Temperature denaturation and aggregation of a multi-domain protein (IgG1) investigated with an array of complementary biophysical methods.

Proteins are used as drugs against different pathologies because of their potential specificity of action with fewer side effects. However, their production and successful storage imposes a greater challenge compared to small molecule drugs. Though the determination of protein thermal stability is commonly used to find the optimum storage conditions for biopharmaceuticals, a multi-technique approach should be applied more often when investigating complex systems to understand the structure of the species that contribute to the different transitions, thereby gaining insight about the processes of both unfolding and aggregation. This knowledge is crucial for identifying those conformational changes which are likely to lead to aggregation/degradation allowing a more rational approach to biopharmaceutical production and formulation. This is particularly important in the case of multi-domain proteins, such as IgGs, which can undergo multiple transitions due to independent unfolding of the domains. In this work, we have followed the thermal denaturation of a monoclonal antibody by using different biophysical techniques with complementary strengths, providing an example of how the information gathered suggests a way to intervene to stabilise the wanted conformation (monomeric protein). Indeed, in this particular case, an optimisation of storage conditions based on only thermal stability studies would have led to the stabilisation of an undesired product, a population of low molecular weight oligomers.

Homochirality as the signature of life: the SETH Cigar.

A characteristic hallmark of life is its homochirality: all biomolecules are usually of one hand, e.g. on Earth life uses only L-amino acids for protein synthesis and not their D mirror images. It is therefore suggested that a search for extra-terrestrial life can be approached as a Search for Extra-Terrestrial Homochirality (SETH). A novel miniaturized space polarimeter, called the SETH Cigar, is described which could he used to detect optical rotation as the homochiral signature of life on other planets. Moving parts are avoided by replacing the normal rotating polarizer by multiple fixed polarizers at different angles as in the eye of the bee. It is believed that homochirality will be found in the subsurface layers on Mars as a relic of extinct life.

Parity violation and the origins of biomolecular handedness.

The violation of parity by the weak interactions ensures that enantiomeric chiral molecules have inequivalent energies, one being inherently stabilized with respect to the other. These parity-violating energy differences have been calculated for a number of fundamental biomolecules including a series of alpha-amino acids, polypeptide structures, and a representative of the sugar series together with its variation over a possible prebiotic reaction path leading to alpha-amino acids. In each case the natural enantiomer found in terrestrial biochemistry was shown to be intrinsically stabilized and preferred over its unnatural enantiomer. The significance of these results in accounting for the prebiotic origins of the terrestrial biomolecular homochirality is discussed and the possible consequences of parity-violating energy differences in mineral catalysts during the prebiotic era considered.

Microbiological quality of Queensland stockfeeds with special reference to salmonella.

One hundred Queensland stockfeeds were examined for their counts of total aerobic bacteria, coliforms, fungi and salmonellas. The total aerobic bacteria, coliform and fungal counts were significantly higher (P < 0.005) for mashes than for crumbles and pellets and salmonellas were isolated from significantly more (P < 0.005) mashes (64%) than pellets and crumbles (8%). Counts of less than 1 salmonella per 100 g were found in 36.4% of the 44 positive feeds. The remainder of the counts ranged from 1.2 per 100 g to greater than 147 salmonellas per 100 g feed.

Examination of stockfeeds for Salmonella.

Of 100 stockfeeds examined for Salmonella 45 were positive by pre-enrichment followed by selective enrichment of 10 x 25 g samples. Forty-three were positive by selective enrichment of pooled aliquots of the pre-enrichment broths from the 10 x 25 g samples. Aliquots of the pre-enrichment broths from the 10 x 25 g samples of 77 of the feeds were stored at 4 degrees C and retested after 6 days. One hundred and ten of these (770) subsamples were found to contain salmonellas initially, and 107 were found to contain salmonellas after storage for 6 days. The testing of feeds by the examination of multiple 25 g samples and pooled pre-enrichment broths is recommended. Aliquots of the pre-enrichment broths may be stored at 4 degrees C for 6 days and retested if an estimation of the numbers in the feed is required. Further pre-enrichment after cold storage is not required.

Conformational plasticity in an HIV-1 antibody epitope.

The structure of a short fragment of the human HIV-1 membrane glycoprotein gp41 has been examined using a combination of parallel tempering molecular dynamics (PTMD) and far UV circular dichroism spectroscopy. The aim is to resolve conflicting reports on the solution state conformational bias in this membrane proximal domain spanning the epitope for the 2F5 monoclonal antibody. We conclude that gp41(659-671) exhibits conformational plasticity in which competing folding propensities are present and can be influenced by local microenvironment. Contrary to previous reports, the 3(10) helix does not emerge as a dominant motif from either simulation or experiment, and this peptide is therefore not a model system for this fold type. Other fold groups such as turn motifs are identifiable at elevated temperatures in the PTMD trajectories and are potentially relevant in antibody binding. Helical populations in pure water are significantly overestimated according to the CHARMM parametrization. However, circular dichroism (CD) data show that helices are promoted in membrane mimetic solvents. As this is a membrane proximal peptide, the helical motif may well have physiological significance.

Metabonomic characterization of genetic variations in toxicological and metabolic responses using probabilistic neural networks.

