Ion exchange liquid chromatography method for the direct determination of small ribonucleic acids

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 characterise the ADME properties of an AOC during development to optimise distribution to target tissues, to minimise the impact of biotransformation on exposure, and to characterise 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 characterisation 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 characterisation 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.

Separation of the diastereomers of phosphorothioated siRNAs by anion-exchange chromatography under non-denaturing conditions

In recent years, several small interfering RNA (siRNA) therapeutics have been approved, and most of them are phosphorothioate (PS)-modified for improving nuclease resistance. This chemical modification induces chirality in the phosphorus atom, leading to the formation of diastereomers. Recent studies have revealed that Sp and Rp configurations of PS modifications of siRNAs have different biological properties, such as nuclease resistance and RNA-induced silencing complex (RISC) loading. These results highlight the importance of determining diastereomeric distribution in quality control. Although various analytical approaches have been used to separate diastereomers (mainly single-stranded oligonucleotides), it becomes more difficult to separate all of them as the number of PS modifications increases. Despite siRNA exhibits efficacy in the double-stranded form, few reports have examined the separation of diastereomers in the double-stranded form. In this study, we investigated the applicability of non-denaturing anion-exchange chromatography (AEX) for the separation of PS-modified siRNA diastereomers. Separation of the four isomers of the two PS bonds tended to improve in the double-stranded form compared to the single-stranded form. In addition, the effects of the analytical conditions and PS-modified position on the separation were evaluated. Moreover, the elution order of the Sp and Rp configurations was confirmed, and the steric difference between them, i.e., the direction of the anionic sulfur atom, appeared to be important for the separation mechanism in non-denaturing AEX. Consequently, all 16 peak tops of the four PS modifications were detected in one sequence, and approximately 30 peak tops were detected out of 64 isomers of six PS bonds, indicating that non-denaturing AEX is a useful technique for the quality control of PS-modified siRNA therapeutics.

Optimization of orthogonal separations for the analysis of oligonucleotides using 2D-LC

Oligonucleotides are commonly analysed using one dimensional chromatography (1D-LC) to resolve and characterise manufacturing impurities, structural isomers and (in respect to emerging oligonucleotide therapeutics) drug substance and drug product. Due to low selectivity and co-elution of closely related oligonucleotides using 1D-LC, analyte resolution is challenged. This leads to the requirement for improved analytical methods. Multidimensional chromatography has demonstrated utility in a range of applications as it increases peak capacity using orthogonal separations, however there are limited studies demonstrating the 2D-LC analysis of closely related oligonucleotides. In this study we optimised OGN size and sequence based separations using a variety of 1D-LC methods and coupled these orthogonal modes of chromatography within a 2D-LC workflow. Theoretical 2D-LC workflows were evaluated for optimal orthogonality using the minimum convex hull metric. The most orthogonal workflow identified in this study was ion-pair reversed phase using tributylammonium acetate (IP-RP-TBuAA) coupled with strong anion exchange in conjunction with sodium perchlorate (SAX-NaClO4) at high mobile phase pH. We developed a heart-cut (IP-RP-TBuAA)-(SAX-NaClO4) 2D-LC method for analysis of closely related size and sequence variant OGNs and OGN manufacturing impurities. The 2D-LC method resulted in an increased orthogonality and a reduction in co-elution (or close elution). Application of a UV based reference mapping strategy in conjunction with the 2D-LC method demonstrated a reduction in analytical complexity by reducing the reliance on mass based detection methods.

Managing nonspecific adsorption to liquid chromatography hardware: A review

The choice of alternative materials over stainless steel hardware in the construction of liquid chromatography systems has unveiled the degree to which nonspecific adsorption impacts the reproducibility of LC methods. Some of the major contributors to nonspecific adsorption losses are charged metallic surfaces and leached metallic impurities, that may interact with the analyte and result in analyte loss and overall poor chromatographic performance. In this review, we describe several mitigation strategies available to chromatographers to minimize nonspecific adsorption to chromatographic systems. Alternative surfaces to stainless steel such as titanium, PEEK, and hybrid surface technologies are discussed. Furthermore, mobile phase additives used to prevent metal ion-analyte interactions are reviewed. Nonspecific adsorption of analytes is not reserved to metallic surfaces, as analytes may adsorb to the surfaces of filters, tubes, and pipette tips during sample preparation. Identifying the source of nonspecific interactions is paramount, as mitigation strategies may differ depending on what stage nonspecific losses are taking place. With this in mind, we discuss diagnostic methods that may help the chromatographer to differentiate losses resulting from sample preparation, and losses during LC runs.

