1
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Hu M, Dong X, Shi Q, Sun Y. Identification of a broad-spectrum high-affinity peptide ligand for the purification of spike proteins. J Chromatogr A 2024; 1723:464912. [PMID: 38643740 DOI: 10.1016/j.chroma.2024.464912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/07/2024] [Accepted: 04/11/2024] [Indexed: 04/23/2024]
Abstract
Since the outbreak of coronavirus disease 2019, the global demand for vaccines has increased rapidly to prevent infection and protect high-risk populations. However, identifying viral mutations poses an additional challenge for chromatographic purification of vaccines and subunit vaccines. In this study, a new affinity peptide model, X1VX2GLNX3WX4RYSK, was established, and a library of 612 peptides was generated for ligand screening. Based on a multistep strategy of ligand screening, 18 candidate peptides were obtained. The top ranking peptide, LP14 (YVYGLNIWLRYSK), and two other representative peptides, LP02 and LP06, with lower rankings were compared via molecular dynamics simulation. The results revealed that peptide binding to the receptor binding domain (RBD) was driven by hydrophobic interactions and the key residues involved in the binding were identified. Surface plasmon resonance analysis further confirmed that LP14 had the highest affinity for the wild RBD (Kd=0.520 μmol/L), and viral mutation had little influence on the affinity of LP14, demonstrating its great potential as a broad-spectrum ligand for RBD purification. Finally, chromatographic performance of LP14-coupled gel-packed column verified that both wild and omicron RBDs could be purified and were eluted by 0.1 mol/L Gly-HCl buffer (pH 3.0). This research identified a broad-spectrum peptide for RBD purification based on rational design and demonstrated its potential application in the purification of RBDs from complex feedstock.
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Affiliation(s)
- Mengke Hu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Xiaoyan Dong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Qinghong Shi
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China.
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China.
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2
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Wong JYK, Ekanayake AI, Kharchenko S, Kirberger SE, Qiu R, Kelich P, Sarkar S, Li J, Fernandez KX, Alvizo-Paez ER, Miao J, Kalhor-Monfared S, John JD, Kang H, Choi H, Nuss JM, Vederas JC, Lin YS, Macauley MS, Vukovic L, Pomerantz WCK, Derda R. Genetically encoded discovery of perfluoroaryl macrocycles that bind to albumin and exhibit extended circulation in vivo. Nat Commun 2023; 14:5654. [PMID: 37704629 PMCID: PMC10499988 DOI: 10.1038/s41467-023-41427-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 08/17/2023] [Indexed: 09/15/2023] Open
Abstract
Peptide-based therapeutics have gained attention as promising therapeutic modalities, however, their prevalent drawback is poor circulation half-life in vivo. In this paper, we report the selection of albumin-binding macrocyclic peptides from genetically encoded libraries of peptides modified by perfluoroaryl-cysteine SNAr chemistry, with decafluoro-diphenylsulfone (DFS). Testing of the binding of the selected peptides to albumin identified SICRFFC as the lead sequence. We replaced DFS with isosteric pentafluorophenyl sulfide (PFS) and the PFS-SICRFFCGG exhibited KD = 4-6 µM towards human serum albumin. When injected in mice, the concentration of the PFS-SICRFFCGG in plasma was indistinguishable from the reference peptide, SA-21. More importantly, a conjugate of PFS-SICRFFCGG and peptide apelin-17 analogue (N3-PEG6-NMe17A2) showed retention in circulation similar to SA-21; in contrast, apelin-17 analogue was cleared from the circulation after 2 min. The PFS-SICRFFC is the smallest known peptide macrocycle with a significant affinity for human albumin and substantial in vivo circulation half-life. It is a productive starting point for future development of compact macrocycles with extended half-life in vivo.
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Affiliation(s)
- Jeffrey Y K Wong
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Arunika I Ekanayake
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Serhii Kharchenko
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Steven E Kirberger
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ryan Qiu
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Payam Kelich
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Susmita Sarkar
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Jiaqian Li
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | | | - Edgar R Alvizo-Paez
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Jiayuan Miao
- Department of Chemistry, Tufts University, Medford, MA, 02155, USA
| | | | - J Dwyer John
- Ferring Research Institute, San Diego, CA, 92121, USA
| | - Hongsuk Kang
- Quantum Intelligence Corp., 31F, One IFC, 10 Gukjegeumyung-ro, Yeongdeungpo-gu-Seoul, Republic of Korea
| | - Hwanho Choi
- Quantum Intelligence Corp., 31F, One IFC, 10 Gukjegeumyung-ro, Yeongdeungpo-gu-Seoul, Republic of Korea
| | - John M Nuss
- Ferring Research Institute, San Diego, CA, 92121, USA
| | - John C Vederas
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, MA, 02155, USA
| | - Matthew S Macauley
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Lela Vukovic
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, TX, 79968, USA
| | | | - Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada.
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3
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Randall JR, Wang X, Groover KE, O'Donnell AC, Davies BW. Using display technologies to identify macrocyclic peptide antibiotics. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119473. [PMID: 37011732 PMCID: PMC10198949 DOI: 10.1016/j.bbamcr.2023.119473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 02/09/2023] [Accepted: 02/19/2023] [Indexed: 04/03/2023]
Abstract
Antibiotic resistant bacterial infections are now a leading cause of global mortality. While drug resistance continues to spread, the clinical antibiotic pipeline has become bare. This discord has focused attention on developing new strategies for antimicrobial discovery. Natural macrocyclic peptide-based products have provided novel antibiotics and antibiotic scaffolds targeting several essential bacterial cell envelope processes, but discovery of such natural products remains a slow and inefficient process. Synthetic strategies employing peptide display technologies can quickly screen large libraries of macrocyclic sequences for specific target binding and general antibacterial potential providing alternative approaches for new antibiotic discovery. Here we review cell envelope processes that can be targeted with macrocyclic peptide therapeutics, outline important macrocyclic peptide display technologies, and discuss future strategies for both library design and screening.
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Affiliation(s)
- Justin R Randall
- University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, USA.
| | - Xun Wang
- University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, USA
| | - Kyra E Groover
- University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, USA
| | - Angela C O'Donnell
- University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, USA
| | - Bryan W Davies
- University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, USA.
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4
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Fang YM, Zhang QL, Lin DQ, Yao SJ. One kind of challenging tetrapeptide biomimetic chromatographic resin for antibody separation. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1208:123407. [DOI: 10.1016/j.jchromb.2022.123407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/24/2022] [Accepted: 08/03/2022] [Indexed: 11/30/2022]
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5
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Emerging affinity ligands and support materials for the enrichment of monoclonal antibodies. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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6
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Lázaro-Mixteco PE, González-Coronel JM, Hernández-Padilla L, Martínez-Alcantar L, Martínez-Carranza E, López-Bucio JS, Guevara-García ÁA, Campos-García J. Transcriptomics Reveals the Mevalonate and Cholesterol Pathways Blocking as Part of the Bacterial Cyclodipeptides Cytotoxic Effects in HeLa Cells of Human Cervix Adenocarcinoma. Front Oncol 2022; 12:790537. [PMID: 35359411 PMCID: PMC8964019 DOI: 10.3389/fonc.2022.790537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/08/2022] [Indexed: 11/23/2022] Open
Abstract
The incidence of human cervix adenocarcinoma (CC) caused by papillomavirus genome integration into the host chromosome is the third most common cancer among women. Bacterial cyclodipeptides (CDPs) exert cytotoxic effects in human cervical cancer HeLa cells, primarily by blocking the PI3K/Akt/mTOR pathway, but downstream responses comprising gene expression remain unstudied. Seeking to understand the cytotoxic and anti-proliferative effects of CDPs in HeLa cells, a global RNA-Seq analysis was performed. This strategy permitted the identification of 151 differentially expressed genes (DEGs), which were either up- or down-regulated in response to CDPs exposure. Database analysis, including Gene Ontology (COG), and the Kyoto Encyclopedia of Genes and Genomes (KEGG), revealed differential gene expression on cancer transduction signals, and metabolic pathways, for which, expression profiles were modified by the CDPs exposure. Bioinformatics confirmed the impact of CDPs in the differential expression of genes from signal transduction pathways such as PI3K-Akt, mTOR, FoxO, Wnt, MAPK, P53, TGF-β, Notch, apoptosis, EMT, and CSC. Additionally, the CDPs exposure modified the expression of cancer-related transcription factors involved in the regulation of processes such as epigenetics, DNA splicing, and damage response. Interestingly, transcriptomic analysis revealed the participation of genes of the mevalonate and cholesterol biosynthesis pathways; in agreement with this observation, total cholesterol diminished, confirming the blockage of the cholesterol synthesis by the exposure of HeLa cells to CDPs. Interestingly, the expression of some genes of the mevalonate and cholesterol synthesis such as HMGS1, HMGCR, IDI1, SQLE, MSMO1, SREBF1, and SOAT1 was up-regulated by CDPs exposure. Accordingly, metabolites of the mevalonate pathway were accumulated in cultures treated with CDPs. This finding further suggests that the metabolism of cholesterol is crucial for the occurrence of CC, and the blockade of the sterol synthesis as an anti-proliferative mechanism of the bacterial CDPs, represents a reasonable chemotherapeutic drug target to explore. Our transcriptomic study supports the anti-neoplastic effects of bacterial CDPs in HeLa cells shown previously, providing new insights into the transduction signals, transcription factors and metabolic pathways, such as mevalonate and cholesterol that are impacted by the CDPs and highlights its potential as anti-neoplastic drugs.
