1
|
Chance R, Kang AS. Eukaryotic ribosome display for antibody discovery: A review. Hum Antibodies 2024:HAB240001. [PMID: 38788063 DOI: 10.3233/hab-240001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Monoclonal antibody biologics have significantly transformed the therapeutic landscape within the biopharmaceutical industry, partly due to the utilisation of discovery technologies such as the hybridoma method and phage display. While these established platforms have streamlined the development process to date, their reliance on cell transformation for antibody identification faces limitations related to library diversification and the constraints of host cell physiology. Cell-free systems like ribosome display offer a complementary approach, enabling antibody selection in a completely in vitro setting while harnessing enriched cellular molecular machinery. This review aims to provide an overview of the fundamental principles underlying the ribosome display method and its potential for advancing antibody discovery and development.
Collapse
|
2
|
Madden SK, Brennan A, Mason JM. A library-derived peptide inhibitor of the BZLF1 transcription factor. J Pept Sci 2024; 30:e3557. [PMID: 38041527 DOI: 10.1002/psc.3557] [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: 04/19/2023] [Revised: 11/12/2023] [Accepted: 11/13/2023] [Indexed: 12/03/2023]
Abstract
Transcription factor dysregulation is associated with many diseases, including cancer. Peptide-based molecules are increasingly recognised as important modulators of difficult intracellular protein-protein interaction targets, with peptide library screening consequently proven to be a viable strategy in developing inhibitors against a wide range of transcription factors (TFs). However, current strategies simply select the highest affinity of binding to a target TF rather than the ability to inhibit TF function. Here, we utilise our Transcription Block Survival (TBS) screening platform to enable high-throughput identification of peptides that inhibit TFs from binding to cognate DNA sites, hence inhibiting functionality. In this study, we explore whether the TBS can be expanded to derive a potent and functional peptide inhibitor of the BZLF1 transcription factor. The library-derived peptide, AcidicW, is shown to form a more stable dimer with BZLF1 than the BZLF1 homodimer, with a thermal denaturation temperature exceeding 80°C. AcidicW can also functionally inhibit the BZLF1:TRE DNA interaction with high potency and an IC50 of 612 nM.
Collapse
Affiliation(s)
- Sarah K Madden
- Department of Life Sciences, University of Bath, Bath, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Andrew Brennan
- Department of Life Sciences, University of Bath, Bath, UK
| | - Jody M Mason
- Department of Life Sciences, University of Bath, Bath, UK
| |
Collapse
|
3
|
Buzas D, Sun H, Toelzer C, Yadav SKN, Borucu U, Gautam G, Gupta K, Bufton JC, Capin J, Sessions RB, Garzoni F, Berger I, Schaffitzel C. Engineering the ADDobody protein scaffold for generation of high-avidity ADDomer super-binders. Structure 2024; 32:342-351.e6. [PMID: 38198950 DOI: 10.1016/j.str.2023.12.010] [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: 09/15/2023] [Revised: 11/17/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024]
Abstract
Adenovirus-derived nanoparticles (ADDomer) comprise 60 copies of adenovirus penton base protein (PBP). ADDomer is thermostable, rendering the storage, transport, and deployment of ADDomer-based therapeutics independent of a cold chain. To expand the scope of ADDomers for new applications, we engineered ADDobodies, representing PBP crown domain, genetically separated from PBP multimerization domain. We inserted heterologous sequences into hyper-variable loops, resulting in monomeric, thermostable ADDobodies expressed at high yields in Escherichia coli. The X-ray structure of an ADDobody prototype validated our design. ADDobodies can be used in ribosome display experiments to select a specific binder against a target, with an enrichment factor of ∼104-fold per round. ADDobodies can be re-converted into ADDomers by genetically reconnecting the selected ADDobody with the PBP multimerization domain from a different species, giving rise to a multivalent nanoparticle, called Chimera, confirmed by a 2.2 Å electron cryo-microscopy structure. Chimera comprises 60 binding sites, resulting in ultra-high, picomolar avidity to the target.
Collapse
Affiliation(s)
- Dora Buzas
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK; Max Planck Bristol Centre for Minimal Biology, Cantock's Close, Bristol BS8 1TS, UK
| | - Huan Sun
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK; Max Planck Bristol Centre for Minimal Biology, Cantock's Close, Bristol BS8 1TS, UK
| | - Christine Toelzer
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Sathish K N Yadav
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Ufuk Borucu
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Gunjan Gautam
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Kapil Gupta
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK; Imophoron Ltd, Science Creates Old Market, Midland Road, Bristol BS2 0JZ, UK
| | - Joshua C Bufton
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Julien Capin
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Frederic Garzoni
- Imophoron Ltd, Science Creates Old Market, Midland Road, Bristol BS2 0JZ, UK
| | - Imre Berger
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK; Max Planck Bristol Centre for Minimal Biology, Cantock's Close, Bristol BS8 1TS, UK; School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
| | | |
Collapse
|
4
|
Nishikawa S, Watanabe H, Terasaka N, Katoh T, Fujishima K. De Novo Single-Stranded RNA-Binding Peptides Discovered by Codon-Restricted mRNA Display. Biomacromolecules 2024; 25:355-365. [PMID: 38051119 PMCID: PMC10777347 DOI: 10.1021/acs.biomac.3c01024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/07/2023]
Abstract
RNA-binding proteins participate in diverse cellular processes, including DNA repair, post-transcriptional modification, and cancer progression through their interactions with RNAs, making them attractive for biotechnological applications. While nature provides an array of naturally occurring RNA-binding proteins, developing de novo RNA-binding peptides remains challenging. In particular, tailoring peptides to target single-stranded RNA with low complexity is difficult due to the inherent structural flexibility of RNA molecules. Here, we developed a codon-restricted mRNA display and identified multiple de novo peptides from a peptide library that bind to poly(C) and poly(A) RNA with KDs ranging from micromolar to submicromolar concentrations. One of the newly identified peptides is capable of binding to the cytosine-rich sequences of the oncogenic Cdk6 3'UTR RNA and MYU lncRNA, with affinity comparable to that of the endogenous binding protein. Hence, we present a novel platform for discovering de novo single-stranded RNA-binding peptides that offer promising avenues for regulating RNA functions.
Collapse
Affiliation(s)
- Shota Nishikawa
- Earth-Life
Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- School
of Life Science and Technology, Tokyo Institute
of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Hidenori Watanabe
- Earth-Life
Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Naohiro Terasaka
- Earth-Life
Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Takayuki Katoh
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kosuke Fujishima
- Earth-Life
Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Graduate
School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| |
Collapse
|
5
|
Zhang P, Wang K, Hu T, Xu M, You X, Chen M, Tang X, Hu H, Jiang Y, Zhao W, Tan S. A novel fully human anti-NT-ANGPTL3 antibody from phage display library exhibits potent ApoB, TG, and LDL-C lowering activities in hyperlipidemia mice. FASEB J 2024; 38:e23399. [PMID: 38174870 DOI: 10.1096/fj.202301564rr] [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: 08/02/2023] [Revised: 12/06/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024]
Abstract
Dyslipidemia is characterized by elevated plasma levels of low-density lipoprotein cholesterol (LDL-C), triglycerides (TG), and TG-rich lipoprotein (TGRLs) in circulation, and is closely associated with the incidence and development of cardiovascular disease. Angiopoietin-like protein 3 (ANGPTL3) deficiency has been identified as a cause of familial combined hypolipidemia in humans, which allows it to be an important therapeutic target for reducing plasma lipids. Here, we report the discovery and characterization of a novel fully human antibody F1519-D95aA against N-terminal ANGPTL3 (NT-ANGPTL3), which potently inhibits NT-ANGPTL3 with a KD as low as 9.21 nM. In hyperlipidemic mice, F1519-D95aA shows higher apolipoprotein B (ApoB) and TG-lowering, and similar LDL-C reducing activity as compared to positive control Evinacumab (56.50% vs 26.01% decrease in serum ApoB levels, 30.84% vs 25.28% decrease in serum TG levels, 23.32% vs 22.52% decrease in serum LDLC levels, relative to vehicle group). Molecular docking and binding energy calculations reveal that the F1519-D95aA-ANGPTL3 complex (10 hydrogen bonds, -65.51 kcal/mol) is more stable than the Evinacumab-ANGPTL3 complex (4 hydrogen bonds, -63.76 kcal/mol). Importantly, F1519-D95aA binds to ANGPTL3 with different residues in ANGPTL3 from Evinacumab, suggesting that F1519-D95aA may be useful for the treatment of patients resistant to Evinacumab. In conclusion, F1519-D95aA is a novel fully human anti-NT-ANGPTL3 antibody with potent plasma ApoB, TG, and LDL-C lowering activities, which can potentially serve as a therapeutic agent for hyperlipidemia and relevant cardiovascular diseases.
