A streamlined search technology for identification of synergistic drug combinations

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Weiss, Andrea ^a,b   Berndsen, Robert H ^a   Ding, Xianting ^c   Ho, Chih Ming ^d   Dyson, Paul J ^a   Van Den Bergh, Hubert ^a   Griffioen, Arjan W ^b   Nowak Sliwinska, Patrycja ^a,b  

^a EPFL   (Switzerland)

^b VU UNIVERSITY MEDICAL CENTER   (Netherlands)

^c SHANGHAI JIAO TONG UNIVERSITY   (China)

^d Engineering IV   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTINEOPLASTIC AGENT; AXITINIB; AZD 4547; BENZAMIDE DERIVATIVE; DASATINIB; DRUG COMBINATION; ERLOTINIB; IMIDAZOLE DERIVATIVE; INDAZOLE DERIVATIVE; PIPERAZINE DERIVATIVE; PYRAZOLE DERIVATIVE;

CELL SURVIVAL; DOSE RESPONSE; DRUG COMBINATION; DRUG EFFECTS; DRUG POTENTIATION; DRUG SCREENING; EPITHELIUM CELL; HUMAN; KIDNEY; PATHOLOGY; TUMOR CELL LINE;

ANTINEOPLASTIC AGENTS; BENZAMIDES; CELL LINE, TUMOR; CELL SURVIVAL; DASATINIB; DOSE-RESPONSE RELATIONSHIP, DRUG; DRUG COMBINATIONS; DRUG SCREENING ASSAYS, ANTITUMOR; DRUG SYNERGISM; EPITHELIAL CELLS; ERLOTINIB HYDROCHLORIDE; HUMANS; IMIDAZOLES; INDAZOLES; KIDNEY; PIPERAZINES; PYRAZOLES;

EID: 84942795835     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep14508     Document Type: Article

References (52)

