Safety Testing of Drug 
Metabolites 
Guidance for Industry 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
U.S. Department of Health and Human Services 
Food and Drug Administration 
Center for Drug Evaluation and Research (CDER) 
 
March 2020 
Pharmacology/Toxicology 
 
Revision 2 
   
Safety Testing of Drug 
Metabolites 
Guidance for Industry 
 
 
 
Additional copies are available from: 
 
Office of Communications, Division of Drug Information 
Center for Drug Evaluation and Research 
Food and Drug Administration 
10001 New Hampshire Ave., Hillandale Bldg., 4th Floor 
Silver Spring, MD  20993-0002 
Phone: 855-543-3784 or 301-796-3400; Fax: 301-431-6353; Email: druginfo@fda.hhs.gov 
https://www.fda.gov/drugs/guidance-compliance-regulatory-information/guidances-drugs 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
U.S. Department of Health and Human Services 
Food and Drug Administration 
Center for Drug Evaluation and Research (CDER) 
 
March 2020 
Pharmacology/Toxicology 
 
Revision 2 
   
TABLE OF CONTENTS 
 
I.  INTRODUCTION............................................................................................................. 1 
II.  BACKGROUND ............................................................................................................... 2 
III.  GENERAL CONCEPTS IN METABOLITE SAFETY TESTING ............................. 3 
A.  General Approaches for Assessing Metabolite Safety ................................................................ 4 
B.  Identification of Metabolites ......................................................................................................... 5 
C.  General Considerations for Nonclinical Study Design ............................................................... 5 
IV.  RECOMMENDED STUDIES FOR ASSESSING THE SAFETY OF 
METABOLITES ............................................................................................................... 6 
A.  General Toxicity Studies ............................................................................................................... 6 
B.  Genotoxicity Studies ...................................................................................................................... 6 
C.  Embryo-Fetal Development Toxicity Studies .............................................................................. 6 
D.  Carcinogenicity Studies ................................................................................................................. 7 
V.  TIMING OF SAFETY ASSESSMENTS ........................................................................ 7 
GLOSSARY................................................................................................................................... 8 
APPENDIX A:  DECISION TREE FLOW DIAGRAM ........................................................... 9 
APPENDIX B:  CASE EXAMPLES OF DRUG METABOLITES ....................................... 10 
 
 
  Contains Nonbinding Recommendations 
Safety Testing of Drug Metabolites 
Guidance for Industry1 
 
 
 
 
This guidance represents the current thinking of the Food and Drug Administration (FDA or Agency) on 
this topic.  It does not establish any rights for any person and is not binding on FDA or the public.  You 
can use an alternative approach if it satisfies the requirements of the applicable statutes and regulations.  
To discuss an alternative approach, contact the FDA office responsible for this guidance as listed on the 
title page. 
 
 
 
 
I.  INTRODUCTION 
 
This guidance provides recommendations to industry on when and how to identify and 
characterize drug metabolites whose nonclinical toxicity needs to be evaluated.  Drug 
metabolites may need to be determined in nonclinical studies when they are disproportionate 
drug metabolites, that is, metabolites identified only in humans or present at higher plasma 
concentrations in humans than in any of the animal species used during standard nonclinical 
toxicology testing.2 
 
This guidance applies to small molecule nonbiologic drug products.  This guidance does not 
apply to some cancer therapies.3 
 
This guidance supersedes the guidance of the same name published in November 2016.  The 
guidance has been revised to align with the ICH guidance for industry M3(R2) Nonclinical Safety 
Studies for the Conduct of Human Clinical Trials and Marketing Authorization for 
Pharmaceuticals (January 2010). 
 
In general, FDAs guidance documents do not establish legally enforceable responsibilities.  
Instead, guidances describe the Agencys current thinking on a topic and should be viewed only 
                                                 
1 This guidance has been prepared by the Pharmacokinetic Subcommittee of the Pharmacology and Toxicology 
Coordinating Committee in the Center for Drug Evaluation and Research at the Food and Drug Administration.  
You may submit comments on this guidance at any time.  Submit comments to Docket No. FDA-2008-D-0065 
(available at https://www.regulations.gov/docket?D=FDA-2008-D-0065).  See the instructions in that docket 
for submitting comments on this and other Level 2 guidances. 
 
