Vol 54: Best Practices for Addressing Impurities in CMC Submissions: A Short Comprehensive Guide for INDs and NDA/BLAs

May 24, 2023The Pathfinder 39 Min Read

Best Practices for Addressing Impurities in CMC Submissions: A Short Comprehensive Guide for INDs and NDA/BLAs in General


Impurities in pharmaceutical products can significantly impact their safety, efficacy, and quality. Therefore, addressing impurities is a crucial aspect of Chemistry, Manufacturing, and Controls (CMC) submissions for both Investigational New Drug (IND) applications and New Drug Application/Biologics License Application (NDA/BLA) submissions. To navigate this complex process successfully, following best practices and regulatory guidelines is essential. 


“Unlocking the Secrets of Impurities: Conquering CMC Submissions for a Flawless Pharmaceutical Future!”


This blog article will explore the best practices for addressing impurities in CMC submissions, focusing on INDs and NDA/BLAs. We will delve into the importance of understanding regulatory guidelines, early impurity profiling, risk assessment, stability studies, analytical method validation, documentation, and collaboration. By implementing these practices, pharmaceutical companies can effectively manage impurities throughout drug development and ensure compliance with regulatory requirements.


“Unmasking Impurities: Mastering the Art of CMC Submissions for a Spotless Pharmaceutical Future”


Additionally, we will discuss the distinction between identified and unidentified impurities and when each requires qualification. We will explore the significance of toxicological evaluations, their impact on efficacy, and the need for investigating and characterizing unidentified impurities. Understanding the qualification process for impurities helps companies demonstrate their commitment to product safety and efficacy and facilitates successful CMC submissions.

At the end of the article, we will refer to key guidance documents issued by regulatory authorities such as the International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use (ICH), the United States Food and Drug Administration (FDA), and the European Medicines Agency (EMA). These guidelines provide invaluable recommendations on impurity control strategies, acceptance criteria, analytical methodologies, stability studies, qualification processes, and reporting requirements.

By following the best practices and regulatory guidelines outlined in this article, pharmaceutical companies can effectively manage impurities in their CMC submissions, leading to the development and approval of high-quality, safe, and effective pharmaceutical products.


The Management and Control of Impurities


One of the critical aspects of CMC submissions is the management and control of impurities. Impurities in drug substances and drug products can arise from various sources and have the potential to impact the safety, efficacy, and quality of the final product. To ensure successful IND applications and New Drug Application/Biologics License Application submissions, following best practices for addressing impurities is vital.

  • Understanding the Regulatory Guidelines

The first step in addressing impurities is to thoroughly understand the regulatory guidelines provided by regulatory authorities such as the U.S. FDA, the EMA, and other relevant authorities. These guidelines outline the acceptable limits, identification, and qualification requirements for impurities in pharmaceutical products. Familiarize yourself with these guidelines to ensure compliance and avoid unnecessary delays in the submission process.

  • Early Impurity Profiling

Impurity profiling should begin early in the drug development process. Conduct a comprehensive characterization of potential impurities from starting materials, synthetic routes, reagents, and degradation products. Analytical methods like high-performance liquid chromatography (HPLC), gas chromatography (GC), and mass spectrometry (MS) should be employed to detect and quantify impurities. Early identification of potential impurities helps in devising effective strategies for their control.

  • Risk Assessment and Control Strategies

Perform a risk assessment to determine the potential impact of impurities on the quality, safety, and efficacy of the drug product. Identify critical impurities and set appropriate specifications to control them. Develop control strategies, including suitable synthetic processes, purification techniques, and storage conditions to minimize or eliminate impurities. Utilize Quality by Design (QbD) principles to establish control strategies based on scientific understanding and risk mitigation.

  • Stability Studies

Stability studies are essential to assess the degradation pathways and profile of impurities over the shelf life of the product. Conduct stress testing under various conditions (e.g., temperature, humidity, light) to induce accelerated degradation and identify degradation products. This information aids in setting appropriate specifications and establishing suitable storage conditions to prevent the formation of impurities during product storage.

  • Analytical Method Validation

Validated analytical methods are crucial for accurately detecting, quantifying, and characterizing impurities. Ensure that the analytical methods used to monitor impurities are adequately validated according to regulatory guidelines. Method validation should include specificity, linearity, accuracy, precision, and robustness. Regularly verify the performance of analytical methods throughout the development process.

  • Documentation and Reporting

Maintain detailed documentation of all impurity-related activities, including method development, validation, and impurity profiling. Ensure that the impurity-related information is reported in the CMC section of INDs and NDA/BLAs. Provide a comprehensive impurity control strategy and data on impurity identification, characterization, and quantification. Justify the control strategies and specifications based on scientific rationale and risk assessment.

