234
Views
4
CrossRef citations to date
0
Altmetric
Research Articles

Structural and theoretical investigations, Hirshfeld surface analysis and anti-SARS CoV-2 of nickel (II) coordination complex

&
Pages 402-422 | Received 09 Sep 2021, Accepted 09 Nov 2021, Published online: 29 Nov 2021

References

  • Acter, T., Uddin, N., Das, J., Akhter, A., Choudhury, T. R., & Kim, S. (2020). Evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as coronavirus disease 2019 (COVID-19) pandemic: A global health emergency. Science of the Total Environment, 730, 138996. https://doi.org/10.1016/j.scitotenv.2020.138996
  • Akitsu, T., & Einaga, Y. (2004). Bis[(R)-3,5-dichloro-N-(1-phenylethyl)salicylideneaminato-k2N,O]- copper(II) and bis[(R)-3-ethoxy-N- (1-phenylethyl)salicylideneaminato-k2 N,O]copper(II). Acta Crystallogr. Part C, 60, 640–642.
  • Al-Janabi, A. S. M., Elzupir, A. O., & Yousef, T. A. (2021). Synthesis, anti-bacterial evaluation, DFT study and molecular docking as a potential 3-chymotrypsin-like protease (3CLpro) of SARS-CoV-2 inhibitors of a novel Schiff bases. Journal of Molecular Structure, 1228, 129454. https://doi.org/10.1016/j.molstruc.2020.129454
  • Al-Resayes, S. I., Azam, M., Kruszynska, A. T., Kruszynski, R., Soliman, S. M., Mohapatra, R. K., & Khan, Z. (2020). Structural and theoretical investigations, Hirshfeld surface analyses, and cytotoxicity of a naphthalene-based chiral compound. ACS Omega, 5(42), 27227–27234. https://doi.org/10.1021/acsomega.0c03376
  • Andreou, A., Trantza, S., Filippou, D., Sipsas, N., & Tsiodras, S. (2020). COVID-19: The potential role of copper and N-acetylcysteine (NAC) in a combination of candidate antiviral treatments against SARS-CoV-2. In Vivo (Athens, Greece), 34(3 Suppl), 1567–1588. https://doi.org/10.21873/invivo.11946
  • Ashfaq, M., Munawar, K. S., Tahir, M. N., Dege, N., Yaman, M., Muhammad, S., Alarfaji, S. S., Kargar, H., & Arshad, M. U. (2021). Synthesis, crystal structure, Hirshfeld surface analysis, and computational study of a novel organic salt obtained from benzylamine and an acidic component. ACS Omega, 6(34), 22357–22366. https://doi.org/10.1021/acsomega.1c03078
  • Bal, T. R., Anand, B., Yogeeswari, P., & Sriram, D. (2005). Synthesis and evaluation of anti-HIV activity of isatin beta-thiosemicarbazone derivatives. Bioorganic & Medicinal Chemistry Letters, 15(20), 4451–4455. https://doi.org/10.1016/j.bmcl.2005.07.046
  • Banti, C. N., Kourkoumelis, N., Hatzidimitriou, A. G., Antoniadou, I., Dimou, A., Rallis, M., Hoffmann, A., Schmidtke, M., McGuire, K., Busath, D., Kolocouris, A., & Hadjikakou, S. K. (2020). Amantadine copper(II) chloride conjugate with possible implementation in influenza virus inhibition. Polyhedron, 185, 114590. https://doi.org/10.1016/j.poly.2020.114590
  • Basu, S., Ramaiah, S., & Anbarasu, A. (2021). In-silico strategies to combat COVID-19: A comprehensive review. Biotechnology & Genetic Engineering Reviews, 37(1), 64–81. https://doi.org/10.1080/02648725.2021.1966920
  • Basu, S., Veeraraghavan, B., Ramaiah, S., & Anbarasu, A. (2020). Novel cyclohexanone compound as a potential ligand against SARS-CoV-2 main-protease. Microbial Pathogenesis, 149, 104546. https://doi.org/10.1016/j.micpath.2020.104546
  • Bauer, D. J., & Sheffield, F. W. (1959). Antiviral chemotherapeutic activity of isatin β-thiosemicarbazone in mice infected with rabbit-pox virus. Nature, 184(4697), 1496–1497. https://doi.org/10.1038/1841496b0
  • Berman, H., Henrick, K., & Nakamura, H. (2003). Announcing the worldwide protein data bank. Nature Structural Biology, 10(12), 980. https://doi.org/10.1038/nsb1203-980
  • Biovia, D. S. (2016). Discovery studio visualizer, v17.2.0.16349. Dassault Systems.
