As the pharmaceutical industry looks for novel modalities and methods to deliver drugs safely and efficiently to patients, a particular therapeutic class is gaining much interest across both biotech and large pharma—but it is not new at all. In fact, it has been around for over a century.

Since insulin was first used to treat diabetes in the 1920s,¹ the use of naturally sourced peptides evolved into the incorporation of non-natural amino acids and backbone modification, and towards synthetic therapeutics. Historically, peptide research has been stifled by drugs having low oral bioavailability, and short half-lives,² however, advances in technology have enabled scientists to enhance peptide functionality and synthesize novel peptides for a particular purpose. As of 2004, more than 80 peptide drugs have been approved worldwide, with over 30 non-insulin peptide therapeutics entering the market since 2000.³

Peptides are big business, with the global peptide therapeutics market having been estimated to be $117.26 billion in 2024, and projected to reach $260.25 billion by 2030.² With their high specificity, precise targeting capabilities, and opportunities for custom design, peptides have become a core focus for many pharmaceutical and biotechnology organizations. One particular class of peptides is currently having a significant impact on the market: GLP-1 analogue drugs have gained high acceptance in recent years, with them shown to be highly beneficial in treating chronic obesity and weight management. These drugs, which are sold under a variety of tradenames include semaglutide, tirzepatide, and liraglutide. The pipeline for other drugs in this class is strong, with fast-follower analogues looking to capitalize on the market potential, as well as for other indications including non-alcoholic steatohepatitis (NASH) and Alzheimer’s disease.⁴

The attraction of synthetic peptides for drug developers comes from the fact that they can be designed to target specific receptors, maximizing therapeutic efficiency while minimizing side effects. This allows for more targeted therapies and supports the development of personalized medicines. Additionally, they are versatile, with naturally occurring peptides playing a role in numerous physiological processes. As a result, peptide drugs can be applied to a wide range of treatment areas including HIV, chronic pain, short bowel syndrome, and numerous other indications, and administered in a variety of ways, including injections, oral formulations, and others.

Customization of Peptides

Peptide engineering and optimization supports the creation of new drugs to be directed against specific indications or pathways, and also enhances physical properties such as stability and bioavailability. For example, CB1 is a custom peptide derived from the naturally occurring Cecropin B to target lung cancer cells while avoiding healthy lung cells.³

Modern peptide therapeutics are generally developed in one of two ways; either through peptide synthesis or using biological routes. In peptide synthesis, amino acids are chemically assembled to create a peptide chain, while biological routes involve cell cultivation to express and then extract the desired peptide.

One of the most common synthetic methods is solid-phase peptide synthesis (SPPS), which builds an amino acid sequence on a solid resin support.⁵ The process uses a series of reactions where the carboxyl group of an amino acid is joined to the amino group of the previous amino acid in the peptide chain. Various reactive groups on the side chains and termini must be chemically protected to prevent side reactions and unwanted by-products during the synthesis, and after each step, the resin must be washed with solvent to remove any excess reagent from the previous coupling. This ensures purity levels remain high for the following steps, and there is no residual amino acid, which could interfere with subsequent coupling steps or cause dimerization.

Synthesis can be carried out in either a column reactor or agitated vessel, and technology has evolved to allow automated synthesizers, such as microwave-assisted peptide synthesizers, to be used to build peptides with greater efficiency than ever.

After synthesis, the product is cleaved from the resin to isolate the active component, and then further purification steps, which are almost always chromatographic, are needed to remove any by-products and isolate the final peptide drug.

In addition to chemical synthesis, therapeutic peptides can be prepared by a number of biological methods, such as isolating bioactive peptides from natural sources by extraction, enzymatic synthesis, fermentation, and recombinant DNA technology.

Commonly used protein production systems include those derived from bacteria, baculovirus/insect cells, mammalian cells and yeast, however, each specific application is dependent upon the selection and optimization of the correct expression system.

Both peptide synthesis and biological approaches to customization can be beneficial in certain use cases. Biological routes offer advantages such as post-translational modifications and can support potentially more complex structures, as well as being seen as a more environmentally sustainable solution. The process to clone and express the gene within a cellular system can take time to develop, and this is a significant disadvantage. 

However, chemical peptide synthesis, especially for applications that only require a short peptide sequence, is often the best way forward. The method offers greater cost-effectiveness, more precise control of sequencing, higher stability, and faster development. Although this route does give developers access to non-natural peptides, interactions that require post-translational modifications, such as glycosylation, are difficult to incorporate synthetically, and it is challenging to create disulfide linkages within products too.

Peptide synthesis involves using excess reagent at each stage to ensure complete coupling. However, process optimization of each step is crucial to reduce the risk of side reactions and to also maximize the efficiency of, for example if an expensive non-natural amino acid was being coupled as a building block. During SPPS, the purity of the final product is unknown until after all couplings have taken place, and the product is cleaved from the resin and isolated. This means that most “in-process” testing methods that would be applicable to standard chemical synthesis are not appropriate to SPPS, so monitoring is done at each step using the Kaiser test, which detects the presence of free amino groups, and indicates the progress of each coupling and deprotection step.

