1
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Ahmad MI, Amorim CG, Abu Qatouseh LF, Montenegro MCBSM. Nanobody-based immunosensor for the detection of H. pylori in saliva. Biosens Bioelectron 2024; 260:116423. [PMID: 38810413 DOI: 10.1016/j.bios.2024.116423] [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: 12/18/2023] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 05/31/2024]
Abstract
Helicobacter pylori (H. pylori) infection is highly prevalent worldwide, affecting more than 43% of world population. The infection can be transmitted through different routes, like oral-oral, fecal-oral, and gastric-oral. Electrochemical sensors play a crucial role in the early detection of various substances, including biomolecules. In this study, the development of nanobody (Nb)-based immunosensor for the detection of H. pylori antigens in saliva samples was investigated. The D2_Nb was isolated and characterized using Western blot and ELISA and employed in the fabrication of the immunosensor. The sensor was prepared using gold screen-printed electrodes, with the immobilization of Nb achieved through chemical linkage using cysteamine-glutaraldehyde. The surface of the electrode was characterized using EIS, FTIR and SEM. Initially, the Nb-based immunosensor's performance was evaluated through cyclic voltammetry (CV), differential pulse voltammetry (DPV), and square wave voltammetry (SWV). The sensor exhibited excellent linearity with an R2 value of 0.96. However, further assessment with the DPV technique revealed both a low limit of detection (5.9 ng/mL, <1 cfu/mL) and high selectivity when exposed to a mixture of similar antigens. Moreover, the immunosensor demonstrated robust recovery rates (96.2%-103.4%) when spiked into artificial saliva and maintained its functionality when stored at room temperature for 24 days.
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Affiliation(s)
- Mohammad Ia Ahmad
- LAQV-REQUIMTE, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Célia G Amorim
- LAQV-REQUIMTE, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal.
| | - Luay F Abu Qatouseh
- Department of Pharmacology and Biomedical Sciences, Faculty of Pharmacy and Medical Sciences, University of Petra, Amman, Jordan.
| | - Maria C B S M Montenegro
- LAQV-REQUIMTE, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
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2
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Nemecz D, Nowak WA, Nemecz Á. VHH Nanobody Versatility against Pentameric Ligand-Gated Ion Channels. J Med Chem 2024; 67:8502-8518. [PMID: 38829690 PMCID: PMC11181324 DOI: 10.1021/acs.jmedchem.4c00231] [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: 01/26/2024] [Revised: 04/17/2024] [Accepted: 05/20/2024] [Indexed: 06/05/2024]
Abstract
Pentameric ligand-gated ion channels provide rapid chemical-electrical signal transmission between cells in the central and peripheral nervous system. Their dysfunction is associated with many nervous system disorders. They are composed of five identical (homomeric receptors) or homologous (heteromeric receptors) subunits. VHH nanobodies, or single-chain antibodies, are the variable domain, VHH, of antibodies that are composed of the heavy chain only from camelids. Their unique structure results in many specific biochemical and biophysical properties that make them an excellent alternative to conventional antibodies. This Perspective explores the published VHH nanobodies which have been isolated against pentameric ligand-gated ion channel subfamilies. It outlines the genetic and chemical modifications available to alter nanobody function. An assessment of the available functional and structural data indicate that it is feasible to create therapeutic agents and impart, through their modification, a given desired modulatory effect of its target receptor for current stoichiometric-specific VHH nanobodies.
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Affiliation(s)
- Dorota Nemecz
- Biochemistry
Department, Nicolaus Copernicus University
in Torun, 87-100 Torun, Poland
| | - Weronika A. Nowak
- Biochemistry
Department, Nicolaus Copernicus University
in Torun, 87-100 Torun, Poland
| | - Ákos Nemecz
- Biochemistry
Department, Nicolaus Copernicus University
in Torun, 87-100 Torun, Poland
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3
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Thompson MK, Sharma N, Thorn A, Prakash A. Deciphering the crystal structure of a novel nanobody against the NEIL1 DNA glycosylase. Acta Crystallogr D Struct Biol 2024; 80:137-146. [PMID: 38289715 PMCID: PMC10836396 DOI: 10.1107/s205979832400038x] [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: 10/18/2023] [Accepted: 01/10/2024] [Indexed: 02/01/2024] Open
Abstract
Nanobodies (VHHs) are single-domain antibodies with three antigenic CDR regions and are used in diverse scientific applications. Here, an ∼14 kDa nanobody (A5) specific for the endonuclease VIII (Nei)-like 1 or NEIL1 DNA glycosylase involved in the first step of the base-excision repair pathway was crystallized and its structure was determined to 2.1 Å resolution. The crystals posed challenges due to potential twinning and anisotropic diffraction. Despite inconclusive twinning indicators, reprocessing in an orthorhombic setting and molecular replacement in space group P21212 enabled the successful modeling of 96% of residues in the asymmetric unit, with final Rwork and Rfree values of 0.199 and 0.229, respectively.
