@article{pmid33242394,

title = {Cross-Neutralization of a SARS-CoV-2 Antibody to a Functionally Conserved Site Is Mediated by Avidity},

author = {Hejun Liu and Nicholas C Wu and Meng Yuan and Sandhya Bangaru and Jonathan L Torres and Tom G Caniels and Jelle van Schooten and Xueyong Zhu and Chang-Chun D Lee and Philip J M Brouwer and Marit J van Gils and Rogier W Sanders and Andrew B Ward and Ian A Wilson},

doi = {10.1016/j.immuni.2020.10.023},

issn = {1097-4180},

year  = {2020},

date = {2020-01-01},

journal = {Immunity},

volume = {53},

number = {6},

pages = {1272--1280.e5},

abstract = {Most antibodies isolated from individuals with coronavirus disease 2019 (COVID-19) are specific to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, COVA1-16 is a relatively rare antibody that also cross-neutralizes SARS-CoV. Here, we determined a crystal structure of the COVA1-16 antibody fragment (Fab) with the SARS-CoV-2 receptor-binding domain (RBD) and negative-stain electron microscopy reconstructions with the spike glycoprotein trimer to elucidate the structural basis of its cross-reactivity. COVA1-16 binds a highly conserved epitope on the SARS-CoV-2 RBD, mainly through a long complementarity-determining region (CDR) H3, and competes with the angiotensin-converting enzyme 2 (ACE2) receptor because of steric hindrance rather than epitope overlap. COVA1-16 binds to a flexible up conformation of the RBD on the spike and relies on antibody avidity for neutralization. These findings, along with the structural and functional rationale for epitope conservation, provide insights for development of more universal SARS-like coronavirus vaccines and therapies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid33275640,

title = {A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody},

author = {Nicholas C Wu and Meng Yuan and Sandhya Bangaru and Deli Huang and Xueyong Zhu and Chang-Chun D Lee and Hannah L Turner and Linghang Peng and Linlin Yang and Dennis R Burton and David Nemazee and Andrew B Ward and Ian A Wilson},

doi = {10.1371/journal.ppat.1009089},

issn = {1553-7374},

year  = {2020},

date = {2020-01-01},

journal = {PLoS Pathog},

volume = {16},

number = {12},

pages = {e1009089},

abstract = {Epitopes that are conserved among SARS-like coronaviruses are attractive targets for design of cross-reactive vaccines and therapeutics. CR3022 is a SARS-CoV neutralizing antibody to a highly conserved epitope on the receptor binding domain (RBD) on the spike protein that is able to cross-react with SARS-CoV-2, but with lower affinity. Using x-ray crystallography, mutagenesis, and binding experiments, we illustrate that of four amino acid differences in the CR3022 epitope between SARS-CoV-2 and SARS-CoV, a single mutation P384A fully determines the affinity difference. CR3022 does not neutralize SARS-CoV-2, but the increased affinity to SARS-CoV-2 P384A mutant now enables neutralization with a similar potency to SARS-CoV. We further investigated CR3022 interaction with the SARS-CoV spike protein by negative-stain EM and cryo-EM. Three CR3022 Fabs bind per trimer with the RBD observed in different up-conformations due to considerable flexibility of the RBD. In one of these conformations, quaternary interactions are made by CR3022 to the N-terminal domain (NTD) of an adjacent subunit. Overall, this study provides insights into antigenic variation and potential cross-neutralizing epitopes on SARS-like viruses.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid33058755,

title = {A Therapeutic Non-self-reactive SARS-CoV-2 Antibody Protects from Lung Pathology in a COVID-19 Hamster Model},

author = {Jakob Kreye and S Momsen Reincke and Hans-Christian Kornau and Elisa Sánchez-Sendin and Victor Max Corman and Hejun Liu and Meng Yuan and Nicholas C Wu and Xueyong Zhu and Chang-Chun D Lee and Jakob Trimpert and Markus Höltje and Kristina Dietert and Laura Stöffler and Niels von Wardenburg and Scott van Hoof and Marie A Homeyer and Julius Hoffmann and Azza Abdelgawad and Achim D Gruber and Luca D Bertzbach and Daria Vladimirova and Lucie Y Li and Paula Charlotte Barthel and Karl Skriner and Andreas C Hocke and Stefan Hippenstiel and Martin Witzenrath and Norbert Suttorp and Florian Kurth and Christiana Franke and Matthias Endres and Dietmar Schmitz and Lara Maria Jeworowski and Anja Richter and Marie Luisa Schmidt and Tatjana Schwarz and Marcel Alexander Müller and Christian Drosten and Daniel Wendisch and Leif E Sander and Nikolaus Osterrieder and Ian A Wilson and Harald Prüss},

doi = {10.1016/j.cell.2020.09.049},

issn = {1097-4172},

year  = {2020},

date = {2020-01-01},

journal = {Cell},

volume = {183},

number = {4},

pages = {1058--1069.e19},

abstract = {The emergence of SARS-CoV-2 led to pandemic spread of coronavirus disease 2019 (COVID-19), manifesting with respiratory symptoms and multi-organ dysfunction. Detailed characterization of virus-neutralizing antibodies and target epitopes is needed to understand COVID-19 pathophysiology and guide immunization strategies. Among 598 human monoclonal antibodies (mAbs) from 10 COVID-19 patients, we identified 40 strongly neutralizing mAbs. The most potent mAb, CV07-209, neutralized authentic SARS-CoV-2 with an IC value of 3.1 ng/mL. Crystal structures of two mAbs in complex with the SARS-CoV-2 receptor-binding domain at 2.55 and 2.70 Å revealed a direct block of ACE2 attachment. Interestingly, some of the near-germline SARS-CoV-2-neutralizing mAbs reacted with mammalian self-antigens. Prophylactic and therapeutic application of CV07-209 protected hamsters from SARS-CoV-2 infection, weight loss, and lung pathology. Our results show that non-self-reactive virus-neutralizing mAbs elicited during SARS-CoV-2 infection are a promising therapeutic strategy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32790871,

title = {A high-affinity antibody against the CSP N-terminal domain lacks Plasmodium falciparum inhibitory activity},

author = {Elaine Thai and Giulia Costa and Anna Weyrich and Rajagopal Murugan and David Oyen and Yevel Flores-Garcia and Katherine Prieto and Alexandre Bosch and Angelo Valleriani and Nicholas C Wu and Tossapol Pholcharee and Stephen W Scally and Ian A Wilson and Hedda Wardemann and Jean-Philippe Julien and Elena A Levashina},

doi = {10.1084/jem.20200061},

issn = {1540-9538},

year  = {2020},

date = {2020-01-01},

journal = {J Exp Med},

volume = {217},

number = {11},

abstract = {Malaria is a global health concern, and research efforts are ongoing to develop a superior vaccine to RTS,S/AS01. To guide immunogen design, we seek a comprehensive understanding of the protective humoral response against Plasmodium falciparum (Pf) circumsporozoite protein (PfCSP). In contrast to the well-studied responses to the repeat region and the C-terminus, the antibody response against the N-terminal domain of PfCSP (N-CSP) remains obscure. Here, we characterized the molecular recognition and functional efficacy of the N-CSP-specific monoclonal antibody 5D5. The crystal structure at 1.85-Å resolution revealed that 5D5 binds an α-helical epitope in N-CSP with high affinity through extensive shape and charge complementarity and the unusual utilization of an antibody N-linked glycan. Nevertheless, functional studies indicated low 5D5 binding to live Pf sporozoites and lack of sporozoite inhibition in vitro and in vivo. Overall, our data do not support the inclusion of the 5D5 N-CSP epitope into the next generation of CSP-based vaccines.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid33027617,

title = {An Alternative Binding Mode of IGHV3-53 Antibodies to the SARS-CoV-2 Receptor Binding Domain},

author = {Nicholas C Wu and Meng Yuan and Hejun Liu and Chang-Chun D Lee and Xueyong Zhu and Sandhya Bangaru and Jonathan L Torres and Tom G Caniels and Philip J M Brouwer and Marit J van Gils and Rogier W Sanders and Andrew B Ward and Ian A Wilson},

doi = {10.1016/j.celrep.2020.108274},

issn = {2211-1247},

year  = {2020},

date = {2020-01-01},

journal = {Cell Rep},

volume = {33},

number = {3},

pages = {108274},

abstract = {IGHV3-53-encoded neutralizing antibodies are commonly elicited during SARS-CoV-2 infection and target the receptor-binding domain (RBD) of the spike (S) protein. Such IGHV3-53 antibodies generally have a short CDR H3 because of structural constraints in binding the RBD (mode A). However, a small subset of IGHV3-53 antibodies to the RBD contain a longer CDR H3. Crystal structures of two IGHV3-53 neutralizing antibodies here demonstrate that a longer CDR H3 can be accommodated in a different binding mode (mode B). These two classes of IGHV3-53 antibodies both target the ACE2 receptor binding site, but with very different angles of approach and molecular interactions. Overall, these findings emphasize the versatility of IGHV3-53 in this common antibody response to SARS-CoV-2, where conserved IGHV3-53 germline-encoded features can be combined with very different CDR H3 lengths and light chains for SARS-CoV-2 RBD recognition and virus neutralization.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32971825,

title = {Structural Biology of Influenza Hemagglutinin: An Amaranthine Adventure},

author = {Nicholas C Wu and Ian A Wilson},

doi = {10.3390/v12091053},

issn = {1999-4915},

year  = {2020},

date = {2020-01-01},

journal = {Viruses},

volume = {12},

number = {9},

abstract = {Hemagglutinin (HA) glycoprotein is an important focus of influenza research due to its role in antigenic drift and shift, as well as its receptor binding and membrane fusion functions, which are indispensable for viral entry. Over the past four decades, X-ray crystallography has greatly facilitated our understanding of HA receptor binding, membrane fusion, and antigenicity. The recent advances in cryo-EM have further deepened our comprehension of HA biology. Since influenza HA constantly evolves in natural circulating strains, there are always new questions to be answered. The incessant accumulation of knowledge on the structural biology of HA over several decades has also facilitated the design and development of novel therapeutics and vaccines. This review describes the current status of the field of HA structural biology, how we got here, and what the next steps might be.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32619441,

title = {Convergent Evolution in Breadth of Two V6-1-Encoded Influenza Antibody Clonotypes from a Single Donor},

