Fluorinated Moieties for Replacement of Amide and Peptide Bonds

Fluorine in Medicinal Chemistry and Chemical Biology

Volumn , Issue , 2009, Pages 257-290

  Taguchi, Takeo ^a   Yanai, Hikaru ^a  

^a TOKYO UNIVERSITY OF PHARMACY AND LIFE SCIENCES   (Japan)

Author keywords

Applications to biologically active peptides and related studies; Conformational analysis and biological aspects; Dipeptidyl peptidase inhibitors; Fluorinated moieties for amide and peptide bond replacement; Fluoro olefins most studied fluorinated peptide mimetics; Fluoroarenes as nucleoside base mimics; Peptide bond mimics; Replacement of amide bonds by (Z) fluoro olefins; Rotameric forms of PNA and structures of alkenic isosteres

Indexed keywords

EID: 84889270642     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9781444312096.ch10     Document Type: Chapter

References (67)

1. Gante, J. (1994) Peptidemimetics-tailored enzyme inhibitors. Angew. Chem. Int. Ed., 33, 1699-1720.
2. Kazmierski, W. M. (1999) Peptidomimetics Protocol, Humana Press. Totawa, NJ.
3. Hann, M. M., Sammes, P. G., Kennewell, P. D. and Taylor, J. B. (1982) On the double bond isostere of the peptide bond: preparation of an enkephalin analogue. J. Chem. Soc. Perkin Trans. I, 307-314.
4. Abraham, R. J., Ellison, S. L. R., Schonholzer, P. and Thomas, W. A. (1986) A theoretical and crystallographic study of the geometries and conformations of fluoro-olefin as peptide analogues. Tetrahedron, 42, 2101-2110.
5. Cieplack, P., Kollmann, P. A. and Radomski, J. P. (1996) Molecular design of fluorine-containing peptide mimetics. in Biomedicinal Frontiers of Fluorine Chemistry, ACS Symposium Series 639, American Chemical Society, Washington, D.C., pp. 143-156.
6. Welch, J. T., Lin, J., Boros, L. G., et al. (1996) Fluoo-olefin isosteres as peptidemimetics in Biomedicinal Frontiers of Fluorine Chemistry, ACS Symposium Series 639,. American Chemical Society, Washington, D.C., pp. 129-142.
7. Wipf, P., Henninger, T. C. and Geib, S. J. (1998) Methyl- and (trifluoromethyl)alkene peptide isosteres: synthesis and evaluation of their potential as ß-turn promoters and peptide mimetics. J. Org. Chem., 63, 6088-6089.
8. Allmendinger, T., Felder, E. and Hungerbuehler, E. (1991) Fluoroolefin dipeptide isosteres, in Selective Fluorination in Organic and Bioorganic Chemistry, ACS Symposium Series 456, American Chemical Society, Washington, D.C., pp. 186-195.
9. Burton, D. J., Yang, Z.-Y. and Qiu, W. (1996) Fluorinated ylides and related compounds. Chem. Rev., 96, 1641-1715.
10. Grison, Ph. C. C. and Sauvetre, R. (1987) 2-Diethoxyphosphoryl alkanoic acid dianions IV. A direct route to 2-fluoro-2-alkenoic acids by the Horner synthesis. Application in the field of pyrethroids. J. Organomet. Chem., 332, 1-8.
11. Sano, S., Saito, K. and Nagao, Y. (2003) Tandem reduction-olefination for the stereoselective synthesis of (Z)-a-fluoro-a,ß-unsaturated esters. Tetrahedron Lett., 44, 3987-3990.
12. Barrma, D. K., Kundeu, A., Zhang, H., et al. (2003) (Z)-a-Haloacrylates: an exceptionally stereoselective preparation via Cr(II)-mediated olefination of aldehydes with trihaloacetate. J. Am. Chem. Soc., 125, 3218-3219.
13. Allmendinger, T., Furet, P. and Hungerbruhler, E. (1990) Fluoroolefin dipeptide isosteres I. The synthesis of GlyΨ[CF=CH]Gly and racemic PheΨ[CF=CH]Gly. Tetrahedron Lett., 31, 7297-7300.