Collapse
Affiliation(s)
- Panpan Zhang
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Ke Wang
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Tuo Hu
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Menglong Xu
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Xiangyan You
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Manman Chen
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Xuan Tang
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Huajing Hu
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Yiwei Jiang
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Wenfeng Zhao
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Shuhua Tan
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| |
Collapse
|
6
|
Liu Y, Lu X, Chen M, Wei Z, Peng G, Yang J, Tang C, Yu P. Advances in screening, synthesis, modification, and biomedical applications of peptides and peptide aptamers. Biofactors 2024; 50:33-57. [PMID: 37646383 DOI: 10.1002/biof.2001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023]
Abstract
Peptides and peptide aptamers have emerged as promising molecules for a wide range of biomedical applications due to their unique properties and versatile functionalities. The screening strategies for identifying peptides and peptide aptamers with desired properties are discussed, including high-throughput screening, display screening technology, and in silico design approaches. The synthesis methods for the efficient production of peptides and peptide aptamers, such as solid-phase peptide synthesis and biosynthesis technology, are described, along with their advantages and limitations. Moreover, various modification techniques are explored to enhance the stability, specificity, and pharmacokinetic properties of peptides and peptide aptamers. This includes chemical modifications, enzymatic modifications, biomodifications, genetic engineering modifications, and physical modifications. Furthermore, the review highlights the diverse biomedical applications of peptides and peptide aptamers, including targeted drug delivery, diagnostics, and therapeutic. This review provides valuable insights into the advancements in screening, synthesis, modification, and biomedical applications of peptides and peptide aptamers. A comprehensive understanding of these aspects will aid researchers in the development of novel peptide-based therapeutics and diagnostic tools for various biomedical challenges.
Collapse
Affiliation(s)
- Yijie Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Xiaoling Lu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Meilun Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Zheng Wei
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Guangnan Peng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Jie Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Chunhua Tang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Peng Yu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| |
Collapse
|
7
|
Singh R, Chandley P, Rohatgi S. Recent Advances in the Development of Monoclonal Antibodies and Next-Generation Antibodies. Immunohorizons 2023; 7:886-897. [PMID: 38149884 PMCID: PMC10759153 DOI: 10.4049/immunohorizons.2300102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/07/2023] [Indexed: 12/28/2023] Open
Abstract
mAbs are highly indispensable tools for diagnostic, prophylactic, and therapeutic applications. The first technique, hybridoma technology, was based on fusion of B lymphocytes with myeloma cells, which resulted in generation of single mAbs against a specific Ag. Along with hybridoma technology, several novel and alternative methods have been developed to improve mAb generation, ranging from electrofusion to the discovery of completely novel technologies such as B cell immortalization; phage, yeast, bacterial, ribosome, and mammalian display systems; DNA/RNA encoded Abs; single B cell technology; transgenic animals; and artificial intelligence/machine learning. This commentary outlines the evolution, methodology, advantages, and limitations of various mAb production techniques. Furthermore, with the advent of next-generation Ab technologies such as single-chain variable fragments, nanobodies, bispecific Abs, Fc-engineered Abs, Ab biosimilars, Ab mimetics, and Ab-drug conjugates, the healthcare and pharmaceutical sectors have become resourceful to develop highly specific mAb treatments against various diseases such as cancer and autoimmune and infectious diseases.
Collapse
Affiliation(s)
- Rohit Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Pankaj Chandley
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Soma Rohatgi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| |
Collapse
|
8
|
Furuhashi T, Sakamoto K, Wada A. Genetic Code Expansion and a Photo-Cross-Linking Reaction Facilitate Ribosome Display Selections for Identifying a Wide Range of Affinity Peptides. Int J Mol Sci 2023; 24:15661. [PMID: 37958644 PMCID: PMC10650079 DOI: 10.3390/ijms242115661] [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: 09/03/2023] [Revised: 10/12/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Cell-free molecular display techniques have been utilized to select various affinity peptides from peptide libraries. However, conventional techniques have difficulties associated with the translational termination through in-frame UAG stop codons and the amplification of non-specific peptides, which hinders the desirable selection of low-affinity peptides. To overcome these problems, we established a scheme for ribosome display selection of peptide epitopes bound to monoclonal antibodies and then applied genetic code expansion with synthetic X-tRNAUAG reprogramming of the UAG codons (X = Tyr, Trp, or p-benzoyl-l-phenylalanine (pBzo-Phe)) to the scheme. Based on the assessment of the efficiency of in vitro translation with X-tRNAUAG, we carried out ribosome display selection with genetic code expansion using Trp-tRNAUAG, and we verified that affinity peptides could be identified efficiently regardless of the presence of UAG codons in the peptide coding sequences. Additionally, after evaluating the photo-cross-linking reactions of pBzo-Phe-incorporated peptides, we performed ribosome display selection of low-affinity peptides in combination with genetic code expansion using pBzo-Phe-tRNAUAG and photo-irradiation. The results demonstrated that sub-micromolar low-affinity peptide epitopes could be identified through the formation of photo-induced covalent bonds with monoclonal antibodies. Thus, the developed ribosome display techniques could contribute to the promotion of diverse peptide-based research.
Collapse
Affiliation(s)
- Takuto Furuhashi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan
- Laboratory for Advanced Biomolecular Engineering, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan
| | - Kensaku Sakamoto
- Laboratory for Nonnatural Amino Acid Technology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan;
- Department of Drug Target Protein Research, School of Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto 390-8621, Nagano, Japan
| | - Akira Wada
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan
- Laboratory for Advanced Biomolecular Engineering, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan
- Laboratory for Nonnatural Amino Acid Technology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan;
| |
Collapse
|
9
|
Zeng Y, Woolley M, Chockalingam K, Thomas B, Arora S, Hook M, Chen Z. Click display: a rapid and efficient in vitro protein display method for directed evolution. Nucleic Acids Res 2023; 51:e89. [PMID: 37548398 PMCID: PMC10484664 DOI: 10.1093/nar/gkad643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/20/2023] [Accepted: 07/22/2023] [Indexed: 08/08/2023] Open
Abstract
We describe a novel method for in vitro protein display-click display-that does not depend on maintaining RNA integrity during biopanning and yields covalently linked protein-cDNA complexes from double-stranded input DNA within 2 h. The display is achieved in a one-pot format encompassing transcription, translation and reverse transcription reactions in series. Stable linkage between proteins and the encoding cDNA is mediated by a modified DNA linker-ML-generated via a click chemistry reaction between a puromycin-containing oligo and a cDNA synthesis primer. Biopanning of a click-displayed mock library coupled with next-generation sequencing analysis revealed >600-fold enrichment of target binders within a single round of panning. A synthetic library of Designed Ankyrin Repeat Proteins (DARPins) with ∼1012 individual members was generated using click display in a 25-μl reaction and six rounds of library panning against a model protein yielded a panel of nanomolar binders. This study establishes click display as a powerful tool for protein binder discovery/engineering and provides a convenient platform for in vitro biopanning selection even in RNase-rich environments such as on whole cells.
Collapse
Affiliation(s)
- Yu Zeng
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Michael Woolley
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Karuppiah Chockalingam
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Benjamin Thomas
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, Houston, TX 77030, USA
| | - Srishtee Arora
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
| | - Magnus Hook
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
| | - Zhilei Chen
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, Houston, TX 77030, USA
| |
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
Ohoka A, Sarkar CA. Facile Display of Homomultivalent Proteins for In Vitro Selections. ACS Synth Biol 2023; 12:634-638. [PMID: 36655840 PMCID: PMC9985468 DOI: 10.1021/acssynbio.2c00563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Low-affinity protein binders are emerging as valuable domains for therapeutic applications because of their higher specificity when presented in multivalent ligands that increase the overall strength and selectivity of receptor binding. De novo discovery of low-affinity binders would be enhanced by the large library sizes attainable with in vitro selection systems, but these platforms generally maximize recovery of high-affinity monovalent binders. Here, we present a facile technology that uses rolling circle amplification to create homomultivalent libraries. We show proof of principle of this approach in ribosome display with off-rate selections of a bivalent ligand against monovalent and bivalent targets, thereby demonstrating high enrichment (up to 166-fold) against a low-affinity target that is bivalent but not monovalent. This approach to homomultivalent library construction can be applied to any binder tolerant of N- and C-terminal fusions and provides a platform for performing in vitro display selections with controlled protein valency and orientation.
