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11(3), 244–251; (d) Bender, A., Bojanic, D., Davies, J. W., Crisman, T. J., Mikhailov, D.,
Scheiber, J., Jenkins, J. L., Deng, Z., Hill, W. A., Popov, M., Jacoby, E., and Glick, M.
Which aspects of HTS are empirically correlated with downstream success? Curr. Opin.
Drug Discov. Devel. 2008, 11(3), 327–337.
4. Bohacek, R. S., McMartin, C., and Guida, W. C. The art and practice of structure-based
drug design: a molecular modeling perspective. Med. Res. Rev. 1996, 16(1), 3–50.
5. Teague, S. J., Davis, A. M., Leeson, P. D., and Oprea, T. The design of leadlike
combinatorial libraries. Angew. Chem. Int. Ed. Engl. 1999, 38(24), 3743–3748.
6. (a) Hann, M. M. and Oprea, T. I. Pursuing the leadlikeness concept in pharmaceutical
research. Curr. Opin. Chem. Biol. 2004, 8(3), 255–263; (b) Rishton, G. M. Molecular
diversity in the context of leadlikeness: compound properties that enable effective
biochemical screening. Curr. Opin. Chem. Biol. 2008, 12(3), 340–351.
7. (a) Wenlock, M. C., Austin, R. P., Barton, P., Davis, A. M., and Leeson, P. D. A comparison
of physiochemical property profiles of development and marketed oral drugs. J. Med.
Chem. 2003, 46(7), 1250–1256; (b) Vieth, M. and Sutherland, J. J. Dependence of
molecular properties on proteomic family for marketed oral drugs. J. Med. Chem. 2006,
49(12), 3451–3453.
8. Leeson, P. D. and Springthorpe, B. The influence of drug-like concepts on decisionmaking in medicinal chemistry. Nat. Rev. Drug Discov. 2007, 6(11), 881–890.
9. Hann, M. M., Leach, A. R., and Harper, G. Molecular complexity and its impact on the
probability of finding leads for drug discovery. J. Chem. Inf. Comp. Sci. 2001, 41(3),
856–864.
10. Hopkins, A. L., Groom, C. R., and Alex, A. Ligand efficiency: a useful metric for lead
selection. Drug Discov. Today 2004, 9(10), 430–431.
11. Lipinski, C. A., Lombardo, F., Dominy, B. W., and Feeney, P. J. Experimental and
computational approaches to estimate solubility and permeability in drug discovery and
development settings. Adv. Drug Deliv. Rev. 1997, 23(1–3), 3–25.
12. (a) Erlanson, D. A., McDowell, R. S., and O’Brien T. Fragment-based drug discovery.
J. Med. Chem. 2004, 47(14), 3463–3482; (b) Rees, D. C., Congreve, M., Murray, C. W.,
and Carr, R. Fragment-based lead discovery.Nat. Rev. Drug Discov. 2004, 3(8), 660–672;
(c) Erlanson, D. A. Fragment-based lead discovery: a chemical update. Curr. Opin.
Biotechnol. 2006, 17(6), 643–652; (d) Hajduk, P. J. and Greer, J. A decade of fragmentbased drug design: strategic advances and lessons learned. Nat. Rev. Drug Discov. 2007, 6
(3), 211–219; (e) Congreve, M., Chessari, G., Tisi, D., and Woodhead, A. J. Recent
developments in fragment-based drug discovery. J. Med. Chem. 2008, 51(13),
3661–3680.
13. Shuker, S. B., Hajduk, P. J., Meadows, R. P., and Fesik, S. W. Discovering high-affinity
ligands for proteins: SAR by NMR.
Science 1996, 274(5292), 1531–1534.
14. Keser€u, G. M. and Makara, G. M. Hit discovery and hit-to-lead approaches. Drug Discov.
Today 2006, 11(15–16), 741–748.
15. (a) Pellecchia, M., Bertini, I., Cowburn, D., Dalvit, C., Giralt, E., Jahnke, W., James, T. L.,
Homans, S. W., Kessler, H., Luchinat, C., Meyer, B., Oschkinat, H., Peng, J., Schwalbe,
H., and Siegal, G. Perspectives on NMR in drug discovery: a technique comes of age. Nat.
Rev. Drug Discov. 2008, 7(9), 738–745; (b) Lepre, C. A., Moore, J. M. and Peng, J. W.
Theory and application of NMR-based screening in pharmaceutical research. Chem. Rev.
2004, 104(8), 3641–3675; (c) Meyer, B. and Peters, T. NMR spectroscopy techniques for
REFERENCES 461
https://t.me/medicina_free

screening and identifying ligand binding to protein receptors. Angew. Chem. Int. Ed.
Engl. 2003, 42(8), 864–890; (d) Pellecchia, M., Sem, D. S., and W€uthrich, K. NMR in
drug discovery. Nat. Rev. Drug Discov. 2002, 1(3), 211–219.
16. (a) Jhoti, H., Cleasby, A., Verdonk,M., and Williams, G. Fragment-based screening using
X-ray crystallography and NMR spectroscopy. Curr. Opin. Chem. Biol. 2007, 11(5),
485–493; (b) Blundell, T. L. and Patel, S. High-throughput X-ray crystallography for drug
discovery. Curr. Opin. Pharmacol. 2004, 4(5), 490–496; (c) Blundell, T. L., Jhoti, H., and
Abell, C. High-throughput crystallography for lead discovery in drug design. Nat. Rev.
Drug Discov. 2002, 1(1), 45–54; (d) Kuhn, P., Wilson, K., Patch, M. G., and Stevens, R. C.
The genesis of high-throughput structure-based drug discovery using protein crystallography. Curr. Opin. Chem. Biol. 2002, 6(5), 704–710.
