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Liu CY, Ahonen CL, Brown ME, Zhou L, Welin M, Krauland EM, Pejchal R, Widboom PF, Battles MB. Structure-based engineering of a novel CD3ε-targeting antibody for reduced polyreactivity. MAbs 2023; 15:2189974. [PMID: 36991534 PMCID: PMC10072072 DOI: 10.1080/19420862.2023.2189974] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
Abstract
Bispecific antibodies continue to represent a growth area for antibody therapeutics, with roughly a third of molecules in clinical development being T-cell engagers that use an anti-CD3 binding arm. CD3 antibodies possessing cross-reactivity with cynomolgus monkey typically recognize a highly electronegative linear epitope at the extreme N-terminus of CD3 epsilon (CD3ε). Such antibodies have high isoelectric points and display problematic polyreactivity (correlated with poor pharmacokinetics for monospecific antibodies). Using insights from the crystal structure of anti-Hu/Cy CD3 antibody ADI-26906 in complex with CD3ε and antibody engineering using a yeast-based platform, we have derived high-affinity CD3 antibody variants with very low polyreactivity and significantly improved biophysical developability. Comparison of these variants with CD3 antibodies in the clinic (as part of bi- or multi-specifics) shows that affinity for CD3 is correlated with polyreactivity. Our engineered CD3 antibodies break this correlation, forming a broad affinity range with no to low polyreactivity. Such antibodies will enable bispecifics with improved pharmacokinetic and safety profiles and suggest engineering solutions that will benefit the large and growing sector of T-cell engagers.
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2
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Rappazzo CG, Tse LV, Kaku CI, Wrapp D, Sakharkar M, Huang D, Deveau LM, Yockachonis TJ, Herbert AS, Battles MB, O'Brien CM, Brown ME, Geoghegan JC, Belk J, Peng L, Yang L, Hou Y, Scobey TD, Burton DR, Nemazee D, Dye JM, Voss JE, Gunn BM, McLellan JS, Baric RS, Gralinski LE, Walker LM. Broad and potent activity against SARS-like viruses by an engineered human monoclonal antibody. Science 2021; 371:823-829. [PMID: 33495307 PMCID: PMC7963221 DOI: 10.1126/science.abf4830] [Citation(s) in RCA: 220] [Impact Index Per Article: 73.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/19/2021] [Indexed: 12/12/2022]
Abstract
The recurrent zoonotic spillover of coronaviruses (CoVs) into the human population underscores the need for broadly active countermeasures. We employed a directed evolution approach to engineer three severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies for enhanced neutralization breadth and potency. One of the affinity-matured variants, ADG-2, displays strong binding activity to a large panel of sarbecovirus receptor binding domains and neutralizes representative epidemic sarbecoviruses with high potency. Structural and biochemical studies demonstrate that ADG-2 employs a distinct angle of approach to recognize a highly conserved epitope that overlaps the receptor binding site. In immunocompetent mouse models of SARS and COVID-19, prophylactic administration of ADG-2 provided complete protection against respiratory burden, viral replication in the lungs, and lung pathology. Altogether, ADG-2 represents a promising broad-spectrum therapeutic candidate against clade 1 sarbecoviruses.
