Fullerene-based amino acids and peptides.

Recent advances in the chemistry of fullerene have allowed the synthesis of many classes of novel fullerene derivatives. Among these classes, fullerene-based amino acids and peptides are particularly interesting, both for structural studies and biological applications. In this review, we will discuss our own achievements in this rapidly growing field. In particular, the application of fulleroproline (Fpr) amino acids and peptides to medicinal chemistry and material science will be highlighted.     

Metabolic regulatory mechanisms and physiological roles of functional amino acids and their applications in yeast

ABSTRACT

In yeast, amino acid metabolism and its regulatory mechanisms vary under different growth environments by regulating anabolic and catabolic processes, including uptake and export, and the metabolic styles form a complicated but robust network. There is also crosstalk with various metabolic pathways, products and signal molecules. The elucidation of metabolic regulatory mechanisms and physiological roles is important fundamental research for understanding life phenomenon. In terms of industrial application, the control of amino acid composition and content is expected to contribute to an improvement in productivity, and to add to the value of fermented foods, alcoholic beverages, bioethanol, and other valuable compounds (proteins and amino acids, etc.). This review article mainly describes our research in constructing yeast strains with high functionality, focused on the metabolic regulatory mechanisms and physiological roles of “functional amino acids”, such as l-proline, l-arginine, l-leucine, l-valine, l-cysteine, and l-methionine, found in yeast.     

Peptidase-mediated storage of amino acids in small peptides

Adult Calliphora contain a large and heterogenous pool of small peptides, which it is supposed come from protein catabolism. Their composition and rapid turn-over appears to be determined in part by a group of peptidases. The activity of the peptidases is inhibited non-competitively by free amino acids and most effectively by the essential amino acids which are also those which stimulate feeding on protein. Thus it seems that as flies feed on protein containing the essential amino acids peptide emerging from catabolized protein tends to remain as peptide until the internal concentrations of the essential amino acids fall. This provides the fly with a physiologically tolerable reservoir of amino acids.     

Free amino acids and γ-glutamyl peptides in fagaceae

Amino acids have been investigated in seeds and fresh parts of members of the Fagaceae. Seeds from the genus Fagus contain willardiine, 5-hydroxy-6-methylpipecolic acids, N-[N-(3-amino-3-carboxypropyl)-3-amino-3-carboxypropyl]azetidine-2-carboxylic acid and γ-glutamyl peptides, mainly γ-glutamylphenylalanine. These compounds are nearly or totally absent from leaves of F. silvatica and from seedlings and immature seeds of F. silvatica var. purpurea; instead, the seedlings contain large amounts of γ-l-glutamyl-l-isoleucine and γ-l-glutamyl-l-leucine. γ-l-Glutamyl-l-tryptophan and γ-l-glutamyl-γ-l-glutamyl-l-phenylalanine, not previously known from nature, have been isolated from seeds of F. silvatica var. purpurea. The structures have been confirmed by syntheses. 4-Hydroxypipecolic acid (with trans-configuration) has been identified in seeds of F. japonica Maxim. and F. sieboldii Endl. None of the above compounds was found in Quercus or Castanea species whereas argininosuccinic acid was identified in Castanea sativa.     

Molecular design of functional peptides by utilizing unnatural amino acids: toward artificial and photofunctional protein

Unnatural amino acids are effective as building blocks to design functional peptides from the following two points: (1) utilization of rigid unnatural amino acids for the incorporated peptides to control the conformation to appear the function, and (2) incorporation of functional and unnatural amino acids into peptides resulting in appearance of the inherent functions. As a combined strategy, molecular design of artificial metalloproteins utilizing 5'-amino-2,2'-bipyridine-5-carboxilic acid (H-5Bpy-OH) as an unnatural amino acid is proposed. The peptide containing three residues of the unnatural amino acid would fold through coordination to a metal ion. In particular, ruthenium(II) ion would yield a ruthenium tris(bipyridine) derivative as the core complex of the artificial protein, which would appear the similar photochemical functions as that of ruthenium(II) tris(bipyridine) complex. The central complex could form two isomers, fac and mer. For selective synthesis of the mer complex, which is expected as the core complex in the artificial protein, dicyclohexylamide as a bulky group is introduced at the C-terminal of the unnatural amino acid to destabilize the fac complex due to steric hindrance. Furthermore, in order to know the photochemical properties and function of the protein mimics, ruthenium(II) tris(2,2'-bipyridine) complexes bearing amide groups at 5,5' positions have been synthesized as the model complexes. As a result, the direction of amide groups (RNHCO-or RCONH-) in ruthenium complexes is found to significantly affect the emission efficiency: the former reduces the quantum yield and the latter enhances it, respectively. The ruthenium(II) tris(5,5'-diamide-2,2'-bipyridine) complexes are also found to strongly bind with various anions [e.g., halogen ions (Cl-, Br-) and acetate anion] in acetonitrile and to detect these anions through the emission spectral changes under air. The molecular design of artificial protein is expected to develop new fields among peptide, organic, inorganic, and physical chemistry.     

