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Becerra JC, Hitchcock L, Vu K, Gach JS. Neutralizing the threat: harnessing broadly neutralizing antibodies against HIV-1 for treatment and prevention. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:207-220. [PMID: 38975023 PMCID: PMC11224682 DOI: 10.15698/mic2024.07.826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 05/06/2024] [Accepted: 05/15/2024] [Indexed: 07/09/2024]
Abstract
Broadly neutralizing antibodies (bnAbs) targeting the human immunodeficiency virus-1 (HIV-1) have played a crucial role in elucidating and characterizing neutralization-sensitive sites on the HIV-1 envelope spike and in informing vaccine development. Continual advancements in identifying more potent bnAbs, along with their capacity to trigger antibody-mediated effector functions, coupled with modifications to extend their half-life, position them as promising candidates for both HIV-1 treatment and prevention. While current pharmacological interventions have made significant progress in managing HIV-1 infection and enhancing quality of life, no definitive cure or vaccines have been developed thus far. Standard treatments involve daily oral anti-retroviral therapy, which, despite its efficacy, can lead to notable long-term side effects. Recent clinical trial data have demonstrated encouraging therapeutic and preventive potential for bnAb therapies in both HIV-1-infected individuals and those without the infection. This review provides an overview of the advancements in HIV-1-specific bnAbs and discusses the insights gathered from recent clinical trials regarding their application in treating and preventing HIV-1 infection.
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Affiliation(s)
- Juan C Becerra
- Department of Medicine, Division of Infectious Diseases, University of CaliforniaCA, Irvine, Irvine, 92697USA
| | - Lauren Hitchcock
- Department of Medicine, Division of Infectious Diseases, University of CaliforniaCA, Irvine, Irvine, 92697USA
| | - Khoa Vu
- Department of Medicine, Division of Infectious Diseases, University of CaliforniaCA, Irvine, Irvine, 92697USA
| | - Johannes S Gach
- Department of Medicine, Division of Infectious Diseases, University of CaliforniaCA, Irvine, Irvine, 92697USA
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2
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Wholey WY, Meyer AR, Yoda ST, Chackerian B, Zikherman J, Cheng W. Minimal Determinants for Lifelong Antiviral Antibody Responses in Mice from a Single Exposure to Virus-like Immunogens at Low Doses. Vaccines (Basel) 2024; 12:405. [PMID: 38675787 PMCID: PMC11054763 DOI: 10.3390/vaccines12040405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
The durability of an antibody (Ab) response is highly important for antiviral vaccines. However, due to the complex compositions of natural virions, the molecular determinants of Ab durability from viral infection or inactivated viral vaccines have been incompletely understood. Here we used a reductionist system of liposome-based virus-like structures to examine the durability of Abs from primary immune responses in mice. This system allowed us to independently vary fundamental viral attributes and to do so without additional adjuvants to model natural viruses. We show that a single injection of protein antigens (Ags) orderly displayed on a virion-sized liposome is sufficient to induce a long-lived neutralizing Ab (nAb) response. The introduction of internal nucleic acids dramatically modulates the magnitude of Ab responses without an alteration of the long-term kinetic trends. These Abs are characterized by very slow off-rates of ~0.0005 s-1, which emerged as early as day 5 after injection and these off-rates are comparable to that of affinity-matured monoclonal Abs. A single injection of these structures at doses as low as 100 ng led to lifelong nAb production in mice. Thus, a minimal virus-like immunogen can give rise to potent and long-lasting antiviral Abs in a primary response in mice without live infection. This has important implications for understanding both live viral infection and for optimizing vaccine design.
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Affiliation(s)
- Wei-Yun Wholey
- Department of Pharmaceutical Sciences, University of Michigan, 428 Church Street, Ann Arbor, MI 48109, USA; (W.-Y.W.); (A.R.M.); (S.-T.Y.)
| | - Alexander R. Meyer
- Department of Pharmaceutical Sciences, University of Michigan, 428 Church Street, Ann Arbor, MI 48109, USA; (W.-Y.W.); (A.R.M.); (S.-T.Y.)
| | - Sekou-Tidiane Yoda
- Department of Pharmaceutical Sciences, University of Michigan, 428 Church Street, Ann Arbor, MI 48109, USA; (W.-Y.W.); (A.R.M.); (S.-T.Y.)
| | - Bryce Chackerian
- Department of Molecular Genetics and Microbiology, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA;
| | - Julie Zikherman
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, University of California, San Francisco, CA 94143, USA;
| | - Wei Cheng
- Department of Pharmaceutical Sciences, University of Michigan, 428 Church Street, Ann Arbor, MI 48109, USA; (W.-Y.W.); (A.R.M.); (S.-T.Y.)
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W. Medical Center Dr., Ann Arbor, MI 48109, USA
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3
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Wholey WY, Meyer AR, Yoda ST, Chackerian B, Zikherman J, Cheng W. Minimal determinants for lifelong antiviral antibody responses in BALB/c mice from a single exposure to virus-like immunogens at low doses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.20.529089. [PMID: 36865112 PMCID: PMC9979986 DOI: 10.1101/2023.02.20.529089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
However, due to the complex compositions of natural virions, the molecular determinants of Ab durability from viral infection or inactivated viral vaccines have been incompletely understood. Here we used a reductionist system of liposome-based virus-like structures to examine the durability of Abs in primary immune responses in mice. This system allowed us to independently vary fundamental viral attributes and to do so without additional adjuvants to model natural viruses. We show that a single injection of antigens (Ags) orderly displayed on a virion-sized liposome is sufficient to induce a long-lived neutralizing Ab (nAb) response. Introduction of internal nucleic acids dramatically modulates the magnitude of long-term Ab responses without alteration of the long-term kinetic trends. These Abs are characterized by exceptionally slow off-rates of ~0.0005 s-1, which emerged as early as day 5 after injection and these off-rates are comparable to that of affinity-matured monoclonal Abs. A single injection of these structures at doses as low as 100 ng led to lifelong nAb production in BALB/c mice. Thus, a minimal virus-like immunogen can give rise to potent and long-lasting antiviral Abs in a primary response in mice without live infection. This has important implications for understanding both live viral infection and for optimized vaccine design.
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4
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Schriek AI, Aldon YLT, van Gils MJ, de Taeye SW. Next-generation bNAbs for HIV-1 cure strategies. Antiviral Res 2024; 222:105788. [PMID: 38158130 DOI: 10.1016/j.antiviral.2023.105788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Despite the ability to suppress viral replication using anti-retroviral therapy (ART), HIV-1 remains a global public health problem. Curative strategies for HIV-1 have to target and eradicate latently infected cells across the body, i.e. the viral reservoir. Broadly neutralizing antibodies (bNAbs) targeting the HIV-1 envelope glycoprotein (Env) have the capacity to neutralize virions and bind to infected cells to initiate elimination of these cells. To improve the efficacy of bNAbs in terms of viral suppression and viral reservoir eradication, next generation antibodies (Abs) are being developed that address the current limitations of Ab treatment efficacy; (1) low antigen (Env) density on (reactivated) HIV-1 infected cells, (2) high viral genetic diversity, (3) exhaustion of immune cells and (4) short half-life of Abs. In this review we summarize and discuss preclinical and clinical studies in which anti-HIV-1 Abs demonstrated potent viral control, and describe the development of engineered Abs that could address the limitations described above. Next generation Abs with optimized effector function, avidity, effector cell recruitment and immune cell activation have the potential to contribute to an HIV-1 cure or durable control.
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Affiliation(s)
- A I Schriek
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology, Meibergdreef 9, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands.
| | - Y L T Aldon
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology, Meibergdreef 9, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - M J van Gils
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology, Meibergdreef 9, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - S W de Taeye
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology, Meibergdreef 9, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands.
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5
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Sprumont A, Rodrigues A, McGowan SJ, Bannard C, Bannard O. Germinal centers output clonally diverse plasma cell populations expressing high- and low-affinity antibodies. Cell 2023; 186:5486-5499.e13. [PMID: 37951212 DOI: 10.1016/j.cell.2023.10.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/05/2023] [Accepted: 10/24/2023] [Indexed: 11/13/2023]
Abstract
Germinal centers (GCs) form in lymph nodes after immunization or infection to facilitate antibody affinity maturation and memory and plasma cell (PC) development. PC differentiation is thought to involve stringent selection for GC B cells expressing the highest-affinity antigen receptors, but how this plays out during complex polyclonal responses is unclear. We combine temporal lineage tracing with antibody characterization to gain a snapshot of PCs developing during influenza infection. GCs co-mature B cell clones with antibody affinities spanning multiple orders of magnitude; however, each generates PCs with similar efficiencies, including weak binders. Within lineages, PC selection is not restricted to variants with the highest-affinity antibodies. Differentiation is commonly associated with proliferative expansion to produce "nodes" of identical PCs. Immunization-induced GCs generate fewer PCs but still of low- and high-antibody affinities. We propose that generating low-affinity antibody PCs reflects an evolutionary compromise to facilitate diverse serum antibody responses.
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Affiliation(s)
- Adrien Sprumont
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Ana Rodrigues
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Simon J McGowan
- Computational Biology Research Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Colin Bannard
- Department of Linguistics and English Language, University of Manchester, Manchester M13 9PL, UK
| | - Oliver Bannard
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
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6
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Tan K, Chen J, Kaku Y, Wang Y, Donius L, Khan RA, Li X, Richter H, Seaman MS, Walz T, Hwang W, Reinherz EL, Kim M. Inadequate structural constraint on Fab approach rather than paratope elicitation limits HIV-1 MPER vaccine utility. Nat Commun 2023; 14:7218. [PMID: 37940661 PMCID: PMC10632514 DOI: 10.1038/s41467-023-42097-6] [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: 04/26/2023] [Accepted: 09/25/2023] [Indexed: 11/10/2023] Open
Abstract
Broadly neutralizing antibodies (bnAbs) against HIV-1 target conserved envelope (Env) epitopes to block viral replication. Here, using structural analyses, we provide evidence to explain why a vaccine targeting the membrane-proximal external region (MPER) of HIV-1 elicits antibodies with human bnAb-like paratopes paradoxically unable to bind HIV-1. Unlike in natural infection, vaccination with MPER/liposomes lacks a necessary structure-based constraint to select for antibodies with an adequate approach angle. Consequently, the resulting Abs cannot physically access the MPER crawlspace on the virion surface. By studying naturally arising Abs, we further reveal that flexibility of the human IgG3 hinge mitigates the epitope inaccessibility and additionally facilitates Env spike protein crosslinking. Our results suggest that generation of IgG3 subtype class-switched B cells is a strategy for anti-MPER bnAb induction. Moreover, the findings illustrate the need to incorporate topological features of the target epitope in immunogen design.
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Affiliation(s)
- Kemin Tan
- Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL, USA
| | - Junjian Chen
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Laboratory of Immunology, Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yu Kaku
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Yi Wang
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- NeoCura Bio-Medical Technology Co., Ltd., Beijing, China
| | - Luke Donius
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- AbbVie Bioresearch Center, AbbVie Inc., Worcester, MA, USA
| | - Rafiq Ahmad Khan
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Xiaolong Li
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Hannah Richter
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY, USA
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
- Department of Materials Science & Engineering, Texas A&M University, College Station, TX, USA
- Department of Physics & Astronomy, Texas A&M University, College Station, TX, USA
| | - Ellis L Reinherz
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Mikyung Kim
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Dermatology, Harvard Medical School, Boston, MA, USA.
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7
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Akiba H, Fujita J, Ise T, Nishiyama K, Miyata T, Kato T, Namba K, Ohno H, Kamada H, Nagata S, Tsumoto K. Development of a 1:1-binding biparatopic anti-TNFR2 antagonist by reducing signaling activity through epitope selection. Commun Biol 2023; 6:987. [PMID: 37758868 PMCID: PMC10533564 DOI: 10.1038/s42003-023-05326-8] [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: 03/07/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Conventional bivalent antibodies against cell surface receptors often initiate unwanted signal transduction by crosslinking two antigen molecules. Biparatopic antibodies (BpAbs) bind to two different epitopes on the same antigen, thus altering crosslinking ability. In this study, we develop BpAbs against tumor necrosis factor receptor 2 (TNFR2), which is an attractive immune checkpoint target. Using different pairs of antibody variable regions specific to topographically distinct TNFR2 epitopes, we successfully regulate the size of BpAb-TNFR2 immunocomplexes to result in controlled agonistic activities. Our series of results indicate that the relative positions of the two epitopes recognized by the BpAb are critical for controlling its signaling activity. One particular antagonist, Bp109-92, binds TNFR2 in a 1:1 manner without unwanted signal transduction, and its structural basis is determined using cryo-electron microscopy. This antagonist suppresses the proliferation of regulatory T cells expressing TNFR2. Therefore, the BpAb format would be useful in designing specific and distinct antibody functions.