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Affiliation(s)
- Marlo K Thompson
- Mitchell Cancer Institute, University of South Alabama Health, 1660 Springhill Avenue, Mobile, AL 36604, USA
| | - Nidhi Sharma
- Mitchell Cancer Institute, University of South Alabama Health, 1660 Springhill Avenue, Mobile, AL 36604, USA
| | - Andrea Thorn
- Institut für Nanostruktur und Festkörperphysik, Universität Hamburg, Hamburg, Germany
| | - Aishwarya Prakash
- Mitchell Cancer Institute, University of South Alabama Health, 1660 Springhill Avenue, Mobile, AL 36604, USA
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4
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Chaudhuri D, Chowdhury D, Chakraborty S, Bhatt M, Chowdhury R, Dutta A, Mistry A, Haldar S. Structurally different chemical chaperones show similar mechanical roles with independent molecular mechanisms. NANOSCALE 2024; 16:2540-2551. [PMID: 38214221 DOI: 10.1039/d3nr00398a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Osmolytes are well known to protect the protein structure against different chemical and physical denaturants. Since their actions with protein surfaces are mechanistically complicated and context dependent, the underlying molecular mechanism is not fully understood. Here, we combined single-molecule magnetic tweezers and molecular dynamics (MD) simulation to explore the mechanical role of osmolytes from two different classes, trimethylamine N-oxide (TMAO) and trehalose, as mechanical stabilizers of protein structure. We observed that these osmolytes increase the protein L mechanical stability by decreasing unfolding kinetics while accelerating the refolding kinetics under force, eventually shifting the energy landscape toward the folded state. These osmolytes mechanically stabilize the protein L and plausibly guide them to more thermodynamically robust states. Finally, we observed that osmolyte-modulated protein folding increases mechanical work output up to twofold, allowing the protein to fold under a higher force regime and providing a significant implication for folding-induced structural stability in proteins.
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Affiliation(s)
- Deep Chaudhuri
- Department of Chemistry, Ashoka University, Sonepat, Haryana, India.
| | - Debojyoti Chowdhury
- Department of Chemical and Biological Sciences, S.N. Bose National Center for Basic Sciences, Kolkata, West Bengal, India
| | - Soham Chakraborty
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana, India
| | - Madhu Bhatt
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana, India
| | - Rudranil Chowdhury
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana, India
| | - Aakashdeep Dutta
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana, India
| | - Ayush Mistry
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana, India
| | - Shubhasis Haldar
- Department of Chemistry, Ashoka University, Sonepat, Haryana, India.
- Department of Chemical and Biological Sciences, S.N. Bose National Center for Basic Sciences, Kolkata, West Bengal, India
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana, India
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5
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Raynaud P, Jugnarain V, Vaugrente O, Vallet A, Boulo T, Gauthier C, Inoue A, Sibille N, Gauthier C, Jean-Alphonse F, Reiter E, Crépieux P, Bruneau G. A single-domain intrabody targeting the follicle-stimulating hormone receptor impacts FSH-induced G protein-dependent signalling. FEBS Lett 2024; 598:220-232. [PMID: 37923554 DOI: 10.1002/1873-3468.14765] [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: 07/17/2023] [Revised: 09/20/2023] [Accepted: 10/06/2023] [Indexed: 11/07/2023]
Abstract
Intracellular variable fragments of heavy-chain antibody from camelids (intra-VHH) have been successfully used as chaperones to solve the 3D structure of active G protein-coupled receptors bound to their transducers. However, their effect on signalling has been poorly explored, although they may provide a better understanding of the relationships between receptor conformation and activity. Here, we isolated and characterized iPRC1, the first intra-VHH recognizing a member of the large glycoprotein hormone receptor family, the follicle-stimulating hormone receptor (FSHR). This intra-VHH recognizes the FSHR third intracellular loop and decreases cAMP production in response to FSH, without altering Gαs recruitment. Hence, iPRC1 behaves as an allosteric modulator and provides a new tool to complete structure/activity studies performed thus far on this receptor.
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Affiliation(s)
- Pauline Raynaud
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l'Equitation (IFCE), Université de Tours, Nouzilly, France
| | - Vinesh Jugnarain
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l'Equitation (IFCE), Université de Tours, Nouzilly, France
| | - Océane Vaugrente
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l'Equitation (IFCE), Université de Tours, Nouzilly, France
| | - Amandine Vallet
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l'Equitation (IFCE), Université de Tours, Nouzilly, France
| | - Thomas Boulo
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l'Equitation (IFCE), Université de Tours, Nouzilly, France
| | - Camille Gauthier
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l'Equitation (IFCE), Université de Tours, Nouzilly, France
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Nathalie Sibille
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, France
| | - Christophe Gauthier
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l'Equitation (IFCE), Université de Tours, Nouzilly, France
| | - Frédéric Jean-Alphonse
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l'Equitation (IFCE), Université de Tours, Nouzilly, France
- Inria, Inria Saclay-Ile-de-France, Palaiseau, France
| | - Eric Reiter
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l'Equitation (IFCE), Université de Tours, Nouzilly, France
- Inria, Inria Saclay-Ile-de-France, Palaiseau, France
| | - Pascale Crépieux
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l'Equitation (IFCE), Université de Tours, Nouzilly, France
- Inria, Inria Saclay-Ile-de-France, Palaiseau, France
| | - Gilles Bruneau
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l'Equitation (IFCE), Université de Tours, Nouzilly, France
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6
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Aoki K, Manabe A, Kimura H, Katoh Y, Inuki S, Ohno H, Nonaka M, Oishi S. Mirror-Image Single-Domain Antibody for a Novel Nonimmunogenic Drug Scaffold. Bioconjug Chem 2023; 34:2055-2065. [PMID: 37883660 DOI: 10.1021/acs.bioconjchem.3c00372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Immunogenic responses by protein therapeutics often lead to reduced therapeutic effects and/or adverse effects via the generation of neutralizing antibodies and/or antidrug antibodies (ADA). Mirror-image proteins of the variable domain of the heavy chain of the heavy chain antibody (VHH) are potential novel protein therapeutics with high-affinity binding to target proteins and reduced immunogenicity because these mirror-image VHHs (d-VHHs) are less susceptible to proteolytic degradation in antigen-presenting cells (APCs). In this study, we investigated the preparation protocols of d-VHHs and their biological properties, including stereoselective target binding and immunogenicity. Initially, we established a facile synthetic process of two model VHHs [anti-GFP VHH and PMP12A2h1 (monomeric VHH of caplacizumab)] and their mirror-image proteins by three-step native chemical ligations (NCLs) from four peptide segments. The folded synthetic VHHs (l-anti-GFP VHH and l-PMP12A2h1) bound to the target proteins (EGFP and vWF-A1 domain, respectively), while their mirror-image proteins (d-anti-GFP VHH and d-PMP12A2h1) showed no binding to the native proteins. For biodistribution studies, l-VHH and d-VHH with single radioactive indium diethylenetriamine-pentaacid (111In-DTPA) labeling at the C-terminus were designed and synthesized by the established protocol. The distribution profiles were essentially similar between l-VHH and d-VHH, in which the probes accumulated in the kidney within 15 min after intravenous administration in mice, because of the small molecular size of VHHs. Comparative assessment of the immunogenicity responses revealed that d-VHH-induced levels of ADA generation were significantly lower than those of native VHH, regardless of the peptide sequences and administration routes. The resulting scaffold investigated should be applicable in the design of d-VHHs with various C-terminal CDR3 sequences, which can be identified by screening using display technologies.
