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Design of Enzyme Inhibitors

Answering Biological Questions Through Organic Synthesis

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Chemical Synthesis

Part of the book series: NATO ASI Series ((NSSE,volume 320))

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Abstract

Mechanistic insight and structural information provide the starting points for two contrasting approaches to the design of enzyme inhibitors. Phosphorus-containing peptides are inhibitors of the zinc and aspartic peptidases that mimic key geometric and electronic characteristics of the transition states of these enzymes. The design of compounds to mimic high-energy structures along the reaction path is also an effective strategy for inhibition of two enzymes of the shikimic acid pathway, EPSP synthase and chorismate mutase. For all of these inhibitors, the structural information available from crystallography has been used to interpret their binding behavior, if not for their initial design. Situations in which structural information does play a role in inhibitor design can be divided into three categories, depending on the kind of information available; examples of two of these are presented, along with some computational tools to facilitate the design process. Macrocyclic, constrained inhibitors of thermolysin were designed from the structures of the enzyme complexes of the acyclic transition state analogs, and cyclic hexapeptide mimics of the α-amylase inhibitor tendamistat were designed from the structure of this 74-residue protein. In this connection, the utility of 3-D structural databases and search tools like CAVEAT has stimulated the development of TRIAD and ILIAD, two large databases of computed, minimized structures.

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References

  1. Pauling, L. (1946) Molecular Architecture and Biological Reactions, Chem. Eng. News, 24, 1375–1377.

    Article  CAS  Google Scholar 

  2. Lienhard, G. E. (1972) Transition State Analogs as Enzyme Inhibitors, Ann. Rep. Med. Chem., 7, 249–258.

    Article  CAS  Google Scholar 

  3. Wolfenden, R. (1969) Transition State Analogues for Enzyme Catalysis, Nature, 223, 704–705.

    Article  Google Scholar 

  4. Wolfenden, R. (1976) Transition State Analog Inhibitors and Enzyme Catalysis, Annu. Rev. Biophys. Bioeng.,5, 271–306.

    Article  CAS  Google Scholar 

  5. Kaplan, A. P. and Bartlett, P. A. (1991) An Inhibitor of Carboxypeptidase A with a Kj Value in the Femtomolar Range, Biochemistry, 30, 8165–8170.

    Article  Google Scholar 

  6. Bartlett, P. A. and Marlowe, C. K. (1983) Phosphonamidates as Transition State Analog Inhibitors of Thermolysin, Biochemistry, 22, 4618–4624.

    Article  Google Scholar 

  7. Morgan, B. P., Scholtz, J. M., Ballinger, M., Zipkin, I. and Bartlett, P. A. (1991) Differential Binding Energy: A Detailed Evaluation of the Influence of Hydrogen-Bonding and Hydrophobic Groups on the Inhibition of Thermolysin by Phosphorus-Containing Inhibitors, J. Am. Chem. Soc, 113, 297–307.

    Google Scholar 

  8. Tronrud, D. E., Holden, H. M. and Matthews, B. W. (1987) Structures of Two Thermolysin Inhibitor Complexes that Differ by a Single Hydrogen Bond, Science, 235, 571–574.

    Article  Google Scholar 

  9. Matthews, B. W. (1988) Structural Basis of the Action of Thermolysin and Related Zinc Peptidases, Acct. Chem. Research, 21, 333–340.

    Google Scholar 

  10. Hanson, J. E., Kaplan, A. P. and Bartlett, P. A. (1989) Phosphonate Analogs of Carboxypeptidase A are Potent Transition State Analog Inhibitors, Biochemistry, 28, 6294–6305.

    Google Scholar 

  11. Phillips, M. A., Fletterick, R. and Rutter, W. J. (1990) Arginine 127 Stabilizes the Transition State in Carboxypeptidase, J. Biol. Chem., 265, 20692–20698.

    CAS  Google Scholar 

  12. Christianson, D. W. and Lipscomb, W. N. (1989) Carboxypeptidase A, Accts. Chem. Research, 22,62–69.

    Article  CAS  Google Scholar 

  13. Phillips, M. A., Kaplan, A. P., Rutter, W. J. and Bartlett, P. A. (1992) Transition State Characterization: A New Approach Combining Inhibitor Analogs and Variation in Enzyme Structure, Biochemistry, 31,959–962.

