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Formulated oligonucleotide APIs: Regulatory aspects

Lee, Judy (2022) Formulated oligonucleotide APIs: Regulatory aspects. Therapeutic innovation & regulatory science, 2022 (56). pp. 386-393. ISSN 2168-4790; 2168-4804


Formulated oligonucleotide APIs: Regulatory aspects
Christian Wetter (Roche), Chris Chorley (Biogen), Corrine Curtis, (Janssen), Nicole del Canto (Biogen), Gair Ford (AstraZeneca), Jenny Franklin (Ionis), Cinzia Gazziola (Roche), Michael T. Jones (Pfizer), Judy Lee (Novartis), Arnold McAuley (Amgen), Floor Saraber (Janssen), Audrey Scott (GSK), Janine Tom (Amgen)

The European Pharma Oligonucleotide Consortium (EPOC) [1] is a collaboration between multiple pharma companies with the aim of sharing chemistry, manufacturing, and control (CMC) knowledge as well as strategies to enable harmonization of oligonucleotide development and commercialization. The objective of the consortium is to publish science-based recommendations for the development of oligonucleotide therapeutics in a series of technical and regulatory white papers, drawing on its collective subject matter expertise and complementing that in the literature and guidelines. This public body of prior knowledge endeavors to serve as a reference for industry practice and help establish development principles for oligonucleotides. The consortium aims at being proactive and inclusive, and it anticipates initiating wider discussion on oligonucleotide CMC practice and policy, thus expediting access to these potentially life changing medicines.
The concept of formulated APIs (also called API mixes by EMA) for oligonucleotides was described by Muslehiddinoglu et al in 2020 [2]. The publication discusses technical aspects related to formulated oligonucleotide APIs, such as their stability, manufacture, microbial control, packaging and storage. Various criteria such as supply chain, scale, dosage strengths, etc., may influence the best choice of the API form – resulting in use of either a solid API, an API in water, or a formulated API. The formulated API may be ready-to-fill, or may require further dilution or addition of excipients. Muslehiddinoglu et al left regulatory aspects out of scope of the published article; therefore, the present communication aims to complement the first manuscript and discuss relevant regulatory and GMP aspects of a formulated API. In addition, this article aims to initiate interaction and discussion with regulators to promote the use of the formulated API approach in oligonucleotide drug manufacture. The authors hope to contribute to EMA’s initiative ‘Regulatory Science to 2025 – Strategic Reflection’, in “developing expertise in novel manufacturing technologies”, “identifying bottlenecks”, and “addressing regulatory challenges” that could be overcome by “modernizing relevant regulations and guidelines”. The authors would like to propose solutions for “promoting a flexible and fit-for-purpose approach in application of GMP”, and “supporting the development of greener manufacturing technologies in line with EU’s ‘Strategic Approach to Pharmaceuticals in the Environment’” [3].
Problem statement
Oligonucleotides are typically synthetically derived and can be isolated as a solid, in water or as formulated APIs. While available guidelines generally provide flexibility with respect to the designation of a formulated API as an API, EMA and Health Canada have set a more restrictive framework in which API-excipient mixtures can be designated as APIs in exceptional cases only. Typically API-excipient mixtures have to be designated as drug product intermediates. A guideline review is provided below.
When designating a formulated API as a drug product intermediate, the manufacturers have to fulfill drug product GMP standards for the manufacturing steps converting the API into a formulated API. The requirements for clean areas as defined in ISO 14644-1 [43] and the EU guideline to GMP, Annex 1 [5] apply. This is typically not possible in facilities designed for manufacture of oligonucleotide APIs.
Further, the designation of a formulated API as a drug product intermediate poses challenges around the shelf-life definition of the oligonucleotide drug product. Per standard requirements for chemical products, the shelf-life is defined by the start of the drug product manufacturing process, i.e., the mixing of the API with other product ingredients [6]. Storage of the formulated API for a prolonged period before further manufacture and/or filling would thereby shorten the shelf-life of the finished product upon release for market distribution.
Similar challenges have been identified when using co-processed APIs [7].