Collapse
Affiliation(s)
| | - Casim A. Sarkar
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| |
Collapse
|
12
|
Su W, Wang Y, Zou S, Zhao Y, Li Y, Zhang C, Guo X, Li S. Construction of Peptide Library in Mammalian Cells by dsDNA-Based Strategy. ACS OMEGA 2023; 8:1037-1046. [PMID: 36643544 PMCID: PMC9835800 DOI: 10.1021/acsomega.2c06402] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/19/2022] [Indexed: 06/16/2023]
Abstract
While different display technologies, represented by phage display, have been widely used in drug discovery, they still can hardly achieve function-based peptide screening, which in most cases is performed in mammalian cells. And most attempts to screen functional peptides with mammalian platforms utilized plasmids to store coding information. Our previous work established double-stranded DNAs (dsDNAs) as innovative biological parts to implement AND-gate genetic circuits in mammalian cells. In the current study, we employ dsDNAs with terminal NNK degenerate codons to implement AND-gate genetic circuits and generate peptide libraries in mammalian cells. This dsDNA-based AND-gate (DBAG) peptide library construction strategy is easy to perform, requiring only PCR reaction and cell transfection. High-throughput sequencing (HTS) and single-cell sequencing results revealed both peptide length and amino acid sequence diversity of DBAG peptide libraries. Moreover, as a feasibility test of this strategy, we identified an MDM2-interacting peptide by applying the DBAG peptide library to a mammalian cell-based two-hybrid system. Our work establishes dsDNAs with terminal degenerate codons as biological parts to build peptide libraries in mammalian cells, which may have great application potential in the future.
Collapse
Affiliation(s)
- Weijun Su
- School
of Medicine, Nankai University, Tianjin 300071, China
| | - Yi Wang
- Department
of Breast Cancer Pathology and Research Laboratory, Tianjin Medical
University Cancer Institute & Hospital, National Clinical Research
Center for Cancer; Key Laboratory of Cancer Prevention and Therapy,
Tianjin, Tianjin’s Clinical Research
Center for Cancer, Tianjin 300060, China
| | - Siqi Zou
- School
of Medicine, Nankai University, Tianjin 300071, China
| | - Yanjie Zhao
- Department
of Breast Cancer Pathology and Research Laboratory, Tianjin Medical
University Cancer Institute & Hospital, National Clinical Research
Center for Cancer; Key Laboratory of Cancer Prevention and Therapy,
Tianjin, Tianjin’s Clinical Research
Center for Cancer, Tianjin 300060, China
| | - Yifan Li
- Department
of Breast Cancer Pathology and Research Laboratory, Tianjin Medical
University Cancer Institute & Hospital, National Clinical Research
Center for Cancer; Key Laboratory of Cancer Prevention and Therapy,
Tianjin, Tianjin’s Clinical Research
Center for Cancer, Tianjin 300060, China
| | - Chunze Zhang
- Department
of Colorectal Surgery, Tianjin Union Medical
Center, Tianjin 300121, China
| | - Xiaojing Guo
- Department
of Breast Cancer Pathology and Research Laboratory, Tianjin Medical
University Cancer Institute & Hospital, National Clinical Research
Center for Cancer; Key Laboratory of Cancer Prevention and Therapy,
Tianjin, Tianjin’s Clinical Research
Center for Cancer, Tianjin 300060, China
| | - Shuai Li
- Department
of Breast Cancer Pathology and Research Laboratory, Tianjin Medical
University Cancer Institute & Hospital, National Clinical Research
Center for Cancer; Key Laboratory of Cancer Prevention and Therapy,
Tianjin, Tianjin’s Clinical Research
Center for Cancer, Tianjin 300060, China
| |
Collapse
|
13
|
Hsieh FL, Chang TH. Antibody Display Technology (ADbody) to Present Challenging and Unstable Target Proteins on Antibodies. Methods Mol Biol 2023; 2681:373-382. [PMID: 37405659 DOI: 10.1007/978-1-0716-3279-6_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
Antibodies are the major components of adaptive immunity for the recognition of diverse antigens. Six complementarity-determining regions (CDRs) from each heavy chain and light chain present the antigen-binding site, which determines the antigen-binding specificity. Here, we describe the detailed method of a novel display technology termed antibody display technology (ADbody) (Hsieh and Chang, bioRxiv, 2021), based on the novel structure of human antibodies from malaria-endemic regions of Africa (Hsieh and Higgins, eLife 6:e27311, 2017). The principle of ADbody is to insert proteins of interest (POI) into the heavy-chain CDR3 while still retaining the biological function of POI on the antibody. In this chapter, we described how to use the ADbody method to display challenging and unstable POI on the antibody in mammalian cells. Collectively, this method is designed to provide an alternative outside the current display systems and to generate novel synthetic antibodies.
Collapse
Affiliation(s)
- Fu-Lien Hsieh
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, USA
| | - Tao-Hsin Chang
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, USA
| |
Collapse
|
14
|
Sellés Vidal L, Isalan M, Heap JT, Ledesma-Amaro R. A primer to directed evolution: current methodologies and future directions. RSC Chem Biol 2023; 4:271-291. [PMID: 37034405 PMCID: PMC10074555 DOI: 10.1039/d2cb00231k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/18/2023] [Indexed: 01/30/2023] Open
Abstract
This review summarises the methods available for directed evolution, including mutagenesis and variant selection techniques. The advantages and disadvantages of each technique are presented, and future challenges in the field are discussed.
Collapse
Affiliation(s)
- Lara Sellés Vidal
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Mark Isalan
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - John T. Heap
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Rodrigo Ledesma-Amaro
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| |
Collapse
|
15
|
Seo K, Hagino K, Ichihashi N. Progresses in Cell-Free In Vitro Evolution. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 186:121-140. [PMID: 37306699 DOI: 10.1007/10_2023_219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Biopolymers, such as proteins and RNA, are integral components of living organisms and have evolved through a process of repeated mutation and selection. The technique of "cell-free in vitro evolution" is a powerful experimental approach for developing biopolymers with desired functions and structural properties. Since Spiegelman's pioneering work over 50 years ago, biopolymers with a wide range of functions have been developed using in vitro evolution in cell-free systems. The use of cell-free systems offers several advantages, including the ability to synthesize a wider range of proteins without the limitations imposed by cytotoxicity, and the capacity for higher throughput and larger library sizes than cell-based evolutionary experiments. In this chapter, we provide a comprehensive overview of the progress made in the field of cell-free in vitro evolution by categorizing evolution into directed and undirected. The biopolymers produced by these methods are valuable assets in medicine and industry, and as a means of exploring the potential of biopolymers.
Collapse
Affiliation(s)
- Kaito Seo
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Tokyo, Japan
| | - Katsumi Hagino
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Tokyo, Japan
| | - Norikazu Ichihashi
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Tokyo, Japan.
- Komaba Institute for Science, The University of Tokyo, Tokyo, Japan.
- Universal Biology Institute, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
16
|
Jeong SL, Zhang H, Yamaki S, Yang C, McKemy D, Lieber M, Pham P, Goodman M. Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization. Nucleic Acids Res 2022; 50:11738-11754. [PMID: 36321646 PMCID: PMC9723645 DOI: 10.1093/nar/gkac995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/10/2022] [Accepted: 10/18/2022] [Indexed: 11/05/2022] Open
Abstract
We describe a purified biochemical system to produce monoclonal antibodies (Abs) in vitro using activation-induced deoxycytidine deaminase (AID) and DNA polymerase η (Polη) to diversify immunoglobulin variable gene (IgV) libraries within a phage display format. AID and Polη function during B-cell affinity maturation by catalyzing somatic hypermutation (SHM) of immunoglobulin variable genes (IgV) to generate high-affinity Abs. The IgV mutational motif specificities observed in vivo are conserved in vitro. IgV mutations occurred in antibody complementary determining regions (CDRs) and less frequently in framework (FW) regions. A unique feature of our system is the use of AID and Polη to perform repetitive affinity maturation on libraries reconstructed from a preceding selection step. We have obtained scFv Abs against human glucagon-like peptide-1 receptor (GLP-1R), a target in the treatment of type 2 diabetes, and VHH nanobodies targeting Fatty Acid Amide Hydrolase (FAAH), involved in chronic pain, and artemin, a neurotropic factor that regulates cold pain. A round of in vitro affinity maturation typically resulted in a 2- to 4-fold enhancement in Ab-Ag binding, demonstrating the utility of the system. We tested one of the affinity matured nanobodies and found that it reduced injury-induced cold pain in a mouse model.