    Google Scholar 

  14. Christianson, D. W. and Lipscomb, W. N. (1988) Comparison of Carboxypeptidase A and Thermolysin: Inhibition by Phosphonamidates, J. Am. Chem. Soc, 110, 5560–5565.

    Article  Google Scholar 

  15. Fraser, M. E., Strynadka, N. C. J., Bartlett, P. A., Hanson, J. E. and James, M. N. G. (1992) Crystallographic Analysis of Transition State Mimics Bound to Penicillopepsin: Phosphorus-Containing Peptide Analogues, Biochemistry, 31, 5201–5214.

    Google Scholar 

  16. Sachdev, G. P. and Fruton, J. S. (1970) Secondary Enzyme-Substrate Interactions and the Specificity of Pepsin, Biochemistry, 9,4465–4470.

    Google Scholar 

  17. Fruton, J. S. (1976) The Mechanism of the Catalytic Action of Pepsin and Related Acid Proteinases, Adv. Enzymol. Relat. Areas Mol. Biol, 44, 1–36.

    Google Scholar 

  18. Haslam, E. (1993) Shikimic Acid Metabolism and Metabolites, John Wiley & Sons, New York.

    Google Scholar 

  19. Bartlett, P.A., McLaren, K.L., Alberg, D.G., Fässler, A., Nyfeler, R., Lauhon, C.T. and Grissom, C.B. (1989) Exploration of the Shikimic Acid Pathway: Opportunities for the Study of Enzyme Mechanisms Through the Synthesis of Intermediates and Inhibitors, In L.G. Copping (ed), Prospects for Amino Acid Biosynthesis Inhibitors in Crop Protection and Pharmaceutical Chemistry, Society of Chemical Industry, pp. 155–170.

    Google Scholar 

  20. Gray, J. V., Eren, D. and Knowles, J. R. (1990) Monofunctional Chorismate Mutase from Bacillus subtilis: Kinetic and 13 C NMR Studies on the Interactions of the Enzyme with Its Ligands, Biochemistry, 29, 8872–8878.

    Article  CAS  Google Scholar 

  21. Andrews, P. R., Cain, E. N., Rizzardo, E. and Smith, G. D. (1977) Rearrangement of Chorismate to Prephenate. Use of Chorismate Mutase Inhibitors to Define the Transition State Structure, Biochemistry, 16, 4848–4852.

    Article  Google Scholar 

  22. Bartlett, P. A., Nakagawa, Y., Johnson, C. R., Reich, S. and Luis, A. (1988) Chorismate Mutase Inhibitors: Synthesis and Evaluation of Some Potential Transition State Analogs, J. Org. Chem., 53, 3195–3210.

    Article  Google Scholar 

  23. Gajewski, JJ., Jurayj, J., Kimbrough, D. R., Gande, M. E., Ganem, B. and Carpenter, B.K. (1987) On the Mechanism of Rearrangement of Chorismic Acid and Related Compounds, J. Am. Chem. Soc, 109, 1170–1186.

    Google Scholar 

  24. Guilford, W. J., Copley, S. D. and Knowles, J. R. (1987) On the Mechanism of the Chorismate Mutase Reaction, J. Am. Chem. Soc, 109, 5013–5019.

    Article  Google Scholar 

  25. Jackson, D. Y., Jacobs, J. W., Sugasawara, R., Reich, S. H., Bartlett, P. A. and Schultz, P. G. (1988) An Antibody–Catalyzed Claisen Rearrangement, J. Am. Chem. Soc, 110, 4841–4842.

    Article  CAS  Google Scholar 

  26. Hilvert, D., Carpenter, S. H., Nared, K. D. and Auditor, M.-T. M. (1988) Catalysis of Concerted Reaction by Antibodies: The Claisen Rearrangement, Proc. Natl. Acad. Sci. U.S.A., 85, 4953–4955.

    Article  CAS  Google Scholar 

  27. Hilvert, D. and Nared, K. D. (1988) Stereospecific Claisen Rearrangement Catalyzed by an Antibody, J. Am. Chem. Soc, 110, 5593–5594.

