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Determination of effectiveness of berberine, a characteristic phytochemical of Berberis species, against human proteome using in-silico analysis

Tika Khan, Imtiaz Ahmed Khan, Abdul Rehman, Zohra Bibi

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J. Bio. Env. Sci.4(5), 53-63, May 2014

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Abstract

Berberis spp. are important representative plants of Family Berberidaceae. Berberis pseudumbellata subsp. gilgitica and Berberis brandisiana are found in Central Karakorum National Park (CKNP) and rest of Gilgit-Baltistan province of Pakistan (formerly Northern mountainous areas of Pakistan). Berberis pseudumbellata subsp. gilgitica is an endemic species and has become critically endangered. They are major source of Berberine which is an essential therapeutic phytochemical agent with anticancer, anti-diabetic, anti-AIDS, anti-jaundice, anti-cholera, anti-diarrhea, anti-leprosy and anti-inflammation effects. Studies illustrate inhibitory effect on oncogene-protein expression and therefore considered as an alternative, safer and effective medicine for chemotherapy. Besides being a multi-potent natural agent to combat Alzheimer’s disease, its effectiveness against cardiovascular, hypertension, musculoskeletal and ocular ailments cannot be ignored. Present in-silico analysis investigated cancer related Berberine-protein, Berberine lead protein-protein metabolic pathways, interactions and level of effect and role in cellular activities of human metabolic process. Moreover, study also attempts to reflect on action mechanism which is not clear so far. Using FDR= <0.001 as filter molecular function, cellular compartment and Biological processes are shortlisted to identify effect of Berberine on human body. Moreover, analysis is also carried out using FI reactome plugging and pathway predicted to be effected by effectors proteins with FDR= <0.001 score are shortlisted. Study reveals that Berberine has strong positive effect and correlation between Berberine and various carcinomic proteins as exhibited through molecular docking filtered on the basis of Z’-score <-0.05. Study contributes into understanding of Berberine as an alternate potential non-toxic anticancer drug.

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Determination of effectiveness of berberine, a characteristic phytochemical of Berberis species, against human proteome using in-silico analysis

Abbas. 2014. Avian diversity in Central Karakoram National Park, Gilgit-Baltistan. International Journal of Agriculture & Biology 16, 377-382.

Abbas Q, Qureshi R, Naqvi AUN, Khan SW, Hussain I. 2013. Floristic inventory and ethnobotanical study of the Naltar valley (Karakoram Range), Gilgit, Pakistan. Pakistan Journal of Botany 45(SI), 269-277.

Abidi. 2005. Extracellular Signal-Regulated Kinase– Dependent Stabilization of Hepatic Low-Density Lipoprotein Receptor mRNA by Herbal Medicine Berberine. Arteriosclerosis, Thrombosis, and Vascular Biology 25, 2170-2176. doi: 10.1161/01.ATV. 0000181761.16341.2b

Aggarwal. 2013. Prevention and Treatment of Colorectal Cancer by Natural Agents From Mother Nature. Current Colorectal Cancer Reports 9(1), 37-56.

Alam J, Ali SI. 2010. Contribution to the red list of the Plants of Pakistan. Pakistan Journal of Botany 42(5), 2967-2971.

Asif A, Kabub G, Mehmood S, Khunum R, Gulfraz M. 2007. Wound healing activity of root extract of Berberis Lyceum Royle in rats. Phytother. Research 21, 589-591.

Auyeung KK, Ko JK. 2009. Coptis chinensis inhibits hepatocellular carcinoma cell growth through nonsteroidal anti-inflammatory drug-activated gene activation. International journal of molecular medicine 24 (4), 571–7. PMID 19724899.

Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Statist.Soc.

Bhandari DK, Nath G, Ray AB, Twari PV. 2000. Antimicrobial activity of crude extracts from Berberis asiatica stem bark. Pharmaceutical Biology 38, 254– 257.

Birdsall TC, Kelly GS. 1997. Berberine: Therapeutic potential of an alkaloid found in several medicinal plants. Altern. Med. Rev. 2, 94-103.

Bolton E, Wang Y, Thiessen PA, Bryant SH. 2008. PubChem: Integrated Platform of Small Molecules and Biological Activities. Annual Reports in Computational Chemistry.