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Affiliation(s)
- Pedro E Lázaro-Mixteco
- Laboratorio de Biotecnología Microbiana, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - José M González-Coronel
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Laura Hernández-Padilla
- Laboratorio de Biotecnología Microbiana, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Lorena Martínez-Alcantar
- Laboratorio de Biotecnología Microbiana, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Enrique Martínez-Carranza
- Laboratorio de Biotecnología Microbiana, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Jesús Salvador López-Bucio
- CONACYT-UMSNH, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Ángel A Guevara-García
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Jesús Campos-García
- Laboratorio de Biotecnología Microbiana, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
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7
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Melsen PRA, Yoshisada R, Jongkees SAK. Opportunities for expanding encoded chemical diversification and improving hit enrichment in mRNA-displayed peptide libraries. Chembiochem 2022; 23:e202100685. [PMID: 35100479 PMCID: PMC9306583 DOI: 10.1002/cbic.202100685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/27/2022] [Indexed: 11/07/2022]
Abstract
DNA‐encoded small‐molecule libraries and mRNA displayed peptide libraries both use numerically large pools of oligonucleotide‐tagged molecules to identify potential hits for protein targets. They differ dramatically, however, in the ‘drug‐likeness’ of the molecules that each can be used to discover. We give here an overview of the two techniques, comparing some advantages and disadvantages of each, and suggest areas where particularly mRNA display can benefit from adopting advances developed with DNA‐encoded small molecule libraries. We outline cases where chemical modification of the peptide library has already been used in mRNA display, and survey opportunities to expand this using examples from DNA‐encoded small molecule libraries. We also propose potential opportunities for encoding such reactions within the mRNA/cDNA tag of an mRNA‐displayed peptide library to allow a more diversity‐oriented approach to library modification. Finally, we outline alternate approaches for enriching target‐binding hits from a pooled and tagged library, and close by detailing several examples of how an adjusted mRNA‐display based approach could be used to discover new ‘drug‐like’ modified small peptides.
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Affiliation(s)
- Paddy R A Melsen
- Vrije Universiteit Amsterdam, Department of Chemistry and Pharmaceutical Sciences, NETHERLANDS
| | - Ryoji Yoshisada
- Vrije Universiteit Amsterdam, Department of Chemistry and Pharmaceutical Sciences, NETHERLANDS
| | - Seino A K Jongkees
- Vrije Universiteit Amsterdam, Chemistry and Pharmaceutical Sciences, de Boelelaan 1108, 1081 HZ, Amsterdam, NETHERLANDS
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8
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Bacon K, Menegatti S, Rao BM. Discovery of Cyclic Peptide Binders from Chemically Constrained Yeast Display Libraries. Methods Mol Biol 2022; 2491:387-415. [PMID: 35482201 DOI: 10.1007/978-1-0716-2285-8_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cyclic peptides with engineered protein-binding activity have great potential as therapeutic and diagnostic reagents owing to their favorable properties, including high affinity and selectivity. Cyclic peptide binders have generally been isolated from phage display combinatorial libraries utilizing panning based selections. As an alternative, we have developed a yeast surface display platform to identify and characterize cyclic peptide binders from genetically encoded combinatorial libraries. Through a combination of magnetic selection and fluorescence-activated cell sorting (FACS), high-affinity cyclic peptide binders can be efficiently isolated from yeast display libraries. In this platform, linear peptide precursors are expressed as yeast surface fusions. To achieve cyclization of the linear precursors, the cells are incubated with disuccinimidyl glutarate, which crosslinks amine groups within the displayed linear peptide sequence. Here, we detail protocols for cyclizing linear peptides expressed as yeast surface fusions. We also discuss how to synthesize a yeast display library of linear peptide precursors. Subsequently, we provide suggestions on how to utilize magnetic selections and FACS to isolate cyclic peptide binders for target proteins of interest from a peptide combinatorial library. Lastly, we detail how yeast surface displayed cyclic peptides can be used to obtain efficient estimates of binding affinity, eliminating the need for chemically synthesized peptides when performing mutant characterization.
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Affiliation(s)
- Kaitlyn Bacon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC, USA
| | - Balaji M Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC, USA.
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9
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Fang YM, Lin DQ, Yao SJ. Tetrapeptide ligands screening for antibody separation and purification by molecular simulation and experimental verification. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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10
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Improved antibody adsorption performance of phenyl-based mixed-mode adsorbents by adjusting the functional group of ligand. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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11
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Peptide Affinity Chromatography Applied to Therapeutic Antibodies Purification. Int J Pept Res Ther 2021; 27:2905-2921. [PMID: 34690622 PMCID: PMC8525457 DOI: 10.1007/s10989-021-10299-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2021] [Indexed: 12/12/2022]
Abstract
The interest in therapeutic monoclonal antibodies (mAbs) has significantly grown in the pharmaceutical industry, exceeding 100 FDA mAbs approved. Although the upstream processing of their industrial production has been significantly improved in the last years, the downstream processing still depends on immobilized protein A affinity chromatography. The high cost, low capacity and short half-life of immobilized protein A chromatography matrices, encouraged the design of alternative short-peptide ligands for mAb purification. Most of these peptides have been obtained by screening combinatorial peptide libraries. These low-cost ligands can be easily produced by solid-phase peptide synthesis and can be immobilized on chromatographic supports, thus obtaining matrices with high capacity and selectivity. Furthermore, matrices with immobilized peptide ligands have longer half-life than those with protein A due to the higher stability of the peptides. In this review the design and synthesis of peptide ligands, their immobilization on chromatographic supports and the evaluation of the affinity supports for their application in mAb purification is described.
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12
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Kamalinia G, Grindel BJ, Takahashi TT, Millward SW, Roberts RW. Directing evolution of novel ligands by mRNA display. Chem Soc Rev 2021; 50:9055-9103. [PMID: 34165126 PMCID: PMC8725378 DOI: 10.1039/d1cs00160d] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
mRNA display is a powerful biological display platform for the directed evolution of proteins and peptides. mRNA display libraries covalently link the displayed peptide or protein (phenotype) with the encoding genetic information (genotype) through the biochemical activity of the small molecule puromycin. Selection for peptide/protein function is followed by amplification of the linked genetic material and generation of a library enriched in functional sequences. Iterative selection cycles are then performed until the desired level of function is achieved, at which time the identity of candidate peptides can be obtained by sequencing the genetic material. The purpose of this review is to discuss the development of mRNA display technology since its inception in 1997 and to comprehensively review its use in the selection of novel peptides and proteins. We begin with an overview of the biochemical mechanism of mRNA display and its variants with a particular focus on its advantages and disadvantages relative to other biological display technologies. We then discuss the importance of scaffold choice in mRNA display selections and review the results of selection experiments with biological (e.g., fibronectin) and linear peptide library architectures. We then explore recent progress in the development of "drug-like" peptides by mRNA display through the post-translational covalent macrocyclization and incorporation of non-proteogenic functionalities. We conclude with an examination of enabling technologies that increase the speed of selection experiments, enhance the information obtained in post-selection sequence analysis, and facilitate high-throughput characterization of lead compounds. We hope to provide the reader with a comprehensive view of current state and future trajectory of mRNA display and its broad utility as a peptide and protein design tool.
