Bioinformatic analysis of the impact of Panax notoginseng and Polygonati Rhizoma on myopia: insights from oxidative stress-related genes

doi:10.5246/jcps.2024.05.033

Abstract

Abstract:

To investigate the material basis and mechanism of Panax notoginseng and Polygonati Rhizoma in the treatment of myopia using network pharmacology, we retrieved the primary active components of Panax notoginseng and Polygonati Rhizoma from the Chinese Medicine Systematic Pharmacology Database and Analysis Platform (TCMSP). The target sites for these components were predicted, and the corresponding gene names were obtained from the UniProt database. Targets associated with myopia and oxidative stress were extracted from the GeneCards database, and the intersection of targets from traditional Chinese medicine (TCM) with those related to myopia and oxidative stress was identified. Subsequently, the String database was utilized to construct a protein interaction network, and Cytoscape software was employed to identify key genes and generate network pharmacological maps. GO and KEGG enrichment analyses were performed on the intersection targets using the DAVID database. The results revealed seven active components of Panax notoginseng and five active ingredients of Polygonati Rhizoma. After removing duplicates, 187 targets were obtained, with 92 targets common to the drugs, myopia, and oxidative stress. Five hub genes were identified through protein-protein interaction analysis. GO analysis indicated enrichment in cellular components such as the nucleus and plasma membrane. KEGG pathway analysis revealed that the signaling pathways of the intersection targets were primarily associated with “Pathways in cancer” and “Lipid and atherosclerosis”. In conclusion, the regulation of target genes such as JUN, TP53, ESR1, IL6, and TNF, particularly in cellular components like the nucleus and plasma membrane, may contribute to the anti-myopic effects of Panax notoginseng and Polygonati Rhizoma.

Key words: Network pharmacology, Myopia, Oxidative stress, Panax notoginseng, Polygonati Rhizoma

Supporting:

Dan Wang. Bioinformatic analysis of the impact of Panax notoginseng and Polygonati Rhizoma on myopia: insights from oxidative stress-related genes[J]. Journal of Chinese Pharmaceutical Sciences, 2024, 33(5): 438-447.

Figures/Tables 10

Table 1. Effective chemical components of drugs.

Table 2. GO function annotation of intersection targets.

Table 3. KEGG pathway enrichment at intersection targets.

