The conformational properties of α,β-dehydroamino acids with a C-terminal ester group

Journal of Peptide Science

Volumn 17, Issue 10, 2011, Pages 690-699

  Siodłak, Dawid ^a   Grondys, Justyna ^a   Broda, Małgorzata A ^a  

^a UNIVERSITY OF OPOLE   (Poland)

Author keywords

Conformational analysis; Dehydroamino acids; Depsipeptides; DFT calculations; FTIR spectra; Phomalide

Indexed keywords

ALPHA,BETA DEHYDROAMINO ACID; AMINO ACID; CARBON TETRACHLORIDE; UNCLASSIFIED DRUG;

ARTICLE; CARBOXY TERMINAL SEQUENCE; INFRARED SPECTROSCOPY; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; PROTEIN ANALYSIS;

AMINO ACIDS; ESTERS; MODELS, MOLECULAR; MOLECULAR CONFORMATION;

EID: 80053185588     PISSN: 10752617     EISSN: 10991387     Source Type: Journal    
DOI: 10.1002/psc.1390     Document Type: Article

References (62)

1. Bagley MC, Dale JW, Merritt EA, Xiong X. Thiopeptide antibiotics. Chem. Rev. 2005; 105: 685-714.
2. Yoshinari T, Okada H, Yamada A, Uemura D, Oka H, Suda H, Okura A. Inhibition of topoisomerase II by a novel antitumor cyclic depsipeptide, BE-22179. Jpn. J. Cancer Res. 1994; 85: 550-555.
3. Teshima T, Nishikava M, Kubota I, Shiba T, Iwa Y, Omura S. The structure of an antibiotic, dityromycin. Tetrahedron Lett. 1988; 29: 1963-1966.
4. Leibold T, Sassa F, Reichenbach H, Höfle G. Cyrmenins, novel antifungal peptides containing a nitrogen-linked β-methoxyacrylate pharmacophore: isolation and structural elucidation. Eur. J. Org. Chem. 2004; 2: 431-435.
5. Williams RH, Fitt BDL. Differentiating α and β groups of Leptosphaeria maculans, causal agent of stem canker (blackleg) of oilseed rape. Plant Pathol. 1999; 48(2): 161-175.
6. Howlett BJ, Idnurm A, Pedras MSC. Leptosphaeria maculans, the causal agent of blackleg disease of Brassicas. Fungal Genet. Biol. 2001; 33: 1-14.
7. Pedras MSC, Biesenthal CJ. Vital staining of plant cell suspension cultures: evaluation of the phytotoxic activity of the phytotoxins phomalide and destruxin B. Plant Cell Rep. 2000; 19: 1135-1138.
8. Pedras MSC, Chumala PB, Yu Y. The phytopathogenic fungi Leptosphaeria maculans and Leptosphaeria biglobosa: chemotaxonomical characterisation of isolates and metabolite production in different culture media. Can. J. Microbiol. 2007; 53: 364-371.
9. Ward DE, Vazquez A, Soledade M, Pedras C. Phytotoxicity: synthesis and biological discrimination of phomalide and its (Z)-isomer. J. Org. Chem. 1996; 61: 8008-8009.
10. Ward DE, Vázquez A, Pedras MSC. Probing host-selective phytotoxicity: synthesis and biological activity of phomalide, isophomalide, and dihydrophomalide. J. Org. Chem. 1999; 64: 1657-1666.
11. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA, Jr, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas O, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ. Gaussian 09, Revision A.1. Gaussian Inc.: Wallingford CT, 2009.
12. Tomasi J, Mennucci B, Cammi R. Quantum mechanical continuum salvation models. Chem. Rev. 2005; 105: 2999-3093.
13. Miertus S, Tomasi J. Approximateevaluationsof theelectrostatic free energy and internal energy changes in solution processes. Chem. Phys. 1982; 65: 239-245.
14. Hudáky I, Kiss R, Perczel A. A nomenclature of peptide conformers. J. Mol. Struct. (Theochem) 2004; 675: 177-183.
15. Schöllkopf U, Meyer R. N-acyldehydro-α-aminosäuren aus N-formyldehydro-α-aminosäure-methylestern. Liebigs Ann. Chem. 1981; 1469-147.
16. Wieland T, Ohnacker G, Ziegler W. Aminosaure-synthesen mit alpha-acylamino-acrylestern. Chem. Ber. 1957; 90: 194-201.
17. Allen FH, Baalham CA, Lommerse JPM, Raithby PR. Carbonyl-carbonyl interactions can be competitive with hydrogen bonds. Acta Crystallogr. B 1998; 54: 320-329.
18. Gallo EA, Gellman SH. Hydrogen-bond-mediated folding in depsipeptide models of β-turns and α-helical turns. J. Am. Chem. Soc. 1993; 115: 9774-9788.
