HTS Reporter displacement assay for fragment screening and fragment evolution toward leads with optimized binding kinetics, binding selectivity, and thermodynamic signature

Methods in Enzymology

Volumn 493, Issue , 2011, Pages 299-320

  Neumann, Lars ^a   Von Knig, Konstanze ^a   Ullmann, Dirk ^a  

^a PROTEROS BIOSTRUCTURES GMBH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

3 HYDROXY 3 METHYLGLUTARYL COENZYME A; HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE; LEAD; SORAFENIB;

ARTICLE; BINDING AFFINITY; BINDING ASSAY; BINDING KINETICS; BINDING SITE; BIOASSAY; CONCENTRATION (PARAMETERS); DISSOCIATION CONSTANT; ENTHALPY; ENTROPY; FRAGMENT BASED LEAD DISCOVERY; HIGH THROUGHPUT SCREENING; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR EVOLUTION; MOLECULAR INTERACTION; PLASMA HALF LIFE; PRIORITY JOURNAL; REPORTER DISPLACEMENT ASSAY; STRUCTURE ACTIVITY RELATION; THERMODYNAMICS;

EID: 79952375489     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-381274-2.00012-1     Document Type: Chapter

References (28)

1. J.B. Chaires Calorimetry and thermodynamics in drug design Annu. Rev. Biophys. 37 2008 135 151
2. M. Chakraborty, A. Sengupta, D. Bhattacharya, S. Banerjee, and A. Chakrabarti DNA binding domain of RFX5: Interactions with X-box DNA and RFXANK Biochim. Biophys. Acta 1804 2010 2016 2024
3. Y. Cheng, and W.H. Prusoff Relationship between the inhibition constant (KI) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction Biochem. Pharmacol. 22 1973 3099 3108
4. R.A. Copeland, D.L. Pompliano, and T.D. Meek Drugtarget residence time and its implications for lead optimization Nat. Rev. Drug Discov. 5 2006 730 739 (Pubitemid 44323700)
5. J. Deinum, L. Gustavsson, E. Gyzander, M. Kullman-Magnusson, A. Edstrm, and R. Karlsson A thermodynamic characterization of the binding of thrombin inhibitors to human thrombin, combining biosensor technology, stopped-flow spectrophotometry, and microcalorimetry Anal. Biochem. 300 2002 152 162 (Pubitemid 34093689)
6. G.G. Ferenczy, and G.M. Keserü Thermodynamics guided lead discovery and optimization Drug Discovery Today 15 2010 919 932
7. E. Freire Do enthalpy and entropy distinguish first in class from best in class? Drug Discov. Today 13 2008 869 874
8. E. Freire A thermodynamic approach to the affinity optimization of drug candidates Chem. Biol. Drug Des. 74 2009 468 472
9. S.S. Hedge, T.K. Dam, F. Brewer, and J.S. Blanchard Thermodynamics of aminoglycoside and acyl-coenzyme A binding to the salmonella enterica AAC(6′)-Iy aminoglycoside N-acetyltransferase Biochemistry 41 2002 7519 7527 (Pubitemid 34602471)
10. Y. Inada, M. Ojima, R. Kanagawa, Y. Misumi, K. Nishikawa, and T. Naka Pharmacologic properties of candesartan cilexetil-possible mechanisms of long-acting antihypertensive action J. Hum. Hypertens. 13 1999 75 80
11. J.E. Ladbury, G. Klebe, and E. Freire Adding calorimetric data to decision making in lead discovery: A hot tip Nat. Drug Discov. 9 2010 23 27
12. T.M. Lohman, L.B. Overman, M.E. Ferrari, and A.G. Kozlov Highly salt-dependent enthalpy change for Escherichia coli SSB protein-nucleic acid binding due to ion-protein interactions Biochemistry 35 1996 5272 5279
13. H. Lu, and P.J. Tonge Drugtarget residence time: Critical information for lead optimization Curr. Opin. Chem. Biol. 14 2010 467 474
14. G. Müller, P.C. Sennhenn, T. Woodcock, and L. Neumann The retro-design concept for novel kinase inhibitors IDrugs 13 2010 457 466
15. I. Navratilova, G.A. Papalia, R.L. Rich, D. Bedinger, S. Brophy, B. Condon, T. Deng, A.W. Emerick, H.W. Guan, T. Hayden, T. Heutmekers, and B. Hoorelbeke Thermodynamic benchmark study using Biacore technology Anal. Biochem. 364 2007 67 77 (Pubitemid 46497949)
16. L. Neumann, R. Abele, and R. Tamp Thermodynamics of peptide binding to the transporter associated with antigen processing (TAP) J. Mol. Biol. 324 2002 965 973 (Pubitemid 41782986)
17. L. Neumann, A. Ritscher, G. Müller, and D. Hafenbradl Fragment based lead generation: Identification of seed fragments by a highly efficient fragment screening technology J. Comput. Aided Mol. Des. 23 2009 501 511
18. T.S.G. Olsson, M.A. Williams, W.R. Pitt, and J.E. Ladbury The thermodynamics of protein-ligand interactions and solvation: Insights for ligand design J. Mol. Biol. 384 2008 1002 1017
19. G.A. Papalia, A.M. Giannetti, N. Arora, and D.G. Myszka Thermodynamic characterization of pyrazole and azaindole derivatives binding to p38 mitogen-activated protein kinase using Biacore T100 technology and van't Hoff analysis Anal. Biochem. 383 2008 255 264
20. C. Paragellis, L. Tong, L. Churchill, P.F. Cirillo, T. Gilmore, and A.G. Graham Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site Nat. Struct. Biol. 9 2002 268 272 (Pubitemid 34289898)
21. J. Regan, C.A. Paragellis, P.F. Cirillo, T. Gilmore, E.R. Hickey, G.W. Peet, A. Proto, A. Swinamer, and N. Moss The kinetics of binding to p38MAP kinase by analogues of BIRB 796 Bioorg. Med. Chem. Lett. 13 2003 3101 3104 (Pubitemid 36993646)
22. D. Swinney Biochemical mechanisms of drug action: What does it take for success? Nat. Rev. Drug Discov. 3 2004 801 808 (Pubitemid 39242832)
23. D. Swinney Opportunities to minimise risk in drug discovery and development Expert Opin. Drug Discov. 1 2006 627 633
24. F.E. Torres, M.I. Recht, J.E. Coyle, R.H. Bruce, and G. Williams Higher throughput calorimetry: Opportunities, approaches and challenges Curr. Opin. Struct. Biol. 20 2010 1 8
25. P.J. Tummino, and R.A. Copeland Residence time of receptor-ligand complexes and its effect on biological function Biochemistry 47 2008 5481 5492 (Pubitemid 351711169)
26. S.T.R. Walsh A biosensor study indicating that entropy, electrostatics, and receptor glycosylation drive the binding interaction between interleukin-7 and its receptor Biochemistry 49 2010 8766 8778
27. G.J. Zaman, M.M. van der Lee, J.J. Kok, R.L. Nelissen, and E.E. Loomans Enzyme fragment complementation binding assay for p38alpha mitogen-activated protein kinase to study the binding kinetics of enzyme inhibitors Assay Drug Dev. Technol. 4 2006 411 420 (Pubitemid 44781632)
28. R. Zhang, and F. Monsma The importance of drug-target residence time Curr. Opin. Drug Discov. Dev. 12 2009 488 496