Bioanalytical Approaches to Support the Development of Antibody-Oligonucleotide Conjugate (AOC) Therapeutic Proteins

RNA interference (RNAi) is a biological process that evolved to protect eukaryotic organisms from foreign genes delivered by viruses. This process has been adapted as a powerful tool to treat numerous diseases through the delivery of small-interfering RNAs (siRNAs) to target cells to alter aberrant gene expression.Antibody-oligonucleotide conjugates (AOCs) are monoclonal antibodies with complexed siRNA or antisense oligonucleotides (ASOs) that have emerged to address some of the challenges faced by naked or chemically conjugated siRNA, which include rapid clearance from systemic circulation and lack of selective delivery of siRNA to target cells.It is essential to characterize the ADME properties of an AOC during development to optimize distribution to target tissues, to minimize the impact of biotransformation on exposure, and to characterize the PK/PD relationship to guide translation. However, owing to the complexity of AOC structure, this presents significant bioanalytical challenges, and multiple bioanalytical measurements are required to investigate the pharmacokinetics and biotransformation of the antibody, linker, and siRNA payload.In this paper, we describe an analytical workflow that details in vivo characterization of AOCs through measurement of their distinct molecular components to provide the basis for greater understanding of their ADME properties. Although the approaches herein can be applied to in vitro characterization of AOCs, this paper will focus on in vivo applications. This workflow relies on high-resolution mass spectrometry as the principal means of detection and leverages chromatographic, affinity-based, and enzymatic sample preparation steps.

Application of middle-down approach in quantitation and catabolite identification of protein by LC-high-resolution mass spectrometry

Aim: To further enhance the detection sensitivity and increase resolving power of top-down intact protein bioanalysis, middle-down approach was explored. Materials & methods: An monoclonal antibody (mAb) was used as a model protein to evaluate quantitative bioanalytical assay performance and a disulfide linked dimer protein was investigated for its pharmacokinetics properties and catabolism in vivo by middle-down approach. Results & Conclusion: For quantitation of the mAb, different subunits generated by middle-down approach provided different level of signal improvement in biological samples with Lc and half Fc giving five-times better sensitivity than intact mAb. For the dimer protein, middle-down analysis by reduction enabled effective differentiation of the unchanged protein and its oxidized form, and clearly elucidated their respective proteolytic catabolites.

Microflow UPLC and high-resolution MS as a sensitive and robust platform for quantitation of intact peptide hormones

Aim: Recent advances in microflow ultra performance liquid chromatography (UPLC) systems offer higher sensitivity with robustness to meet the routine bioanalytical demands. Modern high-resolution mass spectrometers (HRMS) enable the development of highly selective methods with broad dynamic range. Results: The quantitative performances of tandem quadrupole MS and HRMS were comprehensively compared using seven intact peptide hormones up to 9.4 kDa. Results show comparable performance between two platforms in sensitivity, accuracy and linearity. For some peptides, HRMS provided lower background interference. The benefit of increased sensitivity using microflow UPLC was also demonstrated. Conclusion: HRMS is a versatile platform capable of both basic characterization and reliable quantitation in complex matrices. Microflow UPLC provides lower LLOQs than conventional flow systems, even with less sample volume injected.

An ultrasensitive UPLC–MS/MS assay for the quantification of the therapeutic peptide liraglutide in plasma to assess the oral and nasal bioavailability in beagle dogs

Aim: An ultrasensitive UPLC–MS/MS assay for liraglutide was developed and validated according to US FDA and EMA guidelines and applied to the quantification of plasma concentrations after intravenous, nasal and oral administration of liraglutide to beagle dogs. Results: Liraglutide isolation was performed with a combined protein precipitation and solid-phase extraction protocol. The calibrated concentration range of 0.1–200 ng/ml was linear with correlation coefficients >0.998. Precise analysis was achieved through the utilization of an isotopically labeled internal standard. Absolute bioavailability of liraglutide after nasal and oral administration of liraglutide to beagle dogs was 0.03 and 0.006%, respectively. Conclusion: The assay matches the performance in sensitivity of the previously applied immunoassay and optimally covers the therapeutic range of liraglutide.