1. Gonzalez-Angulo, A. M., Hortobagyi, G. N. & Ellis, L. M. Targeted therapies: peaking beneath the surface of recent bevacizumab trials. Nat Rev Clin Oncol 8, 319-320 (2011).
2. Kitano, H. Cancer as a robust system: implications for anticancer therapy. Nat Rev Cancer 4, 227-235 (2004).
3. Gerlinger, M. et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 366, 883-892 (2012).
4. Ebos, J. M., Lee, C. R. & Kerbel, R. S. Tumor and host-mediated pathways of resistance and disease progression in response to antiangiogenic therapy. Clin Cancer Res 15, 5020-5025 (2009).
5. van Beijnum, J. R., Nowak-Sliwinska, P., Huijbers, E. J., Thijssen, V. L. & Griffioen, A. W. The great escape; the hallmarks of resistance to anti-Angiogenic therapy. Pharmacol Rev 67, 441-461 (2015).
6. Bozic, I. et al. Evolutionary dynamics of cancer in response to targeted combination therapy. eLife 2, e00747 (2013).
7. Greenberg, P. A. et al. Long-Term follow-up of patients with complete remission following combination chemotherapy for metastatic breast cancer. J Clin Oncol 14, 2197-2205 (1996).
8. Bonadonna, G. et al. Combination chemotherapy as an adjuvant treatment in operable breast cancer. N Engl J Med 294, 405-410 (1976).
9. Iadevaia, S., Lu, Y., Morales, F. C., Mills, G. B. & Ram, P. T. Identification of optimal drug combinations targeting cellular networks: integrating phospho-proteomics and computational network analysis. Cancer Res 70, 6704-6714 (2010).
10. Zhao, B., Pritchard, J. R., Lauffenburger, D. A. & Hemann, M. T. Addressing genetic tumor heterogeneity through computationally predictive combination therapy. Cancer Discov 4, 166-174 (2014).
11. Tan, X. et al. Systematic identification of synergistic drug pairs targeting HIV. Nat Biotechnol 30, 1125-1130 (2012).
12. Zinner, R. G. et al. Algorithmic guided screening of drug combinations of arbitrary size for activity against cancer cells. Mol Cancer Ther 8, 521-532 (2009).
13. Wong, P. K. et al. Closed-loop control of cellular functions using combinatory drugs guided by a stochastic search algorithm. Proc Nat Acad Sci 105, 5105-5110 (2008).
14. Yoon, B. J. Enhanced stochastic optimization algorithm for finding effective multi-Target therapeutics. BMC Bioinformatics 12 Suppl 1, S18 (2011).
15. Ding, X. et al. Cascade search for HSV-1 combinatorial drugs with high antiviral efficacy and low toxicity. Int J Nanomed 7, 2281-2292 (2012).
16. Tsutsui, H. et al. An optimized small molecule inhibitor cocktail supports long-Term maintenance of human embryonic stem cells. Nat Commun 2, 167 (2011).
17. Honda, Y. et al. Guiding the osteogenic fate of mouse and human mesenchymal stem cells through feedback system control. Sci Rep 3, 3420 (2013).
18. Weiss, A. et al. Rapid Stochastic Optimization Of Drug Combination For Inhibiting Angiogenesis In Cancer Growth. Angiogenesis 18, 233-244 (2015).
19. Wang, H. et al. Mechanism-Independent Optimization of Combinatorial Nanodiamond and Unmodified Drug Delivery Using a Phenotypically Driven Platform Technology. ACS Nano, doi: 10.1021/acsnano.5b00638 (2015).
20. Porta, C. et al. Maximising the duration of disease control in metastatic renal cell carcinoma with targeted agents: An expert agreement. Med Oncol 29, 1896-1907 (2012).
21. Gross-Goupil, M., Francois, L., Quivy, A. & Ravaud, A. Axitinib: A Review of its Safety and Efficacy in the Treatment of Adults with Advanced Renal Cell Carcinoma. Clin Med Insights. Oncol 7, 269-277 (2013).
22. Ling, J. et al. Metabolism and excretion of erlotinib, a small molecule inhibitor of epidermal growth factor receptor tyrosine kinase, in healthy male volunteers. Drug Metab Dispos 34, 420-426 (2006).
23. Bukowski, R. M. et al. Randomized phase II study of erlotinib combined with bevacizumab compared with bevacizumab alone in metastatic renal cell cancer. J Clin Oncol 25, 4536-4541 (2007).
24. CompuSyn for Drug Combinations: PC Software and Users Guide: A Computer Program for Quantitation of Synergism and Antagonism in Drug Combinations, and the Determination of IC50 and ED50 and LD50 Values (Paramus, NJ, 2005).
25. Nowak-Sliwinska, P. et al. Organometallic ruthenium(II) arene compounds with antiangiogenic activity. J Med Chem 54, 3895-3902 (2011).
26. Rugo, H. S., Stopeck, A. & Joy, A. A. A randomized, double-blind phase II study of the oral tyrosine kinase inhibitor (TKI) axitinib (AG-013736) in combination with docetaxel (DOC) compared to DOC plus placebo (PL) in metastatic breast cancer (MBC). J Clin Oncol 25(18 supl) 32 (2007).