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Affiliation(s)
- Golnaz Kamalinia
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
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13
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Focused peptide library screening as a route to a superior affinity ligand for antibody purification. Sci Rep 2021; 11:11650. [PMID: 34079028 PMCID: PMC8173005 DOI: 10.1038/s41598-021-91208-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/24/2021] [Indexed: 12/18/2022] Open
Abstract
Affinity chromatography is the linchpin of antibody downstream processing and typically relies on bacterial immunoglobulin (Ig)-binding proteins, epitomized by staphylococcal protein A-based ligands. However, such affinity ligands are fairly costly and suffer from chemical instability, leading to ligand denaturation and leaching from chromatographic support. Innovations in this area are aimed at developing robust and highly selective antibody ligands capable of withstanding harsh column sanitization conditions. We report the development and first-stage characterization of a selective short linear peptide ligand of the IgG Fc region capable of capturing all four IgG subclasses. The ligand was discovered through in vitro directed evolution. A focused phage-display library based on a previously identified peptide lead was subjected to a single-round screen against a pool of human IgG. The hits were identified with next-generation sequencing and ranked according to the enrichment ratio relative to their frequency in the pre-screened library. The top enriched peptide GSYWYNVWF displaying highest affinity for IgG was coupled to bromohydrin-activated agarose beads via a branched linker. The resulting affinity matrix was characterized with a dynamic binding capacity of approx. 43 mg/mL, on par with commercially employed protein A-based resin.
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14
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A purification platform for antibodies and derived fragments using a de novo designed affinity adsorbent. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2021.118476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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15
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Binzel DW, Li X, Burns N, Khan E, Lee WJ, Chen LC, Ellipilli S, Miles W, Ho YS, Guo P. Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity. Chem Rev 2021; 121:7398-7467. [PMID: 34038115 DOI: 10.1021/acs.chemrev.1c00009] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA nanotechnology is the bottom-up self-assembly of nanometer-scale architectures, resembling LEGOs, composed mainly of RNA. The ideal building material should be (1) versatile and controllable in shape and stoichiometry, (2) spontaneously self-assemble, and (3) thermodynamically, chemically, and enzymatically stable with a long shelf life. RNA building blocks exhibit each of the above. RNA is a polynucleic acid, making it a polymer, and its negative-charge prevents nonspecific binding to negatively charged cell membranes. The thermostability makes it suitable for logic gates, resistive memory, sensor set-ups, and NEM devices. RNA can be designed and manipulated with a level of simplicity of DNA while displaying versatile structure and enzyme activity of proteins. RNA can fold into single-stranded loops or bulges to serve as mounting dovetails for intermolecular or domain interactions without external linking dowels. RNA nanoparticles display rubber- and amoeba-like properties and are stretchable and shrinkable through multiple repeats, leading to enhanced tumor targeting and fast renal excretion to reduce toxicities. It was predicted in 2014 that RNA would be the third milestone in pharmaceutical drug development. The recent approval of several RNA drugs and COVID-19 mRNA vaccines by FDA suggests that this milestone is being realized. Here, we review the unique properties of RNA nanotechnology, summarize its recent advancements, describe its distinct attributes inside or outside the body and discuss potential applications in nanotechnology, medicine, and material science.
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Affiliation(s)
- Daniel W Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Xin Li
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Nicolas Burns
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Eshan Khan
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wen-Jui Lee
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Li-Ching Chen
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Satheesh Ellipilli
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wayne Miles
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yuan Soon Ho
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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16
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González-Muñiz R, Bonache MÁ, Pérez de Vega MJ. Modulating Protein-Protein Interactions by Cyclic and Macrocyclic Peptides. Prominent Strategies and Examples. Molecules 2021; 26:445. [PMID: 33467010 PMCID: PMC7830901 DOI: 10.3390/molecules26020445] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 12/11/2022] Open
Abstract
Cyclic and macrocyclic peptides constitute advanced molecules for modulating protein-protein interactions (PPIs). Although still peptide derivatives, they are metabolically more stable than linear counterparts, and should have a lower degree of flexibility, with more defined secondary structure conformations that can be adapted to imitate protein interfaces. In this review, we analyze recent progress on the main methods to access cyclic/macrocyclic peptide derivatives, with emphasis in a few selected examples designed to interfere within PPIs. These types of peptides can be from natural origin, or prepared by biochemical or synthetic methodologies, and their design could be aided by computational approaches. Some advances to facilitate the permeability of these quite big molecules by conjugation with cell penetrating peptides, and the incorporation of β-amino acid and peptoid structures to improve metabolic stability, are also commented. It is predicted that this field of research could have an important future mission, running in parallel to the discovery of new, relevant PPIs involved in pathological processes.
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Affiliation(s)
- Rosario González-Muñiz
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain; (M.Á.B.); (M.J.P.d.V.)
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Bacon K, Bowen J, Reese H, Rao BM, Menegatti S. Use of Target-Displaying Magnetized Yeast in Screening mRNA-Display Peptide Libraries to Identify Ligands. ACS COMBINATORIAL SCIENCE 2020; 22:738-744. [PMID: 33089990 DOI: 10.1021/acscombsci.0c00171] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This work presents the first use of yeast-displayed protein targets for screening mRNA-display libraries of cyclic and linear peptides. The WW domains of Yes-Associated Protein 1 (WW-YAP) and mitochondrial import receptor subunit TOM22 were adopted as protein targets. Yeast cells displaying WW-YAP or TOM22 were magnetized with iron oxide nanoparticles to enable the isolation of target-binding mRNA-peptide fusions. Equilibrium adsorption studies were conducted to estimate the binding affinity (KD) of select WW-YAP-binding peptides: KD values of 37 and 4 μM were obtained for cyclo[M-AFRLC-K] and its linear cognate, and 40 and 3 μM for cyclo[M-LDFVNHRSRG-K] and its linear cognate, respectively. TOM22-binding peptide cyclo[M-PELNRAI-K] was conjugated to magnetic beads and incubated with yeast cells expressing TOM22 and luciferase. A luciferase-based assay showed a 4.5-fold higher binding of TOM22+ yeast compared to control cells. This work demonstrates that integrating mRNA- and yeast-display accelerates the discovery of peptide ligands.
