title: Utility of redundant combinatorial libraries in distinguishing high and low quality screening hits.
abstract: Large one-bead one-compound (OBOC) combinatorial libraries can be constructed relatively easily by solid-phase split and pool synthesis. The use of resins with hydrophilic surfaces, such as TentaGel, allows the beads to be used directly in screens for compounds that bind selectively to labeled proteins, nucleic acids, or other biomolecules. However, we have found that this method, while useful, has a high false positive rate. In other words, beads that are scored as hits often display compounds that prove to be poor ligands for the target of interest when they are resynthesized and carried through validation trials. This results in a significant waste of time and resources in cases where putative hits cannot be validated without resynthesis. Here, we report that this problem can be largely eliminated through the use of redundant OBOC libraries, where more than one bead displaying the same compound is present in the screen. We show that compounds isolated more than once are likely to be high quality ligands for the target of interest, whereas compounds isolated only once have a much higher likelihood of being poor ligands. While the use of redundant libraries does limit the number of unique compounds that can be screened at one time in this format, the overall savings in time, effort, and materials makes this a more efficient route to the isolation of useful ligands for biomolecules.
authors.affiliation: Departments of Chemistry and Cancer Biology, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States.
authors.forename: Todd M
authors.initials: TM
authors.lastname: Doran
authors.forename: Yu
authors.initials: Y
authors.lastname: Gao
authors.forename: Kimberly
authors.initials: K
authors.lastname: Mendes
authors.forename: Sonja
authors.initials: S
authors.lastname: Dean
authors.forename: Scott
authors.initials: S
authors.lastname: Simanski
authors.forename: Thomas
authors.initials: T
authors.lastname: Kodadek
mesh_terms: D000906:Antibodies / Q000737:chemistry / Q000276:immunology; D020650:Combinatorial Chemistry Techniques; D004353:Drug Evaluation, Preclinical / Q000379:methods*; D008024:Ligands; D015394:Molecular Structure; D010316:Particle Size; D019151:Peptide Library; D011137:Polystyrenes / Q000138:chemical synthesis / Q000737:chemistry*; D011485:Protein Binding; D013499:Surface Properties
chemical_list: D000906:Antibodies; D008024:Ligands; D019151:Peptide Library; D011137:Polystyrenes; C101297:Tentagel resin
references.citation: J Am Chem Soc. 2013 Aug 14;135(32):11990-5
references.pmid: 23865589
references.citation: Cell. 2011 Jan 7;144(1):132-42
references.pmid: 21215375
references.citation: J Am Chem Soc. 2002 Jul 3;124(26):7678-80
references.pmid: 12083920
references.citation: J Am Chem Soc. 2007 Jun 27;129(25):7750-1
references.pmid: 17536803
references.citation: Nature. 1991 Nov 7;354(6348):82-4
references.pmid: 1944576
references.citation: ACS Comb Sci. 2012 Oct 8;14(10):558-64
references.pmid: 22958123
references.citation: J Comb Chem. 2009 Jul-Aug;11(4):604-11
references.pmid: 19397369
references.citation: Chem Commun (Camb). 2011 Oct 14;47(38):10590-2
references.pmid: 21892506
references.citation: Chembiochem. 2003 Nov 7;4(11):1242-5
references.pmid: 14613120
references.citation: J Comb Chem. 2009 Mar 9;11(2):294-302
references.pmid: 19154119
references.citation: Chem Biol. 2009 Jul 31;16(7):724-35
references.pmid: 19635409
references.citation: PLoS Biol. 2004 Jul;2(7):E173
references.pmid: 15221027
references.citation: Nat Chem. 2011 Nov 20;4(2):99-104
references.pmid: 22270625
references.citation: Chem Biol. 2010 Jan 29;17(1):38-45
references.pmid: 20142039
references.citation: Chem Biol. 2013 Mar 21;20(3):360-9
references.pmid: 23521794
references.citation: Lancet. 2004 Dec 11-17;364(9451):2106-12
references.pmid: 15589308
references.citation: Methods Enzymol. 1996;267:437-47
references.pmid: 8743331
references.citation: J Am Chem Soc. 2006 Oct 4;128(39):13000-9
references.pmid: 17002397
references.citation: J Am Chem Soc. 2008 Apr 30;130(17):5744-52
references.pmid: 18386897
references.citation: J Comb Chem. 2006 May-Jun;8(3):417-26
references.pmid: 16677012
references.citation: Chem Biol. 2013 Mar 21;20(3):351-9
references.pmid: 23521793
references.citation: J Am Chem Soc. 2003 Nov 19;125(46):13995-4004
references.pmid: 14611236
references.citation: ACS Chem Biol. 2014 Feb 21;9(2):339-46
references.pmid: 24245981
references.citation: Chemphyschem. 2012 Oct 22;13(15):3472-80
references.pmid: 22829563
references.citation: Proc Natl Acad Sci U S A. 2008 Nov 18;105(46):17670-5
references.pmid: 19001273
references.citation: Nature. 1991 Nov 7;354(6348):84-6
references.pmid: 1719428
references.citation: Nat Chem Biol. 2009 Sep;5(9):647-54
references.pmid: 19648931