Abstract
Speed and throughput are vital ingredients for discovery driven, “-omics” research. The small molecule microarray (SMM) succeeds at delivering phenomenal screening throughput and versatility. The concept at the heart of the technology is elegant, yet simple: by presenting large collections of molecules in high density on a flat surface, one is able to interrogate all possible interactions with desired targets, in just a single step. SMMs have become established as the choice platform for screening, lead discovery, and molecular characterization. This introduction describes the principles governing microarray construction and use, focusing on practical challenges faced when conducting SMM experiments. It will explain the key design considerations and lay the foundation for the chapters that follow. (An earlier version of this chapter appeared in Small Molecule Microarrays: Methods and Protocols, published in 2010.)
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Hu Y, Uttamchandani M, Yao SQ (2006) Microarray: a versatile platform for high-throughput functional proteomics. Comb Chem High Throughput Screen 9:203–212
MacBeath G, Saghatelian A (2009) The promise and challenge of “-omic” approaches. Curr Opin Chem Biol 13:501–502
Foong YM, Fu J, Yao SQ, Uttamchandani M (2012) Current advances in peptide and small molecule microarray technologies. Curr Opin Chem Biol 16:234–242
Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470
Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW (1996) Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci U S A 93:10614–10619
Uttamchandani M, Neo JL, Ong BN, Moochhala S (2009) Applications of microarrays in pathogen detection and biodefence. Trends Biotechnol 27:53–61
Khan J, Bittner ML, Chen Y, Meltzer PS, Trent JM (1999) DNA microarray technology: the anticipated impact on the study of human disease. Biochim Biophys Acta 1423:M17–M28
Yoo SM, Choi JH, Lee SY, Yoo NC (2009) Applications of DNA microarray in disease diagnostics. J Microbiol Biotechnol 19:635–646
Uttamchandani M, Wang J, Yao SQ (2006) Protein and small molecule microarrays: powerful tools for high-throughput proteomics. Mol Biosyst 2:58–68
Templin MF, Stoll D, Schrenk M, Traub PC, Vohringer CF, Joos TO (2002) Protein microarray technology. Trends Biotechnol 20:160–166
Falsey JR, Renil M, Park S, Li S, Lam KS (2001) Peptide and small molecule microarray for high throughput cell adhesion and functional assays. Bioconjug Chem 12:346–353
Park S, Shin I (2002) Fabrication of carbohydrate chips for studying protein–carbohydrate interactions. Angew Chem Int Ed Engl 41:3180–3182
Park S, Lee MR, Pyo SJ, Shin I (2004) Carbohydrate chips for studying high-throughput carbohydrate–protein interactions. J Am Chem Soc 126:4812–4819
Park S, Gildersleeve JC, Blixt O, Shin I (2013) Carbohydrate microarrays. Chem Soc Rev 42:4310–4326
Kuruvilla FG, Shamji AF, Sternson SM, Hergenrother PJ, Schreiber SL (2002) Dissecting glucose signalling with diversity-oriented synthesis and small-molecule microarrays. Nature 416:653–657
Hergenrother PJ, Depew KM, Schreiber SL (2000) Small-molecule microarrays: covalent attachment and screening of alcohol-containing small molecules on glass slides. J Am Chem Soc 122:7849–7850
Wu H, Ge J, Uttamchandani M, Yao SQ (2011) Small molecule microarrays: the first decade and beyond. Chem Commun (Camb) 47:5664–5670
MacBeath G, Koehler AN, Schreiber SL (1999) Printing small molecules as microarrays and detecting protein ligand interactions en masse. J Am Chem Soc 121:7967–7968