    Google Scholar 

  28. Chook, Y. M., Ke, H. and Lipscomb, W. N. (1993) Crystal Structures of the Monofunctional Chorismate Mutase from Bacillus subtilis and its Complex with a Transition State Analog, Proc. Nat. Acad. Sci. USA, 90, 8600–8603.

    Article  Google Scholar 

  29. Haynes, M. R., Sutra, E. A., Hilvert, D. and Wilson, LA. (1994) Routes to Catalysis: Structure of a Catalytic Antibody and Comparison with Its Natural Counterpart, Science, 263, 646–652.

    Article  Google Scholar 

  30. Steinrücken, H. C. and Amrhein, N. (1984) 5-Enolpyruvylshikimate-3-phosphate Synthase of Klebsiella pneumoniae. 2. Inhibition by Glyphosate [N-(phosphonomethyl) glycine], Eur. J. Biochem., 143, 351–357.

    Article  Google Scholar 

  31. Bondinell, W. E., Vnek, J., Knowles, P. F., Sprecher, M. and Sprinson, D. B. (1971) On the Mechanism of 5-Enolpyruvylshikimate 3-Phosphate Synthetase, J. Biol. Chem., 246, 6191–6196.

    Google Scholar 

  32. Anderson, K. A., Sikorski, J. A., Benesi, A. J. and Johnson, K. A. (1988) Isolation and Structural Elucidation of the Tetrahedral Intermediate in the EPSP Synthase Enzymatic Pathway, J. Am. Chem. Soc, 110, 6577–6579.

    Google Scholar 

  33. Sikorski, J.A., personal communication.

    Google Scholar 

  34. Alberg, D. G. and Bartlett, P. A. (1989) Potent Inhibition of 5-Enolpyruvylshikimate-3-phosphate Synthase by a Reaction Intermediate Analog, J. Am. Chem. Soc, 111, 2337–2338.

    Article  CAS  Google Scholar 

  35. Alberg, D. G., Lauhon, C. T., Nyfeler, R., Fassler, A. and Bartlett, P. A. (1992) Inhibition of EPSP Synthase by Analogs of the Tetrahedral Intermediate and of EPSP, J. Am. Chem. Soc, 114, 3535–3546.

    Article  Google Scholar 

  36. Walker, M. C., Jones, C. J., Somerville, R. L. and Sikorski, J. A. (1992) (Z)-3-Fluorophosphoenolpyruvate as a pseudosubstrate of EPSP synthase: enzymatic synthesis of a stable fluoro analog of the catalytic intermediate, Am. Chem. Soc, 114, 7601–7603.

    Google Scholar 

  37. Seto, C.T. and Bartlett, P.A., unpublished results.

    Google Scholar 

  38. Maitra, U. and Bartlett, P.A., unpublished results.

    Google Scholar 

  39. Anderson, K. A. and Johnson, K. A. (1990) “Kinetic Competence” of the 5-Enolpyruvoyl Shikimate-3-phosphate Synthase Tetrahedral Intermediate, J. Biol. Chem., 265, 5567–5572.

    Google Scholar 

  40. Stallings, W., personal communication.

    Google Scholar 

  41. . Holden, H. M., Tronrud, D. E., Monzingo, A. F., Weaver, L. H. and Matthews, B. W. (1987) Slow- and Fast-Binding Inhibitors of Thermolysin Display Different Modes of Binding: Crystallographic Analysis of Extended Phosphonamidate Transition-State Analogues, Biochemistry, 26, 8542–8553.

    Article  Google Scholar 

  42. Bartlett, P.A., Shea, G.T., Telfer, S.J. and Waterman, S. (1989) CAVEAT: A Program to Facilitate the Structure-derived Design of Biologically Active Molecules, In S.M. Roberts (ed), Molecular Recognition: Chemical and Biological Problems, Royal Society of Chemistry, pp. 182-196.

    Google Scholar 

  43. Lauri, G. and Bartlett, P. A. (1994) CAVEAT: A Program to Facilitate the Design of Organic Molecules, J. Comp. Aided Mol. Design, 8, 51–66.

