Retention models for ionizable compounds in reversed-phase liquid chromatography

Two-dimensional sequential selective comprehensive chiral×reversed-phase liquid chromatography of synthetic phosphorothioate oligonucleotide diastereomers

In recent years, many nucleic acid-based pharmaceuticals have been approved and entered the market, and even a larger number are in late stage clinical trials. Conventional oligonucleotides are facing issues in vivo like fast renal clearance and nuclease degradation. Therefore, to increase their stability, phosphorothioation is a frequent modification of therapeutic oligonucleotides (ONs) which also leads to improved binding affinity facilitating cell internalization and intracellular distribution. At the same time, by replacing a phosphodiester linkage with a phosphorothioate group, a phosphorous stereogenic center is generated which causes the formation of Rp- and Sp-diastereomers. It increases the structural diversity. For example, with 15 of those phosphorothioate (PS) linkages, 32,768 different diastereomers are expected. Since the phosphorothioate is introduced non-stereoselectively, the molecular complexity of the resultant phosphorothioate ON products is tremendously increased impeding the chromatographic separation in the course of quality control. Since distinct phosphorothioate diastereomers have different bioactivities and pharmacological properties, there is increasing interest in implications of stereoisomerism of phosphorothiate oligonucleotides. From a quality and regulatory viewpoint, batch-to-batch reproducibility of the diastereomer profile may be of significant concern. In order to address this issue, this study investigates the stereoselectivity of LC methods for two phosphorothioate oligonucleotide (PSO) compounds differing in their molecular size and numbers of PS linkages. Diastereoselectivity of ion-pairing reversed-phase liquid chromatography (IP-RPLC), RPLC without ion-pairing agents and LC with chiral polysaccharide-based column were evaluated for model PSOs and an active pharmaceutical ingredient (API) of PSO with trivalent N-acetylgalactosamine (GalNAc) conjugate. Due to the structural complexity of PSOs, the separation power for the diastereomer mixture was increased by using sequential selective comprehensive two-dimensional chromatography with an amylose tris(α-methylbenzylcarbamate)-immobilized chiral stationary phase (CSP) in the first dimension and ion-pair RPLC with ethylammonium acetate in the second dimension. Improved diastereomer selectivity was obtained and a larger number of peaks could be separated.

Revisiting the dependence of retention factor on the content of organic component in the mobile phase in reversed-phase HPLC

In high-performance liquid chromatography, the dependence of retention factor k on volumetric fraction ϕ of organic phase is expressed by log k = F(ϕ) with F(ϕ) obtained by measuring log k at different ϕ values. From F(ϕ), a value kw is calculated by taking ϕ = 0. The equation log k = F(ϕ) is applied for predicting k, and kw is a descriptor of hydrophobic character of solutes and stationary phases. Calculated kw should not depend on the nature of organic component of mobile phase but extrapolation procedure leads to different kw for different organic components. The present study shows that the expression of F(ϕ) changes depending on the range of ϕ and the same function F(ϕ) cannot be used for the full range of ϕ from 0 to 1. Consequently, kw obtained by extrapolation of ϕ to zero is not correct because the expression of F(ϕ) was generated by fitting the data using ϕ with higher values. The present study shows the proper way to obtain the value of kw .

Polybutylene terephthalate-based stationary phase for ion-pair-free reversed-phase liquid chromatography of small interfering RNA. Part 2: Use for selective comprehensive two-dimensional liquid chromatography

With the increasing numbers of nucleic acid-based pharmaceuticals like antisense oligonucleotides (ASO), small interfering ribonucleic acid (siRNA) entering the market, research facilities, pharmaceutical industries and also regulatory authorities have been looking for efficient analytical methods for these synthetic oligonucleotides (ON). Besides of conventional one-dimensional (1D) reversed-phase liquid chromatography with or without ion-pairing (IP-RP-LC, RP-LC), hydrophilic liquid chromatography (HILIC) and mixed-mode chromatography (MMC), two-dimensional (2D) approaches combining two orthogonal chromatographic techniques also become more relevant due to the high structural complexity of oligonucleotides. Recently, we tested a polybutylene terephthalate(PBT)-based stationary phase under ion-pairing free RP mode for the liquid chromatography electrospray ionization mass spectrometry (LC-ESI-MS) analysis of siRNA (Patisiran). In this study, retention profile and chromatographic orthogonality, respectively, were compared to other LC-modes like HILIC, IP-RPLC, another ion-pair free cholesterol-bonded RPLC and MMC considering their normalized retention times. Finally, because of higher orthogonality, the ion-pairing free PBT-bonded RPLC as first dimension (¹D) was hyphenated with HILIC in the second dimension (²D) in a selective comprehensive 2D-LC setup leading to an enhanced resolution for peak purity evaluation of the main ON entities.

