Studies on the reaction of glutathione and formaldehyde using NMR

Within cells it is proposed that a major mechanism for the metabolism of formaldehyde is via its reaction with glutathione (GSH) to form S-hydroxymethylglutathione (HMG), which undergoes subsequent oxidation. In addition to HMG and the previously reported (5R,10S)-5-(carboxymethylcarbamoyl)-7-oxo-3-thia-1,6-diazabicyclo[4.4.1]undecane-10-carboxylic acid (BiGF(2)), NMR studies on the reaction of GSH with formaldehyde reveal two previously unassigned monocyclic structures. The results imply that the biologically relevant reactions between aldehydes and peptides/proteins may be more complex than presently perceived.

Using NMR solvent water relaxation to investigate metalloenzyme-ligand binding interactions

This report demonstrates that solvent water relaxation measurements can be used for quantitative screening of ligand binding and for mechanistic investigations of enzymes containing paramagnetic metal centers by using conventional NMR instrumentation at high field. The method was exemplified using prolyl hydroxylase domain containing enzyme 2 (PHD2), a human enzyme involved in hypoxic sensing, with Mn(II) substituting for Fe(II) at the active site. K(D) values were determined for inhibitors that hinder access of water to the paramagnetic center. This technique is also useful for investigating the mechanism of suitable metalloenzymes, including order of ligand binding and modes of inhibition.

Group epitope mapping considering relaxation of the ligand (GEM-CRL): including longitudinal relaxation rates in the analysis of saturation transfer difference (STD) experiments

In the application of saturation transfer difference (STD) experiments to the study of protein-ligand interactions, the relaxation of the ligand is one of the major influences on the experimentally observed STD factors, making interpretation of these difficult when attempting to define a group epitope map (GEM). In this paper, we describe a simplification of the relaxation matrix that may be applied under specified experimental conditions, which results in a simplified equation reflecting the directly transferred magnetisation rate from the protein onto the ligand, defined as the summation over the whole protein of the protein-ligand cross-relaxation multiplied by with the fractional saturation of the protein protons. In this, the relaxation of the ligand is accounted for implicitly by inclusion of the experimentally determined longitudinal relaxation rates. The conditions under which this "group epitope mapping considering relaxation of the ligand" (GEM-CRL) can be applied were tested on a theoretical model system, which demonstrated only minor deviations from that predicted by the full relaxation matrix calculations (CORCEMA-ST) [7]. Furthermore, CORCEMA-ST calculations of two protein-saccharide complexes (Jacalin and TreR) with known crystal structures were performed and compared with experimental GEM-CRL data. It could be shown that the GEM-CRL methodology is superior to the classical group epitope mapping approach currently used for defining ligand-protein proximities. GEM-CRL is also useful for the interpretation of CORCEMA-ST results, because the transferred magnetisation rate provides an additional parameter for the comparison between measured and calculated values. The independence of this parameter from the above mentioned factors can thereby enhance the value of CORCEMA-ST calculations.

Carboxymethylproline synthase catalysed syntheses of functionalised N-heterocycles

The utility of wild-type and variant carboxymethylproline synthases for biocatalysis was demonstrated by preparing functionalised 5-, 6- and 7-membered N-heterocycles from amino acid aldehydes and (alkylated) malonyl-coenzyme A derivatives; the N-heterocycles produced were converted to the corresponding bicyclic beta-lactams by a carbapenem synthetase.

Ammonium-directed dihydroxylation of 3-aminocyclohex-1-enes: development of a metal-free dihydroxylation protocol

Treatment of 3-aminocyclohex-1-enes with mCPBA in the presence of trichloroacetic acid gives the corresponding 1,2-anti-2,3-syn-1-trichloroacetoxy-2-hydroxy-3-aminocyclohexane with high levels of diastereoselectivity (90% de). This is consistent with a mechanism of oxidation involving hydrogen-bonded delivery of the oxidant by the allylic ammonium ion formed in situ, followed by highly regioselective ring-opening of the intermediate epoxide by trichloroacetic acid. The effect of conformational constraints upon the oxidation reaction is also examined.