Analysis

As peptides occupy a unique space between small molecules and biologics, this presents a distinct regulatory challenge, and although the respective agencies are actively working to close this regulatory gap, this leaves a dynamic landscape that requires constant vigilance. Recently, both the European Medicines Agency (EMA) and the FDA have issued significant new draft guidelines and USP chapters to address specific aspects of Chemistry, Manufacturing, and Controls (CMC), placing renewed focus on the rigor required for approval.

Within this framework, the impurity profile is paramount. Notably, synthetic peptides are excluded from the scope of ICH Q3A, meaning its standard impurity thresholds do not apply.⁶ This leads to regional divergences; for instance, the EMA refers to thresholds in the European Pharmacopoeia, which the FDA may not recognize, opting instead for a case-by-case assessment. This reality demands a robust, globally-minded impurity control strategy, as any new or significant impurity can be a major obstacle to approval.³

Satisfying global regulators relies on a sophisticated analytical strategy to prove a product’s identity, purity, stability, and safety. This demands a comprehensive panel of orthogonal methods to build a complete quality picture. To unequivocally prove the molecule’s identity and structure, a suite of techniques is essential. Mass spectrometry (MS) and amino acid analysis confirm the exact molecular weight and primary amino acid sequence, while peptide mapping provides more detailed information on modifications such as deamidation or oxidation. Investigating the higher order structure (HOS) using spectroscopy methods including circular dichroism, Fourier transform infrared spectroscopy, fluorescence, microfluidic modulation and nuclear magnetic resonance is also important, as the 3-dimentional conformation dictates biological activity.

Establishing purity requires determining all unwanted by-products. Liquid chromatography (LC) methods are the standard for assay determination and separating peptide-related impurities, and the validation of stability-indicating LC methods is a crucial part of development. A full quality profile also accounts for process-related impurities such as residual solvents and heavy metals, and must navigate regional differences, such as the EMA’s focus on nitrosamines. A thorough immunogenicity risk assessment is also important to evaluate how factors such as impurities and aggregation may provoke an unwanted immune response.⁷

The safety of the drug substance must be demonstrated through microbial and endotoxin analysis. As a final check, a mass balance calculation is performed, summing the percentages of the peptide, counter ions (typically measured by ion chromatography), and water to ensure they total 100%, providing confidence that no significant unaccounted-for impurities remain. This level of testing provides a significant R&D challenge to develop and validate custom analytical methods for each unique peptide molecule. 

Partnering for Success

There are currently over 170 peptide drugs in clinical development, and even more in the preclinical stage.¹ As peptides remain a core area of research and progress in the life sciences space, pharmaceutical and biotechnology organizations require a partner with extensive expertise to ensure timely progression through the development and clinical phases and to maximize the success into commercial launch.

Overcoming challenges in both manufacturing and testing requires extensive experience in this specialized field of drug development and a deep understanding of the constantly evolving regulatory landscape. It also demands the expertise to grasp the complexities of manufacturing and their implications for commercial success. As with every new drug in development, there is no one-size-fits-all solution. However, partnering with an expert CDMO that offers flexible capacity and capabilities, alongside expertise in manufacturing, purification, and analysis, can help ensure that patients gain access to potentially life-changing therapies and drugs in the future.

References

1. Lau, J. & Dunn, M. Therapeutic peptides: Historical perspectives, current development trends, and future directions. Biorganic & Medicinal Chemistry [Online], July 1, 2017. ScienceDirect. https://www.sciencedirect.com/science/article/pii/S0968089617310222 (accessed Feb 14, 2024). 

2. Grand View Research. Peptide Therapeutics Market Size, Share & Trends Analysis Report. Grand View Research; 2024. https://www.grandviewresearch.com/industry-analysis/peptide-therapeutics-market (accessed Oct 23, 2025). 

3. Weng, L. et al. Therapeutic peptides: current applications and future directions. Sig Transduct Target Ther [Online], Feb 14, 2022. Nature.com. https://www.nature.com/articles/s41392-022-00904-4 (accessed Feb 13, 2024).

4. https://www.marketsandmarkets.com/Market-Reports/glp-1-analogues-market-218746186.html#:~:text=Overview,33.2%25%20from%202024%20to%202032

5. Stawikowski, M. & Fields, G.B. Introduction to Peptide Synthesis. Curr Protoc Protein Sci. [Online], Feb 5, 2013. PubMed Central. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3564544/ (accessed Feb 13, 2024).

6. DRLC Group. Synthetic Peptides: Understanding The New CMC Guidelines. https://www.dlrcgroup.com/. December 20, 2023. https://www.dlrcgroup.com/synthetic-peptides-understanding-the-new-cmc-guidelines/

7. U.S. Food and Drug Administration C for DE and R. Clinical Pharmacology Considerations for Peptide Drug Products.; 2023.