A simple and green solid phase extraction method for oligonucleotides using adsorbent with amino and carboxylic moieties

The study aimed to use a material with amino and carboxylic moieties to extract unmodified and phosphorothioate oligonucleotides. The charge of amine and carboxyl groups at the surface has changed with the change in pH of the adsorption (pH 4.5) and desorption solution (pH 9.5). Thus, both the binding and elution of the oligonucleotides were based on electrostatic interactions, and the procedure required only 10 mM ammonium acetate, with the change of pH depending on the extraction step. The developed procedure was successfully applied to extract oligonucleotides from aqueous solutions and serum samples. The method is simple and fast, providing good reproducibility (SD between 1 and 4%) and relatively high oligonucleotide recovery (81-98% for standards, 60-71% for diluted serum samples, and 80-92 for LLE serum extracts). Moreover, only environmentally friendly solvents were used.

Retention behavior of short double-stranded oligonucleotide and its potential impurities by anion-exchange chromatography under non-denaturing conditions

Small interfering RNA (siRNA), consisting of two complementary single-stranded RNAs with overhanging bases, is being adopted as a potent and specific inhibitor of target gene expression. However, non-duplexed single strands and undesired double strands composed of impurities (e.g., n-1 mer) could be produced in addition to the target double strand in the siRNA manufacturing process. Compared to the liquid chromatography analysis of single strands, the analysis of the duplexes under non-denaturing conditions is challenging, since restricted chromatographic conditions are required to maintain the Watson-Crick hydrogen bonds. This study reports the analysis of double-stranded oligomers having approximately 20 base pairs with some overhanging bases as non-denatured forms by anion-exchange chromatography (AEX). Optimization of the chromatographic conditions could potentially achieve the adequate separation of excess single strands from the double strand. Non-optimal duplexes, such as duplexes with long overhangs or bulge structures, were prepared by intentionally deleting terminal or middle nucleotide(s) of either the sense or the antisense strand, and these non-optimal duplexes were eluted at different retention times in most of the cases. Interestingly, under alkaline chromatographic conditions (pH 9.0), non-optimal duplexes containing a shortmer tended to exhibit a stronger retention than their parent duplexes, although they possessed a less negative charge. This study demonstrated some retention behavior of double strands with overhangs by AEX under non-denaturing conditions.

Oligonucleotide separation techniques for purification and analysis: What can we learn for today's tasks?

Nucleic acids are the blueprint of life. They are not only the construction plan of the single cell or higher associations of them, but also necessary for function, communication and regulation. Due to the pandemic, the attention shifted in particular to their therapeutic potential as a vaccine. As pharmaceutical oligonucleotides are unique in terms of their stability and application, special delivery systems were also considered. Oligonucleotide production systems can vary and depend on the feasibility, availability, price and intended application. To achieve good purity, reliable results and match the strict specifications in the pharmaceutical industry, the separation of oligonucleotides is always essential. Besides the separation required for production, additional and specifically different separation techniques are needed for analysis to determine if the product complies with the designated specifications. After a short introduction to ribonucleic acids (RNAs), messenger RNA vaccines, and their production and delivery systems, an overview regarding separation techniques will be provided. This not only emphasises electrophoretic separations but also includes spin columns, extractions, precipitations, magnetic nanoparticles and several chromatographic separation principles, such as ion exchange chromatography, ion-pair reversed-phase, size exclusion and affinity.

Automated ion exchange chromatography screening combined with in silico multifactorial simulation for efficient method development and purification of biopharmaceutical targets

