Clinical side-effects based drug repositioning for anti-epileptic activity

References

• Abdelsayed, M., & Sokolov, S. (2013). Voltage-gated sodium channels: Pharmaceutical targets via anticonvulsants to treat epileptic syndromes. Channels, 7(3), 146–152. https://doi.org/10.4161/chan.24380
   PubMed Web of Science ®Google Scholar
• 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. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Alles, S. R. A., Cain, S. M., & Snutch, T. P. (2020). Pregabalin as a pain therapeutic: Beyond calcium channels. Frontiers in Cellular Neuroscience, 14, 83. https://doi.org/10.3389/fncel.2020.00083
   PubMed Web of Science ®Google Scholar
• Alper, K., Schwartz, K. A., Kolts, R. L., & Khan, A. (2007). Seizure incidence in psychopharmacological clinical trials: An analysis of food and drug administration (FDA) summary basis of approval reports. Biological Psychiatry, 62(4), 345–354. https://doi.org/10.1016/j.biopsych.2006.09.023
   PubMed Web of Science ®Google Scholar
• Anderson, J., & Moor, C. C. (2010). Anti-epileptic drugs: A guide for the non-neurologist. Clinical Medicine, 10(1), 54–58. https://doi.org/10.7861/clinmedicine.10-1-54
   PubMed Web of Science ®Google Scholar
• Banerjee, P. N., Filippi, D., & Allen Hauser, W. (2009). The descriptive epidemiology of epilepsy-A review. Epilepsy Research, 85(1), 31–45. https://doi.org/10.1016/j.eplepsyres.2009.03.003
   PubMed Web of Science ®Google Scholar
• Bastos, A., Bernasconi, A., Bernasconi, N., Duncan, J., Lemieux, L., & Sisodiya, S. (2002). Structural image analysis in epilepsy. Epilepsia, 43, 19–24. https://doi.org/10.1046/j.1528-1157.2002.043s1019.x
   Web of Science ®Google Scholar
• Beghi, E. (2020). The epidemiology of epilepsy. Neuroepidemiology, 54(2), 185–191. https://doi.org/10.1159/000503831
   PubMed Web of Science ®Google Scholar
• Beydoun, A., DuPont, S., Zhou, D., Matta, M., Nagire, V., & Lagae, L. (2020). Current role of carbamazepine and oxcarbazepine in the management of epilepsy. Seizure, 83, 251–263. https://doi.org/10.1016/j.seizure.2020.10.018
   PubMed Web of Science ®Google Scholar
• Brodie, M. J., Besag, F., Ettinger, A. B., Mula, M., Gobbi, G., Comai, S., Aldenkamp, A. P., & Steinhoff, B. J. (2016). Epilepsy, anti-epileptic drugs, and aggression: an evidence-based review. Pharmacological Reviews, 68(3), 563–602. https://doi.org/10.1124/pr.115.012021
   PubMed Web of Science ®Google Scholar
• Campillos, M., Kuhn, M., Gavin, A. C., Jensen, L. J., & Bork, P. (2008). Drug target identification using side-effect similarity. Science, 321(5886), 263–266. https://doi.org/10.1126/science.1158140
   PubMed Web of Science ®Google Scholar
• Coyle, C., Cafferty, F. H., & Langley, R. E. (2016). Aspirin and colorectal cancer prevention and treatment: Is it for everyone? Current Colorectal Cancer Reports, 12(1), 27–34. https://doi.org/10.1007/s11888-016-0306-9
   PubMedGoogle Scholar
• Cunningham, K. L., & Littleton, J. T. (2023). Mechanisms controlling the trafficking, localization, and abundance of presynaptic Ca2+ channels. Frontiers in Molecular Neuroscience, 15, 767. https://doi.org/10.3389/fnmol.2022.1116729
