Hydrophilic interaction in solid-phase extraction of antisense oligonucleotides

Improvement of serum sample preparation and chromatographic analysis of nusinersen used for the treatment of spinal muscular atrophy

The present investigation showed that each of the three different liquid chromatography modes may be successfully used for the qualitative analysis of nusinersen metabolites in a patient's serum sample extract. However, the smallest number was detected by the hydrophilic interaction liquid chromatography. Furthermore, the response of the mass spectrometry is several times greater for ion pair chromatography compared to reversed-phase one. Various extraction methods were applied for the extraction of nusinersen metabolites from serum. Silica with bonded capture strand for hybridization was applied, as well as silica modified with amino and carboxyl groups for dispersive solid phase extraction. The hybridization allows selective extraction of nusinersen analogs, however, it fails in extraction of short metabolites. On the contrary, the efficiency of weak ion exchange-based extraction was high, even in the case of the direct extraction of nusinersen metabolites from diluted serum samples without a protein removal step. The new material is a great alternative to liquid-liquid extraction and hybridization for the isolation of nusinersen metabolites from the serum of patients with spinal muscular atrophy (SMA). It is a very simple method that uses a low concentration of organic salt and desorption occurs after changing its pH. Such complex studies were performed for the first time for nusinersen metabolites extracted from the serum of SMA patients treated with Spinraza.

Targeting FMN, TPP, SAM-I, and glmS Riboswitches with Chimeric Antisense Oligonucleotides for Completely Rational Antibacterial Drug Development

Antimicrobial drug resistance has emerged as a significant challenge in contemporary medicine due to the proliferation of numerous bacterial strains resistant to all existing antibiotics. Meanwhile, riboswitches have emerged as promising targets for discovering antibacterial drugs. Riboswitches are regulatory elements in certain bacterial mRNAs that can bind to specific molecules and control gene expression via transcriptional termination, prevention of translation, or mRNA destabilization. By targeting riboswitches, we aim to develop innovative strategies to combat antibiotic-resistant bacteria and enhance the efficacy of antibacterial treatments. This convergence of challenges and opportunities underscores the ongoing quest to revolutionize medical approaches against evolving bacterial threats. For the first time, this innovative review describes the rational design and applications of chimeric antisense oligonucleotides as antibacterial agents targeting four riboswitches selected based on genome-wide bioinformatic analyses. The antisense oligonucleotides are coupled with the cell-penetrating oligopeptide pVEC, which penetrates Gram-positive and Gram-negative bacteria and specifically targets glmS, FMN, TPP, and SAM-I riboswitches in Staphylococcus aureus, Listeria monocytogenes, and Escherichia coli. The average antibiotic dosage of antisense oligonucleotides that inhibits 80% of bacterial growth is around 700 nM (4.5 μg/mL). Antisense oligonucleotides do not exhibit toxicity in human cell lines at this concentration. The results demonstrate that these riboswitches are suitable targets for antibacterial drug development using antisense oligonucleotide technology. The approach is fully rational because selecting suitable riboswitch targets and designing ASOs that target them are based on predefined criteria. The approach can be used to develop narrow or broad-spectrum antibiotics against multidrug-resistant bacterial strains for a short time. The approach is easily adaptive to new resistance using targeting NGS technology.

Bioanalysis of Oligonucleotide by LC-MS: Effects of Ion Pairing Regents and Recent Advances in Ion-Pairing-Free Analytical Strategies

Oligonucleotides (OGNs) are relatively new modalities that offer unique opportunities to expand the therapeutic targets. Reliable and high-throughput bioanalytical methods are pivotal for preclinical and clinical investigations of therapeutic OGNs. Liquid chromatography-mass spectrometry (LC-MS) is now evolving into being the method of choice for the bioanalysis of OGNs. Ion paring reversed-phase liquid chromatography (IP-RPLC) has been widely used in sample preparation and LC-MS analysis of OGNs; however, there are technical issues associated with these methods. IP-free methods, such as hydrophilic interaction liquid chromatography (HILIC) and anion-exchange techniques, have emerged as promising approaches for the bioanalysis of OGNs. In this review, the state-of-the-art IP-RPLC-MS bioanalytical methods of OGNs and their metabolites published in the past 10 years (2012-2022) are critically reviewed. Recent advances in IP-reagent-free LC-MS bioanalysis methods are discussed. Finally, we describe future opportunities for developing new methods that can be used for the comprehensive bioanalysis of OGNs.

