1
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Azzam T, Du JJ, Flowers MW, Ali AV, Hunn JC, Vijayvargiya N, Knagaram R, Bogacz M, Maravillas KE, Sastre DE, Fields JK, Mirzaei A, Pierce BG, Sundberg EJ. Combinatorially restricted computational design of protein-protein interfaces to produce IgG heterodimers. SCIENCE ADVANCES 2024; 10:eadk8157. [PMID: 38598628 PMCID: PMC11006224 DOI: 10.1126/sciadv.adk8157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 03/08/2024] [Indexed: 04/12/2024]
Abstract
Redesigning protein-protein interfaces is an important tool for developing therapeutic strategies. Interfaces can be redesigned by in silico screening, which allows for efficient sampling of a large protein space before experimental validation. However, computational costs limit the number of combinations that can be reasonably sampled. Here, we present combinatorial tyrosine (Y)/serine (S) selection (combYSelect), a computational approach combining in silico determination of the change in binding free energy (ΔΔG) of an interface with a highly restricted library composed of just two amino acids, tyrosine and serine. We used combYSelect to design two immunoglobulin G (IgG) heterodimers-combYSelect1 (L368S/D399Y-K409S/T411Y) and combYSelect2 (D399Y/K447S-K409S/T411Y)-that exhibit near-optimal heterodimerization, without affecting IgG stability or function. We solved the crystal structures of these heterodimers and found that dynamic π-stacking interactions and polar contacts drive preferential heterodimeric interactions. Finally, we demonstrated the utility of our combYSelect heterodimers by engineering both a bispecific antibody and a cytokine trap for two unique therapeutic applications.
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Affiliation(s)
- Tala Azzam
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jonathan J. Du
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Maria W. Flowers
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Adeela V. Ali
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jeremy C. Hunn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nina Vijayvargiya
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Rushil Knagaram
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Marek Bogacz
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kino E. Maravillas
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Diego E. Sastre
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - James K. Fields
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ardalan Mirzaei
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
| | - Brian G. Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20850, USA
| | - Eric J. Sundberg
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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2
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Gomes PDC, Hin-Chu M, Rickard JJS, Goldberg Oppenheimer P. Advanced Tuneable Micronanoplatforms for Sensitive and Selective Multiplexed Spectroscopic Sensing via Electro-Hydrodynamic Surface Molecular Lithography. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306068. [PMID: 38225756 DOI: 10.1002/advs.202306068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/21/2023] [Indexed: 01/17/2024]
Abstract
Micro- and nanopatterning of materials, one of the cornerstones of emerging technologies, has transformed research capabilities in lab-on-a-chip diagnostics. Herein, a micro- and nanolithographic method is developed, enabling structuring materials at the submicron scale, which can, in turn, accelerate the development of miniaturized platform technologies and biomedical sensors. Underpinning it is the advanced electro-hydrodynamic surface molecular lithography, via inducing interfacial instabilities produces micro- and nanostructured substrates, uniquely integrated with synthetic surface recognition. This approach enables the manufacture of design patterns with tuneable feature sizes, which are functionalized via synthetic nanochemistry for highly sensitive, selective, rapid molecular sensing. The development of a high-precision piezoelectric lithographic rig enables reproducible substrate fabrication with optimum signal enhancement optimized for functionalization with capture molecules on each micro- and nanostructured array. This facilitates spatial separation, which during the spectroscopic sensing, enables multiplexed measurement of target molecules, establishing the detection at minute concentrations. Subsequently, this nano-plasmonic lab-on-a-chip combined with the unconventional computational classification algorithm and surface enhanced Raman spectroscopy, aimed to address the challenges associated with timely point-of-care detection of disease-indicative biomarkers, is utilized in validation assay for multiplex detection of traumatic brain injury indicative glycan biomarkers, demonstrating straightforward and cost-effective micro- and nanoplatforms for accurate detection.
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Affiliation(s)
- Paulo De Carvalho Gomes
- School of Chemical Engineering, Advanced Nanomaterials Structures and Applications Laboratories, College of Engineering and, Physical Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Martin Hin-Chu
- School of Chemical Engineering, Advanced Nanomaterials Structures and Applications Laboratories, College of Engineering and, Physical Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | | | - Pola Goldberg Oppenheimer
- School of Chemical Engineering, Advanced Nanomaterials Structures and Applications Laboratories, College of Engineering and, Physical Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Healthcare Technologies Institute, Institute of Translational Medicine, Mindelsohn Way, Birmingham, B15 2TH, UK
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3
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Zuo J, Chen H, Li H. Two molecule force spectroscopy on ligand-receptor interactions. NANOSCALE 2023; 15:16581-16589. [PMID: 37740375 DOI: 10.1039/d3nr03428c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Many biological processes involve the rupture of multiple ligand-receptors or multivalent ligand-receptors. It is challenging to study the rupture of such parallelly arranged multiple ligand-receptors due to the difficulties in engineering such systems in a well-controlled fashion. Here we report the use of two-molecule force spectroscopy to investigate the rupture of two parallelly arranged monomeric streptavidin (mSA)-biotin complexes. By using SpyCatcher-SpyTag chemistry, we successfully engineered a molecular twin of biotin, in which two biotins are arranged in parallel. By reacting mSA with twin biotin, we constructed parallelly arranged two mSA-biotin complexes for force spectroscopy experiments. The incorporation of single molecule fingerprint domains into our mSA-biotin dimers allowed us to identify and assign the rupture events of the parallelly arranged mSA-biotin complexes without any ambiguity in the two-molecule force spectroscopy experiments. Our results revealed that the rupture force of the parallel dimer mSA-biotin is 172 pN at a pulling speed of 400 nm s-1, which is about 1.6 times of that of single mSA-biotin (105 pN). Furthermore, our findings indicate that the two mSA-biotin behave as non-interacting, independent ligand-receptors. The strategy we demonstrated here can be extended to other ligand-receptors and may open up an avenue toward rigorously testing the theoretic predictions proposed in various models regarding the rupture of multiple parallel ligand-receptors.
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Affiliation(s)
- Jiacheng Zuo
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
| | - Hui Chen
- Department of Chemical Engineering, Nanjing Forestry University, Nanjing, Jiangsu, P. R. China
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
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4
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Greisen PJ, Yi L, Zhou R, Zhou J, Johansson E, Dong T, Liu H, Johnsen LB, Lund S, Svensson LA, Zhu H, Thomas N, Yang Z, Østergaard H. Computational design of N-linked glycans for high throughput epitope profiling. Protein Sci 2023; 32:e4726. [PMID: 37421602 PMCID: PMC10521239 DOI: 10.1002/pro.4726] [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: 04/20/2023] [Revised: 06/12/2023] [Accepted: 07/06/2023] [Indexed: 07/10/2023]
Abstract
Efficient identification of epitopes is crucial for drug discovery and design as it enables the selection of optimal epitopes, expansion of lead antibody diversity, and verification of binding interface. Although high-resolution low throughput methods like x-ray crystallography can determine epitopes or protein-protein interactions accurately, they are time-consuming and can only be applied to a limited number of complexes. To overcome these limitations, we have developed a rapid computational method that incorporates N-linked glycans to mask epitopes or protein interaction surfaces, thereby providing a mapping of these regions. Using human coagulation factor IXa (fIXa) as a model system, we computationally screened 158 positions and expressed 98 variants to test experimentally for epitope mapping. We were able to delineate epitopes rapidly and reliably through the insertion of N-linked glycans that efficiently disrupted binding in a site-selective manner. To validate the efficacy of our method, we conducted ELISA experiments and high-throughput yeast surface display assays. Furthermore, x-ray crystallography was employed to verify the results, thereby recapitulating through the method of N-linked glycans a coarse-grained mapping of the epitope.
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Affiliation(s)
| | - Li Yi
- Global Research TechnologiesNovo Nordisk A/SMaaloevDenmark
| | - Rong Zhou
- Discovery Technology China, Novo Nordisk Research CentreNovo Nordisk A/SBeijingChina
| | - Jian Zhou
- Discovery Technology China, Novo Nordisk Research CentreNovo Nordisk A/SBeijingChina
| | - Eva Johansson
- Global Research TechnologiesNovo Nordisk A/SMaaloevDenmark
| | - Tiantang Dong
- Discovery Technology China, Novo Nordisk Research CentreNovo Nordisk A/SBeijingChina
| | - Haimo Liu
- Discovery Technology China, Novo Nordisk Research CentreNovo Nordisk A/SBeijingChina
| | | | - Søren Lund
- Global Research TechnologiesNovo Nordisk A/SMaaloevDenmark
| | | | - Haisun Zhu
- Discovery Technology China, Novo Nordisk Research CentreNovo Nordisk A/SBeijingChina
| | - Nidhin Thomas
- Digital Science and InnovationNovo Nordisk A/SSeattleUSA
| | - Zhiru Yang
- Discovery Technology China, Novo Nordisk Research CentreNovo Nordisk A/SBeijingChina
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5
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Jiang J, Boughter CT, Ahmad J, Natarajan K, Boyd LF, Meier-Schellersheim M, Margulies DH. SARS-CoV-2 antibodies recognize 23 distinct epitopic sites on the receptor binding domain. Commun Biol 2023; 6:953. [PMID: 37726484 PMCID: PMC10509263 DOI: 10.1038/s42003-023-05332-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/07/2023] [Indexed: 09/21/2023] Open
Abstract
The COVID-19 pandemic and SARS-CoV-2 variants have dramatically illustrated the need for a better understanding of antigen (epitope)-antibody (paratope) interactions. To gain insight into the immunogenic characteristics of epitopic sites (ES), we systematically investigated the structures of 340 Abs and 83 nanobodies (Nbs) complexed with the Receptor Binding Domain (RBD) of the SARS-CoV-2 spike protein. We identified 23 distinct ES on the RBD surface and determined the frequencies of amino acid usage in the corresponding CDR paratopes. We describe a clustering method for analysis of ES similarities that reveals binding motifs of the paratopes and that provides insights for vaccine design and therapies for SARS-CoV-2, as well as a broader understanding of the structural basis of Ab-protein antigen (Ag) interactions.
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Affiliation(s)
- Jiansheng Jiang
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA.
| | - Christopher T Boughter
- Computational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Javeed Ahmad
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Kannan Natarajan
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Lisa F Boyd
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Martin Meier-Schellersheim
- Computational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - David H Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA.
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6
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Jiang J, Boughter CT, Ahmad J, Natarajan K, Boyd LF, Meier-Schellersheim M, Margulies DH. SARS-CoV-2 antibodies recognize 23 distinct epitopic sites on the receptor binding domain. RESEARCH SQUARE 2023:rs.3.rs-2800118. [PMID: 37333174 PMCID: PMC10275037 DOI: 10.21203/rs.3.rs-2800118/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The COVID-19 pandemic and SARS-CoV-2 variants have dramatically illustrated the need for a better understanding of antigen (epitope)-antibody (paratope) interactions. To gain insight into the immunogenic characteristics of epitopic sites (ES), we systematically investigated the structures of 340 Abs and 83 nanobodies (Nbs) complexed with the Receptor Binding Domain (RBD) of the SARS-CoV-2 spike protein. We identified 23 distinct ES on the RBD surface and determined the frequencies of amino acid usage in the corresponding CDR paratopes. We describe a clustering method for analysis of ES similarities that reveals binding motifs of the paratopes and that provides insights for vaccine design and therapies for SARS-CoV-2, as well as a broader understanding of the structural basis of Ab-protein antigen (Ag) interactions.
