Identifying the Mechanisms and Molecular Targets of Yizhiqingxin Formula on Alzheimer’s Disease: Coupling Network Pharmacology with GEO Database

References

• Mebane-Sims I. 2020 Alzheimer’s disease facts and figures. Alzheimers Dement. 2020.
   Google Scholar
• Lane CA, Hardy J, Schott JM. Alzheimer’s disease. Eur J Neurol. 2018;25(1):59–70. doi:10.1111/ene.1343928872215
   PubMed Web of Science ®Google Scholar
• Solanki I, Parihar P, Parihar MS. Neurodegenerative diseases: from available treatments to prospective herbal therapy. Neurochem Int. 2016;95:100–108. doi:10.1016/j.neuint.2015.11.00126550708
   PubMed Web of Science ®Google Scholar
• Majd S, Power JH, Grantham HJ. Neuronal response in Alzheimer’s and Parkinson’s disease: the effect of toxic proteins on intracellular pathways. BMC Neurosci. 2015;16(69).
   Google Scholar
• Morris M, Maeda S, Vossel K, Mucke L. The many faces of tau. Neuron. 2011;70(3):410–426. doi:10.1016/j.neuron.2011.04.00921555069
   PubMed Web of Science ®Google Scholar
• Uddin MS, Kabir MT, Tewari D, et al. Revisiting the role of brain and peripheral Aβ in the pathogenesis of Alzheimer’s disease. J Neurol Sci. 2020;416:116974. doi:10.1016/j.jns.2020.11697432559516
   PubMed Web of Science ®Google Scholar
• Kabir MT, Uddin MS, Setu JR, et al. Exploring the role of PSEN mutations in the pathogenesis of Alzheimer’s disease. Neurotox Res. 2020.
   Web of Science ®Google Scholar
• Uddin MS, Al Mamun A, Rahman MA, et al. Emerging proof of protein misfolding and interaction in multifactorial Alzheimer’s disease. Curr Top Med Chem. 2020;20. doi:10.2174/1568026620666200601161703
   Web of Science ®Google Scholar
• Alzheimer A. Uber eine eigenartige Erkrankung der Hirnride. Centralblatt Nervenheilkunde Psychiatr. 1907;30:177–179.
   Google Scholar
• Patterson C. World Alzheimer report 2018. The state of the art of dementia research: new frontiers. An analysis of prevalence, incidence, cost and trends. Alzheimers Dis Int. 2018.
   Google Scholar
• Ong WY, Farooqui T, Koh HL, Farooqui AA, Ling EA. Protective effects of ginseng on neurological disorders. Front Aging Neurosci. 2015;7:129.26236231
   PubMed Web of Science ®Google Scholar
• Yang Y, Wang Z, Cao Y, et al. Yizhiqingxin formula alleviates cognitive deficits and enhances autophagy via mTOR signaling pathway modulation in early onset alzheimer’s disease mice. Front Pharmacol. 2019;10:1041. doi:10.3389/fphar.2019.0104131607908
   PubMed Web of Science ®Google Scholar
• Liu X, Wu J, Zhang D, Wang K, Duan X, Zhang X. A network pharmacology approach to uncover the multiple mechanisms of hedyotis diffusa willd. on colorectal cancer. Evid Based Complement Alternat Med. 2018;2018:6517034. doi:10.1155/2018/780263929619072
   PubMed Web of Science ®Google Scholar
• Hopkins AL. Network pharmacology. Nat Biotechnol. 2007;25(10):1110–1111. doi:10.1038/nbt1007-111017921993
   PubMed Web of Science ®Google Scholar
• Cao H, Li S, Xie R. Exploring the mechanism of dangguiliuhuang decoction against hepatic fibrosis by network pharmacology and experimental validation. Front Pharmacol. 2018;9:187. doi:10.3389/fphar.2018.0018729556199
   PubMed Web of Science ®Google Scholar
• Huang T, Ning Z, Hu D. Uncovering the mechanisms of chinese herbal medicine (mazirenwan) for functional constipation by focused network pharmacology approach. Front Pharmacol. 2018;9:270. doi:10.3389/fphar.2018.0027029632490
   PubMed Web of Science ®Google Scholar
• Butte A. The use and analysis of microarray data. Nat Rev Drug Discov. 2002;1(12):951–960.12461517
   PubMed Web of Science ®Google Scholar
• Lu Y, Huggins P, Bar-Joseph Z. Cross species analysis of microarray expression data. Bioinformatics. 2009;25(12):1476–1483. doi:10.1093/bioinformatics/btp24719357096
   PubMed Web of Science ®Google Scholar
