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Kumar S, Bajpai P, Joyce C, Kabra SK, Lodha R, Burton DR, Briney B, Luthra K. B cell repertoire sequencing of HIV-1 pediatric elite-neutralizers identifies multiple broadly neutralizing antibody clonotypes. Front Immunol 2024; 15:1272493. [PMID: 38433846 PMCID: PMC10905035 DOI: 10.3389/fimmu.2024.1272493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 02/02/2024] [Indexed: 03/05/2024] Open
Abstract
Introduction A limited subset of HIV-1 infected adult individuals typically after at least 2-3 years of chronic infection, develop broadly neutralizing antibodies (bnAbs), suggesting that highly conserved neutralizing epitopes on the HIV-1 envelope glycoprotein are difficult for B cell receptors to effectively target, during natural infection. Recent studies have shown the evolution of bnAbs in HIV-1 infected infants. Methods We used bulk BCR sequencing (BCR-seq) to profile the B cell receptors from longitudinal samples (3 time points) collected from a rare pair of antiretroviralnaïve, HIV-1 infected pediatric monozygotic twins (AIIMS_329 and AIIMS_330) who displayed elite plasma neutralizing activity against HIV-1. Results BCR-seq of both twins revealed convergent antibody characteristics including V-gene use, CDRH3 lengths and somatic hypermutation (SHM). Further, antibody clonotypes with genetic features similar to highly potent bnAbs isolated from adults showed ongoing development in donor AIIMS_330 but not in AIIMS_329, corroborating our earlier findings based on plasma bnAbs responses. An increase in SHM was observed in sequences of the IgA isotype from AIIMS_330. Discussion This study suggests that children living with chronic HIV-1 can develop clonotypes of HIV-1 bnAbs against multiple envelope epitopes similar to those isolated from adults, highlighting that such B cells could be steered to elicit bnAbs responses through vaccines aimed to induce bnAbs against HIV-1 in a broad range of people including children.
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Affiliation(s)
- Sanjeev Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA, United States
- International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Prashant Bajpai
- International Centre for Genetic Engineering and Biotechnology (ICGEB)-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - Collin Joyce
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA, United States
- International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Sushil Kumar Kabra
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA, United States
- International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA, United States
- Multi-omics Vaccine Evaluation Consortium, The Scripps Research Institute, La Jolla, CA, United States
| | - Kalpana Luthra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
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2
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Yamamoto S, Yamayoshi S, Ito M, Sakai-Tagawa Y, Nakachi I, Baba R, Kamimoto S, Ogura T, Hagiwara S, Kato H, Nakajima H, Uwamino Y, Yagi K, Sugaya N, Nagai H, Saito M, Adachi E, Koga M, Tsutsumi T, Duong C, Okuda M, Murakami J, Furusawa Y, Ujie M, Iwatsuki-Horimoto K, Yotsuyanagi H, Kawaoka Y. Differences among epitopes recognized by neutralizing antibodies induced by SARS-CoV-2 infection or COVID-19 vaccination. iScience 2023; 26:107208. [PMID: 37448563 PMCID: PMC10290734 DOI: 10.1016/j.isci.2023.107208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/21/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
SARS-CoV-2 has gradually acquired amino acid substitutions in its S protein that reduce the potency of neutralizing antibodies, leading to decreased vaccine efficacy. Here, we attempted to obtain mutant viruses by passaging SARS-CoV-2 in the presence of plasma samples from convalescent patients or vaccinees to determine which amino acid substitutions affect the antigenicity of SARS-CoV-2. Several amino acid substitutions in the S2 region, as well as the N-terminal domain (NTD) and receptor-binding domain (RBD), affected the neutralization potency of plasma samples collected from vaccinees, indicating that amino acid substitutions in the S2 region as well as those in the NTD and RBD affect neutralization by vaccine-induced antibodies. Furthermore, the neutralizing potency of vaccinee plasma samples against mutant viruses we obtained or circulating viruses differed among individuals. These findings suggest that genetic backgrounds of vaccinees influence the recognition of neutralizing epitopes.
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Affiliation(s)
- Shinya Yamamoto
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Seiya Yamayoshi
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
| | - Mutsumi Ito
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Yuko Sakai-Tagawa
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Ichiro Nakachi
- Pulmonary Division, Department of Internal Medicine, Saiseikai Utsunomiya Hospital, Tochigi 321-0974, Japan
| | - Rie Baba
- Pulmonary Division, Department of Internal Medicine, Saiseikai Utsunomiya Hospital, Tochigi 321-0974, Japan
| | - Shigenobu Kamimoto
- Pulmonary Division, Department of Internal Medicine, Saiseikai Utsunomiya Hospital, Tochigi 321-0974, Japan
| | - Takayuki Ogura
- Department of Emergency and Intensive Care, Saiseikai Utsunomiya Hospital, Tochigi 321-0974, Japan
| | - Shigehiro Hagiwara
- Department of Clinical Laboratory, Saiseikai Utsunomiya Hospital, Tochigi 321-0974, Japan
| | - Hideaki Kato
- Department of Hematology and Clinical Immunology, Yokohama City University School of Medicine, Kanagawa 236-0004, Japan
| | - Hideaki Nakajima
- Department of Hematology and Clinical Immunology, Yokohama City University School of Medicine, Kanagawa 236-0004, Japan
| | - Yoshifumi Uwamino
- Department of Laboratory Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kazuma Yagi
- Department of Pulmonary Medicine, Keiyu Hospital, Kanagawa 220-8521, Japan
| | - Norio Sugaya
- Department of Pediatrics, Keiyu Hospital, Kanagawa 220-8521, Japan
| | - Hiroyuki Nagai
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Makoto Saito
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Eisuke Adachi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Takeya Tsutsumi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Calvin Duong
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Moe Okuda
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Jurika Murakami
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Yuri Furusawa
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Michiko Ujie
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | | | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA
- The University of Tokyo, Pandemic Preparedness, Infection and Advanced Research Center, Tokyo 108-8639, Japan
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3
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Bruun TUJ, Tang S, Erwin G, Deis L, Fernandez D, Kim PS. Structure-guided stabilization improves the ability of the HIV-1 gp41 hydrophobic pocket to elicit neutralizing antibodies. J Biol Chem 2023; 299:103062. [PMID: 36841484 PMCID: PMC10064241 DOI: 10.1016/j.jbc.2023.103062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023] Open
Abstract
The hydrophobic pocket found in the N-heptad repeat (NHR) region of HIV-1 gp41 is a highly conserved epitope that is the target of various HIV-1-neutralizing monoclonal antibodies. Although the high conservation of the pocket makes it an attractive vaccine candidate, it has been challenging to elicit potent anti-NHR antibodies via immunization. Here, we solved a high-resolution structure of the NHR mimetic IQN17, and, consistent with previous ligand-bound gp41 pocket structures, we observed remarkable conformational plasticity of the pocket. The high malleability of this pocket led us to test whether we could improve the immunogenicity of the gp41 pocket by stabilizing its conformation. We show that the addition of five amino acids at the C terminus of IQN17, to generate IQN22, introduces a stabilizing salt bridge at the base of the peptide that rigidifies the pocket. Mice immunized with IQN22 elicited higher avidity antibodies against the gp41 pocket and a more potent, albeit still weak, neutralizing response against HIV-1 compared with IQN17. Stabilized epitope-focused immunogens could serve as the basis for future HIV-1 fusion-inhibiting vaccines.
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Affiliation(s)
- Theodora U J Bruun
- Sarafan ChEM-H, Stanford University, Stanford, California, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Shaogeng Tang
- Sarafan ChEM-H, Stanford University, Stanford, California, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Graham Erwin
- Sarafan ChEM-H, Stanford University, Stanford, California, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Lindsay Deis
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Daniel Fernandez
- Sarafan ChEM-H, Stanford University, Stanford, California, USA; Chem-H Macromolecular Structure Knowledge Center (MSKC), Stanford University, Stanford, California, USA
| | - Peter S Kim
- Sarafan ChEM-H, Stanford University, Stanford, California, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA; Chan Zuckerberg Biohub, San Francisco, California, USA.
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4
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Bell BN, Bruun TUJ, Friedland N, Kim PS. HIV-1 prehairpin intermediate inhibitors show efficacy independent of neutralization tier. Proc Natl Acad Sci U S A 2023; 120:e2215792120. [PMID: 36795752 PMCID: PMC9974412 DOI: 10.1073/pnas.2215792120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/23/2023] [Indexed: 02/17/2023] Open
Abstract
HIV-1 strains are categorized into one of three neutralization tiers based on the relative ease by which they are neutralized by plasma from HIV-1-infected donors not on antiretroviral therapy; tier-1 strains are particularly sensitive to neutralization while tier-2 and tier-3 strains are increasingly difficult to neutralize. Most broadly neutralizing antibodies (bnAbs) previously described target the native prefusion conformation of HIV-1 Envelope (Env), but the relevance of the tiered categories for inhibitors targeting another Env conformation, the prehairpin intermediate, is not well understood. Here, we show that two inhibitors targeting distinct highly conserved regions of the prehairpin intermediate have strikingly consistent neutralization potencies (within ~100-fold for a given inhibitor) against strains in all three neutralization tiers of HIV-1; in contrast, best-in-class bnAbs targeting diverse Env epitopes vary by more than 10,000-fold in potency against these strains. Our results indicate that antisera-based HIV-1 neutralization tiers are not relevant for inhibitors targeting the prehairpin intermediate and highlight the potential for therapies and vaccine efforts targeting this conformation.
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Affiliation(s)
- Benjamin N. Bell
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Theodora U. J. Bruun
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
| | - Natalia Friedland
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
| | - Peter S. Kim
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Chan Zuckerberg Biohub, San Francisco, CA94158
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5
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Novel chimeric proteins mimicking SARS-CoV-2 spike epitopes with broad inhibitory activity. Int J Biol Macromol 2022; 222:2467-2478. [PMID: 36220405 PMCID: PMC9546781 DOI: 10.1016/j.ijbiomac.2022.10.031] [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: 07/28/2022] [Revised: 09/29/2022] [Accepted: 10/05/2022] [Indexed: 11/05/2022]
Abstract
SARS-CoV-2 spike (S) protein mediates virus attachment to the cells and fusion between viral and cell membranes. Membrane fusion is driven by mutual interaction between the highly conserved heptad-repeat regions 1 and 2 (HR1 and HR2) of the S2 subunit of the spike. For this reason, these S2 regions are interesting therapeutic targets for COVID-19. Although HR1 and HR2 have been described as transiently exposed during the fusion process, no significant antibody responses against these S2 regions have been reported. Here we designed chimeric proteins that imitate highly stable HR1 helical trimers and strongly bind to HR2. The proteins have broad inhibitory activity against WT B.1 and BA.1 viruses. Sera from COVID-19 convalescent donors showed significant levels of reactive antibodies (IgG and IgA) against the HR1 mimetic proteins, whereas these antibody responses were absent in sera from uninfected donors. Moreover, both inhibitory activity and antigenicity of the proteins correlate positively with their structural stability but not with the number of amino acid changes in their HR1 sequences, indicating a conformational and conserved nature of the involved epitopes. Our results reveal previously undetected spike epitopes that may guide the design of new robust COVID-19 vaccines and therapies.