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Affiliation(s)
- Jiansheng Jiang
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 10892, USA
| | - Christopher T. Boughter
- Computational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 10892, USA
| | - Javeed Ahmad
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 10892, USA
| | - Kannan Natarajan
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 10892, USA
| | - Lisa F. Boyd
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 10892, USA
| | - Martin Meier-Schellersheim
- Computational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 10892, USA
| | - David H. Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 10892, USA
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7
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Hogan JM, Lee PS, Wong SC, West SM, Morishige WH, Bee C, Tapia GC, Rajpal A, Strop P, Dollinger G. Residue-Level Characterization of Antibody Binding Epitopes Using Carbene Chemical Footprinting. Anal Chem 2023; 95:3922-3931. [PMID: 36791402 DOI: 10.1021/acs.analchem.2c03091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Characterization of antibody binding epitopes is an important factor in therapeutic drug discovery, as the binding site determines and drives antibody pharmacology and pharmacokinetics. Here, we present a novel application of carbene chemical footprinting with mass spectrometry for identification of antibody binding epitopes at the single-residue level. Two different photoactivated diazirine reagents provide complementary labeling information allowing structural refinement of the antibody binding interface. We applied this technique to map the epitopes of multiple MICA and CTLA-4 antibodies and validated the findings with X-ray crystallography and yeast surface display epitope mapping. The characterized epitopes were used to understand biolayer interferometry-derived competitive binding results at the structural level. We show that carbene footprinting provides fast and high-resolution epitope information critical in the antibody selection process and enables mechanistic understanding of function to accelerate the drug discovery process.
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Affiliation(s)
- Jason M Hogan
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Peter S Lee
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Susan C Wong
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Sean M West
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Winse H Morishige
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Christine Bee
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Gamze Camdere Tapia
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Arvind Rajpal
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Pavel Strop
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Gavin Dollinger
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
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8
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Rouet R, Henry JY, Johansen MD, Sobti M, Balachandran H, Langley DB, Walker GJ, Lenthall H, Jackson J, Ubiparipovic S, Mazigi O, Schofield P, Burnett DL, Brown SHJ, Martinello M, Hudson B, Gilroy N, Post JJ, Kelleher A, Jäck HM, Goodnow CC, Turville SG, Rawlinson WD, Bull RA, Stewart AG, Hansbro PM, Christ D. Broadly neutralizing SARS-CoV-2 antibodies through epitope-based selection from convalescent patients. Nat Commun 2023; 14:687. [PMID: 36755042 PMCID: PMC9907207 DOI: 10.1038/s41467-023-36295-5] [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: 01/19/2022] [Accepted: 01/25/2023] [Indexed: 02/10/2023] Open
Abstract
Emerging variants of concern (VOCs) are threatening to limit the effectiveness of SARS-CoV-2 monoclonal antibodies and vaccines currently used in clinical practice; broadly neutralizing antibodies and strategies for their identification are therefore urgently required. Here we demonstrate that broadly neutralizing antibodies can be isolated from peripheral blood mononuclear cells of convalescent patients using SARS-CoV-2 receptor binding domains carrying epitope-specific mutations. This is exemplified by two human antibodies, GAR05, binding to epitope class 1, and GAR12, binding to a new epitope class 6 (located between class 3 and 5). Both antibodies broadly neutralize VOCs, exceeding the potency of the clinical monoclonal sotrovimab (S309) by orders of magnitude. They also provide prophylactic and therapeutic in vivo protection of female hACE2 mice against viral challenge. Our results indicate that exposure to SARS-CoV-2 induces antibodies that maintain broad neutralization against emerging VOCs using two unique strategies: either by targeting the divergent class 1 epitope in a manner resistant to VOCs (ACE2 mimicry, as illustrated by GAR05 and mAbs P2C-1F11/S2K14); or alternatively, by targeting rare and highly conserved epitopes, such as the new class 6 epitope identified here (as illustrated by GAR12). Our results provide guidance for next generation monoclonal antibody development and vaccine design.
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Affiliation(s)
- Romain Rouet
- Garvan Institute of Medical Research, Sydney, NSW, Australia. .,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia.
| | - Jake Y Henry
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Matt D Johansen
- Center for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, NSW, Australia
| | - Meghna Sobti
- UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia.,Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
| | - Harikrishnan Balachandran
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia.,Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | - David B Langley
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Gregory J Walker
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia.,Kirby Institute, UNSW Sydney, Sydney, NSW, Australia.,Prince of Wales Hospital, Sydney, NSW, Australia
| | - Helen Lenthall
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Jennifer Jackson
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Stephanie Ubiparipovic
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Ohan Mazigi
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Peter Schofield
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Deborah L Burnett
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Simon H J Brown
- Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Marianne Martinello
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia.,Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | | | | | | | - Anthony Kelleher
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia.,Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Friedrich-Alexander University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen-Nürnberg, Germany
| | - Christopher C Goodnow
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Stuart G Turville
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia.,Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | - William D Rawlinson
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia.,Prince of Wales Hospital, Sydney, NSW, Australia
| | - Rowena A Bull
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia.,Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | - Alastair G Stewart
- UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia.,Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
| | | | - Daniel Christ
- Garvan Institute of Medical Research, Sydney, NSW, Australia. .,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia.
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9
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Mejias-Gomez O, Madsen AV, Skovgaard K, Pedersen LE, Morth JP, Jenkins TP, Kristensen P, Goletz S. A window into the human immune system: comprehensive characterization of the complexity of antibody complementary-determining regions in functional antibodies. MAbs 2023; 15:2268255. [PMID: 37876265 PMCID: PMC10601506 DOI: 10.1080/19420862.2023.2268255] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/04/2023] [Indexed: 10/26/2023] Open
Abstract
The human immune system uses antibodies to neutralize foreign antigens. They are composed of heavy and light chains, both with constant and variable regions. The variable region has six hypervariable loops, also known as complementary-determining regions (CDRs) that determine antibody diversity and antigen specificity. Knowledge of their significance, and certain residues present in these areas, is vital for antibody therapeutics development. This study includes an analysis of more than 11,000 human antibody sequences from the International Immunogenetics information system (IMGT). The analysis included parameters such as length distribution, overall amino acid diversity, amino acid frequency per CDR and residue position within antibody chains. Overall, our findings confirm existing knowledge, such as CDRH3's high length diversity and amino acid variability, increased aromatic residue usage, particularly tyrosine, charged and polar residues like aspartic acid, serine, and the flexible residue glycine. Specific residue positions within each CDR influence these occurrences, implying a unique amino acid type distribution pattern. We compared amino acid type usage in CDRs and non-CDR regions, both in globular and transmembrane proteins, which revealed distinguishing features, such as increased frequency of tyrosine, serine, aspartic acid, and arginine. These findings should prove useful for future optimization, improvement of affinity, synthetic antibody library design, or the creation of antibodies de-novo in silico.
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Affiliation(s)
- Oscar Mejias-Gomez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Andreas V. Madsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Kerstin Skovgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lasse E. Pedersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - J. Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Peter Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Steffen Goletz
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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10
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Antibody CDR amino acids underlying the functionality of antibody repertoires in recognizing diverse protein antigens. Sci Rep 2022; 12:12555. [PMID: 35869245 PMCID: PMC9307644 DOI: 10.1038/s41598-022-16841-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/18/2022] [Indexed: 11/21/2022] Open
Abstract
Antibodies recognize protein antigens with exquisite specificity in a complex aqueous environment, where interfacial waters are an integral part of the antibody–protein complex interfaces. In this work, we elucidate, with computational analyses, the principles governing the antibodies’ specificity and affinity towards their cognate protein antigens in the presence of explicit interfacial waters. Experimentally, in four model antibody–protein complexes, we compared the contributions of the interaction types in antibody–protein antigen complex interfaces with the antibody variants selected from phage-displayed synthetic antibody libraries. Evidently, the specific interactions involving a subset of aromatic CDR (complementarity determining region) residues largely form the predominant determinant underlying the specificity of the antibody–protein complexes in nature. The interfacial direct/water-mediated hydrogen bonds accompanying the CDR aromatic interactions are optimized locally but contribute little in determining the epitope location. The results provide insights into the phenomenon that natural antibodies with limited sequence and structural variations in an antibody repertoire can recognize seemingly unlimited protein antigens. Our work suggests guidelines in designing functional artificial antibody repertoires with practical applications in developing novel antibody-based therapeutics and diagnostics for treating and preventing human diseases.
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11
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Warren PD, Dodson MS, Smith MH, Landowski TH, Palting JD, Towne P. High-Resolution Epitope Mapping and Affinity Binding Analysis Comparing a New Anti-Human LAG3 Rabbit Antibody Clone to the Commonly Used Mouse 17B4 Clone. Antibodies (Basel) 2022; 11:antib11040060. [PMID: 36278613 PMCID: PMC9589981 DOI: 10.3390/antib11040060] [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: 08/16/2022] [Revised: 08/30/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Lymphocyte activation gene 3 (LAG3) is a T cell inhibitory receptor that promotes tumor cell immune escape and is a potential target for cancer diagnostic and immunotherapeutic applications. We used automated capillary electrophoresis (ACE), surface plasmon resonance (SPR), and immunohistochemistry (IHC) to compare the binding characteristics of a new anti-LAG3 rabbit antibody clone, SP464, with the thirty-year old and extensively used anti-LAG3 mouse 17B4 clone. The rabbit SP464 clone exhibited between 20× to 30× greater binding to LAG3 than did the mouse 17B4 clone. Using these tools, we precisely mapped the relative locations of the epitopes of these two antibodies. The SP464 and 17B4 minimal epitopes were localized to separate, but overlapping, sub-fragments within the amino-terminal fifteen acids of the original thirty-mer peptide immunogen used to generate both antibodies. Application of this approach for quantifying the effects of alanine substitutions along the minimal SP464 epitope identified two amino acids essential for binding and four amino acids that likely contribute towards binding. Together, ACE, SPR, and IHC constitute a powerful orthologous approach for comparing antibody-binding characteristics and for fine mapping of linear epitopes within short immunogens. Our results indicate that the rabbit clone SP464 may be useful for assessing LAG3 expression.
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12
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Domain-level epitope mapping of polyclonal antibodies against HER-1 and HER-2 receptors using phage display technology. Sci Rep 2022; 12:12268. [PMID: 35851313 PMCID: PMC9293994 DOI: 10.1038/s41598-022-16411-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
HER-1 and HER-2 are tumor-associated antigens overexpressed in several epithelial tumors, and successfully targeted by therapeutic approaches against cancer. Vaccination with their recombinant extracellular domains has had encouraging results in the pre-clinical setting. As complex humoral responses targeting multiple epitopes within each antigen are the ultimate goal of such active immunotherapy strategies, molecular dissection of the mixture of antibody specificities is required. The current work exploits phage display of antigenic versions of HER-1 and HER-2 domains to accomplish domain-level epitope mapping. Recognition of domains I, III and IV of both antigens by antibodies of immunized mice was shown, indicating diverse responses covering a broad range of antigenic regions. The combination of phage display and site-directed mutagenesis allowed mutational screening of antigen surface, showing polyclonal antibodies' recognition of mutated receptor escape variants known to arise in patients under the selective pressure of the anti-HER-1 antibody cetuximab. Phage-displayed HER domains have thus the potential to contribute to fine specificity characterization of humoral responses during future development of anti-cancer vaccines.
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13
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Understanding and Modulating Antibody Fine Specificity: Lessons from Combinatorial Biology. Antibodies (Basel) 2022; 11:antib11030048. [PMID: 35892708 PMCID: PMC9326607 DOI: 10.3390/antib11030048] [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: 06/14/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 02/01/2023] Open
Abstract
Combinatorial biology methods such as phage and yeast display, suitable for the generation and screening of huge numbers of protein fragments and mutated variants, have been useful when dissecting the molecular details of the interactions between antibodies and their target antigens (mainly those of protein nature). The relevance of these studies goes far beyond the mere description of binding interfaces, as the information obtained has implications for the understanding of the chemistry of antibody–antigen binding reactions and the biological effects of antibodies. Further modification of the interactions through combinatorial methods to manipulate the key properties of antibodies (affinity and fine specificity) can result in the emergence of novel research tools and optimized therapeutics.
