Cyclic Peptide Modeling Services
Cyclic peptides, with their unique structures, offer higher target affinity, metabolic stability, and membrane penetration than linear peptides, making them a focus in drug development. However, their complex conformations and verification challenges hinder their design. CD ComputaBio uses a top computational biology platform, combining AI, MD simulations, and QM calculations to offer comprehensive cyclic peptide modeling services, from design to evaluation, overcoming traditional experimental limitations.
Introduction to Cyclic Peptides
Cyclic peptides are molecules with a circular structure formed by amino acids linked end-to-end via amide bonds, lacking free N- and C-termini in their chemical framework. These peptides can be further enhanced in pharmacokinetic properties through the incorporation of non-natural amino acids (like D-amino acids), chemical modifications (such as PEGylation), or rigid linkers (such as benzene rings and disulfide bonds). This allows them to surpass the limitations of traditional small molecule drugs in target selectivity and druggability. Currently, numerous cyclic peptide drugs are in clinical trials globally, targeting areas like anti-tumor, anti-infection, and immunomodulation, including drugs like Glatiramer for multiple sclerosis and Apremilast, an IL-23 targeting immunosuppressant.
Fig 1. De novo development of small cyclic peptides that are orally bioavailable. (Merz M L, et al., 2024)
Cyclic Peptide Modeling
Cyclic peptide modeling is a cross-scale technology that integrates computational biology, medicinal chemistry, and synthetic biology. Its core lies in breaking through the conformational limitations and synthetic barriers of cyclic molecules. Traditional tools for cyclic peptide modeling such as MODPEP 2.0 and PEPstrMOD perform well in standard data sets (such as CyclicPep), with an average Cα RMSD below 1.6 Å, while mETKDG generates a better backbone RMSD distribution in conformational sampling. In recent years, the introduction of AI technology has significantly improved modeling efficiency: for example, PepFlow combines latent space search with Markov chain Monte Carlo (MCMC) methods.
Our Services
CD ComputaBio's cyclic peptide modeling service offers cutting-edge solutions tailored for researchers, pharmaceutical companies, and biotechnology firms looking to unlock the potential of cyclic peptides. With our expertise, state-of-the-art technology, and a commitment to excellence, we aim to facilitate your research and development efforts in this exciting and rapidly evolving field.
By Peptide Types
- Homologous Cyclic Peptides Modeling
- Cyclic Isopeptides Modeling
- Cyclic Dipeptides Modeling
- Dicyclic Peptides Modeling
- Disulfide Bond Cyclic Peptides Modeling
- More
By Modeling Types
Workflow of Cyclic Peptide Modeling Service
01 Customer Inquiry
To best serve your needs, CD ComputaBio will explore your specific cyclic peptide modeling applications, such as targeting protein interfaces or optimizing stability. CD ComputaBio will then work with you to clarify your key objectives, focusing on improving binding affinity or transmembrane efficiency.
02 Project Design
CD ComputaBio provides cyclic peptide thermodynamic analysis, structure, surface properties and other modeling services based on the cyclic peptide information provided by the customer. The proposal contains our specific service content, estimated progress, and cost estimates.
03 Project Execution
Minimize the energy and optimize the side chain of the low-resolution peptide model to ensure the accuracy of the model. Use cutting-edge algorithms to balance parameters such as stability, thermodynamic properties, and surface properties, and output the optimal solution set of the model.
04 Result Delivery
Integrate high-precision cyclic peptide model (PDB format) and analysis methods to create a comprehensive project report that encapsulates the entire modeling process.
Cyclic peptides hold immense potential for drug development and biotechnology applications, owing to their unique properties and diverse biological activities. CD ComputaBio's cyclic peptide modeling service is designed to provide comprehensive and accurate modeling solutions that empower researchers and industry professionals to explore and harness the potential of cyclic peptides. Contact us today to learn more about our cyclic peptide modeling service and discover how we can assist you in your research endeavors.
Reference:
- Merz M L, Habeshian S, Li B, et al. De novo development of small cyclic peptides that are orally bioavailable[J]. Nature Chemical Biology, 2024, 20(5): 624-633.
* For Research Use Only.
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