A novel cyclobutane-derived thiazole–thiourea hybrid with a potency against COVID-19 and tick-borne encephalitis: synthesis, characterization, and computational analysis

References

• https://www.washingtonpost.com/graphics/2020/local/retropolis/coronavirus-deadliest-pandemics/
   Google Scholar
• Valleron AJ, Meurisse S, Boelle PY. Historical analysis of the 1889–1890 pandemic in Europe. Int. J. Infect. Dis. 2008;12:E95. doi:10.1016/j.ijid.2008.05.237
   PubMed Web of Science ®Google Scholar
• Johnson NPAS, Mueller J. Updating the accounts: global mortality of the 1918-1920 ‘Spanish’ influenza pandemic. Bill. Hist. Med. 2002;76:105–115. doi:10.1353/bhm.2002.0022
   PubMed Web of Science ®Google Scholar
• Barré-Sinoussi F, Chermann JC, Rey F, et al. Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS). Science. 1983;220:868–871. doi:10.1126/science.6189183
   PubMed Web of Science ®Google Scholar
• Popovic M, Sarngadharan MG, Read E, et al. Detection, isolation, and continuous production of cytopathic retroviruses (HTLV-III) from patients with AIDS and pre-AIDS. Science. 1984;224:497–500. doi:10.1126/science.6200935
   PubMed Web of Science ®Google Scholar
• Gallo RC, Salahuddin SZ, Popovic M, et al. Frequent detection and isolation of cytopathic retroviruses (HTLV-III) from patients with AIDS and at risk for AIDS. Science. 1984;224:500–503. doi:10.1126/science.6200936
   PubMed Web of Science ®Google Scholar
• Schüpbach J, Popovic M, Gilden RV, et al. Serological analysis of a subgroup of human T-lymphotropic retroviruses (HTLV-III) associated with AIDS. Science. 1984;224:503–505. doi:10.1126/science.6200937
   PubMed Web of Science ®Google Scholar
• Sarngadharan MG, Popovic M, Bruch L, et al. Antibodies reactive with human T-lymphotropic retroviruses (HTLV-III) in the serum of patients with AIDS. Science. 1984;224:506–508. doi:10.1126/science.6324345
   PubMed Web of Science ®Google Scholar
• https://www.who.int/director-general/speeches/detail/who-director-general-s-opening-remarks-at-the-media-briefing-on-covid-19—11-march-2020
   Google Scholar
• https://covid19.who.int/
   Google Scholar
• https://en.wikipedia.org/wiki/Economic_impact_of_the_COVID-19_pandemic
   Google Scholar
• Lindquist L, Vapalahti O. Tick-borne encephalitis. Lancet. 2008;371:1861–1871. doi:10.1016/S0140-6736(08)60800-4
   PubMed Web of Science ®Google Scholar
• https://www.ecdc.europa.eu/en/tick-borne-encephalitis/facts/factsheet
   Google Scholar
• Kuchar E, Zajkowska J, Flisiak R, et al. COVID-19 immunizations in occupational medicine. Med. Pr. 2021;72:701–710. doi:10.13075/mp.5893.01219
   PubMed Web of Science ®Google Scholar
• Czarnowska A, Kapica-Topczewska K, Garkowski A, et al. Severe tick-borne encephalitis in a patient recovered from COVID 19. Ticks Tick-Borne Dis. 2022;13:101940. doi:10.1016/j.ttbdis.2022.101940
   PubMed Web of Science ®Google Scholar
• Zając Z, Bartosik K, Kulisz J, et al. Incidence of tick-borne encephalitis during the COVID-19 pandemic in selected European countries. J. Clin. Med. 2022;11:803. doi:10.3390/jcm11030803
   PubMed Web of Science ®Google Scholar
• Martins P, Jesus J, Santos S, et al. Heterocyclic anticancer compounds: recent advances and the paradigm shift towards the Use of nanomedicine’s tool Box. Molecules. 2015;20:16852–16891. doi:10.3390/molecules200916852
   PubMed Web of Science ®Google Scholar
• Pathania S, Narang RK, Rawal RK. Role of sulphur-heterocycles in medicinal chemistry: an update. Eur. J. Med. Chem. 2019;180:486–508. doi:10.1016/j.ejmech.2019.07.043
   PubMed Web of Science ®Google Scholar
• Jampilek J. Heterocycles in medicinal chemistry. Molecules. 2019;24:3839. doi:10.3390/molecules24213839
   PubMed Web of Science ®Google Scholar
• https://www.mdpi.com/journal/molecules/special_issues/Heterocycles_Medicinal_Chemistry
   Google Scholar
• Thematic issue ‘Heterocyclic Compounds in Medicinal Chemistry’. Chem. Heterocycl. Comp. 2020;56:625. doi:10.1007/s10593-020-02711-7
   Web of Science ®Google Scholar
• https://link.springer.com/journal/10593/volumes-and-issues/56-6
   Google Scholar
• Heravi MM, Zadsirjan V. Prescribed drugs containing nitrogen heterocycles: an overview. RSC Adv. 2020;10:44247–44311. doi:10.1039/D0RA09198G
   PubMed Web of Science ®Google Scholar
• Maertens JA. History of the development of azole derivatives. Clin. Microbiol. Infect. 2004;10:1–10. doi:10.1111/j.1470-9465.2004.00841.x
   PubMed Web of Science ®Google Scholar
• https://www.drugs.com/search.php?searchterm=thiamine
   Google Scholar
• https://go.drugbank.com/drugs/DB00152
   Google Scholar
• https://www.drugs.com/search.php?searchterm=Bleomycin
   Google Scholar
• https://go.drugbank.com/drugs/DB00290
   Google Scholar
• Avotins FM. Aminoacids of the cyclobutane series, Russ. Chem. Rev. 1993;62:897–906.