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14
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Wang Y, Wang X, Gao T, Lou C, Wang H, Liu Y, Cao A. Folding of Flexible Protein Fragments and Design of Nanoparticle-Based Artificial Antibody Targeting Lysozyme. J Phys Chem B 2022; 126:5045-5054. [PMID: 35763806 DOI: 10.1021/acs.jpcb.2c03200] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
It is generally believed that a protein's sequence solely determines its native structure, but how the long- and short-range interactions jointly determine the native structure/conformation of the protein or every local fragment of the protein is still not fully understood. Since most protein fragments are unstructured on their own, direct observation of the folding of flexible protein fragments is very difficult. Interestingly, we show that it is possible to graft the complementary-determining regions (CDRs) of antibodies onto the surface of a gold nanoparticle (AuNP) to create AuNP-based artificial antibodies (denoted as Goldbodies), such as an antilysozyme Goldbody. Goldbodies can specifically recognize the corresponding antigens like the original natural antibodies do, but direct structural evidence for the refolding or restoration of native conformation of the grafted CDRs on AuNPs is still missing and in high demand. Herein we design a new Goldbody that targets an epitope on the lysozyme different from that of the previous antilysozyme Goldbody, and the one circle of helix in the CDR makes it possible to distinguish the unfolded conformation of the free CDR and its folded conformation on AuNPs by circular dichroism (CD) spectroscopy. The refolding of flexible protein fragments on NPs provides unique evidence and inspiration for understanding the fundamental principles of protein folding.
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Affiliation(s)
- Yan Wang
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Xinping Wang
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Tiange Gao
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Chenxi Lou
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Haifang Wang
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Yuanfang Liu
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China.,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Aoneng Cao
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
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15
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Kim S, Ryu H, Tai S, Pedowitz M, Rzasa JR, Pennachio DJ, Hajzus JR, Milton DK, Myers-Ward R, Daniels KM. Real-time ultra-sensitive detection of SARS-CoV-2 by quasi-freestanding epitaxial graphene-based biosensor. Biosens Bioelectron 2022; 197:113803. [PMID: 34814034 PMCID: PMC8595974 DOI: 10.1016/j.bios.2021.113803] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/06/2021] [Accepted: 11/13/2021] [Indexed: 12/30/2022]
Abstract
We report the rapid detection of SARS-CoV-2 in infected patients (mid-turbinate swabs and exhaled breath aerosol samples) in concentrations as low as 60 copies/mL of the virus in seconds by electrical transduction of the SARS-CoV-2 S1 spike protein antigen via SARS-CoV-2 S1 spike protein antibodies immobilized on bilayer quasi-freestanding epitaxial graphene without gate or signal amplification. The sensor demonstrates the spike protein antigen detection in a concentration as low as 1 ag/mL. The heterostructure of the SARS-CoV-2 antibody/graphene-based sensor is developed through a simple and low-cost fabrication technique. Furthermore, sensors integrated into a portable testing unit distinguished B.1.1.7 variant positive samples from infected patients (mid-turbinate swabs and saliva samples, 4000-8000 copies/mL) with a response time of as fast as 0.6 s. The sensor is reusable, allowing for reimmobilization of the crosslinker and antibodies on the biosensor after desorption of biomarkers by NaCl solution or heat treatment above 40 °C.
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Affiliation(s)
- Soaram Kim
- Department of Electrical and Computer Engineering, University of Maryland, College Park, MD, 20742, USA; Institute for Research in Electronics and Applied Physics, University of Maryland, College Park, MD, 20742, USA.
| | - Heeju Ryu
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Sheldon Tai
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, 20742, USA
| | - Michael Pedowitz
- Department of Electrical and Computer Engineering, University of Maryland, College Park, MD, 20742, USA; Institute for Research in Electronics and Applied Physics, University of Maryland, College Park, MD, 20742, USA
| | - John Robertson Rzasa
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | | | | | - Donald K Milton
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, 20742, USA
| | | | - Kevin M Daniels
- Department of Electrical and Computer Engineering, University of Maryland, College Park, MD, 20742, USA; Institute for Research in Electronics and Applied Physics, University of Maryland, College Park, MD, 20742, USA
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16
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Jafari N, Khoradmehr A, Moghiminasr R, Seyed Habashi M. Mesenchymal Stromal/Stem Cells-Derived Exosomes as an Antimicrobial Weapon for Orodental Infections. Front Microbiol 2022; 12:795682. [PMID: 35058912 PMCID: PMC8764367 DOI: 10.3389/fmicb.2021.795682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/08/2021] [Indexed: 11/14/2022] Open
Abstract
The oral cavity as the second most various microbial community in the body contains a broad spectrum of microorganisms which are known as the oral microbiome. The oral microbiome includes different types of microbes such as bacteria, fungi, viruses, and protozoa. Numerous factors can affect the equilibrium of the oral microbiome community which can eventually lead to orodental infectious diseases. Periodontitis, dental caries, oral leukoplakia, oral squamous cell carcinoma are some multifactorial infectious diseases in the oral cavity. In defending against infection, the immune system has an essential role. Depending on the speed and specificity of the reaction, immunity is divided into two different types which are named the innate and the adaptive responses but also there is much interaction between them. In these responses, different types of immune cells are present and recent evidence demonstrates that these cell types both within the innate and adaptive immune systems are capable of secreting some extracellular vesicles named exosomes which are involved in the response to infection. Exosomes are 30-150 nm lipid bilayer vesicles that consist of variant molecules, including proteins, lipids, and genetic materials and they have been associated with cell-to-cell communications. However, some kinds of exosomes can be effective on the pathogenicity of various microorganisms and promoting infections, and some other ones have antimicrobial and anti-infective functions in microbial diseases. These discrepancies in performance are due to the origin of the exosome. Exosomes can modulate the innate and specific immune responses of host cells by participating in antigen presentation for activation of immune cells and stimulating the release of inflammatory factors and the expression of immune molecules. Also, mesenchymal stromal/stem cells (MSCs)-derived exosomes participate in immunomodulation by different mechanisms. Ease of expansion and immunotherapeutic capabilities of MSCs, develop their applications in hundreds of clinical trials. Recently, it has been shown that cell-free therapies, like exosome therapies, by having more advantages than previous treatment methods are emerging as a promising strategy for the treatment of several diseases, in particular inflammatory conditions. In orodental infectious disease, exosomes can also play an important role by modulating immunoinflammatory responses. Therefore, MSCs-derived exosomes may have potential therapeutic effects to be a choice for controlling and treatment of orodental infectious diseases.
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Affiliation(s)
- Nazanin Jafari
- Department of Endodontics, School of Dentistry, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Arezoo Khoradmehr
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Reza Moghiminasr
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mina Seyed Habashi
- Department of Endodontics, School of Dentistry, Bushehr University of Medical Sciences, Bushehr, Iran
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17
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Biby A, Wang X, Liu X, Roberson O, Henry A, Xia X. Rapid testing for coronavirus disease 2019 (COVID-19). MRS COMMUNICATIONS 2022; 12:12-23. [PMID: 35075405 PMCID: PMC8769796 DOI: 10.1557/s43579-021-00146-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 09/29/2021] [Indexed: 05/03/2023]
Abstract
Rapid testing, generally refers to the paper-based diagnostic platform known as "lateral flow assay" (LFA), has emerged as a critical asset to the containment of coronavirus disease 2019 (COVID-19) around the world. LFA technology stands out amongst peer platforms due to its cost-effective design, user-friendly interface, and low sample-to-readout times. This article aims to introduce its design, use, and practicality for the purpose of diagnosing SARS-CoV-2 infection. A connection is made from the normal COVID-19 immune response to the design and efficacy of rapid testing. Interference in test results is a challenge shared by most diagnostic platforms and can be rooted in various underlying issues. The current knowledge and situation about interference in rapid COVID-19 tests due to variant strains as well as vaccination are discussed. The cost and societal impact are reviewed as they play important roles in determining how to properly implement public testing practices. Perspectives on improving the performance, especially detection sensitivity, of LFA for COVID-19 are provided.
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Affiliation(s)
- Alexander Biby
- Department of Chemistry, University of Central Florida, Orlando, FL 32816 USA
| | - Xiaochuan Wang
- School of Social Work, University of Central Florida, Orlando, FL 32816 USA
| | - Xinliang Liu
- School of Global Health Management & Informatics, University of Central Florida, Orlando, FL 32816 USA
| | - Olivia Roberson
- Department of Chemistry, University of Central Florida, Orlando, FL 32816 USA
| | - Allya Henry
- School of Social Work, University of Central Florida, Orlando, FL 32816 USA
| | - Xiaohu Xia
- Department of Chemistry, University of Central Florida, Orlando, FL 32816 USA
- NanoScience Technology Center, University of Central Florida, Orlando, FL 32816 USA
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18
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Chen H, Lin Y, Long YT, Minteer SD, Ying YL. Nanopore-based measurement of the interaction of P450cam monooxygenase and putidaredoxin at the single-molecule level. Faraday Discuss 2021; 233:295-302. [PMID: 34889330 DOI: 10.1039/d1fd00042j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protein-protein interactions occur in a wide range of biological processes and are of great significance to life function. Characterization of transient protein-protein interactions remains a significant barrier to our understanding of cellular processes. Nanopores provide unique nanoscale environments that accommodate single molecules from the surrounding bulk solution. This method permits label-free sensing at the single-molecule level with extremely high sensitivity. Herein, the interaction between a single P450cam monooxygenase and its redox partner putidaredoxin (Pdx) was monitored via transient ionic current by using functionalized glass nanopores. Results show that the volume of P450cam determines the blockage current while the interactions between the P450cam and Pdx give a long blockage duration. Our glass nanopore sensor with adjustable diameter could be applied for real-time sensing of protein-protein interactions between individual proteins with a wide range of molecular weight.
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Affiliation(s)
- Hui Chen
- Department of Chemistry, University of Utah, USA.
