The life and work of Robert (Bob) C. Sheppard.

The life and work of Robert Charles Sheppard (1932-2019), Bob Sheppard informally among friends, is outlined. He was a leading pioneer of solid phase peptide synthesis and made the most significant and fundamental European contribution to the art of peptide synthesis since Emil Fischer.

Structural determinant for inducing RORgamma specific inverse agonism triggered by a synthetic benzoxazinone ligand.

BACKGROUND: The nuclear hormone receptor RORγ regulates transcriptional genes involved in the production of the pro-inflammatory interleukin IL-17 which has been linked to autoimmune diseases such as rheumatoid arthritis, multiple sclerosis and inflammatory bowel disease. This transcriptional activity of RORγ is modulated through a protein-protein interaction involving the activation function 2 (AF2) helix on the ligand binding domain of RORγ and a conserved LXXLL helix motif on coactivator proteins. Our goal was to develop a RORγ specific inverse agonist that would help down regulate pro-inflammatory gene transcription by disrupting the protein protein interaction with coactivator proteins as a therapeutic agent. RESULTS: We identified a novel series of synthetic benzoxazinone ligands having an agonist (BIO592) and inverse agonist (BIO399) mode of action in a FRET based assay. We show that the AF2 helix of RORγ is proteolytically sensitive when inverse agonist BIO399 binds. Using x-ray crystallography we show how small modifications on the benzoxazinone agonist BIO592 trigger inverse agonism of RORγ. Using an in vivo reporter assay, we show that the inverse agonist BIO399 displayed specificity for RORγ over ROR sub-family members α and ß. CONCLUSION: The synthetic benzoxazinone ligands identified in our FRET assay have an agonist (BIO592) or inverse agonist (BIO399) effect by stabilizing or destabilizing the agonist conformation of RORγ. The proteolytic sensitivity of the AF2 helix of RORγ demonstrates that it destabilizes upon BIO399 inverse agonist binding perturbing the coactivator protein binding site. Our structural investigation of the BIO592 agonist and BIO399 inverse agonist structures identified residue Met358 on RORγ as the trigger for RORγ specific inverse agonism.

Isotope ratios of H, C, and O in CO2 and H2O of the martian atmosphere.

Stable isotope ratios of H, C, and O are powerful indicators of a wide variety of planetary geophysical processes, and for Mars they reveal the record of loss of its atmosphere and subsequent interactions with its surface such as carbonate formation. We report in situ measurements of the isotopic ratios of D/H and (18)O/(16)O in water and (13)C/(12)C, (18)O/(16)O, (17)O/(16)O, and (13)C(18)O/(12)C(16)O in carbon dioxide, made in the martian atmosphere at Gale Crater from the Curiosity rover using the Sample Analysis at Mars (SAM)'s tunable laser spectrometer (TLS). Comparison between our measurements in the modern atmosphere and those of martian meteorites such as ALH 84001 implies that the martian reservoirs of CO2 and H2O were largely established ~4 billion years ago, but that atmospheric loss or surface interaction may be still ongoing.

Primordial argon isotope fractionation in the atmosphere of Mars measured by the SAM instrument on Curiosity and implications for atmospheric loss.

[1] The quadrupole mass spectrometer of the Sample Analysis at Mars (SAM) instrument on Curiosity rover has made the first high-precision measurement of the nonradiogenic argon isotope ratio in the atmosphere of Mars. The resulting value of 36Ar/38Ar = 4.2 ± 0.1 is highly significant for it provides excellent evidence that "Mars" meteorites are indeed of Martian origin, and it points to a significant loss of argon of at least 50% and perhaps as high as 85-95% from the atmosphere of Mars in the past 4 billion years. Taken together with the isotopic fractionations in N, C, H, and O measured by SAM, these results imply a substantial loss of atmosphere from Mars in the posthydrodynamic escape phase.

Isotopes of nitrogen on Mars: Atmospheric measurements by Curiosity's mass spectrometer.