19. Broda MA, Rzeszotarska B, Smełka L, Rospenk M. Confor mational investigation of α, β-dehydropeptides. VIII. N-acetyl-α, β-dehydroamino acid N'-methylamides: conformation and electron density perturbation from infrared and theoretical studies. J. Pept. Res. 1997; 50: 342-351.
20. Broda MA, Rzeszotarska B, Smełka L, Pietrzyński G. Conformational investigation of α, β-dehydropeptides. IX. N-acetyl-(E)-α, β-dehy- drobutyrine N'-methylamide: stereoelectronic properties from infrared and theoretical studies. J. Pept. Res. 1998; 52: 72-79.
21. Sobczyk L, Grabowski SJ, Krygowski TM. Interrelation between H-bond and Pi-electron delocalization. Chem. Rev. 2005; 105: 3513-3560.
22. Crisma M, Formaggio F, Toniolo C, Yoshikawa T, Wakamiya T. Flat peptides. J. Am. Chem. Soc. 1999; 121: 3272-3278.
23. Herrebout W, Clou K, Desseyn HO, Blaton N. Vibrational characterization of the peptide bond. Spectrochimica Acta A 2003; 59: 47-59.
24. Allen FH. The cambridge structural database: a quarter of a million crystal structures and rising. Acta Crystallogr. B 2002; 58: 380-388. ().
25. Dey S, Vijayaraghavan R, Goel VK, Kumar S, Kumar P, Singh TP. Design rules for peptides with α, β-dehydro-residues: synthesis of a model peptide Boc-Ile-δAla-OCH3 and its crystal structures obtained from two different solvents. J. Mol. Struct. 2005; 737(2-3): 109-116.
26. GolobiŠ A, Koller J. Conformational analysis of 2, 3-substituted propenoates. J. Mol. Struct. (THEOCHEM) 2002; 532: 109-126.
27. Piazzesi AM, Bardi R, Crisma M, Toniolo C, Singh M, Chauhan VS. Molecular and crystal structure of a dehydroalanine dipeptide. Z. Kristallogr. 1993; 207: 25-32.
28. 3. Biopolymers 1992; 32(10): 1271-1276.
29. Mapelli C, Elrod LF, Holt EM, Stammer CH. The synthesis and characterization of 2, 3-methanopyroglutamic acid. Tetrahedron 1989; 45(14): 4377-4382.
30. Crisma M, Formaggio F, Toniolo C, Yoshikawa T, Wakamiya T. Flat peptides. J. Am. Chem. Soc. 1999; 121(14): 3272-3278.
31. Schumann S, Steglich W, Polborn K. Private communication to the Cambridge Structural Database, 2004; deposition number CCDC 258144.
32. Schwarz T, Steglich W, Polborn K. Private communication to the Cambridge Structural Database, 2004; deposition number CCDC 258148.
33. Pinheiro AC, Kaiser CR, Lourenço MCS, De Souza MVN, Wardell SMSV, Wardell JL. Synthesis and in vitro activity towards Mycobacterium tuberculosis of L-serinyl ester and amino derivatives of pyrazinoic acid. J. Chem. Res. 2007; 3: 180-184.
34. Haug C, Steglich W, Polborn K. Private communication to the Cambridge Structural Database, 2004; deposition number CCDC 255310.
35. Busetti V, Ajo D, De Zuane F. Crystal state conformation of a β, β'-disubstituted dehydroaminoacid derivative. Z. Kristallogr. 1988; 184(3-4): 203-208.
36. Schumann S, Steglich W, Polborn K. Private communication to the Cambridge Structural Database, 2005; deposition numbers CCDC 265787, 266628, 265915, 266004, 263359, 263479.
37. Parsons S, Bell S, Turner NJ, Johnstone R. Private communication to the Cambridge Structural Database, 2006; deposition number CCDC 611728.
38. Michaux J, Retailleau P, Campagne J-M. Synthesis of the central tryptophan-leucine residue of celogentin C. Synlett 2008; 10: 1532-1536.
39. 5. Z. Kristallogr. 1996; 211: 195.
40. Landreau CAS, LePla RC, Shipman M, Slawin AMZ, Hartley JA. Delineating noncovalent interactions between the azinomycins and double-stranded DNA: importance of the naphthalene substitution pattern on interstrand cross-linking efficiency. Org. Lett. 2004; 6(20): 3505-3507.
41. Avenoza A, Cativiela C, Peregrina JM, Zurbano MM. Synthesis of meso-2, 4-diaminoglutaric acid. Tetrahedron: Asymm. 1996; 7(6): 1555-1558.
42. De Risi C, Pollini GP, Veronese AC, Bertolasi V. A new simple route for the synthesis of (±)-2-azetidinones starting from β-enaminoketoesters. Tetrahedron 2001; 57(51): 10155-10161.
