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Schiffner T, Phung I, Ray R, Irimia A, Tian M, Swanson O, Lee JH, Lee CCD, Marina-Zárate E, Cho SY, Huang J, Ozorowski G, Skog PD, Serra AM, Rantalainen K, Allen JD, Baboo S, Rodriguez OL, Himansu S, Zhou J, Hurtado J, Flynn CT, McKenney K, Havenar-Daughton C, Saha S, Shields K, Schultze S, Smith ML, Liang CH, Toy L, Pecetta S, Lin YC, Willis JR, Sesterhenn F, Kulp DW, Hu X, Cottrell CA, Zhou X, Ruiz J, Wang X, Nair U, Kirsch KH, Cheng HL, Davis J, Kalyuzhniy O, Liguori A, Diedrich JK, Ngo JT, Lewis V, Phelps N, Tingle RD, Spencer S, Georgeson E, Adachi Y, Kubitz M, Eskandarzadeh S, Elsliger MA, Amara RR, Landais E, Briney B, Burton DR, Carnathan DG, Silvestri G, Watson CT, Yates JR, Paulson JC, Crispin M, Grigoryan G, Ward AB, Sok D, Alt FW, Wilson IA, Batista FD, Crotty S, Schief WR. Vaccination induces broadly neutralizing antibody precursors to HIV gp41. Nat Immunol 2024; 25:1073-1082. [PMID: 38816615 PMCID: PMC11147780 DOI: 10.1038/s41590-024-01833-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: 02/24/2024] [Accepted: 04/04/2024] [Indexed: 06/01/2024]
Abstract
A key barrier to the development of vaccines that induce broadly neutralizing antibodies (bnAbs) against human immunodeficiency virus (HIV) and other viruses of high antigenic diversity is the design of priming immunogens that induce rare bnAb-precursor B cells. The high neutralization breadth of the HIV bnAb 10E8 makes elicitation of 10E8-class bnAbs desirable; however, the recessed epitope within gp41 makes envelope trimers poor priming immunogens and requires that 10E8-class bnAbs possess a long heavy chain complementarity determining region 3 (HCDR3) with a specific binding motif. We developed germline-targeting epitope scaffolds with affinity for 10E8-class precursors and engineered nanoparticles for multivalent display. Scaffolds exhibited epitope structural mimicry and bound bnAb-precursor human naive B cells in ex vivo screens, protein nanoparticles induced bnAb-precursor responses in stringent mouse models and rhesus macaques, and mRNA-encoded nanoparticles triggered similar responses in mice. Thus, germline-targeting epitope scaffold nanoparticles can elicit rare bnAb-precursor B cells with predefined binding specificities and HCDR3 features.
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Affiliation(s)
- Torben Schiffner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Institute for Drug Discovery, Leipzig University Medical Faculty, Leipzig, Germany
| | - Ivy Phung
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Rashmi Ray
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Adriana Irimia
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ming Tian
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Olivia Swanson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Jeong Hyun Lee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Chang-Chun D Lee
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ester Marina-Zárate
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - So Yeon Cho
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jiachen Huang
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gabriel Ozorowski
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Patrick D Skog
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Andreia M Serra
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Kimmo Rantalainen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Sabyasachi Baboo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Oscar L Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | | | - Jianfu Zhou
- Department of Computer Science, Dartmouth College, Hanover, NH, USA
| | - Jonathan Hurtado
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Claudia T Flynn
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Katherine McKenney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Colin Havenar-Daughton
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Swati Saha
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Kaitlyn Shields
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Steven Schultze
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Melissa L Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Chi-Hui Liang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Laura Toy
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Simone Pecetta
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Ying-Cing Lin
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Jordan R Willis
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Fabian Sesterhenn
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Daniel W Kulp
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Xiaozhen Hu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Christopher A Cottrell
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Xiaoya Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Jennifer Ruiz
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Xuesong Wang
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Usha Nair
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Kathrin H Kirsch
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Hwei-Ling Cheng
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jillian Davis
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Alessia Liguori
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Julia T Ngo
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Vanessa Lewis
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Nicole Phelps
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Ryan D Tingle
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Skye Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Erik Georgeson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Yumiko Adachi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Michael Kubitz
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Saman Eskandarzadeh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Marc A Elsliger
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rama R Amara
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory School of Medicine, Atlanta, GA, USA
| | - Elise Landais
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Multi-omics Vaccine Evaluation Consortium, The Scripps Research Institute, La Jolla, CA, USA
- San Diego Center for AIDS Research, The Scripps Research Institute, La Jolla, CA, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Diane G Carnathan
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Guido Silvestri
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - James C Paulson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Gevorg Grigoryan
- Department of Computer Science, Dartmouth College, Hanover, NH, USA
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
- Generate Biomedicines, Inc., Somerville, MA, USA
| | - Andrew B Ward
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Devin Sok
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ian A Wilson
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Facundo D Batista
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Shane Crotty
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - William R Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA.
- Moderna, Inc., Cambridge, MA, USA.
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2
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Ray R, Schiffner T, Wang X, Yan Y, Rantalainen K, Lee CCD, Parikh S, Reyes RA, Dale GA, Lin YC, Pecetta S, Giguere S, Swanson O, Kratochvil S, Melzi E, Phung I, Madungwe L, Kalyuzhniy O, Warner J, Weldon SR, Tingle R, Lamperti E, Kirsch KH, Phelps N, Georgeson E, Adachi Y, Kubitz M, Nair U, Crotty S, Wilson IA, Schief WR, Batista FD. Affinity gaps among B cells in germinal centers drive the selection of MPER precursors. Nat Immunol 2024; 25:1083-1096. [PMID: 38816616 PMCID: PMC11147770 DOI: 10.1038/s41590-024-01844-7] [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: 08/01/2023] [Accepted: 04/16/2024] [Indexed: 06/01/2024]
Abstract
Current prophylactic human immunodeficiency virus 1 (HIV-1) vaccine research aims to elicit broadly neutralizing antibodies (bnAbs). Membrane-proximal external region (MPER)-targeting bnAbs, such as 10E8, provide exceptionally broad neutralization, but some are autoreactive. Here, we generated humanized B cell antigen receptor knock-in mouse models to test whether a series of germline-targeting immunogens could drive MPER-specific precursors toward bnAbs. We found that recruitment of 10E8 precursors to germinal centers (GCs) required a minimum affinity for germline-targeting immunogens, but the GC residency of MPER precursors was brief due to displacement by higher-affinity endogenous B cell competitors. Higher-affinity germline-targeting immunogens extended the GC residency of MPER precursors, but robust long-term GC residency and maturation were only observed for MPER-HuGL18, an MPER precursor clonotype able to close the affinity gap with endogenous B cell competitors in the GC. Thus, germline-targeting immunogens could induce MPER-targeting antibodies, and B cell residency in the GC may be regulated by a precursor-competitor affinity gap.
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Affiliation(s)
- Rashmi Ray
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Torben Schiffner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, USA
- Institute for Drug Discovery, Leipzig University Medical Faculty, Leipzig, Germany
| | - Xuesong Wang
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Yu Yan
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Kimmo Rantalainen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, USA
| | - Chang-Chun David Lee
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Shivang Parikh
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Raphael A Reyes
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Gordon A Dale
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Ying-Cing Lin
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Simone Pecetta
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
- Moderna, Inc., Cambridge, MA, USA
| | - Sophie Giguere
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Olivia Swanson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, USA
| | - Sven Kratochvil
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Eleonora Melzi
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Ivy Phung
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, USA
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Lisa Madungwe
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, USA
| | - John Warner
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Stephanie R Weldon
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Ryan Tingle
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, USA
| | - Edward Lamperti
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Kathrin H Kirsch
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Nicole Phelps
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, USA
| | - Erik Georgeson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, USA
| | - Yumiko Adachi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, USA
| | - Michael Kubitz
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, USA
| | - Usha Nair
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Shane Crotty
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, USA
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ian A Wilson
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - William R Schief
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA.
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, USA.
- Moderna, Inc., Cambridge, MA, USA.
| | - Facundo D Batista
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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3
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García-Porras M, Torralba J, Insausti S, Valle J, Andreu D, Apellániz B, Nieva JL. A two-step mechanism for the binding of the HIV-1 MPER epitope by the 10E8 antibody onto biosensor-supported lipid bilayers. FEBS Lett 2024; 598:787-800. [PMID: 38339834 DOI: 10.1002/1873-3468.14814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 02/12/2024]
Abstract
HIV-1 antibodies targeting the carboxy-terminal area of the membrane-proximal external region (ctMPER) are close to exerting viral pan-neutralization. Here, we reconstituted the ctMPER epitope as the N-terminal extremity of the Env glycoprotein transmembrane domain helix and immobilized it onto biosensor-supported lipid bilayers. We assessed the binding mechanism of anti-MPER antibody 10E8 through Surface Plasmon Resonance, and found, through equilibrium and kinetic binding analyses as a function of bilayer thickness, peptide length, and paratope mutations, that 10E8 engages first with the epitope peptide (encounter), limited by ctMPER helix accessibility at the membrane surface, and then inserts into the lipid bilayer assisted by favorable Fab-membrane interactions (docking). This mechanistic information may help in devising new strategies to develop more efficient MPER-targeting vaccines.
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Affiliation(s)
- Miguel García-Porras
- Instituto Biofisika (CSIC-UPV/EHU), University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Johana Torralba
- Instituto Biofisika (CSIC-UPV/EHU), University of the Basque Country (UPV/EHU), Bilbao, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Sara Insausti
- Instituto Biofisika (CSIC-UPV/EHU), University of the Basque Country (UPV/EHU), Bilbao, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Javier Valle
- Laboratory of Proteomics and Protein Chemistry, Department of Medicine and Life Sciences, Pompeu Fabra University, Barcelona, Spain
| | - David Andreu
- Laboratory of Proteomics and Protein Chemistry, Department of Medicine and Life Sciences, Pompeu Fabra University, Barcelona, Spain
| | - Beatriz Apellániz
- Department of Physiology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - José L Nieva
- Instituto Biofisika (CSIC-UPV/EHU), University of the Basque Country (UPV/EHU), Bilbao, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
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4
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Wang Q, Zhang S, Nguyen HT, Sodroski J. Inhibition of human immunodeficiency virus (HIV-1) infectivity by expression of poorly or broadly neutralizing antibodies against Env in virus-producing cells. J Virol 2024; 98:e0159423. [PMID: 38289101 PMCID: PMC10878270 DOI: 10.1128/jvi.01594-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/19/2023] [Indexed: 02/21/2024] Open
Abstract
The human immunodeficiency virus (HIV-1) envelope (Env) glycoprotein precursor (gp160) trimerizes, is modified by high-mannose glycans in the endoplasmic reticulum, and is transported via Golgi and non-Golgi secretory pathways to the infected cell surface. In the Golgi, gp160 is partially modified by complex carbohydrates and proteolytically cleaved to produce the mature functional Env trimer, which is preferentially incorporated into virions. Broadly neutralizing antibodies (bNAbs) generally recognize the cleaved Env trimer, whereas poorly neutralizing antibodies (pNAbs) bind the conformationally flexible gp160. We found that expression of bNAbs, pNAbs, or soluble/membrane forms of the receptor, CD4, in cells producing HIV-1 all decreased viral infectivity. Four patterns of co-expressed ligand:Env were observed: (i) ligands (CD4, soluble CD4-Ig, and some pNAbs) that specifically recognize the CD4-bound Env conformation resulted in uncleaved Envs lacking complex glycans that were not incorporated into virions; (ii) other pNAbs produced Envs with some complex carbohydrates and severe defects in cleavage, which were relieved by brefeldin A treatment; (iii) bNAbs that recognize gp160 as well as mature Envs resulted in Envs with some complex carbohydrates and moderate decreases in virion Env cleavage; and (iv) bNAbs that preferentially recognize mature Envs produced cleaved Envs with complex glycans in cells and on virions. The low infectivity observed upon co-expression of pNAbs or CD4 could be explained by disruption of Env trafficking, reducing the level of Env and/or increasing the fraction of uncleaved Env on virions. In addition to bNAb effects on virion Env cleavage, the secreted bNAbs neutralized the co-expressed viruses.IMPORTANCEThe Env trimers on the HIV-1 mediate virus entry into host cells. Env is synthesized in infected cells, modified by complex sugars, and cleaved to form a mature, functional Env, which is incorporated into virus particles. Env elicits antibodies in infected individuals, some of which can neutralize the virus. We found that antibodies co-expressed in the virus-producing cell can disrupt Env transit to the proper compartment for cleavage and sugar modification and, in some cases, block incorporation into viruses. These studies provide insights into the processes by which Env becomes functional in the virus-producing cell and may assist attempts to interfere with these events to inhibit HIV-1 infection.
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Affiliation(s)
- Qian Wang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Hanh T. Nguyen
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
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5
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Newby ML, Allen JD, Crispin M. Influence of glycosylation on the immunogenicity and antigenicity of viral immunogens. Biotechnol Adv 2024; 70:108283. [PMID: 37972669 PMCID: PMC10867814 DOI: 10.1016/j.biotechadv.2023.108283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 10/04/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
A key aspect of successful viral vaccine design is the elicitation of neutralizing antibodies targeting viral attachment and fusion glycoproteins that embellish viral particles. This observation has catalyzed the development of numerous viral glycoprotein mimetics as vaccines. Glycans can dominate the surface of viral glycoproteins and as such, the viral glycome can influence the antigenicity and immunogenicity of a candidate vaccine. In one extreme, glycans can form an integral part of epitopes targeted by neutralizing antibodies and are therefore considered to be an important feature of key immunogens within an immunization regimen. In the other extreme, the existence of peptide and bacterially expressed protein vaccines shows that viral glycosylation can be dispensable in some cases. However, native-like glycosylation can indicate native-like protein folding and the presence of conformational epitopes. Furthermore, going beyond native glycan mimicry, in either occupancy of glycosylation sites or the glycan processing state, may offer opportunities for enhancing the immunogenicity and associated protection elicited by an immunogen. Here, we review key determinants of viral glycosylation and how recombinant immunogens can recapitulate these signatures across a range of enveloped viruses, including HIV-1, Ebola virus, SARS-CoV-2, Influenza and Lassa virus. The emerging understanding of immunogen glycosylation and its control will help guide the development of future vaccines in both recombinant protein- and nucleic acid-based vaccine technologies.