    Article  Google Scholar 

  44. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Jr., Brice, M. D., Rogers, J. R., Kennard, O., Shimanouchi, T. and Tasumi, M. (1977) The Protein Data Bank: A Computer-Based Archival File for Macromolecular Structures, J. Mol. Biol, 111, 535–542.

    Google Scholar 

  45. Morgan, B. P., Bartlett, P. A., Holland, D. R. and Matthews, B. W. (1994) Structure-Based Design of an Inhibitor of the Zinc Peptidase Thermolysin, J. Am. Chem. Soc., 116, 3251–3260.

    Article  Google Scholar 

  46. Pyun, H.-J. and Bartlett, P.A., unpublished results.

    Google Scholar 

  47. Vértesy, L., Oeding, V., Bender, R., Zepf, K. and Nesemann, G. (1984) Tendamistat (HOE 467), a tight-binding α-amylase inhibitor from Streptomyces tendae 4158, Eur. J. Biochem., 141, 505–512.

    Article  Google Scholar 

  48. Pflugrath, J. W., Wiegand, G., Huber, R. and Vertesy, L. (1986) Crystal Structure Determination, Refinement and the Molecular Model of the α-amylase Inhibitor Hoe-467A, J. Mol. Biol, 189, 383–386.

    Article  Google Scholar 

  49. Kline, A. D., Braun, W. and Wüthrich, K. (1986) Studies by 1H Nuclear Magnetic Resonance and Distance Geometry of the Solution Conformation of the α-Amylase Inhibitor Tendamistat,. J. Mol Biol, 189, 367–382.

    Google Scholar 

  50. Billeter, M., Kline, A. D., Braun, W., Huber, R. and Wüthrich, K. (1986) Comparison of the High-resolution Structures of the α-amylase Inhibitor Tendamistat Determined by Nuclear Magnetic Resonance in Solution and by X-ray Diffraction in Single Crystals, J. Mol Biol, 206, 677–687.

    Google Scholar 

  51. Huber, R., personal communication.

    Google Scholar 

  52. Laszlo, E., Hollo, J., Hoschke, A. and Sarosi, G. (1978) The active center of amylolytic enzymes. I. A study by means of lactone inhibition of the role of “halfchair” glycosyl conformation at the active center of amylolytic enzymes, Carbohydr. Res., 61, 387–394.

    Article  Google Scholar 

  53. Kessler, H., Bats, J. W., Griesinger, C, Koll, S., Will, M. and Wagner, K. (1988) Peptide Conformations. 46. Conformational Analysis of a Superpotent Cytoprotective Cyclic Somatostatin Analogue, J. Am. Chem. Soc, 110, 1033–1049.

    Article  CAS  Google Scholar 

  54. Etzkorn, F.A., Guo, T., Lipton, M.A., Goldberg, S.D. and Bartlett, P.A. (1994) Cyclic Hexapeptides and Chimeric Peptides as Mimics of Tendamistat, J. Am. Chem. Soc, submitted for publication.

    Google Scholar 

  55. Bax, A. and Subramanian, S. (1986) Sensitivity-Enhanced Two-Dimensional Heteronuclear Shift Correlation NMR Spectroscopy, J. Mag. Res., 67, 565–569.

    CAS  Google Scholar 

  56. Bax, A. (1988) Correction of Cross-Peak Intensities in 2D Spin-Locked NOE Spectroscopy for Offset and Hartmann-Hahn Effects, J. Mag. Res., 77,134–147.

    Google Scholar 

  57. Bothner-By, A. A., Stephens, R. L., Lee, J., Warren, CD. and Jeanloz, R. W. (1984) Structure Determination of a Tetrasaccharide: Transient Nuclear Overhauser Effects in the Rotating Frame, J. Am. Chem. Soc, 106, 811–813.

    Article  CAS  Google Scholar 

  58. Dorman, D. E. and Bovey, F. A. (1973) Carbon-13 Magnetic Resonance Spectroscopy. The Spectrum of Proline in Oligopeptides, J. Org. Chem., 38, 2379–2383.

    Article  CAS  Google Scholar 

  59. Kessler, H. (1982) Conformation and Biological Activity of Cyclic Peptides, Angew. Chem.t Int. Ed. Engl, 21, 512–523.

