Utilization of NMR-derived fragment leads in drug design

Methods in Enzymology

Volumn 394, Issue , 2005, Pages 549-571

  Huth, Jeffrey R ^a   Sun, Chaohong ^a   Sauer, Daryl R ^a   Hajduk, Philip J ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

2,3 DIMETHYLPHENYLOXALYLAMINOBENZOIC ACID; LIGAND; MATRIX METALLOPROTEINASE INHIBITOR; PROTEIN TYROSINE PHOSPHATASE 1B INHIBITOR; UNCLASSIFIED DRUG;

ANALYTIC METHOD; ARTICLE; BINDING AFFINITY; CALCULATION; CHEMICAL COMPOSITION; CHEMICAL PROCEDURES; CHEMICAL REACTION; CHEMISTRY; CONCENTRATION (PARAMETERS); DRUG ACTIVITY; DRUG CONFORMATION; DRUG DESIGN; DRUG INDUSTRY; DRUG MECHANISM; DRUG POTENCY; DRUG SCREENING; DRUG SELECTIVITY; DRUG SPECIFICITY; DRUG STRUCTURE; DRUG TARGETING; ENERGY TRANSFER; EXPERIMENT; LIGAND BINDING; MACROMOLECULE; MOLECULAR WEIGHT; MOLECULE; MONITORING; NUCLEAR MAGNETIC RESONANCE; PARAMETER; PRIORITY JOURNAL; PROTEIN TARGETING; REACTION ANALYSIS; SENSITIVITY ANALYSIS; STRUCTURE ANALYSIS; VALIDATION PROCESS;

EID: 16244391116     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(05)94023-8     Document Type: Article

References (64)