Review of approaches and examples for monitoring biotransformation in protein and peptide therapeutics by MS

Biotherapeutic drugs have emerged in quantity in pharmaceutical pipelines, and increasingly diverse biomolecules are progressed through preclinical and clinical development. As purification, separation, mass spectrometer detection and data processing capabilities improve, there is opportunity to monitor drug concentration by traditional ligand-binding assay or MS measurement and to monitor metabolism, catabolism or other biomolecular mass variants present in circulation. This review highlights approaches and examples of monitoring biotransformation of biotherapeutics by MS as these techniques are poised to add value to drug development in years to come. The increased use of such approaches, and the successful quantitation of biotherapeutic structural modifications, will provide insightful data for the benefit of both researchers and patients.

Improving selectivity and sensitivity of protein quantitation by LC–HR–MS/MS: determination of somatropin in rat plasma

Aim: Protein quantitation by digestion of a biological sample followed by LC–MS analysis of a signature peptide can be a challenge because of the high complexity of the digested matrix. Results/methodology: The use of LC with high-resolution (quadrupole-TOF) MS detection allowed quantitation of the 22-kDa biopharmaceutical somatropin in 60 μl of rat plasma down to 25 ng/ml with minimal further sample treatment. Reducing the mass extraction window to 0.01 Da considerably decreased the interference of tryptic peptides, enhanced sensitivity and improved accuracy and precision. Analysis with LC–MS/MS resulted in a less favorable limit of quantitation of 100 ng/ml. Conclusion: HRMS is an interesting option for the quantitation of proteins after digestion and has the potential to improve sensitivity with minimal method development.

Quantitation of intact monoclonal antibody in biological samples: comparison of different data processing strategies

Aim: Sample extraction using immuno-affinity capture coupled with LC–high-resolution mass spectrometer has recently emerged as a novel approach for the determination of concentrations of large molecules at intact level in biological matrix. Methodology: In the current work, different data processing strategies for intact protein bioanalysis, deconvoluted mass spectra or extracted ion chromatogram, were applied to quantitate monoclonal antibody in biological samples for comparison of assay performance. Conclusion: Both deconvolution and extracted ion chromatogram strategies showed similar selectivity, sensitivity, accuracy and precision. The monkey pharmacokinetics data obtained from both approaches agreed well with each other, and agreed with data obtained from surrogate peptide approach. The pros and cons, and optimal parameters of each approach were discussed.

Bioanalysis of farnesyl pyrophosphate in human plasma by high-performance liquid chromatography coupled to triple quadrupole tandem mass spectrometry and hybrid quadrupole Orbitrap high-resolution mass spectrometry

The isoprenoids farnesyl pyrophosphate (FPP) and geranylgeranyl pyrophosphate (GGPP) are pivotal intermediates for cholesterol homeostasis and cell signaling in the mevalonate pathway. We developed a sensitive and selective high-performance liquid chromatography tandem triple quadrupole mass spectrometry (LC-QQQ-MS) method for FPP in human plasma without the need for a derivatization process. We optimized the sample preparation procedure to extract FPP and ¹³C₅-FPP (as internal standard) from sample fluids using methanol. Phosphate-buffered saline was used as the surrogate matrix for the preparation of calibration curves and quality control samples. Using an XBridge C18 column (3.5 μm, 2.1 × 100-mm ID) with gradient elution composed of 10 mmol/L ammonium carbonate/ammonium hydroxide (1000:5, v/v) and acetonitrile/ammonium hydroxide (1000:5, v/v) provided the sharp peaks of FPP and ¹³C₅-FPP in human plasma. The calibration curve ranged from 0.2 to 20 ng/mL in human plasma with acceptable intra-day and inter-day precision and accuracy. The sensitivity of this bioanalytical method was sufficient for clinical analysis. The endogenous FPP plasma concentrations in 40 human healthy volunteers ascertained by LC-QQQ-MS and high-performance liquid chromatography tandem hybrid quadrupole Orbitrap high-resolution mass spectrometry (LC-Q-Orbi-MS) were comparable. Furthermore, the endogenous GGPP in human plasma was selectively detected for the first time by LC-Q-Orbi-MS. In conclusion, a sensitive bioanalytical method for FPP in human plasma by means of LC-QQQ-MS and LC-Q-Orbi-MS was developed in this study. Taking into account the versatility of LC-Q-Orbi-MS, the simultaneous detection of FPP and GGPP may be feasible in clinical practice.

