Terpenoid analogues as putative therapeutic agents towards glutathione peroxidase (GPX4) in neurodegenerative disorders: a dynamic computational approach

References

• Banerjee, P., Eckert, A. O., Schrey, A. K., & Preissner, R. (2018). ProTox-II: A webserver for the prediction of toxicity of chemicals. Nucleic Acids Research, 46(W1), W257–W263.
   PubMed Web of Science ®Google Scholar
• Bowers, K. J., Chow, D. E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, K., Kolossvary, I., Moraes, M. A., Sacerdoti, F. D., Salmon, J. K., Shaw, D. E. (2006). Scalable algorithms for molecular dynamics simulations on commodity clusters [Paper presentation]. In SC'06: Proceedings of the 2006 ACM/IEEE Conference on Supercomputing, November (pp. 43–43). IEEE.
   Google Scholar
• Chen, W., Xu, B., Xiao, A., Liu, L., Fang, X., Liu, R., Turlova, E., Barszczyk, A., Zhong, X., Sun, C. L., Britto, L. R., Feng, Z. P., & Sun, H. S. (2015). TRPM7 inhibitor carvacrol protects brain from neonatal hypoxic-ischemic injury. Molecular Brain, 8, 11.
   PubMed Web of Science ®Google Scholar
• Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7, 42717. https://doi.org/10.1038/srep42717
   PubMed Web of Science ®Google Scholar
• Dati, L. M., Ulrich, H., Real, C. C., Feng, Z. P., Sun, H. S., & Britto, L. R. (2017). Carvacrol promotes neuroprotection in the mouse hemiparkinsonian model. Neuroscience, 356, 176–181.
   PubMed Web of Science ®Google Scholar
• DeGoey, D. A., Chen, H. J., Cox, P. B., & Wendt, M. D. (2018). Beyond the rule of 5: Lessons learned from AbbVie's drugs and compound collection. Journal of Medicinal Chemistry, 61(7), 2636–2651. https://doi.org/10.1021/acs.jmedchem.7b00717
   PubMed Web of Science ®Google Scholar
• Dixon, S. J. (2014). The role of iron and reactive oxygen species in cell death. NatChemBiol, 10(1), 9.
   Google Scholar
• Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., Sanschagrin, P. C., & Mainz, D. T. (2006). Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. Journal of Medicinal Chemistry, 49(21), 6177–6196. https://doi.org/10.1021/jm051256o
   PubMed Web of Science ®Google Scholar
• Gaonkar R, Singh J, Chauhan A, Avti PK, Hegde G. Geraniol and Citral as potential therapeutic agents targeting the HSP90 activity: An in silico and experimental approach. Phytochemistry. 195, 2022, 1;195:113058. https://doi.org/10.1016/j.phytochem.2021.113058
   PubMed Web of Science ®Google Scholar
• Gaonkar, R., Avti, P. K., & Hegde, G. (2018). Differential antifungal efficiency of geraniol and citral. Natural Product Communications, 13(12), 1934578X1801301. 1934578X1801301210. https://doi.org/10.1177/1934578X1801301210
   Web of Science ®Google Scholar
• Guan, X., Li, X., Yang, X., Yan, J., Shi, P., Ba, L., Cao, Y., & Wang, P. (2019). The neuroprotective effects of carvacrol on ischemia/reperfusion-induced hippocampal neuronal impairment by ferroptosis mitigation. Life Sciences, 235, 116795.
   PubMed Web of Science ®Google Scholar
• Haddadi, H., Rajaei, Z., Alaei, H., & Shahidani, S. (2018). Chronic treatment with carvacrol improves passive avoidance memory in a rat model of Parkinson's disease. Arquivos de Neuro-Psiquiatria, 76(2), 71–77. https://doi.org/10.1590/0004-282x20170193
   PubMed Web of Science ®Google Scholar
• Herrera-Calderon, O., Yepes-Pérez, A. F., Quintero-Saumeth, J., Rojas-Armas, J. P., Palomino-Pacheco, M., Ortiz-Sánchez, J. M., Cieza-Macedo, E. C., Arroyo-Acevedo, J. L., Figueroa-Salvador, L., Peña-Rojas, G., & Andía-Ayme, V. (2020). Carvacrol: An in silico approach of a candidate drug on HER2, PI3Kα, mTOR, hER-α, PR, and EGFR receptors in the breast cancer. Evidence-Based Complementary and Alternative Medicine, 2020, 1–12. https://doi.org/10.1155/2020/8830665
   Web of Science ®Google Scholar
• Holdgate, G. A., Meek, T. D., & Grimley, R. L. (2018). Mechanistic enzymology in drug discovery: A fresh perspective. Nature Reviews. Drug Discovery, 17(2), 115–132. Febhttps://doi.org/10.1038/nrd.2017.219
   PubMed Web of Science ®Google Scholar
• Huang, B. (2009). MetaPocket: A meta approach to improve protein ligand binding site prediction. Omics, 13(4), 325–330. https://doi.org/10.1089/omi.2009.0045
   PubMed Web of Science ®Google Scholar
• Javed, H., Meeran, M., Jha, N. K., & Ojha, S. (2020). Carvacrol, a plant metabolite targeting viral protease (Mpro) and ACE2 in host cells can be a possible candidate for COVID-19. Frontiers in Plant Science, 11, 601335.
