Biophysical methods for identifying fragment-based inhibitors of protein-protein interactions

Methods in Molecular Biology

Volumn 1278, Issue , 2015, Pages 587-613

  Pfaff, Samuel J ^a   Chimenti, Michael S ^a   Kelly, Mark J S ^a   Arkin, Michelle R ^a  

^a NONE

Author keywords

Biophysics; Crystallography; Discovery; DSF; Fragment; Interaction; Ligand; NMR; Protein protein; SPR

Indexed keywords

PROTEIN;

ARTICLE; CHEMICAL ANALYSIS; DIFFERENTIAL SCANNING CALORIMETRY; FLUOROMETRY; FRAGMENT BASED LEAD DISCOVERY; HETERONUCLEAR MULTIPLE QUANTUM COHERENCE; HETERONUCLEAR SINGLE QUANTUM COHERENCE; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SURFACE PLASMON RESONANCE; X RAY CRYSTALLOGRAPHY;

EID: 84927919934     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-2425-7_39     Document Type: Article

References (42)

1. Rees DC, Congreve M, Murray CW et al (2004) Fragment-based lead discovery. Nat Rev Drug Discov 3: 660-672.
2. Hajduk PJ, Greer J (2007) A decade of fragment-based drug design: Strategic advances and lessons learned. Nat Rev Drug Discov 6: 211-219.
3. Scott DE, Ehebauer MT, Pukala T et al (2013) Using a fragment-based approach to target protein-protein interactions. Chembiochem 14: 332-342.
4. 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.
5. 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.
6. 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.
7. Fuller JC, Burgoyne NJ, Jackson RM (2009) Predicting druggable binding sites at the protein-protein interface. Drug Discov Today 14: 155-161.
8. 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.
9. Na J, Hu Q (2011) Design of screening collections for successful fragment-based lead discovery. Methods Mol Biol 685: 219-240.
10. 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.
11. Erlanson DA, Wells JA, Braisted AC (2004) Tethering: fragment-based drug discovery. Annu Rev Biophys Biomol Struct 33: 199-223.
12. Wilson CG, Arkin MR (2013) Probing structural adaptivity at PPI interfaces with small molecules Drug Discovery Today: Technologies 10 (4): e501-e508.
13. 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.
14. 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.
15. 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.
16. Kranz JK, Schalk-Hihi C (2011) Protein thermal shifts to identify low molecular weight fragments. Methods Enzymol 493: 277-298.
17. Rizo J, Rosen MK, Gardner KH (2012) Enlightening molecular mechanisms through study of protein interactions. J Mol Cell Biol 4: 270-283.
18. 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.
19. Ito Y, Selenko P (2010) Cellular structural biology. Curr Opin Struct Biol 20: 640-648.
20. Dalvit C, Fagerness PE, Hadden DT et al (2003) Fluorine-NMR experiments for highthroughput screening: theoretical aspects, practical considerations, and range of applicability. J Am Chem Soc 125: 7696-7703.
21. 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.
22. Hajduk PJ, Meadows RP, Fesik SW (1999) NMR-based screening in drug discovery. Q Rev Biophys 32: 211-240.
23. Hajduk PJ, Gerfin T, Boehlen JM et al (1999) High-throughput nuclear magnetic resonancebased screening. J Med Chem 42: 2315-2317.
24. Murray CW, Blundell TL (2010) Structural biology in fragment-based drug design. Curr Opin Struct Biol 20: 497-507.
25. Spurlino JC (2011) Fragment screening purely with protein crystallography. Methods Enzymol 493: 321-356.
26. 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.
27. 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.
28. Giannetti AM (2011) From experimental design to validated hits a comprehensive walkthrough of fragment lead identification using surface plasmon resonance. Methods Enzymol 493: 169-218.
29. 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.
30. Niesen FH, Berglund H, VedadiM(2007) The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Nat Protoc 2: 2212-2221.
31. 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.
32. Maurer T (2011) Advancing fragment binders to lead-like compounds using ligand and protein-based NMR spectroscopy. Methods Enzymol 493: 469-485.
33. Bertini I, Molinari H, Niccolai N (1991) NMR and biomolecular structure, vol xvii. VCH, Weinheim, 209 p.
34. 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.
35. Gossert AD, Henry C, Blommers MJ et al (2009) Time efficient detection of proteinligand interactions with the polarization optimized PO-WaterLOGSY NMR experiment. J Biomol NMR 43: 211-217.
36. Shuker SB, Hajduk PJ, Meadows RP et al (1996) Discovering high-affinity ligands for proteins: SAR by NMR. Science 274: 1531-1534.
37. Kabsch W (2010) Xds. Acta Crystallogr D Biol Crystallogr 66: 125-132.
38. Holton J, Alber T (2004) Automated protein crystal structure determination using ELVES. Proc Natl Acad Sci U S A 101: 1537-1542.
39. Adams PD, Afonine PV, BunkocziGet al (2010) Phenix: a comprehensive python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66: 213-221.
40. Emsley P, Cowtan K (2004) Coot: modelbuilding tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60: 2126-2132.
41. 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.
42. Schrodinger, Llc (2010) The PyMOL molecular graphics system, version 1. 3r1.