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Affiliation(s)
- Keisuke Aoki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- Laboratory of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
| | - Asako Manabe
- Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hiroyuki Kimura
- Laboratory of Analytical and Bioinorganic Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8414, Japan
| | - Yohei Katoh
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shinsuke Inuki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroaki Ohno
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Motohiro Nonaka
- Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- Laboratory of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
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7
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Malatji K, Singh A, Thobakgale C, Alexandre K. Development of a Multiplex HIV/TB Diagnostic Assay Based on the Microarray Technology. BIOSENSORS 2023; 13:894. [PMID: 37754128 PMCID: PMC10526232 DOI: 10.3390/bios13090894] [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: 07/18/2023] [Revised: 09/11/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023]
Abstract
Currently there are diagnostic tests available for human immunodeficiency virus (HIV) and tuberculosis (TB); however, they are still diagnosed separately, which can delay treatment in cases of co-infection. Here we report on a multiplex microarray technology for the detection of HIV and TB antibodies using p24 as well as TB CFP10, ESAT6 and pstS1 antigens on epoxy-silane slides. To test this technology for antigen-antibody interactions, immobilized antigens were exposed to human sera spiked with physiological concentrations of primary antibodies, followed by secondary antibodies conjugated to a fluorescent reporter. HIV and TB antibodies were captured with no cross-reactivity observed. The sensitivity of the slides was compared to that of high-binding plates. We found that the slides were more sensitive, with the detection limit being 0.000954 µg/mL compared to 4.637 µg/mL for the plates. Furthermore, stability studies revealed that the immobilized antigens could be stored dry for at least 90 days and remained stable across all pH and temperatures assessed, with pH 7.4 and 25 °C being optimal. The data collectively suggested that the HIV/TB multiplex detection technology we developed has the potential for use to diagnose HIV and TB co-infection, and thus can be developed further for the purpose.
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Affiliation(s)
- Kanyane Malatji
- Array Technology Laboratory, Synthetic Biology and Precision Medicine Centre: Next Generation Health Cluster, Council for Scientific and Industrial Research, Brummeria, Pretoria 0001, South Africa (K.A.)
- Department of Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Braamfontein, Johannesburg 2000, South Africa;
| | - Advaita Singh
- Future Production: Chemicals Cluster, Council for Scientific and Industrial Research, Brummeria, Pretoria 0001, South Africa
| | - Christina Thobakgale
- Department of Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Braamfontein, Johannesburg 2000, South Africa;
- Centre for HIV and STIs, National Institute for Communicable Diseases, Sandringham, Johannesburg 2192, South Africa
| | - Kabamba Alexandre
- Array Technology Laboratory, Synthetic Biology and Precision Medicine Centre: Next Generation Health Cluster, Council for Scientific and Industrial Research, Brummeria, Pretoria 0001, South Africa (K.A.)
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8
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Jiang X, Sun L, Hu C, Zheng F, Lyu Z, Shao J. Shark IgNAR: The Next Broad Application Antibody in Clinical Diagnoses and Tumor Therapies? Mar Drugs 2023; 21:496. [PMID: 37755109 PMCID: PMC10532743 DOI: 10.3390/md21090496] [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: 08/21/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023] Open
Abstract
Antibodies represent a relatively mature detection means and serve as therapeutic drug carriers in the clinical diagnosis and treatment of cancer-among which monoclonal antibodies (mAbs) currently occupy a dominant position. However, the emergence and development of small-molecule monodomain antibodies are inevitable due to the many limitations of mAbs, such as their large size, complex structure, and sensitivity to extreme temperature, and tumor microenvironments. Thus, since first discovered in Chondroid fish in 1995, IgNAR has become an alternative therapeutic strategy through which to replace monoclonal antibodies, thus entailing that this novel type of immunoglobulin has received wide attention with respect to clinical diagnoses and tumor therapies. The variable new antigen receptor (VNAR) of IgNAR provides an advantage for the development of new antitumor drugs due to its small size, high stability, high affinity, as well as other structural and functional characteristics. In that respect, a better understanding of the unique characteristics and therapeutic potential of IgNAR/VNAR in clinical and anti-tumor treatment is needed. This article reviews the advantages of its unique biochemical conditions and molecular structure for clinical diagnoses and novel anti-tumor drugs. At the same time, the main advantages of the existing conjugated drugs, which are based on single-domain antibodies, are introduced here, thereby providing new ideas and methods for the development of clinical diagnoses and anti-tumor therapies in the future.