   PubMed Web of Science ®Google Scholar
• Jee, B., Kumar, S., Yadav, R., Singh, Y., Kumar, A., & Sharma, N. (2018). Ursolic acid and carvacrol may be potential inhibitors of dormancy protein small heat shock protein16.3 of Mycobacterium tuberculosis. Journal of Biomolecular Structure & Dynamics, 36(13), 3434–3443. https://doi.org/10.1080/07391102.2017.1389305
   PubMed Web of Science ®Google Scholar
• Jukic, M., Politeo, O., Maksimovic, M., Milos, M., & Milos, M. (2007). In vitro acetylcholinesterase inhibitory properties of thymol, carvacrol and their derivatives thymoquinone and thymohydroquinone. Phytotherapy Research, 21(3), 259–261.
   PubMed Web of Science ®Google Scholar
• Khalil, A., Kovac, S., Morris, G., & Walker, M. C. (2017). Carvacrol after status epilepticus (SE) prevents recurrent SE, early seizures, cell death, and cognitive decline. Epilepsia, 58(2), 263–273.
   PubMed Web of Science ®Google Scholar
• Khan, I., Bahuguna, A., Kumar, P., Bajpai, V. K., & Kang, S. C. (2018). In vitro and in vivo antitumor potential of carvacrol nanoemulsion against human lung adenocarcinoma A549 cells via mitochondrial mediated apoptosis. Scientific Reports, 8(1), 144. https://doi.org/10.1038/s41598-017-18644-9
   PubMedGoogle Scholar
• Khanduja, K. L., Avti, P. K., Kumar, S., Mittal, N., Sohi, K. K., & Pathak, C. M. (2006). Anti-apoptotic activity of caffeic acid, ellagic acid and ferulic acid in normal human peripheral blood mononuclear cells: A Bcl-2 independent mechanism. Biochimica et Biophysica Acta (BBA) - General Subjects, 1760(2), 283–289. https://doi.org/10.1016/j.bbagen.2005.12.017
   PubMed Web of Science ®Google Scholar
• Konovalova, J., Gerasymchuk, D., Parkkinen, I., Chmielarz, P., & Domanskyi, A. (2019). Interplay between MicroRNAs and oxidative stress in neurodegenerative diseases. International Journal of Molecular Sciences, 20(23), 6055.
   PubMed Web of Science ®Google Scholar
• Li, C., Deng, X., Zhang, W., Xie, X., Conrad, M., Liu, Y., Angeli, J., & Lai, L. (2019). Novel allosteric activators for ferroptosis regulator glutathione peroxidase 4. Journal of Medicinal Chemistry, 62(1), 266–275.
   PubMed Web of Science ®Google Scholar
• Liu, Z., Zhou, T., Ziegler, A. C., Dimitrion, P., & Zuo, L. (2017). Oxidative stress in neurodegenerative diseases: from molecular mechanisms to clinical applications. Oxidative Medicine and Cellular Longevity, 2017, 2525967. https://doi.org/10.1155/2017/2525967
   PubMed Web of Science ®Google Scholar
• Mahmoodi, M., Amiri, H., Ayoobi, F., Rahmani, M., Taghipour, Z., Ghavamabadi, R. T., Jafarzadeh, A., & Sankian, M. (2019). Carvacrol ameliorates experimental autoimmune encephalomyelitis through modulating pro- and anti-inflammatory cytokines. Life Sciences, 219, 257–263. https://doi.org/10.1016/j.lfs.2018.11.051
   PubMed Web of Science ®Google Scholar
• Manouchehrabadi, M., Farhadi, M., Azizi, Z., & Torkaman-Boutorabi, A. (2020). Carvacrol protects against 6-hydroxydopamine-induced neurotoxicity in in vivo and in vitro models of Parkinson's disease. Neurotoxicity Research, 37(1), 156–170.
   PubMed Web of Science ®Google Scholar
• Mbese, Z., & Aderibigbe, B. A. (2018). Biological efficacy of carvacrol analogues. Recent Patents on anti-Infective Drug Discovery, 13(3), 207–216.
   PubMedGoogle Scholar
• McBean, G. J., López, M. G., & Wallner, F. K. (2017). Redox‐based therapeutics in neurodegenerative disease. British Journal of Pharmacology, 174(12), 1750–1770.
