@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 = {2019-05-01},

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 = {2019-05-01},

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 = {2019-05-01},

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 = {2019-04-01},

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 = {2019-04-01},

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 = {2019-04-01},

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}

}

@article{pmid30535315,

title = {Immunodominance and Antigenic Variation of Influenza Virus Hemagglutinin: Implications for Design of Universal Vaccine Immunogens},

author = {Seth J Zost and Nicholas C Wu and Scott E Hensley and Ian A Wilson},

doi = {10.1093/infdis/jiy696},

issn = {1537-6613},

year  = {2019},

date = {2019-04-01},

journal = {J Infect Dis},

volume = {219},

number = {Suppl_1},

pages = {S38--S45},

abstract = {Influenza viruses routinely acquire mutations in their hemagglutinin (HA) and neuraminidase (NA) glycoproteins that abrogate binding of pre-existing antibodies in a process known as antigenic drift. Most human antibodies against HA and NA are directed against epitopes that are hypervariable and not against epitopes that are conserved among different influenza virus strains. Universal influenza vaccines are currently being developed to elicit protective responses against functionally conserved sites on influenza proteins where viral escape mutations can result in large fitness costs [1]. Universal vaccine targets include the highly conserved HA stem domain [2-12], the less conserved HA receptor-binding site (RBS) [13-16], as well as conserved sites on NA [17-19]. One central challenge of universal vaccine efforts is to steer human antibody responses away from immunodominant, variable epitopes and towards subdominant, functionally conserved sites. Overcoming this challenge will require further understanding of the structural basis of broadly neutralizing HA and NA antibody binding epitopes and factors that influence immunodominance hierarchies of human antibody responses.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30728245,

title = {Stabilization of the V2 loop improves the presentation of V2 loop-associated broadly neutralizing antibody epitopes on HIV-1 envelope trimers},

author = {Steven W de Taeye and Eden P Go and Kwinten Sliepen and Alba Torrents de la Peña and Kimberly Badal and Max Medina-Ramírez and Wen-Hsin Lee and Heather Desaire and Ian A Wilson and John P Moore and Andrew B Ward and Rogier W Sanders},

doi = {10.1074/jbc.RA118.005396},

issn = {1083-351X},

year  = {2019},

date = {2019-04-01},

journal = {J Biol Chem},

volume = {294},

number = {14},

pages = {5616--5631},

abstract = {A successful HIV-1 vaccine will likely need to elicit broadly neutralizing antibodies (bNAbs) that target the envelope glycoprotein (Env) spike on the virus. Native-like recombinant Env trimers of the SOSIP design now serve as a platform for achieving this challenging goal. However, SOSIP trimers usually do not bind efficiently to the inferred germline precursors of bNAbs (gl-bNAbs). We hypothesized that the inherent flexibilities of the V1 and V2 variable loops in the Env trimer contribute to the poor recognition of gl-bNAb epitopes at the trimer apex that extensively involve V2 residues. To reduce local V2 flexibility and improve the binding of V2-dependent bNAbs and gl-bNAbs, we designed BG505 SOSIP.664 trimer variants containing newly created disulfide bonds intended to stabilize the V2 loop in an optimally antigenic configuration. The first variant, I184C/E190C, contained a new disulfide bond within the V2 loop, whereas the second variant, E153C/R178C, had a new disulfide bond that cross-linked V2 and V1. The resulting engineered native-like trimer variants were both more reactive with and were neutralized by V2 bNAbs and gl-bNAbs, a finding that may be valuable in the design of germline targeting and boosting trimer immunogens to create an antigenic conformation optimal for HIV vaccine development.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30846569,

title = {A small-molecule fusion inhibitor of influenza virus is orally active in mice},

author = {Maria J P van Dongen and Rameshwar U Kadam and Jarek Juraszek and Edward Lawson and Boerries Brandenburg and Frederike Schmitz and Wim B G Schepens and Bart Stoops and Harry A van Diepen and Mandy Jongeneelen and Chan Tang and Jan Vermond and Alida van Eijgen-Obregoso Real and Sven Blokland and Divita Garg and Wenli Yu and Wouter Goutier and Ellen Lanckacker and Jaco M Klap and Daniëlle C G Peeters and Jin Wu and Christophe Buyck and Tim H M Jonckers and Dirk Roymans and Peter Roevens and Ronald Vogels and Wouter Koudstaal and Robert H E Friesen and Pierre Raboisson and Dashyant Dhanak and Jaap Goudsmit and Ian A Wilson},

doi = {10.1126/science.aar6221},

issn = {1095-9203},

year  = {2019},

date = {2019-03-01},

journal = {Science},

volume = {363},

number = {6431},

abstract = {Recent characterization of broadly neutralizing antibodies (bnAbs) against influenza virus identified the conserved hemagglutinin (HA) stem as a target for development of universal vaccines and therapeutics. Although several stem bnAbs are being evaluated in clinical trials, antibodies are generally unsuited for oral delivery. Guided by structural knowledge of the interactions and mechanism of anti-stem bnAb CR6261, we selected and optimized small molecules that mimic the bnAb functionality. Our lead compound neutralizes influenza A group 1 viruses by inhibiting HA-mediated fusion in vitro, protects mice against lethal and sublethal influenza challenge after oral administration, and effectively neutralizes virus infection in reconstituted three-dimensional cell culture of fully differentiated human bronchial epithelial cells. Cocrystal structures with H1 and H5 HAs reveal that the lead compound recapitulates the bnAb hotspot interactions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30884330,

title = {V1-69 antiviral broadly neutralizing antibodies: genetics, structures, and relevance to rational vaccine design},

author = {Fang Chen and Netanel Tzarum and Ian A Wilson and Mansun Law},

doi = {10.1016/j.coviro.2019.02.004},

issn = {1879-6265},

year  = {2019},

date = {2019-02-01},

journal = {Curr Opin Virol},

volume = {34},

pages = {149--159},

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 V1-69-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.},

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{pmid30487280,

title = {Closing and Opening Holes in the Glycan Shield of HIV-1 Envelope Glycoprotein SOSIP Trimers Can Redirect the Neutralizing Antibody Response to the Newly Unmasked Epitopes},

author = {Rajesh P Ringe and Pavel Pugach and Christopher A Cottrell and Celia C LaBranche and Gemma E Seabright and Thomas J Ketas and Gabriel Ozorowski and Sonu Kumar and Anna Schorcht and Marit J van Gils and Max Crispin and David C Montefiori and Ian A Wilson and Andrew B Ward and Rogier W Sanders and P J Klasse and John P Moore},

doi = {10.1128/JVI.01656-18},

issn = {1098-5514},

year  = {2019},

date = {2019-02-01},

journal = {J Virol},

volume = {93},

number = {4},

abstract = {In HIV-1 vaccine research, native-like, soluble envelope glycoprotein SOSIP trimers are widely used for immunizing animals. The epitopes of autologous neutralizing antibodies (NAbs) induced by the BG505 and B41 SOSIP trimers in rabbits and macaques have been mapped to a few holes in the glycan shields that cover most of the protein surfaces. For BG505 trimers, the dominant autologous NAb epitope in rabbits involves residues that line a cavity caused by the absence of a glycan at residue 241. Here, we blocked this epitope in BG505 SOSIPv4.1 trimer immunogens by knocking in an N-linked glycan at residue 241. We then opened holes elsewhere on the trimer by knocking out single N-linked glycans at residues 197, 234, 276, 332, and 355 and found that NAb responses induced by the 241-glycan-bearing BG505 trimers were frequently redirected to the newly opened sites. The strongest evidence for redirection of the NAb response to neoepitopes, through the opening and closing of glycan holes, was obtained from trimer immunogen groups with the highest occupancy of the N241 site. We also attempted to knock in the N289-glycan to block the sole autologous NAb epitope on the B41 SOSIP.v4.1 trimer. Although a retrospective analysis showed that the new N289-glycan site was substantially underoccupied, we found some evidence for redirection of the NAb response to a neoepitope when this site was knocked in and the N356-glycan site knocked out. In neither study, however, was redirection associated with increased neutralization of heterologous tier 2 viruses. Engineered SOSIP trimers mimic envelope-glycoprotein spikes, which stud the surface of HIV-1 particles and mediate viral entry into cells. When used for immunizing test animals, they elicit antibodies that neutralize resistant sequence-matched HIV-1 isolates. These neutralizing antibodies recognize epitopes in holes in the glycan shield that covers the trimer. Here, we added glycans to block the most immunogenic neutralization epitopes on BG505 and B41 SOSIP trimers. In addition, we removed selected other glycans to open new holes that might expose new immunogenic epitopes. We immunized rabbits with the various glycan-modified trimers and then dissected the specificities of the antibody responses. Thus, in principle, the antibody response might be diverted from one site to a more cross-reactive one, which would help in the induction of broadly neutralizing antibodies by HIV-1 vaccines based on envelope glycoproteins.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30770829,

title = {Capturing the inherent structural dynamics of the HIV-1 envelope glycoprotein fusion peptide},

author = {Sonu Kumar and Anita Sarkar and Pavel Pugach and Rogier W Sanders and John P Moore and Andrew B Ward and Ian A Wilson},