Borderies. 2003. Proteomics of loosely bound cell wall proteins of Arabidopsis thaliana cell suspension cultures: A critical analysis. Electrophoresis 24(19-20), 3421–3432. DOI: 10.1002/elps.200305608

Brennera StE, Chothiab C, Hubbard TimJP. 1997. Population statistics of protein structures: lessons from structural classifications. Current Opinion in Structural Biology 7(3), 369–376. DOI: http://dx.doi.org/10.1016/S0959-440X(97)80054-1

Burley StK. 1999. Structural genomics: beyond the Human Genome Project. Nature Genetics 23, 15. DOI:10.1038/13783

Cao HL, Wang BM, Yan F, Chen X. 2011. The effects of Berberine on growth of Immorto-Min colonic epithelial cell line. Zhonghua Nei Ke Za Zhi 50(5), 420-3.

Caraballo A, Caraballo B, Rodríguez-Acosta A. 2004. Preliminary assessment of medicinal plants used as antimalarials in the southeastern Venezuelan Amazon. Revista da SociedadeBrasileira de Medicina Tropical 37(2), 186–188.

Chandra P, Purohit AN. 1980. Berberine contents and alkaloid profile of Berberis species from different altitudes. Biochemical Systematics and Ecology 8(4), 379–380.

ChemSpider, 2014. Berberine. ChemSpider. Retrieved from http://www.chemspider.com/ Chemical -Structure.2263.html on March 17, 2014

Chen YZ, Ung CY. 2002. Computer Automated Prediction of Potential Therapeutic and Toxicity Protein Targets of Bioactive Compounds from Chinese Medicinal Plants. American Journal of Chinese Medicine 30(139). DOI: 10.1142/S0192415 X02000156

Chopra M, Chatterji A, Pakrashi SC. 1981.The treatise on Indian medicinal plants CSIR, New Delhi, pp. 33-35.

CKNP. 2013. History/Background. Retrieved from http://www.cknp.org.pk/ on November 26, 2013.

Clackson T, Wells JA. 1995. A hot spot of binding energy in a hormone-receptor interface. Science 267(5196), 383-386. DOI: 10.1126/science.7529940

Creasey WA. 1979. Biochemical effects of Berberine. Biochemical Pharmacology 28(7), 1081–1084 DOI: http://dx.doi.org/10.1016/0006-2952(79)90308-3

Diogo CV, Machado NG, Barbosa IA, Serafim TL, Burgeiro A, Oliveira PJ. 2011. Berberine as a promising safe anti-cancer agent – is there a role for mitochondria? Curr. Drug Targets 12, 850-859.

Domadia PN. 2008. Berberine Targets Assembly of Escherichia coli Cell Division Protein FtsZ. Biochemistry 47 (10), 3225–3234. DOI: 10.1021/ bi7018546

Drews J. 2000. Drug Discovery: A Historical Perspective. Science 287(5460), 1960-1964. DOI: 10.1126/science.287.5460.1960

Fatehi M, Saleh TM, Fatehi-Hassanabad Z, Farrokhfal K, Jafarzadeh M, Davodi S. 2005. A pharmacological study on Berberis vulgaris fruit extract. Journal of Ethnopharmacology 102(1), 46–52.

Fukuda K. 1999. Inhibition by berberine of cyclooxygenase-2 transcriptional activity in human colon cancer cells. Journal of Ethnopharmacology 66(2), 227–233. DOI: http://dx.doi.org/10.1016/ S0378-8741(98)00162-7

Girke T, Cheng Li-Chang, Raikhel N. 2005 . ChemMine. A Compound Mining Database for Chemical Genomics. Plant Physiology 138(2), 573-577. doi: http://dx.doi.org/10.1104/pp.105.062687

Ho YT, Lu CC, Yang JS. 2009. “Berberine induced apoptosis via promoting the expression of caspase-8, -9 and -3, apoptosis-inducing factor and endonuclease G in SCC-4 human tongue squamous carcinoma cancer cells”. Anticancer research 29 (10), 4063–70. PMID 19846952.

Hu JP, Nishishita K, Saka E, Yoshida H, Kato Y, Tsukuba T, Okamoto K. 2008. Berberine inhibits RANKL-induced osteoclast formation and survival through suppressing the NF-kBabdAkt pathways. European Journal of Pharmacology 580, 70-79.