Current regulatory landscape
In the ICH Q7 [8] glossary, an API is defined as “any substance or mixture of substances intended to be used in the manufacture of a drug (medicinal) product (...)”. As per ICH Q7 Q&A [9], “when a mixture is classified in the regulatory filing as an API in a region or country in which it is used in a drug product, ICH Q7 should be applied to the manufacturing of these mixtures [ICH Q7, Section 1.2, 20 – see Glossary for definition of ‘API’]”.
As per ICH Q6B [10], for biological products, the drug substance (bulk material) “may also contain excipients including other components such as buffers”.
The WHO Annex 3 on ‘Pharmaceutical development of multisource (generic) finished pharmaceutical products – points to consider’ from 2012 [11] defines an API as “Any substance or mixture of substances intended to be used in the manufacture of a pharmaceutical dosage form and that, when so used, becomes an active ingredient of that pharmaceutical dosage form”.
In their Q&A document [12] the CHMP quality working party (QWP) defines an API mix as a “mixture of an API with one or more excipients”, and “the manufacture of an API mix is considered to be the first step of the manufacture of a finished product”. Further, “in certain circumstances, i.e. stability or safety reasons, the applicant can submit data on such a mixture under part 3.2.S (...).” However, “In case of an API mix prepared due to workability purposes or reasons other than safety and stability, the manufacturing steps from the addition of the excipient to the API should be described in the appropriate part of CTD 3.2.P. In addition the steps following addition of the excipient must be conducted in accordance with GMP Part I and an appropriate manufacturing authorisation”. Moreover, “a justification based only on workability reasons, e.g. to ease handling when processed into final dosage form, is not acceptable. Toxicological considerations (e.g. very potent drugs) fall under workability reasons and are not accepted as justifications.”
In their quality (chemistry and manufacturing) guidance, Health Canada states the following related to the start of drug product manufacture and possible exceptions based on safety and stability reasons [13]. The expectations are aligned with the QWP Q&A discussed above, and Health Canada encourages a discussion with their pre-market approval bureau/office.
That first processing step of the drug substance in the presence of any other substance would be considered a drug product manufacturing activity, subject to Part C, Division 2 of the Food and Drug Regulations, and would define the date from which the expiry date for the drug product would be established. (…) Sponsors having situations that might be an alternative to the above interpretation (e.g. inability to isolate the drug substance in a pure and stable form or mixing with excipients for safety or stability purposes, e.g. nitroglycerin, cholecalciferol) should discuss their case and scientific justification in advance with the pre-market approval bureau/office.”
Proposed path forward
The authors recognize that two elements need to be addressed to enable the designation of formulated APIs as APIs: First, designation of an API-excipient mixture as an API should not be justified solely by the benefits from a usability perspective [12], [13]. Second, applicants should address concerns related to the GMP standards of API manufacturing facilities [4], [5]. The following proposed path forward is intended to address these two hurdles.
For biological products, the use of formulated APIs is a generally accepted common practice, originally mandated by the stability behavior of the proteins. Oligonucleotides are generally stable in formulation; however, certain factors can impact stability. For example, the pH of the formulation strongly influences oligonucleotide degradation [14] and the addition of buffers to an oligonucleotide API can have a stability benefit. For example, Poecheim et al. showed in 2018 that buffered solutions of a model oligonucleotide API show superior stability behavior compared to the aqueous solution [15]. Furthermore, while a solid API is typically stable when stored at -20°C, the use of a buffered solution may allow storage and shipment at 2°C to 8°C or even at room temperature, which is of high relevance for oligonucleotides manufactured at a larger scale. The stability promoting properties conferred by a buffered formulation support use of formulated oligonucleotide APIs as a meaningful option.
In order to address the requirements defined in the QWP Q&A, stability data should be generated for both the API (in solid state or in water) and the formulated API under ICH long-term conditions for up to 6 months. If it can be demonstrated that the formulated API provides superior or equivalent stability behavior, the use of formulated API should be permissible. In case the stability behavior is equivalent, the authors propose that additional aspects can be considered for justification, as detailed below.