• Ru J, Li P, Wang J, et al. TCMSP: a database of systems pharmacology for drug discovery from herbal medicines. J Cheminform. 2014;6(1):13. doi:10.1186/1758-2946-6-1324735618
   PubMed Web of Science ®Google Scholar
• Barton HA, Pastoor TP, Baetcke K, et al. The acquisition and application of absorption, distribution, metabolism, and excretion (ADME) data in agricultural chemical safety assessments. Crit Rev Toxicol. 2006;36(1):9–35. doi:10.1080/1040844050053436216708693
   PubMed Web of Science ®Google Scholar
• Xu X, Zhang W, Huang C, et al. A novel chemometric method for the prediction of human oral bioavailability. Int J Mol Sci. 2012;13(6):6964–6982. doi:10.3390/ijms1306696422837674
   PubMed Web of Science ®Google Scholar
• Tao W, Xu X, Wang X, et al. Network pharmacology-based prediction of the active ingredients and potential targets of Chinese herbal Radix Curcumae formula for application to cardiovascular disease. J Ethnopharmacol. 2013;145(1):1–10. doi:10.1016/j.jep.2012.09.05123142198
   PubMed Web of Science ®Google Scholar
• Law V, Knox C, Djoumbou Y, et al. DrugBank 4.0: shedding new light on drug metabolism. Nucleic Acids Res. 2014;42(Databaseissue):D1091–1097. doi:10.1093/nar/gkt106824203711
   PubMed Web of Science ®Google Scholar
• Martin A, Ochagavia ME, Rabasa LC, Miranda J, Fernandez-de-Cossio J, Bringas R. BisoGenet: a new tool for gene network building, visualization and analysis. BMC Bioinform. 2010;11(1):91. doi:10.1186/1471-2105-11-91
   PubMed Web of Science ®Google Scholar
• Tang Y, Li M, Wang J, Pan Y, Wu FX. CytoNCA: a cytoscape plugin for centrality analysis and evaluation of protein interaction networks. BioSystems. 2015;127:67–72. doi:10.1016/j.biosystems.2014.11.00525451770
   PubMed Web of Science ®Google Scholar
• Newman MEJ. A measure of betweenness centrality based on random walks. Soc Networks. 2005;27(1):39–54. doi:10.1016/j.socnet.2004.11.009
   Web of Science ®Google Scholar
• Jeong H, Mason SP, Barabási AL, Oltvai ZN. Lethality and centrality in protein networks. Nature. 2001;411(6833):41–42. doi:10.1038/3507513811333967
   PubMed Web of Science ®Google Scholar
• Bonacich P. Power and centrality: a family of measures. Am J Sociol. 1987;92(5):1170–1182. doi:10.1086/228631
   Web of Science ®Google Scholar
• Li M, Wang J, Chen X, Wang H, Pan Y. A local average connectivity-based method for identifying essential proteins from the network level. Comput Biol Chem. 2011;35(3):143–150. doi:10.1016/j.compbiolchem.2011.04.00221704260
   PubMed Web of Science ®Google Scholar
• Wang J, Li M, Wang H, Pan Y. Identification of essential proteins based on edge clustering coefficient. IEEE/ACM Trans Comput Biol Bioinform. 2012;9(4):1070–1080. doi:10.1109/TCBB.2011.14722084147
   PubMed Web of Science ®Google Scholar
• Li S, Zhang ZQ, Wu LJ, Zhang XG, Li YD, Wang YY. Understanding ZHENG in traditional Chinese medicine in the context of neuro-endocrine-immune network. IET Syst Biol. 2007;1(1):51–60. doi:10.1049/iet-syb:2006003217370429
   PubMed Web of Science ®Google Scholar
• Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–287. doi:10.1089/omi.2011.011822455463
   PubMed Web of Science ®Google Scholar
• Wang F, Feng J, Yang Y, et al. The Chinese herbal formula fuzheng quxie decoction attenuates cognitive impairment and protects cerebrovascular function in SAMP8 mice. Neuropsychiatr Dis Treat. 2018;14:3037–3051. doi:10.2147/NDT.S17548430519025
   PubMed Web of Science ®Google Scholar
• Moradi SZ, Momtaz S, Bayrami Z, Farzaei MH, Abdollahi M. Nanoformulations of herbal extracts in treatment of neurodegenerative disorders. Front Bioeng Biotechnol. 2020;8:238.32318551
   PubMed Web of Science ®Google Scholar
• Suganthy N, Devi KP, Nabavi SF, Braidy N, Nabavi SM. Bioactive effects of quercetin in the central nervous system: focusing on the mechanisms of actions. Biomed Pharmacother. 2016;84:892–908. doi:10.1016/j.biopha.2016.10.01127756054