17. (a) Erlanson, D. A. and Hansen, S. K. Making drugs on proteins: site-directed ligand
discovery for fragment-based lead assembly. Curr. Opin. Chem. Biol. 2004, 8(4),
399–406; (b) Hofstadler, S. A. and Sannes-Lowery, K. A. Applications of ESI-MS in
drug discovery: interrogation of noncovalent complexes. Nat. Rev. Drug Discov. 2006, 5
(7), 585–595.
18. Neumann, T., Junker, H.-D., Schmidt, K., and Sekul, R. SPR-based fragment screening:
advantages and applications. Curr. Top. Med. Chem. 2007, 7(16), 1630–1642.
19. Ciulli, A. and Abell, C. Fragment-based approaches to enzyme inhibition. Curr. Opin.
Biotechnol. 2007, 18(6), 489–496.
20. Hesterkamp, T. and Whittaker, M. Fragment-based activity space: smaller is better. Curr.
Opin. Chem. Biol. 2008, 12(3), 260–268.
21. (a) Jacoby, E., Davies, J., and Blommers, M. J. Design of small molecule libraries for
NMR screening and other applications in drug discovery. Curr. Top. Med. Chem. 2003, 3
(1), 11–23; (b) Lepre, C. A. Library design for NMR-based screening. Drug Discov.
Today 2001, 6(3), 133–140; (c) Schuffenhauer, A., Ruedisser, S., Marzinzik, A. L.,
Jahnke, W., Blommers, M., Selzer, P., and Jacoby, E. Library design for fragment based
screening. Curr. Top. Med. Chem. 2005, 5(8), 751–762; (d) Baurin, N., Aboul-Ela, F.,
Barril, X., Davis, B., Drysdale, M., Dymock, B., Finch, H., Fromont, C., Richardson, C.,
Simmonite, H., and Hubbard, R. E. Design and characterization of libraries of molecular
fragments for use in NMR screening against protein targets. J. Chem. Inf. Comput. Sci.
2004, 44(6), 2157–2166.
22. Siegel, M. G. and Vieth, M. Drugs in other drugs: a new look at drugs as fragments. Drug
Discov. Today 2007, 12(1–2), 71–79.
23. MDL Comprehensive Medicinal Chemistry, (CMC). Available at http://www.symyx
.com/.
24. Maccs drug data report (MDDR). Available at http://www.symyx.com/.
25. World Drug Index (WDI). Available at http://www.thomsonreuters.com/.
26. Congreve, M., Carr R., Murray, C., and Jhoti, H. A
rule of three for fragment base
discovery. Drug Discov. Today, 2003, 8(19), 876–877.
27. Hajduk, P. J. Fragment-based drug design: how big is too big? J. Med. Chem. 2006, 49
(24), 6972–6976.
28. Siegal, G., AB, E., and Schultz, J. Integration of fragment screening and library design.
Drug Discov. Today 2007, 12(23–24), 1032–1039.
29. Babaoglu, K. and Shoichet, B. K. Deconstructing fragment-based inhibitor discovery.
Nat. Chem. Biol. 2006, 2(12), 720–723.
462
FRAGMENT-BASED DRUG DESIGN: CONSIDERATIONS FOR GOOD ADME PROPERTIES
https://t.me/medicina_free

30. Hajduk, P. J., Huth, J. R., and Fesik, S. W. Druggability indices for protein targets derived
from NMR-based screening data. J. Med. Chem. 2005, 48(7), 2518–2525.
31. Albert, J. S., Blomberg, N., Breeze, A. L., Brown, A. J., Burrows, J. N., Edwards, P. D.,
Folmer, R. H., Geschwindner, S., Griffen, E. J., Kenny, P. W., Nowak, T., Olsson, L. L.,
Sanganee, H., and Shapiro, A. B. An integrated approach to fragment-based lead
generation: philosophy, strategy and case studies from AstraZeneca’s drug discovery
programmes. Curr. Top. Med. Chem. 2007, 7(16), 1600–1629.
32. (a) Willett, P. Similarity methods in chemoinformatics. Annu. Rev. Inform. Sci. Technol.
2009, 43, 3–71; (b) Bender, A. and Glen, R. C. Molecular similarity: a key technique in
molecular informatics. Org. Biomol. Chem. 2004, 2(22), 3204–3218; (c) Nikolova, N.
and Jaworska, J. Approaches to measure chemical similarity—a review.QSAR Comb. Sci.
2003, 22(9–10), 1006–1026.
33. (a) Moore, J. M. NMR screening in drug discovery. Curr. Opin. Biotech. 1999, 10(1),
54–58.
34. Zartler, E. R. and Shapiro, M. J. Protein NMR-based screening in drug discovery. Curr.
Pharm. Des. 2006, 12(31), 3963–3972.
35. Diercks, T., Coles, M., and Kessler, H. Applications of NMR in drug discovery. Curr.
Opin. Chem. Biol. 2001, 5(3), 285–291.
36. Hajduk, P. J., Gerfin, T., Boehlen, J. M., H€aberli, M., Marek, D., and Fesik, S. W. Highthroughput nuclear magnetic resonance-based screening. J. Med. Chem. 1999, 42(13),
2315–2317.
37. Klages, J., Coles, M., and Kessler, H. NMR-based screening: a powerful tool in fragmentbased drug discovery. Mol. Biosyst. 2006, 2(6–7), 318–331.
38. Hajduk, P. J., Augeri, D. J., and Mack, J., Mendoza, R., Yang, J., Betz, S. F., and Fesik, S.
W. NMR-based screening of proteins containing
13
C-labeled methyl groups. J. Am.
Chem. Soc. 2000, 122(33), 7898–7904.
39. Weigelt, J., van Dongen, M., Uppenberg, J., Schultz, J., and Wikstr€om, M. Site-selective
screening by NMR spectroscopy with labeled amino acid pairs. J. Am. Chem. Soc. 2002,
124(11), 2446–2447.
