Rapid lead discovery through iterative screening of one bead one compound libraries

ACS Combinatorial Science

Volumn 17, Issue 1, 2015, Pages 49-59

  Gao, Yu ^a   Amar, Sabrina ^b   Pahwa, Sonia ^b   Fields, Gregg ^b   Kodadek, Thomas ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b TORREY PINES INSTITUTE FOR MOLECULAR STUDIES   (United States)

Author keywords

iterative screening; one bead one compound (OBOC) libraries; rapid lead discovery; structure activity relationship (SAR)

Indexed keywords

DRUG DEVELOPMENT; HIGH THROUGHPUT SCREENING; STRUCTURE ACTIVITY RELATION;

DRUG DISCOVERY; HIGH-THROUGHPUT SCREENING ASSAYS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84921027940     PISSN: 21568952     EISSN: None     Source Type: Journal    
DOI: 10.1021/co500154e     Document Type: Article

References (32)

1. Jorgensen, W. L. Efficient Drug Lead Discovery and Optimization Acc. Chem. Res. 2009, 42 (6) 724-733
2. Mayr, L. M.; Bojanic, D. Novel trends in high-throughput screening Curr. Opin Pharmacol 2009, 9 (5) 580-588
3. Aina, O. H.; Marik, J.; Liu, R.; Lau, D. H.; Lam, K. S. Identification of novel targeting peptides for human ovarian cancer cells using "one-bead one-compound" combinatorial libraries Mol. Cancer Ther. 2005, 4, 806-813
4. Alluri, P. G.; Reddy, M. M.; Bachhawat-Sikder, K.; Olivos, H. J.; Kodadek, T. Isolation of protein ligands from large peptoid libraries J. Am. Chem. Soc. 2003, 125 (46) 13995-4004
5. Liu, T.; Qian, Z.; Xiao, Q.; Pei, D. High-throughput screening of one-bead-one-compound libraries: identification of cyclic peptidyl inhibitors against calcineurin/NFAT interaction ACS Comb. Sci. 2011, 13 (5) 537-46
6. Wu, H.; Li, Y.; Bai, G.; Niu, Y.; Qiao, Q.; Tipton, J. D.; Cao, C.; Cai, J. γ-AA-peptide-based small-molecule ligands that inhibit Aβ aggregation Chem. Commun. 2014, 50, 5206-5208
7. Lam, K. S.; Salmon, S. E.; Hersh, E. M.; Hruby, V. J.; Kazmierski, W. M.; Knapp, R. J. A new type of synthetic peptide library for identifying ligand-binding activity Nature 1991, 354, 82-84
8. Liu, R.; Marik, J.; Lam, K. S. A novel peptide-based encoding system for "one-bead one-compound" peptidomimetic and small molecule combinatorial libraries J. Am. Chem. Soc. 2002, 124, 7678-7680
9. Lee, J. H.; Kim, H. S.; Lim, H. S. Design and facile solid-phase synthesis of conformationally constrained bicyclic peptoids Org. Lett. 2011, 13, 5012-5015
10. Suwal, S.; Kodadek, T. Synthesis of libraries of peptidomimetic compounds containing a 2-oxopiperazine unit in the main chain Org. Biomol. Chem. 2013, 11, 2088-2092
11. Suwal, S.; Kodadek, T. Solid-phase synthesis of peptoid-like oligomers containing diverse diketopiperazine units Org. Biomol. Chem. 2014, 12 (31) 5831-5834
12. Aditya, A.; Kodadek, T. Incorporation of heterocycles into the backbone of peptoids to generate diverse peptoid-inspired one bead one compound libraries ACS Comb. Sci. 2012, 14 (3) 164-169
13. Seligmann, B.; Abdul-Latif, F.; Al-Obeidi, F.; Flegelova, Z.; Issakova, O.; Kocis, P.; Krchnak, V.; Lam, K. S.; Lebl, M.; Ostrem, J.; Safar, P.; Sepetov, N.; Stierandova, A.; Strop, P.; Wildgoose, P. The construction and use of peptide and non-peptidic combinatorial libraries to discover enzyme inhibitors Eur. J. Med. Chem. 1995, 30 (Suppl. 1) 319s-335s
14. Lian, W.; Upadhyaya, P.; Rhodes, C. A.; Liu, Y.; Pei, D. Screening bicyclic peptide libraries for protein-protein interaction inhibitors: Discovery of a tumor necrosis factor-α antagonist J. Am. Chem. Soc. 2013, 135 (32) 11990-11995
15. Doran, T. M.; Gao, Y.; Mendes, K.; Dean, S.; Simanski, S.; Kodadek, T. The utility of redundant combinatorial libraries in distinguishing high and low quality screening hits ACS Comb. Sci. 2014, 16, 259-270
