How our peptide lead optimization solution drove success

Innovative peptides with high phenotypic potency were identified by our client, but the lack of target engagement data hindered the optimization of the peptide series. In addition, initial in vivo PK studies conducted on the most promising lead revealed pharmacokinetics parameters unsuitable for the desired therapeutic, with a particularly short half-life. We were tasked to concurrently optimize potency and PK parameters to deliver a peptide suitable for in vivo efficacy testing, and eventually provide a development candidate.

Customized target engagement assays – Develop an SPR target engagement assay, not only providing a direct confirmation of target engagement, but also binding affinities and kinetics, providing valuable insights for the pharmacological optimization of the chemical matter.

Peptide-focused ADME cascade – Peptides discovery requires specific ADME cascades which are critical to efficiently triage new compounds. Reshaping the project cascade and including key read outs such as plasma stability, solubility, cellular permeability and in vivo PK profiling in relevant tiers was required.

An integrated medicinal chemistry approach – Co-location of chemistry, biology and DMPK services, means our scientists efficiently communicate, hence providing leaner optimization campaigns.

Early synthesis route optimization – Seamless integration of our discovery and process development teams, which are also co-located means we derisk and accelerate the scale up process, providing faster proof of concept. Thus, unlocking additional funding tranches sooner.

Addressing lack of target engagement data

We produced the full-length target protein as well as its two binding domains separately and immobilized each protein individually on CM5 SPR chips. We measured the binding of a range of peptide hits and demonstrated specific binding to one of the two domains, thus demonstrating target engagement and mechanism of action. This assay not only provided binding affinities, but also kinetics, offering multiple advantages over the phenotypic assay initially developed for the project. Using this assay, we rapidly characterized and triaged new compound, further enhancing affinities and potencies > 5-fold compared to the best peptide Leads.

Developing a peptide-specific assay cascade

The DMPK profiling of cherry-picked Leads was initially performed by our scientists to define in vitro and in vivo parameters. This highlighted metabolic soft spots and development challenges, not only inherent peptides in general, but also specific to this project, and enabled us to develop a fit-for-purpose DMPK cascade. Using this cascade, we identified optimized Leads with in-vitro and in-vivo half-lives enhanced by >50-fold, providing sufficient free levels to engage the target in vivo and elicit the desired pharmacology. The cascade also offered an efficient way to optimize the peptide Lead series, saving months of research and focusing budget on the most promising compounds.

Peptide Lead Optimization in Medicinal Chemistry

Peptides are notoriously challenging to optimize due to their high polarity, low permeability, and often dire metabolic stability. Working hand-in-hand with our biology and DMPK teams, our medicinal chemists designed a critical path for the project and implemented many designs aiming to address liabilities associated with the Lead series. This including the strategic truncation of the peptide sequence, peptidomimetics and the addition of N- and C-terminal capping. In under 6 months of research, the project team addressed a wide range of liabilities and identified a suitable development candidate.

Peptide synthesis and scale-up readiness

As the project quickly progressed, higher quantities of the peptides were required for testing in animal models and other advanced studies. Our process development team worked with the co-located process development team to identify optimized solution-based synthetic route, enabling the production of tens of grams of high purity material. This route was further used by our client to provide material to support IND enabling studies, paving a sound path to the GMP production of the API.

Our strategic, integrated approach delivered a rapid and efficient optimization process, resulting in:

• 5x increase in affinity – A direct outcome of our tailored SPR assay and medicinal chemistry strategy
• >50-fold improvement in peptide stability – Enhanced human and mouse blood stability, overcoming rapid enzymatic degradation challenges
• Lead to development candidate in <6 months – A highly efficient optimization cycle, accelerating project timelines
• Seamless transition to IND-enabling studies – Process optimization allowed for fast scale-up, ensuring readiness for regulatory progression
• Compound due to progress into Phase I 

This data-driven peptide optimization strategy enabled the peptide to advance swiftly, demonstrating the value of our tailored biophysics, ADMET, and medicinal chemistry expertise in peptide drug development.