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Affiliation(s)
- Kaitlyn Bacon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Room 2-009, Raleigh, North Carolina 27606, United States
| | - John Bowen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Room 2-009, Raleigh, North Carolina 27606, United States
| | - Hannah Reese
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Room 2-009, Raleigh, North Carolina 27606, United States
| | - Balaji M Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Room 2-009, Raleigh, North Carolina 27606, United States
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Drive, Raleigh, North Carolina 27606, United States
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Room 2-009, Raleigh, North Carolina 27606, United States
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Drive, Raleigh, North Carolina 27606, United States
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18
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Lei Y, Liu X, Lu L, Liu C, Xu R, Huang S, Shen Y, Deng C, Yu J, Zhang T, Crommen J, Wang Q, Jiang Z. Rapid preparation of 1-vinylimidazole based non-affinity polymers for the highly-selective purification of antibodies from multiple biological sources. J Chromatogr A 2020; 1632:461607. [PMID: 33080535 DOI: 10.1016/j.chroma.2020.461607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/02/2020] [Accepted: 10/04/2020] [Indexed: 10/23/2022]
Abstract
There is an urgent need for developing advanced purification techniques with the merits of low cost and satisfactory capacity in order to meet the challenges in the current downstream purification of monoclonal antibodies (mAbs). Herein, a simple and inexpensive nitrogen heterocycle molecule, 1-vinylimidazole (VIM), was proposed as the capture ligand of antibodies for the first time. The corresponding VIM-based non-affinity polymeric material (polyVIM) was then fabricated via a one-step polymerization for use in the highly selective purification of antibodies. Compared to the previously reported materials, this novel material exhibited many advantages without clearly sacrificing selectivity, such as a simpler and faster fabrication (within 1.5 h), comparable or even higher binding capacity (saturated static adsorption capacity > 190 mg/g polymer, dynamic binding capacity about 31.62 mg/g polymer), lower non-specific protein adsorption, and much lower cost. Notably, the polyVIM can effectively purify the antibodies from multiple biological sources with high purity (95.4% for mAbs in the cell culture medium, 93.3% for hIgG in the human serum), with an acceptable recovery (91.6% for mAbs, 77.0% for hIgG), and good reusability (> 10 times). Moreover, the target ELISA binding assay and NFAT-luc reporter gene assay demonstrated that the enriched antibodies can well maintain their binding activity and bioactivity during the whole purification process. The excellent performance of the polyVIM material may be attributed to the high recognition ability of VIM for antibodies, as well as the biocompatible and antifouling properties of the porous polymer. This study provides a promising alternative material for the purification of mAbs in downstream processes and the enrichment of hIgG in human serum.
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Affiliation(s)
- Yutian Lei
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Xiao Liu
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Li Lu
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Cuihua Liu
- Bio-Thera Solutions, Ltd., Guangzhou 510700, China
| | - Rongrong Xu
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Shengfeng Huang
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Yuan Shen
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | | | - Jinchen Yu
- Bio-Thera Solutions, Ltd., Guangzhou 510700, China
| | - Tingting Zhang
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Jacques Crommen
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou 510632, China; Laboratory of Analytical Pharmaceutical Chemistry, Department of Pharmaceutical Sciences, CIRM, University of Liege, CHU B36, B-4000, Liege, Belgium
| | - Qiqin Wang
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou 510632, China; Department of Pharmacy and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine & New Drug Research, Jinan University, Guangzhou 510632, China.
| | - Zhengjin Jiang
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou 510632, China; Department of Pharmacy and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine & New Drug Research, Jinan University, Guangzhou 510632, China.
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Development of histidine-tagged cyclic peptide functionalized monolithic material for the affinity purification of antibodies in biological matrices. J Chromatogr A 2020; 1635:461707. [PMID: 33254002 DOI: 10.1016/j.chroma.2020.461707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 01/04/2023]
Abstract
The rapidly increasing applications of monoclonal antibodies (mAbs) in therapy have necessitated the development of mAb production and purification technologies for both academic and industrial usage. Herein, a histidine-tagged cyclic peptide (HHHHHHGSGSGSDC*AWHLGELVWC*T, the disulfide-bonded cysteines of which are indicated by asterisks, named HT25-cyclopeptide) functionalized monolithic material was developed by the metal ion chelation-based approach. The resulting material possessed suitable affinity and peptide ligand density (13.8 mg peptide ligand per mL of material), good porosity (67.1 %), acceptable specific surface area (52.95 m2/g), and lots of macropores (4.13 μm). Moreover, excellent antibody-specific selectivity, comparable or even better binding capacity (for dried material, maximum static binding capacity and dynamic binding capacity are about 119.3 mg/g and 17.05 mg/g, respectively) for antibody compared to previously developed affinity materials, acceptable resistance to trypsin digestion, and negligible nonspecific protein adsorption, were also achieved on this novel monolithic material. Compared with the corresponding cyclic peptide-based sepharose material, milder elution conditions were employed for the HT25-cyclopeptide-based monolithic material, which could effectively prevent the aggregation and denaturation of the enriched antibodies. This novel material was then successfully applied to the affinity enrichment and purification of mAbs (including infliximab and rituximab) in different cell culture media or IgG in human serum.
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20
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Chu W, Prodromou R, Day KN, Schneible JD, Bacon KB, Bowen JD, Kilgore RE, Catella CM, Moore BD, Mabe MD, Alashoor K, Xu Y, Xiao Y, Menegatti S. Peptides and pseudopeptide ligands: a powerful toolbox for the affinity purification of current and next-generation biotherapeutics. J Chromatogr A 2020; 1635:461632. [PMID: 33333349 DOI: 10.1016/j.chroma.2020.461632] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 02/08/2023]
Abstract
Following the consolidation of therapeutic proteins in the fight against cancer, autoimmune, and neurodegenerative diseases, recent advancements in biochemistry and biotechnology have introduced a host of next-generation biotherapeutics, such as CRISPR-Cas nucleases, stem and car-T cells, and viral vectors for gene therapy. With these drugs entering the clinical pipeline, a new challenge lies ahead: how to manufacture large quantities of high-purity biotherapeutics that meet the growing demand by clinics and biotech companies worldwide. The protein ligands employed by the industry are inadequate to confront this challenge: while featuring high binding affinity and selectivity, these ligands require laborious engineering and expensive manufacturing, are prone to biochemical degradation, and pose safety concerns related to their bacterial origin. Peptides and pseudopeptides make excellent candidates to form a new cohort of ligands for the purification of next-generation biotherapeutics. Peptide-based ligands feature excellent target biorecognition, low or no toxicity and immunogenicity, and can be manufactured affordably at large scale. This work presents a comprehensive and systematic review of the literature on peptide-based ligands and their use in the affinity purification of established and upcoming biological drugs. A comparative analysis is first presented on peptide engineering principles, the development of ligands targeting different biomolecular targets, and the promises and challenges connected to the industrial implementation of peptide ligands. The reviewed literature is organized in (i) conventional (α-)peptides targeting antibodies and other therapeutic proteins, gene therapy products, and therapeutic cells; (ii) cyclic peptides and pseudo-peptides for protein purification and capture of viral and bacterial pathogens; and (iii) the forefront of peptide mimetics, such as β-/γ-peptides, peptoids, foldamers, and stimuli-responsive peptides for advanced processing of biologics.
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Affiliation(s)
- Wenning Chu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Raphael Prodromou
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kevin N Day
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - John D Schneible
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kaitlyn B Bacon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - John D Bowen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Ryan E Kilgore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Carly M Catella
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Brandyn D Moore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Matthew D Mabe
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kawthar Alashoor
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642
| | - Yiman Xu
- College of Material Science and Engineering, Donghua University, 201620 Shanghai, People's Republic of China
| | - Yuanxin Xiao
- College of Textile, Donghua University, Songjiang District, Shanghai, 201620, People's Republic of China
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606.
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21
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Bowen J, Schloop AE, Reeves GT, Menegatti S, Rao BM. Discovery of Membrane-Permeating Cyclic Peptides via mRNA Display. Bioconjug Chem 2020; 31:2325-2338. [PMID: 32786364 DOI: 10.1021/acs.bioconjchem.0c00413] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Small synthetic peptides capable of crossing biological membranes represent valuable tools in cell biology and drug delivery. While several cell-penetrating peptides (CPPs) of natural or synthetic origin have been reported, no peptide is currently known to cross both cytoplasmic and outer embryonic membranes. Here, we describe a method to engineer membrane-permeating cyclic peptides (MPPs) with broad permeation activity by screening mRNA display libraries of cyclic peptides against embryos at different developmental stages. The proposed method was demonstrated by identifying peptides capable of permeating Drosophila melanogaster (fruit fly) embryos and mammalian cells. The selected peptide cyclo[Glut-MRKRHASRRE-K*] showed a strong permeation activity of embryos exposed to minimal permeabilization pretreatment, as well as human embryonic stem cells and a murine fibroblast cell line. Notably, in both embryos and mammalian cells, the cyclic peptide outperformed its linear counterpart and the control MPPs. Confocal microscopy and single cell flow cytometry analysis were utilized to assess the degree of permeation both qualitatively and quantitatively. These MPPs have potential application in studying and nondisruptively controlling intracellular or intraembryonic processes.