Hu, Yan-Jun. 2010. Binding of berberine to bovine serum albumin: spectroscopic approach.Molecular Biology Reports 37(8), 3827-3832

Hu Yan-Jun, Liu, Yi, Xiao, Xiao-He. 2009. Investigation of the Interaction between Berberine and Human Serum Albumin. Biomacromole-cules 10(3), 517–521 DOI: 10.1021/bm801120k

Hwang, Jin-Ming, Wang, Chau-Jong, Chou, Feu-Pi, Tseng, Tsui-Hwa, Hsieh, Yih-Shou, Lin, Wea-Lung, Chu, Chia-Yih. 2002. Inhibitory effect of berberine on tert-butyl hydroperoxide-induced oxidative damage in rat liver. Archives of Toxicology 76(11), 664-670.

Imanshahidi M, Hosseinzadeh H. 2008. Pharmacological and therapeutic effects of Berberis vulgaris and its active constituent, berberine. Phytother.Res. 22, 999-1012.

Ivanoska N, Philipov S. 1996. Study on the anti-inflammatory action of Berberis vulgaris root extracts, alkaloid fractions and pure alkaloid. International Journal of Immunopharmacology 18(10), 553–561.

Iwasa K, Kamigauchi M, Ueki M, Taniguchi M. 1996. Antibacterial activity and structure-activity relationships of berberine analogs. Eur. J. Med. Chem 31, 469-478.

Janbaza KH, Gilanib AH. 2000. Studies on preventive and curative effects of berberine on chemical-induced hepatotoxicity in rodents. Fitoterapia 71(1), 25–33.

Ji Hong-Fang, Shen L. 2011. Berberine: A Potential Multipotent Natural Product to Combat Alzheimer’s Disease. Molecules 2011(16), 6732-6740. doi:10.3390/molecules16086732

Jongejan A. 2005. The role and application of in silico docking in chemical genomics research. Methods in Molecular Biology 310:63-91. DOI: 10. 1007/978-1-59259-948-6_5; PMID: 16350947

Jung HA, Min BS, Yokozawa T, Lee JH, Kim YS, Choi JS. 2009. Anti-Alzheimer and antioxidant activities of Coptidis Rhizoma alkaloids. Biol. Pharm. Bull 32, 1433-1438.

Kettmann V. 2004. In vitro cytotoxicity of berberine against HeLa and L1210 cancer cell lines. Die Pharmazie 59(7), 548-551(4)

Khan SW, Khatoon S. 2007. Ethnobotanical Studies on useful trees and shrubs of Haramosh and Bugrote valleys, in Gilgit Northern Areas of Pakistan. Pakistan Journal of Botany 39(3), 699-710.

Khan T, Khan IA, Rehman A, Alam J, Ali S. 2013. Exploration of near-extinct folk wisdom on medicinally important plants from Shinaki Valley Hunza, Pakistan. International Journal of Biosciences 3(10), 180-186.

Khan T, Khan IA, Ahmed K, Rehman A. 2014. Differential levels of susceptibility of Berberis species to insect attack at various altitudes in Karakoram Ranges. International Journal of Biosciences 4(5), 92-101. DOI: http://dx.doi.org/10.12692/ijb/4.5.92-101

Kim JB, Yu JH, Ko E. 2009. “The alkaloid Berberine inhibits the growth of Anoikis-resistant MCF-7 and MDA-MB-231 breast cancer cell lines by inducing cell cycle arrest”. Phytomedicine 17 (6), 436–40. doi:10.1016/j.phymed.2009.08.012.

Kong. 2004. Berberine is a novel cholesterol-lowering drug working through a unique mechanism distinct from statins. Nature Medicine 10, 1344 – 1351. doi:10.1038/nm1135

Kong. 2009. Berberine reduces insulin resistance through protein kinase C–dependent up-regulation of insulin receptor expression. Metabolism 58(1), 109– 119. http://dx.doi.org/10.1016/j.metabol.2008.08.013

Kong W, Wei J, Abidi P, Lin M, Inaba S, Li C, Wang Y, Wang Z, Si S, Pan H. 2004. Berberine is a novel cholesterol-lowering drug working through a unique mechanism distinct from statins. Nat. Med. 10, 1344-1351.