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Affiliation(s)
- Hiroki Akiba
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan.
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 562-0011, Japan.
| | - Junso Fujita
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
- JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, 565-0871, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Tomoko Ise
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 562-0011, Japan
| | - Kentaro Nishiyama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Tomoko Miyata
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
- JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Takayuki Kato
- Institute of Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
- JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, 565-0871, Japan
- RIKEN SPring-8 Center, Suita, Osaka, 565-0871, Japan
| | - Hiroaki Ohno
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 562-0011, Japan
| | - Haruhiko Kamada
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 562-0011, Japan
| | - Satoshi Nagata
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 562-0011, Japan.
| | - Kouhei Tsumoto
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 562-0011, Japan.
- School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan.
- Institute of Medical Sciences, The University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan.
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8
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Xu Y, Zheng R, Prasad A, Liu M, Wan Z, Zhou X, Porter RM, Sample M, Poppleton E, Procyk J, Liu H, Li Y, Wang S, Yan H, Sulc P, Stephanopoulos N. High-affinity binding to the SARS-CoV-2 spike trimer by a nanostructured, trivalent protein-DNA synthetic antibody. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558353. [PMID: 37790307 PMCID: PMC10542138 DOI: 10.1101/2023.09.18.558353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Multivalency enables nanostructures to bind molecular targets with high affinity. Although antibodies can be generated against a wide range of antigens, their shape and size cannot be tuned to match a given target. DNA nanotechnology provides an attractive approach for designing customized multivalent scaffolds due to the addressability and programmability of the nanostructure shape and size. Here, we design a nanoscale synthetic antibody ("nano-synbody") based on a three-helix bundle DNA nanostructure with one, two, or three identical arms terminating in a mini-binder protein that targets the SARS-CoV-2 spike protein. The nano-synbody was designed to match the valence and distance between the three receptor binding domains (RBDs) in the spike trimer, in order to enhance affinity. The protein-DNA nano-synbody shows tight binding to the wild-type, Delta, and several Omicron variants of the SARS-CoV-2 spike trimer, with affinity increasing as the number of arms increases from one to three. The effectiveness of the nano-synbody was also verified using a pseudovirus neutralization assay, with the three-arm nanostructure inhibiting two Omicron variants against which the structures with only one or two arms are ineffective. The structure of the three-arm nano-synbody bound to the Omicron variant spike trimer was solved by negative-stain transmission electron microscopy reconstruction, and shows the protein-DNA nanostructure with all three arms attached to the RBD domains, confirming the intended trivalent attachment. The ability to tune the size and shape of the nano-synbody, as well as its potential ability to attach two or more different binding ligands, will enable the high-affinity targeting of a range of proteins not possible with traditional antibodies.
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9
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Molinos-Albert LM, Baquero E, Bouvin-Pley M, Lorin V, Charre C, Planchais C, Dimitrov JD, Monceaux V, Vos M, Hocqueloux L, Berger JL, Seaman MS, Braibant M, Avettand-Fenoël V, Sáez-Cirión A, Mouquet H. Anti-V1/V3-glycan broadly HIV-1 neutralizing antibodies in a post-treatment controller. Cell Host Microbe 2023; 31:1275-1287.e8. [PMID: 37433296 DOI: 10.1016/j.chom.2023.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/08/2023] [Accepted: 06/13/2023] [Indexed: 07/13/2023]
Abstract
HIV-1 broadly neutralizing antibodies (bNAbs) can decrease viremia but are usually unable to counteract autologous viruses escaping the antibody pressure. Nonetheless, bNAbs may contribute to natural HIV-1 control in individuals off antiretroviral therapy (ART). Here, we describe a bNAb B cell lineage elicited in a post-treatment controller (PTC) that exhibits broad seroneutralization and show that a representative antibody from this lineage, EPTC112, targets a quaternary epitope in the glycan-V3 loop supersite of the HIV-1 envelope glycoprotein. The cryo-EM structure of EPTC112 complexed with soluble BG505 SOSIP.664 envelope trimers revealed interactions with N301- and N156-branched N-glycans and the 324GDIR327 V3 loop motif. Although the sole contemporaneous virus circulating in this PTC was resistant to EPTC112, it was potently neutralized by autologous plasma IgG antibodies. Our findings illuminate how cross-neutralizing antibodies can alter the HIV-1 infection course in PTCs and may control viremia off-ART, supporting their role in functional HIV-1 cure strategies.
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Affiliation(s)
- Luis M Molinos-Albert
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, Paris 75015, France
| | - Eduard Baquero
- NanoImaging Core Facility, Centre de Ressources et Recherches Technologiques (C2RT), Université Paris Cité, Institut Pasteur, Paris 75015, France
| | | | - Valérie Lorin
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, Paris 75015, France
| | - Caroline Charre
- Université Cité, Faculté de Médecine, Paris 75014, France; INSERM U1016, CNRS UMR8104, Institut Cochin, Paris 75014, France; AP-HP, Service de Virologie, Hôpital Cochin, Paris 75014, France
| | - Cyril Planchais
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, Paris 75015, France
| | - Jordan D Dimitrov
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Paris 75006, France
| | - Valérie Monceaux
- Viral Reservoirs and Immune control Unit, Institut Pasteur, Université Paris Cité, Paris 75015, France; HIV, Inflammation and Persistence Unit, Institut Pasteur, Université Paris Cité, Paris 75015, France
| | - Matthijn Vos
- NanoImaging Core Facility, Centre de Ressources et Recherches Technologiques (C2RT), Université Paris Cité, Institut Pasteur, Paris 75015, France
| | - Laurent Hocqueloux
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier Universitaire d'Orléans La Source, Orléans 45067, France
| | - Jean-Luc Berger
- Department of Internal Medicine, Clinical Immunology and Infectious Diseases, Reims University Hospital, Reims 51100, France
| | | | | | - Véronique Avettand-Fenoël
- Université Cité, Faculté de Médecine, Paris 75014, France; INSERM U1016, CNRS UMR8104, Institut Cochin, Paris 75014, France; AP-HP, Service de Virologie, Hôpital Cochin, Paris 75014, France
| | - Asier Sáez-Cirión
- Viral Reservoirs and Immune control Unit, Institut Pasteur, Université Paris Cité, Paris 75015, France; HIV, Inflammation and Persistence Unit, Institut Pasteur, Université Paris Cité, Paris 75015, France
| | - Hugo Mouquet
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, Paris 75015, France.
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10
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Tan K, Chen J, Kaku Y, Wang Y, Donius L, Khan RA, Li X, Richter H, Seaman MS, Walz T, Hwang W, Reinherz EL, Kim M. Inadequate structural constraint on Fab approach rather than paratope elicitation limits HIV-1 MPER vaccine utility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546734. [PMID: 37425731 PMCID: PMC10327024 DOI: 10.1101/2023.06.27.546734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Broadly neutralizing antibodies (bnAbs) against HIV-1 target conserved epitopes, thereby inhibiting viral entry. Yet surprisingly, those recognizing linear epitopes in the HIV-1 gp41 membrane proximal external region (MPER) are elicited neither by peptide nor protein scaffold vaccines. Here, we observe that while Abs generated by MPER/liposome vaccines may exhibit human bnAb-like paratopes, B-cell programming without constraints imposed by the gp160 ectodomain selects Abs unable to access the MPER within its native "crawlspace". During natural infection, the flexible hinge of IgG3 partially mitigates steric occlusion of less pliable IgG1 subclass Abs with identical MPER specificity, until affinity maturation refines entry mechanisms. The IgG3 subclass maintains B-cell competitiveness, exploiting bivalent ligation resulting from greater intramolecular Fab arm length, offsetting weak antibody affinity. These findings suggest future immunization strategies.
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11
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Budhadev D, Hooper J, Rocha C, Nehlmeier I, Kempf AM, Hoffmann M, Krüger N, Zhou D, Pöhlmann S, Guo Y. Polyvalent Nano-Lectin Potently Neutralizes SARS-CoV-2 by Targeting Glycans on the Viral Spike Protein. JACS AU 2023; 3:1755-1766. [PMID: 37388683 PMCID: PMC10302749 DOI: 10.1021/jacsau.3c00163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 07/01/2023]
Abstract
Mutations in spike (S) protein epitopes allow SARS-CoV-2 variants to evade antibody responses induced by infection and/or vaccination. In contrast, mutations in glycosylation sites across SARS-CoV-2 variants are very rare, making glycans a potential robust target for developing antivirals. However, this target has not been adequately exploited for SARS-CoV-2, mostly due to intrinsically weak monovalent protein-glycan interactions. We hypothesize that polyvalent nano-lectins with flexibly linked carbohydrate recognition domains (CRDs) can adjust their relative positions and bind multivalently to S protein glycans, potentially exerting potent antiviral activity. Herein, we displayed the CRDs of DC-SIGN, a dendritic cell lectin known to bind to diverse viruses, polyvalently onto 13 nm gold nanoparticles (named G13-CRD). G13-CRD bound strongly and specifically to target glycan-coated quantum dots with sub-nM Kd. Moreover, G13-CRD neutralized particles pseudotyped with the S proteins of Wuhan Hu-1, B.1, Delta variant and Omicron subvariant BA.1 with low nM EC50. In contrast, natural tetrameric DC-SIGN and its G13 conjugate were ineffective. Further, G13-CRD potently inhibited authentic SARS-CoV-2 B.1 and BA.1, with <10 pM and <10 nM EC50, respectively. These results identify G13-CRD as the 1st polyvalent nano-lectin with broad activity against SARS-CoV-2 variants that merits further exploration as a novel approach to antiviral therapy.
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Affiliation(s)
- Darshita Budhadev
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - James Hooper
- School
of Food Science & Nutrition and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Cheila Rocha
- Infection
Biology Unit, German Primate Center −
Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Faculty
of Biology and Psychology, Georg-August-University
Göttingen, 37073 Göttingen, Germany
| | - Inga Nehlmeier
- Infection
Biology Unit, German Primate Center −
Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Amy Madeleine Kempf
- Infection
Biology Unit, German Primate Center −
Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Faculty
of Biology and Psychology, Georg-August-University
Göttingen, 37073 Göttingen, Germany
| | - Markus Hoffmann
- Infection
Biology Unit, German Primate Center −
Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Faculty
of Biology and Psychology, Georg-August-University
Göttingen, 37073 Göttingen, Germany
| | - Nadine Krüger
- Infection
Biology Unit, German Primate Center −
Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Dejian Zhou
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Stefan Pöhlmann
- Infection
Biology Unit, German Primate Center −
Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Faculty
of Biology and Psychology, Georg-August-University
Göttingen, 37073 Göttingen, Germany
| | - Yuan Guo
- School
of Food Science & Nutrition and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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12
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Kapcan E, Lake BM, Rullo AF. Orchestrating Binding Interactions and the Emergence of Avidity Driven Therapeutics. ACS CENTRAL SCIENCE 2023; 9:586-589. [PMID: 37122467 PMCID: PMC10141585 DOI: 10.1021/acscentsci.3c00242] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
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13
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Erickson HP, Corbin Goodman L. Recently Designed Multivalent Spike Binders Cannot Bind Multivalently─How Do They Achieve Enhanced Avidity to SARS-CoV-2? Biochemistry 2023; 62:163-168. [PMID: 35943748 DOI: 10.1021/acs.biochem.2c00291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The trimeric spike protein of SARS-CoV-2 has been targeted by antibody mimics that bind near or at the receptor-binding domain to neutralize the virus. Several independent studies have reported enhanced binding avidity for dimers and trimers, where binding domains are connected by short peptides. The enhanced avidity of the multivalent constructs was attributed to their simultaneously binding two or three sites within a single spike trimer. We argue here that the 15-20 amino acid peptide linkers, when considered as worm-like-chains, are too short to span the binding sites within a single spike. The enhanced avidity of the multivalent constructs may be explained by a rebinding mechanism, which does not involve multivalent binding.