author = {Nicholas C Wu and Sarah F Andrews and Julie E Raab and Sarah O'Connell and Chaim A Schramm and Xintao Ding and Michael J Chambers and Kwanyee Leung and Lingshu Wang and Yi Zhang and John R Mascola and Daniel C Douek and Julie E Ledgerwood and Adrian B McDermott and Ian A Wilson},

doi = {10.1016/j.chom.2020.06.003},

issn = {1934-6069},

year  = {2020},

date = {2020-01-01},

journal = {Cell Host Microbe},

volume = {28},

number = {3},

pages = {434--444.e4},

abstract = {Understanding how broadly neutralizing antibodies (bnAbs) to influenza hemagglutinin (HA) naturally develop in humans is critical to the design of universal influenza vaccines. Several classes of bnAbs directed to the conserved HA stem were found in multiple individuals, including one encoded by heavy-chain variable domain V6-1. We describe two genetically similar V6-1 bnAb clonotypes from the same individual that exhibit different developmental paths toward broad neutralization activity. One clonotype evolved from a germline precursor recognizing influenza group 1 subtypes to gain breadth to group 2 subtypes. The other clonotype recognized group 2 subtypes and developed binding to group 1 subtypes through somatic hypermutation. Crystal structures reveal that the specificity differences are primarily mediated by complementarity-determining region H3 (CDR H3). Thus, while V6-1 provides a framework for development of HA stem-directed bnAbs, sequence differences in CDR H3 junctional regions during VDJ recombination can alter reactivity and evolutionary pathways toward increased breadth.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32866207,

title = {Mapping the immunogenic landscape of near-native HIV-1 envelope trimers in non-human primates},

author = {Christopher A Cottrell and Jelle van Schooten and Charles A Bowman and Meng Yuan and David Oyen and Mia Shin and Robert Morpurgo and Patricia van der Woude and Mariëlle van Breemen and Jonathan L Torres and Raj Patel and Justin Gross and Leigh M Sewall and Jeffrey Copps and Gabriel Ozorowski and Bartek Nogal and Devin Sok and Eva G Rakasz and Celia Labranche and Vladimir Vigdorovich and Scott Christley and Diane G Carnathan and D Noah Sather and David Montefiori and Guido Silvestri and Dennis R Burton and John P Moore and Ian A Wilson and Rogier W Sanders and Andrew B Ward and Marit J van Gils},

doi = {10.1371/journal.ppat.1008753},

issn = {1553-7374},

year  = {2020},

date = {2020-01-01},

journal = {PLoS Pathog},

volume = {16},

number = {8},

pages = {e1008753},

abstract = {The induction of broad and potent immunity by vaccines is the key focus of research efforts aimed at protecting against HIV-1 infection. Soluble native-like HIV-1 envelope glycoproteins have shown promise as vaccine candidates as they can induce potent autologous neutralizing responses in rabbits and non-human primates. In this study, monoclonal antibodies were isolated and characterized from rhesus macaques immunized with the BG505 SOSIP.664 trimer to better understand vaccine-induced antibody responses. Our studies reveal a diverse landscape of antibodies recognizing immunodominant strain-specific epitopes and non-neutralizing neo-epitopes. Additionally, we isolated a subset of mAbs against an epitope cluster at the gp120-gp41 interface that recognize the highly conserved fusion peptide and the glycan at position 88 and have characteristics akin to several human-derived broadly neutralizing antibodies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32661058,

title = {Structural basis of a shared antibody response to SARS-CoV-2},

author = {Meng Yuan and Hejun Liu and Nicholas C Wu and Chang-Chun D Lee and Xueyong Zhu and Fangzhu Zhao and Deli Huang and Wenli Yu and Yuanzi Hua and Henry Tien and Thomas F Rogers and Elise Landais and Devin Sok and Joseph G Jardine and Dennis R Burton and Ian A Wilson},

doi = {10.1126/science.abd2321},

issn = {1095-9203},

year  = {2020},

date = {2020-01-01},

journal = {Science},

volume = {369},

number = {6507},

pages = {1119--1123},

abstract = {Molecular understanding of neutralizing antibody responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could accelerate vaccine design and drug discovery. We analyzed 294 anti-SARS-CoV-2 antibodies and found that immunoglobulin G heavy-chain variable region 3-53 (IGHV3-53) is the most frequently used IGHV gene for targeting the receptor-binding domain (RBD) of the spike protein. Co-crystal structures of two IGHV3-53-neutralizing antibodies with RBD, with or without Fab CR3022, at 2.33- to 3.20-angstrom resolution revealed that the germline-encoded residues dominate recognition of the angiotensin I converting enzyme 2 (ACE2)-binding site. This binding mode limits the IGHV3-53 antibodies to short complementarity-determining region H3 loops but accommodates light-chain diversity. These IGHV3-53 antibodies show minimal affinity maturation and high potency, which is promising for vaccine design. Knowledge of these structural motifs and binding mode should facilitate the design of antigens that elicit this type of neutralizing response.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32540903,

title = {Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model},

author = {Thomas F Rogers and Fangzhu Zhao and Deli Huang and Nathan Beutler and Alison Burns and Wan-Ting He and Oliver Limbo and Chloe Smith and Ge Song and Jordan Woehl and Linlin Yang and Robert K Abbott and Sean Callaghan and Elijah Garcia and Jonathan Hurtado and Mara Parren and Linghang Peng and Sydney Ramirez and James Ricketts and Michael J Ricciardi and Stephen A Rawlings and Nicholas C Wu and Meng Yuan and Davey M Smith and David Nemazee and John R Teijaro and James E Voss and Ian A Wilson and Raiees Andrabi and Bryan Briney and Elise Landais and Devin Sok and Joseph G Jardine and Dennis R Burton},

doi = {10.1126/science.abc7520},

issn = {1095-9203},

year  = {2020},

date = {2020-01-01},

journal = {Science},

volume = {369},

number = {6506},

pages = {956--963},

abstract = {Countermeasures to prevent and treat coronavirus disease 2019 (COVID-19) are a global health priority. We enrolled a cohort of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-recovered participants, developed neutralization assays to investigate antibody responses, adapted our high-throughput antibody generation pipeline to rapidly screen more than 1800 antibodies, and established an animal model to test protection. We isolated potent neutralizing antibodies (nAbs) to two epitopes on the receptor binding domain (RBD) and to distinct non-RBD epitopes on the spike (S) protein. As indicated by maintained weight and low lung viral titers in treated animals, the passive transfer of a nAb provides protection against disease in high-dose SARS-CoV-2 challenge in Syrian hamsters. The study suggests a role for nAbs in prophylaxis, and potentially therapy, of COVID-19. The nAbs also define protective epitopes to guide vaccine design.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32631553,

title = {Structural basis for the stabilization of amyloidogenic immunoglobulin light chains by hydantoins},

author = {Nicholas L Yan and Diogo Santos-Martins and Enrico Rennella and Brittany B Sanchez and Jason S Chen and Lewis E Kay and Ian A Wilson and Gareth J Morgan and Stefano Forli and Jeffery W Kelly},

doi = {10.1016/j.bmcl.2020.127356},

issn = {1464-3405},

year  = {2020},

date = {2020-01-01},

journal = {Bioorg Med Chem Lett},

volume = {30},

number = {16},

pages = {127356},

abstract = {Misfolding and aggregation of immunoglobulin light chains (LCs) leads to the degeneration of post-mitotic tissue in the disease immunoglobulin LC amyloidosis (AL). We previously reported the discovery of small molecule kinetic stabilizers of the native dimeric structure of full-length LCs, which slow or stop the LC aggregation cascade at the outset. A predominant structural category of kinetic stabilizers emerging from the high-throughput screen are coumarins substituted at the 7-position, which bind at the interface between the two variable domains of the light chain dimer. Here, we report the binding mode of another, more polar, LC kinetic stabilizer chemotype, 3,5-substituted hydantoins. Computational docking, solution nuclear magnetic resonance experiments, and x-ray crystallography show that the aromatic substructure emerging from the hydantoin 3-position occupies the same LC binding site as the coumarin ring. Notably, the hydantoin ring extends beyond the binding site mapped out by the coumarin hits. The hydantoin ring makes hydrogen bonds with both LC monomers simultaneously. The alkyl substructure at the hydantoin 5-position partially occupies a novel binding pocket proximal to the pocket occupied by the coumarin substructure. Overall, the hydantoin structural data suggest that a larger area of the LC variable-domain-variable-domain dimer interface is amenable to small molecule binding than previously demonstrated, which should facilitate development of more potent full-length LC kinetic stabilizers.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32690700,

title = {An influenza A hemagglutinin small-molecule fusion inhibitor identified by a new high-throughput fluorescence polarization screen},

author = {Yao Yao and Rameshwar U Kadam and Chang-Chun David Lee and Jordan L Woehl and Nicholas C Wu and Xueyong Zhu and Seiya Kitamura and Ian A Wilson and Dennis W Wolan},

doi = {10.1073/pnas.2006893117},

issn = {1091-6490},

year  = {2020},

date = {2020-01-01},

journal = {Proc Natl Acad Sci U S A},

volume = {117},

number = {31},

pages = {18431--18438},

abstract = {Influenza hemagglutinin (HA) glycoprotein is the primary surface antigen targeted by the host immune response and a focus for development of novel vaccines, broadly neutralizing antibodies (bnAbs), and therapeutics. HA enables viral entry into host cells via receptor binding and membrane fusion and is a validated target for drug discovery. However, to date, only a very few bona fide small molecules have been reported against the HA. To identity new antiviral lead candidates against the highly conserved fusion machinery in the HA stem, we synthesized a fluorescence-polarization probe based on a recently described neutralizing cyclic peptide P7 derived from the complementarity-determining region loops of human bnAbs FI6v3 and CR9114 against the HA stem. We then designed a robust binding assay compatible with high-throughput screening to identify molecules with low micromolar to nanomolar affinity to influenza A group 1 HAs. Our simple, low-cost, and efficient in vitro assay was used to screen H1/Puerto Rico/8/1934 (H1/PR8) HA trimer against ∼72,000 compounds. The crystal structure of H1/PR8 HA in complex with our best hit compound F0045(S) confirmed that it binds to pockets in the HA stem similar to bnAbs FI6v3 and CR9114, cyclic peptide P7, and small-molecule inhibitor JNJ4796. F0045 is enantioselective against a panel of group 1 HAs and F0045(S) exhibits in vitro neutralization activity against multiple H1N1 and H5N1 strains. Our assay, compound characterization, and small-molecule candidate should further stimulate the discovery and development of new compounds with unique chemical scaffolds and enhanced influenza antiviral capabilities.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31871236,