MacBeath G, Schreiber SL (2000) Printing proteins as microarrays for high-throughput function determination. Science 289:1760–1763
Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T, Mitchell T, Miller P, Dean RA, Gerstein M, Snyder M (2001) Global analysis of protein activities using proteome chips. Science 293:2101–2105
Ziauddin J, Sabatini DM (2001) Microarrays of cells expressing defined cDNAs. Nature 411:107–110
Horvath L, Henshall S (2001) The application of tissue microarrays to cancer research. Pathology 33:125–129
Sun H, Chattopadhaya S, Wang J, Yao SQ (2006) Recent developments in microarray-based enzyme assays: from functional annotation to substrate/inhibitor fingerprinting. Anal Bioanal Chem 386:416–426
Uttamchandani M, Walsh DP, Yao SQ, Chang YT (2005) Small molecule microarrays: recent advances and applications. Curr Opin Chem Biol 9:4–13
Uttamchandani M, Lu CH, Yao SQ (2009) Next generation chemical proteomic tools for rapid enzyme profiling. Acc Chem Res 42:1183–1192
Dimova D, Hu Y, Bajorath J (2012) Matched molecular pair analysis of small molecule microarray data identifies promiscuity cliffs and reveals molecular origins of extreme compound promiscuity. J Med Chem 55:10220–10228
Sun H, Lu CH, Uttamchandani M, Xia Y, Liou YC, Yao SQ (2008) Peptide microarray for high-throughput determination of phosphatase specificity and biology. Angew Chem Int Ed Engl 47:1698–1702
Gosalia DN, Salisbury CM, Ellman JA, Diamond SL (2005) High throughput substrate specificity profiling of serine and cysteine proteases using solution-phase fluorogenic peptide microarrays. Mol Cell Proteomics 4:626–636
Shigaki S, Yamaji T, Han X, Yamanouchi G, Sonoda T, Okitsu O, Mori T, Niidome T, Katayama Y (2007) A peptide microarray for the detection of protein kinase activity in cell lysate. Anal Sci 23:271–275
Evans D, Johnson S, Laurenson S, Davies AG, Ko Ferrigno P, Walti C (2008) Electrical protein detection in cell lysates using high-density peptide-aptamer microarrays. J Biol 7:3
Bradner JE, McPherson OM, Mazitschek R, Barnes-Seeman D, Shen JP, Dhaliwal J, Stevenson KE, Duffner JL, Park SB, Neuberg DS, Nghiem P, Schreiber SL, Koehler AN (2006) A robust small-molecule microarray platform for screening cell lysates. Chem Biol 13:493–504
Gao L, Sun H, Uttamchandani M, Yao SQ (2013) Phosphopeptide microarrays for comparative proteomic profiling of cellular lysates. Methods Mol Biol 1002:233–251
Pop MS, Wassaf D, Koehler AN (2014) Probing small-molecule microarrays with tagged proteins in cell lysates. Curr Protoc Chem Biol 6:209–220
Zhu B, Jiang B, Na Z, Yao SQ (2015) Controlled proliferation and screening of mammalian cells on a hydrogel-functionalized small molecule microarray. Chem Commun (Camb) 51:10431–10434
Lee JH, Bao K, Frangioni JV, Choi HS (2015) Screening of small molecule microarrays for ligands targeted to the extracellular epitopes of living cells. Microarrays (Basel) 4:53–63
Stiffler MA, Grantcharova VP, Sevecka M, MacBeath G (2006) Uncovering quantitative protein interaction networks for mouse PDZ domains using protein microarrays. J Am Chem Soc 128:5913–5922
Jones RB, Gordus A, Krall JA, MacBeath G (2006) A quantitative protein interaction network for the ErbB receptors using protein microarrays. Nature 439:168–174
Hong JA, Neel DV, Wassaf D, Caballero F, Koehler AN (2014) Recent discoveries and applications involving small-molecule microarrays. Curr Opin Chem Biol 18:21–28
Eisenstein M (2006) Protein arrays: growing pains. Nature 444:959–962
Lam KS, Renil M (2002) From combinatorial chemistry to chemical microarray. Curr Opin Chem Biol 6:353–358
