Paradigms and paradoxes: decoding the “genetic code”

We propose to keep the term “genetic code” to describe the nucleotide sequence in DNA and RNA and use the term “genetic cipher” to describe the key for decoding the genetic codes of DNA and RNA into the amino acid sequences of proteins.

     

Crystallography in Structural Chemistry

This anniversary article has three functions: It marks Volume 25 of our journal; it honors 2014, the International Year of Crystallography; and it celebrates the centennial from the birth of a great crystallographer, Aleksandr I. Kitaigorodskii.     

Synthesis and Characterisation of Self‐Assembled and Self‐Adjuvanting Asymmetric Multi‐Epitope Lipopeptides of Ovalbumin

Designing a lipopeptide (LP) vaccine with a specific asymmetric arrangement of epitopes may result in an improved display of antigens, increasing host‐cell recognition and immunogenicity. This study aimed to synthesise and characterise the physicochemical properties of a library of asymmetric LP‐based vaccine candidates that contained multiple CD4⁺ and CD8⁺ T‐cell epitopes from the model protein antigen, ovalbumin. These fully synthetic vaccine candidates were prepared by microwave‐assisted solid phase peptide synthesis. The C12 or C16 lipoamino acids were coupled to the N or C terminus of the OVA CD4 peptide epitope. The OVA CD4 LPs and OVA CD8 peptide constructs were then conjugated using azide–alkyne Huisgen cycloaddition to give multivalent synthetic vaccines. Physiochemical characterisation of these vaccines showed a tendency to self‐assemble in aqueous media. Changes in lipid length and position induced self‐assembly with significant changes to their morphology and secondary structure as shown by transmission electron microscopy and circular dichroism.     

Can we use docking and scoring for hit-to-lead optimization?

Docking and scoring is currently one of the tools used for hit finding and hit-to-lead optimization when structural information about the target is known. Docking scores have been found useful for optimizing ligand binding to reproduce experimentally observed binding modes. The question is, can docking and scoring be used reliably for hit-to-lead optimization? To illustrate the challenges of scoring for hit-to-lead optimization, the relationship of docking scores with experimentally determined IC₅₀ values measured in-house were tested. The influences of the particular target, crystal structure, and the precision of the scoring function on the ability to differentiate between actives and inactives were analyzed by calculating the area under the curve of receiver operator characteristic curves for docking scores. It was found that for the test sets considered, MW and sometimes ClogP were as useful as GlideScores and no significant difference was observed between SP and XP scores for differentiating between actives and inactives. Interpretation by an expert is still required to successfully utilize docking and scoring in hit-to-lead optimization.     

Quantitative determination of lipase activity by liquid chromatography-mass spectrometry

We developed a novel in vitro lipase assay based on the quantitation of fatty acids by liquid chromatography-mass spectrometry. Oleic acids enzymatically released from triolein substrates were isolated from the reaction mixture by reverse-phase chromatography, ionized in negative mode electrospray mass spectrometry and quantitated with the aid of [(13)C]-oleic acid internal standard. The enzymatic activity was measured by monitoring oleic acid productions at multiple time points. This method overcomes the substrate and pH limitations of conventional techniques and thus serves as a generic lipase activity assay.     

Preparation of Polymer‐Metal Composites via In Situ Decomposition of Metal Salts by Frontal Polymerization

Composites containing powdered zinc, and zinc/lead acetate were prepared via frontal polymerization. In the case of the acetates, elemental metal was formed in an in situ decomposition process. The local area function was used to demonstrate the distribution of fillers, and the uniformity of the area fraction for the quantitative characterization of the distribution. With the use of metal acetates, composites of uniform metal distribution can be produced, unlike in systems with metal powder, where the metal particles are enriched at the margin of the sample. It can be established that the specific direct‐current resistance significantly decreases in AA‐TGDMA composites by the addition of zinc acetate, compared to that of the initial monomer mixture. On heating, the unreacted zinc acetate decomposes further, which results in the further decrease in electrical resistance.

