Peptide Library Construction and Screening

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Peptide drugs have emerged as a significant class of therapeutics with applications ranging from oncology and metabolic diseases to infectious diseases and beyond. The development of peptide drugs involves the meticulous construction and screening of peptide libraries to identify promising lead compounds. Peptide library is a powerful screening tool in biological and chemical research. It is used to screen peptides with few key biological activities from large quantities of peptides. Peptide libraries have a wide range of applications in proteomics and related fields, such as drug discovery, protein-protein interactions, epitope screening, GPCR ligand screening, protein function analysis, enzyme substrate or inhibitor screening, messenger molecule development, and peptide/protein signal response.

As a leading biopharmaceutical company, Creative Peptides specializes in providing comprehensive peptide library construction and screening services, leveraging advanced technologies and methodologies to accelerate drug discovery and development.

The process of screening target peptide drug molecules in peptide libraries

Peptide library screening

Peptide libraries are essential tools in drug discovery, allowing researchers to explore a vast diversity of peptide sequences and structures. The screening strategies of peptide molecules are mainly divided into semi-artificial screening and artificial screening.

Semi-artificial screening

Semi-artificial screening involves modifying natural peptide molecules through a series of chemical alterations and property assessments, aiming to endow these molecules with drug-like potential.

  • Rational design

In the early days, peptide drugs were predominantly derived from natural peptide molecules through rational design based on medicinal chemistry knowledge. Classic drugs such as Vapreotide, Octreotide, and Pasireotide are derived from somatostatin through various modifications (mainly to extend the half-life). Recently approved radiopharmaceuticals or in vivo diagnostic agents, such as Lutathera, are also made by directly coupling relevant effector molecules to these peptides.

Many successful and developing molecules follow similar logic. For example, Ziconotide is derived from the toxin peptide omega-conotoxin, and approved Linaclotide originates from bacterial enterotoxin. TRPV6 inhibitor SOR-C13, derived from a natural toxin, is currently in Phase I clinical development. Another approach involves using domains directly involved in protein-protein interactions as the main body of the peptide molecule. Such as the integrin-targeting PDC drug BGC0222, whose peptide part directly uses the RGD sequence.

  • Rational design & high-throughput screening

This technology refers to a molecular modification process that combines rational improvements based on medicinal chemistry knowledge with high-throughput screening strategies. With the accumulation of structural biology and pharmaceutical knowledge, and the development of new tools such as computer-aided drug design, rational design of peptide drugs has become increasingly sophisticated and efficient. For example, SPEXIS developed the CXCR4 inhibitor POL6326 by extracting the segment of CXCR4's natural ligand that directly interacts with CXCR4, fusing a supporting structure to form a conformationally stable cyclic peptide (T22), and using this as a template to synthesize a large library of candidate molecules for screening. This process combines various desirable properties.

Fully artificial screening

Fully artificial screening involves creating peptide libraries through purely artificial design and using specific screening strategies to identify lead compounds. Based on fundamental properties, fully artificial screening can be divided into chemistry-based and biology-based categories.

  • Chemistry-based platform for peptide library construction and screening

DNA-encoded compound library (DEL)

The concept of DNA-encoded compounds (DEL) was first proposed by Professors Richard A. Lerner and Sydney Brenner in 1999. Due to the technological limitations at the time (high-throughput sequencing was not yet mature), it remained a theoretical idea. Later, scientists, notably Professor Dario Neri from ETH Zurich, successfully implemented DEL technology for drug development.

Using split-and-pool method, researchers can construct peptide compound libraries with DNA encoding. For specific targets, affinity-based screening and subsequent decoding can identify molecules that bind to the target, facilitating further evaluation and development. DEL is expected to become a mainstream technology in peptide drug discovery after continuous optimization.

One-bead-one-compound (OBOC)

The OBOC technology also employs a split-and-pool method to link a specific peptide molecule to each bead, followed by high-throughput screening. The process is similar to DEL. Screening binders are identified using mass spectrometry, which is more straightforward compared to DEL. However, early OBOC separation was cumbersome, the library size was relatively small compared to biological display technologies, and the screening process was complex. Practically, high-quality molecules are rarely screened from such libraries. Some laboratories are working to improve this system.

  • Biology-based platform for peptide library construction and screening

Phage display peptide library

Phage display technology was initially developed by Professor George Smith and later applied to antibody library display and selection by Sir Gregory Winter. Both were awarded the 2018 Nobel Prize in Chemistry. Notably, George Smith originally developed phage display technology to display peptide libraries.

Phage display for peptide libraries is widely used in academia and by numerous companies in the industry to discover peptide drugs. Gregory Winter et. al innovatively uses chemical molecules at the phage level to cyclize linear peptides, addressing the issue of excessive flexibility in linear peptides and creating high-quality cyclic peptide libraries.

mRNA display

mRNA display combines in vitro transcription with affinity screening. It originated from the groundbreaking work of Professors Jack W. Szostak and Richard W. Roberts, published in PNAS in 1997. They creatively used puromycin, covalently linked to the 3' end of mRNA fragments, as a translation inhibitor. During ribosomal translation of mRNA sequences into peptides, the ribosome recognizes puromycin, covalently links it to the peptide chain, and terminates the translation process. The released peptide chain is thus covalently linked to its encoding mRNA via puromycin, achieving an organic connection between genotype (mRNA) and phenotype (peptide), laying the foundation for high-throughput screening.