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6
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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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7
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Rubio AA, Filsinger Interrante MV, Bell BN, Brown CL, Bruun TUJ, LaBranche CC, Montefiori DC, Kim PS. A Derivative of the D5 Monoclonal Antibody That Targets the gp41 N-Heptad Repeat of HIV-1 with Broad Tier-2-Neutralizing Activity. J Virol 2021; 95:e0235020. [PMID: 33980592 PMCID: PMC8274607 DOI: 10.1128/jvi.02350-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/30/2021] [Indexed: 01/11/2023] Open
Abstract
HIV-1 infection is initiated by the viral glycoprotein Env, which, after interaction with cellular coreceptors, adopts a transient conformation known as the prehairpin intermediate (PHI). The N-heptad repeat (NHR) is a highly conserved region of gp41 exposed in the PHI; it is the target of the FDA-approved drug enfuvirtide and of neutralizing monoclonal antibodies (mAbs). However, to date, these mAbs have only been weakly effective against tier-1 HIV-1 strains, which are most sensitive to neutralizing antibodies. Here, we engineered and tested 11 IgG variants of D5, an anti-NHR mAb, by recombining previously described mutations in four of D5's six antibody complementarity-determining regions. One variant, D5_AR, demonstrated 6-fold enhancement in the 50% inhibitory dose (ID50) against lentivirus pseudotyped with HXB2 Env. D5_AR exhibited weak cross-clade neutralizing activity against a diverse set of tier-2 HIV-1 viruses, which are less sensitive to neutralizing antibodies than tier-1 viruses and are the target of current antibody-based vaccine efforts. In addition, the neutralization potency of D5_AR IgG was greatly enhanced in target cells expressing FcγRI, with ID50 values of <0.1 μg/ml; this immunoglobulin receptor is expressed on macrophages and dendritic cells, which are implicated in the early stages of HIV-1 infection of mucosal surfaces. D5 and D5_AR have equivalent neutralization potency in IgG, Fab, and single-chain variable-fragment (scFv) formats, indicating that neutralization is not impacted by steric hindrance. Taken together, these results provide support for vaccine strategies that target the PHI by eliciting antibodies against the gp41 NHR and support investigation of anti-NHR mAbs in nonhuman primate passive immunization studies. IMPORTANCE Despite advances in antiretroviral therapy, HIV remains a global epidemic and has claimed more than 32 million lives. Accordingly, developing an effective HIV vaccine remains an urgent public health need. The gp41 N-heptad repeat (NHR) of the HIV-1 prehairpin intermediate (PHI) is highly conserved (>90%) and is inhibited by the FDA-approved drug enfuvirtide, making it an attractive vaccine target. However, to date, anti-NHR antibodies have not been potent. Here, we engineered D5_AR, a more potent variant of the anti-NHR antibody D5, and established its ability to inhibit HIV-1 strains that are more difficult to neutralize and are more representative of circulating strains (tier-2 strains). The neutralizing activity of D5_AR was greatly potentiated in cells expressing FcγRI; FcγRI is expressed on cells that are implicated at the earliest stages of sexual HIV-1 transmission. Taken together, these results bolster efforts to target the gp41 NHR and the PHI for vaccine development.
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Affiliation(s)
- Adonis A. Rubio
- Stanford ChEM-H, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University School of Humanities & Sciences, Stanford, California, USA
| | - Maria V. Filsinger Interrante
- Stanford ChEM-H, Stanford University, Stanford, California, USA
- Stanford Biophysics Program, Stanford University School of Medicine, Stanford, California, USA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, California, USA
| | - Benjamin N. Bell
- Stanford ChEM-H, Stanford University, Stanford, California, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA
| | - Clayton L. Brown
- Stanford ChEM-H, Stanford University, Stanford, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Theodora U. J. Bruun
- Stanford ChEM-H, Stanford University, Stanford, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Celia C. LaBranche
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - David C. Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Peter S. Kim
- Stanford ChEM-H, Stanford University, Stanford, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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8
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Roth KDR, Wenzel EV, Ruschig M, Steinke S, Langreder N, Heine PA, Schneider KT, Ballmann R, Fühner V, Kuhn P, Schirrmann T, Frenzel A, Dübel S, Schubert M, Moreira GMSG, Bertoglio F, Russo G, Hust M. Developing Recombinant Antibodies by Phage Display Against Infectious Diseases and Toxins for Diagnostics and Therapy. Front Cell Infect Microbiol 2021; 11:697876. [PMID: 34307196 PMCID: PMC8294040 DOI: 10.3389/fcimb.2021.697876] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/21/2021] [Indexed: 12/30/2022] Open
Abstract
Antibodies are essential molecules for diagnosis and treatment of diseases caused by pathogens and their toxins. Antibodies were integrated in our medical repertoire against infectious diseases more than hundred years ago by using animal sera to treat tetanus and diphtheria. In these days, most developed therapeutic antibodies target cancer or autoimmune diseases. The COVID-19 pandemic was a reminder about the importance of antibodies for therapy against infectious diseases. While monoclonal antibodies could be generated by hybridoma technology since the 70ies of the former century, nowadays antibody phage display, among other display technologies, is robustly established to discover new human monoclonal antibodies. Phage display is an in vitro technology which confers the potential for generating antibodies from universal libraries against any conceivable molecule of sufficient size and omits the limitations of the immune systems. If convalescent patients or immunized/infected animals are available, it is possible to construct immune phage display libraries to select in vivo affinity-matured antibodies. A further advantage is the availability of the DNA sequence encoding the phage displayed antibody fragment, which is packaged in the phage particles. Therefore, the selected antibody fragments can be rapidly further engineered in any needed antibody format according to the requirements of the final application. In this review, we present an overview of phage display derived recombinant antibodies against bacterial, viral and eukaryotic pathogens, as well as microbial toxins, intended for diagnostic and therapeutic applications.
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Affiliation(s)
- Kristian Daniel Ralph Roth
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Esther Veronika Wenzel
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany.,Abcalis GmbH, Braunschweig, Germany
| | - Maximilian Ruschig
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Stephan Steinke
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Nora Langreder
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Philip Alexander Heine
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Kai-Thomas Schneider
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Rico Ballmann
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Viola Fühner
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | | | | | | | - Stefan Dübel
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany.,Abcalis GmbH, Braunschweig, Germany.,YUMAB GmbH, Braunschweig, Germany
| | - Maren Schubert
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Federico Bertoglio
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Giulio Russo
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany.,Abcalis GmbH, Braunschweig, Germany
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany.,YUMAB GmbH, Braunschweig, Germany
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9
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The high-affinity immunoglobulin receptor FcγRI potentiates HIV-1 neutralization via antibodies against the gp41 N-heptad repeat. Proc Natl Acad Sci U S A 2021; 118:2018027118. [PMID: 33431684 PMCID: PMC7826338 DOI: 10.1073/pnas.2018027118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Despite decades of research, an effective HIV-1 vaccine remains elusive. One potential vaccine target is the N-heptad repeat (NHR) region of gp41, which is the target of the FDA-approved drug enfuvirtide. However, monoclonal antibodies and antisera targeting this region have only been modestly neutralizing to date. Here, we show that the neutralization potency of the well-characterized anti-NHR antibody D5 is increased >5,000-fold by expression of FcγRI (CD64) on cells. Since FcγRI is expressed on macrophages and dendritic cells, which are implicated in the early establishment of HIV-1 infection following sexual transmission, these results may be important to HIV-1 vaccine development. The HIV-1 gp41 N-heptad repeat (NHR) region of the prehairpin intermediate, which is transiently exposed during HIV-1 viral membrane fusion, is a validated clinical target in humans and is inhibited by the Food and Drug Administration (FDA)-approved drug enfuvirtide. However, vaccine candidates targeting the NHR have yielded only modest neutralization activities in animals; this inhibition has been largely restricted to tier-1 viruses, which are most sensitive to neutralization by sera from HIV-1–infected individuals. Here, we show that the neutralization activity of the well-characterized NHR-targeting antibody D5 is potentiated >5,000-fold in TZM-bl cells expressing FcγRI compared with those without, resulting in neutralization of many tier-2 viruses (which are less susceptible to neutralization by sera from HIV-1–infected individuals and are the target of current antibody-based vaccine efforts). Further, antisera from guinea pigs immunized with the NHR-based vaccine candidate (ccIZN36)3 neutralized tier-2 viruses from multiple clades in an FcγRI-dependent manner. As FcγRI is expressed on macrophages and dendritic cells, which are present at mucosal surfaces and are implicated in the early establishment of HIV-1 infection following sexual transmission, these results may be important in the development of a prophylactic HIV-1 vaccine.
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10
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Caillat C, Guilligay D, Sulbaran G, Weissenhorn W. Neutralizing Antibodies Targeting HIV-1 gp41. Viruses 2020; 12:E1210. [PMID: 33114242 PMCID: PMC7690876 DOI: 10.3390/v12111210] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/20/2020] [Accepted: 10/20/2020] [Indexed: 12/21/2022] Open
Abstract
HIV-1 vaccine research has obtained an enormous boost since the discovery of many broadly neutralizing antibodies (bnAbs) targeting all accessible sites on the HIV-1 envelope glycoprotein (Env). This in turn facilitated high-resolution structures of the Env glycoprotein in complex with bnAbs. Here we focus on gp41, its highly conserved heptad repeat region 1 (HR1), the fusion peptide (FP) and the membrane-proximal external region (MPER). Notably, the broadest neutralizing antibodies target MPER. Both gp41 HR1 and MPER are only fully accessible once receptor-induced conformational changes have taken place, although some studies suggest access to MPER in the close to native Env conformation. We summarize the data on the structure and function of neutralizing antibodies targeting gp41 HR1, FP and MPER and we review their access to Env and their complex formation with gp41 HR1, MPER peptides and FP within native Env. We further discuss MPER bnAb binding to lipids and the role of somatic mutations in recognizing a bipartite epitope composed of the conserved MPER sequence and membrane components. The problematic of gp41 HR1 access and MPER bnAb auto- and polyreactivity is developed in the light of inducing such antibodies by vaccination.
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Affiliation(s)
- Christophe Caillat
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, Commissariat à L'énergie Atomique et Aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), 38000 Grenoble, France
| | - Delphine Guilligay
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, Commissariat à L'énergie Atomique et Aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), 38000 Grenoble, France
| | - Guidenn Sulbaran
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, Commissariat à L'énergie Atomique et Aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), 38000 Grenoble, France
| | - Winfried Weissenhorn
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, Commissariat à L'énergie Atomique et Aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), 38000 Grenoble, France
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11
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Jurado S, Cano-Muñoz M, Polo-Megías D, Conejero-Lara F, Morel B. Thermodynamic dissection of the interface between HIV-1 gp41 heptad repeats reveals cooperative interactions and allosteric effects. Arch Biochem Biophys 2020; 688:108401. [PMID: 32376316 DOI: 10.1016/j.abb.2020.108401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/03/2020] [Accepted: 04/27/2020] [Indexed: 11/27/2022]
Abstract
HIV-1 glycoprotein 41 (gp41) mediates fusion between virus and target cells by folding into a fusion active state, in which the C-terminal heptad repeat (CHR) regions associate externally to the N-terminal heptad repeat (NHR) trimer and form a very stable six-helix bundle coiled-coil structure. Therefore, interfering with the NHR-CHR interaction of gp41 is a promising therapeutic approach against HIV-1. However, a full understanding of the molecular and mechanistic details of this interaction is still incomplete. Here, we use single-chain, chimeric proteins (named covNHR) that reproduce accurately the CHR-NHR interactions to analyze the binding thermodynamics of several peptides with different length from the CHR region. The results indicate that cooperative binding involving two or more pockets of the NHR groove is necessary to obtain relevant affinities and that the binding energy is broadly distributed along the interface, underlining a crucial role of a middle pocket to achieve tight binding. In contrast, targeting only the deep hydrophobic pocket is insufficient to achieve significant affinity. Moreover, calorimetry experiments in combination with limited proteolysis performed using a mutant with occluded binding in the N-terminal pocket reveal the existence of an allosteric communication between the different regions. This study is the first detailed thermodynamic dissection of the NHR-CHR interaction in gp41 and contributes therefore to a better understanding of HIV fusion. These results are relevant for the development of potential fusion inhibitors.