Current emphasis on efficient screening of novel therapeutic agents in toxicological studies has resulted in the evaluation of novel analytical technologies, including genomic (transcriptomic) and proteomic approaches. We have shown that high-resolution 1H NMR spectroscopy of biofluids and tissues coupled with appropriate chemometric analysis can also provide complementary data for use in in vivo toxicological screening of drugs. Metabonomics concerns the quantitative analysis of the dynamic multiparametric metabolic response of living systems to pathophysiological stimuli or genetic modification [Nicholson, J. K., Lindon, J. C., and Holmes, E. (1999) Xenobiotica 11, 1181-1189]. In this study, we have used 1H NMR spectroscopy to characterize the time-related changes in the urinary metabolite profiles of laboratory rats treated with 13 model toxins and drugs which predominantly target liver or kidney. These 1H NMR spectra were data-reduced and subsequently analyzed using a probabilistic neural network (PNN) approach. The methods encompassed a database of 1310 samples, of which 583 comprised a training set for the neural network, with the remaining 727 (independent cases) employed as a test set for validation. Using these techniques, the 13 classes of toxicity, together with the variations associated with strain, were distinguishable to >90%. Analysis of the 1H NMR spectral data by multilayer perceptron networks and principal components analysis gave a similar but less accurate classification than PNN analysis. This study has highlighted the value of probabilistic neural networks in developing accurate NMR-based metabonomic models for the prediction of xenobiotic-induced toxicity in experimental animals and indicates possible future uses in accelerated drug discovery programs. Furthermore, the sensitivity of this tool to strain differences may prove to be useful in investigating the genetic variation of metabolic responses and for assessing the validity of specific animal models.

NMR and QSAR studies on the transacylation reactivity of model 1beta-O-acyl glucuronides. I: design, synthesis and degradation rate measurement.

1. The products arising from intramolecular acyl migration reactions of drug ester glucuronides are reactive towards cellular proteins and can potentially cause toxic side-effects. The relationship between molecular structure and the degradation rates (kd) of 1beta-O-acyl glucuronides were investigated systematically using a series of model compounds based on 4-substituted benzoic acids. 2. A rational method for selecting suitable compounds for inclusion was used and 10 glucuronide esters, predicted to produce a wide range of transacylation rates, were synthesized via a simple "one-pot" method using an imidazolide intermediate. The 10 substituents, where X = NO2, CN, I, Br, F, H, nPr, Et, OMe, O-nPr, had degradation rate half-lives (t1/2 = loge(2)/kd) ranging from 0.9 to 106.6 h. The reactions resulted in mixtures, which predominantly consisted of the desired 1beta-O-acyl glucuronides. 3. It was demonstrated that further purification was unnecessary for determination of kd of the synthetic 1beta-O-acyl glucuronides. Degradation rates (kd) were calculated by following the disappearance of the 1H-NMR signal from the 1beta-anomeric proton of the glucuronic acid moiety as the reaction progressed in pH 7.4 buffer inside an nuclear magnetic resonance tube. Each measured degradation rate represents a pseudo-first-order rate constant, which is a combination of the transacylation rate (1beta to 2beta isomer) and the hydrolysis rate. 4. Degradation rates show a clear relationship with substituent properties, with half-life increasing as the substituent becomes more electron-donating, e.g. 4-nitro t1/2 = 0.9 h and 4-propoxy t1/2 = 106.6 h.

Nuclear magnetic resonance (NMR) and quantitative structure-activity relationship (QSAR) studies on the transacylation reactivity of model 1beta-O-acyl glucuronides. II: QSAR modelling of the reaction using both computational and experimental NMR parameters.

In a previously reported study, a number of 4-substituted benzoic acid acyl glucuronides were synthesized and their degradation rates determined using nuclear magnetic resonance (NMR) spectroscopy. It was shown that this reaction was strongly influenced by the nature of the substituent at the 4-position of the benzoyl moiety. The overall degradation reaction rates for this series of compounds have been modelled successfully using Hammett substituent constants, computational chemistry-derived partial atomic charges and the experimentally determined carbonyl carbon 13C-NMR chemical shifts of the benzoic acids and their ethyl and glucuronide esters. The primary contribution to reactivity is the scale of the electron-donating or -withdrawing effect of the substituent; however, additional contributions such as steric parameters must also be considered when modelling reactions outside a single chemical series. The derived property-reactivity relationships should find utility in medicinal chemistry efforts for optimizing chemical series in pharmaceutical discovery programmes.

Characterisation of the solution conformation of a cyclic RGD peptide analogue by NMR spectroscopy allied with a genetic algorithm approach and constrained molecular dynamics.

The solution conformation of a cyclic RGD peptide analogue, cyclo-(S,S)-2-mercaptobenzoate-arginine-glycine-aspartate-2-mer captoanilide, has been determined via two independent approaches for the searching of conformational space and identification of conformations consistent with NMR and CD spectroscopic data: (i) the use of a binary genetic algorithm and (ii) a molecular dynamics simulation. Inter-proton distances were obtained via analysis of cross-peak volumes from a two-dimensional ROESY NMR spectroscopy experiment at 600 MHz and were used as constraints for the computational calculations. The mercaptoanilide amide proton resonance chemical shift had a very small temperature coefficient, indicating that this proton was hydrogen-bonded. Circular dichroism data showed that, in solution, the torsion angle about the disulfide bond was negative, consistent with one of the distinct conformations around this bond in the 200 ps molecular dynamics simulation. The backbone conformations of the structures resulting from the two different approaches were very similar.

6,6'-Bis(2-hydroxyphenyl)-2,2'-bipyridine manganese(III) complexes: a novel series of superoxide dismutase and catalase mimetics.

A series of novel manganese(III) complexes is described based on a 6,6'-bis(2-hydroxyphenyl)-2,2'-bipyridine template. These complexes show superoxide dismutase and catalase activity. The effect of the aromatic substitution pattern on the SAR is described.