2 See the Glossary for the definition of disproportionate drug metabolite. 
 
3 See the ICH guidance for industry S9 Nonclinical Evaluation for Anticancer Pharmaceuticals (March 2010) for 
the safety testing of drug metabolites in cancer therapies.  We update guidances periodically.  To make sure you 
have the most recent version of a guidance, check the FDA guidance web page at https://www.fda.gov/regulatory-
information/search-fda-guidance-documents. 
  1  Contains Nonbinding Recommendations 
as recommendations, unless specific regulatory or statutory requirements are cited.  The use of 
the word should in Agency guidances means that something is suggested or recommended, but 
not required. 
 
 
II.  BACKGROUND 
 
Nonclinical evaluation of drug safety usually consists of standard animal toxicology studies.4  
These studies usually include assessing drug exposure, primarily parent drug plasma 
concentration.  Generally, drug plasma concentration and systemic exposure in the nonclinical 
studies are compared with systemic exposure in humans to assess the potential risks suggested by 
nonclinical findings and guide monitoring in clinical trials.  This testing paradigm usually is 
sufficient when the metabolic profile in humans is similar to that in at least one of the animal 
species used in nonclinical studies, but metabolic profiles can vary across species both 
quantitatively and qualitatively, and there are cases for which clinically relevant metabolites 
have not been identified or adequately evaluated during nonclinical safety studies.  This situation 
can occur if the metabolite is formed only in humans and is absent in the animal test species or if 
the metabolite is present at higher levels in humans than in the animal species used in the 
standard toxicology testing with the parent drug.  Such a metabolite is called a disproportionate 
drug metabolite. 
 
It is not standard practice for drug metabolites to be evaluated separately in a cross-species safety 
assessment.  As a result, their specific contribution to the overall toxicity of the parent drug has 
often remained unknown.  This lack of understanding about the role of metabolites in drug 
toxicity may partly reflect the inadequate sensitivity of the analytical methods used to detect and 
characterize metabolites derived from the parent drug.  Technological advances, however, have 
greatly improved the analytical abilities to detect, identify, and characterize metabolites and may 
allow a better understanding of the role metabolites play in drug safety assessment. 
 
Drugs entering the body undergo biotransformation via phase 1 and phase 2 metabolic pathways.  
Based on the nature of the chemical reactions involved, metabolites formed from phase 1 
reactions are more likely to be chemically reactive or pharmacologically active and, therefore, 
more likely to need safety evaluation.  A pharmacologically active metabolite may bind to the 
therapeutic target receptors or other receptors, interact with other targets (e.g., enzymes, 
proteins), and cause unintended effects.  This is a particularly important problem when such a 
metabolite is formed in humans and not in animals, but the occurrence of a metabolite only in 
humans and not in any animal test species is rare.  A more common situation is the formation of 
a metabolite at higher levels in humans than in the animal species used in safety testing of the 
parent drug.  This stems from qualitative and/or quantitative differences in metabolic profiles 
between humans and animals.  If at least one animal test species forms this drug metabolite at 
adequate exposure levels (approximately equal to or greater than human exposure), as 
                                                 
4 See the ICH guidances for industry S6 Preclinical Safety Evaluation of Biotechnology-Derived Pharmaceuticals 
(July 1997) and S7A Safety Pharmacology Studies for Human Pharmaceuticals (July 2001). 
 
  2  Contains Nonbinding Recommendations 
determined during toxicology testing of the parent drug, it can be concluded that the metabolites 
contribution to the overall toxicity assessment has been established.5 
 
Metabolites that form chemically reactive intermediates can be difficult to detect and measure 
because of their short half-lives.  In some cases, however, they can form stable products (e.g., 
glutathione conjugates) that can be measured.  Phase 2 conjugation reactions generally render a 
compound more water soluble and pharmacologically inactive, thereby eliminating the need for 
further evaluation.  However, if the conjugate forms a potentially toxic compound such as acyl 
glucuronide, additional safety assessment may be needed.6 
 
Since general toxicity studies are designed to assess both target and off-target toxicity of the 
drug, demonstrating that a metabolite is pharmacologically inactive at the target receptor (or 
even that it does not meaningfully bind to a receptor or enzyme in a screening test) is not 
sufficient to ensure that the metabolite is not toxic.  Therefore, it may need to be tested in 
nonclinical toxicity studies.7 
 
 
III.  GENERAL CONCEPTS IN METABOLITE SAFETY TESTING 
 
We encourage identifying any differences in drug metabolism between animals used in 
nonclinical safety assessments and humans as early as possible during the drug development 
process.8  Discovering such differences in drug metabolites late in drug development can cause 
development delays. 
 
