Protein Crystallography and Drug Discovery

The Practice of Medicinal Chemistry: Second Edition

Volumn , Issue , 2003, Pages 417-443

  Rondeau, Jean Michel ^a   Schreuder, Herman ^b  

^a NOVARTIS PHARMA AG   (Switzerland)

^b SANOFI AVENTIS DEUTSCHLAND GMBH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATION; CELL DEATH; CRYSTALLOGRAPHY; ENZYMES; GENE EXPRESSION; NEURODEGENERATIVE DISEASES; SIGNAL TRANSDUCTION;

AUTOMATED DATA COLLECTION; CELL-WALL FORMATION; HUMAN GENOME PROJECT; PROTEIN CRYSTALLOGRAPHY; PROTEIN EXPRESSIONS; PROTEIN PURIFICATION; SIGNAL TRANSDUCTION PATHWAYS; THREE-DIMENSIONAL STRUCTURE;

DATA ACQUISITION;

EID: 33845809186     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-012744481-9/50030-1     Document Type: Chapter

References (150)

1. Green N.M. Stereoimages. A practical approach. Structure 1994, 2:85-87.
2. Crystallization of Nucleic Acids and Proteins: A Practical Approach 1999, Oxford University Press, New York. 2nd edn. A. Ducruix, R. Giege (Eds.).
3. McRee D.E. Practical Protein Crystallography 1999, Academic Press, Oxford. 2nd edn.
4. Shakespeare W. Macbeth 1997, Editions Aubier Montaigne, San Diego.
5. Goodwill K.E., Tennant M.G., Stevens R.C. High-throughput X-ray crystallography for structure-based drug design. Drug Discovery Today 2001, 6:S113-S118. (Suppl.).
6. Antel J. Integration of combinatorial chemistry and structure-based drug design. Curr. Opin. Drug Discovery Dev. 1999, 2:224-233.
7. Amzel L.M. Structure-based drug design. Curr. Opin. Biotechnol. 1998, 9:366-369.
8. Gane P.J., Dean P.M. Recent advances in structure-based rational drug design. Curr. Opin. Struct. Biol. 2000, 10:401-404.
9. Klebe G. Recent developments in structure-based drug design. J. Mol. Med. 2000, 78:269-281.
10. Murcko M.A., Caron P.R., Charifson P.S. Structure-based drug design. Annu. Rep. Med. Chem. 1999, 34:297-306.
11. Lunney E.A. Structure-based drug design begins a new era. Med. Chem. Res. 1998, 8:352-361.
12. DeCamp D., Ogden R., Kuntz I., Craik C.S. Site-directed drug design. Protein Eng. 1996, 467-505.
13. Gschwend D.A., Good A.C., Kuntz I.D. Molecular docking towards drug discovery. J. Mol. Recognit. 1996, 9:175-186.
14. Marrone T.J., Briggs J.M., McCammon J.A. Structure-based drug design: computational advances. Annu. Rev. Pharmacol. Toxicol. 1997, 37:71-90.
15. Bohacek R.S., McMartin C., Guida W.C. The art and practice of structure-based drug design: a molecular modeling perspective. Med. Res. Rev. 1996, 16:3-50.
16. Kim S.H. Shining a light on structural genomics. Nature Struct. Biol. 1998, 5:643-645.
17. Sali A. 100 000 Protein structures for the biologist. Nature Struct. Biol. 1998, 5:1029-1032.
18. Shapiro L., Lima C.D. The Argonne structural genomics workshop: Lamaze class for the birth of a new science. Structure 1998, 6:265-267.
19. Montelione G.T., Anderson S. Structural genomics: keystone for a human proteome project. Nature Struct. Biol. 1999, 6:11-12.
20. Ramakrishnan V., Moore P.B. Atomic structures at last: the ribosome in 2000. Curr. Opin. Struct. Biol. 2000, 11:144-154.
21. Brodersen D.E., Clemons W.M., Carter A.P., Morgan-Warren R.J., et al. The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit. Cell 2000, 103:1143-1154.
22. Pioletti M., Schlunzen F., Harms J., Zarivach R., Gluhmann M., et al. Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3. Embo J. 2001, 20:1829-1839.
