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Hutchings CJ, Sato AK. Phage display technology and its impact in the discovery of novel protein-based drugs. Expert Opin Drug Discov 2024; 19:887-915. [PMID: 39074492 DOI: 10.1080/17460441.2024.2367023] [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: 11/28/2023] [Accepted: 06/07/2024] [Indexed: 07/31/2024]
Abstract
INTRODUCTION Phage display technology is a well-established versatile in vitro display technology that has been used for over 35 years to identify peptides and antibodies for use as reagents and therapeutics, as well as exploring the diversity of alternative scaffolds as another option to conventional therapeutic antibody discovery. Such successes have been responsible for spawning a range of biotechnology companies, as well as many complementary technologies devised to expedite the drug discovery process and resolve bottlenecks in the discovery workflow. AREAS COVERED In this perspective, the authors summarize the application of phage display for drug discovery and provide examples of protein-based drugs that have either been approved or are being developed in the clinic. The amenability of phage display to generate functional protein molecules to challenging targets and recent developments of strategies and techniques designed to harness the power of sampling diverse repertoires are highlighted. EXPERT OPINION Phage display is now routinely combined with cutting-edge technologies to deep-mine antibody-based repertoires, peptide, or alternative scaffold libraries generating a wealth of data that can be leveraged, e.g. via artificial intelligence, to enable the potential for clinical success in the discovery and development of protein-based therapeutics.
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2
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Wang N, Mcneer NA, Eton E, Fass J, Kentsis A. Proteomic Barcoding Platform for Macromolecular Screening and Delivery. J Proteome Res 2024; 23:2067-2077. [PMID: 38776430 DOI: 10.1021/acs.jproteome.4c00068] [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: 05/25/2024]
Abstract
Engineered macromolecules offer compelling means for the therapy of conventionally undruggable interactions in human disease. However, their efficacy is limited by barriers to tissue and intracellular delivery. Inspired by recent advances in molecular barcoding and evolution, we developed BarcodeBabel, a generalized method for the design of libraries of peptide barcodes suitable for high-throughput mass spectrometry proteomics. Combined with PeptideBabel, a Monte Carlo sampling algorithm for the design of peptides with evolvable physicochemical properties and sequence complexity, we developed a barcoded library of cell penetrating peptides (CPPs) with distinct physicochemical features. Using quantitative targeted mass spectrometry, we identified CPPS with improved nuclear and cytoplasmic delivery exceeding hundreds of millions of molecules per human cell while maintaining minimal membrane disruption and negligible toxicity in vitro. These studies provide a proof of concept for peptide barcoding as a homogeneous high-throughput method for macromolecular screening and delivery. BarcodeBabel and PeptideBabel are available open-source from https://github.com/kentsisresearchgroup/.
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Affiliation(s)
- Ning Wang
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Nicole A Mcneer
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Elliot Eton
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Josh Fass
- Tri-I PhD Program in Computational Biology and Medicine, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Cornell Medical College, Cornell University, New York, New York 10065, United States
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3
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Thomas B, Chockalingam K, Chen Z. Methods for Engineering Binders to Multi-Pass Membrane Proteins. Bioengineering (Basel) 2023; 10:1351. [PMID: 38135942 PMCID: PMC10741020 DOI: 10.3390/bioengineering10121351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/11/2023] [Accepted: 11/19/2023] [Indexed: 12/24/2023] Open
Abstract
Numerous potential drug targets, including G-protein-coupled receptors and ion channel proteins, reside on the cell surface as multi-pass membrane proteins. Unfortunately, despite advances in engineering technologies, engineering biologics against multi-pass membrane proteins remains a formidable task. In this review, we focus on the different methods used to prepare/present multi-pass transmembrane proteins for engineering target-specific biologics such as antibodies, nanobodies and synthetic scaffold proteins. The engineered biologics exhibit high specificity and affinity, and have broad applications as therapeutics, probes for cell staining and chaperones for promoting protein crystallization. We primarily cover publications on this topic from the past 10 years, with a focus on the different formats of multi-pass transmembrane proteins. Finally, the remaining challenges facing this field and new technologies developed to overcome a number of obstacles are discussed.
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Affiliation(s)
- Benjamin Thomas
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX 77845, USA;
| | - Karuppiah Chockalingam
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA;
| | - Zhilei Chen
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX 77845, USA;
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA;
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4
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Frecot DI, Froehlich T, Rothbauer U. 30 years of nanobodies - an ongoing success story of small binders in biological research. J Cell Sci 2023; 136:jcs261395. [PMID: 37937477 DOI: 10.1242/jcs.261395] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Abstract
A milestone in the field of recombinant binding molecules was achieved 30 years ago with the discovery of single-domain antibodies from which antigen-binding variable domains, better known as nanobodies (Nbs), can be derived. Being only one tenth the size of conventional antibodies, Nbs feature high affinity and specificity, while being highly stable and soluble. In addition, they display accessibility to cryptic sites, low off-target accumulation and deep tissue penetration. Efficient selection methods, such as (semi-)synthetic/naïve or immunized cDNA libraries and display technologies, have facilitated the isolation of Nbs against diverse targets, and their single-gene format enables easy functionalization and high-yield production. This Review highlights recent advances in Nb applications in various areas of biological research, including structural biology, proteomics and high-resolution and in vivo imaging. In addition, we provide insights into intracellular applications of Nbs, such as live-cell imaging, biosensors and targeted protein degradation.
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Affiliation(s)
- Desiree I Frecot
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Reutlingen, Germany
| | - Theresa Froehlich
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
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5
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Miyazaki T, Aoki W, Koike N, Sato T, Ueda M. Application of peptide barcoding to obtain high-affinity anti-PD-1 nanobodies. J Biosci Bioeng 2023; 136:173-181. [PMID: 37487915 DOI: 10.1016/j.jbiosc.2023.07.002] [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: 04/02/2023] [Revised: 07/02/2023] [Accepted: 07/06/2023] [Indexed: 07/26/2023]
Abstract
Cancer treatment has been revolutionized by immune checkpoint inhibitors, which regulate immune cell function by blocking the interactions between immune checkpoint molecules and their ligands. The interaction between programmed cell death-1 (PD-1) and programmed cell death-ligand 1 (PD-L1) is a target for immune checkpoint inhibitors. Nanobodies, which are recombinant variable domains of heavy-chain-only antibodies, can replace existing immune checkpoint inhibitors, such as anti-PD-1 or anti-PD-L1 conventional antibodies. However, the screening process for high-affinity nanobodies is laborious and time-consuming. Here, we identified high-affinity anti-PD-1 nanobodies using peptide barcoding, which enabled reliable and efficient screening by distinguishing each nanobody with a peptide barcode that was genetically appended to each nanobody. We prepared a peptide-barcoded nanobody (PBNb) library with thousands of variants. Three high-affinity PBNbs were identified from the PBNb library by quantifying the peptide barcodes derived from high-affinity PBNbs. Furthermore, these three PBNbs neutralized the interaction between PD-1 and PD-L1. Our results demonstrate the utility of peptide barcoding and the resulting nanobodies can be used as experimental tools and antitumor agents.