Generally, metabolites identified only in human plasma or metabolites present at higher levels in 
humans than in any of the animal test species should be considered for safety assessment.  Such 
metabolites are called disproportionate drug metabolites.  Human metabolites that can raise a 
safety concern are those present at greater than 10 percent of total drug-related exposure at 
steady state.9 
                                                 
5 See Appendix A:  Decision Tree Flow Diagram.  This diagram describes which studies may be needed to 
determine safety of the drug metabolite. 
 
6 Faed, EM, 1984, Properties of Acyl Glucuronides:  Implications for Studies of the Pharmacokinetics and 
Metabolism of Acidic Drugs, Drug Metab Rev, 15, 12131249. 
 
7 See Appendix B:  Case Examples of Drug Metabolites. 
 
8 Baillie, TA, MN Cayen, H Fouda, RJ Gerson, JD Green, SJ Grossman, LJ Klunk, B LeBlanc, DG Perkins, and LA 
Shipley, 2002, Drug Metabolites in Safety Testing, Toxicol Appl Pharmacol, 182(3), 188196; and Hastings, KL, J 
El-Hage, A Jacobs, J Leighton, D Morse, and RE Osterberg, 2003, Drug Metabolites in Safety Testing, Toxicol 
Appl Pharmacol, 190(1), 9192. 
 
9 Exposure should be at steady state unless there is some justification for a different measure of exposure.  
Comparison between human and animal exposure generally is based on area under the curve, but sometimes it may 
be more appropriate to use C .  See ICH M3(R2). 
max
 
  3  Contains Nonbinding Recommendations 
The choice of a level of greater than 10 percent for characterization of drug metabolites reflects 
consistency with FDA10 and Environmental Protection Agency guidances.11 
 
A.  General Approaches for Assessing Metabolite Safety 
 
A metabolite identified in animals that is not present in humans can mean that a toxicity 
observed in that animal species, and that can be attributed to the metabolite, may not be relevant 
to humans.  Conversely, a drug metabolite identified during clinical development that is not 
present in animal test species or is present at much lower levels in animals than in humans can 
suggest the need for further studies in animals to determine the potential toxicity of the 
metabolite.  In such cases, sponsors can consider two approaches to assessing the effect of the 
drug metabolite.  The first approach is to identify an animal species routinely used in toxicity 
studies that forms the metabolite at adequate exposure levels (equivalent to or greater than the 
human exposure), and then investigate the drugs toxicity in that species.  The second approach, 
if a relevant animal species that forms the metabolite cannot be identified, is to synthesize the 
drug metabolite and directly administer it to the animal for further safety evaluation.  In this 
approach, analytical methods that are capable of identifying and measuring the levels of the 
metabolite in the nonclinical toxicity studies should be developed. 
 
We acknowledge the difficulties associated with synthesizing a specific metabolite as well as the 
inherent complexities that accompany its direct administration.  Direct dosing of a metabolite to 
animals may lead to subsequent metabolism that may not reflect the clinical situation and thus 
may complicate the toxicity evaluation.  Moreover, new and different toxicities may arise from 
administration of the metabolite that were not observed with the parent drug.  However, 
notwithstanding these possible complications, identifying and evaluating the potential toxicity of 
the drug metabolite is considered important to ensure clinical safety, and the decision to conduct 
direct safety testing of a metabolite should be based on a comprehensive evaluation of the data 
on the parent drug and any information available for the metabolite. 
 
