Addressing common challenges of biotherapeutic protein peptide mapping using recombinant trypsin.

Peptide mapping is the key method for characterization of primary structure of biotherapeutic proteins. This method relies on digestion of proteins into peptides that are then analyzed for amino acid sequence and post-translational modifications. Owing to its high activity and cleavage specificity, trypsin is the protease of choice for peptide mapping. In this study, we investigated critical requirements of peptide mapping and how trypsin affects these requirements. We found that the commonly used MS-grade trypsins contained non-specific, chymotryptic-like cleavage activity causing generation of semi-tryptic peptides and degradation of tryptic-specific peptides. Furthermore, MS-grade trypsins contained pre-existing autoproteolytic peptides and, moreover, additional autoproteolytic peptides were resulting from prominent autoproteolysis during digestion. In our long-standing quest to improve trypsin performance, we developed novel recombinant trypsin and evaluated whether it could address major trypsin drawbacks in peptide mapping. The study showed that the novel trypsin was free of detectable non-specific cleavage activity, had negligible level of autoproteolysis and maintained high activity over the course of digestion reaction. Taking advantage of the novel trypsin advanced properties, especially high cleavage specificity, we established the application for use of large trypsin quantities to digest proteolytically resistant protein sites without negative side effects. We also tested trypsin/Lys-C mix comprising the novel trypsin and showed elimination of non-specific cleavages observed in the digests with the commonly used trypsins. In addition, the improved features of the novel trypsin allowed us to establish the method for accurate and efficient non-enzymatic PTM analysis in biotherapeutic proteins.

Interlaboratory Evaluation of a User-Friendly Benchtop Mass Spectrometer for Multiple-Attribute Monitoring Studies of a Monoclonal Antibody.

In the quest to market increasingly safer and more potent biotherapeutic proteins, the concept of the multi-attribute method (MAM) has emerged from biopharmaceutical companies to boost the quality-by-design process development. MAM strategies rely on state-of-the-art analytical workflows based on liquid chromatography coupled to mass spectrometry (LC-MS) to identify and quantify a selected series of critical quality attributes (CQA) in a single assay. Here, we aimed at evaluating the repeatability and robustness of a benchtop LC-MS platform along with bioinformatics data treatment pipelines for peptide mapping-based MAM studies using standardized LC-MS methods, with the objective to benchmark MAM methods across laboratories, taking nivolumab as a case study. Our results evidence strong interlaboratory consistency across LC-MS platforms for all CQAs (i.e., deamidation, oxidation, lysine clipping and glycosylation). In addition, our work uniquely highlights the crucial role of bioinformatics postprocessing in MAM studies, especially for low-abundant species quantification. Altogether, we believe that MAM has fostered the development of routine, robust, easy-to-use LC-MS platforms for high-throughput determination of major CQAs in a regulated environment.

A new alternative tool to analyse glycosylation in pharmaceutical proteins based on infrared spectroscopy combined with nonlinear support vector regression.

Almost 60% of commercialized pharmaceutical proteins are glycosylated. Glycosylation is considered a critical quality attribute, as it affects the stability, bioactivity and safety of proteins. Hence, the development of analytical methods to characterise the composition and structure of glycoproteins is crucial. Currently, existing methods are time-consuming, expensive, and require significant sample preparation steps, which can alter the robustness of the analyses. In this work, we suggest the use of a fast, direct, and simple Fourier transform infrared spectroscopy (FT-IR) combined with a chemometric strategy to address this challenge. In this context, a database of FT-IR spectra of glycoproteins was built, and the glycoproteins were characterised by reference methods (MALDI-TOF, LC-ESI-QTOF and LC-FLR-MS) to estimate the mass ratio between carbohydrates and proteins and determine the composition in monosaccharides. The FT-IR spectra were processed first by Partial Least Squares Regression (PLSR), one of the most used regression algorithms in spectroscopy and secondly by Support Vector Regression (SVR). SVR has emerged in recent years and is now considered a powerful alternative to PLSR, thanks to its ability to flexibly model nonlinear relationships. The results provide clear evidence of the efficiency of the combination of FT-IR spectroscopy, and SVR modelling to characterise glycosylation in therapeutic proteins. The SVR models showed better predictive performances than the PLSR models in terms of RMSECV, RMSEP, R2CV, R2Pred and RPD. This tool offers several potential applications, such as comparing the glycosylation of a biosimilar and the original molecule, monitoring batch-to-batch homogeneity, and in-process control.

