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

Affinity capillary electrophoresis and quantum mechanical calculations applied to investigation of [Gly6 ]-antamanide binding with sodium and potassium ions

ACE in a free solution and quantum mechanical density functional theory have been applied to the investigation of interactions of glycine-6-antamanide ([Gly⁶ ]AA), a synthetic derivative of cyclic decapeptide antamanide isolated from the highly poisonous mushroom Amanita phalloides, with sodium or potassium ions in methanol. First, from the dependence of effective electrophoretic mobility of [Gly⁶ ]AA on Na⁺ or K⁺ ions concentration in the BGE (methanolic solution of 20 mM chloroacetic acid, 10 mM Tris, pH_MeOH 7.8, containing 0-50 mM NaCl or 0-40 mM KCl), the apparent binding (stability) constants of [Gly⁶ ]AA-Na⁺ and [Gly⁶ ]AA-K⁺ complexes were evaluated as 26 ± 1 and 14 ± 1 L/mol, respectively. The employed ACE method included correction of the effective mobilities measured at ambient temperature and at variable ionic strength of the BGEs to the mobilities related to the reference temperature 25°C and to the constant ionic strength 10 mM. Second, the interaction energies of the [Gly⁶ ]AA-Na⁺ and [Gly⁶ ]AA-K⁺ complexes (-466.3 and -345.2 kJ/mol, respectively) and the structural details of these complexes, such as position of the Na⁺ and K⁺ ions in the cavity of the [Gly⁶ ]AA molecule and the interatomic distances within these complexes, were determined by the density functional theory calculations.

Antamanide, a derivative of Amanita phalloides, is a novel inhibitor of the mitochondrial permeability transition pore

Antamanide is a cyclic decapeptide derived from the fungus Amanita phalloides. Here we show that antamanide inhibits the mitochondrial permeability transition pore, a central effector of cell death induction, by targeting the pore regulator cyclophilin D. Indeed, (i) permeability transition pore inhibition by antamanide is not additive with the cyclophilin D-binding drug cyclosporin A, (ii) the inhibitory action of antamanide on the pore requires phosphate, as previously shown for cyclosporin A; (iii) antamanide is ineffective in mitochondria or cells derived from cyclophilin D null animals, and (iv) abolishes CyP-D peptidyl-prolyl cis-trans isomerase activity. Permeability transition pore inhibition by antamanide needs two critical residues in the peptide ring, Phe6 and Phe9, and is additive with ubiquinone 0, which acts on the pore in a cyclophilin D-independent fashion. Antamanide also abrogates mitochondrial depolarization and the ensuing cell death caused by two well-characterized pore inducers, clotrimazole and a hexokinase II N-terminal peptide. Our findings have implications for the comprehension of cyclophilin D activity on the permeability transition pore and for the development of novel pore-targeting drugs exploitable as cell death inhibitors.

Exploring the conformational space of cyclic peptides by a stochastic search method

A stochastic search algorithm is applied in order to probe the conformations of cyclic peptides. The search is conducted in two stages. In the first stage, random conformations are generated and evaluated by a penalty function for ring closure ability, following a stepwise construction of each amino acid into the peptide by a random choice of one of its allowed conformations. The allowed conformational ranges of backbone dihedral angles for each amino acid have been extracted from a Data Bank of diverse proteins. Values of dihedral angles that do not contribute favorably to the scoring of ring closure are retained or discarded by a statistical test. Values are discarded up to a point from which all remaining combinations of angles are constructed, scored, sorted, and clustered. In the second stage, side chains have been added and fast optimization was applied to the set of diverse conformations in a "united atoms" approach, with the "Kollman forcefield" of Sybyl 6.8. This iterative stochastic elimination algorithm finds the global minimum and most of the best results, when compared to a full exhaustive search in appropriately sized problems. In larger problems, we compare the results to experimental structures. The root mean square deviation (RMSD) of our best results compared to crystal structures of cyclic peptides with sizes from 4 to 15 amino acids are mostly below 1.0 A up to 8 mers and under 2.0 A for larger cyclic peptides.

The cyclization of peptides and depsipeptides

Constricting the peptide backbone into a more defined conformational form through cyclization is an activity evolved in nature and in synthetic work, the latter straddling only the most recent decades. The resulting conformational constraints increase the probability of an optimum response with bio-receptors. The purpose of this review is to highlight developments that have proved to be reasonably efficient in the macrocyclization of linear precursors into cyclic peptides and depsipeptides.

An investigation of the ionophoric characteristics of destruxin A

Destruxin A, a cyclohexadepsipeptide related to the enniatins and beauvericin, exhibits ionophoric properties. Calcium ion mobilization across liposomal membrane barriers, for example, has been demonstrated using the calcium ion-sensitive dyes Arsenazo III and Fura-2. Initial molecular mechanics/molecular dynamics calculations indicate the potential for destruxin A to form a coordination complex with calcium in which the divalent cation is bound at the center of a sandwich formed by two molecules of destruxin A. This novel calcium ion binding may help explain the diverse biological effects exhibited by the destruxins.