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14
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Snider DM, Pandit S, Coffin ML, Ebrahimi SB, Samanta D. DNA-Mediated Control of Protein Function in Semi-Synthetic Systems. Chembiochem 2022; 23:e202200464. [PMID: 36058885 DOI: 10.1002/cbic.202200464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/02/2022] [Indexed: 01/25/2023]
Abstract
The development of strategies for controlling protein function in a precise and predictable manner has the potential to revolutionize catalysis, diagnostics, and medicine. In this regard, the use of DNA has emerged as a powerful approach for modulating protein activity. The programmable nature of DNA allows for constructing sophisticated architectures wherein proteins can be placed with control over position, orientation, and stoichiometry. This ability is especially useful considering that the properties of proteins can be influenced by their local environment or their proximity to other functional molecules. Here, we chronicle the different strategies that have been developed to interface DNA with proteins in semi-synthetic systems. We further delineate the unique applications unlocked by the unprecedented level of structural control that DNA affords. We end by outlining outstanding challenges in the area and discuss future research directions towards potential solutions.
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Affiliation(s)
- Dylan M Snider
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Austin, TX, 78712, USA
| | - Subrata Pandit
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Austin, TX, 78712, USA
| | - Mackenzie L Coffin
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Austin, TX, 78712, USA
| | - Sasha B Ebrahimi
- Drug Product Development - Steriles, GlaxoSmithKline 1250 S Collegeville Rd, Collegeville, PA 19426, USA
| | - Devleena Samanta
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Austin, TX, 78712, USA
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15
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Scheepers C, Richardson SI, Moyo-Gwete T, Moore PL. Antibody class-switching as a strategy to improve HIV-1 neutralization. Trends Mol Med 2022; 28:979-988. [PMID: 36117072 PMCID: PMC9617786 DOI: 10.1016/j.molmed.2022.08.010] [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: 06/21/2022] [Revised: 08/11/2022] [Accepted: 08/19/2022] [Indexed: 12/01/2022]
Abstract
Broadly neutralizing antibodies (bNAbs), when administered through passive immunization, are protective against HIV-1 infection. Current HIV-1 vaccine strategies are aimed at guiding the immune system to make bNAbs by mimicking their development during infection. Somatic hypermutation of the variable region is known to be crucial for the development of bNAbs. More recently, however, studies have shown how class-switch recombination (CSR) resulting in the generation of different antibody isotypes may serve as an additional mechanism through which antibodies can gain neutralization breadth and potency. In this review, we discuss the importance of different antibody isotypes for HIV-1 neutralization breadth and potency and how this information can be leveraged to improve passive and active immunization against HIV-1.
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Affiliation(s)
- Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa; SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Simone I Richardson
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa; SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Thandeka Moyo-Gwete
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa; SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Penny L Moore
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa; SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), KwaZulu-Natal, South Africa, Discipline of Virology, University of KwaZulu-Natal, South Africa.
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16
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Hooper J, Liu Y, Budhadev D, Ainaga DF, Hondow N, Zhou D, Guo Y. Polyvalent Glycan Quantum Dots as a Multifunctional Tool for Revealing Thermodynamic, Kinetic, and Structural Details of Multivalent Lectin-Glycan Interactions. ACS APPLIED MATERIALS & INTERFACES 2022; 14:47385-47396. [PMID: 36194567 PMCID: PMC9614721 DOI: 10.1021/acsami.2c11111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Multivalent lectin-glycan interactions (MLGIs) are widespread and vital for biology. Their binding biophysical and structural details are thus highly valuable, not only for the understanding of binding affinity and specificity mechanisms but also for guiding the design of multivalent therapeutics against specific MLGIs. However, effective techniques that can reveal all such details remain unavailable. We have recently developed polyvalent glycan quantum dots (glycan-QDs) as a new probe for MLGIs. Using a pair of closely related tetrameric viral-binding lectins, DC-SIGN and DC-SIGNR, as model examples, we have revealed and quantified their large affinity differences in glycan-QD binding are due to distinct binding modes: with simultaneous binding for DC-SIGN and cross-linking for DC-SIGNR. Herein, we further extend the capacity of the glycan-QD probes by investigating the correlation between binding mode and binding thermodynamics and kinetics and further probing a structural basis of their binding nature. We reveal that while both lectins' binding with glycan-QDs is enthalpy driven with similar binding enthalpy changes, DC-SIGN pays a lower binding entropy penalty, resulting in a higher affinity than DC-SIGNR. We then show that DC-SIGN binding gives a single second-order kon rate, whereas DC-SIGNR gives a rapid initial binding followed by a much slower secondary interaction. We further identify a structural element in DC-SIGN, absent in DC-SIGNR, that plays an important role in maintaining DC-SIGN's MLGI character. Its removal switches the binding from being enthalpically to entropically driven and gives mixed binding modes containing both simultaneous and cross-linking binding behavior, without markedly affecting the overall binding affinity and kinetics.
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Affiliation(s)
- James Hooper
- School
of Food Science & Nutrition and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Yuanyuan Liu
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United
Kingdom
| | - Darshita Budhadev
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United
Kingdom
| | - Dario Fernandez Ainaga
- School
of Chemical and Process Engineering, University
of Leeds, Leeds LS2 9JT, United Kingdom
| | - Nicole Hondow
- School
of Chemical and Process Engineering, University
of Leeds, Leeds LS2 9JT, United Kingdom
| | - Dejian Zhou
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United
Kingdom
| | - Yuan Guo
- School
of Food Science & Nutrition and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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17
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Engineering SARS-CoV-2 specific cocktail antibodies into a bispecific format improves neutralizing potency and breadth. Nat Commun 2022; 13:5552. [PMID: 36138032 PMCID: PMC9499943 DOI: 10.1038/s41467-022-33284-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 09/12/2022] [Indexed: 01/20/2023] Open
Abstract
One major limitation of neutralizing antibody-based COVID-19 therapy is the requirement of costly cocktails to reduce emergence of antibody resistance. Here we engineer two bispecific antibodies (bsAbs) using distinct designs and compared them with parental antibodies and their cocktail. Single molecules of both bsAbs block the two epitopes targeted by parental antibodies on the receptor-binding domain (RBD). However, bsAb with the IgG-(scFv)2 design (14-H-06) but not the CrossMAb design (14-crs-06) shows increased antigen-binding and virus-neutralizing activities against multiple SARS-CoV-2 variants as well as increased breadth of neutralizing activity compared to the cocktail. X-ray crystallography and cryo-EM reveal distinct binding models for individual cocktail antibodies, and computational simulations suggest higher inter-spike crosslinking potentials by 14-H-06 than 14-crs-06. In mouse models of infections by SARS-CoV-2 and multiple variants, 14-H-06 exhibits higher or equivalent therapeutic efficacy than the cocktail. Rationally engineered bsAbs represent a cost-effective alternative to antibody cocktails and a promising strategy to improve potency and breadth.
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18
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Hale M, Netland J, Chen Y, Thouvenel CD, Smith KN, Rich LM, Vanderwall ER, Miranda MC, Eggenberger J, Hao L, Watson MJ, Mundorff CC, Rodda LB, King NP, Guttman M, Gale M, Abraham J, Debley JS, Pepper M, Rawlings DJ. IgM antibodies derived from memory B cells are potent cross-variant neutralizers of SARS-CoV-2. J Exp Med 2022; 219:213384. [PMID: 35938988 PMCID: PMC9365875 DOI: 10.1084/jem.20220849] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/22/2022] [Accepted: 07/12/2022] [Indexed: 01/14/2023] Open
Abstract
Humoral immunity to SARS-CoV-2 can be supplemented with polyclonal sera from convalescent donors or an engineered monoclonal antibody (mAb) product. While pentameric IgM antibodies are responsible for much of convalescent sera's neutralizing capacity, all available mAbs are based on the monomeric IgG antibody subtype. We now show that IgM mAbs derived from immune memory B cell receptors are potent neutralizers of SARS-CoV-2. IgM mAbs outperformed clonally identical IgG antibodies across a range of affinities and SARS-CoV-2 receptor-binding domain epitopes. Strikingly, efficacy against SARS-CoV-2 viral variants was retained for IgM but not for clonally identical IgG. To investigate the biological role for IgM memory in SARS-CoV-2, we also generated IgM mAbs from antigen-experienced IgM+ memory B cells in convalescent donors, identifying a potent neutralizing antibody. Our results highlight the therapeutic potential of IgM mAbs and inform our understanding of the role for IgM memory against a rapidly mutating pathogen.
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Affiliation(s)
- Malika Hale
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | - Jason Netland
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Yu Chen
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | | | | | - Lucille M. Rich
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | | | - Marcos C. Miranda
- Institute for Protein Design, University of Washington, Seattle, WA,Department of Biochemistry, University of Washington School of Medicine, Seattle, WA
| | - Julie Eggenberger
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Linhui Hao
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Michael J. Watson
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
| | | | - Lauren B. Rodda
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Neil P. King
- Institute for Protein Design, University of Washington, Seattle, WA,Department of Biochemistry, University of Washington School of Medicine, Seattle, WA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
| | - Michael Gale
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Jonathan Abraham
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA
| | - Jason S. Debley
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | - Marion Pepper
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - David J. Rawlings
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA,Department of Immunology, University of Washington School of Medicine, Seattle, WA,Department of Pediatrics, University of Washington School of Medicine, Seattle, WA,Correspondence to David J. Rawlings:
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19
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Schriek AI, van Haaren MM, Poniman M, Dekkers G, Bentlage AEH, Grobben M, Vidarsson G, Sanders RW, Verrips T, Geijtenbeek TBH, Heukers R, Kootstra NA, de Taeye SW, van Gils MJ. Anti-HIV-1 Nanobody-IgG1 Constructs With Improved Neutralization Potency and the Ability to Mediate Fc Effector Functions. Front Immunol 2022; 13:893648. [PMID: 35651621 PMCID: PMC9150821 DOI: 10.3389/fimmu.2022.893648] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
The most effective treatment for HIV-1, antiretroviral therapy, suppresses viral replication and averts the disease from progression. Nonetheless, there is a need for alternative treatments as it requires daily administration with the possibility of side effects and occurrence of drug resistance. Broadly neutralizing antibodies or nanobodies targeting the HIV-1 envelope glycoprotein are explored as alternative treatment, since they mediate viral suppression and contribute to the elimination of virus-infected cells. Besides neutralization potency and breadth, Fc-mediated effector functions of bNAbs also contribute to the in vivo efficacy. In this study multivalent J3, 2E7 and 1F10 anti-HIV-1 broadly neutralizing nanobodies were generated to improve neutralization potency and IgG1 Fc fusion was utilized to gain Fc-mediated effector functions. Bivalent and trivalent nanobodies, coupled using long glycine-serine linkers, showed increased binding to the HIV-1 Env and enhanced neutralization potency compared to the monovalent variant. Fusion of an IgG1 Fc domain to J3 improved neutralization potency compared to the J3-bihead and restored Fc-mediated effector functions such as antibody-dependent cellular phagocytosis and trogocytosis, and natural killer cell activation. Due to their neutralization breadth and potency and their ability to induce effector functions these nanobody-IgG1 constructs may prove to be valuable towards alternative HIV-1 therapies.
