The conformational properties of dehydrobutyrine and dehydrovaline: Theoretical and solid-state conformational studies

Journal of Peptide Science

Volumn 16, Issue 9, 2010, Pages 496-505

  Siodłak, Dawid ^a   Grondys, Justyna ^a   Lis, Tadeusz ^b   Bujak, Maciej ^a   Broda, Małgorzata A ^a   Rzeszotarska, Barbara ^a  

^a UNIVERSITY OF OPOLE   (Poland)

^b UNIVERSITY OF WROC AW   (Poland)

Author keywords

Antrimycins; Bogorols; Lasiodine A; Laxaphycin; Nisin; Pahayokolides; Stendomycin; Syringopeptin

Indexed keywords

ALANINE; AMINO ACID DERIVATIVE; CHLOROFORM; DEHYDROBUTYRINE; DEHYDROVALINE; UNCLASSIFIED DRUG; WATER;

ARTICLE; CHEMICAL BOND; CRYSTAL STRUCTURE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SOLID STATE; THEORETICAL STUDY; TOPOGRAPHY; X RAY CRYSTALLOGRAPHY;

AMINOBUTYRIC ACIDS; CRYSTALLOGRAPHY, X-RAY; MOLECULAR CONFORMATION; VALINE;

EID: 77957291834     PISSN: 10752617     EISSN: 10991387     Source Type: Journal    
DOI: 10.1002/psc.1267     Document Type: Article

References (62)