40. Yabuki, T., Kigawa, T., Dohmae, N., Takio, K., Terada, T., Ito, Y., Laue, E. D., Cooper, J.
A., Kainosho, M., and Yokoyama, S. Dual amino acid-selective and site-directed stableisotope labeling of the human c-Ha-Ras protein by cell-free synthesis. J. Biomol. NMR
1998, 11(3), 295–306.
41. Pervushin, K., Riek, R., Wider, G., and W€uthrich, K. Attenuated T2 relaxation by mutual
cancellation of dipole–dipole coupling and chemical shift anisotropy indicates an avenue
to NMR structures of very large biological macromolecules in solution. Proc. Natl. Acad.
Sci. USA 1997, 94(23), 12366–12371.
42. Riek, R., Wider, G., Pervushin, K., and W€uthrich, K. Polarization transfer by crosscorrelated relaxation in solution NMR with very large molecules. Proc. Natl. Acad. Sci.
USA 1999, 96(9), 4918–4923.
43. Peng, J. W.,Lepre, C. A., Fejzo, J., Abdul-Manan, N., and Moore, J. M. Nuclear magnetic
resonance-based approaches for lead generation in drug discovery. Methods Enzymol.
2002, 338, 202–230.
44. (a) Hajduk, P. J., Olejniczak, E. T., and Fesik, S. W. One-dimensional relaxation- and
diffusion-edited NMR methods for screening compounds that bind to macromolecules.
J. Am. Chem. Soc. 1997, 119(50), 12257–12261; (b) Lin, M., Shapiro, M. J., and Wareing,
REFERENCES 463
https://t.me/medicina_free

J. R. Diffusion-edited NMR—affinity NMR for direct observation of molecular interactions. J. Am. Chem. Soc. 1997, 119(22), 5249–5250.
45. (a) Meyer, B., Weimar, T., and Peters, T. Screening mixtures for biological activity by
NMR. Eur. J. Biochem. 1997, 246(3), 705–709; (b) Inooka, H., Ohtaki, T., Kitahara, O.,
Ikegami, T., Endo, S., Kitada, C., Ogi, K., Onda, H., Fujino, M., and Shirakawa, M.
Conformation of a peptide ligand bound to its G-protein coupled receptor. Nat. Struct.
Biol. 2001, 8(2), 161–165.
46. (a) Chen, A. and Shapiro, M. J. NOE pumping as high-throughput method to determine
compounds with binding affinity to macromolecules by NMR. J. Am. Chem. Soc. 2000,
122(2), 414–415; (b) Chen, A. and Shapiro, M. J. NOE pumping: a novel NMR technique
for identification of compounds with binding affinity to macromolecules. J. Am. Chem.
Soc. 1998, 120(39), 10258–10259.
47. (a) Mayer, M. and Meyer, B. Characterization of ligand binding by saturation transfer
difference NMR spectroscopy. Angew. Chem. Int. Ed. 1999, 38(12), 1784–1788;
(b) Mayer, M. and 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(25), 6108–6117.
48. (a) Dalvit, C., Pevarello, P., Tato, M., Veronesi, M., Vulpetti, A., and Sundstrom, M.
Identification of compounds with binding affinity to proteins via magnetization transfer
from bulk water.J. Biomol. NMR 2000, 18(1), 65–68; (b) Dalvit, C., Fogliatto, G., Stewart,
A.,Veronesi,M., and Stockman,B. WaterLOGSYasa method for primaryNMR screening:
practical aspects and range of applicability. J. Biomol. NMR. 2001, 21(4), 349–359.
49. Becattini, B., Sareth, S., Zhai, D., Crowell, K. J., Leone, M., Reed, J. C., and Pellecchia,
M. Targetingapoptosis via chemical design: inhibition of bid-induced cell death by small
organic molecules. Chem. Biol. 2004, 11(8), 1107–1117.
50. (a) Jahnke, W., Perez, W. B., Paris, C. G., Strauss, A., Fendrich, G., and Nalin, C. M.
Second-site NMR screening with a spin-labeled first ligand. J. Am. Chem. Soc. 2000, 122
(30), 7394–7395; (b) Jahnke, W., Rdisser, S., and Zurini, M. Spin label enhanced NMR
screening. J. Am. Chem. Soc. 2001, 123(13), 3149–3150.
51. Dalvit, C., Ardini, E., Flocco, M., Fogliatto, G. P., Mongelli, N., and Veronesi, M. A
general NMR method for rapid, efficient, and reliable biochemical screening. J. Am.
Chem. Soc. 2003, 125(47), 14620–14625.
52. (a) Dalvit, C., Mongelli, N., Papeo, G., Giordano, P., Veronesi, M., Moskau, D., and
K€ummerle, R. Sensitivity improvement in
19
F NMR-based screening experiments:
theoretical considerations and experimental applications. J. Am. Chem. Soc. 2005,
127(38), 13380–13385; (b) Forino, M., Johnson, S., Wong, T. Y., Rozanov, D. V.,
Savinov, A. Y., Li, W., Fattorusso, R., Becattini, B., Orry, A. J., Jung, D., Abagyan,
R. A., Smith, J. W., Alibek, K., Liddington, R. C., Strongin, A. Y., and Pellecchia, M.
Efficient synthetic inhibitors of anthrax lethal factor. Proc. Natl. Acad. Sci. USA 2005, 102
(27), 9499–9504.
53. Vanwetswinkel, S., Heetebrij, R. J., van Duynhoven, J., Hollander, J. G., Filippov, D. V.,
Hajduk, P. J., and Siegal, G. TINS, target immobilized NMR screening: an efficient and
sensitive method for ligand discovery. Chem. Biol. 2005, 12(2), 207–216.
