Stapled Peptide Manufacturing: How WuXi AppTec’s CRDMO Platform Helps Advance Complex Peptides to Clinical Supply

Key Takeaways

• Stapled peptides offer important therapeutic potential, but medium- to large- scale manufacturing can be challenging because of complex sequences, sourcing of unnatural amino acids, multiple ring systems, catalyst residue control, purification, and formulation requirements. 
• In this case study, WuXi AppTec helped to address poor process robustness, high catalyst loading, unacceptable ruthenium residue, prep-HPLC purification challenges, and high-concentration formulation requirements through an integrated approach. 
• The project delivered kilogram-scale GMP API within 8 months, reduced residual ruthenium in the final API by approximately 75-fold compared with the crude material, achieved a peptide solution above 100 mg/mL. Project onboarding to Phase 2 CTM release was completed in 11 months.

Peptide therapeutics have become an increasingly important modality in modern drug discovery and development. From insulin and GLP-1 receptor agonists to therapies for oncology, as well as metabolic, infectious, and rare diseases, peptide-based medicines have demonstrated meaningful clinical value across a broad range of indications. Today, over 100 peptide drugs are available globally, and many more are advancing through preclinical and clinical pipelines.

Stapled Peptides in Drug Development: Better Stability, Stronger Target Engagement, and CMC Challenges

Peptide therapeutics bridge small molecules and biologics, combining high target specificity, design flexibility, and strong biological activity. Yet many native peptides have limited drug-like properties, which can restrict their therapeutic use. 

Chemical modification is a key strategy to improve peptide drug-like properties. Macrocyclization, including peptide stapling, can constrain peptide conformation and enhance proteolytic stability. By stabilizing α-helical structures often involved in protein–protein interactions, stapled peptides may expand the therapeutic potential of peptide-based medicines.

Ring-closing olefin metathesis (RCM) is one of the most established methods for creating stapled peptides. Pioneering work by Helen Blackwell and Nobel Laureate Robert H. Grubbs demonstrated that RCM could generate covalently cross-linked peptide helices, helping establish hydrocarbon stapling as an important strategy in stapled peptide design.

However, the structural features that make stapled peptides scientifically compelling can also make them challenging to manufacture. Scaling from laboratory synthesis to kilogram-scale clinical trial material requires more than reaction feasibility. Clinical-scale stapled peptide manufacturing can face Chemistry, Manufacturing, and Controls (CMC) challenges, including unnatural amino acid (UAA) sourcing, RCM conversion, and metal residue control. For clinical-stage biotech companies, these issues are not merely isolated chemistry hurdles but development risks that can affect timelines, cost, quality, and clinical supply.

Image Source: 123RF

Case Study: A Phase 2 Stapled Peptide Facing Low Yield, High Catalyst Loading, and CTM Timeline Pressure

These challenges came into focus for one biotech company developing a Phase 2 triple-stapled peptide. The existing manufacturing process suffered from low purity, low and unstable yield, high catalyst loading, and difficult catalyst residue control. At the same time, the program required an ultra-high concentration injectable formulation and timely Clinical Trial Material (CTM) delivery, with limited room for delay.

How Can Integrated Execution Solve Stapled Peptide Manufacturing Challenges?

After the project experienced extensive challenges at another CDMO, the molecule was transferred to WuXi AppTec, where the WuXi TIDES team helped to address these interconnected challenges. From the beginning, the team recognized that this was not simply a yield-improvement project. It was a broader CMC execution challenge that required coordinated problem-solving across multiple workstreams.

Approach 1: Securing UAA Supply to Reduce Sourcing Risk

For stapled peptide programs, reliable access to non-commercial unnatural amino acids can be critical to keeping process development on schedule. In this case, the peptide required two non-commercial UAAs, creating potential sourcing risk and timeline uncertainty. To reduce this risk, the team developed an in-house synthetic route in 6 weeks and delivered 25 kilograms of UAA with greater than 99% purity. This secured a consistent supply of high-quality building blocks for peptide synthesis and process development, while helping avoid external supply delays.

Approach 2: Re-Engineering RCM Conditions to Improve Conversion and Crude Purity

In parallel with other CMC workstreams, the team re-engineered the RCM process to improve conversion and reduce downstream impurity burden. In the previous process, catalyst loading had been repeatedly increased to compensate for low conversion. However, increasing catalyst loading alone may not resolve the root causes of poor RCM efficiency. Instead, high catalyst loading increases both impurity burden and downstream purification complexity, including elevated residual ruthenium, difficult purification, and greater impurity-control pressure. By contrast, the team optimized key reaction parameters, including the solvent system, substrate concentration, and catalyst addition strategy. These changes improved RCM conversion despite increasing conformational constraints, reduced catalyst burden, and increased crude purity by 33%.

Approach 3: Reducing Ruthenium Residue and Improving Prep-HPLC Purification

Residual ruthenium control and purification robustness were critical to making the stapled peptide process suitable for clinical-scale manufacturing. The previous crude material contained a high level of residual ruthenium and appeared dark, which shortened prep-HPLC column lifetime and increased purification complexity. To improve metal impurity control before purification, the team implemented a pre-column metal-scavenging strategy before prep-HPLC. This strategy reduced residual ruthenium by approximately 75-fold from the crude material to the final API. It also helped protect column integrity and reduced the purification cycle time by 30%.

Results: From an Unstable Process to Kilogram-Scale GMP API in 8 Months

Through coordinated CMC interventions, the team transformed a low-yielding, unstable process into a more robust and scalable manufacturing route. Final yield increased by more than twofold, and several kilograms of GMP API were delivered within 8 months. For a complex triple-stapled peptide involving sequential RCM reactions and challenging metal-residue control, these improvements strengthened both process performance and clinical supply readiness.

Accelerating CTM Delivery Through Parallel CMC Execution

Beyond API process optimization, speed also depended on parallel CMC execution. While GMP API production was underway, analytical method development and validation advanced in parallel. Metal quantification, impurity profiling, and stability-indicating methods were aligned early to reduce the risk of late-stage rework and support timely release.

In parallel with API scale-up, the drug product team screened more than 30 formulation prototypes within approximately 5 weeks. The key challenge was to develop an ultra-high concentration injectable formulation suitable for clinical dosing while maintaining solubility, injectability, and physical stability. Through systematic formulation screening and optimization, the team ultimately achieved a stable injectable peptide solution at a concentration exceeding 100 mg/mL.

Integrated Execution Enabled Phase 2 CTM Release in 11 Months

Because UAA supply, API process optimization, analytical development, formulation screening, and CTM manufacturing were advanced in a coordinated manner, the project moved forward without idle time between functions. CTM manufacturing, packaging, and release were completed within 3 months, and the overall project—from project onboarding to Phase 2 CTM release—was completed in 11 months.

This case shows that clinical-scale stapled peptide manufacturing is not only a chemistry challenge, but also an integrated CMC execution challenge. But by coordinating UAA supply, RCM process optimization, ruthenium residue control, prep-HPLC purification, high-concentration formulation, and CTM release, an integrated platform can help transform a non-scalable process into a GMP-ready manufacturing pathway. In this Phase 2 program, WuXi AppTec’s WuXi TIDES team helped support timely clinical trial material delivery for a complex stapled peptide, reflecting a broader goal: solving difficult development and manufacturing challenges so that promising therapies can advance faster toward the patients who need them.