Deciphering deamidation and isomerization in therapeutic proteins: Effect of neighboring residue.

Deamidation of asparagine (Asn) and isomerization of aspartic acid (Asp) residues are among the most commonly observed spontaneous post-translational modifications (PTMs) in proteins. Understanding and predicting a protein sequence's propensity for such PTMs can help expedite protein therapeutic discovery and development. In this study, we used proton-affinity calculations with semi-empirical quantum mechanics and microsecond long equilibrium molecular dynamics simulations to investigate mechanistic roles of structural conformation and chemical environment in dictating spontaneous degradation of Asn and Asp residues in 131 clinical-stage therapeutic antibodies. Backbone secondary structure, side-chain rotamer conformation and solvent accessibility were found to be key molecular indicators of Asp isomerization and Asn deamidation. Comparative analysis of backbone dihedral angles along with N-H proton affinity calculations provides a mechanistic explanation for the strong influence of the identity of the n + 1 residue on the rate of Asn/Asp degradation. With these findings, we propose a minimalistic physics-based classification model that can be leveraged to predict deamidation and isomerization propensity of proteins.

Fanconi syndrome in a patient receiving pre-exposure prophylaxis for HIV infection: case report.

BACKGROUND: Tenofovir disoproxil is efficacious in the preventing HIV infection as part of a pre-exposure prophylaxis (PrEP) regimen. Although its use has been associated with impaired renal function, instances of Fanconi syndrome are extremely rare. This may change with increased uptake of PrEP. METHODS: A 55-year-old male patient (he/him/his) was commenced on PrEP with a baseline estimated glomerular filtration rate (eGFR) of approximately 60mL/min/1.73m2 . RESULTS: Within 6months, he developed new and worsening proteinuria, glycosuria and aminoaciduria despite no apparent change in eGFR. PrEP was discontinued and his urinary abnormalities rapidly resolved. The patient remains off PrEP. CONCLUSIONS: Fanconi syndrome is a rare, but known complication of tenofovir disoproxil. This is the first report related to PrEP in Australia. While tenofovir associated nephrotoxicity in patients taking PrEP is uncommon, the patient's age and pre-existing renal impairment placed him at substantially higher risk. At-risk patients need more frequent monitoring of their eGFR and proteinuria. Urinary protein to creatinine ratio is the preferred to dipstick testing for proteinuria and the latter does not readily detect the low molecular wight proteinuria characteristic of tenofovir toxicity. Early recognition of these patients is essential, as prompt cessation of PrEP can often reverse renal abnormalities.

External validation of a triage tool for predicting cardiac arrest in the emergency department.

Early recognition and prevention comprise the first ring of the Chain of Survival for in-hospital cardiac arrest (IHCA). We previously developed and internally validated an emergency department (ED) triage tool, Emergency Department In-hospital Cardiac Arrest Score (EDICAS), for predicting ED-based IHCA. We aimed to externally validate this novel tool in another ED population. This retrospective cohort study used electronic clinical warehouse data from a tertiary medical center with approximately 130,000 ED visits per year. We retrieved data from 268,208 ED visits over a 2-year period. We selected one ED visit per person and excluded out-of-hospital cardiac arrest or children. Patient demographics and computerized triage information were retrieved, and the EDICAS was calculated to predict the ED-based IHCA. A total of 145,557 adult ED patients were included. Of them, 240 (0.16%) developed IHCA. The EDICAS showed excellent discrimination with an area under the receiver operating characteristic (AUROC) of 0.88. The AUROC of the EDICAS outperformed those of other early warning scores (0.80 for Modified Early Warning Score [MEWS] and 0.83 for Rapid Emergency Medicine Score [REMS]) in the same ED population. An EDICAS of 6 or above (i.e., high-risk patients) corresponded to a sensitivity of 33%, a specificity of 97%, and a positive likelihood ratio of 12.2. In conclusion, we externally validated a tool for predicting imminent IHCA in the ED and demonstrated its superior performance over other early warning scores. The real-world impact of the EDICAS warning system with appropriate interventions would require a future prospective study.

Best Practices for Aggregate Quantitation of Antibody Therapeutics by Sedimentation Velocity Analytical Ultracentrifugation.

Analytical ultracentrifugation (AUC) is a critical analytical tool supporting the development and manufacture of protein therapeutics. AUC is routinely used as an assay orthogonal to size exclusion chromatography for aggregate quantitation. This article distills the experimental and analysis procedures used by the authors for sedimentation velocity AUC into a series of best-practices considerations. The goal of this distillation is to help harmonize aggregate quantitation approaches across the biopharmaceutical industry. We review key considerations for sample and instrument suitability, experimental design, and data analysis best practices and conversely, highlight potential pitfalls to accurate aggregate analysis. Our goal is to provide experienced users benchmarks against which they can standardize their analyses and to provide guidance for new AUC analysts that will aid them to become proficient in this fundamental technique.