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Affiliation(s)
- Takumi Miyazaki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan; Kyoto Integrated Science and Technology Bio-Analysis Center, Simogyo-ku, Kyoto 600-8813, Japan.
| | - Naoki Koike
- TechnoPro, Inc. TechnoPro R&D, Company, Tokyo 106-6135, Japan
| | - Toshiko Sato
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan; Kyoto Integrated Science and Technology Bio-Analysis Center, Simogyo-ku, Kyoto 600-8813, Japan
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6
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Breine A, Van Holsbeeck K, Martin C, Gonzalez S, Mannes M, Pardon E, Steyaert J, Remaut H, Ballet S, Van der Henst C. Bypassing the Need for Cell Permeabilization: Nanobody CDR3 Peptide Improves Binding on Living Bacteria. Bioconjug Chem 2023. [PMID: 37418494 PMCID: PMC10360062 DOI: 10.1021/acs.bioconjchem.3c00116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
Membrane interaction constitutes to be an essential parameter in the mode of action of entities such as proteins, as well as cell-penetrating and antimicrobial peptides, resulting in noninvasive or lytic activities depending on the membrane compositions and interactions. Recently, a nanobody able to interact with the top priority, multidrug-resistant bacterial pathogen Acinetobacter baumannii was discovered, although binding took place with fixed cells only. To potentially overcome this limitation, linear peptides corresponding to the complementarity-determining regions (CDR) were synthesized and fluorescently labeled. Microscopy data indicated clear membrane interactions of the CDR3 sequence with living A. baumannii cells, indicating both the importance of the CDR3 as part of the parent nanobody paratope and the improved binding ability and thus avoiding the need for permeabilization of the cells. In addition, cyclization of the peptide with an additionally introduced rigidifying 1,2,3-triazole bridge retains its binding ability while proteolytically protecting the peptide. Overall, this study resulted in the discovery of novel peptides binding a multidrug-resistant pathogen.
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Affiliation(s)
- A Breine
- Microbial Resistance and Drug Discovery, VIB-VUB Center for Structural Biology, VIB, Flanders Institute for Biotechnology, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - K Van Holsbeeck
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - C Martin
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - S Gonzalez
- CNRS, BioCIS, CY Cergy-Paris Université, 95000 Neuville sur Oise, France
| | - M Mannes
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - E Pardon
- Microbial Resistance and Drug Discovery, VIB-VUB Center for Structural Biology, VIB, Flanders Institute for Biotechnology, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - J Steyaert
- Microbial Resistance and Drug Discovery, VIB-VUB Center for Structural Biology, VIB, Flanders Institute for Biotechnology, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - H Remaut
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, 1050 Brussels, Belgium
| | - S Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - C Van der Henst
- Microbial Resistance and Drug Discovery, VIB-VUB Center for Structural Biology, VIB, Flanders Institute for Biotechnology, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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7
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Hurley K, Cao M, Huang H, Wang Y. Targeted Alpha Therapy (TAT) with Single-Domain Antibodies (Nanobodies). Cancers (Basel) 2023; 15:3493. [PMID: 37444603 DOI: 10.3390/cancers15133493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/23/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
The persistent threat of cancer necessitates the development of improved and more efficient therapeutic strategies that limit damage to healthy tissues. Targeted alpha therapy (TαT), a novel form of radioimmuno-therapy (RIT), utilizes a targeting vehicle, commonly antibodies, to deliver high-energy, but short-range, alpha-emitting particles specifically to cancer cells, thereby reducing toxicity to surrounding normal tissues. Although full-length antibodies are often employed as targeting vehicles for TαT, their high molecular weight and the presence of an Fc-region lead to a long blood half-life, increased bone marrow toxicity, and accumulation in other tissues such as the kidney, liver, and spleen. The discovery of single-domain antibodies (sdAbs), or nanobodies, naturally occurring in camelids and sharks, has introduced a novel antigen-specific vehicle for molecular imaging and TαT. Given that nanobodies are the smallest naturally occurring antigen-binding fragments, they exhibit shorter relative blood half-lives, enhanced tumor uptake, and equivalent or superior binding affinity and specificity. Nanobody technology could provide a viable solution for the off-target toxicity observed with full-length antibody-based TαT. Notably, the pharmacokinetic properties of nanobodies align better with the decay characteristics of many short-lived α-emitting radionuclides. This review aims to encapsulate recent advancements in the use of nanobodies as a vehicle for TαT.
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Affiliation(s)
- Kate Hurley
- Radiobiology and Health, Canadian Nuclear Laboratories, Chalk River, ON K0J 1J0, Canada
| | - Meiyun Cao
- Radiobiology and Health, Canadian Nuclear Laboratories, Chalk River, ON K0J 1J0, Canada
| | - Haiming Huang
- Research Center, Forlong Biotechnology Inc., Suzhou 215004, China
| | - Yi Wang
- Radiobiology and Health, Canadian Nuclear Laboratories, Chalk River, ON K0J 1J0, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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8
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Mattsson J, Ljungars A, Carlsson A, Svensson C, Nilsson B, Ohlin M, Frendéus B. Sequence enrichment profiles enable target-agnostic antibody generation for a broad range of antigens. CELL REPORTS METHODS 2023; 3:100475. [PMID: 37323567 PMCID: PMC10261905 DOI: 10.1016/j.crmeth.2023.100475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 03/27/2023] [Accepted: 04/17/2023] [Indexed: 06/17/2023]
Abstract
Phenotypic drug discovery (PDD) enables the target-agnostic generation of therapeutic drugs with novel mechanisms of action. However, realizing its full potential for biologics discovery requires new technologies to produce antibodies to all, a priori unknown, disease-associated biomolecules. We present a methodology that helps achieve this by integrating computational modeling, differential antibody display selection, and massive parallel sequencing. The method uses the law of mass action-based computational modeling to optimize antibody display selection and, by matching computationally modeled and experimentally selected sequence enrichment profiles, predict which antibody sequences encode specificity for disease-associated biomolecules. Applied to a phage display antibody library and cell-based antibody selection, ∼105 antibody sequences encoding specificity for tumor cell surface receptors expressed at 103-106 receptors/cell were discovered. We anticipate that this approach will be broadly applicable to molecular libraries coupling genotype to phenotype and to the screening of complex antigen populations for identification of antibodies to unknown disease-associated targets.
