Oligonucleotide Chemistry, Manufacturing & Controls: new tips from the German Federal Institute for Drugs and Medical Devices

The German Federal Institute for Drugs and Medical Devices, has given a workshop about the Oligonucleotide CMC Strategies for Quality Control. Quality management follows the ICH Harmonised Tripartite Guideline Quality Risk Management Q9 for risk assessment, control and review.  For oligonucleotides, starting materials are very important for the overall control strategy, with the usage of the complex phosphoramidites accepted by the agencies. Of course, formation, structure and fate of impurities needs to be described in the regulatory dossier, as well as a demonstration of the understanding of their criticality. If multiple suppliers are used, then they should be mentioned (module 3.2.S.2.3); and, if sourced from different suppliers, then impurity profiles of phosphoramidites should be compared between suppliers. Also, each supplier of aminoacid derivatives needs to provide a statement which includes a basic description of the synthesis principles, and a risk analysis on the potential carry-over of impurities.

If conjugated oligonucleotides are used as starting materials, then a justification based on science and ICH Q11 Q&A should be given; with a comprehensive data set, characterization, suitable and validated analytical methods (which are usually not required for small molecule starting materials), description of synthesis and tight specifications (aka, justification for each attribute should guarantee consistent quality). Also, there needs to be a high number batch of analysis to demonstrate consistency, with an elucidation and criticality assessment of the impurity profile; and genotoxic impurity assessment in line with ICH M7 requirements. In the agency point of view, regulatory consistency is extremely important; as such, if a starting complex material is accepted in a specific procedure, it does not automatically mean that the same or a similar complex starting material will be accepted by another applicant, because it all depends on the data. Therefore, commercial reasons are not acceptable as a justification and scientific advice is always recommended.

In relation to sterilization, there is a new guideline from EMA (EMA/CHMP/CVMP/QWP/850374/2015, 06/03/2019, Guideline on the sterilization of the medicinal product, active substance, excipient, and primary container, in effect since October 2019). This guideline states that substantial efforts should be made to enable terminal sterilization of the finish product and these should be presented in the development section of the file. Also, terminal sterilization should not be ruled out solely based on an increase in degradation products without an additional justification. If impurities are either metabolites or are generated at levels already qualified, then terminal sterilization is still considered feasible. If degradation products are no qualified at the levels at which they occur, then sterile filtration and aseptic processing may be selected. For both agencies and manufactures there are still of course questions, like which level of degradation is acceptable, or which qualification data is needed, which other quality attributes are affected besides purity, what is the criticality of these effects, how to perform risk analysis, impact on changes from Tox to Phase III, or what are the capabilities of CMOs for product specific F0 concepts. With those questions in mind, several development programmes using terminal sterilization of oligonucleotides are on-going at the moment.

Another hot-topic at the moment is the presence of nitrosamine impurities  in an API and drug product; and, with that in mind there is a new Q&A for marketing authorization holders/applicants on the CHMP Opinion for the Article 5(3) of Regulation (EC) N. 726/2004, which referrers on nitrosamine impurities in human medicinal products (03/08/2020, EMA/409815/2020). It states the need to include a risk evaluation in Module 1, in case there’s a risk for the presence of nitrosamines in the product, with testing and according measures implemented before the end of the marketing authorization procedure.

Another topic is stress testing of oligonucleotides, which should not be considered a luxury and should be done early in development, with the identification of degradation products, pathways, intrinsic stability of the molecule formulation, with discriminatory power and validation of analytical methods.

One of the most important questions for the future, is whether drug substance testing for impurities needs to be done, or some risk analysis/theoretical calculations will be accepted. Due to the difference in the manufacturing process of oligonucleotides, theoretical considerations for purging are reasonable; although, risk analysis are extremely important, especially in relation to genotoxic impurities and batch analysis, and these for sure will need to be provided. In the future this could change, but for that to happen, industry would need to share the data and provide peer-reviewed publications.

In the agencies point of view sequencing should always be part of the drug substance specification in identity testing. In relation to the validation of Tm, the question remains which complementary strands are relevant to demonstrate specificity/selectivity; and for drug products, two independent test methods should be included in the drug product specification. A good insight on this topic has been recently by published by Capaldi and colleagues (https://doi.org/10.1089/nat.2020.0878); however, the regulatory agencies may have other views, but always with an on-going dialogue.

In relation to control strategy for early access approaches, even though there is the notion that there are, for example to few batches to assess consistency or limited variability in the clinical batches, the regulatory expectations do not change for an expedited development program, and the product is still expected to be safe and efficient with a positive benefit/risk ratio. In a patient-focused control strategy, an option is to use more attributes, process parameters and in-process testing in the application control strategy; which can be revised once more knowledge is gained. The information that should be always front-loaded is: (1) starting material characterization, (2) impurity profile, and (3) analytical methods used.

Catarina Carrão