10 Steps to Control or Eliminate Genotoxic Impurities in API Manufacturing

Much of the concern in drug substance manufacturing pertains to impurities, which can be a byproduct of the numerous reactive chemicals such as solvents, catalysts and reagents used in the synthesis and manufacture of APIs.  They may also be the result of degradation and the various processes involved in creating New Chemical Entities (NCEs). Impurities reside in just about all drug substances and associated drug products. However, they are held to the lowest acceptable levels by regulatory agencies.

According to ICH guidelines, impurities related to drug substances are generally classified into three main categories: organic impurities, elemental impurities, and residual

solvents.  Within these categories, genotoxic impurities are in a somewhat gray area.  They’re of great concern because even at low concentrations, they can pose significant health risks due their potential to damage DNA, which can lead to mutations and/or cancers.

Genotoxicity refers to all types of DNA damage, regardless, of how the toxic change occurred.  Because genotoxic compounds induce genetic mutations and chromosomal rearrangements which may be carcinogenic, they trigger regulatory concerns worldwide in an effort to limit their potential risk. For example, several months ago the FDA initiated an investigation of diabetes drug Metformin when samples sold in the U.S. were found to contain the carcinogen N-Nitrosodimethylamine (NDMA). The drug has not been pulled off the market.

The most recent guidance on genotoxicity, which we at Seqens North America adhere to  closely, was issued to the FDA in 2018 in a document entitled “M7(R1) Assessment and Control of DNA Reactive (Mutagenic) Impurities in Pharmaceuticals To Limit Potential Carcinogenic Risk: Guidance for Industry.”

Interestingly, the FDA’s guidance does not establish legally enforceable responsibilities, but rather reflects the Agency’s current recommendations.  A primary concern of M7(R1) is identification of the steps where genotoxic compounds could be introduced or created during the manufacturing process.

Genotoxicity in later stage programs

We have found that genotoxicity is not a big issue in early stage programs. It’s usually in later stage programs, in scale-up and manufacturing, that genotoxic impurities may be detected.  

In early drug substance development, methods are developed relatively quickly. In these early stages of development both in-house and sponsors’ technical experts can be expected to evaluate genotoxicity.  This evaluation is often based on a literature review of the compounds and the chemical structures anticipated in drug production.  The early stage process takes a bird’s eye view from 50,000 feet up in the air, doing a gross analysis.

That changes when moving into GMP manufacturing.  Here we are looking at finite levels, perhaps 1/10 of 1 percent, and using more sophisticated instruments to find, and isolate, potential carcinogens.

As programs move to larger scale, purity profiles, analytic methods and process- derived
impurities must be screened for genotoxicity. 

10 steps to reducing the incidence of genotoxic impurities

  1. Source and examine raw materials carefully.  Attempts to reduce genotoxic impurities begin, as every program does, in sourcing raw materials.  In addition to sampling, carefully review the Bill of Goods.
  2. Research levels of any unknown or questionable impurities that arise in the literature.
  3. Classify impurities based on their potential for carcinogenicity.
  4. Be aware of the potential mutagenicity of reagents and compounds utilized at any point in synthesis.
  5. Become well versed in the types of molecules that could be genotoxic and their structure.
  6. Establish a Threshold of Toxicological Concern (TTC) for unstudied chemicals, even those with a negligible risk for carcinogenicity or other toxic effects.
  7. Develop a control strategy to assure that any impurities remain below the TTC. 
  8. Assess the risk of transformation from non-toxic to genotoxic compounds
    at every stage of chemical synthesis and manufacturing.
  9. Employ an Ames test to determine the severity of a potentially genotoxic impurity. 
  10. Assess whether the potentially genotoxic impurity can be eliminated or reduced to an acceptable level.

A multifaceted approach is required

In small molecule synthesis, the good news is that genotoxic impurities don’t surface all that frequently.  However, always be on the lookout for them, employing the 10 steps above to identify and mitigate risk. Also consider this multifaceted general approach:

  1. Marshal experts, including mining your in-house and sponsor expertise as well as that found in the literature.
  2. Use available technical tests, some of which require specialized equipment.
  3. Evaluate the test data and taking action as necessary.
  4. Ask anticipatory questions, such as what level might we expect at scale-up, and if that level is unacceptable, determine how to remove the impurity.
  5. Attempt to limit the 15-20 percent loss of yield that occurs when removing a genotoxic impurity.


Careful consideration of genotoxicity, appropriate identification of
genotoxic impurities, options for assessment and control of impurities, and
steps to control risk are all priorities in drug development.  We’d be happy to talk with you about ways we can coordinate efforts to help you optimize processes to produce a safe and effective product. Drop us a line at info@pcisynthesis.com or call us at (978) 462-5555.