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Affiliation(s)
- Jenny Mattsson
- BioInvent, Research, Lund, Sweden
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anne Ljungars
- BioInvent, Research, Lund, Sweden
- Department of Immunotechnology, Lund University, Lund, Sweden
| | | | - Carolin Svensson
- BioInvent, Research, Lund, Sweden
- Section of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Björn Nilsson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Broad Institute, 415 Main Street, Cambridge, MA, USA
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
- SciLifeLab Human Antibody Therapeutics, Lund University, Lund, Sweden
| | - Björn Frendéus
- BioInvent, Research, Lund, Sweden
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
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9
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Yong Joon Kim J, Sang Z, Xiang Y, Shen Z, Shi Y. Nanobodies: Robust miniprotein binders in biomedicine. Adv Drug Deliv Rev 2023; 195:114726. [PMID: 36754285 DOI: 10.1016/j.addr.2023.114726] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 12/30/2022] [Accepted: 02/02/2023] [Indexed: 02/10/2023]
Abstract
Variable domains of heavy chain-only antibodies (VHH), also known as nanobodies (Nbs), are monomeric antigen-binding domains derived from the camelid heavy chain-only antibodies. Nbs are characterized by small size, high target selectivity, and marked solubility and stability, which collectively facilitate high-quality drug development. In addition, Nbs are readily expressed from various expression systems, including E. coli and yeast cells. For these reasons, Nbs have emerged as preferred antibody fragments for protein engineering, disease diagnosis, and treatment. To date, two Nb-based therapies have been approved by the U.S. Food and Drug Administration (FDA). Numerous candidates spanning a wide spectrum of diseases such as cancer, immune disorders, infectious diseases, and neurodegenerative disorders are under preclinical and clinical investigation. Here, we discuss the structural features of Nbs that allow for specific, versatile, and strong target binding. We also summarize emerging technologies for identification, structural analysis, and humanization of Nbs. Our main focus is to review recent advances in using Nbs as a modular scaffold to facilitate the engineering of multivalent polymers for cutting-edge applications. Finally, we discuss remaining challenges for Nb development and envision new opportunities in Nb-based research.
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Affiliation(s)
- Jeffrey Yong Joon Kim
- Center of Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1, Gustave L. Levy Pl, New York, NY 10029, USA; Medical Scientist Training Program, University of Pittsburgh School of Medicine and Carnegie Mellon University, Pittsburgh, PA, USA
| | - Zhe Sang
- Center of Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1, Gustave L. Levy Pl, New York, NY 10029, USA
| | - Yufei Xiang
- Center of Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1, Gustave L. Levy Pl, New York, NY 10029, USA
| | - Zhuolun Shen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yi Shi
- Center of Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1, Gustave L. Levy Pl, New York, NY 10029, USA.
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10
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Meier G, Thavarasah S, Ehrenbolger K, Hutter CAJ, Hürlimann LM, Barandun J, Seeger MA. Deep mutational scan of a drug efflux pump reveals its structure-function landscape. Nat Chem Biol 2023; 19:440-450. [PMID: 36443574 PMCID: PMC7615509 DOI: 10.1038/s41589-022-01205-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 10/10/2022] [Indexed: 11/30/2022]
Abstract
Drug efflux is a common resistance mechanism found in bacteria and cancer cells, but studies providing comprehensive functional insights are scarce. In this study, we performed deep mutational scanning (DMS) on the bacterial ABC transporter EfrCD to determine the drug efflux activity profile of more than 1,430 single variants. These systematic measurements revealed that the introduction of negative charges at different locations within the large substrate binding pocket results in strongly increased efflux activity toward positively charged ethidium, whereas additional aromatic residues did not display the same effect. Data analysis in the context of an inward-facing cryogenic electron microscopy structure of EfrCD uncovered a high-affinity binding site, which releases bound drugs through a peristaltic transport mechanism as the transporter transits to its outward-facing conformation. Finally, we identified substitutions resulting in rapid Hoechst influx without affecting the efflux activity for ethidium and daunorubicin. Hence, single mutations can convert EfrCD into a drug-specific ABC importer.
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Affiliation(s)
- Gianmarco Meier
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Sujani Thavarasah
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Kai Ehrenbolger
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
- Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Cedric A J Hutter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Linkster Therapeutics AG, Zurich, Switzerland
| | - Lea M Hürlimann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Linkster Therapeutics AG, Zurich, Switzerland
| | - Jonas Barandun
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
- Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
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11
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Kim DE, Jensen DR, Feldman D, Tischer D, Saleem A, Chow CM, Li X, Carter L, Milles L, Nguyen H, Kang A, Bera AK, Peterson FC, Volkman BF, Ovchinnikov S, Baker D. De novo design of small beta barrel proteins. Proc Natl Acad Sci U S A 2023; 120:e2207974120. [PMID: 36897987 PMCID: PMC10089152 DOI: 10.1073/pnas.2207974120] [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: 05/10/2022] [Accepted: 01/27/2023] [Indexed: 03/12/2023] Open
Abstract
Small beta barrel proteins are attractive targets for computational design because of their considerable functional diversity despite their very small size (<70 amino acids). However, there are considerable challenges to designing such structures, and there has been little success thus far. Because of the small size, the hydrophobic core stabilizing the fold is necessarily very small, and the conformational strain of barrel closure can oppose folding; also intermolecular aggregation through free beta strand edges can compete with proper monomer folding. Here, we explore the de novo design of small beta barrel topologies using both Rosetta energy-based methods and deep learning approaches to design four small beta barrel folds: Src homology 3 (SH3) and oligonucleotide/oligosaccharide-binding (OB) topologies found in nature and five and six up-and-down-stranded barrels rarely if ever seen in nature. Both approaches yielded successful designs with high thermal stability and experimentally determined structures with less than 2.4 Å rmsd from the designed models. Using deep learning for backbone generation and Rosetta for sequence design yielded higher design success rates and increased structural diversity than Rosetta alone. The ability to design a large and structurally diverse set of small beta barrel proteins greatly increases the protein shape space available for designing binders to protein targets of interest.
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Affiliation(s)
- David E. Kim
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- HHMI, University of Washington, Seattle, WA98195
| | - Davin R. Jensen
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI53226
| | - David Feldman
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Doug Tischer
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Ayesha Saleem
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Cameron M. Chow
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Xinting Li
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Lukas Milles
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Asim K. Bera
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Francis C. Peterson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI53226
| | - Brian F. Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI53226
| | - Sergey Ovchinnikov
- Division of Science, Faculty of Arts and Sciences, Harvard University, Cambridge, MA02138
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA02138
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- HHMI, University of Washington, Seattle, WA98195
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12
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Cáceres C, del Pilar Garcia Morgado M, Bozo FC, Piletsky S, Moczko E. Rapid Selective Detection and Quantification of β-Blockers Used in Doping Based on Molecularly Imprinted Nanoparticles (NanoMIPs). Polymers (Basel) 2022; 14:polym14245420. [PMID: 36559787 PMCID: PMC9787605 DOI: 10.3390/polym14245420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/11/2022] [Accepted: 11/11/2022] [Indexed: 12/14/2022] Open
Abstract
Human performance enhancing drugs (PEDs), frequently used in sport competitions, are strictly prohibited by the World Anti-Doping Agency (WADA). Biological samples collected from athletes and regular patients are continuously tested regarding the identification and/or quantification of the banned substances. Current work is focused on the application of a new analytical method, molecularly imprinted nanoparticles (nanoMIPs), to detect and determine concentrations of certain prohibited drugs, such as β-blockers, in water and human urine samples. These medications are used in the treatment of cardiovascular conditions, negative effects of adrenaline (helping to relief stress), and hypertension (slowing down the pulse and softening the arteries). They can also significantly increase muscle relaxation and improve heart efficiency. The new method of the detection and quantification of β-blockers is based on synthesis, characterization, and implementation of nanoMIPs (so-called plastic antibodies). It offers numerous advantages over the traditional methods, including high binding capacity, affinity, and selectivity for target molecules. Additionally, the whole process is less complicated, cheaper, and better controlled. The size and shape of the nanoMIPs is evaluated by dynamic light scattering (DLS) and transmission electron microscope (TEM). The affinity and selectivity of the nanoparticles are investigated by competitive pseudo enzyme-linked immunosorbent assay (pseudo-ELISA) similar to common immunoassays employing natural antibodies. To provide reliable results towards either doping detection or therapeutic monitoring using the minimal invasive method, the qualitative and quantitative analysis of these drugs is performed in water and human urine samples. It is demonstrated that the assay can detect β-blockers in water within the linear range 1 nmol·L-1-1 mmol·L-1 for atenolol with the detection limit 50.6 ng mL-1, and the linear range 1 mmol·L-1-10 mmol·L-1 for labetalol with the detection limit of 90.5 ng·mL-1. In human urine samples, the linear range is recorded in the concentration range 0.1 mmol·L-1-10 nmol·L-1 for atenolol and 1 mmol·L-1-10 nmol·L-1 for labetalol with a detection limit of 61.0 ng·mL-1 for atenolol and 99.4 ng·mL-1 for labetalol.