   Web of Science ®Google Scholar
• Devine, B. L., Fife, R., & Trust, P. M. (1977). Minoxidil for severe hypertension after failure of other hypotensive drugs. BMJ, 2(6088), 667–669. https://doi.org/10.1136/bmj.2.6088.667
   PubMedGoogle Scholar
• Docherty, R. J., & Farmer, C. E. (2009). The pharmacology of voltage-gated sodium channels in sensory neurones. In Handbook of experimental pharmacology (pp. 519–561). 194. https://doi.org/10.1007/978-3-540-79090-7_15
   Google Scholar
• Dokkedal-Silva, V., Berro, L. F., Galduróz, J. C. F., Tufik, S., & Andersen, M. L. (2019). Clonazepam: Indications, side effects, and potential for nonmedical use. Harvard Review of Psychiatry, 27(5), 279–289. https://doi.org/10.1097/HRP.0000000000000227
   PubMed Web of Science ®Google Scholar
• Drugs@FDA: FDA-Approved Drugs. Fda. Retrieved October 21, 2022, from https://www.accessdata.fda.gov/scripts/cder/daf/index.cfm?event=overview.process&ApplNo=019537%0Ahttps://www.accessdata.fda.gov/drugsatfda_docs/label/2020/125514s088lbl.pdf
   Google Scholar
• Forli, S., Huey, R., Pique, M. E., Sanner, M. F., Goodsell, D. S., & Olson, A. J. (2016). Computational protein-ligand docking and virtual drug screening with the AutoDock suite. Nature Protocols, 11(5), 905–919. https://doi.org/10.1038/nprot.2016.051
   PubMed Web of Science ®Google Scholar
• Garcia-Albeniz, X., & Chan, A. T. (2011). Aspirin for the prevention of colorectal cancer. Best Practice & Research Clinical Gastroenterology, 25(4-5), 461–472. https://doi.org/10.1016/j.bpg.2011.10.015
   PubMed Web of Science ®Google Scholar
• Gennari, L., Merlotti, D., de Paola, V., & Nuti, R. (2008). Raloxifene in breast cancer prevention. Expert Opinion on Drug Safety, 7(3), 259–270. https://doi.org/10.1517/14740338.7.3.259
   PubMed Web of Science ®Google Scholar
• Ghofrani, H. A., Osterloh, I. H., & Grimminger, F. (2006). Sildenafil: from angina to erectile dysfunction to pulmonary hypertension and beyond. Nature Reviews Drug Discovery, 5(8), 689–702. https://doi.org/10.1038/nrd2030
   PubMed Web of Science ®Google Scholar
• Górska, N., Słupski, J., & Cubała, W. J. (2019). Antipsychotic drugs in epilepsy. Neurologia i Neurochirurgia Polska, 53(6), 408–412. https://doi.org/10.5603/PJNNS.a2019.0052
   PubMed Web of Science ®Google Scholar
• Górska, N., Słupski, J., Cubała, W. J., Wiglusz, M. S., & Gałuszko-Węgielnik, M. (2018). Antidepressants in epilepsy. Neurologia i Neurochirurgia Polska, 52(6), 657–661. https://doi.org/10.1016/j.pjnns.2018.07.005
   PubMed Web of Science ®Google Scholar
• Hatzimouratidis, K. (2006). Sildenafil in the treatment of erectile dysfunction: An overview of the clinical evidence. Clinical Interventions in Aging, 1(4), 403–414., https://doi.org/10.2147/ciia.2006.1.4.403
   PubMed Web of Science ®Google Scholar
• Hebeisen, S., Pires, N., Loureiro, A. I., Bonifácio, M. J., Palma, N., Whyment, A., Spanswick, D., & Soares-Da-Silva, P. (2015). Eslicarbazepine and the enhancement of slow inactivation of voltage-gated sodium channels: A comparison with carbamazepine, oxcarbazepine and lacosamide. Neuropharmacology, 89, 122–135. https://doi.org/10.1016/j.neuropharm.2014.09.008
