1
|
Ma J, Tian Z, Shi Q, Dong X, Sun Y. Affinity chromatography for virus-like particle manufacturing: Challenges, solutions, and perspectives. J Chromatogr A 2024; 1721:464851. [PMID: 38574547 DOI: 10.1016/j.chroma.2024.464851] [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: 01/20/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
The increasing medical application of virus-like particles (VLPs), notably vaccines and viral vectors, has increased the demand for commercial VLP production. However, VLP manufacturing has not yet reached the efficiency level achieved for recombinant protein therapeutics, especially in downstream processing. This review provides a comprehensive analysis of the challenges associated with affinity chromatography for VLP purification with respect to the diversity and complexity of VLPs and the associated upstream and downstream processes. The use of engineered affinity ligands and matrices for affinity chromatography is first discussed. Although several representative affinity ligands are currently available for VLP purification, most of them have difficulty in balancing ligand universality, ligand selectivity and mild operation conditions. Then, phage display technology and computer-assisted design are discussed as efficient methods for the rapid discovery of high-affinity peptide ligands. Finally, the VLP purification by affinity chromatography is analyzed. The process is significantly influenced by virus size and variation, ligand type and chromatographic mode. To address the updated regulatory requirements and epidemic outbreaks, technical innovations in affinity chromatography and process intensification and standardization in VLP purification should be promoted to achieve rapid process development and highly efficient VLP manufacturing, and emphasis is given to the discovery of universal ligands, applications of gigaporous matrices and platform technology. It is expected that the information in this review can provide a better understanding of the affinity chromatography methods available for VLP purification and offer useful guidance for the development of affinity chromatography for VLP manufacturing in the decades to come.
Collapse
Affiliation(s)
- Jing Ma
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Zengquan Tian
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, 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, Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China.
| | - Xiaoyan Dong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, 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, Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China.
| |
Collapse
|
2
|
Catalytic Peptides: the Challenge between Simplicity and Functionality. Isr J Chem 2022. [DOI: 10.1002/ijch.202200029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
3
|
Pina AS, Morgado L, Duncan KL, Carvalho S, Carvalho HF, Barbosa AJM, de P. Mariz B, Moreira IP, Kalafatovic D, Morais Faustino BM, Narang V, Wang T, Pappas CG, Ferreira I, Roque ACA, Ulijn RV. Discovery of phosphotyrosine-binding oligopeptides with supramolecular target selectivity. Chem Sci 2022; 13:210-217. [PMID: 35059169 PMCID: PMC8694286 DOI: 10.1039/d1sc04420f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 12/05/2021] [Indexed: 12/16/2022] Open
Abstract
Phage-display screening on self-assembled tyrosine-phosphate ligands enables the identification of oligopeptides selective to dynamic supramolecular targets, with the lead peptide showing a preferred hairpin-like conformation and catalytic activity.
Collapse
Affiliation(s)
- Ana S. Pina
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), NY 10031, USA
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Leonor Morgado
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Krystyna L. Duncan
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), NY 10031, USA
- Department of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - Sara Carvalho
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Henrique F. Carvalho
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Arménio J. M. Barbosa
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Beatriz de P. Mariz
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Inês P. Moreira
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Daniela Kalafatovic
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), NY 10031, USA
| | - Bruno M. Morais Faustino
- CENIMAT/I3N, Department of Materials Science, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Vishal Narang
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), NY 10031, USA
| | - Tong Wang
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), NY 10031, USA
- Imaging Facility of CUNY ASRC, 85 St Nicholas Terrace, New York 10031, USA
| | - Charalampos G. Pappas
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), NY 10031, USA
- Department of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - Isabel Ferreira
- CENIMAT/I3N, Department of Materials Science, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - A. Cecília A. Roque
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Rein V. Ulijn
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), NY 10031, USA
- Hunter College of CUNY, Department of Chemistry and Biochemistry, 695 Park Avenue, New York 10065, USA
- PhD Programs in Chemistry and Biochemistry, The Graduate Center of CUNY, New York 10016, USA
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Hao J, Wang F, Xing G, Liu Y, Deng R, Zhang H, Cheng A, Zhang G. Design and preliminary application of affinity peptide based on the structure of the porcine circovirus type II Capsid (PCV2 Cap). PeerJ 2019; 7:e8132. [PMID: 31824765 PMCID: PMC6899342 DOI: 10.7717/peerj.8132] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/31/2019] [Indexed: 01/14/2023] Open
Abstract
Background Affinity peptides, as a core part of affinity chromatography, play an important role in the purification of target molecules. Methods Here we describe the use of molecular docking technology for virtual screening of affinity peptides that specifically recognize the PCV2 Cap protein for the first time. Thirteen candidate peptides with high scores were obtained and then further characterized. Experimentally, the affinity and sensitivity of the peptides studied were identified by ELISA and LSPR, respectively. In order to investigate the purification effect of a selected peptide (L11) for the recombinant PCV2 Cap protein, it was coupled to NHS agarose magnetic beads as an affinity adsorbent (NaMB-L11); and the ligand density of the affinity adsorbent and pH value in the purification of the recombinant PCV2 Cap protein were optimized. Results Our data showed that the peptide L11- DYWWQSWE has the smallest KD = 103 nM with higher specificity for PCV2 Cap protein recognition. The NaMB-L11 affinity adsorbent yielded a purified Cap sample with 98% purity at 90% recovery in a single step. Conclusion Based on the structure, we obtained a high affinity peptide L11 binding to the PCV2 Cap protein by molecular docking technology. It not only provides a theoretical basis for the design of PCV2 Cap affinity peptide, but a new method for the purification of the PCV2 Cap protein.
