Overcoming the Challenges of Peptide Drug Development

Peptides are powerful therapeutic candidates, offering high specificity and potency. However, their development comes with unique hurdles that must be carefully managed. From enzymatic degradation to poor solubility, addressing these challenges is key to advancing peptides into successful drug candidates. Here’s how we tackle these issues head-on.

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Dr Ralph Kirk, Group Leader at Concept Life Sciences outlines the key challenges of peptide drug development and how to overcome them.

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1. Stability & degradation

Peptides often have short half-lives due to enzymatic degradation and chemical instability. To enhance stability and extend their therapeutic window, try applying the following strategies:

• Cyclization strengthens structural rigidity, making peptides more resistant to enzymatic breakdown
• D-amino acid substitutions reduce enzymatic recognition, enhancing stability
• Non-canonical amino acid incorporation maintains function while resisting degradation
• Formulation optimization mitigates oxidation, deamidation, and hydrolysis risks

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2. Cell permeability and pharmacokinetics (PK):

Unlike small molecules, peptide soften struggle with cell permeability, which limits their ability to interact with intracellular targets. To evaluate this, cell-based permeability assays(e.g., using Caco-2 cells) are the go-to invitro assessment, coupled with the identification of active transports (e.g.PEPT1). One can also use chromatographic predictions of oral bioavailability and permeability in the form of ChamelogK evaluation which predicts the potential for the peptide to have chameleonic properties. Often, permeability can be improved by:

• Applying lipophilic capping
• Modulating lipophilicity
• Incorporating peptoid or β-peptide units to enhance bioavailability
• Assessing the role of peptide transports (i.e.PEPT-1)

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3. Bioavailability & clearance

One major challenge in peptide drug development is rapid renal clearance, which reduces bioavailability. Implementation of the following can help counteract this:

• Lipidation or PEGylation to increase molecular weight and extend circulation time
• Protein conjugation to slow renal filtration and improve half-life
• Solubility enhancements through kinetic and thermodynamic assays
• Aggregation monitoring using RP-HPLC and SEC-MALS to maintain formulation integrity

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4. Immunogenicity & safety

Peptides can elicit immune responses, ranging from the activation of innate immune cells to the generation of specific T cells. Collectively, these reactions may pose safety risks upon administration and lead to antibody formation, ultimately reducing the efficacy of peptide-based drugs. Predicting an increased risk of such immune responses is essential and can be assessed using various in vitro models. Strategies to mitigate immune-mediated risks may include:

• In vitro assays, including innate immune cell activation and PBMC-based T-cell activation assays, can be used to predict immune-related risk
• Sequence modifications, including PEGylation, D-amino acid substitutions, and truncation, reduces immune recognition while preserving bioactivity

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5. Synthetic and formulation challenges

Beyond biological hurdles, peptides also face critical physicochemical challenges that can impact stability and efficacy. The key considerations are:

• Oxidation: Amino acids such as methionine, cysteine, and tryptophan are prone to oxidative degradation. Mitigation involves stabilizing formulations and monitoring oxidation via LC-MS
• Deamidation: Asparagine and glutamine residues can convert into aspartic and glutamic acids, affecting stability. This is controlled through synthesis adjustments and LC-MS analysis
• Hydrolysis: Peptide bonds near susceptible residues can break down, leading to fragmentation. Employing protective modifications such as cyclization and terminal capping often prevents this
• Racemization: L-amino acids can convert to their D-isomers, potentially altering bioactivity. By using chiral chromatography with MS you can detect and control racemization
• Solubility & Aggregation: Poor solubility can limit bioavailability, while aggregation can lead to reduced activity. Both can be monitored using RP-HPLC and SEC-MALS to optimize peptide formulations

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6. Cost and manufacture

Peptide synthesis can be expensive and time-consuming depending on the complexity of the sequences, use of potentially high cost amino acids and specialized equipment. When to use SPPS and LPPS is an important consideration.

• SPPS is ideal for short to moderate peptide chain lengths – typically up to 40 mers, allowing for automated high throughput synthesis and purification. However for complex peptides, steric hinderance, low yields, aggregation and poor solvation may be an issue
• LPPS may be a valuable alternative in this situation, especially when considering scaling up or convergent synthesis

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Integrated peptide drug development strategies

Developing stable, effective peptides requires overcoming multiple hurdles, from degradation to solubility challenges. Our integrated approach—leveraging advanced analytics, rational design, and strategic modifications—ensures peptide candidates have the stability, bioavailability, and efficacy needed for clinical success.

Learn more about our approach on our peptide webpage.

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