Bead-based screening in chemical biology and drug discovery.

High-throughput screening is an important component of the drug discovery process. The screening of libraries containing hundreds of thousands of compounds requires assays amenable to miniaturisation and automization. Combinatorial chemistry holds a unique promise to deliver structurally diverse libraries for early drug discovery. Among the various library forms, the one-bead-one-compound (OBOC) library, where each bead carries many copies of a single compound, holds the greatest potential for the rapid identification of novel hits against emerging drug targets. However, this potential has not yet been fully realized due to a number of technical obstacles. In this feature article, we review the progress that has been made in bead-based library screening and its application to the discovery of bioactive compounds. We identify the key challenges of this approach and highlight key steps needed for making a greater impact in the field.

[1]  M. Meldal,et al.  Solid-phase combinatorial library of norstatine-type isosters by the nitroaldol reaction. , 2003, Journal of combinatorial chemistry.

[2]  Jason E Hein,et al.  Iterative in situ click chemistry creates antibody-like protein-capture agents. , 2009, Angewandte Chemie.

[3]  William S. Kish,et al.  Reversible cyclic peptide libraries for the discovery of affinity ligands. , 2013, Analytical chemistry.

[4]  K. Lam,et al.  Single-Bead Quantification of Peptide Loading Distribution for One-Bead One-Compound Library Synthesis Using Confocal Raman Spectroscopy. , 2017, Analytical chemistry.

[5]  Leslie A. Walling,et al.  New technologies for chemical genetics , 2001, Journal of cellular biochemistry. Supplement.

[6]  D. Burke,et al.  Selection of a potential diagnostic biomarker for HIV infection from a random library of non-biological synthetic peptoid oligomers , 2016, JIM - Journal of Immunological Methods.

[7]  M. Grøtli,et al.  HYDRA: A novel hydroxy and amine functionalised resin synthesised by reductive amination of PEG aldehyde and a polyamine , 2000 .

[8]  S. Rahman,et al.  COMBINATORIAL CHEMISTRY : DIRECT ANALYSIS OF BEAD SURFACE ASSOCIATED MATERIALS , 1995 .

[9]  G. H. Coombs,et al.  Combinatorial library of peptidotriazoles: identification of [1,2,3]-triazole inhibitors against a recombinant Leishmania mexicana cysteine protease. , 2004, Journal of combinatorial chemistry.

[10]  Stuart L. Schreiber,et al.  Synthesis and Preliminary Evaluation of a Library of Polycyclic Small Molecules for Use in Chemical Genetic Assays , 1999 .

[11]  K. Lam,et al.  High-throughput one-bead-one-compound approach to peptide-encoded combinatorial libraries: MALDI-MS analysis of single TentaGel beads. , 2003, Journal of combinatorial chemistry.

[12]  Hakho Lee,et al.  Design of a Microfluidic Chip for Magnetic-Activated Sorting of One-Bead-One-Compound Libraries. , 2016, ACS combinatorial science.

[13]  Morten Meldal,et al.  Microparticle matrix encoding of beads. , 2010, Angewandte Chemie.

[14]  T. Kodadek,et al.  Encoded combinatorial libraries for the construction of cyclic peptoid microarrays. , 2008, Chemical communications.

[15]  Kit S. Lam,et al.  The “One-Bead-One-Compound” Combinatorial Library Method , 1997 .

[16]  H. Gabius,et al.  Discovery of galectin ligands in fully randomized combinatorial one-bead-one-compound (glyco)peptide libraries. , 2007, Bioorganic & medicinal chemistry letters.

[17]  Christoph A. Merten,et al.  Nanoliter plates--versatile tools for the screening of split-and-mix libraries on-bead and off-bead. , 2010, Chemical communications.

[18]  B. Neel,et al.  Substrate specificity of protein tyrosine phosphatases 1B, RPTPα, SHP-1, and SHP-2. , 2011, Biochemistry.

[19]  J. Frangioni,et al.  High-Throughput Sorting and Placement of One-Bead-One-Compound (OBOC) Libraries from Bulk to Single Wells in Organic Solvent. , 2015, ACS combinatorial science.

[20]  M. Kodama,et al.  Development of calixarene-based host molecules for peptides in aqueous media , 2006 .

[21]  H. Börner,et al.  Fine-tuning Nanocarriers Specifically toward Cargo: A Competitive Study on Solubilizing Related Photosensitizers for Photodynamic Therapy. , 2017, Bioconjugate chemistry.