Welcome to volume 9 of Bioanalysis

Welcome to volume 9 of Bioanalysis and Happy New Year to all of our readers. We would like to take the opportunity to look back 2016, which was another great year for us. We thank all our authors, readers and reviewers, as well as our Editorial Board members for their continued support. We very much look forward to working with everyone in 2017.

A novel sequential electrostatic-HILIC SPE within a quantitative method for bivalirudin in human plasma by LC–SRM

Aim: This work set out to realize an idea for a novel means of extracting the peptide therapeutic bivalirudin from human plasma in what would be a uniquely selective means of SPE, a mixed-mode protocol involving electrostatic interactions followed by HILIC. Results: Inter and intra-assay relative error ranged from 3.52 to 8.23%, and 2.37 to 6.90%, respectively. Inter and intra-assay precision ranged from 2.64 to 7.12%, and 0.855 to 2.90%, respectively. Recoveries of 80% were attained, and there was no hint of discernible manifestation of matrix effects. Conclusion: The method was shown to perform excellently in the assessment tantamount to method validation. The essence of the extraction method presents a new option for highly selective extraction of peptides from biological matrices.

A whole-molecule immunocapture LC–MS approach for the in vivo quantitation of biotherapeutics

Aim: Large-molecule biotherapeutic quantitation in vivo by LC–MS has traditionally relied on enzymatic digestion followed by quantitation of a ‘surrogate peptide’ to infer whole-molecule concentration. MS methods presented here measure the whole molecule and provide a platform to better understand the various circulating drug forms by allowing for variant quantitation. Results: An immunocapture LC–MS method for quantitation of a biotherapeutic monoclonal antibody from human plasma is presented. Sensitivity, precision and accuracy for each molecular portion are presented along with an example of glycoform variant quantitation. Conclusion: The method is presented as a basic platform to be further developed for Good Practice (GxP) applications, critical quality attribute analysis or general understanding of molecular forms present as required for the wide range of drug development processes.

Unconjugated payload quantification and DAR characterization of antibody–drug conjugates using high-resolution MS

Aim: The application of high-resolution MS to antibody–drug conjugate (ADC) drug development may provide insight into their safety and efficacy. Quantification of unconjugated cytotoxic drug (payload) and characterization of drug-to-antibody ratio distribution were determined in plasma using orthogonal acceleration quadrupole-time-of-flight MS. Results: Unconjugated payload quantification determined by quadrupole-time-of-flight-based MRMhighresolution and triple quadrupole-based multiple reaction monitoring were comparable and achieved detection limits of 0.030 and 0.015 ng/ml, respectively. As determined by immunocapture and TOF-MS, drug-to-antibody ratio remained unchanged up to 3-weeks postdose for an ADC containing engineered glutamine linkers, but declined from four to three over 2 weeks in an ADC containing engineered cysteine linkers. Conclusion: The use of high-resolution MS in ADC drug discovery confirms its utility within the bioanalytical discipline.

HRMS using a Q-Exactive series mass spectrometer for regulated quantitative bioanalysis: how, when, and why to implement

High-resolution MS (HRMS) has seen an uptake in use for discovery qual/quan workflows, however, its utilization in late discovery/development has been slow. Past reports comparing HRMS to triple quadrupole (QQQ) instrumentation to date have indicated that HRMS instruments are capable of producing data acceptable for regulated bioanalysis, however lack the sensitivity required for sub ng/ml LLOQ assays. Recent advances in HRMS instrumentation have closed the sensitivity gap with QQQ and have even provided improved selectivity and sensitivity over QQQ SRM assays. Herein, the authors will describe how, when, and why HRMS (specifically Q-Exactive series mass spectrometers) should be considered for implementation in regulated quantitative bioanalysis assays.

Modify on the fly: triple quad to high resolution in support of a dermal clinical study requiring an ultra low LLOQ

Background: FTIH studies can be challenging due to the varying dosing regimens and rapid data delivery. Chemists are asked to provide ultra-low limits of quantitation to provide an understanding of patient efficacy and safety in order to progress drug development. In a recent dermal study it became necessary to reduce the LLOQ of a small molecule drug from 50 to 1 pg/ml due to reductions in the dose and surface area of drug application. Methodology: The 50-fold increase in assay sensitivity necessitated the use of a high-resolution mass spectrometer (LC–HRMS) to separate matrix interferences observed when using a unit resolution triple quadrupole MS. Conclusion: A sensitive, robust assay was validated to support of a FTIH study using a LC–HRMS.