Bioprocess development of increasingly challenging therapeutics and vaccines requires a commensurate level of analytical innovation to deliver critical assays across functional areas. Chromatography hyphenated to numerous choices of detection has undeniably been the preferred analytical tool in the pharmaceutical industry for decades to analyze and isolate targets (e.g., APIs, intermediates, and byproducts) from multicomponent mixtures. Among many techniques, ion exchange chromatography (IEX) is widely used for the analysis and purification of biopharmaceuticals due to its unique selectivity that delivers distinctive chromatographic profiles compared to other separation modes (e.g., RPLC, HILIC, and SFC) without denaturing protein targets upon isolation process. However, IEX method development is still considered one of the most challenging and laborious approaches due to the many variables involved such as elution mechanism (via salt, pH, or salt-mediated-pH gradients), stationary phase's properties (positively or negatively charged; strong or weak ion exchanger), buffer type and ionic strength as well as pH choices. Herein, we introduce a new framework consisting of a multicolumn IEX screening in conjunction with computer-assisted simulation for efficient method development and purification of biopharmaceuticals. The screening component integrates a total of 12 different columns and 24 mobile phases that are sequentially operated in a straightforward automated fashion for both cation and anion exchange modes (CEX and AEX, respectively). Optimal and robust operating conditions are achieved via computer-assisted simulation using readily available software (ACD Laboratories/LC Simulator), showcasing differences between experimental and simulated retention times of less than 0.5%. In addition, automated fraction collection is also incorporated into this framework, illustrating the practicality and ease of use in the context of separation, analysis, and purification of nucleotides, peptides, and proteins. Finally, we provide examples of the use of this IEX screening as a framework to identify efficient first dimension (¹D) conditions that are combined with MS-friendly RPLC conditions in the second dimension (²D) for two-dimensional liquid chromatography experiments enabling purity analysis and identification of pharmaceutical targets.

Impact of Nonspecific Adsorption to Metal Surfaces in Ion Pair-RP LC-MS Impurity Analysis of Oligonucleotides

Nonspecific adsorption has been a consistent challenge in the analysis of oligonucleotides. Nonspecific adsorption is a result of interactions between charged acidic analytes and adsorption sites present in metallic surfaces located in the fluidic path of chromatography systems. Due to their high surface area, adsorption to column frits is especially concerning. Poor peak shape, low recovery and compromised LOQ have been associated with this phenomenon. Alternative methods including substitution of stainless steel for different hardware materials and mobile phase additives have been explored in an attempt to minimize this issue. Chemical modification of metal surfaces using hybrid surface technology (HST) by-passes the limitation of stainless steel construction material by forming a hybrid organic/inorganic layer that acts as a barrier and limits nonspecific interactions. In this study we explore the implications of this new technology in sensitive analysis and determination of relative impurity levels of oligonucleotides. Higher relative impurity levels and better reproducibility were obtained with columns using HST.

BIOANALYSIS AND BIOTRANSFORMATION OF OLIGONUCLEOTIDE THERAPEUTICS BY LIQUID CHROMATOGRAPHY-MASS SPECTROMETRY

Since 2016, eight new oligonucleotide therapies have been approved which has led to increased interest in oligonucleotide analysis. There is a particular need for powerful bioanalytical tools to study the metabolism and biotransformation of these molecules. This review provides the background on the biological basis of these molecules as currently used in therapies. The article also reviews the current state of analytical methodology including state of the art sample preparation techniques, liquid chromatography-mass spectrometry methods, and the current limits of detection/quantitation. Finally, the article summarizes the challenges in oligonucleotide bioanalysis and provides future perspectives for this emerging field. © 2020 John Wiley & Sons Ltd.

Recent developments in the characterization of nucleic acids by liquid chromatography, capillary electrophoresis, ion mobility, and mass spectrometry (2010-2020)

The development of new strategies for the analysis of nucleic acids has gained momentum due to the increased interest in using these biomolecules as drugs or drug targets. The application of new mass spectrometry ion activation techniques and the optimization of separation methods including liquid chromatography, capillary electrophoresis, and ion mobility have allowed more detailed characterization of nucleic acids and oligonucleotide therapeutics including confirmation of sequence, localization of modifications and interaction sites, and structural analysis as well as identification of failed sequences and degradation products. This review will cover tandem mass spectrometry methods as well as the recent developments in liquid chromatography, capillary electrophoresis, and ion mobility coupled to mass spectrometry for the analysis of nucleic acids and oligonucleotides.