   Google Scholar
• The Chemistry of Cyclobutanes, Z. Rappoport, J.F. Liebman, Eds., John Wiley & Sons, Ltd. (2005).
   Google Scholar
• Ortuno RM, Moglioni AG, Moltrasio GY. Cyclobutane biomolecules: synthetic approaches to amino acids, peptides and nucleosides, curr. Org. Chem. 2005;9:237–259.
   Google Scholar
• Ay B, Şahin O, Demir BS, et al. Antitumor effects of novel nickel–hydrazine complexes in lung cancer cells. New J. Chem. 2020;44:9064–9072. doi:10.1039/D0NJ00921K
   Web of Science ®Google Scholar
• Shakeel A, Altaf AA, Qureshi AM, et al. Thiourea derivatives in drug design and medicinal chemistry: a short review. J. Drug. Des. Med. Chem. 2016;2:10–20.
   Google Scholar
• Steppeler F, Iwan D, Wojaczyńska E, et al. Chiral thioureas—preparation and significance in asymmetric synthesis and medicinal chemistry. Molecules. 2020;25:401. doi:10.3390/molecules25020401
   PubMed Web of Science ®Google Scholar
• Ronchetti R, Moroni G, Carotti A, et al. Recent advances in urea- and thiourea-containing compounds: focus on innovative approaches in medicinal chemistry and organic synthesis. RSC Med. Chem. 2021;12:1046–1064. doi:10.1039/D1MD00058F
   PubMedGoogle Scholar
• https://www.mdpi.com/journal/pharmaceuticals/special_issues/urea_thiourea_drug
   Google Scholar
• Sahu S, Sahoo PR, Patel S, et al. Oxidation of thiourea and substituted thioureas: a review. Sulfur Chem. 2011;32:171–197. doi:10.1080/17415993.2010.550294
   Web of Science ®Google Scholar
• Saeed A, Flörke U, Erben MF. A review on the chemistry, coordination, structure and biological properties of 1-(acyl/aroyl)-3-(substituted) thioureas. Sulfur Chem. 2014;35:318–355. doi:10.1080/17415993.2013.834904
   Web of Science ®Google Scholar
• Saeed A, Mustafa MN, Zain-ul-Abideen M, et al. Current developments in chemistry, coordination, structure and biological aspects of 1-(acyl/aroyl)-3- (substituted)thioureas: advances continue … . Sulfur Chem. 2019;40:312–350. doi:10.1080/17415993.2018.1551488
   Web of Science ®Google Scholar
• Seck I, Nguemo F. Triazole, imidazole, and thiazole-based compounds as potential agents against coronavirus. Results Chem. 2021;3:100132. doi:10.1016/j.rechem.2021.100132
   PubMedGoogle Scholar
• Assad M, Parveen Z, Farman S, et al. In vitro screening and MD simulations of thiourea derivatives against SARS-CoV-2 in association with multidrug resistance ABCB1 transporter. ACS Omega. 2022;7:47671–47679. doi:10.1021/acsomega.2c04671
   PubMed Web of Science ®Google Scholar
• Morris GM, Lim-Wilby M. Methods in molecular biology. Methods Mol. Biol. 2008;443:365–382. doi:10.1007/978-1-59745-177-2_19
   PubMedGoogle Scholar
• Meng X-Y, Zhang H-X, Mezei M, et al. Molecular docking: a powerful approach for structure-based drug discovery. Curr. Comput. Aided Drug Des. 2011;7:146–157. doi:10.2174/157340911795677602
   PubMed Web of Science ®Google Scholar
• Pinzi L, Rastelli G. Molecular docking: shifting paradigms in drug discovery. Int. J. Mol. Sci. 2019;20:4331. doi:10.3390/ijms20184331
   PubMed Web of Science ®Google Scholar
• https://royalsocietypublishing.org/toc/rsta/2014/372/2011
   Google Scholar
• Ay B, Şahin O, Demir BS, et al. Antitumor effects of novel nickel–hydrazine complexes in lung cancer cells. New J. Chem. 2020;44:9064–9072. doi:10.1039/D0NJ00921K