16. Astle, J. M.; Simpson, L. S.; Huang, Y.; Reddy, M. M.; Wilson, R.; Connell, S.; Wilson, J.; Kodadek, T. Seamless bead to microarray screening: Rapid identification of the highest affinity protein ligands from large combinatorial libraries Chem. Biol. 2010, 17, 38-45
17. Hintersteiner, M.; Kimmerlin, T.; Kalthoff, F.; Stoeckli, M.; Garavel, G.; Seifert, J. M.; Meisner, N. C.; Uhl, V.; Buehler, C.; Weidemann, T.; Auer, M. Single bead labeling method for combining confocal fluorescence on-bead screening and solution validation of tagged one-bead one-compound libraries Chem. Biol. 2009, 16 (7) 724-35
18. Zheng, L.; Li, D.; Xiang, X.; Tong, L.; Qi, M.; Pu, J.; Huang, K.; Tong, Q. Methyl jasmonate abolishes the migration, invasion and angiogenesis of gastric cancer cells through down-regulation of matrix metalloproteinase 14 BMC Cancer 2013, 13, 74
19. He, L.; Chu, D.; Li, X.; Zheng, J.; Liu, S.; Li, J.; Zhao, Q.; Ji, G. Matrix metalloproteinase-14 is a negative prognostic marker for patients with gastric cancer Dig. Dis. Sci. 2013, 58 (5) 1264-70
20. Zarrabi, K.; Dufour, A.; Li, J.; Kuscu, C.; Pulkoski-Gross, A.; Zhi, J.; Hu, Y.; Sampson, N. S.; Zucker, S.; Cao, J. Inhibition of matrix metalloproteinase 14 (MMP-14)-mediated cancer cell migration J. Biol. Chem. 2011, 286 (38) 33167-77
21. Sagara, Y.; Miyata, Y.; Iwata, T.; Kanda, S.; Hayashi, T.; Sakai, H.; Kanetake, H. Clinical significance and prognostic value of S100A4 and matrix metalloproteinase-14 in patients with organ-confined bladder cancer Exp. Ther. Med. 2010, 1 (1) 27-31
22. Fisher, J. F.; Mobashery, S. Recent advances in MMP inhibitor design Cancer Metast. Rev. 2006, 25 (1) 115-136
23. Dufour, A.; Overall, C. M. Missing the target: Matrix metalloproteinase antitargets in inflammation and cancer Trends Pharmacol. Sci. 2013, 34 (4) 233-42
24. Figliozzi, G. M.; Goldsmith, R.; Ng, S. C.; Banville, S. C.; Zuckermann, R. N. Synthesis of N-substituted glycine peptoid libraries Methods Enzymol. 1996, 267, 437-447
25. Zhang, S.; Prabpai, S.; Kongsaeree, P.; Arvidsson, P. I. Poly-N-methylated alpha-peptides: Synthesis and X-ray structure determination of β-strand forming foldamers Chemical Commun. 2006, 5, 497-9
26. Gao, Y.; Kodadek, T. Synthesis and screening of stereochemically diverse combinatorial libraries of peptide tertiary amides Chem. Biol. 2013, 20, 360-369
27. Shah, N. H.; Butterfoss, G. L.; Nguyen, K.; Yoo, B.; Bonneau, R.; Rabenstein, D. L.; Kirshenbaum, K. Oligo(N -Aryl Glycines): A new twist on structured peptoids J. Am. Chem. Soc. 2008, 130 (49) 16622-16632
28. Lauer, J. L.; Bhowmick, M.; Tokmina-Roszyk, D.; Lin, Y.; Van Doren, S. R.; Fields, G. B. The role of collagen charge clusters in the modulation of matrix metalloproteinase activity J. Biol. Chem. 2014, 289 (4) 1981-92
29. Cao, J.; Kozarekar, P.; Pavlaki, M.; Chiarelli, C.; Bahou, W. F.; Zucker, S. Distinct roles for the catalytic and hemopexin domains of membrane type 1-matrix metalloproteinase in substrate degradation and cell migration J. Biol. Chem. 2004, 279 (14) 14129-39
30. dOrtho, M. P.; Will, H.; Atkinson, S.; Butler, G.; Messent, A.; Gavrilovic, J.; Smith, B.; Timpl, R.; Zardi, L.; Murphy, G. Membrane-type matrix metalloproteinases 1 and 2 exhibit broad-spectrum proteolytic capacities comparable to many matrix metalloproteinases Eur. J. Biochem. 1997, 250 (3) 751-7
31. Hurst, D. R.; Schwartz, M. A.; Ghaffari, M. A.; Jin, Y.; Tschesche, H.; Fields, G. B.; Sang, Q. X. Catalytic- and ecto-domains of membrane type 1-matrix metalloproteinase have similar inhibition profiles but distinct endopeptidase activities Biochem. J. 2004, 377 (Pt 3) 775-9
32. Minond, D.; Lauer-Fields, J. L.; Cudic, M.; Overall, C. M.; Pei, D.; Brew, K.; Visse, R.; Nagase, H.; Fields, G. B. The roles of substrate thermal stability and P2 and P1′ subsite identity on matrix metalloproteinase triple-helical peptidase activity and collagen specificity J. Biol. Chem. 2006, 281 (50) 38302-13