Displacement chromatography of anti-sense oligonucleotide and proteins using saccharin as a non-toxic displacer

Sustainability Challenges and Opportunities in Oligonucleotide Manufacturing

With a renewed and growing interest in therapeutic oligonucleotides across the pharmaceutical industry, pressure is increasing on drug developers to take more seriously the sustainability ramifications of this modality. With 12 oligonucleotide drugs reaching the market to date and hundreds more in clinical trials and preclinical development, the current state of the art in oligonucleotide production poses a waste and cost burden to manufacturers. Legacy technologies make use of large volumes of hazardous reagents and solvents, as well as energy-intensive processes in synthesis, purification, and isolation. In 2016, the American Chemical Society (ACS) Green Chemistry Institute Pharmaceutical Roundtable (GCIPR) identified the development of greener processes for oligonucleotide Active Pharmaceutical Ingredients (APIs) as a critical unmet need. As a result, the Roundtable formed a focus team with the remit of identifying green chemistry and engineering improvements that would make oligonucleotide production more sustainable. In this Perspective, we summarize the present challenges in oligonucleotide synthesis, purification, and isolation; highlight potential solutions; and encourage synergies between academia; contract research, development and manufacturing organizations; and the pharmaceutical industry. A critical part of our assessment includes Process Mass Intensity (PMI) data from multiple companies to provide preliminary baseline metrics for current oligonucleotide manufacturing processes.

Analysis and Purification of Synthetic Nucleic Acids Using HPLC

Chromatographic methods have been essential tools for analysis and purification of synthetic oligonucleotides since the 1970s. Significant developments in terms of instruments and stationary phases (media) have been made during the past several decades; among the latest are sub-micron to micron particles for the media, as well as ultra performance liquid chromatography (UPLC). Micron and sub-micron particles have increased product resolution. Applications of recently developed methods such as IP-RP-HPLC and LC-MS have been discussed for analysis, along with use of various methods for purification. Utilization of UPLC has decreased analysis time, increasing the throughput for analysis. Commonly used methods for analysis and purification of synthetic oligonucleotides have been described in this unit.

Dynamic behavior of binary component ion-exchange displacement chromatography of proteins visualized by confocal laser scanning microscopy

Confocal laser scanning microscopy (CLSM) was introduced to visualize particle-scale binary component protein displacement behavior in Q Sepharose HP column. To this end, displacement chromatography of two intrinsic fluorescent proteins, enhanced green fluorescent protein (eGFP) and red fluorescent protein (RFP), were developed using sodium saccharin (NaSac) as a displacer. The results indicated that RFP as well as eGFP could be effectively displaced in the single-component experiments by 50 mmol/L NaSac at 120 and 140 mmol/L NaCl whereas a fully developed displacement train with eGFP and RFP was only observed at 120 mmol/L NaCl in binary component displacement. At 140 mmol/L NaCl, there was a serious overlapping of the zones of the two proteins, indicating the importance of induced-salt effect on the formation of an isotachic displacement train. CLSM provided particle-scale evidence that induced-salt effect occurred likewise in the interior of an adsorbent and was synchronous to the introduction of the displacer. CLSM results at 140 mmol/L NaCl also demonstrated that both the proteins had the same fading rate at 50 mmol/L NaSac in the initial stage, suggesting the same displacement ability of NaSac to both the proteins. In the final stage, the fading rate of RFP in the adsorbent became slow, particularly at lower displacer concentrations. In the binary component displacement, the two proteins exhibited distinct fading rates as compared to the single component displacement and the remarkable lagging of the fading rate was observed in protein displacements. It suggested that the co-adsorbed proteins had significant influence on the formation of an isotachic train and the displacement chromatography of the proteins. Therefore, this research provided particle-scale insight into the dynamic behavior and complexity in the displacement of proteins.

Detection of trace proteins in multicomponent mixtures using displacement chromatography

Model protein feed mixtures containing three abundant and seven trace proteins at various concentrations were identified and employed in a series of displacement experiments. Reversed-phase liquid chromatography (RPLC) and matrix assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry were used to evaluate the compositions of both the feed mixtures and effluent fractions from the displacement experiments. The results demonstrated that trace proteins were focused at the boundaries between the abundant solutes where they were enriched and concentrated. For many of the multicomponent feed mixtures, mass spectrometry analyses of the displacement column effluent fractions resulted in the identification of trace proteins that were not detectable in the feed. In addition, the use of minimal or no salt in the carrier solutions enabled the analysis of displacement fractions by direct infusion mass spectrometry. These results are significant in that they indicate that while the presence of abundant proteins can often be problematic for the detection of trace components, displacement chromatography may be able to employ these abundant proteins to focus trace proteins in the displacement train, thus facilitating detection.

