Synthesis, characterization, and in silico analysis against SARS CoV-2 of novel benzimidazolium salts

[1]. D. Wu, T. Wu, Q. Liu, Z. Yang, The SARS-CoV-2 outbreak: What we know, International Journal of Infectious Diseases 94 (2020) 44-48. Doi: 10.1016/j.ijid.2020.03.00410.1016/j.ijid.2020.03.004710254332171952 Search in Google Scholar

[2]. https://covid19.who.int/ “visited in 14.12.2021” Search in Google Scholar

[3]. J.A. Singh, COVID-19 vaccine trials: Duty of care and standard of prevention considerations, Vaccine 38 (2020) 7578–7580. Doi: 10.1016/j.vaccine.2020.10.01210.1016/j.vaccine.2020.10.012754626633069443 Search in Google Scholar

[4]. V. Gies, N. Bekaddour, Y. Dieudonné, A. Guffroy, Q. Frenger, F. Gros, M. P. Rodero, J.P. Herbeuval, A.S. Korganow, Beyond Anti-viral Effects of Chloroquine/Hydroxychloroquine, Front. Immunol. 11 (2020) 1409. Doi: 10.3389/fimmu.2020.0140910.3389/fimmu.2020.01409734376932714335 Search in Google Scholar

[5]. L. Runfeng, H. Yunlonge, H. Jicheng, P. Weiqi, M. Qinhai, S. Yongxia, L. Chufang, Z. Jin, J. Zhenhua, J. Haiming, Z. Kui, H. Shuxiang, D. Jun, L. Xiaobo, H. Xiaotao, W. Lin, Z. Nanshan, Y. Zifen, Lianhuaqingwen exerts anti-viral and anti-inflammatory activity against novel coronavirus (SARS-CoV-2), Pharmacological Research 156 (2020) 104761. Doi: 10.1016/j.phrs.2020.10476110.1016/j.phrs.2020.104761710254832205232 Search in Google Scholar

[6]. E. Teirumnieks, I. Balchev, R.S. Ghalot, L. Lazov, Antibacterial and anti-viral effects of silver nanoparticles in medicine against COVID-19—a review, Laser Phys. 31 (2021) 013001. Doi: 10.1088/1555-6611/abc87310.1088/1555-6611/abc873 Search in Google Scholar

[7]. J. Xu, L. Gao, H. Liang, S. Chen, In silico screening of potential anti–COVID-19 bioactive natural constituents from food sources by molecular docking, Nutrition 82 (2021) 111049. Doi: 10.1016/j.nut.2020.11104910.1016/j.nut.2020.111049764818833290972 Search in Google Scholar

[8]. A.B. Gumel, E.A. Iboi, C.N. Ngonghala, E.H. Elbash, A primer on using mathematics to understand COVID-19 dynamics: Modeling, analysis and simulations, Infectious Disease Modelling 6 (2021) 148-168. Doi: 10.1016/j.idm.2020.11.00510.1016/j.idm.2020.11.005778603633474518 Search in Google Scholar

[9]. M. Kubeil, R.R. Vernooij, C. Kubeil, B.R. Wood, B. Graham, H. Stephan, L. Spiccia, Studies of Carbon Monoxide Release from Ruthenium(II) Bipyridine Carbonyl Complexes upon UV-Light Exposure, Inorganic Chemistry 56 (2017) 5941–5952. Doi: 10.1021/acs.inorgchem.7b0059910.1021/acs.inorgchem.7b0059928467070 Search in Google Scholar

[10]. Y. Wang, K. Sarris, D.R. Sauer, S.W. Djuric, A simple and efficient one step synthesis of benzoxazoles and benzimidazoles from carboxylic acids, Tetrahedron Letters 47 (2006) 4823-4826. Doi: 10.1016/j.tetlet.2006.05.05210.1016/j.tetlet.2006.05.052 Search in Google Scholar