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Affiliation(s)
- Xiaofeng Jiang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China; (L.S.); (C.H.); (Z.L.)
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Jiangsu Baiying Biotech Co., Ltd., Taizhou 225300, China;
| | - Ling Sun
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China; (L.S.); (C.H.); (Z.L.)
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Chengwu Hu
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China; (L.S.); (C.H.); (Z.L.)
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Feijian Zheng
- Jiangsu Baiying Biotech Co., Ltd., Taizhou 225300, China;
| | - Zhengbing Lyu
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China; (L.S.); (C.H.); (Z.L.)
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Jianzhong Shao
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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9
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Yang H, Vasylieva N, Wang J, Li Z, Duan W, Chen S, Wen K, Meng H, Yu X, Shen J, Hammock BD, Wang Z. Precise isolation and structural origin of an ultra-specific nanobody against chemical compound. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131958. [PMID: 37429192 PMCID: PMC10686526 DOI: 10.1016/j.jhazmat.2023.131958] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/12/2023]
Abstract
Highly specific antibodies are the key reagents for developing immunoassays with a low false positive rate for environmental monitoring. Here, we provide evidence that nanobodies have the potential to achieve higher specificity than conventional antibodies and explain why from their structural features. Using sulfadimethoxine (SDM) as a model analyte, we constructed an immune phage display library and precisely isolated an ultra-specific nanobody (H1-17) by a crucial homologous antigen counter selection strategy. H1-17 showed no observable cross-reactivity (CR) with other structural analogs of 41 SDM tested, which has never been achieved by conventional antibodies. The structurally original specificity of H1-17 was illuminated and compared with that of one conventional antibody by homology modeling and site-directed mutagenesis validation. It was found that the noncanonical disulfide bond (C50-C104) of H1-17 helped CDR3 form a tailor-made binding pocket and divide it into two parts to accommodate the common structure of sulfonamides and the characteristic methoxyl group of SDM, respectively. Besides, the mutual-checking hydrogen bonds also played important roles in the specific recognition. Lastly, immunoassays with zero false positive rate were developed to screen SDM in water and milk samples, indicating that nanobodies could be reliable reagents for the accurate detection of chemical compounds.
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Affiliation(s)
- Huijuan Yang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing 100193, China
| | - Natalia Vasylieva
- Department of Entomology and UCD Comprehensive Cancer Center, University of California, Davis, CA 95616, United States
| | - Jiaxin Wang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing 100193, China
| | - Zhenfeng Li
- Department of Entomology and UCD Comprehensive Cancer Center, University of California, Davis, CA 95616, United States
| | - Wenbo Duan
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing 100193, China
| | - Shuang Chen
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing 100193, China
| | - Kai Wen
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing 100193, China
| | - Hui Meng
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013 Jiangsu, China
| | - Xuezhi Yu
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing 100193, China
| | - Jianzhong Shen
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing 100193, China
| | - Bruce D Hammock
- Department of Entomology and UCD Comprehensive Cancer Center, University of California, Davis, CA 95616, United States
| | - Zhanhui Wang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing 100193, China.
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10
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Thompson MK, Sharma N, Prakash A. Deciphering the orthorhombic crystal structure of a novel NEIL1 nanobody with pseudo-merohedral twinning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.07.552313. [PMID: 37609231 PMCID: PMC10441366 DOI: 10.1101/2023.08.07.552313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Nanobodies or VHHs (Variable Heavy domains of Heavy chain) are single domain antibodies that comprise three antigenic complementary determining regions (CDR). Nanobodies are used in numerous scientific applications including, bio-imaging, diagnosis, therapeutics, and macromolecular crystallography. We obtained crystals of a ∼14 kDa nanobody specific for the NEIL1 DNA glycosylase (hereafter called A5) in 0.5 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate pH 5.6, and 1.0 M lithium sulfate monohydrate from the Crystal HT Hampton Research screen that were further optimized. Here, we describe the structure determination and refinement of the A5 crystals to a resolution of 2.1 Å. The data collected were complicated by the presence of anisotropy and twinning, and while initial space group determination pointed to a higher apparent tetragonal crystal system, the data statistics suggested twinning, placing the crystal in an orthorhombic system. Twinning was confirmed by the Padilla and Yeates test, H-test, and Britton test based on local intensity differences with a twin fraction of 0.4. Molecular replacement produced the best solution in the orthorhombic space group P2 1 2 1 2 with four molecules in the asymmetric unit and we were able to model over 96% of the residues in the electron density with a final R work and R free of 0.1988 and 0.2289 upon refinement. Synopsis The crystal structure of a specific nanobody against NEIL1 was determined to 2.1 Å. The structure was ultimately solved in an orthorhombic space group after diffraction data analysis revealed mild anisotropy as well as pseudo-merohedral twinning.