54. (a) Jahnke, W., Floersheim, P., Ostermeier, C., Zhang, X., Hemmig, R., Hurth, K., and
Uzunov, D. P. NMR reporter screening for the detection of high-affinity ligands. Angew.
Chem. Int. Ed. Engl. 2002, 41 (18), 3420–3423; (b) Dalvit, C., Fasolini, M., Flocco, M.,
Knapp, S., Pevarello, P., and Veronesi,M. NMR-Based screening with competition water-
464
FRAGMENT-BASED DRUG DESIGN: CONSIDERATIONS FOR GOOD ADME PROPERTIES
https://t.me/medicina_free

ligand observed via gradient spectroscopy experiments: detection of high-affinity ligands.
J. Med. Chem. 2002, 45(12), 2610–2614.
55. (a) Muchmore, S. W., Olson, J., Jones, R., Pan, J., Blum, M., Greer, J., Merrick, S. M.,
Magdalinos, P., and Nienaber, V. L. Automated crystal mounting and data collection for
protein crystallography. Structure 2000, 8(12), R243–R246; (b) Sharff, A. and Jhoti, H.
High-throughput crystallography to enhance drug discovery. Curr. Opin. Chem. Biol.
2003, 7(3), 340–345.
56. Hendrickson, W. A. Synchrotron crystallography. Trends Biochem. Sci. 2000, 25(12),
637–643.
57. (a) Mattos, C. and Ringe, D. Locating and characterizing binding sites on proteins. Nat.
Biotechnol. 1996, 14(5), 595–599; (b) Mattos, C. and Ringe, D. Proteins in organic
solvents. Curr. Opin. Struct. Biol. 2001, 11(6), 761–764.
58. Stout, T. J., Sage, C. R. and Stroud, R. M. The additivity of substrate fragments in
enzyme–ligand binding. Structure 1998, 6(7), 839–848.
59. Bostr€om, J., Hogner, A., and Schmitt, S. Do structurally similar ligands bind in a similar
fashion? J. Med. Chem. 2006, 49(23), 6716–6725.
60. Verlinde, C. L., Rudenko, G., and Hol, W. G. In search of new lead compounds for
trypanosomiasis drug design: a protein structure-based linked-fragment approach.
J. Comput. Aided Mol. Des. 1992, 6(2), 131–147.
61. Nienaber, V.L., Richardson, P. L., Klighofer, V., Bouska, J. J., Giranda, V. L., and Greer, J.
Discovering novel ligands for macromolecules using X-ray crystallographic screening.
Nat. Biotechnol. 2000, 18(10), 1105–1108.
62. Lesuisse, D., Lange, G., Deprez, P., Benard, D., Schoot, B., Delettre, G., Marquette, J. P.,
Broto, P., Jean-Baptiste, V., Bichet, P., Sarubbi, E., and Mandine, E. SAR and X-ray. A
new approach combining fragment-based screening and rational drug design: application
to the discovery of nanomolar inhibitors of Src SH2. J. Med. Chem. 2002, 45(12),
2379–2387.
63. Verdonk, M. L. and Hartshorn, M. J. Structure-guided fragment screening for lead
discovery. Curr. Opin. Drug Discov. Devel. 2004, 7(4), 404–410.
64. Gill, A. New lead generation strategies for protein kinase inhibitors—fragment based
screening approaches. Mini. Rev. Med. Chem. 2004, 4(3), 301–311.
65. Carr, R. and Jhoti, H. Structure-based screening of low-affinity compounds. Drug Discov.
Today 2002, 7(9), 522–527.
66. Accelrys, Inc. 10188 Telesis Court, Suite 100. San Diego, CA 92121, USA. Phone:
(858)799-5000. Fax: (858)799-5100. Available at http://www.accelrys.com.
67. Hartshorn, M. J., Murray, C. W., Cleasby, A., Frederickson, M., Tickle, I. J., and Jhoti, H.
Fragment-based lead discovery using X-ray crystallography. J. Med. Chem. 2005, 48(2),
403–413.
68. (a) Gill, A., Cleasby, A., and Jhoti, H. The discovery of novel protein kinase
inhibitors by using fragment-based high-throughput X-ray crystallography. Chem-
BioChem
2005, 6(3), 506–512; (b) Sanders, W. J., Nienaber, V. L., Lerner, C. G.,
McCall, J. O., Merrick, S. M., Swanson, S. J., Harlan, J. E., Stoll, V. S., Stamper, G.
F., Betz, S. F., Condroski, K. R., Meadows, R. P., Severin, J. M., Walter, K. A.,
Magdalinos, P., Jakob, C. G., Wagner, R., and Beutel, B. A. Discovery of potent
inhibitors of dihydroneopterin aldolase using CrystaLEAD high-throughput X-ray
crystallographic screening and structure-directed lead optimization. J. Med. Chem.
REFERENCES 465
https://t.me/medicina_free

2004, 47(7), 1709–1718; (c) Card, G. L., Blasdel, L., England, B. P., Zhang, C.,
Suzuki, Y., Gillette, S., Fong, D., Ibrahim, P. N., Artis, D. R., Bollag, G., Milburn, M.
V., Kim, S.-H., Schlessinger, J., and Zhang, K. Y. J. A family of phosphodiesterase
inhibitors discovered by cocrystallography and scaffold-based drug design. Nat.
Biotechnol. 2005, 23(2), 201–207.
69. (a) Seth, P. P., Miyaji, A., Jefferson, E. A., Sannes-Lowery,K. A., Osgood, S. A., Propp, S.
S., Ranken, R., Massire, C., Sampath, R., Ecker, D. J., Swayze, E. E., and Griffey, R. H.
