Efficiency of hit generation and structural characterization in fragment-based ligand discovery

Current Opinion in Chemical Biology

Volumn 15, Issue 4, 2011, Pages 482-488

  Larsson, Andreas ^a   Jansson, Anna ^a   Åberg, Anders ^b,c   Nordlund, Pär ^a,b  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^b KAROLINSKA INSTITUTE   (Sweden)

^c Sprint Bioscience   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYLCHOLINE BINDING PROTEIN; BETA SECRETASE 1; BINDING PROTEIN; HEAT SHOCK PROTEIN 90; LIGAND; PROTEIN; UNCLASSIFIED DRUG;

ACCURACY; BINDING AFFINITY; CHEMICAL ANALYSIS; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DIFFERENTIAL SCANNING FLUORIMETRY; DIFFERENTIAL STATIC LIGHT SCATTERING; DRUG DESIGN; DRUG SCREENING; ELECTROSPRAY MASS SPECTROMETRY; FLUOROMETRY; FRAGMENT BASED LIGAND DISCOVERY; HIGH THROUGHPUT SCREENING; ISOTHERMAL TITRATION CALORIMETRY; LIGAND BINDING; LIGHT SCATTERING; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PHYSICAL CHEMISTRY; PROTEIN CONFORMATION; PROTEIN SYNTHESIS; REVIEW; STOICHIOMETRY; SURFACE PLASMON RESONANCE; THERMAL ANALYSIS; THERMAL SHIFT ASSAY; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; DRUG DISCOVERY; DRUG EVALUATION, PRECLINICAL; EFFICIENCY; HUMANS; LIGANDS; PROTEIN BINDING; PROTEINS; SMALL MOLECULE LIBRARIES;

EID: 79960994066     PISSN: 13675931     EISSN: 18790402     Source Type: Journal    
DOI: 10.1016/j.cbpa.2011.06.008     Document Type: Review

References (41)