Appendix B provides three case examples when drug metabolites were formed at higher levels in 
humans than in test animals used in the nonclinical studies and how the safety evaluation was 
approached.  In Case 1, testing the drug metabolite was not needed because the metabolite was 
adequately characterized in nonclinical toxicity studies with the parent drug.  However, in Cases 
2 and 3, the drug metabolites had to be tested in toxicity studies by direct administration to the 
                                                 
10 See the Veterinary International Conference on Harmonization guidances for industry GL46 Studies to Evaluate 
the Metabolism and Residue Kinetics of Veterinary Drugs in Food-producing Animals:  Metabolism Study to 
Determine the Quantity and Identify the Nature of Residues (MRK) (September 2011) and GL47 Studies to Evaluate 
the Metabolism and Residue Kinetics of Veterinary Drugs in Food-Producing Animals:  Comparative Metabolism 
Studies in Laboratory Animals (September 2011) available on the Veterinary International Conference on 
Harmonization (VICH) Guidance Documents web page at https://www.fda.gov/animal-veterinary/guidance-
industry/veterinary-international-conference-harmonization-vich-guidance-documents. 
 
11 U.S. Environmental Protection Agency, 1998, Health Effects Test Guidelines, OPPTS 870.7485, Metabolism and 
Pharmacokinetics (https://www.epa.gov/test-guidelines-pesticides-and-toxic-substances/series-870-health-effects-
test-guidelines). 
 
  4  Contains Nonbinding Recommendations 
animal.  In Case 3, the drug metabolite was pharmacologically inactive at the therapeutic target 
receptor but showed a unique toxicity not observed with the parent molecule. 
 
B.  Identification of Metabolites 
 
Sponsors should identify the metabolic profile of the drug during the drug development process.  
This identification can be accomplished at different stages of development using in vitro and in 
vivo methods.  In vitro studies can use liver microsomes, liver slices, or hepatocytes from 
animals and humans; these studies should generally be conducted before initiating clinical trials.  
In vivo metabolism study results in nonclinical test species generally should be available early in 
drug development, and their results will either confirm the results obtained from the in vitro 
studies or reveal quantitative and/or qualitative differences in metabolism across species.  It is 
the latter situation that may pose a safety concern.  Usually, sponsors have conducted human in 
vivo metabolism studies relatively later in drug development, but we strongly recommend that 
sponsors conduct in vivo metabolic evaluation in humans as early as feasible. 
 
The adequacy of exposure to drug metabolites that are present at lower levels in animals used in 
nonclinical studies is determined on a case-by-case basis.  Generally, systemic exposure is 
assessed by measuring the concentration of the parent drug at steady state in serum or plasma.12  
However, when measurements cannot be made in plasma of the test species for any reason, 
adequate exposure can be verified in other biological matrices such as urine, feces, or bile.13  We 
encourage sponsors to contact the FDA early in drug development to discuss these issues. 
 
C.  General Considerations for Nonclinical Study Design 
 
When designing a nonclinical study for a disproportionate drug metabolite, one should consider 
the following factors: 
 
  Similarity of the metabolite to the parent molecule 
  Pharmacological or chemical class 
  Solubility 
  Stability in stomach pH 
  Phase 1 versus phase 2 metabolite 
  Relative amounts detected in humans versus the amounts detected in animals 
 
Additional factors to be considered include the proposed drug indication and patient population 
(e.g., nonclinical studies can be abbreviated for serious indications such as amyotrophic lateral 
                                                 
12 Although the drug metabolite of toxicological concern usually is one circulating in plasma at greater than 10 
percent of total drug-related exposure, other metabolites also can elicit safety concern.  For example, a drug 
metabolite representing greater than 10 percent of urinary excretion relative to the bioavailable dose, or a human 
fecal metabolite in cases where biliary elimination is the predominant route of excretion in humans, may reflect 
potential localized renal or bile duct toxicity, respectively.  The sponsor should discuss with the appropriate FDA 
review division the need for further characterization in these instances, which are addressed on a case-by-case basis. 
 
13 See the ICH guidance for industry S3A Guidance:  Note for Guidance on Toxicokinetics:  The Assessment of 
Systemic Exposure in Toxicity Studies: Focus on Microsampling  Questions and Answers (March 2018). 
  5  Contains Nonbinding Recommendations 
sclerosis), the proposed duration of use (short term, intermittent use, chronic), and the levels of 
exposure at the therapeutic dose. 
 
 
IV.  RECOMMENDED STUDIES FOR ASSESSING THE SAFETY OF 
METABOLITES 
 
Good laboratory practice guidelines apply to the nonclinical studies with the drug metabolite 
designed to evaluate safety (21 CFR part 58).  Sponsors may need to conduct the following 
studies to assess the safety of the disproportionate drug metabolite. 
 