Structural consequences of metal complexation of cyclo[Pro-Phe-Phe-Ala-Xaa]2 decapeptides

The conformational features of both free and Ca2+-complexed cyclo[Pro-Phe-Phe-Ala-Xaa]2 (with Xaa= Glu(OtBu), Lys(CIZ), Leu, and Ala) in solution have been determined by NMR spectroscopy and extensive distance-geometry calculations. The decapeptides are conformationally homogeneous in solution and show common structural features in their free and complexed forms. The structures of the free form contain only trans peptide bonds and are topologically similar to the structure of gramicidin-S, folded up in two antiparallel extended structures, stabilized by interstrand hydrogen bonds, and closed at both ends by two beta-turns. In contrast, the Ca2+-complexed peptides present two cis peptide bonds and are generally similar to those observed for the metal-complexed forms of antamanide and related analogues, folded into a saddle shape with two beta-turns. The Glu(OtBu)-, Leu-, and Lys(ClZ)-containing peptides examined here maintain the biological activity of the cyclolinopeptide A in their ability to competitively inhibit cholate uptake. The natural antamanide and cyclolinopeptide A are both able to inhibit the uptake of bile salts into hepatocytes. They share the same postulated active sequence Pro-Phe-Phe. Based on our structural results, we conclude that the ability to adopt a global conformation, characterized by a clear amphipathic separation of hydrophobic and hydrophilic surfaces, is an important feature for the functioning of this class of peptides.

Pharmacology of amphibian opiate peptides

In 1980 the skin of certain frogs belonging to the genus Phyllomedusinae was found to contain two new peptides that proved to be selective mu-opioid agonists, and named dermorphins. Since 1987 deltorphins, a family of highly selective delta-opioid peptides were identified either by cloning of the cDNA from frog skins or isolation of the peptides. The distinctive feature of opioid peptides is the presence of a naturally occurring D-enantiomer at the second position in their common N-terminal sequence, Tyr-D-Xaa-Phe. The discovery of the amphibian opiate peptides, provided new insights into the functional role of the mu- and delta-opiate systems. It also provided models for novel analgesics with enhanced therapeutic benefits and reduced toxicity.

What peptides these deltorphins be

The deltorphins are a class of highly selective delta-opioid heptapeptides from the skin of the Amazonian frogs Phyllomedusa sauvagei and P. bicolor. The first of these fascinating peptides came to light in 1987 by cloning of the cDNA of from frog skins, while the other members of this family were identified either by cDNA or isolation of the peptides. The distinctive feature of deltorphins is the presence of a naturally occurring D-enantiomer at the second position in their common N-terminal sequence, Tyr-D-Xaa-Phe, comparable to dermorphin, which is the prototype of a group of mu-selective opioids from the same source. The D-amino acid and the anionic residues, either Glu or Asp, as well as their unique amino acid compositions are responsible for the remarkable biostability, high delta-receptor affinity, bioactivity and peptide conformation. This review summarizes a decade of research from many laboratories that defined which residues and substituents in the deltorphins interact with the delta-receptor and characterized pharmacological and physiological activities in vitro and in vivo. It begins with a historical description of the topic and presents general schema for the synthesis of peptide analogues of deltorphins A, B and C as a means to document the methods employed in producing a myriad of analogues. Structure activity studies of the peptides and their pharmacological activities in vitro are detailed in abundantly tabulated data. A brief compendium of the current level of knowledge of the delta-receptor assists the reader to appreciate the rationale for the design of these analogues. Discussion of the conformation of these peptides addresses how structure leads to further hypotheses regarding ligand receptor interaction. The review ends with a broad discussion of the potential applications of these peptides in clinical and therapeutic settings.

Novel sodium binding properties of some cyclopentapeptide endothelin A selective receptor antagonists: electrospray and fast-atom-bombardment mass spectrometric studies

Electrospray ionization and fast atom bombardment mass spectrometric methods reveal novel interactions of endothelin A selective receptor antagonists, cyclo(D-Trp-D-Asp-Pro-D-Val-Leu), cyclo(D-Trp-D-Glu-Ala-D-allo-Ile-Leu) and cyclo(D-Trp-D-Asp-Pro-D-Ile-Leu) with sodium ions. The peptides have very high intrinsic affinities for sodium ions, and form multiple sodium adducts and sandwich structures: [M + Na]+, [M + 2Na - H]+, [M + 3Na - 2H]+, [M + 4Na - 3H]+, [M + 5Na - 4H]+, [2M + Na]+, [2M + 2Na - H]+, [2M + 3Na - 2H]+, [2M + 4Na - 3H]+, [2M + 5Na - 4H]+, [2M + 6Na - 5H]+, and [2M + 7Na - 6H]+. The three cyclic peptides exhibit similar sodium binding stoichiometries despite differences in their amino acids. The observed sodium binding properties may have implications in understanding their protective effects against ischemia-induced acute renal failure. Those cyclic peptides that offer protection may be those that have high affinities for multiple sodium ions.