Biological Evaluation Service for Therapeutic Oligonucleotide
Overview
At CD BioGlyco, our biological evaluation service for therapeutic oligonucleotides is designed as a deep, integrated preclinical platform. With many years of collective expertise, we provide high-resolution functional, structural, and pharmacokinetic data essential for rapidly prioritizing drug candidates and mitigating failure risk. We move beyond simple sequence screening to provide a holistic view of your oligonucleotide's performance in a relevant biological context.
Core Technologies
- High-Resolution Structural Probing
We utilize techniques such as SHAPE-MaP to determine the secondary structure of RNA targets and oligonucleotides, and critically, to map their interactions with cellular proteins and cofactors in living cells. This in-cellulo structural detail is invaluable for understanding the mechanism and confirming target engagement.
- Advanced Mass Spectrometry (LC-MS/MS)
The gold standard for oligonucleotide bioanalysis, our systems are optimized for the sensitive and selective detection and quantification of parent oligonucleotide and their metabolites in complex biological matrices (plasma, tissue homogenates). This is essential for accurate ADME/DMPK profiling.
- Custom Cell and RNP Models
We develop and employ specialized human cell lines, including primary hepatocytes for toxicity screening, and reconstituted ribonucleoprotein (RNP) complexes for precise mechanistic studies, allowing us to accurately predict in vivo outcomes.
Streamlined Evaluation. Accelerated Decisions.
Our streamlined evaluation workflow provides sequential, data-driven decision points to efficiently identify preclinical candidates. It begins with initial efficacy screening using high-throughput cellular assays to confirm biological activity. This is followed by a mechanistic & specificity assessment to verify the mode of action and evaluate off-target effects. Next, high-resolution profiling quantitatively measures target binding and functional potency (EC50/IC50). A comprehensive safety & ADME profile is then established, assessing toxicity (e.g., hepatotoxicity) and metabolic stability. Finally, integrated data review consolidates all findings into an actionable report, selecting lead candidates and recommending the optimal path to in vivo studies.
RNA-Cell Binding Interaction Analysis Services
Understanding how your oligonucleotide interacts with its target RNA and the cellular environment is paramount. We offer high-precision mapping of oligonucleotide-target engagement, evaluating the structural impact of chemical modifications on binding affinity and stability. We employ RNA pull-down and RBPome analysis to identify critical off-target protein interactions that may influence toxicity or distribution. Our SHAPE-MaP methodology provides single-nucleotide resolution of RNA secondary structure changes in cellulo, revealing the true functional conformation of the target upon oligonucleotide binding.
Off-Target Activity Assessment Service
Safety starts with specificity. Off-target effects, resulting from unintended complementary binding to non-target RNA or gene expression modulation, are a major concern in oligonucleotide development. We perform both in silico and in vitro off-target screening. The service utilizes high-content screening (HCS) and microarray/NGS analysis of global gene expression in human cell lines to identify significant, unexpected changes in gene expression. This proactive assessment allows for sequence refinement before costly in vivo trials, minimizing the risk of adverse clinical outcomes.
Conjugate Potency Assay Service
For complex modalities like oligonucleotide-antibody conjugates (OACs) or GalNAc-siRNAs, we design specific cell-based potency assays. We measure key functional endpoints such as ligand-mediated cellular uptake, intracellular trafficking, and the resulting gene silencing efficacy using high-sensitivity methods like luciferase reporter assays and qPCR. This service confirms that the conjugation strategy successfully retains the oligonucleotide's biological activity.
Our ADME profiling services are essential for designing effective dosing regimens and are specifically tailored to address the unique chemical challenges of oligonucleotides, such as their polyanionic nature and susceptibility to nucleases. The services include metabolic stability assessments through in vitro incubation with liver microsomes, hepatocytes, and plasma/serum to determine half-life, utilizing techniques optimized for highly stable compounds. Furthermore, we evaluate distribution and excretion by analyzing plasma protein binding—typically via ultrafiltration—and predicting tissue distribution.