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MESH Headings
- Angiotensin-Converting Enzyme 2/metabolism
- Animals
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/metabolism
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Antibody Affinity
- Betacoronavirus/immunology
- Binding Sites
- Binding Sites, Antibody
- Broadly Neutralizing Antibodies/genetics
- Broadly Neutralizing Antibodies/immunology
- Broadly Neutralizing Antibodies/metabolism
- COVID-19/prevention & control
- COVID-19/therapy
- Cell Surface Display Techniques
- Directed Molecular Evolution
- Epitopes/immunology
- Humans
- Immunization, Passive
- Immunoglobulin Fc Fragments/immunology
- Mice, Inbred BALB C
- Protein Domains
- Protein Engineering
- Receptors, Coronavirus/metabolism
- Severe acute respiratory syndrome-related coronavirus/immunology
- SARS-CoV-2/immunology
- Severe Acute Respiratory Syndrome/immunology
- Severe Acute Respiratory Syndrome/prevention & control
- Severe Acute Respiratory Syndrome/therapy
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- COVID-19 Serotherapy
- Mice
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Affiliation(s)
| | - Longping V Tse
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Daniel Wrapp
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | - Thomas J Yockachonis
- Paul G. Allen School of Global Animal Health, Washington State University, Pullman, WA 99164, USA
| | - Andrew S Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
- The Geneva Foundation, Tacoma, WA 98402, USA
| | | | - Cecilia M O'Brien
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
- The Geneva Foundation, Tacoma, WA 98402, USA
| | | | | | | | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linlin Yang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yixuan Hou
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Trevor D Scobey
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA 02139, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John M Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - James E Voss
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bronwyn M Gunn
- Paul G. Allen School of Global Animal Health, Washington State University, Pullman, WA 99164, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ralph S Baric
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
- Departments of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lisa E Gralinski
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Laura M Walker
- Adimab, LLC, Lebanon, NH 03766, USA.
- Adagio Therapeutics, Inc., Waltham, MA 02451, USA
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3
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Rappazzo CG, Tse LV, Kaku CI, Wrapp D, Sakharkar M, Huang D, Deveau LM, Yockachonis TJ, Herbert AS, Battles MB, O’Brien CM, Brown ME, Geoghegan JC, Belk J, Peng L, Yang L, Scobey TD, Burton DR, Nemazee D, Dye JM, Voss JE, Gunn BM, McLellan JS, Baric RS, Gralinski LE, Walker LM. An Engineered Antibody with Broad Protective Efficacy in Murine Models of SARS and COVID-19. bioRxiv 2020:2020.11.17.385500. [PMID: 33236009 PMCID: PMC7685319 DOI: 10.1101/2020.11.17.385500] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The recurrent zoonotic spillover of coronaviruses (CoVs) into the human population underscores the need for broadly active countermeasures. Here, we employed a directed evolution approach to engineer three SARS-CoV-2 antibodies for enhanced neutralization breadth and potency. One of the affinity-matured variants, ADG-2, displays strong binding activity to a large panel of sarbecovirus receptor binding domains (RBDs) and neutralizes representative epidemic sarbecoviruses with remarkable potency. Structural and biochemical studies demonstrate that ADG-2 employs a unique angle of approach to recognize a highly conserved epitope overlapping the receptor binding site. In murine models of SARS-CoV and SARS-CoV-2 infection, passive transfer of ADG-2 provided complete protection against respiratory burden, viral replication in the lungs, and lung pathology. Altogether, ADG-2 represents a promising broad-spectrum therapeutic candidate for the treatment and prevention of SARS-CoV-2 and future emerging SARS-like CoVs.
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Affiliation(s)
| | - Longping V. Tse
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Daniel Wrapp
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | - Thomas J. Yockachonis
- Paul G. Allen School of Global Animal Health, Washington State University, Pullman, WA 99164, USA
| | - Andrew S. Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
- The Geneva Foundation, 917 Pacific Avenue, Tacoma, WA 98402, USA
| | | | - Cecilia M. O’Brien
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
- The Geneva Foundation, 917 Pacific Avenue, Tacoma, WA 98402, USA
| | | | | | | | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linlin Yang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Trevor D. Scobey
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA 02139, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John M. Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - James E. Voss
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bronwyn M. Gunn
- Paul G. Allen School of Global Animal Health, Washington State University, Pullman, WA 99164, USA
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ralph S. Baric
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Departments of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lisa E. Gralinski
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Laura M. Walker
