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

Yıl 2023, Cilt: 44 Sayı: 4, 723 - 732, 28.12.2023

Sultan Erkan , Niyazi Bulut , Duran Karakaş

https://doi.org/10.17776/csj.1375105

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 Kelimeler

Fukui function indices Molecular Docking Crimean-Congo

Etik Beyan

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Teşekkür

The numerical calculations reported in this paper were fully/partially performed at TUBITAK ULAKBIM, High Performance and Grid Computing Center (TRUBA resources). NB would like to thank FIRAT University Scientific Research Projects Unit (Project number: FF.20.22).

Kaynakça

  • [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.

Yıl 2023, Cilt: 44 Sayı: 4, 723 - 732, 28.12.2023

Sultan Erkan , Niyazi Bulut , Duran Karakaş

https://doi.org/10.17776/csj.1375105

Öz

Kaynakça

  • [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.
Toplam 34 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Konular Organometalik Kimya
Bölüm Natural Sciences
Yazarlar

Sultan Erkan 0000-0001-6744-929X

Niyazi Bulut 0000-0003-2863-7700

Duran Karakaş 0000-0002-6770-3726

Yayımlanma Tarihi 28 Aralık 2023
Gönderilme Tarihi 12 Ekim 2023
Kabul Tarihi 14 Aralık 2023
Yayımlandığı Sayı Yıl 2023 Cilt: 44 Sayı: 4

Kaynak Göster

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. https://doi.org/10.17776/csj.1375105
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