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Affiliation(s)
- Samuel Jurado
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Mario Cano-Muñoz
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Daniel Polo-Megías
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Francisco Conejero-Lara
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| | - Bertrand Morel
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
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12
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Lin M, Da LT. Refolding Dynamics of gp41 from Pre-fusion to Pre-hairpin States during HIV-1 Entry. J Chem Inf Model 2019; 60:162-174. [DOI: 10.1021/acs.jcim.9b00746] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Mengna Lin
- Key Laboratory of System Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Lin-Tai Da
- Key Laboratory of System Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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13
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Pinto D, Fenwick C, Caillat C, Silacci C, Guseva S, Dehez F, Chipot C, Barbieri S, Minola A, Jarrossay D, Tomaras GD, Shen X, Riva A, Tarkowski M, Schwartz O, Bruel T, Dufloo J, Seaman MS, Montefiori DC, Lanzavecchia A, Corti D, Pantaleo G, Weissenhorn W. Structural Basis for Broad HIV-1 Neutralization by the MPER-Specific Human Broadly Neutralizing Antibody LN01. Cell Host Microbe 2019; 26:623-637.e8. [PMID: 31653484 PMCID: PMC6854463 DOI: 10.1016/j.chom.2019.09.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/29/2019] [Accepted: 09/27/2019] [Indexed: 11/24/2022]
Abstract
Potent and broadly neutralizing antibodies (bnAbs) are the hallmark of HIV-1 protection by vaccination. The membrane-proximal external region (MPER) of the HIV-1 gp41 fusion protein is targeted by the most broadly reactive HIV-1 neutralizing antibodies. Here, we examine the structural and molecular mechansims of neutralization by anti-MPER bnAb, LN01, which was isolated from lymph-node-derived germinal center B cells of an elite controller and exhibits broad neutralization breadth. LN01 engages both MPER and the transmembrane (TM) region, which together form a continuous helix in complex with LN01. The tilted TM orientation allows LN01 to interact simultaneously with the peptidic component of the MPER epitope and membrane via two specific lipid binding sites of the antibody paratope. Although LN01 carries a high load of somatic mutations, most key residues interacting with the MPER epitope and lipids are germline encoded, lending support for the LN01 epitope as a candidate for lineage-based vaccine development. bNAb LN01 neutralizes 92% of a 118-strain virus panel LN01 targets the HIV-1 gp41 MPER, the TM region, and lipids LN01-complexed MPER forms a continuous helix with TM Most LN01 paratope residues interacting with MPER-TM and lipids are germline encoded
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Affiliation(s)
- Dora Pinto
- Institute for Research in Biomedicine, Bellinzona 6500, Ticino, Switzerland
| | - Craig Fenwick
- Swiss Vaccine Research Institute, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Christophe Caillat
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38000 Grenoble, France
| | - Chiara Silacci
- Institute for Research in Biomedicine, Bellinzona 6500, Ticino, Switzerland
| | - Serafima Guseva
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38000 Grenoble, France
| | - François Dehez
- LPCT, UMR 7019 Université de Lorraine CNRS, 54500 Vandœuvre-lès-Nancy, France; Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, LPCT, UMR 7019 Universiteé de Lorraine CNRS, Vandœuvre-lès-Nancy 54500, France
| | - Christophe Chipot
- LPCT, UMR 7019 Université de Lorraine CNRS, 54500 Vandœuvre-lès-Nancy, France; Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, LPCT, UMR 7019 Universiteé de Lorraine CNRS, Vandœuvre-lès-Nancy 54500, France; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sonia Barbieri
- Institute for Research in Biomedicine, Bellinzona 6500, Ticino, Switzerland
| | - Andrea Minola
- Humabs Biomed SA, Vir Biotechnology, 6500 Bellinzona, Ticino, Switzerland
| | - David Jarrossay
- Institute for Research in Biomedicine, Bellinzona 6500, Ticino, Switzerland
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Paris Diderot University, Sorbonne Paris Cité, Paris 75013, France
| | | | - Agostino Riva
- Department of Biomedical and Clinical Sciences, Luigi Sacco University Hospital, Università di Milano, 20157 Milan, Italy; III Division of Infectious Diseases, ASST Fatebenefratelli-Sacco, 20157 Milan, Italy
| | - Maciej Tarkowski
- Department of Biomedical and Clinical Sciences, Luigi Sacco University Hospital, Università di Milano, 20157 Milan, Italy
| | - Olivier Schwartz
- Institut Pasteur, Virus & Immunity Unit, CNRS UMR 3569, Paris 75015, France; Vaccine Research Institute, 94000 Créteil, France
| | - Timothée Bruel
- Institut Pasteur, Virus & Immunity Unit, CNRS UMR 3569, Paris 75015, France; Vaccine Research Institute, 94000 Créteil, France
| | - Jérémy Dufloo
- Institut Pasteur, Virus & Immunity Unit, CNRS UMR 3569, Paris 75015, France; Vaccine Research Institute, 94000 Créteil, France; Paris Diderot University, Sorbonne Paris Cité, Paris 75013, France
| | - Michael S Seaman
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - David C Montefiori
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Davide Corti
- Humabs Biomed SA, Vir Biotechnology, 6500 Bellinzona, Ticino, Switzerland.
| | - Giuseppe Pantaleo
- Swiss Vaccine Research Institute, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland; Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland.
| | - Winfried Weissenhorn
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38000 Grenoble, France.
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14
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Bennett MR, Dong J, Bombardi RG, Soto C, Parrington HM, Nargi RS, Schoeder CT, Nagel MB, Schey KL, Meiler J, Skaar EP, Crowe JE. Human VH1-69 Gene-Encoded Human Monoclonal Antibodies against Staphylococcus aureus IsdB Use at Least Three Distinct Modes of Binding To Inhibit Bacterial Growth and Pathogenesis. mBio 2019; 10:e02473-19. [PMID: 31641091 PMCID: PMC6805997 DOI: 10.1128/mbio.02473-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 09/18/2019] [Indexed: 12/30/2022] Open
Abstract
Staphylococcus aureus is an important human pathogen that infects nearly every human tissue. Like most organisms, the acquisition of nutrient iron is necessary for its survival. One route by which it obtains this metal is through the iron-regulated surface determinant (Isd) system that scavenges iron from the hemoglobin of the host. We show that the heavy chain variable region IGHV1-69 gene commonly encodes human monoclonal antibodies (mAbs) targeting IsdB-NEAT2. Remarkably, these antibodies bind to multiple antigenic sites. One class of IGHV1-69-encoded mAbs blocks S. aureus heme acquisition by binding to the heme-binding site of NEAT2, while two additional classes reduce the bacterial burden in vivo by an alternative Fc receptor-mediated mechanism. We further identified clonal lineages of IGHV1-69-encoded mAbs using donor samples, showing that each lineage diversifies during infection by somatic hypermutation. These studies reveal that IGHV1-69-encoded antibodies contribute to a protective immune response, furthering our understanding of the correlates of protection against S. aureus infection.IMPORTANCE The human pathogen Staphylococcus aureus causes a wide range of infections, including skin abscesses and sepsis. There is currently no licensed vaccine to prevent S. aureus infection, and its treatment has become increasingly difficult due to antibiotic resistance. One potential way to inhibit S. aureus pathogenesis is to prevent iron acquisition. The iron-regulated surface determinant (Isd) system has evolved in S. aureus to acquire hemoglobin from the human host as a source of heme-iron. In this study, we investigated the molecular and structural basis for antibody-mediated correlates against a member of the Isd system, IsdB. The association of immunoglobulin heavy chain variable region IGHV1-69 gene-encoded human monoclonal antibodies with the response against S. aureus IsdB is described using structural and functional studies to define the importance of this antibody class. We also determine that somatic hypermutation in the development of these antibodies hinders rather than fine-tunes the immune response to IsdB.
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Affiliation(s)
- Monique R Bennett
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jinhui Dong
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Robin G Bombardi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Cinque Soto
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Helen M Parrington
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Rachel S Nargi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Clara T Schoeder
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Marcus B Nagel
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Kevin L Schey
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Jens Meiler
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - James E Crowe
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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15
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Monoclonal Antibody 2C6 Targets a Cross-Clade Conformational Epitope in gp41 with Highly Active Antibody-Dependent Cell Cytotoxicity. J Virol 2019; 93:JVI.00772-19. [PMID: 31217246 DOI: 10.1128/jvi.00772-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/13/2019] [Indexed: 12/11/2022] Open
Abstract
Previous studies in our laboratory characterized a panel of highly mutated HIV-specific conformational epitope-targeting antibodies (Abs) from a panel of HIV-infected long-term nonprogressors (LTNPs). Despite binding HIV envelope protein and having a high number of somatic amino acid mutations, these Abs had poor neutralizing activity. Because of the evidence of antigen-driven selection and the long CDR3 region (21 amino acids [aa]), we further characterized the epitope targeting of monoclonal Ab (MAb) 76-Q3-2C6 (2C6). We confirmed that 2C6 binds preferentially to trimeric envelope and recognizes the clades A, B, and C SOSIP trimers. 2C6 binds gp140 constructs of clades A, B, C, and D, suggesting a conserved binding site that we localized to the ectodomain of gp41. Ab competition with MAb 50-69 suggested this epitope localizes near aa 579 to 613 (referenced to HXB2 gp160). Peptide library scanning showed consistent binding in this region but to only a single peptide. Lack of overlapping peptide binding supported a nonlinear epitope structure. The significance of this site is supported by 2C6 having Ab-dependent cell cytotoxicity (ADCC) against envelope proteins from two clades. Using 2C6 and variants, alanine scanning mutagenesis identified three amino acids (aa 592, 595, and 596) in the overlapping region of the previously identified peptide. Additional amino acids at sites 524 and 579 were also identified, helping explain its conformational requirement. The fact that different amino acids were included in the epitope depending on the targeted protein supports the conclusion that 2C6 targets a native conformational epitope. When we mapped these amino acids on the trimerized structure, they spanned across oligomers, supporting the notion that the epitope targeted by 2C6 lies in a recessed pocket between two gp41 oligomers. A complete understanding of the epitope specificity of ADCC-mediating Abs is essential for developing effective immunization strategies that optimize protection by these Abs.IMPORTANCE This paper further defines the function and area of the HIV trimeric envelope protein targeted by the monoclonal antibody 2C6. 2C6 binding is influenced by amino acid mutations across two separate gp41 sections of the envelope trimer. This epitope is recognized on multiple clades (variant groups of circulating viruses) of gp41, gp140 trimers, and SOSIP trimers. For the clades tested, 2C6 has robust ADCC. As the target of 2C6 is available in the major clades of HIV and has robust ADCC activity, further definition and appreciation of targeting of antibodies similar to 2C6 during vaccine development should be considered.
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16
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Pu J, Wang Q, Xu W, Lu L, Jiang S. Development of Protein- and Peptide-Based HIV Entry Inhibitors Targeting gp120 or gp41. Viruses 2019; 11:v11080705. [PMID: 31374953 PMCID: PMC6722851 DOI: 10.3390/v11080705] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/26/2019] [Accepted: 07/26/2019] [Indexed: 01/08/2023] Open
Abstract
Application of highly active antiretroviral drugs (ARDs) effectively reduces morbidity and mortality in HIV-infected individuals. However, the emergence of multiple drug-resistant strains has led to the increased failure of ARDs, thus calling for the development of anti-HIV drugs with targets or mechanisms of action different from those of the current ARDs. The first peptide-based HIV entry inhibitor, enfuvirtide, was approved by the U.S. FDA in 2003 for treatment of HIV/AIDS patients who have failed to respond to the current ARDs, which has stimulated the development of several series of protein- and peptide-based HIV entry inhibitors in preclinical and clinical studies. In this review, we highlighted the properties and mechanisms of action for those promising protein- and peptide-based HIV entry inhibitors targeting the HIV-1 gp120 or gp41 and discussed their advantages and disadvantages, compared with the current ARDs.
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Affiliation(s)
- Jing Pu
- Shanghai Public Health Clinical Center and School of Basic Medical Sciences, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Fudan University, Shanghai 200032, China
| | - Qian Wang
- Shanghai Public Health Clinical Center and School of Basic Medical Sciences, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Fudan University, Shanghai 200032, China
| | - Wei Xu
- Shanghai Public Health Clinical Center and School of Basic Medical Sciences, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Fudan University, Shanghai 200032, China
| | - Lu Lu
- Shanghai Public Health Clinical Center and School of Basic Medical Sciences, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Fudan University, Shanghai 200032, China.
| | - Shibo Jiang
- Shanghai Public Health Clinical Center and School of Basic Medical Sciences, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Fudan University, Shanghai 200032, China.
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA.
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17
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Weiss RA, Verrips CT. Nanobodies that Neutralize HIV. Vaccines (Basel) 2019; 7:vaccines7030077. [PMID: 31370301 PMCID: PMC6789485 DOI: 10.3390/vaccines7030077] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 07/22/2019] [Accepted: 07/26/2019] [Indexed: 11/16/2022] Open
Abstract
Nanobodies or VHH (variable domains of heavy-chain only antibodies) are derived from camelid species such as llamas and camels. Nanobodies isolated and selected through phage display can neutralize a broad range of human immunodeficiency virus type 1 (HIV-1) strains. Nanobodies fit into canyons on the HIV envelope that may not be accessible to IgG (immunoglobulin G) containing both heavy and light chains, and they tend to have long CDR3 (complementarity-determining region 3) loops that further enhance recognition of otherwise cryptic epitopes. Nanobodies are readily expressed at high levels in bacteria and yeast, as well as by viral vectors, and they form relatively stable, heat-resistant molecules. Nanobodies can be linked to human Fc chains to gain immune effector functions. Bivalent and trivalent nanobodies recognizing the same or distinct epitopes on the envelope glycoproteins, gp120 and gp41, greatly increase the potency of HIV-1 neutralization. Nanobodies have potential applications for HIV-1 diagnostics, vaccine design, microbicides, immunoprophylaxis, and immunotherapy.