Swarm formation in the desert locust Schistocerca gregaria:isolation and NMR analysis of the primary maternal gregarizing agent

Depending on their rearing density, female desert locusts Schistocerca gregaria epigenetically endow their offspring with differing phenotypes. To identify the chemical basis for such maternal transmission, we compared solitarious and gregarious locust egg pod foam using high performance liquid chromatography (HPLC). We revealed causal relationships between foam chemistry and hatchling phenotype (phase state) by iteratively applying HPLC fractions from gregarious locust egg foam extracts to solitarious eggs and assessing resulting hatchlings with a behavioural bioassay involving logistic regression. Selection and application of increasingly specific HPLC fractions allowed us to isolate compounds with gregarizing properties. Hatchling gregarization was triggered only by certain fractions and was dose dependent. In a final series of experiments, we characterized the most specific gregarizing fraction by nuclear magnetic resonance (NMR) spectroscopy. Here we present tentative structural features of the primary locust maternal gregarizing agent, which appears to be an alkylated l-dopa analogue. In addition, we propose a mechanism for phase-dependent regulation of this compound's activity.

Inhibition of mycobacterial arylamine N-acetyltransferase contributes to anti-mycobacterial activity of Warburgia salutaris

In this study, we show that extracts and a purified compound of Warburgia salutaris exhibit anti-mycobacterial activity against Mycobacterium tuberculosis H37Rv and Mycobacterium bovis BCG Pasteur. The extracts did not inhibit growth of Escherichia coli and were not toxic to cultured mammalian macrophage cells at the concentrations at which anti-mycobacterial activity was observed. The extract and pure compound inhibited pure recombinant arylamine N-acetyltransferase (NAT), an enzyme involved in mycobacterial cell wall lipid synthesis. Moreover, neither extract nor pure compound inhibited growth of a strain of M. bovis BCG in which nat has been deleted suggesting that NAT may indeed be a target within the mycobacterial cell. The purified compound is a novel drimane sesquiterpenoid lactone, 11alpha-hydroxycinnamosmolide. These studies show that W. salutaris is a useful source of anti-tubercular compounds for further analysis and supports the hypothesis of a link between NAT inhibition and anti-mycobacterial activity.

Metal-driven ligand assembly in the synthesis of cyclodextrin [2] and [3]rotaxanes

Cyclodextrin [2] and [3]rotaxanes have been synthesised by use of a metal-driven ligand formation methodology. The kinetically stable cobalt(III) complexes formed act as either linking or capping groups, the function being selected by manipulation of the reaction conditions to promote the formation of either 2:1 or 1:1 complexes, respectively. In all cases, mixtures of isomers containing different alpha-cyclodextrin orientations were observed. All three orientational isomers of the [3]rotaxane were isolated and structurally characterized by 2D NMR.

Sequential Desymmetrization–Fluorination: Enantioselective Synthesis of Fluorinated Cyclitols

An asymmetric synthesis of enantioenriched, highly functionalized fluorinated carbocycles has been developed based on an enantioselective Sharpless dihydroxylation of cyclohexadienylsilanes, combined with a diastereoselective electrophilic fluorodesilylation. Several parameters define the level of diastereocontrol for the fluorination step. These include the relative stereochemistry of the starting endocyclic allylsilanes and the structural features of the reactants. As expected for an S(E)2' mechanism, the fluorodesilylation occurred with clean transposition of the double bond, with the attack of the electrophilic fluorinating agent taking place preferentially anti to the silyl group. For the fluorination step, the best selectivities were observed for the monocyclic anti,syn benzyl-protected precursors and for the syn,syn starting allylsilane. Full NMR spectroscopic analysis of the fluorinated monocyclic compounds, which possess an endocyclic double bond flanked by two electronegative groups (the methoxy group and the fluorine substituent) revealed that a subtle combination of steric (1,3-axial/pseudoaxial interaction) and stereoelectronic effects (pi-sigma* interaction) favours the preferential conformers featuring the methoxy group in a pseudoaxial position.