| | - Yao Lin
- Department of Chemistry, University of Utah, USA. .,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
| | | | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China. .,Chemistry and Biomedicine Innovation Center, Nanjing University, China
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19
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Targeting conserved N-glycosylation blocks SARS-CoV-2 variant infection in vitro. EBioMedicine 2021; 74:103712. [PMID: 34839261 PMCID: PMC8613501 DOI: 10.1016/j.ebiom.2021.103712] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 01/11/2023] Open
Abstract
Background Despite clinical success with anti-spike vaccines, the effectiveness of neutralizing antibodies and vaccines has been compromised by rapidly spreading SARS-CoV-2 variants. Viruses can hijack the glycosylation machinery of host cells to shield themselves from the host's immune response and attenuate antibody efficiency. However, it remains unclear if targeting glycosylation on viral spike protein can impair infectivity of SARS-CoV-2 and its variants. Methods We adopted flow cytometry, ELISA, and BioLayer interferometry approaches to assess binding of glycosylated or deglycosylated spike with ACE2. Viral entry was determined by luciferase, immunoblotting, and immunofluorescence assays. Genome-wide association study (GWAS) revealed a significant relationship between STT3A and COVID-19 severity. NF-κB/STT3A-regulated N-glycosylation was investigated by gene knockdown, chromatin immunoprecipitation, and promoter assay. We developed an antibody-drug conjugate (ADC) that couples non-neutralization anti-spike antibody with NGI-1 (4G10-ADC) to specifically target SARS-CoV-2-infected cells. Findings The receptor binding domain and three distinct SARS-CoV-2 surface N-glycosylation sites among 57,311 spike proteins retrieved from the NCBI-Virus-database are highly evolutionarily conserved (99.67%) and are involved in ACE2 interaction. STT3A is a key glycosyltransferase catalyzing spike glycosylation and is positively correlated with COVID-19 severity. We found that inhibiting STT3A using N-linked glycosylation inhibitor-1 (NGI-1) impaired SARS-CoV-2 infectivity and that of its variants [Alpha (B.1.1.7) and Beta (B.1.351)]. Most importantly, 4G10-ADC enters SARS-CoV-2-infected cells and NGI-1 is subsequently released to deglycosylate spike protein, thereby reinforcing the neutralizing abilities of antibodies, vaccines, or convalescent sera and reducing SARS-CoV-2 variant infectivity. Interpretation Our results indicate that targeting evolutionarily-conserved STT3A-mediated glycosylation via an ADC can exert profound impacts on SARS-CoV-2 variant infectivity. Thus, we have identified a novel deglycosylation method suitable for eradicating SARS-CoV-2 variant infection in vitro. Funding A full list of funding bodies that contributed to this study can be found in the Acknowledgements section
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20
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de O Araújo J, Pinheiro S, Zamora WJ, Alves CN, Lameira J, Lima AH. Structural, energetic and lipophilic analysis of SARS-CoV-2 non-structural protein 9 (NSP9). Sci Rep 2021; 11:23003. [PMID: 34837010 PMCID: PMC8626507 DOI: 10.1038/s41598-021-02366-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/08/2021] [Indexed: 12/02/2022] Open
Abstract
In SARS-CoV-2 replication complex, the Non-structural protein 9 (Nsp9) is an important RNA binding subunit in the RNA-synthesizing machinery. The dimeric forms of coronavirus Nsp9 increase their nucleic acid binding affinity and the N-finger motif appears to play a critical role in dimerization. Here, we present a structural, lipophilic and energetic study about the Nsp9 dimer of SARS-CoV-2 through computational methods that complement hydrophobicity scales of amino acids with molecular dynamics simulations. Additionally, we presented a virtual N-finger mutation to investigate whether this motif contributes to dimer stability. The results reveal for the native dimer that the N-finger contributes favorably through hydrogen bond interactions and two amino acids bellowing to the hydrophobic region, Leu45 and Leu106, are crucial in the formation of the cavity for potential drug binding. On the other hand, Gly100 and Gly104, are responsible for stabilizing the α-helices and making the dimer interface remain stable in both, native and mutant (without N-finger motif) systems. Besides, clustering results for the native dimer showed accessible cavities to drugs. In addition, the energetic and lipophilic analysis reveal that the higher binding energy in the native dimer can be deduced since it is more lipophilic than the mutant one, increasing non-polar interactions, which is in line with the result of MM-GBSA and SIE approaches where the van der Waals energy term has the greatest weight in the stability of the native dimer. Overall, we provide a detailed study on the Nsp9 dimer of SARS-CoV-2 that may aid in the development of new strategies for the treatment and prevention of COVID-19.
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Affiliation(s)
- Jéssica de O Araújo
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, 66075-110, Belém, Pará, Brasil
| | - Silvana Pinheiro
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, 66075-110, Belém, Pará, Brasil
| | - William J Zamora
- School of Chemistry & Faculty of Pharmacy, University of Costa Rica, San Pedro, San José, Costa Rica
- Advanced Computing Lab (CNCA), National High Technology Center (CeNAT-CONARE), Pavas, San José, Costa Rica
| | - Cláudio Nahum Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, 66075-110, Belém, Pará, Brasil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, 66075-110, Belém, Pará, Brasil
| | - Anderson H Lima
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, 66075-110, Belém, Pará, Brasil.
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21
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Wagner TR, Rothbauer U. Nanobodies - Little helpers unravelling intracellular signaling. Free Radic Biol Med 2021; 176:46-61. [PMID: 34536541 DOI: 10.1016/j.freeradbiomed.2021.09.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/26/2021] [Accepted: 09/08/2021] [Indexed: 11/21/2022]
Abstract
The identification of diagnostic and therapeutic targets requires a comprehensive understanding of cellular processes, for which advanced technologies in biomedical research are needed. The emergence of nanobodies (Nbs) derived from antibody fragments of camelid heavy chain-only antibodies as intracellular research tools offers new possibilities to study and modulate target antigens in living cells. Here we summarize this rapidly changing field, beginning with a brief introduction of Nbs, followed by an overview of how target-specific Nbs can be generated, and introduce the selection of intrabodies as research tools. Intrabodies, by definition, are intracellular functional Nbs that target ectopic or endogenous intracellular antigens within living cells. Such binders can be applied in various formats, e.g. as chromobodies for live cell microscopy or as biosensors to decipher complex intracellular signaling pathways. In addition, protein knockouts can be achieved by target-specific Nbs, while modulating Nbs have the potential as future therapeutics. The development of fine-tunable and switchable Nb-based systems that simultaneously provide spatial and temporal control has recently taken the application of these binders to the next level.
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Affiliation(s)
- Teresa R Wagner
- Pharmaceutical Biotechnology, Eberhard Karls University, Tübingen, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University, Tübingen, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany; Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University, Tübingen, Germany.
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22
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NIgPred: Class-Specific Antibody Prediction for Linear B-Cell Epitopes Based on Heterogeneous Features and Machine-Learning Approaches. Viruses 2021; 13:v13081531. [PMID: 34452396 PMCID: PMC8402714 DOI: 10.3390/v13081531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022] Open
Abstract
Upon invasion by foreign pathogens, specific antibodies can identify specific foreign antigens and disable them. As a result of this ability, antibodies can help with vaccine production and food allergen detection in patients. Many studies have focused on predicting linear B-cell epitopes, but only two prediction tools are currently available to predict the sub-type of an epitope. NIgPred was developed as a prediction tool for IgA, IgE, and IgG. NIgPred integrates various heterologous features with machine-learning approaches. Differently from previous studies, our study considered peptide-characteristic correlation and autocorrelation features. Sixty kinds of classifier were applied to construct the best prediction model. Furthermore, the genetic algorithm and hill-climbing algorithm were used to select the most suitable features for improving the accuracy and reducing the time complexity of the training model. NIgPred was found to be superior to the currently available tools for predicting IgE epitopes and IgG epitopes on independent test sets. Moreover, NIgPred achieved a prediction accuracy of 100% for the IgG epitopes of a coronavirus data set. NIgPred is publicly available at our website.
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23
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Mello MG, Westerhausen MT, Singh P, Doble PA, Wanagat J, Bishop DP. Assessing the reproducibility of labelled antibody binding in quantitative multiplexed immuno-mass spectrometry imaging. Anal Bioanal Chem 2021; 413:5509-5516. [PMID: 34304281 DOI: 10.1007/s00216-021-03536-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/09/2021] [Accepted: 07/08/2021] [Indexed: 11/27/2022]
Abstract
Immuno-mass spectrometry imaging (iMSI) uses laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) to determine the spatial expression of biomolecules in tissue sections following immunolabelling with antibodies conjugated to a metal reporter. As with all immunolabelling techniques, the binding efficiency of multiplexed staining can be affected by a number of factors including epitope blocking and other forms of steric hindrance. To date, the effects on the binding of metal-conjugated antibodies to their epitopes in a multiplexed analysis have yet to be quantitatively explored by iMSI. Here we describe a protocol to investigate the effects of multiplexing on reproducible binding using the muscle proteins, dystrophin, sarcospan, and myosin as a model, with antibodies conjugated with Maxpar® reagents before histological application to murine quadriceps sections using standard immunolabelling protocols and imaging with LA-ICP-MS. The antibodies were each individually applied to eight sections, and multiplexed to another eight sections. The average concentrations of the lanthanide analytes were determined, before statistical analyses found there was no significant difference between the individual and multiplexed application of the antibodies. These analyses provide a framework for ensuring reproducibility of antibody binding during multiplexed iMSI, which will allow quantitative exploration of protein-protein interactions and provide a greater understanding of fundamental biological processes during healthy and diseased states.
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Affiliation(s)
- Monique G Mello
- Atomic Medicine Initiative, Faculty of Science, University of Technology Sydney, P.O. Box 123, Broadway, Ultimo, NSW, 2007, Australia
| | - Mika T Westerhausen
- Atomic Medicine Initiative, Faculty of Science, University of Technology Sydney, P.O. Box 123, Broadway, Ultimo, NSW, 2007, Australia
| | - Prashina Singh
- Atomic Medicine Initiative, Faculty of Science, University of Technology Sydney, P.O. Box 123, Broadway, Ultimo, NSW, 2007, Australia
| | - Philip A Doble
- Atomic Medicine Initiative, Faculty of Science, University of Technology Sydney, P.O. Box 123, Broadway, Ultimo, NSW, 2007, Australia
| | - Jonathan Wanagat
- Division of Geriatrics, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA.
| | - David P Bishop
- Atomic Medicine Initiative, Faculty of Science, University of Technology Sydney, P.O. Box 123, Broadway, Ultimo, NSW, 2007, Australia.
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Cheung CHP, Xu J, Lee CL, Zhang Y, Wei R, Bierer D, Huang X, Li X. Construction of diverse peptide structural architectures via chemoselective peptide ligation. Chem Sci 2021; 12:7091-7097. [PMID: 34123337 PMCID: PMC8153220 DOI: 10.1039/d1sc01174j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/13/2021] [Indexed: 12/22/2022] Open
Abstract
Herein, we report the development of a facile synthetic strategy for constructing diverse peptide structural architectures via chemoselective peptide ligation. The key advancement involved is to utilize the benzofuran moiety as the peptide salicylaldehyde ester surrogate, and Dap-Ser/Lys-Ser dipeptide as the hydroxyl amino functionality, which could be successfully introduced at the side chain of peptides enabling peptide ligation. With this method, the side chain-to-side chain cyclic peptide, branched/bridged peptides, tailed cyclic peptides and multi-cyclic peptides have been designed and successfully synthesized with native peptidic linkages at the ligation sites. This strategy has provided an alternative strategic opportunity for synthetic peptide development. It also serves as an inspiration for the structural design of PPI inhibitors with new modalities.
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Affiliation(s)
- Carina Hey Pui Cheung
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Hong Kong
| | - Jianchao Xu
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Hong Kong
| | - Chi Lung Lee
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Hong Kong
| | - Yanfeng Zhang
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Hong Kong
| | - Ruohan Wei
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Hong Kong
| | - Donald Bierer
- Department of Medicinal Chemistry, Bayer AG Aprather Weg 18A 42096 Wuppertal Germany
| | - Xuhui Huang
- Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Xuechen Li
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Hong Kong
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25
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Gramlich M, Hays HCW, Crichton S, Kaiser PD, Heine A, Schneiderhan-Marra N, Rothbauer U, Stoll D, Maier S, Zeck A. HDX-MS for Epitope Characterization of a Therapeutic ANTIBODY Candidate on the Calcium-Binding Protein Annexin-A1. Antibodies (Basel) 2021; 10:11. [PMID: 33808657 PMCID: PMC8006148 DOI: 10.3390/antib10010011] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/15/2021] [Accepted: 03/02/2021] [Indexed: 12/25/2022] Open
Abstract
Annexin-A1 (ANXA1) belongs to a class of highly homologous Ca2+-dependent phospholipid-binding proteins. Its structure consists of a core region composed of four homologous repeats arranged in a compact, hydrolysis-resistant structure and an N-terminal region with a Ca2+-dependent conformation. ANXA1 is involved in several processes, including cell proliferation, apoptosis, metastasis, and the inflammatory response. Therefore, the development of antibodies blocking selected regions on ANXA1 holds great potential for the development of novel therapeutics treating inflammatory and cancer diseases. Here, we report the interaction site between an ANXA1-specific antibody known to inhibit T cell activation without adverse cytotoxic effects and ANXA1 using amide hydrogen-deuterium exchange mass spectrometry (HDX-MS). For the epitope determination, we applied two bottom-up HDX-MS approaches with pepsin digestion in solution and immobilized on beads. Both strategies revealed the interaction region within domain III of ANXA1 in Ca2+-bound conformation. The antibody-binding region correlates with the hydrophobic binding pocket of the N-terminal domain formed in the absence of calcium. This study demonstrates that even cryptic and flexible binding regions can be studied by HDX-MS, allowing a fast and efficient determination of the binding sites of antibodies which will help to define a mode of action profile for their use in therapy.
