Rectifying cancer drug discovery through network pharmacology

Future Medicinal Chemistry

Volumn 6, Issue 5, 2014, Pages 529-539

  Azmi, Asfar S ^a   Mohammad, Ramzi M ^a,b  

^a WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b HAMAD MEDICAL CORPORATION   (Qatar)

Author keywords

[No Author keywords available]

Indexed keywords

ANTINEOPLASTIC AGENT; NATURAL PRODUCT;

CANCER THERAPY; DRUG DESIGN; DRUG MECHANISM; DRUG TARGETING; PRIORITY JOURNAL; REVIEW;

ANTINEOPLASTIC AGENTS; ANTINEOPLASTIC COMBINED CHEMOTHERAPY PROTOCOLS; BIOLOGICAL PRODUCTS; CYCLOPHOSPHAMIDE; DOXORUBICIN; DRUG DISCOVERY; DRUG REPOSITIONING; DRUG RESISTANCE, NEOPLASM; HUMANS; METABOLIC NETWORKS AND PATHWAYS; NEOPLASMS; PREDNISONE; PROTEIN INTERACTION MAPS; SYSTEMS BIOLOGY; VINCRISTINE;

EID: 84897008823     PISSN: 17568919     EISSN: 17568927     Source Type: Journal    
DOI: 10.4155/fmc.14.6     Document Type: Review

References (80)

