High-throughput affinity-based technologies are rapidly growing in use as primary screening methods in drug discovery. In this review, their principles and applications are described and their impact on small-molecule drug discovery is evaluated. In general, these technologies can be divided into 2 groups: those that detect binding interactions by measuring changes to the protein target and those that detect bound compounds. Technologies detecting binding interactions by focusing on the protein have limited throughput but can reveal mechanistic information about the binding interaction; technologies detecting bound compounds have very high throughput, some even significantly higher than current high-throughput screening technologies, but offer limited information about the binding interaction. In addition, the appropriate use of affinity-based technologies is discussed. Finally, nanotechnology is predicted to generate a significant impact on the future of affinity-based technologies. (Journal of Biomolecular Screening 2009:1157-1164)
Goodnow RA: Hit and lead identification: integrated technology-based approaches . Drug Discov Today2006;3:367-375.
2.
Janzen WP: High Throughput Screening: Methods and Protocols. Totowa, NJ: Humana, 2002.
3.
Wemuth CG: The Practice of Medicinal Chemistry. San Diego : Academic Press, 2003.
4.
Spring DR: Chemical genetics to chemical genomics: small molecules offer big insights . Chem Soc Rev2005;34:472-482.
5.
Wagner BK, Haggarty SJ, Clemons PA: Chemical genomics: probing protein function using small molecules . Am J Pharmacogenomics2004;4:313-320.
6.
Hämäläinen MD, Markgren PO, Schaal W., Karlén A., Classon B., Vrang L.: Characterization of a set of HIV-1 protease inhibitors using binding kinetics data from a biosensor-based screen. J Biomol Screen2000;5:353-360.
7.
Thurmond RL, Wadsworth SA, Schafer PH, Zivin RA, Siekierka JJ: Kinetics of small molecule inhibitor binding to p38 kinase. Eur J Biochem2001;268:5747-5754.
Cunningham BT , Li P., Schulz S., Lin B., Baird C., Gerstenmaier J.: Label-free assays on the BIND system. J Biomol Screen2004;9:481-490.
10.
Backman D., Danielson UH: Kinetic and mechanistic analysis of the association and dissociation of inhibitors interacting with secreted aspartic acid proteases 1 and 2 from Candida albicans . Biochim Biophys Acta2003 ;1646:184-195.
11.
Stenlund P. , Frostell-Karlsson A., Karlsson OP: Studies of small molecule interactions with protein phosphatases using biosensor technology . Anal Biochem2006;353:217-225.
12.
Day YS, Baird CL, Rich RL, Myszka DG: Direct comparison of binding equilibrium, thermodynamic, and rate constants determined by surface- and solution-based biophysical methods. Protein Sci2002; 11:1017-1025.
13.
Nordin H., Jungnelius M., Karlsson R., Karlsson OP: Kinetic studies of small molecule interactions with protein kinases using biosensor technology. Anal Biochem2005 ;340:359-368.
14.
Rajagopalan R., Misialek S., Stevens S., Myszka D., Brandhuber B., Ballard J.: Inhibition and binding kinetics of the hepatitis C virus NS3 protease inhibitor ITMN-191 reveals tight binding and slow dissociative behavior. Biochemistry2009;48:2559-2568.
15.
Touil F., Pratt S., Mutter R., Chen B.: Screening a library of potential prion therapeutics against cellular prion proteins and insights into their mode of biological activities by surface plasmon resonance. J Pharm Biomed Anal2006 ;40:822-832.
16.
Fattori D., Squarcia A., Bartoli S.: Fragment-based approach to drug lead discovery: overview and advances in various techniques. Drugs R D2008; 9:217-227.
17.
Perspicace S., Banner D., Benz J., Müller F., Schlatter D., Huber W.: Fragment-based screening using surface plasmon resonance technology. J Biomol Screen2009 ;14:337-349.
18.
Nordström H., Gossas T., Hämäläinen M., Källblad P., Nyström S., Wallberg H., et al: Identification of MMP-12 inhibitors by using biosensor-based screening of a fragment library . J Med Chem2008;51:3449-3459.
19.
Pantoliano MW, Petrella EC, Kwasnoski JD, Lobanov VS, Myslik J., Graf E.: High-density miniaturized thermal shift assays as a general strategy for drug discovery. J Biomol Screen2001;6:429-440.
20.
Lo MC, Aulabaugh A., Jin G., Cowling R., Bard J., Malamas M.: Evaluation of fluorescence-based thermal shift assays for hit identification in drug discovery. Anal Biochem2004;332:153-159.
21.
Pantoliano MW, Petrella EC, Kwasnoski JD, Lobanov VS, Myslik J., Graf E.: High-density miniaturized thermal shift assays as a general strategy for drug discovery. J Biomol Screen2001;6:429-440.