doi = {10.1038/s41467-019-08738-5},

issn = {2041-1723},

year  = {2019},

date = {2019-02-01},

journal = {Nat Commun},

volume = {10},

number = {1},

pages = {763},

abstract = {The N-terminal fusion peptide (FP) of the human immunodeficiency virus (HIV)-1 envelope glycoprotein (Env) gp41 subunit plays a critical role in cell entry. However, capturing the structural flexibility in the unbound FP is challenging in the native Env trimer. Here, FP conformational isomerism is observed in two crystal structures of a soluble clade B transmitted/founder virus B41 SOSIP.664 Env with broadly neutralizing antibodies (bNAbs) PGT124 and 35O22 to aid in crystallization and that are not specific for binding to the FP. Large rearrangements in the FP and fusion peptide proximal region occur around M530, which remains anchored in the tryptophan clasp (gp41 W623, W628, W631) in the B41 Env prefusion state. Further, we redesigned the FP at position 518 to reinstate the bNAb VRC34.01 epitope. These findings provide further structural evidence for the dynamic nature of the FP and how a bNAb epitope can be restored during vaccine design.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30716060,

title = {Potent anti-influenza H7 human monoclonal antibody induces separation of hemagglutinin receptor-binding head domains},

author = {Hannah L Turner and Jesper Pallesen and Shanshan Lang and Sandhya Bangaru and Sarah Urata and Sheng Li and Christopher A Cottrell and Charles A Bowman and James E Crowe and Ian A Wilson and Andrew B Ward},

doi = {10.1371/journal.pbio.3000139},

issn = {1545-7885},

year  = {2019},

date = {2019-02-01},

journal = {PLoS Biol},

volume = {17},

number = {2},

pages = {e3000139},

abstract = {Seasonal influenza virus infections can cause significant morbidity and mortality, but the threat from the emergence of a new pandemic influenza strain might have potentially even more devastating consequences. As such, there is intense interest in isolating and characterizing potent neutralizing antibodies that target the hemagglutinin (HA) viral surface glycoprotein. Here, we use cryo-electron microscopy (cryoEM) to decipher the mechanism of action of a potent HA head-directed monoclonal antibody (mAb) bound to an influenza H7 HA. The epitope of the antibody is not solvent accessible in the compact, prefusion conformation that typifies all HA structures to date. Instead, the antibody binds between HA head protomers to an epitope that must be partly or transiently exposed in the prefusion conformation. The "breathing" of the HA protomers is implied by the exposure of this epitope, which is consistent with metastability of class I fusion proteins. This structure likely therefore represents an early structural intermediate in the viral fusion process. Understanding the extent of transient exposure of conserved neutralizing epitopes also may lead to new opportunities to combat influenza that have not been appreciated previously.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30642961,

title = {Multistate design of influenza antibodies improves affinity and breadth against seasonal viruses},

author = {Alexander M Sevy and Nicholas C Wu and Iuliia M Gilchuk and Erica H Parrish and Sebastian Burger and Dina Yousif and Marcus B M Nagel and Kevin L Schey and Ian A Wilson and James E Crowe and Jens Meiler},

doi = {10.1073/pnas.1806004116},

issn = {1091-6490},

year  = {2019},

date = {2019-01-01},

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

volume = {116},

number = {5},

pages = {1597--1602},

abstract = {Influenza is a yearly threat to global public health. Rapid changes in influenza surface proteins resulting from antigenic drift and shift events make it difficult to readily identify antibodies with broadly neutralizing activity against different influenza subtypes with high frequency, specifically antibodies targeting the receptor binding domain (RBD) on influenza HA protein. We developed an optimized computational design method that is able to optimize an antibody for recognition of large panels of antigens. To demonstrate the utility of this multistate design method, we used it to redesign an antiinfluenza antibody against a large panel of more than 500 seasonal HA antigens of the H1 subtype. As a proof of concept, we tested this method on a variety of known antiinfluenza antibodies and identified those that could be improved computationally. We generated redesigned variants of antibody C05 to the HA RBD and experimentally characterized variants that exhibited improved breadth and affinity against our panel. C05 mutants exhibited improved affinity for three of the subtypes used in design by stabilizing the CDRH3 loop and creating favorable electrostatic interactions with the antigen. These mutants possess increased breadth and affinity of binding while maintaining high-affinity binding to existing targets, surpassing a major limitation up to this point.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30552025,

title = {Vaccine-Induced Protection from Homologous Tier 2 SHIV Challenge in Nonhuman Primates Depends on Serum-Neutralizing Antibody Titers},

author = {Matthias G Pauthner and Joseph P Nkolola and Colin Havenar-Daughton and Ben Murrell and Samantha M Reiss and Raiza Bastidas and Jérémie Prévost and Rebecca Nedellec and Benjamin von Bredow and Peter Abbink and Christopher A Cottrell and Daniel W Kulp and Talar Tokatlian and Bartek Nogal and Matteo Bianchi and Hui Li and Jeong Hyun Lee and Salvatore T Butera and David T Evans and Lars Hangartner and Andrés Finzi and Ian A Wilson and Richard T Wyatt and Darrell J Irvine and William R Schief and Andrew B Ward and Rogier W Sanders and Shane Crotty and George M Shaw and Dan H Barouch and Dennis R Burton},

doi = {10.1016/j.immuni.2018.11.011},

issn = {1097-4180},

year  = {2019},

date = {2019-01-01},

journal = {Immunity},

volume = {50},

number = {1},

pages = {241--252.e6},

abstract = {Passive administration of HIV neutralizing antibodies (nAbs) can protect macaques from hard-to-neutralize (tier 2) chimeric simian-human immunodeficiency virus (SHIV) challenge. However, conditions for nAb-mediated protection after vaccination have not been established. Here, we selected groups of 6 rhesus macaques with either high or low serum nAb titers from a total of 78 animals immunized with recombinant native-like (SOSIP) Env trimers. Repeat intrarectal challenge with homologous tier 2 SHIV led to rapid infection in unimmunized and low-titer animals. High-titer animals, however, demonstrated protection that was gradually lost as nAb titers waned over time. An autologous serum ID nAb titer of ∼1:500 afforded more than 90% protection from medium-dose SHIV infection. In contrast, antibody-dependent cellular cytotoxicity and T cell activity did not correlate with protection. Therefore, Env protein-based vaccination strategies can protect against hard-to-neutralize SHIV challenge in rhesus macaques by inducing tier 2 nAbs, provided appropriate neutralizing titers can be reached and maintained.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30613781,

title = {Genetic and structural insights into broad neutralization of hepatitis C virus by human V1-69 antibodies},

author = {Netanel Tzarum and Erick Giang and Leopold Kong and Linling He and Jannick Prentoe and Elias Augestad and Yuanzi Hua and Shaun Castillo and Georg M Lauer and Jens Bukh and Jiang Zhu and Ian A Wilson and Mansun Law},

doi = {10.1126/sciadv.aav1882},

issn = {2375-2548},

year  = {2019},

date = {2019-01-01},

journal = {Sci Adv},

volume = {5},

number = {1},

pages = {eaav1882},

abstract = {An effective vaccine to the antigenically diverse hepatitis C virus (HCV) must target conserved immune epitopes. Here, we investigate cross-neutralization of HCV genotypes by broadly neutralizing antibodies (bNAbs) encoded by the relatively abundant human gene family   . We have deciphered the molecular requirements for cross-neutralization by this unique class of human antibodies from crystal structures of HCV E2 in complex with bNAbs. An unusually high binding affinity is found for germ line-reverted versions of V1-69 precursor antibodies, and neutralization breadth is acquired during affinity maturation. Deep sequencing analysis of an HCV-immune B cell repertoire further demonstrates the importance of the    gene family in the generation of HCV bNAbs. This study therefore provides critical insights into immune recognition of HCV with important implications for rational vaccine design.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30318466,

title = {Structural Basis for Recognition of a Unique Epitope by a Human Anti-tau Antibody},

author = {Heng Zhang and Xueyong Zhu and Gabriel Pascual and Jehangir S Wadia and Elissa Keogh and Jeroen J Hoozemans and Berdien Siregar and Hanna Inganäs and Esther J M Stoop and Jaap Goudsmit and Adrian Apetri and Wouter Koudstaal and Ian A Wilson},

doi = {10.1016/j.str.2018.08.012},

issn = {1878-4186},

year  = {2018},

date = {2018-12-01},

journal = {Structure},

volume = {26},

number = {12},

pages = {1626--1634.e4},

abstract = {Aggregation of the hyperphosphorylated protein tau into neurofibrillary tangles and neuropil threads is a hallmark of Alzheimer disease (AD). Identification and characterization of the epitopes recognized by anti-tau antibodies might shed light on the molecular mechanisms of AD pathogenesis. Here we report on the biochemical and structural characterization of a tau-specific monoclonal antibody CBTAU-24.1, which was isolated from the human memory B cell repertoire. Immunohistochemical staining with CBTAU-24.1 specifically detects pathological tau structures in AD brain samples. The crystal structure of CBTAU-24.1 Fab with a phosphorylated tau peptide revealed recognition of a unique epitope (Ser235-Leu243) in the tau proline-rich domain. Interestingly, the antibody can bind tau regardless of phosphorylation state of its epitope region and also recognizes both monomeric and paired helical filament tau irrespective of phosphorylation status. This human anti-tau antibody and its unique epitope may aid in development of diagnostics and/or therapeutic AD strategies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30474059,