   PubMed Web of Science ®Google Scholar
• Paula PC, Angelica Maria SG, Luis CH, Gloria Patricia CG. Preventive effect of quercetin in a triple transgenic alzheimer’s disease mice model. Molecules. 2019;24(12):2287. doi:10.3390/molecules24122287
   PubMed Web of Science ®Google Scholar
• Zaplatic E, Bule M, Shah SZA, Uddin MS, Niaz K. Molecular mechanisms underlying protective role of quercetin in attenuating Alzheimer’s disease. Life Sci. 2019;224:109–119. doi:10.1016/j.lfs.2019.03.05530914316
   PubMed Web of Science ®Google Scholar
• Chen AY, Chen YC. A review of the dietary flavonoid, kaempferol on human health and cancer chemoprevention. Food Chem. 2013;138(4):2099–2107. doi:10.1016/j.foodchem.2012.11.13923497863
   PubMed Web of Science ®Google Scholar
• Tsai MS, Wang YH, Lai YY, et al. Kaempferol protects against propacetamol-induced acute liver injury through CYP2E1 inactivation, UGT1A1 activation, and attenuation of oxidative stress, inflammation and apoptosis in mice. Toxicol Lett. 2018;290:97–109. doi:10.1016/j.toxlet.2018.03.02429574133
   PubMed Web of Science ®Google Scholar
• Yang EJ, Kim GS, Jun M, Song KS. Kaempferol attenuates the glutamate-induced oxidative stress in mouse-derived hippocampal neuronal HT22 cells. Food Funct. 2014;5(7):1395–1402. doi:10.1039/c4fo00068d24770605
   PubMed Web of Science ®Google Scholar
• Benesch MG, McElhaney RN. A comparative calorimetric study of the effects of cholesterol and the plant sterols campesterol and brassicasterol on the thermotropic phase behavior of dipalmitoylphosphatidylcholine bilayer membranes. Biochim Biophys Acta. 2014;1838(7):1941–1949. doi:10.1016/j.bbamem.2014.03.01924704414
   PubMed Web of Science ®Google Scholar
• Burg VK, Grimm HS, Rothhaar TL, et al. Plant sterols the better cholesterol in Alzheimer’s disease? A mechanistical study. J Neurosci. 2013;33(41):16072–16087. doi:10.1523/JNEUROSCI.1506-13.201324107941
   PubMed Web of Science ®Google Scholar
• Wang J, Wu F, Shi C. Substitution of membrane cholesterol with β-sitosterol promotes nonamyloidogenic cleavage of endogenous amyloid precursor protein. Neuroscience. 2013;247:227–233. doi:10.1016/j.neuroscience.2013.05.02223707801
   PubMed Web of Science ®Google Scholar
• Ye JY, Li L, Hao QM, Qin Y, Ma CS. β-Sitosterol treatment attenuates cognitive deficits and prevents amyloid plaque deposition in amyloid protein precursor/presenilin 1 mice. Korean J Physiol Pharmacol. 2020;24(1):39–46. doi:10.4196/kjpp.2020.24.1.3931908573
   PubMed Web of Science ®Google Scholar
• Guo LL, Guan ZZ, Huang Y, Wang YL, Shi JS. The neurotoxicity of β-amyloid peptide toward rat brain is associated with enhanced oxidative stress, inflammation and apoptosis, all of which can be attenuated by scutellarin. Exp Toxicol Pathol. 2013;65(5):579–584. doi:10.1016/j.etp.2012.05.00322739358
   PubMedGoogle Scholar
• Uddin MS, Kabir MT, Mamun AA, et al. Pharmacological approaches to mitigate neuroinflammation in Alzheimer’s disease. Int Immunopharmacol. 2020;84:106479.32353686
   PubMed Web of Science ®Google Scholar
• Persson T, Popescu BO, Cedazo-Minguez A. Oxidative stress in Alzheimer’s disease: why did antioxidant therapy fail? Oxid Med Cell Longev. 2014;2014:427318. doi:10.1155/2014/42731824669288
   PubMed Web of Science ®Google Scholar
• Heras-Sandoval D, Pérez-Rojas JM, Hernández-Damián J, Pedraza-Chaverri J. The role of PI3K/AKT/mTOR pathway in the modulation of autophagy and the clearance of protein aggregates in neurodegeneration. Cell Signal. 2014;26(12):2694–2701. doi:10.1016/j.cellsig.2014.08.01925173700
   PubMed Web of Science ®Google Scholar
• Li Q, Liu Y, Sun M. Autophagy and Alzheimer’s disease. Cell Mol Neurobiol. 2017;37(3):377–388. doi:10.1007/s10571-016-0386-827260250