  • Blundell, T. L., Sibanda, B. L., Montalvão, R. W., Brewerton, S., Chelliah, V., Worth, C. L., Harmer, N. J., Davies, O., & Burke, D. (2006). Structural biology and bioinformatics in drug design: Opportunities and challenges for target identification and lead discovery. Philosophical Transactions of the Royal Society B: Biological Sciences, 361(1467), 413–423. https://doi.org/10.1098/rstb.2005.1800
  • Boopathi, S., Poma, A. B., & Kolandaivel, P. (2020). Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment. Journal of Biomolecular Structure and Dynamics, 30, 1–10.
  • Chai, J. D., & Gordon, M. H. (2008). Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections. Physical Chemistry Chemical Physics: PCCP, 10(44), 6615–6620. https://doi.org/10.1039/b810189b
  • Chandra, S., & Sharma, A. K. (2009). Applications of several spectral techniques to characterize coordination compounds derived from 2,6-diacetylpyridine derivative. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy, 74(1), 271–276. https://doi.org/10.1016/j.saa.2009.06.014
  • Chaturvedi, D., & Kambij, M. (2016). Role of Schiff Base in Drug Discovery Research. Chemical Science Journal, 7(2). https://doi.org/10.4172/2150-3494.1000e114
  • Chen, L. R., Wang, Y. C., Lin, Y. W., Chou, S. Y., Chen, S. F., Liu, L. T., Wu, Y. T., Kuo, C. J., Chen, T. S., & Juang, S. H. (2005). Synthesis and evaluation of isatin derivatives as effective SARS coronavirus 3CL protease inhibitors. Bioorganic & Medicinal Chemistry Letters, 15(12), 3058–3062. https://doi.org/10.1016/j.bmcl.2005.04.027
  • Chen, N., Zhou, M., Dong, X., Qu, J., Gong, F., Han, Y., Qiu, Y., Wang, J., Liu, Y., Wei, Y., Xia, J., Yu, T., Zhang, X., & Zhang, L. (2020). Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: A descriptive study. The Lancet, 395(10223), 507–513. https://doi.org/10.1016/S0140-6736(20)30211-7
  • Dai, W., Zhang, B., Jiang, X.-M., Su, H., Li, J., Zhao, Y., Xie, X., Jin, Z., Peng, J., Liu, F., Li, C., Li, Y., Bai, F., Wang, H., Cheng, X., Cen, X., Hu, S., Yang, X., Wang, J., … Liu, H. (2020). Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease, RCSB PDB-6LZE: The crystal strcutre of COVID-19 main protease in complex with an inhibitor 11a. Science (New York, N.Y.), 368(6497), 1331–1335. https://doi.org/10.1126/science.abb4489
  • Das, P., Majumder, R., Mandal, M., & Basak, P. (2020). In-Silico approach for identification of effective and stable inhibitors for COVID-19 main protease (Mpro) from flavonoid based phytochemical constituents of Calendula officinalis. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1796799
  • El-Gammal, O. A., Sh. Mohamed, F., Rezk, G. N., & El-Bindary, A. A. (2021). Structural characterization and biological activity of a new metal complexes based of Schiff base. Journal of Molecular Liquids, 330, 115522. https://doi.org/10.1016/j.molliq.2021.115522
  • Eryilmaz, S., Gul, M., & Inkaya, E. (2019). Investigation of global reactivity descriptors of some perillaldehyde derivatives in different solvents by DFT method. Indian Journal of Chemical Technology, 26, 235–238.
  • Ferreira, L. G., Dos Santos, R. N., Oliva, G., & Andricopulo, A. D. (2015). Molecular docking and structure-based drug design strategies. Molecules (Basel, Switzerland), 20(7), 13384–13421. https://doi.org/10.3390/molecules200713384
  • Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J., Scalmani, R. G., Barone, V., Mennucci, B., & Petersson, G. A. (2016). Gaussian 16 Rev. A.03. Wallingford, CT: Gaussian, Inc.
  • Gage, A., Brunson, K., Morris, K., Wallen, S. L., Dhau, J., Gohel, H., & Kaushik, A. (2021). Perspectives of Manipulative and High-Performance Nanosystems to Manage Consequences of Emerging New Severe Acute Respiratory Syndrome Coronavirus 2 Varian. Frontiers in Nanotechnology. https://doi.org/10.3389/frano.2021.700888
  • Gao, X.-S., Dai, H.-J., Tang, Y., Ding, M.-J., Pei, W.-B., & Ren, X.-M. (2019). Crystal structures, photoluminescence, and magnetism of two novel transition-metal complex cocrystals with three-dimensional h-bonding organic framework or alternating noncovalent anionic and cationic layers. ACS Omega, 4(7), 12230–12237. https://doi.org/10.1021/acsomega.9b01584
  • Hamre, D., Brownlee, K. A., & Donovick, R. (1951). Studies on the chemotherapy of vaccinia virus. II. The activity of some thiosemicarbazones. Journal of Immunology, 67, 305.