Profiling of N-Linked Oligosaccharides of a Glycoprotein by UPLC-FLR-ESI-MS After Derivatization with Fluorescent Anthranilamide.

N-glycans are described to have a large influence on the properties of therapeutic proteins, including safety and efficacy. For this reason, the extent and type of glycosylation is a characterization parameter for the analysis of antibodies and other therapeutic proteins. The method described here is a fast and high-throughput method for identification and semiquantification of N-glycans by HILIC-FLR-ESI-MS. Sample preparation has been optimized and simultaneous preparation of a large number of samples can be achieved within a day. The use of MS coupled to fluorescence detection is an additional tool for identifying the N-glycan type.

Profiling, Relative Quantification, and Identification of Sialylated N-Linked Oligosaccharides by UPLC-FLR-ESI/MS After Derivatization with Fluorescent Anthranilamide.

The presence of sialic acids is one characteristic of glycosylated therapeutic proteins. The presence of these charged monosaccharides is critical for the immunogenicity properties and structural properties of the proteins. Profiling of the N-glycans and their charge state is a requisite for complete protein characterization. Two analytical methods developed on released N-glycans are described in this chapter, allowing for the determination of the sialoglycosylation with different levels of details. In the first method (AEX-HILIC/FLR), N-glycans are separated based on their charge and the average charge state can be determined from the fluorescence profile. In the second method (AEX-RP-FLR-MS), N-glycans are also separated based on their charge and the sialylation level is determined based on the fluorescence signal. In addition, in this method, the N-glycans are also separated by type and identified with the hyphenated MS. For both methods, an optimized protocol with fast and high-throughput sample preparation and purification is presented.

Analysis of Glycoproteins by ATR-FTIR Spectroscopy: Comparative Assessment.

FTIR spectroscopy has been widely used to characterize biopharmaceuticals for many years, in particular to analyze protein structure. More recently, it was demonstrated to be a useful tool to study and compare protein samples in terms of glycosylation. Based on a spectral region specific to carbohydrate absorption, we present here a detailed protocol to compare the FTIR spectra of glycoproteins in terms of global glycosylation level and in terms of glycan composition. This FTIR information is compared to MS information. Both approaches yield consistent results but it appears FTIR analysis is easier and more rapid to perform comparisons.

Apparent ileal digestibility of Maillard reaction products in growing pigs.

The absorption of Maillard reaction products (MRP) from dietary origin has been linked to the occurrence of chronic diseases. The aim of the present study was to determine the effects of toasting time of rapeseed meal (RSM) and the processing method of the diets (pelleting and extrusion) that included RSM on the apparent ileal digestibility (AID) of total lysine, fructosyl-lysine (FL), carboxymethyl-lysine (CML), carboxyethyl-lysine (CEL), lanthionine (LAN) and lysinoalanine (LAL) in growing pigs. The study consisted of a 2×3 factorial design with toasting time of RSM (60, 120 min) and diet processing method (mash, pelleted, extruded) as factors. Fifty growing pigs were individually fed one of the experimental diets for 4.5 consecutive days. Following euthanasia, samples of digesta were collected from the terminal 1.5 m of the small intestine. Increasing the toasting time of RSM increased the contents of FL, CML and CEL, whereas the additional effects of the diet processing methods were relatively small. Lysinoalanine and lanthionine were not detected in the diets; therefore, digestibility of these compounds could not be determined. The contents of FL, CML and CEL in the ileal chyme were positively correlated to their contents in the diets. The AID of the MRP from thermally-treated RSM were overall low and were not related to their contents in the diets. The AID of FL ranged between -8.5 and 19.1%, whilst AID of CML and CEL ranged from -0.2 to 18.3 and 3.6 to 30%, respectively. In conclusion, thermal treatments have clear effects on the contents of MRP in the diets. These compounds have relatively low digestibility in growing pigs.

Spontaneous, non-enzymatic breakdown of peptides during enzymatic protein hydrolysis.