   Web of Science ®Google Scholar
• Alkhimova LE, Babashkina MG, Safin DA. α-Aminophosphonates 4-XC6H4–NH–CH(4-BrC6H4)–P(O)(OiPr)2 (X = H, Br, MeO): crystal structures, Hirshfeld surface analysis, computational studies and in silico molecular docking with the SARS-CoV-2 proteins. Tetrahedron. 2021;97:132376. doi:10.1016/j.tet.2021.132376
   PubMed Web of Science ®Google Scholar
• Shiryaev AA, Goncharenko AN, Burkhanova TM, et al. A chiral (1R,2R)-N,N′-bis-(salicylidene)−1,2-diphenyl-1,2-ethanediamine Schiff base dye: synthesis, crystal structure, Hirshfeld surface analysis, computational study, photophysical properties and in silico antifungal activity. J. Iran. Chem. Soc. 2021;18:2897–2911. doi:10.1007/s13738-021-02237-5
   Web of Science ®Google Scholar
• Babashkina MG, Frontera A, Kertman AV, et al. Favipiravir: insight into the crystal structure, Hirshfeld surface analysis and computational study. J. Iran. Chem. Soc. 2022;19:85–94. doi:10.1007/s13738-021-02285-x
   Web of Science ®Google Scholar
• Alkhimova LE, Babashkina MG, Safin DA. Computational analysis of aspirin. J. Mol. Struct. 2022;1251:131975. doi:10.1016/j.molstruc.2021.131975
   Web of Science ®Google Scholar
• Burkhanova TM, Babashkina MG, Taskin-Tok T, et al. Naphthalene-based bis-N-salicylidene aniline dyes: crystal structures, Hirshfeld surface analysis, computational study and molecular docking with the SARS-CoV-2 proteins. J. Iran. Chem. Soc. 2022;19:1979–1991. doi:10.1007/s13738-021-02438-y
   Web of Science ®Google Scholar
• Alkhimova LE, Burkhanova TM, Babashkina MG, et al. A readily available structural analogue of integrastatins A and B: insight into the crystal structure, Hirshfeld surface analysis and computational study. Tetrahedron. 2022;109:132671. doi:10.1016/j.tet.2022.132671
   Web of Science ®Google Scholar
• Sharov AV, Burkhanova TM, Taskın Tok T, et al. Computational analysis of molnupiravir. Int. J. Mol. Sci. 2022;23:1508. doi:10.3390/ijms23031508
   PubMed Web of Science ®Google Scholar
• Alkhimova LE, Sharov AV, Burkhanova TM, et al. Ambroxol: insight into the crystal structure, Hirshfeld surface analysis and computational study. Polycycl. Aromat. Comp. 2023;43:2599–2617. doi:10.1080/10406638.2022.2049323
   Web of Science ®Google Scholar
• Omar RA, Koparir P, Sarac K, et al. A novel coumarin-triazole-thiophene hybrid: synthesis, characterization, ADMET prediction, molecular docking and molecular dynamics studies with a series of SARS-CoV-2 proteins. J. Chem. Sci. 2023;135:6. doi:10.1007/s12039-022-02127-0
   Web of Science ®Google Scholar
• Garkusha NA, Anikeeva OP, Bayıl I, et al. DFT, DFT, ADMET, molecular docking and molecular dynamics studies of pyridoxal. J. Indian Chem. Soc. 2023;100:100926. doi:10.1016/j.jics.2023.100926
   Web of Science ®Google Scholar
• Garcia-Santos I, Castiñeiras A, Sis BE, et al. N'-isonicotinoylpicolinohydrazonamide: synthesis, crystal structure, DFT and ADMET studies, and in silico inhibition properties toward a series of COVID-19 proteins. Polyhedron. 2023;235:116362. doi:10.1016/j.poly.2023.116362
   Web of Science ®Google Scholar
