The demand for peptide therapeutics has grown rapidly in recent years, as the success of GLP-1 drugs has catapulted them to the forefront of developers’ and sponsors’ minds. Although peptides still represent a relatively small share of FDA-approved therapeutics, they offer distinct advantages in treating diseases where small-molecule drugs or therapeutic antibodies fall short.
The most commercially visible peptides, GLP-1 drugs, have been favored for the dramatic impact they can have on obesity, but other applications have shown promise, including treating cardiovascular, neurological and psychiatric disorders.
As peptides move beyond single-target GLP-1 analogs into dual agonists, triple agonists, oral peptides and conjugated constructs, metabolic stability has emerged as one of the most significant development hurdles researchers must overcome. Structural modifications, while enabling enhanced functionality, can also introduce new clearance mechanisms, increase susceptibility to degradation and create uncertainties in translational outcomes.
As modern peptides advance rapidly, it is essential for researchers to prioritize metabolic stability at the center of ADME, DMPK and toxicology strategies.
The major challenges of peptide development
Drug metabolism plays a central role in both pharmacology and safety, influencing how quickly a drug is activated or deactivated, how long it remains in circulation, and whether it produces toxic or therapeutically effective metabolites. Although peptides and small molecules share broad pharmacokinetic and metabolic principles, important differences exist.
Small molecules are typically metabolized by cytochrome P450 (CYP450) enzymes into active or inactive metabolites, whereas peptides are primarily degraded by proteases. As a result, peptide developers must contend with inherently poor metabolic stability, along with challenges such as higher molecular weight and limited membrane permeability, which can restrict broader applications. These factors also complicate oral delivery and shorten the duration of action in circulation.
But to facilitate the GLP-1 boom, developers have successfully introduced innovative and effective strategies to address stability issues in single-target analogs.
Addressing metabolic stability in GLP-1 drugs
One of the most impressive achievements of new GLP-1 analogs is their weekly and potentially monthly dosing schedules. This has been achieved through strategies such as lipidation to enhance albumin binding, incorporation of non-natural amino acids to improve stability, and depot formulations to extend absorption.
Semaglutide, for example, boasts a half-life of 165 hours, enabling once-a-week dosing. Researchers achieved this feat through amino acid modifications, structural design and lipid conjugation, thereby enhancing plasma protein binding, reducing renal clearance and prolonging systemic exposure.
While the above strategies can extend half-life or improve efficacy, they can also alter the way the drug is cleared, where it’s degraded, and which metabolites are produced. For developers, the challenge is not just to make the molecule last longer, but also to understand how each stabilizing modification affects the full metabolic profile.
The engineering innovations behind GLP-1 single agonists have inspired a new wave of long-acting peptide therapeutics. This new generation is already here. In 2022, tirzepatide became the first FDA-approved GIP/GLP-1 dual agonist, and others followed. Mazdutide, a GLP-1R/GCGR dual-target therapy, was approved by China’s National Medical Products Administration in 2025. Retatrutide, a triple agonist, is highly anticipated and has shown encouraging results in clinical trials.
As these advances accelerate, understanding tissue-specific peptide metabolism is increasingly critical for designing more stable and predictable therapies.
Why tissue-specific stability studies matter
Characterizing peptide-metabolizing enzymes is essential, along with evaluating those responsible for degrade peptides in the GI tract, liver, kidney and plasma. Each of these tissues brings its own nuances to testing.
Plasma
Plasma is the preferred matrix for in vitro metabolic stability studies of peptides due to its accessibility and abundance of proteases. During preparation, anticoagulants are added to prevent clotting. However, EDTA-K2 can interfere with enzyme activity because it chelates the metal ions required for certain enzyme reactions.
Plasma stability was tested using three reference peptides (fast, medium and slow metabolism) to assess the effects of anticoagulants (EDTA-K2 vs. heparin sodium), plasma status (fresh vs. frozen), and matrix type (plasma vs. serum). It revealed shorter peptide half-lives in heparin sodium-anticoagulated plasma versus EDTA-K2 plasma. No significant differences were observed between fresh and frozen plasma or between plasma and serum. These findings support the use of frozen plasma collected with sodium heparin for peptide metabolic studies.
GI tract
Most peptide drugs are administered through IV or subcutaneous injection, as they are quickly broken down by digestive enzymes in the gut and are poorly absorbed. However, Novo Nordisk’s oral semaglutide is an exception. The drug combines semaglutide with salcaprozate sodium (SNAC), an absorption enhancer that helps the peptide pass through the stomach lining.
For developers pursuing oral peptides, GI metabolic studies are essential to guide structural design. These typically involve evaluating peptide stability against key digestive enzymes such as pepsin, trypsin, pancreatin, chymotrypsin and elastase.
Liver
The liver is the principal organ of drug metabolism, containing Phase I and II enzymes that drive a drug’s biotransformation and metabolism. In studies, researchers compared different liver-based lab systems (liver microsome, liver S9, hepatocyte and liver homogenate) and found that liver S9 fraction exhibited higher or similar intrinsic clearance for five commercial peptides than other systems and produced data that correlated most closely with in vivo results.
Kidney
Kidney metabolism is commonly assessed using kidney microsomes, kidney S9 fractions and kidney homogenates. For peptides, kidney S9 and kidney homogenate are most relevant because microsomes are more commonly used for small-molecule metabolism studies. Research by WuXi AppTec showed that peptides exhibited higher or similar intrinsic clearance for five commercial peptides in kidney S9 than in kidney homogenate. A 2023 study also found that S9 fraction from kidney and intestinal tissue produced the fastest peptide clearance.
A final word on multifunctional peptides
The staggering commercial success of GLP-1 drugs has proven what is possible when peptide stability is effectively engineered. With longer half-lives, enhancing plasma protein binding, reduced renal clearance and more durable exposure, peptides have been transformed into highly impactful therapeutics.
However, the next phase of peptide development is much more complex: Unlocking dual and triple agonists, oral peptides, and conjugated constructs. Each modification aimed at improving potency, exposure or delivery can alter how the drug is metabolized and cleared.
This highlights metabolic stability as a key challenge among the many challenges facing multifunctional peptides. Developers must understand where and how it is metabolized, which enzymes are involved, what metabolites are formed, and how these processes translate across tissues and species. Integrated studies across plasma, GI enzymes, liver S9 fractions and kidney models are essential.
Going forward, metabolic stability will increasingly shape decisions on molecular design, administration route, species choice and study strategies, and will become one of the defining principles of modern peptide drug development.
Author bios
Dr. Hanlin Tao
Dr. Hanlin Tao is an Associate Director in the DMPK Department at WuXi AppTec, where he leads the in vitro ADME team at the Cranbury, New Jersey site. He has extensive experience in ADME and drug-drug interaction (DDI) studies and oversees a broad portfolio of services supporting drug discovery, IND-enabling studies, and definitive in vitro ADME and DDI evaluations for pharmaceutical companies worldwide.
Haijuan Liu
Haijuan Liu is an Associate Director in the DMPK Department at WuXi AppTec, responsible for in vitro drug metabolism research. She has extensive experience in drug metabolism studies, has established slow-metabolizer and non-CYP enzyme platforms, and developed new in vitro metabolism capability platforms for modalities such as ADCs and peptides. She provides support to global pharmaceutical companies for drug discovery, IND-enabling studies.
Filed Under: Drug Discovery