23. Ban N., Nissen P., Hansen J., Moore P.B., Steitz T.A. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 2000, 289:905-920.
24. Nissen P., Hansen J., Ban N., Moore P.B., Steitz T.A. The structural basis of ribosome activity in peptide bond synthesis. Science 2000, 289:920-930.
25. Moult J., Melamud E. From fold to function. Curr. Opin. Struct. Biol. 2000, 10:384-389.
26. Hwang K.Y., Chung J.H., Kim S.-H., Han Y.S., Cho Y. Structure-based identification of a novel NTPase from Methanococcus jannaschii. Nature Struct. Biol. 1999, 6:691-696.
27. Yang F., Gustafson K.R., Boyd M.R., Wlodawer A. Crystal structure of Escherichia coli HdeA. Nature Struct. Biol. 1998, 5:763-764.
28. Lolis, E. and Petsko, G.A. Transition-state analogues in protein crystallography: probes of the structural source of enzyme catalysis. Ann. Rev. Biochem.59: 597-630.
29. Verschueren K.H.G., Seljée F., Rozeboom H.J., Kalk K.H., Dijkstra B.W. Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase. Nature 1993, 363:693-698.
30. Strynadka N.C.J., Adachi H., Jensen S.E., Johns K., Sielecki A., et al. Molecular structure of the acyl-enzyme intermediate in β-lactam hydrolysis at 1.7 resolution. Nature 1992, 359:700-705.
31. Davies T.G., Tunnah P., Meijer L., Marko D., Eisenbrand G., et al. Inhibitor binding to active and inactive CDK2. The crystal structure of CDK2-cyclin A/indirubin-5-sulphonate. Structure 2001, 9:389-397.
32. Schindler T., Bornmann W., Pellicena P., Miller W.T., et al. Structural mechanism for STI-571 inhibition of Abelson tyrosine kinase. Science 2000, 289:1938-1942.
33. Boyd D.B. Compendium of software for molecular modeling. Rev. Comput. Chem. 1995, 6:383-437.
34. Martin Y.C. Accomplishments and challenges in integrating software for computer-aided ligand design in drug discovery. Perspect. Drug Discovery Des. 1995, 3:139-150.
35. Walsh C.T. Suicide substrates, mechanism-based enzyme inactivators: recent developments. Ann. Rev. Biochem. 1984, 53:493-535.
36. Radzicka A., Wolfenden R. Transition state and multisubstrate analog inhibitors. Methods Enzymol. 1995, 249:284-312.
37. Schramm V.L. Enzymic transition states and transition state analog design. Annu. Rev. Biochem. 1998, 67:693-720.
38. Kirkpatrick D.L., Watson S., Ulhaq S. Structure-based drug design: combinatorial chemistry and molecular modeling. Comb. Chem. High Throughput Screening 1999, 2:211-221.
39. Ghose A.K., Viswanadhan V.N., Wendoloski J.J. Adapting structure-based drug design in the paradigm of combinatorial chemistry and high-throughput screening: an overview and new examples with important caveats for newcomers to combinatorial library design using pharmacophore models or multiple copy simultaneous search fragments. ACS Symp. Ser. 1999, 719:226-238.
40. Illig C., Eisennagel S., Bone R., Radzicka A., Murphy L., et al. Expanding the envelope of structure-based drug design using chemical libraries: application to small-molecule inhibitors of thrombin. Med. Chem. Res. 1998, 8:244-260.
41. Aronov A.M., Munagala N.R., Ortiz de Montellano P.R., Kuntz I.D., Wang C.C. Rational design of selective submicromolar inhibitors of tritrichomonas foetus hypoxanthine-guanine-xanthine phosphoribosyltransferase. Biochemistry 2000, 39:4684-4691.
42. Bressi J.C., Verlinde C.L.M.J., Aronov A.M., Shaw M.L., Shin S.S., et al. Adenosine analogues as selective inhibitors of glyceraldehyde-3-phosphate dehydrogenase of tryanosomatidae via structure-based drug design. J. Med. Chem. 2001, 44:2080-2093.
