Abstract
Fragment-based lead discovery complements high-throughput screening and computer-aided drug design for the discovery of small-molecule inhibitors of protein-protein interactions. Fragments are molecules with molecular masses ca 280 Da or smaller, and are generally screened using structural or biophysical approaches. Several methods of fragment-based screening are feasible for any soluble protein that can be expressed and purified; specific techniques also have size limitations and/or require multiple milligrams of protein. This chapter describes some of the most common fragment-discovery methods, including surface plasmon resonance, nuclear magnetic resonance, differential scanning fluorimetry, and X-ray crystallography.
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References
Rees DC, Congreve M, Murray CW et al (2004) Fragment-based lead discovery. Nat Rev Drug Discov 3:660–672
Hajduk PJ, Greer J (2007) A decade of fragment-based drug design: Strategic advances and lessons learned. Nat Rev Drug Discov 6:211–219
Scott DE, Ehebauer MT, Pukala T et al (2013) Using a fragment-based approach to target protein-protein interactions. Chembiochem 14:332–342
Braisted AC, Oslob JD, Delano WL et al (2003) Discovery of a potent small molecule IL-2 inhibitor through fragment assembly. J Am Chem Soc 125:3714–3715
Arkin MR, Randal M, Delano WL et al (2003) Binding of small molecules to an adaptive protein-protein interface. Proc Natl Acad Sci U S A 100:1603–1608
Petros AM, Huth JR, Oost T et al (2010) Discovery of a potent and selective bcl-2 inhibitor using SAR by NMR. Bioorg Med Chem Lett 20:6587–6591
Fuller JC, Burgoyne NJ, Jackson RM (2009) Predicting druggable binding sites at the protein-protein interface. Drug Discov Today 14:155–161
Lau WF, Withka JM, Hepworth D et al (2011) Design of a multi-purpose fragment screening library using molecular complexity and orthogonal diversity metrics. J Comput Aided Mol Des 25:621–636
Na J, Hu Q (2011) Design of screening collections for successful fragment-based lead discovery. Methods Mol Biol 685:219–240
Chen IJ, Hubbard RE (2009) Lessons for fragment library design: analysis of output from multiple screening campaigns. J Comput Aided Mol Des 23:603–620
Erlanson DA, Wells JA, Braisted AC (2004) Tethering: fragment-based drug discovery. Annu Rev Biophys Biomol Struct 33:199–223
Wilson CG, Arkin MR (2013) Probing structural adaptivity at PPI interfaces with small molecules Drug Discovery Today: Technologies 10 (4):e501–e508
Giannetti AM, Koch BD, Browner MF (2008) Surface plasmon resonance based assay for the detection and characterization of promiscuous inhibitors. J Med Chem 51:574–580
Babaoglu K, Simeonov A, Irwin JJ et al (2008) Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase. J Med Chem 51:2502–2511
Cimmperman P, Baranauskiene L, Jachimoviciute S et al (2008) A quantitative model of thermal stabilization and destabilization of proteins by ligands. Biophys J 95:3222–3231
Kranz JK, Schalk-Hihi C (2011) Protein thermal shifts to identify low molecular weight fragments. Methods Enzymol 493:277–298
Rizo J, Rosen MK, Gardner KH (2012) Enlightening molecular mechanisms through study of protein interactions. J Mol Cell Biol 4:270–283
Pellecchia M, Bertini I, Cowburn D et al (2008) Perspectives on NMR in drug discovery: a technique comes of age. Nat Rev Drug Discov 7:738–745
Ito Y, Selenko P (2010) Cellular structural biology. Curr Opin Struct Biol 20:640–648
Dalvit C, Fagerness PE, Hadden DT et al (2003) Fluorine-NMR experiments for high-throughput screening: theoretical aspects, practical considerations, and range of applicability. J Am Chem Soc 125:7696–7703
Dalvit C, Flocco M, Veronesi M et al (2002) Fluorine-NMR competition binding experiments for high-throughput screening of large compound mixtures. Comb Chem High Throughput Screen 5:605–611
Hajduk PJ, Meadows RP, Fesik SW (1999) NMR-based screening in drug discovery. Q Rev Biophys 32:211–240
Hajduk PJ, Gerfin T, Boehlen JM et al (1999) High-throughput nuclear magnetic resonance-based screening. J Med Chem 42:2315–2317
Murray CW, Blundell TL (2010) Structural biology in fragment-based drug design. Curr Opin Struct Biol 20:497–507
Spurlino JC (2011) Fragment screening purely with protein crystallography. Methods Enzymol 493:321–356
Bottcher J, Jestel A, Kiefersauer R et al (2011) Key factors for successful generation of protein-fragment structures requirement on protein, crystals, and technology. Methods Enzymol 493:61–89
Prakash O, Eisenberg MA (1979) Biotinyl 5'-adenylate: corepressor role in the regulation of the biotin genes of Escherichia coli k-12. Proc Natl Acad Sci U S A 76:5592–5595
Giannetti AM (2011) From experimental design to validated hits a comprehensive walk-through of fragment lead identification using surface plasmon resonance. Methods Enzymol 493:169–218
Zhang JH, Chung TD, Oldenburg KR (1999) A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J Biomol Screen 4:67–73
Niesen FH, Berglund H, Vedadi M (2007) The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Nat Protoc 2:2212–2221
Matulis D, Kranz JK, Salemme FR et al (2005) Thermodynamic stability of carbonic anhydrase: measurements of binding affinity and stoichiometry using thermofluor. Biochemistry 44:5258–5266
Maurer T (2011) Advancing fragment binders to lead-like compounds using ligand and protein-based NMR spectroscopy. Methods Enzymol 493:469–485
Bertini I, Molinari H, Niccolai N (1991) NMR and biomolecular structure, vol xvii. VCH, Weinheim, 209 p
Dalvit C, Pevarello P, Tato M et al (2000) Identification of compounds with binding affinity to proteins via magnetization transfer from bulk water. J Biomol NMR 18:65–68
Gossert AD, Henry C, Blommers MJ et al (2009) Time efficient detection of protein-ligand interactions with the polarization optimized PO-WaterLOGSY NMR experiment. J Biomol NMR 43:211–217
Shuker SB, Hajduk PJ, Meadows RP et al (1996) Discovering high-affinity ligands for proteins: SAR by NMR. Science 274:1531–1534
Kabsch W (2010) Xds. Acta Crystallogr D Biol Crystallogr 66:125–132
Holton J, Alber T (2004) Automated protein crystal structure determination using ELVES. Proc Natl Acad Sci U S A 101:1537–1542
Adams PD, Afonine PV, Bunkoczi G et al (2010) Phenix: a comprehensive python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66:213–221
Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60:2126–2132
Hamalainen MD, Zhukov A, Ivarsson M et al (2008) Label-free primary screening and affinity ranking of fragment libraries using parallel analysis of protein panels. J Biomol Screen 13:202–209
Schrodinger, Llc (2010) The PyMOL molecular graphics system, version 1.3r1
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Pfaff, S.J., Chimenti, M.S., Kelly, M.J.S., Arkin, M.R. (2015). Biophysical Methods for Identifying Fragment-Based Inhibitors of Protein-Protein Interactions. In: Meyerkord, C., Fu, H. (eds) Protein-Protein Interactions. Methods in Molecular Biology, vol 1278. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2425-7_39
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DOI: https://doi.org/10.1007/978-1-4939-2425-7_39
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2424-0
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