RNA Drugs and RNA Targets for Small Molecules: Principles, Progress, and Challenges

RNA-based therapies, including RNA molecules as drugs and RNA-targeted small molecules, offer unique opportunities to expand the range of therapeutic targets. Various forms of RNAs may be used to selectively act on proteins, transcripts, and genes that cannot be targeted by conventional small molecules or proteins. Although development of RNA drugs faces unparalleled challenges, many strategies have been developed to improve RNA metabolic stability and intracellular delivery. A number of RNA drugs have been approved for medical use, including aptamers (e.g., pegaptanib) that mechanistically act on protein target and small interfering RNAs (e.g., patisiran and givosiran) and antisense oligonucleotides (e.g., inotersen and golodirsen) that directly interfere with RNA targets. Furthermore, guide RNAs are essential components of novel gene editing modalities, and mRNA therapeutics are under development for protein replacement therapy or vaccination, including those against unprecedented severe acute respiratory syndrome coronavirus pandemic. Moreover, functional RNAs or RNA motifs are highly structured to form binding pockets or clefts that are accessible by small molecules. Many natural, semisynthetic, or synthetic antibiotics (e.g., aminoglycosides, tetracyclines, macrolides, oxazolidinones, and phenicols) can directly bind to ribosomal RNAs to achieve the inhibition of bacterial infections. Therefore, there is growing interest in developing RNA-targeted small-molecule drugs amenable to oral administration, and some (e.g., risdiplam and branaplam) have entered clinical trials. Here, we review the pharmacology of novel RNA drugs and RNA-targeted small-molecule medications, with a focus on recent progresses and strategies. Challenges in the development of novel druggable RNA entities and identification of viable RNA targets and selective small-molecule binders are discussed. SIGNIFICANCE STATEMENT: With the understanding of RNA functions and critical roles in diseases, as well as the development of RNA-related technologies, there is growing interest in developing novel RNA-based therapeutics. This comprehensive review presents pharmacology of both RNA drugs and RNA-targeted small-molecule medications, focusing on novel mechanisms of action, the most recent progress, and existing challenges.

Current State of Oligonucleotide Characterization Using Liquid Chromatography-Mass Spectrometry: Insight into Critical Issues

As interests increase in oligonucleotide therapeutics, there has been a greater need for analytical techniques to properly analyze and quantitate these biomolecules. This article looks into some of the existing chromatographic approaches for oligonucleotide analysis, including anion exchange, hydrophilic interaction liquid chromatography, and ion pair chromatography. Some of the key advantages and challenges of these chromatographic techniques are discussed. Colloid formation in mobile phases of alkylamines and fluorinated alcohols, a recently discovered analytical challenge, is discussed. Mass spectrometry is the method of choice to directly obtain structural information about oligonucleotide therapeutics. Mass spectrometry sensitivity challenges are reviewed, including comparison to other oligonucleotide techniques, salt adduction, and the multiple charge state envelope. Ionization of oligonucleotides through the charge residue model, ion evaporation model, and chain ejection model are analyzed. Therapeutic oligonucleotides have to undergo approval from major regulatory agencies, and the impurities and degradation products must be well-characterized to be approved. Current accepted thresholds for oligonucleotide impurities are reported. Aspects of the impurities and degradation products from these types of molecules are discussed as well as optimal analytical strategies to determine oligonucleotide related substances. Finally, ideas are proposed on how the field of oligonucleotide therapeutics may improve to aid in future analysis.

Introducing an In Vitro Liver Stability Assay Capable of Predicting the In Vivo Pharmacodynamic Efficacy of siRNAs for IVIVC

There has been a renewed interest in therapeutic small interfering RNAs (siRNAs) over the past few years. This is particularly the result of successful and efficient delivery of N-acetylgalactosamine (GalNAc)-conjugated siRNAs to the liver. In general, the lead selection process for siRNA drugs is faster and more straightforward than traditional small molecules. Nevertheless, many siRNAs of different sequences and chemical modification patterns must still be evaluated before arriving at a final candidate. One of the major difficulties in streamlining this workflow is the well-known phenomenon that the in vitro data obtained from oligonucleotides transfected into cells are not directly predictive of their in vivo activity. Consequently, all oligonucleotides with some degree of in vitro activity are typically screened in vivo before final lead selection. Here, we demonstrate that the stability of liver-targeting GalNAc-conjugated siRNAs in a mouse liver homogenate shows an acceptable correlation to their in vivo target knockdown efficacy. Therefore, we suggest the incorporation of an in vitro liver homogenate stability assay during the lead optimization process for siRNAs. The addition of this assay to a flow scheme may decrease the need for animal studies, and it could bring cost savings and increase efficiency in siRNA drug development.

Modeling cationic adduction of oligonucleotides using electrospray desorption ionization

RATIONALE

Cationic adduction causes poor sensitivity and increases spectral complexity during mass spectral analysis of oligonucleotides and alkylamines are used to reduce this adduction. It is unclear the effect of the physiochemical properties of the alkylamines on the reduction of the cationic adduction.

