Identification of Acyl-Protein Thioesterase-1 as a Polysorbate-Degrading Host Cell Protein in a Monoclonal Antibody Formulation Using Activity-Based Protein Profiling.

Polysorbate (PS) degradation in monoclonal antibody (mAb) formulations poses a significant challenge in the biopharmaceutical industry. PS maintains protein stability during drug product's shelf life but is vulnerable to breakdown by low-abundance residual host cell proteins (HCPs), particularly hydrolytic enzymes such as lipases and esterases. In this study, we used activity-based protein profiling (ABPP) coupled with mass spectrometry to identify acyl-protein thioesterase-1 (APT-1) as a polysorbate-degrading HCP in one case of mAb formulation with stability problems. We validated the role of APT1 by matching the polysorbate degradation fingerprint in the mAb formulation with that of a recombinant APT1 protein. Furthermore, we found an agreement between APT1 levels and PS degradation rates in the mAb formulation, and we successfully halted PS degradation using APT1-specific inhibitors ML348 and ML211. APT1 was found to co-purify with a specific mAb via hitchhiking mechanism. Our work provides a streamlined approach to identifying critical HCPs in PS degradation, supporting quality-by-design principles in pharmaceutical development.

Bioconversion and P-gp-Mediated Transport of Depot Fluphenazine Prodrugs after Intramuscular Injection.

Fluphenazine (FPZ) decanoate, an ester-type prodrug formulated as a long-acting injection (LAI), is used in the treatment of schizophrenia. FPZ enanthate was also developed as an LAI formulation, but is no longer in use clinically because of the short elimination half-life of FPZ, the parent drug, after intramuscular injection. In the present study, the hydrolysis of FPZ prodrugs was evaluated in human plasma and liver to clarify the reason for this difference in elimination half-lives. FPZ prodrugs were hydrolyzed in human plasma and liver microsomes. The rate of hydrolysis of FPZ enanthate in human plasma and liver microsomes was 15-fold and 6-fold, respectively, faster than that of FPZ decanoate. Butyrylcholinesterase (BChE) and human serum albumin (HSA) present in human plasma, and two carboxylesterase (CES) isozymes, hCE1 and hCE2, expressed in ubiquitous organs including liver, were mainly responsible for the hydrolysis of FPZ prodrugs. FPZ prodrugs may not be bioconverted in human skeletal muscle at the injection site because of lack of expression of BChE and CESs in muscle. Interestingly, although FPZ was a poor substrate for human P-glycoprotein, FPZ caproate was a good substrate. In conclusion, it is suggested that the shorter elimination half-life of FPZ following administration of FPZ enanthate compared with FPZ decanoate can be attributed to the more rapid hydrolysis of FPZ enanthate by BChE, HSA and CESs.

Evaluation of a Five-Probe Metabolic Control Cocktail in Long-Term Cocultured Human Hepatocytes.

Hepatocyte cocultures like HepatoPac have become more frequently used for the assessment of the intrinsic clearance of slowly metabolised drugs during drug discovery due to a superiority in enzymatic activity over time compared to liver microsomal fractions and suspended primary hepatocytes. However, the relatively high cost and practical limitations prevent several quality control compounds to be included in studies and the activities of many important metabolic enzymes are consequently often not monitored. In this study, we have evaluated the possibility for a cocktail approach of quality control compounds in the human HepatoPac system to ensure adequate activity of the major metabolising enzymes. Five reference compounds were selected based on their known metabolic substrate profile in order to capture major CYP and non-CYP metabolic pathways in the incubation cocktail. The intrinsic clearance of the reference compounds when incubated as singlets or in a cocktail was compared and no considerable difference was observed. We show here that a cocktail approach of quality control compounds allows for easy and efficient evaluation of the metabolic competency of the hepatic coculture system over an extended incubation period.

Characterization of Recombinantly-Expressed Hydrolytic Enzymes from Chinese Hamster Ovary Cells: Identification of Host Cell Proteins that Degrade Polysorbate.