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Affiliation(s)
- Robin A Weiss
- Division of Infection & Immunity, University College London, 90 Gower Street, London WC1E 6BT, UK.
| | - C Theo Verrips
- QVQ Holding bv, Padualaan 8, 3584 CL Utrecht, The Netherlands.
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18
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Jurado S, Cano-Muñoz M, Morel B, Standoli S, Santarossa E, Moog C, Schmidt S, Laumond G, Cámara-Artigas A, Conejero-Lara F. Structural and Thermodynamic Analysis of HIV-1 Fusion Inhibition Using Small gp41 Mimetic Proteins. J Mol Biol 2019; 431:3091-3106. [PMID: 31255705 DOI: 10.1016/j.jmb.2019.06.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/21/2019] [Accepted: 06/21/2019] [Indexed: 11/25/2022]
Abstract
Development of effective inhibitors of the fusion between HIV-1 and the host cell membrane mediated by gp41 continues to be a grand challenge due to an incomplete understanding of the molecular and mechanistic details of the fusion process. We previously developed single-chain, chimeric proteins (named covNHR) that accurately mimic the N-heptad repeat (NHR) region of gp41 in a highly stable coiled-coil conformation. These molecules bind strongly to peptides derived from the gp41 C-heptad repeat (CHR) and are potent and broad HIV-1 inhibitors. Here, we investigated two covNHR variants differing in two mutations, V10E and Q123R (equivalent to V38E and Q40R in gp41 sequence) that reproduce the effect of HIV-1 mutations associated with resistance to fusion inhibitors, such as T20 (enfuvirtide). A detailed calorimetric analysis of the binding between the covNHR proteins and CHR peptides (C34 and T20) reveals drastic changes in affinity due to the mutations as a result of local changes in interactions at the site of T20 resistance. The crystallographic structure of the covNHR:C34 complex shows a virtually identical CHR-NHR binding interface to that of the post-fusion structure of gp41 and underlines an important role of buried interfacial water molecules in binding affinity and in development of resistance against CHR peptides. Despite the great difference in affinity, both covNHR variants demonstrate strong inhibitory activity for a wide variety of HIV-1 strains. These properties support the high potential of these covNHR proteins as new potent HIV-1 inhibitors. Our results may guide future inhibition approaches.
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Affiliation(s)
- Samuel Jurado
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Mario Cano-Muñoz
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Bertrand Morel
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Sara Standoli
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Elisabetta Santarossa
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Christiane Moog
- INSERM U1109, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Sylvie Schmidt
- INSERM U1109, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Géraline Laumond
- INSERM U1109, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Ana Cámara-Artigas
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento, 04120 Almeria, Spain
| | - Francisco Conejero-Lara
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
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19
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Strokappe NM, Hock M, Rutten L, Mccoy LE, Back JW, Caillat C, Haffke M, Weiss RA, Weissenhorn W, Verrips T. Super Potent Bispecific Llama VHH Antibodies Neutralize HIV via a Combination of gp41 and gp120 Epitopes. Antibodies (Basel) 2019; 8:antib8020038. [PMID: 31544844 PMCID: PMC6640723 DOI: 10.3390/antib8020038] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 05/19/2019] [Accepted: 05/30/2019] [Indexed: 11/20/2022] Open
Abstract
Broad and potent neutralizing llama single domain antibodies (VHH) against HIV-1 targeting the CD4 binding site (CD4bs) have previously been isolated upon llama immunization. Here we describe the epitopes of three additional VHH groups selected from phage libraries. The 2E7 group binds to a new linear epitope in the first heptad repeat of gp41 that is only exposed in the fusion-intermediate conformation. The 1B5 group competes with co-receptor binding and the 1F10 group interacts with the crown of the gp120 V3 loop, occluded in native Env. We present biophysical and structural details on the 2E7 interaction with gp41. In order to further increase breadth and potency, we constructed bi-specific VHH. The combination of CD4bs VHH (J3/3E3) with 2E7 group VHH enhanced strain-specific neutralization with potencies up to 1400-fold higher than the mixture of the individual VHHs. Thus, these new bivalent VHH are potent new tools to develop therapeutic approaches or microbicide intervention.
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Affiliation(s)
- Nika M Strokappe
- Department of Biology, Faculty of Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands.
- QVQ Holding bv, Yalelaan 1, 3584 CL Utrecht, The Netherlands.
| | - Miriam Hock
- Institute de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, F-38000 Grenoble, France.
- Immunocore Ltd., 101 Park Drive, Milto, Abingdon OX14 4RY, UK.
| | - Lucy Rutten
- Department of Biology, Faculty of Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands.
- QVQ Holding bv, Yalelaan 1, 3584 CL Utrecht, The Netherlands.
| | - Laura E Mccoy
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK.
| | - Jaap W Back
- Pepscan B.V., Zuidersluisweg 2, 8243 RC Lelystad, The Netherlands.
| | - Christophe Caillat
- Institute de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, F-38000 Grenoble, France.
| | - Matthias Haffke
- European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France.
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4002 Basel, Switzerland.
| | - Robin A Weiss
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK.
| | - Winfried Weissenhorn
- Institute de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, F-38000 Grenoble, France.
| | - Theo Verrips
- Department of Biology, Faculty of Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands.
- QVQ Holding bv, Yalelaan 1, 3584 CL Utrecht, The Netherlands.
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20
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V H1-69 antiviral broadly neutralizing antibodies: genetics, structures, and relevance to rational vaccine design. Curr Opin Virol 2019; 34:149-159. [PMID: 30884330 DOI: 10.1016/j.coviro.2019.02.004] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/07/2019] [Indexed: 12/15/2022]
Abstract
Broadly neutralizing antibodies (bnAbs) are potential therapeutic molecules and valuable tools for studying conserved viral targets for vaccine and drug design. Interestingly, antibody responses to conserved epitopes can be highly convergent at the molecular level. Human antibodies targeting a number of viral antigens have often been found to utilize a restricted set of immunoglobulin germline genes in different individuals. Here we review recent knowledge on VH1-69-encoded antibodies in antiviral responses to influenza virus, HCV, and HIV-1. These antibodies share common genetic and structural features, and often develop neutralizing activity against a broad spectrum of viral strains. Understanding the genetic and structural characteristics of such antibodies and the target epitopes should help advance novel strategies to elicit bnAbs through vaccination.
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21
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Yang Z, Liu X, Sun Z, Li J, Tan W, Yu W, Zhang M. Identification of a HIV Gp41-Specific Human Monoclonal Antibody With Potent Antibody-Dependent Cellular Cytotoxicity. Front Immunol 2018; 9:2613. [PMID: 30519238 PMCID: PMC6251304 DOI: 10.3389/fimmu.2018.02613] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/23/2018] [Indexed: 01/23/2023] Open
Abstract
Antibody-Dependent Cellular Cytotoxicity (ADCC) is a major mechanism of protection against viral infections in vivo. Identification of HIV-1-specific monoclonal antibodies (mAbs) with potent ADCC activity may help develop an effective HIV-1 vaccine. In present study, we isolated such human mAb, designated E10, from an HIV-1-infected patient sample by single B cell sorting and single cell PCR. E10 bound to gp140 trimer and linear peptides derived from gp41 membrane proximal external region (MPER). E10 epitope (QEKNEQELLEL) overlapped with mAb 2F5 epitope. However, E10 differentiated from 2F5 in neutralization breadth and potency, as well as ADCC activity. E10 showed low neutralization activity and narrow spectrum of neutralization compared to 2F5, but it mediated higher ADCC activity than 2F5 at low antibody concentration. Fine mapping of E10 epitope may potentiate MPER-based subunit vaccine development.
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Affiliation(s)
- Zheng Yang
- Department of Tuberculosis Prevention, Shenzhen Center for Chronic Disease Control, Shenzhen, China.,AIDS Institute, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Xi Liu
- Department of Infectious Diseases, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Zehua Sun
- National Jewish Health, Denver, CO, United States
| | - Jingjing Li
- AIDS Institute, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Weiguo Tan
- Department of Tuberculosis Prevention, Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Weiye Yu
- Department of Tuberculosis Prevention, Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Meiyun Zhang
- AIDS Institute, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
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22
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Imkeller K, Wardemann H. Assessing human B cell repertoire diversity and convergence. Immunol Rev 2018; 284:51-66. [DOI: 10.1111/imr.12670] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | - Hedda Wardemann
- German Cancer Research Center; B Cell Immunology; Heidelberg Germany
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23
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Setliff I, McDonnell WJ, Raju N, Bombardi RG, Murji AA, Scheepers C, Ziki R, Mynhardt C, Shepherd BE, Mamchak AA, Garrett N, Karim SA, Mallal SA, Crowe JE, Morris L, Georgiev IS. Multi-Donor Longitudinal Antibody Repertoire Sequencing Reveals the Existence of Public Antibody Clonotypes in HIV-1 Infection. Cell Host Microbe 2018; 23:845-854.e6. [PMID: 29861170 PMCID: PMC6002606 DOI: 10.1016/j.chom.2018.05.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 01/27/2018] [Accepted: 04/24/2018] [Indexed: 01/01/2023]
Abstract
Characterization of single antibody lineages within infected individuals has provided insights into the development of Env-specific antibodies. However, a systems-level understanding of the humoral response against HIV-1 is limited. Here, we interrogated the antibody repertoires of multiple HIV-infected donors from an infection-naive state through acute and chronic infection using next-generation sequencing. This analysis revealed the existence of "public" antibody clonotypes that were shared among multiple HIV-infected individuals. The HIV-1 reactivity for representative antibodies from an identified public clonotype shared by three donors was confirmed. Furthermore, a meta-analysis of publicly available antibody repertoire sequencing datasets revealed antibodies with high sequence identity to known HIV-reactive antibodies, even in repertoires that were reported to be HIV naive. The discovery of public antibody clonotypes in HIV-infected individuals represents an avenue of significant potential for better understanding antibody responses to HIV-1 infection, as well as for clonotype-specific vaccine development.
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Affiliation(s)
- Ian Setliff
- Program in Chemical & Physical Biology, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wyatt J McDonnell
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Center for Translational Immunology and Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nagarajan Raju
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Robin G Bombardi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Amyn A Murji
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cathrine Scheepers
- Center for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Rutendo Ziki
- Center for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Charissa Mynhardt
- Center for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Bryan E Shepherd
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), 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, Durban, South Africa; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Simon A Mallal
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Center for Translational Immunology and Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, USA; Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, USA; Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lynn Morris
- Center for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Ivelin S Georgiev
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, USA.
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24
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Chu S, Zhou G, Gochin M. Evaluation of ligand-based NMR screening methods to characterize small molecule binding to HIV-1 glycoprotein-41. Org Biomol Chem 2017; 15:5210-5219. [PMID: 28590477 PMCID: PMC5530879 DOI: 10.1039/c7ob00954b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small molecule inhibitors of glycoprotein-41 (gp41) are able to prevent HIV infection by binding to a hydrophobic pocket (HP) contained within the gp41 ectodomain, and preventing progression of fusion. There is little structural information on gp41-ligand complexes, owing to hydrophobicity of the ligands, occlusion of the HP in folded gp41 ectodomain, and failure to form crystals of complexes. Here we used an engineered gp41 ectodomain protein containing an exposed HP and a small molecule designed to bind with weak affinity to the HP. We evaluated NMR methods, including WaterLOGSY, Saturation Transfer Difference spectroscopy (STD-NMR) and 1H relaxation rate difference spectroscopy with and without target irradiation (DIRECTION) for their ability to probe complex formation and structure. WaterLOGSY was the most sensitive technique for monitoring formation of the complex. STD-NMR and DIRECTION experiments gave similar pharmacophore mapping profiles, although the low dynamic range of the DIRECTION experiment limited its discrimination and sensitivity. A unique binding pose was identified from the STD data and provided clues for future optimization. Advantages and disadvantages of the techniques are discussed. This is the first example of the use of STD for structural analysis of a gp41-small molecule complex.