METHODS

All samples were directly infused into a Synapt G2 HDMS quadrupole time-of-flight (TOF) hybrid mass spectrometer in negative ion electrospray ionization mode through the native built-in fluidics system. The infusion flow rate was set to 50 μL/min. The TOFMS tuning parameters were as follows: capillary voltage -2.0 kV, cone voltage 25 V, extraction cone voltage 2 V, source temperature 125°C, desolvation temperature 450°C, cone gas flow rate 0 L/h, and desolvation gas (nitrogen) flow rate 1000 L/h.

RESULTS

A quantitative model was created to predict the optimized alkylamine for MS analysis, while a qualitative model was generated to explain the most important physiochemical properties: proton affinity (13.83%), gas-phase basicity (11.79%), pKa (11.47%), boiling point (10.73%), MW (10.3%), Henry's Law Constant (9.56%), and partition coefficient (logP) (9.44%). The quantitative model was applied to RNA (microRNA) and a phosphorothioate and predicts the trend of cationic adduction.

CONCLUSIONS

Two models are described to understand the physiochemical properties that contribute to the adduction and to provide users a quick mathematical tool to predict the best choice of alkylamine to lower cationic adduction and decrease spectral complexity while enhancing sensitivity.

LC–TOF–MS methods to quantify siRNAs and major metabolite in plasma, urine and tissues

There are a few different bioanalytical approaches that have been used for the quantification of siRNA in biological matrices, such as S1 nuclease protection ‘cutting ELISA’, fluorescent probe hybridization HPLC, HPLC UV, LC–MS/high-resolution accurate-mass (HRAM) and LC–MS/MS. We have developed and validated plasma assays for several oligonucleotides such as GalNAc-conjugated siRNA, using uHPLC and high-resolution mass spectrometer by TOF detection. Although the molecular weights are in the range of 7000–9000, we were able to meet the same assay acceptance criteria as for the small molecules based on regulatory bioanalytical method validation guidance. The antisense strand and the sense strand can both be monitored. The method was also used in the tissue lysate matrices without a full validation.

Importance of probe design for bioanalysis of oligonucleotides using hybridization-based LC-fluorescence assays

Aim: The importance of the length and/or structure of fluorescently labeled PNA (peptide nucleic acid) probes for quantitative determination of oligodeoxynucleotides (ODNs) is demonstrated in human plasma using hybridization-based LC-fluorescence assays. The length of the PNA probes impacts the peak shape and chromatographic separation of the resulting PNA/ODN hybridization complexes and affects assay sensitivity, dynamic range and carryover. Methods: For quantitative determination of an 18-mer phosphodiester ODN (DNL1818) in human plasma, an assay utilizing an Atto dye-labeled 12-mer PNA probe provided a linear quantitation range of 0.1-50 ng/ml with excellent accuracy and precision (within -5.3-7.73%). Conclusion: This method provides a convenient method for sensitive and specific quantification of ODNs in biological matrix with limited sample volume and no special extraction.

Metabolite Profiling of the Antisense Oligonucleotide Eluforsen Using Liquid Chromatography-Mass Spectrometry

Eluforsen (previously known as QR-010) is a 33-mer 2′-O-methyl modified phosphorothioate antisense oligonucleotide targeting the F508del mutation in the gene encoding CFTR protein of cystic fibrosis patients. In this study, eluforsen was incubated with endo- and exonucleases and mouse liver homogenates to elucidate its in vitro metabolism. Mice and monkeys were used to determine in vivo liver and lung metabolism of eluforsen following inhalation. We developed a liquid chromatography-mass spectrometry method for the identification and semi-quantitation of the metabolites of eluforsen and then applied the method for in vitro and in vivo metabolism studies. Solid-phase extraction was used following proteinase K digestion for sample preparation. Chain-shortened metabolites of eluforsen by 3′ exonuclease were observed in mouse liver in an in vitro incubation system and by either 3′ exonuclease or 5′ exonuclease in liver and lung samples from an in vivo mouse and monkey study. This study provides approaches for further metabolite characterization of 2′-ribose-modified phosphorothioate oligonucleotides in in vitro and in vivo studies to support the development of oligonucleotide therapeutics.