43. Smith T.J., Kremer M.J., Luo M., Vriend G., Arnold E., et al. The site of attachment in human rhinovirus 14 for antiviral agents that inhibit uncoating. Science 1986, 233:1286-1293.
44. Kallen J., Welzenbach K., Ramage P., Geyl D., Kriwacki R., et al. Structural basis for LFA-1 inhibition upon lovastatin binding to the CD11a I-domain. J. Mol. Biol. 1999, 292:1-9.
45. Weber C., Wider G., von Freyberg B., Traber R., Braun W., et al. The NMR structure of cyclosporin A bound to cyclophilin in aqueous solution. Biochemistry 1991, 30:6563-6574.
46. Fesik S.W., Gampe R.T., Eaton H.L., Gemmecker G., Olejniczak E.T., et al. NMR studies of [U-13C]cyclosporin A bound to cyclophilin: bound conformation and portions of cyclosporin involved in binding. Biochemistry 1991, 30:6574-6583.
47. Pflügl G., Kallen J., Schirmer T., Jansonius J.N., et al. X-ray structure of a decameric cyclophilin-cyclosporin crystal complex. Nature 1993, 361:91-94.
48. Van Duyne G.D., Standaert R.F., Karplus P.A., Schreiber S.L., Clardy J. Atomic structure of FKBP-FK506, an immunophilin-immunosuppressant complex. Science 1991, 252:839-842.
49. Badger J., Minor I., Kremer M.J., Oliveira M.A., Smith T.J., et al. Structural analysis of a series of antiviral agents complexed with human rhinovirus 14. Proc. Natl. Acad. Sci. USA 1988, 85:3304-3308.
50. Rich D.H., Sun C.Q., Vara Prasad J.V.N., Pathiasseril A., Toth M.V., et al. Effect of hydroxyl group configuration in hydroxyethylamine dipeptide isosteres on HIV protease inhibition. Evidence for multiple binding modes. J. Med. Chem. 1991, 34:1222-1225.
51. Krohn A., Redshaw S., Ritchie J.C., Graves B.J., Hatada M.H. Novel binding mode of highly potent HIV-proteinase inhibitors uncorporating the (R)-hydroxyethylamine isostere. J. Med. Chem. 1991, 34:3340-3342.
52. Banner D.W., Hadváry P. Crystallographic analysis at 3.0 resolution of the binding to human thrombin of four active site-directed inhibitors. J. Biol. Chem. 1991, 266:20085-20093.
53. Stubbs M.T., Bode W. Crystal structures of thrombin and thrombin complexes as a framework for antithrombotic drug design. Perspect. Drug Dis. Design 1993, 1:431-452.
54. Chirgadze N.Y., Sall D.J., Briggs S.L., Clawson D.K., Zhang M., et al. The crystal structures of human α-thrombin complexed with active site-directed diamino benzo[b]thiophene derivatives: a binding mode for a structurally novel class of inhibitors. Protein Sci. 2000, 9:29-36.
55. Brandstetter H., Engh R.A., Von Roedern E.G., Moroder L., Huber R., et al. Structure of malonic acid-based inhibitors bound to human neutrophil collagenase. A new binding mode explains apparently anomalous data. Protein Sci. 1998, 7:1303-1309.
56. Bartolucci C., Perola E., Pilger C., Fels G., Lamba D. Three-dimensional structure of a complex of galanthamine (nivalin) with acetylcholinesterase from Torpedo californica: implications for the design of new anti-Alzheimer drugs. Proteins. Struct. Funct. Genet. 2001, 42:182-191.
57. Chand P., Babu Y.S., Bantia S., Chu N., Cole L.B., et al. Design and synthesis of benzoic acid derivatives as influenza neuraminidase inhibitors using structure-based drug design. J. Med. Chem. 1997, 40:4030-4052.
58. Schulze-Gahmen U., Brandsen J., Jones H.D., Morgan D.O., Meijer L., et al. Multiple modes of ligand recognition: crystal structures of cyclin-dependent protein kinase 2 in complex with ATP and two inhibitors, olomoucine and isopentenyladenine. Proteins 1995, 22:378-391.