Inpatient Outcomes Following a Return Visit to the Emergency Department: A Nationwide Cohort Study.

INTRODUCTION: Emergency department (ED) revisits are traditionally used to measure potential lapses in emergency care. However, recent studies on in-hospital outcomes following ED revisits have begun to challenge this notion. We aimed to examine inpatient outcomes and resource use among patients who were hospitalized following a return visit to the ED using a national database. METHODS: This was a retrospective cohort study using the National Health Insurance Research Database in Taiwan. One-third of ED visits from 2012-2013 were randomly selected and their subsequent hospitalizations included. We analyzed the inpatient outcomes (mortality and intensive care unit [ICU] admission) and resource use (length of stay [LOS] and costs). Comparisons were made between patients who were hospitalized after a return visit to the ED and those who were hospitalized during the index ED visit. RESULTS: Of the 3,019,416 index ED visits, 477,326 patients (16%) were directly admitted to the hospital. Among the 2,504,972 patients who were discharged during the index ED visit, 229,059 (9.1%) returned to the ED within three days. Of them, 37,118 (16%) were hospitalized. In multivariable analyses, the inpatient mortality rates and hospital LOS were similar between the two groups. Compared with the direct-admission group, the return-admission group had a lower ICU admission rate (adjusted odds ratio, 0.78; 95% confidence interval [CI], 0.72-0.84), and lower costs (adjusted difference, -5,198 New Taiwan dollars, 95% CI, -6,224 to -4,172). CONCLUSION: Patients who were hospitalized after a return visit to the ED had a lower ICU admission rate and lower costs, compared to those who were directly admitted. Our findings suggest that ED revisits do not necessarily translate to poor initial care and that subsequent inpatient outcomes should also be considered for better assessment.

Impact of Silicone Oil on Free Fatty Acid Particle Formation due to Polysorbate 20 Degradation.

PURPOSE: Polysorbate 20 (PS20), a commonly used surfactant in biopharmaceutical formulations, can undergo hydrolytic degradation resulting in free fatty acids (FFAs) that precipitate to form particles. This work investigates the ability for silicone oil (si-oil) coated on the interior walls of prefilled syringes (PFSs) to act as a sink for FFAs and potentially delay FFA particle formation. METHODS: Myristic acid distribution coefficient was measured in a two-phase system containing si-oil and formulation buffer at a range of aqueous conditions. An empirical model was built from these data to predict distribution coefficient based on aqueous conditions. To verify the model, PS20 was degraded using model lipases side-by-side in glass vials and PFSs while monitoring sub-visible particles. RESULTS: The empirical model demonstrates that the partitioning of myristic acid into si-oil is maximized at low pH and low PS20 concentration. The model predicts that the presence of si-oil at levels typical in PFSs provides at most an 8.5% increase in the total carrying capacity for myristic acid compared to a non-coated glass vial. The time to onset of FFA particles was equivalent between degradations performed in two PFS models coated with differing levels of silicone oil and in non-coated glass vials. CONCLUSION: Herein, we demonstrate that FFAs partition from aqueous solution into si-oil. However, the extent of the partitioning effect is not large enough to delay PS20-related FFA particle formation at typical formulation conditions (pH 5.0-7.5, 0.01% - 0.1% w/v PS20) filled in typical PFSs (<1.0 mg si-oil/mL aqueous fill).

Toward in silico CMC: An industrial collaborative approach to model-based process development.

The Third Modeling Workshop focusing on bioprocess modeling was held in Kenilworth, NJ in May 2019. A summary of these Workshop proceedings is captured in this manuscript. Modeling is an active area of research within the biotechnology community, and there is a critical need to assess the current state and opportunities for continued investment to realize the full potential of models, including resource and time savings. Beyond individual presentations and topics of novel interest, a substantial portion of the Workshop was devoted toward group discussions of current states and future directions in modeling fields. All scales of modeling, from biophysical models at the molecular level and up through large scale facility and plant modeling, were considered in these discussions and are summarized in the manuscript. Model life cycle management from model development to implementation and sustainment are also considered for different stages of clinical development and commercial production. The manuscript provides a comprehensive overview of bioprocess modeling while suggesting an ideal future state with standardized approaches aligned across the industry.

Highland games: A benchmarking exercise in predicting biophysical and drug properties of monoclonal antibodies from amino acid sequences.