title = {HIV-1 vaccine design through minimizing envelope metastability},

author = {Linling He and Sonu Kumar and Joel D Allen and Deli Huang and Xiaohe Lin and Colin J Mann and Karen L Saye-Francisco and Jeffrey Copps and Anita Sarkar and Gabrielle S Blizard and Gabriel Ozorowski and Devin Sok and Max Crispin and Andrew B Ward and David Nemazee and Dennis R Burton and Ian A Wilson and Jiang Zhu},

doi = {10.1126/sciadv.aau6769},

issn = {2375-2548},

year  = {2018},

date = {2018-11-01},

journal = {Sci Adv},

volume = {4},

number = {11},

pages = {eaau6769},

abstract = {Overcoming envelope metastability is crucial to trimer-based HIV-1 vaccine design. Here, we present a coherent vaccine strategy by minimizing metastability. For 10 strains across five clades, we demonstrate that the gp41 ectodomain (gp41) is the main source of envelope metastability by replacing wild-type gp41 with BG505 gp41 of the uncleaved prefusion-optimized (UFO) design. These gp41-swapped trimers can be produced in CHO cells with high yield and high purity. The crystal structure of a gp41-swapped trimer elucidates how a neutralization-resistant tier 3 virus evades antibody recognition of the V2 apex. UFO trimers of transmitted/founder viruses and UFO trimers containing a consensus-based ancestral gp41 suggest an evolutionary root of metastability. The gp41-stabilized trimers can be readily displayed on 24- and 60-meric nanoparticles, with incorporation of additional T cell help illustrated for a hyperstable 60-mer, I3-01. In mice and rabbits, these gp140 nanoparticles induced tier 2 neutralizing antibody responses more effectively than soluble trimers.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30351002,

title = {Structure-Activity Relationships in Metal-Binding Pharmacophores for Influenza Endonuclease},

author = {Cy V Credille and Benjamin L Dick and Christine N Morrison and Ryjul W Stokes and Rebecca N Adamek and Nicholas C Wu and Ian A Wilson and Seth M Cohen},

doi = {10.1021/acs.jmedchem.8b01363},

issn = {1520-4804},

year  = {2018},

date = {2018-11-01},

journal = {J Med Chem},

volume = {61},

number = {22},

pages = {10206--10217},

abstract = {Metalloenzymes represent an important target space for drug discovery. A limitation to the early development of metalloenzyme inhibitors has been the lack of established structure-activity relationships (SARs) for molecules that bind the metal ion cofactor(s) of a metalloenzyme. Herein, we employed a bioinorganic perspective to develop an SAR for inhibition of the metalloenzyme influenza RNA polymerase PA endonuclease. The identified trends highlight the importance of the electronics of the metal-binding pharmacophore (MBP), in addition to MBP sterics, for achieving improved inhibition and selectivity. By optimization of the MBPs for PA endonuclease, a class of highly active and selective fragments was developed that displays IC values <50 nM. This SAR led to structurally distinct molecules that also displayed IC values of ∼10 nM, illustrating the utility of a metal-centric development campaign in generating highly active and selective metalloenzyme inhibitors.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30385580,

title = {Universal protection against influenza infection by a multidomain antibody to influenza hemagglutinin},

author = {Nick S Laursen and Robert H E Friesen and Xueyong Zhu and Mandy Jongeneelen and Sven Blokland and Jan Vermond and Alida van Eijgen and Chan Tang and Harry van Diepen and Galina Obmolova and Marijn van der Neut Kolfschoten and David Zuijdgeest and Roel Straetemans and Ryan M B Hoffman and Travis Nieusma and Jesper Pallesen and Hannah L Turner and Steffen M Bernard and Andrew B Ward and Jinquan Luo and Leo L M Poon and Anna P Tretiakova and James M Wilson and Maria P Limberis and Ronald Vogels and Boerries Brandenburg and Joost A Kolkman and Ian A Wilson},

doi = {10.1126/science.aaq0620},

issn = {1095-9203},

year  = {2018},

date = {2018-11-01},

journal = {Science},

volume = {362},

number = {6414},

pages = {598--602},

abstract = {Broadly neutralizing antibodies against highly variable pathogens have stimulated the design of vaccines and therapeutics. We report the use of diverse camelid single-domain antibodies to influenza virus hemagglutinin to generate multidomain antibodies with impressive breadth and potency. Multidomain antibody MD3606 protects mice against influenza A and B infection when administered intravenously or expressed locally from a recombinant adeno-associated virus vector. Crystal and single-particle electron microscopy structures of these antibodies with hemagglutinins from influenza A and B viruses reveal binding to highly conserved epitopes. Collectively, our findings demonstrate that multidomain antibodies targeting multiple epitopes exhibit enhanced virus cross-reactivity and potency. In combination with adeno-associated virus-mediated gene delivery, they may provide an effective strategy to prevent infection with influenza virus and other highly variable pathogens.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30324137,

title = {Cryo-EM structure of  circumsporozoite protein with a vaccine-elicited antibody is stabilized by somatically mutated inter-Fab contacts},

author = {David Oyen and Jonathan L Torres and Christopher A Cottrell and C Richter King and Ian A Wilson and Andrew B Ward},

doi = {10.1126/sciadv.aau8529},

issn = {2375-2548},

year  = {2018},

date = {2018-10-01},

journal = {Sci Adv},

volume = {4},

number = {10},

pages = {eaau8529},

abstract = {The circumsporozoite protein (CSP) on the surface of  sporozoites is important for parasite development, motility, and host hepatocyte invasion. However, intrinsic disorder of the NANP repeat sequence in the central region of CSP has hindered its structural and functional characterization. Here, the cryo-electron microscopy structure at ~3.4-Å resolution of a recombinant shortened CSP construct with the variable domains (Fabs) of a highly protective monoclonal antibody reveals an extended spiral conformation of the central NANP repeat region surrounded by antibodies. This unusual structure appears to be stabilized and/or induced by interaction with an antibody where contacts between adjacent Fabs are somatically mutated and enhance the interaction. This maturation in non-antigen contact residues may be an effective mechanism for antibodies to target tandem repeat sequences and provide novel insights into malaria vaccine design.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30308159,

title = {Recurring and Adaptable Binding Motifs in Broadly Neutralizing Antibodies to Influenza Virus Are Encoded on the D3-9 Segment of the Ig Gene},

author = {Nicholas C Wu and Seiya Yamayoshi and Mutsumi Ito and Ryuta Uraki and Yoshihiro Kawaoka and Ian A Wilson},

doi = {10.1016/j.chom.2018.09.010},

issn = {1934-6069},

year  = {2018},

date = {2018-10-01},

journal = {Cell Host Microbe},

volume = {24},

number = {4},

pages = {569--578.e4},

abstract = {Discovery and characterization of broadly neutralizing antibodies (bnAbs) to the influenza hemagglutinin (HA) stem have provided insights for the development of a universal flu vaccine. Identification of signature features common to bnAbs from different individuals will be key to guiding immunogen design. S9-3-37 is a bnAb isolated from a healthy H5N1 vaccinee. Here, structural characterization reveals that the D3-9 gene segment of S9-3-37 contributes most of the interaction surface with the highly conserved stem epitope on HA. Comparison with other influenza bnAb crystal structures indicates that the D3-9 segment provides a general mechanism for targeting HA stem. Interestingly, such bnAbs can approach the HA stem with vastly different angles and orientations. Moreover, D3-9 can be translated in different reading frames in different bnAbs yet still target the same HA stem pocket. Thus, the D3-9 gene segment in the human immune repertoire can provide a robust defense against influenza virus.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30232260,

title = {Structural basis for cooperative regulation of KIX-mediated transcription pathways by the HTLV-1 HBZ activation domain},

author = {Ke Yang and Robyn L Stanfield and Maria A Martinez-Yamout and H Jane Dyson and Ian A Wilson and Peter E Wright},

doi = {10.1073/pnas.1810397115},

issn = {1091-6490},

year  = {2018},

date = {2018-10-01},

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

volume = {115},

number = {40},

pages = {10040--10045},

abstract = {The human T cell leukemia virus I basic leucine zipper protein (HTLV-1 HBZ) maintains chronic viral infection and promotes leukemogenesis through poorly understood mechanisms involving interactions with the KIX domain of the transcriptional coactivator CBP and its paralog p300. The KIX domain binds regulatory proteins at the distinct MLL and c-Myb/pKID sites to form binary or ternary complexes. The intrinsically disordered N-terminal activation domain of HBZ (HBZ AD) deregulates cellular signaling pathways by competing directly with cellular and viral transcription factors for binding to the MLL site and by allosterically perturbing binding of the transactivation domain of the hematopoietic transcription factor c-Myb. Crystal structures of the ternary KIX:c-Myb:HBZ complex show that the HBZ AD recruits two KIX:c-Myb entities through tandem amphipathic motifs (L/V)(V/L)DGLL and folds into a long α-helix upon binding. Isothermal titration calorimetry reveals strong cooperativity in binding of the c-Myb activation domain to the KIX:HBZ complex and in binding of HBZ to the KIX:c-Myb complex. In addition, binding of KIX to the two HBZ (V/L)DGLL motifs is cooperative; the structures suggest that this cooperativity is achieved through propagation of the HBZ α-helix beyond the first binding motif. Our study suggests that the unique structural flexibility and the multiple interaction motifs of the intrinsically disordered HBZ AD are responsible for its potency in hijacking KIX-mediated transcription pathways. The KIX:c-Myb:HBZ complex provides an example of cooperative stabilization in a transcription factor:coactivator network and gives insights into potential mechanisms through which HBZ dysregulates hematopoietic transcriptional programs and promotes T cell proliferation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29846612,