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Affiliation(s)
- Angela I Schriek
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | - Marlies M van Haaren
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | - Meliawati Poniman
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | | | - Arthur E H Bentlage
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Marloes Grobben
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | - Gestur Vidarsson
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands.,Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, United States
| | - Theo Verrips
- Department of Biology, Faculty of Sciences, Utrecht University, Utrecht, Netherlands.,VerLin BV, Utrecht, Netherlands
| | - Teunis B H Geijtenbeek
- Department of Experimental Immunology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | | | - Neeltje A Kootstra
- Department of Experimental Immunology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | - Steven W de Taeye
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
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20
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Serrano I, Luque A, Mitjavila F, Blom AM, Rodríguez de Córdoba S, Vega MC, Torras J, Aran JM. The Hidden Side of Complement Regulator C4BP: Dissection and Evaluation of Its Immunomodulatory Activity. Front Immunol 2022; 13:883743. [PMID: 35547734 PMCID: PMC9084231 DOI: 10.3389/fimmu.2022.883743] [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: 02/25/2022] [Accepted: 03/28/2022] [Indexed: 11/18/2022] Open
Abstract
C4b-binding protein (C4BP) is a well-known regulator of the complement system that holds additional and important activities unrelated to complement inhibition. Recently, we have described a novel immunomodulatory activity in the minor C4BP(β-) isoform directly acting over inflammatory phagocytes. Here we show that incorporation of the β-chain to the C4BP α-chain oligomer interferes with this immunomodulatory activity of C4BP. Moreover, an oligomeric form including only the complement control protein 6 (CCP6) domain of the C4BP α-chain (PRP6-HO7) is sufficient to “reprogram” monocyte-derived DCs (Mo-DCs) from a pro-inflammatory and immunogenic phenotype to an anti-inflammatory and tolerogenic state. PRP6-HO7 lacks complement regulatory activity but retains full immunomodulatory activity over inflammatory Mo-DCs induced by TLRs, characterized by downregulation of relevant surface markers such as CD83, HLA-DR, co-stimulatory molecules such as CD86, CD80 and CD40, and pro-inflammatory cytokines such as IL-12 and TNF-α. Furthermore, PRP6-HO7-treated Mo-DCs shows increased endocytosis, significantly reduced CCR7 expression and CCL21-mediated chemotaxis, and prevents T cell alloproliferation. Finally, PRP6-HO7 shows also full immunomodulatory activity over Mo-DCs isolated from lupus nephritis patients with active disease, even without further pro-inflammatory stimulation. Therefore PRP6-HO7, retaining the immunomodulatory activity of C4BP(β-) and lacking its complement regulatory activity, might represent a promising and novel alternative to treat autoimmune diseases.
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Affiliation(s)
- Inmaculada Serrano
- Immune-inflammatory Processes and Gene Therapeutics Group, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ana Luque
- Immune-inflammatory Processes and Gene Therapeutics Group, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Francesca Mitjavila
- Internal Medicine Service, Bellvitge University Hospital, University of Barcelona and Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Anna M Blom
- Department of Translational Medicine, Section of Medical Protein Chemistry, Lund University, Malmö, Sweden
| | - Santiago Rodríguez de Córdoba
- Molecular Pathology/Genetics of Complement Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC) and Ciber de Enfermedades Raras (CIBERER), Madrid, Spain
| | - M Cristina Vega
- Structural Biology of Host-Pathogen Interactions Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Joan Torras
- Nephrology Department, Bellvitge University Hospital, Experimental Nephrology Lab., University of Barcelona and Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Josep M Aran
- Immune-inflammatory Processes and Gene Therapeutics Group, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
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21
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Brown JWP, Alford RG, Walsh JC, Spinney RE, Xu SY, Hertel S, Berengut JF, Spenkelink LM, van Oijen AM, Böcking T, Morris RG, Lee LK. Rapid Exchange of Stably Bound Protein and DNA Cargo on a DNA Origami Receptor. ACS NANO 2022; 16:6455-6467. [PMID: 35316035 DOI: 10.1021/acsnano.2c00699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Biomolecular complexes can form stable assemblies yet can also rapidly exchange their subunits to adapt to environmental changes. Simultaneously allowing for both stability and rapid exchange expands the functional capacity of biomolecular machines and enables continuous function while navigating a complex molecular world. Inspired by biology, we design and synthesize a DNA origami receptor that exploits multivalent interactions to form stable complexes that are also capable of rapid subunit exchange. The system utilizes a mechanism first outlined in the context of the DNA replisome, known as multisite competitive exchange, and achieves a large separation of time scales between spontaneous subunit dissociation, which requires days, and rapid subunit exchange, which occurs in minutes. In addition, we use the DNA origami receptor to demonstrate stable interactions with rapid exchange of both DNA and protein subunits, thus highlighting the applicability of our approach to arbitrary molecular cargo, an important distinction with canonical toehold exchange between single-stranded DNA. We expect this study to benefit future studies that use DNA origami structures to exploit multivalent interactions for the design and synthesis of a wide range of possible kinetic behaviors.
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Affiliation(s)
- James W P Brown
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Rokiah G Alford
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - James C Walsh
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Richard E Spinney
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
- School of Physics, University of New South Wales, Sydney 2052, Australia
| | - Stephanie Y Xu
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Sophie Hertel
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Jonathan F Berengut
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
- School of Chemistry, University of Sydney, Sydney 2006, Australia
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Till Böcking
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Richard G Morris
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
- School of Physics, University of New South Wales, Sydney 2052, Australia
| | - Lawrence K Lee
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney 2052, Australia
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22
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Ovchinnikov V, Karplus M. A Coarse-Grained Model of Affinity Maturation Indicates the Importance of B-Cell Receptor Avidity in Epitope Subdominance. Front Immunol 2022; 13:816634. [PMID: 35371013 PMCID: PMC8971376 DOI: 10.3389/fimmu.2022.816634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/24/2022] [Indexed: 12/02/2022] Open
Abstract
The elicitation of broadly neutralizing antibodies (bnAbs) is a major goal in the design of vaccines against rapidly-mutating viruses. In the case of influenza, many bnAbs that target conserved epitopes on the stem of the hemagglutinin protein (HA) have been discovered. However, these antibodies are rare, are not boosted well upon reinfection, and often have low neutralization potency, compared to strain-specific antibodies directed to the HA head. Different hypotheses have been proposed to explain this phenomenon. We use a coarse-grained computational model of the germinal center reaction to investigate how B-cell receptor binding valency affects the growth and affinity maturation of competing B-cells. We find that receptors that are unable to bind antigen bivalently, and also those that do not bind antigen cooperatively, have significantly slower rates of growth, memory B-cell production, and, under certain conditions, rates of affinity maturation. The corresponding B-cells are predicted to be outcompeted by B-cells that bind bivalently and cooperatively. We use the model to explore strategies for a universal influenza vaccine, e.g., how to boost the concentrations of the slower growing cross-reactive antibodies directed to the stem. The results suggest that, upon natural reinfections subsequent to vaccination, the protectiveness of such vaccines would erode, possibly requiring regular boosts. Collectively, our results strongly support the importance of bivalent antibody binding in immunodominance, and suggest guidelines for developing a universal influenza vaccine.
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Affiliation(s)
- Victor Ovchinnikov
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, United States
- *Correspondence: Victor Ovchinnikov, ; ; Martin Karplus,
| | - Martin Karplus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, United States
- Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, Strasbourg, France
- *Correspondence: Victor Ovchinnikov, ; ; Martin Karplus,
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23
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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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24
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Viral surface geometry shapes influenza and coronavirus spike evolution through antibody pressure. PLoS Comput Biol 2021; 17:e1009664. [PMID: 34898597 PMCID: PMC8699686 DOI: 10.1371/journal.pcbi.1009664] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 12/23/2021] [Accepted: 11/19/2021] [Indexed: 01/02/2023] Open
Abstract
The evolution of circulating viruses is shaped by their need to evade antibody response, which mainly targets the viral spike. Because of the high density of spikes on the viral surface, not all antigenic sites are targeted equally by antibodies. We offer here a geometry-based approach to predict and rank the probability of surface residues of SARS spike (S protein) and influenza H1N1 spike (hemagglutinin) to acquire antibody-escaping mutations utilizing in-silico models of viral structure. We used coarse-grained MD simulations to estimate the on-rate (targeting) of an antibody model to surface residues of the spike protein. Analyzing publicly available sequences, we found that spike surface sequence diversity of the pre-pandemic seasonal influenza H1N1 and the sarbecovirus subgenus highly correlates with our model prediction of antibody targeting. In particular, we identified an antibody-targeting gradient, which matches a mutability gradient along the main axis of the spike. This identifies the role of viral surface geometry in shaping the evolution of circulating viruses. For the 2009 H1N1 and SARS-CoV-2 pandemics, a mutability gradient along the main axis of the spike was not observed. Our model further allowed us to identify key residues of the SARS-CoV-2 spike at which antibody escape mutations have now occurred. Therefore, it can inform of the likely functional role of observed mutations and predict at which residues antibody-escaping mutation might arise. The immune system responds to viruses by making neutralizing antibodies to regions of the viral spike protein, which mutates to escape. To inform vaccine design and understand how the fitness landscape of the viral spike changes over time, it is necessary to identify and quantify the factors directing its evolution. Based on the 3D structure of the viral surface and spike as captured with Cryo-EM and crystallography, we aimed to create a coarse-grained model for the effect of antibodies in forcing surface residues of the spike to mutate. We found that for pre-pandemic influenza (hemagglutinin) and the corona sarbecovirus subgenus (S protein), the location of a residue on the spike protein, which modulates its accessibility to antibodies, highly correlates with its propensity to mutate. Hence, a mechanistic approach can be used to identify aspects of viral spike sequence diversity related to antibody escape.
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25
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Abstract
Monoclonal antibodies (mAbs) that efficiently neutralize SARS-CoV-2 have been developed at an unprecedented speed. Notwithstanding, there is a vague understanding of the various Ab functions induced beyond antigen binding by the heavy-chain constant domain. To explore the diverse roles of Abs in SARS-CoV-2 immunity, we expressed a SARS-CoV-2 spike protein (SP) binding mAb (H4) in the four IgG subclasses present in human serum (IgG1-4) using glyco-engineered Nicotiana benthamiana plants. All four subclasses, carrying the identical antigen-binding site, were fully assembled in planta and exhibited a largely homogeneous xylose- and fucose-free glycosylation profile. The Ab variants ligated to the SP with an up to fivefold increased binding activity of IgG3. Furthermore, all H4 subtypes were able to neutralize SARS-CoV-2. However, H4-IgG3 exhibited an up to 50-fold superior neutralization potency compared with the other subclasses. Our data point to a strong protective effect of IgG3 Abs in SARS-CoV-2 infection and suggest that superior neutralization might be a consequence of cross-linking the SP on the viral surface. This should be considered in therapy and vaccine development. In addition, we underscore the versatile use of plants for the rapid expression of complex proteins in emergency cases.
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26
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Onodera T, Kita S, Adachi Y, Moriyama S, Sato A, Nomura T, Sakakibara S, Inoue T, Tadokoro T, Anraku Y, Yumoto K, Tian C, Fukuhara H, Sasaki M, Orba Y, Shiwa N, Iwata N, Nagata N, Suzuki T, Sasaki J, Sekizuka T, Tonouchi K, Sun L, Fukushi S, Satofuka H, Kazuki Y, Oshimura M, Kurosaki T, Kuroda M, Matsuura Y, Suzuki T, Sawa H, Hashiguchi T, Maenaka K, Takahashi Y. A SARS-CoV-2 antibody broadly neutralizes SARS-related coronaviruses and variants by coordinated recognition of a virus-vulnerable site. Immunity 2021; 54:2385-2398.e10. [PMID: 34508662 PMCID: PMC8382582 DOI: 10.1016/j.immuni.2021.08.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/02/2021] [Accepted: 08/19/2021] [Indexed: 11/23/2022]
Abstract
Potent neutralizing SARS-CoV-2 antibodies often target the spike protein receptor-binding site (RBS), but the variability of RBS epitopes hampers broad neutralization of multiple sarbecoviruses and drifted viruses. Here, using humanized mice, we identified an RBS antibody with a germline VH gene that potently neutralized SARS-related coronaviruses, including SARS-CoV and SARS-CoV-2 variants. X-ray crystallography revealed coordinated recognition by the heavy chain of non-RBS conserved sites and the light chain of RBS with a binding angle mimicking the angiotensin-converting enzyme 2 (ACE2) receptor. The minimum footprints in the hypervariable region of RBS contributed to the breadth of neutralization, which was enhanced by immunoglobulin G3 (IgG3) class switching. The coordinated binding resulted in broad neutralization of SARS-CoV and emerging SARS-CoV-2 variants of concern. Low-dose therapeutic antibody treatment in hamsters reduced the virus titers and morbidity during SARS-CoV-2 challenge. The structural basis for broad neutralizing activity may inform the design of a broad spectrum of therapeutics and vaccines.