Collapse
Affiliation(s)
- Junfang Hao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Henan Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Fangyu Wang
- Henan Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Guangxu Xing
- Henan Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yunchao Liu
- Henan Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Ruiguang Deng
- Henan Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Hao Zhang
- Henan Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China.,College of Life Science, Henan Agricultural University, Zhengzhou, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Gaiping Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Henan Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China.,College of Life Science, Henan Agricultural University, Zhengzhou, China
| |
Collapse
|
7
|
Cervera L, Gòdia F, Tarrés-Freixas F, Aguilar-Gurrieri C, Carrillo J, Blanco J, Gutiérrez-Granados S. Production of HIV-1-based virus-like particles for vaccination: achievements and limits. Appl Microbiol Biotechnol 2019; 103:7367-7384. [DOI: 10.1007/s00253-019-10038-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 12/20/2022]
|
8
|
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]
|
9
|
Aires-Barros R, Büchs J, Ferreira G. Editorial: ECAB focus issue: Engineered catalysts, robust, cost-effective and integrated bioprocesses and high-throughput screening. Biotechnol J 2017; 11:1475-1476. [PMID: 27966843 DOI: 10.1002/biot.201600662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
How can technology and industrial biotechnology contribute to a more bio-based economy? At the 3rd European Congress of Applied Biotechnology (ECAB3) in Nice in 2015, relevant topics and technologies and their contribution to sustainability were presented and discussed. In this issue of Biotechnology Journal, five special articles are selected from this conference, highlighting processes and technologies envisaging the development of engineered catalysts, robust bioprocesses, as well as high-throughput screening methods for process development.
Collapse
|
10
|
Zheng G, Lu Q, Wang F, Jin Q, Teng M, Zhang N, Ren T, Ding P, Zhang G. Selection of affinity peptides for the purification potential of porcine circovirus type 2 (PCV2) Cap virus-like particles (VLPs). RSC Adv 2017. [DOI: 10.1039/c7ra05790c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this study, we describe the use of a M13 phage-displayed random peptide library for screening novel peptide motifs that specifically recognize recombinant PCV2 Cap protein for the first time.
Collapse
Affiliation(s)
- Guanmin Zheng
- College of Animal Husbandry and Veterinary Science
- Henan Agricultural University
- Zhengzhou 450002
- People's Republic of China
- Key Laboratory of Animal Immunology of the Ministry of Agriculture
| | - Qingxia Lu
- Key Laboratory of Animal Immunology of the Ministry of Agriculture
- Henan Provincial Key Laboratory of Animal Immunology
- Henan Academy of Agricultural Sciences
- Zhengzhou 450002
- People's Republic of China
| | - Fangyu Wang
- Key Laboratory of Animal Immunology of the Ministry of Agriculture
- Henan Provincial Key Laboratory of Animal Immunology
- Henan Academy of Agricultural Sciences
- Zhengzhou 450002
- People's Republic of China
| | - Qianyue Jin
- Key Laboratory of Animal Immunology of the Ministry of Agriculture
- Henan Provincial Key Laboratory of Animal Immunology
- Henan Academy of Agricultural Sciences
- Zhengzhou 450002
- People's Republic of China
| | - Man Teng
- Key Laboratory of Animal Immunology of the Ministry of Agriculture
- Henan Provincial Key Laboratory of Animal Immunology
- Henan Academy of Agricultural Sciences
- Zhengzhou 450002
- People's Republic of China
| | - Nana Zhang
- Key Laboratory of Animal Immunology of the Ministry of Agriculture
- Henan Provincial Key Laboratory of Animal Immunology
- Henan Academy of Agricultural Sciences
- Zhengzhou 450002
- People's Republic of China
| | - Tingting Ren
- College of Animal Husbandry and Veterinary Science
- Henan Agricultural University
- Zhengzhou 450002
- People's Republic of China
- Key Laboratory of Animal Immunology of the Ministry of Agriculture
| | - Peiyang Ding
- Key Laboratory of Animal Immunology of the Ministry of Agriculture
- Henan Provincial Key Laboratory of Animal Immunology
- Henan Academy of Agricultural Sciences
- Zhengzhou 450002
- People's Republic of China
| | - Gaiping Zhang
- College of Animal Husbandry and Veterinary Science
- Henan Agricultural University
- Zhengzhou 450002
- People's Republic of China
- Key Laboratory of Animal Immunology of the Ministry of Agriculture
| |
Collapse
|