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Affiliation(s)
- Marius Gramlich
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
| | - Henry C. W. Hays
- Medannex Ltd., 1 Lochrin Square, Fountainbridge, Edinburgh EH3 9QA, UK; (H.C.W.H.); (S.C.)
| | - Scott Crichton
- Medannex Ltd., 1 Lochrin Square, Fountainbridge, Edinburgh EH3 9QA, UK; (H.C.W.H.); (S.C.)
| | - Philipp D. Kaiser
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
| | - Anne Heine
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
| | - Nicole Schneiderhan-Marra
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
| | - Ulrich Rothbauer
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Geschwister-Scholl-Platz, 72074 Tuebingen, Germany
| | - Dieter Stoll
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
- Department of Life Sciences, University of Applied Sciences Albstadt-Sigmaringen, Anton-Guentherstr. 51, 72488 Sigmaringen, Germany
| | - Sandra Maier
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
| | - Anne Zeck
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
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26
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Taherinia D, Mahmoodi MM, Fattahi A. Theoretical investigation of the effect of hydrogen bonding on the stereoselectivity of the Diels–Alder reaction. NEW J CHEM 2021. [DOI: 10.1039/d1nj01373d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here, we report the computational prediction of high exo selectivities in a series of Diels–Alder reactions with H-bonding interaction.
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Affiliation(s)
- Davood Taherinia
- Department of Chemistry, Sharif University of Technology, Tehran 11155-9516, Iran
| | - M. Mohsen Mahmoodi
- Department of Chemistry, Sharif University of Technology, Tehran 11155-9516, Iran
| | - Alireza Fattahi
- Department of Chemistry, Sharif University of Technology, Tehran 11155-9516, Iran
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27
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Scheepers MRW, Haenen SRR, Coers JM, van IJzendoorn LJ, Prins MWJ. Inter-particle biomolecular reactivity tuned by surface crowders. NANOSCALE 2020; 12:14605-14614. [PMID: 32614022 DOI: 10.1039/d0nr03125a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The rate at which colloidal particles can form biomolecular bonds controls the kinetics of applications such as particle-based biosensing, targeted drug delivery and directed colloidal assembly. Here we study how the reactivity of the particle surface depends on its molecular composition, quantified by the inter-particle rate of aggregation in an optomagnetic cluster experiment. Particles were functionalized with DNA or with proteins for specific binding, and with polyethylene glycol as a passive surface crowder. The data show that the inter-particle binding kinetics are dominated by specific interactions, which surprisingly can be tuned by the passive crowder molecules for both the DNA and the protein system. The experimental results are interpreted using model simulations, which show that the crowder-induced decrease of the particle surface reactivity can be described as a reduced reactivity of the specific binder molecules on the particle surface.
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Affiliation(s)
- M R W Scheepers
- Eindhoven University of Technology, Department of Applied Physics, PO Box 513, 5600 MB Eindhoven, The Netherlands
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28
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Dagbay KB, Treece E, Streich FC, Jackson JW, Faucette RR, Nikiforov A, Lin SC, Boston CJ, Nicholls SB, Capili AD, Carven GJ. Structural basis of specific inhibition of extracellular activation of pro- or latent myostatin by the monoclonal antibody SRK-015. J Biol Chem 2020; 295:5404-5418. [PMID: 32075906 PMCID: PMC7170532 DOI: 10.1074/jbc.ra119.012293] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/05/2020] [Indexed: 12/27/2022] Open
Abstract
Myostatin (or growth/differentiation factor 8 (GDF8)) is a member of the transforming growth factor β superfamily of growth factors and negatively regulates skeletal muscle growth. Its dysregulation is implicated in muscle wasting diseases. SRK-015 is a clinical-stage mAb that prevents extracellular proteolytic activation of pro- and latent myostatin. Here we used integrated structural and biochemical approaches to elucidate the molecular mechanism of antibody-mediated neutralization of pro-myostatin activation. The crystal structure of pro-myostatin in complex with 29H4-16 Fab, a high-affinity variant of SRK-015, at 2.79 Å resolution revealed that the antibody binds to a conformational epitope in the arm region of the prodomain distant from the proteolytic cleavage sites. This epitope is highly sequence-divergent, having only limited similarity to other closely related members of the transforming growth factor β superfamily. Hydrogen/deuterium exchange MS experiments indicated that antibody binding induces conformational changes in pro- and latent myostatin that span the arm region, the loops contiguous to the protease cleavage sites, and the latency-associated structural elements. Moreover, negative-stain EM with full-length antibodies disclosed a stable, ring-like antigen-antibody structure in which the two Fab arms of a single antibody occupy the two arm regions of the prodomain in the pro- and latent myostatin homodimers, suggesting a 1:1 (antibody:myostatin homodimer) binding stoichiometry. These results suggest that SRK-015 binding stabilizes the latent conformation and limits the accessibility of protease cleavage sites within the prodomain. These findings shed light on approaches that specifically block the extracellular activation of growth factors by targeting their precursor forms.
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Affiliation(s)
| | - Erin Treece
- Scholar Rock Inc., Cambridge, Massachusetts 02139
| | | | | | | | | | - Susan C Lin
- Scholar Rock Inc., Cambridge, Massachusetts 02139
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29
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Trofimov AV, Sokolov AV, Rak AY, Ischenko AM, Kudling TV, Vakhrushev AV, Gorbunov AA. Epitope specificity of two anti-morphine monoclonal antibodies: In vitro and in silico studies. J Mol Recognit 2020; 33:e2846. [PMID: 32219918 DOI: 10.1002/jmr.2845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/18/2020] [Accepted: 03/06/2020] [Indexed: 11/06/2022]
Abstract
Monoclonal antibodies (mAbs) against morphine are important in the development of immunotherapeutic and diagnostic methods for the treatment and prevention of drug addiction. By the surface plasmon resonance (SPR) and enzyme immunoassay techniques, we characterized two previously obtained mAbs 3K11 and 6G1 and showed their ability to recognize free morphine and morphine-containing antigens in different ways because of the epitope specificity thereof. Using the defined amino acid sequences, we obtained three-dimensional models of the variable regions of Fab fragments of these antibodies and compared them with the known sequence and spatial structure of the anti-morphine antibody 9B1. Docking simulations are performed to obtain models of the antibodies complexes with morphine. Differences in the models of 3K11 and 6G1 complexes with morphine correlate with their experimentally detected epitope specificity. The results, in particular, can be used for the structure-based design of the corresponding humanized antibodies. According to our modeling and docking results, the very different modes of morphine binding to mAbs 3K11 and 6G1 are qualitatively similar to those previously reported for cocaine and two anti-cocaine antibodies. Thus, the obtained structural information brings more insight into the hapten recognition diversity.
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Affiliation(s)
- Alexander V Trofimov
- Laboratory of Protein Biochemistry, Institute for Highly Pure Biopreparations, St. Petersburg, Russian Federation
| | - Alexey V Sokolov
- Department of Molecular Genetics, Institute of Experimental Medicine, St. Petersburg, Russian Federation
| | - Alexandra Y Rak
- Laboratory of Protein Biochemistry, Institute for Highly Pure Biopreparations, St. Petersburg, Russian Federation
| | - Alexander M Ischenko
- Laboratory of Protein Biochemistry, Institute for Highly Pure Biopreparations, St. Petersburg, Russian Federation
| | - Tatiana V Kudling
- Laboratory of Protein Biochemistry, Institute for Highly Pure Biopreparations, St. Petersburg, Russian Federation
| | - Andrey V Vakhrushev
- Laboratory of Protein Biochemistry, Institute for Highly Pure Biopreparations, St. Petersburg, Russian Federation
| | - Alexei A Gorbunov
- Laboratory of Protein Biochemistry, Institute for Highly Pure Biopreparations, St. Petersburg, Russian Federation
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30
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Broadly Protective Multivalent OspA Vaccine against Lyme Borreliosis, Developed Based on Surface Shaping of the C-Terminal Fragment. Infect Immun 2020; 88:IAI.00917-19. [PMID: 31932330 DOI: 10.1128/iai.00917-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 12/22/2019] [Indexed: 12/14/2022] Open
Abstract
The development of vaccines for prevention of diseases caused by pathogenic species can encounter major obstacles if high sequence diversity is observed between individual strains. Therefore, development might be restricted either to conserved antigens, which are often rare, or to multivalent vaccines, which renders the production more costly and cumbersome. In light of this complexity, we applied a structure-based surface shaping approach for the development of a Lyme borreliosis (LB) vaccine suitable for the United States and Europe. The surface of the C-terminal fragment of outer surface protein A (OspA) was divided into distinct regions, based primarily on binding sites of monoclonal antibodies (MAbs). In order to target the six clinically most relevant OspA serotypes (ST) in a single protein, exposed amino acids of the individual regions were exchanged to corresponding amino acids of a chosen OspA serotype. Six chimeric proteins were constructed, and, based on their immunogenicity, four of these chimeras were tested in mouse challenge models. Significant protection could be demonstrated for all four proteins following challenge with infected ticks (OspA ST1, OspA ST2, and OspA ST4) or with in vitro-grown spirochetes (OspA ST1 and OspA ST5). Two of the chimeric proteins were linked to form a fusion protein, which provided significant protection against in vitro-grown spirochetes (OspA ST1) and infected ticks (OspA ST2). This article presents the proof-of-concept study for a multivalent OspA vaccine targeting a wide range of pathogenic LB Borrelia species with a single recombinant antigen for prevention of Lyme borreliosis.
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31
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Zhang D, Liang P, Yu Z, Xia J, Ni D, Wang D, Zhou Y, Cao Y, Chen J, Chen J, Jin S. Self-assembled "bridge" substance for organochlorine pesticides detection in solution based on Surface Enhanced Raman Scattering. JOURNAL OF HAZARDOUS MATERIALS 2020; 382:121023. [PMID: 31476717 DOI: 10.1016/j.jhazmat.2019.121023] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 05/29/2023]
Abstract
Pesticide residues pose a great threat to human health, and it is an urgent matter to realize fast and accurate detection of pesticide. SERS (Surface Enhanced Raman Scattering), as a nondestructive detection technology, performs a prominent role in fast detection field due to the strong surface plasmon resonance from short range effect between analyte and nanoparticle. Therefore, in order to solve the incompatibility between organochlorine pesticides molecules and noble metal nanoparticles, this paper proposed a concept of "bridge" substances acting as an interconnect function role to achieve a binding model (object-binder-metal (OBM)) and developed a droplet concentration method to enhance Raman signals. Both combination mode of pesticide molecules to bridge molecules and energy transfer of SERS experiment may relate to the compound ring according to the changes of peaks based on surface plasmon resonance. The selectivity and stability of different bridge substances interacting with pesticides molecules were illumined via binding energy of these two substances obtained by DFT calculations. A droplet can capture nanoparticles and analytes, which is conducive to SERS performance. Chloride ions in the solution contribute to rearrangement of nanoparticles and can validly promote surface activation of Ag nanoparticles to improve energy transfer efficiency of plasma resonance, resulting in superior SERS effect.