Direct identification of microribonucleic acid miR-451 from plasma using liquid chromatography mass spectrometry

In recent years, small endogenous RNAs have come to the forefront of both basic and translational research. For example, many studies have pointed to the potential role of microRNAs (miRNAs) as disease biomarkers. However, precise quantitative methods for the analysis of miRNAs are still lacking. In this study, we report the first mass spectrometry-based quantitation of miR-451, a circulatory microRNA. Using a highly selective sample preparation method with an average recovery of 83.6% and a novel mobile phase chemistry, we were able to reach an LOQ of 0.5 ng/mL. Because of such high sensitivity, we could detect and quantify the endogenous miR-451 from both human and rat plasma. Considering the increased precision of LC-MS compared to other methods, these results usher in a new era of miRNA biomarker discovery and validation.

Alkylamine ion-pairing reagents and the chromatographic separation of oligonucleotides

Alkylamines are commonly used to improve both chromatographic and mass spectral performance of electrospray ionization liquid chromatography mass spectrometry based methods for the analysis of oligonucleotides. Recently several new alkylamines have been introduced to enhance the electrospray mass spectral response for oligonucleotides; however, the chromatographic properties of these new alkylamines have not been rigorously assessed. We have investigated the retention, peak width, resolution and general chromatographic performance of fifteen different alkylamines for the separation of a model DNA, RNA and an antisense therapeutic oligonucleotide. Eleven of the fifteen alkylamines were shown to provide similar chromatographic performance across all three classes of oligonucleotides. Based on these findings, a model for the mechanism of retention of oligonucleotides using alkylamines and hexafluoroisopropanol mobile phases is proposed. Depending on the concentrations of alkylamines and pH adjustment, oligonucleotides can be retained by micellar chromatography and not the generally held ion-pairing mechanism. This conclusion is supported by light scattering, transmission electron microscopy and ion mobility experiments detecting three micron aggregates in the mobile phase at concentrations that are routinely used for LC-MS analysis of oligonucleotides. These aggregates are not detected at lower alkylamine concentrations where the retention mechanism follows an ion-pairing mechanism. The formation of these aggregates appears to be dependent on the pH of the mobile phase.

Development of SPE method for the extraction of phosphorothioate oligonucleotides from serum samples

AIM

Comprehensive development of a method for SPE extraction of antisense phosphorothioate oligonucleotide and its metabolites and their determination with the use of UHPLC.

RESULTS

Polymer-based adsorbent and high percentage of methanol in elution solvent provided high recoveries compared with silica-based octadecyl cartridge. As to the type and concentration of ion pair reagent and organic solvent, the mixture of 5 mM of N,N-dimethylbutylamine/150 mM of 1,1,1,3,3,3-hexafluoroisopropanol and methanol was selected. Relatively high recoveries in the range of 79.2-81.2% with the SDs of 3.4-6.2% were obtained for the oligonucleotide and its metabolites extracted from human serum.

CONCLUSION

The developed method may be successfully applied for routine analysis of antisense oligonucleotides in serum since it is relatively easy, quick and reliable.

Review on sample preparation methods for oligonucleotides analysis by liquid chromatography

Antisense oligonucleotides have been successfully investigated for the treatment of different types of diseases. Detection and determination of antisense oligonucleotides and their metabolites are necessary for drug development and evaluation. This review focuses mainly on the first step of the analysis of oligonucleotides i.e. the sample preparation stage, and in particular on the techniques used for liquid chromatography and liquid chromatography coupled with mass spectrometry. Exceptional sample preparation techniques are required as antisense oligonucleotides need to be determined in complex biological matrices. The text discusses general issues in oligonucleotide sample preparation and approaches to their solution. The most popular techniques i.e. protein precipitation, protein enzyme digestion and liquid-liquid extraction are reviewed. Solid phase extraction methods are discussed and the issues connected with the application of each method are highlighted. Other newly reported promising techniques are also described. Finally, there is a summary of actually used techniques and the indication of the direction of future research.

