System-level multi-target drug discovery from natural products with applications to cardiovascular diseases

Molecular Diversity

Volumn 18, Issue 3, 2014, Pages 621-635

  Zheng, Chunli ^a   Wang, Jinan ^a   Liu, Jianling ^b   Pei, Mengjie ^b   Huang, Chao ^a   Wang, Yonghua ^a  

^a NORTHWEST A F UNIVERSITY   (China)

^b NORTHWEST UNIVERSITY   (China)

Author keywords

Cardiovascular diseases; Multi target drugs; Natural products; Polypharmacology; Systems pharmacology

Indexed keywords

CURCUMIN; LICOCHALCONE A; NATURAL PRODUCT; ROSMARINIC ACID; SALVIANOLIC ACID A; SALVIANOLIC ACID B; UNCLASSIFIED DRUG; BIOLOGICAL PRODUCT;

ADRENERGIC NERVE CELL; ANTIINFLAMMATORY ACTIVITY; ARTICLE; ASTRAGALUS PLANT; ATRACTYLODES MACROCEPHALA; BINDING AFFINITY; CARDIOVASCULAR DISEASE; CARDIOVASCULAR SYSTEM; CINNAMOMI RAMULUS; CORYDALIS; CORYDALIS YANHUSUO; CURCUMA AROMATIC; DALBERGIA; DALBERGIA ODORIFERA; DRUG BINDING; DRUG CONFORMATION; DRUG TARGETING; GLYCYRRHIZAE URALENSIS; HUMAN; HYDROGEN BOND; IN VITRO STUDY; LIGUSTICUM CHUANXIONG; METABOLISM; MITOCHONDRION; NONHUMAN; PANAX NOTOGINSENG; PINELLIA; POLYPHARMACOLOGY; PORIA COCOS; PRIORITY JOURNAL; PULMONARY ARTERY; RENIN ANGIOTENSIN ALDOSTERONE SYSTEM; SALVIA MILTIORRHIZA; SPATHOLOBUS SUBERECTUS; ANIMAL; BIOLOGY; CARDIOVASCULAR DISEASES; CHEMICAL STRUCTURE; DRUG DATABASE; DRUG DEVELOPMENT; ENZYME ACTIVE SITE; ENZYMOLOGY; IC50; PROCEDURES;

ANIMALS; BIOLOGICAL PRODUCTS; CARDIOVASCULAR DISEASES; CATALYTIC DOMAIN; COMPUTATIONAL BIOLOGY; DATABASES, PHARMACEUTICAL; DRUG DISCOVERY; HUMANS; INHIBITORY CONCENTRATION 50; MODELS, MOLECULAR;

EID: 84903821282     PISSN: 13811991     EISSN: 1573501X     Source Type: Journal    
DOI: 10.1007/s11030-014-9521-y     Document Type: Article

References (52)