title = {Influenza Hemagglutinin Structures and Antibody Recognition},

author = {Nicholas C Wu and Ian A Wilson},

doi = {10.1101/cshperspect.a038778},

issn = {2157-1422},

year  = {2020},

date = {2020-01-01},

journal = {Cold Spring Harb Perspect Med},

volume = {10},

number = {8},

abstract = {Hemagglutinin (HA) is most abundant glycoprotein on the influenza virus surface. Influenza HA promotes viral entry by engaging the receptor and mediating virus-host membrane fusion. At the same time, HA is the major antigen of the influenza virus. HA antigenic shift can result in pandemics, whereas antigenic drift allows human circulating strains to escape herd immunity. Most antibody responses against HA are strain-specific. However, antibodies that have neutralizing activities against multiple strains or even subtypes have now been discovered and characterized. These broadly neutralizing antibodies (bnAbs) target conserved regions on HA, such as the receptor-binding site and the stem domain. Structural studies of such bnAbs have provided important insight into universal influenza vaccine and therapeutic design. This review discusses the HA functions as well as HA-antibody interactions from a structural perspective.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32387642,

title = {Innovations in structure-based antigen design and immune monitoring for next generation vaccines},

author = {Andrew B Ward and Ian A Wilson},

doi = {10.1016/j.coi.2020.03.013},

issn = {1879-0372},

year  = {2020},

date = {2020-01-01},

journal = {Curr Opin Immunol},

volume = {65},

pages = {50--56},

abstract = {The recent explosion of atomic-level structures of glycoproteins that comprise the surface antigens of human enveloped viruses, such as RSV, influenza, and HIV, provide tremendous opportunities for rational, structure-based vaccine design. Several concepts in structure-based vaccine design have been put into practice and are are well along preclinical and clinical implementation. Testing of these designed immunogens will provide key insights into the ability to induce the desired immune responses, namely neutralizing antibodies. Many of these immunogens in human clinical trials represent only the first wave of designs and will likely require continued tweaking and elaboration to achieve the ultimate goal of enhanced breadth and potency. Considerable effort is now being invested in germline targeting, epitope focusing, and improved immune presentation such as multivalent nanoparticle incorporation. This review highlights some of the recent advances in these areas as we prepare for the next generation of immunogens for subsequent rounds of iterative vaccine development.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32554590,

title = {Different genetic barriers for resistance to HA stem antibodies in influenza H3 and H1 viruses},

author = {Nicholas C Wu and Andrew J Thompson and Juhye M Lee and Wen Su and Britni M Arlian and Jia Xie and Richard A Lerner and Hui-Ling Yen and Jesse D Bloom and Ian A Wilson},

doi = {10.1126/science.aaz5143},

issn = {1095-9203},

year  = {2020},

date = {2020-01-01},

journal = {Science},

volume = {368},

number = {6497},

pages = {1335--1340},

abstract = {The discovery and characterization of broadly neutralizing human antibodies (bnAbs) to the highly conserved stem region of influenza hemagglutinin (HA) have contributed to considerations of a universal influenza vaccine. However, the potential for resistance to stem bnAbs also needs to be more thoroughly evaluated. Using deep mutational scanning, with a focus on epitope residues, we found that the genetic barrier to resistance to stem bnAbs is low for the H3 subtype but substantially higher for the H1 subtype owing to structural differences in the HA stem. Several strong resistance mutations in H3 can be observed in naturally circulating strains and do not reduce in vitro viral fitness and in vivo pathogenicity. This study highlights a potential challenge for development of a truly universal influenza vaccine.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32467165,

title = {Inhibitory antibodies identify unique sites of therapeutic vulnerability in rhinovirus and other enteroviruses},

author = {Bing Meng and Keke Lan and Jia Xie and Richard A Lerner and Ian A Wilson and Bei Yang},

doi = {10.1073/pnas.1918844117},

issn = {1091-6490},

year  = {2020},

date = {2020-01-01},

journal = {Proc Natl Acad Sci U S A},

volume = {117},

number = {24},

pages = {13499--13508},

abstract = {The existence of multiple serotypes renders vaccine development challenging for most viruses in the  genus. An alternative and potentially more viable strategy for control of these viruses is to develop broad-spectrum antivirals by targeting highly conserved proteins that are indispensable for the virus life cycle, such as the 3C protease. Previously, two single-chain antibody fragments, YDF and GGVV, were reported to effectively inhibit human rhinovirus 14 proliferation. Here, we found that both single-chain antibody fragments target sites on the 3C protease that are distinct from its known drug site (peptidase active site) and possess different mechanisms of inhibition. YDF does not block the active site but instead noncompetitively inhibits 3C peptidase activity through an allosteric effect that is rarely seen for antibody protease inhibitors. Meanwhile, GGVV antagonizes the less-explored regulatory function of 3C in genome replication. The interaction between 3C and the viral genome 5' noncoding region has been reported to be important for enterovirus genome replication. Here, the interface between human rhinovirus 14 3C and its 5' noncoding region was probed by hydrogen-deuterium exchange coupled mass spectrometry and found to partially overlap with the interface between GGVV and 3C. Consistently, prebinding of GGVV completely abolishes interaction between human rhinovirus 14 3C and its 5' noncoding region. The epitopes of YDF and GGVV, therefore, represent two additional sites of therapeutic vulnerability in rhinovirus. Importantly, the GGVV epitope appears to be conserved across many enteroviruses, suggesting that it is a promising target for pan-enterovirus inhibitor screening and design.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32426212,

title = {Cross-reactive Antibody Response between SARS-CoV-2 and SARS-CoV Infections},

author = {Huibin Lv and Nicholas C Wu and Owen Tak-Yin Tsang and Meng Yuan and Ranawaka A P M Perera and Wai Shing Leung and Ray T Y So and Jacky Man Chun Chan and Garrick K Yip and Thomas Shiu Hong Chik and Yiquan Wang and Chris Yau Chung Choi and Yihan Lin and Wilson W Ng and Jincun Zhao and Leo L M Poon and J S Malik Peiris and Ian A Wilson and Chris K P Mok},

doi = {10.1016/j.celrep.2020.107725},

issn = {2211-1247},

year  = {2020},

date = {2020-01-01},

journal = {Cell Rep},

volume = {31},

number = {9},

pages = {107725},

abstract = {The World Health Organization has declared the ongoing outbreak of COVID-19, which is caused by a novel coronavirus SARS-CoV-2, a pandemic. There is currently a lack of knowledge about the antibody response elicited from SARS-CoV-2 infection. One major immunological question concerns antigenic differences between SARS-CoV-2 and SARS-CoV. We address this question by analyzing plasma from patients infected by SARS-CoV-2 or SARS-CoV and from infected or immunized mice. Our results show that, although cross-reactivity in antibody binding to the spike protein is common, cross-neutralization of the live viruses may be rare, indicating the presence of a non-neutralizing antibody response to conserved epitopes in the spike. Whether such low or non-neutralizing antibody response leads to antibody-dependent disease enhancement needs to be addressed in the future. Overall, this study not only addresses a fundamental question regarding antigenicity differences between SARS-CoV-2 and SARS-CoV but also has implications for immunogen design and vaccine development.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32461612,

title = {Vulnerabilities in coronavirus glycan shields despite extensive glycosylation},

author = {Yasunori Watanabe and Zachary T Berndsen and Jayna Raghwani and Gemma E Seabright and Joel D Allen and Oliver G Pybus and Jason S McLellan and Ian A Wilson and Thomas A Bowden and Andrew B Ward and Max Crispin},

doi = {10.1038/s41467-020-16567-0},

issn = {2041-1723},

year  = {2020},

date = {2020-01-01},

journal = {Nat Commun},

volume = {11},

number = {1},

pages = {2688},

abstract = {Severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses (CoVs) are zoonotic pathogens with high fatality rates and pandemic potential. Vaccine development focuses on the principal target of the neutralizing humoral immune response, the spike (S) glycoprotein. Coronavirus S proteins are extensively glycosylated, encoding around 66-87 N-linked glycosylation sites per trimeric spike. Here, we reveal a specific area of high glycan density on MERS S that results in the formation of oligomannose-type glycan clusters, which were absent on SARS and HKU1 CoVs. We provide a comparison of the global glycan density of coronavirus spikes with other viral proteins including HIV-1 envelope, Lassa virus glycoprotein complex, and influenza hemagglutinin, where glycosylation plays a known role in shielding immunogenic epitopes. Overall, our data reveal how organisation of glycosylation across class I viral fusion proteins influence not only individual glycan compositions but also the immunological pressure across the protein surface.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32245784,

title = {A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV},

author = {Meng Yuan and Nicholas C Wu and Xueyong Zhu and Chang-Chun D Lee and Ray T Y So and Huibin Lv and Chris K P Mok and Ian A Wilson},

doi = {10.1126/science.abb7269},

issn = {1095-9203},

year  = {2020},

date = {2020-01-01},

journal = {Science},

volume = {368},

number = {6491},

pages = {630--633},

abstract = {The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) has now become a pandemic, but there is currently very little understanding of the antigenicity of the virus. We therefore determined the crystal structure of CR3022, a neutralizing antibody previously isolated from a convalescent SARS patient, in complex with the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) protein at 3.1-angstrom resolution. CR3022 targets a highly conserved epitope, distal from the receptor binding site, that enables cross-reactive binding between SARS-CoV-2 and SARS-CoV. Structural modeling further demonstrates that the binding epitope can only be accessed by CR3022 when at least two RBDs on the trimeric S protein are in the "up" conformation and slightly rotated. These results provide molecular insights into antibody recognition of SARS-CoV-2.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32348769,

title = {HIV-1 Envelope and MPER Antibody Structures in Lipid Assemblies},

author = {Kimmo Rantalainen and Zachary T Berndsen and Aleksandar Antanasijevic and Torben Schiffner and Xi Zhang and Wen-Hsin Lee and Jonathan L Torres and Lei Zhang and Adriana Irimia and Jeffrey Copps and Kenneth H Zhou and Young D Kwon and William H Law and Chaim A Schramm and Raffaello Verardi and Shelly J Krebs and Peter D Kwong and Nicole A Doria-Rose and Ian A Wilson and Michael B Zwick and John R Yates and William R Schief and Andrew B Ward},