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Affiliation(s)
- César Cáceres
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Viña del Mar 2562307, Chile
| | - Macarena del Pilar Garcia Morgado
- Laboratorio de Procesos Fotónicos y Electroquímicos, Departamento de Ciencias y Geografia, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Subida Carvallo 270, Playa Ancha, Valparaiso 2340000, Chile
| | - Freddy Celis Bozo
- Laboratorio de Procesos Fotónicos y Electroquímicos, Departamento de Ciencias y Geografia, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Subida Carvallo 270, Playa Ancha, Valparaiso 2340000, Chile
| | - Sergey Piletsky
- Department of Chemistry, University of Leicester, Leicester LE1 7RH, UK
| | - Ewa Moczko
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Viña del Mar 2562307, Chile
- Correspondence:
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13
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Panse C, Trachsel C, Türker C. Bridging data management platforms and visualization tools to enable ad-hoc and smart analytics in life sciences. J Integr Bioinform 2022; 19:jib-2022-0031. [PMID: 36073980 PMCID: PMC9800043 DOI: 10.1515/jib-2022-0031] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/29/2022] [Accepted: 08/11/2022] [Indexed: 01/09/2023] Open
Abstract
Core facilities have to offer technologies that best serve the needs of their users and provide them a competitive advantage in research. They have to set up and maintain instruments in the range of ten to a hundred, which produce large amounts of data and serve thousands of active projects and customers. Particular emphasis has to be given to the reproducibility of the results. More and more, the entire process from building the research hypothesis, conducting the experiments, doing the measurements, through the data explorations and analysis is solely driven by very few experts in various scientific fields. Still, the ability to perform the entire data exploration in real-time on a personal computer is often hampered by the heterogeneity of software, the data structure formats of the output, and the enormous data sizes. These impact the design and architecture of the implemented software stack. At the Functional Genomics Center Zurich (FGCZ), a joint state-of-the-art research and training facility of ETH Zurich and the University of Zurich, we have developed the B-Fabric system, which has served for more than a decade, an entire life sciences community with fundamental data science support. In this paper, we sketch how such a system can be used to glue together data (including metadata), computing infrastructures (clusters and clouds), and visualization software to support instant data exploration and visual analysis. We illustrate our in-daily life implemented approach using visualization applications of mass spectrometry data.
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Affiliation(s)
- Christian Panse
- Functional Genomics Center Zurich (FGCZ), University of Zurich/ETH Zurich, Winterthurerstrasse 190, CH-8057Zurich, Switzerland
| | - Christian Trachsel
- Functional Genomics Center Zurich (FGCZ), University of Zurich/ETH Zurich, Winterthurerstrasse 190, CH-8057Zurich, Switzerland
| | - Can Türker
- Functional Genomics Center Zurich (FGCZ), University of Zurich/ETH Zurich, Winterthurerstrasse 190, CH-8057Zurich, Switzerland
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14
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Sorgenfrei M, Hürlimann LM, Remy MM, Keller PM, Seeger MA. Biomolecules capturing live bacteria from clinical samples. Trends Biochem Sci 2022; 47:673-688. [PMID: 35487808 DOI: 10.1016/j.tibs.2022.03.018] [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: 11/23/2021] [Revised: 02/04/2022] [Accepted: 03/22/2022] [Indexed: 10/18/2022]
Abstract
Rapid phenotypic antimicrobial susceptibility testing (AST) requires the enrichment of live bacteria from patient samples, which is particularly challenging in the context of life-threatening bloodstream infections (BSIs) due to low bacterial titers. Over two decades, an extensive array of pathogen-specific biomolecules has been identified to capture live bacteria. The prevailing biomolecules are immune proteins of the complement system, antibodies, aptamers, phage proteins, and antimicrobial peptides. These biomolecules differ by their binder generation technologies and exhibit highly variable specificities, ranging from bacterial strains to most pathogenic bacteria. Here, we summarize how these diverse biomolecules were identified, list examples of successfully reported capture assays, and provide an outlook on the use of nanobodies raised against conserved surface-accessible proteins as promising biomolecules for pathogen capture.
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Affiliation(s)
- Michèle Sorgenfrei
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Lea M Hürlimann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Mélissa M Remy
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Peter M Keller
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
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15
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Walter JD, Scherer M, Hutter CAJ, Garaeva AA, Zimmermann I, Wyss M, Rheinberger J, Ruedin Y, Earp JC, Egloff P, Sorgenfrei M, Hürlimann LM, Gonda I, Meier G, Remm S, Thavarasah S, van Geest G, Bruggmann R, Zimmer G, Slotboom DJ, Paulino C, Plattet P, Seeger MA. Biparatopic sybodies neutralize SARS-CoV-2 variants of concern and mitigate drug resistance. EMBO Rep 2022; 23:e54199. [PMID: 35253970 PMCID: PMC8982573 DOI: 10.15252/embr.202154199] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 12/15/2022] Open
Abstract
The ongoing COVID‐19 pandemic represents an unprecedented global health crisis. Here, we report the identification of a synthetic nanobody (sybody) pair, Sb#15 and Sb#68, that can bind simultaneously to the SARS‐CoV‐2 spike RBD and efficiently neutralize pseudotyped and live viruses by interfering with ACE2 interaction. Cryo‐EM confirms that Sb#15 and Sb#68 engage two spatially discrete epitopes, influencing rational design of bispecific and tri‐bispecific fusion constructs that exhibit up to 100‐ and 1,000‐fold increase in neutralization potency, respectively. Cryo‐EM of the sybody‐spike complex additionally reveals a novel up‐out RBD conformation. While resistant viruses emerge rapidly in the presence of single binders, no escape variants are observed in the presence of the bispecific sybody. The multivalent bispecific constructs further increase the neutralization potency against globally circulating SARS‐CoV‐2 variants of concern. Our study illustrates the power of multivalency and biparatopic nanobody fusions for the potential development of therapeutic strategies that mitigate the emergence of new SARS‐CoV‐2 escape mutants.
