60
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Synthesis, biological application, and computational study of a thymol-based molecule

&
Pages 35-50 | Received 24 Dec 2023, Accepted 08 Feb 2024, Published online: 18 Mar 2024

References

  • Sathe, P.S., Rajput, J.D., Gunaga, S.S., Patel, H.M., Bendre, R.S. (2019). Synthesis, characterization, and antioxidant activity of thymol-based paracetamol analogues, Res. Chem. Intermed. 45: 5487-5498. doi: 10.1007/s11164-019-03914-0
  • Riella, K.R., Marinho, R.R., Santos, J.S., Pereira-Filho, R.N., Cardoso, J.C., Albuquerque-Junior, R.L.C., Thomazzi, S.M. (2012). Anti-inflammatory and cicatrizing activities of thymol, a monoterpene of the essential oil from Lippia gracilis, in rodents, J. Ethnopharmacol. 143: 656-663. doi: 10.1016/j.jep.2012.07.028
  • Diab-Assaf, M., Semaan, J., El-Sabban, M., Al Jaouni, S.K., Azar, R., Kamal, M.A., Harakeh, S. (2018). Inhibition of Proliferation and Induction of Apoptosis by Thymoquinone via Modulation of TGF Family, p53, p21 and Bcl-2α in Leukemic Cells, Anticancer. Agents Med. Chem. 18: 210-215. doi: 10.2174/1871520617666170912133054
  • Kurt, B.Z., Gazioglu, I., Dag, A., Salmas, R.E., Kayık, G., Durdagi, S., Sonmez, F. (2017). Synthesis, anticholinesterase activity and molecular modeling study of novel carbamate-substituted thymol/carvacrol derivatives, Bioorg. Med. Chem. 25: 1352-1363. doi: 10.1016/j.bmc.2016.12.037
  • Kachur, K., Suntres, Z. (2019). The antibacterial properties of phenolic isomers, carvacrol and thymol, 60: 3042-3053.
  • Wang, K., Jiang, S., Yang, Y., Fan, L., Su, F., Ye, M. (2018). Synthesis and antifungal activity of carvacrol and thymol esters with heteroaromatic carboxylic acids, 33: 1924-1930.
  • Dominguez-Uscanga, A., Aycart, D.F., Li, K., Witola, W.H., Andrade Laborde, J.E. (2021). Anti-protozoal activity of Thymol and a Thymol ester against Cryptosporidium parvum in cell culture, Int. J. Parasitol. Drugs Drug Resist. 15: 126-133. doi: 10.1016/j.ijpddr.2021.02.003
  • Muhammed, M.T., Aki-Yalcin, E. (2021). Pharmacophore modeling in drug discovery: methodology and current status, J. Turkish Chem. Soc. Sect. A Chem. 8: 759-772.