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Affiliation(s)
- Maddy L Newby
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
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6
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Nguyen HT, Wang Q, Anang S, Sodroski JG. Characterization of the Human Immunodeficiency Virus (HIV-1) Envelope Glycoprotein Conformational States on Infectious Virus Particles. J Virol 2023; 97:e0185722. [PMID: 36815832 PMCID: PMC10062176 DOI: 10.1128/jvi.01857-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/01/2023] [Indexed: 02/24/2023] Open
Abstract
Human immunodeficiency virus (HIV-1) entry into cells involves triggering of the viral envelope glycoprotein (Env) trimer ([gp120/gp41]3) by the primary receptor, CD4, and coreceptors, CCR5 or CXCR4. The pretriggered (State-1) conformation of the mature (cleaved) Env is targeted by broadly neutralizing antibodies (bNAbs), which are inefficiently elicited compared with poorly neutralizing antibodies (pNAbs). Here, we characterize variants of the moderately triggerable HIV-1AD8 Env on virions produced by an infectious molecular proviral clone; such virions contain more cleaved Env than pseudotyped viruses. We identified three types of cleaved wild-type AD8 Env trimers on virions: (i) State-1-like trimers preferentially recognized by bNAbs and exhibiting strong subunit association; (ii) trimers recognized by pNAbs directed against the gp120 coreceptor-binding region and exhibiting weak, detergent-sensitive subunit association; and (iii) a minor gp41-only population. The first Env population was enriched and the other Env populations reduced by introducing State-1-stabilizing changes in the AD8 Env or by treatment of the virions with crosslinker or the State-1-preferring entry inhibitor, BMS-806. These stabilized AD8 Envs were also more resistant to gp120 shedding induced by a CD4-mimetic compound or by incubation on ice. Conversely, a State-1-destabilized, CD4-independent AD8 Env variant exhibited weaker bNAb recognition and stronger pNAb recognition. Similar relationships between Env triggerability and antigenicity/shedding propensity on virions were observed for other HIV-1 strains. State-1 Envs on virions can be significantly enriched by minimizing the adventitious incorporation of uncleaved Env; stabilizing the pretriggered conformation by Env modification, crosslinking or BMS-806 treatment; strengthening Env subunit interactions; and using CD4-negative producer cells. IMPORTANCE Efforts to develop an effective HIV-1 vaccine have been frustrated by the inability to elicit broad neutralizing antibodies that recognize multiple virus strains. Such antibodies can bind a particular shape of the HIV-1 envelope glycoprotein trimer, as it exists on a viral membrane but before engaging receptors on the host cell. Here, we establish simple yet powerful assays to characterize the envelope glycoproteins in a natural context on virus particles. We find that, depending on the HIV-1 strain, some envelope glycoproteins change shape and fall apart, creating decoys that can potentially divert the host immune response. We identify requirements to keep the relevant envelope glycoprotein target for broad neutralizing antibodies intact on virus-like particles. These studies suggest strategies that should facilitate efforts to produce and use virus-like particles as vaccine immunogens.
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Affiliation(s)
- Hanh T. Nguyen
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Qian Wang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Saumya Anang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph G. Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
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7
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Enhancing HIV-1 Neutralization by Increasing the Local Concentration of Membrane-Proximal External Region-Directed Broadly Neutralizing Antibodies. J Virol 2023; 97:e0164722. [PMID: 36541800 PMCID: PMC9888200 DOI: 10.1128/jvi.01647-22] [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] [Indexed: 12/24/2022] Open
Abstract
Broadly neutralizing antibodies (bNAbs) against the membrane-proximal external region (MPER) of the gp41 component of the human immunodeficiency virus type 1 (HIV-1) envelope (Env) are characterized by long, hydrophobic, heavy chain complementarity-determining region 3s (HCDR3s) that interact with the MPER and some viral membrane lipids to achieve increased local concentrations. Here, we show that increasing the local concentration of MPER-directed bNAbs at the cell surface via binding to the high-affinity Fc receptor FcγRI potentiates their ability to prevent viral entry in a manner analogous to the previously reported observation wherein the lipid-binding activity of MPER bNAbs increases their concentration at the viral surface membrane. However, binding of MPER-directed bNAb 10E8 to FcγRI abolishes the neutralization synergy that is seen with the N-heptad repeat (NHR)-targeting antibody D5_AR and NHR-targeting small molecule enfuvirtide (T20), possibly due to decreased accessibility of the NHR in the FcγRI-10E8-MPER complex. Taken together, our results suggest that lipid-binding activity and FcγRI-mediated potentiation function in concert to improve the potency of MPER-directed bNAbs by increasing their local concentration near the site of viral fusion. Therefore, lipid binding may not be a strict requirement for potent neutralization by MPER-targeting bNAbs, as alternative methods can achieve similar increases in local concentrations while avoiding potential liabilities associated with immunologic host tolerance. IMPORTANCE The trimeric glycoprotein Env, the only viral protein expressed on the surface of HIV-1, is the target of broadly neutralizing antibodies and the focus of most vaccine development efforts. Broadly neutralizing antibodies targeting the membrane proximal external region (MPER) of Env show lipid-binding characteristics, and modulating this interaction affects neutralization. In this study, we tested the neutralization potencies of variants of the MPER-targeting antibody 10E8 with different viral-membrane-binding and host FcγRI-binding capabilities. Our results suggest that binding to both lipid and FcγRI improves the neutralization potency of MPER-directed antibodies by concentrating the antibodies at sites of viral fusion. As such, lipid binding may not be uniquely required for MPER-targeting broadly neutralizing antibodies, as alternative methods to increase local concentration can achieve similar improvements in potency.
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8
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Vesga AG, Villegas L, Vequi-Suplicy CC, Sorzano COS, Requejo-Isidro J. Quantitative characterization of membrane-protein reversible association using FCS. Biophys J 2023:S0006-3495(23)00042-5. [PMID: 36698316 DOI: 10.1016/j.bpj.2023.01.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 01/09/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
Functionally meaningful reversible protein-membrane interactions mediate many biological events. Fluorescence correlation spectroscopy (FCS) is increasingly used to quantitatively study the non-reversible binding of proteins to membranes using lipid vesicles in solution. However, the lack of a complete description of the phase and statistical equilibria in the case of reversible protein-membrane partitioning has hampered the application of FCS to quantify the partition coefficient (Kx). In this work, we further extend the theory that describes membrane-protein partitioning to account for spontaneous protein-membrane dissociation and reassociation to the same or a different lipid vesicle. We derive the probability distribution of proteins on lipid vesicles for reversible binding and demonstrate that FCS is a suitable technique for accurate Kx quantification of membrane-protein reversible association. We also establish the limits to Kx determination by FCS studying the Cramer-Rao bound on the variance of the retrieved parameters. We validate the mathematical formulation against reaction-diffusion simulations to study phase and statistical equilibria and compare the Kx obtained from a computational FCS titration experiment with the experimental ground truth. Finally, we demonstrate the application of our methodology studying the association of anti-HIV broadly neutralizing antibody (10E8-3R) to the membrane.
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Affiliation(s)
- Arturo G Vesga
- Centro Nacional de Biotecnología (CNB), CSIC, 28049 Madrid, Spain; Unidad de Nanobiotecnología, CNB-CSIC-IMDEA Nanociencia Associated Unit, 28049 Madrid, Spain
| | - Lupe Villegas
- Centro Nacional de Biotecnología (CNB), CSIC, 28049 Madrid, Spain
| | | | | | - Jose Requejo-Isidro
- Centro Nacional de Biotecnología (CNB), CSIC, 28049 Madrid, Spain; Unidad de Nanobiotecnología, CNB-CSIC-IMDEA Nanociencia Associated Unit, 28049 Madrid, Spain.
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9
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Torralba J, de la Arada I, Partida-Hanon A, Rujas E, Arribas M, Insausti S, Valotteau C, Valle J, Andreu D, Caaveiro JMM, Jiménez MA, Apellániz B, Redondo-Morata L, Nieva JL. Molecular recognition of a membrane-anchored HIV-1 pan-neutralizing epitope. Commun Biol 2022; 5:1265. [DOI: 10.1038/s42003-022-04219-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022] Open
Abstract
AbstractAntibodies against the carboxy-terminal section of the membrane-proximal external region (C-MPER) of the HIV-1 envelope glycoprotein (Env) are considered as nearly pan-neutralizing. Development of vaccines capable of producing analogous broadly neutralizing antibodies requires deep understanding of the mechanism that underlies C-MPER recognition in membranes. Here, we use the archetypic 10E8 antibody and a variety of biophysical techniques including single-molecule approaches to study the molecular recognition of C-MPER in membrane mimetics. In contrast to the assumption that an interfacial MPER helix embodies the entire C-MPER epitope recognized by 10E8, our data indicate that transmembrane domain (TMD) residues contribute to binding affinity and specificity. Moreover, anchoring to membrane the helical C-MPER epitope through the TMD augments antibody binding affinity and relieves the effects exerted by the interfacial MPER helix on the mechanical stability of the lipid bilayer. These observations support that addition of TMD residues may result in more efficient and stable anti-MPER vaccines.
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10
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Yang S, Hiotis G, Wang Y, Chen J, Wang JH, Kim M, Reinherz EL, Walz T. Dynamic HIV-1 spike motion creates vulnerability for its membrane-bound tripod to antibody attack. Nat Commun 2022; 13:6393. [PMID: 36302771 PMCID: PMC9610346 DOI: 10.1038/s41467-022-34008-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/06/2022] [Indexed: 12/25/2022] Open
Abstract
Vaccines targeting HIV-1's gp160 spike protein are stymied by high viral mutation rates and structural chicanery. gp160's membrane-proximal external region (MPER) is the target of naturally arising broadly neutralizing antibodies (bnAbs), yet MPER-based vaccines fail to generate bnAbs. Here, nanodisc-embedded spike protein was investigated by cryo-electron microscopy and molecular-dynamics simulations, revealing spontaneous ectodomain tilting that creates vulnerability for HIV-1. While each MPER protomer radiates centrally towards the three-fold axis contributing to a membrane-associated tripod structure that is occluded in the upright spike, tilting provides access to the opposing MPER. Structures of spike proteins with bound 4E10 bnAb Fabs reveal that the antibody binds exposed MPER, thereby altering MPER dynamics, modifying average ectodomain tilt, and imposing strain on the viral membrane and the spike's transmembrane segments, resulting in the abrogation of membrane fusion and informing future vaccine development.
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Affiliation(s)
- Shuang Yang
- grid.134907.80000 0001 2166 1519Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY USA
| | - Giorgos Hiotis
- grid.134907.80000 0001 2166 1519Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY USA ,grid.134907.80000 0001 2166 1519Tri-Institutional PhD Program in Chemical Biology, The Rockefeller University, New York, NY USA
| | - Yi Wang
- grid.65499.370000 0001 2106 9910Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Harvard Medical School, Boston, MA USA
| | - Junjian Chen
- grid.65499.370000 0001 2106 9910Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Harvard Medical School, Boston, MA USA
| | - Jia-huai Wang
- grid.65499.370000 0001 2106 9910Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA USA ,grid.65499.370000 0001 2106 9910Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Pediatrics, Harvard Medical School, Boston, MA USA
| | - Mikyung Kim
- grid.65499.370000 0001 2106 9910Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Dermatology, Harvard Medical School, Boston, MA USA
| | - Ellis L. Reinherz
- grid.65499.370000 0001 2106 9910Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Harvard Medical School, Boston, MA USA
| | - Thomas Walz
- grid.134907.80000 0001 2166 1519Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY USA
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11
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Insausti S, Garcia-Porras M, Torralba J, Morillo I, Ramos-Caballero A, de la Arada I, Apellaniz B, Caaveiro JMM, Carravilla P, Eggeling C, Rujas E, Nieva JL. Functional Delineation of a Protein-Membrane Interaction Hotspot Site on the HIV-1 Neutralizing Antibody 10E8. Int J Mol Sci 2022; 23:ijms231810767. [PMID: 36142694 PMCID: PMC9504841 DOI: 10.3390/ijms231810767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/29/2022] Open
Abstract
Antibody engagement with the membrane-proximal external region (MPER) of the envelope glycoprotein (Env) of HIV-1 constitutes a distinctive molecular recognition phenomenon, the full appreciation of which is crucial for understanding the mechanisms that underlie the broad neutralization of the virus. Recognition of the HIV-1 Env antigen seems to depend on two specific features developed by antibodies with MPER specificity: (i) a large cavity at the antigen-binding site that holds the epitope amphipathic helix; and (ii) a membrane-accommodating Fab surface that engages with viral phospholipids. Thus, besides the main Fab-peptide interaction, molecular recognition of MPER depends on semi-specific (electrostatic and hydrophobic) interactions with membranes and, reportedly, on specific binding to the phospholipid head groups. Here, based on available cryo-EM structures of Fab-Env complexes of the anti-MPER antibody 10E8, we sought to delineate the functional antibody-membrane interface using as the defining criterion the neutralization potency and binding affinity improvements induced by Arg substitutions. This rational, Arg-based mutagenesis strategy revealed the position-dependent contribution of electrostatic interactions upon inclusion of Arg-s at the CDR1, CDR2 or FR3 of the Fab light chain. Moreover, the contribution of the most effective Arg-s increased the potency enhancement induced by inclusion of a hydrophobic-at-interface Phe at position 100c of the heavy chain CDR3. In combination, the potency and affinity improvements by Arg residues delineated a protein-membrane interaction site, whose surface and position support a possible mechanism of action for 10E8-induced neutralization. Functional delineation of membrane-interacting patches could open new lines of research to optimize antibodies of therapeutic interest that target integral membrane epitopes.