[22]  Kit S. Lam,et al.  Rapid Discovery of Functional Small Molecule Ligands against Proteomic Targets through Library-Against-Library Screening , 2016, ACS combinatorial science.

[23]  D. Spiegel,et al.  Encoded Silicon-Chip-Based Platform for Combinatorial Synthesis and Screening. , 2017, ACS combinatorial science.

[24]  Kit S Lam,et al.  A novel peptide-based encoding system for "one-bead one-compound" peptidomimetic and small molecule combinatorial libraries. , 2002, Journal of the American Chemical Society.

[25]  D. Pei,et al.  High-throughput screening of one-bead-one-compound libraries: identification of cyclic peptidyl inhibitors against calcineurin/NFAT interaction. , 2011, ACS combinatorial science.

[26]  G. Whitesides,et al.  A miniaturized arrayed assay format for detecting small molecule-protein interactions in cells. , 1997, Chemistry & biology.

[27]  D. Pei,et al.  On-bead screening of combinatorial libraries: reduction of nonspecific binding by decreasing surface ligand density. , 2009, Journal of combinatorial chemistry.

[28]  F. Albericio,et al.  Screening of one-bead-one-peptide combinatorial library using red fluorescent dyes. Presence of positive and false positive beads. , 2009, Journal of combinatorial chemistry.

[29]  L. Brunsveld,et al.  An on-bead assay for the identification of non-natural peptides targeting the androgen receptor-cofactor interaction. , 2011, Bioorganic & medicinal chemistry.

[30]  D. Pei,et al.  Traceless capping agent for peptide sequencing by partial edman degradation and mass spectrometry. , 2006, Analytical chemistry.

[31]  Kristin M. Brinner,et al.  Cleavable hydrophilic linker for one-bead-one-compound sequencing of oligomer libraries by tandem mass spectrometry. , 2006, Journal of combinatorial chemistry.

[32]  T. Kodadek,et al.  Direct Comparison of Linear and Macrocyclic Compound Libraries as a Source of Protein Ligands , 2015, ACS combinatorial science.

[33]  M. Auer,et al.  Analysis of protein-small molecule interactions by microscale equilibrium dialysis and its application as a secondary confirmation method for on-bead screening. , 2010, Journal of combinatorial chemistry.

[34]  Thomas Kodadek,et al.  Optimized protocols for the isolation of specific protein-binding peptides or peptoids from combinatorial libraries displayed on beads. , 2006, Molecular bioSystems.

[35]  C. Schmuck,et al.  Hydrolytic activity of histidine-containing octapeptides in water identified by quantitative screening of a combinatorial library. , 2009, Organic & biomolecular chemistry.

[36]  Morten Meldal,et al.  'One bead two compound libraries' for detecting chemical and biochemical conversions. , 2004, Current opinion in chemical biology.

[37]  Kit S Lam,et al.  Combinatorial Library Screening with Liposomes for Discovery of Membrane Active Peptides. , 2017, ACS combinatorial science.

[38]  R. Zubarev,et al.  Introducing an Asp-Pro linker in the synthesis of random one-bead-one-compound hexapeptide libraries compatible with ESI-MS analysis. , 2012, ACS combinatorial science.

[39]  T. Groth,et al.  Automated Sorting of Beads from a “One-Bead-Two-Compounds” Combinatorial Library of Metalloproteinase Inhibitors , 2003 .

[40]  G. Siuzdak,et al.  Direct characterization of solid phase resin-bound molecules by mass spectrometry , 1996 .

[41]  M. Meldal Pega: a flow stable polyethylene glycol dimethyl acrylamide copolymer for solid phase synthesis. , 1992 .

[42]  K. Lam,et al.  Discovery of selective aldo-keto reductase ligands--an on-bead assay strategy. , 2005, Bioorganic & medicinal chemistry letters.

[43]  M. Przybylski,et al.  De novo sequencing of peptides on single resin beads by MALDI-FTICR tandem mass spectrometry , 2010, Journal of the American Society for Mass Spectrometry.

[44]  F. Albericio,et al.  An efficient strategy for the preparation of one-bead-one-peptide libraries on a new biocompatible solid support , 2005 .

[45]  C. Schmuck,et al.  Peptide Binding by One‐Armed Receptors in Water: Screening of a Combinatorial Library for the Binding of Val‐Val‐Ile‐Ala , 2003, Chembiochem : a European journal of chemical biology.