- Adimab LLC, Lebanon, NH 03766, USA
- Adagio Therapeutics, Inc., Waltham, MA 02451, USA
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4
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Vendeville S, Tahri A, Hu L, Demin S, Cooymans L, Vos A, Kwanten L, Van den Berg J, Battles MB, McLellan JS, Koul A, Raboisson P, Roymans D, Jonckers THM. Discovery of 3-({5-Chloro-1-[3-(methylsulfonyl)propyl]-1H-indol-2-yl}methyl)-1-(2,2,2-trifluoroethyl)-1,3-dihydro-2H-imidazo[4,5-c]pyridin-2-one (JNJ-53718678), a Potent and Orally Bioavailable Fusion Inhibitor of Respiratory Syncytial Virus. J Med Chem 2020; 63:8046-8058. [DOI: 10.1021/acs.jmedchem.0c00226] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Sandrine Vendeville
- Janssen Pharmaceutica NV, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Abdellah Tahri
- Janssen Pharmaceutica NV, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Lili Hu
- Janssen Pharmaceutica NV, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Samuel Demin
- Janssen Pharmaceutica NV, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Ludwig Cooymans
- Janssen Pharmaceutica NV, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Ann Vos
- Janssen Pharmaceutica NV, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Leen Kwanten
- Janssen Pharmaceutica NV, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Joke Van den Berg
- Janssen Pharmaceutica NV, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Michael B. Battles
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, United States
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Anil Koul
- Janssen Pharmaceutica NV, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Pierre Raboisson
- Janssen Pharmaceutica NV, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Dirk Roymans
- Janssen Pharmaceutica NV, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Tim H. M. Jonckers
- Janssen Pharmaceutica NV, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
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5
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Abstract
Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract disease in young children and elderly people. Although the virus was isolated in 1955, an effective RSV vaccine has not been developed, and the only licensed intervention is passive immunoprophylaxis of high-risk infants with a humanized monoclonal antibody. During the past 5 years, however, there has been substantial progress in our understanding of the structure and function of the RSV glycoproteins and their interactions with host cell factors that mediate entry. This period has coincided with renewed interest in developing effective interventions, including the isolation of potent monoclonal antibodies and small molecules and the design of novel vaccine candidates. In this Review, we summarize the recent findings that have begun to elucidate RSV entry mechanisms, describe progress on the development of new interventions and conclude with a perspective on gaps in our knowledge that require further investigation. Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract disease in young children and elderly people. In this Review, Battles and McLellan summarize our current understanding of RSV entry, describe progress on the development of new interventions and conclude with a perspective on gaps in our knowledge that require further investigation.
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Affiliation(s)
- Michael B Battles
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
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6
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Jones HG, Battles MB, Lin CC, Bianchi S, Corti D, McLellan JS. Alternative conformations of a major antigenic site on RSV F. PLoS Pathog 2019; 15:e1007944. [PMID: 31306469 PMCID: PMC6658013 DOI: 10.1371/journal.ppat.1007944] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/25/2019] [Accepted: 06/25/2019] [Indexed: 01/18/2023] Open
Abstract
The respiratory syncytial virus (RSV) fusion (F) glycoprotein is a major target of neutralizing antibodies arising from natural infection, and antibodies that specifically bind to the prefusion conformation of RSV F generally demonstrate the greatest neutralization potency. Prefusion-stabilized RSV F variants have been engineered as vaccine antigens, but crystal structures of these variants have revealed conformational differences in a key antigenic site located at the apex of the trimer, referred to as antigenic site Ø. Currently, it is unclear if flexibility in this region is an inherent property of prefusion RSV F or if it is related to inadequate stabilization of site Ø in the engineered variants. Therefore, we set out to investigate the conformational flexibility of antigenic site Ø, as well as the ability of the human immune system to recognize alternative conformations of this site, by determining crystal structures of prefusion RSV F bound to neutralizing human-derived antibodies AM22 and RSD5. Both antibodies bound with high affinity and were specific for the prefusion conformation of RSV F. Crystal structures of the complexes revealed that the antibodies recognized distinct conformations of antigenic site Ø, each diverging at a conserved proline residue located in the middle of an α-helix. These data suggest that antigenic site Ø exists as an ensemble of conformations, with individual antibodies recognizing discrete states. Collectively, these results have implications for the refolding of pneumovirus and paramyxovirus fusion proteins and should inform development of prefusion-stabilized RSV F vaccine candidates.