Enzymatic hydrolysis of polysorbate in drug products is a major challenge for the biopharmaceutical industry. Polysorbate hydrolysis caused by host cell proteins (HCPs) co-purified during bioprocessing can reduce the protective effects of the surfactant for the active pharmaceutical ingredient and cause the accumulation of low-solubility degradation products over the long-term storage. The identities of such HCPs are elusive due to their extremely low concentrations after the efficient purification processes of most biopharmaceuticals. In this work, 20 enzymes-selected for their known or putative hydrolytic activity and potential to degrade polysorbate-were recombinantly expressed, purified, and characterized via orthogonal methods. First, these recombinant HCPs were assessed for hydrolytic activity against a fluorogenic esterase substrate in a recently-developed, high-throughput assay. Second, these HCPs were screened for hydrolytic activity against polysorbate in a representative mAb formulation. Third, HCPs that displayed hydrolytic activities in the first two assays were subjected to more detailed characterization of their enzyme kinetics against polysorbates. Finally, these HCPs were evaluated for substrate specificity towards different sub-species of polysorbates. This work provides critical new insights for targeted LC-MS/MS approaches for identification of relevant polysorbate-degrading enzymes and supports improvements to remove such HCPs, including knockouts or targeted removal during purification.

Biocatalytic membranes through aqueous phase separation.

HYPOTHESIS: Polymer membranes play a critical role in water treatment, chemical industry, and medicine. Unfortunately, the current standard for polymer membrane production requires unsustainable and harmful organic solvents. Aqueous phase separation (APS) has recently been proposed as a method to produce membranes in a more sustainable manner through induced polyelectrolyte complexation in aqueous solutions. EXPERIMENTS: We demonstrate that APS has another natural advantage that goes beyond sustainability: the easy incorporation of enzymes in the membrane structure. Biocatalytic membranes hold great promise in for example biorefinery, but the most common current post-production processes to immobilize enzymes on the membrane surface are complicated and expensive. FINDINGS: In this study we demonstrated the first biocatalytic membrane produced via APS. We demonstrate an easy procedure to incorporate lysozyme in polyelectrolyte complex membranes made via APS. Our functionalized membranes have the same structure, water permeability (in the range of high nanofiltration, low ultrafiltration), and retention as membranes without lysozyme. Lysozyme is antibacterial by catalysing the hydrolysis of specific peptidoglycan bonds in bacteria walls. We demonstrate that the functionalized membranes are also capable of catalysing this reaction. The membranes remain enzymatically active for a period of at least one week. This opens new routes to produce polymer membranes with added biological function.

Identification and Characterization of Polysorbate-Degrading Enzymes in a Monoclonal Antibody Formulation.

Degradation of polysorbate (PS) by hydrolytically active host cell proteins (HCPs) in drug products may impair the protein-stabilizing properties of PS and lead to the formation of particles due to the accumulation of poorly soluble free fatty acids upon long-term storage. The identification of the causative enzymes is challenging due to their low-abundance even when using state-of-the-art instrumentation and workflows. To overcome these challenges, we developed a rigorous enrichment strategy for HCPs, utilizing both Protein A and anti-HCP affinity chromatography, which facilitated the in-depth characterization of the HCP population in a monoclonal antibody formulation prone to PS hydrolysis. Based on the HCPs identified by liquid chromatography coupled to tandem mass spectrometry, a number of enzymes annotated as hydrolases were recombinantly expressed and characterized in terms of polysorbate degradation. Among the selected candidates, Lipoprotein Lipase, Lysosomal Acid Lipase (LIPA) and Palmitoyl-Protein Thioesterase 1 (PPT1) exhibited notable activity towards PS. To our knowledge, this is the first report to identify LIPA and PPT1 as residual HCPs that can contribute to PS degradation in a biological product.

Near Infrared and Frequency Modulated Spectroscopy as Non-Invasive Methods for Moisture Assessment of Freeze-Dried Biologics.

Near-infrared (NIR) and frequency modulated spectroscopy (FMS) were employed, for non-invasive moisture determination of a lyophilized biologic drug product (DP). Development of NIR and FMS provides a rapid non-invasive means of residual moisture measurement, and would be beneficial compared with traditional time consuming, product destructive methods such as Karl Fischer (KF). A model therapeutic enzyme in a sucrose-based formulation was employed for proof of concept studies, and NIR and FMS methods were compared side by side for residual moisture analysis. Moisture models were created using lyophilized vials and comparisons were made between the methods using different moisture preparation approaches:1) direct water droplet addition to the vial headspace, 2) use of elevated temperature (80°C), and 3) using various levels of moisture in stoppers generated during the washing and drying procedures, then lyophilizing using the stoppers and placing the sealed vials on stability. The results for direct water addition gave an average percent error for residual moisture of 5.7% for NIR and 9.4% for FMS when compared to KF. The elevated temperature method resulted in an average percent error for residual moisture of 54% for NIR and 43% for FMS compared to KF. The stopper moisture stability study, for FMS, provided an average percent error for residual moisture of 31% compared to KF. The error was greater for the elevated temperature and stopper methods, due to the low moisture values, which resulted in greater error. At this lower range of moisture (<1%) both NIR and FMS were less accurate, but from 1 to 5% their accuracy increased, based on the models used in this study. NIR and FMS methods can be used to complement KF at these lower moisture levels and models could be further improved with additional data points. NIR and FMS methods have advantages and disadvantages for residual moisture analysis when compared to each other, but both provided an accurate measurement of drug product moisture (depending on the method used for moisture increase), they can be used as process analytical technology (PAT), and both can be used for fast non-invasive moisture determination.