Koo L, Seang K. 1996. Inhibitory effect of protoberberine alkaloids from the roots of Coptis japonica on chatecolamine biosynthesis in PC12 cells. PlantaMedica 62(1), 31-34

Kroemer RT. 2007. Structure-Based Drug Design: Docking and Scoring. Current Protein and Peptide Science, Bentham Science Publishers Ltd. 8, pp. 312-328

Kulkarni GT, Sharma VN, Agrawal S. 2012. Antimicrobial and Anti-inflammatory Activities of Bark of Four Plant Species from Indian Origin. WebmedCentral Pharmaceutical Sciences 3(10), WMC002010.

Kuo CL, Chi CW, Liu TY. 2004. The anti-inflammatory potential of Berberine in vitro and in vivo. Cancer Letters 203(2), 127–137.

Lengauer T, Rarey M. 1996. Computational methods for biomolecular docking. Current Opinion in Structural Biology 6(3), 402-6. DOI:10.1016 /S0959-440X(96)80061-3

Li B, Zhu WL, Chen KX. 2008 Advances in the study of berberine and its derivatives. Yao Xue Xue Bao 43(8), 773-87.

Li. 2005.The effect of Berberine on the secondary structure of human serum lbumin. Journal of Molecular Structure 743(1–3), 79–84 http://dx. doi.org/10.1016/j.molstruc.2005.02.032

Li. 2011. Berberine suppresses androgen receptor signaling in prostate cancer. Molecular Cancer Therapeutics 10(8), 1346-56. doi: 10.1158/1535-7163.MCT-10-0985.

LI-NA XU. 2012. Mechanisms involved in the cytotoxic effects of berberine on human colon cancer HCT-8 cells. BIOCELL 36(3), 113-120

Lindley PF. 1999. Macromolecular crystallography with a third-generation synchrotron source. Acta Crystallographica Section D 55(10), 1654-1662. doi:10.1107/S0907444999008288

Lu B, Hu M, liu K,Peng J. 2010.Cytotoxicity of berberine on human cervical carcinoma HeLa cells through mitochondria, death receptor and MAPK pathways, and in-silico drug-target prediction. Toxicology in vitro 24(6), 1482–1490. http://dx.doi.org/10.1016/j.tiv.2010.07.017

Luo H. 2011. DRAR-CPI: a server for identifying drug repositioning potential and adverse drug reactions via the chemical–protein Interactome. Nucleic Acids Research 39(2), W492-W498. doi: 10.1093/nar/gkr299

Marszalek M, Konarska A, Szajdzinska-Pietek E, Wolszczak M. 2013. Interaction of Cationic Protoberberine Alkaloids with Human Serum Albumin. No Spectroscopic Evidence on Binding to Sudlow’s Site 1. The Journal of Physical Chemistry B 117 (50), 15987-15993 PDB. 2014. www.rcsb.org/pdb/home/home.do

Pinto-Garcia L, Efferth T, Torres A, Hoheisel JD, Youns M.2010. “Berberine Inhibits Cell Growth and Mediates Caspase-Independent Cell Death in Human Pancreatic Cancer Cells”. Planta Medica 76 (11),1155–61. doi:10.1055/s-0030-1249931. PMID 20455200.

Popov D. 2011. Novel protein tyrosine phosphatase 1B inhibitors: interaction requirements for improved intracellular efficacy in type 2 diabetes mellitus and obesity control. Biochemical and Biophysical Research Communications 410(3), 377–381. http://dx.doi.org/10.1016/j.bbrc.2011.06.009

Racková L, Májeková M, Kost’álová D, Stefek M. 2003. Antiradical and antioxidant activities of alkaloids isolated from Mahoniaaquifoliu. Structural aspects. Bioorg. Med. Chem. 2003, 12, 4709-4715. RDb. 2014. http://www.reactome.org

Sakai. 2002. Characterization of berberine transport intoCoptis japonica cells and the involvement of ABC protein. J. Exp. Bot. 53 (376), 1879-1886. doi: 10. 1093/jxb/erf052

Serafim TL, Oliveira PJ, Sardao VA, Perkins E, Parke D, Holy J. 2008. “Different concentrations of berberine result in distinct cellular localization patterns and cell cycle effects in a melanoma cell line”. Cancer Chemotherapy and Pharmacology 61 (6), 1007–18.doi:10.1007/s00280-007-0558-9. PMID 17661039.

Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. 2011.Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27(3),431-432.

Stermitz FR, Lorenz P, Tawara JN, Zenewicz, LA, Lewis K. 2000a. Synergy in a medicinal plant: antimicrobial action of berberine potentiated by 5-methoxyhydnocarpin, a multidrug pump inhibitor. In: Proceedings of the National Academy of Sciences of the United States of America 97, 1433–1437.

Stermitz FR, Lorenz P, Tawara JN, Zenewicz LA, Lewis K. 2000. Synergy in a medicinal plant: Antimicrobial action of berberine potentiated by 5-methoxyhydrocarpin, a multidrug pump inhibitor. Proc. Natl. Acad. Sci. USA 97, 1433-1437.

Stigers KD, Soth MJ, Nowick JS. 1999. Designed molecules that fold to mimic protein secondary structures.Current Opinion in Chemical Biology 3(6), 714–723. http://dx.doi.org/10.1016/S1367-5931(99) 00030-7

Tang F, Wang D, Duan C. 2009. “Berberine inhibits metastasis of nasopharyngeal carcinoma 5-8F cells by targeting Rho kinase-mediated Ezrin phosphorylation at threonine 567”. The Journal of Biological Chemistry 284 (40), 27456–66. doi:10. 1074/jbc.M109.033795. PMC 2785675. PMID 196517 79.

Tang J, Feng Y, Tsao S, Wang N, Curtain R, Wang Y. 2009. Berberine and Coptidis Rhizoma as novel antineoplastic agent: A review of traditional use and biomedical investigations. Journal of Ethnophar-macology 126: 5-17

Tang LQ, Wei W, Chen LM and Liu S. 2006. Effects of berberine on diabetes induced by alloxan and a high-fat/high-cholesterol diet in rats. J. Ethnopharmacol.; 108: 109-115

Tsang. 2009. Berberine inhibits Rho GTPases and cell migration at low doses but induces G2 arrest and apoptosis at high doses in human cancer cells. International Journal of Molecular Medicine 24(1), 131-8. DOI: 10.3892/ijmm_00000216

UofMHealth.  2014.  Oregon  Grape.  UofMHealth.org. retrieved from http://www.uofmhealth.org/health-library/hn-2141009#hn-2141009-uses on March 24, 2014. Vega-ZZ. 2014. www.nova.colombo58.unimi.it/cms/ index.php?Software _projects: VEGA _ZZ

Villinski RJ, Dumas ER, Chai HB, Pezzuto JM, Angerhofer CK, Gafner S. 2003. Antibacterial activity and alkaloid content of Berberis thunbergii, Berberis vulgaris and Hydrastiscanadensis. Pharma-ceutical Biology 41( 8) , 551-557.

Virk AT, Sheikh KM, Marwat AH. 2003. NASSD Background Paper: Biodiversity. IUCN Pakistan, Northern Areas Progamme, Gilgit. x+74 pp. Retrieved from https://cmsdata.iucn.org/downloads/bpbiodive -rsity. pdf on April 7, 2014.

Wells JA et al. 1993.The molecular basis for growth hormone-receptor interactions. Recent progress in hormone Research 48:253-75

Zhang P, Agarwal P, Obradovic Z. 2013. Computational Drug Repositioning by Ranking and Integrating Multiple Data Sources. PloS Computational biology 6(11), 569-581.

Zhang Q. 2010. Simultaneous determination of jatrorrhizine, palmatine, berberine, and obacunone in PhellodendriAmurensis Cortex by RP-HPLC. Journal of Chinese materiamedica 35(16), 2061–4. PMID 21046728

Zhang X. 2010. Degradation of MDM2 by the Interaction between Berberine and DAXX Leads to Potent Apoptosis in MDM2-Overexpressing Cancer Cells. Cancer Research 70(23), 9895–904. doi: 10.1158/0008-5472.CAN-10-1546

Zhu F, Qian C. 2006. Berberine chloride can ameliorate the spatial memory impairment and increase the expression of interleukin-1beta and inducible nitric oxide synthase in the rat model of Alzheimer’s disease. BMC Neurosci 7, 78.

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