   PubMed Web of Science ®Google Scholar
• Moeini, M., Lu, X., Avti, P. K., Damseh, R., Bélanger, S., Picard, F., Boas, D., Kakkar, A., & Lesage, F. (2018). Compromised microvascular oxygen delivery increases brain tissue vulnerability with age. Scientific Reports, 8(1), 1–17. https://doi.org/10.1038/s41598-018-26543-w
   PubMedGoogle Scholar
• Mysinger, M. M., Carchia, M., Irwin, J. J., & Shoichet, B. K. (2012). Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. Journal of Medicinal Chemistry, 55(14), 6582–6594. Jul 26https://doi.org/10.1021/jm300687e
   PubMed Web of Science ®Google Scholar
• Needleman, S. B., & Wunsch, C. D. (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology, 48(3), 443–453. https://doi.org/10.1016/0022-2836(70)90057-4
   PubMed Web of Science ®Google Scholar
• Pires, L. F., Costa, L. M., de Almeida, A. A., Silva, O. A., Cerqueira, G. S., de Sousa, D. P., & de Freitas, R. M. (2014). Is there a correlation between in vitro antioxidant potential and in vivo effect of carvacryl acetate against oxidative stress in mice hippocampus? Neurochemical Research, 39(4), 758–769. https://doi.org/10.1007/s11064-014-1267-5
   PubMed Web of Science ®Google Scholar
• Ritchie, T. J., & Macdonald, S. J. (2009). The impact of aromatic ring count on compound developability–are too many aromatic rings a liability in drug design? Drug Discovery Today, 14(21–22), 1011–1020. https://doi.org/10.1016/j.drudis.2009.07.014
   PubMed Web of Science ®Google Scholar
• Samarghandian, S., Farkhondeh, T., Samini, F., & Borji, A. (2016). Protective effects of carvacrol against oxidative stress induced by chronic stress in rat's brain, liver, and kidney. Biochemistry Research International, 2016, 1–7. https://doi.org/10.1155/2016/2645237
   Google Scholar
• Samuele, A., Crespan, E., Garbelli, A., Bavagnoli, L., & Maga, G. (2013). The power of enzyme kinetics in the drug development process. Current Pharmaceutical Biotechnology, 14(5), 551–560. Jun 1https://doi.org/10.2174/138920101405131111105023
   PubMed Web of Science ®Google Scholar
• Shahrokhi Raeini, A., Hafizibarjin, Z., Rezvani, M. E., Safari, F., Afkhami Aghda, F., & Zare Mehrjerdi, F. (2020). Carvacrol suppresses learning and memory dysfunction and hippocampal damages caused by chronic cerebral hypoperfusion. Naunyn-Schmiedeberg's Archives of Pharmacology, 393(4), 581–589.
   PubMed Web of Science ®Google Scholar
• Singh, J., Raina, A., Sangwan, N., Chauhan, A., & Avti, P. K. (2022). Structural, molecular hybridization and network based identification of miR-373-3p and miR-520e-3p as regulators of NR4A2 human gene involved in neurodegeneration. Nucleosides, Nucleotides & Nucleic Acids, 10, 1–25. https://doi.org/10.1080/15257770.2022.2048851
   Google Scholar
• Valera, E., & Masliah, E. (2013). Immunotherapy for neurodegenerative diseases: Focus on α-synucleinopathies. Pharmacology & Therapeutics, 138(3), 311–322. https://doi.org/10.1016/j.pharmthera.2013.01.013
   PubMed Web of Science ®Google Scholar
• Vašková, J., De Martino, L., Caputo, L., & De Feo, V. (2022). Two representatives of lamiaceae essential oils and their main components cause changes in glutathione related enzymatic activities. Natural Product Research, 36(2), 1–7.
   PubMed Web of Science ®Google Scholar
• Vuolo, M. M., Lima, V. S., & Junior, M. R. M. (2019). Phenolic compounds: Structure, classification, and antioxidant power. In Bioactive compounds (pp. 33–50). Woodhead Publishing.
   Google Scholar
• Wang, P., Luo, Q., Qiao, H., Ding, H., Cao, Y., Yu, J., Liu, R., Zhang, Q., Zhu, H., & Qu, L. (2017). The neuroprotective effects of carvacrol on ethanol-induced hippocampal neurons impairment via the antioxidative and antiapoptotic pathways. Oxidative Medicine and Cellular Longevity, 2017, 4079425. https://doi.org/10.1155/2017/4079425
   PubMed Web of Science ®Google Scholar
• Ward, S. E., & Beswick, P. (2014). What does the aromatic ring number mean for drug design? Expert Opinion on Drug Discovery, 9(9), 995–1003.
   PubMed Web of Science ®Google Scholar
• Yu, H., Zhang, Z. L., Chen, J., Pei, A., Hua, F., Qian, X., He, J., Liu, C. F., & Xu, X. (2012). Carvacrol, a food-additive, provides neuroprotection on focal cerebral ischemia/reperfusion injury in mice. PLoS One, 7(3), e33584.
   PubMed Web of Science ®Google Scholar
• Zamanian, M., Kujawska, M., Zadeh, M. N., Hassanshahi, A., Ramezanpour, S., Kamiab, Z., & Bazmandegan, G. (2021). Carvacrol as a potential neuroprotective agent for neurological diseases: A systematic review article. CNS & Neurological Disorders Drug Targets, 20(10), 942-953. https://doi.org/10.2174/1871527320666210506185042.
   Google Scholar
• Zotti, M., Colaianna, M., Morgese, M. G., Tucci, P., Schiavone, S., Avato, P., & Trabace, L. (2013). Carvacrol: from ancient flavoring to neuromodulatory agent. Molecules (Basel, Switzerland), 18(6), 6161–6172.
   PubMed Web of Science ®Google Scholar