Professor Hiroaki Suga's laboratory introduced non-natural amino acids into the mRNA display system, achieving the translation of peptide chains with various non-natural amino acids and developing an improved mRNA display platform. This platform can quickly construct and screen libraries with over 1012 non-natural cyclic peptide compounds.

Integration of computational tools

In addition to experimental techniques, we integrate computational tools into our peptide library construction and screening processes. These tools enhance the efficiency and accuracy of our services, enabling the design and optimization of peptide libraries and the interpretation of screening results.

  • Computer-aided drug design (CADD)

CADD techniques, including molecular modeling, docking studies, and molecular dynamics simulations, are utilized to design peptides with optimal properties. These computational approaches help predict the binding affinity, stability, and specificity of peptides, guiding the construction of focused libraries and enhancing screening success rates.

  • Bioinformatics and data analysis

Advanced bioinformatics tools are employed to analyze screening data and identify promising lead compounds. Techniques such as sequence alignment, motif analysis, and machine learning algorithms are used to identify patterns and optimize peptide sequences. Our bioinformatics capabilities ensure the efficient processing and interpretation of large datasets, accelerating the identification of high-potential peptides.

Peptide library services

  • Custom peptide library construction

Based on the structure of known compounds, a series of peptides are constructed and designed in ways including but not limited to the following, and screened according to the functions and indications of the target compounds, in order to obtain new molecules or new structures with target efficacy.

N-terminus, C-terminus, side-chain modification: acylation, esterylation, PEGylation, beta-amino acid substitution, D-amino acid substitution, backbone aminomethylation, disulfide bond substitution, conformational locking (helix, beta-sheet), mirror polypeptide, cyclic peptide (end-to-head cyclization, side-chain cyclization), special molecular markers, hydroxy acid substitution.

  • High-throughput screening (HTS)

Our HTS platform enables the rapid testing of large peptide libraries against your target of interest, integrating robotics, advanced detection systems, and sophisticated data analysis tools to ensure high sensitivity and specificity.

  • Affinity-based screening

We use techniques such as surface plasmon resonance (SPR), biolayer interferometry (BLI), and enzyme-linked immunosorbent assays (ELISA) to measure binding interactions, providing detailed insights into binding kinetics and thermodynamics.

  • Functional screening

Our functional screening services include cell-based assays, enzymatic assays, and other bioassays to determine the biological activity of peptides, identifying those with desired therapeutic effects.

  • Peptide drug AI design and screening technology platform

Why choose Creative Peptides?

  • Comprehensive expertise

Our team comprises experts in peptide chemistry, molecular biology, bioinformatics, and pharmacology, ensuring a multidisciplinary approach to peptide library construction and screening.

  • Cutting-edge technology

We utilize the latest technologies and methodologies, including automated peptide synthesizers, high-throughput screening platforms, and advanced computational tools, to deliver high-quality results.

  • Customization and flexibility

We offer customizable services tailored to the specific needs of our clients, from small-scale pilot studies to large-scale screening projects, ensuring flexibility and scalability.

  • Speed and efficiency

Our streamlined processes and integrated workflows enable rapid turnaround times, allowing you to accelerate your drug discovery projects and bring novel therapeutics to market faster.

  • Quality and reliability

We adhere to stringent quality control measures and industry standards, ensuring the reliability and reproducibility of our results.

FAQ

1. What types of peptide libraries can you construct?

We construct a variety of peptide libraries, including linear, cyclic, and modified peptides, using techniques such as SPPS, OBOC, phage display, and mRNA display. We can also incorporate non-natural amino acids for enhanced diversity.

2. How do you ensure the quality and diversity of your peptide libraries?

We utilize advanced synthesis technologies and rigorous quality control measures. Each library undergoes thorough verification for sequence accuracy, purity, and diversity before being used in screening.

3. What screening technologies do you offer?

We offer high-throughput screening (HTS), affinity-based screening (SPR, BLI, ELISA), and functional screening (cell-based and enzymatic assays). These technologies allow us to identify peptides with high affinity, specificity, and desired biological activity.

4. Can you customize the peptide libraries and screening assays to specific targets?

Yes, we provide highly customizable services. We work closely with our clients to design peptide libraries and screening assays tailored to their specific targets and research needs.

5. What is the typical turnaround time for your services?

Turnaround times vary depending on the complexity and scale of the project. However, our streamlined processes and integrated workflows ensure rapid and efficient delivery of results, typically within a few weeks to a few months.

6. How do you handle data confidentiality and intellectual property?

We adhere to strict confidentiality agreements and respect our clients' intellectual property. All project data and results are handled with the utmost confidentiality and integrity.

7. Can you assist with the development of lead peptides identified through screening?

Yes, we offer additional services for the optimization and development of lead peptides, including structure-activity relationship (SAR) studies, stability assessments, and preclinical testing.

If you have any peptide synthesis requirement in mind, please do not hesitate to contact us at . We will endeavor to provide highly satisfying products and services.
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Creative Peptides has accumulated a huge library of peptide knowledge including frontier peptide articles, application of peptides, useful tools, and more!

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