title = {Clinical Correlations of Transcriptional Profile in Patients Infected With Avian Influenza H7N9 Virus},

author = {Wenda Guan and Zifeng Yang and Nicholas C Wu and Horace H Y Lee and Yimin Li and Wenxin Jiang and Lihan Shen and Douglas C Wu and Rongchang Chen and Nanshan Zhong and Ian A Wilson and Malik Peiris and Chris K P Mok},

doi = {10.1093/infdis/jiy317},

issn = {1537-6613},

year  = {2018},

date = {2018-09-01},

journal = {J Infect Dis},

volume = {218},

number = {8},

pages = {1238--1248},

abstract = {BACKGROUND: Avian influenza A (H7N9) viruses emerged in China in 2013 and caused zoonotic disease associated with a case-fatality ratio of over 30%. Transcriptional profiles in peripheral blood reflect host responses and can help to elucidate disease pathogenesis.nnMETHODS: We correlated serial blood transcriptomic profiles of patients with avian influenza A (H7N9) virus infection and determined the biological significances from the analysis.nnRESULTS: We found that specific gene expression profiles in the blood were strongly correlated with the Pao 2/Fio 2 ratio and viral load in the lower respiratory tract. Cell cycle and leukocyte-related immunity were activated at the acute stage of the infection while T-cell functions and various metabolic processes were associated with the recovery phase of the illness. A transition from systemic innate to adaptive immunity was found.nnCONCLUSIONS: We developed a novel approach for transcriptomic analysis to identify key host responses that were strongly correlated with specific clinical and virologic parameters in patients with H7N9 infection.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30198895,

title = {Crystal structure of the post-fusion core of the Human coronavirus 229E spike protein at 1.86 Å resolution},

author = {Lei Yan and Bing Meng and Jiangchao Xiang and Ian A Wilson and Bei Yang},

doi = {10.1107/S2059798318008318},

issn = {2059-7983},

year  = {2018},

date = {2018-09-01},

journal = {Acta Crystallogr D Struct Biol},

volume = {74},

number = {Pt 9},

pages = {841--851},

abstract = {Human coronavirus 229E (HCoV-229E) usually causes mild upper respiratory infections in heathy adults, but may lead to severe complications or mortality in individuals with weakened immune systems. Virus entry of HCoV-229E is mediated by its spike (S) protein, where the S1 domain facilitates attachment to host cells and the S2 domain is involved in subsequent fusion of the virus and host membranes. During the fusion process, two heptad repeats, HR1 and HR2, in the S2 domain assemble into a six-helix membrane-fusion structure termed the fusion core. Here, the complete fusion-core structure of HCoV-229E has been determined at 1.86 Å resolution, representing the most complete post-fusion conformation thus far among published human alphacoronavirus (α-HCoV) fusion-core structures. The overall structure of the HCoV-229E fusion core is similar to those of SARS, MERS and HCoV-NL63, but the packing of its 3HR1 core differs from those of SARS and MERS in that it contains more noncanonical `x' and `da' layers. Side-by-side electrostatic surface comparisons reveal that the electrostatic surface potentials are opposite in α-HCoVs and β-HCoVs at certain positions and that the HCoV-229E surface also appears to be the most hydrophobic among the various HCoVs. In addition to the highly conserved hydrophobic interactions between HR1 and HR2, some polar and electrostatic interactions are also well preserved across different HCoVs. This study adds to the structural profiling of HCoVs to aid in the structure-based design of pan-coronavirus small molecules or peptides to inhibit viral fusion.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30097292,

title = {Electron-Microscopy-Based Epitope Mapping Defines Specificities of Polyclonal Antibodies Elicited during HIV-1 BG505 Envelope Trimer Immunization},

author = {Matteo Bianchi and Hannah L Turner and Bartek Nogal and Christopher A Cottrell and David Oyen and Matthias Pauthner and Raiza Bastidas and Rebecca Nedellec and Laura E McCoy and Ian A Wilson and Dennis R Burton and Andrew B Ward and Lars Hangartner},

doi = {10.1016/j.immuni.2018.07.009},

issn = {1097-4180},

year  = {2018},

date = {2018-08-01},

journal = {Immunity},

volume = {49},

number = {2},

pages = {288--300.e8},

abstract = {Characterizing polyclonal antibody responses via currently available methods is inherently complex and difficult. Mapping epitopes in an immune response is typically incomplete, which creates a barrier to fully understanding the humoral response to antigens and hinders rational vaccine design efforts. Here, we describe a method of characterizing polyclonal responses by using electron microscopy, and we applied this method to the immunization of rabbits with an HIV-1 envelope glycoprotein vaccine candidate, BG505 SOSIP.664. We detected known epitopes within the polyclonal sera and revealed how antibody responses evolved during the prime-boosting strategy to ultimately result in a neutralizing antibody response. We uncovered previously unidentified epitopes, including an epitope proximal to one recognized by human broadly neutralizing antibodies as well as potentially distracting non-neutralizing epitopes. Our method provides an efficient and semiquantitative map of epitopes that are targeted in a polyclonal antibody response and should be of widespread utility in vaccine and infection studies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29954862,

title = {Immunogenetic and structural analysis of a class of HCV broadly neutralizing antibodies and their precursors},

author = {Fernando Aleman and Netanel Tzarum and Leopold Kong and Kenna Nagy and Jiang Zhu and Ian A Wilson and Mansun Law},

doi = {10.1073/pnas.1802378115},

issn = {1091-6490},

year  = {2018},

date = {2018-07-01},

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

volume = {115},

number = {29},

pages = {7569--7574},

abstract = {Elicitation of broadly neutralizing antibodies (bnAbs) is a leading strategy in rational vaccine design against antigenically diverse pathogens. Here, we studied a panel of monoclonal antibodies (mAbs) from mice immunized with the hepatitis C virus (HCV) envelope glycoproteins E1E2. Six of the mAbs recognize the conserved E2 antigenic site 412-423 (AS412) and cross-neutralize diverse HCV genotypes. Immunogenetic and structural analysis revealed that the antibodies originated from two different germline (GL) precursors and bind AS412 in a β-hairpin conformation. Intriguingly, the anti-HCV activity of one antibody lineage is associated with maturation of the light chain (LC), whereas the other lineage is dependent on heavy-chain (HC) maturation. Crystal structures of GL precursors of the LC-dependent lineage in complex with AS412 offer critical insights into the maturation process of bnAbs to HCV, providing a scientific foundation for utilizing the mouse model to study AS412-targeting vaccine candidates.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29991715,

title = {A multifunctional human monoclonal neutralizing antibody that targets a unique conserved epitope on influenza HA},

author = {Sandhya Bangaru and Heng Zhang and Iuliia M Gilchuk and Thomas G Voss and Ryan P Irving and Pavlo Gilchuk and Pranathi Matta and Xueyong Zhu and Shanshan Lang and Travis Nieusma and Juergen A Richt and Randy A Albrecht and Hillary A Vanderven and Robin Bombardi and Stephen J Kent and Andrew B Ward and Ian A Wilson and James E Crowe},

doi = {10.1038/s41467-018-04704-9},

issn = {2041-1723},

year  = {2018},

date = {2018-07-01},

journal = {Nat Commun},

volume = {9},

number = {1},

pages = {2669},

abstract = {The high rate of antigenic drift in seasonal influenza viruses necessitates frequent changes in vaccine composition. Recent seasonal H3 vaccines do not protect against swine-origin H3N2 variant (H3N2v) strains that recently have caused severe human infections. Here, we report a human V1-69 gene-encoded monoclonal antibody (mAb) designated H3v-47 that exhibits potent cross-reactive neutralization activity against human and swine H3N2 viruses that circulated since 1989. The crystal structure and electron microscopy reconstruction of H3v-47 Fab with the H3N2v hemagglutinin (HA) identify a unique epitope spanning the vestigial esterase and receptor-binding subdomains that is distinct from that of any known neutralizing antibody for influenza A H3 viruses. MAb H3v-47 functions largely by blocking viral egress from infected cells. Interestingly, H3v-47 also engages Fcγ receptor and mediates antibody dependent cellular cytotoxicity (ADCC). This newly identified conserved epitope can be used in design of novel immunogens for development of broadly protective H3 vaccines.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29973404,

title = {The human naive B cell repertoire contains distinct subclasses for a germline-targeting HIV-1 vaccine immunogen},

author = {Colin Havenar-Daughton and Anita Sarkar and Daniel W Kulp and Laura Toy and Xiaozhen Hu and Isaiah Deresa and Oleksandr Kalyuzhniy and Kirti Kaushik and Amit A Upadhyay and Sergey Menis and Elise Landais and Liwei Cao and Jolene K Diedrich and Sonu Kumar and Torben Schiffner and Samantha M Reiss and Grégory Seumois and John R Yates and James C Paulson and Steven E Bosinger and Ian A Wilson and William R Schief and Shane Crotty},

