Helix stabilization
Stapled Peptide Design for Protein-Protein Interaction Targets
Protein-protein interactions mediated by alpha-helical interfaces represent some of the most important — and most challenging — targets in drug discovery. Stapled peptides, stabilized by hydrocarbon or other crosslinks, maintain helical conformation, resist proteolysis, and can penetrate cells to engage intracellular PPI targets. We apply computational methods to design and optimize stapled peptides for your PPI target.
The PPI Targeting Challenge
Protein-protein interactions mediated by alpha-helical peptide segments are critical regulators of cellular signaling — but they present a flat, extended binding surface that is difficult to target with small molecules. Peptides that mimic the helical interface can disrupt these interactions, but linear peptides are rapidly degraded and cannot penetrate cells to reach intracellular targets.
Stapling — the introduction of a covalent crosslink that locks the peptide in a helical conformation — addresses both limitations. But designing stapled peptides that maintain helical structure, retain target binding, and achieve cell penetration requires precise computational optimization.
Our Stapled Peptide Design Approach
Helical propensity prediction
Computational assessment of helical propensity and identification of optimal staple positions that reinforce rather than disrupt the bioactive conformation.
Staple position optimization
Systematic evaluation of i, i+4 and i, i+7 staple positions to identify configurations that maximize helical content and target engagement.
Cell penetration modeling
Prediction of cell penetration efficiency based on amphipathicity, charge distribution, and membrane interaction modeling.
Protease stability assessment
Evaluation of protease resistance conferred by stapling and identification of additional modifications to improve metabolic stability.
Stapled Peptide Design Workflow
PPI target characterization
Structural analysis of the target PPI interface to identify the helical binding epitope.
Peptide sequence definition
Definition of the peptide sequence corresponding to the helical binding interface.
Staple position screening
Computational screening of staple positions for helical content and target binding preservation.
Candidate design and optimization
AI-assisted sequence optimization within the stapled scaffold for potency, selectivity, and cell penetration.
Property prediction
Prediction of helical content, cell penetration, protease stability, and target affinity.
Candidate prioritization
Selection of priority candidates for synthesis and experimental validation.
What Can Be Evaluated
What You May Receive
Stapled peptide candidate library
Designed stapled sequences with predicted helical content, cell penetration, and target binding profiles.
Staple position analysis
Computational assessment of staple position options and rationale for the selected configuration.
Conformational analysis
Predicted helical content and bioactive conformation for priority candidates.
Optimization strategy
Recommended modifications to improve cell penetration, stability, or potency.
Deliverables depend on project scope and target characteristics. Helical content and cell penetration outcomes cannot be guaranteed computationally.
Who This Is For
Oncology drug discovery teams
Programs targeting intracellular PPI targets in cancer — MDM2/p53, BCL-2 family, RAS effectors — where stapled peptides offer a path to intracellular engagement.
Medicinal chemists
Teams exploring constrained peptide space for helical PPI targets where linear peptides have insufficient stability or cell penetration.
Biotech companies
Companies developing stapled peptide therapeutics or constrained peptide-based drug candidates for intracellular targets.
Screen Your Peptide Sequence First
Use our free tools to assess the physicochemical properties of your stapled peptide candidate. The Peptide Property Analyzer calculates GRAVY score and aliphatic index — key indicators of helical character and hydrophobicity relevant to stapled peptide design.
Frequently Asked Questions
Design Stapled Peptides for Your PPI Target
Submit your PPI target and helical binding interface. We will assess the stapled peptide design opportunity and outline a computational approach for your program.
Confidential project discussions available under NDA.