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Affiliation(s)
- Taishi Onodera
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Shunsuke Kita
- Laboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Yu Adachi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Saya Moriyama
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Akihiko Sato
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; Drug Discovery & Disease Research Laboratory, Shionogi & Co., Ltd., Osaka 561-0825, Japan
| | - Takao Nomura
- Laboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Shuhei Sakakibara
- Laboratory of Immune Regulation, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Takeshi Inoue
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Takashi Tadokoro
- Laboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Yuki Anraku
- Laboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Kohei Yumoto
- Laboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Cong Tian
- Laboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Hideo Fukuhara
- Laboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan; Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo 060-0812, Japan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan
| | - Nozomi Shiwa
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
| | - Naoko Iwata
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
| | - Noriyo Nagata
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
| | - Tateki Suzuki
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Jiei Sasaki
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomic Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Keisuke Tonouchi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; Department of Life Science and Medical Bioscience, Waseda University, Tokyo 162-8480, Japan
| | - Lin Sun
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Shuetsu Fukushi
- Department of Virology I, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Hiroyuki Satofuka
- Chromosome Engineering Research Center, Tottori University, Tottori 683-8503, Japan
| | - Yasuhiro Kazuki
- Chromosome Engineering Research Center, Tottori University, Tottori 683-8503, Japan; Division of Genome and Cellular Functions, Department of Molecular and Cellular Biology, School of Life Science, Faculty of Medicine, Tottori University, Tottori 683-8503, Japan
| | | | - Tomohiro Kurosaki
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Makoto Kuroda
- Pathogen Genomic Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Yoshiharu Matsuura
- Laboratory of Virus Control, Center for Infectious Diseases Education and Research, Osaka University, Osaka 565-0871, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan
| | - Takao Hashiguchi
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan; Laboratory of Medical Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan; Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo 060-0812, Japan.
| | - Yoshimasa Takahashi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan.
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27
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Lee TJ, Vazquez JA, Rao ASRS. Mathematical modeling of impact of eCD4-Ig molecule in control and management of HIV within a host. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:6887-6906. [PMID: 34517562 DOI: 10.3934/mbe.2021342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Eradication and eventually cure of the HIV virus from the infected individual should be the primary goal in all HIV therapy. This has yet to be achieved, however development of broadly neutralizing antibodies (bNabs) and eCD4-Ig and its related particles are promising therapeutic alternatives to eliminate the HIV virus from the host. Past studies have found superior protectivity and efficacy eradicating the HIV virus with the use of eCD4-Igs over bNabs, which has proposed the antibody-dependent cell-mediated cytotoxicity (ADCC) effect as one of the key-factors for antibody design. In this study, we evaluated the dynamics of the HIV virus, CD4 T-cells, and eCD4-Ig in humans using a gene-therapy approach which has been evaluated in primates previously. We utilized a mathematical model to investigate the relationship between eCD4-Ig levels, ADCC effects, and the neutralization effect on HIV elimination. In addition, a balance between ADCC and viral neutralization effect of eCD4-Ig has been investigated in order to understand the condition of which HIV eliminating antibodies needs to satisfy. Our analysis indicated some level of ADCC effect, which was missing from ART, was required for viral elimination. The results will be helpful in designing future drugs or therapeutic strategies.
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Affiliation(s)
- Tae Jin Lee
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
| | - Jose A Vazquez
- Division of Infectious Diseases, Department of Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
| | - Arni S R Srinivasa Rao
- Division of Infectious Diseases, Department of Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
- Laboratory for Theory and Mathematical Modeling, Division of Infectious Diseases, Department of Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
- Department of Mathematics, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
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28
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Nasal delivery of an IgM offers broad protection from SARS-CoV-2 variants. Nature 2021; 595:718-723. [PMID: 34082438 PMCID: PMC8742224 DOI: 10.1038/s41586-021-03673-2] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/26/2021] [Indexed: 02/04/2023]
Abstract
Resistance represents a major challenge for antibody-based therapy for COVID-191-4. Here we engineered an immunoglobulin M (IgM) neutralizing antibody (IgM-14) to overcome the resistance encountered by immunoglobulin G (IgG)-based therapeutics. IgM-14 is over 230-fold more potent than its parental IgG-14 in neutralizing SARS-CoV-2. IgM-14 potently neutralizes the resistant virus raised by its corresponding IgG-14, three variants of concern-B.1.1.7 (Alpha, which first emerged in the UK), P.1 (Gamma, which first emerged in Brazil) and B.1.351 (Beta, which first emerged in South Africa)-and 21 other receptor-binding domain mutants, many of which are resistant to the IgG antibodies that have been authorized for emergency use. Although engineering IgG into IgM enhances antibody potency in general, selection of an optimal epitope is critical for identifying the most effective IgM that can overcome resistance. In mice, a single intranasal dose of IgM-14 at 0.044 mg per kg body weight confers prophylactic efficacy and a single dose at 0.4 mg per kg confers therapeutic efficacy against SARS-CoV-2. IgM-14, but not IgG-14, also confers potent therapeutic protection against the P.1 and B.1.351 variants. IgM-14 exhibits desirable pharmacokinetics and safety profiles when administered intranasally in rodents. Our results show that intranasal administration of an engineered IgM can improve efficacy, reduce resistance and simplify the prophylactic and therapeutic treatment of COVID-19.
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29
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Peterhoff D, Thalhauser S, Sobczak JM, Mohsen MO, Voigt C, Seifert N, Neckermann P, Hauser A, Ding S, Sattentau Q, Bachmann MF, Breunig M, Wagner R. Augmenting the Immune Response against a Stabilized HIV-1 Clade C Envelope Trimer by Silica Nanoparticle Delivery. Vaccines (Basel) 2021; 9:642. [PMID: 34208059 PMCID: PMC8230641 DOI: 10.3390/vaccines9060642] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/03/2021] [Accepted: 06/09/2021] [Indexed: 12/19/2022] Open
Abstract
The delivery of HIV-1 envelope (Env) trimer-based immunogens on the surface of nanoparticles holds promise to promote immunogenicity with the aim of inducing a potent, durable and broad neutralizing antibody (bnAb) response. Towards that goal, we examined the covalent conjugation of Env to 100 nm and 200 nm silica nanoparticles (SiNPs) to optimize conjugation density and attachment stability. Env was redesigned to enable site-specific cysteine-mediated covalent conjugation while maintaining its structural integrity and antigenicity. Env was anchored to different sized SiNPs with a calculated spacing of 15 nm between adjacent trimers. Both particle sizes exhibited high in vitro stability over a seven-day period. After attachment, 100 nm particles showed better colloidal stability compared to 200 nm particles. Importantly, the antigenic profile of Env was not impaired by surface attachment, indicating that the quaternary structure was maintained. In vitro Env uptake by dendritic cells was significantly enhanced when Env was delivered on the surface of nanoparticles compared to soluble Env. Furthermore, multivalent Env displayed efficiently activated B cells even at Env concentrations in the low nanomolar range. In mice, antibody responses to nanoparticle-coupled Env were stronger compared to the free protein and had equivalent effects at lower doses and without adjuvant.
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Affiliation(s)
- David Peterhoff
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, 93053 Regensburg, Germany; (C.V.); (N.S.); (P.N.); (A.H.)
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Stefanie Thalhauser
- Institute of Pharmaceutical Technology, University of Regensburg, 93053 Regensburg, Germany; (S.T.); (M.B.)
| | - Jan M. Sobczak
- Department for BioMedical Research, University of Bern, 3010 Bern, Switzerland; (J.M.S.); (M.O.M.); (M.F.B.)
- Department of Immunology RI, University Hospital Bern, 3010 Bern, Switzerland
| | - Mona O. Mohsen
- Department for BioMedical Research, University of Bern, 3010 Bern, Switzerland; (J.M.S.); (M.O.M.); (M.F.B.)
- Department of Immunology RI, University Hospital Bern, 3010 Bern, Switzerland
| | - Christoph Voigt
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, 93053 Regensburg, Germany; (C.V.); (N.S.); (P.N.); (A.H.)
| | - Nicole Seifert
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, 93053 Regensburg, Germany; (C.V.); (N.S.); (P.N.); (A.H.)
| | - Patrick Neckermann
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, 93053 Regensburg, Germany; (C.V.); (N.S.); (P.N.); (A.H.)
| | - Alexandra Hauser
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, 93053 Regensburg, Germany; (C.V.); (N.S.); (P.N.); (A.H.)
| | - Song Ding
- EuroVacc Foundation, 1002 Lausanne, Switzerland;
| | - Quentin Sattentau
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK;
| | - Martin F. Bachmann
- Department for BioMedical Research, University of Bern, 3010 Bern, Switzerland; (J.M.S.); (M.O.M.); (M.F.B.)
- Department of Immunology RI, University Hospital Bern, 3010 Bern, Switzerland
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Miriam Breunig
- Institute of Pharmaceutical Technology, University of Regensburg, 93053 Regensburg, Germany; (S.T.); (M.B.)
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, 93053 Regensburg, Germany; (C.V.); (N.S.); (P.N.); (A.H.)
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, 93053 Regensburg, Germany
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30
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Differential expression of HIV envelope epitopes on the surface of HIV-Infected macrophages and CD4 + T cells. Antiviral Res 2021; 191:105085. [PMID: 33961905 DOI: 10.1016/j.antiviral.2021.105085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/28/2021] [Accepted: 05/01/2021] [Indexed: 11/23/2022]
Abstract
HIV-infected macrophages contribute to persistence of HIV reservoirs in people living with HIV receiving antiretroviral therapy. A potential strategy to eliminate reservoirs is the use of antibody-dependent cellular cytotoxicity (ADCC) against infected cells expressing the HIV envelope (Env) protein on their surface. Designing ADCC strategies requires knowledge of exposed Env epitopes on the cell surface and identifying antibodies capable of opsonising infected cells, yet little is known regarding the ability of HIV-infected macrophages to be targeted with such strategies. Using a panel of neutralising and poorly-neutralising anti-Env antibodies we compared Env epitopes expressed on infected monocyte-derived macrophages (MDM) and autologous T cells. Our results reveal potential differences in epitope expression on macrophage- and T cell-expressed Env. Notably, HIVBaL-infected macrophages were more susceptible to opsonisation by NIH45-46 (median = 40.4%) compared to infected T cells (13.6%; p = 0.002), which were more susceptible to opsonisation by 17b and 447.52D (88.6% and 45.6% respectively) compared to MDM (30% and 6.7%, p = 0.002 and 0.004 respectively). Furthermore, neutralising antibodies 10E8 and PGT145 were relatively ineffective at opsonising Env expressed on the surface of infected T cells or macrophages, indicating that the context in which Env is presented on infected cells may differ to that of cell-free virions.
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31
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Remmel JL, Frei JC, Butler SE, Lai JR, Ackerman ME. Diverse contributions of avidity to the broad neutralization of Dengue virus by antibodies targeting the E dimer epitope. Virology 2021; 559:57-64. [PMID: 33819753 DOI: 10.1016/j.virol.2021.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/05/2021] [Accepted: 03/21/2021] [Indexed: 10/21/2022]
Abstract
Antibodies (Abs) recognizing the Dengue virus (DENV) E dimer epitope (EDE) that potently neutralize all DENV serotypes are promising templates for vaccine design. As an important feature for some Abs is their bivalency, we sought to define the role avidity plays in neutralization by EDE Abs. We compared neutralization activity between bivalent IgGs and monovalent Ab fragments (Fabs) for two EDE Abs, A11 and C10. IgG forms of both Abs exhibited more potent neutralization activity than their counterpart Fabs, yet only for C10 was this enhanced activity associated with bivalent binding. A11 and C10 also exhibited differential binding profiles to DENV virus-like particles under acidic conditions mimicking the environment that triggers viral membrane fusion, suggesting that EDE Abs employ diverse neutralization mechanisms despite sharing an epitope. Delineating the full range of Ab binding modes and neutralization mechanisms against a single epitope may inform therapeutic approaches and refine vaccine design.
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Affiliation(s)
- Jennifer L Remmel
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA
| | - Julia C Frei
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Savannah E Butler
- Geisel School of Medicine, Dartmouth College, Hanover, NH, 03755, USA
| | - Jonathan R Lai
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Margaret E Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA; Geisel School of Medicine, Dartmouth College, Hanover, NH, 03755, USA.