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Affiliation(s)
- Justin D Walter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Melanie Scherer
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Cedric A J Hutter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Alisa A Garaeva
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Department of Membrane Enzymology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Iwan Zimmermann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Linkster Therapeutics AG, Zurich, Switzerland
| | - Marianne Wyss
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jan Rheinberger
- Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Yelena Ruedin
- Institute of Virology and Immunology, Bern & Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jennifer C Earp
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Pascal Egloff
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Linkster Therapeutics AG, Zurich, Switzerland
| | - Michèle Sorgenfrei
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Lea M Hürlimann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Imre Gonda
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Gianmarco Meier
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Sille Remm
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Sujani Thavarasah
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Geert van Geest
- Interfaculty Bioinformatics Unit and Swiss, Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss, Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Gert Zimmer
- Institute of Virology and Immunology, Bern & Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Dirk J Slotboom
- Department of Membrane Enzymology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Cristina Paulino
- Department of Membrane Enzymology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.,Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Philippe Plattet
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
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16
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Ji F, Ren J, Vincke C, Jia L, Muyldermans S. Nanobodies: From Serendipitous Discovery of Heavy Chain-Only Antibodies in Camelids to a Wide Range of Useful Applications. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2446:3-17. [PMID: 35157266 DOI: 10.1007/978-1-0716-2075-5_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The presence of unique heavy chain-only antibodies (HCAbs) in camelids was discovered at Vrije Universiteit Brussel (VUB, Brussels, Belgium) at a time when many researchers were exploring the cloning and expression of smaller antigen-binding fragments (Fv and Fab) from hybridoma-derived antibodies. The potential importance of this discovery was anticipated, and efforts were immediately undertaken to understand the emergence and ontogeny of these HCAbs as well as to investigate the applications of the single-domain antigen-binding variable domains of HCAbs (nanobodies). Nanobodies were demonstrated to possess multiple biochemical and biophysical advantages over other antigen-binding antibody fragments and alternative scaffolds. Today, nanobodies have a significant and growing impact on research, biotechnology, and medicine.
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Affiliation(s)
- Fangling Ji
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Jun Ren
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Cécile Vincke
- Cellular and Molecular Immunology Laboratory, Vrije Universiteit Brussel, Brussels, Belgium.,Myeloid Cell Immunology Laboratory, VIB Center for Inflammation Research, Brussels, Belgium
| | - Lingyun Jia
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Serge Muyldermans
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China. .,Cellular and Molecular Immunology Laboratory, Vrije Universiteit Brussel, Brussels, Belgium.
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17
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Oloketuyi S, Bernedo R, Christmann A, Borkowska J, Cazzaniga G, Schuchmann HW, Niedziółka-Jönsson J, Szot-Karpińska K, Kolmar H, de Marco A. Native llama Nanobody Library Panning Performed by Phage and Yeast Display Provides Binders Suitable for C-Reactive Protein Detection. BIOSENSORS 2021; 11:bios11120496. [PMID: 34940253 PMCID: PMC8699515 DOI: 10.3390/bios11120496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/22/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
C-reactive protein (CRP) is an inflammation biomarker that should be quantified accurately during infections and healing processes. Nanobodies are good candidates to replace conventional antibodies in immunodiagnostics due to their inexpensive production, simple engineering, and the possibility to obtain higher binder density on capture surfaces. Starting from the same pre-immune library, we compared the selection output resulting from two independent panning strategies, one exclusively exploiting the phage display and another in which a first round of phage display was followed by a second round of yeast display. There was a partial output convergence between the two methods, since two clones were identified using both panning protocols but the first provided several further different sequences, whereas the second favored the recovery of many copies of few clones. The isolated anti-CRP nanobodies had affinity in the low nanomolar range and were suitable for ELISA and immunoprecipitation. One of them was fused to SpyTag and exploited in combination with SpyCatcher as the immunocapture element to quantify CRP using electrochemical impedance spectroscopy. The sensitivity of the biosensor was calculated as low as 0.21 μg/mL.
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Affiliation(s)
- Sandra Oloketuyi
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, 5000 Nova Gorica, Slovenia; (S.O.); (R.B.); (G.C.)
| | - Robert Bernedo
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, 5000 Nova Gorica, Slovenia; (S.O.); (R.B.); (G.C.)
| | - Andreas Christmann
- Applied Biochemistry, Technical University of Darmstadt, 64200 Darmstadt, Germany; (A.C.); (H.W.S.); (H.K.)
| | - Justyna Borkowska
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland; (J.B.); (J.N.-J.); (K.S.-K.)
| | - Giulia Cazzaniga
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, 5000 Nova Gorica, Slovenia; (S.O.); (R.B.); (G.C.)
| | - Horst Wilhelm Schuchmann
- Applied Biochemistry, Technical University of Darmstadt, 64200 Darmstadt, Germany; (A.C.); (H.W.S.); (H.K.)
| | - Joanna Niedziółka-Jönsson
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland; (J.B.); (J.N.-J.); (K.S.-K.)
| | - Katarzyna Szot-Karpińska
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland; (J.B.); (J.N.-J.); (K.S.-K.)
| | - Harald Kolmar
- Applied Biochemistry, Technical University of Darmstadt, 64200 Darmstadt, Germany; (A.C.); (H.W.S.); (H.K.)
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, 5000 Nova Gorica, Slovenia; (S.O.); (R.B.); (G.C.)
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18
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Matsuzaki Y, Aoki W, Miyazaki T, Aburaya S, Ohtani Y, Kajiwara K, Koike N, Minakuchi H, Miura N, Kadonosono T, Ueda M. Peptide barcoding for one-pot evaluation of sequence-function relationships of nanobodies. Sci Rep 2021; 11:21516. [PMID: 34728738 PMCID: PMC8563947 DOI: 10.1038/s41598-021-01019-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 10/21/2021] [Indexed: 11/17/2022] Open
Abstract
Optimisation of protein binders relies on laborious screening processes. Investigation of sequence–function relationships of protein binders is particularly slow, since mutants are purified and evaluated individually. Here we developed peptide barcoding, a high-throughput approach for accurate investigation of sequence–function relationships of hundreds of protein binders at once. Our approach is based on combining the generation of a mutagenised nanobody library fused with unique peptide barcodes, the formation of nanobody–antigen complexes at different ratios, their fine fractionation by size-exclusion chromatography and quantification of peptide barcodes by targeted proteomics. Applying peptide barcoding to an anti-GFP nanobody as a model, we successfully identified residues important for the binding affinity of anti-GFP nanobody at once. Peptide barcoding discriminated subtle changes in KD at the order of nM to sub-nM. Therefore, peptide barcoding is a powerful tool for engineering protein binders, enabling reliable one-pot evaluation of sequence–function relationships.