Workflow
Publication Data
Journal: Pharmaceutics
IF: 5.5
DOI: 10.3390/pharmaceutics14020260
Published: 2022
Results: This white paper by the oligonucleotide safety working group (OSWG) ADME subcommittee provides comprehensive recommendations for the nonclinical pharmacokinetic characterization of therapeutic oligonucleotides. It highlights that while the general approach aligns with small molecules, key differences arise from the consistent ADME profiles across oligonucleotide classes, enabling platform-based strategies where data from one compound can support others. The document covers study design, timing, species selection, bioanalytical methods, protein binding, tissue distribution, metabolism, excretion, and drug-drug interactions, with specific guidance for various oligonucleotide types such as ASOs, siRNAs, and mRNA, including novel formulations like lipid nanoparticles. These recommendations aim to streamline nonclinical development and serve as a foundation for regulatory discussions to advance oligonucleotide therapeutics.
Applications
- Assessment of Biological Activity
We employ this service to quantitatively measure the functional effects of oligonucleotide candidates in various in vitro and in vivo models. This allows us to confirm target engagement and validate their potential for advancing research therapies.
- Safety and Toxicity Profiling
A critical part of our development process involves utilizing this service to conduct comprehensive toxicological assessments. We systematically evaluate potential adverse effects to establish a preliminary safety profile for candidate oligonucleotides, which is essential for regulatory submissions in drug development.
- Pharmacokinetic and Pharmacodynamic Studies
We rely on this service to analyze the absorption, distribution, metabolism, and excretion (ADME) properties of our oligonucleotide constructs. This data is fundamental for understanding their behavior in biological systems and for optimizing dosing regimens in pre-clinical studies.
- Investigation of Mechanism of Action
We use this service to delve deeply into the biochemical pathways and molecular interactions modulated by the oligonucleotide. This helps us elucidate the precise mechanism behind its observed effects, strengthening the scientific rationale for further investment in its development.
- Optimization of Lead Candidates
This service is integral to our lead optimization workflow. By providing comparative biological data on multiple oligonucleotide variants, it enables us to select the most promising lead compound based on efficacy and preliminary safety metrics for further development.
Advantages
- High-Resolution In Cellulo Structural Probing
Our expertise in techniques like SHAPE-MaP allows for the determination of RNA secondary structure and the mapping of interactions with cellular proteins directly in living cells, providing invaluable mechanistic insights.
- Advanced and Sensitive Bioanalytical Capabilities
We utilize gold-standard techniques like hybrid LC-MS/MS, optimized for the sensitive and selective detection and quantification of oligonucleotides and their metabolites in complex biological matrices.
- Predictive Custom Biological Models
We develop and employ specialized human cell lines, including primary hepatocytes, and reconstituted ribonucleoprotein (RNP) complexes to accurately predict in vivo outcomes during mechanistic studies and toxicity screening.
- Accelerated and Data-Driven Workflow
Our streamlined, sequential workflow, supported by high-throughput automation, enables efficient identification of preclinical candidates, saving critical months in the discovery phase.
- Modality-Agnostic and Versatile Expertise
Our platform is adaptable to various oligonucleotide types, including ASOs (both gapmers and steric-blockers), siRNAs, and aptamers, with customized assay strategies for each mechanism of action.
Frequently Asked Questions
Customer Review
- "CD BioGlyco' off-target assessment service was instrumental in de-risking our lead gapmer candidate. Their data was rigorous, comprehensive, and stood up flawlessly during our internal safety review."
—Dr. Peterson, Senior Director, Molecular R&D
- "The ADME profiling data, particularly the Hybrid LC-MS/MS bioanalysis, were the most sensitive we’ve seen. Their expertise in oligonucleotide metabolite profiling is truly world-class."
— Manager, Drug Manufacturing
- "The custom conjugate potency assay CD BioGlyco designed for our lipid-oligonucleotide platform was perfect. They accurately confirmed the cellular internalization efficiency and functional knockdown, validating our delivery strategy."
— M. Al-Farsi, Research Director, Bioanalysis
Associated Services
Our biological evaluation service for therapeutic oligonucleotides assesses the efficacy and safety profiles of nucleic acid therapeutics, where reliable results depend critically on sample purity. To support this requirement, we provide specialized Oligonucleotide Fragment Purification Service utilizing multiple methodologies, including:
CD BioGlyco is your dedicated partner in transforming innovative nucleic acid sequences into viable therapeutic candidates. If you are interested in our integrated, high-science solution, encompassing high-throughput functional screening, high-resolution structural characterization (SHAPE-MaP), rigorous off-target safety assessment, and custom ADME/PK profiling, contact us.
Reference
- Moumné, L.; et al. Oligonucleotide therapeutics: from discovery and development to patentability. Pharmaceutics. 2022, 14(2): 260. (Open Access)