[11]. S.D. Düşünceli, D. Ayaz, E. Üstün, S. Günal, N. Özdemir, M. Dinçer, İ. Özdemir, Synthesis, antimicrobial properties, and theoretical analysis of benzimidazole-2-ylidene silver(I) complexes, Journal of Coordination Chemistry 73 (2020) 1967-1986. Doi: 10.1080/00958972.2020.181258710.1080/00958972.2020.1812587 Search in Google Scholar

[12]. J. Valdez, R. Cedillo, A. Hernández-Campos, L. Yépez, F. Hernández-Luis, G. Navarrete-Vázquez, A. Tapia, R. Cortés, M. Hernández, R. Castillo, Synthesis and antiparasitic activity of 1H-benzimidazole derivatives, Bioorganic & Medicinal Chemistry Letters 12 (2002) 2221-2224. Doi: 10.1016/S0960-894X(02)00346-310.1016/S0960-894X(02)00346-3 Search in Google Scholar

[13]. M. Tonelli, M. Simone, B. Tasso, F. Novelli, V. Boido, F. Sparatore, G. Paglietti, S. Pricl, G. Giliberti, S. Blois, C. Ibba, G. Sanna, R. Loddo, P. Colla, Antiviral activity of benzimidazole derivatives. II. Antiviral activity of 2-phenylbenzimidazole derivatives, Bioorganic & Medicinal Chemistry 18 (2010) 2937-2953. Doi: 10.1016/j.bmc.2010.02.03710.1016/j.bmc.2010.02.037 Search in Google Scholar

[14]. E. Üstün, A. Özgür, K.A. Coşkun, S.D. Düşünceli, İ. Özdemir, Y. Tutar, Anticancer activities of manganese-based photoactivatable CO-releasing complexes (PhotoCORMs) with benzimidazole derivative ligands, Transition Metal Chemistry 42 (2017) 331–337. Doi: 10.1007/s11243-017-0136-x10.1007/s11243-017-0136-x Search in Google Scholar

[15]. M. Gaba, S. Singh, C. Mohan, Benzimidazole: An emerging scaffold for analgesic and anti-inflammatory agents, European Journal of Medicinal Chemistry 76 (2014) 494-505. Doi: 10.1016/j.ejmech.2014.01.03010.1016/j.ejmech.2014.01.030 Search in Google Scholar

[16]. J. Velík, V. Baliharová, J. Fink-Gremmels, S. Bull, J. Lamka, L. Skálová, Benzimidazole drugs and modulation of biotransformation enzymes, Research in Veterinary Science 76 (2004) 95-108. Doi: 10.1016/j.rvsc.2003.08.00510.1016/j.rvsc.2003.08.005 Search in Google Scholar

[17]. A.G. Saimot, A.C. Cremieux, J.M. Hay, A. Meulemans, M.D. Giovanangeli, B. Delaitre, J.P. Coulaud, Albendazole as a potential treatment for human hydatidosis, The Lancet 322 (1983) 652-656. Doi: 10.1016/S0140-6736(83)92533-310.1016/S0140-6736(83)92533-3 Search in Google Scholar

[18]. R.R. Nadendla, Molecular modeling: A powerful tool for drug design and molecular docking, Resonance 9 (2004) 51–60. Doi: 10.1007/BF0283401510.1007/BF02834015 Search in Google Scholar

[19]. J.C. Phillips, Generalized Koopmans’ Theorem, Phys. Rev. 123, 420. Doi: 10.1103/PhysRev.123.42010.1103/PhysRev.123.420 Search in Google Scholar

[20]. https://www.rcsb.org/structure/2GTB (for 2gtb); https://www.rcsb.org/structure/5R82 (for5r82); https://www.rcsb.org/structure/6W9C (for 6w9c) Search in Google Scholar

[21]. T.W. Lee, M.M. Cherney, J. Liu, K.E. James, J.C. Powers, L.D. Eltis, M.N.G. James, Crystal structures reveal an induced-fit binding of a substrate-like aza-peptide epoxide to SARS coronavirus main peptidase, J. Mol. Biol. 366 (2007) 916-932. Doi: 10.1016/j.jmb.2006.11.07810.1016/j.jmb.2006.11.078709432317196984 Search in Google Scholar