1. Hughes JP, Rees S, Kalindjian SB, Philpott KL. Principles of early drug discovery. Br. J. Pharmacol. 162(6), 1239-1249 (2011).
2. Sams-Dodd F. Target-based drug discovery: is something wrong? Drug Discov. Today 10(2), 139-147 (2005).
3. Arrowsmith J, Miller P. Trial watch: Phase II and Phase III attrition rates 2011-2012. Nat. Rev. Drug Discov. 12(8), 569 (2013).
4. Shapiro DM, GOLDIN A. Cancer chemotherapy; analysis of results of different screening techniques with nitrogen-mustard analogues. Cancer 2(1), 100-112 (1949).
5. Rosenberg B, Vancamp L, Krigas T. Inhibition of cell division in escherichia coli by electrolysis products from a platinum electrode. Nature 205, 698-699 (1965).
6. Rosenberg B. Noble metal complexes in cancer chemotherapy. Adv. Exp. Med. Biol. 91, 129-150 (1977).
7. Rosenberg B. Anticancer activity of cis-dichlorodiammineplatinum(II) and some relevant chemistry. Cancer Treat. Rep. 63(9-10), 1433-1438 (1979).
8. Gaynor ER, Fisher RI. CHOP therapy: has shorter-course therapy had an impact on lymphomas? Cancer Invest. 16(1), 26-32 (1998).
9. Habermann TM, Weller EA, Morrison VA et al. Rituximab-CHOP versus CHOP alone or with maintenance rituximab in older patients with diffuse large B-cell lymphoma. J. Clin. Oncol. 24(19), 3121-3127 (2006).
10. Kath R, Blumenstengel K, Fricke HJ, Hoffken K. Bendamustine monotherapy in advanced and refractory chronic lymphocytic leukemia. J. Cancer Res. Clin. Oncol. 127(1), 48-54 (2001).
11. Alian OM, Azmi AS, Mohammad RM. Network insights on oxaliplatin anti-cancer mechanisms. Clin. Transl. Med. 1(1), 26 (2012).
12. Lee WL, Wen TN, Shiau JY, Shyur LF. Differential proteomic profiling identifies novel molecular targets of paclitaxel and phytoagent deoxyelephantopin against mammary adenocarcinoma cells. J. Proteome. Res. 9(1), 237-253 (2010).
13. Ma WW, Hidalgo M. The winning FORMULA-tion: the development of paclitaxel in pancreatic cancer. Clin. Cancer Res. (2013).
14. Kitano H. Biological robustness. Nat. Rev. Genet. 5(11), 826-837 (2004).
15. Kitano H. The theory of biological robustness and its implication in cancer. In: Systems Biology. Springer Berlin Heidelberg, Germany, 69-88 (2007).
16. Kitano H. Cancer robustness: tumour tactics. Nature 426(6963), 125 (2003).
17. Kitano H. Cancer as a robust system: implications for anticancer therapy. Nat. Rev. Cancer 4(3), 227-235 (2004).
18. Srihari S , Leong HW. Temporal dynamics of protein complexes in PPI networks: a case study using yeast cell cycle dynamics. BMC. Bioinform. 13(Suppl. 17), S16 (2012).
19. Lopez-Bigas N, Audit B, Ouzounis C, Parra G, Guigo R. Are splicing mutations the most frequent cause of hereditary disease? FEBS Lett. 579(9), 1900-1903 (2005).
20. Martin DI, Cropley JE, Suter CM. Epigenetics in disease: leader or follower? Epigenetics 6(7), 843-848 (2011).
21. Esteller M, Fraga MF, Paz MF et al. Cancer epigenetics and methylation. Science 297(5588), 1807-1808 (2002).
22. Esteller M. Non-coding RNAs in human disease. Nat. Rev. Genet. 12(12), 861-874 (2011).
23. Eaton S, Simons K. Apical, basal, and lateral cues for epithelial polarization. Cell 82(1), 5-8 (1995).
24. Darland DC, DAmore PA. Cell-cell interactions in vascular development. Curr. Top. Dev. Biol. 52, 107-149 (2001).
25. Karagiannis GS, Poutahidis T, Erdman SE, Kirsch R, Riddell RH, Diamandis EP. Cancer-associated fibroblasts drive the progression of metastasis through both paracrine and mechanical pressure on cancer tissue. Mol. Cancer Res. 10(11), 1403-1418 (2012).
26. Croci DO, Salatino M. Tumor immune escape mechanisms that operate during metastasis. Curr. Pharm. Biotechnol. 12(11), 1923-1936 (2011).
27. Azmi AS, Bao B, Sarkar FH. Exosomes in cancer development, metastasis, and drug resistance: a comprehensive review. Cancer Metastasis Rev. 32(3-4), 623-642 (2013).
28. Dean M, Fojo T, Bates S. Tumour stem cells and drug resistance. Nat. Rev. Cancer 5(4), 275-284 (2005).
29. Semsarian C, Seidman CE. Molecular medicine in the 21st century. Intern. Med. J. 31(1), 53-59 (2001).
30. Azmi AS. Adopting network pharmacology for cancer drug discovery. Curr. Drug Discov. Technol. 10(2), 95-105 (2013).