59. Powers J.C., Oleksyszyn J., Narasimhan S.L., Kam C.M., Radhakrishnan R., et al. Reaction of porcine pancreatic elastase with 7-substituted 3-alkoxy-4-chloroisocoumarins: design of potent inhibitors using the crystal structure of the complex formed with 4-chloro-3-ethoxy-7-guanidinoisocoumarin. Biochemistry 1990, 29:3108-3118.
60. Singh J., Dobrusin E.M., Fry D.W., Haske T., Whitty A., McNamara D.J. Structure-based design of a potent, selective, and irreversible inhibitor of the catalytic domain of the erbB receptor subfamily of protein tyrosine kinases. J. Med. Chem. 1997, 40:1130-1135.
61. Maignan S., Mikol V. The use of 3D structural data in the design of specific Factor Xa inhibitors. Curr. Top. Med. Chem. 2001, 1:161-174.
62. Aronov A.M., Suresh S., Buckner F.S., Van Voorhis W.C., Verlinde C.L.M.J., et al. Structure-based design of submicromolar, biologically active inhibitors of trypanosomatid glyceraldehyde-3-phosphate dehydrogenase. Proc. Natl Acad. Sci. USA 1999, 96:4273-4278.
63. Aronov A.M., Verlinde C.L.M.J., Hol W.G.J., Gelb M.H. Selective tight binding inhibitors of trypanosomal glyceraldehyde-3-phosphate dehydrogenase via structure-based drug design. J. Med. Chem. 1998, 41:4790-4799.
64. Nienaber V.L., Davidson D., Edalji R., Giranda V.L., Klinghofer V., et al. Structure-directed discovery of potent non-peptidic inhibitors of human urokinase that access a novel binding subsite. Structure 2000, 8:553-563.
65. Mao C., Sudbeck E.A., Venkatachalam T.K., Uckun F.M. Structure-based drug design of non-nucleoside inhibitors for wild-type and drug-resistant HIV reverse transcriptase. Biochem. Pharmacol. 2000, 60:1251-1265.
66. Rahuel J., Rasetti V., Maibaum J., Rueger H., Goschke R., et al. Structure-based drug design: the discovery of novel nonpeptide orally active inhibitors of human renin. Chem. Biol. 2000, 7:493-504.
67. Mihelich E.D., Schevitz R.W. Structure-based design of a new class of anti-inflammatory drugs: secretory phospholipase A2 inhibitors, SPI. Biochim. Biophys. Acta 1999, 1441:223-228.
68. Wlodawer A., Vondrasek J. Inhibitors of HIV-1 protease: a major success of structure-assisted drug design. Annu. Rev. Biophys. Biomol. Struct. 1998, 27:249-284.
69. Wade R.C. 'Flu' and structure-based drug design. Structure 1997, 5:1139-1145.
70. Montgomery J.A., Niwas S., Rose J.D., Secrist J.A., Babu Y.S., et al. Structure-based design of inhibitors of purine nucleoside phosphorylase. Part 1. 9-(Arylmethyl) derivatives of 9-deazaguanine. J. Med. Chem. 1993, 36:55-69.
71. Secrist J.A., Niwas S., Rose J.D., Babu Y.S., Bugg C.E., et al. Structure-based design of inhibitors of purine nucleoside phosphorylase. Part 2. 9-Alicyclic and 9-heteroalicyclic derivatives of 9-deazaguanine. J. Med. Chem. 1993, 36:1847-1854.
72. Erion M.D., Niwas S., Rose J.D., Ananthan S., Allen M., et al. Structure-based design of inhibitors of purine nucleoside phosphorylase. Part 3. 9-Arylmethyl derivatives of 9-deazaguanine substitued on the methylene group. J. Med. Chem. 1993, 36:3771-3783.
73. Guida W.C., Elliott R.D., Thomas H.J., Secrist J.A., Babu Y.S., et al. Structure-based design of inhibitors of purine nucleoside phosphorylase. Part 4. A study of phosphate mimics. J. Med. Chem. 1994, 37:1109-1114.
74. Baldwin J.J., Ponticello G.S., Anderson P.S., Christy M.E., Murcko M.A., et al. Thienothiopyran-2-sulfonamides: novel topically active carbonic anhydrase inhibitors for the treatment of glaucoma. J. Med. Chem. 1989, 32:2510-2513.
