Review on biomimetic affinity chromatography with short peptide ligands and its application to protein purification

doi:10.1016/j.chroma.2018.07.082

Journal of Chromatography A

Volume 1571, 12 October 2018, Pages 1-15

https://doi.org/10.1016/j.chroma.2018.07.082 Get rights and content

Highlights

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The rational designs of short peptide ligands were reviewed.
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The screening technologies for short peptide ligands were reviewed.
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The designs of the resins grafted with short peptide ligands were introduced.
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Applications of the resins grafted with short peptide ligands were discussed.

Abstract

Biomimetic affinity chromatography with short peptide ligands, as a promising bioseparation technique, has great potential to protein separation and purification, which is based on highly specific biological interactions between specially-designed ligands and target proteins. Generally, short peptide ligands with the chain length ranging from two to nine amino acids could be divided into two types, linear peptide ligands and cyclic peptide ligands. To obtain the desired short peptide ligands, rational design strategies could be applied by knowing the 3-dimensional (3D) information of the receptors or just knowing the surface cavities and the active site of the receptors. Subsequently, several technologies could be used to screen the optimal peptide ligands from the designed peptide ligands, such as combinatorial chemistry, phage display, mRNA display and computer-based screening technology. The screening efficiency is dependent on the different technology for individual target proteins. After screening, the chromatographic resin could be prepared by coupling the optimal short peptide ligand onto a matrix with some spacer arms. The suitable matrix and spacer arms are also important to enhance the ability of the peptide ligand for protein purification. With the advantages of high affinity, high adsorption capacity, structural stability, low immunogenicity and low cost, biomimetic affinity chromatography with short peptides as the functional ligands have shown an extensive development and application potentiality to protein purification. In this review, we focused on the strategies of rational designs and screening for short peptide ligands, and some items on the perpetration of new resins and their applications for protein purification would also be discussed.

Introduction

Affinity chromatography is widely used for protein purification, while the most commonly used adsorbents are natural ligands, such as enzyme substrates, coenzymes, inhibitors, effectors and antigens [1]. However, these natural ligands have some shortcomings, such as high cost, harsh elution condition and ligand leakage [[2], [3], [4]]. As a part of affinity chromatography, biomimetic affinity chromatography, which was first proposed by Lowe in 1992 has been developed to avoid these problems [5]. Ligands of biomimetic affinity chromatography are synthetic compounds that mimicking the properties of natural ligands with the advantages of low cost, low immunogenicity and high chemical stability [6,7]. In the early studies, compounds like metal chelates [8,9] and reactive dyes [10,11] were applied as biomimetic affinity ligands, which normally showed low selectivity toward specific receptors. With the development of several novel technologies, for example, high-throughput screening [12], combinatorial chemistry [13], crystallization technique [14] and computer simulation [15], biomimetic ligands with high specificity and selectivity have been better designed and applied for protein separation.

Short peptide ligands as an important part of biomimetic ligands have raised increasing interest in recent years [16,17]. Typically, there are many interactions between receptors and affinity resins, including hydrophobic interaction, electrostatic interaction and hydrogen bond [18]. Therefore, it is necessary to have a comprehensive understanding of the molecular interactions between ligands and receptors to aid the design of appropriate affinity ligands. In earlier researches, Geysen and coworkers [19] found that the binding effects of natural ligands and receptors were mainly dominated by critical residues. Meanwhile, short peptides with those critical residues could mimic the epitopes and are able to compete with the natural ligands for protein binding [20]. These discoveries indicated the great potential of peptide ligands to bind receptors with high affinity. To obtain the optimal short peptide ligands, a vast peptide library should be established at first [21]. Then, several screening technologies would be used to screen the peptide ligand with high affinity. After that, the screened ligand could be coupled onto the matrix to prepare biomimetic chromatography resin and its ability for protein purification would be tested. In addition, some advanced methods could be beneficial to simplify the screening steps to save time, manpower and cost of the research. For instance, molecular docking would be useful to reduce the number of candidate peptides in library.

In this review, the lasted developments of short peptide ligands for biomimetic affinity chromatography as seen in Table 1 would be introduced, and their characteristics and potential applications would be discussed. It is expected that this article could provide some insight into the future development of novel short peptide ligands for biomimetic affinity chromatography.

Section snippets

Linear and cyclic short peptide ligands

Many bioactive peptides with critical residues from natural ligands have been found to have common structural properties that include a relatively short peptide length ranging from two to nine amino acids [22,23]. Generally, short peptide ligands could be divided into two types, linear short peptide ligands and cyclic short peptide ligands. To simplify the expression of short peptide ligands, all the amino acids in the following article are abbreviated (Table 2).