Collapse
Affiliation(s)
- Soo Lim Jeong
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Hongyu Zhang
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Shanni Yamaki
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Chenyu Yang
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - David D McKemy
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Michael R Lieber
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA,Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Phuong Pham
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Myron F Goodman
- To whom correspondence should be addressed. Tel: +1 213 740 5190; Fax: +1 213 821 1138;
| |
Collapse
|
17
|
Xu Y, Zhu TF. Mirror-image T7 transcription of chirally inverted ribosomal and functional RNAs. Science 2022; 378:405-412. [DOI: 10.1126/science.abm0646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
To synthesize a chirally inverted ribosome with the goal of building mirror-image biology systems requires the preparation of kilobase-long mirror-image ribosomal RNAs that make up the structural and catalytic core and about two-thirds of the molecular mass of the mirror-image ribosome. Here, we chemically synthesized a 100-kilodalton mirror-image T7 RNA polymerase, which enabled efficient and faithful transcription of the full-length mirror-image 5
S
, 16
S
, and 23
S
ribosomal RNAs from enzymatically assembled long mirror-image genes. We further exploited the versatile mirror-image T7 transcription system for practical applications such as biostable mirror-image riboswitch sensor, long-term storage of unprotected kilobase-long
l
-RNA in water, and
l
-ribozyme–catalyzed
l
-RNA polymerization to serve as a model system for basic RNA research.
Collapse
Affiliation(s)
- Yuan Xu
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
- School of Life Sciences, Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Ting F. Zhu
- School of Life Sciences, Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| |
Collapse
|
18
|
Kulmala A, Lappalainen M, Lamminmäki U, Huovinen T. Synonymous Codons and Hydrophobicity Optimization of Post-translational Signal Peptide PelB Increase Phage Display Efficiency of DARPins. ACS Synth Biol 2022; 11:3174-3181. [PMID: 36178799 PMCID: PMC9594773 DOI: 10.1021/acssynbio.2c00260] [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] [Indexed: 01/24/2023]
Abstract
DsbA leader peptide targets proteins for cotranslational translocation by signal recognition particle (SRP) pathway and has been the standard signal sequence for filamentous phage display of fast-folding Designed Ankyrin Repeat Proteins (DARPins). In contrast, translocation of DARPins via the post-translational pathway, for example, with the commonly used PelB leader, has been reported to be highly inefficient. In this study, two PelB signal sequence libraries were screened covering different regions of the leader peptide for identifying mutants with improved display of DARPins on phage. A PelB variant with the most favorable combination of synonymous mutations in the n-region and hydrophobic substitutions in the h-region increased the display efficiency of a DARPin library 44- and 12-fold compared to PelBWT and DsbA, respectively. Based on thioredoxin-1 (TrxA) export studies the triple valine mutant PelB DN5 V3 leader was capable of more efficient cotranslational translocation than PelBWT, but the overall display efficiency improvement over DsbA suggests that besides increased cotranslational translocation other factors contribute to the observed enhancement in DARPin display efficiency.
Collapse
Affiliation(s)
- Antti Kulmala
- Department
of Life Technologies, University of Turku Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Matias Lappalainen
- Department
of Life Technologies, University of Turku Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Urpo Lamminmäki
- Department
of Life Technologies, University of Turku Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Tuomas Huovinen
- Department
of Life Technologies, University of Turku Kiinamyllynkatu 10, 20520 Turku, Finland,
| |
Collapse
|
19
|
Katoh T, Suga H. In Vitro Genetic Code Reprogramming for the Expansion of Usable Noncanonical Amino Acids. Annu Rev Biochem 2022; 91:221-243. [PMID: 35729073 DOI: 10.1146/annurev-biochem-040320-103817] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetic code reprogramming has enabled us to ribosomally incorporate various nonproteinogenic amino acids (npAAs) into peptides in vitro. The repertoire of usable npAAs has been expanded to include not only l-α-amino acids with noncanonical sidechains but also those with noncanonical backbones. Despite successful single incorporation of npAAs, multiple and consecutive incorporations often suffer from low efficiency or are even unsuccessful. To overcome this stumbling block, engineering approaches have been used to modify ribosomes, EF-Tu, and tRNAs. Here, we provide an overview of these in vitro methods that are aimed at optimal expansion of the npAA repertoire and their applications for the development of de novo bioactive peptides containing various npAAs.
Collapse
Affiliation(s)
- Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan; ,
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan; ,
| |
Collapse
|
20
|
Ledsgaard L, Ljungars A, Rimbault C, Sørensen CV, Tulika T, Wade J, Wouters Y, McCafferty J, Laustsen AH. Advances in antibody phage display technology. Drug Discov Today 2022; 27:2151-2169. [PMID: 35550436 DOI: 10.1016/j.drudis.2022.05.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/24/2022] [Accepted: 05/04/2022] [Indexed: 01/06/2023]
Abstract
Phage display technology can be used for the discovery of antibodies for research, diagnostic, and therapeutic purposes. In this review, we present and discuss key parameters that can be optimized when performing phage display selection campaigns, including the use of different antibody formats and advanced strategies for antigen presentation, such as immobilization, liposomes, nanodiscs, virus-like particles, and whole cells. Furthermore, we provide insights into selection strategies that can be used for the discovery of antibodies with complex binding requirements, such as targeting a specific epitope, cross-reactivity, or pH-dependent binding. Lastly, we provide a description of specialized phage display libraries for the discovery of bispecific antibodies and pH-sensitive antibodies. Together, these methods can be used to improve antibody discovery campaigns against all types of antigen. Teaser: This review provides an overview of the different strategies that can be exploited to improve the success rate of antibody phage display discovery campaigns, addressing key parameters, such as antigen presentation, selection methodologies, and specialized libraries.
Collapse
Affiliation(s)
- Line Ledsgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
| | - Anne Ljungars
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Charlotte Rimbault
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Christoffer V Sørensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Tulika Tulika
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Jack Wade
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Yessica Wouters
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - John McCafferty
- Department of Medicine, Addenbrookes Hospital, Box 157, Hills Road, Cambridge, CB2 0QQ, UK; Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
| |
Collapse
|
21
|
Lu J, Ding J, Liu Z, Chen T. Retrospective analysis of the preparation and application of immunotherapy in cancer treatment (Review). Int J Oncol 2022; 60:12. [PMID: 34981814 PMCID: PMC8759346 DOI: 10.3892/ijo.2022.5302] [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: 10/05/2021] [Accepted: 12/20/2021] [Indexed: 12/11/2022] Open
Abstract
Monoclonal antibody technology plays a vital role in biomedical and immunotherapy, which greatly promotes the study of the structure and function of genes and proteins. To date, monoclonal antibodies have gone through four stages: murine monoclonal antibody, chimeric monoclonal antibody, humanised monoclonal antibody and fully human monoclonal antibody; thousands of monoclonal antibodies have been used in the fields of biology and medicine, playing a special role in the pathogenesis, diagnosis and treatment of disease. In this review, we compare the advantages and disadvantages of hybridoma technology, phage display technology, ribosome display technology, transgenic mouse technology, single B cell monoclonal antibody generation technologies, and forecast the promising applications of these technologies in clinical medicine, disease diagnosis and tumour treatment.
Collapse
Affiliation(s)
- Jiachen Lu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Jianing Ding
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Zhaoxia Liu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Tingtao Chen
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| |
Collapse
|
22
|
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.