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MESH Headings
- Amino Acid Sequence
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- Antigen-Antibody Complex/chemistry
- Antigen-Antibody Complex/immunology
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Binding Sites/genetics
- Crystallography, X-Ray
- Humans
- Models, Molecular
- Proline/chemistry
- Protein Conformation
- Respiratory Syncytial Virus, Human/chemistry
- Respiratory Syncytial Virus, Human/genetics
- Respiratory Syncytial Virus, Human/immunology
- Viral Fusion Proteins/chemistry
- Viral Fusion Proteins/genetics
- Viral Fusion Proteins/immunology
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Affiliation(s)
- Harrison G. Jones
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Michael B. Battles
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Chun-Chi Lin
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Siro Bianchi
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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7
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Jones HG, Wrapp D, Gilman MSA, Battles MB, Wang N, Sacerdote S, Chuang GY, Kwong PD, McLellan JS. Iterative screen optimization maximizes the efficiency of macromolecular crystallization. Acta Crystallogr F Struct Biol Commun 2019; 75:123-131. [PMID: 30713164 PMCID: PMC6360444 DOI: 10.1107/s2053230x18017338] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/06/2018] [Indexed: 11/11/2022] Open
Abstract
Advances in X-ray crystallography have streamlined the process of determining high-resolution three-dimensional macromolecular structures. However, a rate-limiting step in this process continues to be the generation of crystals that are of sufficient size and quality for subsequent diffraction experiments. Here, iterative screen optimization (ISO), a highly automated process in which the precipitant concentrations of each condition in a crystallization screen are modified based on the results of a prior crystallization experiment, is described. After designing a novel high-throughput crystallization screen to take full advantage of this method, the value of ISO is demonstrated by using it to successfully crystallize a panel of six diverse proteins. The results suggest that ISO is an effective method to obtain macromolecular crystals, particularly for proteins that crystallize under a narrow range of precipitant concentrations.
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Affiliation(s)
- Harrison G Jones
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Daniel Wrapp
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Morgan S A Gilman
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Michael B Battles
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Nianshuang Wang
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Sofia Sacerdote
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Gwo Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason S McLellan
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
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8
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Battles MB, Más V, Olmedillas E, Cano O, Vázquez M, Rodríguez L, Melero JA, McLellan JS. Structure and immunogenicity of pre-fusion-stabilized human metapneumovirus F glycoprotein. Nat Commun 2017; 8:1528. [PMID: 29142300 PMCID: PMC5688127 DOI: 10.1038/s41467-017-01708-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/06/2017] [Indexed: 01/10/2023] Open
Abstract
Human metapneumovirus (hMPV) is a frequent cause of bronchiolitis in young children. Its F glycoprotein mediates virus-cell membrane fusion and is the primary target of neutralizing antibodies. The inability to produce recombinant hMPV F glycoprotein in the metastable pre-fusion conformation has hindered structural and immunological studies. Here, we engineer a pre-fusion-stabilized hMPV F ectodomain and determine its crystal structure to 2.6 Å resolution. This structure reveals molecular determinants of strain-dependent acid-induced fusion, as well as insights into refolding from pre- to post-fusion conformations. A dense glycan shield at the apex of pre-fusion hMPV F suggests that antibodies against this site may not be elicited by host immune responses, which is confirmed by depletion studies of human immunoglobulins and by mouse immunizations. This is a major difference with pre-fusion F from human respiratory syncytial virus (hRSV), and collectively our results should facilitate development of effective hMPV vaccine candidates.
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Affiliation(s)
- Michael B Battles
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Vicente Más
- Unidad de Biología Viral, Centro Nacional de Microbiología and CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220, Madrid, Spain
| | - Eduardo Olmedillas
- Unidad de Biología Viral, Centro Nacional de Microbiología and CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220, Madrid, Spain
| | - Olga Cano
- Unidad de Biología Viral, Centro Nacional de Microbiología and CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220, Madrid, Spain
| | - Mónica Vázquez
- Unidad de Biología Viral, Centro Nacional de Microbiología and CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220, Madrid, Spain
| | - Laura Rodríguez
- Unidad de Biología Viral, Centro Nacional de Microbiología and CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220, Madrid, Spain.,University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - José A Melero
- Unidad de Biología Viral, Centro Nacional de Microbiología and CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220, Madrid, Spain.
| | - Jason S McLellan
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.