[22]. A. Douangamath, D. Fearon, P. Gehrtz, T. Krojer, P. Lukacik, C.D. Owen, E. Resnick, C. Strain-Damerell, A. Aimon, P. Abranyi-Balogh, J. Brandao-Neto, A. Carbery, G. Davison, A. Dias, T.D. Downes, L. Dunnett, M. Fairhead, J.D. Firth, S.P. Jones, A. Keeley, G.M. Keseru, H.F. Klein, M.P. Martin, M.E.M. Noble, P. O’Brien, A. Powell, R.N. Reddi, R. Skyner, M. Snee, M.J: Waring, C. Wild, N. London, F. von Delft, M.A. Walsh, Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease, Nat Commun 11 (2020) 5047. Doi: 10.1038/s41467-020-18709-w10.1038/s41467-020-18709-w754244233028810 Search in Google Scholar

[23]. J. Osipiuk, R. Jedrzejczak, C. Tesar, M. Endres, L. Stols, G. Babnigg, Y. Kim, K. Michalska, A. Joachimiak, The crystal structure of papain-like protease of SARS CoV-2, Center for Structural Genomics of Infectious Diseases, to be published. Search in Google Scholar

[24]. N. Şahin, G. Serdaroğlu, S. D. Düşünceli, M. N. Tahir, C. Arıcı, İ. Özdemir, Direct arylation of heteroarenes by PEPPSI-type palladium–NHC complexes and representative quantum chemical calculations for the compound which the structure was determined by X-ray crystallography, Journal of Coordination Chemistry 72 (2019) 3258-3284. Doi: 10.1080/00958972.2019.1692202.10.1080/00958972.2019.1692202 Search in Google Scholar

[25]. A.D. Becke, Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A Gen Phys. 38 (1988) 3098-3100. Doi: 10.1103/PhysRevA.38.3098.10.1103/PhysRevA.38.3098 Search in Google Scholar

[26]. J.P. Perdew, K. Burke, M. Ernzerhof, Generalized Gradient Approximation Made Simple, Phys. Rev. Lett. 77 (1996) 3865-3868. Doi: 10.1103/PhysRevLett.77.386510.1103/PhysRevLett.77.386510062328 Search in Google Scholar

[27]. D.A. Pantazis, X.Y. Chen, C.R. Landis, F. Neese, All-Electron Scalar Relativistic Basis Sets for Third-Row Transition Metal Atoms, J. Chem. Theory Comput. 4 (2008) 908-919. Doi: 10.1021/ct800047t10.1021/ct800047t26621232 Search in Google Scholar

[28]. C. Lee, W. Yang, R.G. Parr, Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Phys. Rev. B 37 (1988) 785–789. Doi: /10.1103/PhysRevB.37.78510.1103/PhysRevB.37.785 Search in Google Scholar

[29]. F. Neese, The ORCA program system, WIREs Computational Molecular Science 2 (2011)73-78. Doi: 10.1002/wcms.8110.1002/wcms.81 Search in Google Scholar

[30]. J. P. Perdew, Density-functional approximation for the correlation energy of the inhomogeneous electron gas, Phys. Rev. B. 33 (1986) 8822. Doi: 10.1103/PhysRevB.33.882210.1103/PhysRevB.33.88229938299 Search in Google Scholar

[31]. F. Weigend, R. Ahlrichs, Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy, Phys. Chem. Chem. Phys. 7 (2005) 3297–3305. Doi: /10.1039/B508541A10.1039/b508541a16240044 Search in Google Scholar

[32]. G.M. Morris, R. Huey, W. Lindstrom, M.F. Sanner, R.K. Belew, D.S. Goodsell, A.J. Olson, Autodock4 and AutoDockTools4: automated docking with selective receptor flexibility, J. Computational Chemistry 16 (2009) 2785-2791. Doi: 10.1002/jcc.2125610.1002/jcc.21256276063819399780 Search in Google Scholar