Wang J, Uttamchandani M, Sun H, Yao SQ (2006) Small molecule microarrays: applications using specially tagged chemical libraries. QSAR Comb Sci 25:1009–1019
Lee A, Breitenbucher JG (2003) The impact of combinatorial chemistry on drug discovery. Curr Opin Drug Discov Devel 6:494–508
Koehler AN, Shamji AF, Schreiber SL (2003) Discovery of an inhibitor of a transcription factor using small molecule microarrays and diversity-oriented synthesis. J Am Chem Soc 125:8420–8421
Xiao XY, Li R, Zhuang H, Ewing B, Karunaratne K, Lillig J, Brown R, Nicolaou KC (2000) Solid-phase combinatorial synthesis using MicroKan reactors, Rf tagging, and directed sorting. Biotechnol Bioeng 71:44–50
Kanoh N, Asami A, Kawatani M, Honda K, Kumashiro S, Takayama H, Simizu S, Amemiya T, Kondoh Y, Hatakeyama S, Tsuganezawa K, Utata R, Tanaka A, Yokoyama S, Tashiro H, Osada H (2006) Photo-cross-linked small-molecule microarrays as chemical genomic tools for dissecting protein–ligand interactions. Chem Asian J 1:789–797
Kanoh N, Takayama H, Honda K, Moriya T, Teruya T, Simizu S, Osada H, Iwabuchi Y (2009) Cleavable linker for photo-cross-linked small-molecule affinity matrix. Bioconjug Chem 21(1):182–186
Kwon K, Grose C, Pieper R, Pandya GA, Fleischmann RD, Peterson SN (2009) High quality protein microarray using in situ protein purification. BMC Biotechnol 9:72
Lesaicherre ML, Uttamchandani M, Chen GY, Yao SQ (2002) Developing site-specific immobilization strategies of peptides in a microarray. Bioorg Med Chem Lett 12:2079–2083
Ramachandran N, Raphael JV, Hainsworth E, Demirkan G, Fuentes MG, Rolfs A, Hu Y, LaBaer J (2008) Next-generation high-density self-assembling functional protein arrays. Nat Methods 5:535–538
Hu Y, Chen GY, Yao SQ (2005) Activity-based high-throughput screening of enzymes by using a DNA microarray. Angew Chem Int Ed Engl 44:1048–1053
Winssinger N, Harris JL (2005) Microarray-based functional protein profiling using peptide nucleic acid-encoded libraries. Expert Rev Proteomics 2:937–947
Melkko S, Scheuermann J, Dumelin CE, Neri D (2004) Encoded self-assembling chemical libraries. Nat Biotechnol 22:568–574
Gao X, Pellois JP, Na Y, Kim Y, Gulari E, Zhou X (2004) High density peptide microarrays. In situ synthesis and applications. Mol Divers 8:177–187
Beyer M, Nesterov A, Block I, Konig K, Felgenhauer T, Fernandez S, Leibe K, Torralba G, Hausmann M, Trunk U, Lindenstruth V, Bischoff FR, Stadler V, Breitling F (2007) Combinatorial synthesis of peptide arrays onto a microchip. Science 318:1888
Fodor SP, Rava RP, Huang XC, Pease AC, Holmes CP, Adams CL (1993) Multiplexed biochemical assays with biological chips. Nature 364:555–556
Breitling F, Nesterov A, Stadler V, Felgenhauer T, Bischoff FR (2009) High-density peptide arrays. Mol Biosyst 5:224–234
Duffner JL, Clemons PA, Koehler AN (2007) A pipeline for ligand discovery using small-molecule microarrays. Curr Opin Chem Biol 11:74–82
Pilobello KT, Mahal LK (2007) Deciphering the glycocode: the complexity and analytical challenge of glycomics. Curr Opin Chem Biol 11:300–305
Kohn M, Wacker R, Peters C, Schroder H, Soulere L, Breinbauer R, Niemeyer CM, Waldmann H (2003) Staudinger ligation: a new immobilization strategy for the preparation of small-molecule arrays. Angew Chem Int Ed Engl 42:5830–5834
Dillmore WS, Yousaf MN, Mrksich M (2004) A photochemical method for patterning the immobilization of ligands and cells to self-assembled monolayers. Langmuir 20:7223–7231
Shaginian A, Patel M, Li MH, Flickinger ST, Kim C, Cerrina F, Belshaw PJ (2004) Light-directed radial combinatorial chemistry: orthogonal safety-catch protecting groups for the synthesis of small molecule microarrays. J Am Chem Soc 126:16704–16705