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9
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Roymans D, Alnajjar SS, Battles MB, Sitthicharoenchai P, Furmanova-Hollenstein P, Rigaux P, Berg JVD, Kwanten L, Ginderen MV, Verheyen N, Vranckx L, Jaensch S, Arnoult E, Voorzaat R, Gallup JM, Larios-Mora A, Crabbe M, Huntjens D, Raboisson P, Langedijk JP, Ackermann MR, McLellan JS, Vendeville S, Koul A. Therapeutic efficacy of a respiratory syncytial virus fusion inhibitor. Nat Commun 2017; 8:167. [PMID: 28761099 PMCID: PMC5537225 DOI: 10.1038/s41467-017-00170-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 06/07/2017] [Indexed: 01/16/2023] Open
Abstract
Respiratory syncytial virus is a major cause of acute lower respiratory tract infection in young children, immunocompromised adults, and the elderly. Intervention with small-molecule antivirals specific for respiratory syncytial virus presents an important therapeutic opportunity, but no such compounds are approved today. Here we report the structure of JNJ-53718678 bound to respiratory syncytial virus fusion (F) protein in its prefusion conformation, and we show that the potent nanomolar activity of JNJ-53718678, as well as the preliminary structure–activity relationship and the pharmaceutical optimization strategy of the series, are consistent with the binding mode of JNJ-53718678 and other respiratory syncytial virus fusion inhibitors. Oral treatment of neonatal lambs with JNJ-53718678, or with an equally active close analog, efficiently inhibits established acute lower respiratory tract infection in the animals, even when treatment is delayed until external signs of respiratory syncytial virus illness have become visible. Together, these data suggest that JNJ-53718678 is a promising candidate for further development as a potential therapeutic in patients at risk to develop respiratory syncytial virus acute lower respiratory tract infection. Respiratory syncytial virus causes lung infections in children, immunocompromised adults, and in the elderly. Here the authors show that a chemical inhibitor to a viral fusion protein is effective in reducing viral titre and ameliorating infection in rodents and neonatal lambs.
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Affiliation(s)
- Dirk Roymans
- Janssen Infectious Diseases and Vaccines, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Sarhad S Alnajjar
- College of Veterinary Medicine, Iowa State University, 1800 Christensen Dr, Ames, IA, 50010, USA
| | - Michael B Battles
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, 1 Rope Ferry Road, Hanover, NH, 03755, USA
| | | | | | - Peter Rigaux
- Janssen Infectious Diseases and Vaccines, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Joke Van den Berg
- Janssen Infectious Diseases and Vaccines, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Leen Kwanten
- Janssen Infectious Diseases and Vaccines, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Marcia Van Ginderen
- Janssen Infectious Diseases and Vaccines, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Nick Verheyen
- Janssen Infectious Diseases and Vaccines, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Luc Vranckx
- Janssen Infectious Diseases and Vaccines, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Steffen Jaensch
- Computational Biology, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Eric Arnoult
- Computational Chemistry, Janssen R&D LLC, 1400 Mckean Road, Spring House, PA, 19477, USA
| | - Richard Voorzaat
- Janssen Vaccines and Prevention, Newtonweg 1, 2333-CP, Leiden, The Netherlands
| | - Jack M Gallup
- College of Veterinary Medicine, Iowa State University, 1800 Christensen Dr, Ames, IA, 50010, USA
| | - Alejandro Larios-Mora
- College of Veterinary Medicine, Iowa State University, 1800 Christensen Dr, Ames, IA, 50010, USA
| | - Marjolein Crabbe
- Non-Clinical Statistics, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Dymphy Huntjens
- Clinical Pharmacology and Pharmacometrics, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Pierre Raboisson
- Janssen Infectious Diseases and Vaccines, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | | | - Mark R Ackermann