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Affiliation(s)
- Yusei Matsuzaki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan. .,Kyoto Integrated Science and Technology Bio-Analysis Center, Simogyo-ku, Kyoto, 600-8813, Japan. .,JST, CREST, Chiyoda-ku, Tokyo, 102-0076, Japan. .,JST, COI-NEXT, Chiyoda-ku, Tokyo, 102-0076, Japan. .,JST, FOREST, Chiyoda-ku, Tokyo, 102-0076, Japan.
| | - Takumi Miyazaki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Shunsuke Aburaya
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yuta Ohtani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kaho Kajiwara
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Naoki Koike
- TechnoPro, Inc. TechnoPro R&D, Company, Tokyo, 106-6135, Japan
| | | | - Natsuko Miura
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Naka-ku, Sakai, 599-8531, Japan
| | - Tetsuya Kadonosono
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, 226-8501, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.,Kyoto Integrated Science and Technology Bio-Analysis Center, Simogyo-ku, Kyoto, 600-8813, Japan.,JST, CREST, Chiyoda-ku, Tokyo, 102-0076, Japan.,JST, COI-NEXT, Chiyoda-ku, Tokyo, 102-0076, Japan
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19
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Chen X, Gentili M, Hacohen N, Regev A. A cell-free nanobody engineering platform rapidly generates SARS-CoV-2 neutralizing nanobodies. Nat Commun 2021; 12:5506. [PMID: 34535642 PMCID: PMC8448731 DOI: 10.1038/s41467-021-25777-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 09/01/2021] [Indexed: 11/21/2022] Open
Abstract
Antibody engineering technologies face increasing demands for speed, reliability and scale. We develop CeVICA, a cell-free nanobody engineering platform that uses ribosome display for in vitro selection of nanobodies from a library of 1011 randomized sequences. We apply CeVICA to engineer nanobodies against the Receptor Binding Domain (RBD) of SARS-CoV-2 spike protein and identify >800 binder families using a computational pipeline based on CDR-directed clustering. Among 38 experimentally-tested families, 30 are true RBD binders and 11 inhibit SARS-CoV-2 pseudotyped virus infection. Affinity maturation and multivalency engineering increase nanobody binding affinity and yield a virus neutralizer with picomolar IC50. Furthermore, the capability of CeVICA for comprehensive binder prediction allows us to validate the fitness of our nanobody library. CeVICA offers an integrated solution for rapid generation of divergent synthetic nanobodies with tunable affinities in vitro and may serve as the basis for automated and highly parallel nanobody engineering.
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Affiliation(s)
- Xun Chen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | | | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Genentech, 1 DNA Way, South San Francisco, CA, USA.
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20
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Khunweeraphong N, Kuchler K. Multidrug Resistance in Mammals and Fungi-From MDR to PDR: A Rocky Road from Atomic Structures to Transport Mechanisms. Int J Mol Sci 2021; 22:4806. [PMID: 33946618 PMCID: PMC8124828 DOI: 10.3390/ijms22094806] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/19/2022] Open
Abstract
Multidrug resistance (MDR) can be a serious complication for the treatment of cancer as well as for microbial and parasitic infections. Dysregulated overexpression of several members of the ATP-binding cassette transporter families have been intimately linked to MDR phenomena. Three paradigm ABC transporter members, ABCB1 (P-gp), ABCC1 (MRP1) and ABCG2 (BCRP) appear to act as brothers in arms in promoting or causing MDR in a variety of therapeutic cancer settings. However, their molecular mechanisms of action, the basis for their broad and overlapping substrate selectivity, remains ill-posed. The rapidly increasing numbers of high-resolution atomic structures from X-ray crystallography or cryo-EM of mammalian ABC multidrug transporters initiated a new era towards a better understanding of structure-function relationships, and for the dynamics and mechanisms driving their transport cycles. In addition, the atomic structures offered new evolutionary perspectives in cases where transport systems have been structurally conserved from bacteria to humans, including the pleiotropic drug resistance (PDR) family in fungal pathogens for which high resolution structures are as yet unavailable. In this review, we will focus the discussion on comparative mechanisms of mammalian ABCG and fungal PDR transporters, owing to their close evolutionary relationships. In fact, the atomic structures of ABCG2 offer excellent models for a better understanding of fungal PDR transporters. Based on comparative structural models of ABCG transporters and fungal PDRs, we propose closely related or even conserved catalytic cycles, thus offering new therapeutic perspectives for preventing MDR in infectious disease settings.
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Affiliation(s)
| | - Karl Kuchler
- Center for Medical Biochemistry, Max Perutz Labs Vienna, Campus Vienna Biocenter, Medical University of Vienna, Dr. Bohr-Gasse 9/2, A-1030 Vienna, Austria;
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21
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Xiang Y, Sang Z, Bitton L, Xu J, Liu Y, Schneidman-Duhovny D, Shi Y. Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies. Cell Syst 2021; 12:220-234.e9. [PMID: 33592195 PMCID: PMC7979497 DOI: 10.1016/j.cels.2021.01.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 10/13/2020] [Accepted: 01/20/2021] [Indexed: 12/15/2022]
Abstract
The antibody immune response is essential for the survival of mammals. However, we still lack a systematic understanding of the antibody repertoire. Here, we developed a proteomic strategy to survey, at an unprecedented scale, the landscape of antigen-engaged, circulating camelid heavy-chain antibodies, whose minimal binding fragments are called VHH antibodies or nanobodies. The sensitivity and robustness of this approach were validated with three antigens spanning orders of magnitude in immune responses; thousands of distinct, high-affinity nanobody families were reliably identified and quantified. Using high-throughput structural modeling, cross-linking mass spectrometry, mutagenesis, and deep learning, we mapped and analyzed the epitopes of >100,000 antigen-nanobody complexes. Our results revealed a surprising diversity of ultrahigh-affinity camelid nanobodies for specific antigen binding on various dominant epitope clusters. Nanobodies utilize both shape and charge complementarity to enable highly selective antigen binding. Interestingly, we found that nanobody-antigen binding can mimic conserved intracellular protein-protein interactions. A record of this paper's Transparent Peer Review process is included in the Supplemental information.
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Affiliation(s)
- Yufei Xiang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhe Sang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA; University of Pittsburgh, Carnegie Mellon University Program for Computational Biology, Pittsburgh, PA, USA
| | - Lirane Bitton
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Jianquan Xu
- Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yang Liu
- Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel.
| | - Yi Shi
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA; University of Pittsburgh, Carnegie Mellon University Program for Computational Biology, Pittsburgh, PA, USA.
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22
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Njeru FN, Kusolwa PM. Nanobodies: their potential for applications in biotechnology, diagnosis and antiviral properties in Africa; focus on application in agriculture. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1974943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Faith Njeri Njeru
- Department of Veterinary Microbiology, Parasitology and Biotechnology, Southern African Centre for Infectious Disease Surveillance (SACIDS), Sokoine University of Agriculture, Morogoro, Tanzania
| | - Paul Mbogo Kusolwa
- Department of Crop Science and Horticulture, College of Agriculture, Sokoine University of Agriculture, Morogoro, Tanzania
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23
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Muyldermans S. A guide to: generation and design of nanobodies. FEBS J 2020; 288:2084-2102. [PMID: 32780549 PMCID: PMC8048825 DOI: 10.1111/febs.15515] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/03/2020] [Accepted: 08/07/2020] [Indexed: 01/09/2023]
Abstract
A nanobody (Nb) is a registered trademark of Ablynx, referring to the single antigen-binding domain of heavy chain-only antibodies (HCAbs) that are circulating in Camelidae. Nbs are produced recombinantly in micro-organisms and employed as research tools or for diagnostic and therapeutic applications. They were - and still are - also named single-domain antibodies (sdAbs) or variable domain of the heavy chain of HCAbs (VHH). A variety of methods are currently in use for the fast and efficient generation of target-specific Nbs. Such Nbs are produced at low cost and associate with high affinity to their cognate antigen. They are robust, strictly monomeric and easy to tailor into more complex entities to meet the requirements of their application. Here, we review the various sources and different strategies that have been developed to identify rapidly, target-specific Nbs. We further discuss a variety of engineering technologies that have been explored to broaden the application range of Nbs and summarise those applications where designed Nbs might offer a marked advantage over other affinity reagents.
