Utility of redundant combinatorial libraries in distinguishing high and low quality screening hits

ACS Combinatorial Science

Volumn 16, Issue 6, 2014, Pages 259-270

  Doran, Todd M ^a   Gao, Yu ^a   Mendes, Kimberly ^b   Dean, Sonja ^b   Simanski, Scott ^a   Kodadek, Thomas ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b OPKO Health Inc   (United States)

Author keywords

antibody screen; antigen surrogate; nonspecific binding; OBOC library; peptoids; redundant library; serum screen

Indexed keywords

ANTIBODY; LIGAND; PEPTIDE LIBRARY; POLYSTYRENE DERIVATIVE; PROTEIN BINDING; TENTAGEL RESIN;

CHEMICAL STRUCTURE; CHEMISTRY; COMBINATORIAL CHEMISTRY; DRUG SCREENING; IMMUNOLOGY; PARTICLE SIZE; PEPTIDE LIBRARY; PROCEDURES; SURFACE PROPERTY; SYNTHESIS;

ANTIBODIES; COMBINATORIAL CHEMISTRY TECHNIQUES; DRUG EVALUATION, PRECLINICAL; LIGANDS; MOLECULAR STRUCTURE; PARTICLE SIZE; PEPTIDE LIBRARY; POLYSTYRENES; PROTEIN BINDING; SURFACE PROPERTIES;

EID: 84902213551     PISSN: 21568952     EISSN: None     Source Type: Journal    
DOI: 10.1021/co500030f     Document Type: Article

References (27)

1. Houghten, R. A.; Pinilla, C.; Blondelle, S. E.; Appel, J. R.; Dooley, C. T.; Cuervo, J. H. Generation and use of synthetic peptide combinatorial libraries for basic research and drug discovery Nature 1991, 354, 84-86
2. 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
3. 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, 13995-14004
4. Paulick, M. G.; Hart, K. M.; Brinner, K. M.; Tjandra, M.; Charych, D. H.; Zuckermann, R. N. Cleavable hydrophilic linker for one-bead-one-compound sequencing of oligomer libraries by tandem mass spectrometry J. Comb. Chem. 2006, 8, 417-426
5. Joo, S. H.; Xiao, Q.; Ling, Y.; Gopishetty, B.; Pei, D. High-throughput sequence determination of cyclic peptide library members by partial Edman degradation/mass spectrometry J. Am. Chem. Soc. 2006, 128, 13000-13009
6. Thakkar, A.; Cohen, A. S.; Connolly, M. D.; Zuckermann, R. N.; Pei, D. High-throughput sequencing of peptoids and peptide-peptoid hybrids by partial Edman degradation and mass spectrometry J. Comb. Chem. 2009, 11 (2) 294-302
7. 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
8. Halpin, D. R.; Harbury, P. DNA display 1. Sequence-encoded routing of DNA populations PLoS Biol. 2004, 2, 1015-1021
9. Mannocci, L.; Zhang, Y.; Scheuermann, J.; Leimbacher, M.; De Bellis, G.; Rizzi, E.; Dumelin, C.; Melkko, S.; Neri, D. High-throughput sequencing allows the identification of binding molecules isolated from DNA-encoded chemical libraries Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 17670-17675
10. Clark, M. A.; Acharya, R. A.; Arico-Muendel, C. C.; Belyanskaya, S. L.; Benjamin, D. R.; Carlson, N. R.; Centrella, P. A.; Chiu, C. H.; Creaser, S. P.; Cuozzo, J. W.; Davie, C. P.; Ding, Y.; Franklin, G. J.; Franzen, K. D.; Gefter, M. L.; Hale, S. P.; Hansen, N. J.; Israel, D. I.; Jiang, J.; Kavarana, M. J.; Kelley, M. S.; Kollmann, C. S.; Li, F.; Lind, K.; Mataruse, S.; Medeiros, P. F.; Messer, J. A.; Myers, P.; O'Keefe, H.; Oliff, M. C.; Rise, C. E.; Satz, A. L.; Skinner, S. R.; Svendsen, J. L.; Tang, L.; van Vloten, K.; Wagner, R. W.; Yao, G.; Zhao, B.; Morgan, B. A. Design, synthesis and selection of DNA-encoded small-molecule libraries Nat. Chem. Biol. 2009, 5, 647-654
11. Olivos, H. J.; Bachhawat-Sikder, K.; Kodadek, T. Quantum dots as a visual aid for screening bead-bound combinatorial libraries ChemBioChem 2003, 4, 1242-1245
12. Lim, H. S.; Archer, C. T.; Kodadek, T. Identification of a peptoid inhibitor of the proteasome 19S regulatory particle J. Am. Chem. Soc. 2007, 129, 7750-7751
13. Udugamasooriya, D. G.; Dineen, S. P.; Brekken, R. A.; Kodadek, T. A peptoid "antibody surrogate" that antagonizes VEGF receptor 2 activity J. Am. Chem. Soc. 2008, 130, 5744-5752
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, 11990-11995
15. Chen, X.; Tan, P. H.; Zhang, Y.; Pei, D. On-bead screening of combinatorial libraries: Reduction of nonspecific binding by decreasing surface ligand density J. Comb. Chem. 2009, 11, 604-611
16. 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, 724-735
17. Raveendra, B.; Hao, W.; Baccala, R.; Reddy, M. M.; Schilke, J.; Bennett, J. L.; Theofiliopolous, A. N.; Kodadek, T. Discovery of peptoid ligands for anti-Aquaporin 4 antibodies Chem. Biol. 2013, 20, 350-359
18. Lennon, V. A.; Wingerchuk, D. M.; Kryzer, T. J.; Pittock, S. J.; Lucchinetti, C. F.; Fujihara, K.; Nakashima, I.; Weinshenker, B. G. A serum autoantibody marker of neuromyelitis optica: Distinction from multiple sclerosis Lancet 2004, 364, 2106-2112
19. 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
20. Hintersteiner, M.; Buehler, C.; Auer, M. On-bead screens sample narrower affinity ranges of protein-ligand interactions compared to equivalent solution assays ChemPhysChem 2012, 13, 3472-3480
21. Reddy, M. M.; Wilson, R.; Wilson, J.; Connell, S.; Gocke, A.; Hynan, L.; German, D.; Kodadek, T. Identification of candidate IgG biomarkers for Alzheimer's Disease via combinatorial library screening Cell 2011, 144, 132-142
22. Doran, T. M.; Kodadek, T. A liquid array platform for the multiplexed analysis of synthetic molecule-protein interactions ACS Chem. Biol. 2014, 9 (2) 339-346
23. Gao, Y.; Kodadek, T. Synthesis and screening of stereochemically diverse combinatorial libraries of peptide tertiary amides Chem. Biol. 2013, 20, 360-369
24. Aquino, C.; Sarkar, M.; Chalmers, M. J.; Mendes, K.; Kodadek, T.; Micalizio, G. A biomimetic polyketide-inspired approach to small molecule ligand discovery Nat. Chem. 2011, 4, 99-104
25. 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
26. Sarma, B. K.; Kodadek, T. Acylhydrazides as peptoid sub-monomers Chem. Commun. 2011, 47, 10590-10592
27. Sarma, B. K.; Kodadek, T. Sub-monomer synthesis of a hybrid peptoid-azapeptoid library ACS Comb. Sci. 2012, 14, 558-564