[46]  A. Berkessel,et al.  Organogel media for on-bead screening in combinatorial catalysis , 2005 .

[47]  J. Ndungu,et al.  High-throughput Identification of DNA-Encoded IgG Ligands that Distinguish Active and Latent Mycobacterium tuberculosis Infections. , 2017, ACS chemical biology.

[48]  Judit Tulla-Puche,et al.  ChemMatrix, a poly(ethylene glycol)-based support for the solid-phase synthesis of complex peptides. , 2006, Journal of combinatorial chemistry.

[49]  H. Fenniri,et al.  Barcoded resins: a new concept for polymer-supported combinatorial library self-deconvolution. , 2001, Journal of the American Chemical Society.

[50]  T. Kodadek,et al.  Seamless bead to microarray screening: rapid identification of the highest affinity protein ligands from large combinatorial libraries. , 2010, Chemistry & biology.

[51]  E. Bayer Towards the Chemical Synthesis of Proteins , 1991 .

[52]  M. Grøtli,et al.  SPOCC : A RESIN FOR SOLID-PHASE ORGANIC CHEMISTRY AND ENZYMATIC REACTIONS ON SOLID PHASE , 1999 .

[53]  Anne-Sophie Wavreille,et al.  Cyclic peptidyl inhibitors of Grb2 and tensin SH2 domains identified from combinatorial libraries. , 2008, Journal of combinatorial chemistry.

[54]  Kevin L. Bicker,et al.  Peptoid Library Agar Diffusion (PLAD) Assay for the High-Throughput Identification of Antimicrobial Peptoids. , 2016, ACS combinatorial science.

[55]  J. Reymond,et al.  Identification of catalytic Peptide dendrimers by "off-bead" in silica high-throughput screening of combinatorial libraries. , 2009, Journal of combinatorial chemistry.

[56]  Darryn Bryant,et al.  Toward larger chemical libraries: Encoding with fluorescent colloids in combinatorial chemistry , 2000 .

[57]  J. E. Rasmussen,et al.  Small-molecule affinity ligands for protein purification: combined computational enrichment and automated in-line screening of an optically encoded library. , 2010, Angewandte Chemie.

[58]  M. Kodama,et al.  On-bead screening of a library to detect host-guest complexation by an aniline reporter. , 2006, Chemical communications.

[59]  C. Buehler,et al.  On-bead screens sample narrower affinity ranges of protein-ligand interactions compared to equivalent solution assays. , 2012, Chemphyschem : a European journal of chemical physics and physical chemistry.

[60]  Manfred Auer,et al.  Single bead labeling method for combining confocal fluorescence on-bead screening and solution validation of tagged one-bead one-compound libraries. , 2009, Chemistry & biology.

[61]  C. Cao,et al.  γ-AApeptide-based small-molecule ligands that inhibit Aβ aggregation. , 2014, Chemical communications.

[62]  T. Kodadek,et al.  Rapid Lead Discovery Through Iterative Screening of One Bead One Compound Libraries , 2014, ACS combinatorial science.

[63]  R. CruickshankDana,et al.  The development of organometallic OBOC peptide libraries and sequencing of N-terminal rhenium(I) tricarbonyl-containing peptides utilizing MALDI tandem mass spectrometry , 2015 .

[64]  A. Jäschke,et al.  Isolation and characterization of fluorescence-enhancing RNA tags. , 2011, Bioorganic & medicinal chemistry.

[65]  B. Pentelute,et al.  Library Design-Facilitated High-Throughput Sequencing of Synthetic Peptide Libraries. , 2017, ACS combinatorial science.

[66]  Ji Hoon Lee,et al.  A simple strategy for the construction of combinatorial cyclic peptoid libraries. , 2010, Chemical communications.

[67]  K. Lam,et al.  A new type of synthetic peptide library for identifying ligand-binding activity , 1992, Nature.

[68]  S. Schreiber,et al.  Small molecule-dependent genetic selection in stochastic nanodroplets as a means of detecting protein-ligand interactions on a large scale. , 1997, Chemistry & biology.

[69]  M. Auer,et al.  A Wide-Field Fluorescence Microscope Extension for Ultrafast Screening of One-Bead One-Compound Libraries Using a Spectral Image Subtraction Approach. , 2016, ACS combinatorial science.

[70]  D. Pei,et al.  Reverse interactomics: decoding protein-protein interactions with combinatorial peptide libraries. , 2007, Molecular bioSystems.