75. Appelt K. Crystal structures of HIV-1 protease-inhibitor complexes. Perspect. Drug Dis. Design 1993, 1:23-48.
76. Vacca J.P., Fitzgerald P.M.D., Holloway M.K., Hungate R.W., Starbuck K.E., Chen L.J., Darke P.L., Anderson P.S., Huff J.R. Conformationally constrained HIV-1 protease inhibitors. Bioorg. Med. Chem. Lett. 1994, 4:499-504.
77. Lam P.Y.S., Jadhav P.K., Eyermann C.J., Hodge C.N., Ru Y., et al. Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors. Science 1994, 263:380-384.
78. Morgan B.P., Holland D.R., Matthews B.W., Bartlett P.A. Structure-based design of an inhibitor of the zinc peptidase thermolysin. J. Am. Chem. Soc. 1994, 116:3251-3260.
79. 4 tripeptide portion of the angiotensinogen template. J. Med. Chem. 1991, 34:1276-1282.
80. Weber, A. E., Halgren, T. A., Doyle, J. J., Lynch, R. J., Siegl, P. K. S., et al. Design and synthesis of P2-P1'-linked macrocyclic human renin inhibitors. J. Med. Chem. 34: 2692-2701.
81. Alberg D.G., Schreiber S.L. Structure-based design of a cyclophilin-calcineurin bridging ligand. Science 1993, 262:248-250.
82. Furet P., Garcia-Echeverria C., Gay B., Schoepfer J., et al. Structure-based design, synthesis, and X-ray crystallography of a high-affinity antagonist of the Grb2-SH2 domain containing an asparagine mimetic. J. Med. Chem. 1999, 42:2358-2363.
83. Toledo L.M., Lydon N.B., Elbaum D. The structure-based design of ATP-site directed protein kinase inhibitors. Curr. Med. Chem. 1999, 6:775-805.
84. Borkakoti N. Matrix metalloproteases: variations on a theme. Prog. Biophys. Mol. Biol. 1998, 70:73-94.
85. Somoza J.R., Skillman A.G., Munagala N.R., Oshiro C.M., Knegtel R.M.A., et al. Rational design of novel antimicrobials: blocking purine salvage in a parasitic protozoan. Biochemistry 1998, 37:5344-5348.
86. Gschwend D.A., Sirawaraporn W., Santi D.V., Kuntz I.D. Specificity in structure-based drug design: identification of a novel, selective inhibitor of Pneumocystis carinii dihydrofolate reductase. Proteins Struct. Funct. Genet. 1997, 29:59-67.
87. Schevitz R.W., Bach N.J., Carlson D.G., Chirgadze N.Y., Clawson D.K., et al. Structure-based design of the first potent and selective inhibitor of human non-pancreatic secretory phospholipase A2. Nat. Struct. Biol. 1995, 2:458-465.
88. Kim E.E., Baker C.T., Dwyer M.D., Mucko M.A., Rao B.G., et al. Crystal structure of HIV-1 protease in complex with VX-478, a potent and orally bioavailable inhibitor of the enzyme. J. Am. Chem. Soc. 1995, 117:1181-1182.
89. MacPherson L.J., Bayburt E.K., Capparelli M.P., Bohacek R.S., Clarke F.H., et al. Design and synthesis of an orally active macrocyclic neutral endopeptidase 24.11 inhibitor. J. Med. Chem. 1993, 36:3821-3828.
90. Brown F.J., Andisik D.W., Bernstein P.R., Bryant C.B., Ceccarelli C., et al. Design of orally active, non-peptidic inhibitors of human leukocyte elastase. J. Med. Chem. 1994, 37:1259-1261.
91. Varney M.D., Marzoni G.P., Palmer C.L., Deal J.G., Webber S., et al. Crystal-structure-based design and synthesis of benz[cd]indole-containing inhibitors of thymidylate synthase. J. Med. Chem. 1992, 35:663-676.
92. Reich S.H., Fuhry M.A.M., Nguyen D., Pino M.J., Welsh K.M., et al. Design and synthesis of novel 6,7-imidazotetrahydroquinoline inhibitors of thymidylate synthase using iterative protein crystal structure analysis. J. Med. Chem. 1992, 35:847-858.