doi = {10.1126/scitranslmed.aat0381},

issn = {1946-6242},

year  = {2018},

date = {2018-07-01},

journal = {Sci Transl Med},

volume = {10},

number = {448},

abstract = {Traditional vaccine development to prevent some of the worst current pandemic diseases has been unsuccessful so far. Germline-targeting immunogens have potential to prime protective antibodies (Abs) via more targeted immune responses. Success of germline-targeting vaccines in humans will depend on the composition of the human naive B cell repertoire, including the frequencies and affinities of epitope-specific B cells. However, the human naive B cell repertoire remains largely undefined. Assessment of antigen-specific human naive B cells among hundreds of millions of B cells from multiple donors may be used as pre-phase 1 ex vivo human testing to potentially forecast B cell and Ab responses to new vaccine designs. VRC01 is an HIV broadly neutralizing Ab (bnAb) against the envelope CD4-binding site (CD4bs). We characterized naive human B cells recognizing eOD-GT8, a germline-targeting HIV-1 vaccine candidate immunogen designed to prime VRC01-class Abs. Several distinct subclasses of VRC01-class naive B cells were identified, sharing sequence characteristics with inferred precursors of known bnAbs VRC01, VRC23, PCIN63, and N6. Multiple naive B cell clones exactly matched mature VRC01-class bnAb L-CDR3 sequences. Non-VRC01-class B cells were also characterized, revealing recurrent public light chain sequences. Unexpectedly, we also identified naive B cells related to the IOMA-class CD4bs bnAb. These different subclasses within the human repertoire had strong initial affinities () to the immunogen, up to 13 nM, and represent encouraging indications that multiple independent pathways may exist for vaccine-elicited VRC01-class bnAb development in most individuals. The frequencies of these distinct eOD-GT8 B cell specificities give insights into antigen-specific compositional features of the human naive B cell repertoire and provide actionable information for vaccine design and advancement.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29898396,

title = {Co-evolution of HIV Envelope and Apex-Targeting Neutralizing Antibody Lineage Provides Benchmarks for Vaccine Design},

author = {Kimmo Rantalainen and Zachary T Berndsen and Sasha Murrell and Liwei Cao and Oluwarotimi Omorodion and Jonathan L Torres and Mengyu Wu and Jeffrey Umotoy and Jeffrey Copps and Pascal Poignard and Elise Landais and James C Paulson and Ian A Wilson and Andrew B Ward},

doi = {10.1016/j.celrep.2018.05.046},

issn = {2211-1247},

year  = {2018},

date = {2018-06-01},

journal = {Cell Rep},

volume = {23},

number = {11},

pages = {3249--3261},

abstract = {Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at serial time points during infection provide a basis for understanding the co-evolutionary contest between HIV and the humoral immune system. Here, we describe the structural characterization of an apex-targeting antibody lineage and autologous clade A viral Env from a donor in the Protocol C cohort. Comparison of Ab-Env complexes at early and late time points reveals that, within the antibody lineage, the CDRH3 loop rigidifies, the bnAb angle of approach steepens, and surface charges are mutated to accommodate glycan changes. Additionally, we observed differences in site-specific glycosylation between soluble and full-length Env constructs, which may be important for tuning optimal immunogenicity in soluble Env trimers. These studies therefore provide important guideposts for design of immunogens that prime and mature nAb responses to the Env V2-apex.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29855358,

title = {A common antigenic motif recognized by naturally occurring human V5-51/V4-1 anti-tau antibodies with distinct functionalities},

author = {Adrian Apetri and Rosa Crespo and Jarek Juraszek and Gabriel Pascual and Roosmarijn Janson and Xueyong Zhu and Heng Zhang and Elissa Keogh and Trevin Holland and Jay Wadia and Hanneke Verveen and Berdien Siregar and Michael Mrosek and Renske Taggenbrock and Jeroenvan Ameijde and Hanna Inganäs and Margot van Winsen and Martin H Koldijk and David Zuijdgeest and Marianne Borgers and Koen Dockx and Esther J M Stoop and Wenli Yu and Els C Brinkman-van der Linden and Kimberley Ummenthum and Kristof van Kolen and Marc Mercken and Stefan Steinbacher and Donata de Marco and Jeroen J Hoozemans and Ian A Wilson and Wouter Koudstaal and Jaap Goudsmit},

doi = {10.1186/s40478-018-0543-z},

issn = {2051-5960},

year  = {2018},

date = {2018-05-01},

journal = {Acta Neuropathol Commun},

volume = {6},

number = {1},

pages = {43},

abstract = {Misfolding and aggregation of tau protein are closely associated with the onset and progression of Alzheimer's Disease (AD). By interrogating IgG memory B cells from asymptomatic donors with tau peptides, we have identified two somatically mutated V5-51/V4-1 antibodies. One of these, CBTAU-27.1, binds to the aggregation motif in the R3 repeat domain and blocks the aggregation of tau into paired helical filaments (PHFs) by sequestering monomeric tau. The other, CBTAU-28.1, binds to the N-terminal insert region and inhibits the spreading of tau seeds and mediates the uptake of tau aggregates into microglia by binding PHFs. Crystal structures revealed that the combination of V5-51 and V4-1 recognizes a common Pro-X-Lys motif driven by germline-encoded hotspot interactions while the specificity and thereby functionality of the antibodies are defined by the CDR3 regions. Affinity improvement led to improvement in functionality, identifying their epitopes as new targets for therapy and prevention of AD.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29595997,

title = {Structure and Immune Recognition of the HIV Glycan Shield},

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

doi = {10.1146/annurev-biophys-060414-034156},

issn = {1936-1238},

year  = {2018},

date = {2018-05-01},

journal = {Annu Rev Biophys},

volume = {47},

pages = {499--523},

abstract = {Vaccine design efforts against the human immunodeficiency virus (HIV) have been greatly stimulated by the observation that many infected patients eventually develop highly potent broadly neutralizing antibodies (bnAbs). Importantly, these bnAbs have evolved to recognize not only the two protein components of the viral envelope protein (Env) but also the numerous glycans that form a protective barrier on the Env protein. Because Env is heavily glycosylated compared to host glycoproteins, the glycans have become targets for the antibody response. Therefore, considerable efforts have been made in developing and validating biophysical methods to elucidate the complex structure of the Env-spike glycoprotein, with its combination of glycan and protein epitopes. We illustrate here how the application of robust biophysical methods has transformed our understanding of the structure and function of the HIV Env spike and stimulated innovation in vaccine design strategies that takes into account the essential glycan components.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29769533,

title = {Structure of a cleavage-independent HIV Env recapitulates the glycoprotein architecture of the native cleaved trimer},

author = {Anita Sarkar and Shridhar Bale and Anna-Janina Behrens and Sonu Kumar and Shailendra Kumar Sharma and Natalia de Val and Jesper Pallesen and Adriana Irimia and Devan C Diwanji and Robyn L Stanfield and Andrew B Ward and Max Crispin and Richard T Wyatt and Ian A Wilson},

doi = {10.1038/s41467-018-04272-y},

issn = {2041-1723},

year  = {2018},

date = {2018-05-01},

journal = {Nat Commun},

volume = {9},

number = {1},

pages = {1956},

abstract = {Furin cleavage of the HIV envelope glycoprotein is an essential step for cell entry that enables formation of well-folded, native-like glycosylated trimers, releases constraints on the fusion peptide, and limits enzymatic processing of the N-glycan shield. Here, we show that a cleavage-independent, stabilized, soluble Env trimer mimic (BG505 NFL.664) exhibits a "closed-form", native-like, prefusion conformation akin to furin-cleaved Env trimers. The crystal structure of BG505 NFL.664 at 3.39 Å resolution with two potent bNAbs also identifies the full epitopes of PGV19 and PGT122 that target the receptor binding site and N332 supersite, respectively. Quantitative site-specific analysis of the glycan shield reveals that native-like glycan processing is maintained despite furin-independent maturation in the secretory pathway. Thus, cleavage-independent NFL Env trimers exhibit quaternary protein and carbohydrate structures similar to the native viral spike that further validate their potential as vaccine immunogen candidates.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29554084,

title = {A public antibody lineage that potently inhibits malaria infection through dual binding to the circumsporozoite protein},

author = {Joshua Tan and Brandon K Sack and David Oyen and Isabelle Zenklusen and Luca Piccoli and Sonia Barbieri and Mathilde Foglierini and Chiara Silacci Fregni and Jessica Marcandalli and Said Jongo and Salim Abdulla and Laurent Perez and Giampietro Corradin and Luca Varani and Federica Sallusto and Betty Kim Lee Sim and Stephen L Hoffman and Stefan H I Kappe and Claudia Daubenberger and Ian A Wilson and Antonio Lanzavecchia},