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Affiliation(s)
- De Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, China
| | - Pei Liang
- College of Optical and Electronic Technology, China Jiliang University, 310018, Hangzhou, China.
| | - Zhi Yu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, China.
| | - Jing Xia
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, China
| | - Dejiang Ni
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, China
| | - Dan Wang
- College of Optical and Electronic Technology, China Jiliang University, 310018, Hangzhou, China
| | - Yongfeng Zhou
- College of Optical and Electronic Technology, China Jiliang University, 310018, Hangzhou, China
| | - Yu Cao
- College of Optical and Electronic Technology, China Jiliang University, 310018, Hangzhou, China
| | - Jie Chen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, China
| | - Jinlei Chen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, China
| | - Shangzhong Jin
- College of Optical and Electronic Technology, China Jiliang University, 310018, Hangzhou, China
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32
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Wen Z, Kim W, Yoo SJ, Chae CG, Seo HB, Bak IG, Changez M, Lee JS. Highly ordered supramolecular structure built from poly(4-(4-vinylphenylpyridine)) and 1,1′-ferrocenedicarboxylic acid via hydrogen bonding. Polym Chem 2020. [DOI: 10.1039/d0py00066c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A molecular-level ordered supramolecular nanostructure is formed of P4VPPy and FDA, using a solvent vapor thermal annealing process that initiates hydrogen bonding directed self-assembly.
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Affiliation(s)
- Zuwang Wen
- School of Materials Science and Engineering
- Gwangju Institute of Science and Technology (GIST)
- Gwangju 61005
- Republic of Korea
| | - Wonbin Kim
- School of Materials Science and Engineering
- Gwangju Institute of Science and Technology (GIST)
- Gwangju 61005
- Republic of Korea
| | - Seung Jo Yoo
- Electron Microscopy Research Center
- Korea Basic Science Institute (KBSI)
- Daejeon 34133
- Republic of Korea
- Department of Materials Science and Engineering
| | - Chang-Geun Chae
- School of Materials Science and Engineering
- Gwangju Institute of Science and Technology (GIST)
- Gwangju 61005
- Republic of Korea
| | - Ho-Bin Seo
- School of Materials Science and Engineering
- Gwangju Institute of Science and Technology (GIST)
- Gwangju 61005
- Republic of Korea
| | - In-Gyu Bak
- School of Materials Science and Engineering
- Gwangju Institute of Science and Technology (GIST)
- Gwangju 61005
- Republic of Korea
| | - Mohammad Changez
- School of Materials Science and Engineering
- Gwangju Institute of Science and Technology (GIST)
- Gwangju 61005
- Republic of Korea
- Department of Basic Sciences
| | - Jae-Suk Lee
- School of Materials Science and Engineering
- Gwangju Institute of Science and Technology (GIST)
- Gwangju 61005
- Republic of Korea
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33
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Chiu ML, Goulet DR, Teplyakov A, Gilliland GL. Antibody Structure and Function: The Basis for Engineering Therapeutics. Antibodies (Basel) 2019; 8:antib8040055. [PMID: 31816964 PMCID: PMC6963682 DOI: 10.3390/antib8040055] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/25/2019] [Accepted: 11/28/2019] [Indexed: 12/11/2022] Open
Abstract
Antibodies and antibody-derived macromolecules have established themselves as the mainstay in protein-based therapeutic molecules (biologics). Our knowledge of the structure–function relationships of antibodies provides a platform for protein engineering that has been exploited to generate a wide range of biologics for a host of therapeutic indications. In this review, our basic understanding of the antibody structure is described along with how that knowledge has leveraged the engineering of antibody and antibody-related therapeutics having the appropriate antigen affinity, effector function, and biophysical properties. The platforms examined include the development of antibodies, antibody fragments, bispecific antibody, and antibody fusion products, whose efficacy and manufacturability can be improved via humanization, affinity modulation, and stability enhancement. We also review the design and selection of binding arms, and avidity modulation. Different strategies of preparing bispecific and multispecific molecules for an array of therapeutic applications are included.
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Affiliation(s)
- Mark L. Chiu
- Drug Product Development Science, Janssen Research & Development, LLC, Malvern, PA 19355, USA
- Correspondence:
| | - Dennis R. Goulet
- Department of Medicinal Chemistry, University of Washington, P.O. Box 357610, Seattle, WA 98195-7610, USA;
| | - Alexey Teplyakov
- Biologics Research, Janssen Research & Development, LLC, Spring House, PA 19477, USA; (A.T.); (G.L.G.)
| | - Gary L. Gilliland
- Biologics Research, Janssen Research & Development, LLC, Spring House, PA 19477, USA; (A.T.); (G.L.G.)
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34
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Crystal structure and receptor-interacting residues of MYDGF - a protein mediating ischemic tissue repair. Nat Commun 2019; 10:5379. [PMID: 31772377 PMCID: PMC6879528 DOI: 10.1038/s41467-019-13343-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/04/2019] [Indexed: 12/14/2022] Open
Abstract
Myeloid-derived growth factor (MYDGF) is a paracrine-acting protein that is produced by bone marrow-derived monocytes and macrophages to protect and repair the heart after myocardial infarction (MI). This effect can be used for the development of protein-based therapies for ischemic tissue repair, also beyond the sole application in heart tissue. Here, we report the X-ray structure of MYDGF and identify its functionally relevant receptor binding epitope. MYDGF consists of a 10-stranded β-sandwich with a folding topology showing no similarities to other cytokines or growth factors. By characterizing the epitope of a neutralizing antibody and utilizing functional assays to study the activity of surface patch-mutations, we were able to localize the receptor interaction interface to a region around two surface tyrosine residues 71 and 73 and an adjacent prominent loop structure of residues 97–101. These findings enable structure-guided protein engineering to develop modified MYDGF variants with potentially improved properties for clinical use. Myeloid-derived growth factor (MYDGF) is an angiogenic growth factor with therapeutic potential for ischemic tissue repair and the receptor is still unknown. Here the authors present the crystal structure of human MYDGF and identify its functional epitope through mutagenesis studies.
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35
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Zhang H, Miller BL. Immunosensor-based label-free and multiplex detection of influenza viruses: State of the art. Biosens Bioelectron 2019; 141:111476. [PMID: 31272058 PMCID: PMC6717022 DOI: 10.1016/j.bios.2019.111476] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/18/2019] [Accepted: 06/24/2019] [Indexed: 12/20/2022]
Abstract
The ability of influenza viruses to rapidly evolve has caused significant challenges in viral surveillance, diagnosis, and therapeutic development. Molecular sequencing methods, though powerful tools for monitoring influenza evolution at the genetic level, are not able to fully characterize the antigenic properties of influenza viruses. Understanding influenza virus antigenicity is critical to vaccine development and disease prevention. Traditional immunoassays which have been widely used for evaluating influenza antigenicity have limited throughput. To alleviate these problems, new bioanalytical tools to investigate influenza antigenicity by measuring antibody-antigen binding are an active area of research. Herein, we review immunosensor technologies from the aspects of various sensing principles, while highlighting recent developments in multiplex, label-free detection strategies. Highlighted technologies include electrochemical immunosensors relying on impedimetric detection; these demonstrate simple design and cost effectiveness for mass production. Antibody arrays implemented on an optical interferometric sensor system allow systematic characterization of influenza antigenicity. Quartz microbalance immunosensors are highly sensitive but have yet to be explored for multiplex sensing. Immunosensors made on lateral flow strips have shown promise in rapid diagnosis of influenza subtypes. We anticipate that these and other technologies discussed in the review will facilitate advances in the study of influenza, and other viral pathogens.
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Affiliation(s)
- Hanyuan Zhang
- Department of Dermatology, University of Rochester Medical Center, 601 Elmwood Avenue Box 697, Rochester, NY, 14642, USA; Materials Science Program, University of Rochester, 500 Joseph C. Wilson Blvd. Box 270216, Rochester, NY, 14627, USA
| | - Benjamin L Miller
- Department of Dermatology, University of Rochester Medical Center, 601 Elmwood Avenue Box 697, Rochester, NY, 14642, USA; Materials Science Program, University of Rochester, 500 Joseph C. Wilson Blvd. Box 270216, Rochester, NY, 14627, USA.
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36
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Heat and Chemical Treatments Affect the Viability, Morphology, and Physiology of Staphylococcus aureus and Its Subsequent Antibody Labeling for Flow Cytometric Analysis. Appl Environ Microbiol 2019; 85:AEM.01006-19. [PMID: 31253681 DOI: 10.1128/aem.01006-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 06/21/2019] [Indexed: 11/20/2022] Open
Abstract
The effects of heat and chemical treatments on Staphylococcus aureus viability and physiology and their subsequent effects on antibody binding ability and cell morphology were measured. Treatments included lethal and sublethal heat; exposure to organic acids, salt, and sodium hydroxide; and freeze-thawing. Strain-related differences in viability were noted depending on treatment and were reflected in changes in physiology as monitored by flow cytometry (FCM) using three different staining protocols: SYTO 9/propidium iodide (PI), DiOC2(3), or calcein acetoxymethyl ester (calcein-AM)/PI. Treatments that resulted in significant losses in viability as measured by plate counting were reflected better by the first two staining combinations, as intracellular calcein-AM uptake may have been impaired by certain treatments. FCM analysis using labeling by commercial anti-S. aureus antibodies indicated that differences in cell physiology as a result of treatments influenced immunofluorescence detection. The ratio of the mean fluorescence intensities of stained cells to those of unstained cells [MFI/MFI(us)] varied with treatment, five of these treatments, including freeze-thaw, citric acid, oxalic acid, NaCl, and NaOH treatments, resulted in significantly lower fluorescence values compared to controls.IMPORTANCE FCM data indicated that cells conventionally considered to be dead and which would not give rise to CFU in a plate count assay, e.g., cells heated to 80°C, were labeled by antibody staining. This finding suggests that without the inclusion of a live/dead discriminating dye, these cells would be erroneously detected as viable within an FCM assay. Reductions in antibody staining due to physicochemical treatment were strain related, reflecting the complexity of the phenomenon under study and illustrating that substantial validation of any new antibody detection-based method, including physiological staining and cell sorting, should be undertaken. Researchers should be aware of physicochemical treatments causing false-negative results: in this study, freeze-thawing severely reduced antibody binding without affecting the viability of a substantial percentage of cells. Scanning electron microscopy carried out on treated cells revealed a range of morphological changes resulting from physicochemical treatments which may have hindered antibody binding.
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Rapid isolation of a potent human antibody against H7N9 influenza virus from an infected patient. Antiviral Res 2019; 170:104564. [PMID: 31336147 DOI: 10.1016/j.antiviral.2019.104564] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 07/16/2019] [Accepted: 07/19/2019] [Indexed: 11/23/2022]
Abstract
Influenza virus A H7N9 remains a serious threat to public health due to the lack of effective vaccines and drugs. In this study, a neutralizing human antibody named 3L11 was rapidly isolated from the switched memory B cells of a patient infected with H7N9. The antibody 3L11 was encoded by the heavy-chain VH1-8 gene and the light-chain VL2-13 gene that had undergone somatic mutations, and conferred high affinity binding to H7N9 hemagglutinins (HAs). It promoted killing of infected cells by antibody-dependent cell-mediated cytotoxicity (ADCC). Epitope mapping by mass spectroscopy (MS) indicated that 3L11 bound to the peptide 149-175 of HAs that contained the 150-loop of the receptor-binding site (RBS). Additionally, the 3L11 escape strains had G151R (Gly151→Arg151) and S152P (Ser152→Pro152) mutations within a conserved antigenic site A near the RBS that were not observed in field strains. Importantly, 3L11 fully protected mice against a lethal H7N9 virus challenge, in both pre- and postexposure administration regimens. Altogether, this work demonstrates the feasibility of rapid isolation of neutralizing H7N9 antibodies from infected patients and provides a potential prophylactic and therapeutic agent against H7N9 viruses.