Synthesis of N-glycan oxazolines: donors for endohexosaminidase catalysed glycosylation

Oxazoline mono-, di-, tri- and hexasaccharides, corresponding to the core components of N-linked glycoprotein high mannose glycans, are synthesised as potential glycosyl donors for endohexosaminidase catalysed glycosylation of glycopeptides and glycoprotein remodelling. The crucial beta-D-Manp-(1-->4)-D-GlcpNAc linkage is synthesised via epimerisation of gluco disaccharide substrates by sequential triflation and nucleophilic substitution. Oxazolines are formed directly from the anomeric OPMP protected N-acetyl glucosamine derivatives. Efficient endohexosaminidase catalysed glycosylation of a synthetic beta-D-GlcpNAcAsn glycosyl amino acid is demonstrated with the trisaccharide oxazoline donor.

Hypoxia-inducible factor prolyl hydroxylase 2 has a high affinity for ferrous iron and 2-oxoglutarate

Regulation of the hypoxic response in humans is regulated by the post-translational hydroxylation of hypoxia inducible transcription factor; a recombinant form of a human prolyl-4-hydroxylase (PHD2) was characterised and shown to have an unexpectedly high affinity for, and to copurify with endogenous levels of, its Fe(ii) cofactor and 2-oxoglutarate cosubstrate.

Helix-Forming Carbohydrate Amino Acids

[reaction: see text] The solution-phase conformational properties of tetrameric and octameric chains of C-glycosyl alpha-d-lyxofuranose configured tetrahydrofuran amino acids (where the C-2 and C-5 substituents on the tetrahydrofuran ring are trans to each other) were examined using NMR and IR and CD in organic solvents. Studies by NMR and IR demonstrated that in chloroform solution, the tetramer 7 does not adopt a hydrogen-bonded conformation whereas the octamer 10 populates a well-defined helical secondary structure stabilized by 16-membered (i, i - 3) interresidue hydrogen bonds, similar to a pi-helix. Circular dichroism studies in trifluoroethanol are consistent with this conformation for the octamer 10, and also indicate that the tetramer 7 adopts a rigid conformation not stabilized by hydrogen bonds.

Synthesis, structure and dynamics of methoxynaphthalene-substituted phospha-ruthenocenes and -ferrocenes

The syntheses of potassium 2-(2'-methoxynaphth-1'-yl)-3,4-dimethyl-5-phenylphospholide 4 and eta5-pentamethylcyclopentadienyl(eta5-2-(2-methoxynaphth-1-yl)-3,4-dimethyl-5-phenylphospholyl)-ruthenium(II)5 and -iron(II)6 are described. The barrier to rotation of the naphthyl group (79 kJ mol-1 and 72 kJ mol-1 in CD2Cl2 respectively) characterises 5 and 6 as potential tropos type ligands. Coordination of 5 to [PtCl2(PEt3)] gives two cis and two trans complexes [PtCl2(PEt3)5] wherein rotation about the phospholyl-naphthyl vector is slow.

Conformational studies of oligomeric oxetane-based dipeptide isosteres derived fromL-rhamnose orD-xylose

Conformational investigations have been undertaken on oligomers (dimers, tetramers, hexamers) of five closely related oxetane-based dipeptide isosteres. All the oligomers were subjected to a range of studies by NMR, FT-IR and CD spectroscopy. The oligomers derived from methyl 2,4-anhydro-5-azido-3-O-tert-butyldimethylsilyl-5-deoxy-L-rhamnonate 'monomer' all exhibited evidence of ordered conformations in chloroform and 2,2,2-trifluoroethanol (TFE) solution. 5-Acetamido and N-methylamide derivatives of the L-rhamnonate 'monomer', along with a 'dimer' lacking silyl protection at C-3, were synthesized to ascertain the role of intramolecular interactions. This led to the conclusion that, for the L-rhamnonate oligomers, steric interactions govern the conformational preference observed. The equivalent silyl-protected D-lyxonate oligomers gave ordered CD spectra in TFE solution, but NMR and FT-IR spectroscopy in chloroform solution suggested an irregular, non-hydrogen bonded system. The remaining silyl-protected 6-deoxy-L-altronate, 6-deoxy-D-gulonate and D-fuconate oligomers appear to be characterized by their lack of ordered conformation in TFE and chloroform solution.

