Skip to main content
SpringerLink
Log in

Solid-Phase Synthesis and NMR Structural Studies of the Marine Antibacterial Cyclic Tetrapeptide: Cyclo[GSPE]

  • Published:
International Journal of Peptide Research and Therapeutics Aims and scope Submit manuscript

Abstract

Twelve-membered head-to-tail cyclic tetrapeptides (CTPs) are rigid molecules found in nature and possess a diverse range of biological activities. A possible reason may be due to their ability to adopt rigid conformations in solution mimicking reverse-turns. Reverse-turns are common structural motifs which serve as molecular recognition sites in many protein-receptor interactions. In this paper, we describe the solid-phase synthesis of the antibacterial cyclic tetrapeptide cyclo[Gly-Ser-Pro-Glu] (cyclo[GSPE]), first isolated from the Ruegeria strain of marine bacteria by Mitova et al. (J Nat Prod 67:1178–1181, 2004). Our NMR experiments in H2O:D2O:DMSO (18:1:1) revealed that it possessed three conformations in an approximate ratio of 4:2:1 based on NMR amide peak intensities. 2D NMR studies and computer calculations revealed that the major conformer adopted a reverse-turn conformation and have ω torsion angles twisted by up to 2°, with two transoid amide bonds between Gly-Ser, Pro-Glu and two cisoid amide bonds between Ser-Pro, Glu-Gly in a cis–trans-cis–trans (ctct) pattern. This supports previous reports that majority of CTPs adopt a ctct pattern when dissolved in hydrogen-bond disrupting solvents (Che and Marshall in J Med Chem 49:111–124, 2006 and references cited therein). An ensemble of ten lowest-energy-minimised 3D structures generated using XPLOR-NIH software revealed that cyclo[GSPE] possessed a rigid backbone ring scaffold. The remaining two minor conformers were present in quantities too low for NMR structural studies.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Scheme 1
Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

Abbreviations

1D:

One-dimensional

2D:

Two-dimensional

3D:

Three-dimensional

CTPs:

Cyclic tetrapeptides

DIPEA:

N,N-diisopropylethylamine

DMSO:

Dimethyl sulfoxide

DQF-COSY:

Double-quantum filtered correlation spectroscopy

DSS:

Sodium-2,2-dimethyl-2-silapentane-5-sulphonate

eq:

Mole equivalents

Fmoc:

Fluorenylmethyloxycarbonyl

HBTU:

O-benzotriazole-N,N,N′,N′-tetramethyluroniumhexafluorophosphate

HOBt:

Hydroxybenzotriazole

HPLC:

High performance liquid chromatography

NMR:

Nuclear magnetic resonance

NOESY:

Nuclear Overhauser effect spectroscopy

ppm:

Parts per million

TFA:

Trifluoroacetic acid

TOCSY:

Total correlation spectroscopy

tBu:

Tertiary butyl

References

  • Alcaro MC, Sabatino G, Uziel J et al (2004) On-resin head-to-tail cyclization of cyclotetrapeptides: optimization of crucial parameters. J Pept Sci 10:218–228

    Article  CAS  PubMed  Google Scholar 

  • Arbor S, Marshall GR (2009) A virtual library of constrained cyclic tetrapeptides that mimics all four side-chain orientations for over half the reverse-turns in the protein data bank. J Comput Aided Mol Des 23:87–95

    Article  CAS  PubMed  Google Scholar 

  • Bernardi E, Fauchere JL, Atassi G, Viallefont P, Lazaro R (1993) Antitumoral cyclic peptide analogues of Chlamydocin. Peptides 14:1091–1093

    Article  CAS  PubMed  Google Scholar 

  • Bernstein HJ (2000) Recent changes to RasMol, recombining the variants. Trends Biochem Sci 25:453–455

    Article  CAS  PubMed  Google Scholar 

  • Che Y, Marshall GR (2006) Engineering cyclic tetrapeptides containing chimeric amino acids as preferred reverse-turn scaffolds. J Med Chem 49:111–124

    Article  CAS  PubMed  Google Scholar 

  • Darkin-Rattray SJ, Gurnett AM, Myers RW et al (1996) Apicidin: a novel antiprotozoal agent that inhibits parasite histone deacetylase. Proc Natl Acad Sci USA 93:13143–13147

    Article  CAS  PubMed  Google Scholar 

  • Daura X, Gademann K, Schäfer H et al (2001) The β-peptide hairpin in solution: conformational study of a β-hexapeptide in methanol by NMR spectroscopy and MD simulation. J Am Chem Soc 123:2393–2404

    Article  CAS  PubMed  Google Scholar 

  • DeLano WL (2002) The PyMol molecular graphics system. DeLano Scientific, Palo Alto, CA, USA. www.pymol.org