Lin PC, Ueng SH, Tseng MC, Ko JL, Huang KT, Yu SC, Adak AK, Chen YJ, Lin CC (2006) Site-specific protein modification through Cu(I)-catalyzed 1,2,3-triazole formation and its implementation in protein microarray fabrication. Angew Chem Int Ed Engl 45:4286–4290
Zhang CJ, Tan CY, Ge J, Na Z, Chen GY, Uttamchandani M, Sun H, Yao SQ (2013) Preparation of small-molecule microarrays by trans-cyclooctene tetrazine ligation and their application in the high-throughput screening of protein–protein interaction inhibitors of bromodomains. Angew Chem Int Ed Engl 52:14060–14064
Wang P, Na Z, Fu J, Tan CY, Zhang H, Yao SQ, Sun H (2014) Microarray immobilization of biomolecules using a fast trans-cyclooctene (TCO)-tetrazine reaction. Chem Commun (Camb) 50:11818–11821
Lee MR, Shin I (2005) Facile preparation of carbohydrate microarrays by site-specific, covalent immobilization of unmodified carbohydrates on hydrazide-coated glass slides. Org Lett 7:4269–4272
Hsiao HY, Chen ML, Wu HT, Huang LD, Chien WT, Yu CC, Jan FD, Sahabuddin S, Chang TC, Lin CC (2011) Fabrication of carbohydrate microarrays through boronate formation. Chem Commun (Camb) 47:1187–1189
Camarero JA, Kwon Y, Coleman MA (2004) Chemoselective attachment of biologically active proteins to surfaces by expressed protein ligation and its application for “protein chip” fabrication. J Am Chem Soc 126:14730–14731
Marsden DM, Nicholson RL, Skindersoe ME, Galloway WR, Sore HF, Givskov M, Salmond GP, Ladlow M, Welch M, Spring DR (2010) Discovery of a quorum sensing modulator pharmacophore by 3D small-molecule microarray screening. Org Biomol Chem 8:5313–5323
Kanoh N, Kumashiro S, Simizu S, Kondoh Y, Hatakeyama S, Tashiro H, Osada H (2003) Immobilization of natural products on glass slides by using a photoaffinity reaction and the detection of protein-small-molecule interactions. Angew Chem Int Ed Engl 42:5584–5587
Fodor SP, Read JL, Pirrung MC, Stryer L, Lu AT, Solas D (1991) Light-directed, spatially addressable parallel chemical synthesis. Science 251:767–773
Pellois JP, Zhou X, Srivannavit O, Zhou T, Gulari E, Gao X (2002) Individually addressable parallel peptide synthesis on microchips. Nat Biotechnol 20:922–926
Wang H, Zhang Y, Yuan X, Chen Y, Yan M (2011) A universal protocol for photochemical covalent immobilization of intact carbohydrates for the preparation of carbohydrate microarrays. Bioconjug Chem 22:26–32
Diamond SL (2007) Methods for mapping protease specificity. Curr Opin Chem Biol 11:46–51
Gosalia DN, Salisbury CM, Maly DJ, Ellman JA, Diamond SL (2005) Profiling serine protease substrate specificity with solution phase fluorogenic peptide microarrays. Proteomics 5:1292–1298
Angenendt P, Lehrach H, Kreutzberger J, Glokler J (2005) Subnanoliter enzymatic assays on microarrays. Proteomics 5:420–425
Monton MR, Lebert JM, Little JR, Nair JJ, McNulty J, Brennan JD (2010) A sol-gel-derived acetylcholinesterase microarray for nanovolume small-molecule screening. Anal Chem 82:9365–9373
Wang J, Uttamchandani M, Sun LP, Yao SQ (2006) Activity-based high-throughput profiling of metalloprotease inhibitors using small molecule microarrays. Chem Commun (Camb) 717–719
Uttamchandani M, Huang X, Chen GY, Yao SQ (2005) Nanodroplet profiling of enzymatic activities in a microarray. Bioorg Med Chem Lett 15:2135–2139
Bailey SN, Sabatini DM, Stockwell BR (2004) Microarrays of small molecules embedded in biodegradable polymers for use in mammalian cell-based screens. Proc Natl Acad Sci U S A 101:16144–16149