References 29

[1]	Tian, X.T.; Liu, F.; Li, Z.X.; Lin, Y.F.; Liu, H.; Hu, P.; Chen, M.C.; Sun, Z.L.; Xu, Z.; Zhang, Y.T.; Han, L.; Zhang, Y.Y.; Pan, G.Y.; Huang, C.G. Enhanced anti-diabetic effect of berberine combined with timosaponin B2 in goto-kakizaki rats, associated with increased variety and exposure of effective substances through intestinal absorption. Front Pharmacol. 2019, 10, 19.
[2]	Guo, M.F.; Dai, Y.J.; Gao, J.R.; Chen, P.J. Uncovering the mechanism of astragalus membranaceus in the treatment of diabetic nephropathy based on network pharmacology. J. Diabetes Res. 2020, 2020, 5947304.
[3]	Xu, C.C.; Wang, W.W.; Wang, B.; Zhang, T.; Cui, X.M.; Pu, Y.Q.; Li, N. Analytical methods and biological activities of Panax notoginseng saponins: recent trends. J. Ethnopharmacol. 2019, 236, 443–465.
[4]	Piao, C.L.; Sun, Z.Y.; Jin, D.; Wang, H.; Wu, X.M.; Zhang, N.W.; Lian, F.M.; Tong, X.L. Network pharmacology-based investigation of the underlying mechanism of panax notoginseng treatment of diabetic retinopathy. Comb. Chem. High Throughput Screen. 2020, 23, 334–344.
[5]	Guo, X.; Sun, W.; Luo, G.B.; Wu, L.L.; Xu, G.Y.; Hou, D.; Hou, Y.; Guo, X.Y.; Mu, X.H.; Qin, L.L.; Liu, T.H. Panax notoginseng saponins alleviate skeletal muscle insulin resistance by regulating the IRS1-PI3K-AKT signaling pathway and GLUT4 expression. FEBS Open Bio. 2019, 9, 1008–1019.
[6]	Yang, X.X.; Wang, X.; Shi, T.T.; Dong, J.C.; Li, F.J.; Zeng, L.X.; Yang, M.; Gu, W.; Li, J.P.; Yu, J. Mitochondrial dysfunction in high-fat diet-induced nonalcoholic fatty liver disease: the alleviating effect and its mechanism of Polygonatum kingianum. Biomed. Pharmacother. 2019, 117, 109083.
[7]	Yan, H.L.; Lu, J.M.; Wang, Y.F.; Gu, W.; Yang, X.X.; Yu, J. Intake of total saponins and polysaccharides from Polygonatum kingianum affects the gut microbiota in diabetic rats. Phytomedicine. 2017, 26, 45–54.
[8]	Yang, X.X.; Wei, J.D.; Mu, J.K.; Liu, X.; Li, F.J.; Li, Y.Q.; Gu, W.; Li, J.P.; Yu, J.E. Mitochondrial metabolomic profiling for elucidating the alleviating potential of Polygonatum kingianum against high-fat diet-induced nonalcoholic fatty liver disease. World J. Gastroenterol. 2019, 25, 6404–6415.
[9]	Han, C.Y.; Sun, T.T.; Fan, G.T.; Liu, Y.W.; Liu, C.Y. Protective effects of Polygonatum sibiricum against CCl₄-induced acute liver injury in rats through oxidative stress and mitochondrial apoptotic pathways. J. Chin. Pharm. Sci. 2021, 30, 306–318.
[10]	Miura, T.; Kato, A.; Usami, M.; Kadowaki, S.; Seino, Y. Effect of polygonati rhizoma on blood glucose and facilitative glucose transporter isoform 2(GLUT2) mRNA expression in wistar fatty rats. Biol. Pharm. Bull. 1995, 18, 624–625.
[11]	Cui, X.Y.; Wu, X.A.; Lu, D.; Wang, D. Network pharmacology-based strategy for predicting therapy targets of Sanqi and Huangjing in diabetes mellitus. World J. Clin. Cases. 2022, 10, 6900–6914.
[12]	Wu, D.Y.; Wang, X.D.; Chai, J.M.; Li, Q.Q.; Li, Y.; Bi, M.; Gui, W.W. Cao, H.M. Study on the mechanism of Danggui Buxue Decoction in the treatment of diabetic retinopathy based on network pharmacology and experiment. J. Chin. Pharm. Sci. 2023, 32, 527.
[13]	Yan, H.; Wang, J.; Fu, H.; Yang, M.; Qu, M.; Fang, Z.E. Discussion on the potential target and mechanism of Dachaihu Decoction in treating hyperlipidemia based on network pharmacology. J. Chin. Pharm. Sci. 2023, 32, 446.
