Structure and dynamic simulation-based interactions of benzenoids, pyrroles and organooxygen compounds for effective targeting of GPX4 in ischemic stroke

References

• “Sun, D., Gao, W., Hu, H., & Zhou, S. (2022). Why 90% of clinical drug development fails and how to improve it? Acta Pharmaceutica Sinica B, 12(7), 3049–3062. https://doi.org/10.1016/j.apsb.2022.02.002
   PubMed Web of Science ®Google Scholar
• Avti, P., Chauhan, A., Shekhar, N., Prajapat, M., Sarma, P., Kaur, H., Bhattacharyya, A., Kumar, S., Prakash, A., Sharma, S., & Medhi, B. (2021). Computational basis of SARS-CoV 2 main protease inhibition: an insight from molecular dynamics simulation based findings. Journal of Biomolecular Structure and Dynamics, 1–11. https://doi.org/10.1080/07391102.2021.1922310
   Google Scholar
• Boguski, M. S., Mandl, K. D., & Sukhatme, V. P. (2009). Drug discovery. Repurposing with a difference. Science (New York, N.Y.), 324(5933), 1394–1395. https://doi.org/10.1126/science.1169920
   PubMed Web of Science ®Google Scholar
• Bowers, K. J. (2006). Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters [Paper presentation]. SC '06: Proceedings of the 2006 ACM/IEEE Conference on Supercomputing (pp. 43–43). https://doi.org/10.1109/SC.2006.54.
   Google Scholar
• Cardoso, B. R., Hare, D. J., Bush, A. I., & Roberts, B. R. (2017). Glutathione peroxidase 4: A new player in neurodegeneration? Molecular Psychiatry, 22(3), 328–335. https://doi.org/10.1038/mp.2016.196.–20
   PubMed Web of Science ®Google Scholar
• Chauhan, A., Avti, P., Shekhar, N., Prajapat, M., Sarma, P., Bhattacharyya, A., Kumar, S., Kaur, H., Prakash, A., & Medhi, B. (2021). Structural and conformational analysis of SARS CoV 2 N-CTD revealing monomeric and dimeric active sites during the RNA-binding and stabilization: Insights towards potential inhibitors for N-CTD. Computers in Biology and Medicine, 134, 104495. https://doi.org/10.1016/j.compbiomed.2021.104495
   PubMed Web of Science ®Google Scholar
• Chen, J.-H., Yang, L.-K., Chen, L., Wang, Y.-H., Wu, Y., Jiang, B.-J., Zhu, J., & Li, P.-P. (2016). Atorvastatin ameliorates early brain injury after subarachnoid hemorrhage via inhibition of AQP4 expression in rabbits. International Journal of Molecular Medicine, 37(4), 1059–1066. https://doi.org/10.3892/ijmm.2016.2506.–42
   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.7b00717–35
   PubMed Web of Science ®Google Scholar
• Dubin, A., Lattanzio, B., & Gatti, L. (2017). The spectrum of cardiovascular effects of dobutamine - from healthy subjects to septic shock patients. Espectro dos efeitos cardiovasculares da dobutamina - de voluntários saudáveis a pacientes em choque séptico. Revista Brasileira de Terapia Intensiva, 29(4), 490–498. https://doi.org/10.5935/0103-507X.20170068–39
   PubMedGoogle Scholar
