Didemnin B. Conformation and dynamics of an antitumour and antiviral depsipeptide studied in solution by 1H and 13C. n.m.r. spectroscopy.
The solution conformation of didemnin B, the most potent member of a family of depsipeptides that shows antitumour, antiviral, and immunosuppressive activity, has been studied in chloroform solution using n.m.r. spectroscopy. 1H and 13C spectra have been assigned from analysis of a number of two-dimensional homonuclear and heteronuclear chemical shift correlation experiments which confirm the recently corrected primary structure of the molecule. The conformation of the peptide has been deduced from measurements of the temperature dependence of the NH chemical shifts, analysis of coupling constant data and primarily through NOE effects observed in the rotating frame. Interproton distance bounds determined from a quantitative analysis of the ROE data provide 41 constraints from which a family of closely related structures were calculated using distance geometry algorithms. A type II beta-turn involving residues Thr6, Leu7, and Pro8 is well represented in the computed conformers as is a hydrogen bonding interaction between the NH of Leu3 and the carbonyl oxygen of Thr6. This latter interaction causes the linear portion of the structure to fold back over the depsipeptide ring, imparting to it a degree of structural stability as well as giving the molecule a somewhat globular character. Only one transannular hydrogen bond, between Ist1 NH and Leu3 carbonyl, stabilizes the conformation of the depsipeptide, which has an irregular non-planar configuration. The small temperature coefficients (less than 2.0 x 10(-3) ppm/degrees C) for the NHs of Ist1 and Leu3 are consistent with their involvement in these hydrogen bonding interactions. We find that many of the structural features observed in the crystalline form of didemnin B are conserved in solution. Analysis of the 13C spin-lattice relaxation rates of the protonated carbons reveals small variations in effective correlation times at specific sites in the molecule. The data suggests that the peptide segment encompassing residues Leu3 through to Thr6 is in a more motionally restricted part of the structure.
Searle
M S
MS
Molecular Pharmacology Group, Peter MacCallum Cancer Institute, Melbourne, Victoria, Australia.
Hall
J G
JG
Kyratzis
I
I
Wakelin
L P
LP
D000595:Amino Acid Sequence; D000970:Antineoplastic Agents; D000998:Antiviral Agents; D002247:Carbon Isotopes; D047630:Depsipeptides; D007166:Immunosuppressive Agents; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D010456:Peptides, Cyclic / Q000494:pharmacology; D011487:Protein Conformation; D011522:Protons; D012399:Rotation; D013329:Structure-Activity Relationship; D013696:Temperature
D000970:Antineoplastic Agents; D000998:Antiviral Agents; D002247:Carbon Isotopes; D047630:Depsipeptides; D007166:Immunosuppressive Agents; D010456:Peptides, Cyclic; D011522:Protons; C030051:didemnins