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Affiliation(s)
- Shidong Chu
- Department of Basic Sciences, Touro University-California, Vallejo, CA 94592, USA.
| | - Guangyan Zhou
- Department of Basic Sciences, Touro University-California, Vallejo, CA 94592, USA.
| | - Miriam Gochin
- Department of Basic Sciences, Touro University-California, Vallejo, CA 94592, USA. and Department of Pharmaceutical Chemistry, University of California San Francisco, CA 94143, USA
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25
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Kuhn P, Fühner V, Unkauf T, Moreira GMSG, Frenzel A, Miethe S, Hust M. Recombinant antibodies for diagnostics and therapy against pathogens and toxins generated by phage display. Proteomics Clin Appl 2016; 10:922-948. [PMID: 27198131 PMCID: PMC7168043 DOI: 10.1002/prca.201600002] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 03/30/2016] [Accepted: 05/17/2016] [Indexed: 12/11/2022]
Abstract
Antibodies are valuable molecules for the diagnostic and treatment of diseases caused by pathogens and toxins. Traditionally, these antibodies are generated by hybridoma technology. An alternative to hybridoma technology is the use of antibody phage display to generate recombinant antibodies. This in vitro technology circumvents the limitations of the immune system and allows—in theory—the generation of antibodies against all conceivable molecules. Phage display technology enables obtaining human antibodies from naïve antibody gene libraries when either patients are not available or immunization is not ethically feasible. On the other hand, if patients or immunized/infected animals are available, it is common to construct immune phage display libraries to select in vivo affinity‐matured antibodies. Because the phage packaged DNA sequence encoding the antibodies is directly available, the antibodies can be smoothly engineered according to the requirements of the final application. In this review, an overview of phage display derived recombinant antibodies against bacterial, viral, and eukaryotic pathogens as well as toxins for diagnostics and therapy is given.
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Affiliation(s)
- Philipp Kuhn
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | - Viola Fühner
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | - Tobias Unkauf
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | | | - André Frenzel
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany.,YUMAB GmbH, Braunschweig, Germany
| | - Sebastian Miethe
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | - Michael Hust
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany.
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26
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Strauli NB, Hernandez RD. Statistical inference of a convergent antibody repertoire response to influenza vaccine. Genome Med 2016; 8:60. [PMID: 27255379 PMCID: PMC4891843 DOI: 10.1186/s13073-016-0314-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 05/05/2016] [Indexed: 12/31/2022] Open
Abstract
Background Vaccines dramatically affect an individual’s adaptive immune system and thus provide an excellent means to study human immunity. Upon vaccination, the B cells that express antibodies (Abs) that happen to bind the vaccine are stimulated to proliferate and undergo mutagenesis at their Ab locus. This process may alter the composition of B cell lineages within an individual, which are known collectively as the antibody repertoire (AbR). Antibodies are also highly expressed in whole blood, potentially enabling RNA sequencing (RNA-seq) technologies to query this diversity. Less is known about the diversity of AbR responses across individuals to a given vaccine and if individuals tend to yield a similar response to the same antigenic stimulus. Methods Here we implement a bioinformatic pipeline that extracts the AbR information from a time-series RNA-seq dataset of five patients who were administered a seasonal trivalent influenza vaccine (TIV). We harness the detailed time-series nature of this dataset and use methods based in functional data analysis (FDA) to identify the Abs that respond to the vaccine. We then design and implement rigorous statistical tests in order to ask whether or not these patients exhibit a convergent AbR response to the same TIV. Results We find that high-resolution time-series data can be used to help identify the Abs that respond to an antigenic stimulus and that this response can exhibit a convergent nature across patients inoculated with the same vaccine. However, correlations in AbR diversity among individuals prior to inoculation can confound inference of a convergent signal unless it is taken into account. Conclusions We developed a framework to identify the elements of an AbR that respond to an antigen. This information could be used to understand the diversity of different immune responses in different individuals, as well as to gauge the effectiveness of the immune response to a given stimulus within an individual. We also present a framework for testing a convergent hypothesis between AbRs; a hypothesis that is more difficult to test than previously appreciated. Our discovery of a convergent signal suggests that similar epitopes do select for antibodies with similar sequence characteristics. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0314-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicolas B Strauli
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, Byers Hall, 1700 4th Street, San Francisco, CA, 94158, USA. .,Institute for Human Genetics, University of California, San Francisco, CA, USA. .,Institute for Quantitative Biosciences (QB3), University of California, San Francisco, CA, USA.
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27
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Henry Dunand CJ, Wilson PC. Restricted, canonical, stereotyped and convergent immunoglobulin responses. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0238. [PMID: 26194752 DOI: 10.1098/rstb.2014.0238] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
It is becoming evident that B-cell responses to particular epitopes or in particular contexts can be highly convergent at the molecular level. That is, depending on the epitope targeted, persons of diverse genetic backgrounds and immunological histories can use highly similar, stereotyped B-cell receptors (BCRs) for a particular response. In some cases, multiple people with immunity to a particular epitope or with a type of B-cell neoplasia will elicit antibodies encoded by essentially identical immunoglobulin gene rearrangements. In other cases, particular VH genes encode antibodies important for immunity against pathogens such as influenza and HIV. It appears that the conserved antibody structures driving these stereotyped responses are highly limited and selected. There are interesting and important convergences in the types of stereotyped BCRs induced in conditions of immunity and B-cell-related pathology such as cancer and autoimmunity. By characterizing and understanding stereotyped B-cell responses, novel approaches to B-cell immunity and in understanding the underlying causes of B-cell pathology may be discovered. In this paper, we will review stereotyped BCR responses in various contexts of B-cell immunity and pathology.
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Affiliation(s)
- Carole J Henry Dunand
- Department of Medicine, Section of Rheumatology, Knapp Center for Lupus and Immunology Research, Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Patrick C Wilson
- Department of Medicine, Section of Rheumatology, Knapp Center for Lupus and Immunology Research, Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
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28
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Abstract
In this article, we highlight the advantages of isolating human monoclonal antibodies from the human memory B cells and plasma cell repertoires by using high-throughput cellular screens. Memory B cells are immortalized with high efficiency using Epstein-Barr virus (EBV) in the presence of a toll-like receptor (TLR) agonist, while plasma cells are maintained in single-cell cultures by using interleukin 6 (IL-6) or stromal cells. In both cases, multiple parallel assays, including functional assays, can be used to identify rare cells that produce antibodies with unique properties. Using these methods, we have isolated potent and broadly neutralizing antibodies against a variety of viruses, in particular, a pan-influenza-A-neutralizing antibody and an antibody that neutralizes four different paramyxoviruses. Given the high throughput and the possibility of directly screening for function (rather than just binding), these methods are instrumental to implement a target-agnostic approach to identify the most effective antibodies and, consequently, the most promising targets for vaccine design. This approach is exemplified by the identification of unusually potent cytomegalovirus-neutralizing antibodies that led to the identification of the target, a pentameric complex that we are developing as a candidate vaccine.
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29
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Louis JM, Baber JL, Clore GM. The C34 Peptide Fusion Inhibitor Binds to the Six-Helix Bundle Core Domain of HIV-1 gp41 by Displacement of the C-Terminal Helical Repeat Region. Biochemistry 2015; 54:6796-805. [PMID: 26506247 DOI: 10.1021/acs.biochem.5b01021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conformational transition of the core domain of HIV-1 gp41 from a prehairpin intermediate to a six-helix bundle is responsible for virus-cell fusion. Several inhibitors which target the N-heptad repeat helical coiled-coil trimer that is fully accessible in the prehairpin intermediate have been designed. One such inhibitor is the peptide C34 derived from the C-heptad repeat of gp41 that forms the exterior of the six-helix bundle. Here, using a variety of biophysical techniques, including dye tagging, size-exclusion chromatography combined with multiangle light scattering, double electron-electron resonance EPR spectroscopy, and circular dichroism, we investigate the binding of C34 to two six-helix bundle mimetics comprising N- and C-heptad repeats either without (core(SP)) or with (core(S)) a short spacer connecting the two. In the case of core(SP), C34 directly exchanges with the C-heptad repeat. For core(S), up to two molecules of C34 bind the six-helix bundle via displacement of the C-heptad repeat. These results suggest that fusion inhibitors such as C34 can target a continuum of transitioning conformational states from the prehairpin intermediate to the six-helix bundle prior to the occurrence of irreversible fusion of viral and target cell membranes.
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Affiliation(s)
- John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
| | - James L Baber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
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30
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Williams WB, Liao HX, Moody MA, Kepler TB, Alam SM, Gao F, Wiehe K, Trama AM, Jones K, Zhang R, Song H, Marshall DJ, Whitesides JF, Sawatzki K, Hua A, Liu P, Tay MZ, Seaton KE, Shen X, Foulger A, Lloyd KE, Parks R, Pollara J, Ferrari G, Yu JS, Vandergrift N, Montefiori DC, Sobieszczyk ME, Hammer S, Karuna S, Gilbert P, Grove D, Grunenberg N, McElrath MJ, Mascola JR, Koup RA, Corey L, Nabel GJ, Morgan C, Churchyard G, Maenza J, Keefer M, Graham BS, Baden LR, Tomaras GD, Haynes BF. HIV-1 VACCINES. Diversion of HIV-1 vaccine-induced immunity by gp41-microbiota cross-reactive antibodies. Science 2015; 349:aab1253. [PMID: 26229114 DOI: 10.1126/science.aab1253] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 07/09/2015] [Indexed: 01/04/2023]
Abstract
An HIV-1 DNA prime vaccine, with a recombinant adenovirus type 5 (rAd5) boost, failed to protect from HIV-1 acquisition. We studied the nature of the vaccine-induced antibody (Ab) response to HIV-1 envelope (Env). HIV-1-reactive plasma Ab titers were higher to Env gp41 than to gp120, and repertoire analysis demonstrated that 93% of HIV-1-reactive Abs from memory B cells responded to Env gp41. Vaccine-induced gp41-reactive monoclonal antibodies were non-neutralizing and frequently polyreactive with host and environmental antigens, including intestinal microbiota (IM). Next-generation sequencing of an immunoglobulin heavy chain variable region repertoire before vaccination revealed an Env-IM cross-reactive Ab that was clonally related to a subsequent vaccine-induced gp41-reactive Ab. Thus, HIV-1 Env DNA-rAd5 vaccine induced a dominant IM-polyreactive, non-neutralizing gp41-reactive Ab repertoire response that was associated with no vaccine efficacy.
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Affiliation(s)
- Wilton B Williams
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.
| | - Hua-Xin Liao
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
| | - S Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Feng Gao
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Ashley M Trama
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Kathryn Jones
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Ruijun Zhang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Hongshuo Song
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Dawn J Marshall
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - John F Whitesides
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Kaitlin Sawatzki
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
| | - Axin Hua
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
| | - Pinghuang Liu
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Matthew Z Tay
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Kelly E Seaton
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Andrew Foulger
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Krissey E Lloyd
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Justin Pollara
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Jae-Sung Yu
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Nathan Vandergrift
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Scott Hammer
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Shelly Karuna
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Peter Gilbert
- The Statistical Center for HIV/AIDS Research and Prevention (SCHARP), Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Doug Grove
- The Statistical Center for HIV/AIDS Research and Prevention (SCHARP), Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nicole Grunenberg
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Gary J Nabel
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Cecilia Morgan
- The Statistical Center for HIV/AIDS Research and Prevention (SCHARP), Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Janine Maenza
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michael Keefer
- University of Rochester School of Medicine, Rochester, NY, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.