- College of Veterinary Medicine, Iowa State University, 1800 Christensen Dr, Ames, IA, 50010, USA
| | - Jason S McLellan
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, 1 Rope Ferry Road, Hanover, NH, 03755, USA
| | - Sandrine Vendeville
- Janssen Infectious Diseases and Vaccines, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Anil Koul
- Janssen Infectious Diseases and Vaccines, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
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10
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Wrapp D, Jones H, Gilman MSA, Battles MB, Sacerdote S, Wang N, Handing KB, Gualtieri E, Kwong PD, McLellan JS. Automated method for iterative optimization of macromolecular crystallization screens. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s0108767317098609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
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11
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Godbersen C, Coupet TA, Huehls AM, Zhang T, Battles MB, Fisher JL, Ernstoff MS, Sentman CL. NKG2D Ligand-Targeted Bispecific T-Cell Engagers Lead to Robust Antitumor Activity against Diverse Human Tumors. Mol Cancer Ther 2017; 16:1335-1346. [PMID: 28500232 DOI: 10.1158/1535-7163.mct-16-0846] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 03/16/2017] [Accepted: 04/28/2017] [Indexed: 01/06/2023]
Abstract
Two new bispecific T-cell engaging (BiTE) molecules with specificity for NKG2D ligands were developed and functionally characterized. One, huNKG2D-OKT3, was derived from the extracellular portion of the human NKG2D receptor fused to a CD3ε binding single-chain variable fragment (scFv), known as OKT3. NKG2D has multiple ligands, including MICA, which are expressed by a variety of malignant cells. A second molecule, B2-OKT3, was created in the tandem scFv BiTE format that targets MICA on tumor cells and CD3ε on human T cells. Both BiTEs specifically activated T cells to kill human tumor cell lines. Cytotoxicity by B2-OKT3, but not huNKG2D-OKT3, is blocked by soluble rMICA. The huNKG2D-OKT3 induced greater T-cell cytokine production in comparison with B2-OKT3. No T-cell pretreatment was required for IFNγ production upon coculture of B2-OKT3 or huNKG2D-OKT3 with T cells and target cells. The effector memory T-cell compartment was the primary source of IFNγ, and culture of T cells and these BiTEs with plate-bound rMICA showed ligand density-dependent production of IFNγ from both CD4+ and CD8+ T cells. There was 2-fold more IFNγ produced per CD8+ T cell and 5-fold greater percentage of CD8+ T cells producing IFNγ compared with CD4+ T cells. In addition, both BiTEs elicited significant antitumor responses against human metastatic melanoma tumor samples using autologous or healthy donor T cells. These data demonstrate the robust antitumor activity of these NKG2D ligand-binding bispecific proteins and support their further development for clinical use. Mol Cancer Ther; 16(7); 1335-46. ©2017 AACR.
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Affiliation(s)
- Claire Godbersen
- Department of Microbiology & Immunology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
- The Center for Synthetic Immunity, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
| | - Tiffany A Coupet
- Department of Microbiology & Immunology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
- The Center for Synthetic Immunity, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
| | - Amelia M Huehls
- Department of Microbiology & Immunology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
- The Center for Synthetic Immunity, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
| | - Tong Zhang
- Department of Microbiology & Immunology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
- The Center for Synthetic Immunity, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
| | - Michael B Battles
- Department of Microbiology & Immunology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
- The Center for Synthetic Immunity, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
| | | | | | - Charles L Sentman
- Department of Microbiology & Immunology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire.