doi = {10.1016/j.celrep.2020.107583},

issn = {2211-1247},

year  = {2020},

date = {2020-01-01},

journal = {Cell Rep},

volume = {31},

number = {4},

pages = {107583},

abstract = {Structural and functional studies of HIV envelope glycoprotein (Env) as a transmembrane protein have long been complicated by challenges associated with inherent flexibility of the molecule and the membrane-embedded hydrophobic regions. Here, we present approaches for incorporating full-length, wild-type HIV-1 Env, as well as C-terminally truncated and stabilized versions, into lipid assemblies, providing a modular platform for Env structural studies by single particle electron microscopy. We reconstitute a full-length Env clone into a nanodisc, complex it with a membrane-proximal external region (MPER) targeting antibody 10E8, and structurally define the full quaternary epitope of 10E8 consisting of lipid, MPER, and ectodomain contacts. By aligning this and other Env-MPER antibody complex reconstructions with the lipid bilayer, we observe evidence of Env tilting as part of the neutralization mechanism for MPER-targeting antibodies. We also adapt the platform toward vaccine design purposes by introducing stabilizing mutations that allow purification of unliganded Env with a peptidisc scaffold.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32347204,

title = {Serological assays for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), March 2020},

author = {Ranawaka Apm Perera and Chris Kp Mok and Owen Ty Tsang and Huibin Lv and Ronald Lw Ko and Nicholas C Wu and Meng Yuan and Wai Shing Leung and Jacky Mc Chan and Thomas Sh Chik and Chris Yc Choi and Kathy Leung and Kin Ho Chan and Karl Ck Chan and Ka-Chi Li and Joseph T Wu and Ian A Wilson and Arnold S Monto and Leo Lm Poon and Malik Peiris},

doi = {10.2807/1560-7917.ES.2020.25.16.2000421},

issn = {1560-7917},

year  = {2020},

date = {2020-01-01},

journal = {Euro Surveill},

volume = {25},

number = {16},

abstract = {BackgroundThe ongoing coronavirus disease (COVID-19) pandemic has major impacts on health systems, the economy and society. Assessing infection attack rates in the population is critical for estimating disease severity and herd immunity which is needed to calibrate public health interventions. We have previously shown that it is possible to achieve this in real time to impact public health decision making.AimOur objective was to develop and evaluate serological assays applicable in large-scale sero-epidemiological studies.MethodsWe developed an ELISA to detect IgG and IgM antibodies to the receptor-binding domain (RBD) of the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We evaluated its sensitivity and specificity in combination with confirmatory microneutralisation (MN) and 90% plaque reduction neutralisation tests (PRNT) in 51 sera from 24 patients with virologically confirmed COVID-19 and in age-stratified sera from 200 healthy controls.ResultsIgG and IgM RBD ELISA, MN and PRNT were reliably positive after 29 days from illness onset with no detectable cross-reactivity in age-stratified controls. We found that PRNT tests were more sensitive in detecting antibody than MN tests carried out with the conventional 100 tissue culture infectious dose challenge. Heparinised plasma appeared to reduce the infectivity of the virus challenge dose and may confound interpretation of neutralisation test.ConclusionUsing IgG ELISA based on the RBD of the spike protein to screen sera for SARS-CoV-2 antibody, followed by confirmation using PRNT, is a valid approach for large-scale sero-epidemiology studies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32109354,

title = {The Impact of Sustained Immunization Regimens on the Antibody Response to Oligomannose Glycans},

author = {Dung N Nguyen and Richard L Redman and Satoru Horiya and Jennifer K Bailey and Bokai Xu and Robyn L Stanfield and J Sebastian Temme and Celia C LaBranche and Shiyu Wang and Avital A Rodal and David C Montefiori and Ian A Wilson and Isaac J Krauss},

doi = {10.1021/acschembio.0c00053},

issn = {1554-8937},

year  = {2020},

date = {2020-01-01},

journal = {ACS Chem Biol},

volume = {15},

number = {3},

pages = {789--798},

abstract = {The high mannose patch (HMP) of the HIV envelope protein (Env) is the structure most frequently targeted by broadly neutralizing antibodies; therefore, many researchers have attempted to use mimics of this region as a vaccine immunogen. In our previous efforts, vaccinating rabbits with evolved HMP mimic glycopeptides containing Man resulted in an overall antibody response targeting the glycan core and linker rather than the full glycan or Manα1→2Man tips of Man glycans. A possible reason could be processing of our immunogen by host serum mannosidases. We sought to test whether more prolonged dosing could increase the antibody response to intact glycans, possibly by increasing the availability of intact Man to germinal centers. Here, we describe a study investigating the impact of immunization regimen on antibody response by testing immunogen delivery through bolus, an exponential series of mini doses, or a continuously infusing mini-osmotic pump. Our results indicate that, with our glycopeptide immunogens, standard bolus immunization elicited the strongest HIV Env-binding antibody response, even though higher overall titers to the glycopeptide were elicited by the exponential and pump regimens. Antibody selectivity for intact glycan was, if anything, slightly better in the bolus-immunized animals.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31941772,

title = {Autologous Antibody Responses to an HIV Envelope Glycan Hole Are Not Easily Broadened in Rabbits},

author = {Yuhe R Yang and Laura E McCoy and Marit J van Gils and Raiees Andrabi and Hannah L Turner and Meng Yuan and Christopher A Cottrell and Gabriel Ozorowski and James Voss and Matthias Pauthner and Thomas M Polveroni and Terrence Messmer and Ian A Wilson and Rogier W Sanders and Dennis R Burton and Andrew B Ward},

doi = {10.1128/JVI.01861-19},

issn = {1098-5514},

year  = {2020},

date = {2020-01-01},

journal = {J Virol},

volume = {94},

number = {7},

abstract = {Extensive studies with subtype A BG505-derived HIV envelope glycoprotein (Env) immunogens have revealed that the dominant autologous neutralizing epitope in rabbits is located in an exposed region of the heavily glycosylated trimer that lacks potential N-linked glycosylation sites at positions 230, 241, and 289. The Env derived from B41, a subtype B virus, shares a glycan hole centered on positions 230 and 289. To test whether broader neutralization to the common glycan hole can be achieved, we immunized rabbits with B41 SOSIP (gp120-gp41 disulfide [SOS] with an isoleucine-to-proline mutation [IP] in gp41) alone, as well as B41 and BG505 coimmunization. We isolated autologous neutralizing antibodies (nAbs) and described their structure in complex with the B41 Env. Our data suggest that distinct autologous nAb lineages are induced by BG505 and B41 immunogens, even when both were administered together. In contrast to previously described BG505 glycan hole antibodies, the B41-specific nAbs accommodate the >97% conserved N241 glycan, which is present in B41. Single-particle cryo-electron microscopy studies confirmed that B41- and BG505-specific nAbs bind to overlapping glycan hole epitopes. We then used our high-resolution data to guide mutations in the BG505 glycan hole epitope in an attempt to broaden the reactivity of a B41-specific nAb, but we recovered only partial binding. Our data demonstrate that the lack of cross-reactivity in glycan hole antibodies is due to amino acid differences within the epitope, and our attempts to rationally design cross-reactive trimers resulted in only limited success. Thus, even for the immunodominant glycan hole shared between BG505 and B41, the prospect of designing prime-boost immunogens remains difficult. A glycan hole is one of the most dominant autologous neutralizing epitopes targeted on BG505 and B41 SOSIP trimer-immunized rabbits. Our high-resolution cryo-electron microscopy (cryoEM) studies of B41 in complex with a B41-specific antibody complex elucidate the molecular basis of this strain-specific glycan hole response. We conclude that even for the immunodominant glycan hole shared between BG505 and B41, the prospect of designing prime-boost immunogens remains difficult.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32150583,

title = {Structure and mechanism of monoclonal antibody binding to the junctional epitope of Plasmodium falciparum circumsporozoite protein},

author = {David Oyen and Jonathan L Torres and Phillip C Aoto and Yevel Flores-Garcia and Špela Binter and Tossapol Pholcharee and Sean Carroll and Sini Reponen and Rachael Wash and Qi Liang and Franck Lemiale and Emily Locke and Allan Bradley and C Richter King and Daniel Emerling and Paul Kellam and Fidel Zavala and Andrew B Ward and Ian A Wilson},

doi = {10.1371/journal.ppat.1008373},

issn = {1553-7374},

year  = {2020},

date = {2020-01-01},

journal = {PLoS Pathog},

volume = {16},

number = {3},

pages = {e1008373},

abstract = {Lasting protection has long been a goal for malaria vaccines. The major surface antigen on Plasmodium falciparum sporozoites, the circumsporozoite protein (PfCSP), has been an attractive target for vaccine development and most protective antibodies studied to date interact with the central NANP repeat region of PfCSP. However, it remains unclear what structural and functional characteristics correlate with better protection by one antibody over another. Binding to the junctional region between the N-terminal domain and central NANP repeats has been proposed to result in superior protection: this region initiates with the only NPDP sequence followed immediately by NANP. Here, we isolated antibodies in Kymab mice immunized with full-length recombinant PfCSP and two protective antibodies were selected for further study with reactivity against the junctional region. X-ray and EM structures of two monoclonal antibodies, mAb667 and mAb668, shed light on their differential affinity and specificity for the junctional region. Importantly, these antibodies also bind to the NANP repeat region with equal or better affinity. A comparison with an NANP-only binding antibody (mAb317) revealed roughly similar but statistically distinct levels of protection against sporozoite challenge in mouse liver burden models, suggesting that junctional antibody protection might relate to the ability to also cross-react with the NANP repeat region. Our findings indicate that additional efforts are necessary to isolate a true junctional antibody with no or much reduced affinity to the NANP region to elucidate the role of the junctional epitope in protection.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32144244,

title = {Major antigenic site B of human influenza H3N2 viruses has an evolving local fitness landscape},

author = {Nicholas C Wu and Jakub Otwinowski and Andrew J Thompson and Corwin M Nycholat and Armita Nourmohammad and Ian A Wilson},