1. Boran AD, Iyengar R (2010) Systems approaches to polypharmacology and drug discovery. Curr Opin Drug Disc 13:297-309. doi:10.1371/journal.pone.0040262
2. Csermely P, Agoston V, Pongor S (2005) The efficiency of multitarget drugs: the network approach might help drug design. Trends Pharmacol Sci 26:178-182. doi:10.1016/j.tips.2005.02.007 (Pubitemid 40432652)
3. Wist AD, Berger SI, Iyengar R (2009) Systems pharmacology and genomemedicine: a future perspective. Genome Med 1:11. doi:10.1186/gm11
4. Morrow JK, Tian L, Zhang S (2010) Molecular networks in drug discovery. Crit Rev Biomed Eng 38:143-156. doi:10.1615/CritRevBiomedEng.v38.i2.30
5. Kell D (2006) Systems biology, metabolic modelling and metabolomics in drug discovery and development. Drug Discov Today 11:1085-1092. doi:10.1016/j.drudis.2006.10.004
6. Cascante M, Boros LG, Comin-Anduix B, de Atauri P, Centelles JJ, Lee PW-N (2002) Metabolic control analysis in drug discovery and disease. Nat Biotechnol 20:243-249. doi:10.1038/nbt0302-243 (Pubitemid 34205416)
7. Murthy D, Attri KS, Gokhale RS (2013) Network, nodes and nexus: systems approach to multitarget therapeutics. Curr Opin Biotech 24:1129-1136. doi:10.1016/j.copbio
8. Huang C, Zheng C, Li Y, Wang Y, Lu A, Yang L (2013) Systems pharmacology in drug discovery and therapeutic insight for herbal medicines. Brief Bioinform (in press). doi:10.1093/bib/bbt035
9. Liu H, Wang J, Zhou W, Wang Y, Yang L (2013) Systems approaches and polypharmacology for drug discovery from herbal medicines: an example using licorice. J Ethnopharmacol 146:773-793. doi:10.1016/j.jep.2013.02.004
10. Wang X, Xu X, Li Y, Li X, Tao W, Li B, Wang Y, Yang L (2013) Systems pharmacology uncovers Janus functions of botanical drugs: activation of host defense system and inhibition of influenza virus replication. Integr Biol 5:351-371. doi:10.1039/c2ib20204b
11. Li B, Xu X, Wang X, Yu H, Li X, Tao W, Wang Y, Yang L (2012) A systems biology approach to understanding the mechanisms of action of Chinese herbs for treatment of cardiovascular disease. Int J Mol Sci 13:13501-13520. doi:10.3390/ijms131013501
12. Wang X, Xu X, Tao W, Li Y, Wang Y, Yang L (2012) A systems biology approach to uncovering pharmacological synergy in herbal medicines with applications to cardiovascular disease. Evid-Based Compl Alt (in press). doi:10.1155/2012/519031
13. Tao W, Xu X, Wang X, Li B, Wang Y, Li Y, Yang L (2012) Network pharmacology-based prediction of the active ingredients and potential targets of Chinese herbal Radix Curcumae formula for application to cardiovascular disease. J Ethnopharmacol 145:1-10. doi:10.1016/j.jep.2012.09.051
14. Zhou W, Wang Y (2014) A network-based analysis of the types of coronary artery disease from traditional Chinese medicine perspective: Potential for therapeutics and drug discovery. J Ethnopharmacol 151:66-77. doi:10.1016/j.jep.2013.11.007
15. Singh N, Guha R, Giulianotti MA, Pinilla C, Houghten RA, Medina-Franco JL (2009) Chemoinformatic analysis of combinatorial libraries, drugs, natural products, and molecular libraries small molecule repository. J Chem Inf Model 49:1010-1024. doi:10.1021/ci800426u
16. Austin CP, Brady LS, Insel TR, Collins FS (2004) NIH molecular libraries initiative. Science 306:1138-1139. doi:10.1126/science.1105511 (Pubitemid 39488980)
17. Irwin JJ, Shoichet BK (2005) ZINC-a free database of commercially available compounds for virtual screening. JChem Inf Model 45:177-182. doi:10.1021/ci049714+ (Pubitemid 40736970)