- The Center for Synthetic Immunity, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
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12
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Badarau A, Rouha H, Malafa S, Battles MB, Walker L, Nielson N, Dolezilkova I, Teubenbacher A, Banerjee S, Maierhofer B, Weber S, Stulik L, Logan DT, Welin M, Mirkina I, Pleban C, Zauner G, Gross K, Jägerhofer M, Magyarics Z, Nagy E. Context matters: The importance of dimerization-induced conformation of the LukGH leukocidin of Staphylococcus aureus for the generation of neutralizing antibodies. MAbs 2016; 8:1347-1360. [PMID: 27467113 PMCID: PMC5058624 DOI: 10.1080/19420862.2016.1215791] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
LukGH (LukAB) is a potent leukocidin of Staphylococcus aureus that lyses human phagocytic cells and is thought to contribute to immune evasion. Unlike the other bi-component leukocidins of S. aureus, LukGH forms a heterodimer before binding to its receptor, CD11b expressed on professional phagocytic cells, and displays significant sequence variation. We employed a high diversity human IgG1 library presented on yeast cells to discover monoclonal antibodies (mAbs) neutralizing the cytolytic activity of LukGH. Recombinant LukG and LukH monomers or a LukGH dimer were used as capture antigens in the library selections. We found that mAbs identified with LukG or LukH as bait had no or very low toxin neutralization potency. In contrast, LukGH dimer-selected antibodies proved to be highly potent, and several mAbs were able to neutralize even the most divergent LukGH variants. Based on biolayer interferometry and mesoscale discovery, the high affinity antibody binding site on the LukGH complex was absent on the individual monomers, suggesting that it was generated upon formation of the LukG-LukH dimer. X-ray crystallography analysis of the complex between the LukGH dimer and the antigen-binding fragment of a very potent mAb (PDB code 5K59) indicated that the epitope is located in the predicted cell binding region (rim domain) of LukGH. The corresponding IgG inhibited the binding of LukGH dimer to target cells. Our data suggest that knowledge of the native conformation of target molecules is essential to generate high affinity and functional mAbs.
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Affiliation(s)
- Adriana Badarau
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Harald Rouha
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Stefan Malafa
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | | | | | | | | | | | - Srijib Banerjee
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | | | - Susanne Weber
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Lukas Stulik
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Derek T Logan
- c SARomics Biostructures AB , Medicon Village, Lund , Sweden
| | - Martin Welin
- c SARomics Biostructures AB , Medicon Village, Lund , Sweden
| | - Irina Mirkina
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Clara Pleban
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Gerhild Zauner
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Karin Gross
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | | | - Zoltán Magyarics
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Eszter Nagy
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
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13
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Rouha H, Badarau A, Visram ZC, Battles MB, Prinz B, Magyarics Z, Nagy G, Mirkina I, Stulik L, Zerbs M, Jägerhofer M, Maierhofer B, Teubenbacher A, Dolezilkova I, Gross K, Banerjee S, Zauner G, Malafa S, Zmajkovic J, Maier S, Mabry R, Krauland E, Wittrup KD, Gerngross TU, Nagy E. Five birds, one stone: neutralization of α-hemolysin and 4 bi-component leukocidins of Staphylococcus aureus with a single human monoclonal antibody. MAbs 2015; 7:243-54. [PMID: 25523282 PMCID: PMC5045134 DOI: 10.4161/19420862.2014.985132] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Staphylococcus aureus is a major human pathogen associated with high mortality. The emergence of antibiotic resistance and the inability of antibiotics to counteract bacterial cytotoxins involved in the pathogenesis of S. aureus call for novel therapeutic approaches, such as passive immunization with monoclonal antibodies (mAbs). The complexity of staphylococcal pathogenesis and past failures with single mAb products represent considerable barriers for antibody-based therapeutics. Over the past few years, efforts have focused on neutralizing α-hemolysin. Recent findings suggest that the concerted actions of several cytotoxins, including the bi-component leukocidins play important roles in staphylococcal pathogenesis. Therefore, we aimed to isolate mAbs that bind to multiple cytolysins by employing high diversity human IgG1 libraries presented on the surface of yeast cells. Here we describe cross-reactive antibodies with picomolar affinity for α-hemolysin and 4 different bi-component leukocidins that share only ∼26% overall amino acid sequence identity. The molecular basis of cross-reactivity is the recognition of a conformational epitope shared by α-hemolysin and F-components of gamma-hemolysin (HlgAB and HlgCB), LukED and LukSF (Panton-Valentine Leukocidin). The amino acids predicted to form the epitope are conserved and known to be important for cytotoxic activity. We found that a single cross-reactive antibody prevented lysis of human phagocytes, epithelial and red blood cells induced by α-hemolysin and leukocidins in vitro, and therefore had superior effectiveness compared to α-hemolysin specific antibodies to protect from the combined cytolytic effect of secreted S. aureus toxins. Such mAb afforded high levels of protection in murine models of pneumonia and sepsis.