Synthesis and characterization of fluorescent displacers for online monitoring of displacement chromatography

One of the major impediments to the implementation of displacement chromatography for the purification of biomolecules is the need to collect fractions from the column effluent for time-consuming offline analysis. The ability to employ direct online monitoring of displacement chromatography would have significant implications for applications ranging from analytical to preparative bioseparations. To this end, a set of novel fluorescent displacers were rationally designed using known chemically selective displacers as a template. Fluorescent cores were functionalized with different charge moieties, creating a homologous library of displacers. These compounds were then tested on two protein pairs, alpha-chymotrypsinogen A/ribonuclease A and cytochrome c/lysozyme, using batch and column displacement experiments. Of the synthesized displacers, two were found to be highly selective while one was determined to be a high-affinity displacer. Column displacements using one of the selective displacers yielded complete separation of both protein pairs while facilitating direct online detection using UV and fluorescence detection. Saturation transfer difference NMR was also carried out to investigate the binding of the fluorescent displacers to proteins. The results indicated a selective binding between the selective displacers and alpha-chymotrypsinogen A, while no binding was observed for ribonuclease A, confirming that protein-displacer binding is responsible for the selectivity in these systems. This work demonstrates the utility of fluorescent displacers to enable online monitoring of displacer breakthroughs while also acting as efficient displacers for protein purification.

Purification of proteins using displacement chromatography

Displacement chromatography has several advantages over the nonlinear elution technique, as well as the linear elution mode, such as the recovery of purified components at high concentrations, less tailing during elution, high throughput and high resolution. Displacer affinity and its utilization are the critical components of displacement chromatography. Particularly, the nonspecific interactions between the displacer and the stationary phase can be exploited to generate high affinity displacers. This chapter will discuss the design and execution of displacer selection and implementation in a separation specifically focusing on its utilization in ion exchange chromatography.

Displacement chromatography of proteins on hydrophobic charge induction adsorbent column

Displacement chromatography of protein mixtures is proposed on hydrophobic charge induction chromatography (HCIC). We have used an HCIC medium, MEP-Hypercel as the stationary phase and a quaternary ammonium salt, benzethonium chloride, as the displacer. It was found that the multiple interactions between proteins/displacer and the HCIC sorbent, i.e. hydrophobic interaction and charge repulsion, enabled a greater flexibility for the design of displacement processes and ease of column regeneration by adjustment of pH. The capacity factors of proteins and displacers were used to predict their performances in column displacement, and the experimental results agreed well with the prediction. An isotachic displacement train of lysozyme and alpha-chymotrypsinogen A was formed with benzethonium chloride as the displacer at pH 5.0 with good yields and purities of the two proteins. Column regeneration was efficiently achieved by charge repulsion between the displacer and the adsorbent at lower pH values (pH 3 and 4). The results indicate that the displacement chromatography on HCIC is a good alternative to traditional hydrophobic displacement chromatography.

Influence of polyfunctional interactions between organic zwitter-ion eremomycin and carboxylic cation exchangers on forming concentration front

The nature of the polyfunctional interactions between the organic zwitter-ions of eremomycin and the carboxylic sorbents was studied. A cation exchange and hydrophobic mechanisms of interactions in the studied sorption system were determined as preponderant over other ones. The typical features of the eremomycin diffusion into the pores of the structurally segregated carboxylic sorbents were studied. The physical-chemical properties of the sorption system which influence the formation of the target product concentration zone with sharp boundary were investigated. The effect of column sizes on the eremomycin unified elution peak formation was shown. The height to diameter ratio leading to the eremomycin concentration front division into two zones was determined.

Calorimetric investigation of the adsorption of nitrogen bases and nucleosides on a hydrophobic interaction sorbent

Heats of adsorption for nitrogen bases and nucleosides on Sepharose CL-6B, a hydrophobic interaction adsorbent, were collected through flow microcalorimetry in order to ascertain the thermodynamic driving force for adsorption in each case. It was determined that enthalpy changes associated with base stacking self-interactions can contribute significantly to the observed heats of adsorption. Accordingly, the observed heats were the net effect of the adsorbate/adsorbent interactions and the adsorbate stacking self-interactions. Since base stacking proceeds beyond the dimer stage, multi-layer adsorption of these compounds is possible, even at low solution concentrations.

Parallel screening of selective and high-affinity displacers for proteins in ion-exchange systems

This paper employs a parallel batch screening technique for the identification of both selective and high-affinity displacers for a model binary mixture of proteins in a cation-exchange system. A variety of molecules were screened as possible displacers for the proteins ribonuclease A (RNAseA) and alpha-chymotrypsinogen A (alpha-chyA) on high performance Sepharose SP. The batch screening data for each protein was used to select leads for selective and high-affinity displacers and column experiments were carried out to evaluate the performance of the selected leads. The data from the batch displacements was also employed to generate quantitative structure-efficacy relationship (QSER) models based on a support vector machine regression approach. The resulting models had high correlation coefficients and were able to predict the behaviour of molecules not included in the training set. The descriptors selected in the QSER models for both proteins were examined to provide insights into factors influencing displacer selectivity in ion-exchange systems. The results presented in this paper demonstrate that this parallel batch screening-QSER approach can be employed for the identification of selective and high-affinity displacers for protein mixtures.