1. Goldberg J, Huang H-b, Kwon Y-g, Greengard P, Nairn AC, Kuriyan J. Three-dimensional structure of the catalytic sub unit of protein serine/threonine phosphatase-1. Nature 1995; 376: 745-753.
2. Namikoshi M, Choi BW, Sun F, Rinehart KL, Evans WR, Carmichael WW. Chemical characterization and toxicity of dihydro derivatives of nodularin and microcystin-LR, potent cyanobacterial cyclic peptide hepatotoxins. Chem. Res. Toxicol. 1993; 6: 151-158.
3. 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.
4. Rich DH, Bhatnagar PK. Conformational studies of tentoxin by nuclear magnetic resonance spectroscopy. Evidence for a new conformation for a cyclic tetrapeptide. J. Am. Chem. Soc. 1978; 100: 2212-2218.
5. Rich DH, Bhatnagar PK. Isolation and conformational analysis of two conformers of D-methylalanine1-tentoxin. J. Am. Chem. Soc. 1978; 100: 2218-2224.
6. Libermann B, Ellinger R, Pinet E. Isotentoxin, a conversion product of the phytotoxin tentoxin. Phytochemistry 1996; 42: 1537-1540.
7. Chatterjee C, Paul M, Xie L, van der Donk WA. Biosynthesis and mode of action of lantibiotics. Chem. Rev. 2005; 105: 633-683.
8. Bagley MC, Dale JW, Merritt EA, Xiong X. Thiopeptide antibiotics. Chem. Rev. 2005; 105: 685-714.
9. Bodanszky M, Izdebski J, Muramatsu I. The structure of the peptide antibiotic stendomycin. J. Am. Chem. Soc. 1969; 91: 2351-2358.
10. López-Marcià À, Jiménez JC, Royo M, Giralt E, Albericio F. Synthesis and structure determination of kahalalide F. J. Am. Chem. Soc. 2001; 123: 11398-11401.
11. Ballard CE, Yu H, Wang B. Recent developments in depsipeptide research. Curr. Med. Chem. 2002; 9: 471-498.
12. Furumai R, Matsuyama A, Kobashi N, Lee K-H, Nishiyama M, Nakajima H, Tanaka A, Komatsu Y, Nishino N, Yoshida M, Horinouchi S. FK228 (depsipeptide) as a natural prodrug that inhibits class I histone deacetylases. Cancer Res. 2002; 62: 4916-4921.
13. Piekarz RL, Robey R, Sandor V, Bakke S, Wilson WH, Dahmoush L, Kingma DM, Turner ML, Altemus R, Bates SE. Inhibitor of histone deacetylation, depsipeptides (FR901228), in the treatment of peripheral and cutaneous T-cell lymphoma: A case report. Blood 2001; 98: 2865-2868.
14. Scaloni A, Dalla Serra M, Amodeo P, Mannina L, Vitale RM, Segre AL, Cruciani O, Lodovichetti F, Greco ML, Fiore A, Gallo M, D'Ambrosio C, Coraiola M, Menestrina G, Graniti A, Fogliano V. Structure, conformation and biological activity of a novel lipodepsipeptide from Pseudomonas corrugata: Cormycin A. Biochem. J. 2004; 384: 25-36.
15. Grgurina I, Mariotti F, Fogliano V, Gallo M, Scaloni A, Iacobellis NS, Cantore PL, Mannina L, vanAxel Castelli V, Greco ML, Graniti A. A new syringopeptin produced by bean strains of Pseudomonas syringae pv. Syringae. BBA 2002; 1597: 81-89.
16. Ballio A, Bossaa F, Giorgio DD, Ferrantib P, Paci M, Puccib P, Scalonia A, Segred A, Strobel GA. Novel bioactive lipodepsipeptides from Pseudomonas syringae: The pseudomycins. FEBSLett. 1994; 355: 96-100.
17. Sun X, Zeckner DJ, Zhang Y-z, Sachs RK, Current WL, Rodriguez M, Chen S-H. Prodrugs of 3-amido bearing pseudomycin analogues: Novel antifungal agents. Bioorg. Med. Chem. Lett. 2001; 11: 1881-1884.
18. Barsby T, Warabi K, Sørensen D, Zimmerman WT, Kelly MT, Andersen RJ. The bogorol family of antibiotics: Template-based structure elucidation and a new approach to positioning enantiomeric pairs of aminoacids. J. Org. Chem. 2006;71:6031-6037.
19. Bonnard I, Rolland M, Salmon J-M, Debiton E, Barthomeuf C, Banaigs B. Total structure and inhibition of tumor cell proliferation of laxaphycins. J. Med. Chem. 2007; 50: 1266-1279.
20. MacMillan J, Ernst-Russell MA, de Ropp JS, Molinski TF. Lobocyclamides A-C, lipopeptides from a cryptic cyanobacterial mat containing Lyngbya confervoides. J. Org. Chem. 2002;67:8210-8215.
21. Yokokawa F, Shioiri T. Total synthesis of somamide A, an Ahp (3-amino-6-hydroxy-2-piperidone)-containing cyclic depsipeptide. Tetrahedron Lett. 2002; 43: 8673-8677. (Pubitemid 35300062)
22. Tan LT. Bioactive natural products from marine cyanobacteria. Phytochemistry 2007; 68: 954-979.
23. Plaza A, Bewley CA, Largamides A-H. Unusual cyclic peptides from the marine cyanobacterium Oscillatoria sp. J. Org. Chem. 2006; 71: 6898-6907.
24. An T, Kumar TKS, Wang M, Liu L, Lay JO Jr, Liyanage R, Berry J, Gantar M, Marks V, Gawley RE, Rein KS. Structures of pahayokolides A and B, cyclic peptides from a Lyngbya sp. J. Nat. Prod. 2007; 70: 730-735.
25. Berry JP, Gantar M, Gawley RE, Wang M, Rein KS. Pharmacology and toxicology of pahayokolide A, a bioactive metabolite from a freshwater species of Lyngbya isolated from the Florida Everglades. Comp Biochem. Physiol., Part C 2004; 139: 231-238.
26. Tan N-H, Zhou J. Plant cyclopeptides. Chem. Rev. 2006;106:840-895.
27. Schmidt U, Riedl B. The total synthesis of antrimycin D. J. Chem. Soc., Chem. Commun. 1992; 17: 1186-1187.
28. Ohtsu Y, Sasamura H, Shibata T, Nakajima H, Hino M, Fujii T. The novel gluconeogenesis inhibitors FR225659 and related compounds that originate from Helicomyces sp. No. 19353. II. Biological profiles. J. Antibiot. 2003; 56: 689-693.
29. Stohlmeyer MM, Tanaka H, Wandless TJ. A stereospecific elimination to form dehydroamino acids: Synthesis of the phomopsin tripeptide side chain. J. Am. Chem. Soc. 1999; 121: 6100-6101.