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Affiliation(s)
- John Bowen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, North Carolina 27606, United States
| | - Allison E Schloop
- Genetics Program, North Carolina State University, 112 Derieux Place, Raleigh, North Carolina 27695, United States
| | - Gregory T Reeves
- Department of Chemical Engineering, Texas A&M University, 200 Jack E. Brown Engineering Building, College Station, Texas 77843, United States
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, North Carolina 27606, United States
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Drive, Raleigh, North Carolina 27606, United States
| | - Balaji M Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, North Carolina 27606, United States
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Drive, Raleigh, North Carolina 27606, United States
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22
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Bacon K, Blain A, Burroughs M, McArthur N, Rao BM, Menegatti S. Isolation of Chemically Cyclized Peptide Binders Using Yeast Surface Display. ACS COMBINATORIAL SCIENCE 2020; 22:519-532. [PMID: 32786323 DOI: 10.1021/acscombsci.0c00076] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cyclic peptides with engineered protein-binding activity have gained increasing attention for use in therapeutic and biotechnology applications. We describe the efficient isolation and characterization of cyclic peptide binders from genetically encoded combinatorial libraries using yeast surface display. Here, peptide cyclization is achieved by disuccinimidyl glutarate-mediated cross-linking of amine groups within a linear peptide sequence that is expressed as a yeast cell surface fusion. Using this approach, we first screened a library of cyclic heptapeptides using magnetic selection, followed by fluorescence activated cell sorting (FACS) to isolate binders for a model target (lysozyme) with low micromolar binding affinity (KD ∼ 1.2-3.7 μM). The isolated peptides bind lysozyme selectively and only when cyclized. Importantly, we showed that yeast surface displayed cyclic peptides can be used to efficiently obtain quantitative estimates of binding affinity, circumventing the need for chemical synthesis of the selected peptides. Subsequently, to demonstrate broader applicability of our approach, we isolated cyclic heptapeptides that bind human interleukin-17 (IL-17) using yeast-displayed IL-17 as a target for magnetic selection, followed by FACS using recombinant IL-17. Molecular docking simulations and follow-up experimental analyses identified a candidate cyclic peptide that likely binds IL-17 in its receptor binding region with moderate apparent affinity (KD ∼ 300 nM). Taken together, our results show that yeast surface display can be used to efficiently isolate and characterize cyclic peptides generated by chemical modification from combinatorial libraries.
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Affiliation(s)
- Kaitlyn Bacon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Box 7905, Engineering Building I, Raleigh, North Carolina 27695, United States
| | - Abigail Blain
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Box 7905, Engineering Building I, Raleigh, North Carolina 27695, United States
| | - Matthew Burroughs
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Box 7905, Engineering Building I, Raleigh, North Carolina 27695, United States
| | - Nikki McArthur
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Box 7905, Engineering Building I, Raleigh, North Carolina 27695, United States
| | - Balaji M Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Box 7905, Engineering Building I, Raleigh, North Carolina 27695, United States
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Box 7905, Engineering Building I, Raleigh, North Carolina 27695, United States
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina 27695, United States
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23
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Li Y, Yuan S, Yong X, zhao T, Liu J. Research progress on small peptides in Chinese Baijiu. J Funct Foods 2020. [DOI: 10.1016/j.jff.2020.104081] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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24
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Perret G, Boschetti E. Aptamer-Based Affinity Chromatography for Protein Extraction and Purification. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 174:93-139. [PMID: 31485702 DOI: 10.1007/10_2019_106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Aptamers are oligonucleotide molecules able to recognize very specifically proteins. Among the possible applications, aptamers have been used for affinity chromatography with effective results and advantages over most advanced protein separation technologies. This chapter first discusses the context of the affinity chromatography with aptamer ligands. With the adaptation of SELEX, the chemical modifications of aptamers to comply with the covalent coupling and the separation process are then extensively presented. A focus is then made about the most important applications for protein separation with real-life examples and the comparison with immunoaffinity chromatography. In spite of well-advanced demonstrations and the extraordinary potential developments, a significant optimization work is still due to deserve large-scale applications with all necessary validations. Graphical Abstract Aptamer-protein complexes by X-ray crystallography.
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25
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Newton MS, Cabezas-Perusse Y, Tong CL, Seelig B. In Vitro Selection of Peptides and Proteins-Advantages of mRNA Display. ACS Synth Biol 2020; 9:181-190. [PMID: 31891492 DOI: 10.1021/acssynbio.9b00419] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
mRNA display is a robust in vitro selection technique that allows the selection of peptides and proteins with desired functions from libraries of trillions of variants. mRNA display relies upon a covalent linkage between a protein and its encoding mRNA molecule; the power of the technique stems from the stability of this link, and the large degree of control over experimental conditions afforded to the researcher. This article describes the major advantages that make mRNA display the method of choice among comparable in vivo and in vitro methods, including cell-surface display, phage display, and ribosomal display. We also describe innovative techniques that harness mRNA display for directed evolution, protein engineering, and drug discovery.
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Affiliation(s)
- Matilda S. Newton
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
- Department of Molecular, Cellular, and Developmental Biology & Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Yari Cabezas-Perusse
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Cher Ling Tong
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
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26
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Engel BJ, Grindel BJ, Gray JP, Millward SW. Purification of poly-dA oligonucleotides and mRNA-protein fusions with dT 25-OAS resin. Bioorg Med Chem Lett 2020; 30:126934. [PMID: 31919017 PMCID: PMC6986445 DOI: 10.1016/j.bmcl.2019.126934] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/17/2019] [Accepted: 12/23/2019] [Indexed: 11/21/2022]
Abstract
Solid-phase resins functionalized with poly-deoxythymidine (dT) oligos facilitate purification of poly-adenylated molecules from solution through high affinity, high selectivity base-pairing interactions. These resins are commonly used to purify messenger RNA (mRNA) from complex biological mixtures as well as mRNA-protein fusion molecules for mRNA Display selections. Historically, dT-conjugated cellulose was the primary resin for poly-dA purification, but its scarcity has prompted the development of alternative resins, most notably dT-functionalized magnetic beads. In order to develop a cost-effective alternative to commercially available poly-dT resins for large-scale purifications of mRNA-protein fusions, we investigated the purification properties of dT25-conjugated Oligo Affinity Support resin (dT25-OAS) alongside poly-dT14 magnetic beads and dT25-cellulose. dT25-OAS was found to have the highest dA21 oligo binding capacity at 4 pmol/µg, followed by dT14-magnetic beads (1.1 pmol/µg) and dT25-cellulose (0.7 pmol/µg). To determine the resin specificity in the context of a complex biological mixture, we translated mRNA-protein fusions consisting of a radiolabeled Her2 affibody fused to its encoding mRNA. Commercial dT25-cellulose showed the highest mRNA-affibody purification specificity, followed by dT25-OAS and dT14-magnetic beads. Overall, dT25-OAS showed exceptionally high binding capacity and low background binding, making it an attractive alternative for large-scale mRNA purification and mRNA Display library enrichment.
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Affiliation(s)
- Brian J Engel
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, United States
| | - Brian J Grindel
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, United States
| | - Joshua P Gray
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, United States
| | - Steven W Millward
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, United States.
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27
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Matos MJB, Pina AS, Roque ACA. Rational design of affinity ligands for bioseparation. J Chromatogr A 2020; 1619:460871. [PMID: 32044126 DOI: 10.1016/j.chroma.2020.460871] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/05/2020] [Accepted: 01/08/2020] [Indexed: 11/25/2022]
Abstract
Affinity adsorbents have been the cornerstone in protein purification. The selective nature of the molecular recognition interactions established between an affinity ligands and its target provide the basis for efficient capture and isolation of proteins. The plethora of affinity adsorbents available in the market reflects the importance of affinity chromatography in the bioseparation industry. Ligand discovery relies on the implementation of rational design techniques, which provides the foundation for the engineering of novel affinity ligands. The main goal for the design of affinity ligands is to discover or improve functionality, such as increased stability or selectivity. However, the methodologies must adapt to the current needs, namely to the number and diversity of biologicals being developed, and the availability of new tools for big data analysis and artificial intelligence. In this review, we offer an overview on the development of affinity ligands for bioseparation, including the evolution of rational design techniques, dating back to the years of early discovery up to the current and future trends in the field.
