Bioinformatics & Analytics

Peptide Library Design

JPT has developed an algorithm called PepSelector that performs a manufacturability assessment and feasibility ranking of peptide sequences. The PepSelector applies its algorithm based on literature and experimental data from several tens of thousands of synthetic peptides. It considers amino acid coupling efficiencies, peptide library side reactions during synthesis, peptide stability, peptide solubility, correlation of physicochemical properties and secondary structure propensities with manufacturability, ability to be purified and reconstituted in aqueous buffers. 

The aim is to predict potential difficulties and rank peptides according to their overall manufacturability. Although the PepSelector does not provide a go/no-go differentiation of peptides for production, it does allow the selection of peptides with a higher probability of success over peptides with an increased risk of failure. As a result, it is an effective tool for ranking peptides for fast, efficient and successful synthesis in turnaround sensitive studies such as neo-epitope-based individualised immunotherapies. In addition to the manufacturability assessment, the program can provide access to potential sequence optimisations that can be achieved by simply shortening, extending or frame-shifting the peptide sequences along their parental antigen sequences.

Peptide solubility is a critical factor in almost all peptide-based projects. This includes the robustness of in vitro assays and in vivo bioavailability. In both cases, lack of complete solubility at the desired effective concentration will result in reduced activity and/or false negative results. A prerequisite for effective solubility assessment and optimization is the availability of a rapid and sensitive solubility assay.  

Turbidimetric Solubility Assay (TSA) allows a rapid determination of solubility using only small peptide amounts. Depending on applications of the target peptides, different organic and inorganic solvents and solvent additives can be applied.

JJPT has a long-standing and focused expertise in supporting biomedical screening and peptide lead optimisation programmes with its comprehensive bioinformatics and cheminformatics capabilities. Statistical evaluation, visualisation and presentation of complex data are performed using state-of-the-art tools. We offer this unique know-how and expertise as part of our services or in Contracted Research Projects. 

Service Specifications 

• Detailed discussion of your project and definition of a suitable strategy based on scientific feasibility and experience 
• Receive project proposal on how our bioinformatics and cheminformatic expertise can support your project
• Obtain detailed and comprehensive service reports 

• Design of peptide content for high-density peptide microarrays and complex peptide libraries
• Design of peptide libraries based on biological pathways, literature data or complex database search strategies 
• Generation of homology models and use of available structural information for peptide selection 
• Support for optimization of hit and lead structures (affinity, physicochemical properties, ADME)
• Prediction and modeling of data
• Interpretation, management and integration of data 
• Visualization and presentation of complex data sets 

• Long-term track record in the discovery and development of peptides in drug discovery and diagnostic development 
• State-of-the-art prediction, data interpretation and data mining algorithms and software paired with chemical and biological know-how 
• Expertise available as a fee-for-service or in collaborative partnerships