SAR by MS: discovery of a new class of RNA-binding small molecules for the hepatitis C
virus: internal ribosome entry site IIA subdomain. J. Med. Chem. 2005, 48(23),
7099–7102; (b) Swayze, E. E., Jefferson, E. A., Sannes-Lowery, K. A., Blyn, L. B.,
Risen, L. M., Arakawa, S., Osgood, S. A., Hofstadler, S. A., and Griffey, R. H. SAR by
MS: a ligand based technique for drug lead discovery against structured RNA targets.
J. Med. Chem. 2002, 45(18) , 3816–3819.
70. Erlanson, D. A., Wells, J. A., and Braisted, A. C. Tethering: fragment-based drug
discovery. Annu. Rev. Biophys. Biomol. Struct. 2004, 33, 199–223.
71. (a) Huber, W. and Mueller, F. Biomolecular interaction analysis in drug discovery using
surface plasmon resonance technology. Curr. Pharm. Des. 2006, 12(31), 3999–4021;
(b) Baird, C. L. and Myszka, D. G. Current and emerging commercial optical biosensors.
J. Mol. Recognit. 2001, 14(5), 261–268.
72. Pr€oll, F., Fechner, P., and Proll, G. Direct optical detection in fragment-based screening.
Anal. Bioanal. Chem. 2009, 393(6–7), 1557–1562.
73. Day, Y. S., Baird, C. L., Rich, R. L., and Myszka, D. G. Direct comparison of binding
equilibrium, thermodynamic, and rate constants determined by surface- and solutionbased biophysical methods. Protein Sci. 2002, 11(5), 1017–1025.
74. Cooper, M. A. Optical biosensors in drug discovery. Nat. Rev. Drug Discov. 2002, 1(7),
515–528.
75. Cooper, M. A. Advances in membrane receptor screening and analysis. J. Mol. Recognit.
2004, 17(4), 286–315.
76. Gribbon, P. and Sewing, A. Fluorescence readouts in HTS: no gain without pain? Drug
Discov. Today. 2003, 8(22), 1035–1043.
77. Dai, W.-G., Pollock-Dove, C., Dong, L. C., and Li, S. Advanced screening assays to
rapidly identify solubility-enhancing formulations: high-throughput, miniaturization and
automation. Adv. Drug Deliv. Rev. 2008, 60(6), 657–672.
78. (a) McGovern, S. L., Caselli, E., Grigorieff, N., and Shoichet, B. K. A common
mechanism underlying promiscuous inhibitors from virtual and high-throughput screening. J. Med. Chem. 2002, 45(8), 1712–1722; (b) McGovern, S. L., Helfand, B. T., Feng,
B., and Shoichet, B. K. A specific mechanism of nonspecific inhibition. J. Med. Chem.
2003, 46(20), 4265–4272.
79. (a) Rishton, G. M. Reactive compounds and in vitro false positives in HTS. Drug Discov.
Today 1997, 2(9), 382–384; (b) Huth, J. R., Mendoza, R., Olejniczak, E. T., Johnson, R.
W., Cothron, D. A., Liu, Y., Lerner, C. G., Chen, J., and Hajduk, P. J. ALARM NMR:
a rapid and robust experimental method to detect reactive false positives in biochemical
screens. J. Am. Chem. Soc.
2005, 127(1), 217–224.
80. (a) Maly, D. J., Choong, I. C., and Ellman, J. A. Combinatorial target-guided ligand
assembly: identification of potent subtype-selective c-Src inhibitors. Proc. Natl. Acad.
Sci. USA 2000, 97(6), 2419–2424; (b) He, M. M., Smith, A. S., Oslob, J. D., Flanagan, W.
466
FRAGMENT-BASED DRUG DESIGN: CONSIDERATIONS FOR GOOD ADME PROPERTIES
https://t.me/medicina_free

M., Braisted, A. C., Whitty,A., Cancilla, M. T.,Wang,J., Lugovskoy,A. A., Yoburn, J. C.,
Fung, A. D., Farrington, G., Eldredge, J. K., Day, E. S., Cruz, L. A., Cachero, T.G., Miller,
S. K., Friedman, J. E., Choong, I. C., and Cunningham, B. C. Small-molecule inhibition of
TNF-a. Science 2005, 310(5750), 1022–1025.
81. (a) Wang, X., Choe, Y., Craik, C. S., and Ellman, J. A. Design and synthesis of novel
inhibitors of gelatinase B. Bioorg. Med. Chem. Lett. 2002, 12(16), 2201–2204; (b)
Boehm, H.-J., Boehringer, M., Bur, D., Gmuender, H., Huber, W., Klaus, W., Kostrewa,
D., Kuehne, H., Luebbers, T., Meunier-Keller, N., and Mueller, F. Novel inhibitors of
DNA gyrase: 3D structure based biased needle screening, hit validation by biophysical
methods, and 3D guided optimization. A promising alternative to random screening. J.
Med. Chem. 2000, 43(14), 2664–2674; (c) Black, E., Breed, J., Breeze, A. L., Embrey, K.,
Garcia, R., Gero, T. W., Godfrey, L., Kenny, P. W., Morley, A. D., Minshull, C. A.,
Pannifer, A. D., Read, J., Rees, A., Russell, D. J., Toader, D., and Tucker, J. Structurebased design of protein tyrosine phosphatase-1B inhibitors. Bioorg. Med. Chem. Lett.
2005, 15(10), 2503–2507; (d) Schilling, S., Niestroj, A. J., Rahfeld, J. U., Hoffmann, T.,
Wermann, M., Zunkel, K., Wasternack, C., and Demuth, H. U. Identification of human
glutaminyl cyclase as a metalloenzyme. Potent inhibition by imidazole derivatives and
heterocyclic chelators. J. Biol. Chem. 2003, 278(50), 49773–49779; (e) Buchholz, M.,
Heiser, U., Schilling, S., Niestroj, A. J., Zunkel, K., and Demuth, H. U. The first potent
inhibitors for human glutaminyl cyclase: synthesis and structure–activity relationship.
