1,272
Views
68
CrossRef citations to date
0
Altmetric
Original Research

Network Pharmacology Prediction and Molecular Docking-Based Strategy to Discover the Potential Pharmacological Mechanism of Huai Hua San Against Ulcerative Colitis

, , , ORCID Icon, , , , & show all
Pages 3255-3276 | Published online: 28 Jul 2021

References

  • Tatiya-AphiradeeN, ChatuphonprasertW, JarukamjornK. Immune response and inflammatory pathway of ulcerative colitis. J Basic Clin Physiol Pharmacol. 2018;30(1):1–10. doi:10.1515/jbcpp-2018-003630063466
  • MatsuokaK, KobayashiT, UenoF, et al. Evidence-based clinical practice guidelines for inflammatory bowel disease. J Gastroenterol. 2018;53(3):305–353.29429045
  • GalloG, KotzePG, SpinelliA. Surgery in ulcerative colitis: When? How? Best Pract Res Clin Gastroenterol. 2018;32–33:71–78. doi:10.1016/j.bpg.2018.05.017
  • NgSC, ShiHY, HamidiN, et al. Worldwide incidence and prevalence of inflammatory bowel disease in the 21st century: a systematic review of population-based studies. Lancet. 2017;390(10114):2769–2778. doi:10.1016/S0140-6736(17)32448-029050646
  • CowardS, ClementF, BenchimolEI, et al. Past and future burden of inflammatory bowel diseases based on modeling of population-based data. Gastroenterology. 2019;156(5):1345–1353. doi:10.1053/j.gastro.2019.01.00230639677
  • KaplanGG, NgSC. Understanding and preventing the global increase of inflammatory bowel disease. Gastroenterology. 2017;152(2):313–321.e312. doi:10.1053/j.gastro.2016.10.02027793607
  • CohenRD, YuAP, WuEQ, XieJ, MulaniPM, ChaoJ. Systematic review: the costs of ulcerative colitis in Western countries. Aliment Pharmacol Ther. 2010;31(7):693–707. doi:10.1111/j.1365-2036.2010.04234.x20064142
  • XiangY, GuoZ, ZhuP, ChenJ, HuangY. Traditional Chinese medicine as a cancer treatment: modern perspectives of ancient but advanced science. Cancer Med. 2019;8(5):1958–1975. doi:10.1002/cam4.210830945475
  • WangJ, MaQ, LiY, et al. Research progress on Traditional Chinese Medicine syndromes of diabetes mellitus. Biomed Pharmacother. 2020;121:109565. doi:10.1016/j.biopha.2019.10956531704615
  • CorsonTW, CrewsCM. Molecular understanding and modern application of traditional medicines: triumphs and trials. Cell. 2007;130(5):769–774. doi:10.1016/j.cell.2007.08.02117803898
  • StoneR. Biochemistry. Lifting the veil on traditional Chinese medicine. Science. 2008;319(5864):709–710. doi:10.1126/science.319.5864.70918258866
  • ZhaoZ, LiY, ZhouL, et al. Prevention and treatment of COVID-19 using Traditional Chinese Medicine: a review. Phytomedicine. 2020;153308.32843234
  • ZhangL, YuJ, ZhouY, ShenM, SunL. Becoming a faithful defender: traditional Chinese medicine against coronavirus disease 2019 (COVID-19). Am J Chin Med. 2020;48(4):763–777. doi:10.1142/S0192415X2050038X32349517
  • WuXV, DongY, ChiY, YuM, WangW. Traditional Chinese medicine as a complementary therapy in combat with COVID-19-A review of evidence-based research and clinical practice. J Adv Nurs. 2020;77(4):1635–1644. doi:10.1111/jan.1467333174654
  • GuoJ, XiaQ, DunW, WuK, HuangS. A study on the effect and mechanism of huaihua powder in the treatment of ulcerative colitis by emulating the intestinal subwind blood syndrome. Modern Traditional Chinese Medicine. 2020;40(05):9–14+21.
  • LiuP, BianY, LiuT, et al. Huai hua san alleviates dextran sulphate sodium-induced colitis and modulates colonic microbiota. J Ethnopharmacol. 2020;259:112944. doi:10.1016/j.jep.2020.11294432387236
  • WangX, ZhangY. Clinical study on the clinical effect of Sophora powder combined with Xianfang-Huoming decoction for ulcerative colitis. Int J Tradit Chin Med. 2017;39(08):701–704.