Rational designs for short peptide ligands

Compared to the random assortment of 20 natural amino acids, rational designs of short peptide ligands have been performed to reduce the complexity of the huge screening. The crucial point for the binding of short peptide ligands and target proteins is the interactions between them. Therefore, rational designs for short peptide ligands normally relay on the detailed knowledge of binding force [39]. In addition, molecular recognition and binding affinity of short peptide ligands are driven by a

Methods of screening short peptide ligands

Numbers of methods have been applied for screening the short peptide ligands after the rational designs, such as combinatorial chemistry, mRNA display, phage display, and computer-based virtual screening technology.

Rational designs for the resins coupled with short peptide ligands

After screening the short peptide ligand, the ligand should be coupled onto some matrix with a spacer arm to prepare the resin for protein separation. Some short (cyclic) peptides coupled onto some matrix with specific spacer arms are summarized in Table 1, which can specifically bind target proteins reported before.

Application of biomimetic affinity chromatography with short peptide ligands

With the advantages of high affinity, high stability and adsorption capacity, low immunogenicity and low cost, short peptide ligands have shown an extensive development and application potentials for protein purification with biomimetic affinity chromatography. The adsorption behaviors and applications of short peptide resins reported for protein purification are reviewed as follows.

Conclusions

Biomimetic affinity chromatography with short peptide ligands has a great potential for protein purification, due to the benefits of high affinity, strong stability, low immunogenicity and low cost. In order to obtain high-affinity ligands for target proteins, the first step is to design the structure of short peptide ligands and establish a ligand library. Subsequently, several technologies, such as combinatorial chemistry, mRNA display, phage display and computer-based screening, could be

Acknowledgment

This work was supported by the National Natural Science Foundation of China.

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Review articleReview on biomimetic affinity chromatography with short peptide ligands and its application to protein purification

Highlights

Abstract

Introduction

Section snippets

Linear and cyclic short peptide ligands

Rational designs for short peptide ligands

Methods of screening short peptide ligands

Rational designs for the resins coupled with short peptide ligands

Application of biomimetic affinity chromatography with short peptide ligands

Conclusions

Acknowledgment

Sep. Purif. Technol.

Bioconjugate Chem.

Trends Biotechnol.

J. Chromatogr. A

J. Chromatogr. B.

J. Immunol. Methods

Method Enzymol.

J. Chromatogr. A

Arch. Biochem. Biophys.

Mol. Immunol.

J. Chromatogr. A

J. Chromatogr. A

Biochem. Eng. J.

J. Chromatogr. A

J. Chromatogr. A

J. Chromatogr. A

J. Chromatogr. A

Tetrahedron

Drug Discov. Today

J. Chromatogr. B.

J. Chromatogr. A

J. Chromatogr. A

J. Chromatogr. A

Curr. Opin. Chem. Biol.

Anal. Biochem.

Clin. Biochem.

Drug Discov. Today

J. Virol. Methods

Bioorg. Med. Chem. Lett.

J. Biotechnol.

Enzyme Microb. Technol.

Biomaterials

Int. J. Biol. Macromol.

J. Chromatogr. A

Peptide ligands of the immunoglobulin G Fc region identified by screening phage libraries and site-directed mutagenesis

FEBS J.

A strategy for the generation of biomimetic ligands for affinity chromatography. Combinatorial synthesis and biological evaluation of an IgG binding ligand

J. Mol. Recognit.

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J. Mol. Recognit.: JMR

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SpeedScreen, a label-free, affinity-based high-throughput screening technology for the discovery of orphan protein ligands

Chimia

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Cryst. Growth Des.

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Biochem. Eng. J.

Chromatography of amino acids and short peptides. New advances

Biomed. Chromatogr.

Molecular insights into the binding selectivity of a synthetic ligand DAAG to Fc fragment of IgG

J. Mol. Recognit.

A synthetic mimic of a discontinuous binding site on interleukin-10

Nat. Biotechnol.

Fc-binding ligands of immunoglobulin G: an overview of high affinity proteins and peptides

Materials

Bioactive proteins and peptides from food sources. Applications of bioprocesses used in isolation and recovery

Curr. Pharm. Design.

Recent progress in the solid-state NMR studies of short peptides: techniques, structure and dynamics

A hexamer peptide ligand that binds selectively to staphylococcal enterotoxin B: isolation from a solid phase combinatorial library

J. Pept. Res.

Hexamer peptide affinity resins that bind the Fc region of human immunoglobulin G

J. Pept. Res.

Binding site on human immunoglobulin G for the affinity ligand HWRGWV

J. Mol. Recognit.

Review article
Review on biomimetic affinity chromatography with short peptide ligands and its application to protein purification