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Affiliation(s)
- Sara Insausti
- Instituto Biofisika (CSIC-UPV/EHU), University of the Basque Country (UPV/EHU), 48080 Bilbao, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), 48080 Bilbao, Spain
| | - Miguel Garcia-Porras
- Instituto Biofisika (CSIC-UPV/EHU), University of the Basque Country (UPV/EHU), 48080 Bilbao, Spain
| | - Johana Torralba
- Instituto Biofisika (CSIC-UPV/EHU), University of the Basque Country (UPV/EHU), 48080 Bilbao, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), 48080 Bilbao, Spain
| | - Izaskun Morillo
- Instituto Biofisika (CSIC-UPV/EHU), University of the Basque Country (UPV/EHU), 48080 Bilbao, Spain
| | - Ander Ramos-Caballero
- Instituto Biofisika (CSIC-UPV/EHU), University of the Basque Country (UPV/EHU), 48080 Bilbao, Spain
| | - Igor de la Arada
- Instituto Biofisika (CSIC-UPV/EHU), University of the Basque Country (UPV/EHU), 48080 Bilbao, Spain
| | - Beatriz Apellaniz
- Department of Physiology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad, 7, 01006 Vitoria-Gasteiz, Spain
| | - Jose M. M. Caaveiro
- Laboratory of Global Healthcare, School of Pharmaceutical Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Pablo Carravilla
- Leibniz Institute of Photonic Technology e.V., 07745 Jena, Germany
| | - Christian Eggeling
- Leibniz Institute of Photonic Technology e.V., 07745 Jena, Germany
- Faculty of Physics and Astronomy, Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, 07743 Jena, Germany
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX1 2JD, UK
| | - Edurne Rujas
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
- Pharmacokinetic, Nanotechnology and Gene Therapy Group, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
- Microbiology, Infectious Disease, Antimicrobial Agents, and Gene Therapy, Bioaraba, 01006 Vitoria-Gasteiz, Spain
- Correspondence: (E.R.); (J.L.N.)
| | - Jose L. Nieva
- Instituto Biofisika (CSIC-UPV/EHU), University of the Basque Country (UPV/EHU), 48080 Bilbao, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), 48080 Bilbao, Spain
- Correspondence: (E.R.); (J.L.N.)
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12
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Lee JH, Yin R, Ofek G, Pierce BG. Structural Features of Antibody-Peptide Recognition. Front Immunol 2022; 13:910367. [PMID: 35874680 PMCID: PMC9302003 DOI: 10.3389/fimmu.2022.910367] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/08/2022] [Indexed: 11/22/2022] Open
Abstract
Antibody recognition of antigens is a critical element of adaptive immunity. One key class of antibody-antigen complexes is comprised of antibodies targeting linear epitopes of proteins, which in some cases are conserved elements of viruses and pathogens of relevance for vaccine design and immunotherapy. Here we report a detailed analysis of the structural and interface features of this class of complexes, based on a set of nearly 200 nonredundant high resolution antibody-peptide complex structures that were assembled from the Protein Data Bank. We found that antibody-bound peptides adopt a broad range of conformations, often displaying limited secondary structure, and that the same peptide sequence bound by different antibodies can in many cases exhibit varying conformations. Propensities of contacts with antibody loops and extent of antibody binding conformational changes were found to be broadly similar to those for antibodies in complex with larger protein antigens. However, antibody-peptide interfaces showed lower buried surface areas and fewer hydrogen bonds than antibody-protein antigen complexes, while calculated binding energy per buried interface area was found to be higher on average for antibody-peptide interfaces, likely due in part to a greater proportion of buried hydrophobic residues and higher shape complementarity. This dataset and these observations can be of use for future studies focused on this class of interactions, including predictive computational modeling efforts and the design of antibodies or epitope-based vaccine immunogens.
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Affiliation(s)
- Jessica H. Lee
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
| | - Rui Yin
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States,University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, United States
| | - Gilad Ofek
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States,University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, United States
| | - Brian G. Pierce
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States,University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, United States,University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, United States,*Correspondence: Brian G. Pierce,
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13
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Global Increases in Human Immunodeficiency Virus Neutralization Sensitivity Due to Alterations in the Membrane-Proximal External Region of the Envelope Glycoprotein Can Be Minimized by Distant State 1-Stabilizing Changes. J Virol 2022; 96:e0187821. [PMID: 35289647 DOI: 10.1128/jvi.01878-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Binding to the receptor, CD4, drives the pretriggered, "closed" (State-1) conformation of the human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer ([gp120/gp41]3) into more "open" conformations. HIV-1 Env on the viral membrane is maintained in a State-1 conformation that resists binding and neutralization by commonly elicited antibodies. Premature triggering of Env before the virus engages a target cell typically leads to increased susceptibility to spontaneous inactivation or ligand-induced neutralization. Here, we showed that single amino acid substitutions in the gp41 membrane-proximal external region (MPER) of a primary HIV-1 strain resulted in viral phenotypes indicative of premature triggering of Env to downstream conformations. Specifically, the MPER changes reduced viral infectivity and globally increased virus sensitivity to poorly neutralizing antibodies, soluble CD4, a CD4-mimetic compound, and exposure to cold. In contrast, the MPER mutants exhibited decreased sensitivity to the State 1-preferring inhibitor, BMS-806, and to the PGT151 broadly neutralizing antibody. Depletion of cholesterol from virus particles did not produce the same State 1-destabilizing phenotypes as MPER alterations. Notably, State 1-stabilizing changes in Env distant from the MPER could minimize the phenotypic effects of MPER alteration but did not affect virus sensitivity to cholesterol depletion. Thus, membrane-proximal gp41 elements contribute to the maintenance of the pretriggered Env conformation. The conformationally disruptive effects of MPER changes can be minimized by distant State 1-stabilizing Env modifications, a strategy that may be useful in preserving the native pretriggered state of Env. IMPORTANCE The pretriggered shape of the human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) is a major target for antibodies that can neutralize many strains of the virus. An effective HIV-1 vaccine may need to raise these types of antibodies, but this goal has proven difficult. One reason is that the pretriggered shape of Env is unstable and dependent on interactions near the viral membrane. Here, we showed that the membrane-proximal external region (MPER) of Env plays an important role in maintaining Env in a pretriggered shape. Alterations in the MPER resulted in global changes in Env conformation that disrupted its pretriggered shape. We also found that these disruptive effects of MPER changes could be minimized by distant Env modifications that stabilized the pretriggered shape. These modifications may be useful for preserving the native shape of Env for structural and vaccine studies.
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14
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Single-chain variable fragments of broadly neutralizing antibodies prevent HIV cell-cell transmission. J Virol 2021; 96:e0193421. [PMID: 34935437 DOI: 10.1128/jvi.01934-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Broadly neutralizing antibodies (bNAbs) are able to prevent HIV infection following passive administration. Single-chain variable fragments (scFv) may have advantages over IgG as their smaller size permits improved diffusion into mucosal tissues. We have previously shown that scFv of bNAbs retain significant breadth and potency against cell-free viral transmission in a TZM-bl assay. However, scFv have not been tested for their ability to block cell-cell transmission, a model in which full-sized bNAbs lose potency. We tested 4 scFv (CAP256.25, PGT121, 3BNC117 and 10E8v4) compared to IgG, in free-virus and cell-cell neutralization assays in A3.01 cells, against a panel of seven heterologous viruses. We show that free-virus neutralization titers in the TZM-bl and A3.01 assays were not significantly different, and confirm that scFv show a 1 to 32-fold reduction in activity in the cell-free model, compared to IgG. However, whereas IgG show 3.4 to 19-fold geometric mean potency loss in cell-cell neutralization compared to free-virus transmission, scFv had more comparable activity in the two assays, with only a 1.3 to 2.3-fold reduction. Geometric mean IC50 of scFv for cell-cell transmission ranged from 0.65 μg/ml (10E8v4) to 2.3 μg/ml (3BNC117) with IgG and scFv neutralization showing similar potency against cell-associated transmission. Therefore, despite the reduced activity of scFv in cell-free assays, their retention of activity in the cell-cell format may make scFv useful for the prevention of both modes of transmission in HIV prevention studies. Importance Broadly neutralizing antibodies (bNAbs) are a major focus for passive immunization against HIV, with the recently concluded HVTN AMP (Antibody Mediated Protection) trial providing proof of concept. Most studies focus on cell-free HIV, however cell-associated virus may play a significant role in HIV infection, pathogenesis and latency. Single-chain variable fragments (scFv) of antibodies may have increased tissue penetration, and reduced immunogenicity. We previously demonstrated that scFv of four HIV-directed bNAbs (CAP256-VRC26.25, PGT121, 3BNC117 and 10E8v4) retain significant potency and breadth against cell-free HIV. As some bNAbs have been shown to lose potency against cell-associated virus, we investigated the ability of bNAb scFv to neutralize this mode of transmission. We demonstrate that unlike IgG, scFv of bNAbs are able to neutralize cell-free and cell-associated virus with similar potency. These scFv, which show functional activity in the therapeutic range, may therefore be suitable for further development as passive immunity for HIV prevention.
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15
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McIlwain BC, Erwin AL, Davis AR, Ben Koff B, Chang L, Bylund T, Chuang GY, Kwong PD, Ohi MD, Lai YT, Stockbridge RB. N-terminal Transmembrane-Helix Epitope Tag for X-ray Crystallography and Electron Microscopy of Small Membrane Proteins. J Mol Biol 2021; 433:166909. [PMID: 33676924 PMCID: PMC8292168 DOI: 10.1016/j.jmb.2021.166909] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 12/21/2022]
Abstract
Structural studies of membrane proteins, especially small membrane proteins, are associated with well-known experimental challenges. Complexation with monoclonal antibody fragments is a common strategy to augment such proteins; however, generating antibody fragments that specifically bind a target protein is not trivial. Here we identify a helical epitope, from the membrane-proximal external region (MPER) of the gp41-transmembrane subunit of the HIV envelope protein, that is recognized by several well-characterized antibodies and that can be fused as a contiguous extension of the N-terminal transmembrane helix of a broad range of membrane proteins. To analyze whether this MPER-epitope tag might aid structural studies of small membrane proteins, we determined an X-ray crystal structure of a membrane protein target that does not crystallize without the aid of crystallization chaperones, the Fluc fluoride channel, fused to the MPER epitope and in complex with antibody. We also demonstrate the utility of this approach for single particle electron microscopy with Fluc and two additional small membrane proteins that represent different membrane protein folds, AdiC and GlpF. These studies show that the MPER epitope provides a structurally defined, rigid docking site for antibody fragments that is transferable among diverse membrane proteins and can be engineered without prior structural information. Antibodies that bind to the MPER epitope serve as effective crystallization chaperones and electron microscopy fiducial markers, enabling structural studies of challenging small membrane proteins.
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Affiliation(s)
- Benjamin C McIlwain
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Amanda L Erwin
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48019, United States
| | - Alexander R Davis
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, United States
| | - B Ben Koff
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Louise Chang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States
| | - Tatsiana Bylund
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, United States
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, United States
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, United States
| | - Melanie D Ohi
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48019, United States.
| | - Yen-Ting Lai
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, United States; Moderna Therapeutics, 200 Technology Square, Cambridge, MA 02139, United States.
| | - Randy B Stockbridge
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, United States; Program in Biophysics, University of Michigan, Ann Arbor, MI 48109, United States.
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16
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Do Kwon Y, Wang XE, Bender MF, Yang R, Li Y, McKee K, Rawi R, O’Dell S, Schneck NA, Shaddeau A, Zhang B, Arnold FJ, Connors M, Doria-Rose NA, Kwong PD, Lei QP. Structures of HIV-1 Neutralizing Antibody 10E8 Delineate the Mechanistic Basis of Its Multi-Peak Behavior on Size-Exclusion Chromatography. Antibodies (Basel) 2021; 10:antib10020023. [PMID: 34200826 PMCID: PMC8293163 DOI: 10.3390/antib10020023] [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: 02/19/2021] [Revised: 05/20/2021] [Accepted: 05/30/2021] [Indexed: 11/16/2022] Open
Abstract
Antibody 10E8 is capable of effectively neutralizing HIV through its recognition of the membrane-proximal external region (MPER), and a suitably optimized version of 10E8 might have utility in HIV therapy and prophylaxis. However, 10E8 displays a three-peak profile on size-exclusion chromatography (SEC), complicating its manufacture. Here we show cis-trans conformational isomerization of the Tyr-Pro-Pro (YPP) motif in the heavy chain 3rd complementarity-determining region (CDR H3) of antibody 10E8 to be the mechanistic basis of its multipeak behavior. We observed 10E8 to undergo slow conformational isomerization and delineate a mechanistic explanation for effective comodifiers that were able to resolve its SEC heterogeneity and to allow an evaluation of the critical quality attribute of aggregation. We determined crystal structures of single and double alanine mutants of a key di-proline motif and of a light chain variant, revealing alternative conformations of the CDR H3. We also replicated both multi-peak and delayed SEC behavior with MPER-antibodies 4E10 and VRC42, by introducing a Tyr-Pro (YP) motif into their CDR H3s. Our results show how a conformationally dynamic CDR H3 can provide the requisite structural plasticity needed for a highly hydrophobic paratope to recognize its membrane-proximal epitope.
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Affiliation(s)
- Young Do Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
| | - Xiangchun E. Wang
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
| | - Michael F. Bender
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
| | - Rong Yang
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
| | - Yile Li
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
| | - Sijy O’Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
| | - Nicole A. Schneck
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
| | - Andrew Shaddeau
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
| | - Frank J. Arnold
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
| | - Mark Connors
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Nicole A. Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.D.K.); (M.F.B.); (K.M.); (R.R.); (S.O.); (B.Z.); (N.A.D.-R.)
- Correspondence: (P.D.K.); (Q.P.L.)
| | - Q. Paula Lei
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD 20878, USA; (X.E.W.); (R.Y.); (Y.L.); (N.A.S.); (A.S.); (F.J.A.)
- Correspondence: (P.D.K.); (Q.P.L.)