Evaluation of limulus amebocyte lysate and recombinant endotoxin alternative assays for an assessment of endotoxin detection specificity.

The United States Pharmacopeia (USP), European Pharmacopeia (EP), and Parenteral Drug Association (PDA) provide guidance on the validation of alternative microbiological methods (U.S. Pharmacopeia National Formulary 2019, Parenteral Drug Association Technical Report No. 33 2013, European Pharmacopoeia (Ph. Eur.) 2017). They define "specificity" as the ability to detect a range of microorganisms. In the context of alternative methods to the compendial Bacterial Endotoxin Test (BET) a range of endotoxins must be considered. This range should represent environmental endotoxins that present risks to pharmaceutical manufacturing processes, final products, and to the most important stakeholder: the patient. This study examines several alternative methods for the bacterial endotoxin detection test. It compares the official and harmonized BET test from two Limulus Amebocyte Lysate (LAL) suppliers to three commercially available recombinant Factor C (rFC) reagents that contain only one of the three enzymes in the horseshoe crab clotting cascade. The study also includes a recombinant reagent that has been developed to include all three of the enzymes involved in the LAL coagulation cascade, occurring in the presence of endotoxins. Pharmaceutically relevant water samples from various points in pharmaceutical water purification processes were used as a source of natural environmental endotoxins. While these water samples are not routinely tested for bacterial endotoxins, they do exist within manufacturing facilities and thus present risks to manufacturing operations (Sandle, 2019). A statistical analysis of 128 samples containing environmental endotoxin has shown that at the 5% level of significance, non-inferiority between the two compendial LAL methods was achieved. However, the non-inferiority claim could not be made with any of the recombinant reagents. The link between the BET and recombinant alternatives remains unresolved and, therefore, requires caution, continued development, and testing.

Correlation of Body Weight and Composition With Hepatic Activities of Cytochrome P450 Enzymes.

Obesity is associated with comorbidities of which pharmacological treatment is needed. Physiological changes associated with obesity may influence the pharmacokinetics of drugs, but the effect of body weight on drug metabolism capacity remains uncertain. The aim of this study was to investigate ex vivo activities of hepatic drug metabolizing CYP enzymes in patients covering a wide range of body weight. Liver biopsies from 36 individuals with a body mass index (BMI) ranging from 18 to 63 kg/m2 were obtained. Individual hepatic microsomes were prepared and activities of CYP3A, CYP2B6, CYP2C8, CYP2D6, CYP2C9, CYP2C19 and CYP1A2 were determined. The unbound intrinsic clearance (CLint,u) values for CYP3A correlated negatively with body weight (r = -0.43, p < 0.01), waist circumference (r = -0.47, p < 0.01), hip circumference (r = -0.51, p < 0.01), fat percent (r = -0.41, p < 0.05), fat mass (r = -0.48, p < 0.01) and BMI (r = -0.46, p < 0.01). Linear regression analysis showed that CLint,u values for CYP3A decreased with 5% with each 10% increase in body weight (r2 = 0.12, ß = -0.558, p < 0.05). There were no correlations between body weight measures and CLint,u values for the other CYP enzymes investigated. These results indicate reduced hepatic metabolizing capacity of CYP3A substrates in patients with increasing body weight.

Dilemmas With Absolute Quantification of Pharmacologically Relevant Proteins Using Mass Spectrometry.

Determination of abundances of proteins involved in uptake, distribution, metabolism and excretion of xenobiotics is a prerequisite to understand and predict elimination mechanisms in tissue. Mass spectrometry promises simple and accurate measurements of individual proteins in complex mixtures using isotopically labeled peptide standards. However, comparisons of measurements performed in different laboratories have shown considerable discrepancies in the data generated. Even when very similar approaches are compared, the results differ significantly. An alternative method of measuring protein titers is global proteomics. Depending on sample type, this allows quantification of hundreds to thousands of proteins in a single analysis. It enables system-wide insights by providing protein copy numbers and cell sizes. Regardless of differences, the workflows of both the labeled standard-based and the proteomic approach share several steps. Each can be critical. Selection of optimal techniques is the prerequisite for accurate and reproducible protein quantification.