• Dubus, E., Ijjaali, I., Barberan, O., & Petitet, F. (2009). Drug repurposing using in silico compound profiling. Future Medicinal Chemistry, 1(9), 1723–1736. https://doi.org/10.4155/fmc.09.123
   PubMed Web of Science ®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-25
   PubMed Web of Science ®Google Scholar
• Gaonkar, R., Singh, J., Chauhan, A., Avti, P. K., & Hegde, G. (2022). Geraniol and Citral as potential therapeutic agents targeting the HSP90 activity: An in silico and experimental approach. Phytochemistry, 195, 113058. https://doi.org/10.1016/j.phytochem.2021.113058
   PubMed Web of Science ®Google Scholar
• Ghosh, D., Sehgal, K., Sodnar, B., Bhosale, N., Sarmah, D., Datta, A., Chaudhary, A., Kalia, K., Wang, X., & Bhattacharya, P. (2022). Drug repurposing for stroke intervention. Drug Discovery Today, 1359–6446. https://doi.org/10.1016/j.drudis.2022.03.003–18
   Google Scholar
• Halgren, T. A., Murphy, R. B., Friesner, R. A., Beard, H. S., Frye, L. L., Pollard, W. T., & Banks, J. L. (2004). Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. Journal of Medicinal Chemistry, 47(7), 1750–1759. https://doi.org/10.1021/jm030644s
   PubMed Web of Science ®Google Scholar
• Hsu, P.-F., Sung, S.-H., Cheng, H.-M., Shin, S.-J., Lin, K.-D., Chong, K., Yen, F.-S., Yu, B.-H., Huang, C.-T., & Hsu, C.-C. (2018). Cardiovascular benefits of acarbose vs sulfonylureas in patients with type 2 diabetes treated with metformin. The Journal of Clinical Endocrinology and Metabolism, 103 (10), 3611–3619. https://doi.org/10.1210/jc.2018-00040.–37
   PubMed Web of Science ®Google Scholar
• Huang, B. (2009). MetaPocket: A meta approach to improve protein ligand active site prediction. OMICS: A Journal of Integrative Biology, 13(4), 325–330. https://doi.org/10.1089/omi.2009.0045.–26
   PubMed Web of Science ®Google Scholar
• Irwin, J. J., & Shoichet, B. K. (2005). ZINC–a free database of commercially available compounds for virtual screening. Journal of Chemical Information and Modeling, 45(1), 177–182. https://doi.org/10.1021/ci049714+.
   PubMed Web of Science ®Google Scholar
• Li, C., Deng, X., Zhang, W., Xie, X., Conrad, M., Liu, Y., Angeli, J. P. F., & Lai, L. (2019). Novel allosteric agonists for ferroptosis regulator glutathione peroxidase 4. Journal of Medicinal Chemistry, 62(1), 266–275. https://doi.org/10.1021/acs.jmedchem.8b00315–31
   PubMed Web of Science ®Google Scholar
• Liu, J., Guo, Z.-N., Yan, X.-L., Huang, S., Ren, J.-X., Luo, Y., & Yang, Y. (2020). Crosstalk between autophagy and ferroptosis and its putative role in ischemic stroke. Frontiers in Cellular Neuroscience, 14, 577403. https://doi.org/10.3389/fncel.2020.577403–-12
   PubMed Web of Science ®Google Scholar
• Lobanov, M. I., Bogatyreva, N. S., & Galzitskaia, O. V. (2008). Radius of gyration is indicator of compactness of protein structure. Molekuliarnaia Biologiia, 42(4), 701–706.