J. Med. Chem. 2006, 49(2), 664–677.
82. Kehoe, J. W., Maly, D. J., Verdugo, D. E., Armstrong, J. I., Cook, B. N., Ouyang, Y. B.,
Moore, K. L., Ellman, J. A., and Bertozzi, C. R. Tyrosylprotein sulfotransferase inhibitors
generated by combinatorial target-guided ligand assembly. Bioorg. Med. Chem. Lett.
2002, 12(3), 329–332.
83. Hesterkamp, T., Barker, J., Davenport, A., and Whittaker, M. Fragment based drug
discovery using fluorescence correlation: spectroscopy techniques: challenges and
solutions. Curr. Top. Med. Chem. 2007, 7(16), 1582–1591.
84. Barker,J.J., Barker, O., Boggio,R., Chauhan, V.,Cheng, R.K., Corden, V.,Courtney,S. M.,
Edwards, N., Falque, V. M., Fusar, F., Gardiner, M., Hamelin, E. M., Hesterkamp, T.,
Ichihara, O., Jones, R. S., Mather, O., Mercurio, C., Minucci, S., Montalbetti, C. A., M€uller,
A., Patel, D., Phillips, B. G., Varasi, M., Whittaker, M., Winkler, D., and Yarnold, C. J.
Fragment-based identification of Hsp90 inhibitors. ChemMedChem 2009, 4(6), 963–966.
85. (a) Wood,W. J. L., Patterson, A. W., Tsuruoka, H., Jain, R. K., and Ellman, J. A. Substrate
activity screening: a fragment-based method for the rapid identification of nonpeptidic
protease inhibitors. J. Am. Chem. Soc. 2005, 127(44), 15521–15527; (b) Brak, K., Doyle,
P. S., McKerrow, J. H., and Ellman, J. A. Identification of a new class of nonpeptidic
inhibitors of cruzain. J. Am. Chem. Soc. 2008, 130(20), 6404–6410; (c) Soellner, M. B.,
Rawls, K. A., Grundner, C., Alber, T., and Ellman, J. A. Fragment-based substrate activity
screening method for the identification of potent inhibitors of the Mycobacterium
tuberculosis phosphatase PtpB. J. Am. Chem. Soc. 2007, 129(31), 9613–9635.
86. (a) Oprea, T. I., Davis, A. M. Teague, S. J., and Lesson, P. D. Is there a difference between
leads and drugs? A historial perspective. J. Chem. Inf. Comput. Sci. 2001, 41(5),
1308–1315; (b) Baurin, N., Baker, R., Richardson, C., Chen, I., Foloppe, N., Potter,
A., Jordan, A., Roughley, S., Parratt, M., Greaney, P., Morley, D., and Hubbard, R. E.
Drug-like annotation and duplicate analysis of a 23-supplier chemical database totalling
2.7 million compounds. J. Chem. Inf. Comput. Sci. 2004, 44(2), 643–651.
REFERENCES 467
https://t.me/medicina_free

87. Scapin, G. Structural biology and drug discovery. Curr. Pharm. Des. 2006, 12(17),
2087–2097.
88. (a) Jencks, W. P. On the attribution and additivity of binding energies. Proc. Natl. Acad.
Sci. USA 1981, 78(7), 4046–4050; (b) Saxty, G., Woodhead, S. J., Berdini, V., Davies, T.
G., Verdonk, M. L., Wyatt, P. G., Boyle, R. G., Barford, D., Downham, R., Garrett, M. D.,
and Carr, R. A. Identification of inhibitors of protein kinase B using fragment-based lead
discovery. J. Med. Chem. 2007, 50(10), 2293–2296.
89. Patel, Y., Gillet, V. J., Howe, T., Pastor, J., Oyarzabal, J., and Willett, P. Assessment of
additive/nonadditive effects in structure–activity relationships: implications for iterative
drug design. J. Med. Chem. 2008, 51(23), 7552–7562.
90. Green, N. M. Avidin. Adv. Protein Chem. 1975; 29, 85–133.
91. Murray, C. W. and Verdonk, M. L. The consequences of translational and rotational
entropy lost by small molecules on binding to proteins. J. Comput. Aided Mol. Des. 2002,
16(10), 741–753.
92. (a) Ganesan, A. Strategies for the dynamic integration of combinatorial synthesis and
screening. Angew. Chem. Int. Ed. 1998, 37(20), 2828–2831; (b) Otto, S., Furlan, R. L.,
and Sanders, J. K. Recent developments in dynamic combinatorial chemistry. Curr. Opin.
Chem. Biol. 2002, 6(3), 321–327; (c) Ramstr€om, O. and Lehn, J.-M. Drug discovery by
dynamic combinatorial libraries. Nat. Rev. Drug Discov. 2002, 1(1), 26–36.
93. Kolb, H. C., Finn, M. G., and Sharpless, K. B. Click chemistry: diverse chemical function
from a few good reactions. Angew. Chem. Int. Ed. Engl. 2001, 40(11), 2004–2021.
94. Lehn, J.-M. and Eliseev, A. V. Dynamic combinatorial chemistry. Science 2001, 291
(5512), 2331–2332.
95. (a) Eliseev, A. V. and Nelen, M. I. Use of molecular recognition to drive chemical
evolution. 1. Controlling the composition of an equilibrating mixture of simple arginine
receptors. J. Am. Chem. Soc. 1997, 119(5), 1147–1148; (b) Ramstr€om, O. and Lehn J.-M.
In situ generation and screening of a dynamic combinatorial carbohydrate library against
concanavalin A. ChemBioChem 2000, 1(1), 41–48; (c) Bunyapaiboonsri, T., Ramstr€om,
O., Lohmann, S., Lehn, J.-M., Peng, L., and Goeldner, M. Dynamic deconvolution of
a pre-equilibrated dynamic combinatorial library of acetylcholinesterase inhibitors.