Noblin DJ, Page CM, Tae HS, Gareiss PC, Schneekloth JS, Crews CM (2012) A HaloTag-based small molecule microarray screening methodology with increased sensitivity and multiplex capabilities. ACS Chem Biol 7:2055–2063
O’Donnell B, Maurer A, Papandreou-Suppappola A, Stafford P (2015) Time-frequency analysis of peptide microarray data: application to brain cancer immunosignatures. Cancer Inform 14:219–233
Valentini D, Ferrara G, Advani R, Hallander HO, Maeurer MJ (2015) Serum reactome induced by Bordetella pertussis infection and Pertussis vaccines: qualitative differences in serum antibody recognition patterns revealed by peptide microarray analysis. BMC Immunol 16:40
Wang D, Tang J, Liu S, Huang J (2015) Carbohydrate microarrays identify blood group precursor cryptic epitopes as potential immunological targets of breast cancer. J Immunol Res 2015:510810
Blake TA, Ouyang Z, Wiseman JM, Takats Z, Guymon AJ, Kothari S, Cooks RG (2004) Preparative linear ion trap mass spectrometer for separation and collection of purified proteins and peptides in arrays using ion soft landing. Anal Chem 76:6293–6305
Yu X, Xu D, Cheng Q (2006) Label-free detection methods for protein microarrays. Proteomics 6:5493–5503
Lausted C, Hu Z, Hood L, Campbell CT (2009) SPR imaging for high throughput, label-free interaction analysis. Comb Chem High Throughput Screen 12:741–751
Souplet V, Desmet R, Melnyk O (2007) Imaging of protein layers with an optical microscope for the characterization of peptide microarrays. J Pept Sci 13:451–457
Inoue Y, Mori T, Yamanouchi G, Han X, Sonoda T, Niidome T, Katayama Y (2008) Surface plasmon resonance imaging measurements of caspase reactions on peptide microarrays. Anal Biochem 375:147–149
Ozkumur E, Needham JW, Bergstein DA, Gonzalez R, Cabodi M, Gershoni JM, Goldberg BB, Unlu MS (2008) Label-free and dynamic detection of biomolecular interactions for high-throughput microarray applications. Proc Natl Acad Sci U S A 105:7988–7992
Uttamchandani M, Walsh DP, Khersonsky SM, Huang X, Yao SQ, Chang YT (2004) Microarrays of tagged combinatorial triazine libraries in the discovery of small-molecule ligands of human IgG. J Comb Chem 6:862–868
Disney MD, Seeberger PH (2004) The use of carbohydrate microarrays to study carbohydrate-cell interactions and to detect pathogens. Chem Biol 11:1701–1707
Fu J, Na Z, Peng B, Uttamchandani M, Yao SQ (2016) Accelerated cellular on- and off-target screening of bioactive compounds using microarrays. Org Biomol Chem 14:59–64
Funeriu DP, Eppinger J, Denizot L, Miyake M, Miyake J (2005) Enzyme family-specific and activity-based screening of chemical libraries using enzyme microarrays. Nat Biotechnol 23:622–627
Gordus A, MacBeath G (2006) Circumventing the problems caused by protein diversity in microarrays: implications for protein interaction networks. J Am Chem Soc 128:13668–13669
Zhu Q, Uttamchandani M, Li D, Lesaicherre ML, Yao SQ (2003) Enzymatic profiling system in a small-molecule microarray. Org Lett 5:1257–1260
Salisbury CM, Maly DJ, Ellman JA (2002) Peptide microarrays for the determination of protease substrate specificity. J Am Chem Soc 124:14868–14870
Uttamchandani M, Chen GY, Lesaicherre ML, Yao SQ (2004) Site-specific peptide immobilization strategies for the rapid detection of kinase activity on microarrays. Methods Mol Biol 264:191–204
Stoevesandt O, Elbs M, Kohler K, Lellouch AC, Fischer R, Andre T, Brock R (2005) Peptide microarrays for the detection of molecular interactions in cellular signal transduction. Proteomics 5:2010–2017