doi = {10.1038/nm.4513},

issn = {1546-170X},

year  = {2018},

date = {2018-05-01},

journal = {Nat Med},

volume = {24},

number = {4},

pages = {401--407},

abstract = {Immunization with attenuated Plasmodium falciparum sporozoites (PfSPZs) has been shown to be protective against malaria, but the features of the antibody response induced by this treatment remain unclear. To investigate this response in detail, we isolated IgM and IgG monoclonal antibodies from Tanzanian volunteers who were immunized with repeated injection of Sanaria PfSPZ Vaccine and who were found to be protected from controlled human malaria infection with infectious homologous PfSPZs. All isolated IgG monoclonal antibodies bound to P. falciparum circumsporozoite protein (PfCSP) and recognized distinct epitopes in its N terminus, NANP-repeat region, and C terminus. Strikingly, the most effective antibodies, as determined in a humanized mouse model, bound not only to the repeat region, but also to a minimal peptide at the PfCSP N-terminal junction that is not in the RTS,S vaccine. These dual-specific antibodies were isolated from different donors and were encoded by VH3-30 or VH3-33 alleles that encode tryptophan or arginine at position 52. Using structural and mutational data, we describe the elements required for germline recognition and affinity maturation. Our study provides potent neutralizing antibodies and relevant information for lineage-targeted vaccine design and immunization strategies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29596914,

title = {VLR Recognition of TLR5 Expands the Molecular Characterization of Protein Antigen Binding by Non-Ig-based Antibodies},

author = {Robin J Gunn and Brantley R Herrin and Sharmistha Acharya and Max D Cooper and Ian A Wilson},

doi = {10.1016/j.jmb.2018.03.016},

issn = {1089-8638},

year  = {2018},

date = {2018-04-01},

journal = {J Mol Biol},

volume = {430},

number = {9},

pages = {1350--1367},

abstract = {Variable lymphocyte receptors (VLRs) are unconventional adaptive immune receptors relatively recently discovered in the phylogenetically ancient jawless vertebrates, lamprey and hagfish. VLRs bind antigens using a leucine-rich repeat fold and are the only known adaptive immune receptors that do not utilize an immunoglobulin fold for antigen recognition. While immunoglobulin antibodies have been studied extensively, there are comparatively few studies on antigen recognition by VLRs, particularly for protein antigens. Here we report isolation, functional and structural characterization of three VLRs that bind the protein toll-like receptor 5 (TLR5) from zebrafish. Two of the VLRs block binding of TLR5 to its cognate ligand flagellin in functional assays using reporter cells. Co-crystal structures revealed that these VLRs bind to two different epitopes on TLR5, both of which include regions involved in flagellin binding. Our work here demonstrates that the lamprey adaptive immune system can be used to generate high-affinity VLR clones that recognize different epitopes and differentially impact natural ligand binding to a protein antigen.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29610325,

title = {A small-molecule fragment that emulates binding of receptor and broadly neutralizing antibodies to influenza A hemagglutinin},

author = {Rameshwar U Kadam and Ian A Wilson},

doi = {10.1073/pnas.1801999115},

issn = {1091-6490},

year  = {2018},

date = {2018-04-01},

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

volume = {115},

number = {16},

pages = {4240--4245},

abstract = {The influenza virus hemagglutinin (HA) glycoprotein mediates receptor binding and membrane fusion during viral entry in host cells. Blocking these key steps in viral infection has applications for development of novel antiinfluenza therapeutics as well as vaccines. However, the lack of structural information on how small molecules can gain a foothold in the small, shallow receptor-binding site (RBS) has hindered drug design against this important target on the viral pathogen. Here, we report on the serendipitous crystallization-based discovery of a small-molecule -cyclohexyltaurine, commonly known as the buffering agent CHES, that is able to bind to both group-1 and group-2 HAs of influenza A viruses. X-ray structural characterization of group-1 H5N1 A/Vietnam/1203/2004 (H5/Viet) and group-2 H3N2 A/Hong Kong/1/1968 (H3/HK68) HAs at 2.0-Å and 2.57-Å resolution, respectively, revealed that -cyclohexyltaurine binds to the heart of the conserved HA RBS. -cyclohexyltaurine mimics the binding mode of the natural receptor sialic acid and RBS-targeting bnAbs through formation of similar hydrogen bonds and CH-π interactions with the HA. In H3/HK68, -cyclohexyltaurine also binds to a conserved pocket in the stem region, thereby exhibiting a dual-binding mode in group-2 HAs. These long-awaited structural insights into RBS recognition by a noncarbohydrate-based small molecule enhance our knowledge of how to target this important functional site and can serve as a template to guide the development of novel broad-spectrum small-molecule therapeutics against influenza virus.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29150937,

title = {cGMP production and analysis of BG505 SOSIP.664, an extensively glycosylated, trimeric HIV-1 envelope glycoprotein vaccine candidate},

author = {Antu K Dey and Albert Cupo and Gabriel Ozorowski and Vaneet K Sharma and Anna-Janina Behrens and Eden P Go and Thomas J Ketas and Anila Yasmeen and Per J Klasse and Eddy Sayeed and Heather Desaire and Max Crispin and Ian A Wilson and Rogier W Sanders and Thomas Hassell and Andrew B Ward and John P Moore},

doi = {10.1002/bit.26498},

issn = {1097-0290},

year  = {2018},

date = {2018-04-01},

journal = {Biotechnol Bioeng},

volume = {115},

number = {4},

pages = {885--899},

abstract = {We describe the properties of BG505 SOSIP.664 HIV-1 envelope glycoprotein trimers produced under current Good Manufacturing Practice (cGMP) conditions. These proteins are the first of a new generation of native-like trimers that are the basis for many structure-guided immunogen development programs aimed at devising how to induce broadly neutralizing antibodies (bNAbs) to HIV-1 by vaccination. The successful translation of this prototype demonstrates the feasibility of producing similar immunogens on an appropriate scale and of an acceptable quality for Phase I experimental medicine clinical trials. BG505 SOSIP.664 trimers are extensively glycosylated, contain numerous disulfide bonds and require proteolytic cleavage, all properties that pose a substantial challenge to cGMP production. Our strategy involved creating a stable CHO cell line that was adapted to serum-free culture conditions to produce envelope glycoproteins. The trimers were then purified by chromatographic methods using a 2G12 bNAb affinity column and size-exclusion chromatography. The chosen procedures allowed any adventitious viruses to be cleared from the final product to the required extent of >12 log . The final cGMP production run yielded 3.52 g (peptidic mass) of fully purified trimers (Drug Substance) from a 200 L bioreactor, a notable yield for such a complex glycoprotein. The purified trimers were fully native-like as judged by negative-stain electron microscopy, and were stable over a multi-month period at room temperature or below and for at least 1 week at 50°C. Their antigenicity, disulfide bond patterns, and glycan composition were consistent with trimers produced on a research laboratory scale. The methods reported here should pave the way for the cGMP production of other native-like Env glycoprotein trimers of various designs and genotypes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29593268,

title = {A complex epistatic network limits the mutational reversibility in the influenza hemagglutinin receptor-binding site},

author = {Nicholas C Wu and Andrew J Thompson and Jia Xie and Chih-Wei Lin and Corwin M Nycholat and Xueyong Zhu and Richard A Lerner and James C Paulson and Ian A Wilson},

doi = {10.1038/s41467-018-03663-5},

issn = {2041-1723},

year  = {2018},

date = {2018-03-01},

journal = {Nat Commun},

volume = {9},

number = {1},

pages = {1264},

abstract = {The hemagglutinin (HA) receptor-binding site (RBS) in human influenza A viruses is critical for attachment to host cells, which imposes a functional constraint on its natural evolution. On the other hand, being part of the major antigenic sites, the HA RBS of human H3N2 viruses needs to constantly mutate to evade the immune system. From large-scale mutagenesis experiments, we here show that several of the natural RBS substitutions become integrated into an extensive epistatic network that prevents substitution reversion. X-ray structural analysis reveals the mechanistic consequences as well as changes in the mode of receptor binding. Further studies are necessary to elucidate whether such entrenchment limits future options for immune escape or adversely affect long-term viral fitness.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29420040,

title = {Integrity of Glycosylation Processing of a Glycan-Depleted Trimeric HIV-1 Immunogen Targeting Key B-Cell Lineages},

author = {Anna-Janina Behrens and Abhinav Kumar and Max Medina-Ramirez and Albert Cupo and Kevin Marshall and Victor M Cruz Portillo and David J Harvey and Gabriel Ozorowski and Nicole Zitzmann and Ian A Wilson and Andrew B Ward and Weston B Struwe and John P Moore and Rogier W Sanders and Max Crispin},

doi = {10.1021/acs.jproteome.7b00639},

issn = {1535-3907},

year  = {2018},

date = {2018-03-01},

journal = {J Proteome Res},

volume = {17},

number = {3},

pages = {987--999},

abstract = {Broadly neutralizing antibodies (bNAbs) that target the trimeric HIV-1 envelope glycoprotein spike (Env) are tools that can guide the design of recombinant Env proteins intended to engage the predicted human germline precursors of bNAbs (gl-bNAbs). The protein components of gl-bNAb epitopes are often masked by glycans, while mature bNAbs can evolve to accommodate or bypass these shielding glycans. The design of germline-targeting Env immunogens therefore includes the targeted deletion of specific glycan sites. However, the processing of glycans on Env trimers can be influenced by the density with which they are packed together, a highly relevant point given the essential contributions under-processed glycans make to multiple bNAb epitopes. We sought to determine the impact of the removal of 15 potential N-glycan sites (5 per protomer) from the germline-targeting soluble trimer, BG505 SOSIP.v4.1-GT1, using quantitative, site-specific N-glycan mass spectrometry analysis. We find that, compared with SOSIP.664, there was little overall change in the glycan profile but only subtle increases in the extent of processing at sites immediately adjacent to where glycans had been deleted. We conclude that multiple glycans can be deleted from BG505 SOSIP trimers without perturbing the overall integrity of the glycan shield.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29474444,