Different effects of peptides and their amino acids on antibody production and phagocytic activity of the neutrophils in mice

The effects of some natural polypeptides fragments and amino acids which were incorporated in them on the thymus-dependent SRBC immune response and on the phagocytosis of Staphylococcus by murine peritoneal neutrophils were compared. It was found that the peptides LGIP and PYIK which consisted of those amino acids that stimulated phagocytosis but did influence the immune response (K, P, Y, L) did not change the immune response as well as phagocytosis. The peptides TKPR, TTKD and LGIPE which included those amino acids that were able to stimulate both immune response and phagocytosis (T, E, D) enhanced both activities. Nevertheless the peptide PYIKV containing valine (that stimulated the antibody production as well as phagocytosis) did not effect the immune response but enhanced the phagocytic index. The existence of two immunoregulatory systems--the peptide system and the amino acid one--was suggested.     

Adsorption of amino acids and peptides on an activated carbon-fibrous material

The adsorption process of amino acids and peptides by the activated carbon-fibrous material has been studied. The adsorption depends on availability of aromatic and some hydrophobic (isoleucine, leucine, methionine) amino acids. These data permit explaining the mechanism of the adsorption of protein fragments by the carbon-fibrous material and elaborating principles of the bioassay of carbon-fibrous sorbents and purifying some proteins and other substances.     

Hypochlorite-induced oxidation of amino acids, peptides and proteins

Summary. Activated phagocytes generate the potent oxidant hypochlorite (HOCl) via the release of the enzyme myeloperoxidase and hydrogen peroxide. HOCl is known to react with a number of biological targets including proteins, DNA, lipids and cholesterol. Proteins are likely to be major targets for reaction with HOCl within a cell due to their abundance and high reactivity with HOCl. This review summarizes information on the rate of reaction of HOCl with proteins, the nature of the intermediates formed, the mechanisms involved in protein oxidation and the products of these reactions. The predicted targets for reaction with HOCl from kinetic modeling studies and the consequences of HOCl-induced protein oxidation are also discussed.     

Computer-assisted assignment of peptides with non-standard amino acids

Summary A comprehensive peptide assignment program and its application to a cyclic peptide, cyclosporin A, are presented in this paper. A group of graph theoretical algorithms using fuzzy logic are discussed with the aid of examples from cyclosporin A. The algorithms deal with heavily overlapped peaks, recover disjointed and distorted spin coupling networks, and include strategies for sequence-specific assignment. A procedure to extend the Protein Knowledge Base for automatically assigning non-standard amino acid residues is also presented. The program is capable of completely automated assignment for small peptides (20 residues). For such molecules, it is insensitive to whether the peptide chain is cyclic or acyclic, and to whether amide protons are present or absent. For larger peptides/proteins, more user interaction is required and the sequence-specific assignment step usually must proceed through fragments smaller than the full length to avoid problems due to occurrence of a combinatorial explosion. The program can be applied as a rigorous tool to check manual assignments. The fuzzy graph theoretical concepts built in the program are illustrated with 2D proton spectra of a peptide, but may be extended to higher-dimensional spectra, other biopolymers, natural products and other organic structures.     

Solution- and solid-phase synthesis and anti-HIV activity of maslinic acid derivatives containing amino acids and peptides

Maslinic acid (1) has been coupled at C-28 with several α- and ω-amino acids by using solution- and solid-phase synthetic procedures. Twelve derivatives (2–13) with a single amino acid residue were prepared in solution phase, whereas a dipeptide (14), a tripeptide (15), and a series of conjugate dipeptides (16–24) were synthesized in solid phase. The anti-HIV activity of these compounds was assessed on MT-2 cells infected with viral clones carrying the luciferase gene as a reporter. While in maslinic acid (1) were present both cytotoxic and antiviral activities, only the derivatives 13 and 24 showed anti-HIV-1 activity and therefore represent a novel class of anti-HIV-1 compounds.     

Design and synthesis of biologically active peptides: a 'tail' of amino acids can modulate activity of synthetic cyclic peptides

In earlier work, we synthesized a cyclic 9-amino acid peptide (AFPep, cyclo[EKTOVNOGN]) and showed it to be useful for prevention and therapy of breast cancer. In an effort to explore the structure–function relationships of AFPep, we have designed analogs that bear a short ‘tail’ (one or two amino acids) attached to the cyclic peptide distal to its pharmacophore. Analogs that bore a tail of either one or two amino acids, either of which had a hydrophilic moiety in the side chain (e.g., cyclo[EKTOVNOGN]FS) exhibited greatly diminished biological activity (inhibition of estrogen-stimulated uterine growth) relative to AFPep. Analogs that bore a tail of either one or two amino acids which had hydrophobic (aliphatic or aromatic) side chains (e.g., cyclo[EKTOVNOGN]FI) retained (or had enhanced) growth inhibition activity. Combining in the same biological assay a hydrophilic-tailed analog with either AFPep or a hydrophobic-tailed analog resulted in decreased activity relative to that for AFPep or for the hydrophobic-tailed analog alone, suggesting that hydrophilic-tailed analogs are binding to a biologically active receptor. An analog with a disrupted pharmacophore (cyclo[EKTOVGOGN]) exhibited little or no growth inhibition activity. An analog with a hydrophilic tail and a disrupted pharmacophore (cyclo[EKTOVGOGN]FS) exhibited no growth inhibition activity of its own and did not affect the activity of a hydrophobic-tailed analog, but enhanced the growth inhibition activity of AFPep. These results are discussed in the context of a two-receptor model for binding of AFPep and ring-and-tail analogs. We suggest that tails on cyclic peptides may comprise a useful method to enhance diversity of peptide design and specificity of ligand–receptor interactions.