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11
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Valdés-Tresanco MS, Valdés-Tresanco ME, Molina-Abad E, Moreno E. NbThermo: a new thermostability database for nanobodies. Database (Oxford) 2023; 2023:baad021. [PMID: 37042467 PMCID: PMC10091358 DOI: 10.1093/database/baad021] [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: 11/25/2022] [Revised: 02/08/2023] [Accepted: 03/16/2023] [Indexed: 04/13/2023]
Abstract
We present NbThermo-a first-in-class database that collects melting temperatures (Tm), amino acid sequences and several other categories of useful data for hundreds of nanobodies (Nbs), compiled from an extensive literature search. This so-far unique database currently contains up-to-date, manually curated data for 564 Nbs. It represents a contribution to efforts aimed at developing new algorithms for reliable Tm prediction to assist Nb engineering for a wide range of applications of these unique biomolecules. Nbs from the two most common source organisms-llama and camel-show similar distributions of melting temperatures. A first exploratory research that takes advantage of this large data collection evidences that understanding the structural bases of Nb thermostability is a complex task, since there are no apparent differences in sequence patterns between the frameworks of Nbs with lower and higher melting temperatures, indicating that the highly variable loops play a relevant role in defining Nb thermostability. Database URL https://valdes-tresanco-ms.github.io/NbThermo.
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Affiliation(s)
- Mario S Valdés-Tresanco
- Faculty of Basic Sciences, University of Medellin, Cra. 87 No. 30-65, Medellin 050026, Colombia
| | - Mario E Valdés-Tresanco
- Centre for Molecular Simulations and Department of Biological Sciences, University of Calgary, 2500 University Drive N.W, Calgary, AB T2N 1N4, Canada
| | | | - Ernesto Moreno
- Faculty of Basic Sciences, University of Medellin, Cra. 87 No. 30-65, Medellin 050026, Colombia
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12
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Dumas L, Marfoglia M, Yang B, Hijazi M, Larabi AN, Lau K, Pojer F, Nash MA, Barth P. Uncovering and engineering the mechanical properties of the adhesion GPCR ADGRG1 GAIN domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.05.535724. [PMID: 37066252 PMCID: PMC10104041 DOI: 10.1101/2023.04.05.535724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Key cellular functions depend on the transduction of extracellular mechanical signals by specialized membrane receptors including adhesion G-protein coupled receptors (aGPCRs). While recently solved structures support aGPCR activation through shedding of the extracellular GAIN domain, the molecular mechanisms underpinning receptor mechanosensing remain poorly understood. When probed using single-molecule atomic force spectroscopy and molecular simulations, ADGRG1 GAIN dissociated from its tethered agonist at forces significantly higher than other reported signaling mechanoreceptors. Strong mechanical resistance was achieved through specific structural deformations and force propagation pathways under mechanical load. ADGRG1 GAIN variants computationally designed to lock the alpha and beta subdomains and rewire mechanically-induced structural deformations were found to modulate the GPS-Stachel rupture forces. Our study provides unprecedented insights into the molecular underpinnings of GAIN mechanical stability and paves the way for engineering mechanosensors, better understanding aGPCR function, and informing drug-discovery efforts targeting this important receptor class.
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13
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Raynaud P, Gauthier C, Jugnarain V, Jean-Alphonse F, Reiter E, Bruneau G, Crépieux P. Intracellular VHHs to monitor and modulate GPCR signaling. Front Endocrinol (Lausanne) 2022; 13:1048601. [PMID: 36465650 PMCID: PMC9708903 DOI: 10.3389/fendo.2022.1048601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 10/24/2022] [Indexed: 11/17/2022] Open
Abstract
Single-domain antibody fragments, also known as VHHs or nanobodies, have opened promising avenues in therapeutics and in exploration of intracellular processes. Because of their unique structural properties, they can reach cryptic regions in their cognate antigen. Intracellular VHHs/antibodies primarily directed against cytosolic proteins or transcription factors have been described. In contrast, few of them target membrane proteins and even less recognize G protein-coupled receptors. These receptors are major therapeutic targets, which reflects their involvement in a plethora of physiological responses. Hence, they elicit a tremendous interest in the scientific community and in the industry. Comprehension of their pharmacology has been obscured by their conformational complexity, that has precluded deciphering their structural properties until the early 2010's. To that respect, intracellular VHHs have been instrumental in stabilizing G protein-coupled receptors in active conformations in order to solve their structure, possibly bound to their primary transducers, G proteins or β-arrestins. In contrast, the modulatory properties of VHHs recognizing the intracellular regions of G protein-coupled receptors on the induced signaling network have been poorly studied. In this review, we will present the advances that the intracellular VHHs have permitted in the field of GPCR signaling and trafficking. We will also discuss the methodological hurdles that linger the discovery of modulatory intracellular VHHs directed against GPCRs, as well as the opportunities they open in drug discovery.
