Reversed-phase liquid chromatography as a tool in the determination of the hydrophilicity/hydrophobicity of amino acid side-chains at a ligand-receptor interface in the presence of different aqueous environments. I. Effect of varying receptor hydrophobicity

We have developed further a chromatographic model for studying the hydrophobic interactions which characterize the way a ligand binds to its receptor. This model is based on observing the retention behaviour of de novo designed model 18-residue amphipathic alpha-helical peptides (representing the hydrophobic binding domain of a ligand) on reversed-phase packings by varying hydrophobicity (representing a receptor protein with a hydrophobic binding pocket). Mutants of the "native" peptide ligand (which contains seven Leu residues in its non-polar face) were designed by replacing one residue in the center of the extremely non-polar face of the amphipathic alpha-helix. Through reversed-phase liquid chromatography of these peptides at pH 2.0 on cyano and C18 columns, we have demonstrated how an increase in receptor hydrophobicity (represented by an increase in column stationary phase hydrophobicity; cyano --> C18) significantly enhances hydrophilicity of polar amino acid side-chains at the ligand-receptor interface while moderately enhancing the hydrophobicity of non-polar side-chains. The addition of salt (100 mM sodium perchlorate) to the aqueous environment surrounding the binding site of receptor and ligand was also shown to have a profound effect on side-chain hydrophilicity/hydrophobicity in the binding interface. This effect was particularly dramatic for the positively charged side-chains Arg, Lys and His, whose significant enhancement of hydrophobicity in the presence of the cyano column contrasted with their increase in hydrophilicity in the presence of the considerably more hydrophobic C18 stationary phase. Our results have major implications to understanding the influence of hydrophobic and aqueous environment on hydrophilicity/hydrophobicity of amino acid side-chains and the role side-chains play in the folding and stability of proteins.     

Synthetic studies related to diketopyrrolopyrrole (DPP) pigments. Part 2: The use of esters in place of nitriles in standard DPP syntheses: Claisen-type acylations and furopyrrole intermediates

Ethyl 2-aryl-4,5-dihydro-5-oxopyrrole-3-carboxylates react with esters or acyl halides in the presence of a strong base to give 4-acyl derivatives, which exist predominantly as either E- or Z-enols. These are cyclised, either in solution at temperatures >200 °C or by microwave irradiation, to 3,6-disubstituted 1H-furo[3,4-c]pyrrolediones which, after N-protection, are convertible by reaction with primary amines into novel N,N′-disubstituted DPP derivatives.     

Application of positive ion chemical ionisation and tandem mass spectrometry combined with gas chromatography to the trace level analysis of ethyl carbamate in bread

A rapid, sensitive and selective method has been developed and validated for the analysis of the contaminant ethyl carbamate (EC) in bread products at the part-per-billion level. The new procedure uses positive ion chemical ionisation (PICI) and tandem mass spectrometry (MS/MS), combined with gas chromatography (GC), on a 'bench-top' triple-quadrupole mass spectrometer. Ammonia was the PICI reagent gas of choice because of its ability to produce abundant [M+H]+ and [M+NH4]+ ions from EC and deuterium-labelled EC (LEC) used as an internal standard. For identification and quantification, selected reaction monitoring (SRM) was used to follow the precursor-to-product ion transitions of m/z 107 --> 90, m/z 107 --> 62 and m/z 90 --> 62 for EC, as well as m/z 112 --> 63 for the LEC internal standard. The limits of detection and quantification were 0.6 and 1.2 microg kg(-1), respectively, and the recovery of the method was 101 +/- 10% at 10 microg kg(-1) and 98 +/- 5% at 100 microg kg(-1). The precision of the method, established under conditions of intermediate reproducibility, did not exceed a relative standard deviation of 7%. The quantitative performance of the new GC/PICI-SRM procedure compared favourably with that of a reference method based on GC/MS and selected ion monitoring (correlation coefficient, r = 0.997). However, the new method had the advantages of reduced sample preparation time, improved sensitivity and unambiguous identification of EC at all concentrations. Application of the new method to the analysis of 50 UK breads showed that levels of EC ranged from 0.6 to 2.3 microg kg(-1) in retail products and from 3.1 to 12.2 microg kg(-1) for breads prepared using domestic breadmaking machines (dry weight basis). Toasting bread in a domestic toaster led to increases of between two- and three-fold in mean EC concentrations.     