    Article  Google Scholar 

  60. Kessler, H., Griesinger, C, Lautz, J., Muller, A., van Gunsteren, W. F. and Berendsen, HJ. (1988) Conformational Dynamics Detected by Nuclear Magnetic Resonance NOE Values and J Coupling Constants, J. Am. Chem. Soc, 110, 3393–3396.

    Article  CAS  Google Scholar 

  61. Blaney, J. and Crippen, G., DGEOM (available from QCPE, University of Indiana, Dept. of Chemistry, Bloomington, IN).

    Google Scholar 

  62. Dspace, Dspace vl.O (available from Hare Research Inc., Woodinville, WA).

    Google Scholar 

  63. Lipton, M. and Still, W. C. (1988) The Multiple Minimum Problem in Molecular Modeling. Tree Searching Internal Coordinate Conformational Space, J. Comp. Chem., 9, 343–355.

    Article  CAS  Google Scholar 

  64. Mohamadi, F., Richards, N. G. J., Guida, W. C., Liskamp, R., Lipton, M., Caufield, C, Chang, G., Hendrickson, T. and Still, W. C. (1990) MacroModel—An Integrated Software System for Modeling Organic and Bioorganic Molecules Using Molecular Mechanics, J. Comp. Chem., 11, 440–467.

    Article  Google Scholar 

  65. Peishoff, C. E., Dixon, J. S. and Kopple, K. D. (1990) Application of the Distance Geometry Algorithm to Cyclic Oligopeptide Conformation Searches, Biopolymers, 30, 45–56.

    Article  Google Scholar 

  66. Blaney, J., COMPARE, unpublished results.

    Google Scholar 

  67. Lauri, G., unpublished results.

    Google Scholar 

  68. Ohlmeyer, M. H. J., Swanson, R. N., Dillard, L. W., Reader, J. C., Asouline, G., Kobayashi, R., Wigler, M. and Still, W. C. (1993) Complex Synthetic Chemical Libraries Indexed with Molecular Tags, Proc. Nat. Acad. Sci. USA, 90, 10922–10926.

    Article  Google Scholar 

  69. Borchardt, A. and Still, W. C. (1994) Synthetic Receptor Binding Elucidated With an Encoded Combinatorial Library, J. Am. Chem. Soc, 116, 373–374.

    Google Scholar 

  70. Simon, R. J., Kania, R. S., Zuckermann, R. N., Huebner, V. D., Jewell, D. A., Banville, S., Ng, S., Wang, L., Rosenberg, S., Marlowe, C. K., Spellmeyer, D. C., Tan, R., Frankel, A. D., Santi, D. V., Cohen, F. E. and Bartlett, P. A. (1992) Peptoids: A Modular Approach to Drug Discovery, Proc Nat. Acad. Sci. USA, 89, 9367–9371.

    Google Scholar 

  71. Bunin, B. A. and Ellman, J. A. (1992) A General and Expedient Method for the Solid-Phase Synthesis of 1,4-Benzodiazepine Derivatives, J. Amer. Chem. Soc, 114, 10646–10647.

    Article  Google Scholar 

  72. DeWitt, S. H., Kiely, J. S., Stankovic, C. J., Schroeder, M. C., Reynolds Cody, D. M. and Pavia, M. R. (1993) “Diversomers”: An approach to Nonpeptide, Nonoligomeric Chemical Diversity, Proc Nat. Acad. Sci. USA, 90, 6909–6913.

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Chemistry, University of California, Berkeley, California, 94720, USA

    Paul A. Bartlett

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  1. Paul A. Bartlett
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  1. I.Co.C.E.A., Consiglio Nazionale delle Ricerche, Bologna, Italy

    Chryssostomos Chatgilialoglu

  2. Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada

    Victor Snieckus

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© 1996 Kluwer Academic Publishers

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Bartlett, P.A. (1996). Design of Enzyme Inhibitors. In: Chatgilialoglu, C., Snieckus, V. (eds) Chemical Synthesis. NATO ASI Series, vol 320. Springer, Dordrecht. https://doi.org/10.1007/978-94-009-0255-8_6

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  • DOI: https://doi.org/10.1007/978-94-009-0255-8_6

  • Publisher Name: Springer, Dordrecht

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