   PubMed Web of Science ®Google Scholar
• Hill, T., Coupland, C., Morriss, R., Arthur, A., Moore, M., & Hippisley-Cox, J. (2015). Antidepressant use and risk of epilepsy and seizures in people aged 20 to 64 years: Cohort study using a primary care database. BMC Psychiatry, 15, 1–13. https://doi.org/10.1186/s12888-015-0701-9
   PubMed Web of Science ®Google Scholar
• Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins: Structure, Function, and Bioinformatics, 65(3), 712–725. https://doi.org/10.1002/prot.21123
   PubMed Web of Science ®Google Scholar
• Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., de Groot, B. L., Grubmüller, H., & MacKerell, A. D. (2017). CHARMM36m: An improved force field for folded and intrinsically disordered proteins. Nature Methods, 14(1), 71–73. https://doi.org/10.1038/nmeth.4067
   PubMed Web of Science ®Google Scholar
• Jarada, T. N., Rokne, J. G., & Alhajj, R. A. (2020). Review of computational drug repositioning: Strategies, approaches, opportunities, challenges, and directions. Journal of Cheminformatics, 12(1), 46. https://doi.org/10.1186/s13321-020-00450-7
   PubMed Web of Science ®Google Scholar
• Jo, S., Jiang, W., Lee, H. S., Roux, B., & Im, W. (2013). CHARMM-GUI ligand binder for absolute binding free energy calculations and its application. Journal of Chemical Information and Modeling, 53(1), 267–277. https://doi.org/10.1021/ci300505n
   PubMed Web of Science ®Google Scholar
• Jo, S., Kim, T., Iyer, V. G., & Im, W. (2008). CHARMM-GUI: A web-based graphical user interface for CHARMM. Journal of Computational Chemistry, 29(11), 1859–1865. https://doi.org/10.1002/jcc.20945
   PubMed Web of Science ®Google Scholar
• Jourdan, J. P., Bureau, R., Rochais, C., & Dallemagne, P. (2020). Drug repositioning: A brief overview. Journal of Pharmacy and Pharmacology, 72(9), 1145–1151. https://doi.org/10.1111/jphp.13273
   PubMed Web of Science ®Google Scholar
• Kenyon, K., Mintzer, S., & Nei, M. (2014). Carbamazepine treatment of generalized tonic-clonic seizures in idiopathic generalized epilepsy. Seizure, 23(3), 234–236. https://doi.org/10.1016/j.seizure.2013.11.016
   PubMed Web of Science ®Google Scholar
• Kim, J. H., & Scialli, A. R. (2011). Thalidomide: The tragedy of birth defects and the effective treatment of disease. Toxicological Sciences, 122(1), 1–6. https://doi.org/10.1093/toxsci/kfr088
   PubMed Web of Science ®Google Scholar
• Koch-Stoecker, S. (2002). Antipsychotic drugs and epilepsy: Indications and treatment guidelines. Epilepsia, 43(S2), 19–24. https://doi.org/10.1046/j.1528-1157.2002.043s2019.x
   PubMedGoogle Scholar
• Kuhn, M., Letunic, I., Jensen, L. J., & Bork, P. (2016). The SIDER database of drugs and side effects. Nucleic Acids Research, 44(D1), D1075–D1079. https://doi.org/10.1093/nar/gkv1075
   PubMed Web of Science ®Google Scholar
• Kumar, P., Sheokand, D., Grewal, A., Saini, V., Gupta, D., & Kumar, A. (2022). BBBper: A machine learning based online tool for Blood Brain Barrier (BBB) permeability prediction. Bioinformatics (under Review).