93. Reich S.H., Webber S.E. Structure-based drug design (SBDD): every structure tells a story. Perspect. Drug Dis. Design 1993, 1:371-390.
94. Erickson J.W. Design and structure of symmetry-based inhibitors of HIV-1 protease. Perspect. Drug Dis. Design 1993, 1:109-128.
95. Sintchak M.D., Nimmesgern E. The structure of inosine 5'-monophosphate dehydrogenase and the design of novel inhibitors. Immunopharmacology 2000, 47:163-184.
96. Fretz H., Furet P., Garcia-Echeverria C., Rahuel J., Schoepfer J. Structure-based design of compounds inhibiting Grb2-SH2 mediated protein-protein interactions in signal transduction pathways. Curr. Pharm. Des. 2000, 6:1777-1796.
97. Gubernator, K., Heinze-Krauss, I., angehrn, P., Charnas, R.L., Hubschwerlen, C., et al. Structure-based design of potent β-lactamase inhibitors. Methods Princ. Med. Chem.6: 89-103.
98. Joseph-McCarthy D. Computational approaches to structure-based ligand design. Pharmacol. Ther. 1999, 84:179-191.
99. Nienaber V.L., Richardson P.L., Klighofer V., Bouska J.J., et al. Discovering novel ligands for macromolecules using X-ray crystallographic screening. Nat. Biotechnol. 2000, 18:1105-1108.
100. Ducruix A., Giege R. Crystallization of Nucleic Acids and Proteins: A Practical Approach 1999, Oxford University Press, Paris. 2nd edn.
101. McPherson A. Crystallization of Biological Macromolecules 1999, Cold Spring Harbor Laboratory Press, Oxford.
102. McRee D.E. Practical Protein Crystallography 1999, Academic Press, Cold Spring Harbor, NY. 2nd edn.
103. Drenth J. Principles of Protein X-ray Crystallography 1999, Springer Verlag, San Diego. 2nd edn.
104. Viterbo D. Solution and refinement of crystal structures. Fundamentals of Crystallography 1992, 319-401. Oxford University Press, New York. C. Giacovazzo (Ed.).
105. Dauter Z., Dauter M. Entering a new phase: using solvent halide ions in protein structure determination. Structure 2001, 9:R21-R26.
106. Bricogne G. Direct phase determination by entropy maximization and likelihood ranking: status report and perspectives. Acta Crystallogr. Sect. D 1993, D49:37-60.
107. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., et al. The protein data bank. Nucleic Acids Res. 2000, 28:235-242.
108. Brünger A.T. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 1992, 355:472-475.
109. Jia Z., Vandonselaar M., Quail J.W., Delbaere L.T.J. Active-centre torsion-angle strain revealed in 1.6 -resolution structure of histidine-containing phosphocarrier protein. Nature 1993, 361:94-97.
110. Chevrier B., Schalk C., D'Orchymont H., Rondeau J.-M., et al. Crystal structure of Aeromonas proteolytica aminopeptidase: a prototypical member of the co-catalytic zinc enzyme family. Structure 1994, 2:283-291.
111. Perutz M. Protein Structure. New Approaches to Disease and Therapy 1992, W. H. Freeman and Company, Oxford.
112. Brange J., Ribel U., Hansen J.F., Dodson G., Hansen M.T., et al. Monomeric insulins obtained by protein engineering and their medical implications. Nature 1988, 333:679-682.
113. Ring C.S., Sun E., McKerrow J.H., Lee G.K., Rosenthal P.J., et al. Structure-based inhibitor design by using protein models for the development of antiparasitic agents. Proc. Natl. Acad. Sci. USA 1993, 90:3583-3587.
114. Cushman D.W., Cheung H.S., Sabo E.F., Ondetti M.A. Design of potent competitive inhibitors of angiotensin-converting enzyme. Carboxyalkanoyl and mercaptalkanoyl amino acids. Biochemistry 1977, 16:5484-5491.
115. Hassall C.H., Kröhn A., Moody C.H., Thomas W.A. The design of a new group of angiotensin-converting enzyme inhibitors. FEBS Lett. 1982, 147:175-179.