doi = {10.1038/s41467-020-15102-5},

issn = {2041-1723},

year  = {2020},

date = {2020-01-01},

journal = {Nat Commun},

volume = {11},

number = {1},

pages = {1233},

abstract = {Antigenic drift of influenza virus hemagglutinin (HA) is enabled by facile evolvability. However, HA antigenic site B, which has become immunodominant in recent human H3N2 influenza viruses, is also evolutionarily constrained by its involvement in receptor binding. Here, we employ deep mutational scanning to probe the local fitness landscape of HA antigenic site B in six different human H3N2 strains spanning from 1968 to 2016. We observe that the fitness landscape of HA antigenic site B can be very different between strains. Sequence variants that exhibit high fitness in one strain can be deleterious in another, indicating that the evolutionary constraints of antigenic site B have changed over time. Structural analysis suggests that the local fitness landscape of antigenic site B can be reshaped by natural mutations via modulation of the receptor-binding mode. Overall, these findings elucidate how influenza virus continues to explore new antigenic space despite strong functional constraints.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31852794,

title = {Neutralizing Antibody Induction by HIV-1 Envelope Glycoprotein SOSIP Trimers on Iron Oxide Nanoparticles May Be Impaired by Mannose Binding Lectin},

author = {Rajesh P Ringe and Victor M Cruz Portillo and Pia Dosenovic and Thomas J Ketas and Gabriel Ozorowski and Bartek Nogal and Lautaro Perez and Celia C LaBranche and Jillian Lim and Erik Francomano and Ian A Wilson and Rogier W Sanders and Andrew B Ward and David C Montefiori and Michel C Nussenzweig and P J Klasse and Albert Cupo and John P Moore},

doi = {10.1128/JVI.01883-19},

issn = {1098-5514},

year  = {2020},

date = {2020-01-01},

journal = {J Virol},

volume = {94},

number = {6},

abstract = {We covalently attached human immunodeficiency virus type 1 (HIV-1) Env SOSIP trimers to iron oxide nanoparticles (IO-NPs) to create a particulate immunogen for neutralizing antibody (NAb) induction. The attached trimers, ∼20 per particle, retained native-like antigenicity, judged by reactivity with NAbs and non-NAbs. Bivalent (BG505 and B41) trimer IO-NPs were made, as were IO-NPs displaying B41 trimers carrying a PADRE T-cell helper epitope (TCHE). We immunized mice with B41 soluble or IO-NP trimers after PADRE peptide priming. After two immunizations, IO-NP presentation and the TCHE tag independently and substantially increased anti-trimer antibody responses, but titer differences waned after two further doses. Notable and unexpected findings were that autologous NAbs to the N289 glycan hole epitope were consistently induced in mice given soluble but not IO-NP trimers. Various recombinant mannose binding lectins (MBLs) and MBLs in sera of both murine and human origin bound to soluble and IO-NP trimers. MBL binding occluded the autologous NAb epitope on the B41 IO-NP trimers, which may contribute to its poor immunogenicity. The exposure of a subset of broadly active NAb epitopes was also impaired by MBL binding, which could have substantial implications for the utility of trimer-bearing nanoparticles in general and perhaps also for soluble Env proteins. Recombinant trimeric SOSIP proteins are vaccine components intended to induce neutralizing antibodies (NAbs) that prevent cells from infection by human immunodeficiency virus type 1 (HIV-1). A way to increase the strength of antibody responses to these proteins is to present them on the surface of nanoparticles (NPs). We chemically attached about 20 SOSIP trimers to NPs made of iron oxide (IO). The resulting IO-NP trimers had appropriate properties when we studied them in the laboratory but, unexpectedly, were less able to induce NAbs than nonattached trimers when used to immunize mice. We found that mannose binding lectins, proteins naturally present in the serum of mice and other animals, bound strongly to the soluble and IO-NP trimers, blocking access to antibody epitopes in a way that may impede the development of NAb responses. These findings should influence how trimer-bearing NPs of various designs are made and used.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31883801,

title = {Diverse Antibody Responses to Conserved Structural Motifs in Plasmodium falciparum Circumsporozoite Protein},

author = {Tossapol Pholcharee and David Oyen and Jonathan L Torres and Yevel Flores-Garcia and Gregory M Martin and Gonzalo E González-Páez and Daniel Emerling and Wayne Volkmuth and Emily Locke and C Richter King and Fidel Zavala and Andrew B Ward and Ian A Wilson},

doi = {10.1016/j.jmb.2019.12.029},

issn = {1089-8638},

year  = {2020},

date = {2020-01-01},

journal = {J Mol Biol},

volume = {432},

number = {4},

pages = {1048--1063},

abstract = {Malaria vaccine candidate RTS,S/AS01 is based on the central and C-terminal regions of the circumsporozoite protein (CSP) of P. falciparum. mAb397 was isolated from a volunteer in an RTS,S/AS01 clinical trial, and it protects mice from infection by malaria sporozoites. However, mAb397 originates from the less commonly used VH3-15 germline gene compared to the VH3-30/33 antibodies generally elicited by RTS,S to the central NANP repeat region of CSP. The crystal structure of mAb397 with an NPNA peptide shows that the central NPNA forms a type I β-turn and is the main recognition motif. In most anti-NANP antibodies studied to date, a germline-encoded Trp is used to engage the Pro in NPNA β-turns, but here the Trp interacts with the first Asn. This "conserved" Trp, however, can arise from different germline genes and be located in the heavy or the light chain. Variation in the terminal ψ angles of the NPNA β-turns results in different dispositions of the subsequent NPNA and, hence, different stoichiometries and modes of antibody binding to rsCSP. Diverse protective antibodies against NANP repeats are therefore not limited to a single germline gene response or mode of binding.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31151913,

title = {Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility},

author = {Nicholas C Wu and Huibin Lv and Andrew J Thompson and Douglas C Wu and Wilson W S Ng and Rameshwar U Kadam and Chih-Wei Lin and Corwin M Nycholat and Ryan McBride and Weiwen Liang and James C Paulson and Chris K P Mok and Ian A Wilson},

doi = {10.1016/j.chom.2019.04.013},

issn = {1934-6069},

year  = {2019},

date = {2019-06-01},

journal = {Cell Host Microbe},

volume = {25},

number = {6},

pages = {836--844.e5},

abstract = {Egg-based seasonal influenza vaccines are the major preventive countermeasure against influenza virus. However, their effectiveness can be compromised when antigenic changes arise from egg-adaptive mutations on influenza hemagglutinin (HA). The L194P mutation is commonly observed in egg-based H3N2 vaccine seed strains and significantly alters HA antigenicity. An approach to prevent L194P would therefore be beneficial. We show that emergence of L194P during egg passaging can be impeded by preexistence of a G186V mutation, revealing strong incompatibility between these mutations. X-ray structures illustrate that individual G186V and L194P mutations have opposing effects on the HA receptor-binding site (RBS), and when both G186V and L194P are present, the RBS is severely disrupted. Importantly, wild-type HA antigenicity is maintained with G186V, but not L194P. Our results demonstrate that these epistatic interactions can be used to prevent the emergence of mutations that adversely alter antigenicity during egg adaptation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30834312,

title = {Oligomannose Glycopeptide Conjugates Elicit Antibodies Targeting the Glycan Core Rather than Its Extremities},

author = {Dung N Nguyen and Bokai Xu and Robyn L Stanfield and Jennifer K Bailey and Satoru Horiya and J Sebastian Temme and Deborah R Leon and Celia C LaBranche and David C Montefiori and Catherine E Costello and Ian A Wilson and Isaac J Krauss},

doi = {10.1021/acscentsci.8b00588},

issn = {2374-7943},

year  = {2019},

date = {2019-02-01},

journal = {ACS Cent Sci},

volume = {5},

number = {2},

pages = {237--249},

abstract = {Up to ∼20% of HIV-infected individuals eventually develop broadly neutralizing antibodies (bnAbs), and many of these antibodies (∼40%) target a region of dense high-mannose glycosylation on gp120 of the HIV envelope protein, known as the "high-mannose patch" (HMP). Thus, there have been numerous attempts to develop glycoconjugate vaccine immunogens that structurally mimic the HMP and might elicit bnAbs targeting this conserved neutralization epitope. Herein, we report on the immunogenicity of glycopeptides, designed by  selection, that bind tightly to anti-HMP antibody 2G12. By analyzing the fine carbohydrate specificity of rabbit antibodies elicited by these immunogens, we found that they differ from some natural human bnAbs, such as 2G12 and PGT128, in that they bind primarily to the core structures within the glycan, rather than to the Manα1 → 2Man termini (2G12) or to the whole glycan (PGT128). Antibody specificity for the glycan core may result from extensive serum mannosidase trimming of the immunogen in the vaccinated animals. This finding has broad implications for vaccine design aiming to target glycan-dependent HIV neutralizing antibodies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31794659,

title = {A Dynamic Switch in Inactive p38γ Leads to an Excited State on the Pathway to an Active Kinase},

author = {Phillip C Aoto and Robyn L Stanfield and Ian A Wilson and H Jane Dyson and Peter E Wright},

doi = {10.1021/acs.biochem.9b00932},

issn = {1520-4995},

year  = {2019},

date = {2019-01-01},

journal = {Biochemistry},

volume = {58},

number = {51},

pages = {5160--5172},

abstract = {The inactive state of mitogen-activated protein kinases (MAPKs) adopts an open conformation while the active state exists in a compact form stabilized by phosphorylation. In the active state, eukaryotic kinases undergo breathing motions related to substrate binding and product release that have not previously been detected in the inactive state. However, docking interactions of partner proteins with inactive MAPK kinases exhibit allostery in binding of activating kinases. Interactions at a site distant from the activation loop are coupled to the configuration of the activation loop, suggesting that the inactive state may also undergo concerted dynamics. X-ray crystallographic studies of nonphosphorylated, inactive p38γ reveal differences in domain orientations and active site structure in the two molecules in the asymmetric unit. One molecule resembles an inactive kinase with an open active site. The second molecule has a rotation of the N-lobe that leads to partial compaction of the active site, resulting in a conformation that is intermediate between the inactive open state and the fully closed state of the activated kinase. Although the compact state of apo p38γ displays several of the features of the activated enzyme, it remains catalytically inert. In solution, the kinase fluctuates on a millisecond time scale between the open ground state and a weakly populated excited state that is similar in structure to the compact state observed in the crystal. The nuclear magnetic resonance and crystal structure data imply that interconversion between the open and compact states involves a molecular switch associated with the DFG loop.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31875553,

title = {Identification of Antibodies Targeting the H3N2 Hemagglutinin Receptor Binding Site following Vaccination of Humans},