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32
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Bracken CJ, Lim SA, Solomon P, Rettko NJ, Nguyen DP, Zha BS, Schaefer K, Byrnes JR, Zhou J, Lui I, Liu J, Pance K, Zhou XX, Leung KK, Wells JA. Bi-paratopic and multivalent VH domains block ACE2 binding and neutralize SARS-CoV-2. Nat Chem Biol 2021; 17:113-121. [PMID: 33082574 PMCID: PMC8356808 DOI: 10.1038/s41589-020-00679-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 09/25/2020] [Indexed: 11/14/2022]
Abstract
Neutralizing agents against SARS-CoV-2 are urgently needed for the treatment and prophylaxis of COVID-19. Here, we present a strategy to rapidly identify and assemble synthetic human variable heavy (VH) domains toward neutralizing epitopes. We constructed a VH-phage library and targeted the angiotensin-converting enzyme 2 (ACE2) binding interface of the SARS-CoV-2 Spike receptor-binding domain (Spike-RBD). Using a masked selection approach, we identified VH binders to two non-overlapping epitopes and further assembled these into multivalent and bi-paratopic formats. These VH constructs showed increased affinity to Spike (up to 600-fold) and neutralization potency (up to 1,400-fold) on pseudotyped SARS-CoV-2 virus when compared to standalone VH domains. The most potent binder, a trivalent VH, neutralized authentic SARS-CoV-2 with a half-maximal inhibitory concentration (IC50) of 4.0 nM (180 ng ml-1). A cryo-EM structure of the trivalent VH bound to Spike shows each VH domain engaging an RBD at the ACE2 binding site, confirming our original design strategy.
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MESH Headings
- Angiotensin-Converting Enzyme 2/antagonists & inhibitors
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/immunology
- Animals
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Binding Sites, Antibody/genetics
- Binding Sites, Antibody/immunology
- Chlorocebus aethiops
- Cryoelectron Microscopy
- HEK293 Cells
- Humans
- Models, Molecular
- Peptide Library
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- SARS-CoV-2
- Single-Chain Antibodies/chemistry
- Single-Chain Antibodies/genetics
- Single-Chain Antibodies/immunology
- Spike Glycoprotein, Coronavirus/antagonists & inhibitors
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Vero Cells
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Affiliation(s)
- Colton J Bracken
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Shion A Lim
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Paige Solomon
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Nicholas J Rettko
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Duy P Nguyen
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Lyell Immunopharma Inc., Seattle, WA, USA
| | - Beth Shoshana Zha
- Department of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kaitlin Schaefer
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - James R Byrnes
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Jie Zhou
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Irene Lui
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Jia Liu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Merck & Co., South San Francisco, CA, USA
| | - Katarina Pance
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Xin X Zhou
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Kevin K Leung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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33
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Chu TH, Patz EF, Ackerman ME. Coming together at the hinges: Therapeutic prospects of IgG3. MAbs 2021; 13:1882028. [PMID: 33602056 PMCID: PMC7899677 DOI: 10.1080/19420862.2021.1882028] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/08/2021] [Accepted: 01/22/2021] [Indexed: 01/22/2023] Open
Abstract
The human IgG3 subclass is conspicuously absent among the formats for approved monoclonal antibody therapies and Fc fusion protein biologics. Concern about the potential for rapid degradation, reduced plasma half-life, and increased immunogenicity due to marked variation in allotypes has apparently outweighed the potential advantages of IgG3, which include high affinity for activating Fcγ receptors, effective complement fixation, and a long hinge that appears better suited for low abundance targets. This review aims to highlight distinguishing features of IgG3 and to explore its functional role in the immune response. We present studies of natural immunity and recombinant antibody therapies that elucidate key contributions of IgG3 and discuss historical roadblocks that no longer remain clearly relevant. Collectively, this body of evidence motivates thoughtful reconsideration of the clinical advancement of this distinctive antibody subclass for treatment of human diseases. Abbreviations: ADCC - Antibody-Dependent Cell-mediated CytotoxicityADE - Antibody-dependent enhancementAID - Activation-Induced Cytidine DeaminaseCH - Constant HeavyCHF - Complement factor HCSR - Class Switch RecombinationEM - Electron MicroscopyFab - Fragment, antigen bindingFc - Fragment, crystallizableFcRn - Neonatal Fc ReceptorFcγR - Fc gamma ReceptorHIV - Human Immunodeficiency VirusIg - ImmunoglobulinIgH - Immunoglobulin Heavy chain geneNHP - Non-Human Primate.
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Affiliation(s)
- Thach H. Chu
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Edward F. Patz
- Department of Radiology and Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, NC, USA
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Surowka M, Schaefer W, Klein C. Ten years in the making: application of CrossMab technology for the development of therapeutic bispecific antibodies and antibody fusion proteins. MAbs 2021; 13:1967714. [PMID: 34491877 PMCID: PMC8425689 DOI: 10.1080/19420862.2021.1967714] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/03/2021] [Accepted: 08/10/2021] [Indexed: 12/15/2022] Open
Abstract
Bispecific antibodies have recently attracted intense interest. CrossMab technology was described in 2011 as novel approach enabling correct antibody light-chain association with their respective heavy chain in bispecific antibodies, together with methods enabling correct heavy-chain association using existing pairs of antibodies. Since the original description, CrossMab technology has evolved in the past decade into one of the most mature, versatile, and broadly applied technologies in the field, and nearly 20 bispecific antibodies based on CrossMab technology developed by Roche and others have entered clinical trials. The most advanced of these are the Ang-2/VEGF bispecific antibody faricimab, currently undergoing regulatory review, and the CD20/CD3 T cell bispecific antibody glofitamab, currently in pivotal Phase 3 trials. In this review, we introduce the principles of CrossMab technology, including its application for the generation of bi-/multispecific antibodies with different geometries and mechanisms of action, and provide an overview of CrossMab-based therapeutics in clinical trials.
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35
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Amitai A. Viral surface geometry shapes influenza and coronavirus spike evolution through antibody pressure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.10.20.347641. [PMID: 33106808 PMCID: PMC7587782 DOI: 10.1101/2020.10.20.347641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The evolution of circulating viruses is shaped by their need to evade antibody response, which mainly targets the glycoprotein (spike). However, not all antigenic sites are targeted equally by antibodies, leading to complex immunodominance patterns. We used 3D computational models to estimate antibody pressure on the seasonal influenza H1N1 and SARS spikes. Analyzing publically available sequences, we show that antibody pressure, through the geometrical organization of spikes on the viral surface, shaped their mutability. Studying the mutability patterns of SARS-CoV-2 and the 2009 H1N1 pandemic spikes, we find that they are not predominantly shaped by antibody pressure. However, for SARS-CoV-2, we find that over time, it acquired mutations at antibody-accessible positions, which could indicate possible escape as define by our model. We offer a geometry-based approach to predict and rank the probability of surface resides of SARS-CoV-2 spike to acquire antibody escaping mutations.
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Affiliation(s)
- Assaf Amitai
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
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36
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Cheloha RW, Harmand TJ, Wijne C, Schwartz TU, Ploegh HL. Exploring cellular biochemistry with nanobodies. J Biol Chem 2020; 295:15307-15327. [PMID: 32868455 PMCID: PMC7650250 DOI: 10.1074/jbc.rev120.012960] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/27/2020] [Indexed: 12/21/2022] Open
Abstract
Reagents that bind tightly and specifically to biomolecules of interest remain essential in the exploration of biology and in their ultimate application to medicine. Besides ligands for receptors of known specificity, agents commonly used for this purpose are monoclonal antibodies derived from mice, rabbits, and other animals. However, such antibodies can be expensive to produce, challenging to engineer, and are not necessarily stable in the context of the cellular cytoplasm, a reducing environment. Heavy chain-only antibodies, discovered in camelids, have been truncated to yield single-domain antibody fragments (VHHs or nanobodies) that overcome many of these shortcomings. Whereas they are known as crystallization chaperones for membrane proteins or as simple alternatives to conventional antibodies, nanobodies have been applied in settings where the use of standard antibodies or their derivatives would be impractical or impossible. We review recent examples in which the unique properties of nanobodies have been combined with complementary methods, such as chemical functionalization, to provide tools with unique and useful properties.
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Affiliation(s)
- Ross W Cheloha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Thibault J Harmand
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Charlotte Wijne
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas U Schwartz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA.
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37
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Schmidt F, Weisblum Y, Muecksch F, Hoffmann HH, Michailidis E, Lorenzi JC, Mendoza P, Rutkowska M, Bednarski E, Gaebler C, Agudelo M, Cho A, Wang Z, Gazumyan A, Cipolla M, Caskey M, Robbiani DF, Nussenzweig MC, Rice CM, Hatziioannou T, Bieniasz PD. Measuring SARS-CoV-2 neutralizing antibody activity using pseudotyped and chimeric viruses. J Exp Med 2020; 217:e20201181. [PMID: 32692348 PMCID: PMC7372514 DOI: 10.1084/jem.20201181] [Citation(s) in RCA: 408] [Impact Index Per Article: 102.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/05/2020] [Accepted: 07/07/2020] [Indexed: 12/18/2022] Open
Abstract
The emergence of SARS-CoV-2 and the ensuing explosive epidemic of COVID-19 disease has generated a need for assays to rapidly and conveniently measure the antiviral activity of SARS-CoV-2-specific antibodies. Here, we describe a collection of approaches based on SARS-CoV-2 spike-pseudotyped, single-cycle, replication-defective human immunodeficiency virus type-1 (HIV-1), and vesicular stomatitis virus (VSV), as well as a replication-competent VSV/SARS-CoV-2 chimeric virus. While each surrogate virus exhibited subtle differences in the sensitivity with which neutralizing activity was detected, the neutralizing activity of both convalescent plasma and human monoclonal antibodies measured using each virus correlated quantitatively with neutralizing activity measured using an authentic SARS-CoV-2 neutralization assay. The assays described herein are adaptable to high throughput and are useful tools in the evaluation of serologic immunity conferred by vaccination or prior SARS-CoV-2 infection, as well as the potency of convalescent plasma or human monoclonal antibodies.
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MESH Headings
- Animals
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/analysis
- Antibodies, Neutralizing/blood
- Antibodies, Viral/analysis
- Antibodies, Viral/blood
- Betacoronavirus/genetics
- Betacoronavirus/immunology
- COVID-19
- Cell Line
- Chimera/genetics
- Chimera/immunology
- Chlorocebus aethiops
- Coronavirus Infections/immunology
- Coronavirus Infections/virology
- HEK293 Cells
- HIV-1/genetics
- HIV-1/immunology
- Humans
- Immunoassay/methods
- Neutralization Tests/methods
- Pandemics
- Pneumonia, Viral/immunology
- Pneumonia, Viral/virology
- Recombination, Genetic
- SARS-CoV-2
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Vero Cells
- Vesicular stomatitis Indiana virus/genetics
- Vesicular stomatitis Indiana virus/immunology
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Affiliation(s)
- Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, NY
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY
| | | | | | - Julio C.C. Lorenzi
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Pilar Mendoza
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | | | - Eva Bednarski
- Laboratory of Retrovirology, The Rockefeller University, New York, NY
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Marianna Agudelo
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Davide F. Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | | | - Paul D. Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY
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38
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Abstract
PURPOSE OF REVIEW Immunotherapy strategies alternative to current antiretroviral therapies will need to address viral diversity while increasing the immune system's ability to efficiently target the latent virus reservoir. Antibody-based molecules can be designed based on broadly neutralizing and non-neutralizing antibodies that target free virions and infected cells. These multispecific molecules, either by IgG-like or non-IgG-like in structure, aim to target several independent HIV-1 epitopes and/or engage effector cells to eliminate the replicating virus and infected cells. This detailed review is intended to stimulate discussion on future requirements for novel immunotherapeutic molecules. RECENT FINDINGS Bispecific and trispecific antibodies are engineered as a single molecules to target two or more independent epitopes on the HIV-1 envelope (Env). These antibody-based molecules have increased avidity for Env, leading to improved neutralization potency and breadth compared with single parental antibodies. Furthermore, bispecific and trispecific antibodies that engage cellular receptors with one arm of the molecule help concentrate inhibitory molecules to the sites of potential infection and facilitate engagement of immune effector cells and Env-expressing target cells for their elimination. SUMMARY Recently engineered antibody-based molecules of different sizes and structures show promise in vitro or in vivo and are encouraging candidates for HIV treatment.