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Affiliation(s)
- Manuel J B Matos
- UCIBIO, Chemistry Department, School of Sciences and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Ana S Pina
- UCIBIO, Chemistry Department, School of Sciences and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - A C A Roque
- UCIBIO, Chemistry Department, School of Sciences and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal.
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28
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Day K, Prodromou R, Saberi Bosari S, Lavoie A, Omary M, Market C, San Miguel A, Menegatti S. Discovery and Evaluation of Peptide Ligands for Selective Adsorption and Release of Cas9 Nuclease on Solid Substrates. Bioconjug Chem 2019; 30:3057-3068. [DOI: 10.1021/acs.bioconjchem.9b00703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Kevin Day
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Engineering Building 1, 911 Partners Way, Raleigh 27695-7905, United States
| | - Raphael Prodromou
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Engineering Building 1, 911 Partners Way, Raleigh 27695-7905, United States
| | - Sahand Saberi Bosari
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Engineering Building 1, 911 Partners Way, Raleigh 27695-7905, United States
| | - Ashton Lavoie
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Engineering Building 1, 911 Partners Way, Raleigh 27695-7905, United States
| | - Mohammad Omary
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Engineering Building 1, 911 Partners Way, Raleigh 27695-7905, United States
| | - Connor Market
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Engineering Building 1, 911 Partners Way, Raleigh 27695-7905, United States
| | - Adriana San Miguel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Engineering Building 1, 911 Partners Way, Raleigh 27695-7905, United States
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Engineering Building 1, 911 Partners Way, Raleigh 27695-7905, United States
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Drive, Raleigh, North Carolina 27606, United States
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29
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Wang W, Hao D, Ge J, Zhao L, Huang Y, Zhu K, Wu X, Su Z, Yu R, Ma G. A minimalist peptide ligand for IgG by minimizing the binding domain of protein A. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.107327] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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30
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Fang YM, Chen SG, Lin DQ, Yao SJ. A new tetrapeptide biomimetic chromatographic resin for antibody separation with high adsorption capacity and selectivity. J Chromatogr A 2019; 1604:460474. [DOI: 10.1016/j.chroma.2019.460474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/16/2019] [Accepted: 08/21/2019] [Indexed: 01/03/2023]
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31
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Li Y, Stern D, Lock LL, Mills J, Ou SH, Morrow M, Xu X, Ghose S, Li ZJ, Cui H. Emerging biomaterials for downstream manufacturing of therapeutic proteins. Acta Biomater 2019; 95:73-90. [PMID: 30862553 DOI: 10.1016/j.actbio.2019.03.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/26/2019] [Accepted: 03/06/2019] [Indexed: 12/23/2022]
Abstract
Downstream processing is considered one of the most challenging phases of industrial manufacturing of therapeutic proteins, accounting for a large portion of the total production costs. The growing demand for therapeutic proteins in the biopharmaceutical market in addition to a significant rise in upstream titers have placed an increasing burden on the downstream purification process, which is often limited by high cost and insufficient capacities. To achieve efficient production and reduced costs, a variety of biomaterials have been exploited to improve the current techniques and also to develop superior alternatives. In this work, we discuss the significance of utilizing traditional biomaterials in downstream processing and review the recent progress in the development of new biomaterials for use in protein separation and purification. Several representative methods will be highlighted and discussed in detail, including affinity chromatography, non-affinity chromatography, membrane separations, magnetic separations, and precipitation/phase separations. STATEMENT OF SIGNIFICANCE: Nowadays, downstream processing of therapeutic proteins is facing great challenges created by the rapid increase of the market size and upstream titers, starving for significant improvements or innovations in current downstream unit operations. Biomaterials have been widely used in downstream manufacturing of proteins and efforts have been continuously devoted to developing more advanced biomaterials for the implementation of more efficient and economical purification methods. This review covers recent advances in the development and application of biomaterials specifically exploited for various chromatographic and non-chromatographic techniques, highlighting several promising alternative strategies.
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Affiliation(s)
- Yi Li
- Department of Chemical and Biomolecular Engineering, and Institute for NanoBioTechnology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, United States
| | - David Stern
- Department of Chemical and Biomolecular Engineering, and Institute for NanoBioTechnology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, United States
| | - Lye Lin Lock
- Biologics Process Development, Global Product Development and Supply, Bristol-Myers Squibb, Devens, MA 01434, United States
| | - Jason Mills
- Biologics Process Development, Global Product Development and Supply, Bristol-Myers Squibb, Devens, MA 01434, United States
| | - Shih-Hao Ou
- Department of Chemical and Biomolecular Engineering, and Institute for NanoBioTechnology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, United States
| | - Marina Morrow
- Department of Chemical and Biomolecular Engineering, and Institute for NanoBioTechnology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, United States
| | - Xuankuo Xu
- Biologics Process Development, Global Product Development and Supply, Bristol-Myers Squibb, Devens, MA 01434, United States.
| | - Sanchayita Ghose
- Biologics Process Development, Global Product Development and Supply, Bristol-Myers Squibb, Devens, MA 01434, United States
| | - Zheng Jian Li
- Biologics Process Development, Global Product Development and Supply, Bristol-Myers Squibb, Devens, MA 01434, United States
| | - Honggang Cui
- Department of Chemical and Biomolecular Engineering, and Institute for NanoBioTechnology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, United States; Department of Oncology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States.
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32
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Hirose H, Hideshima T, Katoh T, Suga H. A Case Study on the Keap1 Interaction with Peptide Sequence Epitopes Selected by the Peptidomic mRNA Display. Chembiochem 2019; 20:2089-2100. [PMID: 31169361 DOI: 10.1002/cbic.201900039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/12/2019] [Indexed: 11/08/2022]
Abstract
Many protein-protein and peptide-protein interactions (PPIs) play key roles in the regulation of biological functions, and therefore, the modulation of PPIs has become an attractive target of new drug development. Although a number of PPIs have already been identified, over 100 000 unknown PPIs are predicted to exist. To uncover such unknown PPIs, it is important to devise a conceptually distinct method from that of currently available methods. Herein, an mRNA display by using a total RNA library derived from various human tissues, which serves as a unique method to physically isolate peptide epitopes that potentially bind to a target protein of interest, is reported. In this study, selection was performed against Kelch-like ECH-associated protein (Keap1) as a model target protein, leading to a peptide epitope originating from astrotactin-1 (ASTN1). It turned out that this ASTN1 peptide was able to interact with Keap1 more strongly than that with a known peptide derived from Nrf2; a well-known, naturally occurring Keap1 binder. This case study demonstrates the applicability of peptidomic mRNA display for the rapid exploration of consensus binding peptide motifs and the potential for the discovery of unknown PPIs with other proteins of interest.
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Affiliation(s)
- Hisaaki Hirose
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Tomoki Hideshima
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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33
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Moczko E, Guerreiro A, Cáceres C, Piletska E, Sellergren B, Piletsky SA. Epitope approach in molecular imprinting of antibodies. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1124:1-6. [DOI: 10.1016/j.jchromb.2019.05.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 11/25/2022]
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34
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Zorzi A, Linciano S, Angelini A. Non-covalent albumin-binding ligands for extending the circulating half-life of small biotherapeutics. MEDCHEMCOMM 2019; 10:1068-1081. [PMID: 31391879 PMCID: PMC6644573 DOI: 10.1039/c9md00018f] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/01/2019] [Indexed: 12/13/2022]
Abstract
Peptides and small protein scaffolds are gaining increasing interest as therapeutics. Similarly to full-length antibodies, they can bind a target with a high binding affinity and specificity while remaining small enough to diffuse into tissues. However, despite their numerous advantages, small biotherapeutics often suffer from a relatively short circulating half-life, thus requiring frequent applications that ultimately restrict their ease of use and user compliance. To overcome this limitation, a large variety of half-life extension strategies have been developed in the last decades. Linkage to ligands that non-covalently bind to albumin, the most abundant serum protein with a circulating half-life of ∼19 days in humans, represents one of the most successful approaches for the generation of long-lasting biotherapeutics with improved pharmacokinetic properties and superior efficacy in the clinic.