It is expected that during the hydrolysis of proteins with specific enzymes only peptides are formed that result from hydrolysis of the specific cleavage sites (i.e. specific peptides). It is, however, quite common to find a-specific peptides (i.e. resulting from a-specific cleavage), which are often ignored, or explained by impurities in the enzyme preparation. In recent work in a whey protein isolate (WPI) hydrolysate obtained with the specific Bacillus licheniformis protease (BLP), 13 peptides of 77 identified were found to be the result of a-specific cleavage. These were formed after degradation of 6 specific peptides, after 5 different types of amino acids. The fact that other peptides were not hydrolyzed after these 5 amino acids suggests that the cleavages were not the result of a contamination with a different enzyme. In other systems, certain peptide sequences have been described to degrade chemically, under relatively mild conditions. This process is referred to as spontaneous cleavage. To test if the a-specific peptides observed in the WPI hydrolysis are the results of spontaneous cleavages, the parental peptides were synthesized. Surprisingly, 4 of the 5 synthesized peptides were indeed spontaneously cleaved under the mild conditions used in this study (i.e. 40°C and pH 8) showing that peptides are less stable than typically considered. The rate of cleavage on the a-specific bonds was found to be enhanced in the presence of BLP. This suggests that the formation of a-specific peptides is not due to side activity but rather an enhancement of intrinsic instability of the peptides.

Determination of the influence of substrate concentration on enzyme selectivity using whey protein Isolate and Bacillus licheniformis protease.

Increasing substrate concentration during enzymatic protein hydrolysis results in a decrease in hydrolysis rate. To test if changes in the mechanism of hydrolysis also occur, the enzyme selectivity was determined. The selectivity is defined quantitatively as the relative rate of hydrolysis of each cleavage site in the protein. It was determined from the identification and quantification of the peptides present in the hydrolysates. Solutions of 0.1-10% (w/v) whey protein isolate (WPI) were hydrolyzed by Bacillus licheniformis protease at constant enzyme-to-substrate ratio. The cleavage sites were divided into five groups, from very high (>10%) to very low selectivity (<0.1%). The selectivity toward cleavage sites after Glu 62 and 134 was 2 times higher at 10% (w/v) WPI than at the lower protein concentrations. This finding shows that both the rate of hydrolysis and the enzyme selectivity were influenced by the substrate concentration.

Introducing enzyme selectivity: a quantitative parameter to describe enzymatic protein hydrolysis.

Enzyme selectivity is introduced as a quantitative parameter to describe the rate at which individual cleavage sites in a protein substrate are hydrolyzed relative to other cleavage sites. Whey protein isolate was hydrolyzed by Bacillus licheniformis protease, which is highly specific for Glu and Asp residues. The molar concentration of all peptides (58) from ß-lactoglobulin formed during hydrolysis was determined from the UV214 signal. The quality of identification and quantification of the peptides were described by newly defined parameters: the peptide sequence coverage (on average 94 %) and the molar sequence coverage (on average 75 %). The selectivity was calculated from the rate of hydrolysis of each cleavage site, and showed differences of up to a factor of 5,000. The ability to quantitatively discriminate the enzyme preference towards individual cleavage sites is considered essential to the understanding of enzymatic protein hydrolysis.

Effects of ionic strength on the enzymatic hydrolysis of diluted and concentrated whey protein isolate.

To identify the parameters that affect enzymatic hydrolysis at high substrate concentrations, whey protein isolate (1-30% w/v) was hydrolyzed by Alcalase and Neutrase at constant enzyme-to-substrate ratio. No changes were observed in the solubility and the aggregation state of the proteins. With increasing concentration, both the hydrolysis rate and the final DH decreased, from 0.14 to 0.015 s(-1) and from 24 to 15%, respectively. The presence of 0.5 M NaCl decreased the rate of hydrolysis for low concentrations (to 0.018 s(-1) for 1% WPI), resulting in similar rates of hydrolysis for all substrate concentrations. The conductivity increase (by increasing the protein concentration, or by addition of NaCl) has significant effects on the hydrolysis kinetics, but the reason for this is not yet well understood. The results show the importance of conductivity as a factor that influences the kinetics of the hydrolysis, as well as the composition of the hydrolysates.