116. Attwood M.R., Hassall C.H., Kröhn A., Lawton G., Redshaw S. The design and synthesis of the angiotensin-converting enzyme inhibitor cilazapril and related bicyclic compounds. J. Chem. Soc. Perkins Trans. 1986, 1:1011-1019.
117. Blundell T.L., Cooper J., Foundling S.I., Jones D.M., et al. On the rational design of renin inhibitors: X-ray studies of aspartic proteinases complexed with transition-state analogues. Biochemistry 1987, 26:5585-5590.
118. Greenlee W.J. Renin inhibitors. Med. Res. Rev. 1990, 10:173-236.
119. Lunney E.A., Hamilton H.W., Hodges J.C., Kaltenbronn J.S., Repine J.T., et al. Analyses of ligand binding in five endothiapepsin crystal complexes and their use in the design and evaluation of novel renin inhibitors. J. Med. Chem. 1993, 36:3809-3820.
120. Iizuka K., Kamijo T., Harada H., Akahane K., Kubota T., et al. Orally potent human renin inhibitors derived from angiotensinogen transition state: design, synthesis, and mode of interaction. J. Med. Chem. 1990, 33:2707-2714.
121. Takahashi L.H., Radhakrishnan R., Rosenfield R.E., Meyer E.F., et al. X-ray diffraction analysis of the inhibition of porcine oancreatic elastase by a peptidyl trifluoromethylketone. J. Mol. Biol. 1988, 201:423-428.
122. Luo M., Jedrzejas M.J., Singh S., White C.L., Brouillette W.J., et al. Benzoic acid inhibitors of influenza virus neuraminidase. Acta Crystallogr. Sect. D 1995, D51:504-510.
123. Bethell R.C., Smith P.W. Sialidase as a target for inhibitors of influenza virus replication. Expert Opin. Invest. Drugs 1997, 6:1501-1509.
124. Luo M., Air G.M., Brouillette W.J. Design of aromatic inhibitors of influenza virus neuraminidase. J. Infect. Dis. 1997, 176(Suppl. 1):S62-S65.
125. Babu Y.S., Chand P., Bantia S., Kotian P., Dehghani A., et al. Bcx-1812 (rwj-270201): discovery of a novel, highly potent, orally active, and selective influenza neuraminidase inhibitor through structure-based drug design. J. Med. Chem. 2000, 43:3482-3486.
126. Watenpaugh K.D. Structure-based drug design and informatics: the development of potent HIV protease inhibitors as clinical drug candidates. Folding Des. 1996, 1(Suppl. 1):S67.
127. Aristoff P.A. Dihydropyrone sulfonamides as a promising new class of HIV protease inhibitors. Drugs Future 1988, 23:995-999.
128. Thaisrivongs S., Strohbach J.W. Structure-based discovery of Tipranavir Disodium (PNU-140690E): a potent, orally bioavailable, nonpeptidic HIV protease inhibitor. Biopolymers 1999, 51:51-58.
129. Rastelli G., Vianello P., Barlocco D., Costantino L., et al. Structure-based design of an inhibitor modeled at the substrate active site of aldose reductase. Bioorg. Med. Chem. Lett. 1997, 7:1897-1902.
130. Iwata Y., Arisawa M., Hamada R., Kita Y., Mizutani M.Y., et al. Discovery of novel aldose reductase inhibitors using a protein structure-based approach: 3D-database search followed by design and Synthesis. J. Med. Chem. 2001, 44:1718-1728.
131. Du X., Hansell E., Engel J.C., Caffrey C.R., et al. Aryl ureas represent a new class of anti-trypanosomal agents. Chem. Biol. 2000, 7:733-742.
132. Matthews D.A., Dragovich P.S., Webber S.E., Fuhrman S.A., Patick A.K., et al. Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes. Proc. Natl Acad. Sci. USA 1999, 96:11000-11007.
133. Frecer V., Maliar T., Miertus S. Protease inhibitors as anticancer drugs: role of molecular modelling and combinatorial chemistry in drug design. Int. J. Med. Biol. Environ. 2000, 28:161-173.