   PubMed Web of Science ®Google Scholar
• Chiarini A, Dal Pra I, Marconi M, Chakravarthy B, Whitfield JF, Armato U. Calcium-sensing receptor (CaSR) in human brain’s pathophysiology: roles in late-onset Alzheimer’s disease (LOAD). Curr Pharm Biotechnol. 2009;10(3):317–326. doi:10.2174/13892010978784750119355942
   PubMed Web of Science ®Google Scholar
• Puig B, Gómez-Isla T, Ribé E, et al. Expression of stress-activated kinases c-Jun N-terminal kinase (SAPK/JNK-P) and p38 kinase (p38-P), and tau hyperphosphorylation in neurites surrounding betaA plaques in APP Tg2576 mice. Neuropathol Appl Neurobiol. 2004;30(5):491–502. doi:10.1111/j.1365-2990.2004.00569.x15488025
   PubMed Web of Science ®Google Scholar
• Marques CA, Keil U, Bonert A, et al. Neurotoxic mechanisms caused by the Alzheimer’s disease-linked Swedish amyloid precursor protein mutation: oxidative stress, caspases, and the JNK pathway. J Biol Chem. 2003;278(30):28294–28302. doi:10.1074/jbc.M21226520012730216
   PubMed Web of Science ®Google Scholar
• Hashimoto Y, Tsuji O, Niikura T, et al. Involvement of c-Jun N-terminal kinase in amyloid precursor protein-mediated neuronal cell death. J Neurochem. 2003;84(4):864–877. doi:10.1046/j.1471-4159.2003.01585.x12562529
   PubMed Web of Science ®Google Scholar
• Tamagno E, Parola M, Bardini P, et al. Beta-site APP cleaving enzyme up-regulation induced by 4-hydroxynonenal is mediated by stress-activated protein kinases pathways. J Neurochem. 2005;92(3):628–636. doi:10.1111/j.1471-4159.2004.02895.x15659232
   PubMed Web of Science ®Google Scholar
• Shen C, Chen Y, Liu H, et al. Hydrogen peroxide promotes Abeta production through JNK-dependent activation of gamma-secretase. J Biol Chem. 2008;283(25):17721–17730. doi:10.1074/jbc.M80001320018436531
   PubMed Web of Science ®Google Scholar
• Schnöder L, Hao W, Qin Y, et al. Deficiency of neuronal p38α MAPK attenuates amyloid pathology in Alzheimer disease mouse and cell models through facilitating lysosomal degradation of BACE1. J Biol Chem. 2016;291(5):2067–2079. doi:10.1074/jbc.M115.69591626663083
   PubMed Web of Science ®Google Scholar
• Layfield R, Cavey JR, Lowe J. Role of ubiquitin-mediated proteolysis in the pathogenesis of neurodegenerative disorders. Ageing Res Rev. 2003;2(4):343–356. doi:10.1016/S1568-1637(03)00025-414522239
   PubMed Web of Science ®Google Scholar
• Hegde AN, Smith SG, Duke LM, Pourquoi A, Vaz S. Perturbations of ubiquitin-proteasome-mediated proteolysis in aging and Alzheimer’s disease. Front Aging Neurosci. 2019;11:324. doi:10.3389/fnagi.2019.0032431866849
   PubMed Web of Science ®Google Scholar
• Chu J, Li JG, Hoffman NE, Madesh M, Praticò D. Degradation of gamma secretase activating protein by the ubiquitin-proteasome pathway. J Neurochem. 2015;133(3):432–439. doi:10.1111/jnc.1301125533523
   PubMed Web of Science ®Google Scholar
• Hong L, Huang HC, Jiang ZF. Relationship between amyloid-beta and the ubiquitin-proteasome system in Alzheimer’s disease. Neurol Res. 2014;36(3):276–282. doi:10.1179/1743132813Y.000000028824512022
   PubMed Web of Science ®Google Scholar
• Gong B, Radulovic M, Figueiredo-Pereira ME, Cardozo C. The ubiquitin-proteasome system: potential therapeutic targets for Alzheimer’s disease and spinal cord injury. Front Mol Neurosci. 2016;9:4. doi:10.3389/fnmol.2016.0000426858599
   PubMed Web of Science ®Google Scholar
• Thiel G, Rössler OG. Resveratrol stimulates AP-1-regulated gene transcription. Mol Nutr Food Res. 2014;58(7):1402–1413. doi:10.1002/mnfr.20130091324753227
   PubMed Web of Science ®Google Scholar
• Meng J, Li Y, Zhang M, et al. A combination of curcumin, vorinostat and silibinin reverses Aβ-induced nerve cell toxicity via activation of AKT-MDM2-p53 pathway. PeerJ. 2019;7:e6716. doi:10.7717/peerj.671631086728
   PubMed Web of Science ®Google Scholar