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Affiliation(s)
- Marina Tuyishime
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Guido Ferrari
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
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39
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Bracken CJ, Lim SA, Solomon P, Rettko NJ, Nguyen DP, Zha BS, Schaefer K, Byrnes JR, Zhou J, Lui I, Liu J, Pance K, Zhou XX, Leung KK, Wells JA. Bi-paratopic and multivalent human VH domains neutralize SARS-CoV-2 by targeting distinct epitopes within the ACE2 binding interface of Spike. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.08.08.242511. [PMID: 32817948 PMCID: PMC7430580 DOI: 10.1101/2020.08.08.242511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Neutralizing agents against SARS-CoV-2 are urgently needed for treatment and prophylaxis of COVID-19. Here, we present a strategy to rapidly identify and assemble synthetic human variable heavy (VH) domain binders with high affinity toward neutralizing epitopes without the need for high-resolution structural information. We constructed a VH-phage library and targeted a known neutralizing site, the angiotensin-converting enzyme 2 (ACE2) binding interface of the trimeric SARS-CoV-2 Spike receptor-binding domain (Spike-RBD). Using a masked selection approach, we identified 85 unique VH binders to two non-overlapping epitopes within the ACE2 binding site on Spike-RBD. This enabled us to systematically link these VH domains into multivalent and bi-paratopic formats. These multivalent and bi-paratopic VH constructs showed a marked increase in affinity to Spike (up to 600-fold) and neutralization potency (up to 1400-fold) on pseudotyped SARS-CoV-2 virus when compared to the standalone VH domains. The most potent binder, a trivalent VH, neutralized authentic SARS-CoV-2 with half-minimal inhibitory concentration (IC 50 ) of 4.0 nM (180 ng/mL). A cryo-EM structure of the trivalent VH bound to Spike shows each VH domain bound an RBD at the ACE2 binding site, explaining its increased neutralization potency and confirming our original design strategy. Our results demonstrate that targeted selection and engineering campaigns using a VH-phage library can enable rapid assembly of highly avid and potent molecules towards therapeutically important protein interfaces.
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Affiliation(s)
- Colton J. Bracken
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Shion A. Lim
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Paige Solomon
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Nicholas J. Rettko
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Duy P. Nguyen
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Beth Shoshana Zha
- Department of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kaitlin Schaefer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - James R. Byrnes
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Jie Zhou
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Irene Lui
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Jia Liu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Katarina Pance
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - QCRG Structural Biology Consortium
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Xin X. Zhou
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Kevin K. Leung
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - James A. Wells
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, CA
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40
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Nanoparticles presenting clusters of CD4 expose a universal vulnerability of HIV-1 by mimicking target cells. Proc Natl Acad Sci U S A 2020; 117:18719-18728. [PMID: 32690692 PMCID: PMC7414181 DOI: 10.1073/pnas.2010320117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
CD4-based decoy approaches against HIV-1 are attractive options for long-term viral control, but initial designs, including soluble CD4 (sCD4) and CD4-Ig, were ineffective. To evaluate a therapeutic that more accurately mimics HIV-1 target cells compared with monomeric sCD4 and dimeric CD4-Ig, we generated virus-like nanoparticles that present clusters of membrane-associated CD4 (CD4-VLPs) to permit high-avidity binding of trimeric HIV-1 envelope spikes. In neutralization assays, CD4-VLPs were >12,000-fold more potent than sCD4 and CD4-Ig and >100-fold more potent than the broadly neutralizing antibody (bNAb) 3BNC117, with >12,000-fold improvements against strains poorly neutralized by 3BNC117. CD4-VLPs also neutralized patient-derived viral isolates that were resistant to 3BNC117 and other bNAbs. Intraperitoneal injections of CD4-CCR5-VLP produced only subneutralizing plasma concentrations in HIV-1-infected humanized mice but elicited CD4-binding site mutations that reduced viral fitness. All mutant viruses showed reduced sensitivity to sCD4 and CD4-Ig but remained sensitive to neutralization by CD4-VLPs in vitro. In vitro evolution studies demonstrated that CD4-VLPs effectively controlled HIV-1 replication at neutralizing concentrations, and viral escape was not observed. Moreover, CD4-VLPs potently neutralized viral swarms that were completely resistant to CD4-Ig, suggesting that escape pathways that confer resistance against conventional CD4-based inhibitors are ineffective against CD4-VLPs. These findings suggest that therapeutics that mimic HIV-1 target cells could prevent viral escape by exposing a universal vulnerability of HIV-1: the requirement to bind CD4 on a target cell. We propose that therapeutic and delivery strategies that ensure durable bioavailability need to be developed to translate this concept into a clinically feasible functional cure therapy.
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41
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Schmidt F, Weisblum Y, Muecksch F, Hoffmann HH, Michailidis E, Lorenzi JCC, Mendoza P, Rutkowska M, Bednarski E, Gaebler C, Agudelo M, Cho A, Wang Z, Gazumyan A, Cipolla M, Caskey M, Robbiani DF, Nussenzweig MC, Rice CM, Hatziioannou T, Bieniasz PD. Measuring SARS-CoV-2 neutralizing antibody activity using pseudotyped and chimeric viruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.08.140871. [PMID: 32577658 PMCID: PMC7302213 DOI: 10.1101/2020.06.08.140871] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The emergence of SARS-CoV-2 and the ensuing explosive epidemic of COVID19 disease has generated a need for assays to rapidly and conveniently measure the antiviral activity of SARSCoV-2-specific antibodies. Here, we describe a collection of approaches based on SARS-CoV-2 spike-pseudotyped, single-cycle, replication-defective human immunodeficiency virus type-1 (HIV-1) and vesicular stomatitis virus (VSV), as well as a replication-competent VSV/SARS-CoV-2 chimeric virus. While each surrogate virus exhibited subtle differences in the sensitivity with which neutralizing activity was detected, the neutralizing activity of both convalescent plasma and human monoclonal antibodies measured using each virus correlated quantitatively with neutralizing activity measured using an authentic SARS-CoV-2 neutralization assay. The assays described herein are adaptable to high throughput and are useful tools in the evaluation of serologic immunity conferred by vaccination or prior SARS-CoV-2 infection, as well as the potency of convalescent plasma or human monoclonal antibodies.
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Affiliation(s)
- Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10028
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10028
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10028
| | - Hans-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, 1230 York Avenue, New York NY 10028
| | - Eleftherios Michailidis
- Laboratory of Virology and Infectious Disease, The Rockefeller University, 1230 York Avenue, New York NY 10028
| | - Julio C C Lorenzi
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York NY 10028
| | - Pilar Mendoza
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York NY 10028
| | - Magdalena Rutkowska
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10028
| | - Eva Bednarski
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10028
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York NY 10028
| | - Marianna Agudelo
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York NY 10028
| | - Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York NY 10028
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York NY 10028
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York NY 10028
| | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York NY 10028
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York NY 10028
| | - Davide F Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York NY 10028
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York NY 10028
- Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York NY 10028
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, 1230 York Avenue, New York NY 10028
| | - Theodora Hatziioannou
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10028
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10028
- Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York NY 10028
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42
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Berengut JF, Berengut JC, Doye JPK, Prešern D, Kawamoto A, Ruan J, Wainwright MJ, Lee LK. Design and synthesis of pleated DNA origami nanotubes with adjustable diameters. Nucleic Acids Res 2020; 47:11963-11975. [PMID: 31728524 PMCID: PMC7145641 DOI: 10.1093/nar/gkz1056] [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: 01/14/2019] [Revised: 10/22/2019] [Accepted: 10/25/2019] [Indexed: 12/31/2022] Open
Abstract
DNA origami allows for the synthesis of nanoscale structures and machines with nanometre precision and high yields. Tubular DNA origami nanostructures are particularly useful because their geometry facilitates a variety of applications including nanoparticle encapsulation, the construction of artificial membrane pores and as structural scaffolds that can uniquely spatially arrange nanoparticles in circular, linear and helical arrays. Here we report a system of parametrization for the design of radially symmetric DNA origami nanotubes with adjustable diameter, length, crossover density, pleat angle and chirality. The system is implemented into a computational algorithm that provides a practical means to navigate the complex geometry of DNA origami nanotube design. We apply this in the design, synthesis and characterization of novel DNA origami nanotubes. These include structures with pleated walls where the same number of duplexes can form nanotubes with different diameters, and to vary the diameter within the same structure. We also construct nanotubes that can be reconfigured into different chiral shapes. Finally, we explore the effect of strain on the local and global geometry of DNA origami nanotubes and demonstrate how pleated walls can provide a strategy to rigidify nanotubes and to construct closely packed parallel duplexes.
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Affiliation(s)
- Jonathan F Berengut
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, UNSW Sydney, Kensington, NSW 2052, Australia.,Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | | | - Jonathan P K Doye
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Domen Prešern
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Akihiro Kawamoto
- Institute for Protein Research, Osaka University, Osaka, Kansai, 565-0871, Japan
| | - Juanfang Ruan
- Electron Microscopy Unit, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Madeleine J Wainwright
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Lawrence K Lee
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, UNSW Sydney, Kensington, NSW 2052, Australia.,Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
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43
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Abstract
Bispecific therapeutics target two distinct antigens simultaneously and provide novel functionalities that are not attainable with single monospecific molecules or combinations of them. The unique potential of bispecific therapeutics is driving extensive efforts to discover synergistic dual targets, design molecular formats to integrate bispecific elements, and accelerate successful clinical translation. In particular, the past decade has witnessed a boom in the design and development of bispecific antibody formats with more than 100 collections to date. Despite the remarkable progress that has been made to expand the number of formats, qualitative fine-tuning of bispecific formats is needed to achieve optimal dual-target engagement based on understanding of the spatiotemporal interdependence of the two physically linked binding specificities and the complex target biology associated with bispecific approaches. This review provides insights into the design parameters - including affinity, valency, and geometry - that need to be considered at an early stage of development in order to take the best advantage of bispecific therapeutics.
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Affiliation(s)
- Sung In Lim
- Department of Chemical Engineering, Pukyong National University, Yongso-ro 45, Nam-gu, Busan, South Korea.
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44
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Reed SA, Brzovic DA, Takasaki SS, Boyko KV, Antos JM. Efficient Sortase-Mediated Ligation Using a Common C-Terminal Fusion Tag. Bioconjug Chem 2020; 31:1463-1473. [PMID: 32324377 PMCID: PMC7357393 DOI: 10.1021/acs.bioconjchem.0c00156] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sortase-mediated ligation is a powerful method for generating site-specifically modified proteins. However, this process is limited by the inherent reversibility of the ligation reaction. To address this, here we report the continued development and optimization of an experimentally facile strategy for blocking reaction reversibility. This approach, which we have termed metal-assisted sortase-mediated ligation (MA-SML), relies on the use of a solution additive (Ni2+) and a C-terminal tag (LPXTGGHH5) that is widely used for converting protein targets into sortase substrates. In a series of model systems utilizing a 1:1 molar ratio of sortase substrate and glycine amine nucleophile, we find that MA-SML consistently improves the extent of ligation. This enables the modification of proteins with fluorophores, PEG, and a bioorthogonal cyclooctyne moiety without the need to use precious reagents in excess. Overall, these results demonstrate the potential of MA-SML as a general strategy for improving reaction efficiency in a broad range of sortase-based protein engineering applications.
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Affiliation(s)
- Sierra A. Reed
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, United States
| | - David A. Brzovic
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, United States
| | - Savanna S. Takasaki
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, United States
| | - Kristina V. Boyko
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, United States
| | - John M. Antos
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, United States
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45
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Mesoscale computational protocols for the design of highly cooperative bivalent macromolecules. Sci Rep 2020; 10:7992. [PMID: 32409687 PMCID: PMC7224399 DOI: 10.1038/s41598-020-64646-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 04/07/2020] [Indexed: 11/09/2022] Open
Abstract
The last decade has witnessed a swiftly increasing interest in the design and production of novel multivalent molecules as powerful alternatives for conventional antibodies in the fight against cancer and infectious diseases. However, while it is widely accepted that large-scale flexibility (10–100 nm) and free/constrained dynamics (100 ns -μs) control the activity of such novel molecules, computational strategies at the mesoscale still lag behind experiments in optimizing the design of crucial features, such as the binding cooperativity (a.k.a. avidity). In this study, we introduced different coarse-grained models of a polymer-linked, two-nanobody composite molecule, with the aim of laying down the physical bases of a thorough computational drug design protocol at the mesoscale. We show that the calculation of suitable potentials of mean force allows one to apprehend the nature, range and strength of the thermodynamic forces that govern the motion of free and wall-tethered molecules. Furthermore, we develop a simple computational strategy to quantify the encounter/dissociation dynamics between the free end of a wall-tethered molecule and the surface, at the roots of binding cooperativity. This procedure allows one to pinpoint the role of internal flexibility and weak non-specific interactions on the kinetic constants of the nanobody-wall encounter and dissociation. Finally, we quantify the role and weight of rare events, which are expected to play a major role in real-life situations, such as in the immune synapse, where the binding kinetics is likely dominated by fluctuations.