ChemBioChem 2001, 2(6), 438–444; (d) Edwards, P. Fragment-based drug discovery
of carbonic anhydrase II inhibitors by dynamic combinatorial chemistry. Drug Discov.
Today 2007, 12(11/12), 497–498.
96. (a)Huc, I. and Lehn, J.-M. Virtualcombinatoriallibraries: dynamic generation of molecular
and supramolecular diversity by self-assembly. Proc. Natl. Acad. Sci. USA 1997, 94(6),
2106–2110; (b) Hochg
€
urtel, M., Kroth, H., Piecha, D., Hofmann, M. W., Nicolau, C.,
Krause, S., Schaaf, O., Sonnenmoser, G., and Eliseev, A. V. Target-induced formation of
neuraminidase inhibitors from in vitro virtual combinatorial libraries.Proc. Natl. Acad. Sci.
USA 2002, 99(6), 3382–3387; (c) Hochg€urtel, M., Biesinger, R., Kroth, H., Piecha, D.,
Hofmann,M. W.,Krause, S., Schaaf, O., Nicolau,C., and Eliseev, A. V. Ketonesas building
blocks for dynamic combinatorial libraries: highly active neuraminidase inhibitors generated via selection pressure of the biological target. J. Med. Chem. 2003, 46(3), 356–358;
(d)Zameo, S., Vauzeilles, B., and Beau, J.-M. Dynamic combinatorialchemistry: lysozyme
selects an aromatic motif that mimics a carbohydrate residue. Angew. Chem. Int. Ed. Engl.
2005, 44(6), 965–969;(e) Bugaut, A., Bathany,K., Schmitter, J.-M., and Rayner, B. Targetinduced selection of ligands from a dynamic combinatorial library of mono- and biconjugated oligonucleotides. Tetrahedron Lett. 2005, 46(4), 687–690.
468
FRAGMENT-BASED DRUG DESIGN: CONSIDERATIONS FOR GOOD ADME PROPERTIES
https://t.me/medicina_free

97. (a) Cousins, G. R. L., Poulsen, S.-A., and Sanders, J. K. M. Dynamic combinatorial
libraries of pseudo-peptide hydrazone macrocycles. Chem. Commun. 1999, (16),
1575–1576; (b) Bunyapaiboonsri, T., Ramstr€om, H., Ramstr€om, O., Haiech, J., and
Lehn, J.-M. Generation of bis-cationic heterocyclic inhibitors of Bacillus subtilis HPr
kinase/phosphatase from a ditopic dynamic combinatorial library. J. Med. Chem. 2003,
46(26), 5803–5811; (c) Ramstr€om, O., Lohmann, S., Bunyapaiboonsri, T., and Lehn, J.-
M. Dynamic combinatorial carbohydrate libraries: probing the binding site of the
concanavalin A lectin. Chem. Eur. J. 2004, 10(7), 1711–1715.
98. (a) Swann, P. G., Casanova, R. A., Desai, A., Frauenhoff, M. M., Urbancic, M.,
Slomczynska, U., Hopfinger, A. J., Le Breton, G. C., and Venton, D. L. Nonspecific
protease-catalyzed hydrolysis/synthesis of a mixture of peptides: product diversity and
ligand amplification by a molecular trap. Biopolymers 1996, 40(6), 617–625; (b) Burger,
M. T., and Bartlett, P. A. Enzymatic, polymer-supported formation of an analog of the
trypsin inhibitor A90720A: a screening strategy for macrocyclic peptidase inhibitors.
J. Am. Chem. Soc. 1997, 119(51), 12697–12698.
99. (a) Nicolaou, K. C., Hughes, R., Cho, S. Y., Winssinger, N., Smethurst, C., Labischinski,
H., and Endermann, R. Target-accelerated combinatorial synthesis and discovery of
highly potent antibiotics effective against vancomycinn-resistant bacteria. Angew.
Chem. Int. Ed. 2000, 39(21), 3823–3828; (b) Ladame, S., Whitney, A. M., and
Balasubramanian S. Targeting nucleic acid secondary structures with polyamides
using an optimized dynamic combinatorial approach. Angew. Chem. Int. Ed. Engl.
2005, 44(35), 5736–5739; (c) Hotchkiss, T., Kramer, H. B., Doores, K. J., Gamblin, D. P.,
Oldham, N. J., and Davis, B. G. Ligand amplification in a dynamic combinatorial
glycopeptide library. Chem. Commun. 2005, (34), 4264–4266.
100. (a) Shi, B. and Greaney, M. F. Reversible Michael addition of thiols as a new tool for
dynamic combinatorial chemistry. Chem. Commun. 2005, (7), 886–888; (b) Shi, B.,
Stevenson, R., Campopiano, D. J., and Greaney, M. F. Discovery of glutathione Stransferase inhibitors using dynamic combinatorial chemistry. J. Am. Chem. Soc. 2006,
128(26), 8459–8467.
101. Poulsen, S. A. and Bornaghi, L. F. Fragment-based drug discovery of carbonic anhydrase
II inhibitors by dynamic combinatorial chemistry utilizing alkene cross metathesis.
Bioorg. Med. Chem. 2006, 14(10), 3275–3284.
102. Lienard, B. M. R., Selevsek, N., Oldham, N. J., and Schofield, C. J. Combined mass
spectrometry and dynamic chemistry approach to identify metalloenzyme inhibitors.
ChemMedChem 2007, 2(2), 175–179.
103. Congreve, M. S., Davis, D. J., Devine, L., Granata, C., O’Reilly, M., Wyatt, P. G., and
Jhoti, H. Detection of ligands from a dynamic combinatorial library by X-ray crystallography. Angew. Chem. Int. Ed. Engl. 2003, 42(37), 4479–4482.