Biopharmaceutical product and process development do not yet take advantage of predictive computational modeling to nearly the degree seen in industries based on smaller molecules. To assess and advance progress in this area, spirited coopetition (mutually beneficial collaboration between competitors) was successfully used to motivate industrial scientists to develop, share, and compare data and methods which would normally have remained confidential. The first "Highland Games" competition was held in conjunction with the October 2018 Recovery of Biological Products Conference in Ashville, NC, with the goal of benchmarking and assessment of the ability to predict development-related properties of six antibodies from their amino acid sequences alone. Predictions included purification-influencing properties such as isoelectric point and protein A elution pH, and biophysical properties such as stability and viscosity at very high concentrations. Essential contributions were made by a large variety of individuals, including companies which consented to provide antibody amino acid sequences and test materials, volunteers who undertook the preparation and experimental characterization of these materials, and prediction teams who attempted to predict antibody properties from sequence alone. Best practices were identified and shared, and areas in which the community excels at making predictions were identified, as well as areas presenting opportunities for considerable improvement. Predictions of isoelectric point and protein A elution pH were especially good with all-prediction average errors of 0.2 and 1.6 pH unit, respectively, while predictions of some other properties were notably less good. This manuscript presents the events, methods, and results of the competition, and can serve as a tutorial and as a reference for in-house benchmarking by others. Organizations vary in their policies concerning disclosure of methods, but most managements were very cooperative with the Highland Games exercise, and considerable insight into common and best practices is available from the contributed methods. The accumulated data set will serve as a benchmarking tool for further development of in silico prediction tools.

Measurement and Characterization of Hydrogen-Deuterium Exchange Chemistry Using Relaxation Dispersion NMR Spectroscopy.

One-dimensional heteronuclear relaxation dispersion NMR spectroscopy at 13C natural abundance successfully characterized the dynamics of the hydrogen-deuterium exchange reaction occurring at the Nε position in l-arginine by monitoring Cδ in varying amounts of D2O. A small equilibrium isotope effect was observed and quantified, corresponding to ΔG = -0.14 kcal mol-1. A bimolecular rate constant of kD = 5.1 × 109 s-1 M-1 was determined from the pH*-dependence of kex (where pH* is the direct electrode reading of pH in 10% D2O and kex is the nuclear spin exchange rate constant), consistent with diffusion-controlled kinetics. The measurement of ΔG serves to bridge the millisecond time scale lifetimes of the detectable positively charged arginine species with the nanosecond time scale lifetime of the nonobservable low-populated neutral arginine intermediate species, thus allowing for characterization of the equilibrium lifetimes of the various arginine species in solution as a function of fractional solvent deuterium content. Despite the system being in fast exchange on the chemical shift time scale, the magnitude of the secondary isotope shift due to the exchange reaction at Nε was accurately measured to be 0.12 ppm directly from curve-fitting D2O-dependent dispersion data collected at a single static field strength. These results indicate that relaxation dispersion NMR spectroscopy is a robust and general method for studying base-catalyzed hydrogen-deuterium exchange chemistry at equilibrium.

Effects of Gender on the Association of Urinary Phthalate Metabolites with Thyroid Hormones in Children: A Prospective Cohort Study in Taiwan.

Phthalates are considered endocrine disruptors. Our study assessed the gender-specific effects of phthalate exposure on thyroid function in children. In total, 189 Taiwanese children were enrolled in the study. One-spot urine and blood samples were collected for analyzing 12 phthalate metabolites in urine and thyroid hormones. The association between urinary phthalate metabolites and serum thyroid hormones was determined using a generalized linear model with a log link function; the children were categorized into groups for analysis according to the 33rd and 66th percentiles. The data were stratified according to gender and adjusted for a priori defined covariates. In girls, a positive association existed between urinary di-2-ethylhexyl phthalate (DEHP) metabolites (mono-(2-ethylhexyl) phthalate, mono-(2-ethyl-5-oxohexyl) phthalate, and mono-(2-ethyl-5-hydroxyhexyl) phthalate) and free thyroxine (T4). In boys, urinary dibutyl phthalate (DBP) metabolites (mono-i-butyl phthalate and mono-n-butyl phthalate) were positively associated with free triiodothyronine (T3). After categorizing each exposure into three groups, urinary DEHP metabolites were positively associated with free T3 levels in boys. Our results suggested that DEHP is associated with free T4 in girls and that DBP is associated with free T3 in boys. Higher DEHP metabolite concentrations exerted larger effects on free T3 in boys. These results reveal the gender-specific relationships between phthalate metabolites and thyroid hormones.