1. Hajduk P., Greer J. A decade of fragment-based drug design: strategic advances and lessons learned. Nat Rev Drug Discov 2007, 6:211-219.
2. Leeson P.D., Springthorpe B. The influence of drug-like concepts on decision-making in medicinal chemistry. Nat Rev Drug Discov 2007, 6:881-890.
3. Coyne A.G., Scott D.E., Abell C. Drugging challenging targets using fragment based approaches. Curr Opin Chem Biol 2010, 14:299-307.
4. Edwards A.M., Isserlin R., Bader G.D., Frye S.V., Willson T.M., Yu F.H. Too many roads not taken. Nature 2011, 470:163-165.
5. Murray C.E., Blundell T.L. Structural biology in fragment-based drug design. Curr Opin Struct Biol 2010, 20:497-507.
6. Hubbard R.E., Murray J.B. Experiences in fragment-based lead discovery. Meth Enzymol 2011, 493:509-531.
7. Kranz J.K., Schalk-Hihi C. Protein thermal shifts to identify low molecular weight fragments. Meth Enzymol 2011, 493:277-298.
8. Giannetti A.M. From experimental design to validated hits comprehensive walk-through of fragment lead identification using surface plasmon resonance. Meth Enzymol 2011, 493:169-218.
9. Maurer T. Advancing fragment binders to lead-like compounds using ligand and protein-based NMR spectroscopy. Meth Enzymol 2011, 493:469-485.
10. Mayer M., Meyer B. Group epitope mapping by saturation transfer difference NMR to identify segments of a ligand in direct contact with a protein receptor. J Am Chem Soc 2001, 123:6108-6117.
11. Dalvit C. NMR methods in fragment screening: theory and a comparison with other biophysical techniques. Drug Discov Today 2009, 14:1051-1057.
12. Navratilova I., Hopkins A.L. Fragment screening by surface plasmon resonance. ACS Med Chem Lett 2010, 1:44-48.
13. Rich R.L., Quinn J.G., Morton T., Stepp D., Myszka D.G. Biosensor-based fragment screening using FastStep injections. Anal Biochem 2010, 407:270-277.
14. Rich R.L., Myszka D.G. Kinetic analysis and fragment screening with Fujifilm AP-3000. Anal Biochem 2010, 402:170-178.
15. Edink E., Rucktooa P., Retra K., Akdemir A., Nahar T., Zuiderveld O., Van Elk R., Janssen E., van Nierop P., van Muijlwijk-Koezen J., et al. Fragment growing induces conformational changes in acetylcholine-binding protein: a structural and thermodynamic analysis. J Am Chem Soc 2011, 133:5363-5371.
16. Basse N., Kaar J.L., Settanni G., Joerger A.C., Rutherford T.J., Fersht A.R. Toward the rational design of p53-stabilizing drugs: probing the surface of the oncogenic Y220C mutant. Chem Biol 2010, 17:46-56.
17. Ericsson U.B., Hallberg B.M., Detitta G.T., Dekker N., Nordlund P. Thermofluor-based high-throughput stability optimization of proteins for structural studies. Anal Biochem 2006, 357:289-298.
18. Senisterra G.A., Markin E., Yamazaki K., Hui R., Vedadi M., Awrey D.E. Screening for ligands using a generic and high-throughput light-scattering-based assay. J Biomol Screen 2006, 11:940-948.
19. Vedadi M., Niesen F., Allali-Hassani A., Fedorov O., Finerty P., Wasney G., Yeung R., Arrowsmith C., Ball L., Berglund H., et al. Chemical screening methods to identify ligands that promote protein stability, protein crystallization, and structure determination. Proc Natl Acad Sci 2006, 103:15835-15840.
20. Niesen F., Berglund H., Vedadi M. The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Nat Protoc 2007, 2:2212-2221.
21. Drinkwater N., Vu H., Lovell K.M., Criscione K.R., Collins B.M., Prisinzano T.E., Poulsen S.-A., McLeish M.J., Grunewald G.L., Martin J.L. Fragment-based screening by X-ray crystallography, MS and isothermal titration calorimetry to identify PNMT (phenylethanolamine N-methyltransferase) inhibitors. Biochem J 2010, 431:51-61.
22. Vivat Hannah V., Atmanene C., Zeyer D., Van Dorsselaer A., Sanglier-Cianférani S. Native MS: an 'ESI' way to support structure- and fragment-based drug discovery. Future Med Chem 2010, 2:35-50.
23. Bornhop D.J., Latham J.C., Kussrow A., Markov D.A., Jones R.D., Sørensen H.S. Free-solution, label-free molecular interactions studied by back-scattering interferometry. Science 2007, 317:1732-1736.
24. Abdiche Y., Malashock D., Pinkerton A., Pons J. Determining kinetics and affinities of protein interactions using a parallel real-time label-free biosensor, the Octet. Anal Biochem 2008, 377:209-217.
25. Englebienne P., Van Hoonacker A., Verhas M., Khlebtsov N.G. Advances in high-throughput screening: biomolecular interaction monitoring in real-time with colloidal metal nanoparticles. Comb Chem High Throughput Screen 2003, 6:777-787.
26. Duong-Thi M.-D., Meiby E., Bergström M., Fex T., Isaksson R., Ohlson S. Weak affinity chromatography as a new approach for fragment screening in drug discovery. Anal Biochem 2011, 414:138-146.
27. Cressina E., Chen L., Abell C., Leeper F.J., Smith A.G. Fragment screening against the thiamine pyrophosphate riboswitch thiM. Chem Sci 2011, 2:157.
28. Früh V., Zhou Y., Chen D., Loch C., Ab E., Grinkova Y.N., Verheij H., Sligar S.G., Bushweller J.H., Siegal G. Application of fragment-based drug discovery to membrane proteins: identification of ligands of the integral membrane enzyme DsbB. Chem Biol 2010, 17:881-891.
29. Congreve M., Rich R.L., Myszka D.G., Figaroa F., Siegal G., Marshall F.H. Fragment screening of stabilized G-protein-coupled receptors using biophysical methods. Meth Enzymol 2011, 493:115-136.
30. Senisterra G.A., Ghanei H., Khutoreskaya G., Dobrovetsky E., Edwards A.M., Prive G.G., Vedadi M. Assessing the stability of membrane proteins to detect ligand binding using differential static light scattering. J Biomol Screen 2010, 15:314-320.
31. Nienaber V.L., Richardson P.L., Klighofer V., Bouska J.J., Giranda V.L., Greer J. Discovering novel ligands for macromolecules using X-ray crystallographic screening. Nat Biotechnol 2000, 18:1105-1108.
32. Jhoti H., Cleasby A., Verdonk M., Williams G. Fragment-based screening using X-ray crystallography and NMR spectroscopy. Curr Opin Chem Biol 2007, 11:485-493.
33. Verlinde C.L.M.J., Fan E., Shibata S., Zhang Z., Sun Z., Deng W., Ross J., Kim J., Xiao L., Arakaki T.L., et al. Fragment-based cocktail crystallography by the medical structural genomics of pathogenic protozoa consortium. Curr Top Med Chem 2009, 9:1678-1687.
34. Gibbs A.C., Abad M.C., Zhang X., Tounge B.A., Lewandowski F.A., Struble G.T., Sun W., Sui Z., Kuo L.C. Electron density guided fragment-based lead discovery of ketohexokinase inhibitors. J Med Chem 2010, 53:7979-7991.
35. Wang Y.-S., Strickland C., Voigt J.H., Kennedy M.E., Beyer B.M., Senior M.M., Smith E.M., Nechuta T.L., Madison V.S., Czarniecki M., et al. Application of fragment-based NMR screening, X-ray crystallography, structure-based design, and focused chemical library design to identify novel microM leads for the development of nM BACE-1 (beta-site APP cleaving enzyme 1) inhibitors. J Med Chem 2010, 53:942-950.
36. Godemann R., Madden J., Krämer J., Smith M., Fritz U., Hesterkamp T., Barker J., Höppner S., Hallett D., Cesura A., et al. Fragment-based discovery of BACE1 inhibitors using functional assays. Biochemistry 2009, 48:10743-10751.
37. Abad M.C., Gibbs A.C., Zhang X. Electron density guided fragment-based drug design-a lead generation example. Meth Enzymol 2011, 493:487-508.
38. Chim N., Habel J.E., Johnston J.M., Krieger I., Miallau L., Sankaranarayanan R., Morse R.P., Bruning J., Swanson S., Kim H., et al. The TB structural genomics consortium: a decade of progress. Tuberculosis (Edinb) 2011, 91:155-172.
39. Fan E., Baker D., Fields S., Gelb M.H., Buckner F.S., Van Voorhis W.C., Phizicky E., Dumont M., Mehlin C., Grayhack E., et al. Structural genomics of pathogenic protozoa: an overview. Methods Mol Biol 2008, 426:497-513.
40. Weigelt J. Structural genomics-impact on biomedicine and drug discovery. Exp Cell Res 2010, 316:1332-1338.
41. Bembenek S.D., Tounge B.A., Reynolds C.H. Ligand efficiency and fragment-based drug discovery. Drug Discov Today 2009, 14:278-283.