Oligonucleotides Isolation and Separation—A Review on Adsorbent Selection

Oligonucleotides have many important applications, including as primers in polymerase chain reactions and probes for DNA sequencing. They are proposed as a diagnostic and prognostic tool for various diseases and therapeutics in antisense therapy. Accordingly, it is necessary to develop liquid chromatography and solid phase extraction methods to separate oligonucleotides and isolate them from biological samples. Many reviews have been written about the determination of these compounds using the separation technique or sample preparation for their isolation. However, presumably, there are no articles that critically review the adsorbents used in liquid chromatography or solid phase extraction. The present publication reviews the literature from the last twenty years related to supports (silica, polymers, magnetic nanoparticles) and their modifications. The discussed issues concern reversed phase (alkyl, aromatic, cholesterol, mixed ligands), ion-exchange (strong and weak ones), polar (silica, polyhydroxy, amide, zwitterionic), and oligonucleotide-based adsorbents.

Titanium-based metal-organic framework MIL-125(Ti) for the highly selective isolation and purification of immunoglobulin G from human serum

Titanium-based metal-organic framework MIL-125(Ti) was synthesized by the hydrothermal method of terephthalic acid and tetra butyl titanate in N-N dimethylformamide and methanol. MIL-125(Ti) was characterized by Fourier transform infrared spectroscopy, X-ray diffraction, thermogravimetric analysis, nitrogen adsorption-desorption, energy-dispersive X-ray spectroscopy, zeta potential, scanning electron microscope and transmission electron microscopy. The results showed MIL-125(Ti) could be used as a potential adsorbent for protein separation and purification due to the high specific surface area, high stability and strong hydrophobicity. As a result, MIL-125(Ti) had adsorption selectivity for immunoglobulin G, which was due to hydrogen bond between MIL-125(Ti) and protein. At pH 8.0, the maximum adsorption efficiency of 0.25 mg MIL-125(Ti) for 300 μL 100 μg mL^-1 immunoglobulin G was 98.3%, and its maximum adsorption capacity was 232.56 mg g^-1 . The elution efficiency of immunoglobulin G was 92.4% by 0.1% SDS. SDS-PAGE result demonstrated the successful isolation of highly purified immunoglobulin G from the human serum. Therefore, a new method of separation and purification of immunoglobulin G in human serum using titanium-based metal-organic framework MIL-125(Ti) as a solid-phase adsorbent was established, which broadened the application scope of metal-organic frameworks. This article is protected by copyright. All rights reserved.

Hydrophilic-Phase Extraction: A New Avenue of Solid-Phase Extraction for Oligonucleotide Bioanalysis

A novel mode of bioanalytical solid-phase extraction (SPE) has been developed and used for a quantitative application involving an RNA oligonucleotide therapeutic candidate. Previously established protocols and media showed very little recovery, and so this new approach, based on hydrophilic interaction liquid chromatography (HILIC) with an aminopropyl-bonded phase on a silica support and providing an essentially uncharted avenue of selectivity, was explored. The procedure featured only one step prior to sample load, high-organic sorbent conditioning, two washes following the load that switched between low and high pH, followed by elution in an a highly eluotropic HILIC composition. The moniker of “hydrophilic-phase extraction” (HPE) was given to the procedure. The HPE was proven to be a critical part of a fully quantitative HILIC–high-resolution mass spectrometry (HRMS) method for the RNA oligonucleotide and has potential for general application.

Novel hydrophilic-phase extraction, HILIC and high-resolution MS quantification of an RNA oligonucleotide in plasma

Aim: In the theme of quantitative LC-MS bioanalysis of oligonucleotides free of ion-pairing, a 22-mer RNA oligonucleotide took center stage. The focus was on a unique polar-based retention scheme to produce a high-recovery extraction presenting a high-performance alternative extraction means, also there was the opportunity to involve hydrophilic-interaction liquid chromatography and contemporary high-resolution MS as the end point. Results: Original LC-MS methodology was developed for the oligonucleotide and the performance was robust for both nominal and accurate mass detection, the latter affording 10× improvement in sensitivity and 4000-fold linear dynamic range, 500 pM to 2000 nM. Conclusion: A novel means of solid-phase extraction is exhibited within a robust pair-free methodology, reaching pM sensitivity with the demonstrably beneficial accurate mass platform.