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Affiliation(s)
- Alessandro Zorzi
- Institute of Chemical Sciences and Engineering , School of Basic Sciences , Ecole Polytechnique Fédérale de Lausanne (EPFL) , Lausanne CH-1015 , Switzerland
| | - Sara Linciano
- Department of Molecular Sciences and Nanosystems , Ca' Foscari University of Venice , Via Torino 155 , Venezia Mestre 30172 , Italy
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems , Ca' Foscari University of Venice , Via Torino 155 , Venezia Mestre 30172 , Italy
- European Centre for Living Technologies (ECLT) , San Marco 2940 , Venice 30124 , Italy .
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35
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Silica resins and peptide ligands to develop disposable affinity adsorbents for antibody purification. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2018.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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36
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Islam T, Naik AD, Hashimoto Y, Menegatti S, Carbonell RG. Optimization of Sequence, Display, and Mode of Operation of IgG-Binding Peptide Ligands to Develop Robust, High-Capacity Affinity Adsorbents That Afford High IgG Product Quality. Int J Mol Sci 2019; 20:E161. [PMID: 30621158 PMCID: PMC6337475 DOI: 10.3390/ijms20010161] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 12/20/2018] [Accepted: 12/26/2018] [Indexed: 11/16/2022] Open
Abstract
This work presents the use of peptide ligand HWRGWV and its cognate sequences to develop affinity adsorbents that compete with Protein A in terms of binding capacity and quality of the eluted product. First, the peptide ligand was conjugated to crosslinked agarose resins (WorkBeads) at different densities and using different spacer arms. The optimization of ligand density and display resulted in values of static and dynamic binding capacity of 85 mg/mL and 65 mg/mL, respectively. A selected peptide-WorkBeads adsorbent was utilized for purifying Mabs from Chinese Hamster Ovary (CHO) cell culture supernatants. The peptide-WorkBeads adsorbent was found able to withstand sanitization with strong alkaline solutions (0.5 M NaOH). The purity of the eluted product was consistently higher than 95%, with logarithmic removal value (LRV) of 1.5 for host cell proteins (HCPs) and 4.0 for DNA. HCP clearance was significantly improved by adding a post-load washing step with either 0.1 M Tris HCl pH 9 or 1 M NaCl. The cognate peptide of HWRGWV, constructed by replacing arginine (R) with citrulline, further increased the HCP LRV to 2.15. The peptide-based adsorbent also showed a remarkable performance in terms of removal of Mab aggregates; unlike Protein A, in fact, HWRGWV was found to bind only monomeric IgG. Collectively, these results demonstrate the potential of peptide-based adsorbents as alternative to Protein A for the purification of therapeutic antibodies.
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Affiliation(s)
- Tuhidul Islam
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA.
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695-7928, USA.
| | - Amith D Naik
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695-7928, USA.
| | - Yasuhiro Hashimoto
- Department of Research and Development, Fuji Silysia Chemical LTD, Kasugai Aichi 487-0013, Japan.
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA.
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695-7928, USA.
| | - Ruben G Carbonell
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA.
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695-7928, USA.
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37
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Abstract
Communication between and within communities of cells or independent organisms is a crucial prerequisite for species survival. In response to variations in the extracellular environment, the collective behavior of cell populations can be coordinated by regulating community-level gene expression. This mechanism is strongly conserved during evolution, being shared both by bacterial communities and central nervous system cells. Notably, cyclic dipeptides (CDPs) are molecules that are implicated in these quorum sensing behaviors in both settings. Bacteria coordinate their collective behavior by producing CDPs (quorum sensing inducers) that enhance the capacity of individual members of the community to detect these signals and thus amplify the community-level response. In this review, we highlight recent data indicating that strikingly similar molecular mechanisms control communications between glial and neuronal cells to maintain homeostasis in the central nervous system, with a specific focus on the role of the thyrotropin-releasing hormone—derived CDP cyclo(His-Pro) in the protection against neurotoxic insults.
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38
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Dong Y, Bai Y, Zhang S, Xu W, Xu J, Zhou Y, Zhang S, Wu Y, Yu H, Cao N, Liu H, Wang W. Cyclic peptide RD808 reduces myocardial injury induced by β 1-adrenoreceptor autoantibodies. Heart Vessels 2018; 34:1040-1051. [PMID: 30554265 DOI: 10.1007/s00380-018-1321-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 12/07/2018] [Indexed: 10/27/2022]
Abstract
Autoantibodies against the second extracellular loop of β1-adrenergic receptor (β1-AA) have been shown to be involved in the development of cardiovascular diseases. Recently, there has been considerable interest in strategies to remove these autoantibodies, particularly therapeutic peptides to neutralize β1-AA. Researchers are investigating the roles of cyclic peptides that mimic the structure of relevant epitopes on the β1-AR-ECII in a number of immune-mediated diseases. Here, we used a cyclic peptide, namely, RD808, to neutralize β1-AA, consequently alleviating β1-AA-induced myocardial injury. We investigated the protective effects of RD808 on the myocardium both in vitro and in vivo. RD808 was found to increase the survival rate of cardiomyocytes; furthermore, it decreased myocardial necrosis and apoptosis and improved the cardiac function of BalB/c mice in a β1-AA transfer model. In vitro and in vivo experiments showed that myocardial autophagy was increased in the presence of RD808, which might contribute to its cardioprotective effects. Our findings indicate that RD808 reduced myocardial injury induced by β1-AA.
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Affiliation(s)
- Yu Dong
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, No. 10 Xitoutiao, You An Men Wai, Beijing, 100069, China.,Beijing Key Laboratory of Metabolic Disorders Related Cardiovascular Diseases, Capital Medical University, Beijing, China
| | - Yan Bai
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, No. 10 Xitoutiao, You An Men Wai, Beijing, 100069, China.,Beijing Key Laboratory of Metabolic Disorders Related Cardiovascular Diseases, Capital Medical University, Beijing, China
| | - Shangyue Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, No. 10 Xitoutiao, You An Men Wai, Beijing, 100069, China.,Beijing Key Laboratory of Metabolic Disorders Related Cardiovascular Diseases, Capital Medical University, Beijing, China
| | - Wenli Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, No. 10 Xitoutiao, You An Men Wai, Beijing, 100069, China.,Beijing Key Laboratory of Metabolic Disorders Related Cardiovascular Diseases, Capital Medical University, Beijing, China
| | - Jiahui Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, No. 10 Xitoutiao, You An Men Wai, Beijing, 100069, China.,Beijing Key Laboratory of Metabolic Disorders Related Cardiovascular Diseases, Capital Medical University, Beijing, China
| | - Yi Zhou
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, No. 10 Xitoutiao, You An Men Wai, Beijing, 100069, China.,Beijing Key Laboratory of Metabolic Disorders Related Cardiovascular Diseases, Capital Medical University, Beijing, China
| | - Suli Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, No. 10 Xitoutiao, You An Men Wai, Beijing, 100069, China.,Beijing Key Laboratory of Metabolic Disorders Related Cardiovascular Diseases, Capital Medical University, Beijing, China
| | - Ye Wu
- Beijing Key Laboratory of Metabolic Disorders Related Cardiovascular Diseases, Capital Medical University, Beijing, China
| | - Haicun Yu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, No. 10 Xitoutiao, You An Men Wai, Beijing, 100069, China.,Beijing Key Laboratory of Metabolic Disorders Related Cardiovascular Diseases, Capital Medical University, Beijing, China
| | - Ning Cao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, No. 10 Xitoutiao, You An Men Wai, Beijing, 100069, China.,Beijing Key Laboratory of Metabolic Disorders Related Cardiovascular Diseases, Capital Medical University, Beijing, China
| | - Huirong Liu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, No. 10 Xitoutiao, You An Men Wai, Beijing, 100069, China. .,Beijing Key Laboratory of Metabolic Disorders Related Cardiovascular Diseases, Capital Medical University, Beijing, China.
| | - Wen Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, No. 10 Xitoutiao, You An Men Wai, Beijing, 100069, China. .,Beijing Key Laboratory of Metabolic Disorders Related Cardiovascular Diseases, Capital Medical University, Beijing, China.