Industrial Approach to Determine the Relative Contribution of Seven Major UGT Isoforms to Hepatic Glucuronidation.

The pharma industry designs increasingly less cytochrome P450 dependent and more metabolically stable drugs, and consequently UGT-metabolism becomes more frequently involved. This study compares 2 glucuronidation RAF-scaling approaches, product formation and substrate depletion, regarding their potential for prediction of in vivo DDI and the relative contribution of UGT-mediated phase II reactions in an industrial setting. RAFs were developed for UGT1A1, 1A3, 1A4, 1A6, 1A9, 2B7 and 2B15 recombinant UGT isoforms and a large 150-donor pooled human liver microsome batch. The RAF-values ranged from small values of 0.06 (UGT1A3), over 0.24 and 0.48 (UGT1A9 and UGT1A4), to values around 1 (1.11 for UGT2B7, 1.14 for UGT1A1), and high RAFs of 4.8 (UGT1A6) and 6.57 (UGT2B15). Both approaches identified the same primarily involved isoforms (≥75% relative contribution) of 5 clinical reference compounds (raloxifene, haloperidol, laropiprant, telmisartan and naloxone), in concordance with reported in vitro (R2 = 0.65) and clinical results for UGT1A1, 1A3, 1A4, 1A9, 2B7 and 2B15. This study is distinctive in that it is reporting the glucuronide formation in addition to substrate depletion. The product formation approach proved more sensitive and enables UGT phenotyping of slowly metabolized drugs, additionally it allows identification of structurally different glucuronides.

Effect of Calcium on the Hydrolysis Activity of Human Butyrylcholinesterase.

The aim of this experiment was to study the effects of calcium ion on the hydrolysis of cationic and anionic substrate by human butyrylcholinesterase (HuBChE). The hydrolysis of aspirin, an anionic substrate, by HuBChE was markedly increased in the presence of increasing concentrations of calcium ion (∼20 mM), as shown by the increasing kcat (∼18-fold). Butyrylthiocholine (BTC), a cationic substrate, was biphasically hydrolyzed with substrate activation; a second BTC molecule caused a 3-fold increase in kcat. At both lower and higher concentrations of BTC, its hydrolysis by HuBChE was slightly slowed down by the addition of calcium ion. Other cationic substrates, propranolol derivatives with butyryl and valeryl groups, were R-preferentially hydrolyzed by HuBChE; the rate of hydrolysis of these compounds was nearly the same in the absence and presence of calcium ion. These data indicate differential effects of calcium ion on HuBChE activity with anionic and cationic substrates. Furthermore, during the hydrolysis of aspirin in the presence of calcium ions, we demonstrated the existence of 2 additional binding sites for calcium, with Km values of 1.8 and 5.9 mM. These binding sites exhibited much lower affinities than the EF-hand motif, previously identified as a high-affinity calcium-binding site.

Identification of Major Esterase Involved in Hydrolysis of Soft Anticholinergic (2R3'R-SGM) Designed From Glycopyrrolate in Human and Rat Tissues.

The glycopyrrolate soft analog, SGM, designed to be easily hydrolyzed into the significantly less active zwitterionic metabolite, SGa, typifies soft drug that reduces systemic side effects (a problem often seen with traditional anticholinergics) following local administration. In this study, hydrolysis of 2R3'R-SGM, the highest pharmacologically active stereoisomer of SGM, was investigated in human and rat tissues. In both species, 2R3'R-SGM was metabolized to 2R3'R-SGa in plasma but was stable in liver and intestine. The half-life of 2R3'R-SGM was found to be 16.9 min and 9.8 min in human and rat plasma, respectively. The enzyme inhibition and stimulation experiments showed that plasma paraoxonase 1 (PON1) is responsible for the hydrolysis of 2R3'R-SGM in humans and rats. The PON1-mediated hydrolysis of 2R3'R-SGM was confirmed in the lipoprotein-rich fractions of human plasma. As PON1 is naturally attached to high-density lipoprotein, it might be absent in topical tissues where 2R3'R-SGM is applied, supporting its local stability and efficacy. The metabolic behavior of 2R3'R-SGM indicates that it is an ideal soft drug to be detoxified as soon as it moves into systemic circulation. Furthermore, the similarity of 2R3'R-SGM metabolism in humans and rats showed that the rat is a suitable animal for preclinical study.

Pulse Proteolysis: An Orthogonal Tool for Protein Formulation Screening.