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17
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Caillat C, Guilligay D, Sulbaran G, Weissenhorn W. Neutralizing Antibodies Targeting HIV-1 gp41. Viruses 2020; 12:E1210. [PMID: 33114242 PMCID: PMC7690876 DOI: 10.3390/v12111210] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/20/2020] [Accepted: 10/20/2020] [Indexed: 12/21/2022] Open
Abstract
HIV-1 vaccine research has obtained an enormous boost since the discovery of many broadly neutralizing antibodies (bnAbs) targeting all accessible sites on the HIV-1 envelope glycoprotein (Env). This in turn facilitated high-resolution structures of the Env glycoprotein in complex with bnAbs. Here we focus on gp41, its highly conserved heptad repeat region 1 (HR1), the fusion peptide (FP) and the membrane-proximal external region (MPER). Notably, the broadest neutralizing antibodies target MPER. Both gp41 HR1 and MPER are only fully accessible once receptor-induced conformational changes have taken place, although some studies suggest access to MPER in the close to native Env conformation. We summarize the data on the structure and function of neutralizing antibodies targeting gp41 HR1, FP and MPER and we review their access to Env and their complex formation with gp41 HR1, MPER peptides and FP within native Env. We further discuss MPER bnAb binding to lipids and the role of somatic mutations in recognizing a bipartite epitope composed of the conserved MPER sequence and membrane components. The problematic of gp41 HR1 access and MPER bnAb auto- and polyreactivity is developed in the light of inducing such antibodies by vaccination.
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Affiliation(s)
- Christophe Caillat
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, Commissariat à L'énergie Atomique et Aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), 38000 Grenoble, France
| | - Delphine Guilligay
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, Commissariat à L'énergie Atomique et Aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), 38000 Grenoble, France
| | - Guidenn Sulbaran
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, Commissariat à L'énergie Atomique et Aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), 38000 Grenoble, France
| | - Winfried Weissenhorn
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, Commissariat à L'énergie Atomique et Aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), 38000 Grenoble, France
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18
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The influence of proline isomerization on potency and stability of anti-HIV antibody 10E8. Sci Rep 2020; 10:14313. [PMID: 32868832 PMCID: PMC7458915 DOI: 10.1038/s41598-020-71184-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/27/2020] [Indexed: 12/22/2022] Open
Abstract
Monoclonal antibody (mAb) 10E8 recognizes a highly conserved epitope on HIV and is capable of neutralizing > 95% of circulating viral isolates making it one of the most promising Abs against HIV. Solution instability and biochemical heterogeneity of 10E8 has hampered its development for clinical use. We identify the source of 10E8 heterogeneity being linked to cis/trans isomerization at two prolines within the YPP motif in the CRD3 loop that exists as two predominant conformers that interconvert on a slow timescale. The YtransP conformation conformer can bind the HIV gp41 epitope, while the YcisP is not binding competent and shows a higher aggregation propensity. The high barrier of isomerization and propensity to adopt non-binding competent proline conformers provides novel insight into the slow binding kinetics, low potency, and poor solubility of 10E8. This study highlights how proline isomerization should be considered a critical quality attribute for biotherapeutics with paratopes containing potential cis proline amide bonds.
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19
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Rujas E, Insausti S, Leaman DP, Carravilla P, González-Resines S, Monceaux V, Sánchez-Eugenia R, García-Porras M, Iloro I, Zhang L, Elortza F, Julien JP, Saéz-Cirión A, Zwick MB, Eggeling C, Ojida A, Domene C, Caaveiro JMM, Nieva JL. Affinity for the Interface Underpins Potency of Antibodies Operating In Membrane Environments. Cell Rep 2020; 32:108037. [PMID: 32814041 PMCID: PMC7861656 DOI: 10.1016/j.celrep.2020.108037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/02/2020] [Accepted: 07/23/2020] [Indexed: 11/29/2022] Open
Abstract
The contribution of membrane interfacial interactions to recognition of membrane-embedded antigens by antibodies is currently unclear. This report demonstrates the optimization of this type of antibodies via chemical modification of regions near the membrane but not directly involved in the recognition of the epitope. Using the HIV-1 antibody 10E8 as a model, linear and polycyclic synthetic aromatic compounds are introduced at selected sites. Molecular dynamics simulations predict the favorable interactions of these synthetic compounds with the viral lipid membrane, where the epitope of the HIV-1 glycoprotein Env is located. Chemical modification of 10E8 with aromatic acetamides facilitates the productive and specific recognition of the native antigen, partially buried in the crowded environment of the viral membrane, resulting in a dramatic increase of its capacity to block viral infection. These observations support the harnessing of interfacial affinity through site-selective chemical modification to optimize the function of antibodies that target membrane-proximal epitopes.
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Affiliation(s)
- Edurne Rujas
- Instituto Biofisika (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain; Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Sara Insausti
- Instituto Biofisika (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
| | - Daniel P Leaman
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pablo Carravilla
- Instituto Biofisika (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain; Institute of Applied Optics and Biophysics Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743 Jena, Germany; Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745 Jena, Germany
| | | | - Valérie Monceaux
- Institut Pasteur, Unité HIV Inflammation et Persistance, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Rubén Sánchez-Eugenia
- Instituto Biofisika (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
| | - Miguel García-Porras
- Instituto Biofisika (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
| | - Ibon Iloro
- Proteomics Platform, CIC bioGUNE, Parque Tecnológico de Vizcaya, 48160 Derio, Spain
| | - Lei Zhang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Félix Elortza
- Proteomics Platform, CIC bioGUNE, Parque Tecnológico de Vizcaya, 48160 Derio, Spain
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Asier Saéz-Cirión
- Institut Pasteur, Unité HIV Inflammation et Persistance, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Michael B Zwick
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christian Eggeling
- Institute of Applied Optics and Biophysics Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743 Jena, Germany; Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Akio Ojida
- Department of Chemical Biology, School of Pharmaceutical Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Carmen Domene
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AX, UK; Department of Chemistry, University of Oxford, Oxford OX1 3TF, UK
| | - Jose M M Caaveiro
- Laboratory of Global Health Care, School of Pharmaceutical Sciences, Kyushu University, Fukuoka 819-0395, Japan.
| | - José L Nieva
- Instituto Biofisika (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain.
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20
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Torralba J, de la Arada I, Carravilla P, Insausti S, Rujas E, Largo E, Eggeling C, Arrondo JLR, Apellániz B, Nieva JL. Cholesterol Constrains the Antigenic Configuration of the Membrane-Proximal Neutralizing HIV-1 Epitope. ACS Infect Dis 2020; 6:2155-2168. [PMID: 32584020 DOI: 10.1021/acsinfecdis.0c00243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The envelope glycoprotein (Env) enables HIV-1 cell entry through fusion of host-cell and viral membranes induced by the transmembrane subunit gp41. Antibodies targeting the C-terminal sequence of the membrane-proximal external region (C-MPER) block the fusogenic activity of gp41 and achieve neutralization of divergent HIV-1 strains and isolates. Thus, recreating the structure that generates broadly neutralizing C-MPER antibodies during infection is a major goal in HIV vaccine development. Here, we have reconstituted a peptide termed CpreTM-TMD in a membrane environment. This peptide contains the C-MPER epitope and the minimum TMD residues required for the anchorage of the Env glycoprotein to the viral membrane. In addition, we have used antibody 10E8 variants to gauge the antigenic configuration attained by CpreTM-TMD as a function of the membrane cholesterol content, a functional determinant of the HIV envelope and liposome-based vaccines. Differential binding of the 10E8 variants and the trend of the IgG responses recovered from rabbits immunized with liposome-peptide formulations, suggested that cholesterol may restrict 10E8 accessibility to the C-MPER epitope. Our data ruled out the destabilization of the lipid bilayer architecture in CpreTM-TMD-containing membranes, and pointed to the perturbation of the helical conformation by lipid packing as the cause of the antigenic configuration loss induced by cholesterol. Overall, our results provide additional insights into the structural basis of the Env complex anchoring to membranes, and suggest new approaches to the design of effective immunogens directed against the near pan-neutralizing HIV-1 epitope C-MPER.
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Affiliation(s)
- Johana Torralba
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
| | - Igor de la Arada
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
| | - Pablo Carravilla
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien Platz 1, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Sara Insausti
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
| | - Edurne Rujas
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
| | - Eneko Largo
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
- Department of Immunology, Microbiology and Parasitology, Medicine and Odontology Faculty, University of Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
| | - Christian Eggeling
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien Platz 1, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745 Jena, Germany
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, OX3 9DS Oxford, U.K
| | - José L R Arrondo
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
| | - Beatriz Apellániz
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
- Department of Physiology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad, 7, 01006 Vitoria-Gasteiz, Spain
| | - José L Nieva
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
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21
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Kwon B, Mandal T, Elkins MR, Oh Y, Cui Q, Hong M. Cholesterol Interaction with the Trimeric HIV Fusion Protein gp41 in Lipid Bilayers Investigated by Solid-State NMR Spectroscopy and Molecular Dynamics Simulations. J Mol Biol 2020; 432:4705-4721. [PMID: 32592698 PMCID: PMC7781112 DOI: 10.1016/j.jmb.2020.06.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/07/2020] [Accepted: 06/18/2020] [Indexed: 12/13/2022]
Abstract
HIV-1 entry into cells is mediated by the fusion protein gp41. Cholesterol plays an important role in this virus-cell fusion, but molecular structural information about cholesterol-gp41 interaction is so far absent. Here, we present experimental and computational data about cholesterol complexation with gp41 in lipid bilayers. We focus on the C-terminal region of the protein, which comprises a membrane-proximal external region (MPER) and the transmembrane domain (TMD). We measured peptide-cholesterol contacts in virus-mimetic lipid bilayers using solid-state NMR spectroscopy, and augmented these experimental data with all-atom molecular dynamics simulations. 2D 19F NMR spectra show correlation peaks between MPER residues and the cholesterol isooctyl tail, indicating that cholesterol is in molecular contact with the MPER-TMD trimer. 19F-13C distance measurements between the peptide and 13C-labeled cholesterol show that C17 on the D ring and C9 at the intersection of B and C rings are ~7.0 Å from the F673 side-chain 4-19F. At high peptide concentrations in the membrane, the 19F-13C distance data indicate three cholesterol molecules bound near F673 in each trimer. Mutation of a cholesterol recognition amino acid consensus motif did not change these distances, indicating that cholesterol binding does not require this sequence motif. Molecular dynamics simulations further identify two hotspots for cholesterol interactions. Taken together, these experimental data and simulations indicate that the helix-turn-helix conformation of the MPER-TMD is responsible for sequestering cholesterol. We propose that this gp41-cholesterol interaction mediates virus-cell fusion by recruiting gp41 to the boundary of the liquid-disordered and liquid-ordered phases to incur membrane curvature.
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Affiliation(s)
- Byungsu Kwon
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA
| | - Taraknath Mandal
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA
| | - Matthew R Elkins
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA
| | - Younghoon Oh
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA; Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA.
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22
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New GMP manufacturing processes to obtain thermostable HIV-1 gp41 virosomes under solid forms for various mucosal vaccination routes. NPJ Vaccines 2020; 5:41. [PMID: 32435515 PMCID: PMC7235025 DOI: 10.1038/s41541-020-0190-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/28/2020] [Indexed: 01/02/2023] Open
Abstract
The main objective of the MACIVIVA European consortium was to develop new Good Manufacturing Practice pilot lines for manufacturing thermostable vaccines with stabilized antigens on influenza virosomes as enveloped virus-like particles. The HIV-1 gp41-derived antigens anchored in the virosome membrane, along with the adjuvant 3M-052 (TLR7/8 agonist) on the same particle, served as a candidate vaccine for the proof of concept for establishing manufacturing processes, which can be directly applied or adapted to other virosomal vaccines or lipid-based particles. Heat spray-dried powders suitable for nasal or oral delivery, and freeze-dried sublingual tablets were successfully developed as solid dosage forms for mucosal vaccination. The antigenic properties of vaccinal antigens with key gp41 epitopes were maintained, preserving the original immunogenicity of the starting liquid form, and also when solid forms were exposed to high temperature (40 °C) for up to 3 months, with minimal antigen and adjuvant content variation. Virosomes reconstituted from the powder forms remained as free particles with similar size, virosome uptake by antigen-presenting cells in vitro was comparable to virosomes from the liquid form, and the presence of excipients specific to each solid form did not prevent virosome transport to the draining lymph nodes of immunized mice. Virosome integrity was also preserved during exposure to <−15 °C, mimicking accidental freezing conditions. These “ready to use and all-in-one” thermostable needle-free virosomal HIV-1 mucosal vaccines offer the advantage of simplified logistics with a lower dependence on the cold chain during shipments and distribution.
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23
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Rantalainen K, Berndsen ZT, Antanasijevic A, Schiffner T, Zhang X, Lee WH, Torres JL, Zhang L, Irimia A, Copps J, Zhou KH, Kwon YD, Law WH, Schramm CA, Verardi R, Krebs SJ, Kwong PD, Doria-Rose NA, Wilson IA, Zwick MB, Yates JR, Schief WR, Ward AB. HIV-1 Envelope and MPER Antibody Structures in Lipid Assemblies. Cell Rep 2020; 31:107583. [PMID: 32348769 PMCID: PMC7196886 DOI: 10.1016/j.celrep.2020.107583] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 03/05/2020] [Accepted: 04/07/2020] [Indexed: 11/25/2022] Open
Abstract
Structural and functional studies of HIV envelope glycoprotein (Env) as a transmembrane protein have long been complicated by challenges associated with inherent flexibility of the molecule and the membrane-embedded hydrophobic regions. Here, we present approaches for incorporating full-length, wild-type HIV-1 Env, as well as C-terminally truncated and stabilized versions, into lipid assemblies, providing a modular platform for Env structural studies by single particle electron microscopy. We reconstitute a full-length Env clone into a nanodisc, complex it with a membrane-proximal external region (MPER) targeting antibody 10E8, and structurally define the full quaternary epitope of 10E8 consisting of lipid, MPER, and ectodomain contacts. By aligning this and other Env-MPER antibody complex reconstructions with the lipid bilayer, we observe evidence of Env tilting as part of the neutralization mechanism for MPER-targeting antibodies. We also adapt the platform toward vaccine design purposes by introducing stabilizing mutations that allow purification of unliganded Env with a peptidisc scaffold.