• Babashkina MG, Safin DA. 6-Amino-2-(4-fluorophenyl)-4-(trifluoromethyl)quinoline: insight into the crystal structure, Hirshfeld surface analysis and computational study. Aromat. Comp. 2023;43:3324–3341. doi:10.1080/10406638.2022.2068622
   Web of Science ®Google Scholar
• Babashkina MG, Taskin-Tok T, Burkhanova TM, et al. 1-hydroxy-6,6-Dimethyl-3-Phenyl-1,6-Dihydropyridine-2,5-Dione as a promising inhibitor of the SARS-CoV-2 proteins: insight into the crystal structure, Hirshfeld surface analysis and computational study. Polycycl. Aromat. Comp. 2023;43:4729–4749. doi:10.1080/10406638.2022.2094420
   Web of Science ®Google Scholar
• Babashkina MG, Panova EV, Alkhimova LE, et al. Salen: insight into the crystal structure, Hirshfeld surface analysis, optical properties, DFT, and molecular docking studies. Polycycl. Aromat. Comp. 2023;43:5116–5138. doi:10.1080/10406638.2022.2097281
   Web of Science ®Google Scholar
• Koparir P, Omar RA, Sarac K, et al. Synthesis, characterization and computational analysis of thiophene-2,5-diylbis((3-mesityl-3-methylcyclobutyl)methanone). Polycycl. Aromat. Comp. 2023;43:6107–6125. doi:10.1080/10406638.2022.2112712
   Web of Science ®Google Scholar
• Burkhanova TM, Krysantieva AI, Babashkina MG, et al. In silico analyses of Betulin: DFT studies, corrosion inhibition properties, ADMET prediction and molecular docking with a series of SARS-CoV-2 and monkeypox proteins. Struct Chem 2023;34:1545–1556. doi:10.1007/s11224-022-02079-8
   Web of Science ®Google Scholar
• Douglass IB, Dains FB. The structure of ethyl Di-diphenylmethylmalonate. J. Am. Chem. Soc. 1934;56:719–721. doi:10.1021/ja01318a058
   Google Scholar
• Krishnan R, Binkley JS, Seeger R, et al. Self-consistent molecular orbital methods. XX. A basis set for correlated wave functions. J. Chem. Phys. 1980;72:650–654. doi:10.1063/1.438955
   Web of Science ®Google Scholar
• Becke AD. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 1993;98:5648–5652.
   Web of Science ®Google Scholar
• Frisch MJ, Pople JA, Binkley JS. Self-consistent molecular orbital methods 25. Supplementary functions for Gaussian basis sets. J. Chem. Phys. 1984;80:3265–3269. doi:10.1063/1.447079
   Web of Science ®Google Scholar
• Dennington R, Keith TA, Millam JM. GaussView, Version 6.0, Semichem Inc., Shawnee Mission, KS (2016).
   Google Scholar
• Frisch MJ, Trucks GW, Schlegel HB, et al., Gaussian 09, Revision D.01 (2013).
   Google Scholar
• https://cadd.labshare.cn/cb-dock2/php/index.php
   Google Scholar
• Liu Y, Yang X, Gan J, et al. CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting. Nucl. Acids Res. 2022;50:W159–W164. doi:10.1093/nar/gkac394
   PubMed Web of Science ®Google Scholar
• Eberhardt J, Santos-Martins D, Tillack AF, et al. Autodock vina 1.2.0: new docking methods, expanded force field, and Python bindings. J. Chem. Inf. Model. 2021;61:3891–3898. doi:10.1021/acs.jcim.1c00203
   PubMed Web of Science ®Google Scholar
• Rose Y, Duarte JM, Lowe R, et al. RCSB protein data bank: architectural advances towards integrated searching and efficient access to macromolecular structure data from the PDB archive. J. Mol. Biol. 2021;433:166704. doi:10.1016/j.jmb.2020.11.003
   PubMed Web of Science ®Google Scholar
• Accelrys Software Inc. Discovery Studio Modeling Environment; Release 3.5; Accelrys Software Inc.: San Diego, CA, USA, 2013.