31. Azmi AS. Network pharmacology: an emerging field in cancer drug discovery. Curr. Drug Discov. Technol. 10(2), 93-94 (2013).
32. Azmi AS. Systems and network biology in pharmaceutical drug discovery. Curr. Pharm. Des. 20(1), 2-3 (2014).
33. Prasasya RD, Tian D, Kreeger PK. Analysis of cancer signaling networks by systems biology to develop therapies. Semin. Cancer Biol. 21(3), 200-206 (2011).
34. Azmi AS, Wang Z, Philip PA, Mohammad RM, Sarkar FH. Proof of concept: network and systems biology approaches aid in the discovery of potent anticancer drug combinations. Mol. Cancer Ther. 9(12), 3137-3144 (2010).
35. Azmi AS, Mohammad RM, Sarkar FH. Can network pharmacology rescue neutraceutical cancer research? Drug Discov. Today 17(15-16), 807-809 (2012).
36. Hopkins AL. Network pharmacology: the next paradigm in drug discovery. Nat. Chem. Biol. 4(11), 682-690 (2008).
37. Pawson T, Linding R. Network medicine. FEBS Lett. 582(8), 1266-1270 (2008).
38. Pujol A, Mosca R, Farres J, Aloy P. Unveiling the role of network and systems biology in drug discovery. Trends Pharmacol. Sci. 31(3), 115-123 (2010).
39. Zhao S, Iyengar R. Systems pharmacology: network analysis to identify multiscale mechanisms of drug action. Annu. Rev. Pharmacol. Toxicol. 52, 505-521 (2012).
40. Tang J, Karhinen L, Xu T et al. Target inhibition networks: predicting selective combinations of druggable targets to block cancer survival pathways. PLoS Comput. Biol. 9(9), e1003226 (2013).
41. Tang J, Aittokallio T. Network pharmacology strategies toward multi-target anticancer therapies: from computational models to experimental design principles. Curr. Pharm. Des. 20(1), 23-36 (2013).
42. Strogatz SH. Exploring complex networks. Nature 410(6825), 268-276 (2001).
43. Beisser D, Brunkhorst S, Dandekar T, Klau GW, Dittrich MT, Muller T. Robustness and accuracy of functional modules in integrated network analysis. Bioinformatics 28(14), 1887-1894 (2012).
44. Dittrich MT, Klau GW, Rosenwald A, Dandekar T, Muller T. Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics 24(13), i223-i231 (2008).
45. Nacher JC, Schwartz JM. Modularity in protein complex and drug interactions reveals new polypharmacological properties. PLoS ONE 7(1), e30028 (2012).
46. Wu G, Feng X, Stein L. A human functional protein interaction network and its application to cancer data analysis. Genome Biol. 11(5), R53 (2010).
47. Gordo S, Giralt E. Knitting and untying the protein network: modulation of protein ensembles as a therapeutic strategy. Protein Sci. 18(3), 481-493 (2009).
48. Xu Y, Xu D, Gabow HN. Protein domain decomposition using a graph-theoretic approach. Bioinformatics 16(12), 1091-1104 (2000).
49. Chen JL, Li J, Stadler WM, Lussier YA. Protein-network modeling of prostate cancer gene signatures reveals essential pathways in disease recurrence. J. Am. Med. Inform. Assoc. 18(4), 392-402 (2011).
50. Berger SI, Iyengar R. Network analyses in systems pharmacology. Bioinformatics 25(19), 2466-2472 (2009).
51. Stumpf MP, Thorne T, de Silva E et al. Estimating the size of the human interactome. Proc. Natl Acad. Sci. USA 105(19), 6959-6964 (2008).
52. Taboureau O, Nielsen SK, Audouze K et al. ChemProt: a disease chemical biology database. Nucleic Acids Res. 39(database issue), D367-D372 (2011).
53. Schrattenholz A, Groebe K, Soskic V. Systems biology approaches and tools for analysis of interactomes and multi-target drugs. Methods Mol. Biol. 662, 29-58 (2010).
54. Dancik V, Seiler KP, Young DW, Schreiber SL, Clemons PA. Distinct biological network properties between the targets of natural products and disease genes. J. Am. Chem. Soc. 132(27), 9259-9261 (2010).
55. Pemovska T, Kontro M, Yadav B et al. Individualized systems medicine strategy to tailor treatments for patients with chemorefractory acute myeloid leukemia. Cancer Discov. 3(12), 1416-1429 (2013).
56. Pan J, Mott M, Xi B et al. Phase I study of nelfinavir in liposarcoma. Cancer Chemother. Pharmacol. 70(6), 791-799 (2012).
57. Rengan R, Mick R, Pryma D et al. A Phase I trial of the HIV protease inhibitor nelfinavir with concurrent chemoradiotherapy for unresectable stage IIIA/IIIB non-small cell lung cancer: a report of toxicities and clinical response. J. Thorac. Oncol. 7(4), 709-715 (2012).