14. Van der Veken, P., Kertesz, I., Senten, K., et al. (2003) Synthesis of (E)- and (Z)-fluoro-olefin analogues of potent dipeptidyl peptidase IV inhibitors. Tetrahedron Lett., 44, 6231-6234.
15. Boros, L. G., De Corte, B., Gimi, R. H., et al. (1994) Fluoroolefin peptide isosteres-tools for controlling peptide conformations. Tetrahedron Lett., 35, 6033-6036.
16. Allmendinger, T., Felder, E. and Hungerbruhler, E. (1990) Fluoroolefin dipeptide isosteres II. Enantioselective synthesis of both antipodes of the Phe-Gly dipeptide mimic. Tetrahedron Lett., 31, 7301-7304.
17. Dolbier, Jr., W. R., Medinger, K. S., Greenberg, A. and Liebman, J. F. (1982) The thermodynamic effect of fluorine as a substituent. Tetrahedron, 38, 2415-2420.
18. Watanabe, D., Koura, M., Saito, A., et al. (2005) A highly stereoselective synthesis of fluoroolefin dipeptide isostere. 125th Annual Meeting of the Pharmaceutical Society of Japan, Tokyo, Japan. Pharmaceutical Society of Japan, Abstract 31-0205.
19. Bartlett, P. A. and Otake, A. (1995) Fluoroalkenes as peptide isosteres: ground state inhibitors of thermolysin. J. Org. Chem., 60, 3107-3111.
20. Lamy, C., Hofmann, J., Parrot-Lopez, H. and Goekjian, P. (2007) Synthesis of a fluoroalkene peptidemimetic precursor of VV-acetyl-L-glutamyl-L-alanine. Tetrahedron Lett., 48, 6177-6180.
21. Allmendinger, T. (1991) Ethyl phenylsulfinyl fluoroacetate, a new and versatile reagent for the preparation of a-fluoro-a,ß-unsaturated carboxylic acid esters. Tetrahedron, 47, 4905-1914.
22. Okada, M., Nakamura, Y., Saito, A., et al. (2002) Synthesis of a-alkylated (Z)-y-fluoro-ß,y-enoates through organocopper mediated reaction of y,y-difluoro-a,ß-enoates: a different reactivity of R3Al-Cu(I) and Me2CuLi. Chem. Lett., 28-29.
23. Nakamura, Y., Okada, M., Koura, M., et al. (2006) An efficient synthetic method for Z-fluoro-alkene dipeptide isosteres: application to the synthesis of the dipeptide isostere of Sta- Ala. J. Fluorine Chem., 127, 627-636.
24. Otaka, A., Watanabe, H., Yukimasa, A., et al. (2001) New access to a-substituted (Z)-fluoro-alkene dipeptide isosteres utilizing organocopper reagents under "reduction-oxidative alkylation (R-OA)" conditions. Tetrahedron Lett., 42, 5443-5446.
25. Narumi, T., Niida, A., Tomita, K., et al. (2006) A novel one-pot reaction involving organocop-per-mediated reduction/transmetalation/asymmetric alkylation, leading to the diastereoselective synthesis of functionalized (Z)-fluoroalkene dipeptide isosteres. Chem. Commun., 4720-4722.
26. Narumi, T., Tomita, K., Inokuchi, E., et al. (2007) Facile synthesis of fluoroalkenes by palladium-catalyzed reductive defluorination of allylic gem-difluorides. Org. Lett., 9, 3465-3468.
27. Babine, R. E. and Bender, S. L. (1997) Molecular recognition of protein-ligand complexes: applications to drug design. Chem. Rev., 97, 1359-1472.
28. Lide, D. R. (1997) CRC Handbook of Chemistry and Physics, 78th edn, CRC Press, New York.
29. Okada, M., Nakamura, Y., Saito, A., et al. (2002) Stereoselective construction of functionalized (Z)-fluoroalkenes directed to depsipeptide isosteres. Tetrahedron Lett., 43, 5845-5848.