Collapse
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.
| |
Collapse
|
23
|
Chen J, Chen M, Zhu TF. Directed evolution and selection of biostable L-DNA aptamers with a mirror-image DNA polymerase. Nat Biotechnol 2022; 40:1601-1609. [PMID: 35668324 PMCID: PMC9646512 DOI: 10.1038/s41587-022-01337-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/28/2022] [Indexed: 12/30/2022]
Abstract
Mirror-image aptamers made from chirally inverted nucleic acids are nuclease-resistant and exceptionally biostable, opening up opportunities for unique applications. However, the directed evolution and selection of mirror-image aptamers directly from large randomized L-DNA libraries has, to our knowledge, not been demonstrated previously. Here, we developed a 'mirror-image selection' scheme for the directed evolution and selection of biostable L-DNA aptamers with a mirror-image DNA polymerase. We performed iterative rounds of enrichment and mirror-image polymerase chain reaction (PCR) amplification of L-DNA sequences that bind native human thrombin, in conjunction with denaturing gradient gel electrophoresis (DGGE) to isolate individual aptamers and L-DNA sequencing-by-synthesis to determine their sequences. Based on the selected L-DNA aptamers, we designed biostable thrombin sensors and inhibitors, which remained functional in physiologically relevant nuclease-rich environments, even in the presence of human serum that rapidly degraded D-DNA aptamers. Mirror-image selection of biostable L-DNA aptamers directly from large randomized L-DNA libraries greatly expands the range of biomolecules that can be targeted, broadening their applications as biostable sensors, therapeutics and basic research tools.
Collapse
Affiliation(s)
- Ji Chen
- grid.12527.330000 0001 0662 3178School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Mengyin Chen
- grid.12527.330000 0001 0662 3178School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Ting F. Zhu
- grid.12527.330000 0001 0662 3178School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China ,grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang China
| |
Collapse
|
24
|
Jaroszewicz W, Morcinek-Orłowska J, Pierzynowska K, Gaffke L, Węgrzyn G. Phage display and other peptide display technologies. FEMS Microbiol Rev 2021; 46:6407522. [PMID: 34673942 DOI: 10.1093/femsre/fuab052] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 10/19/2021] [Indexed: 12/13/2022] Open
Abstract
Phage display technology, which is based on the presentation of peptide sequences on the surface of bacteriophage virions, was developed over 30 years ago. Improvements in phage display systems have allowed us to employ this method in numerous fields of biotechnology, as diverse as immunological and biomedical applications, the formation of novel materials and many others. The importance of phage display platforms was recognized by awarding the Nobel Prize in 2018 "for the phage display of peptides and antibodies". In contrast to many review articles concerning specific applications of phage display systems published in recent years, we present an overview of this technology, including a comparison of various display systems, their advantages and disadvantages, and examples of applications in various fields of science, medicine, and the broad sense of biotechnology. Other peptide display technologies, which employ bacterial, yeast and mammalian cells, as well as eukaryotic viruses and cell-free systems, are also discussed. These powerful methods are still being developed and improved; thus, novel sophisticated tools based on phage display and other peptide display systems are constantly emerging, and new opportunities to solve various scientific, medical and technological problems can be expected to become available in the near future.
Collapse
Affiliation(s)
- Weronika Jaroszewicz
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | | | - Karolina Pierzynowska
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Lidia Gaffke
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| |
Collapse
|
25
|
Shabani S, Moghadam MF, Gargari SLM. Isolation and characterization of a novel GRP78-specific single-chain variable fragment (scFv) using ribosome display method. Med Oncol 2021; 38:115. [PMID: 34390413 DOI: 10.1007/s12032-021-01561-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/18/2021] [Indexed: 01/07/2023]
Abstract
Glucose-regulated protein 78 (GRP78) is a well-characterized endoplasmic reticulum (ER) chaperon frequently overexpressed at the surface of tumor cells and associated with tumor survival, metastasis, and chemoresistance. Hence, potential GRP78 binders emerge as promising candidates for cancer therapy and diagnosis. We applied ribosome display to isolate a single-chain variable domain (scFv) specific for the C-terminal domain of a recombinant human GRP78 (CGRP). Six female BALB/c mice were immunized and then splenocyte mRNA was extracted. An scFv-ribosome display library was established by joining the amplified VH/Vκ fragments through a 72-bp linker using overlap extension PCR. Then, selection was performed by applying two rounds of eukaryotic ribosome display panning with stepwise decreased amount of CGRP. Ultimately, the selected scFv was characterized using the indirect-ELISA assay, competitive-ELISA assay, Western blotting, Surface Plasmon Resonance (SPR), and in-silico analyses. The constructed library had a length of ~ 1100 bp and the high-affinity scFvs were isolated using the outputs of the final panning round. Among 60 positive clones, GSF3 was selected and its expression, purification, and binding capacity was confirmed by SDS-PAGE and Western blotting. GSF3 exhibited an affinity of 13 × 107 M-1 to CGRP as assessed by SPR. Moreover, the in-silico analyses indicated that GSF3 binds the C-terminal domain of GRP78 through key residues engaged in antibody-antigen interactions. We found that ribosome display is a swift and reliable technique for specific and high-affinity scFv isolation. Moreover, our results suggest that GSF3 might be applied as a potential cancer immunotherapeutic and diagnostic tool if this approach is carefully followed by successful preclinical and clinical evaluations to validate the findings for further confirmation.
Collapse
Affiliation(s)
- Shima Shabani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box 14115/111, Tehran, Iran
| | - Mehdi Forouzandeh Moghadam
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box 14115/111, Tehran, Iran.
| | | |
Collapse
|
26
|
Kim SW, Yumoto A, Minagawa N, Son K, Heo Y, Ito Y, Uzawa T. Selection of Ovalbumin-specific Binding Peptides through Instant Translation in Ribosome Display Using E. coli Extract. ANAL SCI 2021; 37:707-712. [PMID: 33487600 DOI: 10.2116/analsci.20scp20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In vitro selection has been widely used to generate molecular-recognition elements in analytical sciences. Although reconstituted types of in vitro transcription and translation (IVTT) system, such as PURE system, are nowadays widely used for ribosome display and mRNA/cDNA display, use of E. coli extract is often avoided, presumably because it contains unfavorable contaminants, such as ribonuclease. Nevertheless, the initial speed of protein translation in E. coli extract is markedly faster than that of PURE system. We thus hypothesized that E. coli extract is more appropriate for instant translation in ribosome display than PURE system. Here, we first revisit the potency of E. coli extract for ribosome display by shortening the translation time, and then applied the optimized condition for selecting peptide aptamers for ovalbumin (OVA). The OVA-binding peptides selected using E. coli extract exhibited specific binding to OVA, even in the presence of 50% serum. We conclude that instant translation in ribosome display using E. coli extract has the potential to generate easy-to-use and economical molecular-recognition elements in analytical sciences.
Collapse
Affiliation(s)
- Shin-Woong Kim
- Department of Biological Sciences, Tokyo Metropolitan University.,Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research
| | - Akiko Yumoto
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science
| | - Noriko Minagawa
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science
| | - Kon Son
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science
| | - Yun Heo
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science
| | - Yoshihiro Ito
- Department of Biological Sciences, Tokyo Metropolitan University.,Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research.,Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science
| | - Takanori Uzawa
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research.,Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science
| |
Collapse
|
27
|
Valldorf B, Hinz SC, Russo G, Pekar L, Mohr L, Klemm J, Doerner A, Krah S, Hust M, Zielonka S. Antibody display technologies: selecting the cream of the crop. Biol Chem 2021; 403:455-477. [PMID: 33759431 DOI: 10.1515/hsz-2020-0377] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/05/2021] [Indexed: 02/07/2023]
Abstract
Antibody display technologies enable the successful isolation of antigen-specific antibodies with therapeutic potential. The key feature that facilitates the selection of an antibody with prescribed properties is the coupling of the protein variant to its genetic information and is referred to as genotype phenotype coupling. There are several different platform technologies based on prokaryotic organisms as well as strategies employing higher eukaryotes. Among those, phage display is the most established system with more than a dozen of therapeutic antibodies approved for therapy that have been discovered or engineered using this approach. In recent years several other technologies gained a certain level of maturity, most strikingly mammalian display. In this review, we delineate the most important selection systems with respect to antibody generation with an emphasis on recent developments.