If the API is isolated as a solid, the solid API can be used for the stability comparison with the formulated API. If the API is processed further as an aqueous solution, without isolation, the API in water can be used for comparison with the formulated API.
Oligonucleotide APIs in water should not be considered as API mixtures. The oligonucleotide in water is isolated as such from the API manufacturing process, and hence water is not added as a first (and new) excipient to the final API. An oligonucleotide API in its solid state can contain up to 20% of water, and water is an integral part of the nucleic acid structure [16]. Therefore, an oligonucleotide API can be considered as an amorphous hydrate [17].
Indeed, this concept can be extended further. Downstream processing following oligonucleotide synthesis may afford an API in a solution containing so called processing salts (e.g., phosphates), which are present due to their necessity in the process. Examples could include use of a buffer to control pH, or utilization of salts from a previous chromatographic step to maintain adequate flux during UF/DF. If these components are also required as part of the drug product formulation, it should not be necessary to remove them from the API in solution, and they would consequently be part of the final composition. In such cases, an API with processing salts in water, requiring further compounding and/or dilution at the drug product stage, can be designated as an API, and not a formulated API. This is justified because the API, even if lyophilized, would not be isolated without these processing salts.
In addition to the stability and formulation considerations detailed above, a comprehensive control strategy should be implemented. The control strategy will mitigate any potential risk inherent to the management and addition of excipients as part of the formulated API manufacturing process. The elements of the control strategy include design of the manufacturing process (e.g. closed or controlled manufacturing systems), design of manufacturing facilities and utilities, and implementation of appropriate quality systems (“fit-for-purpose approach in application of GMP” [3]). They are complemented with risk assessments and implementation of risk mitigation activities (“use of risk-based approaches to manufacturing processes and control strategies” [3]), and evaluation of process validation results to ensure sufficient controls are in place. In totality, the control strategy demonstrates delivery of safe and efficacious product. In detail:
• Manufacturing facilities should be used that allow handling of excipients under appropriate GMP standards.
• Purification and final dispensing operations are typically carried out in a multi-product facility with established product segregation procedures. The facility design and controls developed should support the manufacture of low bioburden formulated APIs.
• Microbial controls incorporated into the process should assure consistent delivery of low bioburden, low endotoxin formulated API appropriate for further parenteral drug product processing. The microbial control strategy should be risk-based and include elements of facility design, process controls, personnel requirements, environmental and utility monitoring systems and procedural responses to contamination.
• Excipients used in the manufacture of drug substance could be controlled as critical raw materials. Following the standards defined in EU Directive 2001/83/EC, Annex I, Section [18], “the specifications (of the used excipients) and their justifications shall be detailed. The analytical procedures shall be described and duly validated”. The used excipients should be handled in a facility offering an appropriate clean area concept as per ISO [4] and EU guidance on GMP [5].
• In compliance with the EMA guideline on water for pharmaceutical use, dated 2020, [19], it is proposed to use water for injection (WFI) starting with the UF/DF of the formulated oligonucleotide API, as the WFI will remain in the final medicinal product. The steps prior to UF/DF need not use WFI.
• API manufacturing process risk assessments should cover the whole process down to the formulated API: Risk assessments should show no high-risk parameters in the API manufacturing process. The downstream process must be adequately characterized and controlled to consistently produce API meeting its quality targets.
• The Quality Management System (QMS) should support all operations associated with raw material receipt/inspection, production, packaging, labeling, Quality Control testing, product disposition, release, storage, and distribution of GMP materials.
• Process validation of the formulated API manufacturing process must be performed to ensure the process consistently meets its quality targets.
The requirements for formulated APIs detailed above will provide sufficient controls to permit their production at the site of API manufacture.