  • Chen, Y.C. (2015). Beware of docking!, Trends Pharmacol. Sci. 36: 78-95. doi: 10.1016/j.tips.2014.12.001
  • Muhammed, M.T., Aki-Yalcin, E. (2024). Molecular Docking: Principles, Advances, and its Applications in Drug Discovery, Lett. Drug Des. Discov. 21(3): 480-495. doi: 10.2174/1570180819666220922103109
  • Wu, X., Xu, L.Y., Li, E.M., Dong, G. (2022). Application of molecular dynamics simulation in biomedicine, Chem. Biol. Drug Des. 99: 789-800. doi: 10.1111/cbdd.14038
  • Han, Y., Ali, I., Wang, Z., Cai, J., Wu, S., Tang, J., Zhang, L., Ren, J., Xiao, R., Lu, Q., Hang, L., Luo, H., Li, J. (2021). Machine learning accelerates quantum mechanics predictions of molecular crystals, Phys. Rep. 934: 1-71. doi: 10.1016/j.physrep.2021.08.002
  • Alqahtani, S. (2017). In silico ADME-Tox modeling: progress and prospects, Expert Opin. Drug Metab. Toxicol. 13: 1147–1158. doi: 10.1080/17425255.2017.1389897
  • Li, Y., Wen, J.-m., Du, C.-j., Hu, S.-m., Chen, J.-x., Zhang, S.-g., Zhang, N., Gao, F., Li, S.-j., Mao, X.-w., Miyamoto, H., Ding, K.-f. (2017). Thymol inhibits bladder cancer cell proliferation via inducing cell cycle arrest and apoptosis. Bio-chem. Biophys. Res. Commun. 491(2): 530-536. doi: 10.1016/j.bbrc.2017.04.009
  • Laamari, Y., Bimoussa, A., Fawzi, M., Oubella, A., Rohand, T., Meervelt, L.V., Itto, M.Y.A., Morjani, H., Auhmani, A. (2023). Synthesis, crystal structure and evaluation of anticancer activities of some novel heterocyclic compounds based on thymol. J. Mol. Struct. 1278: 134906. doi: 10.1016/j.molstruc.2023.134906
  • Sahin, D., Kepekci, R.A., Türkmenoğlu, B., Akkoc, S. (2024). Biological evaluations and computational studies of newly synthesized thymol-based Schiff bases as anticancer, anti-microbial and antioxidant agents. J. Biomol. Struct. Dyn., 1-15.
  • Negi, B., Rawat, D.S. (2018). Antituberculosis activity evaluation of thymol Schiff bases, Chem. Biol. Interface. 8: 244-254.
  • Beena, Kumar, D., Rawat, D.S. (2013). Synthesis and antioxidant activity of thymol and carvacrol based Schiff bases, Bioorg. Med. Chem. Lett. 23: 641-645. doi: 10.1016/j.bmcl.2012.12.001
  • Akkoç, S. (2019). Derivatives of 1-(2-(Piperidin-1-yl)ethyl)-1H-benzo[d]imidazole: Synthesis, Characterization, Determining of Electronic Properties and Cytotoxicity Studies, Chemistry Select. 4: 4938-4943.
  • Akkoç, S. (2019). Antiproliferative activities of 2-hydroxyethyl substituted benzimidazolium salts and their palladium complexes against human cancerous cell lines, Synth. Commun. 49: 2903-2914.
  • Wu, C.Y., Hu, I.C., Yang, Y.C., Ding, W.C., Lai, C.H., Lee, Y.Z., Liu, Y.C., Cheng, H.C., Lyu, P.C. (2020). An essential role of acetyl coenzyme A in the catalytic cycle of insect arylalkylamine N-acetyltransferase, Commun. Biol. 3: 441. doi: 10.1038/s42003-020-01177-9.
  • Pemovska, T., Johnson, E., Kontro, M., Repasky, G.A., Chen, J., Wells, P., Cronin, C.N., Mctigue, M., Kallioniemi, O., Porkka, K., Murray, B.W., Wennerberg, K. (2015). Axitinib effectively inhibits BCR-ABL1(T315I) with a distinct binding conformation, Nature. 519: 102-105. doi: 10.1038/nature14119
  • Trott, O., Olson, A. (2010). Autodock vina: improving the speed and accuracy of docking, J. Comput. Chem. 31: 455-461. doi: 10.1002/jcc.21334
  • Cousins, K.R. (2011). Computer review of Chem Draw ultra 12.0, J. Am. Chem. Soc. 133: 8388. doi: 10.1021/ja204075s
  • Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B.A., Thiessen, P.A., Yu, B., Zaslavsky, L., Zhang, J., Bolton, E.E. (2021). PubChem in 2021: New data content and improved web interfaces, Nucleic Acids Res. 49: D1388-D1395. doi: 10.1093/nar/gkaa971
  • Hanwell, M.D., Curtis, D.E., Lonie, D.C., Vandermeersch, T., Zurek, E., Hutchison, G.R. (2012). Avogadro: an advanced semantic chemical editor, visualization, and analysis platform, J. Cheminform. 262: 476-483.
