Amino acidic scaffolds bearing unnatural side chains: an old idea generates new and versatile tools for the life sciences.

The unnatural amino acids (UAAs) are members of a class of molecules with relevant impacts in the life sciences. Due to the role of these molecules in the modulation of the chemical and physical properties of biological and inorganic materials, UAAs have attracted increasing interest in recent years. The aim of this review is to highlight (i) the most recent and innovative synthetic routes for the preparation of UAAs, (ii) the recently marketed UAA-based drugs, and (iii) the most promising technological applications involving novel UAA-containing molecular entities.

The Mycobacterium tuberculosis chaperonin 10 monomer exhibits structural plasticity.

The conditions which favor dissociation of oligomeric Mycobacterium tuberculosis chaperonin 10 and the solution structure of the monomer were studied by analytical ultracentrifugation, size exclusion chromatography, fluorescence, and circular dichroism spectroscopies. At neutral pH and in the absence of divalent cations, the protein is fully monomeric below approximately a 4.7 microM concentration.

Mycobacterium tuberculosis chaperonin 10 is secreted in the macrophage phagosome: is secretion due to dissociation and adoption of a partially helical structure at the membrane?

To confirm that Mycobacterium tuberculosis chaperonin 10 (Cpn10) is secreted outside the live bacillus, infected macrophages were examined by electron microscopy. This revealed that the mycobacterial protein accumulates both in the wall of the bacterium and in the matrix of the phagosomes in which ingested mycobacteria survive within infected macrophages. To understand the structural implications underlying this secretion, a structural study of M.

Global 3D-QSAR methods: MS-WHIM and autocorrelation.

The recently proposed MS-WHIM indices, a set of theoretical descriptors containing information about size, shape and electrostatic distribution of a molecule, have been further investigated. The main objectives of this work were: (i) to confirm the descriptive power of MS-WHIM in modelling specific biological interactions, (ii) to analyse the dependence of MS-WHIM on the type of atomic charges used for computing electrostatic potential and (iii) to compare the performances of MS-WHIM with those provided by other global 3D molecular descriptors. The spatial autocorrelation of atomic and molecular surface properties were selected for comparison purposes.

Pharmacokinetics of ITF 296 (Sinitrodil) a novel organic nitrate, in healthy volunteers.

ITF 296 is a new orally active nitrate acting selectively on large arterial vessels over a wide range of doses. In healthy volunteers it causes less reduction in vascular resistance and less venodilatation than classic nitrates. Its pharmacokinetic profile was evaluated after intravenous infusion and oral (solution and immediate-release tablet) administration in a randomised cross-over design on 11 healthy volunteers.

The interaction of myristylated peptides with the catalytic domain of protein kinase C revealed by their sequence palindromy and the identification of a myristyl binding site.

Using a model of the enzyme structure and the results from a series of free and myristylated peptides, we provide evidence that peptides corresponding to the pseudosubstrate sequence of protein kinase C bind to the enzyme substrate binding site in an essentially extended conformation. This and the nearly symmetrical location of positive charges around the substrate phosphoritable site allow the peptide to bind to the enzyme in either an N-to-C orientation or its C-to-N opposite orientation. The latter is favoured by a change in residue chirality or when the peptide bears a myristoyl chain at its N-terminus.

Application of reversible biotinylated label for directed immobilization of synthetic peptides and proteins: isolation of ligates from crude cell lysates.

Chaperonin 10 protein from Rattus norvegicus (Rat cpn 10) has been reported to bind chaperonin 60 from Escherichia coli (GroEL) in an ATP-dependent manner. Chemically synthesized Rat cpn10 was immobilized in a defined orientation to agarose-bound monomeric avidin using a reversible biotinylated affinity label (1), attached to the N alpha-terminal residue. The resulting affinity chromatographic matrix was then used to isolate binding proteins from a crude cell lysate.

The structural and aggregation properties of the synthetic C-terminal half (104-mer) polypeptide from HIV p24gag resemble those of full-length protein.

The aggregation and structural properties of the synthetic C-terminal half [Ala330, Ala350(270-373; 104-mer)] polypeptide from HIV-1 p24gag were studied. In concentrated solutions the synthetic polypeptide aggregated to tetramers which, upon dilution, gave a mixture of monomeric and dimeric and dimeric species. These results correlated well with the in vitro aggregation properties of recombinant p24.