  • Collaboration and Communication

Effective communication and collaboration between different departments within the organization and with regulatory authorities are critical. Establish cross-functional teams involving experts from analytical chemistry, process development, formulation, and regulatory affairs to address impurity-related issues collectively. Timely communication with regulatory authorities regarding impurity concerns or changes in control strategies can help prevent surprises during the review


How and When to Identify Impurities


The identification of impurities is a critical step in the CMC submission process. It involves the characterization and understanding of impurities present in drug substances and drug products. Here are some vital considerations for identifying impurities:

1.    Analytical Techniques: Utilize advanced analytical techniques such as HPLC, GC, MS, nuclear magnetic resonance (NMR), and Fourier-transform infrared spectroscopy (FTIR) to identify impurities. These techniques enable the separation, quantification, and structural elucidation of impurities.

2.    Reference Standards: Employ reference standards for impurity identification. Compare the impurity peaks’ retention time, peak purity, spectral characteristics, and chromatographic behavior with those of authentic reference standards. This helps in confirming the identity of known impurities.

3.    Comparative Studies: Perform comparative studies between impurity profiles of drug substances and products manufactured using different synthetic processes, manufacturing sites, or batches. This aids in identifying and understanding the sources of impurities.

4.    Forced Degradation Studies: Conduct forced degradation studies under various stress conditions (e.g., heat, humidity, light, acid/base hydrolysis) to induce degradation and generate impurities. By analyzing the degradation products, you can identify potential impurities that may arise during the drug’s lifecycle.

5.    Literature Review: Refer to scientific literature, compendia, and databases to gather information on known impurities reported for similar drug substances or related compounds. This can provide valuable insights into potential impurities that may arise during the manufacturing process.


Identified versus Unidentified Impurities


Impurities can be broadly categorized as identified or unidentified based on their known or unknown structures. Understanding the difference between these two types is essential for effective impurity control:

1.    Identified Impurities: These are impurities for which the chemical structure and identity are known. Identified impurities can include known starting material impurities, intermediate impurities, degradation products, or impurities introduced during manufacturing. The structure and characteristics of identified impurities should be well-documented, and their control strategies should be established to ensure compliance with regulatory guidelines.

2.    Unidentified Impurities: Unidentified impurities refer to impurities whose chemical structure and identity are not known or not fully characterized. They may appear as unknown peaks during analysis or at trace levels. Unidentified impurities can arise from various sources, including process-related impurities or impurities formed during storage or degradation. It is essential to investigate and characterize these impurities to assess their potential impact on product quality and safety. Techniques such as advanced spectroscopic methods, mass spectrometry, and other advanced analytical tools can be employed for their identification.

Addressing unidentified impurities requires a systematic approach, including isolation, purification, and characterization. These impurities should be monitored, and their levels should be controlled to acceptable limits. In some cases, further toxicological assessments and impurity qualification may be necessary if unidentified impurities are present at significant levels or suspected to be potentially harmful.


When Impurities Need to be Qualified


Regarding the qualification of impurities, both identified and unidentified impurities may need to be addressed based on regulatory requirements. Here’s a closer look at when impurities need to be qualified according to regulations:

Identified Impurities:

•    Known Safety Concern: If an identified impurity is known or suspected of a safety concern, it should be subjected to a thorough toxicological evaluation. Regulatory authorities may require qualification data, including genotoxicity studies, to assess the potential risks associated with the impurity. The qualification process involves establishing an acceptable limit for the impurity based on its toxicological profile and ensuring that the impurity remains within that limit during manufacturing and throughout the product’s lifecycle.

•    Impact on Efficacy: Identified impurities that can potentially affect the drug product’s efficacy may also need to be qualified. In such cases, additional studies may be required to assess the impact of the impurity on the therapeutic activity or performance of the drug. These studies help determine whether the impurity needs to be controlled to a specific limit or eliminated.

Unidentified Impurities:

•    Significant Levels: Unidentified impurities present at significant levels, even if their structures are unknown, may require further investigation and qualification. These impurities can impact product safety or efficacy, and regulatory authorities may request additional data to assess their potential risks. This can involve isolation, purification, and structural elucidation of the impurities to understand their nature and establish their qualification status.

•    Known Impurities in Unknown Structure: In some cases, an impurity may be known but not fully characterized, meaning its exact structure is not determined. If such impurities are present at levels of concern, regulatory authorities may require efforts to identify and characterize the impurity to evaluate its impact on product quality, safety, or efficacy. This may involve applying advanced analytical techniques and conducting toxicological studies, if necessary.