58. Bao B, Wang Z, Ali S et al. Metformin inhibits cell proliferation, migration and invasion by attenuating CSC function mediated by deregulating miRNAs in pancreatic cancer cells. Cancer Prev. Res. (Phila) 5(3), 355-364 (2012).
59. Clinicaltrials: NCT01579812. http://clinicaltrials.gov/show/ NCT01579812
60. Clinicaltrials.gov website. http://clinicaltrials.gov
61. Cote TR, Xu K, Pariser AR. Accelerating orphan drug development. Nat. Rev. Drug Discov. 9(12), 901-902 (2010).
62. Xu K, Cote TR. Database identifies FDA-approved drugs with potential to be repurposed for treatment of orphan diseases. Brief. Bioinform. 12(4), 341-345 (2011).
63. von Eichborn J, Murgueitio MS, Dunkel M, Koerner S, Bourne PE, Preissner R. PROMISCUOUS: a database for networkbased drug-repositioning. Nucleic Acids Res. 39(database issue), D1060-D1066 (2011).
64. Koehn FE, Carter GT. Rediscovering natural products as a source of new drugs. Discov. Med. 5(26), 159-164 (2005).
65. Koehn FE, Carter GT. The evolving role of natural products in drug discovery. Nat. Rev. Drug Discov. 4(3), 206-220 (2005).
66. Sarkar FH, Li Y. Harnessing the fruits of nature for the development of multi-targeted cancer therapeutics. Cancer Treat. Rev. 35(7), 597-607 (2009).
67. Sarkar FH, Li Y, Wang Z, Padhye S. Lesson learned from nature for the development of novel anti-cancer agents: implication of isoflavone, curcumin, and their synthetic analogs. Curr. Pharm. Des. 16(16), 1801-1812 (2010).
68. Tan Y, Wu Q, Xia J, Miele L, Sarkar FH, Wang Z. Systems biology approaches in identifying the targets of natural compounds for cancer therapy. Curr. Drug Discov. Technol. 10(2), 139-146 (2013).
69. Gertsch J. Botanical drugs, synergy, and network pharmacology: forth and back to intelligent mixtures. Planta Med. 77(11), 1086-1098 (2011).
70. Sun H, Zhang A, Yan G et al. Proteomics study on the hepatoprotective effects of traditional Chinese medicine formulae Yin-Chen-Hao-Tang by a combination of two-dimensional polyacrylamide gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry. J. Pharm. Biomed. Anal. 75, 173-179 (2013).
71. Klein A, Wrulich OA, Jenny M et al. Pathway-focused bioassays and transcriptome analysis contribute to a better activity monitoring of complex herbal remedies. BMC.Genomics 14, 133 (2013).
72. Hur M, Campbell AA, meida-de-Macedo M et al. A global approach to analysis and interpretation of metabolic data for plant natural product discovery. Nat. Prod. Rep. 30(4), 565-583 (2013).
73. Pei L, Bao Y, Liu S, Zheng J, Chen X. Material basis of Chinese herbal formulas explored by combining pharmacokinetics with network pharmacology. PLoS ONE 8(2), e57414 (2013).
74. Gu J, Gui Y, Chen L, Yuan G, Lu HZ, Xu X. Use of natural products as chemical library for drug discovery and network pharmacology. PLoS ONE 8(4), e62839 (2013).
75. Daguanno S, Dagnano I, De CM et al. Shotgun proteomics and network analysis of neuroblastoma cell lines treated with curcumin. Mol. Biosyst. 8(4), 1068-1077 (2012).
76. Daminelli S, Haupt VJ, Reimann M, Schroeder M. Drug repositioning through incomplete bi-cliques in an integrated drug-target-disease network. Integr. Biol. (Camb.) 4(7), 778-788 (2012).
77. Fu XJ, Wang ZG, Qu Y, Wang P, Zhou Y, Yu HY. Study on the networks of Nature- Family-Component of Chinese medicinal herbs based on association rules mining. Chin J. Integr. Med. 19(9), 663-667 (2013).
78. Huang C, Zheng C, Li Y, Wang Y, Lu A, Yang L. Systems pharmacology in drug discovery and therapeutic insight for herbal medicines. Brief. Bioinform. doi:10.1039/ c2ib20204b (2013) (Epub ahead of print).
79. Wang X, Xu X, Tao W, Li Y, Wang Y, Yang L. A systems biology approach to uncovering pharmacological synergy in herbal medicines with applications to cardiovascular disease. Evid. Based Complement Alternat. Med. 2012, 519031 (2012).
80. Li B, Xu X, Wang X et al. A systems biology approach to understanding the mechanisms of action of chinese herbs for treatment of cardiovascular disease. Int. J. Mol. Sci. 13(10), 13501-13520 (2012).