1. Bartolozzi A., Grogan M.J., Kates S.A. Advances in the applications of polymer-supported reagents for organic synthesis. Methods Enzymol. 369:2003;347-366
2. Bhattacharyya S., Fan L., Vo L., Labadie J. Comb. Chem. High Throughput Screen. 3:2000;117-124
3. Bhattacharyya S., Rana S., Gooding O.W., Labadie J. Tetrahedron Lett. 44:2003;4957-4960
4. Bohacek R.S., McMartin C. Multiple highly diverse structures complementary to enzyme binding sites: Results of extensive application of a de novo design method incorporating combinatorial growth. J. Am. Chem. Soc. 116:1994;5560-5571
5. Bohm H.J. Site-directed structure generation by fragment-joining. Perspect. Drug Disc. Des. 3:1995;21-33
6. Booth R.J., Hodges J.C. Polymer-supported quenching reagents for parallel purification. J. Am. Chem. Soc. 119:1997;4882-4886
7. Booth R.J., Hodges J.C. Solid-supported reagent strategies for rapid purification of combinatorial synthesis products. Acc. Chem. Res. 32:1999;18-26
8. Chen A., Shapiro M.J. NOE pumping: A novel NMR technique for identification of compounds with binding affinity to macromolecules. J. Am. Chem. Soc. 120:1998;10258-10259
9. Clore G.M., Gronenborn A.M. Theory and applications of the transferred nuclear Overhauser effect to the study of the conformations of small ligands bound to proteins. J. Magn. Reson. 48:1983;402-417
10. Colacot T.J., Gore E.S., Kuber A. High-throughput screening studies of fiber-supported catalysts leading to room-temperature Suzuki coupling. Organometallics. 21:2002;3301-3304
11. Coles M., Heller M., Kessler H. NMR-based screening technologies. DDT. 8:2003;803-810
12. Dalvit C., Flocco M., Knapp S., Mostardini M., Perego R., Stockman B.J., Veronesi M., Varasi M. High-throughput NMR-based screening with competition binding experiments. J. Am. Chem. Soc. 124:2002;7702-7709
13. Fauchere J.L., Boutin J.A., Henlin J.M., Kucharczyk N., Ortuno J.C. Combinatorial chemistry for the generation of molecular diversity and the discovery of bioactive leads. Chemom. Intell. Lab. Sys. 43:1998;43-68
14. Fecik R.A., Frank K.E., Gentry E.J., Menon S.R., Mitscher L.A., Telikepalli H. The search for orally active medications through combinatorial chemistry. Med. Res. Rev. 18:1998;149-185
15. Fejzo J., Lepre C.A., Peng J.W., Bemis G.W., Ajay Murcko, M. A., Moore J.M. The SHAPES strategy: An NMR-based approach for lead generation in drug discovery. Chem. Biol. 6:1999;755-769
16. Fernandez C., Wider G. TROSY in NMR studies of the structure and function of large biological macromolecules. Curr. Opin. Struct. Biol. 13:2003;570-580
17. Gentles R.G., Wodka D., Park D.C., Vasudevan A. Standardization protocols and optimized precursor sets for the efficient application of automated parallel synthesis to lead optimization: A Mitsunobu example. J. Comb. Chem. 4:2002;442-456
18. Gerig J.T. Fluorine NMR of proteins. Prog. NMR Spectrosc. 26:1994;293-370
19. Ghose A.K., Viswanadhan V.N., Wendoloski J.J. A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases. J. Comb. Chem. 1:1999;55-68
20. Hajduk P.J., Meadows R.P., Fesik S.W. Discovering high-affinity ligands for proteins. Science. 278:1997a;497-499
21. Hajduk P.J., Olejniczak E.T., Fesik S.W. One-dimensional relaxation- and diffusion-edited NMR methods for screening compounds that bind to macromolecules. J. Am. Chem. Soc. 119:1997b;12257-12261
22. Hajduk P.J., Sheppard G., Nettesheim D.G., Olejniczak E.T., Shuker S.B., Meadows R.P., Steinman D.H., Carrera G.M., Marcotte P.A., Severin J., Walter K., Smith H., Gubbins E., Simmer R., Holzman T.F., Morgan D.W., Davidsen S.K., Fesik S.W. Discovery of potent nonpeptide inhibitors of stromelysin using SAR by NMR. J. Am. Chem. Soc. 119:1997c;5818-5827
23. Hajduk P.J., Dinges J., Schkeryantz J.M., Janowick D., Kaminski M., Tufano M., Augeri D.J., Petros A., Nienaber V., Zhong P., Hammond R., Coen M., Beutel B., Katz L., Fesik S.W. Novel inhibitors of erm methyltransferases from NMR and parallel synthesis. J. Med. Chem. 42:1999a;3852-3859