  • Hussein, R. K., & Elkhair, H. M. (2021). Molecular docking identification for the efficacy of some zinc complexes with chloroquine and hydroxychloroquine against main protease of COVID-19. Journal of Molecular Structure, 1231, 129979. https://doi.org/10.1016/j.molstruc.2021.129979
  • Johnson, D. K., Murphy, T. B., Rose, N. J., Goodwin, W. H., & Pickart, L. (1982). Cytotoxic chelators and chelates 1. Inhibition of DNA synthesis in cultured rodent and human cells by aroylhydrazones and by a copper(II) complex of salicylaldehyde benzoyl hydrazone. Inorganica Chimica Acta, 67, 159–165. https://doi.org/10.1016/S0020-1693(00)85058-6
  • Kargar, H., F-Mehrjardi, M., Ardakani, B. B., Tahir, M. N., Ashfaq, M., & Munawar, K. S. (2021). Synthesis, crystal structure determination, Hirshfeld surface analysis, spectral characterization, theoretical and computational studies of titanium(IV) Schiff base complex. Journal of Coordination Chemistry. https://doi.org/10.1080/00958972.2021.1972984
  • Khan, I., Panini, P., Khan, S. U.-D., Rana, U. A., Andleeb, H., Chopra, D., Hameed, S., & Simpson, J. (2016). Exploiting the role of molecular electrostatic potential, deformation density, topology, and energetics in the characterization of S···N and Cl···N supramolecular motifs in crystalline triazolothiadiazoles. Crystal Growth and Design, 16(3), 1371–1386. https://doi.org/10.1021/acs.cgd.5b01499
  • Kotian, A., Kamat, V., Naik, K., Kokare, D. G., Kumara, K., Neratur, K. L., Kumbar, V., Bhat, K., & Revankar, V. K. (2021). 8-Hydroxyquinoline derived p-halo N4-phenyl substituted thiosemicarbazones: Crystal structures, spectral characterization and in vitro cytotoxic studies of their Co(III), Ni(II) and Cu(II) complexes. Bioorganic Chemistry, 112, 104962. https://doi.org/10.1016/j.bioorg.2021.104962
  • Kulkarni, B. S., Mishra, D., & Pal, S. (2013). Role of substituents on the reactivity and electron density profile of diimine ligands: A density functional theory based study. Journal of Chemical Sciences, 125(5), 1247–1258. https://doi.org/10.1007/s12039-013-0469-8
  • Lambert, H., Mohan, N., & Lee, T. C. (2019). Ultrahigh binding affinity of a hydrocarbon guest inside cucurbit[7]uril enhanced by strong host-guest charge matching. Physical Chemistry Chemical Physics: PCCP, 21(27), 14521–14529. https://doi.org/10.1039/c9cp01762c
  • Li, G., & Clercq, E. D. (2020). Therapeutic options for the 2019 novel coronavirus (2019-nCoV). Nature Reviews Drug Discovery, 19(3), 149–150. https://doi.org/10.1038/d41573-020-00016-0
  • Lobana, T. S., Kumari, P., Castineiras, A., & Butcher, R. J. (2013). The effect of C-2 substituents of salicylaldehyde-based thiosemicarbazones on the synthesis, spectroscopy, structures, and fluorescence of nickel(II) complexes. European Journal of Inorganic Chemistry, 2013(20), 3557–3566. https://doi.org/10.1002/ejic.201300209
  • Maldonado, N., & Amo-Ochoa, P. (2021). The role of coordination compounds in virus research. Different approaches and trends. Dalton Transactions, 50(7), 2310–2323. https://doi.org/10.1039/d0dt04066e
  • Mckinnon, J. J., Mitchell, A. S., & Spackman, M. A. (1998). Hirshfeld surfaces: A new tool for visualising and exploring molecular crystals. Chemistry - A European Journal, 4(11), 2136–2141. https://doi.org/10.1002/(SICI)1521-3765(19981102)4:11<2136::AID-CHEM2136>3.0.CO;2-G
  • Mckinnon, J. J., Spackman, M. A., & Mitchell, A. S. (2004). Novel tools for visualizing and exploring intermolecular interactions in molecular crystals. Acta Crystallographica. Section B, Structural Science, 60(Pt 6), 627–668. https://doi.org/10.1107/S0108768104020300
  • Mengist, H. M., Dilnessa, T., & Jin, T. (2021). Structural basis of potential inhibitors targeting SARS-CoV-2 main protease. Frontiers in Chemistry, 9, 622898. https://doi.org/10.3389/fchem.2021.622898
  • Mir, J. M., Majid, S. A., & Shalla, A. H. (2021). Enhancement of Schiff base biological efficacy by metal coordination and introduction of metallic compounds as anticovid candidates: a simple overview. Reviews in Inorganic Chemistry. https://doi.org/10.1515/revic-2020-0020
  • Mohan, B., & Choudhary, M. (2021). Synthesis, crystal structure, computational study and anti-virus effect of mixed ligand copper (II) complex with ONS donor Schiff base and 1, 10-phenanthroline. Journal of Molecular Structure, 1246, 131246.