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Affiliation(s)
- Pauline Raynaud
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l’Equitation (IFCE), Université de Tours, Nouzilly, France
| | - Camille Gauthier
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l’Equitation (IFCE), Université de Tours, Nouzilly, France
| | - Vinesh Jugnarain
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l’Equitation (IFCE), Université de Tours, Nouzilly, France
| | - Frédéric Jean-Alphonse
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l’Equitation (IFCE), Université de Tours, Nouzilly, France
- Inria, Inria Saclay-Ile-de-France, Palaiseau, France
| | - Eric Reiter
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l’Equitation (IFCE), Université de Tours, Nouzilly, France
- Inria, Inria Saclay-Ile-de-France, Palaiseau, France
| | - Gilles Bruneau
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l’Equitation (IFCE), Université de Tours, Nouzilly, France
| | - Pascale Crépieux
- Physiologie de la Reproduction et des Comportements (PRC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l’Equitation (IFCE), Université de Tours, Nouzilly, France
- Inria, Inria Saclay-Ile-de-France, Palaiseau, France
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14
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Smardz P, Sieradzan AK, Krupa P. Mechanical Stability of Ribonuclease A Heavily Depends on the Redox Environment. J Phys Chem B 2022; 126:6240-6249. [PMID: 35975925 PMCID: PMC9421896 DOI: 10.1021/acs.jpcb.2c04718] [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] [Indexed: 11/30/2022]
Abstract
Disulfide bonds are covalent bonds that connect nonlocal fragments of proteins, and they are unique post-translational modifications of proteins. They require the oxidizing environment to be stable, which occurs for example during oxidative stress; however, in a cell the reductive environment is maintained, lowering their stability. Despite many years of research on disulfide bonds, their role in the protein life cycle is not fully understood and seems to strictly depend on a system or process in which they are involved. In this article, coarse-grained UNited RESidue (UNRES), and all-atom Assisted Model Building with Energy Refinement (AMBER) force fields were applied to run a series of steered molecular dynamics (SMD) simulations of one of the most studied, but still not fully understood, proteins─ribonuclease A (RNase A). SMD simulations were performed to study the mechanical stability of RNase A in different oxidative-reductive environments. As disulfide bonds (and any other covalent bonds) cannot break/form in any classical all-atom force field, we applied additional restraints between sulfur atoms of reduced cysteines which were able to mimic the breaking of the disulfide bonds. On the other hand, the coarse-grained UNRES force field enables us to study the breaking/formation of the disulfide bonds and control the reducing/oxidizing environment owing to the presence of the designed distance/orientation-dependent potential. This study reveals that disulfide bonds have a strong influence on the mechanical stability of RNase A only in a highly oxidative environment. However, the local stability of the secondary structure seems to play a major factor in the overall stability of the protein. Both our thermal unfolding and mechanical stretching studies show that the most stable disulfide bond is Cys65-Cys72. The breaking of disulfide bonds Cys26-Cys84 and Cys58-Cys110 is associated with large force peaks. They are structural bridges, which are mostly responsible for stabilizing the RNase A conformation, while the presence of the remaining two bonds (Cys65-Cys72 and Cys40-Cys95) is most likely connected with the enzymatic activity rather than the structural stability of RNase A in the cytoplasm. Our results prove that disulfide bonds are indeed stabilizing fragments of the proteins, but their role is strongly redox environment-dependent.
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Affiliation(s)
- Pamela Smardz
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
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15
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Liu H, Liu Z, Yang B, Lopez Morales J, Nash MA. Optimal Sacrificial Domains in Mechanical Polyproteins: S. epidermidis Adhesins Are Tuned for Work Dissipation. JACS AU 2022; 2:1417-1427. [PMID: 35783175 PMCID: PMC9241160 DOI: 10.1021/jacsau.2c00121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
The opportunistic pathogen Staphylococcus epidermidis utilizes a multidomain surface adhesin protein to bind host components and adhere to tissues. While it is known that the interaction between the SdrG receptor and its fibrinopeptide target (FgB) is exceptionally mechanostable (∼2 nN), the influence of downstream B domains (B1 and B2) is unclear. Here, we studied the mechanical relationships between folded B domains and the SdrG receptor bound to FgB. We used protein engineering, single-molecule force spectroscopy (SMFS) with an atomic force microscope (AFM), and Monte Carlo simulations to understand how the mechanical properties of folded sacrificial domains, in general, can be optimally tuned to match the stability of a receptor-ligand complex. Analogous to macroscopic suspension systems, sacrificial shock absorber domains should neither be too weak nor too strong to optimally dissipate mechanical energy. We built artificial molecular shock absorber systems based on the nanobody (VHH) scaffold and studied the competition between domain unfolding and receptor unbinding. We quantitatively determined the optimal stability of shock absorbers that maximizes work dissipation on average for a given receptor and found that natural sacrificial domains from pathogenic S. epidermidis and Clostridium perfringens adhesins exhibit stabilities at or near this optimum within a specific range of loading rates. These findings demonstrate how tuning the stability of sacrificial domains in adhesive polyproteins can be used to maximize mechanical work dissipation and serve as an adhesion strategy by bacteria.
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Affiliation(s)
- Haipei Liu
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Zhaowei Liu
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Byeongseon Yang
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Joanan Lopez Morales
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Michael A. Nash
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
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16
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Haueis L, Stech M, Kubick S. A Cell-free Expression Pipeline for the Generation and Functional Characterization of Nanobodies. Front Bioeng Biotechnol 2022; 10:896763. [PMID: 35573250 PMCID: PMC9096027 DOI: 10.3389/fbioe.2022.896763] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Cell-free systems are well-established platforms for the rapid synthesis, screening, engineering and modification of all kinds of recombinant proteins ranging from membrane proteins to soluble proteins, enzymes and even toxins. Also within the antibody field the cell-free technology has gained considerable attention with respect to the clinical research pipeline including antibody discovery and production. Besides the classical full-length monoclonal antibodies (mAbs), so-called "nanobodies" (Nbs) have come into focus. A Nb is the smallest naturally-derived functional antibody fragment known and represents the variable domain (VHH, ∼15 kDa) of a camelid heavy-chain-only antibody (HCAb). Based on their nanoscale and their special structure, Nbs display striking advantages concerning their production, but also their characteristics as binders, such as high stability, diversity, improved tissue penetration and reaching of cavity-like epitopes. The classical way to produce Nbs depends on the use of living cells as production host. Though cell-based production is well-established, it is still time-consuming, laborious and hardly amenable for high-throughput applications. Here, we present for the first time to our knowledge the synthesis of functional Nbs in a standardized mammalian cell-free system based on Chinese hamster ovary (CHO) cell lysates. Cell-free reactions were shown to be time-efficient and easy-to-handle allowing for the "on demand" synthesis of Nbs. Taken together, we complement available methods and demonstrate a promising new system for Nb selection and validation.