Collapse
Affiliation(s)
- Bernhard Valldorf
- Chemical and Pharmaceutical Development, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Steffen C Hinz
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287Darmstadt, Germany
| | - Giulio Russo
- Abcalis GmbH, Inhoffenstrasse 7, D-38124Braunschweig, Germany.,Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106Braunschweig, Germany
| | - Lukas Pekar
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Laura Mohr
- Institute of Cell Biology and Neuroscience and Buchmann Institute for Molecular Life Sciences, University of Frankfurt, Max-von-Laue-Strasse 13, D-60438Frankfurt am Main, Germany
| | - Janina Klemm
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287Darmstadt, Germany
| | - Achim Doerner
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106Braunschweig, Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| |
Collapse
|
28
|
Katoh T, Suga H. Development of Bioactive Foldamers Using Ribosomally Synthesized Nonstandard Peptide Libraries. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200326] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- 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
| |
Collapse
|
29
|
Bhatwa A, Wang W, Hassan YI, Abraham N, Li XZ, Zhou T. Challenges Associated With the Formation of Recombinant Protein Inclusion Bodies in Escherichia coli and Strategies to Address Them for Industrial Applications. Front Bioeng Biotechnol 2021; 9:630551. [PMID: 33644021 PMCID: PMC7902521 DOI: 10.3389/fbioe.2021.630551] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
Recombinant proteins are becoming increasingly important for industrial applications, where Escherichia coli is the most widely used bacterial host for their production. However, the formation of inclusion bodies is a frequently encountered challenge for producing soluble and functional recombinant proteins. To overcome this hurdle, different strategies have been developed through adjusting growth conditions, engineering host strains of E. coli, altering expression vectors, and modifying the proteins of interest. These approaches will be comprehensively highlighted with some of the new developments in this review. Additionally, the unique features of protein inclusion bodies, the mechanism and influencing factors of their formation, and their potential advantages will also be discussed.
Collapse
Affiliation(s)
- Arshpreet Bhatwa
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Weijun Wang
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Yousef I. Hassan
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Nadine Abraham
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Xiu-Zhen Li
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Ting Zhou
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| |
Collapse
|
30
|
Dotter H, Boll M, Eder M, Eder AC. Library and post-translational modifications of peptide-based display systems. Biotechnol Adv 2021; 47:107699. [PMID: 33513435 DOI: 10.1016/j.biotechadv.2021.107699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 01/04/2021] [Accepted: 01/14/2021] [Indexed: 12/27/2022]
Abstract
Innovative biotechnological methods empower the successful identification of new drug candidates. Phage, ribosome and mRNA display represent high throughput screenings, allowing fast and efficient progress in the field of targeted drug discovery. The identification range comprises low molecular weight peptides up to whole antibodies. However, a major challenge poses the stability and affinity in particular of peptides. Chemical modifications e.g. the introduction of unnatural amino acids or cyclization, have been proven to be essential tools to overcome these limitations. This review article particularly focuses on available methods for the targeted chemical modification of peptides and peptide libraries in selected display approaches.
Collapse
Affiliation(s)
- Hanna Dotter
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Melanie Boll
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Matthias Eder
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Ann-Christin Eder
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| |
Collapse
|
31
|
Peptide library screening as a tool to derive potent therapeutics: current approaches and future strategies. Future Med Chem 2020; 13:95-98. [PMID: 33275071 DOI: 10.4155/fmc-2020-0324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
|
32
|
Li H, Liu L, Ning B, Sun Z, Yao S, Jiang Y, Liu J. Selection of an artificial paraquat-specific binding protein from a ribosome display library based on a lipocalin scaffold. Biotechnol Appl Biochem 2020; 68:1372-1385. [PMID: 33169873 DOI: 10.1002/bab.2059] [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: 03/09/2020] [Accepted: 10/15/2020] [Indexed: 11/06/2022]
Abstract
In this study, an anticalin that could specifically bind paraquat (PQ), a quaternary nitrogen herbicide, as a new set of engineered receptor protein with antibody-like properties was generated to detect PQ concentration. To this end, a native and random library was constructed and engineered to allow in vitro transcription and translation using an Escherichia coli lysate system. Meanwhile, a PQ derivative that carries an active aliphatic carboxylate group at the end of an aliphatic spacer arm was synthesized. Then, this compound was coupled covalently to the carrier protein bovine serum albumin/ovalbumin and amino-functionalized paramagnetic beads. Alternating selection in solution and immobilization in microtiter wells were used to pan mRNA-ribosome-antibody complexes. After several rounds of ribosome display, three variants were selected from a random library of the bilin-binding protein. The variants that could bind complex PQ with high affinity and exhibit IC50 values as low as 14.039 ± 0.970 ng/mL were identified. Moreover, the limits of detection reached 0.083 ± 0.011 ng/mL. Our data suggest that the generation of anticalins may provide a promising alternative to recombinant antibody fragments to create a stable receptor protein against hapten with bioanalytical relevance.
Collapse
Affiliation(s)
- Hua Li
- Department of Endoscopy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin, People's Republic of China
| | - Li Liu
- Inner Mongolia, Baotou Teachers College of Inner Mongolia University of Science and Technology, Baotou, People's Republic of China
| | - Baoan Ning
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Health and Environmental Medicine, Tianjin, People's Republic of China
| | - Zhiyong Sun
- NO.946 Hospital of PLA, Yining, Xinjiang, People's Republic of China
| | - Sun Yao
- Inner Mongolia North Heavy Industry No.5 Middle School, Baotou, Inner Mongolia, People's Republic of China
| | - Yongqiang Jiang
- Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People's Republic of China
| | - Jianqing Liu
- Inner Mongolia, Baotou Teachers College of Inner Mongolia University of Science and Technology, Baotou, People's Republic of China
| |
Collapse
|
33
|
Elter A, Bogen JP, Hinz SC, Fiebig D, Macarrón Palacios A, Grzeschik J, Hock B, Kolmar H. Humanization of Chicken-Derived scFv Using Yeast Surface Display and NGS Data Mining. Biotechnol J 2020; 16:e2000231. [PMID: 33078896 DOI: 10.1002/biot.202000231] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 10/06/2020] [Indexed: 01/17/2023]
Abstract
Generation of high-affinity monoclonal antibodies by immunization of chickens is a valuable strategy, particularly for obtaining antibodies directed against epitopes that are conserved in mammals. A generic procedure is established for the humanization of chicken-derived antibodies. To this end, high-affinity binders of the epidermal growth factor receptor extracellular domain are isolated from immunized chickens using yeast surface display. Complementarity determining regions (CDRs) of two high-affinity binders are grafted onto a human acceptor framework. Simultaneously, Vernier zone residues, responsible for spatial CDR arrangement, are partially randomized. A yeast surface display library comprising ≈300 000 variants is screened for high-affinity binders in the scFv and Fab formats. Next-generation sequencing discloses humanized antibody variants with restored affinity and improved protein characteristics compared to the parental chicken antibodies. Furthermore, the sequencing data give new insights into the importance of antibody format, used during the humanization process. Starting from the antibody repertoire of immunized chickens, this work features an effective and fast high-throughput approach for the generation of multiple humanized antibodies with potential therapeutic relevance.
Collapse
Affiliation(s)
- Adrian Elter
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Strasse 4, Darmstadt, D-64287, Germany.,Merck Lab @ Technical University of Darmstadt, Alarich-Weiss-Strasse 4, Darmstadt, D-64287, Germany
| | - Jan P Bogen
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Strasse 4, Darmstadt, D-64287, Germany.,Ferring Darmstadt Laboratory, Biologics Technology and Development, Alarich-Weiss-Strasse 4, Darmstadt, D-64287, Germany
| | - Steffen C Hinz
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Strasse 4, Darmstadt, D-64287, Germany.,Merck Lab @ Technical University of Darmstadt, Alarich-Weiss-Strasse 4, Darmstadt, D-64287, Germany
| | - David Fiebig
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Strasse 4, Darmstadt, D-64287, Germany.,Ferring Darmstadt Laboratory, Biologics Technology and Development, Alarich-Weiss-Strasse 4, Darmstadt, D-64287, Germany
| | - Arturo Macarrón Palacios
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Strasse 4, Darmstadt, D-64287, Germany
| | - Julius Grzeschik
- Ferring Darmstadt Laboratory, Biologics Technology and Development, Alarich-Weiss-Strasse 4, Darmstadt, D-64287, Germany
| | - Björn Hock
- Ferring International Center S.A., Chemin de la Vergognausaz 50, Saint-Prex, 1162, Switzerland
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Strasse 4, Darmstadt, D-64287, Germany.,Merck Lab @ Technical University of Darmstadt, Alarich-Weiss-Strasse 4, Darmstadt, D-64287, Germany
| |
Collapse
|
34
|
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.