43. Enders D, Chen Z-X, Raabe G. Stereoselective synthesis of 3-substituted ethyl (Z)-4, 4, 4-trifluoro-2- formylamino-2-butenoates. Synthesis 2005; 2: 306-310.
44. Vaswani RG, Chamberlin AR. Stereocontrolled total synthesis of (-)-kaitocephalin. J. Org. Chem. 2008; 73(5): 1661-1681.
45. UršiŠ U, Grošelj U, Meden A, Svete J, Stanovnik B. Regiospecific [2 + 2] cycloadditions of electron-poor acetylenes to (Z)-2-acylamino-3-dimethylaminopropenoates: synthesis of highly functionalised buta-1, 3-dienes. Tetrahedron Lett. 2008; 49(23): 3775-3778.
46. Singh J, Kronenthal DR, Schwinden M, Godfrey JD, Fox R, Vawter EJ, Zhang B, Kissick TP, Patel B, Mneimne O, Humora M, Papaioannou CG, Szymanski W, Wong MKY, Chen CK, Heikes JE, DiMarco JD, Qiu J, Deshpande RP, Gougoutas JZ, Mueller RH. Efficient asymmetric synthesis of the vasopeptidase inhibitor BMS-189921. Org. Lett. 2003; 5(17): 3155-3158.
47. Reetz MT, Kayser F, Harms K. Cycloaddition reactions of γ-amino α, β-didehydro amino acid esters: a test case for the principle of 1, 3-allylic strain. Tetrahedron Lett. 1992; 33: 3453-3456.
48. Klepp KO, Hiebl J, Kollmann H, Rovenszky F. The crystal structure of dimethyl (2Z, 6Z)-2, 7-bis-(benzyloxycarbonylamino)octa-2, 6-diendioate: A useful precursor for optically pure 2, 7-diaminosuberic acid. Z. Naturforsch. B: Chem. Sci. 1999; 54(4): 447-450.
49. Djinovic-Carugo K, Golic L, Leban I, Svete J, Stanovnik B, Tisler M, Tate C. Three substituted 3-amino-2-benzoylaminopropenoic acid derivatives. Acta Crystallogr. C: Cryst. Struct. Commun. 1994; 50: 239-245.
50. Zeitler K, Steglich W, Polborn K. Private communication to the Cambridge Structural Database, 2005; deposition numbers CCDC 267220, 267595.
51. 3. Z. Kristallogr. New Crystal. Struct. 2001; 216: 599-600.
52. Mulzer J, Schulzchen F, Bats J-W. Rigid dipeptide mimetics. Stereocontrolled synthesis of all eight stereoisomers of 2-oxo-3-(N-Cbz-amino)-1-azabicyclo[4.3.0]nonane-9-carboxylic Acid ester. Tetrahedron 2000; 56(25): 4289-4298.
53. Parsons S, Eve T, Turner NJ, Johnstone R. Private communication to the Cambridge Structural Database, 2006; deposition number CCDC 611747.
54. Groundwater PW, Sharif T, Arany A, Hibbs DE, Hursthouse MB, Nyerges M. Tetrahedron Lett. A new synthesis of didehydroamino acid esters. Tetrahedron Lett. 1998; 39(11): 1433-1436.
55. Parsons S, Roff G, Turner NJ, Johnstone R, Johnstone R. Private communication to the Cambridge Structural Database, 2006; deposition numbers CCDC 611749, 611750.
56. Groundwater PW, Sharif T, Arany A, Hibbs DE, Hursthouse MB, Nyerges M. A novel synthesis of didehydroamino acid esters from azomethine ylides. J. Chem. Soc., Perkin Trans. 1998; 1(17): 2837-2846.
57. 3. Biopolymers Pept. Sci. Sect. 1988; 27(10): 1595-1606.
58. Jones PG, Jäger S. Ethyl (Z)-3-bromo-2-[(tert-butoxycarbonyl)-amino]-3-phenylacrylate. Acta Crystallogr. E: Struct. Rep. Online 2003; 59(3): 369-371.
59. Gunda TE. Rearrangement and degradation of cephalosporins and penicillins in the presence of mercury(II) trifluoroacetate. Org. Lett. 2000; 2: 103-105.
60. Crescenza A, Botta M, Corelli F, Santini A, Tafi A. Cyclic dipeptides. 3.1 Synthesis of methyl (R)-6-[(tert-butoxycarbonyl)amino]-4, 5, 6, 7-tetrahydro-2-methyl-5-oxo-1, 4-thiazepine-3-carboxylate and its hexahydro analogues: elaboration of a novel dual ACE/NEP inhibitor. J. Org. Chem. 1999; 64(9): 3019-3025.
61. Siodłak D, Janicki A. Conformational properties of the residues connected by ester and methylated amide bonds. Theoretical and solid state conformational studies. J. Pept. Sci. 2010; 16: 126-135.
62. Siodłak D, Grondys J, Lis T, Bujak M, Broda MA, Rzeszotarska B. The conformational properties of dehydrobutyrine and dehydrovaline: theoretical and solid state conformational studies. J. Pept. Sci. 2010; 16: 496-505.