Polybutylene terephthalate-based stationary phase for ion-pair-free reversed-phase liquid chromatography of small interfering RNA. Part 1: Direct coupling with mass spectrometry

Nowadays, ion-pairing reversed-phase liquid chromatography (IP-RPLC) is the dominating generic method for the analysis of nucleic acid related compounds, such as antisense-oligonucleotides (ASO), small-interfering ribonucleic acid (siRNA) or other DNA or RNA type molecules and their conjugates. Despite of its effective performance, the usage of a high concentration of ion-pairing reagent in the eluent in IP-RPLC is unfavorable for the hyphenation with mass spectrometry (MS) which is required for a detailed structural characterization of the analytes and their structurally related impurities. In this work, we tested a polybutylene terephthalate (PBT)-bonded silica-based stationary phase for the separation of generically synthesized Patisiran as siRNA (antisense and sense single strands as well as their annealed double strand) giving some unexpected selectivity without any presence of ion-pairing reagents. Important chromatographic conditions affecting the separation have been investigated and evaluated. Furthermore, MS and tandem MS (MS/MS) characterization was possible without contamination of the MS system with ion-pair agent and related problems.

Impact of changes in physicochemical parameters of the mobile phase along the column on the retention time in gradient liquid chromatography. Part A - temperature gradient

Gradient chromatography has been widely applied in analytical and preparative chromatography since it provides better peak shapes and the ability to elute analytes in a shorter time frame. Apart from changes in the composition of a mobile phase also alteration of process temperature can be applied during separation procedures to improve efficiency. However, proper mathematical modeling of the gradient chromatography and further correct prediction of solutes' retention behavior have become a serious challenge as it involves the need to develop computational procedures that accurately account for the time and spatial gradients of crucial parameters. In this work, a computational procedure including the equilibrium-dispersive two-dimensional mass transfer model, the two-dimensional (2D) heat transfer model together with Darcy's law and the continuity equation have been proposed. Additionally, the calculation procedure was simplified by replacing the 2D model with the one-dimensional (1D) mass transfer model in order to speed up the computations. Both proposed solutions were validated employing external experimental data of temperature gradient HPLC [1] as well as with predictions based on the linear elution strength (LES) model available therein. The proposed procedures made it possible to efficiently predict the concentration profiles with average relative errors of calculated retention times not exceeding 3.22%. Moreover, the effect of the axial dispersion coefficient determination method on the obtained peak shapes was examined involving the Gunn, the Wen-Fan, and the Chung-Wen correlations, indicating that the latter produces the most accurate results. Finally, the proposed mathematical procedures were tested under UHPLC conditions, and due to a significant difference in retention times found the 2D model is strongly advised.

Comparison of the Fitting Performance of Retention Models and Elution Strength Behaviour in Hydrophilic-Interaction and Reversed-Phase Liquid Chromatography

Hydrophilic interaction liquid chromatography (HILIC) is able to separate from polar to highly polar solutes, using similar eluents to those in the reversed-phase mode (RPLC) and a polar stationary phase, where water is adsorbed onto its surface. It is widely accepted that multiple modes of interaction take place in the HILIC environment, which can be far more complex than the interactions in an RPLC column. The behaviour in HILIC should be adequately modelled to predict the retention with optimisation purposes and improve the understanding on retention mechanisms, as is the case for RPLC. In this work, the prediction performance of several retention models is studied for seven HILIC columns (underivatised silica, and silica containing diol, amino and sulfobetaine functional groups, together with three columns recently manufactured with neutral, anionic, and cationic character), using uracil and six polar nucleosides (adenosine, cytidine, guanosine, thymidine, uridine, and xanthosine) as probe compounds. The results in HILIC are compared with those that were offered by the elution of several polar sulphonamides and diuretics analysed with two C18 columns (Chromolith Speed ROD and Zorbax Eclipse XDB). It is shown that eight retention models, which only consider partitioning or both partitioning and adsorption, give similar good accuracy in predictions for both HILIC and RPLC columns. However, the study on the elution strength behaviour, at varying mobile phase composition, reveals similarities (or differences) between RPLC and HILIC columns of diverse nature. The particular behaviour for the HILIC and RPLC columns was also revealed when the retention, in both modes, was fitted to a model that describes the change in the elution strength with the modifier concentration.

Comparison of the Retention and Separation Selectivity of Aromatic Hydrocarbons with Polar Groups in RP-HPLC Systems with Different Stationary Phases and Eluents

In this manuscript, the retention of aromatic hydrocarbons with polar groups has been compared for systems with various nonpolar columns of the types from C3 to C18 and different mobile phases composed of methanol, acetonitrile, or tetrahydrofuran as modifiers. The selectivity separation of the solutes in systems with different adsorbents, when one eluent modifier is swapped by another, has been explained, taking into account molecular interactions of the solutes with components of the stationary phase region (i.e., extracted modifier depending on the chain length of the stationary phase).