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Puchades C, Kűkrer B, Diefenbach O, Sneekes-Vriese E, Juraszek J, Koudstaal W, Apetri A. Epitope mapping of diverse influenza Hemagglutinin drug candidates using HDX-MS. Sci Rep 2019; 9:4735. [PMID: 30894620 PMCID: PMC6427009 DOI: 10.1038/s41598-019-41179-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/27/2019] [Indexed: 01/22/2023] Open
Abstract
Epitope characterization is critical for elucidating the mechanism of action of drug candidates. However, traditional high-resolution epitope mapping techniques are not well suited for screening numerous drug candidates recognizing a similar target. Here, we use Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) to explore the conformational impact of diverse drug molecules binding on Hemagglutinin (HA), the major surface antigen of influenza viruses. We optimized a semi-automated HDX-MS workflow to systematically probe distantly related HA subtypes in complex with 4 different drug candidates, ranging from a monoclonal antibody to a small synthetic peptide. This fast, cost-effective HDX-MS epitope mapping approach accurately determined the main antigenic site in all cases. Moreover, our studies reveal distinct changes in the local conformational dynamics of HA associated to the molecular mechanism of neutralization, establishing a marker for broad anti-HA activity. Taken together, these findings highlight the potential for HDX-MS epitope mapping-based screening to identify promising candidates against HA at early stages of drug discovery.
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Affiliation(s)
- Cristina Puchades
- Janssen Vaccines and Prevention, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN, Leiden, The Netherlands
| | - Başak Kűkrer
- Janssen Vaccines and Prevention, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN, Leiden, The Netherlands
| | - Otto Diefenbach
- Janssen Vaccines and Prevention, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN, Leiden, The Netherlands
| | - Eveline Sneekes-Vriese
- Janssen Vaccines and Prevention, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN, Leiden, The Netherlands
| | - Jarek Juraszek
- Janssen Vaccines and Prevention, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN, Leiden, The Netherlands
| | - Wouter Koudstaal
- Janssen Vaccines and Prevention, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN, Leiden, The Netherlands
| | - Adrian Apetri
- Janssen Vaccines and Prevention, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN, Leiden, The Netherlands.
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Abstract
Background:
B-cell epitope prediction is an essential tool for a variety of
immunological studies. For identifying such epitopes, several computational predictors have been
proposed in the past 10 years.
Objective:
In this review, we summarized the representative computational approaches developed
for the identification of linear B-cell epitopes.
</P><P>
Methods: We mainly discuss the datasets, feature extraction methods and classification methods
used in the previous work.
Results:
The performance of the existing methods was not very satisfying, and so more effective
approaches should be proposed by considering the structural information of proteins.
Conclusion:
We consider existing challenges and future perspectives for developing reliable
methods for predicting linear B-cell epitopes.
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Affiliation(s)
- Cangzhi Jia
- School of Science, Dalian Maritime University, No. 1 Linghai Road, Dalian 116026, China
| | - Hongyan Gong
- School of Science, Dalian Maritime University, No. 1 Linghai Road, Dalian 116026, China
| | - Yan Zhu
- School of Science, Dalian Maritime University, No. 1 Linghai Road, Dalian 116026, China
| | - Yixia Shi
- Department of Mathematics and Statistics, Lingnan Normal University, Zhanjiang, China
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40
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Li C, Wang Y, Liu T, Niklasch M, Qiao K, Durand S, Chen L, Liang M, Baumert TF, Tong S, Nassal M, Wen YM, Wang YX. An E. coli-produced single-chain variable fragment (scFv) targeting hepatitis B virus surface protein potently inhibited virion secretion. Antiviral Res 2019; 162:118-129. [DOI: 10.1016/j.antiviral.2018.12.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 12/06/2018] [Accepted: 12/28/2018] [Indexed: 01/14/2023]
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Wolf Pérez AM, Sormanni P, Andersen JS, Sakhnini LI, Rodriguez-Leon I, Bjelke JR, Gajhede AJ, De Maria L, Otzen DE, Vendruscolo M, Lorenzen N. In vitro and in silico assessment of the developability of a designed monoclonal antibody library. MAbs 2019; 11:388-400. [PMID: 30523762 DOI: 10.1080/19420862.2018.1556082] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Despite major advances in antibody discovery technologies, the successful development of monoclonal antibodies (mAbs) into effective therapeutic and diagnostic agents can often be impeded by developability liabilities, such as poor expression, low solubility, high viscosity and aggregation. Therefore, strategies to predict at the early phases of antibody development the risk of late-stage failure of antibody candidates are highly valuable. In this work, we employ the in silico solubility predictor CamSol to design a library of 17 variants of a humanized mAb predicted to span a broad range of solubility values, and we examine their developability potential with a battery of commonly used in vitro and in silico assays. Our results demonstrate the ability of CamSol to rationally enhance mAb developability, and provide a quantitative comparison of in vitro developability measurements with each other and with more resource-intensive solubility measurements, as well as with in silico predictors that offer a potentially faster and cheaper alternative. We observed a strong correlation between predicted and experimentally determined solubility values, as well as with measurements obtained using a panel of in vitro developability assays that probe non-specific interactions. These results indicate that computational methods have the potential to reduce or eliminate the need of carrying out laborious in vitro quality controls for large numbers of lead candidates. Overall, our study provides support to the emerging view that the implementation of in silico tools in antibody discovery campaigns can ensure rapid and early selection of antibodies with optimal developability potential.
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Affiliation(s)
- Adriana-Michelle Wolf Pérez
- a Large Protein Biophysics , Novo Nordisk A/S , Måløv , Denmark.,b iNANO , Aarhus University , Aarhus C , Denmark
| | - Pietro Sormanni
- c Centre for Misfolding Diseases, Department of Chemistry , University of Cambridge , Cambridge , UK
| | | | | | | | | | | | | | | | - Michele Vendruscolo
- c Centre for Misfolding Diseases, Department of Chemistry , University of Cambridge , Cambridge , UK
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Blanco Y, de Diego-Castilla G, Viúdez-Moreiras D, Cavalcante-Silva E, Rodríguez-Manfredi JA, Davila AF, McKay CP, Parro V. Effects of Gamma and Electron Radiation on the Structural Integrity of Organic Molecules and Macromolecular Biomarkers Measured by Microarray Immunoassays and Their Astrobiological Implications. ASTROBIOLOGY 2018; 18:1497-1516. [PMID: 30070898 PMCID: PMC6276817 DOI: 10.1089/ast.2016.1645] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 04/10/2018] [Indexed: 05/20/2023]
Abstract
High-energy ionizing radiation in the form of solar energetic particles and galactic cosmic rays is pervasive on the surface of planetary bodies with thin atmospheres or in space facilities for humans, and it may seriously affect the chemistry and the structure of organic and biological material. We used fluorescent microarray immunoassays to assess how different doses of electron and gamma radiations affect the stability of target compounds such as biological polymers and small molecules (haptens) conjugated to large proteins. The radiation effect was monitored by measuring the loss in the immunoidentification of the target due to an impaired ability of the antibodies for binding their corresponding irradiated and damaged epitopes (the part of the target molecule to which antibodies bind). Exposure to electron radiation alone was more damaging at low doses (1 kGy) than exposure to gamma radiation alone, but this effect was reversed at the highest radiation dose (500 kGy). Differences in the dose-effect immunoidentification patterns suggested that the amount (dose) and not the type of radiation was the main factor for the cumulative damage on the majority of the assayed molecules. Molecules irradiated with both types of radiation showed a response similar to that of the individual treatments at increasing radiation doses, although the pattern obtained with electrons only was the most similar. The calculated radiolysis constant did not show a unique pattern; it rather suggested a different behavior perhaps associated with the unique structure of each molecule. Although not strictly comparable with extraterrestrial conditions because the irradiations were performed under air and at room temperature, our results may contribute to understanding the effects of ionizing radiation on complex molecules and the search for biomarkers through bioaffinity-based systems in planetary exploration.
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Affiliation(s)
- Yolanda Blanco
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, Madrid, Spain
| | - Graciela de Diego-Castilla
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, Madrid, Spain
| | - Daniel Viúdez-Moreiras
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, Madrid, Spain
| | - Erika Cavalcante-Silva
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, Madrid, Spain
| | | | - Alfonso F. Davila
- Space Science Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Christopher P. McKay
- Space Science Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Victor Parro
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, Madrid, Spain
- Address correspondence to: Victor Parro, Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir km 4, Torrejón de Ardoz, Madrid 28850, Spain
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Yitzchaik S, Gutierrez R, Cuniberti G, Yerushalmi R. Diversification of Device Platforms by Molecular Layers: Hybrid Sensing Platforms, Monolayer Doping, and Modeling. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14103-14123. [PMID: 30253096 DOI: 10.1021/acs.langmuir.8b02369] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Inorganic materials such as semiconductors, oxides, and metals are ubiquitous in a wide range of device technologies owing to the outstanding robustness and mature processing technologies available for such materials. However, while the important contribution of inorganic materials to the advancement of device technologies has been well established for decades, organic-inorganic hybrid device systems, which merge molecular functionalities with inorganic platforms, represent a newer domain that is rapidly evolving at an increasing pace. Such devices benefit from the great versatility and flexibility of the organic building blocks merged with the robustness of the inorganic platforms. Given the overwhelming wealth of literature covering various approaches for modifying and using inorganic devices, this feature article selectively highlights some of the advances made in the context of the diversification of devices by surface chemistry. Particular attention is given to oxide-semiconductor systems and metallic surfaces modified with organic monolayers. The inorganic device components, such as semiconductors, metals, and oxides, are modified by organic monolayers, which may serve as either active, static, or sacrificial components. We portray research directions within the broader field of organic-inorganic hybrid device systems that can be viewed as specific examples of the potential of such hybrid device systems given their comprehensive capabilities of design and diversification. Monolayer doping techniques where sacrificial organic monolayers are introduced into semiconducting elements are reviewed as a specific case, together with associated requirements for nanosystems, devices, and sensors for controlling doping levels and doping profiles on the nanometric scale. Another series of examples of the flexibility provided by the marriage of organic functional monolayers and inorganic device components are represented by a new class of biosensors, where the organic layer functionality is exploited in a functioning device for sensing. Considerations for relying on oxide-terminated semiconductors rather than the pristine semiconductor material as a platform both for processing and sensing are discussed. Finally, we cover aspects related to the use of various theoretical and computational approaches to model organic-inorganic systems. The main objectives of the topics covered here are (i) to present the advances made in each respective domain and (ii) to provide a comprehensive view of the potential uses of organic monolayers and self-assembly processes in the rapidly evolving field of molecular-inorganic hybrid device platforms and processing methodologies. The directions highlighted here provide a perspective on a future, not yet fully realized, integrated approach where organic monolayers are combined with inorganic platforms in order to obtain versatile, robust, and flexible systems with enhanced capabilities.
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Affiliation(s)
- Shlomo Yitzchaik
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology , The Hebrew University of Jerusalem , Edmond J. Safra Campus , Givat Ram Jerusalem , 91904 Israel
| | | | | | - Roie Yerushalmi
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology , The Hebrew University of Jerusalem , Edmond J. Safra Campus , Givat Ram Jerusalem , 91904 Israel
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44
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Szlag VM, Rodriguez RS, He J, Hudson-Smith N, Kang H, Le N, Reineke TM, Haynes CL. Molecular Affinity Agents for Intrinsic Surface-Enhanced Raman Scattering (SERS) Sensors. ACS APPLIED MATERIALS & INTERFACES 2018; 10:31825-31844. [PMID: 30134102 DOI: 10.1021/acsami.8b10303] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Research at the interface of synthetic materials, biochemistry, and analytical techniques has enabled sensing platforms for applications across many research communities. Herein we review the materials used as affinity agents to create surface-enhanced Raman spectroscopy (SERS) sensors. Our scope includes those affinity agents (antibody, aptamer, small molecule, and polymer) that facilitate the intrinsic detection of targets relevant to biology, medicine, national security, environmental protection, and food safety. We begin with an overview of the analytical technique (SERS) and considerations for its application as a sensor. We subsequently describe four classes of affinity agents, giving a brief overview on affinity, production, attachment chemistry, and first uses with SERS. Additionally, we review the SERS features of the affinity agents, and the analytes detected by intrinsic SERS with that affinity agent class. We conclude with remarks on affinity agent selection for intrinsic SERS sensing platforms.