24. Hajduk P.J., Gerfin T., Boehlen J.-M., Häberli M., Marek D., Fesik S.W. High-throughput nuclear magnetic resonance-based screening. J. Med. Chem. 42:1999b;2315-2317
25. Hajduk P.J., Meadows R.P., Fesik S.W. NMR-based screening in drug discovery. Q. Rev. Biophys. 32:1999c;211-240
26. Hajduk P.J., Augeri D.A., Mack J., Mendoza R., Yang J., Betz S.F., Fesik S.W. NMR-based screening of proteins containing 13C-labeled methyl groups. J. Med. Chem. 122:2000a;7898-7904
27. Hajduk P.J., Boyd S., Nettesheim D., Nienaber V., Severin J., Smith R., Davidson D., Rockway T., Fesik S.W. The identification of novel inhibitors of urokinase using NMR-based screening. J. Med. Chem. 43:2000b;3862-3866
28. Hajduk P.J., Gomtsyan A., Didomenico S., Cowart M., Bayburt E.K., Solomon L., Severin Smith, R., Walter K., Holzman T.F., Stewart A., McGaraughty S., Jarvis M.F., Kowaluk E.S., Fesik S.W. Design of adenosine kinase inhibitors from the NMR-based screening of fragments. J. Med. Chem. 43:2000c;4781-4786
29. Hajduk P.J., Shuker S.B., Nettesheim D.G., Xu L., Augeri D.J., Betebenner D., Craig R., Albert D.H., Guo Y., Meadows R.P., Michaelides M., Davidsen S.K., Fesik S.W. NMR-based optimization of MMP inhibitors with improved bioavailability. J. Med. Chem. 45:2002;5628-5639
30. Hinzen B. Polymer-supported reagents: Preparation and use in parallel organic synthesis. Methods Princ. Med. Chem. 9:2000;209-237
31. Huth J.R., Sun C. Utility of NMR in lead optimization: Fragment-based approaches. Comb. Chem. High Throughput Screen. 5:2002;631-644
32. Jahnke W. Spin labels as a tool to identify and characterize protein-ligand interactions by NMR spectroscopy. Chembiochem. 3:2002;167-173
33. Jahnke W., Perez L.B., Paris C.G., Strauss A., Fendrich G., Nalin C.M. Second-site NMR screening with a spin-labeled first ligand. J. Am. Chem. Soc. 122:2000;7394-7395
34. Jahnke W., Rudisser S., Zurini M. Spin label enhanced NMR screening. J. Am. Chem. Soc. 123:2001;3149-3150
35. Jahnke W., Florsheimer A., Blommers M.J.J., Paris C.G., Heim J., Nalin C.M., Perez L.B. Second-site NMR screening and linker design. Curr. Top. Med. Chem. 3:2003;69-80
36. Kortemme T., Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Proc. Natl. Acad. Sci. USA. 99:2002;14116-14121
37. Kuntz I.D., Chen K., Sharp K.A., Kollman P.A. The maximal affinity of ligands. Proc. Natl. Acad. Sci. USA. 96:1999;9997-10002
38. Lepre C.A., Peng J.W., Fejzo J., Abdul-Manan N., Pocas J., Jacobs M., Xie X., Moore J.M. Applications of SHAPES screening in drug discovery. Comb. Chem. High Throughput Screen. 5:2002;583-590
39. Li D., DeRose E., London R. The inter-ligand Overhauser effect: A powerful new NMR approach for mapping structural relationships of macromolecular ligands. J. Biomol. NMR. 15:1999;71-76
40. Liu G., Huth J.R., Olejniczak E.T., Mendoza R., DeVries P., Leitza S., Reilly E.B., Okasinski G.F., Fesik S.W., von Geldern T.W. Novel p-arylthio cinnamides as antagonists of leukocyte function-associated antigen-1/ intracellular adhesion molecule-1 interaction. 2. Mechanism of inhibition and structure-based improvement of pharmaceutical properties. J. Med. Chem. 44:2001;1202-1210
41. London R.E. Theoretical analysis of the inter-ligand Overhauser effect: A new approach for mapping structural relationships of macromolecular ligands. J. Magn. Reson. 141:1999;301-311
42. Mayer M., Meyer B. Characterization of ligand binding by saturation transfer difference NMR spectroscopy. Angew. Chem. Int. Ed. 38:1999;1784-1788
43. McCoy M.A., Wyss D.F. Alignment of weakly interacting molecules to protein surfaces using simulations of chemical shift perturbations. J. Biomol. NMR. 18:2000;189-198
44. McGovern S.L., Caselli E., Grigorieff N., Shoichet B.K. A common mechanism underlying promiscuous inhibitors from virtual and high-throughput screening. J. Med. Chem. 45:2002;1712-1722
45. McMartin C., Bohacek R.S. QXP: Powerful, rapid computer algorithms for structure-based design. J. Comp. Aided Mol. Des. 11:1997;333-344