[1] The Sample Analysis at Mars (SAM) instrument suite on the Mars Science Laboratory (MSL) measured a Mars atmospheric14N/15N ratio of 173 ± 11 on sol 341 of the mission, agreeing with Viking's measurement of 168 ± 17. The MSL/SAM value was based on Quadrupole Mass Spectrometer measurements of an enriched atmospheric sample, with CO2 and H2O removed. Doubly ionized nitrogen data at m/z 14 and 14.5 had the highest signal/background ratio, with results confirmed by m/z 28 and 29 data. Gases in SNC meteorite glasses have been interpreted as mixtures containing a Martian atmospheric component, based partly on distinctive14N/15N and40Ar/14N ratios. Recent MSL/SAM measurements of the40Ar/14N ratio (0.51 ± 0.01) are incompatible with the Viking ratio (0.35 ± 0.08). The meteorite mixing line is more consistent with the atmospheric composition measured by Viking than by MSL.

Building block syntheses of gallic acid monomers and tris-(O-gallyl)-gallic acid dendrimers chemically attached to graphite powder: a comparative study of their uptake of Al(III) ions.

A synthesis of graphite powder covalently modified with gallic acid (3,4,5-trihydroxybenzoic acid), via a 1,2-diaminoethane "linker" molecule, to form gallylaminoethylaminocarbonyl graphite (gallic-carbon) is reported. The synthesis was used as a model for a "ground-upwards building-block" approach to a primary dendrimer of gallic acid covalently attached to the surface of graphite powder, tris-(O-gallyl)-gallylaminoethylaminocarbonyl graphite (TGGA-carbon). The resulting modified carbon materials were characterized at each stage of the syntheses using X-ray photoelectron spectroscopy (XPS) analysis. The effects of increasing the modifier's structural complexity from monomeric gallic-carbon to the analogous primary dendrimer TGGA-carbon were explored by comparing each material's efficacy toward the adsorption of Al(III) ions from water. The uptake of Al(III) ions by gallic-carbon and TGGA-carbon was measured using UV-vis spectroscopy. In comparison to the case of monomeric gallic-carbon, the rate of adsorption of Al(III) ions by the TGGA-carbon was found to be 2.3 times more rapid. Furthermore, the total uptake of Al(III) ions was greater (reducing the concentration of 1000 ppb Al(III) solutions to below the WHO legal limit of 100 ppb in less than 5 min) and irreversible, in contrast to the gallic-carbon where the adsorption was found to be under thermodynamic control and to follow a Freundlich isotherm.

Synthesis and biological characterisation of novel N-alkyl-deoxynojirimycin alpha-glucosidase inhibitors.

The N-alkylated deoxynojirimycin compound, N-(6'-(4''-azido-2''-nitrophenylamino)hexyl)-1-deoxynojirimycin (6) was synthesised as a potential photoaffinity probe for endoplasmic reticulum (ER) alpha-glucosidases I and II. Surprisingly this compound was a highly potent inhibitor of alpha-glucosidase I (IC(50), 17 nM) in an in vitro assay and proved equally effective at inhibiting cellular ER glucosidases, as determined by a free oligosaccharide (FOS) analysis. A modest library of compounds was synthesised to obtain structure-activity information by variation of the N-alkyl chain length and modifications to the azido-nitrophenyl group. All of these compounds failed to improve on the efficacy of compound 6, but most showed greater enzyme inhibitory potency than N-butyl-deoxynojirimycin (NB-DNJ), a pharmacological agent that has been evaluated for the treatment of several viruses for which infectivity is dependent on host cell glycosylation.

Contrasting pKa of protonated bis(3-aminopropyl)-terminated polyethylene glycol "Jeffamine" and the associated thermodynamic parameters in solution and covalently attached to graphite surfaces.

The pKa value of protonated Jeffamine (bis(3-aminopropyl) terminated polyethylene glycol) in solution and attached as a monolayer to graphite surfaces has been determined using potentiometric titration. The protonated Jeffamine was found to have a pKa value of 9.7 in solution at 25 degrees C, whereas this value decreases to 7.1 when it is attached to a graphite surface. Potentiometric titrations from 25 to 40 degrees C allowed us to determine the surface pKa of the protonated Jeffamine at each temperature studied and hence to determine the enthalpy, entropy and Gibbs energy changes associated with the deprotonation of the amino-terminated surface bound Jeffamine groups. It was found that the enthalpic contribution is negligibly small and the evaluation of these thermodynamic parameters controlling the shift in surface pKa value indicates that this process is controlled by entropic contribution arising from the ordering/disordering of solvent molecules at the carbon-water interface. This suggests that the long chain Jeffamine molecules are oriented on the carbon surface rather than existing in the bulk solution.

