Solution conformational analysis of sodium complexed [Gly6]. - and [Gly9]. -antamanide analogs

To investigate the conformational flexibility of metal-complexed cyclodecapeptides, we synthesized and studied two antamanide analogs, in which the phenylalanine residue in position 6 or 9 of the sequence was substituted by Gly. Previous conformational studies on antamanide suggested that these backbone regions are affected by conformational variation. The NMR conformational study showed a high degree of flexibility for the two analogs. With sodium ions, on the other hand, [Gly⁹]. -antamanide was able to form a fairly stable equimolar complex, whereas [Gly⁶]. -antamanide showed a conformational heterogeneity, with one prevailing conformer. For the [Gly⁹]. -antamanide analog, the whole NMR data, combined with extensive theoretical calculations, were consistent with the presence of 1) two (β-turns of type I, centered on Gly⁹-Phe¹⁰ and Ala⁴-Phe⁵, respectively; 2) a central cavity with a six-carbonyl oxygen cage, optimal for a Na⁺ hexacoordination; 3) strongly H-bonded amide protons for residues 1 and 6, both involved in the formation of the two type I β-turns, which, however, exhibited some fluctuations during the molecular dynamics simulations. For the [Gly⁶]. -antamanide-Na⁺ complex the prevailing conformer was consistent with a more open structure, with the partial solvent exposure of all the amide protons; that is, the Gly residue in position 6 increases the flexibility of this critical site more than does the Gly in position 9. These data in some way parallel the results of the cytotoxicity tests on B16-F10 transformed cells for the two analogs: [Gly⁹]. -antamanide is cytotoxic after 48 h exposure, whereas [Gly⁶]. -antamanide is almost inactive. On the contrary, both analogs are practically inactive in vivo against phalloidin.     

Conformational study of cyclolinopeptide A

The conformation of cyclolinopeptide A, c(Pro-Pro-Phe-Phe-Leu-Ile-Ile-Leu-Val), a naturally occurring peptide with remarkable cytoprotective activity, has been investigated by means of distance geometry calculations and molecular dynamics simulations. The starting points for all the calculations were an X-ray structure and other structures obtained from distance geometry calculations based on NMR data. Restrained and unrestrained molecular dynamics simulations are reported in vacuo and in CCI₄. Structural and dynamic properties are investigated and compared with those experimentally determined. The conformation obtained from the MD simulations which best reproduces the NMR parameters is at the same time one of the most stable ones and is also fairly similar to the crystal structure. An explanation for the occurrence of multiple conformations in solution at room temperature is given.     

Cyclic hexapeptides related to somatostatin Conformational analysis employing 1H-NMR and molecular dynamics

We report the conformational analysis of a series of cyclic hexapeptides related to the hormone somatostatin utilizing ¹H NMR spectroscopy and NOE restrained molecular dynamics. The conformational preferences and results from biological analysis of these analogs (previous paper) allow for refinement of the current understanding of the structure-activity relationship of somatostatin. For most of the molecules examined, a βII′ turn about the d -tryptophan-lysine residues, postulated to be required for biological activity, was present. From the NOE restrained molecular dynamics, it can be seen that the turn structure is important for the maintenance of the proper orientation of the side chains of the adjacent phenylalanine, tryptophan and lysine. The biologically active analogs have the side chains of lysine and d -tryptophan extended away from the 18-membered ring in close proximity to each other for a significant portion of the dynamic simulations. Although other conformations are accessible and monitored during the simulations, we believe this is important for biological recognition. The absence of the βII′ turn at the d -tryptophan-lysine disrupts this side chain array producing inactive molecules. The role of the bridging region, the Phe-Pro dipeptide, is to stabilize the βII′ turn and help maintain the proper orientation of the biologically important side chains.     

Structure of cyclic peptides: the crystal and solution conformation of cyclo(Phe-Phe-Aib-Leu-Pro)

A solid-state and solution conformation analyses of the cyclopentapeptide cyclo(Phe-Phe-Aib-Leu-Pro) has been carried out by X-ray diffraction and nuclear magnetic resonance techniques. The structure of the hexagonal crystals, grown from a methanol solution [a=b= 16.530(4) Å, c= 21.356(9) Å, space group P6₅, Z = 6], shows the presence of one intramolecular N-H?O=C hydrogen bond with the formation of a γ-turn (C₇). The Aib³ residue, at the center of the γ-turn, presents unexpected values of the torsion angles [φ= 70.5° and ψ= -73.8°], which have been observed only once before for this helicogenic residue. A cis peptide bond occurs between Leu⁴ and Pro⁵; all other peptide bonds are trans. The overall conformation for the cyclopentapeptide with one cis-peptide bond on one side and an intramolecular γ-turn on the opposite side results in an equatorial topology of the side-chains of the Phe¹, Phe² and Leu⁴ residues. Indeed, the C^α-C^βand C^β-C^γ bonds of these residues lie approximately in the mean plane of the cyclic ring system. The structure is compared with data in the literature on cyclic pentapeptides. In addition the Pro-Phe-Phe moiety shows a conformation similar to that observed in other larger cyclic bioactive peptides, which indicates a reduced number of conformations for this sequence. The solution study was carried out in three different solvent systems: chloroform, acetonitrile and methanol in the temperature interval 220–300 K. In all three solvents the room temperature spectra show that the peptide is conformationally nonhomogeneous. In acetonitrile at low temperatures it is possible to reduce the conformational equilibrium to two predominant conformers which differ for the cis-trans isomerism of the Leu⁴-Pro⁵ peptide bond.     

Solution and solid-state structure of the diketopiperazine of tyrosyl-tetrahydroisoquinoline-3-carboxylic acid

δSelective antagonism of [L-Tic²]-peptides, including the simple dipeptide Tyr-L-Tic-NH₂, is linked to the Tyr-Tic-“recognition site”. In order to gain further information on the conformational preferences of the Tyr-Tic-moiety we have undertaken a structural study of a cyclic analog, the diketopiperazine of Tyr-Tic. A conformational study of cycle[-Tyr-Tic-], that is almost devoid of opioid activity, can also be useful to discriminate between the role of the two aromatic rings and of the basic nitrogen in determining antagonism. The structure of cycle[-Tyr-Tic-] has been solved in a DMSO/water solution at 278 K by NMR spectros-copy and in the solid state by X-ray diffraction methods. The two informations are almost identical, with an arrangement of the aromatic rings rather different from that of the putative bioactive conformation of the parent linear dipeptide. This difference points to the importance of coformational effects and is in agreement with the hypothesis that the positive center may be not essential for antogonism. © Munksgaard 1995.