  • Muhammed, M.T., Kuyucuklu, G., Kaynak-Onurdag, F., Aki-Yalcin, E. (2022). Synthesis, antimicrobial activity, and molecular modeling studies of some benzoxazole derivatives, Lett. Drug Des. Discov. 19: 757-768. doi: 10.2174/1570180819666220408133643
  • Abraham, M.J., Murtola, T., Schulz, R., Páll, S., Smith, J.C., Hess, B., Lindah, E. (2015). Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers, SoftwareX. 1-2: 19-25.
  • Vanommeslaeghe, K., MacKerell, A.D. (2012). Automation of the CHARMM general force field (CGenFF) I: Bond perception and atom typing, J. Chem. Inf. Model. 52: 3144-3154. doi: 10.1021/ci300363c
  • Lindahl, E., Bjelkmar, P., Larsson, P., Cuendet, M.A., Hess, B. (2010). Implementation of the charmm force field in GROMACS: Analysis of protein stability effects from correction maps, virtual interaction sites, and water models, J. Chem. Theory Comput. 6: 459-466. doi: 10.1021/ct900549r
  • Muhammed, M.T., Er, M., Akkoç, S. (2023). Molecular Modeling and In Vitro Antiproliferative Activity Studies of Some Imidazole and Isoxazole Derivatives, J. Mol. Struct. 1282: 135066. doi: 10.1016/j.molstruc.2023.135066
  • Naturalscienceedition, J., View, G., Dft, T., Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Barone, V., Petersson, G.A., Nakatsuji, H., Li, X., Caricato, M., Marenich, A., Bloino, J., Janesko, B.G., Gomperts, R., Mennucci, B., Hratchian, H.P., Ort, J.V., Fox, D.J. (2009). Gaussian 09, 53-54.
  • Becke, A.D. (1996). Density-functional thermo-chemistry. IV. A new dynamical correlation functional and implications for exact-exchange mixing, J. Chem. Phys. 104: 1040-1046. doi: 10.1063/1.470829
  • Perdew, J.P., Kurth, S. (1999). Accurate density functional with correct formal properties: A step beyond the generalized gradient approximation, Phys. Rev. Lett. 82: 2544-2547. doi: 10.1103/PhysRevLett.82.2544
  • Dennington, J.M., Keith, R.D., Millam, T.A. (2008). GaussView 5.0.
  • Accelrys Software, Disovery Studio, (2012).
  • Rodrigues-Lima, F., Dairou, J., Busi, F., Dupret, J.-M. (2010). Human Arylamine N-Acetyltransferase 1: A Drug-Metabolizing Enzyme and a Drug Target?, Curr. Drug Targets. 11: 759-766. doi: 10.2174/138945010791170905
  • Leggett, C.S., Doll, M.A., Salazar-González, R.A., Habil, M.R., Trent, J.O., Hein, D.W. (2022). Identification and characterization of potent, selective, and efficacious inhibitors of human arylamine N-acetyltransferase 1, Arch. Toxicol. 96: 511-524. doi: 10.1007/s00204-021-03194-x
  • 39. van der Zanden, S.Y., Qiao, X., Neefjes, J. (2021). New insights into the activities and toxicities of the old anticancer drug doxorubicin, FEBS J. 288: 6095–6111. doi: 10.1111/febs.15583
  • Liu, Y., Cao, J., Zhu, Y.N., Ma, Y., Murtaza, G., Li, Y., Wang, J.H., Pu, Y.S. (2020). C1222C Deletion in Exon 8 of ABL1 Is Involved in Carcinogenesis and Cell Cycle Control of Colorectal Cancer Through IRS1/PI3K/Akt Pathway, Front. Oncol. 10: 1-12. doi: 10.3389/fonc.2020.00001
  • Zhou, S., Tan, S., Fang, D., Zhang, R., Lin, W., Wu, W., Zheng, K. (2016). Computational analysis of binding between benzamide-based derivatives and Abl wt and T315I mutant kinases, RSC Adv. 6: 85355-85366. doi: 10.1039/C6RA19494J
  • Rodrigues, F.C., Hari, G., Pai, K.S.R., Suresh, A., Nayak, U.Y., Anilkumar, N.V., Thakur, G. (2021). Molecular modeling piloted analysis for semicarbazone derivative of curcumin as a potent Abl-kinase inhibitor targeting colon cancer, 3 Biotech. 11: 1-15.