title = {Epitopes for neutralizing antibodies induced by HIV-1 envelope glycoprotein BG505 SOSIP trimers in rabbits and macaques},

author = {P J Klasse and Thomas J Ketas and Christopher A Cottrell and Gabriel Ozorowski and Gargi Debnath and Diawoye Camara and Erik Francomano and Pavel Pugach and Rajesh P Ringe and Celia C LaBranche and Marit J van Gils and Christine A Bricault and Dan H Barouch and Shane Crotty and Guido Silvestri and Sudhir Kasturi and Bali Pulendran and Ian A Wilson and David C Montefiori and Rogier W Sanders and Andrew B Ward and John P Moore},

doi = {10.1371/journal.ppat.1006913},

issn = {1553-7374},

year  = {2018},

date = {2018-02-01},

journal = {PLoS Pathog},

volume = {14},

number = {2},

pages = {e1006913},

abstract = {The native-like, soluble SOSIP.664 trimer based on the BG505 clade A env gene of HIV-1 is immunogenic in various animal species, of which the most studied are rabbits and rhesus macaques. The trimer induces autologous neutralizing antibodies (NAbs) consistently but at a wide range of titers and with incompletely determined specificities. A precise delineation of immunogenic neutralization epitopes on native-like trimers could help strategies to extend the NAb response to heterologous HIV-1 strains. One autologous NAb epitope on the BG505 Env trimer is known to involve residues lining a hole in the glycan shield that is blocked by adding a glycan at either residue 241 or 289. This glycan-hole epitope accounts for the NAb response of most trimer-immunized rabbits but not for that of a substantial subset. Here, we have used a large panel of mutant BG505 Env-pseudotyped viruses to define additional sites. A frequently immunogenic epitope in rabbits is blocked by adding a glycan at residue 465 near the junction of the gp120 V5 loop and β24 strand and is influenced by amino-acid changes in the structurally nearby C3 region. We name this new site the "C3/465 epitope". Of note is that the C3 region was under selection pressure in the infected infant from whom the BG505 virus was isolated. A third NAb epitope is located in the V1 region of gp120, although it is rarely immunogenic. In macaques, NAb responses induced by BG505 SOSIP trimers are more often directed at the C3/465 epitope than the 241/289-glycan hole.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29396418,

title = {Structural insights into the design of novel anti-influenza therapies},

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

doi = {10.1038/s41594-018-0025-9},

issn = {1545-9985},

year  = {2018},

date = {2018-02-01},

journal = {Nat Struct Mol Biol},

volume = {25},

number = {2},

pages = {115--121},

abstract = {A limited arsenal of therapies is currently available to tackle the emergence of a future influenza pandemic or even to deal effectively with the continual outbreaks of seasonal influenza. However, recent findings hold great promise for the design of novel vaccines and therapeutics, including the possibility of more universal treatments. Structural biology has been a major contributor to those advances, in particular through the many studies on influenza hemagglutinin (HA), the major surface antigen. HA's primary function is to enable the virus to enter host cells, and structural work has revealed the various HA conformational forms generated during the entry process. Other studies have explored how human broadly neutralizing antibodies (bnAbs), designed proteins, peptides and small molecules, can inhibit and neutralize the virus. Here we review milestones in HA structural biology and how the recent insights from bnAbs are paving the way to design novel vaccines and therapeutics.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29222332,

title = {Stabilization of the gp120 V3 loop through hydrophobic interactions reduces the immunodominant V3-directed non-neutralizing response to HIV-1 envelope trimers},

author = {Steven W de Taeye and Alba Torrents de la Peña and Andrea Vecchione and Enzo Scutigliani and Kwinten Sliepen and Judith A Burger and Patricia van der Woude and Anna Schorcht and Edith E Schermer and Marit J van Gils and Celia C LaBranche and David C Montefiori and Ian A Wilson and John P Moore and Andrew B Ward and Rogier W Sanders},

doi = {10.1074/jbc.RA117.000709},

issn = {1083-351X},

year  = {2018},

date = {2018-02-01},

journal = {J Biol Chem},

volume = {293},

number = {5},

pages = {1688--1701},

abstract = {To provide protective immunity against circulating primary HIV-1 strains, a vaccine most likely has to induce broadly neutralizing antibodies to the HIV-1 envelope glycoprotein (Env) spike. Recombinant Env trimers such as the prototype BG505 SOSIP.664 that closely mimic the native Env spike can induce autologous neutralizing antibodies (NAbs) against relatively resistant (tier 2) primary viruses. Ideally, Env immunogens should present broadly neutralizing antibody epitopes but limit the presentation of immunodominant non-NAb epitopes that might induce off-target and potentially interfering responses. The V3 loop in gp120 is such a non-NAb epitope that can effectively elicit non-NAbs when animals are immunized with SOSIP.664 trimers. V3 immunogenicity can be diminished, but not abolished, by reducing the conformational flexibility of trimers via targeted sequence changes, including an A316W substitution in V3, that create the SOSIP.v4.1 and SOSIP.v5.2 variants. Here, we further modified these trimer designs by introducing leucine residues at V3 positions 306 and 308 to create hydrophobic interactions with the tryptophan residue at position 316 and with other topologically proximal sites in the V1V2 domain. Together, these modifications further stabilized the resulting SOSIP.v5.2 S306L/R308L trimers in the prefusion state in which V3 is sequestered. When we tested these trimers as immunogens in rabbits, the induction of V3 non-NAbs was significantly reduced compared with the SOSIP.v5.2 trimers and even more so compared with the SOSIP.664 prototype, without affecting the autologous NAb response. Hence, these additional trimer sequence modifications may be beneficial for immunization strategies that seek to minimize off-target non-NAb responses.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29951061,

title = {The Neutralizing Face of Hepatitis C Virus E2 Envelope Glycoprotein},

author = {Netanel Tzarum and Ian A Wilson and Mansun Law},

doi = {10.3389/fimmu.2018.01315},

issn = {1664-3224},

year  = {2018},

date = {2018-01-01},

journal = {Front Immunol},

volume = {9},

pages = {1315},

abstract = {The high genetic variability of hepatitis C virus, together with the high level of glycosylation on the viral envelope proteins shielding potential neutralizing epitopes, pose a difficult challenge for vaccine development. An effective hepatitis C virus (HCV) vaccine must target conserved epitopes and the HCV E2 glycoprotein is the main target for such neutralizing antibodies (NAbs). Recent structural investigations highlight the presence of a highly conserved and accessible surface on E2 that is devoid of N-linked glycans and known as the E2 neutralizing face. This face is defined as a hydrophobic surface comprising the front layer (FL) and the CD81 binding loop (CD81bl) that overlap with the CD81 receptor binding site on E2. The neutralizing face consists of highly conserved residues for recognition by cross-NAbs, yet it appears to be high conformationally flexible, thereby presenting a moving target for NAbs. Three main overlapping neutralizing sites have been identified in the neutralizing face: antigenic site 412 (AS412), antigenic site 434 (AS434), and antigenic region 3 (AR3). Here, we review the structural analyses of these neutralizing sites, either as recombinant E2 or epitope-derived linear peptides in complex with bNAbs, to understand the functional and preferred conformations for neutralization, and for viral escape. Collectively, these studies provide a foundation and molecular templates to facilitate structure-based approaches for HCV vaccine development.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29455846,

title = {The Unusual Genetics and Biochemistry of Bovine Immunoglobulins},

author = {Robyn L Stanfield and Jeremy Haakenson and Thaddeus C Deiss and Michael F Criscitiello and Ian A Wilson and Vaughn V Smider},

doi = {10.1016/bs.ai.2017.12.004},

issn = {1557-8445},

year  = {2018},

date = {2018-01-01},

journal = {Adv Immunol},

volume = {137},

pages = {135--164},

abstract = {Antibodies are the key circulating molecules that have evolved to fight infection by the adaptive immune system of vertebrates. Typical antibodies of most species contain six complementarity-determining regions (CDRs), where the third CDR of the heavy chain (CDR H3) has the greatest diversity and often makes the most significant contact with antigen. Generally, the process of V(D)J recombination produces a vast repertoire of antibodies; multiple V, D, and J gene segments recombine with additional junctional diversity at the V-D and D-J joints, and additional combinatorial possibilities occur through heavy- and light-chain pairing. Despite these processes, the overall structure of the resulting antibody is largely conserved, and binding to antigen occurs predominantly through the CDR loops of the immunoglobulin V domains. Bovines have deviated from this general paradigm by having few VH regions and thus little germline combinatorial diversity, but their antibodies contain long CDR H3 regions, with substantial diversity generated through somatic hypermutation. A subset of the repertoire comprises antibodies with ultralong CDR H3s, which can reach over 70 amino acids in length. Structurally, these unusual antibodies form a β-ribbon "stalk" and disulfide-bonded "knob" that protrude far from the antibody surface. These long CDR H3s allow cows to mount a particularly robust immune response when immunized with viral antigens, particularly to broadly neutralizing epitopes on a stabilized HIV gp140 trimer, which has been a challenge for other species. The unusual genetics and structural biology of cows provide for a unique paradigm for creation of immune diversity and could enable generation of antibodies against especially challenging targets and epitopes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29386130,