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Affiliation(s)
- Victoria M Szlag
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Rebeca S Rodriguez
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Jiayi He
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Natalie Hudson-Smith
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Hyunho Kang
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Ngoc Le
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Theresa M Reineke
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Christy L Haynes
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
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45
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Ono M, Horita S, Sato Y, Nomura Y, Iwata S, Nomura N. Structural basis for tumor necrosis factor blockade with the therapeutic antibody golimumab. Protein Sci 2018; 27:1038-1046. [PMID: 29575262 DOI: 10.1002/pro.3407] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/09/2018] [Accepted: 03/21/2018] [Indexed: 12/29/2022]
Abstract
Tumor necrosis factor α (TNFα) is a proinflammatory cytokine, and elevated levels of TNFα in serum are associated with various autoimmune diseases, including rheumatoid arthritis (RA), ankylosing spondylitis (AS), Crohn's disease (CD), psoriasis, and systemic lupus erythaematosus. TNFα performs its pleiotropic functions by binding to two structurally distinct transmembrane receptors, TNF receptor (TNFR) 1 and TNFR2. Antibody-based therapeutic strategies that block excessive TNFα signaling have been shown to be effective in suppressing such harmful inflammatory conditions. Golimumab (Simponi®) is an FDA-approved fully human monoclonal antibody targeting TNFα that has been widely used for the treatment of RA, AS, and CD. However, the structural basis underlying the inhibitory action of golimumab remains unclear. Here, we report the crystal structure of the Fv fragment of golimumab in complex with TNFα at a resolution of 2.73 Å. The resolved structure reveals that golimumab binds to a distinct epitope on TNFα that does not overlap with the binding residues of TNFR2. Golimumab exerts its inhibitory effect by preventing binding of TNFR1 and TNFR2 to TNFα by steric hindrance. Golimumab does not induce conformational changes in TNFα that could affect receptor binding. This mode of action is specific to golimumab among the four anti-TNFα therapeutic antibodies currently approved for clinical use.
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Affiliation(s)
- Masatsugu Ono
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Shoichiro Horita
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yumi Sato
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yayoi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.,RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Norimichi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
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Sanada H, Kobayashi K, Oyama K, Maru T, Nakanishi T, Umetsu M, Asano R, Kumagai I. Affinity maturation of humanized anti-epidermal growth factor receptor antibody using a modified phage-based open sandwich selection method. Sci Rep 2018; 8:5414. [PMID: 29615700 PMCID: PMC5882652 DOI: 10.1038/s41598-018-23796-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/21/2018] [Indexed: 11/09/2022] Open
Abstract
Affinity maturation is one of the cardinal strategies for improving antibody function using in vitro evolutionary methods; one such well-established method is phage display. To minimise gene deletion, we previously developed an open sandwich (OS) method wherein selection was performed using only phage-displaying VH fragments after mixing with soluble VL fragments. The decrease in anti-EGFR antibody 528 affinity through humanization was successfully recovered by selecting VH mutants using this OS method. However, the affinity was not similar to that of parental 528. For further affinity maturation, we aimed to isolate VL mutants that act in synergy with VH mutants. However, the OS method could not be applied for selecting VL fragments because the preparation of soluble VH fragments was hampered by their instability and insolubility. Therefore, we initially designed a modified OS method based on domain-swapping of VH fragments, from added soluble Fv fragments to phage-displaying VL fragments. Using this novel Fv-added OS selection method, we successfully isolated VL mutants, and one of the Fv comprising VH and VL mutants showed affinity almost equivalent to that of parental 528. This method is applicable for engineering other VL fragments for affinity maturation.
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Affiliation(s)
- Hideaki Sanada
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Kazuki Kobayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Kenji Oyama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Takamitsu Maru
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Takeshi Nakanishi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Ryutaro Asano
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan. .,Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, 184-8588, Japan.
| | - Izumi Kumagai
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan.
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Feng T, Chen F, Kang Y, Sun H, Liu H, Li D, Zhu F, Hou T. HawkRank: a new scoring function for protein-protein docking based on weighted energy terms. J Cheminform 2017; 9:66. [PMID: 29282565 PMCID: PMC5745212 DOI: 10.1186/s13321-017-0254-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/14/2017] [Indexed: 01/09/2023] Open
Abstract
Deciphering the structural determinants of protein–protein interactions (PPIs) is essential to gain a deep understanding of many important biological functions in the living cells. Computational approaches for the structural modeling of PPIs, such as protein–protein docking, are quite needed to complement existing experimental techniques. The reliability of a protein–protein docking method is dependent on the ability of the scoring function to accurately distinguish the near-native binding structures from a huge number of decoys. In this study, we developed HawkRank, a novel scoring function designed for the sampling stage of protein–protein docking by summing the contributions from several energy terms, including van der Waals potentials, electrostatic potentials and desolvation potentials. First, based on the solvation free energies predicted by the Generalized Born model for ~ 800 proteins, a SASA (solvent accessible surface area)-based solvation model was developed, which can give the aqueous solvation free energies for proteins by summing the contributions of 21 atom types. Then, the van der Waals potentials and electrostatic potentials based on the Amber ff14SB force field were computed. Finally, the HawkRank scoring function was derived by determining the most optimal weights for five energy terms based on the training set. Here, MSR (modified success rate), a novel protein–protein scoring quality index, was used to assess the performance of HawkRank and three other popular protein–protein scoring functions, including ZRANK, FireDock and dDFIRE. The results show that HawkRank outperformed the other three scoring functions according to the total number of hits and MSR. HawkRank is available at http://cadd.zju.edu.cn/programs/hawkrank.
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Affiliation(s)
- Ting Feng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Fu Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yu Kang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Huiyong Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Hui Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China. .,State Key Lab of CAD&CG, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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48
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Artificial antibody created by conformational reconstruction of the complementary-determining region on gold nanoparticles. Proc Natl Acad Sci U S A 2017; 115:E34-E43. [PMID: 29255034 PMCID: PMC5776806 DOI: 10.1073/pnas.1713526115] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mimicking protein-like specific interactions and functions has been a long-pursued goal in nanotechnology. The key challenge is to precisely organize nonfunctional surface groups on nanoparticles into specific 3D conformations to function in a concerted and orchestrated manner. Here, we develop a method to graft the complementary-determining regions of natural antibodies onto nanoparticles and reconstruct their “active” conformation to create nanoparticle-based artificial antibodies that recognize the corresponding antigens. Our work demonstrates that it is possible to create functions on nanoparticles by conformational engineering, namely tuning flexible surface groups into specific conformations. Our straightforward strategy could be used further to create other artificial antibodies for various applications and provides a new tool to understand the structure and folding of natural proteins. To impart biomedical functions to nanoparticles (NPs), the common approach is to conjugate functional groups onto NPs by dint of the functions of those groups per se. It is still beyond current reach to create protein-like specific interactions and functions on NPs by conformational engineering of nonfunctional groups on NPs. Here, we develop a conformational engineering method to create an NP-based artificial antibody, denoted “Goldbody,” through conformational reconstruction of the complementary-determining regions (CDRs) of natural antibodies on gold NPs (AuNPs). The seemingly insurmountable task of controlling the conformation of the CDR loops, which are flexible and nonfunctional in the free form, was accomplished unexpectedly in a simple way. Upon anchoring both terminals of the free CDR loops on AuNPs, we managed to reconstruct the “active” conformation of the CDR loops by tuning the span between the two terminals and, as a result, the original specificity was successfully reconstructed on the AuNPs. Two Goldbodies have been created by this strategy to specifically bind with hen egg white lysozyme and epidermal growth factor receptor, with apparent affinities several orders of magnitude stronger than that of the original natural antibodies. Our work demonstrates that it is possible to create protein-like functions on NPs in a protein-like way, namely by tuning flexible surface groups to the correct conformation. Given the apparent merits, including good stability, of Goldbodies, we anticipate that a category of Goldbodies could be created to target different antigens and thus used as substitutes for natural antibodies in various applications.
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Arts R, Ludwig SKJ, van Gerven BCB, Estirado EM, Milroy LG, Merkx M. Semisynthetic Bioluminescent Sensor Proteins for Direct Detection of Antibodies and Small Molecules in Solution. ACS Sens 2017; 2:1730-1736. [PMID: 29037030 PMCID: PMC5706068 DOI: 10.1021/acssensors.7b00695] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/17/2017] [Indexed: 01/07/2023]
Abstract
Single-step immunoassays that can be performed directly in solution are ideally suited for point-of-care diagnostics. Our group recently developed a new platform of bioluminescent sensor proteins (LUMABS; LUMinescent AntiBody Sensor) that allow antibody detection in blood plasma. Thus far, LUMABS has been limited to the detection of antibodies recognizing natural peptide epitopes. Here, we report the development of semisynthetic LUMABS sensors that recognize nonpeptide epitopes. The non-natural amino acid para-azidophenylalanine was introduced at the position of the original antibody-recognition sites as a chemical handle to enable site-specific conjugation of synthetic epitope molecules coupled to a dibenzocylcooctyne moiety via strain-promoted click chemistry. The approach was successfully demonstrated by developing semisynthetic LUMABS sensors for antibodies targeting the small molecules dinitrophenol and creatinine (DNP-LUMABS and CR-LUMABS) with affinities of 5.8 pM and 1.3 nM, respectively. An important application of these semisynthetic LUMABS is the detection of small molecules using a competitive assay format, which is demonstrated here for the detection of creatinine. Using a preassembled complex of CR-LUMABS and an anti-creatinine antibody, the detection of high micromolar concentrations of creatinine was possible both in buffer and in 1:1 diluted blood plasma. The use of semisynthetic LUMABS sensors significantly expands the range of antibody targets and enables the application of LUMABS sensors for the ratiometric bioluminescent detection of small molecules using a competitive immunoassay format.
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Affiliation(s)
- Remco Arts
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Susann K. J. Ludwig
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Benice C. B. van Gerven
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Eva Magdalena Estirado
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
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Sequence composition predicts immunoglobulin superfamily members that could share the intrinsically disordered properties of antibody CH1 domains. Sci Rep 2017; 7:12404. [PMID: 28963509 PMCID: PMC5622106 DOI: 10.1038/s41598-017-12616-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/01/2017] [Indexed: 12/02/2022] Open
Abstract
Antibodies are central to the growing sector of protein therapeutics, and increasingly they are being manipulated as fragments and combinations. An improved understanding of the properties of antibody domains in isolation would aid in their engineering. We have conducted an analysis of sequence and domain interactions for IgG antibodies and Fab fragments in the structural database. Of sequence-related properties studied, relative lysine to arginine content was found to be higher in CH1 and CL than in variable domains. As earlier work shows that lysine is favoured over arginine in more soluble proteins, this suggests that individual domains may not be optimised for greater solubility, giving scope for fragment engineering. Across other sequence-based features, CH1 is anomalous. A sequence-based scheme predicts CH1 to be folded, although it is known that CH1 folding is linked to IgG assembly and secretion. Calculations indicate that charge interactions in CH1 domains contribute less to folded state stability than in other Fab domains. Expanding to the immunoglobulin superfamily reveals that a subset of non-antibody domains shares sequence composition properties with CH1, leading us to suggest that some of these may also couple folding, assembly and secretion.
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