Thermodynamic signatures of fragment binding: Validation of direct versus displacement ITC titrations

Biochimica et Biophysica Acta - General Subjects

Volumn 1850, Issue 4, 2015, Pages 647-656

  Rühmann, Eggert ^a   Betz, Michael ^a   Fricke, Marie ^b   Heine, Andreas ^a   Schäfer, Martina ^b   Klebe, Gerhard ^a  

^a PHILIPPS UNIVERSITY MARBURG   (Germany)

^b BAYER PHARMA AG   (Germany)

Author keywords

Displacement titrations; Isothermal titration calorimetry; Low c value titration; Protein fragment binding; Thermodynamic signature; Thrombin

Indexed keywords

THROMBIN; PROTEIN BINDING;

ARTICLE; BINDING AND RELATED PHENOMENA; COMPARATIVE STUDY; CONTROLLED STUDY; ENERGY; ENTHALPY; ENTROPY; FRAGMENT BINDING; ISOTHERMAL TITRATION CALORIMETRY; MEASUREMENT ACCURACY; PROTEIN BINDING; THERMODYNAMICS; TITRIMETRY; VALIDATION PROCESS; CALORIMETRY; PROCEDURES; VALIDATION STUDY;

CALORIMETRY; PROTEIN BINDING; THERMODYNAMICS;

EID: 84921059243     PISSN: 03044165     EISSN: 18728006     Source Type: Journal    
DOI: 10.1016/j.bbagen.2014.12.007     Document Type: Article

References (33)