30. Nakamura, Y., Okada, M., Sato, A., et al. (2005) Stereoselective synthesis of (Z)-fluoroalkenes directed to peptide isosteres: Cu(I) mediated reaction of trialkylaluminum with 4,4-difluoro-5-hydroxyallylic alcohol derivatives. Tetrahedron, 43, 5741-5743.
31. Xu, J. and Burton, D. J. (2002) Kinetic separation methodology for the stereoselective synthesis of (E)- and (Z)-a-fluoro-a,ß-unsaturated esters via the palladium-catalyzed carboalkoxylation of 1-bromo-1-fluoroalkenes. Org. Lett., 4, 831-833.
32. Dutheuil, G., Paturel, C, Lei, X., et al. (2006) First stereospecific synthesis of (E)- or (Z)-a-fluoroenones via a kinetically controlled Negishi coupling reaction. J. Org. Chem., 71, 4316-4319.
33. Dutheuil, G., Couve-Bonnaire, S. and Pannecoucke, X. (2007) Diastereomeric fluoroolefins as peptide bond mimics prepared by asymmetric reductive amination of a-fluoroenones. Angew. Chem. Int. Ed., 46, 1290-1292.
34. Augustyns, K., Bal, G., Thonus, G., et al. (1999) The unique properties of dipeptidyl-peptidase IV (DPP IV/CD26) and the therapeutic potential of DPP IV inhibitors. Curr. Med. Chem., 6, 311-327.
35. Ashworth, D. M., Atrash, B., Baker, G. R., et al. (1996) 2-Cyanopyrrolidines as potent, stable inhibitors of dipeptidyl peptidase IV. Bioorg. Med. Chem. Lett., 6, 1163-1166.
36. Lin, J., Toscano, P. J. and Welch, J. T. (1998) Inhibition of dipeptidyl peptidase IV (DPP IV) by fluoroolefin-containing N-peptidyl-O-hydroxylamine peptidemimetics. Proc. Natl Acad. Sci. U. S. A., 95, 14020-14024.
37. Zhao, K., Lim, D. S., Funaki, T. and Welch, J. T. (2003) Inhibition of dipeptidyl peptidase IV (DPP IV) by 2-(2-amino-1-fluoropropylidene)-cyanopentanecarbonitrile, a fluoroolefin containing peptidemimetic. Bioorg. Med. Chem., 11, 207-215.
38. Van der Veken, P., Senten, K., Kertesz, I., et al. (2005) Fluoro-olefins as peptidomimetic inhibitors of dipeptidyl peptidases. J. Med. Chem., 48, 1768-1780.
39. Egholm, M., Buchardt, O., Christensen, L., et al. (1993) PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules. Nature, 365, 566-568.
40. Armitage, B. A. (2003) The impact of nucleic acid secondary structure on PNA hybridization. Drug Discov. Today, 8, 222-228.
41. Koppelhus, U. and Nielsen, P. E. (2003) Cellular delivery of peptide nucleic acid (PNA) Adv. Drug Del. Rev., 55, 267-280.
42. Hollenstein, M., Gautschi, D. and Leumann, C. J. (2003) Fluorinated peptide nucleic acids. Nucleosides Nucleotides Nucleic Acids, 22, 1191-1194.
43. Hollenstein, M. and Leumann, C. J. (2003) Synthesis and incorporation into PNA of fluorinated olefinic PNA (F-OPA) monomers. Org. Lett., 5, 1987-1990.
44. Hollenstein, M. and Leumann, C. J. (2005) Fluorinated olefinic peptide nucleic acid: synthesis and pairing properties with complementary DNA. J. Org. Chem., 70, 3205-3217.
45. Schutz, R., Cantin, M., Roberts, C., et al. (2000) Oleinic peptide nucleic acids (OPAs): new aspects of the molecular recognition of DNA by PNA. Angew. Chem. Int. Ed., 39, 1250-1253.
46. Will, D. W., Breipohl, G., Langner, D., et al. (1995) The synthesis of polyamide nucleic acids using a novel monomethoxytrityl protecting-group strategy. Tetrahedron, 51, 12069-12082.
47. For a review, see: Kool, E. T., Morales, J. C. and Guckian, K. M. (2000) Mimicking the structure and function of DNA: insights into DNA stability and replication. Angew. Chem. Int. Ed., 39, 990-1009.