It is important to note that the qualification of impurities is a dynamic process and can vary based on different regulatory authorities’ specific regulations and guidelines. Companies should stay updated on the latest regulatory expectations and discuss with regulatory agencies to determine the appropriate qualification strategy for identified and unidentified impurities.

Proactively addressing identified and unidentified impurities through qualification demonstrates a commitment to ensuring pharmaceutical products’ safety, efficacy, and quality, and contributes to successful CMC submissions.


The Guidances to Consider when It Comes to Dealing with Impurities


When dealing with impurities in pharmaceutical products, it is essential to refer to regulatory guidelines and guidance documents issued by regulatory authorities. Here are some important guidances to consider:

International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use (ICH):

•    ICH Q3A(R2): Impurities in New Drug Substances
•    ICH Q3B(R2): Impurities in New Drug Products
•    ICH Q3C(R6): Impurities: Guideline for Residual Solvents
•    ICH Q11: Development and Manufacture of Drug Substances (Chemical Entities and Biotechnological/Biological Entities)

United States Food and Drug Administration (FDA):

•    FDA Guidance for Industry: Q3A Impurities in New Drug Substances
•    FDA Guidance for Industry: Q3B Impurities in New Drug Products
•    FDA Guidance for Industry: Q3C Impurities: Residual Solvents
•    FDA Guidance for Industry: Analytical Procedures and Methods Validation for Drugs and Biologics

European Medicines Agency (EMA):

•    EMA Guideline on the Limits of Genotoxic Impurities
•    EMA Guideline on Setting Health-Based Exposure Limits for Use in Risk Identification in the Manufacture of Different Medicinal Products in Shared Facilities
•    EMA Guideline on Residual Solvents

Pharmacopoeial Monographs:

•    United States Pharmacopeia (USP)
•    European Pharmacopoeia (Ph. Eur.)
•    Japanese Pharmacopoeia (JP)

Other National Regulatory Authorities:

•    Each country may have its specific guidelines and requirements related to impurities. It is important to consult the regulatory authority’s guidance documents for comprehensive information.

These guidance documents provide recommendations on impurity control strategies, acceptance criteria, analytical methodologies, stability studies, qualification processes, and reporting requirements for impurities in drug substances and drug products. They help ensure compliance with regulatory expectations and facilitate the development and approval of pharmaceutical products.

It is crucial to regularly check for updates and revisions to these guidances as regulatory requirements may evolve over time. Additionally, engaging in discussions with regulatory authorities and seeking their input can provide further clarity and guidance specific to your product and development process.

By adhering to these guidelines, pharmaceutical companies can establish robust impurity control strategies and ensure their products’ safety, efficacy, and quality, leading to successful CMC submissions.




Addressing impurities in CMC submissions is paramount for pharmaceutical companies seeking regulatory approval for their products. By following the best practices outlined in this article, companies can establish robust impurity control strategies and ensure their pharmaceutical products’ safety, efficacy, and quality.

Understanding and adhering to regulatory guidelines, conducting early impurity profiling, performing risk assessments, conducting stability studies, and validating analytical methods are critical steps in managing impurities effectively. Thorough documentation, transparent reporting, and proactive communication with regulatory authorities contribute to successful CMC submissions.

The distinction between identified and unidentified impurities requires careful consideration. Identified impurities should undergo toxicological evaluation if they raise safety concerns or may impact product efficacy. Unidentified impurities, especially those at significant levels, require further investigation and characterization to assess their potential risks.

By referring to key guidance documents from regulatory authorities such as ICH, FDA, and EMA, pharmaceutical companies can ensure compliance with regulatory requirements and stay updated on evolving expectations.

Addressing impurities in CMC submissions demonstrates a commitment to patient safety and product quality. By implementing these best practices and following regulatory guidelines, companies can navigate the complex landscape of impurity control, leading to the successful development and approval of pharmaceutical products that meet stringent regulatory standards.



By embracing these guidelines, companies can enhance their understanding of critical quality attributes, implement effective risk management strategies, establish robust quality systems, and manage post-approval changes in a harmonized manner. Staying informed about regulatory changes, engaging in early interactions with regulatory authorities, and leveraging regulatory expertise and partnerships are also crucial elements of a successful CMC regulatory strategy. Ultimately, by adopting a proactive and globally-minded approach, pharmaceutical companies can navigate the complexities of CMC regulations, ensure compliance, and achieve market access in various regions worldwide.

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