22.
Ross A., Schlotterbeck G., Klaus W., Senn H.: Automation of NMR measurements and data evaluation for systematically screening interactions of small molecules with target proteins. J Biomol NMR2000;16:139-146.
23.
Hajduk PJ, Burns DJ: Integration of NMR and high-throughput screening. Comb Chem High Throughput Screen2002;5:613-621.
24.
Rupp B.: High-throughput crystallography at an affordable cost: the TB Structural Genomics Consortium Crystallization Facility. Acc Chem Res2003;36:173-181.
25.
Lesley SA, Kuhn P., Godzik A., Deacon AM, Mathews I., Kreusch A.: Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc Natl Acad Sci USA2002;99:11664-11669.
26.
Hajduk PJ, Betz SF, Mack J., Ruan X., Towne DL, Lerner CG: A strategy for high-throughput assay development using leads derived from nuclear magnetic resonance-based screening. J Biomol Screen2002;7:429-432.
27.
Claasen B., Axmann M., Meinecke R., Meyer B.: Direct observation of ligand binding to membrane proteins in living cells by a saturation transfer double difference (STDD) NMR spectroscopy method shows a significantly higher affinity of integrin alpha(IIb)beta3 in native platelets than in liposomes. J Am Chem Soc2005;127:916-919.
28.
Hajduk PJ, Olejniczak ET, Fesik SW: One-dimensional relaxation and diffusion-edited NMR methods for screening compounds that bind to macromolecules. J Am Chem Soc1997;119:12257-12261.
29.
Mercier KA, Powers R.: Determining the optimal size of small molecule mixtures for high throughput NMR screening. J Biomol NMR2005 ; 31:243-258.
30.
Murray CW, Callaghan O., Chessari G., Cleasby A., Congreve M., Frederickson M.: Application of fragment screening by X-ray crystallography to beta-secretase . J Med Chem2007;50:1116-1123.
31.
Petros AM, Dinges J., Augeri DJ, Baumeister SA, Betebenner DA, Bures MG: Discovery of a potent inhibitor of the antiapoptotic protein Bcl-xL from NMR and parallel synthesis. J Med Chem2006;49:656-663.
32.
Stockman BJ , Kothe M., Kohls D., Weibley L., Connolly BJ, Sheils AL: Identification of allosteric PIF-pocket ligands for PDK1 using NMRbased fragment screening and 1H-15N TROSY experiments . Chem Biol Drug Des2009;73:179-188.
33.
Gill AL, Frederickson M., Cleasby A., Woodhead SJ, Carr MG, Woodhead AJ: Identification of novel p38alpha MAP kinase inhibitors using fragment-based lead generation. J Med Chem2005;48:414-426.
34.
Gao J., Winslow SL, Vander-Velde D., Aubé J., Borchardt RT: Transport characteristics of peptides and peptidomimetics: II. Hydroxyethylamine bioisostere-containing peptidomimetics as substrates for the oligopeptide transporter and P-glycoprotein in the intestinal mucosa. J Pept Res2001; 57:361-373.
35.
Congreve M. , Aharony D., Albert J., Callaghan O., Campbell J., Carr RA: Application of fragment screening by X-ray crystallography to the discovery of aminopyridines as inhibitors of beta-secretase . J Med Chem2007;50:1124-1132.
36.
Zehender H. , Le Goff F., Lehmann N., Filipuzzi I., Mayr LM: SpeedScreen: The "missing link" between genomics and lead discovery. J Biomol Screen2004;9:498-505.
37.
Annis DA, Athanasopoulos J., Curran PJ, Felsch JS, Kalghatgi K., Lee WH, et al: An affinity selection-mass spectrometry method for the identification of small molecule ligands from self-encoded combinatorial libraries. Int J Mass Spec2004;238:77-83.
38.
Comess KM, Schurdak ME, Voorbach MJ, Coen M., Trumbull JD, Yang H., et al: An ultraefficient affinity-based high-throughput screening process: application to bacterial cell wall biosynthesis enzyme MurF. J Biomol Screen2006;11:743-754.
39.
Slon-Usakiewicz JJ, Ng W., Dai JR, Pasternak A., Redden PR: Frontal affinity chromatography with MS detection (FAC-MS) in drug discovery. Drug Discov Today2005;10:409-416.
40.
Annis DA, Nickbarg E., Yang X., Ziebell MR, Whitehurst CE: Affinity selection-mass spectrometry screening techniques for small molecule drug discovery. Curr Opin Chem Biol2007;11:518-526.
41.
Hannewald P. , Maunit B., Muller JF: Screening of DHFR-binding drugs by MALDI-TOFMS . Anal Bioanal Chem2008;392:1335-1344.