[33]. U.C. Singh, P.A. Kollman, An approach to computing electrostatic charges for molecules, Journal of Computational Chemistry 5 (1984) 129-145. Doi: 10.1002/jcc.54005020410.1002/jcc.540050204 Search in Google Scholar

[34]. B.D. Bursulaya, M. Totrov, R. Abagyan, C.L. Brooks, Comparative study of several algorithms for flexible ligand docking, Journal of Computer-Aided Molecular Design 17 (2004) 755–763. Doi: 10.1023/B:JCAM.0000017496.76572.6f10.1023/B:JCAM.0000017496.76572.6f Search in Google Scholar

[35]. G.M. Morris, D.S. Goodsell, R.S. Halliday, R. Huey, W.E. Hart, R.K. Belew, A.J. Olson, Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function, Journal of Computational Chemistry 19 (1999) 1639-1662. Doi: 10.1002/(SICI)1096-987X(19981115)19:14<1639::AIDJCC10>3.0.CO;2-B10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B Search in Google Scholar

[36]. BIOVIA, Dassault Systèmes, Discovery Studio, [4.1.0], San Diego: Dassault Systèmes, [2019]. Search in Google Scholar

[37]. G. Serdaroğlu, N. Şahin, The synthesis and characterization of 1-(Allyl)-3-(2-methylbenzyl) benzimidazolium chloride: FT-IR, NMR, and DFT computational investigation, Journal of Molecular Structure 1178 (2019) 212-221. Doi: 10.1016/j.molstruc.2018.10.02810.1016/j.molstruc.2018.10.028 Search in Google Scholar

[38]. N. Uludağ, G. Serdaroğlu, An improved synthesis, spectroscopic (FT-IR, NMR) study and DFT computational analysis (IR, NMR, UV–Vis, MEP diagrams, NBO, NLO, FMO) of the 1,5-methanoazocino[4,3-b]indole core structure, Journal of Molecular Structure 1155 (2018) 548-560. Doi: 10.1016/j.molstruc.2017.11.03210.1016/j.molstruc.2017.11.032 Search in Google Scholar

[39]. M.M.L. Kadam, D. Patil, N. Sekar, 4-(Diethyl-amino) salicylaldehyde based fluorescent Salen ligand with red-shifted emission – A facile synthesis and DFT investigation, Journal of Luminescence 204 (2018) 354-367. Doi: 10.1016/j.jlumin.2018.08.04010.1016/j.jlumin.2018.08.040 Search in Google Scholar

[40]. R. Vijayaraj, V. Subramanian, P.K. Chattaraj, Comparison of Global Reactivity Descriptors Calculated Using Various Density Functionals: A QSAR Perspective, J. Chem. Theory Comput. 5 (2009) 2744–2753. Doi: 10.1021/ct900347f10.1021/ct900347f26631787 Search in Google Scholar

[41]. M. Berkowitz, R.G. Parr, Molecular hardness and softness, local hardness and softness, hardness and softness kernels, and relations among these quantities, J. Chem. Phys. 88 (1988) 2554. Doi: 10.1063/1.45403410.1063/1.454034 Search in Google Scholar

[42]. R.G. Parr, L. Szentpály, S. Liu, Electrophilicity Index, Am. Chem. Soc. 121 (1999) 1922–1924. Doi: 10.1021/ja983494x10.1021/ja983494x Search in Google Scholar

[43]. B. Salim, M. Noureddine, Identification of Compounds from Nigella Sativa as New Potential Inhibitors of 2019 Novel Coronasvirus (Covid-19): Molecular Docking Study, ChemRxiv. Cambridge: Cambridge Open Engage, (2020). Doi: 10.26434/chemrxiv.12055716.v110.26434/chemrxiv.12055716.v1 Search in Google Scholar

[44]. A.A. Al-Zahrani, Rutin as a Promising Inhibitor of Main Protease and Other Protein Targets of COVID-19: In Silico Study, Nat. Prod. Commun. 15 (2020) 1–4. Doi: 10. 1177/1934 578X 2095395110.1177/1934578X20953951 Search in Google Scholar