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Chu S, Kaur H, Nemati A, Walsh JD, Partida V, Zhang SQ, Gochin M. Swapped-domain constructs of the glycoprotein-41 ectodomain are potent inhibitors of HIV infection. ACS Chem Biol 2015; 10:1247-57. [PMID: 25646644 DOI: 10.1021/cb501021j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The conformational rearrangement of N- and C-heptad repeats (NHR, CHR) of the HIV-1 glycoprotein-41 (gp41) ectodomain into a trimer of hairpins triggers virus-cell fusion by bringing together membrane-spanning N- and C-terminal domains. Peptides derived from the NHR and CHR inhibit fusion by targeting a prehairpin intermediate state of gp41. Typically, peptides derived from the CHR are low nanomolar inhibitors, whereas peptides derived from the NHR are low micromolar inhibitors. Here, we describe the inhibitory activity of swapped-domain gp41 mimics of the form CHR-loop-NHR, which were designed to form reverse hairpin trimers exposing NHR grooves. We observed low nanomolar inhibition of HIV fusion in constructs that possessed the following properties: an extended NHR C-terminus, an exposed conserved hydrophobic pocket on the NHR, high helical content, and trimer stability. Low nanomolar activity was independent of CHR length. CD studies in membrane mimetic dodecylphosphocholine micelles suggested that bioactivity could be related to the ability of the inhibitors to interact with a membrane-associated prehairpin intermediate. The swapped-domain design resolves the problem of unstable and weakly active NHR peptides and suggests a different mechanism of action from that of CHR peptides in inhibition of HIV-1 fusion.
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Affiliation(s)
- Shidong Chu
- Department
of Basic Sciences, Touro University−California, Vallejo, California 94592, United States
| | - Hardeep Kaur
- Department
of Basic Sciences, Touro University−California, Vallejo, California 94592, United States
| | - Ariana Nemati
- Department
of Basic Sciences, Touro University−California, Vallejo, California 94592, United States
| | - Joseph D. Walsh
- Department
of Basic Sciences, Touro University−California, Vallejo, California 94592, United States
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - Vivian Partida
- Department
of Basic Sciences, Touro University−California, Vallejo, California 94592, United States
| | - Shao-Qing Zhang
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19014, United States
| | - Miriam Gochin
- Department
of Basic Sciences, Touro University−California, Vallejo, California 94592, United States
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
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Walsh JD, Chu S, Zhang SQ, Gochin M. Design and characterization of swapped-domain constructs of HIV-1 glycoprotein-41 as receptors for drug discovery. Protein Eng Des Sel 2015; 28:107-16. [PMID: 25792539 PMCID: PMC4366113 DOI: 10.1093/protein/gzv006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 01/08/2015] [Accepted: 01/28/2015] [Indexed: 11/14/2022] Open
Abstract
Four new swapped-domain constructs of the ectodomain of human immunodeficiency virus type 1 glycoprotein-41 (gp41) were prepared. The gp41 ectodomain consists of 50-residue N-heptad repeat (NHR), 36-residue disulfide-bonded loop and 39-residue C-heptad repeat (CHR). It folds into a hairpin structure that forms a trimer along the NHR axis. The swapped-domain proteins feature CHR domains of length 39, 28 or 21 residues preceding a 4-residue loop and a 49- or 50-residue NHR domain. The effect of CHR truncation was to expose increasing lengths of the NHR groove, including the conserved hydrophobic pocket, an important drug target. A novel method for preparing proteins with extended exposed hydrophobic surfaces was demonstrated. Biophysical measurements, including analytical ultracentrifugation and ligand-detected Water-Ligand Observed via Gradient Spectroscopy and (1)H-(15)N-HSQC NMR experiments, were used to confirm that the proteins formed stable trimers in solution with exposed binding surfaces. These proteins could play an important role as receptors in structure-based drug discovery.
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Affiliation(s)
- Joseph D Walsh
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University California, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
| | - Shidong Chu
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University California, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA
| | - Shao-Qing Zhang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19014, USA
| | - Miriam Gochin
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University California, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
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Miglietta R, Pastori C, Venuti A, Ochsenbauer C, Lopalco L. Synergy in monoclonal antibody neutralization of HIV-1 pseudoviruses and infectious molecular clones. J Transl Med 2014; 12:346. [PMID: 25496375 PMCID: PMC4274758 DOI: 10.1186/s12967-014-0346-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 11/26/2014] [Indexed: 12/26/2022] Open
Abstract
Background Early events in HIV infection are still poorly understood; virus derived from acute infections, the transmitted/founders IMCs, could provide more reliable information as they represent strains that established HIV infection in vivo, and therefore are investigated to elucidate potentially shared biological features. Methods This study examined synergy in neutralization by six monoclonal antibodies targeting different domains in gp120 and gp41 and assayed in pairwise combination against 11 HIV-1 clade B strains, either Env pseudoviruses (PV, n = 5) or transmitted/founder infectious molecular clones (T/F IMCs, n = 6). Three of the early-infection env tested as PV were juxtaposed with T/F viruses derived from the same three patients, respectively. Results All antibodies reaching IC50 were assayed pairwise (n = 50). T/F IMCs showed overall lower sensitivity to neutralization by single antibodies than PV, including within the three patient-matched pairs. Remarkably, combination index (CI) calculated using the Chow and Talalay method indicated synergy (CI < 0.9) in 42 data sets, and occurred in T/F IMC at similar proportions (15 of 17 antibody-T/F IMC combinations tested) as in pseudoviruses (27 of 33). CI values indicative of additivity and low-level antagonism were seen in 5 and 3 cases, respectively. Most pairs showed comparable synergic neutralizing effects on both virus groups, with the 4E10 + PG16 pair achieving the best synergic effects. Variability in neutralization was mostly observed on pseudovirus isolates, suggesting that factors other than virus isolation technology, such as env conformation, epitope accessibility and antibody concentration, are likely to affect polyclonal neutralization. Conclusions The findings from this study suggest that inhibitory activity of bNAbs can be further augmented through appropriate combination, even against viruses representing circulating strains, which are likely to exhibit a less sensitive Tier 2 neutralization phenotype. This notion has important implications for the design and development of anti-Env bNAb-inducing vaccines and polyclonal sera for passive immunization. Electronic supplementary material The online version of this article (doi:10.1186/s12967-014-0346-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Riccardo Miglietta
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy. .,Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Claudia Pastori
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy.
| | - Assunta Venuti
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy.
| | - Christina Ochsenbauer
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA. .,CFAR, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Lucia Lopalco
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy.
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Single-chain protein mimetics of the N-terminal heptad-repeat region of gp41 with potential as anti-HIV-1 drugs. Proc Natl Acad Sci U S A 2014; 111:18207-12. [PMID: 25489108 DOI: 10.1073/pnas.1413592112] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During HIV-1 fusion to the host cell membrane, the N-terminal heptad repeat (NHR) and the C-terminal heptad repeat (CHR) of the envelope subunit gp41 become transiently exposed and accessible to fusion inhibitors or Abs. In this process, the NHR region adopts a trimeric coiled-coil conformation that can be a target for therapeutic intervention. Here, we present an approach to rationally design single-chain protein constructs that mimic the NHR coiled-coil surface. The proteins were built by connecting with short loops two parallel NHR helices and an antiparallel one with the inverse sequence followed by engineering of stabilizing interactions. The constructs were expressed in Escherichia coli, purified with high yield, and folded as highly stable helical coiled coils. The crystal structure of one of the constructs confirmed the predicted fold and its ability to accurately mimic an exposed gp41 NHR surface. These single-chain proteins bound to synthetic CHR peptides with very high affinity, and furthermore, they showed broad inhibitory activity of HIV-1 fusion on various pseudoviruses and primary isolates.
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35
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Ma X, Tan J, Su M, Li C, Zhang X, Wang C. Molecular dynamics studies of the inhibitor C34 binding to the wild-type and mutant HIV-1 gp41: inhibitory and drug resistant mechanism. PLoS One 2014; 9:e111923. [PMID: 25393106 PMCID: PMC4230944 DOI: 10.1371/journal.pone.0111923] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 10/08/2014] [Indexed: 11/20/2022] Open
Abstract
Mutations on NHR (N-terminal heptad repeat) associated with resistance to fusion inhibitor were observed. In addition, mutations on CHR (C-terminal heptad repeat) accompanied NHR mutations of gp41 are noted in many cases, like N43D/S138A double mutation. In this work, we explored the drug resistant mechanism of N43D mutation and the role of S138A second mutation in drug resistance. The binding modes of the wild type gp41 and the two mutants, N43D and N43D/S138A, with the HIV-1 fusion inhibitor C34, a 34-residue peptide mimicking CHR of gp41, were carried out by using molecular dynamics simulations. Based on the MD simulations, N43D mutation affects not only the stability of C34 binding, but also the binding energy of the inhibitor C34. Because N43D mutation may also affect the stable conformation of 6-HB, we introduced S138A second mutation into CHR of gp41 and determined the impact of this mutation. Through the comparative analysis of MD results of the N43D mutant and the N43D/S138A mutant, we found that CHR with S138A mutation shown more favorable affinity to NHR. Compelling differences in structures have been observed for these two mutants, particularly in the binding modes and in the hydrophobic interactions of the CHR (C34) located near the hydrophobic groove of the NHR. Because the conformational stability of 6-HB is important to HIV-1 infection, we suggested a hypothetical mechanism for the drug resistance: N43D single mutation not only impact the binding of inhibitor, but also affect the affinity between NHR and CHR of gp41, thus may reduce the rate of membrane fusion; compensatory mutation S138A would induce greater hydrophobic interactions between NHR and CHR, and render the CHR more compatible to NHR than inhibitors.
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Affiliation(s)
- Xueting Ma
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China
| | - Jianjun Tan
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China
- * E-mail:
| | - Min Su
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China
| | - Chunhua Li
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China
| | - Xiaoyi Zhang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China
| | - Cunxin Wang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China
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36
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Pancera M, Zhou T, Druz A, Georgiev IS, Soto C, Gorman J, Huang J, Acharya P, Chuang GY, Ofek G, Stewart-Jones GBE, Stuckey J, Bailer RT, Joyce MG, Louder MK, Tumba N, Yang Y, Zhang B, Cohen MS, Haynes BF, Mascola JR, Morris L, Munro JB, Blanchard SC, Mothes W, Connors M, Kwong PD. Structure and immune recognition of trimeric pre-fusion HIV-1 Env. Nature 2014; 514:455-61. [PMID: 25296255 PMCID: PMC4348022 DOI: 10.1038/nature13808] [Citation(s) in RCA: 602] [Impact Index Per Article: 60.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 09/01/2014] [Indexed: 12/17/2022]
Abstract
The human immunodeficiency virus type 1 (HIV-1) envelope (Env) spike, comprising three gp120 and three gp41 subunits, is a conformational machine that facilitates HIV-1 entry by rearranging from a mature unliganded state, through receptor-bound intermediates, to a post-fusion state. As the sole viral antigen on the HIV-1 virion surface, Env is both the target of neutralizing antibodies and a focus of vaccine efforts. Here we report the structure at 3.5 Å resolution for an HIV-1 Env trimer captured in a mature closed state by antibodies PGT122 and 35O22. This structure reveals the pre-fusion conformation of gp41, indicates rearrangements needed for fusion activation, and defines parameters of immune evasion and immune recognition. Pre-fusion gp41 encircles amino- and carboxy-terminal strands of gp120 with four helices that form a membrane-proximal collar, fastened by insertion of a fusion peptide-proximal methionine into a gp41-tryptophan clasp. Spike rearrangements required for entry involve opening the clasp and expelling the termini. N-linked glycosylation and sequence-variable regions cover the pre-fusion closed spike; we used chronic cohorts to map the prevalence and location of effective HIV-1-neutralizing responses, which were distinguished by their recognition of N-linked glycan and tolerance for epitope-sequence variation.