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39
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Fang YM, Lin DQ, Yao SJ. Review on biomimetic affinity chromatography with short peptide ligands and its application to protein purification. J Chromatogr A 2018; 1571:1-15. [DOI: 10.1016/j.chroma.2018.07.082] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 07/12/2018] [Accepted: 07/29/2018] [Indexed: 10/28/2022]
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40
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41
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Wang X, Xia D, Han H, Peng K, Zhu P, Crommen J, Wang Q, Jiang Z. Biomimetic small peptide functionalized affinity monoliths for monoclonal antibody purification. Anal Chim Acta 2018. [DOI: 10.1016/j.aca.2018.02.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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42
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Kruljec N, Molek P, Hodnik V, Anderluh G, Bratkovič T. Development and Characterization of Peptide Ligands of Immunoglobulin G Fc Region. Bioconjug Chem 2018; 29:2763-2775. [DOI: 10.1021/acs.bioconjchem.8b00395] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nika Kruljec
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Biology, SI-1000 Ljubljana, Slovenia
- University of Ljubljana, Faculty of Medicine, Graduate School of Biomedicine, Ljubljana, SI-1000 Slovenia
| | - Peter Molek
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Biology, SI-1000 Ljubljana, Slovenia
| | - Vesna Hodnik
- University of Ljubljana, Biotechnical Faculty, Department of Biology, SI-1000 Ljubljana, Slovenia
- National Institute of Chemistry, Department of Molecular Biology and Nanobiotechnology, SI-1000 Ljubljana, Slovenia
| | - Gregor Anderluh
- National Institute of Chemistry, Department of Molecular Biology and Nanobiotechnology, SI-1000 Ljubljana, Slovenia
| | - Tomaž Bratkovič
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Biology, SI-1000 Ljubljana, Slovenia
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43
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Mishra AK, Choi J, Choi SJ, Baek KH. Cyclodipeptides: An Overview of Their Biosynthesis and Biological Activity. Molecules 2017; 22:molecules22101796. [PMID: 29065531 PMCID: PMC6151668 DOI: 10.3390/molecules22101796] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 10/18/2017] [Accepted: 10/19/2017] [Indexed: 01/06/2023] Open
Abstract
Cyclodipeptides (CDP) represent a diverse family of small, highly stable, cyclic peptides that are produced as secondary functional metabolites or side products of protein metabolism by bacteria, fungi, and animals. They are widespread in nature, and exhibit a broad variety of biological and pharmacological activities. CDP synthases (CDPSs) and non-ribosomal peptide synthetases (NRPSs) catalyze the biosynthesis of the CDP core structure, which is further modified by tailoring enzymes often associated with CDP biosynthetic gene clusters. In this review, we provide a comprehensive summary of CDP biosynthetic pathways and modifying enzymes. We also discuss the biological properties of some known CDPs and their possible applications in metabolic engineering.
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Affiliation(s)
- Awdhesh Kumar Mishra
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea.
| | - Jaehyuk Choi
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea.
| | - Seong-Jin Choi
- Department of Biotechnology, Daegu Catholic University, Gyeongsan 38430, Korea.
| | - Kwang-Hyun Baek
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea.
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44
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Tong HF, Cavallotti C, Yao SJ, Lin DQ. Molecular insight into protein binding orientations and interaction modes on hydrophobic charge-induction resin. J Chromatogr A 2017; 1512:34-42. [DOI: 10.1016/j.chroma.2017.06.071] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/15/2017] [Accepted: 06/29/2017] [Indexed: 11/28/2022]
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45
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Affiliation(s)
- Nika Kruljec
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Tomaž Bratkovič
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
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46
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Affiliation(s)
- Judit Randek
- Division of Biotechnology, IFM, Linköping University, Linköping, Sweden
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47
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Saito F, Bode JW. Synthesis and stabilities of peptide-based [1]rotaxanes: molecular grafting onto lasso peptide scaffolds. Chem Sci 2017; 8:2878-2884. [PMID: 28553526 PMCID: PMC5427998 DOI: 10.1039/c7sc00021a] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 01/25/2017] [Indexed: 12/14/2022] Open
Abstract
The chemical synthesis of peptide-based [1]rotaxanes (lasso peptides) was achieved by [2]rotaxane formation followed by two chemoselective ligation reactions. Our approach enabled incorporation of various peptide sequences into a common rotaxane structure. The synthetic lasso peptides were characterized by NMR, chromatography, and partial degradation by proteases. A linear peptide epitope grafted onto the rotaxane scaffold showed significantly improved proteolytic stability.
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Affiliation(s)
- Fumito Saito
- Laboratorium füer Organische Chemie , Department of Chemistry and Applied Biosciences , ETH Zürich , Zürich , Switzerland 8093 . ; http://www.bode.ethz.ch
| | - Jeffrey W Bode
- Laboratorium füer Organische Chemie , Department of Chemistry and Applied Biosciences , ETH Zürich , Zürich , Switzerland 8093 . ; http://www.bode.ethz.ch
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48
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Abstract
Cyclic peptides are an important class of molecules that are increasingly viewed as an ideal scaffold for inhibition of protein-protein interactions (PPI). Here we detail an approach that enables the intracellular synthesis of cyclic peptide libraries of around 108 members. The method utilizes split intein mediated circular ligation of peptides and proteins (SICLOPPS), taking advantage of split intein splicing to cyclize a library of peptide sequences. SICLOPPS allows the ring size, set residues and number of random residues within a library to be predetermined by the user. SICLOPPS libraries have been combined with a variety of cell-based screens to identify cyclic peptide inhibitors of a variety of enzymes and protein-protein interactions.
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Affiliation(s)
- Eliot L Osher
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - Ali Tavassoli
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK.
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49
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Fc-Binding Ligands of Immunoglobulin G: An Overview of High Affinity Proteins and Peptides. MATERIALS 2016; 9:ma9120994. [PMID: 28774114 PMCID: PMC5456964 DOI: 10.3390/ma9120994] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 11/26/2016] [Accepted: 11/29/2016] [Indexed: 01/20/2023]
Abstract
The rapidly increasing application of antibodies has inspired the development of several novel methods to isolate and target antibodies using smart biomaterials that mimic the binding of Fc-receptors to antibodies. The Fc-binding domain of antibodies is the primary binding site for e.g., effector proteins and secondary antibodies, whereas antigens bind to the Fab region. Protein A, G, and L, surface proteins expressed by pathogenic bacteria, are well known to bind immunoglobulin and have been widely exploited in antibody purification strategies. Several difficulties are encountered when bacterial proteins are used in antibody research and application. One of the major obstacles hampering the use of bacterial proteins is sample contamination with trace amounts of these proteins, which can invoke an immune response in the host. Many research groups actively develop synthetic ligands that are able to selectively and strongly bind to antibodies. Among the reported ligands, peptides that bind to the Fc-domain of antibodies are attractive tools in antibody research. Besides their use as high affinity ligands in antibody purification chromatography, Fc-binding peptides are applied e.g., to localize antibodies on nanomaterials and to increase the half-life of proteins in serum. In this review, recent developments of Fc-binding peptides are presented and their binding characteristics and diverse applications are discussed.
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50
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Wang RZ, Lin DQ, Chu WN, Zhang QL, Yao SJ. New tetrapeptide ligands designed for antibody purification with biomimetic chromatography: Molecular simulation and experimental validation. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.06.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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