   PubMed Web of Science ®Google Scholar
• Luong, L., Duckles, H., Schenkel, T., Mahmoud, M., Tremoleda, J. L., Wylezinska-Arridge, M., Ali, M., Bowden, N. P., Villa-Uriol, M.-C., van der Heiden, K., Xing, R., Gijsen, F. J., Wentzel, J., Lawrie, A., Feng, S., Arnold, N., Gsell, W., Lungu, A., Hose, R., … Evans, P. C. (2016). Heart rate reduction with ivabradine promotes shear stress-dependent anti-inflammatory mechanisms in arteries. Thrombosis and Haemostasis, 116(1), 181–190. https://doi.org/10.1160/TH16-03-0214.–43
   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), 1–7. https://doi.org/10.1038/s41598-018-26543-w
   PubMedGoogle Scholar
• Mujwar, S., Deshmukh, R., Harwansh, R. K., Gupta, J. K., & Gour, A. (2019). Drug repurposing approach for developing novel therapy against mupirocin-resistant Staphylococcus aureus. Assay and Drug Development Technologies, 17(7), 298–309. https://doi.org/10.1089/adt.2019.944
   PubMed Web of Science ®Google Scholar
• Mujwar, S., & Tripathi, A. (2022). Repurposing Benzbromarone as antifolate to develop novel antifungal therapy for Candida albicans. Journal of Molecular Modeling, 28(7), 1–9. https://doi.org/10.1007/s00894-022-05185-w
   Web of Science ®Google 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. https://doi.org/10.1021/jm300687e–23
   PubMed Web of Science ®Google Scholar
• Park, J. Y., Lee, S. K., Kim, J. Y., Je, K. H., Schellingerhout, D., & Kim, D. E. (2014). A new micro-computed tomography-based high-resolution blood-brain barrier imaging technique to study ischemic stroke. Stroke, 45(8), 2480–2484. https://doi.org/10.1161/STROKEAHA.114.006297.–38
   PubMed Web of Science ®Google Scholar
• Paul, S., & Candelario-Jalil, E. (2021). Emerging neuroprotective strategies for the treatment of ischemic stroke: An overview of clinical and preclinical studies. Experimental Neurology, 335, 113518. https://doi.org/10.1016/j.expneurol.2020.113518 –11
   PubMed Web of Science ®Google Scholar
• Pouliot, P., Gagnon, L., Lam, T., Avti, P. K., Bowen, C., Desjardins, M., Kakkar, A. K., Thorin, E., Sakadzic, S., Boas, D. A., & Lesage, F. (2017). Magnetic resonance fingerprinting based on realistic vasculature in mice. NeuroImage, 149, 436–445. https://doi.org/10.1016/j.neuroimage.2016.12.060
   PubMed Web of Science ®Google Scholar
• Pushpakom, S., Iorio, F., Eyers, P. A., Escott, K. J., Hopper, S., Wells, A., Doig, A., Guilliams, T., Latimer, J., McNamee, C., Norris, A., Sanseau, P., Cavalla, D., & Pirmohamed, M. (2019). Drug repurposing: progress, challenges and recommendations. Nature Reviews. Drug Discovery, 18(1), 41–58. https://doi.org/10.1038/nrd.2018.168
   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. –33 https://doi.org/10.1016/j.drudis.2009.07.014.
   PubMed Web of Science ®Google Scholar
• Sangwan, N., & Avti, P. K. (2022). Nanomedicine-mediated stem cell therapeutics in stroke. In regenerative therapies in ischemic stroke recovery (pp. 157–197). Springer.
   Google Scholar
• Sangwan, N., Singh, J., Chauhan, A., Prakash, A., Khanduja, K. L., Medhi, B., & Avti, P. K. (2022). Terpenoid analogues as putative therapeutic agents towards glutathione peroxidase (GPX4) in neurodegenerative disorders: A dynamic computational approach. Journal of Biomolecular Structure and Dynamics, 1–11.–32 https://doi.org/10.1080/07391102.2022.2086923
   Web of Science ®Google Scholar
• Santos, D., Batoreu, M. C., Aschner, M., & Marreilha dos Santos, A. P. (2013). Comparison between 5-aminosalicylic acid (5-ASA) and para-aminosalicylic acid (4-PAS) as potential protectors against Mn-induced neurotoxicity. Biological Trace Element Research, 152(1), 113–116. https://doi.org/10.1007/s12011-012-9597-0–44
   PubMed Web of Science ®Google Scholar
• Schrödinger Release. (2021). Schrödinger Release 2022-3: LigPrep., Schrödinger, LLC.
   Google Scholar
• Sievers, F., & Higgins, D. G. (2014). Clustal omega. Current Protocols in Bioinformatics, 48(1), 3–13. https://doi.org/10.1002/0471250953.bi0313s48
   PubMedGoogle Scholar
• Singh, G., Kumar, N., & Avti, P. K. (2019). Bioheat physics for hyperthermia therapy. In Application of biomedical engineering in neuroscience (pp. 381–397). Springer.