Rychlewski L, Kschischo M, Dong L, Schutkowski M, Reimer U (2004) Target specificity analysis of the Abl kinase using peptide microarray data. J Mol Biol 336:307–311
Ikeda H, Kamimoto J, Yamamoto T, Hata A, Otsubo Y, Niidome T, Fukushima M, Mori T, Katayama Y (2013) A peptide microarray fabricated on a non-fouling phosphatidylcholine-polymer-coated surface for a high-fidelity analysis of a cellular kinome. Curr Med Chem 20:4419–4425
Sun H, Tan LP, Gao L, Yao SQ (2009) High-throughput screening of catalytically inactive mutants of protein tyrosine phosphatases (PTPs) in a phosphopeptide microarray. Chem Commun (Camb) 677–679
Kohn M, Gutierrez-Rodriguez M, Jonkheijm P, Wetzel S, Wacker R, Schroeder H, Prinz H, Niemeyer CM, Breinbauer R, Szedlacsek SE, Waldmann H (2007) A microarray strategy for mapping the substrate specificity of protein tyrosine phosphatase. Angew Chem Int Ed Engl 46:7700–7703
Park S, Shin I (2007) Carbohydrate microarrays for assaying galactosyltransferase activity. Org Lett 9:1675–1678
Bryan MC, Lee LV, Wong CH (2004) High-throughput identification of fucosyltransferase inhibitors using carbohydrate microarrays. Bioorg Med Chem Lett 14:3185–3188
Ban L, Mrksich M (2008) On-chip synthesis and label-free assays of oligosaccharide arrays. Angew Chem Int Ed Engl 47:3396–3399
Rauh D, Fischer F, Gertz M, Lakshminarasimhan M, Bergbrede T, Aladini F, Kambach C, Becker CF, Zerweck J, Schutkowski M, Steegborn C (2013) An acetylome peptide microarray reveals specificities and deacetylation substrates for all human sirtuin isoforms. Nat Commun 4:2327
Scheuermann J, Dumelin CE, Melkko S, Zhang Y, Mannocci L, Jaggi M, Sobek J, Neri D (2008) DNA-encoded chemical libraries for the discovery of MMP-3 inhibitors. Bioconjug Chem 19:778–785
Chen GY, Uttamchandani M, Zhu Q, Wang G, Yao SQ (2003) Developing a strategy for activity-based detection of enzymes in a protein microarray. Chembiochem 4:336–339
Reddy MM, Kodadek T (2005) Protein “fingerprinting” in complex mixtures with peptoid microarrays. Proc Natl Acad Sci U S A 102:12672–12677
Usui K, Ojima T, Takahashi M, Nokihara K, Mihara H (2004) Peptide arrays with designed secondary structures for protein characterization using fluorescent fingerprint patterns. Biopolymers 76:129–139
Usui K, Tomizaki KY, Mihara H (2006) Protein-fingerprint data mining of a designed alpha-helical peptide array. Mol Biosyst 2:417–420
Uttamchandani M, Wang J, Li J, Hu M, Sun H, Chen KY, Liu K, Yao SQ (2007) Inhibitor fingerprinting of matrix metalloproteases using a combinatorial peptide hydroxamate library. J Am Chem Soc 129:7848–7858
Horlacher T, Oberli MA, Werz DB, Krock L, Bufali S, Mishra R, Sobek J, Simons K, Hirashima M, Niki T, Seeberger PH (2010) Determination of carbohydrate-binding preferences of human galectins with carbohydrate microarrays. Chembiochem 11:1563–1573
Kuhne Y, Reese G, Ballmer-Weber BK, Niggemann B, Hanschmann KM, Vieths S, Holzhauser T (2015) A novel multipeptide microarray for the specific and sensitive mapping of linear IgE-binding epitopes of food allergens. Int Arch Allergy Immunol 166:213–224
Huang M, Ma Q, Liu X, Li B, Ma H (2015) Initiator integrated poly(dimethysiloxane)-based microarray as a tool for revealing the relationship between nonspecific interactions and irreproducibility. Anal Chem 87:7085–7091
Miyazaki I, Simizu S, Okumura H, Takagi S, Osada H (2010) A small-molecule inhibitor shows that pirin regulates migration of melanoma cells. Nat Chem Biol 6:667–673