104. (a) O’Brien, T., Fahr, B. T., Sopko, M. M., Lam, J. W., Waal, N. D., Raimundo, B. C.,
Purkey,H. E., Pham, P.,and Romanowski, M. J. Structural analysis of caspase-1 inhibitors
derived from Tethering. Acta Crystallogr. Sec. F Struct. Biol. Cryst. Commun. 2005, 61
(5), 451–458; (b) Fahr, B. T., O’Brien, T., Pham, P., Waal, N. D., Baskaran, S., Raimundo,
B. C., Lam, J. W., Sopko, M. M., Purkey, H. E., and Romanowski, M. J. Tethering
identifies fragment that yields potent inhibitors of human caspase-1. Bioorg. Med. Chem.
Lett. 2006, 16(3), 559–62.
105. (a) Erlanson, D. A., Lam, J. W., Wiesmann, C., Luong, T. N., Simmons, R. L., DeLano, W.
L., Choong, I. C., Burdett, M. T., Flanagan, W. M., Lee, D., Gordon, E. M., and O’Brien, T.
REFERENCES 469
https://t.me/medicina_free

In situ assembly of enzyme inhibitors using extended tethering. Nat. Biotechnol. 2003, 21
(3), 308–314; (b) Choong, I. C., Lew, W., Lee, D., Pham, P., Burdett, M. T., Lam, J. W.,
Wiesmann, C., Luong, T. N., Fahr, B., DeLano, W. L., McDowell, R. S., Allen, D. A.,
Erlanson, D. A., Gordon, E. M., and O’Brien, T. Identification of potent and selective
small-molecule inhibitors of caspase-3 through the use of extended tethering and
structure-based drug design. J. Med. Chem. 2002, 45(23), 5005–5022.
106. Inglese, J., Blatchly, R. A., and Benkovic, S. J. A multisubstrate adduct inhibitor of
a purine biosynthetic enzyme with a picomolar dissociation constant. J. Med. Chem.
1989, 32(5), 937–940.
107. Greasley, S. E., Marsilje, T. H., Cai, H., Baker, S., Benkovic, S. J., Boger, D. L., and
Wilson, I. A. Unexpected formation of an epoxide-derived multisubstrate adduct
inhibitor on the active site of GAR transformylase. Biochemistry 2001, 40(45),
13538–13547.
108. Nguyen, R. and Huc, I. Using an enzyme’s active site to template inhibitors. Angew.
Chem. Int. Ed. Engl. 2001, 40(9), 1774–1776.
109. Huisgen, R. In 1,3-Dipolar Cycloaddition Chemistry, Vol. 1, Padwa, A. (ed.), Wiley,
New York, 1984, pp. 1–176.
110. (a) Kolb, H. C. and Sharpless, K. B. The growing impact of click chemistry on drug
discovery. Drug Discov. Today 2003, 8(24), 1128–1137; (b) Moorhouse, A. D. and
Moses, J. E. Click chemistry and medicinal chemistry: a case of “cyclo-addiction”.
ChemMedChem 2008, 3(5), 715–723; (c) Tron, G. C., Pirali, T., Billington, R. A.,
Canonico, P. L., Sorba, G., and Genazzani, A. A. Click chemistry reactions in medicinal
chemistry: applications of the 1, 3-dipolar cycloaddition between azides and alkynes.
Med. Res. Rev. 2008, 28(2), 278–308.
111. (a) Lewis, W. G., Green, L. G., Grynszpan, F., Radic, Z., Carlier, P. R., Taylor, P., Finn, M.
G., and Sharpless, K. B. Click chemistry in situ: acetylcholinesterase as a reaction vessel
for the selective assembly of a femtomolar inhibitor from an array of building blocks.
Angew. Chem. Int. Ed. Engl. 2002, 41(6), 1053–1057; (b) Manetsch, R., Krasinski, A.,
Radic, Z., Raushel, J., Taylor, P., Sharpless, K. B., and Kolb, H. C. In situ click chemistry:
enzyme inhibitors made to their own specifications. J. Am. Chem. Soc. 2004, 126(40),
12809–12818; (c) Krasinski, A., Radic, Z., Manetsch, R., Raushel, J., Taylor, P.,
Sharpless, K. B., and Kolb, H. C. In situ selection of lead compounds by click chemistry:
target-guided optimization of acetylcholinesterase inhibitors. J. Am. Chem. Soc. 2005,
127(18), 6686–6692.
112. Mocharla, V. P., Colasson, B., Lee, L. V., R€oper, S., Sharpless, K. B., Wong, C. H., and
Kolb, H. C. In situ click chemistry: enzyme-generated inhibitors of carbonic anhydrase II.
Angew. Chem. Int. Ed Engl. 2004, 44(1), 116–120.
113. Whiting, M., Muldoon, J., Lin, Y. C., Silverman, S. M., Lindstrom, W.,Olson, A. J., Kolb,
H. C., Finn, M. G., Sharpless, K. B., Elder, J. H., and Fokin, V. V. Inhibitors of HIV-1
protease by using in situ click chemistry. Angew. Chem. Int. Ed. Engl. 2006, 45(9),
1435–1439.
114. Hajduk, P. J., Gomtsyan, A., Didomenico, S., Cowart, M., Bayburt, E. K., Solomon,
L., Severin, J., Smith, R., Walter, K., Holzman, T. F., Stewart, A., McGaraughty, S.,
Jarvis, M. F., Kowaluk, E. A., and Fesik, S. W. Design of adenosine kinase inhibitors
from the NMR-based screening of fragments. J. Med. Chem. 2000, 43(25),
4781–4786.
470
FRAGMENT-BASED DRUG DESIGN: CONSIDERATIONS FOR GOOD ADME PROPERTIES
https://t.me/medicina_free
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