Investigation of native and aggregated therapeutic proteins in human plasma with asymmetrical flow field-flow fractionation and mass spectrometry.

Physiochemical degradation of therapeutic proteins in vivo during plasma circulation after administration can have a detrimental effect on their efficacy and safety profile. During drug product development, in vivo animal studies are necessary to explore in vivo protein behaviour. However, these studies are very demanding and expensive, and the industry is working to decrease the number of in vivo studies. Consequently, there is considerable interest in the development of methods to pre-screen the behaviour of therapeutic proteins in vivo using in vitro analysis. In this work, asymmetrical flow field-flow fractionation (AF4) and liquid chromatography-mass spectrometry (LC-MS) were combined to develop a novel analytical methodology for predicting the behaviour of therapeutic proteins in vivo. The method was tested with two proteins, a monoclonal antibody and a serum albumin binding affibody. After incubation of the proteins in plasma, the method was successfully used to investigate and quantify serum albumin binding, analyse changes in monoclonal antibody size, and identify and quantify monoclonal antibody aggregates.

Optimizing selectivity of anion hydrophobic multimodal chromatography for purification of a single-chain variable fragment.

Single-chain variable fragments (scFv) are widely used in several fields. However, they can be challenging to purify unless using expensive Protein L-based affinity adsorbents or affinity tags. In this work, a purification process for a scFv using mixed-mode (MM) chromatography was developed by design of experiments (DoE) and proteomics for host cell protein (HCP) quantification. Capture of scFv from human embryonic kidney 293 (HEK293) cell feedstocks was performed by hydrophobic charge induction chromatography (MEP HyperCel™), whereafter polishing was performed by anion hydrophobic MM chromatography (Capto Adhere™). The DoE designs of the polishing step included both binding and flow-through modes, the latter being the standard mode for HCP removal. Chromatography with Capto Adhere™ in binding-mode with elution by linear salt gradient at pH 7.5 resulted in optimal yield, purity and HCP reduction factor of 98.9 > 98.5%, and 14, respectively. Totally, 258 different HCPs were removed, corresponding to 84% of identified HCPs. The optimized conditions enabled binding of the scFv to Capto Adhere™ below its theoretical pI, while the majority of HCPs were in the flow-through. Surface property maps indicated the presence of hydrophobic patches in close proximity to negatively charged patches that could potentially play a role in this unique selectivity.

Assessment and improvement of statistical tools for comparative proteomics analysis of sparse data sets with few experimental replicates.

Large-scale quantitative analyses of biological systems are often performed with few replicate experiments, leading to multiple nonidentical data sets due to missing values. For example, mass spectrometry driven proteomics experiments are frequently performed with few biological or technical replicates due to sample-scarcity or due to duty-cycle or sensitivity constraints, or limited capacity of the available instrumentation, leading to incomplete results where detection of significant feature changes becomes a challenge. This problem is further exacerbated for the detection of significant changes on the peptide level, for example, in phospho-proteomics experiments. In order to assess the extent of this problem and the implications for large-scale proteome analysis, we investigated and optimized the performance of three statistical approaches by using simulated and experimental data sets with varying numbers of missing values. We applied three tools, including standard t test, moderated t test, also known as limma, and rank products for the detection of significantly changing features in simulated and experimental proteomics data sets with missing values. The rank product method was improved to work with data sets containing missing values. Extensive analysis of simulated and experimental data sets revealed that the performance of the statistical analysis tools depended on simple properties of the data sets. High-confidence results were obtained by using the limma and rank products methods for analyses of triplicate data sets that exhibited more than 1000 features and more than 50% missing values. The maximum number of differentially represented features was identified by using limma and rank products methods in a complementary manner. We therefore recommend combined usage of these methods as a novel and optimal way to detect significantly changing features in these data sets. This approach is suitable for large quantitative data sets from stable isotope labeling and mass spectrometry experiments and should be applicable to large data sets of any type. An R script that implements the improved rank products algorithm and the combined analysis is available.

Using mass spectrometry to explore the neglected glycan moieties of the antiophidic proteins DM43 and DM64.

The resistance of the opossum Didelphis aurita to Bothrops snake venoms is attributed to the opossum's antihemorrhagic (DM43) and antimyotoxic (DM64) acidic serum glycoproteins. The aim of this study was to characterize the N-glycosylation sites of these antiophidic proteins and to determine whether their glycans influence the biological activity measured by in vitro assays. Our experimental pipeline included the sequential enzymatic digestion of the inhibitors with two different proteinases (trypsin and endoproteinase Asp-N) and eventually with trypsin, peptide-N-glycosidase F (PNGase F) and endoproteinase Asp-N, used in that order. All of the peptide and protein samples were analyzed by MALDI-TOF/TOF MS. The results experimentally confirmed the putative N-glycosylation sites of DM43 (Asn23, Asn156, Asn160, and Asn175) and DM64 (Asn46, Asn179, Asn183, and Asn379). Following treatments with specific glycosidases, complex-type oligosaccharides containing galactose and sialic acid could be assigned to both proteins. The removal of these monosaccharide units by exoglycosidase digestion did not measurably affect the inhibitory activity. In contrast, partially deglycosylated DM43 treated with PNGase F under nondenaturing conditions was half as effective as native DM43. In conclusion, we have demonstrated that the contribution of the carbohydrate portion of these potentially therapeutic molecules, for their mechanism of action, should not be overlooked.