  • LiuF, LeiN, TangX. Clinical observation of addition and subtraction therapy of Danggui Shaoyaosan combined with Huaihuasan to ulcerative colitis with syndrome of dampness-heat in large intestine during active stage. Chin J Exp Tradit Med Formulae. 2019;25(20):82–87.
  • LeiN, KongP, ChenS, TangX. Regulatory effect of Huaihuasan combined with Taohuatang on immune inflammation during active period of ulcerative colitis with cold-heat syndrome. Chin J Exp Tradit Med Formulae. 2020;26(07):86–91.
  • ZhangY, LiS. Progress in network pharmacology for modern research of traditional Chinese medicine. Chin J Pharmacol Toxicol. 2015;29(06):883–892.
  • GohKI, CusickME, ValleD, ChildsB, VidalM, BarabásiAL. The human disease network. Proc Natl Acad Sci U S A. 2007;104(21):8685–8690. doi:10.1073/pnas.070136110417502601
  • LiuZ, SunX. Network pharmacology: new opportunity for the modernization of traditional Chinese medicine. Acta Pharmaceutica Sinica. 2012;47(6):696–703.22919715
  • LuoTT, LuY, YanSK, XiaoX, RongXL, GuoJ. Network pharmacology in research of Chinese medicine formula: methodology, application and prospective. Chin J Integr Med. 2020;26(1):72–80. doi:10.1007/s11655-019-3064-030941682
  • LiangX, LiH, LiS. A novel network pharmacology approach to analyse traditional herbal formulae: the Liu-Wei-Di-Huang pill as a case study. Mol Biosyst. 2014;10(5):1014–1022. doi:10.1039/C3MB70507B24492828
  • LiS, ZhangB. Traditional Chinese medicine network pharmacology: theory, methodology and application. Chin J Nat Med. 2013;11(2):110–120. doi:10.3724/SP.J.1009.2013.0011023787177
  • XueLC, DobbsD, BonvinAM, HonavarV. Computational prediction of protein interfaces: a review of data driven methods. FEBS Lett. 2015;589(23):3516–3526. doi:10.1016/j.febslet.2015.10.00326460190
  • VilloutreixBO, BastardK, SperandioO, et al. In silico-in vitro screening of protein-protein interactions: towards the next generation of therapeutics. Curr Pharm Biotechnol. 2008;9(2):103–122. doi:10.2174/13892010878395521818393867
  • VakserIA. Protein-protein docking: from interaction to interactome. Biophys J. 2014;107(8):1785–1793. doi:10.1016/j.bpj.2014.08.03325418159
  • RuJ, LiP, WangJ, 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
  • LiuZ, GuoF, WangY, et al. BATMAN-TCM: a bioinformatics analysis tool for molecular mechANism of traditional Chinese medicine. Sci Rep. 2016;6:21146. doi:10.1038/srep2114626879404
  • XuHY, ZhangYQ, LiuZM, et al. ETCM: an encyclopaedia of traditional Chinese medicine. Nucleic Acids Res. 2019;47(D1):D976–d982. doi:10.1093/nar/gky98730365030
  • ChenCY. TCM database@Taiwan: the world’s largest traditional Chinese medicine database for drug screening in silico. PLoS One. 2011;6(1):e15939. doi:10.1371/journal.pone.001593921253603
  • TianS, WangJ, LiY, XuX, HouT. Drug-likeness analysis of traditional Chinese medicines: prediction of drug-likeness using machine learning approaches. Mol Pharm. 2012;9(10):2875–2886. doi:10.1021/mp300198d22738405
  • GiménezBG, SantosMS, FerrariniM, FernandesJP. Evaluation of blockbuster drugs under the rule-of-five. Pharmazie. 2010;65(2):148–152.20225662
  • LipinskiCA, LombardoF, DominyBW, FeeneyPJ. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev. 2001;46(1–3):3–26. doi:10.1016/S0169-409X(00)00129-011259830
  • GongJ, CaiC, LiuX, et al. ChemMapper: a versatile web server for exploring pharmacology and chemical structure association based on molecular 3D similarity method. Bioinformatics. 2013;29(14):1827–1829. doi:10.1093/bioinformatics/btt27023712658
  • WangX, ShenY, WangS, et al. PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database. Nucleic Acids Res. 2017;45(W1):W356–w360. doi:10.1093/nar/gkx37428472422