18. Ertl P, Roggo S, Schuffenhauer A (2008) Natural product-likeness score and its application for prioritization of compound libraries. J Chem Inf Model 48:68-74. doi:10.1021/ci700286x (Pubitemid 351271051)
19. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT (2000) Gene Ontology: tool for the unification of biology. Nat Genet 25:25-29. doi:10.1038/75556 (Pubitemid 30257031)
20. Smoot ME, Ono K, Ruscheinski J, Wang P-L, Ideker T (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27:431-432. doi:10.1093/bioinformatics/btq675
21. Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267:727-748. doi:10.1006/jmbi.1996.0897 (Pubitemid 27170693)
22. Xu X, Zhang W, Huang C, Li Y, Yu H, Wang Y, Duan J, Ling Y (2012) A novel chemometric method for the prediction of human oral bioavailability. Int J Mol Sci 13:6964-6982. doi:10.3390/ijms13066964
23. Yamanishi Y, Kotera M, Kanehisa M, Goto S (2010) Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework. Bioinformatics 26:i246-i254. doi:10.1093/bioinformatics/btq176
24. Korcsmáros T, Szalay MS, Böde C, Kovács IA, Csermely P (2007) How to design multi-target drugs: target search options in cellular networks. Expert Opin Drug Discov 2:1-10
25. Barabási A-L, Gulbahce N, Loscalzo J (2011) Network medicine: a network-based approach to human disease. Nat Rev Genet 12:56-68. doi:10.1038/nrg2918
26. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman W-H, Pagès F, Trajanoski Z, Galon J (2009) ClueGO: a cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25:1091-1093. doi:10.1093/bioinformatics/btp101
27. Gao F, de Beer VJ, Hoekstra M, Xiao C, Duncker DJ, Merkus D (2010) Both β1-and β2-adrenoceptors contribute to feedforward coronary resistance vessel dilation during exercise. Am J Physiol Heart C 298:H921-H929. doi:10.1152/ajpheart.00135.2009
28. Yoshioka T, Fujii E, Endo M, Wada K, Tokunaga Y, Shiba N, Hohsho H, Shibuya H, Muraki T (1998) Antiinflammatory potency of dehydrocurdione, a zedoary-derived sesquiterpene. Inflamm Res 47:476-481. doi:10.1007/s000110050361 (Pubitemid 29015636)
29. Pan M-H, Huang T-M, Lin J-K (1999) Biotransformation of curcumin through reduction and glucuronidation inmice. Drug Metab Dispos 27:486-494 (Pubitemid 29177642)
30. Kurahashi K, Fujiwara M (1976) Adrenergic neuron blocking action of dehydrocorydaline isolated from Corydalis bulbosa. Can J Physiol Pharm 54:287-293. doi:10.1139/y76-042
31. Xu Z, Chen X, Fu S, Bao J, Dang Y, Huang M, Chen L, Wang Y (2012) Dehydrocorydaline inhibits breast cancer cells proliferation by inducing apoptosis in MCF-7 cells. Am J Chin Med 40:177-185. doi:10.1142/ S0192415X12500140
32. Pujol A, Mosca R, Farrés J, Aloy P (2010) Unveiling the role of network and systems biology in drug discovery. Trends Pharmacol Sci 31:115-123. doi:10.1016/j.tips.2009.11.006
33. Masferrer JL, Zweifel BS, Manning PT, Hauser SD, Leahy KM, Smith WG, Isakson PC, Seibert K (1994) Selective inhibition of inducible cyclooxygenase 2 in vivo is antiinflammatory and nonulcerogenic. Proc Natl Acad Sci USA 91:3228-3232. doi:10.1073/pnas.91.8.3228 (Pubitemid 24130209)
34. Li N, Liu JY, Qiu H, Harris TR, Sirish P, Hammock BD, Chiamvimonvat N (2011) Use of metabolomic profiling in the study of arachidonic acid metabolism in cardiovascular disease. Congest Heart Fail 17:42-46. doi:10.1111/j.1751-7133. 2010.00209.x
35. Wang Y, Liu Z, Li C, Li D, Ouyang Y, Yu J, Guo S, He F, Wang W (2012) Drug target prediction based on the herbs components: the study on themultitargets pharmacological mechanism of qishenkeli acting on the coronary heart disease. Evid Based Complement Altern (in press). doi:10.1155/2012/698531