author = {Seth J Zost and Juhye Lee and Megan E Gumina and Kaela Parkhouse and Carole Henry and Nicholas C Wu and Chang-Chun D Lee and Ian A Wilson and Patrick C Wilson and Jesse D Bloom and Scott E Hensley},

doi = {10.1016/j.celrep.2019.11.084},

issn = {2211-1247},

year  = {2019},

date = {2019-01-01},

journal = {Cell Rep},

volume = {29},

number = {13},

pages = {4460--4470.e8},

abstract = {Antibodies targeting the receptor binding site (RBS) of the influenza virus hemagglutinin (HA) protein are usually not broadly reactive because their footprints are typically large and extend to nearby variable HA residues. Here, we identify several human H3N2 HA RBS-targeting monoclonal antibodies (mAbs) that are sensitive to substitutions in conventional antigenic sites and are therefore not broadly reactive. However, we also identify an H3N2 HA RBS-targeting mAb that is exceptionally broadly reactive despite being sensitive to substitutions in residues outside of the RBS. We show that similar antibodies are present at measurable levels in the sera of some individuals but that they are inefficiently elicited by conventional vaccines. Our data indicate that HA RBS-targeting antibodies can be effective against variable viral strains even when they are somewhat sensitive to substitutions in HA residues adjacent to the RBS.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31757769,

title = {Influenza H7N9 Virus Neuraminidase-Specific Human Monoclonal Antibodies Inhibit Viral Egress and Protect from Lethal Influenza Infection in Mice},

author = {Iuliia M Gilchuk and Sandhya Bangaru and Pavlo Gilchuk and Ryan P Irving and Nurgun Kose and Robin G Bombardi and Natalie J Thornburg and C Buddy Creech and Kathryn M Edwards and Sheng Li and Hannah L Turner and Wenli Yu and Xueyong Zhu and Ian A Wilson and Andrew B Ward and James E Crowe},

doi = {10.1016/j.chom.2019.10.003},

issn = {1934-6069},

year  = {2019},

date = {2019-01-01},

journal = {Cell Host Microbe},

volume = {26},

number = {6},

pages = {715--728.e8},

abstract = {H7N9 avian influenza virus causes severe infections and might have the potential to trigger a major pandemic. Molecular determinants of human humoral immune response to N9 neuraminidase (NA) proteins, which exhibit unusual features compared with seasonal influenza virus NA proteins, are ill-defined. We isolated 35 human monoclonal antibodies (mAbs) from two H7N9 survivors and two vaccinees. These mAbs react to NA in a subtype-specific manner and recognize diverse antigenic sites on the surface of N9 NA, including epitopes overlapping with, or distinct from, the enzyme active site. Despite recognizing multiple antigenic sites, the mAbs use a common mechanism of action by blocking egress of nascent virions from infected cells, thereby providing an antiviral prophylactic and therapeutic protection in vivo in mice. Studies of breadth, potency, and diversity of antigenic recognition from four subjects suggest that vaccination with inactivated adjuvanted vaccine induce NA-reactive responses comparable to that of H7N9 natural infection.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31757767,

title = {Structural Basis of Protection against H7N9 Influenza Virus by Human Anti-N9 Neuraminidase Antibodies},

author = {Xueyong Zhu and Hannah L Turner and Shanshan Lang and Ryan McBride and Sandhya Bangaru and Iuliia M Gilchuk and Wenli Yu and James C Paulson and James E Crowe and Andrew B Ward and Ian A Wilson},

doi = {10.1016/j.chom.2019.10.002},

issn = {1934-6069},

year  = {2019},

date = {2019-01-01},

journal = {Cell Host Microbe},

volume = {26},

number = {6},

pages = {729--738.e4},

abstract = {Influenza virus neuraminidase (NA) is a major target for small-molecule antiviral drugs. Antibodies targeting the NA surface antigen could also inhibit virus entry and egress to provide host protection. However, our understanding of the nature and range of target epitopes is limited because of a lack of human antibody structures with influenza neuraminidase. Here, we describe crystal and cryogenic electron microscopy (cryo-EM) structures of NAs from human-infecting avian H7N9 viruses in complex with five human anti-N9 antibodies, systematically defining several antigenic sites and antibody epitope footprints. These antibodies either fully or partially block the NA active site or bind to epitopes distant from the active site while still showing neuraminidase inhibition. The inhibition of antibodies to NAs was further analyzed by glycan array and solution-based NA activity assays. Together, these structural studies provide insights into protection by anti-NA antibodies and templates for the development of NA-based influenza virus vaccines and therapeutics.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31672916,

title = {A generalized HIV vaccine design strategy for priming of broadly neutralizing antibody responses},

author = {Jon M Steichen and Ying-Cing Lin and Colin Havenar-Daughton and Simone Pecetta and Gabriel Ozorowski and Jordan R Willis and Laura Toy and Devin Sok and Alessia Liguori and Sven Kratochvil and Jonathan L Torres and Oleksandr Kalyuzhniy and Eleonora Melzi and Daniel W Kulp and Sebastian Raemisch and Xiaozhen Hu and Steffen M Bernard and Erik Georgeson and Nicole Phelps and Yumiko Adachi and Michael Kubitz and Elise Landais and Jeffrey Umotoy and Amanda Robinson and Bryan Briney and Ian A Wilson and Dennis R Burton and Andrew B Ward and Shane Crotty and Facundo D Batista and William R Schief},

doi = {10.1126/science.aax4380},

issn = {1095-9203},

year  = {2019},

date = {2019-01-01},

journal = {Science},

volume = {366},

number = {6470},

abstract = {Vaccine induction of broadly neutralizing antibodies (bnAbs) to HIV remains a major challenge. Germline-targeting immunogens hold promise for initiating the induction of certain bnAb classes; yet for most bnAbs, a strong dependence on antibody heavy chain complementarity-determining region 3 (HCDR3) is a major barrier. Exploiting ultradeep human antibody sequencing data, we identified a diverse set of potential antibody precursors for a bnAb with dominant HCDR3 contacts. We then developed HIV envelope trimer-based immunogens that primed responses from rare bnAb-precursor B cells in a mouse model and bound a range of potential bnAb-precursor human naïve B cells in ex vivo screens. Our repertoire-guided germline-targeting approach provides a framework for priming the induction of many HIV bnAbs and could be applied to most HCDR3-dominant antibodies from other pathogens.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31772165,

title = {An MPER antibody neutralizes HIV-1 using germline features shared among donors},

author = {Lei Zhang and Adriana Irimia and Lingling He and Elise Landais and Kimmo Rantalainen and Daniel P Leaman and Thomas Vollbrecht and Armando Stano and Daniel I Sands and Arthur S Kim and  and Pascal Poignard and Dennis R Burton and Ben Murrell and Andrew B Ward and Jiang Zhu and Ian A Wilson and Michael B Zwick},

doi = {10.1038/s41467-019-12973-1},

issn = {2041-1723},

year  = {2019},

date = {2019-01-01},

journal = {Nat Commun},

volume = {10},

number = {1},

pages = {5389},

abstract = {The membrane-proximal external region (MPER) of HIV-1 envelope glycoprotein (Env) can be targeted by neutralizing antibodies of exceptional breadth. MPER antibodies usually have long, hydrophobic CDRH3s, lack activity as inferred germline precursors, are often from the minor IgG3 subclass, and some are polyreactive, such as 4E10. Here we describe an MPER broadly neutralizing antibody from the major IgG1 subclass, PGZL1, which shares germline V/D-region genes with 4E10, has a shorter CDRH3, and is less polyreactive. A recombinant sublineage variant pan-neutralizes a 130-isolate panel at 1.4 μg/ml (IC). Notably, a germline revertant with mature CDR3s neutralizes 12% of viruses and still binds MPER after DJ reversion. Crystal structures of lipid-bound PGZL1 variants and cryo-EM reconstruction of an Env-PGZL1 complex reveal how these antibodies recognize MPER and viral membrane. Discovery of common genetic and structural elements among MPER antibodies from different patients suggests that such antibodies could be elicited using carefully designed immunogens.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31649200,

title = {Broadly protective human antibodies that target the active site of influenza virus neuraminidase},

author = {Daniel Stadlbauer and Xueyong Zhu and Meagan McMahon and Jackson S Turner and Teddy J Wohlbold and Aaron J Schmitz and Shirin Strohmeier and Wenli Yu and Raffael Nachbagauer and Philip A Mudd and Ian A Wilson and Ali H Ellebedy and Florian Krammer},

doi = {10.1126/science.aay0678},

issn = {1095-9203},

year  = {2019},

date = {2019-01-01},

journal = {Science},

volume = {366},

number = {6464},

pages = {499--504},

abstract = {Better vaccines against influenza virus are urgently needed to provide broader protection against diverse strains, subtypes, and types. Such efforts are assisted by the identification of novel broadly neutralizing epitopes targeted by protective antibodies. Influenza vaccine development has largely focused on the hemagglutinin, but the other major surface antigen, the neuraminidase, has reemerged as a potential target for universal vaccines. We describe three human monoclonal antibodies isolated from an H3N2-infected donor that bind with exceptional breadth to multiple different influenza A and B virus neuraminidases. These antibodies neutralize the virus, mediate effector functions, are broadly protective in vivo, and inhibit neuraminidase activity by directly binding to the active site. Structural and functional characterization of these antibodies will inform the development of neuraminidase-based universal vaccines against influenza virus.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31121217,

title = {Exploitation of glycosylation in enveloped virus pathobiology},

author = {Yasunori Watanabe and Thomas A Bowden and Ian A Wilson and Max Crispin},

doi = {10.1016/j.bbagen.2019.05.012},

issn = {1872-8006},

year  = {2019},

date = {2019-01-01},

journal = {Biochim Biophys Acta Gen Subj},

volume = {1863},

number = {10},

pages = {1480--1497},

abstract = {Glycosylation is a ubiquitous post-translational modification responsible for a multitude of crucial biological roles. As obligate parasites, viruses exploit host-cell machinery to glycosylate their own proteins during replication. Viral envelope proteins from a variety of human pathogens including HIV-1, influenza virus, Lassa virus, SARS, Zika virus, dengue virus, and Ebola virus have evolved to be extensively glycosylated. These host-cell derived glycans facilitate diverse structural and functional roles during the viral life-cycle, ranging from immune evasion by glycan shielding to enhancement of immune cell infection. In this review, we highlight the imperative and auxiliary roles glycans play, and how specific oligosaccharide structures facilitate these functions during viral pathogenesis. We discuss the growing efforts to exploit viral glycobiology in the development of anti-viral vaccines and therapies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31306512,