  • Dolle RE, Michaut M, Martinez-Teipel B et al (2009) Nascent structure-activity relationship study of a diastereomeric series of kappa opioid receptor antagonists derived from CJ-15,208. Bioorg Med Chem Lett 19:3647–3650

    Article  CAS  PubMed  Google Scholar 

  • Flippen J, Karle IL (1976) Conformation of the cyclic tetrapeptide dihydrochlamydocin by X-ray diffraction. Biopolymers 15:1081–1092

    Article  CAS  PubMed  Google Scholar 

  • Gattin Z, Zaugg J, van Gunsteren WF (2010) Structure determination of a flexible cyclic peptide based on NMR and MD simulation. ChemPhysChem 11:830–835

    Article  CAS  PubMed  Google Scholar 

  • Goddard TD, Kneller DG (2004) Sparky 3. University of California, San Francisco, USA. www.cgl.ucsf.edu/home/sparky/

  • Grathwohl C, Tun-Kyi A, Bundi A, Schwyzer R, Wüthrich K (1975) 1H- and 13C-NMR studies of molecular conformations of cyclo-tetraglycyl. Helv Chim Acta 58:415–423

    Article  CAS  PubMed  Google Scholar 

  • Guéron M, Plateau P, Decorps M (1991) Solvent signal suppression in NMR. Prog NMR Spectrosc 23:135–209

    Article  Google Scholar 

  • Horton DA, Bourne GT, Coughlan J et al (2008) Cyclic tetrapeptides via the ring contraction strategy: chemical techniques useful for their identification. Org Biomol Chem 6:1386–1395

    Article  CAS  PubMed  Google Scholar 

  • Itazaki H, Nagashima K, Sugita K et al (1990) Isolation and structural elucidation of new cyclotetrapeptides Trapoxin-A and Trapoxin-B having detransformation activities as antitumor agents. J Antibiot 43:1524–1532

    CAS  PubMed  Google Scholar 

  • IUPAC-IUB (1970) IUPAC-IUB commission on biochemical nomenclature. Abbreviations and symbols for the description of the conformation of polypeptide chains. Biochemistry 9:3471–3479

    Article  Google Scholar 

  • Kawagishi H, Somoto A, Kuranari J, Kimura A, Chiba S (1993) A novel cyclotetrapeptide produced by Lactobacillus helveticus as a tyrosinase inhibitor. Tetrahedron Lett 34:3439–3440

    Article  CAS  Google Scholar 

  • Kawai M, Jasensky RD, Rich DH (1983) Conformational analysis by NMR spectrometry of the highly substituted cyclic tetrapeptides, Chlamydocin and Ala4-Chlamydocin. Evidence for a unique amide bond sequence in Dimethyl-d 6 sulfoxide. J Am Chem Soc 105:4456–4462

    Article  CAS  Google Scholar 

  • Kawai M, Pottorf RS, Rich DH (1986) Structure and solution conformation of the cytostatic cyclic tetrapeptide WF-3161. J Med Chem 29:2409–2411

    Article  CAS  PubMed  Google Scholar 

  • Kessler H (1982) Conformation and biological activity of cyclic peptides. Angew Chem Int Ed 21:512–523

    Article  Google Scholar 

  • Liesch JM, Sweeley CC, Staffeld GD, Anderson MS, Weber DJ, Scheffer RP (1982) Structure of HC-Toxin, a cyclic tetrapeptide from Helminthosporium carbonum. Tetrahedron 38:45–48

    Article  CAS  Google Scholar 

  • Meutermans WDF, Bourne GT, Golding SW et al (2003) Difficult macrocyclizations: new strategies for synthesizing highly strained cyclic tetrapeptides. Org Lett 5:2711–2714

    Article  CAS  PubMed  Google Scholar 

  • Mitova M, Popov S, De Rosa S (2004) Cyclic peptides from the Ruegeria strain of bacteria associated with the sponge Suberites domuncula. J Nat Prod 67:1178–1181

    Article  CAS  PubMed  Google Scholar 

  • Ngu-Schwemlein M, Zhou Z, Bowie T, Eden R (2003) Cyclotetrapeptides with alternating D-Ala residues: synthesis and spectroscopic studies. J Mol Struct 655:59–68

    Article  CAS  Google Scholar 

  • Nishino N, Xu M, Mihara H, Fujimoto T, Ueno Y, Kumagai H (1992) Sequence dependence in solid-phase synthesis-cyclization-cleavage for cyclo(-arginyl-glycylaspartyl-phenylglycyl-). Tetrahedron Lett 33:1479–1482

    Article  CAS  Google Scholar 

  • Pardi A, Billeter M, Wüthrich K (1984) Calibration of the angular dependence of the amide proton-C alpha proton coupling constants, 3 J HNα in a globular protein. J Mol Biol 180:741–751