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Affiliation(s)
- Lisa Haueis
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany.,Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.,Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus-Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
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17
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Obeng EM, Dzuvor CKO, Danquah MK. Anti-SARS-CoV-1 and -2 nanobody engineering towards avidity-inspired therapeutics. NANO TODAY 2022; 42:101350. [PMID: 34840592 PMCID: PMC8608585 DOI: 10.1016/j.nantod.2021.101350] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/22/2021] [Accepted: 11/18/2021] [Indexed: 05/15/2023]
Abstract
In the past two decades, the emergence of coronavirus diseases has been dire distress on both continental and global fronts and has resulted in the search for potent treatment strategies. One crucial challenge in this search is the recurrent mutations in the causative virus spike protein, which lead to viral escape issues. Among the current promising therapeutic discoveries is the use of nanobodies and nanobody-like molecules. While these nanobodies have demonstrated high-affinity interaction with the virus, the unpredictable spike mutations have warranted the need for avidity-inspired therapeutics of potent inhibitors such as nanobodies. This article discusses novel approaches for the design of anti-SARS-CoV-1 and -2 nanobodies to facilitate advanced innovations in treatment technologies. It further discusses molecular interactions and suggests multivalent protein nanotechnology and chemistry approaches to translate mere molecular affinity into avidity.
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Affiliation(s)
- Eugene M Obeng
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Bioengineering Laboratory, Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Christian K O Dzuvor
- Bioengineering Laboratory, Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Michael K Danquah
- Department of Chemical Engineering, University of Tennessee, Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, United States
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18
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Yang B, Liu H, Liu Z, Doenen R, Nash MA. Influence of Fluorination on Single-Molecule Unfolding and Rupture Pathways of a Mechanostable Protein Adhesion Complex. NANO LETTERS 2020; 20:8940-8950. [PMID: 33191756 PMCID: PMC7729889 DOI: 10.1021/acs.nanolett.0c04178] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/08/2020] [Indexed: 05/25/2023]
Abstract
We investigated the influence of fluorination on unfolding and unbinding reaction pathways of a mechanostable protein complex comprising the tandem dyad XModule-Dockerin bound to Cohesin. Using single-molecule atomic force spectroscopy, we mapped the energy landscapes governing the unfolding and unbinding reactions. We then used sense codon suppression to substitute trifluoroleucine in place of canonical leucine globally in XMod-Doc. Although TFL substitution thermally destabilized XMod-Doc, it had little effect on XMod-Doc:Coh binding affinity at equilibrium. When we mechanically dissociated global TFL-substituted XMod-Doc from Coh, we observed the emergence of a new unbinding pathway with a lower energy barrier. Counterintuitively, when fluorination was restricted to Doc, we observed mechano-stabilization of the non-fluorinated neighboring XMod domain. This suggests that intramolecular deformation is modulated by fluorination and highlights the differences between equilibrium thermostability and non-equilibrium mechanostability. Future work is poised to investigate fluorination as a means to modulate mechanical properties of synthetic proteins and hydrogels.
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Affiliation(s)
- Byeongseon Yang
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Haipei Liu
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Zhaowei Liu
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Regina Doenen
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Michael A. Nash
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
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19
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Gettemans J, De Dobbelaer B. Transforming nanobodies into high-precision tools for protein function analysis. Am J Physiol Cell Physiol 2020; 320:C195-C215. [PMID: 33264078 DOI: 10.1152/ajpcell.00435.2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Single-domain antibodies, derived from camelid heavy antibodies (nanobodies) or shark variable new antigen receptors, have attracted increasing attention in recent years due to their extremely versatile nature and the opportunities they offer for downstream modification. Discovered more than three decades ago, these 120-amino acid (∼15-kDa) antibody fragments are known to bind their target with high specificity and affinity. Key features of nanobodies that make them very attractive include their single-domain nature, small size, and affordable high-level expression in prokaryotes, and their cDNAs are routinely obtained in the process of their isolation. This facilitates and stimulates new experimental approaches. Hence, it allows researchers to formulate new answers to complex biomedical questions. Through elementary PCR-based technologies and chemical modification strategies, their primary structure can be altered almost at leisure while retaining their specificity and biological activity, transforming them into highly tailored tools that meet the increasing demands of current-day biomedical research. In this review, various aspects of camelid nanobodies are expounded, including intracellular delivery in recombinant format for manipulation of, i.e., cytoplasmic targets, their derivatization to improve nanobody orientation as a capturing device, approaches to reversibly bind their target, their potential as protein-silencing devices in cells, the development of strategies to transfer nanobodies through the blood-brain barrier and their application in CAR-T experimentation. We also discuss some of their disadvantages and conclude with future prospects.
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Affiliation(s)
- Jan Gettemans
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Brian De Dobbelaer
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
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20
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Ma H, Ó'Fágáin C, O'Kennedy R. Antibody stability: A key to performance - Analysis, influences and improvement. Biochimie 2020; 177:213-225. [PMID: 32891698 DOI: 10.1016/j.biochi.2020.08.019] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 02/01/2023]
Abstract
An antibody's stability greatly influences its performance (i.e. its specificity and affinity). Thus, stability is a major issue for researchers and manufacturers, especially with the increasing use of antibodies in therapeutics, diagnostics and rapid analytical platforms. Here we review antibody stability under five headings: (i) measurement techniques; (ii) stability issues in expression and production (expression, proteolysis, aggregation); (iii) effects of antibody format and engineering on stability and (iv) formulation, drying and storage conditions. We consider more than 100 sources, including patents, and conclude with (v) recommendations to promote antibody stability.