title = {Structures of single-layer β-sheet proteins evolved from β-hairpin repeats},

author = {Qingping Xu and Matthew Biancalana and Joanna C Grant and Hsiu-Ju Chiu and Lukasz Jaroszewski and Mark W Knuth and Scott A Lesley and Adam Godzik and Marc-André Elsliger and Ashley M Deacon and Ian A Wilson},

doi = {10.1002/pro.3683},

issn = {1469-896X},

year  = {2019},

date = {2019-01-01},

journal = {Protein Sci},

volume = {28},

number = {9},

pages = {1676--1689},

abstract = {Free-standing single-layer β-sheets are extremely rare in naturally occurring proteins, even though β-sheet motifs are ubiquitous. Here we report the crystal structures of three homologous, single-layer, anti-parallel β-sheet proteins, comprised of three or four twisted β-hairpin repeats. The structures reveal that, in addition to the hydrogen bond network characteristic of β-sheets, additional hydrophobic interactions mediated by small clusters of residues adjacent to the turns likely play a significant role in the structural stability and compensate for the lack of a compact hydrophobic core. These structures enabled identification of a family of secreted proteins that are broadly distributed in bacteria from the human gut microbiome and are putatively involved in the metabolism of complex carbohydrates. A conserved surface patch, rich in solvent-exposed tyrosine residues, was identified on the concave surface of the β-sheet. These new modular single-layer β-sheet proteins may serve as a new model system for studying folding and design of β-rich proteins.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31243995,

title = {Structure and Dynamics of Stacking Interactions in an Antibody Binding Site},

author = {Ramkrishna Adhikary and Jörg Zimmermann and Robyn L Stanfield and Ian A Wilson and Wayne Yu and Masayuki Oda and Floyd E Romesberg},

doi = {10.1021/acs.biochem.9b00119},

issn = {1520-4995},

year  = {2019},

date = {2019-01-01},

journal = {Biochemistry},

volume = {58},

number = {27},

pages = {2987--2995},

abstract = {For years, antibodies (Abs) have been used as a paradigm for understanding how protein structure contributes to molecular recognition. However, with the ability to evolve Abs that recognize specific chromophores, they also have great potential as models for how protein dynamics contribute to molecular recognition. We previously raised murine Abs to different chromophores and, with the use of three-pulse photon echo peak shift spectroscopy, demonstrated that the immune system is capable of producing Abs with widely varying flexibility. We now report the characterization of the complexes formed between two Abs, 5D11 and 10A6, and the chromophoric ligand that they were evolved to recognize, 8-methoxypyrene-1,3,6-trisulfonic acid (MPTS). The sequences of the Ab genes indicate that they evolved from a common precursor. We also used a variety of spectroscopic methods to probe the photophysics and dynamics of the Ab-MPTS complexes and found that they are similar to each other but distinct from previously characterized anti-MPTS Abs. Structural studies revealed that this difference likely results from a unique mode of binding in which MPTS is sandwiched between the side chain of Phe98, which interacts with the chromophore via T-stacking, and the side chain of Trp91, which interacts with the chromophore via parallel stacking. The T-stacking interaction appears to mediate relaxation on the picosecond time scale, while the parallel stacking appears to mediate relaxation on an ultrafast, femtosecond time scale, which dominates the response. The anti-MPTS Abs thus not only demonstrate the simultaneous use of the two limiting modes of stacking for molecular recognition, but also provide a unique opportunity to characterize how dynamics might contribute to molecular recognition. Both types of stacking are common in proteins and protein complexes where they may similarly contribute to dynamics and molecular recognition.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31130486,

title = {Structural Insights into the Lipid A Transport Pathway in MsbA},

author = {Pius S Padayatti and Sung Chang Lee and Robyn L Stanfield and Po-Chao Wen and Emad Tajkhorshid and Ian A Wilson and Qinghai Zhang},

doi = {10.1016/j.str.2019.04.007},

issn = {1878-4186},

year  = {2019},

date = {2019-01-01},

journal = {Structure},

volume = {27},

number = {7},

pages = {1114--1123.e3},

abstract = {MsbA is an essential ATP-binding cassette transporter in Gram-negative bacteria that transports lipid A and lipopolysaccharide from the cytoplasmic leaflet to the periplasmic leaflet of the inner membrane. Here we report the X-ray structure of MsbA from Salmonella typhimurium at 2.8-Å resolution in an inward-facing conformation after cocrystallization with lipid A and using a stabilizing facial amphiphile. The structure displays a large amplitude opening in the transmembrane portal, which is likely required for lipid A to pass from its site of synthesis into the protein-enclosed transport pathway. Putative lipid A density is observed further inside the transmembrane cavity, consistent with a trap and flip model. Additional electron density attributed to lipid A is observed near an outer surface cleft at the periplasmic ends of the transmembrane helices. These findings provide new structural insights into the lipid A transport pathway through comparative analysis with existing MsbA structures.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31194940,

title = {Conformational Plasticity in the HIV-1 Fusion Peptide Facilitates Recognition by Broadly Neutralizing Antibodies},

author = {Meng Yuan and Christopher A Cottrell and Gabriel Ozorowski and Marit J van Gils and Sonu Kumar and Nicholas C Wu and Anita Sarkar and Jonathan L Torres and Natalia de Val and Jeffrey Copps and John P Moore and Rogier W Sanders and Andrew B Ward and Ian A Wilson},

doi = {10.1016/j.chom.2019.04.011},

issn = {1934-6069},

year  = {2019},

date = {2019-01-01},

journal = {Cell Host Microbe},

volume = {25},

number = {6},

pages = {873--883.e5},

abstract = {The fusion peptide (FP) of HIV-1 envelope glycoprotein (Env) is essential for mediating viral entry. Detection of broadly neutralizing antibodies (bnAbs) that interact with the FP has revealed it as a site of vulnerability. We delineate X-ray and cryo-electron microscopy (cryo-EM) structures of bnAb ACS202, from an HIV-infected elite neutralizer, with an FP and with a soluble Env trimer (AMC011 SOSIP.v4.2) derived from the same patient. We show that ACS202 CDRH3 forms a "β strand" interaction with the exposed hydrophobic FP and recognizes a continuous region of gp120, including a conserved N-linked glycan at N88. A cryo-EM structure of another previously identified bnAb VRC34.01 with AMC011 SOSIP.v4.2 shows that it also penetrates through glycans to target the FP. We further demonstrate that the FP can twist and present different conformations for recognition by bnAbs, which enables approach to Env from diverse angles. The variable recognition of FP by bnAbs thus provides insights for vaccine design.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31189111,

title = {N-Glycolylneuraminic Acid as a Receptor for Influenza A Viruses},

author = {Frederik Broszeit and Netanel Tzarum and Xueyong Zhu and Nikoloz Nemanichvili and Dirk Eggink and Tim Leenders and Zeshi Li and Lin Liu and Margreet A Wolfert and Andreas Papanikolaou and Carles Martínez-Romero and Ivan A Gagarinov and Wenli Yu and Adolfo García-Sastre and Tom Wennekes and Masatoshi Okamatsu and Monique H Verheije and Ian A Wilson and Geert-Jan Boons and Robert P de Vries},

doi = {10.1016/j.celrep.2019.05.048},

issn = {2211-1247},

year  = {2019},

date = {2019-01-01},

journal = {Cell Rep},

volume = {27},

number = {11},

pages = {3284--3294.e6},

abstract = {A species barrier for the influenza A virus is the differential expression of sialic acid, which can either be α2,3-linked for avians or α2,6-linked for human viruses. The influenza A virus hosts also express other species-specific sialic acid derivatives. One major modification at C-5 is N-glycolyl (NeuGc), instead of N-acetyl (NeuAc). N-glycolyl is mammalian specific and expressed in pigs and horses, but not in humans, ferrets, seals, or dogs. Hemagglutinin (HA) adaptation to either N-acetyl or N-glycolyl is analyzed on a sialoside microarray containing both α2,3- and α2,6-linkage modifications on biologically relevant N-glycans. Binding studies reveal that avian, human, and equine HAs bind either N-glycolyl or N-acetyl. Structural data on N-glycolyl binding HA proteins of both H5 and H7 origin describe this specificity. Neuraminidases can cleave N-glycolyl efficiently, and tissue-binding studies reveal strict species specificity. The exclusive manner in which influenza A viruses differentiate between N-glycolyl and N-acetyl is indicative of selection.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31142746,

title = {Structure and immunogenicity of a stabilized HIV-1 envelope trimer based on a group-M consensus sequence},

author = {Kwinten Sliepen and Byung Woo Han and Ilja Bontjer and Petra Mooij and Fernando Garces and Anna-Janina Behrens and Kimmo Rantalainen and Sonu Kumar and Anita Sarkar and Philip J M Brouwer and Yuanzi Hua and Monica Tolazzi and Edith Schermer and Jonathan L Torres and Gabriel Ozorowski and Patricia van der Woude and Alba Torrents de la Peña and Mariëlle J van Breemen and Juan Miguel Camacho-Sánchez and Judith A Burger and Max Medina-Ramírez and Nuria González and Jose Alcami and Celia LaBranche and Gabriella Scarlatti and Marit J van Gils and Max Crispin and David C Montefiori and Andrew B Ward and Gerrit Koopman and John P Moore and Robin J Shattock and Willy M Bogers and Ian A Wilson and Rogier W Sanders},

doi = {10.1038/s41467-019-10262-5},

issn = {2041-1723},

year  = {2019},

date = {2019-01-01},

journal = {Nat Commun},

volume = {10},

number = {1},

pages = {2355},

abstract = {Stabilized HIV-1 envelope glycoproteins (Env) that resemble the native Env are utilized in vaccination strategies aimed at inducing broadly neutralizing antibodies (bNAbs). To limit the exposure of rare isolate-specific antigenic residues/determinants we generated a SOSIP trimer based on a consensus sequence of all HIV-1 group M isolates (ConM). The ConM trimer displays the epitopes of most known bNAbs and several germline bNAb precursors. The crystal structure of the ConM trimer at 3.9 Å resolution resembles that of the native Env trimer and its antigenic surface displays few rare residues. The ConM trimer elicits strong NAb responses against the autologous virus in rabbits and macaques that are significantly enhanced when it is presented on ferritin nanoparticles. The dominant NAb specificity is directed against an epitope at or close to the trimer apex. Immunogens based on consensus sequences might have utility in engineering vaccines against HIV-1 and other viruses.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31116986,