  • Mohan, B., Choudhary, M., Bharti, S., Jana, A., Das, N., Muhammad, S., Al-Sehemi, A. G., & Kumar, S. (2019). Syntheses, characterizations, crystal structures and efficient NLO applications of new organic compounds bearing 2-methoxy-4-nitrobenzeneamine moiety and copper (II) complex of (E)-N'-(3, 5-dichloro-2-hydroxybenzylidene) benzohydrazide. Journal of Molecular Structure, 1190, 54–67. https://doi.org/10.1016/j.molstruc.2019.04.059
  • Mohan, B., Choudhary, M., Muhammad, S., Das, N., Singh, K., Jana, A., Bharti, S., Algarni, H., Al-Sehemi, A. G., & Kumar, S. (2020). Synthesis, characterizations, crystal structures, and theoretical studies of copper(II) and nickel(II) coordination complexes. Journal of Coordination Chemistry, 73(8), 1256–1279. https://doi.org/10.1080/00958972.2020.1761961
  • Mohan, B., Jana, A., Das, N., Bharti, S., Choudhary, M., Muhammad, S., Kumar, S., Sehemi, A. G. A., & Algarni, H. (2019). A dual approach to study the key features of nickel (II) and copper (II) coordination complexes: Synthesis, crystal structure, optical and nonlinear properties. Inorganica Chimica Acta, 484, 148–159. https://doi.org/10.1016/j.ica.2018.09.037
  • Mohan, B., Muhammad, S., Al-Sehemi, A. G., Bharti, S., Kumar, S., & Choudhary, M. (2021). Synthesis of copper(II) coordination complex, its molecular docking and computational exploration for novel functional properties: A dual approach. ChemistrySelect, 6(4), 738–745. https://doi.org/10.1002/slct.202003738
  • Morris, G., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
  • Pal, M., Musib, D., & Roy, M. (2021). Transition metal complexes as potential tools against SARS-CoV-2: An in silico approach. New Journal of Chemistry, 45(4), 1924–1933. https://doi.org/10.1039/D0NJ04578K
  • Parr, R. G., Szentpaly, L. V., & Liu, S. (1999). Electrophilicity index. Journal of the American Chemical Society, 121(9), 1922–1924. https://doi.org/10.1021/ja983494x
  • Patel, R. N., Gundla, V. L. N., & Patel, D. K. (2008). Synthesis, structure and properties of some copper(II) complexes containing an ONO donor Schiff base and substituted imidazole ligands. Polyhedron, 27(3), 1054–1060. https://doi.org/10.1016/j.poly.2007.11.042
  • Patel, R. N., Singh, N., & Gundla, V. L. N. (2006). Synthesis, structure and properties of ternary copper(II) complexes of ONO donor Schiff base, imidazole, 2,2′-bipyridine and 1,10-phenanthroline. Polyhedron, 25(17), 3312–3318. https://doi.org/10.1016/j.poly.2006.06.017
  • Petrasheuskaya, T. V., Kiss, M. A., Dömötör, O., Holczbauer, T., May, N. V., Spengler, G., Kincses, A., Čipak Gašparović, A., Frank, É., & Enyedy, É. A. (2020). Salicylaldehyde thiosemicarbazone copper complexes: Impact of hybridization with estrone on cytotoxicity, solution stability and redox activity. New Journal of Chemistry, 44(28), 12154–12168. https://doi.org/10.1039/D0NJ01070G
  • Polakis, P. G., Snyderman, R., & Evans, T. (1989). Characterization of G25K, A GTP-binding protein containing a novel putative nucleotide binding domain. Biochemical and Biophysical Research Communications, 160(1), 25–32. https://doi.org/10.1016/0006-291X(89)91615-X
  • Prescott, B., & Li, C. P. (1964). Long-chain thiosemicarbazones as potential anticancer and antiviral agents. Journal of Medicinal Chemistry, 7(3), 383–385. https://doi.org/10.1021/jm00333a044
  • Rogolino, D., Bacchi, A., Luca, L. D., Rispoli, G., Sechi, M., Stevaert, A., Naesens, L., & Carcelli, M. (2015). Investigation of the salicylaldehyde thiosemicarbazone scaffold for inhibition of influenza virus PA endonuclease. Journal of Biological Inorganic Chemistry: JBIC: A Publication of the Society of Biological Inorganic Chemistry, 20(7), 1109–1121. https://doi.org/10.1007/s00775-015-1292-0