    Article  CAS  PubMed  Google Scholar 

  • Proksch P, Ebel R, Edrada RA et al (2008) Sponge-associated fungi and their bioactive compounds: the Suberites case. Bot Mar 51:209–218

    Article  CAS  Google Scholar 

  • Rich DH, Kawai M, Jasensky RD (1983) Conformational studies of cyclic tetrapeptides: evidence for a bis γ-turn conformation for Chlamydocin and Ala4-Chlamydocin in non-polar solvents. Int J Pept Protein Res 21:35–42

    Article  CAS  PubMed  Google Scholar 

  • Rose GD, Gierasch LM, Smith JA (1985) Turns in peptides and proteins. Adv Protein Chem 37:1–109

    Article  CAS  PubMed  Google Scholar 

  • Saito T, Hirai H, Kim YJ et al (2002) CJ-15, 208, a novel kappa opioid receptor antagonist from a fungus, Ctenomyces serratus ATCC15502. J Antibiot 55:847–854

    CAS  PubMed  Google Scholar 

  • Sayle R, Milner-White EJ (1995) RasMol: biomolecular graphics for all. Trends Biochem Sci 20:374–376

    Article  CAS  PubMed  Google Scholar 

  • Schwieters CD, Kuszewski JJ, Tjandra N, Clore GM (2003) The XPLOR-NIH NMR molecular structure determination package. J Magn Reson 160:66–74

    Article  Google Scholar 

  • Schwieters CD, Kuszewski JJ, Tjandra N, Clore GM (2006) Using XPLOR-NIH for NMR molecular structure determination. Prog NMR Spectrosc 48:47–62

    Article  CAS  Google Scholar 

  • Seebach D, Bezencon O, Jaun B et al (1996) Further C-alkylations of cyclotetrapeptides via lithium and phosphazenium enolates: discovery of a new conformation. Helv Chim Acta 79:588–608

    Article  CAS  Google Scholar 

  • Shin J, Seo Y, Lee HS, Rho JR, Mo SJ (2003) A new cyclic peptide from a marine-derived bacterium of the genus Nocardiopsis. J Nat Prod 66:883–884

    Article  CAS  PubMed  Google Scholar 

  • Shute RE, Kawai M, Rich DH (1988) Conformationally constrained biologically active peptides: tentative identification of the antimitogenic bioactive conformer of the naturally occurring cyclic tetrapeptides. Tetrahedron 44:685–695

    Article  CAS  Google Scholar 

  • Singh EK, Ravula S, Pan CM et al (2008) Synthesis and biological evaluation of histone deacetylase inhibitors that are based on FR235222: a cyclic tetrapeptide scaffold. Bioorg Med Chem Lett 18:2549–2554

    Article  CAS  PubMed  Google Scholar 

  • Skubatz H, Brot MD, Stock KM, Klatt B, Thomas GP (2009) Analgesic and antipyretic activities of a novel tetrapeptide in rats. Int J Pept Res Ther 15:293–301

    Article  CAS  Google Scholar 

  • Terui Y, Chu YW, Li JY et al (2008) WSS2220, a novel cyclic tetrapeptide with a new sulfonoamino acid, exhibits potent and selective inhibitory activity against GlyT1. Tetrahedron Lett 49:3067–3070

    Article  CAS  Google Scholar 

  • Tyndall JDA, Pfeiffer B, Abbenante G, Fairlie DP (2005) Over one hundred peptide-activated G protein-coupled receptors recognize ligands with turn structure. Chem Rev 105:793–826

    Article  CAS  PubMed  Google Scholar 

  • Umehara K, Nakahara K, Kiyoto S et al (1983) Studies on WF-3181, a new antitumor antibiotic. J Antibiot 36:478–483

    CAS  PubMed  Google Scholar 

  • Yang L, Tan RX, Wang Q, Huang WY, Yin YX (2002) Antifungal cyclopeptides from Halobacillus litoralis YS3106 of marine origin. Tetrahedron Lett 44:685–695

    Google Scholar 

Download references

Acknowledgments

We thank A*STAR Biomedical Research Council for financial support.

Author information

Authors and Affiliations

  1. Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, Singapore, 138669, Singapore

    Huichang Annie Lim, CongBao Kang & Cheng San Brian Chia

Authors
  1. Huichang Annie Lim
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. CongBao Kang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Cheng San Brian Chia
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Cheng San Brian Chia.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Lim, H.A., Kang, C. & Chia, C.S.B. Solid-Phase Synthesis and NMR Structural Studies of the Marine Antibacterial Cyclic Tetrapeptide: Cyclo[GSPE]. Int J Pept Res Ther 16, 145–152 (2010). https://doi.org/10.1007/s10989-010-9216-x

Download citation

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10989-010-9216-x

Keywords

Search

Navigation