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Affiliation(s)
- Serge Muyldermans
- Cellular and Molecular Immunology, Vrije Universiteit Brussel, Belgium.,Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, China
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24
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Konwarh R. Nanobodies: Prospects of Expanding the Gamut of Neutralizing Antibodies Against the Novel Coronavirus, SARS-CoV-2. Front Immunol 2020; 11:1531. [PMID: 32655584 PMCID: PMC7324746 DOI: 10.3389/fimmu.2020.01531] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 06/10/2020] [Indexed: 11/25/2022] Open
Affiliation(s)
- Rocktotpal Konwarh
- Department of Biotechnology, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
- Centre of Excellence-Nanotechnology, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
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25
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Zimmermann I, Egloff P, Hutter CAJ, Kuhn BT, Bräuer P, Newstead S, Dawson RJP, Geertsma ER, Seeger MA. Generation of synthetic nanobodies against delicate proteins. Nat Protoc 2020; 15:1707-1741. [PMID: 32269381 DOI: 10.1038/s41596-020-0304-x] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 01/16/2020] [Indexed: 12/21/2022]
Abstract
Here, we provide a protocol to generate synthetic nanobodies, known as sybodies, against any purified protein or protein complex within a 3-week period. Unlike methods that require animals for antibody generation, sybody selections are carried out entirely in vitro under controlled experimental conditions. This is particularly relevant for the generation of conformation-specific binders against labile membrane proteins or protein complexes and allows selections in the presence of non-covalent ligands. Sybodies are especially suited for cases where binder generation via immune libraries fails due to high sequence conservation, toxicity or insufficient stability of the target protein. The procedure entails a single round of ribosome display using the sybody libraries encoded by mRNA, followed by two rounds of phage display and binder identification by ELISA. The protocol is optimized to avoid undesired reduction in binder diversity and enrichment of non-specific binders to ensure the best possible selection outcome. Using the efficient fragment exchange (FX) cloning method, the sybody sequences are transferred from the phagemid to different expression vectors without the need to amplify them by PCR, which avoids unintentional shuffling of complementary determining regions. Using quantitative PCR (qPCR), the efficiency of each selection round is monitored to provide immediate feedback and guide troubleshooting. Our protocol can be carried out by any trained biochemist or molecular biologist using commercially available reagents and typically gives rise to 10-30 unique sybodies exhibiting binding affinities in the range of 500 pM-500 nM.
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Affiliation(s)
- Iwan Zimmermann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Linkster Therapeutics AG, Zurich, Switzerland
| | - Pascal Egloff
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Linkster Therapeutics AG, Zurich, Switzerland
| | - Cedric A J Hutter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Benedikt T Kuhn
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Philipp Bräuer
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Roger J P Dawson
- Linkster Therapeutics AG, Zurich, Switzerland.,Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Eric R Geertsma
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
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26
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Arnold FM, Weber MS, Gonda I, Gallenito MJ, Adenau S, Egloff P, Zimmermann I, Hutter CAJ, Hürlimann LM, Peters EE, Piel J, Meloni G, Medalia O, Seeger MA. The ABC exporter IrtAB imports and reduces mycobacterial siderophores. Nature 2020; 580:413-417. [PMID: 32296173 PMCID: PMC7170716 DOI: 10.1038/s41586-020-2136-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/24/2020] [Indexed: 12/17/2022]
Abstract
Intracellular replication of the deadly pathogen Mycobacterium tuberculosis relies on the production of small organic molecules called siderophores to scavenge iron from host proteins1. M. tuberculosis produces two classes of siderophores, lipid-bound mycobactin and soluble carboxymycobactin2, 3. Functional studies revealed that iron-loaded carboxymycobactin is imported into the cytoplasm by the ABC transporter IrtAB4, which features an additional cytoplasmic siderophore interaction domain (SID)5. However, IrtAB’s predicted ABC exporter fold seemingly contradicts its import function. Here, we show that membrane-reconstituted IrtAB is sufficient to import mycobactins, which are then reduced by the SID to facilitate iron release. Structure determination by X-ray crystallography and cryo-EM confirms IrtAB’s ABC exporter fold, but also reveals structural peculiarities at the transmembrane region of IrtAB resulting in a partially collapsed inward-facing substrate binding cavity. The SID is positioned in close proximity to the inner membrane leaflet, which allows the reduction of membrane-inserted mycobactin. Enzymatic ATPase activity and in vivo growth assays show that IrtAB prefers mycobactin over carboxymycobactin as its substrate. Our study provides insights into an unusual ABC exporter that evolved as highly specialized siderophore import machinery in mycobacteria.
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Affiliation(s)
- Fabian M Arnold
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Miriam S Weber
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Imre Gonda
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Marc J Gallenito
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, USA
| | - Sophia Adenau
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Pascal Egloff
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Linkster Therapeutics, Zurich, Switzerland
| | - Iwan Zimmermann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Linkster Therapeutics, Zurich, Switzerland
| | - Cedric A J Hutter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Lea M Hürlimann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Eike E Peters
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Jörn Piel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Gabriele Meloni
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, USA
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
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27
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Ding R, Hung KC, Mitra A, Ung LW, Lightwood D, Tu R, Starkie D, Cai L, Mazutis L, Chong S, Weitz DA, Heyman JA. Rapid isolation of antigen-specific B-cells using droplet microfluidics. RSC Adv 2020; 10:27006-27013. [PMID: 35515810 PMCID: PMC9055518 DOI: 10.1039/d0ra04328a] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 06/30/2020] [Indexed: 12/19/2022] Open
Abstract
Monoclonal antibodies are powerful tools for scientific research and are the basis of numerous therapeutics. However, traditional approaches to generate monoclonal antibodies against a desired target, such as hybridoma-based techniques and display library methods, are laborious and suffer from fusion inefficiency and display bias, respectively. Here we present a platform, featuring droplet microfluidics and a bead-based binding assay, to rapidly identify and verify antigen-binding antibody sequences from primary cells. We used a defined mixture of hybridoma cells to characterize the system, sorting droplets at up to 100 Hz and isolating desired hybridoma cells, comprising 0.1% of the input, with a false positive rate of less than 1%. We then applied the system to once-frozen primary B-cells to isolate rare cells secreting target-binding antibody. We performed RT-PCR on individual sorted cells to recover the correctly paired heavy- and light-chain antibody sequences, and we used rapid cell-free protein synthesis to generate single-chain variable fragment-format (scFv) antibodies from fourteen of the sorted cells. Twelve of these showed antigen-specific binding by ELISA. Our platform facilitates screening animal B-cell repertoires within days at low cost, increasing both rate and range of discovering antigen-specific antibodies from living organisms. Further, these techniques can be adapted to isolate cells based on virtually any secreted product. We use a droplet-microfluidics-based platform to rapidly identify and isolate individual primary cells that secrete desired antibodies. We then retrieve the antibody-encoding sequences and create recombinant antibodies that bind the target protein.![]()