  • YaoZJ, DongJ, CheYJ, et al. TargetNet: a web service for predicting potential drug-target interaction profiling via multi-target SAR models. J Comput Aided Mol Des. 2016;30(5):413–424. doi:10.1007/s10822-016-9915-227167132
  • UniProt Consortium. UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 2019;47(D1):D506–D515. doi:10.1093/nar/gky104930395287
  • StelzerG, RosenN, PlaschkesI, et al. The geneCards suite: from gene data mining to disease genome sequence analyses. Curr Protoc Bioinformatics. 2016;54:1.30.31–31.30.33. doi:10.1002/cpbi.5
  • AmbergerJS, HamoshA. Searching online mendelian inheritance in man (OMIM): a knowledgebase of human genes and genetic phenotypes. Curr Protoc Bioinformatics. 2017;58:1.2.1–1.2.12. doi:10.1002/cpbi.27
  • Whirl-CarrilloM, McDonaghEM, HebertJM, et al. Pharmacogenomics knowledge for personalized medicine. Clin Pharmacol Ther. 2012;92(4):414–417. doi:10.1038/clpt.2012.9622992668
  • WangY, ZhangS, LiF, et al. Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics. Nucleic Acids Res. 2020;48(D1):D1031–D1041. doi:10.1093/nar/gkz98131691823
  • WishartDS, FeunangYD, GuoAC, et al. DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Res. 2018;46(D1):D1074–d1082. doi:10.1093/nar/gkx103729126136
  • SzklarczykD, GableAL, LyonD, et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019;47(D1):D607–D613. doi:10.1093/nar/gky113130476243
  • López-VallejoF, CaulfieldT, Martínez-MayorgaK, et al. Integrating virtual screening and combinatorial chemistry for accelerated drug discovery. Comb Chem High Throughput Screen. 2011;14(6):475–487. doi:10.2174/13862071179576786621521151
  • MengXY, ZhangHX, MezeiM, CuiM. Molecular docking: a powerful approach for structure-based drug discovery. Curr Comput Aided Drug Des. 2011;7(2):146–157. doi:10.2174/15734091179567760221534921
  • TrottO, OlsonAJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010;31(2):455–461. doi:10.1002/jcc.2133419499576
  • ClyneA, YangL, YangM, MayB, YangAWH. Molecular docking and network connections of active compounds from the classical herbal formula Ding Chuan Tang. PeerJ. 2020;8:e8685. doi:10.7717/peerj.868532185106
  • LaskowskiRA, SwindellsMB. LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J Chem Inf Model. 2011;51(10):2778–2786. doi:10.1021/ci200227u21919503
  • MartinezX, KroneM, AlharbiN, et al. Molecular graphics: bridging structural biologists and computer scientists. Structure. 2019;27(11):1617–1623. doi:10.1016/j.str.2019.09.00131564470
  • PeiC, ShaoL, LiuJ, ShiH, FengJ. Study on the mechanism of Carthami Flos in treating retinal vein occlusion based on network pharmacology and molecular docking technology. Nat Prod Res Dev. 2020;32(11):1844–1851+1865.
  • Mechta-GrigoriouF, GeraldD, YanivM. The mammalian Jun proteins: redundancy and specificity. Oncogene. 2001;20(19):2378–2389. doi:10.1038/sj.onc.120438111402334
  • LamphWW, WamsleyP, Sassone-CorsiP, VermaIM. Induction of proto-oncogene JUN/AP-1 by serum and TPA. Nature. 1988;334(6183):629–631. doi:10.1038/334629a02457172
  • WisdomR. AP-1: one switch for many signals. Exp Cell Res. 1999;253(1):180–185. doi:10.1006/excr.1999.468510579922
  • JochumW, PasseguéE, WagnerEF. AP-1 in mouse development and tumorigenesis. Oncogene. 2001;20(19):2401–2412. doi:10.1038/sj.onc.120438911402336
  • JiangW, HanYP, HuM, BaoXQ, YanY, ChenG. A study on regulatory mechanism of miR-223 in ulcerative colitis through PI3K/Akt-mTOR signaling pathway. Eur Rev Med Pharmacol Sci. 2019;23(11):4865–4872. doi:10.26355/eurrev_201906_1807431210320
  • LiuP, ZhongJ, BianY, ZhongY, LiuZ. The protective effect of Huaihua San on rat experimental colitis. Chin J Vet Med. 2020;56(12):29–31+35+127.