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Affiliation(s)
- Marie Pancera
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Aliaksandr Druz
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ivelin S. Georgiev
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Cinque Soto
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jason Gorman
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jinghe Huang
- HIV-Specific Immunity Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Priyamvada Acharya
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Gilad Ofek
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Guillaume B. E. Stewart-Jones
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jonathan Stuckey
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Robert T. Bailer
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - M. Gordon Joyce
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Mark K. Louder
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Nancy Tumba
- Center for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service (NHLS), and University of the Witwatersrand, Johannesburg, South Africa, and Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Yongping Yang
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Myron S. Cohen
- Departments of Medicine, Epidemiology, Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Barton F. Haynes
- Duke University Human Vaccine Institute, Departments of Medicine, Surgery, Pediatrics and Immunology, Duke University School of Medicine, and the Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery at Duke University, Durham, North Carolina 27710, USA
| | - John R. Mascola
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Lynn Morris
- Center for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service (NHLS), and University of the Witwatersrand, Johannesburg, South Africa, and Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - James B. Munro
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Scott C. Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10021, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Mark Connors
- HIV-Specific Immunity Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Peter D. Kwong
- Vaccine Research Center, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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37
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Novel neutralising antibodies targeting the N-terminal helical region of the transmembrane envelope protein p15E of the porcine endogenous retrovirus (PERV). Immunol Res 2014; 58:9-19. [PMID: 23729215 DOI: 10.1007/s12026-013-8430-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Previously, immunising different species with the transmembrane envelope protein p15E of the porcine endogenous retrovirus (PERV), neutralising antibodies were induced which recognised epitopes in the fusion peptide proximal region (FPPR) and in the membrane-proximal external region (MPER). Only the MPER-specific antibodies were shown to neutralise and these antibodies targeted epitopes in the MPER similarly localised as the epitopes recognised by antibodies broadly neutralising HIV-1 such as 2F5 and 4E10. To study whether neutralising antibodies could be induced immunising with subunits of p15E, recombinant proteins corresponding to the N-terminal, the C-terminal helical region (NHR, CHR) and a p15E with a mutation in the Cys-Cys loop were produced. Whereas none of these antigens induced MPER-specific neutralising antibodies, the animals immunised with the FPPR/NHR subunit and the mutated p15E produced neutralising antibodies binding to the NHR. Therefore, for the first time, antibodies specific for the NHR and neutralising PERV were described.
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38
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Radzimanowski J, Effantin G, Weissenhorn W. Conformational plasticity of the Ebola virus matrix protein. Protein Sci 2014; 23:1519-27. [PMID: 25159197 DOI: 10.1002/pro.2541] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 08/01/2014] [Accepted: 08/04/2014] [Indexed: 12/14/2022]
Abstract
Filoviruses are the causative agents of a severe and often fatal hemorrhagic fever with repeated outbreaks in Africa. They are negative sense single stranded enveloped viruses that can cross species barriers from its natural host bats to primates including humans. The small size of the genome poses limits to viral adaption, which may be partially overcome by conformational plasticity. Here we review the different conformational states of the Ebola virus (EBOV) matrix protein VP40 that range from monomers, to dimers, hexamers, and RNA-bound octamers. This conformational plasticity that is required for the viral life cycle poses a unique opportunity for development of VP40 specific drugs. Furthermore, we compare the structure to homologous matrix protein structures from Paramyxoviruses and Bornaviruses and we predict that they do not only share the fold but also the conformational flexibility of EBOV VP40.
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Affiliation(s)
- Jens Radzimanowski
- University Grenoble Alpes, UVHCI, F-38000, Grenoble, France; CNRS, UVHCI, F-38000, Grenoble, France
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Affinity maturation in an HIV broadly neutralizing B-cell lineage through reorientation of variable domains. Proc Natl Acad Sci U S A 2014; 111:10275-80. [PMID: 24982157 DOI: 10.1073/pnas.1409954111] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Rapidly evolving pathogens, such as human immunodeficiency and influenza viruses, escape immune defenses provided by most vaccine-induced antibodies. Proposed strategies to elicit broadly neutralizing antibodies require a deeper understanding of antibody affinity maturation and evolution of the immune response to vaccination or infection. In HIV-infected individuals, viruses and B cells evolve together, creating a virus-antibody "arms race." Analysis of samples from an individual designated CH505 has illustrated the interplay between an antibody lineage, CH103, and autologous viruses at various time points. The CH103 antibodies, relatively broad in their neutralization spectrum, interact with the CD4 binding site of gp120, with a contact dominated by CDRH3. We show by analyzing structures of progenitor and intermediate antibodies and by correlating them with measurements of binding to various gp120s that there was a shift in the relative orientation of the light- and heavy-chain variable domains during evolution of the CH103 lineage. We further show that mutations leading to this conformational shift probably occurred in response to insertions in variable loop 5 (V5) of the HIV envelope. The shift displaced the tips of the light chain away from contact with V5, making room for the inserted residues, which had allowed escape from neutralization by the progenitor antibody. These results, which document the selective mechanism underlying this example of a virus-antibody arms race, illustrate the functional significance of affinity maturation by mutation outside the complementarity determining region surface of the antibody molecule.
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40
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Zhou G, Sofiyev V, Kaur H, Snyder BA, Mankowski MK, Hogan PA, Ptak RG, Gochin M. Structure-activity relationship studies of indole-based compounds as small molecule HIV-1 fusion inhibitors targeting glycoprotein 41. J Med Chem 2014; 57:5270-81. [PMID: 24856833 PMCID: PMC4216203 DOI: 10.1021/jm500344y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
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We
previously described indole-containing compounds with the potential
to inhibit HIV-1 fusion by targeting the hydrophobic pocket of transmembrane
glycoprotein gp41. Here we report optimization and structure–activity
relationship studies on the basic scaffold, defining the role of shape,
contact surface area, and molecular properties. Thirty new compounds
were evaluated in binding, cell–cell fusion, and viral replication
assays. Below a 1 μM threshold, correlation between binding
and biological activity was diminished, indicating an amphipathic
requirement for activity in cells. The most active inhibitor 6j exhibited 0.6 μM binding affinity and 0.2 μM
EC50 against cell–cell fusion and live virus replication
and was active against T20 resistant strains. Twenty-two compounds
with the same connectivity displayed a consensus pose in docking calculations,
with rank order matching the biological activity. The work provides
insight into requirements for small molecule inhibition of HIV-1 fusion
and demonstrates a potent low molecular weight fusion inhibitor.
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Affiliation(s)
- Guangyan Zhou
- Department of Basic Sciences, Touro University-California , 1310 Club Drive, Mare Island, Vallejo, California 94592, United States
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41
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Particle conformation regulates antibody access to a conserved GII.4 norovirus blockade epitope. J Virol 2014; 88:8826-42. [PMID: 24872579 DOI: 10.1128/jvi.01192-14] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
UNLABELLED GII.4 noroviruses (NoVs) are the primary cause of epidemic viral acute gastroenteritis. One primary obstacle to successful NoV vaccination is the extensive degree of antigenic diversity among strains. The major capsid protein of GII.4 strains is evolving rapidly, resulting in the emergence of new strains with altered blockade epitopes. In addition to characterizing these evolving blockade epitopes, we have identified monoclonal antibodies (MAbs) that recognize a blockade epitope conserved across time-ordered GII.4 strains. Uniquely, the blockade potencies of MAbs that recognize the conserved GII.4 blockade epitope were temperature sensitive, suggesting that particle conformation may regulate functional access to conserved blockade non-surface-exposed epitopes. To map conformation-regulating motifs, we used bioinformatics tools to predict conserved motifs within the protruding domain of the capsid and designed mutant VLPs to test the impacts of substitutions in these motifs on antibody cross-GII.4 blockade. Charge substitutions at residues 310, 316, 484, and 493 impacted the blockade potential of cross-GII.4 blockade MAbs with minimal impact on the blockade of MAbs targeting other, separately evolving blockade epitopes. Specifically, residue 310 modulated antibody blockade temperature sensitivity in the tested strains. These data suggest access to the conserved GII.4 blockade antibody epitope is regulated by particle conformation, temperature, and amino acid residues positioned outside the antibody binding site. The regulating motif is under limited selective pressure by the host immune response and may provide a robust target for broadly reactive NoV therapeutics and protective vaccines. IMPORTANCE In this study, we explored the factors that govern norovirus (NoV) cross-strain antibody blockade. We found that access to the conserved GII.4 blockade epitope is regulated by temperature and distal residues outside the antibody binding site. These data are most consistent with a model of NoV particle conformation plasticity that regulates antibody binding to a distally conserved blockade epitope. Further, antibody "locking" of the particle into an epitope-accessible conformation prevents ligand binding, providing a potential target for broadly effective drugs. These observations open lines of inquiry into the mechanisms of human NoV entry and uncoating, fundamental biological questions that are currently unanswerable for these noncultivatable pathogens.
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42
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Abstract
Virus-cell fusion is the primary means by which the human immunodeficiency virus-1 (HIV) delivers its genetic material into the human T-cell host. Fusion is mediated in large part by the viral glycoprotein 41 (gp41) which advances through four distinct conformational states: (i) native, (ii) pre-hairpin intermediate, (iii) fusion active (fusogenic), and (iv) post-fusion. The pre-hairpin intermediate is a particularly attractive step for therapeutic intervention given that gp41 N-terminal heptad repeat (NHR) and C-terminal heptad repeat (CHR) domains are transiently exposed prior to the formation of a six-helix bundle required for fusion. Most peptide-based inhibitors, including the FDA-approved drug T20, target the intermediate and there are significant efforts to develop small molecule alternatives. Here, we review current approaches to studying interactions of inhibitors with gp41 with an emphasis on atomic-level computer modeling methods including molecular dynamics, free energy analysis, and docking. Atomistic modeling yields a unique level of structural and energetic detail, complementary to experimental approaches, which will be important for the design of improved next generation anti-HIV drugs.
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43
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Hwang KK, Trama AM, Kozink DM, Chen X, Wiehe K, Cooper AJ, Xia SM, Wang M, Marshall DJ, Whitesides J, Alam M, Tomaras GD, Allen SL, Rai KR, McKeating J, Catera R, Yan XJ, Chu CC, Kelsoe G, Liao HX, Chiorazzi N, Haynes BF. IGHV1-69 B cell chronic lymphocytic leukemia antibodies cross-react with HIV-1 and hepatitis C virus antigens as well as intestinal commensal bacteria. PLoS One 2014; 9:e90725. [PMID: 24614505 PMCID: PMC3948690 DOI: 10.1371/journal.pone.0090725] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 02/03/2014] [Indexed: 11/21/2022] Open
Abstract
B-cell chronic lymphocytic leukemia (B-CLL) patients expressing unmutated immunoglobulin heavy variable regions (IGHVs) use the IGHV1-69 B cell receptor (BCR) in 25% of cases. Since HIV-1 envelope gp41 antibodies also frequently use IGHV1-69 gene segments, we hypothesized that IGHV1-69 B-CLL precursors may contribute to the gp41 B cell response during HIV-1 infection. To test this hypothesis, we rescued 5 IGHV1-69 unmutated antibodies as heterohybridoma IgM paraproteins and as recombinant IgG1 antibodies from B-CLL patients, determined their antigenic specificities and analyzed BCR sequences. IGHV1-69 B-CLL antibodies were enriched for reactivity with HIV-1 envelope gp41, influenza, hepatitis C virus E2 protein and intestinal commensal bacteria. These IGHV1-69 B-CLL antibodies preferentially used IGHD3 and IGHJ6 gene segments and had long heavy chain complementary determining region 3s (HCDR3s) (≥21 aa). IGHV1-69 B-CLL BCRs exhibited a phenylalanine at position 54 (F54) of the HCDR2 as do rare HIV-1 gp41 and influenza hemagglutinin stem neutralizing antibodies, while IGHV1-69 gp41 antibodies induced by HIV-1 infection predominantly used leucine (L54) allelic variants. These results demonstrate that the B-CLL cell population is an expansion of members of the innate polyreactive B cell repertoire with reactivity to a number of infectious agent antigens including intestinal commensal bacteria. The B-CLL IGHV1-69 B cell usage of F54 allelic variants strongly suggests that IGHV1-69 B-CLL gp41 antibodies derive from a restricted B cell pool that also produces rare HIV-1 gp41 and influenza hemagglutinin stem antibodies.