[14]	Huo, L.; Sun, Y.L.; Xu, X.W.; Qiang, T.T.; Ruan, X.F. Meta Analysis on Rhizoma Polygonati and Notoginseng Compatibility in the Treatment of Coronary Heart Disease Angina Pectoris. World Chin. Med. 2021, 16, 3033–3039.
[15]	Yang, Y.Q.; Li, Y.Q.; Yu, L.P.; Li, X.E.; Mu, J.K.; Shang, J.; Gu, W.; Li, J.P.; Yu, J.E.; Yang, X.X. Muscle fatigue-alleviating effects of a prescription composed of polygonati rhizoma and notoginseng radix et rhizoma. BioMed Res. Int. 2020, 2020, 1–6, article number: 3963045.
[16]	Xiong, Y.; Du, C.X.; Duan, Y.S.; Yuan, C.M.; Huang, L.J.; Gu, W.; Hao, X.J. Chemical constituents and pharmacological activities of Sedum aizoon form Guizhou province. Chin. Tradit. Herbal Drugs. 2019, 50, 5404–5410.
[17]	Wang, Y.R.; Yuan, M.; Zhang, L.; Zhang, Y.Y.; Liao, P.; Yao, Z.X. Reseatch progress on antioxidant actions and resated mechanisms of querchtin. Acta Nutr. Sin. 2022, 44, 204–208.
[18]	He, Z.W.; Hu, X.; Chen, G.F.; Liu, C. Antioxidant: a new therapy for thyroid associated ophthalmopathy. Rec. Adv. Ophthalmol. 2022, 42, 417–420.
[19]	Mai, J.L.; Li, J.L.; Xiao, J.C.; Liang, D.; Wang, H.B. Mechanism of polygonatiRhizoma on treating osteoporosis based on network pharmacology and preliminary verification. Chin. J. Exp. Tradit. Med. Form. 2022, 28, 210–217.
[20]	Huang, Y.P; Wu, D.Z; Wang, S. Research progress on pharmacological action of scutellariae radix and its drug pair. China Pharm. 2022, 31, 129–133.
[21]	Gao, X.S.; Wang, Q.; Zhang, Z.; Sun, R.Q. Effect of baicalin on retinal injury in mice with acute ocular hypertension. Shandong Med. J. 2021, 61, 34–37.
[22]	Lu, Q.; Zou L.F.; Gao Y.Z.; Ye, T.; Li, M.J.; Zhang, Y.K.; Liang, B.; Yuan,Y.; Sun, WS.; Xing, D.M. The protective effect and mechanism of liquiritigenin on UVA-induced photoaging. Chin. J. New Drugs. 2022, 31, 2056–2066.
[23]	Cai, Q.; Yu, T.; Tang, H.J.; Zhang, R.; Yang L.; Wang Z.Q. Ginsenoside Rh2 regulates TNF/MAPK and NF-κB signaling pathway to inhibit TGF- β1 induced activation of LX-2 cells. Tradit. Chin. Drug Res. Clin. Pharm. 2022, 33, 1047–1054.
[24]	Fan, Z.X.; Zhang, W.; Tang, Y.H.; Wang, X.I.; Li, Y.H.; Huang, C.X. Effects of ginsenoside Rh2 on the levels of NLRP3, IL-1β, TNF-α and SOD activity in rats with myocardial ischemia-reperfusion injury. J. Emerg. Tradit. Chin. Med. 2021, 30, 1541–1544+1549.
[25]	Dan, Y.J.; Gao, X.R.; Chen, J.; Luo, B.; Huang, L.; Gan, J.H.; Ou, Y.K.; Lü, H.B.; He, Y. Effects and mechanism of panax notoginseng saponins on the apoptosis of retinal ganglion cells induced by hypoxia. Chin. J. Clin. Pharm. 2021, 37, 2295–2298.
[26]	Jin, R.N.; Guo, H.; Xu, J.; Du, XY.; Zhan, G.T.; Chen, Y. Intervention effect and mechanism of Panax notoginseng Saponins on Neovascular retinopathy. World Sci. Technol. Mod. Tradit. Chin. Med. 2021, 23, 108–116.
[27]	Ai, H.; Xia, F.; Li, B.; Chen, X.D.; Peng, J.; Peng Q.H. Comprehensive treatment of Retinitis Pigmentosa in traditional Chinese medicine and analysis of medication rules. J. Tradit. Chin. Med. Univ. Hunan. 2020, 40, 165–169.
[28]	Qiao, L.Y.; Cheng, J. Research on the mechanism of Bidens pilosa L on dry eye based on network pharma-cology. Chin. J. Chin. Ophthal. 2022, 32, 164–168.
[29]	Jiang, M.N.; Ma, X.Y.; Zhao, Q.Q.; Li, Y.; Xing, Y.Q.; Deng, Q.Q.; Shen, Y. The neuroprotective effects of novel estrogen receptor GPER1 in mouse retinal ganglion cell degeneration. Exp. Eye Res. 2019, 189, 107826.