Assessing the Utility of Circular Dichroism and FTIR Spectroscopy in Monoclonal-Antibody Comparability Studies.

Protein characterization is a necessary activity during development, technical transfers, and licensure. One important aspect of protein characterization is higher order structure assessment, which can be accomplished in a variety of ways. Circular dichroism (CD) and Fourier transform infrared (FTIR) spectroscopies provide global higher order structure and are routinely used to measure the overall structure for product characterization; however, their use as comparability tools is uncertain because of their insensitivity to local or small structure changes. We use a monoclonal antibody (mAb) to explore the usefulness of CD and FTIR compared with other indirect methods of structure characterization such as size-exclusion and ion-exchange chromatographies (SEC and IEC). A panel of degraded samples of a mAb was generated; their higher order structure evaluated using CD and FTIR and was found to be largely unchanged. However, the SEC and IEC chromatograms of certain degraded samples were found to have measurable changes. Based on these studies, we conclude that the application of CD and FTIR should be reserved for global higher order structure identification or product characterization only. The use of CD or FTIR comparability of mAbs should be carefully evaluated, as comparability can be sensitively determined using indirect methods based on chromatography.

Six amino acid residues in a 1200 Å2 interface mediate binding of factor VIII to an IgG4κ inhibitory antibody.

The development of neutralizing anti-factor VIII (FVIII) antibodies complicates the treatment of many hemophilia A patients. The C-terminal C2 domain is a particularly antigenic FVIII region. A crystal structure of recombinant FVIII-C2 bound to an Fab fragment of the patient-derived monoclonal antibody BO2C11, which recognizes an immunodominant inhibitor epitope on FVIII and blocks its ability to bind von Willebrand factor (VWF) and phospholipids, revealed that 15 amino acids in FVIII contact this antibody. Forty-three recombinant FVIII-C2 proteins, each with a surface-exposed side chain mutated to alanine or another residue, were generated, and surface plasmon resonance studies were carried out to evaluate effects of these substitutions on BO2C11/FVIII-C2 binding affinity. Thermodynamic analysis of experiments carried out at three temperatures indicated that one beta hairpin turn at the antigen-antibody interface (FVIII-F2196, N2198, M2199 and F2200) plus two non-contiguous arginines (FVIII-R2215 and R2220), contributed appreciably to the affinity. B-domain-deleted (BDD) FVIII-F2196A, FVIII-F2196K and FVIII-M2199A were generated and characterized. Their pro-coagulant activities and binding to VWF were similar to those of WT-BDD-FVIII, and FVIII-F2196K avoided neutralization by BO2C11 and murine inhibitory mAb 1B5. This study suggests specific sites for amino acid substitutions to rationally design FVIII variants capable of evading immunodominant neutralizing anti-FVIII antibodies.

Fatal falls from height in Taiwan.

This study conducts an investigation of fatal falls from height, examines gender differences, and compares our findings with those of Western countries. We review deaths in Taiwan caused by falls from height that underwent forensic autopsy from 1994 to 2010. Among the examined cases, 182 were suicide, 156 were accidents, and 18 were homicides. Men who fell from greater heights had a lower probability of fatal head trauma (p = 0.045), and women exhibited a lower fatal head trauma rate when falling from heights of between 10 and 25 m in accident group (p = 0.003). There was no significant difference between cases of falling from greater and lower heights within the suicide group (p = 0.834). Psychiatric illness was only reported in 20.3% and 28.8% cases in suicide and accident groups. Only in male cases was the use of psychotropic substances higher in the suicide groups than in the accident groups (p = 0.047).

High-resolution mapping of epitopes on the C2 domain of factor VIII by analysis of point mutants using surface plasmon resonance.

Neutralizing anti-factor VIII (FVIII) antibodies that develop in patients with hemophilia A and in murine hemophilia A models, clinically termed "inhibitors," bind to several distinct surfaces on the FVIII-C2 domain. To map these epitopes at high resolution, 60 recombinant FVIII-C2 proteins were generated, each having a single surface-exposed residue mutated to alanine or a conservative substitution. The binding kinetics of these muteins to 11 monoclonal, inhibitory anti-FVIII-C2 antibodies were evaluated by surface plasmon resonance and the results compared with those obtained for wild-type FVIII-C2. Clusters of residues with significantly altered binding kinetics identified "functional" B-cell epitopes, defined as those residues contributing appreciable antigen-antibody avidity. These antibodies were previously shown to neutralize FVIII activity by interfering with proteolytic activation of FVIII by thrombin or factor Xa, or with its binding to phospholipid surfaces, von Willebrand factor, or other components of the intrinsic tenase complex. Fine mapping of epitopes by surface plasmon resonance also indicated surfaces through which FVIII interacts with proteins and phospholipids as it participates in coagulation. Mutations that significantly altered the dissociation times/half-lives identified functionally important interactions within antigen-antibody interfaces and suggested specific sequence modifications to generate novel, less antigenic FVIII proteins with possible therapeutic potential for treatment of inhibitor patients.