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Affiliation(s)
- Kimmo Rantalainen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Zachary T Berndsen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Torben Schiffner
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xi Zhang
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Lei Zhang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Adriana Irimia
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kenneth H Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Young D Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - William H Law
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Raffaello Verardi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Shelly J Krebs
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael B Zwick
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - William R Schief
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02129, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA.
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24
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Neutralization Breadth and Potency of Single-Chain Variable Fragments Derived from Broadly Neutralizing Antibodies Targeting Multiple Epitopes on the HIV-1 Envelope. J Virol 2020; 94:JVI.01533-19. [PMID: 31619559 DOI: 10.1128/jvi.01533-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 10/08/2019] [Indexed: 12/25/2022] Open
Abstract
Passive administration of HIV-directed broadly neutralizing antibodies (bNAbs) can prevent infection in animal models, and human efficacy trials are under way. Single-chain variable fragments (scFv), comprised of only the variable regions of antibody heavy and light chains, are smaller molecules that may offer advantages over full-length IgG. We designed and expressed scFv of HIV bNAbs prioritized for clinical testing that target the V2-apex (CAP256-VRC26.25), V3-glycan supersite (PGT121), CD4 binding site (3BNC117), and MPER (10E8v4). The use of either a 15- or 18-amino-acid glycine-serine linker between the heavy- and light-chain fragments provided adequate levels of scFv expression. When tested against a 45-multisubtype virus panel, all four scFv retained good neutralizing activity, although there was variable loss of function compared to the parental IgG antibodies. For CAP256-VRC26.25, there was a significant 138-fold loss of potency that was in part related to differential interaction with charged amino acids at positions 169 and 170 in the V2 epitope. Potency was reduced for the 3BNC117 (13-fold) and PGT121 (4-fold) scFv among viruses lacking the N276 and N332 glycans, respectively, and in viruses with a longer V1 loop for PGT121. This suggested that scFv interacted with their epitopes in subtly different ways, with variation at key residues affecting scFv neutralization more than the matched IgGs. Remarkably, the scFv of 10E8v4 maintained breadth of 100% with only a minor reduction in potency. Overall, scFv of clinically relevant bNAbs had significant neutralizing activity, indicating that they are suitable for passive immunization to prevent HIV-1 infection.IMPORTANCE Monoclonal antibodies have been isolated against conserved epitopes on the HIV trimer and are being investigated for passive immunization. Some of the challenges associated with full-sized antibody proteins may be overcome by using single-chain variable fragments (scFv). These smaller forms of antibodies can be produced more efficiently, may show fewer off-target effects with increased tissue penetration, and are more adaptable to vectored-mediated expression than IgG. Here, we demonstrate that scFv of four HIV-directed bNAbs (CAP256-VRC26.25, PGT121, 3BNC117, and 10E8v4) had significant neutralizing activity against diverse global strains of HIV. Loss of potency and/or breadth was shown to be due to increased dependence of the scFv on key residues within the epitope. These smaller antibody molecules with functional activity in the therapeutic range may be suitable for further development as passive immunity for HIV prevention.
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25
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Zhang L, Irimia A, He L, Landais E, Rantalainen K, Leaman DP, Vollbrecht T, Stano A, Sands DI, Kim AS, Poignard P, Burton DR, Murrell B, Ward AB, Zhu J, Wilson IA, Zwick MB. An MPER antibody neutralizes HIV-1 using germline features shared among donors. Nat Commun 2019; 10:5389. [PMID: 31772165 PMCID: PMC6879610 DOI: 10.1038/s41467-019-12973-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 10/11/2019] [Indexed: 11/09/2022] Open
Abstract
The membrane-proximal external region (MPER) of HIV-1 envelope glycoprotein (Env) can be targeted by neutralizing antibodies of exceptional breadth. MPER antibodies usually have long, hydrophobic CDRH3s, lack activity as inferred germline precursors, are often from the minor IgG3 subclass, and some are polyreactive, such as 4E10. Here we describe an MPER broadly neutralizing antibody from the major IgG1 subclass, PGZL1, which shares germline V/D-region genes with 4E10, has a shorter CDRH3, and is less polyreactive. A recombinant sublineage variant pan-neutralizes a 130-isolate panel at 1.4 μg/ml (IC50). Notably, a germline revertant with mature CDR3s neutralizes 12% of viruses and still binds MPER after DJ reversion. Crystal structures of lipid-bound PGZL1 variants and cryo-EM reconstruction of an Env-PGZL1 complex reveal how these antibodies recognize MPER and viral membrane. Discovery of common genetic and structural elements among MPER antibodies from different patients suggests that such antibodies could be elicited using carefully designed immunogens.
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Affiliation(s)
- Lei Zhang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- CTK Biotech, Inc., 3855 Stowe Drive, Poway, California, 92064, USA
| | - Adriana Irimia
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Lingling He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Elise Landais
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative, New York, New York, 10004, USA
| | - Kimmo Rantalainen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Daniel P Leaman
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Thomas Vollbrecht
- Department of Medicine, University of California, San Diego, California, 92093, USA
| | - Armando Stano
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Daniel I Sands
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Arthur S Kim
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- Departments of Medicine, Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, 63110, USA
| | - Pascal Poignard
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative, New York, New York, 10004, USA
- Institut de Biologie Structurale, Université Grenoble Alpes, Commissariat a l'Energie Atomique, Centre National de Recherche Scientifique and Centre Hospitalier Universitaire Grenoble Alpes, 38044, Grenoble, France
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, 92037, USA
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge, Massachussetts, 02114, USA
| | - Ben Murrell
- Department of Medicine, University of California, San Diego, California, 92093, USA
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Jiang Zhu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA.
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA.
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA.
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, 92037, USA.
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, 92037, USA.
| | - Michael B Zwick
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA.
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26
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Carravilla P, Darré L, Oar-Arteta IR, Vesga AG, Rujas E, de Las Heras-Martínez G, Domene C, Nieva JL, Requejo-Isidro J. The Bilayer Collective Properties Govern the Interaction of an HIV-1 Antibody with the Viral Membrane. Biophys J 2019; 118:44-56. [PMID: 31787208 DOI: 10.1016/j.bpj.2019.11.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 10/31/2019] [Accepted: 11/05/2019] [Indexed: 01/15/2023] Open
Abstract
Efficient engagement with the envelope glycoprotein membrane-proximal external region (MPER) results in robust blocking of viral infection by a class of broadly neutralizing antibodies (bnAbs) against human immunodeficiency virus (HIV). Developing an accommodation surface that engages with the viral lipid envelope appears to correlate with the neutralizing potency displayed by these bnAbs. The nature of the interactions established between the antibody and the lipid is nonetheless a matter of debate, with some authors arguing that anti-MPER specificity arises only under pathological conditions in autoantibodies endowed with stereospecific binding sites for phospholipids. However, bnAb-lipid interactions are often studied in systems that do not fully preserve the biophysical properties of lipid bilayers, and therefore, questions on binding specificity and the effect of collective membrane properties on the interaction are still open. Here, to evaluate the specificity of lipid interactions of an anti-MPER bnAb (4E10) in an intact membrane context, we determine quantitatively its association with lipid bilayers by means of scanning fluorescence correlation spectroscopy and all-atom molecular dynamic simulations. Our data support that 4E10 establishes electrostatic and hydrophobic interactions with the viral membrane surface and that the collective physical properties of the lipid bilayer influence 4E10 dynamics therein. We conclude that establishment of peripheral, nonspecific electrostatic interactions with the viral membrane through accommodation surfaces may assist high-affinity binding of HIV-1 MPER epitope at membrane interfaces. These findings highlight the importance of considering antibody-lipid interactions in the design of antibody-based anti-HIV strategies.
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Affiliation(s)
- Pablo Carravilla
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Spain; Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain; Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Jena, Germany
| | - Leonardo Darré
- Functional Genomics Laboratory & Biomolecular Simulations Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Itziar R Oar-Arteta
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Spain; Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Arturo G Vesga
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Spain; Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Edurne Rujas
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Spain; Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | | | - Carmen Domene
- Department of Chemistry, University of Bath, Claverton Down, Bath, United Kingdom; Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Jose L Nieva
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Spain; Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain.
| | - Jose Requejo-Isidro
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Spain; Centro Nacional de Biotecnología, CSIC, Madrid, Spain; Unidad de Nanobiotecnología, CNB-CSIC-IMDEA Nanociencia Associated Unit, Madrid, Spain.
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Pinto D, Fenwick C, Caillat C, Silacci C, Guseva S, Dehez F, Chipot C, Barbieri S, Minola A, Jarrossay D, Tomaras GD, Shen X, Riva A, Tarkowski M, Schwartz O, Bruel T, Dufloo J, Seaman MS, Montefiori DC, Lanzavecchia A, Corti D, Pantaleo G, Weissenhorn W. Structural Basis for Broad HIV-1 Neutralization by the MPER-Specific Human Broadly Neutralizing Antibody LN01. Cell Host Microbe 2019; 26:623-637.e8. [PMID: 31653484 PMCID: PMC6854463 DOI: 10.1016/j.chom.2019.09.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/29/2019] [Accepted: 09/27/2019] [Indexed: 11/24/2022]
Abstract
Potent and broadly neutralizing antibodies (bnAbs) are the hallmark of HIV-1 protection by vaccination. The membrane-proximal external region (MPER) of the HIV-1 gp41 fusion protein is targeted by the most broadly reactive HIV-1 neutralizing antibodies. Here, we examine the structural and molecular mechansims of neutralization by anti-MPER bnAb, LN01, which was isolated from lymph-node-derived germinal center B cells of an elite controller and exhibits broad neutralization breadth. LN01 engages both MPER and the transmembrane (TM) region, which together form a continuous helix in complex with LN01. The tilted TM orientation allows LN01 to interact simultaneously with the peptidic component of the MPER epitope and membrane via two specific lipid binding sites of the antibody paratope. Although LN01 carries a high load of somatic mutations, most key residues interacting with the MPER epitope and lipids are germline encoded, lending support for the LN01 epitope as a candidate for lineage-based vaccine development. bNAb LN01 neutralizes 92% of a 118-strain virus panel LN01 targets the HIV-1 gp41 MPER, the TM region, and lipids LN01-complexed MPER forms a continuous helix with TM Most LN01 paratope residues interacting with MPER-TM and lipids are germline encoded
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Affiliation(s)
- Dora Pinto
- Institute for Research in Biomedicine, Bellinzona 6500, Ticino, Switzerland
| | - Craig Fenwick
- Swiss Vaccine Research Institute, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Christophe Caillat
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38000 Grenoble, France
| | - Chiara Silacci
- Institute for Research in Biomedicine, Bellinzona 6500, Ticino, Switzerland
| | - Serafima Guseva
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38000 Grenoble, France
| | - François Dehez
- LPCT, UMR 7019 Université de Lorraine CNRS, 54500 Vandœuvre-lès-Nancy, France; Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, LPCT, UMR 7019 Universiteé de Lorraine CNRS, Vandœuvre-lès-Nancy 54500, France
| | - Christophe Chipot
- LPCT, UMR 7019 Université de Lorraine CNRS, 54500 Vandœuvre-lès-Nancy, France; Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, LPCT, UMR 7019 Universiteé de Lorraine CNRS, Vandœuvre-lès-Nancy 54500, France; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sonia Barbieri
- Institute for Research in Biomedicine, Bellinzona 6500, Ticino, Switzerland
| | - Andrea Minola
- Humabs Biomed SA, Vir Biotechnology, 6500 Bellinzona, Ticino, Switzerland
| | - David Jarrossay
- Institute for Research in Biomedicine, Bellinzona 6500, Ticino, Switzerland
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Paris Diderot University, Sorbonne Paris Cité, Paris 75013, France
| | | | - Agostino Riva
- Department of Biomedical and Clinical Sciences, Luigi Sacco University Hospital, Università di Milano, 20157 Milan, Italy; III Division of Infectious Diseases, ASST Fatebenefratelli-Sacco, 20157 Milan, Italy
| | - Maciej Tarkowski
- Department of Biomedical and Clinical Sciences, Luigi Sacco University Hospital, Università di Milano, 20157 Milan, Italy
| | - Olivier Schwartz
- Institut Pasteur, Virus & Immunity Unit, CNRS UMR 3569, Paris 75015, France; Vaccine Research Institute, 94000 Créteil, France
| | - Timothée Bruel
- Institut Pasteur, Virus & Immunity Unit, CNRS UMR 3569, Paris 75015, France; Vaccine Research Institute, 94000 Créteil, France
| | - Jérémy Dufloo
- Institut Pasteur, Virus & Immunity Unit, CNRS UMR 3569, Paris 75015, France; Vaccine Research Institute, 94000 Créteil, France; Paris Diderot University, Sorbonne Paris Cité, Paris 75013, France
| | - Michael S Seaman
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - David C Montefiori
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Davide Corti
- Humabs Biomed SA, Vir Biotechnology, 6500 Bellinzona, Ticino, Switzerland.
| | - Giuseppe Pantaleo
- Swiss Vaccine Research Institute, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland; Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland.
| | - Winfried Weissenhorn
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38000 Grenoble, France.
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Topological analysis of the gp41 MPER on lipid bilayers relevant to the metastable HIV-1 envelope prefusion state. Proc Natl Acad Sci U S A 2019; 116:22556-22566. [PMID: 31624123 DOI: 10.1073/pnas.1912427116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The membrane proximal external region (MPER) of HIV-1 envelope glycoprotein (gp) 41 is an attractive vaccine target for elicitation of broadly neutralizing antibodies (bNAbs) by vaccination. However, current details regarding the quaternary structural organization of the MPER within the native prefusion trimer [(gp120/41)3] are elusive and even contradictory, hindering rational MPER immunogen design. To better understand the structural topology of the MPER on the lipid bilayer, the adjacent transmembrane domain (TMD) was appended (MPER-TMD) and studied. Membrane insertion of the MPER-TMD was sensitive both to the TMD sequence and cytoplasmic residues. Antigen binding of MPER-specific bNAbs, in particular 10E8 and DH511.2_K3, was significantly impacted by the presence of the TMD. Furthermore, MPER-TMD assembly into 10-nm diameter nanodiscs revealed a heterogeneous membrane array comprised largely of monomers and dimers, as enumerated by bNAb Fab binding using single-particle electron microscopy analysis, arguing against preferential trimeric association of native MPER and TMD protein segments. Moreover, introduction of isoleucine mutations in the C-terminal heptad repeat to induce an extended MPER α-helical bundle structure yielded an antigenicity profile of cell surface-arrayed Env variants inconsistent with that found in the native prefusion state. In line with these observations, electron paramagnetic resonance analysis suggested that 10E8 inhibits viral membrane fusion by lifting the MPER N-terminal region out of the viral membrane, mandating the exposure of residues that would be occluded by MPER trimerization. Collectively, our data suggest that the MPER is not a stable trimer, but rather a dynamic segment adapted for structural changes accompanying fusion.