Mycobacterium tuberculosis chaperonin 10 and N-truncated fragments. Their synthesis and purification by the isoelectric focusing technique carried out in solution.

The Mycobacterium tuberculosis chaperonin 10 protein and fragments corresponding to sequences 59-99, 51-99 and 26-99 were synthesised by the solid-phase methodology using a double coupling protocol and without the aid of capping agents. After the final acid cleavage using the low TFMSA-high HF protocol the polypeptides were purified by either the ion exchange chromatography/RP-HPLC combination or the isoelectric separation carried out in solution and followed by semi-preparative RP-HPLC. Comparison of the results obtained through the two approaches indicated that in general the isoelectricfocusing/HPLC combination was superior both in terms of recovery of final material and its purity.

MS-WHIM, new 3D theoretical descriptors derived from molecular surface properties: a comparative 3D QSAR study in a series of steroids.

The recently proposed WHIM (Weighted Holistic Invariant Molecular) approach [Todeschini, R., Lasagni, M. and Marengo, E.

The use of crown ethers in peptide chemistry-V. Solid-phase synthesis of peptides by the fragment condensation approach using crown ethers as non-covalent protecting groups.

We have previously described the conditions by which peptide synthesis by the solid-phase fragment condensation approach can be carried out using crown ethers as non-covalent protection for the N alpha-amino group. Here we demonstrate that the procedure can be extended to large, partially protected peptide fragments possessing free Lys and/or Arg residues. The first step was to ensure that complex formation on the side chain of amino acids was not detrimental to the methodology and exhibited the same solubility and coupling properties as N alpha-complexed peptides.

Chemical synthesis and purification of proteins: a methodology.

Classical stepwise solid-phase peptide synthesis (SPPS) has been used successfully for the synthesis of proteins up to 150 residues in length, although usually with poor yields and homogeneity. The major limitation has been the inability to separate chromatographically similar deletion and truncated impurities from the target sequence. We have developed a highly effective protocol for stepwise SPPS and 'one-step' purification of small proteins.

Rational design of a new C-myristylamido peptide exerting potent and selective PKC inhibitory activity.

A 3D model of the catalytic domain of PKC was built based on the X-ray structure of the homologous PKA enzyme. The two enzymes were found to have similar general architecture although differing for the number of negatively charged clusters and their location near the phosphorylation site. These differences were consistent with the charge requirements deduced from the consensus sequence of PKC and PKA substrates.

The solution conformational features of two highly homologous antigenic peptides of foot-and-mouth disease virus serotype A, variant A and USA, correlate with their serological properties.

The solution structure of a peptide corresponding to the VP1 region 141-160 of foot-and-mouth disease virus (FMDV) serotype A variant USA has been studied by NMR and computer calculations and compared with the results from a study on a highly homologous peptide deriving from serotype A, variant A. The two peptides differ in their serological behavior and contain the immunodominant epitope of the virus which partly overlaps with its receptor binding region. Distance constraints, derived both from 2D and 3D homonuclear NMR and 2D-heteronuclear NMR experiments, were combined with DG calculations to yield 50 structures.

Mycobacterium tuberculosis chaperonin 10 forms stable tetrameric and heptameric structures. Implications for its diverse biological activities.

The chaperonin activity of sequence-related chaperonin 10 proteins requires their aggregation into heptameric structures. We describe size-exclusion chromatography and ultracentrifugation studies that reveal that while Escherichia coli chaperonin 10 exists as a heptamer, the Mycobacterium tuberculosis chaperonin 10 is tetrameric in dilute solutions and in whole M. tuberculosis lysate.

Affinity purification of 101 residue rat cpn10 using a reversible biotinylated probe.

The purification of large synthetic peptides using conventional separation techniques often results in poor yields and homogeneity due to the accumulation of chromatographically similar deletion and truncated impurities. We have developed a highly effective synthetic strategy and one-step purification procedure that is based on (i) the application of single coupling using HBTU/HOBt activation to reduce incomplete couplings, (ii) the use of N-(2-chlorobenzyloxycarbonyloxy)succinimide as a capping agent to terminate deletion sequences and (iii) the N-terminal derivatization of the complete peptidyl-resin with a reversible Fmoc-based chromatographic probe possessing enhanced physico-chemical properties (i.e.