134. Morris P.E., Omura G.A. Inhibitors of the enzyme purine nucleoside phosphorylase as potential therapy for psoriasis. Curr. Pharm. Des. 2000, 6:943-959.
135. Matthews D.A., Appelt K., Oatley S.J., Xuong Ng.H. Crystal structure of Escherichia coli thymidylate synthase containing bound 5-fluoro-2'-deoxyuridylate and 10-propargyl-5,8-dideazafolate. J. Mol. Biol. 1990, 214:923-936.
136. Appelt K., Bacquet R.J., Bartlett C.A., et al. Design of enzyme inhibitors using iterative protein crystallographic analysis. J. Med. Chem. 1991, 34:1925-1934.
137. Wlodawer A., Miller M., Jaskolski M., Sathyanarayana B.K., Baldwin E., et al. Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease. Science 1989, 245:616-621.
138. Lapatto R., Blundell T., Hemmings A., Overington J., Wilderspin A., et al. X-ray analysis of HIV-1 proteinase at 2.7 resolution confirms structural homology among retroviral enzymes. Nature 1989, 342:299-302.
139. Wlodawer A., Erickson J.W. Structure-based inhibitors of HIV-1 protease. Annu. Rev. Biochem. 1993, 62:543-585.
140. Clare M. HIV protease: structure-based design. Perspect. Drug Dis. Des. 1993, 1:49-68.
141. Kalish V.J., Tatlock J.H., Davies J.F., Kaldor S.W., Dressman B.A., et al. Structure-based drug design of nonpeptidic P2 substituents for HIV-1 protease inhibitors. Bioorg. Med. Chem. Lett. 1995, 5:727-732.
142. Romero D.L., Tommasi R.A., Janakiraman M.N., Strohbach J.W., Turner S.R., et al. Structure-based design of HIV protease inhibitors: 5,6-dihydro-4-hydroxy-2-pyrones as effective, nonpeptidic inhibitors. J. Med. Chem. 1996, 39:4630-4642.
143. Skulnick H.I., Turner S.R., Strohbach J.W., Tommasi R.A., Johnson P.D., et al. Structure-based design of HIV protease inhibitors: sulfonamide-containing 5,6-dihydro-4-hydroxy-2-pyrones as non-peptidic inhibitors. J. Med. Chem. 1996, 39:4349-4353.
144. Skulnick H.I., Johnson P.D., Aristoff P.A., Morris J.K., Lovasz K.D., et al. Structure-based design of nonpeptidic HIV protease inhibitors: the sulfonamide-substituted cyclooctylpyranones. J. Med. Chem. 1997, 40:1149-1164.
145. Babine R.E., Zhang N., Jurgens A.R., Schow S.R., Desai P.R., et al. The use of HIV-1 protease structure in inhibitor design. Bioorg. Med. Chem. Lett. 1992, 2:541-546.
146. Kempf D.J., Codacovi L., Wang X.C., Kohlbrenner W.E., Wideburg N.E., et al. Symmetry-based inhibitors of HIV protease structure-activity studies of acylated 2,4-diamino-1,5-diphenyl-3-hydroxypentane and 2,5-diamino-1,6-diphenylhexane-3,4-diol. J. Med. Chem. 1993, 36:320-330.
147. Swain A.L., Miller M.M., Green J., Rich D.H., Schneider J., et al. X-ray crystallographic structure of a complex between a synthetic protease of human immunodeficiency virus 1 and a substrate-based hydroxyethylamine inhibitor. Proc. Natl Acad. Sci. USA 1990, 87:8805-8809.
148. Nienaber V., Wang J., Davidson D., Henkin J. Reengineering of human urokinase provides a system for structure-based drug design at high resolution and reveals a novel structural subsite. J. Biol. Chem. 2000, 275:7239-7248.
149. Knight S., Andersson I., Brändén C.-I. Reexamination of the three-dimensional structure of the small subunit of RuBisCO from higher plants. Science 1989, 244:702-705.
150. Curmi P.M.G., Cascio D., Sweet R.M., Eisenberg D., Schreuder H. Crystal structure of the unactivated form of ribulose-1,5-bisphosphate carboxylase/oxygenase from tobacco refined at 2.0 resolution. J. Biol. Chem. 1992, 267:16980-16989.