42.
Coburn CA, Stachel SJ, Li YM, Rush DM, Steele TG, Chen-Dodson E.: Identification of a small molecule nonpeptide active site beta-secretase inhibitor that displays a nontraditional binding mode for aspartyl proteases . J Med Chem2004;47:6117-6119.
43.
Whitehurst CE, Nazef N., Annis DA, Hou Y., Murphy DM, Spacciapoli P.: Discovery and characterization of orthosteric and allosteric muscarinic M2 acetylcholine receptor ligands by affinity selection-mass spectrometry. J Biomol Screen2006;11:194-207.
44.
Hofstadler SA, Sannes-Lowery KA: Applications of ESI-MS in drug discovery: interrogation of noncovalent complexes. Nat Rev Drug Discov2006;5:585-595.
45.
Vu H., Pham NB, Quinn RJ: Direct screening of natural product extracts using mass spectrometry . J Biomol Screen2008;13:265-275.
46.
Hopper ED, Roulhac PL, Campa MJ, Patz EF Jr, Fitzgerald MC: Throughput and efficiency of a mass spectrometry-based screening assay for protein-ligand binding detection. J Am Soc Mass Spectrom2008;19: 1303-1311.
47.
Sano T., Smith CL, Cantor CR: Immuno-PCR: very sensitive antigen detection by means of specific antibody-DNA conjugates. Science1992;258:120-122.
48.
Pedersen H., Gouilaev AH, Franch T., Sams CK, Olsen EK, Slok FA: Templated molecules and methods for using such molecules. US Patent Application 20040049008.
49.
Gartner ZJ, Tse BN, Grubina R., Doyon JB, Snyder TM, Liu DR: DNA-templated organic synthesis and selection of a library of macrocycles . Science2004;305:1601-1605.
50.
Pedersen H., Holtmann A., Franch T., Gouilaev AH, Felding J.: Method for synthesising templated molecules. US Patent 7413854.
51.
Melkko S., Zhang Y., Dumelin CE, Scheuermann J., Neri D.: Isolation of high-affinity trypsin inhibitors from a DNA-encoded chemical library. Angew Chem Int Ed Engl2007 ;46:4671-4674.
52.
Clark MA, Acharya1 RA, Arico-Muendel CC, Belyanskaya SL, Benjamin DR, Carlson NR: Design, synthesis, and selection of DNA encoded small molecule libraries . Nat Chem Biol2009;5:647-654.
53.
Mannocci L. , Zhang Y., Scheuermann J., Leimbacher M., De Bellis G., Rizzi E.: High-throughput sequencing allows the identification of binding molecules isolated from DNA-encoded chemical libraries. Proc Natl Acad Sci USA2008;105:17670-17675.
54.
Aich P., Ritchie S., Bonham K., Lee JS: Thermodynamic and kinetic studies of the formation of triple helices between purine-rich deoxyribo-oligonucleotides and the promoter region of the human c-src proto-oncogene. Nucleic Acids Res1998 ;26:4173-4177.
Tagore DM, Sprinz KI, Fletcher S., Jayawickramarajah J., Hamilton AD: Protein recognition and denaturation by self-assembling fragments on a DNA quadruplex scaffold. Angew Chem Int Ed Engl2007;46:223-225.
57.
Hoen PA, Ariyurek Y., Thygesen HH, Vreugdenhil E., Vossen RH, de Menezes RX: Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms . Nucleic Acids Res2008;36:1-12.
58.
GSK continues acquisition spree with Praecis Pharmaceuticals. GEN News, Dec 21, 2006.
59.
Nuevolution announces progress in its collaboration with Merck & Co. Inc. GEN News, Apr 2, 2009.
60.
BMS taps ensemble discovery with $5m up front. GEN News, Apr 15, 2009.
61.
Wang WU, Chen C, Lin KH, Fang Y, Lieber CM: Label-free detection of small-molecule-protein interactions by using nanowire nanosensors. Proc Natl Acad Sci USA 2005;102:3208-3212.
62.
Marchesini GR, Buijs J., Haasnoot W., Hooijerink D., Jansson O., Nielen MWF: Nanoscale affinity chip interface for coupling inhibition SPR immunosensor screening with nano-LC TOF MS. Anal Chem2008;80: 1159-1168.
63.
Mayr LM, Fuerst P.: The future of high-throughput screening. J Biomol Screen2008;13:443-448.
64.
Schröter T., Minond D., Weiser A., Dao C., Habel J., Spicer T.: Comparison of miniaturized time-resolved fluorescence resonance energy transfer and enzyme-coupled luciferase high-throughput screening assays to discover inhibitors of Rho-kinase II (ROCK-II). J Biomol Screen2008;13:17-28.
