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Monoclonal antibodies are mainly produced by mammalian cell culture, which due to its complexity, results in a wide range of product variants/isoforms. With the growing implementation of Quality by Design (QbD) and Process Analytical Technology (PAT) in drug manufacturing, monitoring and controlling quality attributes within a predefined range during manufacturing may provide added consistency to product quality. To implement these concepts, more robust analytical tools could reduce the time needed for monitoring quality attributes during upstream processing. The formation of protein aggregates is one such quality attribute that can lead to safety and efficacy issues in the final drug product. Described in this study is a fully automated two-dimensional high performance liquid chromatography (2D-HPLC) method for characterizing protein aggregation of crude in-process bioreactor samples. It combines protein A purification and separation by size exclusion into a single analytical module that has the potential to be employed at-line within a bioprocessing system. This method utilizes a novel in-line fraction collection device allowing for the collection of up to twelve fractions from a single sample or peak which facilitates the subsequent linked analysis of multiple protein peaks of interest in one chromatography module. [ABSTRACT FROM AUTHOR]

We surveyed 23 antibody-related marketing applications for glycoform analytical and functional information. Our database analysis shows a clear trend of increasing sophistication of analytical methods used to identify and quantify glycans. These have revealed a high degree of complexity and heterogeneity of glycans attached to antibody products. The nature of the complexity is influenced by product type and expression system, and may be associated with functional consequences in some but not all cases. [ABSTRACT FROM AUTHOR]

The major outer membrane proteins Pgm6 (41 kDa) and Pgm7 (40 kDa) of Porphyromonas gingivalis ATCC 33277 are encoded by open reading frames pg0695 and pg0694, respectively, which form a single operon. Pgm6 and Pgm7 (Pgm6/7) have a high degree of similarity to Escherichia coli OmpA in the C-terminal region and are predicted to form eight-stranded β-barrels in the N-terminal region. By sodium dodecyl sulfate-polyacrylamide gel electrophoresis, Pgm6/7 appear as bands with apparent molecular masses of 40 and 120 kDa, with and without a reducing agent, suggesting a monomer and trimer, respectively. To verify the predicted trimeric structure and function of Pgm6/7, we constructed three mutants with pg0695, pg0694, or both deleted. The double mutant produced no Pgm6/7. The single-deletion mutants appeared to contain less Pgm7 and Pgm6 and to form homotrimers that migrated slightly faster (115 kDa) and slower (130 kDa), respectively, than wild-type Pgm6/7 under nonreducing conditions. N-terminal amino acid sequencing and mass spectrometry analysis of partially digested Pgm6/7 detected only fragments from Pgm6 and Pgm7. Two-dimensional, diagonal electrophoresis and chemical cross-linking experiments with or without a reducing agent clearly showed that Pgm6/7 mainly form stable heterotrimers via intermolecular disulfide bonds. Furthermore, growth retardation and arrest of the three mutants and increased permeability of their outer membranes indicated that Pgm6/7 play an important role in outer membrane integrity. Based on results of liposome swelling experiments, these proteins are likely to function as a stabilizer of the cell wall rather than as a major porin in this organism. [ABSTRACT FROM AUTHOR]

Integration host factor (IHF) is a DNA–bending protein that recognizes its cognate sites through indirect readout. Previous studies have shown that binding of wild-type (WT)-IHF is disrupted by a T to A mutation at the center position of a conserved TTR motif in its binding site, and that substitution of βGlu44 with Ala prevented IHF from discriminating between A and T at this position. We have determined the crystal structures and relative binding affinities for all combinations of WT-IHF and IHF-βGlu44Ala bound to the WT and mutant DNAs. Comparison of these structures reveals that DNA twist plays a major role in DNA recognition by IHF, and that this geometric parameter is dependent on the dinucleotide step and not on the bound IHF variant. [Copyright &y& Elsevier]