Degradation product characterization of therapeutic oligonucleotides using liquid chromatography mass spectrometry

Synthetic antisense phosphorothioate oligonucleotides (PS) have undergone rapid development as novel therapeutic agents. The increasing significance of this class of drugs requires significant investment in the development of quality control methods. The determination of the many degradation pathways of such complex molecules presents a significant challenge. However, an understanding of the potential impurities that may arise is necessary to continue to advance these powerful new therapeutics. In this study, four different antisense oligonucleotides representing several generations of oligonucleotide therapeutic agents were evaluated under various stress conditions (pH, thermal, and oxidative stress) using ion-pairing reversed-phase liquid chromatography tandem mass spectrometry (IP-RPLC-MS/MS) to provide in-depth characterization and identification of the degradation products. The oligonucleotide samples were stressed under different pH values at 45 and 90 °C. The main degradation products were observed to be losses of nucleotide moieties from the 3'- and 5'-terminus, depurination, formation of terminal phosphorothioates, and production of ribose, ribophosphorothioates (Rp), and phosphoribophosphorothioates (pRp). Moreover, the effects of different concentrations of hydrogen peroxide were studied resulting in primarily extensive desulfurization and subsequent oxidation of the phosphorothioate linkage to produce the corresponding phosphodiester. The reaction kinetics for the degradation of the oligonucleotides under the different stress conditions were studied and were found to follow pseudo-first-order kinetics. Differences in rates exist even for oligonucleotides of similar length but consisting of different sequences. Graphical abstract Identification of degradation products across several generations of oligonucleotide therapeutics using LC-MS.

Quantitative analysis of imetelstat in plasma with LC-MS/MS using solid-phase or hybridization extraction

AIM

Imetelstat, a 13-mer oligonucleotide with a lipid tail is being evaluated for treating hematologic myeloid malignancies. This report describes the development of extraction and quantification methods for imetelstat. Methodology & results: Imetelstat was extracted using SPE (rat plasma) or by hybridization using a biotinylated capture probe (human plasma) and was quantified by LC-MS/MS. Calibration curves were established (0.1-50 μg/ml). Stability of imetelstat in plasma was demonstrated. Concentrations of imetelstat extracted using either of the methods and quantified with LC-MS/MS were comparable with a validated ELISA.

CONCLUSION

Two extraction methods (solid phase and hybridization) were developed for quantifying imetelstat in plasma using LC-MS/MS. The hybridization extraction in combination with LC-MS/MS is a novel extraction approach.

Chromatographic approaches for the characterization and quality control of therapeutic oligonucleotide impurities

Phosphorothioate (PS) oligonucleotides are a rapidly rising class of drugs with significant therapeutic applications. However, owing to their complex structure and multistep synthesis and purification processes, generation of low-level impurities and degradation products are common. Therefore, they require significant investment in quality control and impurity identification. This requires the development of advanced methods for analysis, characterization and quantitation. In addition, the presence of the PS linkage leads to the formation of chiral centers which can affect their biological properties and therapeutic efficiency. In this review, the different types of oligonucleotide impurities and degradation products, with an emphasis on their origin, mechanism of formation and methods to reduce, prevent or even eliminate their production, will be extensively discussed. This review will focus mainly on the application of chromatographic techniques to determine these impurities but will also discuss other approaches such as mass spectrometry, capillary electrophoresis and nuclear magnetic resonance spectroscopy. Finally, the chirality and formation of diastereomer mixtures of PS oligonucleotides will be covered as well as approaches used for their characterization and the application for the development of stereochemically-controlled PS oligonucleotides.

Bridging small interfering RNA with giant therapeutic outcomes using nanometric liposomes

The scope of RNAi based therapeutics is unquestionable. However, if we dissect the current trend of clinical trials for afore mentioned drug class, some stark trends appear: 1) naked siRNA only exerts influence in topical mode whilst systemic delivery requires a carrier and 2) even after two decades of extensive efforts, not even a single siRNA containing product is commercially available. It was therefore felt that a perspective simplifying the unique intricacies of working with a merger of siRNA and liposomes from a pharmaceutical viewpoint could draw the attention of a wider array of interested researchers. We begin from the beginning and attempt to conduit the gap between theoretical logic and experimental/actual constraints. This, in turn could stimulate the next generation of investigators, gearing them to tackle the conundrum, which is siRNA delivery.

