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CD ComputaBio provides ligand-based peptide design services, which can utilize the biological and chemical information from known active ligands to guide the design of new peptides, even when the structural information of the target protein is unknown or limited, thereby providing solutions for clients.
Ligand-based drug design utilizes information from molecules that can bind to biological targets. These molecules can be used to derive pharmacophore models and establish quantitative structure-activity relationships (QSAR) to design new molecular entities that interact with the target. This design method can also utilize existing peptide molecular information to purposefully optimize peptide structures. It plays an important role in the development of novel peptide drugs and targeted disease therapies, and helps to discover more promising peptide drugs.
Fig. 1 Schematic representation of the model-guided ligand design directed evolution workflow. (Puszkarska A M, et al., 2024)
CD ComputaBio utilizes ligand-based peptide design, extracting biological and chemical information from known active ligands, identifying key functional features to meet clients' diverse needs for peptide design, and helping to discover new peptides with greater potential and value.
Ligand Feature Extraction - Extract physicochemical properties of the ligand binding site (e.g., hydrophobicity, electrostatic potential, hydrogen bonding sites) and identify key functional groups of the ligand.
Peptide Ligand Design - Design peptide sequences using virtual fragment-based, template-based, and sequence-based methods to generate a peptide library.
Molecular Docking - Perform protein-peptide docking using molecular docking software to screen for higher-affinity peptide candidates.
Molecular Dynamics Simulation - Conduct molecular dynamics simulations on high-scoring complexes to analyze RMSD, RMSF, hydrogen bond stability, and calculate binding free energy.
Iterative Optimization and Design - Integrate computational models (e.g., pharmacophore models, QSAR) to guide the next round of peptide design and optimization.
Ligand-based peptide design holds significant importance in fields like drug development and biological sciences. Its strategies can be categorized into fragment-based, template-based, and sequence-based approaches.
Fragment-based peptide design constructs functional peptides by identifying and combining key bioactive fragments from known ligands or structural motifs. This approach balances structural diversity and target compatibility, simplifying the peptide creation process and reducing synthesis complexity.
Template-based peptide design uses established peptide-target complex structures or related sequences as templates to craft new functional peptides. This strategy allows for the rapid development of peptide candidates that maintain critical binding features while enhancing their properties.
Sequence-based peptide design strategies are founded on the assumption that conserved sites and motifs are crucial for function and structure. This approach relies on multiple sequence alignment and analysis of conserved regions, and it is frequently employed in practical design.
Ready to take your peptide drug development to the next level? Contact us today to learn more about our ligand-based peptide design services. Our team is eager to answer your questions and discuss how we can collaborate to achieve your project goals. CD ComputaBio will provide you with professional advice and support to help you make breakthroughs in your research and development.
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CD ComputaBio offers computation-driven peptide design services to research institutions, pharmaceutical, and biotechnology companies.