The authors would like to comment on the fact that a justification for using formulated APIs based only on workability reasons, e.g., to ease handling prior to processing into the final dosage form, is not currently accepted by EMA. Specifically, advantages of a formulated API, such as reduced environmental impact (“support the development of greener manufacturing technologies” [3]) and security of supply could also be considered when justifying the chosen formulated API approach. In addition, if the use of a formulated API affords a demonstrable benefit to the quality of the API and/or drug product, factors other than stability could be considered as appropriate justification. These could include improvements in purity or yield, or introduction of innovative manufacturing processes enhancing the state of the art.
In general, lyophilization is defined as a stabilizing process in which the sample is frozen followed by a reduction of the solvent content by sublimation and then by desorption to values that will no longer allow biological growth or chemical reactions [20]. If microbial growth can be controlled using measures discussed above, and lyophilization is not needed for suppression of degradation, then lyophilization essentially represents additional handling steps and a stress to the API. It is furthermore a highly energy-consuming unit operation. Unless there are clear benefits for transportation and supply chain (see detailed discussion by Muslehiddinoglu et al [2]), skipping the lyophilzation step is in alignment with the aspiration to promote greener manufacturing approaches [3].
As noted in the QWP Q&A [12], “for APIs of an explosive nature the use of an API mix may be justified, and an appropriate explanation is considered sufficient”. Therefore, if powder explosivity data on the API demonstrate a potential safety hazard to pharmaceutical operators, it may be necessary to keep the API in solution during the process, leading to either a partially or fully formulated API, or else an API in water or containing processing salts, as the most pragmatic solution.
Some additional selected aspects are briefly discussed below to promote further alignment.
Regulatory documentation
The location of formulated API-specific information in module 3 of the CTD is provided in Table 1 below. Other locations in the application may be possible in alignment with ICH M4Q [21].
Table 1: Formulated API-specific information and location in module 3 of CTD
CTD section Content Comment
3.2.S.2.2 Description of formulated API manufacture: Oligonucleotide (solid phase) synthesis, cleavage, purification, potential coupling to obtain conjugates, ultrafiltration/diafiltration, concentration, potential annealing, concentration, mixing with excipients Used processing salts (remaining in the drug product) and excipients should be listed in 3.2.P.1 [12]. Their contribution to the drug product composition should be provided.
3.2.S.2.3 Specifications of the materials used to manufacture the formulated API should be provided in this section. This includes the used excipients. Used processing salts and excipients and reference to relevant standards will also be provided in 3.2.P.1
3.2.S.2.6 Justification of formulated API approach, including comparative stability data demonstrating favorable behavior of formulated API compared to API in solid state/in water. Other quality-based justifications (e.g., improvement in overall purity of final drug product) could also be included in this section.
Summary of API manufacturing process risk assessments and process characterization studies to ensure process robustness, including API formulation consistency and microbial attributes. Extractable and leachable substances (if in bags), endotoxin clearance, excipient selection, and API container closure integrity.
Other aspects, such as environmental impact, safety, supply security benefits
Safety-based if this is the principal justification for the API mix. Tight linkage with discussion provided in 3.2.P.2
3.2.S.7.x Re-test period, storage conditions and stability data of the formulated API Information on the formulated API (which is the designated API). Comparative stability data is provided in 3.2.S.2.6
3.2.P.1 Composition, including processing salts and excipients added to the drug substance when manufacturing the formulated API Processing salts and excipients used in the manufacture of the formulated API contribute to the composition of the finished product and should be listed on the label
3.2.P.2.1 Justification of choice and level of excipient Discussion expected to be linked to discussion in 3.2.S.2.6 (e.g., for selected buffers)
When a partially formulated API is used, the choice and level of excipient used in the drug product manufacture should be justified.