     

Attaining control by design over the hydrolytic stability of Fe-TAML oxidation catalysts

The iron(III) complexes of tetra amidato macrocyclic ligands (TAMLs) ([Fe{1-X1-2-X2C6H2-4,5-(NCOCMe2NCO)2CR2}(OH2)]- , 1: X1 = X2 = H, R2 = Me2 (a), R2 = (CH2)2 (b); X1 = X2 = Cl, R2 = F2 (c), etc.), which the proton is known to demetalate at pH < 3, are also subject to catalyzed demetalation by Br?nsted acid buffer components at pH 4-9 such as H2PO4-, HSO3-, and CH3CO2H, HO2CCH2CO2-. Buffers based on pyridine (py) and tris(hydroxymethyl)aminomethane (TRIS) are catalytically inactive. Where reactions proceed, the products are demetalated TAMLs and iron species of variable composition. Pseudo-first-order rate constants for the demetalation (kobs) are linear functions of the acid concentrations, and the effective second-order rate constants k1,eff have a hyperbolic dependence on [H+] (k1,eff = a1[H+]/(b1+[H+]). The rate of demetalation of 1a in H2PO4-/HPO42- buffer is appreciable, but the kobs values for 1b and 1c are immeasurably low, showing that the rates are strongly affected by the CR2 or "tail" fragments, which are known to potently affect the TAML basicity. The reactivities of 1 depend insignificantly on the aromatic ring or "head" group of 1. The proposed mechanism involves precoordination of the acidic buffer species followed by hydrolysis. The demetalating abilities of buffer species depend on their structures and acidities. Thus, although pyridine-2-carboxylic (picolinic) acid catalyzes the demetalation, its 3- and 4-isomers (nicotinic and isonicotininc acids) are inactive. The difference is rationalized to result from the ability that only coordinated picolinic acid has to deliver a proton to an amidato nitrogen in an intramolecular manner. The reaction order in picolinic acid equals one for 1a and two for 1b. For 1b, "inactive" pyridine and nicotinic acid speed up the demetalation in the presence of picolinic acid, suggesting that the second order arises from the axial binding of two pyridine molecules, one of which must be picolinic acid. The binding of pyridine- and imidazole-type ligands was confirmed by UV/vis equilibrium measurements and X-ray crystallography. The implications of these mechanistic findings for designing superior Fe-TAML oxidation catalysts and catalyst formulations are discussed using the results of DFT calculations.     

Complexation of phenols by calix[4]arene Diethers in a low-permittivity solvent. Self-switched complexation by 25,27-Dibenzyloxycalix[4]arene

To improve the selectivity of sensing, the thermodynamics of the complex formation of some calix[4]arene hosts with neutral phenol guests was studied in carbon tetrachloride as nonpolar solvent. The molecular shape of calixarenes was varied by the selective functionalization with tBu and O-CH2-Ph (O-benzyl) or OPr groups at the upper and lower rim, respectively. To vary the electron density on the guest's aromatic rings, the parent phenol was functionalized in the para position with electron-withdrawing Cl, as well as H, and electron-releasing CH3 and tBu groups. To study the interaction between calixarene and the guests, PL and quantum-chemical methods were applied. The results revealed an overall 1:1 complex stoichiometry except for the parent dibenzyloxycalix[4]arene, where 1:2 host-guest stoichiometries were observed irrespective of the quality of phenol. In the latter case, the complex formation shows a self-switched character: the first phenol molecule is included in the calixarene cavity, and only afterward, a second guest molecule is bound by the two benzyloxy aromatics. Although the enthalpy change predicts strong interaction between the host and the guest, the Gibbs free energy change of the complex formation is small, resulting in a relatively low complex stability. The solvent-relaxation measurements support that the unexpected entropy change could be the consequence of the reorientation of solvent molecules around the calixarene building block. The reorientation is assisted by dispersive forces between solute and solvent molecules. IR and RAMAN analysis of the complexes exclude a considerable participation of the phenolic OH group in the stabilization of the complex. This result is in agreement with earlier findings where deterministic role of pi-pi interaction in the complex stability was assumed.