Collapse
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
| |
Collapse
|
35
|
Lagoutte P. [Ribosome display: Evolution and acellular selection of molecular libraries for high affinity binder generation]. Med Sci (Paris) 2020; 36:717-724. [PMID: 32821048 DOI: 10.1051/medsci/2020126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Ribosome display is a powerful method for selection and molecular evolution of proteins and peptides from large libraries. Displayed proteins are recovered from target molecules in multiple rounds of selection in order to enrich specific binders with the desired properties. Nowadays, ribosome display has become one of the most widely-used display technologies thanks to its advantages over cell-display as phage display. Ribosome display is an in vitro method, in which a stable ternary complex is formed between the mRNA, the ribosome and the nascent protein. A selection cycle can be performed in a few days and bacterial transformation is not necessary. Ribosome display has been used to screen and select peptides, proteins or molecular scaffolds in order to increase their affinity, specificity, catalytic activity or stability. In this review, ribosome display systems and their applications in selection and evolution of proteins are described.
Collapse
Affiliation(s)
- Priscillia Lagoutte
- Univ Lyon, CNRS, Laboratoire de biologie tissulaire et ingénierie thérapeutique, LBTI, UMR 5305. 7 passage du Vercors, F-69637, Lyon, France
| |
Collapse
|
36
|
Ribosome Display Technology: Applications in Disease Diagnosis and Control. Antibodies (Basel) 2020; 9:antib9030028. [PMID: 32605027 PMCID: PMC7551589 DOI: 10.3390/antib9030028] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 12/28/2022] Open
Abstract
Antibody ribosome display remains one of the most successful in vitro selection technologies for antibodies fifteen years after it was developed. The unique possibility of direct generation of whole proteins, particularly single-chain antibody fragments (scFvs), has facilitated the establishment of this technology as one of the foremost antibody production methods. Ribosome display has become a vital tool for efficient and low-cost production of antibodies for diagnostics due to its advantageous ability to screen large libraries and generate binders of high affinity. The remarkable flexibility of this method enables its applicability to various platforms. This review focuses on the applications of ribosome display technology in biomedical and agricultural fields in the generation of recombinant scFvs for disease diagnostics and control.
Collapse
|
37
|
Kojima T. Ultra-high-throughput analysis of functional biomolecules using in vitro selection and bioinformatics. Biosci Biotechnol Biochem 2020; 84:1767-1774. [PMID: 32441212 DOI: 10.1080/09168451.2020.1768823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Functional analysis of biomolecules, including nucleic acids and proteins, is important for understanding biological mechanisms in living cells such as gene expression and metabolism. To analyze diverse biomolecular functions, large-scale screening systems for biomolecules have been developed for various applications such as to improve enzyme activity and identify target binding molecules. One of these systems, the Bead Display system, utilizes emulsion technology and is a powerful tool for rapidly screening functional nucleic acids or proteins in vitro. Furthermore, an analytical pipeline that consists of genomic systematic evolution of ligands by exponential enrichment (gSELEX)-Seq, gene expression analysis, and bioinformatics was shown to be a robust platform for comprehensively identifying genes regulated by a transcription factor. This review provides an overview of the biomolecular screening methods developed to date.
Collapse
Affiliation(s)
- Takaaki Kojima
- Graduate School of Bioagricultural Sciences, Nagoya University , Nagoya, Japan
| |
Collapse
|
38
|
Sandomenico A, Caporale A, Doti N, Cross S, Cruciani G, Chambery A, De Falco S, Ruvo M. Synthetic Peptide Libraries: From Random Mixtures to In Vivo Testing. Curr Med Chem 2020; 27:997-1016. [PMID: 30009695 DOI: 10.2174/0929867325666180716110833] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 06/22/2018] [Accepted: 06/29/2018] [Indexed: 01/13/2023]
Abstract
Combinatorially generated molecular repertoires have been largely used to identify novel bioactive compounds. Ever more sophisticated technological solutions have been proposed to simplify and speed up such process, expanding the chemical diversity space and increasing the prospect to select new molecular entities with specific and potent activities against targets of therapeutic relevance. In this context, random mixtures of oligomeric peptides were originally used and since 25 years they represent a continuous source of bioactive molecules with potencies ranging from the sub-nM to microM concentration. Synthetic peptide libraries are still employed as starting "synthetic broths" of structurally and chemically diversified molecular fragments from which lead compounds can be extracted and further modified. Thousands of studies have been reported describing the application of combinatorial mixtures of synthetic peptides with different complexity and engrafted on diverse structural scaffolds for the identification of new compounds which have been further developed and also tested in in vivo models of relevant diseases. We briefly review some of the most used methodologies for library preparation and screening and the most recent case studies appeared in the literature where compounds have reached at least in vivo testing in animal or similar models. Recent technological advancements in biotechnology, engineering and computer science have suggested new options to facilitate the discovery of new bioactive peptides. In this instance, we anticipate here a new approach for the design of simple but focused tripeptide libraries against druggable cavities of therapeutic targets and its complementation with existing approaches.
Collapse
Affiliation(s)
- Annamaria Sandomenico
- Istituto di Biostrutture e Bioimmagini del CNR and CIRPeB, Universita Federico II di Napoli, via Mezzocannone, 16, 80134 Napoli, Italy
| | - Andrea Caporale
- Istituto di Biostrutture e Bioimmagini del CNR and CIRPeB, Universita Federico II di Napoli, via Mezzocannone, 16, 80134 Napoli, Italy
| | - Nunzianna Doti
- Istituto di Biostrutture e Bioimmagini del CNR and CIRPeB, Universita Federico II di Napoli, via Mezzocannone, 16, 80134 Napoli, Italy
| | - Simon Cross
- Molecular Discovery Ltd, Unit 501 Centennial Park, Centennial Avenue Elstree, Borehamwood, Hertfordshire WD6 3FG, United Kingdom
| | - Gabriele Cruciani
- Molecular Discovery Ltd, Unit 501 Centennial Park, Centennial Avenue Elstree, Borehamwood, Hertfordshire WD6 3FG, United Kingdom.,Dipartimento di Chimica, Biologia e Biotecnologia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Angela Chambery
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università della Campania "Luigi Vanvitelli", via Vivaldi, 43, 81100 Caserta, Italy
| | - Sandro De Falco
- Istituto di Genetica e Biofisica del CNR, via Pietro Castellino, 111, 80131, Napoli, Italy
| | - Menotti Ruvo
- Istituto di Biostrutture e Bioimmagini del CNR and CIRPeB, Universita Federico II di Napoli, via Mezzocannone, 16, 80134 Napoli, Italy
| |
Collapse
|
39
|
Hammerling MJ, Fritz BR, Yoesep DJ, Kim DS, Carlson ED, Jewett MC. In vitro ribosome synthesis and evolution through ribosome display. Nat Commun 2020; 11:1108. [PMID: 32111839 PMCID: PMC7048773 DOI: 10.1038/s41467-020-14705-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 01/28/2020] [Indexed: 02/04/2023] Open
Abstract
Directed evolution of the ribosome for expanded substrate incorporation and novel functions is challenging because the requirement of cell viability limits the mutations that can be made. Here we address this challenge by combining cell-free synthesis and assembly of translationally competent ribosomes with ribosome display to develop a fully in vitro methodology for ribosome synthesis and evolution (called RISE). We validate the RISE method by selecting active genotypes from a ~1.7 × 107 member library of ribosomal RNA (rRNA) variants, as well as identifying mutant ribosomes resistant to the antibiotic clindamycin from a library of ~4 × 103 rRNA variants. We further demonstrate the prevalence of positive epistasis in resistant genotypes, highlighting the importance of such interactions in selecting for new function. We anticipate that RISE will facilitate understanding of molecular translation and enable selection of ribosomes with altered properties. Directed evolution of the ribosome is challenging because the requirement of cell viability limits the mutations that can be made. Here the authors develop a platform for in vitro ribosome synthesis and evolution (RISE) to overcome these constraints.
Collapse
Affiliation(s)
- Michael J Hammerling
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208, USA
| | - Brian R Fritz
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208, USA
| | - Danielle J Yoesep
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208, USA
| | - Do Soon Kim
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208, USA
| | - Erik D Carlson
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208, USA.,Department of Chemical Engineering, Stanford University, Stanford, California, 94305, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208, USA. .,Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208, USA. .,Simpson Querrey Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208, USA. .,Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208, USA. .,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208, USA.
| |
Collapse
|
40
|
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.
