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Overcoming Bottlenecks in Quantifying Oligonucleotide Therapeutics Using LC-MS/MS Technology and Expertise to Reduce Risk and Increase Your Speed to Market

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Overcoming Bottlenecks in Quantifying Oligonucleotide Therapeutics Using LC-MS/MS Technology and Expertise to Reduce Risk and Increase Your Speed to Market Overcoming Bottlenecks in Quantifying Oligonucleotide Therapeutics Using LC-MS/MS Technology and Expertise to Reduce Risk and Increase Your Speed to Market Overcoming Bottlenecks in Quantifying Oligonucleotide Therapeutics 1 Introduction Oligonucleotides are a rapidly growing family of biopharmaceutical products whose therapeutic potential is now primed and waiting to be unlocked. First recognized for their ability to modulate gene expression more than three decades ago, advances in fundamental research and enabling technologies have doubled the number of oligonucleotide drugs on the market since the start of 2016, with many more expected in the years to come. This important class of therapeutics is coming of age, and for biopharmaceutical companies, the race is on to launch the next generation of innovative oligonucleotide products. Bringing safe and effective oligonucleotides to market relies on robust bioanalysis workflows. However, given their unique physicochemical properties, oligonucleotides require advanced and unique analytical strategies that go above and beyond those used to study conventional small molecule or even peptide and protein drugs. Implementing ineffective solutions that poorly meet these needs can cause substantial bioanalysis backlogs, lengthy study delays or even suboptimal development decisions based on incomplete or incorrect data. Even the largest and most experienced drug developers are not immune to these challenges. To accelerate the development of your oligonucleotide therapeutics and drive clinical success, you need robust bioanalysis solutions underpinned by industry- leading analytical expertise, cutting-edge technologies and proven workflows built on decades of experience. Abstract Developing bioanalytical solutions to support oligonucleotide drug programs can be challenging due to the unique physicochemical properties of these molecules. This whitepaper outlines both the established and the unique liquid chromatography and extraction technologies Covance has developed to ensure you remain at the forefront of oligonucleotide innovation. Learn how you can benefit from the workflows to: ▶ Eliminate bottlenecks and accelerate timelines with state-of-the-art liquid chromatography, focused detection and extraction technologies that generate accurate and robust data ▶ Rapidly receive the results you need through world-class scientific expertise based on decades of experience in solving complex bioanalytical challenges ▶ Capitalize on the rapidly expanding oligonucleotide marketing with the support of technologies and expertise Now Is the Time to Get Ahead of the Oligonucleotide Therapeutics Field Oligonucleotide therapeutics However, following extensive encompass a wide range of research efforts and a large number different modalities, with antisense of clinical trials, the last few years oligonucleotides (ASOs), small have seen an upsurge in the number interfering RNA (siRNA), micro of oligonucleotide drugs that RNA (miRNA) antagomirs/mimetics have been granted FDA approval, and oligonucleotide aptamers among signaling the start of a new era in the most widely utilized families.1 oligonucleotide therapeutics. Since Each class has been shown to operate 2016, the number of oligonucleotide through different mechanisms, products on the market has more which researchers are exploring to than doubled and a wealth of develop new treatments across a promising candidates are currently broad range of therapeutic fields, in late-stage clinical trials. The oligonucleotide including cancer,2 neurodegenerative This growth shows no sign of conditions3 and infectious diseases.4 therapeutics market stopping, with the oligonucleotide is expected to grow Despite the breadth of targets and therapeutics sector expected to mechanisms of action, translating increase at an annual rate of by 10% annually to all this potential into marketable 10% between 2018 and 2022 to reach $760 million drugs has had something of a an estimated $760 million.6 The by 2022. Now is the slow start (see market milestones oligonucleotide market is currently time to expedite timeline).5 Prior to 2016, just wide open and a new generation of three oligonucleotide therapeutics safe and effective therapeutics now your research in this (pegaptanib, mipomersen and within reach. This represents an exciting drug area, fomivirsen) had been approved enormous opportunity to capitalize before the market by the U.S. Food and Drug on this growing market and get fully matures.6 Administration (FDA), with the latter ahead of the competition. discontinued due to