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Affiliation(s)
- Kwan-Ki Hwang
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Ashley M. Trama
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Daniel M. Kozink
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Xi Chen
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Abby J. Cooper
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Shi-Mao Xia
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Minyue Wang
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Dawn J. Marshall
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - John Whitesides
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Munir Alam
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Georgia D. Tomaras
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Steven L. Allen
- The Karches Center for Chronic Lymphocytic Leukemia Research, The Feinstein Institute for Medical Research, Manhasset, New York, United States of America
| | - Kanti R. Rai
- The Karches Center for Chronic Lymphocytic Leukemia Research, The Feinstein Institute for Medical Research, Manhasset, New York, United States of America
| | - Jane McKeating
- School of Immunity and Infection, Institute of Biomedical Research, University of Birmingham, Birmingham, United Kingdom
| | - Rosa Catera
- The Karches Center for Chronic Lymphocytic Leukemia Research, The Feinstein Institute for Medical Research, Manhasset, New York, United States of America
| | - Xiao-Jie Yan
- The Karches Center for Chronic Lymphocytic Leukemia Research, The Feinstein Institute for Medical Research, Manhasset, New York, United States of America
| | - Charles C. Chu
- The Karches Center for Chronic Lymphocytic Leukemia Research, The Feinstein Institute for Medical Research, Manhasset, New York, United States of America
| | - Garnett Kelsoe
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Hua-Xin Liao
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Nicholas Chiorazzi
- The Karches Center for Chronic Lymphocytic Leukemia Research, The Feinstein Institute for Medical Research, Manhasset, New York, United States of America
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
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44
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A novel gene therapy strategy using secreted multifunctional anti-HIV proteins to confer protection to gene-modified and unmodified target cells. Gene Ther 2013; 21:175-87. [PMID: 24305417 DOI: 10.1038/gt.2013.70] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 08/26/2013] [Accepted: 09/24/2013] [Indexed: 11/08/2022]
Abstract
Current human immunodeficiency virus type I (HIV) gene therapy strategies focus on rendering HIV target cells non-permissive to viral replication. However, gene-modified cells fail to accumulate in patients and the virus continues to replicate in the unmodified target cell population. We have designed lentiviral vectors encoding secreted anti-HIV proteins to protect both gene-modified and unmodified cells from infection. Soluble CD4 (sCD4), a secreted single chain variable fragment (sscFv(17b)) and a secreted fusion inhibitor (sFI(T45)) were used to target receptor binding, co-receptor binding and membrane fusion, respectively. Additionally, we designed bi- and tri-functional fusion proteins to exploit the multistep nature of HIV entry. Of the seven antiviral proteins tested, sCD4, sCD4-scFv(17b), sCD4-FI(T45) and sCD4-scFv(17b)-FI(T45) efficiently inhibited HIV entry. The neutralization potency of the bi-functional fusion proteins sCD4-scFv(17b) and sCD4-FI(T45) was superior to that of sCD4 and the Food and Drug Administration-approved fusion inhibitor T-20. In co-culture experiments, sCD4, sCD4-scFv(17b) and sCD4-FI(T45) secreted from gene-modified producer cells conferred substantial protection to unmodified peripheral blood mononuclear cells. In conclusion, continuous delivery of secreted anti-HIV proteins via gene therapy may be a promising strategy to overcome the limitations of the current treatment.
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45
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Gustchina E, Li M, Ghirlando R, Schuck P, Louis JM, Pierson J, Rao P, Subramaniam S, Gustchina A, Clore GM, Wlodawer A. Complexes of neutralizing and non-neutralizing affinity matured Fabs with a mimetic of the internal trimeric coiled-coil of HIV-1 gp41. PLoS One 2013; 8:e78187. [PMID: 24244293 PMCID: PMC3820714 DOI: 10.1371/journal.pone.0078187] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 09/08/2013] [Indexed: 11/18/2022] Open
Abstract
A series of mini-antibodies (monovalent and bivalent Fabs) targeting the conserved internal trimeric coiled-coil of the N-heptad repeat (N-HR) of HIV-1 gp41 has been previously constructed and reported. Crystal structures of two closely related monovalent Fabs, one (Fab 8066) broadly neutralizing across a wide panel of HIV-1 subtype B and C viruses, and the other (Fab 8062) non-neutralizing, representing the extremes of this series, were previously solved as complexes with 5-Helix, a gp41 pre-hairpin intermediate mimetic. Binding of these Fabs to covalently stabilized chimeric trimers of N-peptides of HIV-1 gp41 (named (CCIZN36)3 or 3-H) has now been investigated using X-ray crystallography, cryo-electron microscopy, and a variety of biophysical methods. Crystal structures of the complexes between 3-H and Fab 8066 and Fab 8062 were determined at 2.8 and 3.0 Å resolution, respectively. Although the structures of the complexes with the neutralizing Fab 8066 and its non-neutralizing counterpart Fab 8062 were generally similar, small differences between them could be correlated with the biological properties of these antibodies. The conformations of the corresponding CDRs of each antibody in the complexes with 3-H and 5-Helix are very similar. The adaptation to a different target upon complex formation is predominantly achieved by changes in the structure of the trimer of N-HR helices, as well as by adjustment of the orientation of the Fab molecule relative to the N-HR in the complex, via rigid-body movement. The structural data presented here indicate that binding of three Fabs 8062 with high affinity requires more significant changes in the structure of the N-HR trimer compared to binding of Fab 8066. A comparative analysis of the structures of Fabs complexed to different gp41 intermediate mimetics allows further evaluation of biological relevance for generation of neutralizing antibodies, as well as provides novel structural insights into immunogen design.
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Affiliation(s)
- Elena Gustchina
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mi Li
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, Maryland, United States of America
- Basic Research Program, SAIC-Frederick, Frederick, Maryland, United States of America
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Peter Schuck
- Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jason Pierson
- FEI Company, Hillsboro, Oregon, United States of America
| | - Prashant Rao
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Sriram Subramaniam
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Alla Gustchina
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, Maryland, United States of America
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, Maryland, United States of America
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46
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Abstract
Neutralizing antibodies (NAbs) typically play a key role in controlling viral infections and contribute to the protective effect of many successful vaccines. In the case of HIV-1 infection, there is compelling data in experimental animal models that NAbs can prevent HIV-1 acquisition, although there is no similar data in humans and their role in controlling established infection in humans is also limited. It is clear HIV-specific NAbs drive the evolution of the HIV-1 envelope glycoprotein within an infected individual. The virus's ability to evade immune selection may be the main reason HIV-1 NAbs exert limited control during infection. The extraordinary antigenic diversity of HIV-1 also presents formidable challenges to defining NAbs that could provide broad protection against diverse circulating HIV-1 strains. Several new potent monoclonal antibodies (MAbs) have been identified, and are beginning to yield important clues into the epitopes common to diverse HIV-1 strains. In addition, antibodies can also act in concert with effector cells to kill HIV-infected cells; this could provide another mechanism for antibody-mediated control of HIV-1 replication. Understanding the impact of antibodies on HIV-1 transmission and pathogenesis is critical to helping move forward with rational HIV-1 vaccine design.
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Affiliation(s)
- Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
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47
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Demirkhanyan L, Marin M, Lu W, Melikyan GB. Sub-inhibitory concentrations of human α-defensin potentiate neutralizing antibodies against HIV-1 gp41 pre-hairpin intermediates in the presence of serum. PLoS Pathog 2013; 9:e1003431. [PMID: 23785290 PMCID: PMC3681749 DOI: 10.1371/journal.ppat.1003431] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 05/02/2013] [Indexed: 12/13/2022] Open
Abstract
Human defensins are at the forefront of the host responses to HIV and other pathogens in mucosal tissues. However, their ability to inactivate HIV in the bloodstream has been questioned due to the antagonistic effect of serum. In this study, we have examined the effect of sub-inhibitory concentrations of human α-defensin HNP-1 on the kinetics of early steps of fusion between HIV-1 and target cells in the presence of serum. Direct measurements of HIV-cell fusion using an enzymatic assay revealed that, in spite of the modest effect on the extent of fusion, HNP-1 prolonged the exposure of functionally important transitional epitopes of HIV-1 gp41 on the cell surface. The increased lifetime of gp41 intermediates in the presence of defensin was caused by a delay in the post-coreceptor binding steps of HIV-1 entry that correlated with the marked enhancement of the virus' sensitivity to neutralizing anti-gp41 antibodies. By contrast, the activity of antibodies to gp120 was not affected. HNP-1 appeared to specifically potentiate antibodies and peptides targeting the first heptad repeat domain of gp41, while its effect on inhibitors and antibodies to other gp41 domains was less prominent. Sub-inhibitory concentrations of HNP-1 also promoted inhibition of HIV-1 entry into peripheral blood mononuclear cells by antibodies and, more importantly, by HIV-1 immune serum. Our findings demonstrate that: (i) sub-inhibitory doses of HNP-1 potently enhance the activity of a number of anti-gp41 antibodies and peptide inhibitors, apparently by prolonging the lifetime of gp41 intermediates; and (ii) the efficiency of HIV-1 fusion inhibitors and neutralizing antibodies is kinetically restricted. This study thus reveals an important role of α-defensin in enhancing adaptive immune responses to HIV-1 infection and suggests future strategies to augment these responses. Human neutrophil peptide 1 (HNP-1) is a small cationic peptide that can directly block HIV-1 entry in the absence of serum. However, since serum attenuates the anti-HIV activity of this peptide, HNP-1 is unlikely to inhibit infection in the bloodstream. Here, we demonstrate that sub-inhibitory doses of HNP-1 in the presence of serum can strongly enhance the activity of neutralizing antibodies and inhibitors targeting transiently exposed intermediate conformations of HIV-1 gp41. HNP-1 appears to exert this effect by delaying post-coreceptor binding steps of fusion and thereby prolonging the exposure of gp41 intermediates. These results imply that the HIV-1 fusion kinetics is an important determinant of sensitivity to neutralizing antibodies and peptides against transiently exposed functional domains of gp41. The surprising synergy between sub-inhibitory concentrations of HNP-1 and anti-gp41 antibodies suggests new strategies to sensitize the virus to circulating antibodies by developing compounds that prolong the exposure of conserved gp41 epitopes on the cell surface.
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Affiliation(s)
- Lusine Demirkhanyan
- Division of Pediatric Infectious Diseases, Emory University Children's Center, Atlanta, Georgia, United States of America
| | - Mariana Marin
- Division of Pediatric Infectious Diseases, Emory University Children's Center, Atlanta, Georgia, United States of America
| | - Wuyuan Lu
- Institute of Human Virology and Department of Biochemistry, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Gregory B. Melikyan
- Division of Pediatric Infectious Diseases, Emory University Children's Center, Atlanta, Georgia, United States of America
- Children's Healthcare of Atlanta, Atlanta, Georgia, United States of America
- * E-mail:
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48
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Wang G, Wang X, Xu Q, Cheng Z. Polyclonal Antibody Against Conserved Peptide in Transmembrane Protein of Avian Leukosis Virus Subgroup J. Monoclon Antib Immunodiagn Immunother 2013; 32:211-5. [DOI: 10.1089/mab.2012.0101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Guihua Wang
- Molecular Pathology Laboratory, Department of Fundamental Veterinary, College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai'an, China
| | - Xiaowei Wang
- Molecular Pathology Laboratory, Department of Fundamental Veterinary, College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Qingqing Xu
- Molecular Pathology Laboratory, Department of Fundamental Veterinary, College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Ziqiang Cheng
- Molecular Pathology Laboratory, Department of Fundamental Veterinary, College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai'an, China
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49
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HIV-1 envelope glycoprotein structure. Curr Opin Struct Biol 2013; 23:268-76. [PMID: 23602427 DOI: 10.1016/j.sbi.2013.03.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/26/2013] [Accepted: 03/26/2013] [Indexed: 11/21/2022]
Abstract
The trimeric envelope glycoprotein of HIV-1, composed of gp120 and gp41 subunits, remains a major target for vaccine development. The structures of the core regions of monomeric gp120 and gp41 have been determined previously by X-ray crystallography. New insights into the structure of trimeric HIV-1 envelope glycoproteins are now coming from cryo-electron tomographic studies of the gp120/gp41 trimer as displayed on intact viruses and from cryo-electron microscopic studies of purified, soluble versions of the ectodomain of the trimer. Here, we review recent developments in these fields as they relate to our understanding of the structure and function of HIV-1 envelope glycoproteins.
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50
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Kwong PD, Mascola JR, Nabel GJ. Rational design of vaccines to elicit broadly neutralizing antibodies to HIV-1. Cold Spring Harb Perspect Med 2013; 1:a007278. [PMID: 22229123 DOI: 10.1101/cshperspect.a007278] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The development of a highly effective AIDS vaccine will likely depend on success in designing immunogens that elicit broadly neutralizing antibodies to naturally circulating strains of HIV-1. Although the antibodies induced after natural infection with HIV-1 are often directed to strain-specific or nonneutralizing determinants, it is now evident that 10%-25% of HIV-infected individuals generate neutralizing antibody responses of considerable breadth. In the past, only four broadly neutralizing monoclonal antibodies had been defined, but more than a dozen monoclonal antibodies of substantial breadth have more recently been isolated. An understanding of their recognition sites, the structural basis of their interaction with the HIV Env, and their development pathways provides new opportunities to design vaccine candidates that will elicit broadly protective antibodies against this virus.
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Affiliation(s)
- Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892
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