3.2.P.2.5 Microbial attributes and control
Microbial attributes discussion in 3.2.P.2 should also include the excipient used in the formulated API in relation to the microbial attributes relevant to the final drug product Tight linkage with information provided in 3.2.S.2.6
3.2.P.3.2 Batch formula of drug product manufacture, starting from the formulated API Formulated API amount, any additional excipients, and/or WFI added as part of DP manufacture
3.2.P.3.3 Description of drug product filling process The drug product manufacturing process consists of the potential addition of further excipients to the formulated API, sterile filtration and aseptic filling. Thawing/equilibration may not be needed if formulated API can be stored at room temperature
3.2.P.8.1 Definition of shelf-life and storage condition Shelf-life starts with the first step of the drug product manufacturing process, i.e., the use of the formulated API

Characterization of API
It is proposed to characterize the API at the stage where it is most suitable. For example, for siRNAs, it may be best to run certain characterization tests at the single strand stage and some others at an annealed stage. For certain parameters of formulated oligonucleotide API, characterization using the solid API may be preferred, for other parameters using dissolved API may be appropriate, and certain tests, like stereogenic composition, can only be performed during synthesis development studies, and not as an end-product test. Therefore, flexible approaches using scientific reasoning can be justified.
A discussion should be provided in section 3.2.S.3.1 if processing salts and excipients added to the formulated API have an impact on the characterization.
Control strategy
Release of API
Release testing per CTD section 3.2.S.4.1 should be performed using the formulated API. The formulated API should be analyzed for identity and content (or relative concentration in final API mix) of excipients used in its manufacture. As proposed above in the section on characterization, certain release tests may be performed upstream in lieu of testing of the formulated API. In addition, the use of Process Analytical Technology (PAT), e.g. for real-time confirmation of sequence identity, may be implemented as part of the synthesis.
Drug product manufacture
The start of the drug product manufacture will be defined by the introduction of the formulated API into further processing steps, i.e., with the potential supplemental addition of excipients required for the finished product formulation and/or prior to the sterile filtration and aseptic filling. The start of the drug product manufacture is also the proposed start of the drug product shelf-life and the proposed start of the drug product manufacturing process.
Processing salts and excipients used in the manufacture of the formulated API, as well as potential additional excipients introduced in the drug product manufacture before filling are required to be listed on the label. In countries where the country of origin has to be provided on the label, only the country of origin of the (formulated) API will be provided; the country of origin of the excipients will not be provided, as the API is defined as the molecule of action.
Summary and conclusions
A formulated API approach for oligonucleotides can provide benefits in terms of quality and safety of the drug. Specifically, a formulated API can provide improved stability, yield, and purity. Greener and safer manufacturing standards may be achieved. The concept also aligns with generally accepted common practices for biological products. From this perspective, based on the nature of the oligonucleotide molecule, the concept should also be generally acceptable for oligonucleotide APIs. Therefore, it should be acceptable to develop and commercialize formulated APIs under the standards described in this manuscript, and upon presentation of positive supportive data serving as a justification.
The EPOC group welcomes further interaction and discussion with regulators to promote the use of the formulated API approach in oligonucleotide drug manufacture. Further, the authors recommend that relevant guidance documents be modernized so that they better reflect the specific needs of therapeutic oligonucleotide manufacture, as outlined in this manuscript.
The authors thank the European Pharmaceutical Oligonucleotide Consortium (EPOC) Steering Committee and other experts in the field for providing insights and comments.
Active pharmaceutical ingredient (API)
In the context of this paper, an API can be an API alone, or can be the API in water with or without processing salts. The processing salts are used in and are needed for the API manufacturing and purification process, e.g., for the UF/DF step.
Depending on the jurisdictions the terms active substance or drug substance are preferred. In the context of this paper, the three terms can be used interchangeably.
Formulated API
A formulated API is a mixture of the API with processing salts and excipients in water and will be presented in 3.2.S of the marketing application dossier. It contains some (partially formulated API) or all (fully formulated API) excipients of the final drug product. The formulated API may be ready-to-fill (fully formulated API), or may require further dilution or addition of excipients (partially formulated API).
Excipients vs processing salts
A processing salt is used in and needed for the drug substance manufacturing or purification process and will not be removed in the last purification or filtration step yielding the API. An excipient is a drug product component added to the API solution after the final purification or filtration step. The processing salts will typically appear in 3.2.P.1 and on the label together with the other excipients.
Drug product intermediate
Formulated APIs are not considered as drug product intermediates.
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Item Type: Article
Date Deposited: 17 May 2022 00:45
Last Modified: 17 May 2022 00:45