Synthesis and reactivity of silyl ruthenium complexes: the importance of trans effects in C-H activation,Si-C bond formation,and dehydrogenative coupling of silanes

A series of octahedral ruthenium silyl hydride complexes, cis-(PMe(3))(4)Ru(SiR(3))H (SiR(3) = SiMe(3), 1a; SiMe(2)CH(2)SiMe(3), 1b; SiEt(3), 1c; SiMe(2)H, 1d), has been synthesized by the reaction of hydrosilanes with (PMe(3))(3)Ru(eta(2)-CH(2)PMe(2))H (5), cis-(PMe(3))(4)RuMe(2) (6), or (PMe(3))(4)RuH(2) (9). Reaction with 6 proceeds via an intermediate product, cis-(PMe(3))(4)Ru(SiR(3))Me (SiR(3) = SiMe(3), 7a; SiMe(2)CH(2)SiMe(3), 7b). Alternatively, 1 and 7 have been synthesized via a fast hydrosilane exchange with another cis-(PMe(3))(4)Ru(SiR(3))H or cis-(PMe(3))(4)Ru(SiR(3))Me, which occurs at a rate approaching the NMR time scale. Compounds 1a, 1b, 1d, and 7a adopt octahedral geometries in solution and the solid state with mutually cis silyl and hydride (or silyl and methyl) ligands. The longest Ru-P distance within a complex is always trans to Si, reflecting the strong trans influence of silicon. The aptitude of phosphine dissociation in these complexes has been probed in reactions of 1a, 1c, and 7a with PMe(3)-d(9) and CO. The dissociation is regioselective in the position trans to a silyl ligand (trans effect of Si), and the rate approaches the NMR time scale. A slower secondary process introduces PMe(3)-d(9) and CO in the other octahedral positions, most likely via nondissociative isomerization. The trans effect and trans influence in 7a are so strong that an equilibrium concentration of dissociated phosphine is detectable (approximately 5%) in solution of pure 7a. Compounds 1a-c also react with dihydrogen via regioselective dissociation of phosphine from the site trans to Si, but the final product, fac-(PMe(3))(3)Ru(SiR(3))H(3) (SiR(3) = SiMe(3), 4a; SiMe(2)CH(2)SiMe(3), 4b; SiEt(3), 4c), features hydrides cis to Si. Alternatively, 4a-c have been synthesized by photolysis of (PMe(3))(4)RuH(2) in the presence of a hydrosilane or by exchange of fac-(PMe(3))(3)Ru(SiR(3))H(3) with another HSiR(3). The reverse manifold - HH elimination from 4a and trapping with PMe(3) or PMe(3)-d(9) - is also regioselective (1a-d(9)() is predominantly produced with PMe(3)-d(9) trans to Si), but is very unfavorable. At 70 degrees C, a slower but irreversible SiH elimination also occurs and furnishes (PMe(3))(4)RuH(2). The structure of 4a exhibits a tetrahedral P(3)Si environment around the metal with the three hydrides adjacent to silicon and capping the P(2)Si faces. Although strong Si...HRu interactions are not indicated in the structure or by IR, the HSi distances (2.13-2.23(5) A) suggest some degree of nonclassical SiH bonding in the H(3)SiR(3) fragment. Thermolysis of 1a in C(6)D(6) at 45-55 degrees C leads to an intermolecular CD activation of C(6)D(6). Extensive H/D exchange into the hydride, SiMe(3), and PMe(3) ligands is observed, followed by much slower formation of cis-(PMe(3))(4)Ru(D)(Ph-d(5)). In an even slower intramolecular CH activation process, (PMe(3))(3)Ru(eta(2)-CH(2)PMe(2))H (5) is also produced. The structure of intermediates, mechanisms, and aptitudes for PMe(3) dissociation and addition/elimination of H-H, Si-H, C-Si, and C-H bonds in these systems are discussed with a special emphasis on the trans effect and trans influence of silicon and ramifications for SiC coupling catalysis.     

Comparison of reversed-phase liquid chromatography and hydrophilic interaction/cation-exchange chromatography for the separation of amphipathic alpha-helical peptides with L- and D-amino acid substitutions in the hydrophilic face

Mixed-mode hydrophilic interaction/cation-exchange chromatography (HILIC/CEX) is a novel high-performance technique which has excellent potential for peptide separations. Separations by HILIX/CEX are carried out by subjecting peptides to linear increasing salt gradients in the presence of high levels of acetonitrile, which promotes hydrophilic interactions overlaid on ionic interactions with the cation-exchange matrix. In the present study, HILIC/CEX has been compared to reversed-phase liquid chromatography (RP-HPLC) for separation of mixtures of diastereomeric amphipathic alpha-helical peptide analogues, where L- and D-amino acid substitutions were made in the centre of the hydrophilic face of the amphipathic alpha-helix. Unlike RP-HPLC, temperature had a substantial effect on HILIC/CEX of the peptides, with a rise in temperature from 25 to 65 degrees C increasing the retention times of the peptides as well as improving resolution. Our results again highlight the potential of HILIC/CEX as a peptide separation mode in its own right as well as an excellent complement to RP-HPLC.     