improvements in HIV treatments. Overcoming Bottlenecks in Quantifying Oligonucleotide Therapeutics 3 Market Milestones in the Development of Oligonucleotide Therapeutics5 FDA Fomivirsen (Vitravene) Approval Developers: Isis (now Ionis) 1998 Pharmaceuticals & Novartis Ophthalmics Pegaptanib (Macugen) FDA Approval Developer: NeXstar Pharmaceuticals 2004 FDA Mipomersen (Kynamro) Approval Developer: Isis (now Ionis) 2013 Pharmaceuticals Defibrotide (Defitelio) FDA Approval Developer: Jazz Pharmaceuticals 2016 FDA Eteplirsen (Exondys 51) Approval Developer: Sarepta 2016 Therapeutics Nusinersen (Spinraza) FDA Approval Developers: Ionis Pharmaceuticals & Biogen 2016 FDA Onpattro (Patisiran) Approval Developer: Alnylam 2018 Pharmaceuticals, Inc. Givlaari (Givosiran) FDA Approval Developer: Alnylam 2019 Pharmaceuticals, Inc. Overcoming Bottlenecks in Quantifying Oligonucleotide Therapeutics 4 Experience and Expertise Are Essential When Developing Oligonucleotide Bioanalysis Workflows Developing and validating The analysis of oligonucleotides Given these challenges, many bioanalytical methods for using traditional LC-MS techniques biopharmaceutical companies choose oligonucleotide therapeutics by is also more challenging than to work with external partners to liquid chromatography-mass for other types of molecules. access the specialist techniques, spectrometry (LC-MS) is widely Oligonucleotides are comprised of technologies and expertise necessary regarded as being more challenging just four alternating nucleobases, for successful oligonucleotide than conventional small molecule meaning that chromatographic bioanalysis. Moreover, with analysis.7 Without capable separation is more mass- and bioanalysis workflows involving technologies and specialist know- size-based than most other extensive protocol development how, bioanalytical strategies may chromatography applications. and careful method optimization, deliver inaccurate or unreliable These molecules are also highly outsourcing to dedicated specialists results and leave oligonucleotide polar and multiply charged, can be a notably more cost-effective development programs vulnerable making conventional reversed- route to achieving successful results to unexpected issues and delays. phase chromatography unsuitable. in the shortest possible timeframe. These potential challenges arise The pronounced polarity and due to the unique physical multiple charging also produce characteristics associated with sensitivity challenges, especially in this biotherapeutic class. high-aqueous reversed-phase LC Outsourcing conditions, where the nebulized oligonucleotide Firstly, the isolation of evaporation process to produce oligonucleotides from biofluids bioanalysis discrete gas phase ions in the mass may often be complicated by ex vivo to dedicated spectrometer source component instability. Oligonucleotides also is that much more difficult due specialists can bind strongly to proteins and can to the high concentration of undergo nonspecific binding be a more water. Furthermore, as some (i.e., secondary binding) to cost-effective oligonucleotides can be thermally equipment and labware. Careful labile at low pH, analytical route to your consideration must therefore be paid parameters such as ion source to methods to minimize unreliable achieving temperature must be systematically quantification and ensure the success in the optimized. As such, it can be difficult collection of accurate data. to develop reliable quantitative shortest possible analysis methods using the LC-MS timeframe. techniques commonly employed for small molecule analysis. Overcoming Bottlenecks in Quantifying Oligonucleotide Therapeutics 5 Benefit from Advanced Oligonucleotide Bioanalysis Techniques To accelerate innovation and hit development deadlines, it’s essential your bioanalysis workflows incorporate the most capable oligonucleotide extraction, separation and detection techniques. Drawing on a global network of expertise with decades of experience in analytical problem-solving, we’ll work together to develop a robust bioanalysis strategy that meets your needs. This includes optimized methods are underpinned by state-of-the-art technologies, ensuring we deliver the results you need to make key decisions, on time and on budget. High-Performance Ion-Pairing Methods State-of-the-Art LC-MS Systems Reversed-phase ion pair chromatography (RP-IPC) Issues around cross-reactivity and interference from is a well-established technology for oligonucleotide other metabolites found in biological samples can bioanalysis.8 It is used to separate polar organic present a serious challenge when using analytical molecules and employs the same types of eluents and techniques such as ELISA. LC-MS and LC-FD based on hydrophobic stationary phases as conventional reversed- tandem chromatographic separations with either mass phase liquid chromatography. However, unlike standard spectrometry or fluorescence detection offer
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