   Google Scholar
• Daina A, Michielin O, Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci. Rep. 2017;7:42717. doi:10.1038/srep42717
   PubMed Web of Science ®Google Scholar
• https://tox-new.charite.de/protox_II/index.php?site=home
   Google Scholar
• Banerjee P, Eckert AO, Schrey AK, et al. ProTox-II: a webserver for the prediction of toxicity of chemicals. Nucl. Acids Res. 2018;46:W257–W263. doi:10.1093/nar/gky318
   PubMed Web of Science ®Google Scholar
• P. Pérez, L.R. Domingo, A. Aizman, R. Contreras, Chapter 9 The electrophilicity index in organic chemistry. In Theoretical and computational chemistry; A. Toro-Labbé, Ed.; Elsevier B.V., 2007, Volume 19, pp. 139–291.
   Google Scholar
• Tok TT, Tatar G. Structures and functions of coronavirus proteins: molecular modeling of viral nucleoprotein. Int. J. Virol. Infect. Dis. 2017;2:001–007.
   Google Scholar
• Tok TT, Gowder SJT. An updated review on COVID-19 with special reference to structural elucidation and functional properties. Biomed. J. Sci. Tech. Res. 2020;31:24345–24351.
   Google Scholar
• Shamsi A, Mohammad T, Anwar S, et al. Potential drug targets of SARS-CoV-2: from genomics to therapeutics. Int. J. Biol. Macromol. 2021;177:1–9. doi:10.1016/j.ijbiomac.2021.02.071
   PubMed Web of Science ®Google Scholar
• Singh V, Somvanshi P. Structural modeling of the NS 3 helicase of tick-borne encephalitis virus and their virtual screening of potent drugs using molecular docking, interdiscip. Sci. Comput. Life Sci. 2009;1:168–172.
   Web of Science ®Google Scholar
• Gejji V, Svoboda P, Stefanik M, et al. An RNA-dependent RNA polymerase inhibitor for tick-borne encephalitis virus. Virology. 2020;546:13–19. doi:10.1016/j.virol.2020.03.006
   PubMed Web of Science ®Google Scholar
• Pulkkinen LIA, Barrass SV, Domanska A, et al. Molecular organisation of tick-borne encephalitis virus. Viruses. 2022;14:792. doi:10.3390/v14040792
   PubMed Web of Science ®Google Scholar
• Eastman RT, Roth JS, Brimacombe KR, et al. Remdesivir: a review of its discovery and development leading to emergency Use authorization for treatment of COVID-19. ACS Cent. Sci. 2020;6:672–683. doi:10.1021/acscentsci.0c00489
   PubMed Web of Science ®Google Scholar
• Du Y-X, Chen X-P. Favipiravir: pharmacokinetics and concerns about clinical trials for 2019-nCoV infection. Clin. Pharmacol. Ther. 2020;108:242–247. doi:10.1002/cpt.1844
   PubMed Web of Science ®Google Scholar
• Schmidt EV, Kropotkina EA, Abdulova GA, et al. Antiviral activity of jodantipyrin – an anti-inflammatory oral therapeutic with interferon-inducing properties. Anti-Inflamm. Anti-Allergy Agents Med. Chem. 2008;7:106–115. doi:10.2174/187152308784533195
   Google Scholar
• Reynolds CH, Tounge BA, Bembenek SD. Ligand binding efficiency: trends, physical basis, and implications. J. Med. Chem. 2008;51:2432–2438. doi:10.1021/jm701255b
   PubMed Web of Science ®Google Scholar
• Schultes S, de Graaf C, haaksma EE, et al. Ligand efficiency as a guide in fragment hit selection and optimization. Drug Discov. Today: Technol. 2010;7:e157–e162. doi:10.1016/j.ddtec.2010.11.003
   Google Scholar
• Hughes JP, Rees S, Kalindjian SB, et al. Principles of early drug discovery. Br. J. Pharmacol. 2011;162:1239–1249. doi:10.1111/j.1476-5381.2010.01127.x
   PubMed Web of Science ®Google Scholar
• Hopkins AL, Keserü GM, Leeson PD, et al. The role of ligand efficiency metrics in drug discovery. Nat. Rev. Drug Discov. 2014;13:105–121. doi:10.1038/nrd4163
   PubMed Web of Science ®Google Scholar
• Abdul-Hammed M, Adedotun IO, Falade VA, et al. Target-based drug discovery, ADMET profiling and bioactivity studies of antibiotics as potential inhibitors of SARS-CoV-2 main protease (Mpro). VirusDisease. 2021;32:642–656. doi:10.1007/s13337-021-00717-z
   PubMedGoogle Scholar
• https://www.molinspiration.com/services/logp.html
   Google Scholar