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Affiliation(s)
- Ruihua Ding
- John A. Paulson School of Engineering and Applied Sciences
- Harvard University
- Cambridge
- USA
- Department of Chemistry and Chemical Biology
| | - Kuo-Chan Hung
- John A. Paulson School of Engineering and Applied Sciences
- Harvard University
- Cambridge
- USA
| | - Anindita Mitra
- John A. Paulson School of Engineering and Applied Sciences
- Harvard University
- Cambridge
- USA
| | - Lloyd W. Ung
- John A. Paulson School of Engineering and Applied Sciences
- Harvard University
- Cambridge
- USA
| | | | - Ran Tu
- John A. Paulson School of Engineering and Applied Sciences
- Harvard University
- Cambridge
- USA
- CAS Key Laboratory of Systems Microbial Biotechnology
| | | | - Liheng Cai
- John A. Paulson School of Engineering and Applied Sciences
- Harvard University
- Cambridge
- USA
- Department of Materials Science and Engineering
| | - Linas Mazutis
- John A. Paulson School of Engineering and Applied Sciences
- Harvard University
- Cambridge
- USA
- Vilnius University
| | | | - David A. Weitz
- John A. Paulson School of Engineering and Applied Sciences
- Harvard University
- Cambridge
- USA
- Department of Physics
| | - John A. Heyman
- John A. Paulson School of Engineering and Applied Sciences
- Harvard University
- Cambridge
- USA
- SphereBio
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28
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Droplet barcoding: tracking mobile micro-reactors for high-throughput biology. Curr Opin Biotechnol 2019; 60:205-212. [DOI: 10.1016/j.copbio.2019.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 05/07/2019] [Indexed: 01/09/2023]
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29
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Lecocq Q, De Vlaeminck Y, Hanssens H, D'Huyvetter M, Raes G, Goyvaerts C, Keyaerts M, Devoogdt N, Breckpot K. Theranostics in immuno-oncology using nanobody derivatives. Am J Cancer Res 2019; 9:7772-7791. [PMID: 31695800 PMCID: PMC6831473 DOI: 10.7150/thno.34941] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 07/11/2019] [Indexed: 12/25/2022] Open
Abstract
Targeted therapy and immunotherapy have become mainstream in cancer treatment. However, only patient subsets benefit from these expensive therapies, and often responses are short‐lived or coincide with side effects. A growing modality in precision oncology is the development of theranostics, as this enables patient selection, treatment and monitoring. In this approach, labeled compounds and an imaging technology are used to diagnose patients and select the best treatment option, whereas for therapy, related compounds are used to target cancer cells or the tumor stroma. In this context, nanobodies and nanobody-directed therapeutics have gained interest. This interest stems from their high antigen specificity, small size, ease of labeling and engineering, allowing specific imaging and design of therapies targeting antigens on tumor cells, immune cells as well as proteins in the tumor environment. This review provides a comprehensive overview on the state-of-the-art regarding the use of nanobodies as theranostics, and their importance in the emerging field of personalized medicine.
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30
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van Veen HW, Singh H, Agboh K, Fagg LA, Guo D, Swain B, de Kruijf RF, Guffick C. Energy coupling in ABC exporters. Res Microbiol 2019; 170:392-398. [PMID: 31442612 DOI: 10.1016/j.resmic.2019.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/27/2019] [Accepted: 08/12/2019] [Indexed: 11/19/2022]
Abstract
Multidrug transporters are important and interesting molecular machines that extrude a wide variety of cytotoxic drugs from target cells. This review summarizes novel insights in the energetics and mechanisms of bacterial ATP-binding cassette multidrug transporters as well as recent advances connecting multidrug transport to ion and lipid translocation processes in other membrane proteins.
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Affiliation(s)
- Hendrik W van Veen
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK.
| | - Himansha Singh
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Kelvin Agboh
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Lisa A Fagg
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Dawei Guo
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Brendan Swain
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Robbin F de Kruijf
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Charlotte Guffick
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
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31
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Sun S, Wang R, Huang Y, Xu J, Yao K, Liu W, Cao Y, Qian K. Design of Hierarchical Beads for Efficient Label-Free Cell Capture. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1902441. [PMID: 31237759 DOI: 10.1002/smll.201902441] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 05/30/2019] [Indexed: 06/09/2023]
Abstract
Defined hierarchical materials promise cell analysis and call for application-driven design in practical use. The further issue is to develop advanced materials and devices for efficient label-free cell capture with minimum instrumentation. Herein, the design of hierarchical beads is reported for efficient label-free cell capture. Silica nanoparticles (size of ≈15 nm) are coated onto silica spheres (size of ≈200 nm) to achieve nanoscale surface roughness, and then the rough silica spheres are combined with microbeads (≈150-1000 µm in diameter) to assemble hierarchical structures. These hierarchical beads are built via electrostatic interaction, covalent bonding, and nanoparticle adherence. Further, after functionalization by hyaluronic acid (HA), the hierarchical beads display desirable surface hydrophilicity, biocompatibility, and chemical/structural stability. Due to the controlled surface topology and chemistry, HA-functionalized hierarchical beads afford high cell capture efficiency up to 98.7% in a facile label-free manner. This work guides the development of label-free cell capture techniques and contributes to the construction of smart interfaces in bio-systems.
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Affiliation(s)
- Shiyu Sun
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Ruimin Wang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yida Huang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jiale Xu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Kuan Yao
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Wanshan Liu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yimei Cao
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Kun Qian
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
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32
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Miura N, Miyamoto K, Ohtani Y, Yaginuma K, Aburaya S, Kitagawa Y, Aoki W, Ueda M. Domain swapping of complementarity-determining region in nanobodies produced by Pichia pastoris. AMB Express 2019; 9:107. [PMID: 31309388 PMCID: PMC6629726 DOI: 10.1186/s13568-019-0833-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/05/2019] [Indexed: 11/10/2022] Open
Abstract
Easy preparation of chimeric nanobodies with various scaffolds is important for customizing abilities of nanobodies toward practical utilization. To accomplish high-throughput production of various nanobodies, utilization of microbes is an attractive option. In the present study, various chimeric nanobodies were prepared using the methylotrophic yeast Pichia pastoris. We designed chimeric nanobodies with complementarity-determining regions (CDRs) against green fluorescent protein (GFP) or cluster of differentiation 4 (CD4) based on the scaffold of GFP-nanobody. FLAG-tagged chimeric nanobodies were prepared by one-step cloning and produced using P. pastoris. Secreted chimeric nanobodies were purified from the culture media of P. pastoris transformants. Relative binding abilities of purified chimeric nanobodies to GFP and CD4 was tested using a BIACORE T-200. P. pastoris successfully produced a high yield of FLAG-tagged chimeric nanobodies. FLAG-tagged GFP- and CD4-nanobodies were shown to specifically bind to GFP and CD4, respectively. Chimeric nanobodies, in which the CDR2 or 3 of GFP-nanobody was replaced with CDRs of CD4-nanobody, acquired the ability to bind to CD4 without binding to GFP. These results demonstrate successful production of functional chimeric nanobodies using P. pastoris. These results also suggest that swapping of CDRs, especially CDRs 2 or 3, potentially enables a novel method of creating nanobodies.
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