Investigating the thermodynamic causes behind the anomalously large shifts in pKa values of benzoic acid-modified graphite and glassy carbon surfaces.

The difference between the values of 4-carboxyphenyl groups, covalently attached to either graphite (BAcarbon) or glassy carbon (BA-GC) surfaces, and benzoic acid in solution is explored using potentiometric titration and cyclic voltammetry. In solution, benzoic acid has a pKa of 4.20 at 25 degrees C. However, the observed pKa value on the graphitic surfaces shows significant deviations, with BAcarbon exhibiting a large shift to higher pKa values (pKa = 6.45) in contrast to BA-GC, which is shifted to lower pKa values (pKa = 3.25). Potentiometric titrations at temperatures between 25 and 50 degrees C allowed us to determine the surface pKa of these materials at each temperature studied and hence to determine the enthalpy, entropy, and Gibbs' energy changes associated with the ionization of the carboxylic acid groups. It was found that the enthalpic contribution is negligible and that the changes in surface pKa values are entropically controlled. This suggests that solvent ordering/disordering around the interface strongly influences the observed pKa value, which then reflects the relative hydrophobicity/hydrophilicity of the different graphitic surfaces.

R.B. Merrifield: European footnotes to his life and work.

Some reflections on the life and work of RB Merrifield in the European context are given.

The shifting sands of serials bibliography: titles using the term "peptide".

A commentary on the confusing nomenclature and bibliography of serial publications which use the term "peptide" in their titles is given, with guidance on citation.

Cyclic oligomers of oxetane-based dipeptide isosteres derived from L-rhamnose.

Two new cyclic oligomers, cyclo-tetra-[2,4-anhydro-3-O-tert-butyldimethylsilyl-5-deoxy-L-rhamnonamido-(N-->5)] and the corresponding 6-deoxy-D-gulonate cyclic "tetramer", have been synthesised from linear tetrameric oligomers, using TBTU- and pentafluorophenyl ester-based methodologies, respectively. These two compounds constitute a novel class of cyclic oligomers derived from oxetane-based sugar amino acids.

Words derived from the noun peptide.

Modifications of the noun peptide are explored and clarified; a few are condemned.

Abbreviations and symbols in peptide science: a revised guide and commentary.

The abbreviations and symbols used in Peptide Science are surveyed, with comment and recommendations.

Removal of toxic metal-ion pollutants from water by using chemically modified carbon powders.

The thermodynamics of and the kinetic parameters controlling the sequestration of the toxic heavy-metal ion Cd(II) from aqueous media by using a novel material consisting of glassy carbon microspheres (10-20 microm in diameter) chemically modified with L-cysteine methyl ester are presented. In an effort to reduce the cost and increase the efficiency of toxic-metal-ion removal, this modification strategy was expanded to attach L-cysteine methyl chemically ester to less-expensive graphite powders (2-20 microm in diameter), and the thermodynamic and kinetic parameters of the sequestration of Cd(II), Cu(II), and As(III) toxic metal ions are presented. It was found that the use of chemically modified graphite powder greatly increased both the rate and the amount of metal ions removed from aqueous media. This work has important potential applications to filtration of drinking water and environmental remediation.

Cysteine methyl ester modified glassy carbon spheres for removal of toxic heavy metals from aqueous media.

Glassy carbon spherical powder (10-20 microm diameter) modified with cysteine methyl ester is found to be an inexpensive, novel material for the rapid removal of large quantities of toxic heavy metal ions such as Cd(II), Cu(II) and As(III) from aqueous media, with wide ranging potential applications such as third world drinking water filtration or environmental cleanup.

The synthesis of oligomers of oxetane-based dipeptide isosteres derived from L-rhamnose or D-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.

Conformational studies of oligomeric oxetane-based dipeptide isosteres derived from L-rhamnose or D-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.

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.