   Google Scholar
• Sinoy, S., Fayaz, S. M., Charles, K. D., Suvanish, V. K., Kapfhammer, J. P., & Rajanikant, G. K. (2017). Amikacin inhibits miR-497 maturation and exerts post-ischemic neuroprotection. Molecular Neurobiology, 54(5), 3683–3694. https://doi.org/10.1007/s12035-016-9940-0.–40
   PubMed Web of Science ®Google Scholar
• Sonaye, H. V., Sheikh, R. Y., & Doifode, C. A. (2021). Drug repurposing: Iron in the fire for older drugs. Biomedicine & Pharmacotherapy = Biomedecine & Pharmacotherapie, 141, 111638. https://doi.org/10.1016/j.biopha.2021.1116389
   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. https://doi.org/10.1517/17460441.2014.932346.–34
   PubMed Web of Science ®Google Scholar
• Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T. A. P., Rempfer, C., Bordoli, L., Lepore, R., & Schwede, T. (2018). SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Research, 46(W1), W296–W303. https://doi.org/10.1093/nar/gky427
   PubMed Web of Science ®Google Scholar
• Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M., & Barton, G. J. (2009). Jalview Version 2 - A multiple sequence alignment editor and analysis workbench. Bioinformatics (Oxford, England), 25(9), 1189–1191. https://doi.org/10.1093/bioinformatics/btp033–29
   PubMed Web of Science ®Google Scholar
• Yuan, Z., Bailey, T. L., & Teasdale, R. D. (2005). Prediction of protein B‐factor profiles. Proteins: Structure, Function, and Bioinformatics, 58(4), 905–912.–45 https://doi.org/10.1002/prot.20375
   PubMed Web of Science ®Google Scholar
• Zhan, P., Yu, B., & Ouyang, L. (2022). Drug repurposing: An effective strategy to accelerate contemporary drug discovery. Drug discovery today, 27(7), 1785–1788. https://doi.org/10.1016/j.drudis.2022.05.026
   Google Scholar
• Zhang, Y., Lu, X., Tai, B., Li, W., & Li, T. (2021). Ferroptosis and its multifaceted roles in cerebral stroke. Frontiers in Cellular Neuroscience, 15, 615372. https://doi.org/10.3389/fncel.2021.615372–19
   PubMed Web of Science ®Google Scholar
• Zhang, X.-L., Yuan, S.-Y., Wan, G., Yuan, M.-X., Yang, G.-R., Fu, H.-J., Zhu, L.-X., Zhang, J.-D., Li, Y.-L., Gao, D-y., Cui, X.-L., Wang, Z-m., Xie, R.-R., & Chen, Y-j (2021). The effects of acarbose therapy on reductions of myocardial infarction and all-cause death in T2DM during 10-year multifactorial interventions (The Beijing Community Diabetes Study 24). Scientific Reports, 11(1), 4839. https://doi.org/10.1038/s41598-021-84015-0–36
   PubMed Web of Science ®Google Scholar
• Zivin, J. A. (2009). Acute stroke therapy with tissue plasminogen activator (tPA) since it is approved by the U.S. Food and Drug Administration (FDA). Annals of Neurology, 66(1), 6–10. https://doi.org/10.1002/ana.21750–13
   PubMed Web of Science ®Google Scholar
• Zulfiqar, Z., Shah, F. A., Shafique, S., Alattar, A., Ali, T., Alvi, A. M., Rashid, S., & Li, S. (2020). Repurposing FDA approved drugs as JNK3 inhibitor for prevention of neuroinflammation induced by MCAO in rats. Journal of Inflammation Research, 13, 1185–1205. https://doi.org/10.2147/JIR.S284471__10
   PubMed Web of Science ®Google Scholar