46. Medek A., Hajduk P.J., Mack J., Fesik S.W. The use of differential chemical shifts for determining the binding site location and orientation of protein-bound ligands. J. Am. Chem. Soc. 122:1999;1241-1242
47. Meyer B., Weimar T., Peters T. Screening mixtures for biological activity by NMR. Eur. J. Biochem. 246:1997;705-709
48. Meyer B., Peters T. NMR spectroscopy techniques for screening and identifying ligand binding to receptors. Angew. Chem. Int. Ed. 42:2003;864-890
49. Murali N., Jarori G.K., Landy S.B., Nageswara Rao B.D. Two-dimensional transferred nuclear Overhauser effect spectroscopy (TRNOESY) studies of nucleotide conformations in creatine kinase complexes: Effects due to weakly nonspecific binding. Biochemistry. 32:1993;12941-12948
50. Peng J.W., Lepre C.A., Fejzo J., Abdul-Manan N., Moore J.M. Nuclear magnetic resonance-based approaches for lead generation in drug discovery. Methods Enzymol. 338:2001;202-230
51. Post C.B. Exchange-transferred NOE spectroscopy and bound ligand structure determination. Curr. Opin. Struct. Biol. 13:2003;581-588
52. Salvino J.M., Dolle R.E. The development and application of tetrafluorophenol-activated resins for rapid amine derivatization. Methods Enzymol. 369:2003;151-163
53. Salvino J.M., Kumar N.V., Orton E., Airey J., Kiesow T., Crawford K., Mathew R., Krolikowski P., Drew M., Engers D., Krolinkowski D., Herpin T., Gardyan M., McGeehan G., Labaudiniere R. Polymer-supported tetrafluorophenol: A new activated resin for chemical library synthesis. J. Comb. Chem. 2:2000;691-697
54. Sauer D.R., Kalvin D., Phelan K.M. Microwave-assisted synthesis utilizing supported reagents: A rapid and efficient acylation procedure. Organic Lett. 5:2003;4721-4724
55. Sem D.S., Bertolaet B., Baker B., Chang E., Costache A.D., Coutts S., Dong Q., Hansen M., Hong V., Huang X., Jack R.M., Kho R., Lang H., Ma C.-T., Meininger D., Pellecchia M., Pierre F., Villar H., Yu L. Systems-based design of bi-ligand inhibitors of oxidoreductases: Filling the chemical proteomic toolbox. Chem. Biol. 11:2004;185-194
56. Shuker S.B., Hajduk P.J., Meadows R.P., Fesik S.W. Discovering high-affinity ligands for proteins: SAR by NMR. Science. 274:1996;1531-1534
57. Stockman B.J., Dalvit C. NMR screening techniques in drug discovery and drug design. Prog. NMR Spectrosc. 41:2002;187-231
58. Stockman B.J., Farley K.A., Angwin D.T. Screening of compound libraries for protein binding using flow-injection nuclear magnetic resonance spectroscopy. Methods Enzymol. 338:2001;231-246
59. Strauss A., Bitsch F., Cutting B., Fendrich G., Graff P., Liebetanz J., Zurini M., Jahnke W. Amino-acid-type selective isotope labeling of proteins expressed in baculovirus-infected insect cells useful for NMR studies. J. Biomol. NMR. 26:2003;367-372
60. Szczepankiewicz B.G., Liu G., Hajduk P.J., Abad-Zapatero C., Pei Z., Xin Z., Lubben T., Trevillyan J.M., Stashko M.A., Ballaron S.J., Liang H., Huang F., Hutchins C.W., Fesik S.W., Jirousek M.R. Discovery of a potent, selective protein tyrosine phosphatase 1B inhibitor using a linked-fragment strategy. J. Am. Chem. Soc. 125:2003;4087-4096
61. Ukkola O., Santaniemi M. Protein tyrosine phosphatase 1B: A new target for the treatment of obesity and associated comorbidities. J. Intern. Med. 251:2002;467-475
62. Wada C.K., Holms J.H., Curtin M.L., Dai Y., Florjancic A.S., Garland R.B., Guo Y., Heyman H.R., Stacey J.R., Steinman D.H., Albert D.H., Bouska J.J., Elmore I.N., Goodfellow C.L., Marcotte P.A., Tapang P., Morgan D.W., Michaelides M.R., Davidsen S.K. Phenoxyphenyl sulfone N-formylhydroxylamines (retrohydroxamates) as potent, selective, orally bioavailable matrix metalloproteinase inhibitors. J. Med. Chem. 45:2002;219-232
63. Xin A., Oost T.K., Abad-Zapatero C., Hajduk P.J., Pei Z., Szczepankiewicz B.G., Hutchins C.W., Ballaron S.J., Stashko M.A., Lubben T., Trevillyan J.M., Jirousek M.R., Liu G. Potent, selective inhibitors of protein tyrosine phosphatase 1B. Biorg. Med. Chem. Lett. 13:2003;1887-1890
64. Yun Y.K., Porco J.A. Jr., Labadie J. Polymer-assisted parallel solution phase synthesis of substituted benzimidazoles. Synlett. 2002;739-742