Temperature selectivity effects in reversed-phase liquid chromatography due to conformation differences between helical and non-helical peptides

In order to characterize the effect of temperature on the retention behaviour and selectivity of separation of polypeptides and proteins in reversed-phase high-performance liquid chromatography (RP-HPLC), the chromatographic properties of four series of peptides, with different peptide conformations, have been studied as a function of temperature (5-80 degrees C). The secondary structure of model peptides was based on either the amphipathic alpha-helical peptide sequence Ac-EAEKAAKEX(D/L)EKAAKEAEK-amide, (position X being in the centre of the hydrophobic face of the alpha-helix), or the random coil peptide sequence Ac-X(D/L)LGAKGAGVG-amide, where position X is substituted by the 19 L- or D-amino acids and glycine. We have shown that the helical peptide analogues exhibited a greater effect of varying temperature on elution behaviour compared to the random coil peptide analogues, due to the unfolding of alpha-helical structure with the increase of temperature during RP-HPLC. In addition, temperature generally produced different effects on the separations of peptides with different L- or D-amino acid substitutions within the groups of helical or non-helical peptides. The results demonstrate that variations in temperature can be used to effect significant changes in selectivity among the peptide analogues despite their very high degree of sequence homology. Our results also suggest that a temperature-based approach to RP-HPLC can be used to distinguish varying amino acid substitutions at the same site of the peptide sequence. We believe that the peptide mixtures presented here provide a good model for studying temperature effects on selectivity due to conformational differences of peptides, both for the rational development of peptide separation optimization protocols and a probe to distinguish between peptide conformations.     

Flexible matching of test ligands to a 3D pharmacophore using a molecular superposition force field: Comparison of predicted and experimental conformations of inhibitors of three enzymes

Summary A computer procedure TFIT, which uses a molecular superposition force field to flexibly match test compounds to a 3D pharmacophore, was evaluated to find out whether it could reliably predict the bioactive conformations of flexible ligands. The program superposition force field optimizes the overlap of those atoms of the test ligand and template that are of similar chemical type, by applying an attractive force between atoms of the test ligand and template which are close together and of similar type (hydrogen bonding, charge, hydrophobicity). A procedure involving Monte Carlo torsion perturbations, followed by torsional energy minimization, is used to find conformations of the test ligand which cominimize the internal energy of the ligand and the superposition energy of ligand and template. The procedure was tested by applying it to a series of flexible ligands for which the bioactive conformation was known experimentally. The 15 molecules tested were inhibitors of thermolysin, HIV-1 protease or endothiapepsin for which X-ray structures of the bioactive conformation were available. For each enzyme, one of the molecules served as a template and the others, after being conformationally randomized, were fitted. The fitted conformation was then compared to the known binding geometry. The matching procedure was successful in predicting the bioactive conformations of many of the structures tested. Significant deviation from experimental results was found only for parts of molecules where it was readily apparent that the template did not contain sufficient information to accurately determine the bioactive conformation.     

Bronsted acid-promoted olefin aziridination and formal anti-aminohydroxylation

A straightforward synthesis of aziridines is reported from an electron-rich azide (alkyl or aryl azide), electron-deficient olefin, and triflic acid in cold acetonitrile. The only coproduct of the reaction is dinitrogen (N2). Active ester substrates bearing a nucleophilic carbonyl engage the putative protonated aziridine intermediate to produce the product of olefin aminohydroxylation in which the nitrogen is benzyl protected and the oxygen is acylated. The possibility that a triazoline need not be an intermediate in aziridine production is advanced.     

Reaction of tris(trimethylsilyl)methylsilicon halides with methanolic sodium methoxide. Probability of sila-olefin intermediates

The compounds TsiSiR₂X [Tsi = Me₃Si)₃C; R = Me, X = Cl, Br, I, or R = Ph, X = F, Cl, Br, I)] react with boiling 2 M MeONa-MeOH to give products of the type (Me₃Si)₂CHSiR₂OMe. It is suggested that the reaction proceeds through an elimination, analogous to E2 eliminations of alkyl halides, involving synchronous attack of MeO^? at an Me₃Si group, liberation of X^?, and formation of (Me₃Si)₂CSiR₂. The compounds TsiSiPhMeF TsiSiPhCl₂ react analogously to give (Me₃Si)₂CHSiPhMe(OMe) and (Me₃Si)₂CHSiPh(OMe)₂ [tha latter presumably by solvolysis of the initially-formed (Me₃Si)₂CHSiPhCl(OMe)]. The compounds TsiSiMe₂OMe and TsiSiMe₃ do not react, while TsiSiMe₂H gives TsiH. The compound TsiSiCl₃ reacts with 0.1 M MeONa-MeOH to give the substitution and elmination products TsiSiCl₂(OMe) and (Me₃Si)₂CHSi(OMe)₃ in ca. $\text{1}\text{2}$ ratio.     

Structural changes in the monomeric despentapeptide (B30-B26) insulin crystal

Insulin modified by the removal of its 5 B chain C terminal residues is monomeric but remains substantially potent. The crystal structures of the beef and insulin (dpi) with two molecules in the asymmetric unit has been determined by x-ray analysis. The 3-dimensional structure ofdpi proves to be generally similar to that of native molecule in 2Zn insulin. More detailed comparison reveals that the slight differences in the two independent molecules of beefdpi are distributed uniformly throughout the structure in contrast to insulin in 2Zn insulin, where the structural changes are concentrated in specific regions. The loss of symmetry in thedpi crystal appears to be the inability of the A9 serine to pack effectively in the C2 cell. The efficient packing of the sheepdpi molecule whose crystal structure has also been determined and where A9 is glycine supports this conclusion.