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29
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Sutar J, Padwal V, Sonawani A, Nagar V, Patil P, Kulkarni B, Hingankar N, Deshpande S, Idicula-Thomas S, Jagtap D, Bhattacharya J, Bandivdekar A, Patel V. Effect of diversity in gp41 membrane proximal external region of primary HIV-1 Indian subtype C sequences on interaction with broadly neutralizing antibodies 4E10 and 10E8. Virus Res 2019; 273:197763. [PMID: 31553924 DOI: 10.1016/j.virusres.2019.197763] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 10/25/2022]
Abstract
Human Immunodeficiency Virus-1 Clade C (HIV-1C) dominates the AIDS epidemic in India, afflicting 2.1 million individuals within the country and more than 15 million people worldwide. Membrane proximal external region (MPER) is an attractive target for broadly neutralizing antibody (bNAb) based therapies. However, information on MPER sequence diversity from India is meagre due to limited sampling of primary viral sequences. In the present study, we examined the variation in MPER of HIV-1C from 24 individuals in Mumbai, India by high throughput sequencing of uncultured viral sequences. Deep sequencing of MPER (662-683; HXB2 envelope amino acid numbering) allowed quantification of intra-individual variation up to 65% at positions 662, 665, 668, 674 and 677 within this region. These variable positions included contact sites targeted by bNAbs 2F5, Z13e1, 4E10 as well as 10E8. Both major and minor epitope variants i.e. 'haplotypes' were generated for each sample dataset. A total of 23, 34 and 25 unique epitope haplotypes could be identified for bNAbs 2F5, Z13e1 and 4E10/10E8 respectively. Further analysis of 4E10 and 10E8 epitopes from our dataset and meta-analysis of previously reported HIV-1 sequences from India revealed 26 epitopes (7 India-specific), heretofore untested for neutralization sensitivity. Peptide-Ab docking predicted 13 of these to be non-binding to 10E8. ELISA, Surface Plasmon Resonance and peptide inhibition of HIV-1 neutralization assays were then performed which validated predicted weak/non-binding interactions for peptides corresponding to six of these epitopes. These results highlight the under-representation of 10E8 non-binding HIV-1C MPER sequences from India. Our study thus underscores the need for increased surveillance of primary circulating envelope sequences for development of efficacious bNAb-based interventions in India.
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Affiliation(s)
- Jyoti Sutar
- Department of Biochemistry, National Institute for Research in Reproductive Health (ICMR-NIRRH), Parel, Mumbai, India
| | - Varsha Padwal
- Department of Biochemistry, National Institute for Research in Reproductive Health (ICMR-NIRRH), Parel, Mumbai, India
| | - Archana Sonawani
- ICMR Biomedical Informatics Centre, National Institute for Research in Reproductive Health (ICMR-NIRRH), Parel, Mumbai, India
| | - Vidya Nagar
- Department of Medicine, Grant Government Medical College, Byculla, Mumbai, India
| | - Priya Patil
- Department of Medicine, Grant Government Medical College, Byculla, Mumbai, India
| | - Bhalachandra Kulkarni
- Department of Structural Biology, National Institute for Research in Reproductive Health (ICMR-NIRRH), Parel, Mumbai, India
| | - Nitin Hingankar
- HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Suprit Deshpande
- HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Susan Idicula-Thomas
- ICMR Biomedical Informatics Centre, National Institute for Research in Reproductive Health (ICMR-NIRRH), Parel, Mumbai, India
| | - Dhanashree Jagtap
- Department of Structural Biology, National Institute for Research in Reproductive Health (ICMR-NIRRH), Parel, Mumbai, India
| | - Jayanta Bhattacharya
- HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Atmaram Bandivdekar
- Department of Biochemistry, National Institute for Research in Reproductive Health (ICMR-NIRRH), Parel, Mumbai, India.
| | - Vainav Patel
- Department of Biochemistry, National Institute for Research in Reproductive Health (ICMR-NIRRH), Parel, Mumbai, India.
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Zhu H, Mathew E, Connelly SM, Zuber J, Sullivan M, Piepenbrink MS, Kobie JJ, Dumont ME. Identification of variant HIV envelope proteins with enhanced affinities for precursors to anti-gp41 broadly neutralizing antibodies. PLoS One 2019; 14:e0221550. [PMID: 31504041 PMCID: PMC6736307 DOI: 10.1371/journal.pone.0221550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 08/09/2019] [Indexed: 11/19/2022] Open
Abstract
HIV envelope protein (Env) is the sole target of broadly neutralizing antibodies (BNAbs) that are capable of neutralizing diverse strains of HIV. While BNAbs develop spontaneously in a subset of HIV-infected patients, efforts to design an envelope protein-based immunogen to elicit broadly neutralizing antibody responses have so far been unsuccessful. It is hypothesized that a primary barrier to eliciting BNAbs is the fact that HIV envelope proteins bind poorly to the germline-encoded unmutated common ancestor (UCA) precursors to BNAbs. To identify variant forms of Env with increased affinities for the UCA forms of BNAbs 4E10 and 10E8, which target the Membrane Proximal External Region (MPER) of Env, libraries of randomly mutated Env variants were expressed in a yeast surface display system and screened using fluorescence activated cell sorting for cells displaying variants with enhanced abilities to bind the UCA antibodies. Based on analyses of individual clones obtained from the screen and on next-generation sequencing of sorted libraries, distinct but partially overlapping sets of amino acid substitutions conferring enhanced UCA antibody binding were identified. These were particularly enriched in substitutions of arginine for highly conserved tryptophan residues. The UCA-binding variants also generally exhibited enhanced binding to the mature forms of anti-MPER antibodies. Mapping of the identified substitutions into available structures of Env suggest that they may act by destabilizing both the initial pre-fusion conformation and the six-helix bundle involved in fusion of the viral and cell membranes, as well as providing new or expanded epitopes with increased accessibility for the UCA antibodies.
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Affiliation(s)
- Hong Zhu
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Elizabeth Mathew
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Sara M. Connelly
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Jeffrey Zuber
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Mark Sullivan
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Michael S. Piepenbrink
- Infectious Diseases Division, University of Rochester Medical Center, Rochester, NY United States of America
| | - James J. Kobie
- Infectious Diseases Division, University of Rochester Medical Center, Rochester, NY United States of America
| | - Mark E. Dumont
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, United States of America
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31
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Torrents de la Peña A, Rantalainen K, Cottrell CA, Allen JD, van Gils MJ, Torres JL, Crispin M, Sanders RW, Ward AB. Similarities and differences between native HIV-1 envelope glycoprotein trimers and stabilized soluble trimer mimetics. PLoS Pathog 2019; 15:e1007920. [PMID: 31306470 PMCID: PMC6658011 DOI: 10.1371/journal.ppat.1007920] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 07/25/2019] [Accepted: 06/17/2019] [Indexed: 01/02/2023] Open
Abstract
The HIV-1 envelope glycoprotein (Env) trimer is located on the surface of the virus and is the target of broadly neutralizing antibodies (bNAbs). Recombinant native-like soluble Env trimer mimetics, such as SOSIP trimers, have taken a central role in HIV-1 vaccine research aimed at inducing bNAbs. We therefore performed a direct and thorough comparison of a full-length unmodified Env trimer containing the transmembrane domain and the cytoplasmic tail, with the sequence matched soluble SOSIP trimer, both based on an early Env sequence (AMC011) from an HIV+ individual that developed bNAbs. The structures of the full-length AMC011 trimer bound to either bNAb PGT145 or PGT151 were very similar to the structures of SOSIP trimers. Antigenically, the full-length and SOSIP trimers were comparable, but in contrast to the full-length trimer, the SOSIP trimer did not bind at all to non-neutralizing antibodies, most likely as a consequence of the intrinsic stabilization of the SOSIP trimer. Furthermore, the glycan composition of full-length and SOSIP trimers was similar overall, but the SOSIP trimer possessed slightly less complex and less extensively processed glycans, which may relate to the intrinsic stabilization as well as the absence of the membrane tether. These data provide insights into how to best use and improve membrane-associated full-length and soluble SOSIP HIV-1 Env trimers as immunogens. HIV-1 envelope glycoprotein (Env) trimer is the primary antigenic target for neutralizing antibodies. As such, it is the focus of subunit vaccine design efforts that aim to recapitulate the structure and native antigenic profile in a soluble, stable form capable of eliciting neutralizing antibody responses. Here, we compare the antigenicity, glycosylation and structure of a full-length, wild-type Env trimer with a corresponding soluble, SOSIP trimer that is representative of many ongoing subunit vaccine design efforts. Overall, both exhibit similar properties, and the SOSIP trimer is an accurate mimic of the wild-type Env.
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Affiliation(s)
- Alba Torrents de la Peña
- Department of Medical Microbiology, Amsterdam UMC - University of Amsterdam, Amsterdam, the Netherlands
| | - Kimmo Rantalainen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Christopher A. Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Joel D. Allen
- Centre for Biological Sciences & Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Marit J. van Gils
- Department of Medical Microbiology, Amsterdam UMC - University of Amsterdam, Amsterdam, the Netherlands
| | - Jonathan L. Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Max Crispin
- Centre for Biological Sciences & Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Rogier W. Sanders
- Department of Medical Microbiology, Amsterdam UMC - University of Amsterdam, Amsterdam, the Netherlands
- * E-mail: (RWS); (ABW)
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail: (RWS); (ABW)
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32
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Kwon YD, Chuang GY, Zhang B, Bailer RT, Doria-Rose NA, Gindin TS, Lin B, Louder MK, McKee K, O'Dell S, Pegu A, Schmidt SD, Asokan M, Chen X, Choe M, Georgiev IS, Jin V, Pancera M, Rawi R, Wang K, Chaudhuri R, Kueltzo LA, Manceva SD, Todd JP, Scorpio DG, Kim M, Reinherz EL, Wagh K, Korber BM, Connors M, Shapiro L, Mascola JR, Kwong PD. Surface-Matrix Screening Identifies Semi-specific Interactions that Improve Potency of a Near Pan-reactive HIV-1-Neutralizing Antibody. Cell Rep 2019; 22:1798-1809. [PMID: 29444432 PMCID: PMC5889116 DOI: 10.1016/j.celrep.2018.01.023] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/02/2017] [Accepted: 01/08/2018] [Indexed: 12/21/2022] Open
Abstract
Highly effective HIV-1-neutralizing antibodies could have utility in the prevention or treatment of HIV-1 infection. To improve the potency of 10E8, an antibody capable of near pan-HIV-1 neutralization, we engineered 10E8-surface mutants and screened for improved neutralization. Variants with the largest functional enhancements involved the addition of hydrophobic or positively charged residues, which were positioned to interact with viral membrane lipids or viral glycan-sialic acids, respectively. In both cases, the site of improvement was spatially separated from the region of antibody mediating molecular contact with the protein component of the antigen, thereby improving peripheral semi-specific interactions while maintaining unmodified dominant contacts responsible for broad recognition. The optimized 10E8 antibody, with mutations to phenylalanine and arginine, retained the extraordinary breadth of 10E8 but with ~10-fold increased potency. We propose surface-matrix screening as a general method to improve antibodies, with improved semi-specific interactions between antibody and antigen enabling increased potency without compromising breadth.
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Affiliation(s)
- Young D Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Tatyana S Gindin
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Bob Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Stephen D Schmidt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Mangaiarkarasi Asokan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Xuejun Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Misook Choe
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Ivelin S Georgiev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Vivian Jin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Marie Pancera
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Keyun Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Rajoshi Chaudhuri
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Lisa A Kueltzo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Slobodanka D Manceva
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - John-Paul Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Diana G Scorpio
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Mikyung Kim
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Ellis L Reinherz
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Kshitij Wagh
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Bette M Korber
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Mark Connors
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA.
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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Antibody responses to viral infections: a structural perspective across three different enveloped viruses. Nat Microbiol 2019; 4:734-747. [PMID: 30886356 PMCID: PMC6818971 DOI: 10.1038/s41564-019-0392-y] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/29/2019] [Indexed: 02/07/2023]
Abstract
Antibodies serve as critical barriers to viral infection. Humoral immunity to a virus is achieved through the dual role of antibodies in communicating the presence of invading pathogens in infected cells to effector cells and interfering with processes essential to the viral lifecycle, chiefly entry into the host cell. For individuals that successfully control infection, virus-elicited antibodies can provide lifelong surveillance and protection from future insults. One approach to understand the nature of a successful immune response has been to utilize structural biology to uncover the molecular details of the antibodies derived from vaccines or natural infection and how they interact with their cognate microbial antigens. The ability to isolate antigen specific B-cells and rapidly solve structures of functional, monoclonal antibodies in complex with viral glycoprotein surface antigens has greatly expanded our knowledge of the sites of vulnerability on viruses. In this review, we compare the adaptive humoral immune responses to HIV, influenza, and filoviruses, with a particular focus on neutralizing antibodies. The pathogenesis of each of these viruses is quite different, providing an opportunity for comparison of immune responses: HIV causes a persistent, chronic infection; influenza an acute infection with multiple exposures during a lifetime and annual vaccination; and filoviruses, a virulent, acute infection. Neutralizing antibodies that develop under these different constraints are therefore sentinels that can provide insight into the underlying humoral immune responses and important lessons to guide future development of vaccines and immunotherapeutics.