48. For a review, see: Kool, E. T. and Sintim, H. O. (2006) The difluorotoluene debate-a decade later. Chem. Commun., 3665-3675.
49. Schweitzer, B. A. and Kool, E. T. (1994) Aromatic nonpolar nucleosides as hydrophobic iso-steres of pyrimidine and purine nucleosides. J. Org. Chem., 59, 7238-7242.
50. Schweitzer, B. A. and Kool, E. T. (1995) Hydrophobic, non-hydrogen-bonding bases and base pairs in DNA. J. Am. Chem. Soc., 117, 1863-1872.
51. Kim, T. W. and Kool, E. T. (2004) A set of nonpolar thymidine nucleoside analogues with gradually increasing size. Org. Lett., 6, 3949-3952.
52. Kim, T. W. and Kool, E. T. (2005) A series of nonpolar thymidine analogues of increasing size: DNA base pairing and stacking properties. J. Org. Chem., 70, 2048-2053.
53. Dunitz, J. D. and Taylor, R. (1997) Organic fluorine hardly ever accepts hydrogen bonds. Chem. Eur. J., 3, 89-98.
54. Thalladi, V. R., Weiss, H.-C., Bläeser, D., et al. (1998) C-H--F interactions in the crystal structures of some fluorobenzenes. J. Am. Chem. Soc., 120, 8702-8710.
55. Parsch, J. and Engeles, J. W. (2002) C-F-H-C hydrogen bonds in ribonucleic acids. J. Am. Chem. Soc., 124, 5664-5672.
56. O'Neill, B. M., Ratto, J. E., Good, K. L., et al. (2002) A highly effective nonpolar isostere of deoxyguanosine: synthesis, structure, stacking, and base pairing. J. Org. Chem., 67, 5869-5875.
57. Guckian, K. M., Schweitzer, B. A., Ren, R. X.-F., et al. (2000) Factors contributing to aromatic stacking in water: evaluation in the context of DNA. J. Am. Chem. Soc., 122, 2213-2222.
58. Kim, T. W., Delaney, J., Essigmann, J. M. and Kool, E. T. (2005) Probing the active site tightness of DNA polymerase in subangstrom increments, Proc. Natl. Acad. Sci. U. S. A., 102, 15803-15808.
59. Sintim, H. O. and Kool, E. T. (2006) Remarkable sensitivity to DNA base shape in the DNA polymerase active site. Angew. Chem. Int. Ed., 45, 1974-1979.
60. Kim, T. W., Brieba, L. G., Ellenberger, T. and Kool, E. T. (2006) Functional evidence for a small and rigid active site in a high fidelity DNA polymerase: probing T7 DNA polymerase with variably sized base pairs. J. Biol. Chem., 281, 2289-2295.
61. Mizukami, S., Kim, T. W., Helquist, S. A. and Kool, E. T. (2006) Varying DNA base-pair size in subangstrom increments: evidence for a loose, not large, active site in low-fidelity Dpo4 polymerase. Biochemistry 45, 2772-2778.
62. Silverman, A. P. and Kool, E. T. (2007) RNA probes of steric effects in active sites: high flexibility of HIV-1 reverse transcriptase. J. Am. Chem. Soc., 129, 10626-10627.
63. Wipf, P., Xiao, J. and Geib, S. J. (2005) Imine additions of internal alkynes for the synthesis of trisubstituted (E)-alkene and cyclopropane peptide isosteres. Adv. Synth. Catal., 347, 1605-1613.
64. Tius, M. A. and Kawakami, J. K. (1992) Vinyl fluorides from vinylstannanes. Synth. Commun., 22, 1461-1471.
65. Chen, Q.-Y. and Wu, S.-W. (1989) Methyl (fluorosulfonyl)difluoroacetate; a new trifluorometh-ylating agent. J. Chem. Soc. Chem. Commun., 705-706.
66. Ball, J. B., Hughes, R. A., Alewood, P. F. and Andrews, P. R. (1993) ß-Turn topography. Tetrahedron, 49, 3467-3478.
67. Xiao, J., Weisblum, B. and Wipf, P. (2005) Electrostatic versus steric effects in peptidomimicry: Synthesis and secondary structure analysis of gramicidin S analogues with (E)-alkene peptide isosteres. J. Am. Chem. Soc., 127, 5742-5743.