Hyphenation of a Deoxyribonuclease I immobilized enzyme reactor with liquid chromatography for the online stability evaluation of oligonucleotides

The stability of antisense oligonucleotides (ONs) toward nucleases is a key aspect for their possible implementation as therapeutic agents. Typically, ON stability studies are performed off-line, where the ONs are incubated with nucleases in solution, followed by their analysis. The problematics of off-line processing render the detailed comparison of relative ON stability quite challenging. Therefore, the development of an online platform based on an immobilized enzyme reactor (IMER) coupled to liquid chromatography (LC) was developed as an alternative for improved ON stability testing. More in detail, Deoxyribonuclease I (DNase I) was immobilized on epoxy-silica particles of different pore sizes and packed into a column for the construction of an IMER. Subsequently, the hyphenation of the IMER with ion-pair chromatography (IPC) and ion-exchange chromatography (IEC) was evaluated, leading to the successful development of two online methodologies: IMER-IPC and IMER-IEC. More specifically, natural and modified DNA and RNA oligonucleotides were used for testing the performance of the methodologies. Both methodologies proved to be simple, automatable, fast and highly reproducible for the quantitative and qualitative evaluation of ON degradation. In addition, the extended IMER life time in combination with a more straightforward control of the reaction kinetics substantiate the applicability of the IMER-LC platform for ON stability tests and its implementation in routine and research laboratories.

LC-MS of oligonucleotides: applications in biomedical research

Recent findings have elucidated numerous novel biological functions for oligonucleotides. Current standard methods for the study of oligonucleotides (i.e., hybridization and PCR) are not fully equipped to deal with the experimental needs arising from these new discoveries. More importantly, as the intracellular capacity of oligonucleotides is being harnessed for biomedical applications, alternative bioanalytical techniques become indispensable in order to comply with ever-increasing regulatory requirements. Owing to its ability to detect oligonucleotides independent of their sequence, LC-MS is emerging as the analytical method of choice for oligonucleotides. In this article, the current applications of LC-MS in the analysis of oligonucleotides, with an emphasis on RNA therapeutics and biomarkers, will be examined. In addition, the theoretical framework of oligonucleotide ESI is carefully inspected with the purpose of identifying the contributing factors to MS signal intensity.

Current state-of-the-art of nontargeted metabolomics based on liquid chromatography-mass spectrometry with special emphasis in clinical applications

Metabolomics, as a part of systems biology, has been widely applied in different fields of life science by studying the endogenous metabolites. The development and applications of liquid chromatography (LC) coupled with high resolution mass spectrometry (MS) greatly improve the achievable data quality in non-targeted metabolic profiling. However, there are still some emerging challenges to be covered in LC-MS based metabolomics. Here, recent approaches about sample collection and preparation, instrumental analysis, and data handling of LC-MS based metabolomics are summarized, especially in the analysis of clinical samples. Emphasis is put on the improvement of analytical techniques including the combination of different LC columns, isotope coded derivatization methods, pseudo-targeted LC-MS method, new data analysis algorithms and structural identification of important metabolites.

Systematic optimization of ion-pairing agents and hexafluoroisopropanol for enhanced electrospray ionization mass spectrometry of oligonucleotides

RATIONALE

New methods to enhance the electrospray ionization (ESI) signals are essential for low-level analysis of oligonucleotides. We report a systematic evaluation comparing 13 ion-pairing agents with and without hexafluoroisopropanol to understand their effect on the ion abundance of hetero-oligonucleotides.

METHODS

A Waters Synapt G2 HDMS quadrupole time-of-flight instrument was used to compare oligonucleotide signal intensity with 13 alkylamine ion-pairing agents at varying concentrations. The alkylamines that yielded the highest signal intensity were further evaluated with hexafluoroisopropanol at concentrations between 5 and 100 mM. The chemical properties of the solution components and analytes were evaluated to identify key factors in predicting optimal mobile phase conditions for different classes of oligonucleotides.

RESULTS

We identified a series of optimized mobile phase systems using diisopropylamine, tripropylamine, dimethylbutylamine, methyldibutylamine, and dimethylhexylamine along with 25 to 50 mM hexafluoroisopropanol that yielded significantly higher MS signal intensity for both siRNA and DNA compared with the traditionally used triethlyamine/hexafluoroisopropanol system. We explored charge state reduction, adduct formation and ESI mechanisms and identify the Henry's Law constant k aq/g as a key chemical property in predicting alkylamines that will increase oligonucleotide ion intensity. We also find that the hydrophobicity of the oligonucleotide plays a major role in choosing ion-pairing agents that will increase ion abundance.

CONCLUSIONS

This comprehensive and systematic optimization finds that the hydrophobicity of the oligonucleotide was a key factor in choosing alkylamine ion-pairing agents to increase ESI abundance. We identified that diisopropylamine and tripropylamine combined with lower concentrations of hexafluoroisopropanol yielded the highest signal intensity for these oligonucleotides.