   Google Scholar
• Kumar, P., Sheokand, D., Grewal, A., Saini, V., & Kumar, A. (2022). Drug repositioning for idiopathic epilepsy using gene expression signature data. Bioinformation, 18(10), 845–852. https://doi.org/10.6026/97320630018845
   PubMedGoogle Scholar
• Kumar, P., Sheokand, D., Saini, V., & Kumar, A. (2022). In-silico identification and analysis of hub proteins for designing novel first line anti-seizure medications. Letters in Drug Design & Discovery, 20(6), 662–673. https://doi.org/10.2174/1570180819666220512122511
   Web of Science ®Google Scholar
• Lee, J., Cheng, X., Swails, J. M., Yeom, M. S., Eastman, P. K., Lemkul, J. A., Wei, S., Buckner, J., Jeong, J. C., Qi, Y., Jo, S., Pande, V. S., Case, D. A., Brooks, C. L., MacKerell, A. D., Klauda, J. B., & Im, W. (2016). CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field. Journal of Chemical Theory and Computation, 12(1), 405–413. https://doi.org/10.1021/acs.jctc.5b00935
   PubMed Web of Science ®Google Scholar
• Lipkind, G. M., & Fozzard, H. A. (2010). Molecular model of anticonvulsant drug binding to the voltage-gated sodium channel inner pore. Molecular Pharmacology, 78(4), 631–638. https://doi.org/10.1124/mol.110.064683
   PubMed Web of Science ®Google Scholar
• Löscher, W., Klitgaard, H., Twyman, R. E., & Schmidt, D. (2013). New avenues for anti-epileptic drug discovery and development. Nature Reviews Drug Discovery, 12(10), 757–776. https://doi.org/10.1038/nrd4126
   PubMed Web of Science ®Google Scholar
• Macindoe, G., Mavridis, L., Venkatraman, V., Devignes, M. D., & Ritchie, D. W. (2010). HexServer: An FFT-based protein docking server powered by graphics processors. Nucleic Acids Research, 38(Web Server), W445–W449. https://doi.org/10.1093/nar/gkq311
   PubMedGoogle Scholar
• Malamiri, R. A., Ghaempanah, M., Khosroshahi, N., Nikkhah, A., Bavarian, B., & Ashrafi, M. R. (2012). Efficacy and safety of intravenous sodium valproate versus phenobarbital in controlling convulsive status epilepticus and acute prolonged convulsive seizures in children: A randomised trial. European Journal of Paediatric Neurology, 16(5), 536–541. https://doi.org/10.1016/j.ejpn.2012.01.012
   PubMed Web of Science ®Google Scholar
• Manjushree, N., Chakraborty, A., Shashidhar, K., & Narayanaswamy, S. (2015). A review of the drug pregabalin. International Journal of Basic and Clinical Pharmacology, 4(4), 601–605. https://doi.org/10.18203/2319-2003.ijbcp20150359
   Google Scholar
• Masiulis, S., Desai, R., Uchański, T., Serna Martin, I., Laverty, D., Karia, D., Malinauskas, T., Zivanov, J., Pardon, E., Kotecha, A., Steyaert, J., Miller, K. W., & Aricescu, A. R. (2019). GABAA receptor signalling mechanisms revealed by structural pharmacology. Nature, 565(7740), 454–459. https://doi.org/10.1038/s41586-018-0832-5
   PubMed Web of Science ®Google Scholar
• Meier-Stephenson, V., Riemer, J., & Narendran, A. (2017). The HIV protease inhibitor, nelfinavir, as a novel therapeutic approach for the treatment of refractory pediatric leukemia. OncoTargets and Therapy, 10, 2581–2593. https://doi.org/10.2147/OTT.S136484
   PubMed Web of Science ®Google Scholar
• Miller, B. R., McGee, T. D., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). MMPBSA.py: An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8(9), 3314–3321. https://doi.org/10.1021/ct300418h
   PubMed Web of Science ®Google Scholar
• Morris, G. M., Ruth, H., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). Software news and updates AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
   PubMed Web of Science ®Google Scholar
• Moshé, S. L., Perucca, E., Ryvlin, P., & Tomson, T. (2015). Epilepsy: New advances. The Lancet, 385(9971), 884–898. https://doi.org/10.1016/S0140-6736(14)60456-6
   PubMed Web of Science ®Google Scholar
• Mruk, A. L., Garlitz, K. L., & Leung, N. R. (2015). Levetiracetam in neonatal seizures: A review. The Journal of Pediatric Pharmacology and Therapeutics, 20(2), 76–89. https://doi.org/10.5863/1551-6776-20.2.76
   PubMedGoogle Scholar
• Napolitano, F., Zhao, Y., Moreira, V. M., Tagliaferri, R., Kere, J., D’Amato, M., & Greco, D. (2013). Drug repositioning: A machine-learning approach through data integration. Journal of Cheminformatics, 5(1), 30. https://doi.org/10.1186/1758-2946-5-30
   PubMedGoogle Scholar
• Okazaki, M., Adachi, N., Ito, M., Watanabe, M., Watanabe, Y., Kato, M., & Onuma, T. (2011). One-year seizure prognosis in epilepsy patients treated with antidepressants. Epilepsy & Behavior, 22(2), 331–335. https://doi.org/10.1016/j.yebeh.2011.07.016
   PubMed Web of Science ®Google Scholar
• Pauig, P. M., Deluca, M. A., & Osterheld, R. G. (1961). Thioridazine hydrochloride in the treatment of behavior disorders in epileptics. American Journal of Psychiatry, 117(9), 832–833.