[71]  T. Kodadek,et al.  Utility of Redundant Combinatorial Libraries in Distinguishing High and Low Quality Screening Hits , 2014, ACS combinatorial science.

[72]  K. Lam,et al.  Application of the "libraries from libraries" concept to "one-bead one-compound" combinatorial chemistry. , 2009, Advances in experimental medicine and biology.

[73]  David K Wilson,et al.  On-bead combinatorial techniques for the identification of selective aldose reductase inhibitors. , 2006, Bioorganic & medicinal chemistry.

[74]  B. Imperiali,et al.  A Powerful Combinatorial Screen to Identify High‐Affinity Terbium(III)‐Binding Peptides , 2003, Chembiochem : a European journal of chemical biology.

[75]  Su Seong Lee,et al.  An efficient strategy to enhance binding affinity and specificity of a known isozyme inhibitor. , 2016, Organic & biomolecular chemistry.

[76]  J. Delaissé,et al.  PEGA supports for combinatorial peptide synthesis and solid‐phase enzymatic library assays , 1998, Journal of peptide science : an official publication of the European Peptide Society.

[77]  Manfred Auer,et al.  Confocal nanoscanning, bead picking (CONA): PickoScreen microscopes for automated and quantitative screening of one-bead one-compound libraries. , 2009, Journal of combinatorial chemistry.

[78]  S. Joo,et al.  High-throughput sequence determination of cyclic peptide library members by partial Edman degradation/mass spectrometry. , 2006, Journal of the American Chemical Society.

[79]  K. Nicolaou,et al.  Radiofrequency Encoded Combinatorial Chemistry , 1995 .

[80]  N. Ede,et al.  Beyond Rf tagging. , 2003, Current opinion in chemical biology.

[81]  F. Albericio,et al.  A simple protocol for combinatorial cyclic depsipeptide libraries sequencing by matrix‐assisted laser desorption/ionisation mass spectrometry , 2015, Journal of peptide science : an official publication of the European Peptide Society.

[82]  T. Kodadek,et al.  Rapid identification of improved protein ligands using peptoid microarrays. , 2009, Bioorganic & medicinal chemistry letters.

[83]  F. Albericio,et al.  Preparation and applications of polyethylene glycol-polystyrene graft resin supports for solid-phase peptide synthesis , 1994 .

[84]  K. Lam,et al.  Global transformation of OBOC combinatorial peptide libraries into OBOC polyamine and small molecule libraries. , 2008, Journal of combinatorial chemistry.

[85]  K. Lam,et al.  Rainbow beads: a color coding method to facilitate high-throughput screening and optimization of one-bead one-compound combinatorial libraries. , 2008, Journal of combinatorial chemistry.

[86]  Kit S Lam,et al.  Jeffamine derivatized TentaGel beads and poly(dimethylsiloxane) microbead cassettes for ultrahigh-throughput in situ releasable solution-phase cell-based screening of one-bead-one-compound combinatorial small molecule libraries. , 2010, Journal of combinatorial chemistry.

[87]  Laurent Mugherli,et al.  Combinatorial discovery of fluorescent pharmacophores by multicomponent reactions in droplet arrays. , 2011, Journal of the American Chemical Society.

[88]  K. Lam,et al.  Encoding method for OBOC small molecule libraries using a biphasic approach for ladder-synthesis of coding tags. , 2004, Journal of the American Chemical Society.

[89]  J. Minna,et al.  Unbiased Selection of Peptide-Peptoid Hybrids Specific for Lung Cancer Compared to Normal Lung Epithelial Cells. , 2015, ACS chemical biology.

[90]  G. H. Coombs,et al.  Combinatorial library of peptide isosters based on Diels-Alder reactions: identification of novel inhibitors against a recombinant cysteine protease from Leishmania mexicana. , 2001, Journal of combinatorial chemistry.

[91]  T. Kodadek,et al.  Identification of a peptoid inhibitor of the proteasome 19S regulatory particle. , 2007, Journal of the American Chemical Society.

[92]  Y. Fukazawa,et al.  On-beads screening of solid-attached diketopiperazines for calix(5)arene-based receptor , 2003 .

[93]  Alexander K. Price,et al.  hνSABR: Photochemical Dose–Response Bead Screening in Droplets , 2016, Analytical chemistry.

[94]  T. Nielsen,et al.  In-Bead Screening of Hydroxamic Acids for the Identification of HDAC Inhibitors. , 2016, Angewandte Chemie.