1. J.E. Ladbury, G. Klebe, and E. Freire Adding calorimetric data to decision making in lead discovery: a hot tip Nat. Rev. Drug Discov. 9 2010 23 27
2. E. Freire A thermodynamic approach to the affinity optimization of drug candidates Chem. Biol. Drug Des. 74 2009 468 472
3. J.B. Chaires Calorimetry and thermodynamics in drug design Annu. Rev. Biophys. 37 2008 135 151
4. T.S.G. Olsson, M.A. Williams, W.R. Pitt, and J.E. Ladbury The thermodynamics of protein-ligand interaction and solvation: insights for ligand design J. Mol. Biol. 384 2008 1002 1017
5. A. Glas, D. Bier, G. Hahne, C. Rademacher, C. Ottmann, and T.N. Grossmann Constrained peptides with target-adapted cross-links as inhibitors of a pathogenic protein-protein interaction Angew. Chem. Int. Ed. Engl. 53 2014 2489 2493
6. G.E. de Kloe, D. Bailey, R. Leurs, and I.J.P. de Esch Transforming fragments into candidates: small becomes big in medicinal chemistry Drug Discov. Today 14 2009 630 646
7. G.G. Ferenczy, and G.M. Keseru Thermodynamics of fragment binding J. Chem. Inf. Model. 52 2012 1039 1045
8. G.G. Ferenczy, and G.M. Keseru How are fragments optimized? A retrospective analysis of 145 fragment optimizations J. Med. Chem. 56 2013 2478 2486
9. V. Borsi, V. Calderone, M. Fragai, C. Luchinat, and N. Sarti Entropic contribution to the linking coefficient in fragment based drug design: a case study J. Med. Chem. 53 2010 4285 4289
10. S.F. Martin, and J.H. Clements Correlating structure and energetics in protein-ligand interactions: paradigms and paradoxes Annu. Rev. Biochem. 82 2013 267 293
11. M. Congreve, G. Chessari, D. Tisi, and A.J. Woodhead Recent developments in fragment-based drug discovery J. Med. Chem. 51 2008 3661 3680
12. J.D. Taylor, P.J. Gilbert, M.A. Williams, W.R. Pitt, and J.E. Ladbury Identification of novel fragment compounds targeted against the pY pocket of v-Src SH2 by computational and NMR screening and thermodynamic evaluation Proteins 67 2007 981 990
13. D.C. Rees, M. Congreve, C.W. Murray, and R. Carr Fragment-based lead discovery Nat. Rev. Drug Discov. 3 2004 660 672
14. Y.L. Zhang, and Z.Y. Zhang Low-affinity binding determined by titration calorimetry using a high-affinity coupling ligand: a thermodynamic study of ligand binding to protein tyrosine phosphatase 1B Anal. Biochem. 261 1998 139 148
15. W.G. Eisert, N. Hauel, J. Stangier, W. Wienen, A. Clemens, and J. van Ryn Dabigatran: an oral novel potent reversible nonpeptide inhibitor of thrombin Arterioscler. Thromb. Vasc. Biol. 30 2010 1885 1889
16. M. Fricke, Diploma Thesis, FU Berlin, Germany, (2013)
17. K. Hilpert, J. Ackermann, D.W. Banner, A. Gast, K. Gubernator, P. Hadváry, L. Labler, K. Müller, G. Schmid, and T.B. Tschopp Design and synthesis of potent and highly selective thrombin inhibitors J. Med. Chem. 37 1994 3889 3901
18. T. Steinmetzer, and J. Stürzebecher Progress in the development of synthetic thrombin inhibitors as new orally active anticoagulants Curr. Med. Chem. 11 2004 2297 2321
19. M. T. Khayat PhD Thesis, University at Buffalo, USA, (2013)
20. B. Baum, M. Mohamed, M. Zayed, C. Gerlach, A. Heine, D. Hangauer, and G. Klebe More than a simple lipophilic contact: a detailed thermodynamic analysis of nonbasic residues in the s1 pocket of thrombin J. Mol. Biol. 390 2009 56 69
21. B. Baum, L. Muley, A. Heine, M. Smolinski, D. Hangauer, and G. Klebe Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin J. Mol. Biol. 391 2009 552 564
22. A. Biela, F. Sielaff, F. Terwesten, A. Heine, T. Steinmetzer, and G. Klebe Ligand binding stepwise disrupts water network in thrombin: enthalpic and entropic changes reveal classical hydrophobic effect J. Med. Chem. 55 2012 6094 6110
23. T. Wiseman, S. Williston, J.F. Brandts, and L.N. Lin Rapid measurement of binding constants and heats of binding using a new titration calorimeter Anal. Biochem. 179 1989 131 137
24. W.B. Turnbull, and A.H. Daranas On the value of c: can low affinity systems be studied by isothermal titration calorimetry? J. Am. Chem. Soc. 125 2003 14859 14866
25. W.B. Turnbull, B.L. Precious, and S.W. Homans Dissecting the cholera toxin-ganglioside GM1 interaction by isothermal titration calorimetry J. Am. Chem. Soc. 126 2004 1047 1054
26. W.B. Turnbull Divided we fall? Studying low-affinity fragments of ligands by ITC GE Application Note 2011
27. J. Broecker, C. Vargas, and S. Keller Revisiting the optimal c-value for isothermal titration calorimetry Anal. Biochem. 418 2011 307 309
28. J. Tellinghuisen Isothermal titration calorimetry at very low c Anal. Biochem. 373 2008 395 397
29. S. Keller, C. Vargas, H. Zhao, G. Piszczek, C.A. Brautigam, and P. Schuck High-precision isothermal titration calorimetry with automated peak-shape analysis Anal. Chem. 84 2012 5066 5073
30. J.C. Houtman, P.H. Brown, B. Bowden, H. Yamaguchi, E. Appella, L.E. Samelson, and P. Schuck Studying multisite binary and ternary protein interactions by global analysis of isothermal titration calorimetry data in SEDPHAT: application to adaptor protein complexes in cell signaling Protein Sci. 16 2007 30 42
31. J. Stürzebecher, U. Stürzebecher, H. Vieweg, G. Wagner, J. Hauptmann, and F. Markwardt Synthetic inhibitors of bovine factor Xa and thrombin comparison of their anticoagulant efficiency Thromb. Res. 54 1989 245 252
32. M. Dixon The graphical determination of Km and Ki Biochem. J. 129 1972 197 202
33. M.J. Bernett, S.I. Blaber, I.A. Scarisbrick, P. Dhanarajan, S.M. Thompson, and M. Blaber Crystal structure and biochemical characterization of human kallikrein 6 reveals that a trypsin-like kallikrein is expressed in the central nervous system J. Biol. Chem. 277 2002 24562 24570