Pop MS, Stransky N, Garvie CW, Theurillat JP, Hartman EC, Lewis TA, Zhong C, Culyba EK, Lin F, Daniels DS, Pagliarini R, Ronco L, Koehler AN, Garraway LA (2014) A small molecule that binds and inhibits the ETV1 transcription factor oncoprotein. Mol Cancer Ther 13:1492–1502
Na Z, Pan S, Uttamchandani M, Yao SQ (2014) Discovery of cell-permeable inhibitors that target the BRCT domain of BRCA1 protein by using a small-molecule microarray. Angew Chem Int Ed Engl 53:8421–8426
Fu J, Na Z, Uttamchandani M, Yao SQ (2013) Profiling human Src homology 2 (SH2) domain proteins and ligand discovery using a peptide-hybrid small molecule microarray. Chem Commun (Camb) 49:9660–9662
Molnar E, Kuntam S, Cingaram PK, Peksel B, Suresh B, Fabian G, Feher LZ, Bokros A, Medgyesi A, Ayaydin F, Puskas LG (2013) Combination of small molecule microarray and confocal microscopy techniques for live cell staining fluorescent dye discovery. Molecules 18:9999–10013
Landry JP, Fei Y, Zhu X, Ke Y, Yu G, Lee P (2013) Discovering small molecule ligands of vascular endothelial growth factor that block VEGF-KDR binding using label-free microarray-based assays. Assay Drug Dev Technol 11:326–332
Na Z, Li L, Uttamchandani M, Yao SQ (2012) Microarray-guided discovery of two-photon (2P) small molecule probes for live-cell imaging of cysteinyl cathepsin activities. Chem Commun (Camb) 48:7304–7306
Stanton BZ, Peng LF, Maloof N, Nakai K, Wang X, Duffner JL, Taveras KM, Hyman JM, Lee SW, Koehler AN, Chen JK, Fox JL, Mandinova A, Schreiber SL (2009) A small molecule that binds Hedgehog and blocks its signaling in human cells. Nat Chem Biol 5:154–156
Vegas AJ, Bradner JE, Tang W, McPherson OM, Greenberg EF, Koehler AN, Schreiber SL (2007) Fluorous-based small-molecule microarrays for the discovery of histone deacetylase inhibitors. Angew Chem Int Ed Engl 46:7960–7964
Uttamchandani M, Lee WL, Wang J, Yao SQ (2007) Quantitative inhibitor fingerprinting of metalloproteases using small molecule microarrays. J Am Chem Soc 129:13110–13117
Na Z, Peng B, Ng S, Pan S, Lee JS, Shen HM, Yao SQ (2015) A small-molecule protein–protein interaction inhibitor of PARP1 that targets its BRCT domain. Angew Chem Int Ed Engl 54:2515–2519
Wu H, Ge J, Yang PY, Wang J, Uttamchandani M, Yao SQ (2011) A peptide aldehyde microarray for high-throughput profiling of cellular events. J Am Chem Soc 133:1946–1954
Childs-Disney JL, Wu M, Pushechnikov A, Aminova O, Disney MD (2007) A small molecule microarray platform to select RNA internal loop–ligand interactions. ACS Chem Biol 2:745–754
Sztuba-Solinska J, Shenoy SR, Gareiss P, Krumpe LR, Le Grice SF, O’Keefe BR, Schneekloth JS Jr (2014) Identification of biologically active, HIV TAR RNA-binding small molecules using small molecule microarrays. J Am Chem Soc 136:8402–8410
Hahm JI (2011) Polymeric surface-mediated, high-density nano-assembly of functional protein arrays. J Biomed Nanotechnol 7:731–742
Acknowledgments
We gratefully acknowledge financial support by Singapore National Medical Research Council (CBRG/0038/2013), the Ministry of Education (MOE2013-T2-1-048), and DSO National Laboratories.
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Science+Business Media New York
About this protocol
Cite this protocol
Uttamchandani, M., Yao, S.Q. (2017). The Expanding World of Small Molecule Microarrays. In: Uttamchandani, M., Yao, S. (eds) Small Molecule Microarrays. Methods in Molecular Biology, vol 1518. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6584-7_1
Download citation
DOI: https://doi.org/10.1007/978-1-4939-6584-7_1
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-6582-3
Online ISBN: 978-1-4939-6584-7
eBook Packages: Springer Protocols