  • Parcha, P., Sarvagalla, S., Madhuri, B., Pajaniradje, S., Baskaran, V., Coumar, M.S., Rajasekaran, B. (2017). Identification of natural inhibitors of Bcr-Abl for the treatment of chronic myeloid leukemia, Chem. Biol. Drug Des. 90: 596-608. doi: 10.1111/cbdd.12983
  • Işık, A., Çevik, U.A., Celik, I., Erçetin, T., Koçak, A., Özkay, Y., Kaplancıklı, Z.A. (2022). Synthesis, characterization, molecular docking, dynamics simulations, and in silico absorption, distribution, metabolism, and excretion (ADME) studies of new thiazolylhydrazone derivatives as butyrylcholinesterase inhibitors, Zeitschrift Für Naturforsch. C. 77(11-12):447-457. doi: 10.1515/znc-2021-0316
  • Dong, Y.W., Liao, M.L., Meng, X.L., Somero, G.N. (2018). Structural flexibility and protein adaptation to temperature: Molecular dynamics analysis of malate dehydrogenases of marine molluscs, Proc. Natl. Acad. Sci. U. S. A. 115: 1274-1279. doi: 10.1073/pnas.1718910115
  • Maity, D., Singh, D., Bandhu, A. (2022). Mce1R of Mycobacterium tuberculosis prefers long -chain fatty acids as specific ligands : a computa-tional study, Mol. Divers. 27(6): 2523-2543. doi: 10.1007/s11030-022-10566-7
  • Politzer, P., Murray, J.S. (2002). The funda-mental nature and role of the electrostatic potential in atoms and molecules, Theor. Chem. Acc. 108: 134-142. doi: 10.1007/s00214-002-0363-9
  • Akman, S., Akkoc, S., Zeyrek, C.T., Muhammed, M.T., Ilhan, I.O. (2023). Density functional modeling , and molecular docking with SARS-CoV-2 spike protein ( Wuhan ) and omicron S protein ( variant ) studies of new heterocyclic compounds including a pyrazoline nucleus, J. Biomol. Struct. Dyn. 41(22): 12951-12965. doi: 10.1080/07391102.2023.2169765
  • Parr, R.G., Donnelly, R.A., Levy, M., Palke, W.E. (1978). Electronegativity: The density functional viewpoint, J. Chem. Phys. 68: 3801. doi: 10.1063/1.436185
  • Chattaraj, P.K., Sarkar, U., Roy, D.R. (2006). Electrophilicity index, Chem. Rev. 106: 2065-2091. doi: 10.1021/cr040109f
  • Koopmans, T. (1934). About the assignment of wave functions and eigenvalues to the individual electrons of an atom, Physica. 1: 104-113. doi: 10.1016/S0031-8914(34)90011-2
  • Miar, M., Shiroudi, A., Pourshamsian, K., Oliaey, A.R., Hatamjafari, F. (2021). Theoreti-cal investigations on the HOMO-LUMO gap and global reactivity descriptor studies, natural bond orbital, and nucleus-independent chemical shifts analyses of 3-phenylbenzo[d]thiazole-2(3H)-imine and its para-substituted derivatives: Solvent and subs, J. Chem. Res. 45: 147-158. doi: 10.1177/1747519820932091
  • Qidwai, T. (2017). QSAR modeling, docking and ADMET studies for exploration of potential anti-malarial compounds against Plasmodium falciparum, Silico Pharmacol. 5: 1-13. doi: 10.1007/s40203-017-0026-0

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.