The 41 kDa heat-modifiable OmpA-like protein from Bacteroides fragilis ATCC 25285 was purified and tryptic peptide sequences were used to design degenerate oligonucleotide primers which were then used in amplification and identification of the omp A gene. The omp A gene was cloned and sequenced (GenBank Accession Number AY028459). Sequence analysis revealed an open reading frame of 1188 bases. The deduced amino acid sequence (which contained the experimentally determined peptide sequences) has 395 amino acids; the mature protein consists of 376 amino acids, has a predicted MW of 41 448 and a theoretical pI of 7.95. It is preceded by 19 amino acids that correspond to elements typical of a signal peptide sequence, including the Lys-Lys sequence near the N-terminus followed by a hydrophobic region (LLALAGV). The C-terminus of B. fragilis OmpA is homologous to the highly characteristic OmpA signature domain (75% similarity with the OmpA consensus domain). Three-dimensional modeling of B. fragilis OmpA predicts an eight-stranded β-barrel; the predicted loops are in agreement with those predicted as hydrophilic maxima in hydrophobicity plots. B. fragilis OmpA was cloned into pET-27b(+) and expressed in E. coli BL21(DE3)pLysS. The recombinant B. fragilis OmpA was recovered from inclusion bodies, solubilized in 8 M urea and refolded in 4 mM Zwittergent 3-14. Recombinant, refolded B. fragilis OmpA was active in a liposome assay (swelling rate for arabinose was 0.495/5.6μg protein) and preliminary analysis indicated that channels of three sizes were formed in a black lipid bilayer assay. This is the first description of an ompA homolog in Bacteroides. [Copyright &y& Elsevier]

The high MW porin protein complex (Omp200, composed of Omp121 and Omp71) from Bacteroides fragilis ATCC 25285 was purified and tryptic peptide sequences were used to design degenerate oligonucleotide primers which were then used as a first step in amplification, identification and sequencing of the omp121 gene (GenBank Accession Number AF357210). Sequence analysis revealed an open reading frame of 3378 bases. The deduced amino acid sequence (which contained the experimentally determined peptide sequences) has 1125 or 1116 amino acids (depending on which start codon is used); the mature protein consists of 1096 amino acids, has a predicted MW of 121.4 and a theoretical pI of 6.32. It is preceded by a 29 or 18 amino acid signal peptide which includes a typical hydrophobic region near the N-terminus (VLVLVL). Hydropathy plots of the deduced amino acid sequence of B. fragilis Omp121 display striking similarity with those of Escherichia coli OmpC (a 16-stranded porin) and FepA (a 22-stranded ligand-gated transport protein). Three-dimensional modeling of B. fragilis Omp121 (based on 1D and 3D sequence profiles, coupled with secondary structure and solvation potential information) indicated that the closest homologues in terms in fold conservation were the E. coli 16-stranded porins (e.g. OsmA) and 22-stranded ligand gated transport proteins (e.g. FepA). The omp71 gene sequence was identified using the tryptic peptides to search the published Bacteroides genome data base. We found that omp71 is located immediately downstream of omp121 and confirmed this with PCR analysis. Omp71 has no known homologues but does share some characteristics with the Porphyromonas RagB antigen. [Copyright &y& Elsevier]

Formulating appropriate storage conditions for biopharmaceutical proteins is essential for ensuring their stability and thereby their purity, potency, and safety over their shelf-life. Using a model murine IgG3 produced in a bioreactor system, multiple formulation compositions were systematically explored in a DoE design to optimize the stability of a challenging antibody formulation worst case. The stability of the antibody in each buffer formulation was assessed by UV/VIS absorbance at 280 nm and 410 nm and size exclusion high performance liquid chromatography (SEC) to determine overall solubility, opalescence, and aggregate formation, respectively. Upon preliminary testing, acetate was eliminated as a potential storage buffer due to significant visible precipitate formation. An additional 24 full factorial DoE was performed that combined the stabilizing effect of arginine with the buffering capacity of histidine. From this final DoE, an optimized formulation of 200 mM arginine, 50 mM histidine, and 100 mM NaCl at a pH of 6.5 was identified to substantially improve stability under long-term storage conditions and after multiple freeze/thaw cycles. Thus, our data highlights the power of DoE based formulation screening approaches even for challenging monoclonal antibody molecules. [ABSTRACT FROM AUTHOR]