  • ChenH. Based on Intestinal sIgA and Inflammatory Factor Change to Explore the Huaihua San on the Treatment Mechanism of UC Model Rats. Hunan University Of Chinese Medicine; 2020.
  • KobayashiT, SiegmundB, Le BerreC, et al. Ulcerative colitis. Nat Rev Dis Primers. 2020;6(1):74. doi:10.1038/s41572-020-0205-x32913180
  • ZuoH, ZhangQ, SuS, ChenQ, YangF, HuY. A network pharmacology-based approach to analyse potential targets of traditional herbal formulas: an example of Yu Ping Feng decoction. Sci Rep. 2018;8(1):11418. doi:10.1038/s41598-018-29764-130061691
  • ZhangH, ZhangH, ZaiX, et al. Study on the effect of three natural compounds in Spartina alterniflora on uric acid. Chin Wild Plant Res. 2019;38(03):9–12.
  • YuanX, JiJ, XuJ, et al. Natural herbs, potential autophagy inducers in cancer therapy. J Modern Oncol. 2019;27(05):879–885.
  • CaoY, HuY, ZhangD, YangJ. Research advances in anti-leukemia activities of natural compounds. J Southwest Med Univ. 2020;43(03):300–305.
  • AzabA, NassarA, AzabAN. Anti-inflammatory activity of natural products. Molecules. 2016;21(10):1321. doi:10.3390/molecules21101321
  • AnJ, ChenB, KangX, et al. Neuroprotective effects of natural compounds on LPS-induced inflammatory responses in microglia. Am J Transl Res. 2020;12(6):2353–2378.32655777
  • ZhangX, YaoG, LiuY, JinP. Analysis on effect of temperature to rutin content in preparing Huaihua powders by HPLC. Lishizhen Med Materia Medica Res. 2002;03:136–137.
  • YaoG, ZhangX, ZhuM, ZhaoZ. Content determination of Rutin in Huaihuasan (Sophora Powder) with HPLC. Herald Med. 2003;02:115–116.
  • HabtemariamS, BelaiA. Natural therapies of the inflammatory bowel disease: the case of rutin and its aglycone, quercetin. Mini Rev Med Chem. 2018;18(3):234–243. doi:10.2174/138955751766617012015241728117024
  • LiuS, LiuJ. Advances in the pharmacological effects of quercetin. Chin J Lung Dis. 2020;13(01):104–106.
  • DoddaD, ChhajedR, MishraJ, PadhyM. Targeting oxidative stress attenuates trinitrobenzene sulphonic acid induced inflammatory bowel disease like symptoms in rats: role of quercetin. Indian J Pharmacol. 2014;46(3):286–291. doi:10.4103/0253-7613.13216024987175
  • AmashehM, SchlichterS, AmashehS, et al. Quercetin enhances epithelial barrier function and increases claudin-4 expression in Caco-2 cells. J Nutr. 2008;138(6):1067–1073. doi:10.1093/jn/138.6.106718492835
  • KimH, KongH, ChoiB, et al. Metabolic and pharmacological properties of rutin, a dietary quercetin glycoside, for treatment of inflammatory bowel disease. Pharm Res. 2005;22(9):1499–1509. doi:10.1007/s11095-005-6250-z16132362
  • FranzaL, CarusiV, NuceraE, PandolfiF. Luteolin, inflammation and cancer: special emphasis on gut microbiota. Biofactors. 2021;47(2):181–189. doi:10.1002/biof.171033507594
  • AzizN, KimMY, ChoJY. Anti-inflammatory effects of luteolin: a review of in vitro, in vivo, and in silico studies. J Ethnopharmacol. 2018;225:342–358. doi:10.1016/j.jep.2018.05.01929801717
  • ZhouZ, LiuB, WuW. Effect of luteolin on ulcerative colitis mice. Chin J Clin Pharmacol Therap. 2005;10:1152–1155.