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34
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Longitudinal Analysis Reveals Early Development of Three MPER-Directed Neutralizing Antibody Lineages from an HIV-1-Infected Individual. Immunity 2019; 50:677-691.e13. [PMID: 30876875 DOI: 10.1016/j.immuni.2019.02.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 11/13/2018] [Accepted: 02/13/2019] [Indexed: 12/21/2022]
Abstract
Lineage-based vaccine design is an attractive approach for eliciting broadly neutralizing antibodies (bNAbs) against HIV-1. However, most bNAb lineages studied to date have features indicative of unusual recombination and/or development. From an individual in the prospective RV217 cohort, we identified three lineages of bNAbs targeting the membrane-proximal external region (MPER) of the HIV-1 envelope. Antibodies RV217-VRC42.01, -VRC43.01, and -VRC46.01 used distinct modes of recognition and neutralized 96%, 62%, and 30%, respectively, of a 208-strain virus panel. All three lineages had modest levels of somatic hypermutation and normal antibody-loop lengths and were initiated by the founder virus MPER. The broadest lineage, VRC42, was similar to the known bNAb 4E10. A multimeric immunogen based on the founder MPER activated B cells bearing the unmutated common ancestor of VRC42, with modest maturation of early VRC42 intermediates imparting neutralization breadth. These features suggest that VRC42 may be a promising template for lineage-based vaccine design.
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Carravilla P, Chojnacki J, Rujas E, Insausti S, Largo E, Waithe D, Apellaniz B, Sicard T, Julien JP, Eggeling C, Nieva JL. Molecular recognition of the native HIV-1 MPER revealed by STED microscopy of single virions. Nat Commun 2019; 10:78. [PMID: 30622256 PMCID: PMC6325134 DOI: 10.1038/s41467-018-07962-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 12/07/2018] [Indexed: 11/09/2022] Open
Abstract
Antibodies against the Membrane-Proximal External Region (MPER) of the Env gp41 subunit neutralize HIV-1 with exceptional breadth and potency. Due to the lack of knowledge on the MPER native structure and accessibility, different and exclusive models have been proposed for the molecular mechanism of MPER recognition by broadly neutralizing antibodies. Here, accessibility of antibodies to the native Env MPER on single virions has been addressed through STED microscopy. STED imaging of fluorescently labeled Fabs reveals a common pattern of native Env recognition for HIV-1 antibodies targeting MPER or the surface subunit gp120. In the case of anti-MPER antibodies, the process evolves with extra contribution of interactions with the viral lipid membrane to binding specificity. Our data provide biophysical insights into the recognition of the potent and broadly neutralizing MPER epitope on HIV virions, and as such is of importance for the design of therapeutic interventions.
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Affiliation(s)
- Pablo Carravilla
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080, Bilbao, Spain
| | - Jakub Chojnacki
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Edurne Rujas
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080, Bilbao, Spain
| | - Sara Insausti
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080, Bilbao, Spain
| | - Eneko Largo
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080, Bilbao, Spain
| | - Dominic Waithe
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Beatriz Apellaniz
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080, Bilbao, Spain
| | - Taylor Sicard
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.
- Institute of Applied Optics Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743, Jena, Germany.
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745, Jena, Germany.
| | - José L Nieva
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080, Bilbao, Spain.
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Li Y, Wang XE, Bender MF, Yang R, Cozine TJ, Atallah KM, Arnold F, Cooper JW, Lei QP. Overcoming the Multiple-Monomeric-Peak Profile of Broadly Neutralizing HIV-1 Antibody 10E8 with a Unique Size-Exclusion-Chromatography Method. Anal Chem 2018; 90:12390-12394. [PMID: 30346697 PMCID: PMC7727924 DOI: 10.1021/acs.analchem.8b03594] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
10E8 is a potent broadly neutralizing antibody (bNAb) that targets the membrane-proximal external region (MPER) of the HIV virus. During early analytical development of this bNAb directed towards clinical evaluation, 10E8 exhibited a multiple-monomeric-peak profile caused by secondary interactions in traditional size-exclusion chromatography (SEC), thereby rendering SEC unfit for the purpose of assessing aggregation, a target critical quality attribute. To overcome this challenge, an innovative and robust SEC method was successfully developed in which the mobile phase was tested for excipients capable of reducing the secondary interactions responsible for the multipeak profile, and an optimal mobile phase composed of 2× PBS and 100 mM arginine at pH 10.55 was established. Application of this optimized mobile phase was shown to allow quantification of the intrinsic level of aggregation of 10E8 without alteration to the SEC matrix itself. Furthermore, the newly developed method was linear, specific, accurate, and precise over an established range. Overall, an SEC method involving optimization of the mobile phase has been successfully developed, which allowed for assessment of antibody aggregation throughout process development, manufacturing, release, and stability testing.
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Affiliation(s)
- Yile Li
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Gaithersburg , Maryland 20878 , United States
| | - Xiangchun E Wang
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Gaithersburg , Maryland 20878 , United States
| | - Michael F Bender
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Gaithersburg , Maryland 20878 , United States
| | - Rong Yang
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Gaithersburg , Maryland 20878 , United States
| | - Taryn J Cozine
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Gaithersburg , Maryland 20878 , United States
| | - Kandace M Atallah
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Gaithersburg , Maryland 20878 , United States
| | - Frank Arnold
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Gaithersburg , Maryland 20878 , United States
| | - Jonathan W Cooper
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Gaithersburg , Maryland 20878 , United States
| | - Q Paula Lei
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Gaithersburg , Maryland 20878 , United States
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37
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Sok D, Burton DR. Recent progress in broadly neutralizing antibodies to HIV. Nat Immunol 2018; 19:1179-1188. [PMID: 30333615 DOI: 10.1038/s41590-018-0235-7] [Citation(s) in RCA: 249] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/12/2018] [Indexed: 12/18/2022]
Abstract
In this Review, we highlight some recent developments in the discovery and application of broadly neutralizing antibodies (bnAbs) to human immunodeficiency virus (HIV); i.e., antibodies able to neutralize diverse isolates of HIV. We consider the characterization of novel bnAbs, recent data on the effects of bnAbs in vivo in humans and animal models, and the importance of both kinds of data for the application of Abs to prophylaxis and therapy and to guide vaccine design. We seek to place newly discovered bnAbs in the context of existing bnAbs, and we explore the various characteristics of the antibodies that are most desirable for different applications.
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Affiliation(s)
- Devin Sok
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA. .,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA. .,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, USA. .,International AIDS Vaccine Initiative, New York, NY, USA.
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA. .,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA. .,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, USA. .,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
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38
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Structure of the membrane proximal external region of HIV-1 envelope glycoprotein. Proc Natl Acad Sci U S A 2018; 115:E8892-E8899. [PMID: 30185554 DOI: 10.1073/pnas.1807259115] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The membrane-proximal external region (MPER) of the HIV-1 envelope glycoprotein (Env) bears epitopes of broadly neutralizing antibodies (bnAbs) from infected individuals; it is thus a potential vaccine target. We report an NMR structure of the MPER and its adjacent transmembrane domain in bicelles that mimic a lipid-bilayer membrane. The MPER lies largely outside the lipid bilayer. It folds into a threefold cluster, stabilized mainly by conserved hydrophobic residues and potentially by interaction with phospholipid headgroups. Antigenic analysis and comparison with published images from electron cryotomography of HIV-1 Env on the virion surface suggest that the structure may represent a prefusion conformation of the MPER, distinct from the fusion-intermediate state targeted by several well-studied bnAbs. Very slow bnAb binding indicates that infrequent fluctuations of the MPER structure give these antibodies occasional access to alternative conformations of MPER epitopes. Mutations in the MPER not only impede membrane fusion but also influence presentation of bnAb epitopes in other regions. These results suggest strategies for developing MPER-based vaccine candidates.
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Flemming J, Wiesen L, Herschhorn A. Conformation-Dependent Interactions Between HIV-1 Envelope Glycoproteins and Broadly Neutralizing Antibodies. AIDS Res Hum Retroviruses 2018; 34:794-803. [PMID: 29905080 DOI: 10.1089/aid.2018.0102] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
HIV type 1 (HIV-1) envelope glycoproteins (Env) mediate virus entry and are the target of neutralizing antibodies. Binding of the metastable HIV-1 Env trimer to the CD4 receptor triggers structural rearrangements that mediate Env conformational transitions from a closed conformation to a more open state through an intermediate step. Recent studies have revealed new insights on the dynamics, regulation, and molecular mechanisms of Env transitions along the entry pathway. In this study, we provide an overview of the current knowledge on Env conformational dynamics and the relationship between Env conformational states and neutralization selectivity of the broadly neutralizing antibodies that develop in 10%-20% of infected individuals and may provide guidance for the development of an effective HIV-1 vaccine.
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Affiliation(s)
- Juliana Flemming
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Lisa Wiesen
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Alon Herschhorn
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
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40
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Vaccine based on antibody-dependent cell-mediated cytotoxicity epitope on the H1N1 influenza virus increases mortality in vaccinated mice. Biochem Biophys Res Commun 2018; 503:1874-1879. [PMID: 30064910 DOI: 10.1016/j.bbrc.2018.07.129] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 07/24/2018] [Indexed: 11/22/2022]
Abstract
Antibody-dependent cell-mediated cytotoxicity bridges humoral immunity and cellular immunity. Thus vaccine candidates which can elicit both broadly neutralizing antibodies and potent antibody-dependent cell-mediated cytotoxicity (ADCC) are recommended. Previously, a panel of functional epitopes that can elicit ADCC effects is isolated and characterized on the H1N1 Influenza Virus. Based on these identified epitopes, an epitope vaccine against H1N1 infection has been designed. The serum of vaccine immunized mice show potent ADCC activities in comparison with vector control group and HA ecto domain vaccinated group. However, the release of IL-6 and TNFα is higher in lung of epitope vaccine immunized mice. The viral load is also higher in epitope vaccine immunized mice. In addition, the epitope vaccine immunized mice showed lower survive rate than both empty vector immunized mice and HA ectodomain immunized mice. Passive transfer of serum from epitope vaccine immunized mice to healthy adult mice can decrease the survival rate of recipients after viral challenge. Our data suggested that ADCC epitope based vaccine has a mortality promoting effect rather than protective effect after H1N1 viral challenge. This result provides indications in future vaccine design with a consideration of balancing humoral immune response and cellular immune response.
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41
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Kwon B, Lee M, Waring AJ, Hong M. Oligomeric Structure and Three-Dimensional Fold of the HIV gp41 Membrane-Proximal External Region and Transmembrane Domain in Phospholipid Bilayers. J Am Chem Soc 2018; 140:8246-8259. [PMID: 29888593 DOI: 10.1021/jacs.8b04010] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The HIV-1 glycoprotein, gp41, mediates fusion of the virus lipid envelope with the target cell membrane during virus entry into cells. Despite extensive studies of this protein, inconsistent and contradictory structural information abounds in the literature about the C-terminal membrane-interacting region of gp41. This C-terminal region contains the membrane-proximal external region (MPER), which harbors the epitopes for four broadly neutralizing antibodies, and the transmembrane domain (TMD), which anchors the protein to the virus lipid envelope. Due to the difficulty of crystallizing and solubilizing the MPER-TMD, most structural studies of this functionally important domain were carried out using truncated peptides either in the absence of membrane-mimetic solvents or bound to detergents and lipid bicelles. To determine the structural architecture of the MPER-TMD in the native environment of lipid membranes, we have now carried out a solid-state NMR study of the full MPER-TMD segment bound to cholesterol-containing phospholipid bilayers. 13C chemical shifts indicate that the majority of the peptide is α-helical, except for the C-terminus of the TMD, which has moderate β-sheet character. Intermolecular 19F-19F distance measurements of singly fluorinated peptides indicate that the MPER-TMD is trimerized in the virus-envelope mimetic lipid membrane. Intramolecular 13C-19F distance measurements indicate the presence of a turn between the MPER helix and the TMD helix. This is supported by lipid-peptide and water-peptide 2D 1H-13C correlation spectra, which indicate that the MPER binds to the membrane surface whereas the TMD spans the bilayer. Together, these data indicate that full-length MPER-TMD assembles into a trimeric helix-turn-helix structure in lipid membranes. We propose that the turn between the MPER and TMD may be important for inducing membrane defects in concert with negative-curvature lipid components such as cholesterol and phosphatidylethanolamine, while the surface-bound MPER helix may interact with N-terminal segments of the protein during late stages of membrane fusion.
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Affiliation(s)
- Byungsu Kwon
- Department of Chemistry , Massachusetts Institute of Technology , 170 Albany Street , Cambridge , Massachusetts 02139 , United States
| | - Myungwoon Lee
- Department of Chemistry , Massachusetts Institute of Technology , 170 Albany Street , Cambridge , Massachusetts 02139 , United States
| | - Alan J Waring
- Department of Medicine , Harbor-UCLA Medical Center , 1000 West Carson Street, Building RB2 , Torrance , California 90502 , United States
| | - Mei Hong
- Department of Chemistry , Massachusetts Institute of Technology , 170 Albany Street , Cambridge , Massachusetts 02139 , United States
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42
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HIV-1 Vaccines Based on Antibody Identification, B Cell Ontogeny, and Epitope Structure. Immunity 2018; 48:855-871. [DOI: 10.1016/j.immuni.2018.04.029] [Citation(s) in RCA: 225] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 12/12/2022]
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43
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The development of HIV vaccines targeting gp41 membrane-proximal external region (MPER): challenges and prospects. Protein Cell 2018; 9:596-615. [PMID: 29667004 PMCID: PMC6019655 DOI: 10.1007/s13238-018-0534-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 03/05/2018] [Indexed: 10/31/2022] Open
Abstract
A human immunodeficiency virus type-1 (HIV-1) vaccine which is able to effectively prevent infection would be the most powerful method of extinguishing pandemic of the acquired immunodeficiency syndrome (AIDS). Yet, achieving such vaccine remains great challenges. The membrane-proximal external region (MPER) is a highly conserved region of the envelope glycoprotein (Env) gp41 subunit near the viral envelope surface, and it plays a key role in membrane fusion. It is also the target of some reported broadly neutralizing antibodies (bNAbs). Thus, MPER is deemed to be one of the most attractive vaccine targets. However, no one can induce these bNAbs by immunization with immunogens containing the MPER sequence(s). The few attempts at developing a vaccine have only resulted in the induction of neutralizing antibodies with quite low potency and limited breadth. Thus far, vaccine failure can be attributed to various characteristics of MPER, such as those involving structure and immunology; therefore, we will focus on these and review the recent progress in the field from the following perspectives: (1) MPER structure and its role in membrane fusion, (2) the epitopes and neutralization mechanisms of MPER-specific bNAbs, as well as the limitations in eliciting neutralizing antibodies, and (3) different strategies for MPER vaccine design and current harvests.