The objective of the study was to analyze the effect of controlled and uncontrolled freezing step of a lyophilization process on the extent of non-enzymatic glycation and aggregation of an IgG1 formulation at two concentrations (1 mg/ml and 20 mg/ml). The degree of glycation (%) was determined through boronate affinity chromatography and its effect on the formation of soluble aggregates and higher molecular weight species was studied using dynamic light scattering (DLS) and size exclusion chromatography with multi-angle light scattering (SEC-MALS). The effect of non-enzymatic glycation on the secondary structure of the formulations was also studied using circular dichroism (CD) spectroscopy and Fourier transform infrared (FT-IR) spectroscopy. Results indicated that controlled nucleation yielded higher residual moisture contents and significantly lower specific surface areas for the two monoclonal antibody concentrations compared with uncontrolled nucleation cycle ( p < 0.05). For the two concentrations, uncontrolled nucleation resulted in significantly higher levels of glycation compared with controlled nucleation samples ( p < 0.05). Further, it was observed that higher storage temperatures (25 °C/60% RH) versus 5 °C resulted in higher glycation. Even though SEC-MALS analyses of the low concentrated formulations did not reveal the formation of higher molecular weight species, DLS analyses at two storage conditions revealed increases in the hydrodynamic radii and polydispersity index of the reconstituted formulations, suggesting the onset of formation of smaller species in the formulations. CD spectroscopy did not reveal any differences in the secondary structure of the mAb for the two concentrations after lyophilization. In conclusion, the freezing step method impacted the extent of glycation in lyophilized samples and the hydrolyzed component of sucrose was critical for increasing glycation. Even though some level of glycation was observed in lyophilized samples, the native structure of the protein was not affected. Further, it was demonstrated that storage of both lyophilized cakes and reconstituted formulations at higher temperatures could increase the extent of glycation in monoclonal antibody formulations. [ABSTRACT FROM AUTHOR]

Highlights: [•] We mapped packaging cleavage sites for phage 80α and pathogenicity island SaPI1. [•] Packaging directed by 80α TerS initiates within the 80α terS coding sequence. [•] SaPI1 TerS-specific packaging initiates in an intergenic region. [•] The SaPI1 pac site determinants were mapped using a plasmid-based assay. [•] Deletion of the pac site from SaPI1 eliminates high frequency transduction. [ABSTRACT FROM AUTHOR]

An efficient and potentially scalable technology was evaluated to control the ice nucleation step of the freezing process for a model monoclonal antibody formulation and the effect on process performance and quality attributes of the final lyophilized product was compared with the conventional shelf ramping method of freezing. Controlled ice nucleation resulted in uniform nucleation at temperatures between −2.3 and −3.2°C while uncontrolled nucleation resulted in random nucleation at temperatures between −10 and −16.4°C. The sublimation rate (dm/dt) during primary drying was higher in the controlled nucleation cycle (0.13g/h/vial) than in the uncontrolled nucleation cycle (0.11g/h/vial). This was due to the formation of larger ice crystals, leading to lower product resistance (R p) and 19% reduction in the primary drying for the controlled nucleation cycle. Controlled ice nucleation resulted in lyophilized cakes with more acceptable appearance, no visible collapse or shrinkage and decreased reconstitution times compared with uncontrolled nucleation. There were no observed differences in the particle size, concentration (A 280nm) and presence of aggregates (A 410nm) between the two nucleation cycles when the lyophilized cakes were reconstituted. These were confirmed by SEC and protein A-HPLC analyses which showed similar peak shapes and retention times between the two cycles. However, uncontrolled nucleation resulted in cakes with larger specific surface area (0.90m2/g) than controlled nucleation (0.46m2/g). SEM images of the lyophilized cakes from uncontrolled nucleation revealed a sponge-like morphology with smaller pores while cakes from controlled nucleation cycle revealed plate-like structures with more open and larger pores. While controlled nucleation resulted in a final product with a higher residual moisture content (2.1±0.08%) than uncontrolled nucleation (1.62±0.11%), this was resolved by increasing the secondary drying temperature. [ABSTRACT FROM AUTHOR]

Consistent high-quality antibody yield is a key goal for cell culture bioprocessing. This endpoint is typically achieved in commercial settings through product and process engineering of bioreactor parameters during development. When the process is complex and not optimized, small changes in composition and control may yield a finished product of less desirable quality. Therefore, changes proposed to currently validated processes usually require justification and are reported to the US FDA for approval. Recently, design-of-experiments-based approaches have been explored to rapidly and efficiently achieve this goal of optimized yield with a better understanding of product and process variables that affect a product's critical quality attributes. Here, we present a laboratory-scale model culture where we apply a Plackett- Burman screening design to parallel cultures to study the main effects of 11 process variables. This exercise allowed us to determine the relative importance of these variables and identify the most important factors to be further optimized in order to control both desirable and undesirable glycan profiles. We found engineering changes relating to culture temperature and nonessential amino acid supplementation significantly impacted glycan profiles associated with fucosylation, β-galactosylation, and sialylation. All of these are important for monoclonal antibody product quality. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 104:1919-1928, 2015 [ABSTRACT FROM AUTHOR]