title = {The Chimpanzee SIV Envelope Trimer: Structure and Deployment as an HIV Vaccine Template},

author = {Raiees Andrabi and Jesper Pallesen and Joel D Allen and Ge Song and Jinsong Zhang and Natalia de Val and Gavin Gegg and Katelyn Porter and Ching-Yao Su and Matthias Pauthner and Amanda Newman and Hilary Bouton-Verville and Fernando Garces and Ian A Wilson and Max Crispin and Beatrice H Hahn and Barton F Haynes and Laurent Verkoczy and Andrew B Ward and Dennis R Burton},

doi = {10.1016/j.celrep.2019.04.082},

issn = {2211-1247},

year  = {2019},

date = {2019-01-01},

journal = {Cell Rep},

volume = {27},

number = {8},

pages = {2426--2441.e6},

abstract = {Epitope-targeted HIV vaccine design seeks to focus antibody responses to broadly neutralizing antibody (bnAb) sites by sequential immunization. A chimpanzee simian immunodeficiency virus (SIV) envelope (Env) shares a single bnAb site, the variable loop 2 (V2)-apex, with HIV, suggesting its possible utility in an HIV immunization strategy. Here, we generate a chimpanzee SIV Env trimer, MT145K, which displays selective binding to HIV V2-apex bnAbs and precursor versions, but no binding to other HIV specificities. We determine the structure of the MT145K trimer by cryo-EM and show that its architecture is remarkably similar to HIV Env. Immunization of an HIV V2-apex bnAb precursor Ab-expressing knockin mouse with the chimpanzee MT145K trimer induces HIV V2-specific neutralizing responses. Subsequent boosting with an HIV trimer cocktail induces responses that exhibit some virus cross-neutralization. Overall, the chimpanzee MT145K trimer behaves as expected from design both in vitro and in vivo and is an attractive potential component of a sequential immunization regimen to induce V2-apex bnAbs.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31100268,

title = {A Site of Vulnerability on the Influenza Virus Hemagglutinin Head Domain Trimer Interface},

author = {Sandhya Bangaru and Shanshan Lang and Michael Schotsaert and Hillary A Vanderven and Xueyong Zhu and Nurgun Kose and Robin Bombardi and Jessica A Finn and Stephen J Kent and Pavlo Gilchuk and Iuliia Gilchuk and Hannah L Turner and Adolfo García-Sastre and Sheng Li and Andrew B Ward and Ian A Wilson and James E Crowe},

doi = {10.1016/j.cell.2019.04.011},

issn = {1097-4172},

year  = {2019},

date = {2019-01-01},

journal = {Cell},

volume = {177},

number = {5},

pages = {1136--1152.e18},

abstract = {Here, we describe the discovery of a naturally occurring human antibody (Ab), FluA-20, that recognizes a new site of vulnerability on the hemagglutinin (HA) head domain and reacts with most influenza A viruses. Structural characterization of FluA-20 with H1 and H3 head domains revealed a novel epitope in the HA trimer interface, suggesting previously unrecognized dynamic features of the trimeric HA protein. The critical HA residues recognized by FluA-20 remain conserved across most subtypes of influenza A viruses, which explains the Ab's extraordinary breadth. The Ab rapidly disrupted the integrity of HA protein trimers, inhibited cell-to-cell spread of virus in culture, and protected mice against challenge with viruses of H1N1, H3N2, H5N1, or H7N9 subtypes when used as prophylaxis or therapy. The FluA-20 Ab has uncovered an exceedingly conserved protective determinant in the influenza HA head domain trimer interface that is an unexpected new target for anti-influenza therapeutics and vaccines.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30886356,

title = {Antibody responses to viral infections: a structural perspective across three different enveloped viruses},

author = {Charles D Murin and Ian A Wilson and Andrew B Ward},

doi = {10.1038/s41564-019-0392-y},

issn = {2058-5276},

year  = {2019},

date = {2019-01-01},

journal = {Nat Microbiol},

volume = {4},

number = {5},

pages = {734--747},

abstract = {Antibodies serve as critical barriers to viral infection. Humoral immunity to a virus is achieved through the dual role of antibodies in communicating the presence of invading pathogens in infected cells to effector cells, and in interfering with processes essential to the viral life cycle (chiefly entry into the host cell). For individuals that successfully control infection, virus-elicited antibodies can provide lifelong surveillance and protection from future insults. One approach to understand the nature of a successful immune response has been to utilize structural biology to uncover the molecular details of antibodies derived from vaccines or natural infection and how they interact with their cognate microbial antigens. The ability to isolate antigen-specific B-cells and rapidly solve structures of functional, monoclonal antibodies in complex with viral glycoprotein surface antigens has greatly expanded our knowledge of the sites of vulnerability on viruses. In this Review, we compare the adaptive humoral immune responses to human immunodeficiency virus (HIV), influenza and filoviruses, with a particular focus on neutralizing antibodies. The pathogenesis of each of these viruses is quite different, providing an opportunity for comparison of immune responses: HIV causes a persistent, chronic infection; influenza, an acute infection with multiple exposures during a lifetime and annual vaccination; filoviruses, a virulent, acute infection. Neutralizing antibodies that develop under these different constraints are therefore sentinels that can provide insight into the underlying humoral immune responses, as well as important lessons to guide future development of vaccines and immunotherapeutics.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30971495,

title = {Stabilization of amyloidogenic immunoglobulin light chains by small molecules},

author = {Gareth J Morgan and Nicholas L Yan and David E Mortenson and Enrico Rennella and Joshua M Blundon and Ryan M Gwin and Chung-Yon Lin and Robyn L Stanfield and Steven J Brown and Hugh Rosen and Timothy P Spicer and Virneliz Fernandez-Vega and Giampaolo Merlini and Lewis E Kay and Ian A Wilson and Jeffery W Kelly},

doi = {10.1073/pnas.1817567116},

issn = {1091-6490},

year  = {2019},

date = {2019-01-01},

journal = {Proc Natl Acad Sci U S A},

volume = {116},

number = {17},

pages = {8360--8369},

abstract = {In Ig light-chain (LC) amyloidosis (AL), the unique antibody LC protein that is secreted by monoclonal plasma cells in each patient misfolds and/or aggregates, a process leading to organ degeneration. As a step toward developing treatments for AL patients with substantial cardiac involvement who have difficulty tolerating existing chemotherapy regimens, we introduce small-molecule kinetic stabilizers of the native dimeric structure of full-length LCs, which can slow or stop the amyloidogenicity cascade at its origin. A protease-coupled fluorescence polarization-based high-throughput screen was employed to identify small molecules that kinetically stabilize LCs. NMR and X-ray crystallographic data demonstrate that at least one structural family of hits bind at the LC-LC dimerization interface within full-length LCs, utilizing variable-domain residues that are highly conserved in most AL patients. Stopping the amyloidogenesis cascade at the beginning is a proven strategy to ameliorate postmitotic tissue degeneration.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30996301,

title = {Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification},

author = {Senlian Hong and Yujie Shi and Nicholas C Wu and Geramie Grande and Lacey Douthit and Hua Wang and Wen Zhou and K Barry Sharpless and Ian A Wilson and Jia Xie and Peng Wu},

doi = {10.1038/s41467-019-09608-w},

issn = {2041-1723},

year  = {2019},

date = {2019-01-01},

journal = {Nat Commun},

volume = {10},

number = {1},

pages = {1799},

abstract = {Chemoenzymatic modification of cell-surface glycan structures has emerged as a complementary approach to metabolic oligosaccharide engineering. Here, we identify Pasteurella multocida α2-3-sialyltransferase M144D mutant, Photobacterium damsela α2-6-sialyltransferase, and Helicobacter mustelae α1-2-fucosyltransferase, as efficient tools for live-cell glycan modification. Combining these enzymes with Helicobacter pylori α1-3-fucosyltransferase, we develop a host-cell-based assay to probe glycan-mediated influenza A virus (IAV) infection including wild-type and mutant strains of H1N1 and H3N2 subtypes. At high NeuAcα2-6-Gal levels, the IAV-induced host-cell death is positively correlated with haemagglutinin (HA) binding affinity to NeuAcα2-6-Gal. Remarkably, an increment of host-cell-surface sialyl Lewis X (sLe) exacerbates the killing by several wild-type IAV strains and a previously engineered mutant HK68-MTA. Structural alignment of HAs from HK68 and HK68-MTA suggests formation of a putative hydrogen bond between Trp222 of HA-HK68-MTA and the C-4 hydroxyl group of the α1-3-linked fucose of sLe, which may account for the enhanced host cell killing of that mutant.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30989115,

title = {A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike},

author = {Shuai Xia and Lei Yan and Wei Xu and Anurodh Shankar Agrawal and Abdullah Algaissi and Chien-Te K Tseng and Qian Wang and Lanying Du and Wenjie Tan and Ian A Wilson and Shibo Jiang and Bei Yang and Lu Lu},

doi = {10.1126/sciadv.aav4580},

issn = {2375-2548},

year  = {2019},

date = {2019-01-01},

journal = {Sci Adv},

volume = {5},

number = {4},

pages = {eaav4580},

abstract = {Continuously emerging highly pathogenic human coronaviruses (HCoVs) remain a major threat to human health, as illustrated in past SARS-CoV and MERS-CoV outbreaks. The development of a drug with broad-spectrum HCoV inhibitory activity would address this urgent unmet medical need. Although previous studies have suggested that the HR1 of HCoV spike (S) protein is an important target site for inhibition against specific HCoVs, whether this conserved region could serve as a target for the development of broad-spectrum pan-CoV inhibitor remains controversial. Here, we found that peptide OC43-HR2P, derived from the HR2 domain of HCoV-OC43, exhibited broad fusion inhibitory activity against multiple HCoVs. EK1, the optimized form of OC43-HR2P, showed substantially improved pan-CoV fusion inhibitory activity and pharmaceutical properties. Crystal structures indicated that EK1 can form a stable six-helix bundle structure with both short α-HCoV and long β-HCoV HR1s, further supporting the role of HR1 region as a viable pan-CoV target site.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}