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44
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Ringel O, Müller K, Koch J, Brill B, Wolf T, Stephan C, Vieillard V, Debré P, Dietrich U. Optimization of the EC26-2A4 Epitope in the gp41 Membrane Proximal External Region Targeted by Neutralizing Antibodies from an Elite Controller. AIDS Res Hum Retroviruses 2018; 34:365-374. [PMID: 29262692 PMCID: PMC5899297 DOI: 10.1089/aid.2017.0250] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The analysis of patient derived HIV neutralizing antibodies (nAbs) and their target epitopes in the viral envelope (Env) protein provides important basic information for vaccine design. In this study we optimized an epitope, EC26-2A4, that is targeted by neutralizing antibodies from an elite controller (EC26) and localizes in the membrane-proximal external region from the gp41 transmembrane protein. Due to its overlap with the epitope of the first generation broadly neutralizing monoclonal Ab (mAb) 2F5 associated with autoreactivity, we first defined the minimal core epitope reacting with antibodies from EC26 plasma, but not with mAb 2F5. The optimized minimal epitope, EC26-2A4ΔM, was able to induce neutralizing antibodies in vaccinated mice. We further analyzed the frequency of antibodies against the EC26-2A4ΔM peptide in HIV-positive patient sera from a treated cohort and an untreated long-term nonprogressor (LTNP) cohort. Interestingly, 27% of the LTNP sera reacted with the peptide, whereas only 9% showed reactivity in the treated cohort. Although there was no association between the presence of antibodies against the EC26-2A4ΔM epitope and viral load or CD4 count in these patients, the CD4 nadir in the treated cohort was higher in patients positive for EC26-2A4ΔM antibodies, in particular in patients having such antibodies at an early and a late timepoint after infection.
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Affiliation(s)
- Oliver Ringel
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt, Germany
| | - Karsten Müller
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt, Germany
- Department of Infectious Diseases, HIV Center, University Hospital, Frankfurt, Germany
| | - Joachim Koch
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt, Germany
| | - Boris Brill
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt, Germany
| | - Timo Wolf
- Department of Infectious Diseases, HIV Center, University Hospital, Frankfurt, Germany
| | - Christoph Stephan
- Department of Infectious Diseases, HIV Center, University Hospital, Frankfurt, Germany
| | - Vincent Vieillard
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1135, CNRS ERL8255, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Patrice Debré
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1135, CNRS ERL8255, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Ursula Dietrich
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt, Germany
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45
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Functional Optimization of Broadly Neutralizing HIV-1 Antibody 10E8 by Promotion of Membrane Interactions. J Virol 2018; 92:JVI.02249-17. [PMID: 29386285 DOI: 10.1128/jvi.02249-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 01/26/2018] [Indexed: 11/20/2022] Open
Abstract
The 10E8 antibody targets a helical epitope in the membrane-proximal external region (MPER) and transmembrane domain (TMD) of the envelope glycoprotein (Env) subunit gp41 and is among the broadest known neutralizing antibodies against HIV-1. Accordingly, this antibody and its mechanism of action valuably inform the design of effective vaccines and immunotherapies. 10E8 exhibits unusual adaptations to attain specific, high-affinity binding to the MPER at the viral membrane interface. Reversing the charge of the basic paratope surface (from net positive to net negative) reportedly lowered its neutralization potency. Here, we hypothesized that by increasing the net positive charge in similar polar surface patches, the neutralization potency of the antibody may be enhanced. We found that an increased positive charge at this paratope surface strengthened an electrostatic interaction between the antibody and lipid bilayers, enabling 10E8 to interact spontaneously with membranes. Notably, the modified 10E8 antibody did not gain any apparent polyreactivity and neutralized virus with a significantly greater potency. Binding analyses indicated that the optimized 10E8 antibody bound with a higher affinity to the epitope peptide anchored in lipid bilayers and to Env spikes on virions. Overall, our data provide a proof of principle for the rational optimization of 10E8 via manipulation of its interaction with the membrane element of its epitope. However, the observation that a similar mutation strategy did not affect the potency of the first-generation anti-MPER antibody 4E10 shows possible limitations of this principle. Altogether, our results emphasize the crucial role played by the viral membrane in the antigenicity of the MPER-TMD of HIV-1.IMPORTANCE The broadly neutralizing antibody 10E8 blocks infection by nearly all HIV-1 isolates, a capacity which vaccine design seeks to reproduce. Engineered versions of this antibody also represent a promising treatment for HIV infection by passive immunization. Understanding its mechanism of action is therefore important to help in developing effective vaccines and biologics to combat HIV/AIDS. 10E8 engages its helical MPER epitope where the base of the envelope spike submerges into the viral membrane. To enable this interaction, this antibody evolved an unusual property: the ability to interact with the membrane surface. Here, we provide evidence that 10E8 can be made more effective by enhancing its interactions with membranes. Our findings strengthen the idea that to elicit antibodies similar to 10E8, vaccines must reproduce the membrane environment where these antibodies perform their function.
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46
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Steinhardt JJ, Guenaga J, Turner HL, McKee K, Louder MK, O'Dell S, Chiang CI, Lei L, Galkin A, Andrianov AK, A Doria-Rose N, Bailer RT, Ward AB, Mascola JR, Li Y. Rational design of a trispecific antibody targeting the HIV-1 Env with elevated anti-viral activity. Nat Commun 2018; 9:877. [PMID: 29491415 PMCID: PMC5830440 DOI: 10.1038/s41467-018-03335-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 02/05/2018] [Indexed: 11/09/2022] Open
Abstract
HIV-1 broadly neutralizing antibodies (bNAbs) are being explored as passively administered therapeutic and preventative agents. However, the extensively diversified HIV-1 envelope glycoproteins (Env) rapidly acquire mutations to evade individual bNAbs in monotherapy regimens. The use of a "single" agent to simultaneously target distinct Env epitopes is desirable to overcome viral diversity. Here, we report the use of tandem single-chain variable fragment (ScFv) domains of two bNAbs, specific for the CD4-binding site and V3 glycan patch, to form anti-HIV-1 bispecific ScFvs (Bi-ScFvs). The optimal Bi-ScFv crosslinks adjacent protomers within one HIV-1 Env spike and has greater neutralization breadth than its parental bNAbs. Furthermore, the combination of this Bi-ScFv with a third bNAb recognizing the Env membrane proximal external region (MPER) results in a trispecific bNAb, which has nearly pan-isolate neutralization breadth and high potency. Thus, multispecific antibodies combining functional moieties of bNAbs could achieve outstanding neutralization capacity with augmented avidity.
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Affiliation(s)
- James J Steinhardt
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA.,Virology Program at the University of Maryland, College Park, MD, 20740, USA
| | - Javier Guenaga
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Chi-I Chiang
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA
| | - Lin Lei
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA
| | - Andrey Galkin
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Alexander K Andrianov
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yuxing Li
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA. .,Virology Program at the University of Maryland, College Park, MD, 20740, USA. .,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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Oakes V, Torralba J, Rujas E, Nieva JL, Domene C, Apellaniz B. Exposure of the HIV-1 broadly neutralizing antibody 10E8 MPER epitope on the membrane surface by gp41 transmembrane domain scaffolds. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1259-1271. [PMID: 29477358 DOI: 10.1016/j.bbamem.2018.02.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 01/30/2018] [Accepted: 02/20/2018] [Indexed: 12/27/2022]
Abstract
The 10E8 antibody achieves near-pan neutralization of HIV-1 by targeting the remarkably conserved gp41 membrane-proximal external region (MPER) and the connected transmembrane domain (TMD) of the HIV-1 envelope glycoprotein (Env). Thus, recreating the structure that generates 10E8-like antibodies is a major goal of the rational design of anti-HIV vaccines. Unfortunately, high-resolution information of this segment in the native Env is lacking, limiting our understanding of the behavior of the crucial 10E8 epitope residues. In this report, two sequences, namely, MPER-TMD1 (gp41 residues 671-700) and MPER-TMD2 (gp41 residues 671-709) were compared both experimentally and computationally, to assess the TMD as a potential membrane integral scaffold for the 10E8 epitope. These sequences were selected to represent a minimal (MPER-TMD1) or full-length (MPER-TMD2) TMD membrane anchor according to mutagenesis results reported by Yue et al. (2009) J. Virol. 83, 11,588. Immunochemical assays revealed that MPER-TMD1, but not MPER-TMD2, effectively exposed the MPER C-terminal stretch, harboring the 10E8 epitope on the surface of phospholipid bilayers containing a cholesterol concentration equivalent to that of the viral envelope. Molecular dynamics simulations, using the recently resolved TMD trimer structure combined with the MPER in a cholesterol-enriched model membrane confirmed these results and provided an atomistic mechanism of epitope exposure which revealed that TMD truncation at position A700 combined with N-terminal addition of lysine residues positively impacts epitope exposure. Overall, these results provide crucial insights into the design of effective MPER-TMD derived immunogens.
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Affiliation(s)
- Victoria Oakes
- Department of Chemistry, Britannia House, 7 Trinity Street, King's College London, London SE1 1DB, UK; Department of Chemistry, 1 South Building, Claverton Down Road, University of Bath, Bath BA2 7AY, UK
| | - Johana Torralba
- Biofisika Institute (CSIC, UPV/EHU), Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
| | - Edurne Rujas
- Biofisika Institute (CSIC, UPV/EHU), Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
| | - José L Nieva
- Biofisika Institute (CSIC, UPV/EHU), Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
| | - Carmen Domene
- Department of Chemistry, 1 South Building, Claverton Down Road, University of Bath, Bath BA2 7AY, UK; Chemistry Research Laboratory, Mansfield Road, University of Oxford, Oxford OX1 3TA, UK.
| | - Beatriz Apellaniz
- Biofisika Institute (CSIC, UPV/EHU), Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain.
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Carravilla P, Nieva JL. HIV antivirals: targeting the functional organization of the lipid envelope. Future Virol 2018. [DOI: 10.2217/fvl-2017-0114] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Most of the surface of the lipid bilayer covering the human immunodeficiency virus type 1 (HIV-1) particle is directly accessible from the aqueous medium. Its peculiar chemical composition and physical properties appear to be critical for infection and, therefore, may comprise a target for selective antiviral activity. The HIV-1 membrane is enriched in raft-type lipids and also displays aminophospholipids on its external leaflet. We contend here that a great deal of membrane-active compounds described to block HIV-1 infection can do so by following a common mechanism of action: alteration of the lateral heterogeneity that supports the functional organization of the lipid envelope. The confirmation of this hypothesis could lay new foundations for the rational development of compounds with anti-HIV activity.
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Affiliation(s)
- Pablo Carravilla
- Biofisika Institute (CSIC, UPV/EHU) & Department of Biochemistry & Molecular Biology, University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
| | - José L Nieva
- Biofisika Institute (CSIC, UPV/EHU) & Department of Biochemistry & Molecular Biology, University of the Basque Country (UPV/EHU), PO Box 644, 48080 Bilbao, Spain
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Hessell AJ, Malherbe DC, Haigwood NL. Passive and active antibody studies in primates to inform HIV vaccines. Expert Rev Vaccines 2018; 17:127-144. [PMID: 29307225 PMCID: PMC6587971 DOI: 10.1080/14760584.2018.1425619] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Prevention of infection remains the ultimate goal for HIV vaccination, and there is compelling evidence that antibodies directed to Envelope are necessary to block infection. Generating antibodies that are sufficiently broad, potent, and sustained to block infection by the diverse HIV-1 strains circulating worldwide remains an area of intense study. AREAS COVERED In this review, we have summarized progress from publications listed as PubMed citations in 2016-17 in the areas of passive antibody studies using human neutralizing monoclonal antibodies in nonhuman primates, HIV Envelope vaccine development and active vaccination studies to generate potent neutralizing antibodies. EXPERT COMMENTARY Passive transfer studies in nonhuman primates using human neutralizing monoclonal antibodies have informed the potency, specificity, and cooperativity of antibodies needed to prevent infection, leading to clinical studies now testing potent antibodies for prevention of HIV. Progress in understanding the structure of Envelope has led to novel vaccine constructs, including mimetics, scaffolds and native-like proteins. As yet, no single approach ensures protection against the circulating global HIV-1 strains, but there is progress in understanding why, and intense research continues in these and other areas for a solution. We offer perspectives on how this knowledge may shape the design of future HIV vaccines.
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Structural Features of Broadly Neutralizing Antibodies and Rational Design of Vaccine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1075:73-95. [PMID: 30030790 DOI: 10.1007/978-981-13-0484-2_4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Despite sequence diversity, glycosylation, and conformational flexibility of the human immunodeficiency virus type 1 (HIV-1) envelope (Env), antibodies that neutralize diverse HIV-1 strains develop in selected HIV-1-infected individuals. The application of single B cell-based approaches has identified many broad and potent human antibodies from infected donors. Structural studies on antibody recognition of HIV Env have revealed that these broadly reactive antibodies target epitopes covering entire exposed and glycosylated surface on the viral spike; several classes of antibodies recognize the viral spike with converged modes. Critical structural features, such as antibody mimicry of cellular receptors, enable effective HIV-1 neutralization. However, other structural and genetic features, such as long CDR H3, fixed length of CDR L3, restricted germline usage, and high rate of somatic hypermutation, may explain the difficulties in eliciting these antibodies by vaccination. Accumulating information on antibody recognition of HIV-1 Env and ontogenesis suggests distinct pathways for generating effective HIV-1 vaccine based on specific antibody ontogeny or specific target site.
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