  • XiongY, ChenD, YuC, et al. Citrus nobiletin ameliorates experimental colitis by reducing inflammation and restoring impaired intestinal barrier function. Mol Nutr Food Res. 2015;59(5):829–842. doi:10.1002/mnfr.20140061425655748
  • HagenlocherY, GommeringerS, HeldA, et al. Nobiletin acts anti-inflammatory on murine IL-10(-/-) colitis and human intestinal fibroblasts. Eur J Nutr. 2019;58(4):1391–1401. doi:10.1007/s00394-018-1661-x29525889
  • LiJ. TLR2 and TLR4 Monoclonal Antibodies Blockade Suppress Murine Dextran-Sulfate-Sodium-Induced Acute Colitis. Fudan University; 2010.
  • LongM. To Investigate the Function of c-Jun in Ulcerative Colitis in Rat by Using Uyghur’s Medicine Kui Jiean and RNA Interference Technique. Xinjiang Medical University; 2007.
  • LongM, Abulaiti·AhemaitiK, Kurexi·yunusiHJ. Expression and significance of interleukin-6 and c-jun in colon tissues of rats with ulcerative colitis. J Xinjiang Med Univ. 2007;5:446–448.
  • VolodkoN, SallaM, EksteenB, FedorakRN, HuynhHQ, BakshS. TP53 codon 72 Arg/Arg polymorphism is associated with a higher risk for inflammatory bowel disease development. World J Gastroenterol. 2015;21(36):10358–10366. doi:10.3748/wjg.v21.i36.1035826420962
  • DuL, KimJJ, ShenJ, ChenB, DaiN. KRAS and TP53 mutations in inflammatory bowel disease-associated colorectal cancer: a meta-analysis. Oncotarget. 2017;8(13):22175–22186. doi:10.18632/oncotarget.1454928077799
  • HirschD, GaiserT. [Crohn’s disease-associated colorectal carcinogenesis: TP53 mutations and copy number gains of chromosome arm 5p as (early) markers of tumor progression]. Pathologe. 2018;39(Suppl 2):253–261. [German]. doi:10.1007/s00292-018-0496-930229283
  • Krela-KaźmierczakI, Skrzypczak-ZielińskaM, Kaczmarek-RyśM, et al. ESR1 gene variants are predictive of osteoporosis in female patients with Crohn’s disease. J Clin Med. 2019;8(9):1306. doi:10.3390/jcm8091306
  • SaitoS, KatoJ, HiraokaS, et al. DNA methylation of colon mucosa in ulcerative colitis patients: correlation with inflammatory status. Inflamm Bowel Dis. 2011;17(9):1955–1965. doi:10.1002/ibd.2157321830274
  • ZhuY, ShiY, KeX, XuanL, MaZ. RNF8 induces autophagy and reduces inflammation by promoting AKT degradation via ubiquitination in ulcerative colitis mice. J Biochem. 2020;168(5):445–453. doi:10.1093/jb/mvaa06832597970
  • BaekSH, KoJH, LeeJH, et al. Ginkgolic acid inhibits invasion and migration and TGF-β-induced EMT of lung cancer cells through PI3K/Akt/mTOR inactivation. J Cell Physiol. 2017;232(2):346–354. doi:10.1002/jcp.2542627177359
  • YangX, SongX, WangX, LiuX, PengZ. Downregulation of TM7SF4 inhibits cell proliferation and metastasis of A549 cells through regulating the PI3K/AKT/mTOR signaling pathway. Mol Med Rep. 2017;16(5):6122–6127. doi:10.3892/mmr.2017.732428849122
  • WangH, ZhangC, XuL, et al. Bufalin suppresses hepatocellular carcinoma invasion and metastasis by targeting HIF-1α via the PI3K/AKT/mTOR pathway. Oncotarget. 2016;7(15):20193–20208. doi:10.18632/oncotarget.793526958938
  • GhayadSE, CohenPA. Inhibitors of the PI3K/Akt/mTOR pathway: new hope for breast cancer patients. Recent Pat Anticancer Drug Discov. 2010;5(1):29–57. doi:10.2174/15748921078970220819751211
  • Guerrero-ZotanoA, MayerIA, ArteagaCL. PI3K/AKT/mTOR: role in breast cancer progression, drug resistance, and treatment. Cancer Metastasis Rev. 2016;35(4):515–524. doi:10.1007/s10555-016-9637-x27896521
  • LiS. Network pharmacology evaluation method guidance-draft. World J Tradit Chin Med. 2021;7(1):165–166. doi:10.4103/wjtcm.wjtcm_11_21