Collapse
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
| |
Collapse
|
41
|
Ayoubi-Joshaghani MH, Dianat-Moghadam H, Seidi K, Jahanban-Esfahalan A, Zare P, Jahanban-Esfahlan R. Cell-free protein synthesis: The transition from batch reactions to minimal cells and microfluidic devices. Biotechnol Bioeng 2020; 117:1204-1229. [PMID: 31840797 DOI: 10.1002/bit.27248] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/23/2019] [Accepted: 12/09/2019] [Indexed: 12/13/2022]
Abstract
Thanks to the synthetic biology, the laborious and restrictive procedure for producing a target protein in living microorganisms by biotechnological approaches can now experience a robust, pliant yet efficient alternative. The new system combined with lab-on-chip microfluidic devices and nanotechnology offers a tremendous potential envisioning novel cell-free formats such as DNA brushes, hydrogels, vesicular particles, droplets, as well as solid surfaces. Acting as robust microreactors/microcompartments/minimal cells, the new platforms can be tuned to perform various tasks in a parallel and integrated manner encompassing gene expression, protein synthesis, purification, detection, and finally enabling cell-cell signaling to bring a collective cell behavior, such as directing differentiation process, characteristics of higher order entities, and beyond. In this review, we issue an update on recent cell-free protein synthesis (CFPS) formats. Furthermore, the latest advances and applications of CFPS for synthetic biology and biotechnology are highlighted. In the end, contemporary challenges and future opportunities of CFPS systems are discussed.
Collapse
Affiliation(s)
| | | | - Khaled Seidi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Peyman Zare
- Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland
| | - Rana Jahanban-Esfahlan
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
42
|
Stern LA, Lown PS, Hackel BJ. Ligand Engineering via Yeast Surface Display and Adherent Cell Panning. Methods Mol Biol 2020; 2070:303-320. [PMID: 31625103 PMCID: PMC6996137 DOI: 10.1007/978-1-4939-9853-1_17] [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: 06/10/2023]
Abstract
High-throughput ligand discovery and evolution-via genotype-phenotype linkage strategies-empower molecularly targeted therapy, diagnostics, and fundamental science. Maintaining high-quality target antigen in these selections, particularly for membrane targets, is often a technical challenge. Panning yeast-displayed ligand libraries on intact mammalian cells expressing the molecular target has emerged as an effective strategy. Herein we describe the techniques used to select target-binding ligands via this approach including the use of target-negative cells to deplete non-specific binders and avidity reduction to preferentially select high-affinity ligands.
Collapse
Affiliation(s)
- Lawrence A Stern
- Department of Hematology and Hematopoietic Cell Transplantation, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Patrick S Lown
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
| |
Collapse
|
43
|
Biyani M, Biyani M, Nishigaki K. Biomolecular display technology: a new tool for drug discovery. Anim Biotechnol 2020. [DOI: 10.1016/b978-0-12-811710-1.00019-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
44
|
Bozovičar K, Bratkovič T. Evolving a Peptide: Library Platforms and Diversification Strategies. Int J Mol Sci 2019; 21:E215. [PMID: 31892275 PMCID: PMC6981544 DOI: 10.3390/ijms21010215] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/22/2019] [Accepted: 12/25/2019] [Indexed: 12/22/2022] Open
Abstract
Peptides are widely used in pharmaceutical industry as active pharmaceutical ingredients, versatile tools in drug discovery, and for drug delivery. They find themselves at the crossroads of small molecules and proteins, possessing favorable tissue penetration and the capability to engage into specific and high-affinity interactions with endogenous receptors. One of the commonly employed approaches in peptide discovery and design is to screen combinatorial libraries, comprising a myriad of peptide variants of either chemical or biological origin. In this review, we focus mainly on recombinant peptide libraries, discussing different platforms for their display or expression, and various diversification strategies for library design. We take a look at well-established technologies as well as new developments and future directions.
Collapse
Affiliation(s)
| | - Tomaž Bratkovič
- Department of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, SI-1000 Ljubljana, Slovenia;
| |
Collapse
|
45
|
Abstract
Engineered protein scaffolds have made a tremendous contribution to the panel of affinity tools owing to their favorable biophysical properties that make them useful for many applications. In 2007, our group paved the way for using archaeal Sul7d proteins for the design of artificial affinity ligands, so-called Affitins. For many years, Sac7d and Sso7d have been used as molecular basis to obtain binders for various targets. Recently, we characterized their old gifted protein family and identified Aho7c, originating from Acidianus hospitalis, as the shortest member (60 amino-acids) with impressive stability (96.5 °C, pH 0-12). Here, we describe the construction of Aho7c combinatorial libraries and their use for selection of binders by ribosome display.
Collapse
|
46
|
Apitius L, Rübsam K, Jakesch C, Jakob F, Schwaneberg U. Ultrahigh‐throughput screening system for directed polymer binding peptide evolution. Biotechnol Bioeng 2019; 116:1856-1867. [DOI: 10.1002/bit.26990] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 03/28/2019] [Accepted: 04/11/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Lina Apitius
- DWI – Leibniz‐Institute for Interactive MaterialsAachen Germany
- RWTH Aachen UniversityAachen Germany
| | - Kristin Rübsam
- DWI – Leibniz‐Institute for Interactive MaterialsAachen Germany
| | | | - Felix Jakob
- DWI – Leibniz‐Institute for Interactive MaterialsAachen Germany
- RWTH Aachen UniversityAachen Germany
| | - Ulrich Schwaneberg
- DWI – Leibniz‐Institute for Interactive MaterialsAachen Germany
- RWTH Aachen UniversityAachen Germany
| |
Collapse
|
47
|
Abstract
Ribosome display has proven to be a powerful in vitro selection and evolution method for generating high-affinity binders from libraries of folded proteins. It works entirely in vitro, and this has two important consequences. First, since no transformation of any cells is required, libraries with much greater diversity can be handled than with most other techniques. Second, since a library does not have to be cloned and transformed, it is very convenient to introduce random errors in the library by PCR-based methods and select improved binders. Thus, a true directed evolution, an iteration between randomization and selection over several generations, can be conveniently carried out, e.g., for affinity maturation, either on a given clone or on the whole library. Ribosome display has been successfully applied to antibody single-chain Fv fragments (scFv), which can be selected not only for specificity but also for stability and catalytic activity. High-affinity binders with new target specificity can be obtained from highly diverse libraries in only a few selection rounds. In this protocol, the selection from the library and the process of affinity maturation and off-rate selection are explained in detail.
Collapse
|
48
|
Liszczak G, Muir TW. Barcoding mit Nukleinsäuren: Anwendung der DNA‐Sequenzierung als molekulares Zählwerk. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201808956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Glen Liszczak
- Department of ChemistryPrinceton University Princeton NJ 08544 USA
- Aktuelle Adresse: Department of BiochemistryUT Southwestern Medical Center Dallas TX 75390 USA
| | - Tom W. Muir
- Department of ChemistryPrinceton University Princeton NJ 08544 USA
| |
Collapse
|
49
|
Wright RC, Nemhauser J. Plant Synthetic Biology: Quantifying the "Known Unknowns" and Discovering the "Unknown Unknowns". PLANT PHYSIOLOGY 2019; 179:885-893. [PMID: 30630870 PMCID: PMC6393784 DOI: 10.1104/pp.18.01222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/14/2018] [Indexed: 05/03/2023]
Abstract
Biosensors, advanced microscopy, and single- cell transcriptomics are advancing plant synthetic biology.
Collapse
Affiliation(s)
- R Clay Wright
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia
| | | |
Collapse
|
50
|
Liszczak G, Muir TW. Nucleic Acid-Barcoding Technologies: Converting DNA Sequencing into a Broad-Spectrum Molecular Counter. Angew Chem Int Ed Engl 2019; 58:4144-4162. [PMID: 30153374 DOI: 10.1002/anie.201808956] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Indexed: 12/17/2022]
Abstract
The emergence of high-throughput DNA sequencing technologies sparked a revolution in the field of genomics that has rippled into many branches of the life and physical sciences. The remarkable sensitivity, specificity, throughput, and multiplexing capacity that are inherent to parallel DNA sequencing have since motivated its use as a broad-spectrum molecular counter. A key aspect of extrapolating DNA sequencing to non-traditional applications is the need to append nucleic-acid barcodes to entities of interest. In this review, we describe the chemical and biochemical approaches that have enabled nucleic-acid barcoding of proteinaceous and non-proteinaceous materials and provide examples of downstream technologies that have been made possible by DNA-encoded molecules. As commercially available high-throughput sequencers were first released less than 15 years ago, we believe related applications will continue to mature and close by proposing new frontiers to support this assertion.
Collapse
Affiliation(s)
- Glen Liszczak
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.,Present address: Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| |
Collapse
|