The synthesis of oligomers of oxetane-based dipeptide isosteres derived fromL-rhamnose orD-xylose

Routes to oligomers (dimers, tetramers, hexamers) of five oxetane-based dipeptide isosteres have been established. Methyl 2,4-anhydro-5-azido-5-deoxy-L-rhamnonate 'monomer' led, by coupling the corresponding carboxylic acid and amine, to a 'dimer'. Reverse-aldol ring-opening occurred on attempted saponification of the dimer, so all further oligomerization was performed using TBDMS C-3 hydroxyl protection. The silyl protected L-rhamnonate monomer led in turn to the dimer (via the monomer acid and amine), the tetramer (via the dimer acid and amine) and finally the hexamer (via the tetramer acid and dimer amine). In each case the acids were obtained through saponification of the respective methyl esters and the amines were obtained by hydrogenation of the azides; coupling was TBTU-mediated. Essentially the same strategy was employed on equivalent D-lyxonate, 6-deoxy-L-altronate, 6-deoxy-D-gulonate and D-fuconate dipeptide isosteres to give the respective dimers, tetramers and hexamers.

An unsaturated peptidomimetic assembly derived from a carbohydrate

A strategy has been established for the synthesis of peptidomimetics derived from unsaturated carbohydrates, and exemplified by the use of methyl 2,6-anhydro-7-azido-3,7-deoxy-4,5-O-isopropylidene-D-lyxo-hept-2-enonate 9 as a dipeptide 'monomer' which can be elaborated from either end. Selective reduction of 9 gives a protected pseudodipeptide ester suitable for use as an amino component, and saponification gives an azido acid suitable for use as a carboxyl component. The 'dimer' product of coupling these two components with TBTU can be similarly elaborated at either end to give a 'trimer' and a further cycle of selective reduction and coupling gave a 'tetramer', 17, a pseudo-octapeptide.

Biomimetic synthesis of the crispatene core

The biomimetic synthesis of the crispatene core is reported. The core framework was efficiently generated from an easily synthesized all (E)-tetraene precursor in one step, in good yield.

Bend ribbon-forming tetrahydrofuran amino acidsThis is one of a number of contributions from the current members of the Dyson Perrins Laboratory to mark the end of almost 90 years of organic chemistry research in that building, as all its current academic staff move across South Parks Road to a new purpose-built laboratory

Short oligomeric chains of C-glycosyl beta-D-arabinofuranose configured tetrahydrofuran amino acids (where the C-2 and C-5 substituents of the tetrahydrofuran ring are cis to each other) exhibit a well-defined repeating turn secondary structure stabilised by (i, i - 2) inter-residue hydrogen bonds. This is in contrast to the epimeric alpha-D-arabinofuranose oligomer (where the C-2 and C-5 substituents of the tetrahydrofuran ring are trans to each other) in which there is no indication of any secondary structure in solution.

Structural basis for the recognition of hydroxyproline in HIF-1 alpha by pVHL

Hypoxia-inducible factor-1 (HIF-1) is a transcriptional complex that controls cellular and systemic homeostatic responses to oxygen availability. HIF-1 alpha is the oxygen-regulated subunit of HIF-1, an alpha beta heterodimeric complex. HIF-1 alpha is stable in hypoxia, but in the presence of oxygen it is targeted for proteasomal degradation by the ubiquitination complex pVHL, the protein of the von Hippel Lindau (VHL) tumour suppressor gene and a component of an E3 ubiquitin ligase complex. Capture of HIF-1 alpha by pVHL is regulated by hydroxylation of specific prolyl residues in two functionally independent regions of HIF-1 alpha. The crystal structure of a hydroxylated HIF-1 alpha peptide bound to VCB (pVHL, elongins C and B) and solution binding assays reveal a single, conserved hydroxyproline-binding pocket in pVHL. Optimized hydrogen bonding to the buried hydroxyprolyl group confers precise discrimination between hydroxylated and unmodified prolyl residues. This mechanism provides a new focus for development of therapeutic agents to modulate cellular responses to hypoxia.