Simplified Oligonucleotide Phosphorus Deprotection Process with Reduced 3-(2-Cyanoethyl) Thymidine Impurities.

Oligonucleotides have emerged as valuable new therapeutics. Presently, oligonucleotide manufacturing consists in a series of stepwise additions until the full-length product is obtained. Deprotection of the phosphorus backbone before cleavage and deprotection (C&D) by ammonolysis is necessary to control the 3-(2-cyanoethyl) thymidine (CNET) impurity. In this study, we demonstrate that the use of piperazine as a scavenger of acrylonitrile allows phosphorus deprotection and C&D to be combined in a single step. This reduces solvent consumption, processing time, and CNET levels. Additionally, we showed that substitution of piperazine for triethylamine in the phosphorus deprotection step of supported-synthesis leads to reduced reaction times and lower levels of CNET impurities.

Use of ultrafiltration/diafiltration for the processing of antisense oligonucleotides.

Ultrafiltration/diafiltration (UF/DF) has been the hallmark for concentrating and buffer exchange of protein and peptide-based therapeutics for years. Here we examine the capabilities and limitations of UF/DF membranes to process oligonucleotides using antisense oligonucleotides (ASOs) as a model. Using a 3 kDa UF/DF membrane, oligonucleotides as small as 6 kDa are shown to have low sieving coefficients (<0.008) and thus can be concentrated to high concentrations (≤200 mg/mL) with high yield (≥95%) and low viscosity (<15 centipoise), provided the oligonucleotide is designed not to undergo self-hybridization. In general, the oligonucleotide should be at least twice the reported membrane molecular weight cutoff for robust retention. Regarding diafiltration, results show that a small amount of salt is necessary to maintain adequate flux at concentrations exceeding about 40 mg/mL. Removal of salts along with residual solvents and small molecule process-related impurities can be robust provided they are not positively charged as the interaction with the oligonucleotide can prevent passage through the membrane, even for common divalent cations such as calcium or magnesium. Overall, UF/DF is a valuable tool to utilize in oligonucleotide processing, especially as a final drug substance formulation step that enables a liquid active pharmaceutical ingredient.

Development of Kilogram-Scale Convergent Liquid-Phase Synthesis of Oligonucleotides.

Oligonucleotide drugs show promise to treat diseases afflicting millions of people. To address the need to manufacture large quantities of oligonucleotide therapeutics, the novel convergent liquid-phase synthesis has been developed for an 18-mer oligonucleotide drug candidate. Fragments containing tetra- and pentamers were synthesized and assembled into the 18-mer without column chromatography, which had a similar impurity profile to material made by standard solid-phase oligonucleotide synthesis. Two of the fragments have been synthesized at ∼3 kg/batch sizes and four additional tetra- and pentamer fragments were synthesized at >300-g scale, and a 34-mer was assembled from the fragments. Critical impurities are controlled in the fragment syntheses to provide oligonucleotides of purities suitable for clinical use after applying standard full-length product purification process. Impurity control in the assembly steps demonstrated the potential to eliminate chromatography of full-length oligonucleotides, which should enhance scalability and reduce the environmental impact of the process. The convergent assembly and telescoping of reactions made the long synthesis (>60 reactions) practical by reducing production time, material loss, and chances for impurity generation.

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.

Solid-Phase Synthesis of Phosphorothioate Oligonucleotides Using Sulfurization Byproducts for in Situ Capping.

Oligonucleotides containing phosphorothioate (PS) linkages have recently demonstrated significant clinical utility. PS oligonucleotides are manufactured via a solid-phase chain elongation process in which a four-reaction cycle consisting of detritylation, coupling, sulfurization, and failure sequence capping with Ac2O is repeated. In the capping step, uncoupled sequences are acetylated at the 5'-OH to stop the chain growth and control the levels of deletion, or ( n-1), impurities. Herein, we report that the byproducts of commonly used sulfurization reagents react with the 5'-OH and cap the failure sequences. The standard Ac2O capping step can therefore be eliminated, and this 3-reaction cycle process affords a higher yield and higher or comparable overall purity compared to the conventional 4-reaction synthesis. This improvement results in reducing the number of reactions from ∼80 to ∼60 for the synthesis of a typical length 20-mer oligonucleotide. For every kilogram of an oligonucleotide intermediate synthesized, > 500 L of reagents and organic solvents is saved, and the E-factor is decreased to <1500 from ∼2000.

Development of a gradient elution preparative high performance liquid chromatography method for the recovery of the antibiotic ertapenem from crystallization process streams.