27. Sumi, T. et al. Expression of matrix metalloproteinases 7 and 2 in human renal cell carcinoma. Oncol Rep 10, 567-570 (2003).
28. Cho, D. C. et al. The efficacy of the novel dual PI3-kinase/mTOR inhibitor NVP-BEZ235 compared with rapamycin in renal cell carcinoma. Ciln Caner Res 16, 3628-3638 (2010).
29. Schoffski, P. et al. A phase I, dose-escalation study of the novel Polo-like kinase inhibitor volasertib (BI 6727) in patients with advanced solid tumours. Eur J Cancer 48, 179-186 (2012).
30. Lombardo, L. J. et al. Discovery of N-(2-chloro-6-methyl-phenyl)-2-(6-(4-(2-hydroxyethyl)-piperazin-1-yl)-2-methylpyrimidin-4-ylamino)thiazole-5-carboxamide (BMS-354825), a dual Src/Abl kinase inhibitor with potent antitumor activity in preclinical assays. J Med Chem 47, 6658-6661 (2004).
31. Li, Y. et al. VX680/MK-0457, a potent and selective Aurora kinase inhibitor, targets both tumor and endothelial cells in clear cell renal cell carcinoma. Am J Transl Res 2, 296-308 (2010).
32. Stillebroer, A., Mulders, P., Boerman, O., Oyen, W. & Oosterwijk, E. Carbonic anhydrase IX in renal cell carcinoma: implications for prognosis, diagnosis, and therapy. Eur Urol 58, 75-83 (2010).
33. Al-Ahmadie, H. A. et al. Carbonic anhydrase IX expression in clear cell renal cell carcinoma: An immunohistochemical study comparing 2 antibodies. Am J surg Pathol 32, 377-382 (2008).
34. Zhang, J. et al. Translating the therapeutic potential of AZD4547 in FGFR1-Amplified non-small cell lung cancer through the use of patient-derived tumor xenograft models. Clin Cancer Res 18, 6658-6667 (2012).
35. Heinrich, M. C. et al. Crenolanib inhibits the drug-resistant PDGFRA D842V mutation associated with imatinib-resistant gastrointestinal stromal tumors. Clin Cancer Res 18, 4375-4384 (2012).
36. Xu, H., Jaynes, J. & Ding, X. Combining two-level and three-level orthogonal arrays for factor screening and response surface exploration. Stat Sinica 24, 269-289 (2014).
37. Wood, K., Nishida, S., Sontag, E. D. & Cluzel, P. Mechanism-independent method for predicting response to multidrug combinations in bacteria. Proc Nat Acad Sci 109, 12254-12259 (2012).
38. Al-Shyoukh, I. et al. Systematic quantitative characterization of cellular responses induced by multiple signals. BMC Syst Biol 5, 88 (2011).
39. Yang, F. et al. Sunitinib induces apoptosis and growth arrest of medulloblastoma tumor cells by inhibiting STAT3 and AKT signaling pathways. Mol Cancer Res 8, 35-45 (2010).
40. Geva-Zatorsky, N. et al. Protein dynamics in drug combinations: A linear superposition of individual-drug responses. Cell 140, 643-651 (2010).
41. Pritchard, J. R. et al. Defining principles of combination drug mechanisms of action. Proc Nat Acad Sci 110, E170-179 (2013).
42. Park, M., Nassar, M. & Vikalo, H. Bayesian active learning for drug combinations. IEEE Trans Biomed Eng 60, 3248-3255 (2013).
43. Feala, J. D. et al. Systems approaches and algorithms for discovery of combinatorial therapies. Wiley Interdiscip Rev Sys Biol Med 2, 181-193 (2010).
44. Tallarida, R. J. Drug synergism: its detection and applications. J Pharmacol Exp Ther 298, 865-872 (2001).
45. Minto, C. F. et al. Response surface model for anesthetic drug interactions. Anesthesiology 92, 1603-1616 (2000).
46. Loges, S., Schmidt, T. & Carmeliet, P. Mechanisms of resistance to anti-Angiogenic therapy and development of third-generation anti-Angiogenic drug candidates. Genes Cancer 1, 12-25 (2010).
47. Li, W. et al. Identifying prognostic features by bottom-up approach and correlating to drug repositioning. PLoS One 10, e0118672 (2015).
48. Allardyce, C. S., Dyson, P. J., Ellis, D. J. & Heath, S. L. [Ru(eta(6)-p-cymene)Cl-2(pta)] (pta= 1,3,5-Triaza-7-phosphatricyclo[3.3.1.1] decane): A water soluble compound that exhibits pH dependent DNA binding providing selectivity for diseased cells. Chem Commun, 1396-1397, doi: 10.1039/B104021a (2001).
49. Boyum, A. Isolation of lymphocytes, granulocytes and macrophages. Scand J Immunol Suppl 5, 9-15 (1976).
50. van Beijnum, J. R. et al. Tumor angiogenesis is enforced by autocrine regulation of high-mobility group box 1. Oncogene 17, 363-374 (2013).
51. Seber, G. A. F. & Lee, A. J. Linear Regression Analysis; 2nd Edition. (Wiley, 2003).
52. Bijnsdorp, I. V., Giovannetti, E. & Peters, G. J. Analysis of drug interactions. Methods Mol Biol 731, 421-434 (2011).