   PubMed Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF chimera - A visualisation system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Piplani, S., Verma, P. K., & Kumar, A. (2016). Neuroinformatics analyses reveal GABAt and SSADH as major proteins involved in anticonvulsant activity of valproic acid. Biomedicine & Pharmacotherapy, 81, 402–410. https://doi.org/10.1016/j.biopha.2016.04.036
   PubMed Web of Science ®Google Scholar
• Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., Shirts, M. R., Smith, J. C., Kasson, P. M., van der Spoel, D., Hess, B., & Lindahl, E. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29(7), 845–854. https://doi.org/10.1093/bioinformatics/btt055
   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
• Ribot, R., Ouyang, B., & Kanner, A. M. (2017). The impact of antidepressants on seizure frequency and depressive and anxiety disorders of patients with epilepsy: Is it worth investigating? Epilepsy & Behavior, 70, 5–9. https://doi.org/10.1016/j.yebeh.2017.02.032
   PubMed Web of Science ®Google Scholar
• Romoli, M., Mazzocchetti, P., D'Alonzo, R., Siliquini, S., Rinaldi, V. E., Verrotti, A., Calabresi, P., & Costa, C. (2019). Valproic acid and epilepsy: From molecular mechanisms to clinical evidences. Current Neuropharmacology, 17(10), 926–946. https://doi.org/10.2174/1570159X17666181227165722
   PubMed Web of Science ®Google Scholar
• Schrör, K. (1997). Aspirin and platelets: The antiplatelet action of aspirin and its role in thrombosis treatment and prophylaxis. Seminars in Thrombosis and Hemostasis, 23(04), 349–356. https://doi.org/10.1055/s-2007-996108
   PubMedGoogle Scholar
• Suchonwanit, P., Thammarucha, S., & Leerunyakul, K. (2019). Minoxidil and its use in hair disorders: A review. Drug Design, Development and Therapy, ume 13, 2777–2786. https://doi.org/10.2147/DDDT.S214907
   Web of Science ®Google Scholar
• Thijs, R. D., Surges, R., O'Brien, T. J., & Sander, J. W. (2019). Epilepsy in adults. The Lancet, 393(10172), 689–701. https://doi.org/10.1016/S0140-6736(18)32596-0
   PubMed Web of Science ®Google Scholar
• Valdés-Tresanco, M. S., Valdés-Tresanco, M. E., Valiente, P. A., & Moreno, E. (2021). Gmx_MMPBSA: A new tool to perform end-state free energy calculations with GROMACS. Journal of Chemical Theory and Computation, 17(10), 6281–6291. https://doi.org/10.1021/acs.jctc.1c00645
   PubMed Web of Science ®Google Scholar
• Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general Amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. https://doi.org/10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• Wishart, D. S., Feunang, Y. D., Guo, A. C., Lo, E. J., Marcu, A., Grant, J. R., Sajed, T., Johnson, D., Li, C., Sayeeda, Z., Assempour, N., Iynkkaran, I., Liu, Y., MacIejewski, A., Gale, N., Wilson, A., Chin, L., Cummings, R., Le, D., … Wilson, M. (2018). DrugBank 5.0: A major update to the DrugBank database for 2018. Nucleic Acids Research, 46(D1), D1074–D1082. https://doi.org/10.1093/nar/gkx1037
   PubMed Web of Science ®Google Scholar
• Wright, C. L., Mist, S. D., Ross, R. L., & Jones, K. D. (2010). Duloxetine for the treatment of fibromyalgia. Expert Review of Clinical Immunology, 6(5), 745–756. https://doi.org/10.1586/eci.10.64
   PubMed Web of Science ®Google Scholar
• Yang, L., & Agarwal, P. (2011). Systematic drug repositioning based on clinical side-effects. PLoS One. 6(12), e28025. https://doi.org/10.1371/journal.pone.0028025
   PubMed Web of Science ®Google Scholar