakaş D (2023). Investigation of Antiviral Activities of Nickel and Copper Complexes with Macrocyclic Ligands against Crimean-Congo Hemorrhagic Fever by In Silico Calculations. Cumhuriyet Science Journal, 44(4), 723 - 732. 10.17776/csj.1375105
Chicago	erkan sultan,BULUT NİYAZİ,Karakaş Duran Investigation of Antiviral Activities of Nickel and Copper Complexes with Macrocyclic Ligands against Crimean-Congo Hemorrhagic Fever by In Silico Calculations. Cumhuriyet Science Journal 44, no.4 (2023): 723 - 732. 10.17776/csj.1375105
MLA	erkan sultan,BULUT NİYAZİ,Karakaş Duran Investigation of Antiviral Activities of Nickel and Copper Complexes with Macrocyclic Ligands against Crimean-Congo Hemorrhagic Fever by In Silico Calculations. Cumhuriyet Science Journal, vol.44, no.4, 2023, ss.723 - 732. 10.17776/csj.1375105
AMA	erkan s,BULUT N,Karakaş D Investigation of Antiviral Activities of Nickel and Copper Complexes with Macrocyclic Ligands against Crimean-Congo Hemorrhagic Fever by In Silico Calculations. Cumhuriyet Science Journal. 2023; 44(4): 723 - 732. 10.17776/csj.1375105
Vancouver	erkan s,BULUT N,Karakaş D Investigation of Antiviral Activities of Nickel and Copper Complexes with Macrocyclic Ligands against Crimean-Congo Hemorrhagic Fever by In Silico Calculations. Cumhuriyet Science Journal. 2023; 44(4): 723 - 732. 10.17776/csj.1375105
IEEE	erkan s,BULUT N,Karakaş D "Investigation of Antiviral Activities of Nickel and Copper Complexes with Macrocyclic Ligands against Crimean-Congo Hemorrhagic Fever by In Silico Calculations." Cumhuriyet Science Journal, 44, ss.723 - 732, 2023. 10.17776/csj.1375105
ISNAD	erkan, sultan vd. "Investigation of Antiviral Activities of Nickel and Copper Complexes with Macrocyclic Ligands against Crimean-Congo Hemorrhagic Fever by In Silico Calculations". Cumhuriyet Science Journal 44/4 (2023), 723-732. https://doi.org/10.17776/csj.1375105