A.  General Toxicity Studies 
 
The potential toxicity of a disproportionate drug metabolite should be evaluated to enable 
comparisons between the metabolite and its parent drug.  The duration of the general toxicity 
study with direct dosing of the metabolite should follow the recommendations listed in ICH 
M3(R2).  Sponsors should investigate the toxicity of the drug metabolite at multiples of the 
human exposure or at least at levels comparable to those measured in humans.  We also 
recommend using the parent drugs intended clinical route of administration.  However, with 
justification, one can use other routes to achieve sufficient exposure to the disproportionate 
metabolite.  If the clinical route is oral, it is important to verify the stability of the metabolite in 
the stomach environment.  It is crucial to gather toxicokinetic data from this type of study to 
ensure adequate exposure. 
 
B.  Genotoxicity Studies 
 
The potential genotoxicity of the drug metabolite should be assessed in an in vitro assay that 
detects point mutations and in another assay that detects chromosomal aberrations.  It is 
important that these assays be conducted according to the recommendations in the ICH guidance 
for industry S2(R1) Genotoxicity Testing and Data Interpretation for Pharmaceuticals Intended 
for Human Use (June 2012).  If one or both of the in vitro tests are equivocal and/or positive, 
results from a complete standard battery of genotoxicity studies may be needed. 
 
C.  Embryo-Fetal Development Toxicity Studies 
 
When a drug is intended for use in a population that includes women of childbearing potential, 
sponsors should conduct embryo-fetal development toxicity studies with the drug metabolite.  
We may ask for other reproductive toxicity studies on a case-by-case basis, depending on results 
of the general toxicity and embryo-fetal development studies.  Sponsors should conduct 
reproductive toxicity studies in accordance with the ICH guidances on reproductive toxicity.  
Sometimes the conduct of an embryo-fetal development toxicity study in only one species that 
forms the drug metabolite can be justified. 
 
  6  Contains Nonbinding Recommendations 
D.  Carcinogenicity Studies 
 
Carcinogenicity studies should be conducted on metabolites of drugs that are administered 
continuously for at least 6 months or that are used intermittently to treat chronic or recurrent 
conditions when the carcinogenic potential of the metabolite cannot be adequately evaluated 
from carcinogenicity studies conducted with the parent drug.  Sponsors should conduct a single 
carcinogenicity study or an alternative bioassay in accordance with the ICH guidances for 
industry S1A The Need for Long-term Rodent Carcinogenicity Studies of Pharmaceuticals 
(March 1996), S1B Testing for Carcinogenicity of Pharmaceuticals (July 1997), and S1C(R2) 
Dose Selection for Carcinogenicity Studies (September 2008). 
 
 
V.  TIMING OF SAFETY ASSESSMENTS 
 
Early identification of disproportionate drug metabolites can provide clear justification for 
nonclinical testing in animals, assist in interpreting and planning clinical studies, and prevent 
delays in drug development.  If toxicity studies of a drug metabolite are warranted, sponsors 
should complete studies and provide study reports to the FDA before beginning large-scale 
clinical trials. 
 
To optimize and expedite drug development for serious or life-threatening diseases other than 
cancer (e.g., amyotrophic lateral sclerosis, stroke, human immunodeficiency virus), the number 
and type of nonclinical studies for the drug metabolites can be modified on a case-by-case basis 
for those drugs with major beneficial therapeutic advances and for drugs for illnesses that lack an 
approved effective therapy.  Sponsors should contact the appropriate review division to discuss 
such situations. 
 
  7  Contains Nonbinding Recommendations 
GLOSSARY 
 
Disproportionate drug metabolite  A metabolite present only in humans or present at higher 
plasma concentrations in humans than in the animals used in nonclinical studies.  In general, 
these metabolites are of interest if they account for plasma levels greater than 10 percent of total 
drug-related exposure, measured as area under the curve at steady state. 
 
Metabolite  A compound derived from the parent drug through phase 1 and/or phase 2 
metabolic pathways. 
 
Pharmacologically active metabolite  A metabolite that has pharmacological activity at the 
target receptor.  The activity may be greater than, equal to, or less than that of the parent drug. 
 