Crystal and NMR structures of a Trp-cage mini-protein benchmark for computational fold prediction.

To provide high-resolution X-ray crystallographic structures of a peptide with the Trp-cage fold, we prepared a cyclized version of this motif. Cyclized Trp-cage is remarkably stable and afforded two crystal forms suitable for X-ray diffraction. The resulting higher resolution crystal structures validate the prior NMR models and provide explanations for experimental observations that could not be rationalized by NMR structural data, including the structural basis for the increase in fold stability associated with motif cyclization and the manner in which a polar serine side chain is accommodated in the hydrophobic interior. A hexameric oligomer of the cyclic peptide is found in both crystal forms and indicates that under appropriate conditions, this minimized system may also serve as a model for protein-protein interactions.

Lysine and arginine residues do not increase the helicity of alanine-rich peptide helices.

The helix-disfavoring, versus alanine, propagation values of lysine (0.8) and arginine (1.0) residues placed centrally in an (Ala)(9) unit have been measured by (13)C NMR.

The Trp-cage: optimizing the stability of a globular miniprotein.

The Trp-cage, as the smallest miniprotein, remains the subject of numerous computational and experimental studies of protein folding dynamics and pathways. The original Trp-cage (NLYIQWLKDGGPSSGRPPPS, Tm = 42 degrees C) can be significantly stabilized by mutations; melting points as high as 64 degrees C are reported. In helical portions of the structure, each allowed replacement of Leu, Ile, Lys or Ser residues by Ala results in a 1.5 (+/-0.35) kJ/mol fold stabilization. No changes in structure or fluxionality of the core results upon stabilization. Contrary to the initial hypothesis, specific Pro/Trp interactions are not essential for core formation. The entropic advantage of Pro versus Ala (DeltaDeltaS(U) = 11 +/- 2 J/mol K) was measured at the solvent-exposed P17 site. Pro-Ala mutations at two of the three prolines (P12 and P18) that encage the indole ring result in less fold destabilization (2.3-3.4 kJ/mol). However, a P19A mutation reduces fold stability by 16 kJ/mol reflecting a favorable Y3/P19 interaction as well as Trp burial. The Y3/P19 hydrophobic staple interaction defines the folding motif as an 18-residue unit. Other stabilizing features that have been identified include a solvent-exposed Arg/Asp salt bridge (3.4-6 kJ/mol) and a buried H-bonded Ser side chain ( approximately 10 kJ/mol).

A pre-existing hydrophobic collapse in the unfolded state of an ultrafast folding protein.

Insights into the conformational passage of a polypeptide chain across its free energy landscape have come from the judicious combination of experimental studies and computer simulations. Even though some unfolded and partially folded proteins are now known to possess biological function or to be involved in aggregation phenomena associated with disease states, experimentally derived atomic-level information on these structures remains sparse as a result of conformational heterogeneity and dynamics. Here we present a technique that can provide such information. Using a 'Trp-cage' miniprotein known as TC5b (ref. 5), we report photochemically induced dynamic nuclear polarization NMR pulse-labelling experiments that involve rapid in situ protein refolding. These experiments allow dipolar cross-relaxation with hyperpolarized aromatic side chain nuclei in the unfolded state to be identified and quantified in the resulting folded-state spectrum. We find that there is residual structure due to hydrophobic collapse in the unfolded state of this small protein, with strong inter-residue contacts between side chains that are relatively distant from one another in the native state. Prior structuring, even with the formation of non-native rather than native contacts, may be a feature associated with fast folding events in proteins.

The helical alanine controversy: an (Ala)6 insertion dramatically increases helicity.

Employing chemical shift melts and hydrogen/deuterium exchange NMR techniques, we have determined the stabilization of the Trp-cage miniprotein due to multiple alanine insertions within the N-terminal alpha-helix. Alanine is shown to be uniquely helix-stabilizing and this stabilization is reflected in the global fold stability of the Trp-cage. The associated free energy change per alanine can be utilized to calculate the alanine propagation value. From the Lifson-Roig formulation, the calculated value (wAla = 1.6) is comparable to those obtained for short, solubilized, alanine-rich helices and is much larger than the values obtained by prior host-guest techniques or in N-terminally templated helices and peptides bearing long contiguous strings of alanines with no capping or solubilizing units present.