Immunochemical and proteomic technologies as tools for unravelling toxins involved in envenoming by accidental contact with Lonomia obliqua caterpillars.

The accidental contact with Lonomia obliqua caterpillar causes local and systemic symptoms (such as fibrinogen depletion), leading, in some cases, to serious clinical complications (acute renal failure and intracranial haemorrhage). Fortunately, a successful therapeutical approach using anti-Lonomic serum, produced in horses against L. obliqua's bristle extract, has already been put in place. However, a global view of immunogenic toxins involved in the coagulation disorders could help to elucidate the envenoming process. In the present study, our aim was to identify bristle extract's immunogenic components, especially those related to the haemostasis, coupling proteomics and immunochemical approaches (bidimensional electrophoresis, mass spectrometry and immunoblotting). The bidimensional map of bristle extract showed a broad profile of 157 silver-stained spots, where at least 153 spots were immunochemically revealed. Twenty-four of these spots were submitted to sequencing by mass spectrometry and three different categories of proteins were identified: lipocalins, cuticle proteins and serpins. From these protein families, it was observed that the most abundant was the lipocalin family, specifically represented by different isoforms of Lopap (a prothrombin activator protein), reinforcing its relevance during envenoming. Peptide sequences of several other immunochemically revealed spots showed no correspondence to any known sequence and were classified as unknown proteins. These proteins could represent new immunogenic molecules and/or toxins. The sequences presented in this article can be used for oligonucleotide design aiming the amplification of cDNAs coding for new molecules using L. obliqua bristles' cDNA libraries or isolated RNAs as template.

Caracterização da N-Glicosilação de DM43 e DM64 por espectrometria de massas e análise de sua contribuição para a atividade antiofídica destas proteínas / Characterization of the N-Glycosylation of DM43 and DM64 for mass spectrometry and analysis of its contribution for the antiophidian activity of these proteins

Em países tropicais e subtropicais, o envenenamento por picadas de venenos de serpentes é um problema de saúde pública. A mortalidade global estimada é de 50 a 100 mil casos por ano. Entretanto, há um elevado número de subnotificações no que tange os índices de morbidade, seqüelas que incluem ulceração crônica, falência renal, dano neurológico e amputações. O tratamento atual é baseado na administração de antisoro de origem animal produzido contra as toxinas antigênicas presentes nos venenos. Contudo, o antiveneno é ineficaz no tratamento do dano tecidual local e sua administração pode provocar sérias reações adversas. Alguns animais apresentam resistência natural ao envenenamento por serpentes, principalmente devido à presença de fatores séricos neutralizantes. O marsupial Didelphis aurita é resistente ao veneno de várias serpentes da família Viperidae e do seu soro foram isoladas duas proteínas com atividades anti-hemorrágica (DM43) e antimiotóxica (DM64). DM43 e DM64 são glicoproteínas ácidas homodiméricas apresentando 21por cento e 15por cento de conteúdo de carboidrato por peso, respectivamente. O objetivo desse trabalho foi implementar e desenvolver diferentes técnicas analíticas para glicoproteínas, utilizando estes inibidores como modelo. Os diferentes peptídeos e glicopeptídeos gerados, após hidrólise enzimática, foram analisados por espectrometria de massas. As estruturas oligossacarídicas e a atividade biológica dos inibidores, após desglicosilação total ou parcial, também foram analisadas. Utilizando digestões seqüênciais com três diferentes proteases, com e sem digestão prévia com PNGase F, aliadas à análise por MALDI-TOF/TOF, quatro sítios de N-glicosilação foram confirmados em DM43 (Asn(elevado a 23), Asn(elevado a 156), Asn(elevado a 160) and Asn(elevado a 175)) e outros quatro determinados experimentalmente em DM64(Asn(elevado a 46), Asn(elevado a 179), Asn(elevado a 183) and Asn(elevado a 379)). Estruturas de oligossacarídeos...toxina.

Antibodies from dogs with canine visceral leishmaniasis recognise two proteins from the saliva of Lutzomyia longipalpis.

The saliva of the sand fly Lutzomyia longipalpis, a major vector of Leishmania, exhibits pharmacological and immunomodulatory activities that may facilitate entry and establishment of parasites into the vertebrate host. Salivary gland components of the sand fly are, therefore, potential candidates in the development of a vaccine against human leishmaniasis. With the objective of identifying sand fly saliva proteins that could be used to immunise animals against canine visceral leishmaniasis, we have evaluated anti-saliva antibody reactivity using serum samples collected from dogs naturally infected with Leishmania chagasi. Two proteins with molecular weights of 28.6 and 47.3 kDa were recognised by dog antibodies in Western blot assays. Protein bands were excised from an SDS-PAGE gel and the sequences determined by mass spectrometry. The proteins were identified as LuLo-D7 and Lulo YELLOW, respectively. The significance of these findings in the context of the development of multi-component vaccination experiments is discussed.