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Affiliation(s)
- Hui Ma
- School of Biotechnology, Dublin City University, Dublin 9, D09 V2O9, Ireland
| | - Ciarán Ó'Fágáin
- School of Biotechnology, Dublin City University, Dublin 9, D09 V2O9, Ireland.
| | - Richard O'Kennedy
- School of Biotechnology, Dublin City University, Dublin 9, D09 V2O9, Ireland; Qatar Foundation, Research Complex, And Hamad Bin Khalifa University, Education City, Doha, Qatar
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21
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Liu Z, Liu H, Vera AM, Bernardi RC, Tinnefeld P, Nash MA. High force catch bond mechanism of bacterial adhesion in the human gut. Nat Commun 2020; 11:4321. [PMID: 32859904 PMCID: PMC7456326 DOI: 10.1038/s41467-020-18063-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 08/04/2020] [Indexed: 12/28/2022] Open
Abstract
Bacterial colonization of the human intestine requires firm adhesion of bacteria to insoluble substrates under hydrodynamic flow. Here we report the molecular mechanism behind an ultrastable protein complex responsible for resisting shear forces and adhering bacteria to cellulose fibers in the human gut. Using single-molecule force spectroscopy (SMFS), single-molecule FRET (smFRET), and molecular dynamics (MD) simulations, we resolve two binding modes and three unbinding reaction pathways of a mechanically ultrastable R. champanellensis (Rc) Dockerin:Cohesin (Doc:Coh) complex. The complex assembles in two discrete binding modes with significantly different mechanical properties, with one breaking at ~500 pN and the other at ~200 pN at loading rates from 1-100 nN s-1. A neighboring X-module domain allosterically regulates the binding interaction and inhibits one of the low-force pathways at high loading rates, giving rise to a catch bonding mechanism that manifests under force ramp protocols. Multi-state Monte Carlo simulations show strong agreement with experimental results, validating the proposed kinetic scheme. These results explain mechanistically how gut microbes regulate cell adhesion strength at high shear stress through intricate molecular mechanisms including dual-binding modes, mechanical allostery and catch bonds.
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Affiliation(s)
- Zhaowei Liu
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Haipei Liu
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Andrés M Vera
- Faculty of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Rafael C Bernardi
- NIH Center for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 61801, Urbana, IL, USA
- Department of Physics, Auburn University, 36849, Auburn, AL, USA
| | - Philip Tinnefeld
- Faculty of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.
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Capturing transient antibody conformations with DNA origami epitopes. Nat Commun 2020; 11:3114. [PMID: 32561744 PMCID: PMC7305102 DOI: 10.1038/s41467-020-16949-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/26/2020] [Indexed: 02/07/2023] Open
Abstract
Revealing antibody-antigen interactions at the single-molecule level will deepen our understanding of immunology. However, structural determination under crystal or cryogenic conditions does not provide temporal resolution for resolving transient, physiologically or pathologically relevant functional antibody-antigen complexes. Here, we develop a triangular DNA origami framework with site-specifically anchored and spatially organized artificial epitopes to capture transient conformations of immunoglobulin Gs (IgGs) at room temperature. The DNA origami epitopes (DOEs) allows programmed spatial distribution of epitope spikes, which enables direct imaging of functional complexes with atomic force microscopy (AFM). We establish the critical dependence of the IgG avidity on the lateral distance of epitopes within 3–20 nm at the single-molecule level. High-speed AFM imaging of transient conformations further provides structural and dynamic evidence for the IgG avidity from monovalent to bivalent in a single event, which sheds light on various applications including virus neutralization, diagnostic detection and cancer immunotherapy. Understanding antibody-antigen interactions is important to deepen the understanding of immunology. Here, the authors report on the application of DNA origami structures for the controlled presentation of antigens to study antibody binding behaviours at room temperature.
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Yang B, Liu Z, Liu H, Nash MA. Next Generation Methods for Single-Molecule Force Spectroscopy on Polyproteins and Receptor-Ligand Complexes. Front Mol Biosci 2020; 7:85. [PMID: 32509800 PMCID: PMC7248566 DOI: 10.3389/fmolb.2020.00085] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/16/2020] [Indexed: 12/31/2022] Open
Abstract
Single-molecule force spectroscopy with the atomic force microscope provides molecular level insights into protein function, allowing researchers to reconstruct energy landscapes and understand functional mechanisms in biology. With steadily advancing methods, this technique has greatly accelerated our understanding of force transduction, mechanical deformation, and mechanostability within single- and multi-domain polyproteins, and receptor-ligand complexes. In this focused review, we summarize the state of the art in terms of methodology and highlight recent methodological improvements for AFM-SMFS experiments, including developments in surface chemistry, considerations for protein engineering, as well as theory and algorithms for data analysis. We hope that by condensing and disseminating these methods, they can assist the community in improving data yield, reliability, and throughput and thereby enhance the information that researchers can extract from such experiments. These leading edge methods for AFM-SMFS will serve as a groundwork for researchers cognizant of its current limitations who seek to improve the technique in the future for in-depth studies of molecular biomechanics.
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Affiliation(s)
- Byeongseon Yang
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Zhaowei Liu
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Haipei Liu
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Michael A. Nash
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
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