 
  8  Contains Nonbinding Recommendations 
APPENDIX A:  DECISION TREE FLOW DIAGRAM 
 
 
Disproportionate Drug Metabolite 
>10% of total drug-
<10% of total drug-
related exposure 
related exposure 
(area under the curve) 
(area under the curve) 
Formed in any 
animal test species? 
No further testing needed 
to evaluate metabolite 
Yes 
No  How much? 
Exposure in animal  Exposure in animal 
studies does not approach  studies does approach 
human exposure  human exposure 
Nonclinical testing with  No further testing needed 
the drug metabolite  to qualify metabolite 
 
 
 
 
 
  9  Contains Nonbinding Recommendations 
APPENDIX B:  CASE EXAMPLES OF DRUG METABOLITES 
 
Case 1. 
From an initial mass balance study, a metabolite represented 1 to 2 percent of total 
radioactive dose in rat plasma, 5 percent in dogs, and 20 percent in humans (radioactivity 
of this metabolite in urine and/or feces was minimal).  Based on the up-to-20-fold greater 
exposure in humans than in animals, nonclinical safety testing was recommended.  
However, the data generated in the general toxicology studies with the parent drug in the 
rat and dog suggested that the maximum doses tested produced metabolite exposures that 
represented at least the therapeutic exposure at the maximum recommended human dose.  
Also, the plasma concentrations of this metabolite measured in the in vivo genetic 
toxicity study, embryo-fetal development toxicity study, and carcinogenicity studies 
conducted with the parent drug provided adequate exposure and characterization of the 
metabolite.  Therefore, no additional testing with the metabolite was needed. 
 
Case 2. 
Two primary hydroxylated metabolites, M1 and M2, were shown to undergo further 
oxidation to form secondary metabolites M3 and M4 using hepatic microsomes and 
hepatocytes from human, monkey, rat, dog, rabbit, and mouse.  This metabolic profile 
was later confirmed by in vivo data.  The results showed the following: 
 
  M1 and M4 were the predominant metabolites in human, monkey, and dog 
microsomes, whereas rat, mouse, and rabbit formed M2 and M3 
 
  M4 was formed in humans at 4-fold higher levels than the parent drug and 75 
percent of the total drug-related exposure, but M4 was formed at very low levels 
in rodents and only represented 20 percent of the total drug-related exposure in 
monkey (see Table 1) 
 
Table 1:  AUC  at the Maximum Dose* 
0-24hr
   Human (MRHD)* Monkey  Rat 
Total drug-  10,220  24,240  15,135 
related exposure 
Parent Exposure 1,800  15,000  12,500 
M4 Exposure  7,700   5,000   135  
* AUC = area under the curve; 
MRHD = maximum recommended human dose 
 
  Severe drug-related and novel target organ toxicities were observed with the 
parent drug in monkeys but not in rats 
 
  M4 was pharmacologically inactive at the drug target receptors 
 
  10  Contains Nonbinding Recommendations 
The following additional studies were done with M4: 
 
  Subchronic toxicity study:  3 months in rats 
 
  Embryo-fetal development study in the rats 
 
  In vitro genotoxicity testing:  M4 was positive for point mutation and 
chromosomal aberration; the parent drug was negative 
 
  Because of the positive genotoxicity, a carcinogenicity study that included M4 
was recommended 
 
Case 3. 
M2 is a phase 1 oxidative metabolite that formed up to 50 percent of total drug-related 
exposure in humans, 10 percent of total drug-related exposure in mice, 15 percent of total 
drug-related exposure in dogs, and only trace amounts in rats.  In vitro metabolism 
studies in these species supported the in vivo findings.  Based on structure activity 
relationship analyses, there was no reason to anticipate any difference or exaggeration in 
toxicity of the metabolite compared with the parent molecule.  The parent drug showed 
no significant toxicity or identifiable target organ of toxicity in any of the animal species 
tested in safety assessment studies.  Because disproportionate human exposure was 
identified, further safety testing was needed.  When M2 was tested in a short-term 
tolerance study in the dog, it produced unexpected and significant cardiotoxicity at all 
doses and in all of the dogs.  M2 was pharmacologically inactive at the therapeutic target 
receptor. 
 
  11