30. Thormann M, Hofmann H-J. Conformational properties of peptides containing dehydro amino acids. J. Mol. Struct. (Theochem) 1998; 431: 79-96.
31. Jain R, Chauhan VS. Conformational characteristics of peptides containing α,β-dehydroamino acid residues. Bioplimers 1996; 40: 105-119.
32. Broda MA, Rzeszotarska B, Smełka L, Rospenk M. Conformational 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.
33. Broda MA, Rzeszotarska B, Smełka L, Pietrzyński G. Conformational investigation of α,β-dehydropeptides. IX. N-acetyl-(E)-α,β- dehydrobutyrine N′-methylamide: Stereoelectronic properties from infrared and theoretical studies. J. Pept Res. 1998; 52: 72-79.
34. 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.
35. Miertus S, Tomasi J. Approximateevaluationsof theelectrostatic free energy and internal energy changes in solution processes. Chem. Phys. 1982; 65: 239-245.
36. Tomasi J, Mennucci B, Cammi R. Quantum mechanical continuum salvation models. Chem. Rev. 2005; 105: 2999-3093.
37. Vargas R, Garza J, Hay BP, Dixon DA. Conformational study of the alanine dipeptide at the MP2 and DFT levels. J. Phys. Chem. A 2002; 106: 3213-3218.
38. Zimmerman SS, Pottle MS, Némethy G, Scheraga HA. Conformational analysis of the 20 naturally occurring amino acid residues using ECEPP. Macromolecules 1977; 10: 1-9.
39. Hudáky I, Kiss R, Perczel A. A nomenclature of peptide conformers. J. Mol. Struct. (Theochem) 2004; 675: 177-183.
40. Smełka L, Rzeszotarska B, Broda MA, Kubica Z. N-acetyl-α, β- dehydroamino acid N′-methylamides and N′, N′-dimethylamides. Org. Prep. Proc. Int. 1997; 29: 696-701.
41. Sheldrick GM. A short history of SHELX. Acta Crystallogr., Sect. A 2008; 64: 112-122.
42. Macrae CF, Bruno IJ, Chisholm JA, Edgington PR, McCabe P, Pidcock E, Rodriguez-Monge L, Taylor R, van de Streek J, Wood PA. Mercury CSD 2.0 - new features for the visualization and investigation of crystal structures. J. Appl. Cryst. 2008; 41: 466-470.
43. 3. J. Pept. Res. 2005; 66: 68-74.
44. 3. J.Mol. Struct. 2005; 738: 189-192.
45. Ciszak E, Pietrzyński G, Rzeszotarska B. Conformational investigation of α,β-dehydropeptides. Part III. Molecular and crystal structure of acetyl-L-prolyl-α,β-dehydrovaline methylamide. Int. J. Pept. Protein Res. 1992; 39: 218-222.
46. Makker J, Dey S, Mukherjee S, Vijayaraghavan R, Kumar P, Singh TP. Design of peptides with α,β-dehydro-residues: Synthesis, crystal structure and molecular conformation of a tetrapeptide Z-ΔVal-Val- ΔPhe-Ile-Ome. J.Mol. Struct. 2003; 654: 119-124.
47. 3. J. Pept. Res. 2003; 62: 63-69.
48. Vijayaraghavan R, Kumar P, Dey S, Singh TP. Design of peptides with α,β-dehydro residues: A dipeptide with a branched β-carbon dehydroresidue atthe (i+1) position,methyl N-(benzyloxycarbonyl)- α,β-didehydrovalyl-L-tryptophanate. Acta Crystallogr., Sect. C 2001; 57: 1220-1221.
49. Broda MA, Ciszak EM, Kozioł AE, Pietrzyński G, Rzeszotarska B. Conformational investigation of α,β-dehydropeptides. XVI. β-turn tendency in Ac-Pro-ΔXaa-NHMe: Crystallographic and theoretical studies. J. Pept. Sci. 2006; 12: 538-549.
50. 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.
51. Nakanishi I, Konishita T, Tada T, Fujita T, Hatanaka H, Sato A. Molecular structure of FR901277, a novel inhibitor of human leukocyte elastase, and its binding mode simulation. Bioorg. Med. Chem. Lett. 1999; 9: 2397-2402.
52. Shigematsu N, Ueda H, Takase S, Tanaka H, Yamamoto K, Tada T. FR901228, a novel antitumor bicyclic depsipeptide produced by chromobacterium violaceum No. 968. II. Structure determination. J. Antibiot. 1994; 47: 311-314.
53. 3. Int. J. Pep Protein Res. 1989; 33: 167-172.
54. Narula P, Patel HC, Singh TP, Chauhan VS. Synthesis, crystal structure, and molecular conformation of N-Boc-L-Phe-dehydro-Leu-L-Val- OCH3. Biopolymers 1990; 29: 935-941.
55. Zecchini PG, Paradisi PM, Torrini I, Lucente G, Gavuzzo E, Mazza F, Pochetti G, Spisani S. For-Met-Δ(z)Leu-Phe-OMe: A new active analog of chemotactic N-formyltripeptides with β-turn crystal conformation. Tetrahedron Lett. 1991; 32: 4375-4376.
56. 3. Acta Crystallogr., Sect.C:Cryst. Struct.Commun. 2002; 58: 212-214.
57. Singh M, Chauhan VS. Synthetic and conformational studies on dehydrovaline-containing model peptides. Proc. Indian Acad. Sci. Chem. Sci. 1994; 106: 1139-1147.
58. Culvenor CCJ, Edgar JA, Mackay MF, Gorst-Allman CP, Marasas WFO, Steyn PS, Vleggaar R, Wessels PL. Structure elucidation and absolute configuration of phomopsin A, a hexapeptide mycotoxin produced by Phomopsis leptostromiformis. Tetrahedron 1989; 45: 2351-2372.
59. Cativiela C, Diaz-de-Villegas MD, Galvez JA. Synthesis and chemical resolution of unique α,β-didehydroamino acids with a chiral axis. Tetrahedron Lett. 1999; 40: 1027-1030.
60. Cativiela C, Diaz-de-Villegas MD, Galvez JA, Su G. Synthesis and conformational properties of model dipeptides containing novel axially chiral α,β-didehydroamino acids at the (i+1) position of a β-turn conformation. Tetrahedron. 2004; 60: 11923-11932.
61. Aubry A, Allier F, Boussard G, Marraud M. Crystal structure of dehydromonopetide, (Z)-N-acetyl-α,β-dehydrophenylalanine methylamide. Biopolymers 1985; 24: 639-646.
62. Palmer DE, Pattaroni C, Nunami K, Chadha RK, Goodman M, Wakamiya T, Fukase K, Horimoto S, Kitazawa M, Fujita H, Kubo A, Shiba T. Effects of dehydroalanine on peptide conformations. J. Am. Chem. Soc. 1992; 114: 5634-5642.