  • Rohl, A. L., Moret, M., Kaminsky, W., Claborn, K., McKinnon, J. J., & Kahr, B. (2008). Cryst. Crystal Growth & Design, 8(12), 4517–4525. https://doi.org/10.1021/cg8005212
  • Rudolph, M. G., Wittinghofer, A., & Vetter, I. R. (1999). Nucleotide binding to the G12V-mutant of Cdc42 investigated by X-ray diffraction and fluorescence spectroscopy: Two different nucleotide states in one crystal . Protein Science: A Publication of the Protein Society, 8(4), 778–789. https://doi.org/10.1110/ps.8.4.778
  • Seshan, G., Kanagasabai, S., Ananthasri, S., Kannappan, B., Suvitha, A., Jaimohan, S. M., Kanagaraj, S., & Kothandn, G. (2020). Insights of structure-based pharmacophore studies and inhibitor design against Gal3 receptor through molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1804452
  • Sheldrick, G. M. (1990). Phase annealing in SHELX-90: Direct methods for larger structures. Acta Crystallographica Section A, Foundations of Crystallography, 46(6), 467–473. https://doi.org/10.1107/S0108767390000277
  • Sheldrick, G. M. (2008). A short history of SHELX. Acta Crystallographica. Section A, Foundations of Crystallography, 64(Pt 1), 112–122. https://doi.org/10.1107/S0108767307043930
  • Spackman, M. A., & Jayatilaka, D. (2009). Hirshfeld surface analysis. CrystEngComm, 11(1), 19–32. )https://doi.org/10.1039/B818330A
  • Spackman, M. A., & Mckinnon, J. J. (2002). Fingerprinting intermolecular interactions in molecular crystals. CrystEngComm, 4(66), 378–392. https://doi.org/10.1039/B203191B
  • Spackman, P. R., Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Jayatilaka, D., & Spackman, M. A. (2021). CrystalExplorer: A program for Hirshfeld surface analysis, visualization and quantitative analysis of molecular crystals. Journal of Applied Crystallography, 54(3), 1006–1011. https://doi.org/10.1107/S1600576721002910
  • Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
  • Uddin, M. N., Amin, M. S., Rahman, M. S., Khandaker, S., Shumi, W., Rahman, M. A., & Rahman, S. M. (2021). Titanium (IV) complexes of some tetra-dentate symmetrical bis-Schiff bases of 1,6-hexanediamine: Synthesis, characterization, and in silico prediction of potential inhibitor against coronavirus (SARS-CoV-2). Applied Organometallic Chemistry, 35(1). https://doi.org/10.1002/aoc.6067
  • Vijayaraj, R., Subramanian, V., & Chattaraj, P. K. (2009). Comparison of global reactivity descriptors calculated using various density functionals: A QSAR perspective. Journal of Chemical Theory and Computation, 5(10), 2744–2753. https://doi.org/10.1021/ct900347f
  • Wolff, S. K., Grimwood, D. J., McKinnon, J. J., Turner, M. J., Jayatilaka, D., & Spackman, M. A. (2012). Crystal Explorer, Version 3.0. Perth: University of Western Australia.
  • Zhang, S., Krumberger, M., Morris, M. A., Parrocha, C. M. T., Griffin, J. H., Kreutzer, A., & Nowick, J. S. (2021). Structure-Based Drug Design of an Inhibitor of the SARS-CoV-2 (COVID-19) Main Protease Using Free Software: A Tutorial for Students and Scientists. ChemRxiv. https://doi.org/10.26434/chemrxiv.12791954
  • Zhao, R., Cang, Z., Tong, Y., & Wei, G.-W. (2018). Protein pocket detection via convex hull surface evolution and associated Reeb graph. Bioinformatics (Oxford, England), 34(17), i830–i837. https://doi.org/10.1093/bioinformatics/bty598

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.