Sequence and structural homologies between M. tuberculosis chaperonin 10 and the MHC class I/II peptide binding cleft.

The peptide corresponding to the C-terminal half of M.tuberculosis hsp10 was synthesised based on the prediction that it might represent an independent structural region of the protein. This hypothesis was confirmed by aggregation and CD studies using this peptide and longer sequences of the protein.

Different cytotoxic activity and intracellular fate of an anti-CD5-momordin immunotoxin in normal compared to tumour cells.

We investigated the different sensitivity of peripheral blood mononuclear cells (PBMC) and human T cell leukaemias (Jurkat and CEM) to an anti-CD5-momordin immunotoxin. In a short-term assay, the immunotoxin displayed different cytotoxic activity on normal and tumour cells: for leukaemic cell lines an incubation time of 72 h was necessary for the immunotoxin to reach the IC50 of 41-53 pM, compared to the 1 h sufficient for 6 pM immunotoxin to inhibit 50% of PBMC protein synthesis. In a long-term clonogenic assay (15 days), the immunotoxin demonstrated a comparable efficacy of clonogenic cell killing for both cell types.

Cochaperonins are histone-binding proteins.

Cochaperonins (cpn10) assist chaperonins (cpn60) in mediating folding of polypeptide substrates in an ATP-dependent reaction. Moreover, they have been shown to be secretory products of living cells and to perform discrete biological activities without the need to interact with cpn60. Here, we have investigated the possible existence of cellular cpn10 binding sites that could mediate such activities.

Chemical synthesis and characterisation of rat chaperonin 10: effect of chain length, ions, heat and N-terminal acetylation on unchaperoned folding into its heptameric form.

Recently, the sequence of mitochondrial chaperonin 10 from Rattus norvegicus (rat cpn10), with N-terminal acetylation, has been published. Two syntheses of rat cpn10 were performed, the first using a classical carbodiimide-mediated double coupling protocol (Method A) and the second a more efficient HBTU/HOBT/single coupling procedure (Method B). The latter also involved the application of a capping procedure, using N-(2-chlorobenzyloxycarbonyloxy)succinimide [Z(2-Cl)-OSu].

In vitro and in vivo properties of an anti-CD5-momordin immunotoxin on normal and neoplastic T lymphocytes.

An anti-CD5 monoclonal antibody (mAb) was linked to the plant toxin momordin, a type-1 ribosome-inactivating protein purified from Momordica charantia. The in vitro cytotoxicity of the immunotoxin was evaluated as the inhibition of protein and/or DNA synthesis on isolated peripheral blood mononuclear cells (PBMC) and on human T cell leukemia Jurkat. The potency of the immunotoxin on PBMC was very high (IC50 = 1 - 10 pM) and was not affected by blood components.

Iron protein succinylate: preclinical safety assessment.

In this brief review the preclinical safety studies on iron protein succinylate (synonym: ITF 282) are presented. Iron protein succinylate is an iron-protein complex, in which iron is present in ferric form. It has been developed for oral iron-supplementation therapy and is characterized by a very favorable tolerability profile.

Mutagenicity testing of imidazole and related compounds.

Ames tests have been performed with imidazole and its principal metabolites, hydantoin and hydantoic acid. N-Acetyl-imidazole, a potential metabolite resulting from the action of intestinal bacteria, and histamine, a structurally related compound which is widely distributed in mammalian tissues, have also been tested. Imidazole and histamine were also tested in the UDS assay in primary rat hepatocytes, while imidazole alone was tested in the M2-C3H mouse fibroblast malignant transformation assay.

Purification of synthetic peptides using reversible chromatographic probes based on the Fmoc molecule.

A rapid, versatile, reversible procedure for purifying synthetic peptides has been developed based on the specific incorporation of 4-carboxylate Fmoc derivatives onto the terminal amino acid of peptidyl-resins. The acid stable 4-COR-Fmoc derivatives were synthesised with a variety of chemical groups thus altering the chromatographic properties of the "target" peptides and permitting their convenient purification, either by reversed-phase HPLC or ion exchange chromatography. The assembly of the peptides involved a capping step to prevent the formation of deletion forms.