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46
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Chu TH, Crowley AR, Backes I, Chang C, Tay M, Broge T, Tuyishime M, Ferrari G, Seaman MS, Richardson SI, Tomaras GD, Alter G, Leib D, Ackerman ME. Hinge length contributes to the phagocytic activity of HIV-specific IgG1 and IgG3 antibodies. PLoS Pathog 2020; 16:e1008083. [PMID: 32092122 PMCID: PMC7058349 DOI: 10.1371/journal.ppat.1008083] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 03/05/2020] [Accepted: 09/16/2019] [Indexed: 12/13/2022] Open
Abstract
Antibody functions such as neutralization require recognition of antigen by the Fab region, while effector functions are additionally mediated by interactions of the Fc region with soluble factors and cellular receptors. The efficacy of individual antibodies varies based on Fab domain characteristics, such as affinity for antigen and epitope-specificity, and on Fc domain characteristics that include isotype, subclass, and glycosylation profile. Here, a series of HIV-specific antibody subclass and hinge variants were constructed and tested to define those properties associated with differential effector function. In the context of the broadly neutralizing CD4 binding site-specific antibody VRC01 and the variable loop (V3) binding antibody 447-52D, hinge truncation and extension had a considerable impact on the magnitude of phagocytic activity of both IgG1 and IgG3 subclasses. The improvement in phagocytic potency of antibodies with extended hinges could not be attributed to changes in either intrinsic antigen or antibody receptor affinity. This effect was specific to phagocytosis and was generalizable to different phagocytes, at different effector cell to target ratios, for target particles of different size and composition, and occurred across a range of antibody concentrations. Antibody dependent cellular cytotoxicity and neutralization were generally independent of hinge length, and complement deposition displayed variable local optima. In vivo stability testing showed that IgG molecules with altered hinges can exhibit similar biodistribution and pharmacokinetic profiles as IgG1. Overall, these results suggest that when high phagocytic activity is desirable, therapeutic antibodies may benefit from being formatted as human IgG3 or engineered IgG1 forms with elongated hinges.
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Affiliation(s)
- Thach H. Chu
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Andrew R. Crowley
- The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
| | - Iara Backes
- The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
| | - Cheryl Chang
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Matthew Tay
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Thomas Broge
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
| | - Marina Tuyishime
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Michael S. Seaman
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Simone I. Richardson
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, Gauteng, South Africa
| | - Georgia D. Tomaras
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
| | - David Leib
- The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
| | - Margaret E. Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, United States of America
- The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
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47
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Richardson SI, Lambson BE, Crowley AR, Bashirova A, Scheepers C, Garrett N, Abdool Karim S, Mkhize NN, Carrington M, Ackerman ME, Moore PL, Morris L. IgG3 enhances neutralization potency and Fc effector function of an HIV V2-specific broadly neutralizing antibody. PLoS Pathog 2019; 15:e1008064. [PMID: 31841557 PMCID: PMC6936867 DOI: 10.1371/journal.ppat.1008064] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 12/30/2019] [Accepted: 09/02/2019] [Indexed: 11/19/2022] Open
Abstract
Broadly neutralizing antibodies (bNAbs) protect against HIV infection in non-human primates and their efficacy may be enhanced through interaction with Fc receptors on immune cells. Antibody isotype is a modulator of this binding with the IgG3 subclass mediating potent Fc effector function and is associated with HIV vaccine efficacy and HIV control. BNAb functions are typically assessed independently of the constant region with which they are naturally expressed. To examine the role of natural isotype in the context of a bNAb lineage we studied CAP256, an HIV-infected individual that mounted a potent V2-specific bNAb response. CAP256 expressed persistently high levels of plasma IgG3 which we found mediated both broad neutralizing activity and potent Fc function. Sequencing of germline DNA and the constant regions of V2-directed bNAbs from this donor revealed the expression of a novel IGHG3 allele as well as IGHG3*17, an allele that produces IgG3 antibodies with increased plasma half-life. Both allelic variants were used to generate CAP256-VRC26.25 and CAP256-VRC26.29 IgG3 bNAbs and these were compared to IgG1 versions. IgG3 variants were shown to have significantly higher phagocytosis and trogocytosis compared to IgG1 versions, which corresponded to increased affinity for FcγRIIa. Neutralization potency was also significantly higher for IgG3 bNAbs, particularly against viruses lacking the N160 glycan. By exchanging hinge regions between subclass variants, we showed that hinge length modulated both neutralization potency and Fc function. This study showed that co-operation between the variable and natural IgG3 constant regions enhanced the polyfunctionality of antibodies, indicating the value of leveraging genetic variation which could be exploited for passive immunity.
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Affiliation(s)
- Simone I. Richardson
- Centre for HIV and STI’s, National Institute for Communicable Diseases, Johannesburg, Gauteng, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Gauteng, South Africa
| | - Bronwen E. Lambson
- Centre for HIV and STI’s, National Institute for Communicable Diseases, Johannesburg, Gauteng, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Gauteng, South Africa
| | - Andrew R. Crowley
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Arman Bashirova
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard University, Boston, Massachusetts, United States of America
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Cathrine Scheepers
- Centre for HIV and STI’s, National Institute for Communicable Diseases, Johannesburg, Gauteng, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Gauteng, South Africa
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Congella, KwaZulu-Natal, South Africa
- Department of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Salim Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Congella, KwaZulu-Natal, South Africa
- Department of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
- Department of Epidemiology, Columbia University, New York, NY, United States of America
| | - Nonhlanhla N. Mkhize
- Centre for HIV and STI’s, National Institute for Communicable Diseases, Johannesburg, Gauteng, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Gauteng, South Africa
| | - Mary Carrington
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard University, Boston, Massachusetts, United States of America
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Margaret E. Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Penny L. Moore
- Centre for HIV and STI’s, National Institute for Communicable Diseases, Johannesburg, Gauteng, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Gauteng, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Congella, KwaZulu-Natal, South Africa
| | - Lynn Morris
- Centre for HIV and STI’s, National Institute for Communicable Diseases, Johannesburg, Gauteng, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Gauteng, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Congella, KwaZulu-Natal, South Africa
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48
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Choi H, Park H, Son K, Kim HM, Jung Y. Fabrication of rigidity and space variable protein oligomers with two peptide linkers. Chem Sci 2019; 10:10428-10435. [PMID: 32110335 PMCID: PMC6988741 DOI: 10.1039/c9sc04158c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 09/11/2019] [Indexed: 12/24/2022] Open
Abstract
Supramolecular protein assemblies have garnered considerable interest due to their potential in diverse fields with unrivaled attainable functionalities and structural accuracy. Despite significant advances in protein assembly strategies, inserting long linkers with varied lengths and rigidity between assembling protein building blocks remains extremely difficult. Here we report a series of green fluorescent protein (GFP) oligomers, where protein building blocks were linked via two independent peptide strands. Assembling protein units for this two-peptide assembly were designed by flopped fusion of three self-assembling GFP fragments with two peptide linkers. Diverse flexible and rigid peptide linkers were successfully inserted into high-valent GFP oligomers. In addition, oligomers with one flexible linker and one rigid linker could also be fabricated, allowing more versatile linker rigidity control. Linker length could be varied from 10 amino acids (aa) even up to 76 aa, which is the longest among reported protein assembling peptide linkers. Discrete GFP oligomers containing diverse linkers with valencies between monomers to decamers were monodispersely purified by gel elution. Furthermore, various functional proteins could be multivalently fused to the present GFP oligomers. Binding assays, size exclusion chromatography, dynamic light scattering, circular dichroism, differential scanning calorimetry, and transmission electron microscopy suggested circular geometries of the GFP oligomers and showed distinct characteristics of GFP oligomers with length/rigidity varied linkers. Lastly, a surface binding study indicated that more spaced oligomeric binding modules offered more effective multivalent interactions than less spaced modules.
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Affiliation(s)
- Hyeokjune Choi
- Department of Chemistry , KAIST , 291 Daehak-ro, Yuseong-gu , Daejeon 34143 , Republic of Korea . ; ; Tel: +82-42-350-2817
| | - Hyoin Park
- Department of Chemistry , KAIST , 291 Daehak-ro, Yuseong-gu , Daejeon 34143 , Republic of Korea . ; ; Tel: +82-42-350-2817
| | - Kabi Son
- Graduate School of Medical Science & Engineering , KAIST , Daejeon 34141 , Republic of Korea
| | - Ho Min Kim
- Graduate School of Medical Science & Engineering , KAIST , Daejeon 34141 , Republic of Korea.,Center for Biomolecular & Cellular Structure , Institute for Basic Science (IBS) , Daejeon 34126 , Republic of Korea
| | - Yongwon Jung
- Department of Chemistry , KAIST , 291 Daehak-ro, Yuseong-gu , Daejeon 34143 , Republic of Korea . ; ; Tel: +82-42-350-2817
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49
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Critical design criteria for engineering a nanoparticulate HIV-1 vaccine. J Control Release 2019; 317:322-335. [PMID: 31786187 DOI: 10.1016/j.jconrel.2019.11.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 12/11/2022]
Abstract
Inducing a long-lasting as well as broad and potent immune response by generating broadly neutralizing antibodies is a major goal and at the same time the main challenge of preventive HIV-1 vaccine design. Immunization with soluble, stabilized and native-like envelope (Env) glycoprotein so far only led to low neutralization breadth and displayed low immunogenicity. A promising approach to generate a potent immune response is the presentation of Env on the surface of nanoparticles. In this review, we will focus on two key processes essential for the induction of immune response that can be addressed by specific features of nanoparticulate carriers: first, the trafficking to and within distinct compartments of the lymph node, and second, the use of multivalent Env display allowing for high avidity interactions. To optimize these pivotal steps critical design criteria should be considered for the presentation of Env on nanoparticles. These include an optimal particle size below 100 nm, distances between two adjacent Env antigens of approximately 10-15 nm, an appropriate orientation of Env, and finally, the stability of both the Env attachment and the nanoparticle platform. Hence, an interdisciplinary approach that combines a suitable delivery system and a straightforward presentation of the Env antigen may have the potential to drive the immune response towards increased breadth and potency.
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50
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Einav T, Yazdi S, Coey A, Bjorkman PJ, Phillips R. Harnessing Avidity: Quantifying the Entropic and Energetic Effects of Linker Length and Rigidity for Multivalent Binding of Antibodies to HIV-1. Cell Syst 2019; 9:466-474.e7. [PMID: 31668801 PMCID: PMC6892280 DOI: 10.1016/j.cels.2019.09.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 12/13/2022]
Abstract
IgG antibodies increase their apparent affinities by using both of their Fabs to simultaneously attach to antigens. HIV-1 foils this strategy by having few, and highly separated, Envelope (Env) spike targets for antibodies, forcing most IgGs to bind monovalently. Here, we develop a statistical mechanics model of synthetic diFabs joined by DNA linkers of different lengths and flexibilities. This framework enables us to translate the energetic and entropic effects of the linker into the neutralization potency of a diFab. We demonstrate that the strongest neutralization potencies are predicted to require a rigid linker that optimally spans the distance between two Fab binding sites on an Env trimer and that avidity can be further boosted by incorporating more Fabs into these constructs. These results inform the design of multivalent anti-HIV-1 therapeutics that utilize avidity effects to remain potent against HIV-1 in the face of the rapid mutation of Env spikes. Synthetic antibodies that bivalently bind to HIV-1 can markedly enhance avidity Linkers that enable bivalent binding are fully characterized by the linker entropy Properly sized rigid linkers outperform long, flexible linkers Avidity can be further enhanced by increasing antibody valency
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Affiliation(s)
- Tal Einav
- Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Shahrzad Yazdi
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Aaron Coey
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Rob Phillips
- Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA.
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