A peculiar chromatographic selectivity of porous graphitic carbon during the separation of dileucine isomers

Porous graphitic carbon is a versatile stationary phase for high-performance liquid chromatography which performs especially well for isomeric separations. Shape-sensitivity of the stationary phase is caused by a steric effect when a molecule interacts with a flat carbon surface. It follows that branched, non-flat molecules are eluted much earlier than flat or linear molecules. In this short communication we show that if a molecule has a highly ionizable group, the "shape" of a molecule part which is farther from the ionizable group affects retention much more than the "shape" of a molecule part which is closer to the ionizable group. Dipeptides which consist of tert-leucine and norleucine were used as an example. Basic and acidic eluents were used. Retention strongly depends on whether a norleucine or tert-leucine residual is located near the non-ionized side in an eluent for both basic and acidic eluents. A residual located on the opposite side is less important. To investigate the possible causes of this peculiar retention behavior we compared the retention behavior of these dipeptides for porous graphitic carbon with the behavior for other types of stationary phases and with the calculated physicochemical properties. Strong and complex dependence of elution order on a mobile phase composition is demonstrated. The separation of other dileucine isomers is also considered. The applicability of porous graphitic carbon for the separation of complex mixtures of isomeric peptides is discussed.

Dual-retention mechanism of dopamine-related compounds on monolithic stationary phase with zwitterion functionality

Seven retention models have been selected to describe a dual-retention behavior of ten dopamine-related compounds on polymer-based monolithic stationary phase with zwitterion sulfobetaine functionality. Regression quality, as well as a statistical significance of individual regression parameters, have been evaluated. Better regression performance showed two four-parameter models when compared to three-parameter models. On the other hand, limited number of experimental points disqualified statistical robustness of four-parameter models. Among three-parameter models, retention description introduced by Horváth and Liang provided comparable quality of regression at significantly improved robustness. Multivariate analysis of the best three-parameter models provided the description of physicochemical properties of dopamine precursors and metabolites. Principal component analysis and logistic regression allowed structural characterization of dopamine-related compounds based solely on regression parameters extracted from an isocratic elution data. Both polarity and type of functional groups has been correctly assigned for 3-methoxytyramine that has not been part of an evaluation study. Among applied dual-retention models, Horváth´s model, initially developed to describe a retention of ionic compounds on nonpolar stationary phases, provided robust regression of experimental data and allowed an extraction of structural characteristics of dopamine-related compounds.

Automated techniques in pKa determination: Low, medium and high-throughput screening methods

Drug discovery programs that generate hundreds of new molecular entities need efficient methodologies for physicochemical profiling. Several high-throughput methods for pK_a screening have been developed in the last 15 years to determine this key physicochemical parameter. Separation techniques such as HPLC-MS or capillary electrophoresis are particularly well-suited due to their high throughput and capacity to deal with impure or complex samples. In addition, potentiometric and (mostly) UV-metric-based methods (plate-based and automated systems), find their place as very precise methodologies for pK_a determination despite of somewhat lower throughput. Finally, pK_a prediction software packages are useful estimator tools but, to date, they cannot replace experimental measurements when accurate pK_a values are required.

Gallic Acid: Review of the Methods of Determination and Quantification

Gallic acid (3,4,5 trihydroxybenzoic acid) is a secondary metabolite present in most plants. This metabolite is known to exhibit a range of bioactivities including antioxidant, antimicrobial, anti-inflammatory, and anticancer. There are various methods to analyze gallic acid including spectrometry, chromatography, and capillary electrophoresis, among others. They have been developed to identify and quantify this active ingredient in most biological matrices. The aim of this article is to review the available information on analytical methods for gallic acid, as well as presenting the advantages and limitations of each technique.

Separation of purine and pyrimidine bases and nucleosides by hydrophilic interaction chromatography

The separation of 12 model compounds chosen among purine and pyrimidine bases and nucleosides was studied by using hydrophilic interaction chromatography (HILIC). The compounds investigated were small molecules with relevant properties for biomedical and pharmaceutical studies. The mixture of pyrimidines and purines was applied on a ZIC-HILIC 150 x 2.1 mm, 5 microm, and two TSKgel Amide-80 150 x 2.0 mm, 5 microm and 3 microm particle size columns. The retention of the analytes was studied by varying ACN%, ammonium formate concentration, pH, and column temperature. The results obtained confirmed the elution order of nucleobases, nucleosides, and nucleotides based on their hydrophobicity. The retention mechanism of the columns was studied considering the models used for describing partitioning and surface adsorption. The influence on retention of chromatographic conditions (ACN%, salt concentration, pH, and temperature) was described and discussed for both columns. The optimization of the conditions studied allowed to assess a gradient method for the separation of the 12 analytes. The developed method is a valuable alternative to existing methods for the separation of the compounds concerned.