Histidine Hydrogen-Deuterium Exchange Mass Spectrometry for Probing the Microenvironment of Histidine Residues in Dihydrofolate Reductase

Histidine Hydrogen-Deuterium Exchange Mass Spectrometry (His-HDX-MS) determines the HDX rates at the imidazole C(2)-hydrogen of histidine residues. This method provides not only the HDX rates but also the pK(a) values of histidine imidazole rings. His-HDX-MS was used to probe the microenvironment of histidine residues of E. coli dihydrofolate reductase (DHFR), an enzyme proposed to undergo multiple conformational changes during catalysis.Using His-HDX-MS, the pK(a) values and the half-lives (t(1/2)) of HDX reactions of five histidine residues of apo-DHFR, DHFR in complex with methotrexate (DHFR-MTX), DHFR in complex with MTX and NADPH (DHFR-MTX-NADPH), and DHFR in complex with folate and NADP+ (DHFR-folate-NADP+) were determined. The results showed that the two parameters (pK(a) and t(1/2)) are sensitive to the changes of the microenvironment around the histidine residues. Although four of the five histidine residues are located far from the active site, ligand binding affected their pK(a), t(1/2) or both. This is consistent with previous observations of ligand binding-induced distal conformational changes on DHFR. Most of the observed pK(a) and t(1/2) changes could be rationalized using the X-ray structures of apo-DHFR, DHFR-MTX-NADPH, and DHFR-folate-NADP+. The availability of the neutron diffraction structure of DHFR-MTX enabled us to compare the protonation states of histidine imidazole rings.Our results demonstrate the usefulness of His-HDX-MS in probing the microenvironments of histidine residues within proteins

Biobased Pyrazine-Containing Polyesters

A set of 12 first-in-class, biobased pyrazine-containing polyesters was synthesized based on dimethylpyrazine dipropionic acid. These new diacid monomers were obtained from underutilized nitrogen-rich biomass. The polyester materials were synthesized via a two-step melt transesterification-polycondensation procedure with molecular weights between 12 300 and 47 500 g/mol and dispersities between 1.9 and 2.3. Six of the obtained polymers were amorphous and six were semi-crystalline. The thermal properties of the materials were studied; thermal degradation was found to take place at the monomer degradation temperature. The effect of methyl groups on the glass transition temperature was investigated, and the materials were found to behave mostly as aliphatic polyesters in this regard. The melting points of the methyl-substituted polyesters were found to be high and within the range of those of current high-performance polyesters. These materials are thus a welcome addition to current biobased polyesters

Syntheses, pharmacological evaluation and molecular modelling of substituted 6-alkoxyimidazo 1,2-b pyridazines as new ligands for the benzodiazepine receptor

A series of 2,3-disubstituted-6-alkoxyimidazo[1,2-b] has been synthesized and evaluated for in vitro affinity for the benzodiazepine receptor (BZR). 3-(Benzamidomethyl or substituted benzamidomethyl)-6-methoxy-2-(3,4-methylenedioxyphenyl)imidazo[1,2-b]pyridazines were found to be the most potent BZR ligands (eg, 4a, IC50 7 nM; 4e, IC50 14 nM; 4v, IC50 8 nM). Imidazo[1,2-b]pyridazines unsubstituted in the 3-position, or containing builder alkoxy groups in the 6-position, were found to bind less strongly to the BZR. Selected compounds from the series were identified from in vitro GABA-shift experiments as BZR agonists. Molecular modelling has been employed to identify the common pharmacophoric points of lipophilic and hydrogen bonding, ligand-receptor interaction and areas of steric hindrance for these substituted imidazo[1,2-b]pyridazines at the BZR

The Forgotten Pyrazines: Exploring the Dakin–West Reaction

Pyrazines are an underreported class of N-heterocycles available from nitrogen-rich biomass presenting an interesting functional alternative for current aromatics. In this work, access to pyrazines obtained from amino acids by using the 90 year old Dakin-West reaction was explored. After a qualitative screening several functional proteinogenic amino acids proved good substrates for this reaction, which were successfully scaled to multigram scale synthesis of the corresponding intermediate alpha-acetamido ketones. Subsequently, the conditions towards pyrazine formation using delta-amino-levulinic acid were optimized, and these were employed to synthesize a relevant set of five functional dimethylpyrazines in high purity. These pyrazines can be considered a versatile toolbox of aromatic building blocks for a wide range of applications, such as in the synthesis of polymers or metal-organic frameworks

A cellular automata model of acid dissociation

A dynamic cellular automata model that simulates the dissociation of an organic acid in solution is described. In the model, acids are represented by a novel cell type in which one face corresponds to the dissociating carboxylic acid group and the remaining faces represent the anionic portion of the acid. Simulations are described that analyze the effects of variable acid strength, changes of solvent temperature, and environmental influences, such as the presence of cosolutes and other acids. Several general features of acid dissociation in solution are replicated by the model and some additional aspects are examined. As a rule, additional solutes depress acid dissociation, the effect being greatest when the added cosolute is Lipophilic, as might occur, for example, in a biological system. In mixtures of two different acids, the dissociation of each is suppressed, the weaker acid experiencing the greater suppression