[95]  Judit Tulla-Puche,et al.  From the one-bead-one-compound concept to one-bead-one-reactor. , 2007, Journal of combinatorial chemistry.

[96]  Kevin Braeckmans,et al.  Encoding microcarriers by spatial selective photobleaching , 2003, Nature materials.

[97]  Mehmet Toner,et al.  Multifunctional Encoded Particles for High-Throughput Biomolecule Analysis , 2007, Science.

[98]  Jonathan A. Ellman,et al.  Synthesis and Applications of Small Molecule Libraries. , 1996, Chemical reviews.

[99]  A. Sherry,et al.  On-bead combinatorial synthesis and imaging of chemical exchange saturation transfer magnetic resonance imaging agents to identify factors that influence water exchange. , 2011, Journal of the American Chemical Society.

[100]  T. Kodadek,et al.  Identification of selective covalent inhibitors of platelet activating factor acetylhydrolase 1B2 from the screening of an oxadiazolone-capped peptoid-azapeptoid hybrid library. , 2016, Bioorganic & medicinal chemistry.

[101]  B. Paegel,et al.  DNA-Encoded Solid-Phase Synthesis: Encoding Language Design and Complex Oligomer Library Synthesis , 2015, ACS combinatorial science.

[102]  Melissa R. Jeddeloh,et al.  Aminodeoxychorismate synthase inhibitors from one-bead one-compound combinatorial libraries: "staged" inhibitor design. , 2006, Journal of medicinal chemistry.

[103]  L. Hood,et al.  Rapid screening of peptide probes through in situ single-bead sequencing microarray. , 2014, Analytical chemistry.

[104]  B. Paegel,et al.  Poisson Statistics of Combinatorial Library Sampling Predict False Discovery Rates of Screening , 2017, ACS combinatorial science.

[105]  R. Liskamp,et al.  Combinatorial solid-phase synthesis and screening of a diverse tripodal triazacyclophane (TAC)-based synthetic receptor library showing a remarkable selectivity towards a d-Ala-d-Ala containing ligand , 2004 .

[106]  K. Lam,et al.  Discovery and Characterization of a Potent and Specific Peptide Ligand Targeting Endothelial Progenitor Cells and Endothelial Cells for Tissue Regeneration. , 2017, ACS chemical biology.

[107]  Manfred Auer,et al.  Single‐bead, Single‐molecule, Single‐cell Fluorescence , 2008, Annals of the New York Academy of Sciences.

[108]  K. Lam,et al.  Development of hydrogel TentaGel shell-core beads for ultrahigh throughput solution-phase screening of encoded OBOC combinatorial small molecule libraries. , 2009, Journal of combinatorial chemistry.

[109]  J. Ndungu,et al.  Optimization of the Magnetic Recovery of Hits from One-Bead-One-Compound Library Screens. , 2015, ACS combinatorial science.

[110]  Su Seong Lee,et al.  Investigating fluorescent dyes in fluorescence-assisted screenings. , 2014, Chemical communications.

[111]  M. Meldal,et al.  POEPOP AND POEPS : INERT POLYETHYLENE GLYCOL CROSSLINKED POLYMERIC SUPPORTS FOR SOLID SYNTHESIS , 1996 .

[112]  K. Lam,et al.  Partial alloc-deprotection approach for ladder synthesis of "one-bead one-compound" combinatorial libraries. , 2005, Journal of combinatorial chemistry.

[113]  T. Kodadek,et al.  A peptoid "antibody surrogate" that antagonizes VEGF receptor 2 activity. , 2008, Journal of the American Chemical Society.

[114]  M. Auer,et al.  Edinburgh Research Explorer Identification of a Small Molecule Inhibitor of Importin Mediated Nuclear Import by Confocal On-Bead Screening of Tagged One-Bead One-Compound Libraries , 2022 .

[115]  Joshua A. Kritzer,et al.  A Rapid Library Screen for Tailoring β-Peptide Structure and Function , 2005 .

[116]  G. Nolan,et al.  Evolution of peptides that modulate the spectral qualities of bound, small-molecule fluorophores. , 1998, Chemistry & biology.

[117]  M. Ghadiri,et al.  Discovery of potent and selective histone deacetylase inhibitors via focused combinatorial libraries of cyclic alpha3beta-tetrapeptides. , 2009, Journal of medicinal chemistry.