36. Ho CY, Seidman CE (2006) A contemporary approach to hypertrophic cardiomyopathy. Circulation 113:e858-e862. doi:10.1161/circulationaha.105.591982 (Pubitemid 44305279)
37. Griendling KK, Murphy T, Alexander RW (1993) Molecular biology of the renin-angiotensin system. Circulation 87:1816-1828. doi:10.1161/01.CIR.87.6.1816 (Pubitemid 23165623)
38. Li X, Xu X, Wang J, Yu H, Wang X, Yang H, Xu H, Tang S, Li Y, Yang L (2012)Asystem-level investigation into the mechanisms of chinese traditional medicine: compound danshen formula for cardiovascular disease treatment. PLoS One 7:e43918. doi:10.1371/journal.pone.0043918
39. Ma XH, Shi Z, Tan C, Jiang Y, Go ML, Low BC, Chen YZ (2010) In-silico approaches to multi-target drug discovery. Pharm Res 27:739-749. doi:10.1007/s11095-010-0065-2
40. Cheng TO (2007) Cardiovascular effects of Danshen. Int J Cardiol 121:9-22. doi:10.1016/j.ijcard.2007.01.004
41. Konik E, Kurtz E, Sam F, Sawyer D (2012) Coronary artery spasm, hypertension, hypokalemia and licorice. J Clin Case Rep 2:143. doi:10.4172/2165-7920.1000143
42. Lü D-Y, Cao Y, Li L, Zhu Z-Y, Dong X, Zhang H, Chai Y-F, Lou Z-Y (2011) Comparative analysis of essential oils found in Rhizomes Curcumae and Radix Curcumae by gas chromatographymass spectrometry. J Pharm Anal 1:203-207. doi:10.1016/j.jpha.2011.05.001
43. Fan HY, Fu FH, Yang MY, Xu H, Zhang AH, Liu K (2010) Antiplatelet and antithrombotic activities of salvianolic acid A. Thromb Res 126:e17-e22. doi:10.1016/j.thromres.2010.04.006
44. Kim YH, Shin EK, Kim DH, Lee HH, Park JHY, Kim J-K (2010) Antiangiogenic effect of licochalcone A. Biochem Pharmacol 80:1152-1159. doi:10.1016/j.bcp. 2010.07.006
45. Kim M, Kim Y (2010) Hypocholesterolemic effects of curcumin via up-regulation of cholesterol 7a-hydroxylase in rats fed a high fat diet. Nutr Res Pract 4:191-195. doi:10.4162/nrp.2010.4.3.191
46. Xie L, Evangelidis T, Xie L, Bourne PE (2011) Drug discovery using chemical systems biology: weak inhibition of multiple kinases may contribute to the anti-cancer effect of nelfinavir. PLoS Comput Biol 7:e1002037. doi:10.1371/journal.pcbi.1002037
47. Wang J-G, Staessen JA (2000) Genetic polymorphisms in the renin-angiotensin system: relevance for susceptibility to cardiovascular disease. Eur J Pharmacol 410:289-302. doi:10.1016/S0014-2999(00)00822-0 (Pubitemid 32008151)
48. Bai JP, Abernethy DR (2013) Systems pharmacology to predict drug toxicity: integration across levels of biological organization. Annu Rev Pharmacol 53:451-473. doi:10.1146/annurev-pharmtox-011112-140248
49. Serena DT, Gianni C, Valentina C, Mauro G, Tiziana C, Chiara S, Simone N, Barbara M, Giuseppina B, Virgilio M (2013) Cytocompatibility evaluation of glycol-chitosan coated boron nitride nanotubes in human endothelial cells. Colloids Surf B Biointerfaces 111:142-149. doi:10.1016/j.colsurfb.2013.05.031
50. Xiong X, Yang X, Liu Y, Zhang Y, Wang P, Wang J (2013) Chinese herbal formulas for treating hypertension in traditional Chinese medicine: perspective of modern science. Hypertens Res 36:570-579. doi:10.1038/hr.2013.18
51. Webb NJ, Bottomley MJ, Watson CJ, Brenchley PE (1998) Vascular endothelial growth factor (VEGF) is released from platelets during blood clotting: implications for measurement of circulating VEGF levels in clinical disease. Clin Sci 94:395-404. doi:10.1042/cs0940395 (Pubitemid 28176624)
52. Thomas T, Advani A (2006) Inflammation in cardiovascular disease and regulation of the actin cytoskeleton in inflammatory cells: the actin cytoskeleton as a target. Cardiovasc Hematol Agents Med Chem 4:165-182. doi:10.2174/187152506776369926 (Pubitemid 43805198)