A gradient elution preparative chromatography method was developed for the recovery of the antibiotic ertapenem from crystallization mother-liquor streams. The preparative HPLC method that was developed on the lab-scale employs an analytical size column of conventional dimensions (25 cm x 0.46 cm) packed with Kromasil C8 stationary phase. Gradient elution was used with aqueous acetic acid and acetonitrile as mobile phases. A target of processing approximately 30 mg of ertapenem per half an hour at a flow rate of 1.5 mL/min with high yield and adequate rejection of all major impurities was achieved. This corresponds to a productivity of approximately 0.6 kg ertapenem as free acid per kilogram of stationary phase per day (kkd). The scalability of the method was demonstrated by using a 5 cm i.d. column configuration to generate 10 g of purified ertapenem. This work complements a previous study improving on the productivity and throughput of the method by employing gradient elution and the use of crystallization to remove some key impurities that are chromatographically difficult to resolve [A. Vailaya, P. Sajonz, O. Sudah, V. Capodanno, R. Helmy, F.D. Antia, J. Chromatogr. A 1079 (2005) 80].

Normal phase high-performance liquid chromatography of pneumocandins: in situ modification of silica with L-proline to separate structural analogues.

Lipopeptides such as pneumocandin B(0) are often produced by fermentation processes. Many compounds with similar structures (structural analogues), and hence similar physiochemical properties, are coproduced in the fermentation. We employed high performance liquid chromatography using silica gel as the stationary phase and a ternary ethyl acetate/MeOH/water mobile phase to separate pneumocandin B(0) from these structural analogues. Despite extensive efforts to optimize this system, two key structural analogues, pneumocandin E(0) and pneumocandin B(5), continued to be poorly resolved from the main product peak (pneumocandin B(0)). As a result, feed load was restricted and productivity was limited. In situ modification of the silica gel stationary phase with l-proline or other amino acids significantly enhances the resolution of the two key structural analogues from the compound of interest, enabling a two-fold increase in productivity. Results of a systematic study showed that the amine group in l-proline and other amino acids plays a key role in the modification of the surface of the silica gel to mediate the selectivity enhancement.

Preparation and evaluation of novel stationary phases for improved chromatographic purification of pneumocandin B0.

Preparation and evaluation of a number of stationary phases for improved chromatographic purification of pneumocandin B0, a key intermediate in the synthesis of the antifungal agent, Cancidas, has led to the identification of several materials with potential for improved performance.

Influence of mobile phase composition and thermodynamics on the normal phase chromatography of echinocandins.

In the normal phase preparative HPLC of fermentation derived echinocandins, resolution of key impurities from the product of interest, pneumocandin B(o), is accomplished using a ternary ethyl acetate/methanol/water mobile phase with silica gel as the sorbent. In this work, previous characterization of the system is extended to define the impact and role of water content on the separation efficiency and retention of pneumocandin B(o). Experimental results indicate that column efficiency, measured using both the product of interest and small molecule tracers (compounds used for pulse tests), is good despite the use of an irregular silica and unusually high levels (greater than 6%) of water in the mobile phase. In contrast to column efficiency measurements using small molecules (MEK and toluene), measurements performed with the product itself indicate improved efficiency with increasing water content of the mobile phase. Building on these results, a scale-up/scale-down protocol was developed based on measurements of column efficiency using theoretical plate counts determined with pneumocandin B(o). Since the solubility of pneumocandin B(o) in the ternary mobile phase is relatively low, a higher strength solvent with higher levels of methanol and water is employed for dissolution of the crude product at concentrations of up to 40g/L. The mismatch between the high strength solvent used for the feed introduction and the mobile phase has the potential to affect column performance. The impact of this mismatch using plate count measurements with the product at both analytical and semi-preparative scales was found not to be significant. Finally, a van't Hoff analysis was performed to characterize the thermodynamics of adsorption of pneumocandin B(o) on silica. The analysis shows that the adsorption process for pneumocandin B(o) on silica in the ternary solvent system is endothermic (DeltaH(ads)>0), implying that the adsorption is entropically driven. Results from an overall water balance across the column indicate significant enrichment of adsorbed water on the silica surface. These results further emphasize the importance of selective partitioning of water between the bulk mobile phase and the silica as a dominant factor in controlling retention.

Exploiting pH mismatch in preparative high-performance liquid chromatographic recovery of ertapenem from mother liquor streams.

Preparative chromatography was successfully employed to recover ertapenem from mother liquor streams. The recovery process involved concentration of mother liquor stream by evaporation, purification by reversed-phase preparative high-performance liquid chromatography (HPLC), and removal of chromatographic solvents in the recovered fractions by evaporation. HPLC feed was prepared by stripping off the organic solvents from the mother liquor using a wiped-film evaporator. Purification was first carried out on a 25 cm x 0.46 cm analytical column packed with 10-microm Kromasil C8 particles and then scaled up to a 25 cm x 5 cm preparative column. Gram-level recovery of ertapenem with high purity was achieved by exploiting a novel approach based on pH mismatch between the feed and the eluent. Purified ertapenem streams from preparative HPLC runs were combined, evaporated and recycled into the crystallizer for ertapenem isolation.