Protein formulation stability is difficult to predict a priori and generally involves long-term stability studies. It is of interest to develop an analytical method that can predict stability trends reliably. Here, pulse proteolysis was evaluated as an analytical tool to predict solution-state stability in different formulations. Four proteins formulated in different buffer and excipient compositions were subjected to urea-induced unfolding and brief enzymatic digestion ("pulse" proteolysis), and relative resistance to proteolysis was measured by microfluidics-based capillary electrophoresis-sodium dodecyl sulfate. Biophysical properties of each formulation were measured using orthogonal biophysical techniques such as differential scanning fluorimetry, differential scanning calorimetry, dynamic light scattering, circular dichroism, and fluorescence spectroscopy. Protein stability in all formulations was monitored by size exclusion chromatography on storage at 5°C and 40°C. For all 4 proteins, formulations with greater proteolytic resistance also showed higher monomer content on thermal stability. In contrast, standard biophysical techniques showed reasonable-to-no correlation with size exclusion chromatography data. The data support the use of pulse proteolysis as an orthogonal, quantitative, and predictive tool to measure protein conformational stability and rank-order formulations.

Evaluation of Cytochrome P450 Selectivity for Hydralazine as an Aldehyde Oxidase Inhibitor for Reaction Phenotyping.

Hydralazine has been reported as a selective mechanism-based inactivator of aldehyde oxidase (AO) and it is widely used in the pharmaceutical industry for reaction phenotyping to estimate fraction metabolized by AO and to identify AO substrates. In this study, however, hydralazine was found to inhibit CYP1A2, 2B6, 2D6, and 3A in human suspension hepatocytes under reaction phenotyping assay conditions, at concentrations that chemically knocked out most of the AO activities (≥50 µM). Furthermore, hydralazine is a time-dependent inhibitor of CYP1A2. Based on these findings, precautions need to be taken when using hydralazine as an AO inhibitor for in vitro studies because fraction metabolized by AO is likely to be overestimated and the likelihood of false positives in identifying AO substrates increases.

Methadone Metabolism and Drug-Drug Interactions: In Vitro and In Vivo Literature Review.

Methadone is utilized for the treatment of individuals with opiate dependence. Methadone undergoes N-demethylation by multiple cytochrome P450 (CYP) enzymes including CYP3A4, CYP2B6, CYP2C19, CYP2D6, CYP2C9, and CYP2C8. In vivo, polymorphism effects on methadone systemic exposure have been noted for CYP2B6, CYP3A4, and CYP2D6. Clinical drug interaction studies with antiviral drugs in methadone maintenance treatment patients yield varying results on methadone pharmacokinetics and pharmacodynamics. In general, CYP inhibitors altered methadone exposure with no adverse effects. CYP inducers generally decreased methadone exposure with some reports of withdrawal symptoms in the subjects. Interaction studies with antiviral drug combinations yielding differing results depend on the enzyme(s) affected. For certain antiviral medicines which are dual inhibitor(s) and inducer(s) for CYP enzymes, their effect on methadone pharmacokinetics can change with time since the effect of induction is usually delayed compared to the effect of inhibition.

Nitrous oxide reduction genetic potential from the microbial community of an intermittently aerated partial nitritation SBR treating mature landfill leachate.

This study investigates the microbial community dynamics in an intermittently aerated partial nitritation (PN) SBR treating landfill leachate, with emphasis to the nosZ encoding gene. PN was successfully achieved and high effluent stability and suitability for a later anammox reactor was ensured. Anoxic feedings allowed denitrifying activity in the reactor. The influent composition influenced the mixed liquor suspended solids concentration leading to variations of specific operational rates. The bacterial community was low diverse due to the stringent conditions in the reactor, and was mostly enriched by members of Betaproteobacteria and Bacteroidetes as determined by 16S rRNA sequencing from excised DGGE melting types. The qPCR analysis for nitrogen cycle-related enzymes (amoA, nirS, nirK and nosZ) demonstrated high amoA enrichment but being nirS the most relatively abundant gene. nosZ was also enriched from the seed sludge. Linear correlation was found mostly between nirS and the organic specific rates. Finally, Bacteroidetes sequenced in this study by 16S rRNA DGGE were not sequenced for nosZ DGGE, indicating that not all denitrifiers deal with complete denitrification. However, nosZ encoding gene bacteria was found during the whole experiment indicating the genetic potential to reduce N2O.

Analysis of DNA by Southern blotting.

The purpose of this protocol is to detect specific DNA sequences in a complex sample by hybridization to a labeled probe.