title = {Elicitation of Neutralizing Antibodies Targeting the V2 Apex of the HIV Envelope Trimer in a Wild-Type Animal Model},

author = {James E Voss and Raiees Andrabi and Laura E McCoy and Natalia de Val and Roberta P Fuller and Terrence Messmer and Ching-Yao Su and Devin Sok and Salar N Khan and Fernando Garces and Laura K Pritchard and Richard T Wyatt and Andrew B Ward and Max Crispin and Ian A Wilson and Dennis R Burton},

doi = {10.1016/j.celrep.2017.10.089},

issn = {2211-1247},

year  = {2018},

date = {2018-01-01},

journal = {Cell Rep},

volume = {22},

number = {4},

pages = {1103},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29265822,

title = {"Inverse Drug Discovery" Strategy To Identify Proteins That Are Targeted by Latent Electrophiles As Exemplified by Aryl Fluorosulfates},

author = {David E Mortenson and Gabriel J Brighty and Lars Plate and Grant Bare and Wentao Chen and Suhua Li and Hua Wang and Benjamin F Cravatt and Stefano Forli and Evan T Powers and K Barry Sharpless and Ian A Wilson and Jeffery W Kelly},

doi = {10.1021/jacs.7b08366},

issn = {1520-5126},

year  = {2018},

date = {2018-01-01},

journal = {J Am Chem Soc},

volume = {140},

number = {1},

pages = {200--210},

abstract = {Drug candidates are generally discovered using biochemical screens employing an isolated target protein or by utilizing cell-based phenotypic assays. Both noncovalent and covalent hits emerge from such endeavors. Herein, we exemplify an "Inverse Drug Discovery" strategy in which organic compounds of intermediate complexity harboring weak, but activatable, electrophiles are matched with the protein(s) they react with in cells or cell lysate. An alkyne substructure in each candidate small molecule enables affinity chromatography-mass spectrometry, which produces a list of proteins that each distinct compound reacts with. A notable feature of this approach is that it is agnostic with respect to the cellular proteins targeted. To illustrate this strategy, we employed aryl fluorosulfates, an underexplored class of sulfur(VI) halides, that are generally unreactive unless activated by protein binding. Reversible aryl fluorosulfate binding, correct juxtaposition of protein side chain functional groups, and transition-state stabilization of the S(VI) exchange reaction all seem to be critical for conjugate formation. The aryl fluorosulfates studied thus far exhibit chemoselective reactivity toward Lys and, particularly, Tyr side chains, and can be used to target nonenzymes (e.g., a hormone carrier or a small-molecule carrier protein) as well as enzymes. The "Inverse Drug Discovery" strategy should be particularly attractive as a means to explore latent electrophiles not typically used in medicinal chemistry efforts, until one reacts with a protein target of exceptional interest. Structure-activity data can then be used to enhance the selectivity of conjugate formation or the covalent probe can be used as a competitor to develop noncovalent drug candidates. Here we use the "Inverse Drug Discovery" platform to identify and validate covalent ligands for 11 different human proteins. In the case of one of these proteins, we have identified and validated a small-molecule probe for the first time.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29253863,

title = {Probing the antigenicity of hepatitis C virus envelope glycoprotein complex by high-throughput mutagenesis},

author = {Radhika Gopal and Kelli Jackson and Netanel Tzarum and Leopold Kong and Andrew Ettenger and Johnathan Guest and Jennifer M Pfaff and Trevor Barnes and Andrew Honda and Erick Giang and Edgar Davidson and Ian A Wilson and Benjamin J Doranz and Mansun Law},

doi = {10.1371/journal.ppat.1006735},

issn = {1553-7374},

year  = {2017},

date = {2017-12-01},

journal = {PLoS Pathog},

volume = {13},

number = {12},

pages = {e1006735},

abstract = {The hepatitis C virus (HCV) envelope glycoproteins E1 and E2 form a non-covalently linked heterodimer on the viral surface that mediates viral entry. E1, E2 and the heterodimer complex E1E2 are candidate vaccine antigens, but are technically challenging to study because of difficulties in producing natively folded proteins by standard protein expression and purification methods. To better comprehend the antigenicity of these proteins, a library of alanine scanning mutants comprising the entirety of E1E2 (555 residues) was created for evaluating the role of each residue in the glycoproteins. The mutant library was probed, by a high-throughput flow cytometry-based assay, for binding with the co-receptor CD81, and a panel of 13 human and mouse monoclonal antibodies (mAbs) that target continuous and discontinuous epitopes of E1, E2, and the E1E2 complex. Together with the recently determined crystal structure of E2 core domain (E2c), we found that several residues in the E2 back layer region indirectly impact binding of CD81 and mAbs that target the conserved neutralizing face of E2. These findings highlight an unexpected role for the E2 back layer in interacting with the E2 front layer for its biological function. We also identified regions of E1 and E2 that likely located at or near the interface of the E1E2 complex, and determined that the E2 back layer also plays an important role in E1E2 complex formation. The conformation-dependent reactivity of CD81 and the antibody panel to the E1E2 mutant library provides a global view of the influence of each amino acid (aa) on E1E2 expression and folding. This information is valuable for guiding protein engineering efforts to enhance the antigenic properties and stability of E1E2 for vaccine antigen development and structural studies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29199989,

title = {Crystal structure of an anti-idiotype variable lymphocyte receptor},

author = {Bernard C Collins and Hiro Nakahara and Sharmistha Acharya and Max D Cooper and Brantley R Herrin and Ian A Wilson},

doi = {10.1107/S2053230X1701620X},

issn = {2053-230X},

year  = {2017},

date = {2017-12-01},

journal = {Acta Crystallogr F Struct Biol Commun},

volume = {73},

number = {Pt 12},

pages = {682--687},

abstract = {Variable lymphocyte receptors (VLRs), the leucine-rich repeat (LRR)-based antigen receptors of jawless fish, have great utility in a wide variety of biochemical and biological applications, similar to classical Ig-based antibodies. VLR-based reagents may be particularly useful when traditional antibodies are not available. An anti-idiotype lamprey VLR, VLR39, has previously been identified that recognizes the heavy-chain CDR3 of the B-cell receptor (BCR) of a leukemic clone from a patient with chronic lymphocytic leukemia (CLL). VLR39 was used successfully to track the re-emergence of this clone in the patient following chemotherapy. Here, the crystal structure of VLR39 is presented at 1.5 Å resolution and compared with those of other protein-specific VLRs. VLR39 adopts a curved solenoid fold and exhibits substantial structural similarity to other protein-binding VLRs. VLR39 has a short LRRCT loop that protrudes outwards away from the concave face and is similar to those of its protein-specific VLR counterparts. Analysis of the VLR39-BCR interaction by size-exclusion chromatography and biolayer interferometry using the scFv version of the BCR confirms that VLR39 recognizes the BCR Fv region. Such VLR-based reagents may be useful for identifying and monitoring leukemia in CLL patients and in other clinical diagnostic assays.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29138320,

title = {Structural basis for antibody recognition of the NANP repeats in  circumsporozoite protein},

author = {David Oyen and Jonathan L Torres and Ulrike Wille-Reece and Christian F Ockenhouse and Daniel Emerling and Jacob Glanville and Wayne Volkmuth and Yevel Flores-Garcia and Fidel Zavala and Andrew B Ward and C Richter King and Ian A Wilson},

doi = {10.1073/pnas.1715812114},

issn = {1091-6490},

year  = {2017},

date = {2017-11-01},

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

volume = {114},

number = {48},

pages = {E10438--E10445},

abstract = {Acquired resistance against antimalarial drugs has further increased the need for an effective malaria vaccine. The current leading candidate, RTS,S, is a recombinant circumsporozoite protein (CSP)-based vaccine against  that contains 19 NANP repeats followed by a thrombospondin repeat domain. Although RTS,S has undergone extensive clinical testing and has progressed through phase III clinical trials, continued efforts are underway to enhance its efficacy and duration of protection. Here, we determined that two monoclonal antibodies (mAbs 311 and 317), isolated from a recent controlled human malaria infection trial exploring a delayed fractional dose, inhibit parasite development in vivo by at least 97%. Crystal structures of antibody fragments (Fabs) 311 and 317 with an (NPNA) peptide illustrate their different binding modes. Notwithstanding, one and three of the three NPNA repeats adopt similar well-defined type I β-turns with Fab311 and Fab317, respectively. Furthermore, to explore antibody binding in the context of  CSP, we used negative-stain electron microscopy on a recombinant shortened CSP (rsCSP) construct saturated with Fabs. Both complexes display a compact rsCSP with multiple Fabs bound, with the rsCSP-Fab311 complex forming a highly organized helical structure. Together, these structural insights may aid in the design of a next-generation malaria vaccine.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}