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Key Words
- BLI, biolayer interferometry
- EC50, effective concentration
- Hla, α-hemolysin
- HlgAB and HlgCB, gamma-hemolysins
- IC50, inhibitory concentration
- LukED, leukocidin ED
- LukSF, leukocidin SF
- PMN, polymorphonuclear cells
- RBC, red blood cell
- Staphylococcus aureus
- engineered cross-reactivity
- exotoxins
- in vitro potency
- in vivo efficacy
- mAb, monoclonal antibody
- monoclonal antibody
- toxin neutralization
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14
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Grimm SK, Battles MB, Ackerman ME. Directed evolution of a yeast-displayed HIV-1 SOSIP gp140 spike protein toward improved expression and affinity for conformational antibodies. PLoS One 2015; 10:e0117227. [PMID: 25688555 PMCID: PMC4331506 DOI: 10.1371/journal.pone.0117227] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 12/22/2014] [Indexed: 11/19/2022] Open
Abstract
Design of an envelope-based immunogen capable of inducing a broadly neutralizing antibody response is thought to be key to the development of a protective HIV-1 vaccine. However, the broad diversity of viral variants and a limited ability to produce native envelope have hampered such design efforts. Here we describe adaptation of the yeast display system and use of a combinatorial protein engineering approach to permit directed evolution of HIV envelope variants. Because the intrinsic instability and complexity of this trimeric glycoprotein has greatly impeded the development of immunogens that properly represent the structure of native envelope, this platform addresses an essential need for methodologies with the capacity to rapidly engineer HIV spike proteins towards improved homogeneity, stability, and presentation of neutralizing epitopes. We report for the first time the display of a designed SOSIP gp140 on yeast, and the in vitro evolution of derivatives with greatly improved expression and binding to conformation-dependent antibodies. These efforts represent an initial and critical step toward the ability to rapidly engineer HIV-1 envelope immunogens via directed evolution.
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Affiliation(s)
- Sebastian K. Grimm
- Thayer School of Engineering at Dartmouth, Hanover, New Hampshire, United States of America
| | - Michael B. Battles
- Thayer School of Engineering at Dartmouth, Hanover, New Hampshire, United States of America
| | - Margaret E. Ackerman
- Thayer School of Engineering at Dartmouth, Hanover, New Hampshire, United States of America
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15
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Du M, Battles MB, Nett JH. A color-based stable multi-copy integrant selection system for Pichia pastoris using the attenuated ADE1 and ADE2 genes as auxotrophic markers. Bioeng Bugs 2012; 3:32-7. [PMID: 22126802 DOI: 10.4161/bbug.3.1.17936] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The methylotropic yeast Pichia pastoris has been used for more than two decades to successfully produce a large number of recombinant proteins. Currently, a wide variety of auxotrophic and drug based selection markers are employed to screen for clones expressing the protein of interest. For most proteins an increased copy number of the integrated plasmid results in higher levels of expression, but these multi-copy integrants can be unstable due to the propensity of P. pastoris for homologous recombination. Here we describe a multi-copy selection system based on ade1 and ade2 auxotrophic parent strains and the respective attenuated markers with truncated promoter regions. We show that for all four proteins we tested, the use of the attenuated markers leads to increased protein expression when compared with selection based on the full strength markers. The fact that the adenine auxotrophic strains grow more slowly than the complemented counterparts essentially ensures the stability of multi-copy integration. At the same time, the accumulation of a red dye in the auxotrophic strains also provides an easy, color-based selection for transformants with multiple copies.
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Affiliation(s)
- Min Du
- GlycoFi, Inc., Lebanon, NH, USA
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