@article{pmid39521150,

title = {Cladophorol-A is an inhibitor of cyclic GMP-AMP synthase},

author = {Mildred Kissai and Emily N Chin and Francisco Martínez-Peña and Ariana Sulpizio and E Paige Stout and Ippei Usui and Farhana Barmare and Brittany Sanchez and Eduardo Esquenazi and Robyn L Stanfield and Ian A Wilson and Luke L Lairson},

doi = {10.1016/j.bmcl.2024.130007},

issn = {1464-3405},

year  = {2025},

date = {2025-01-01},

journal = {Bioorg Med Chem Lett},

volume = {115},

pages = {130007},

abstract = {Cyclic guanosine monophosphate (GMP)-adenosine monophosphate (AMP) synthase (cGAS) is an enzyme sensor of double-stranded DNA (dsDNA) that serves to trigger activation of the cGAS-stimulator of interferon genes (STING) pathway. Excessive activation of this pathway has been demonstrated to contribute to various forms of inflammatory disease. As such, cGAS has arisen as a potential therapeutic target with broad potential applications. Using a pathway-targeted cell-based screening approach, we identified the natural product Cladophorol-A as a new class of non-cytotoxic cGAS inhibitor (cell-based IC = 370 nM). An X-ray co-crystal structure at 2.75 Å resolution revealed that Cladophorol-A inhibits cGAS by binding to its active site within the conserved adenosine nucleobase binding site.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39563066,

title = {Plant-produced SARS-CoV-2 antibody engineered towards enhanced potency and in vivo efficacy},

author = {Steven W de Taeye and Loïc Faye and Bertrand Morel and Angela I Schriek and Jeffrey C Umotoy and Meng Yuan and Natalia A Kuzmina and Hannah L Turner and Xueyong Zhu and Clemens Grünwald-Gruber and Meliawati Poniman and Judith A Burger and Tom G Caniels and Anne-Catherine Fitchette and Réjean Desgagnés and Virginie Stordeur and Lucie Mirande and Guillaume Beauverger and Godelieve de Bree and Gabriel Ozorowski and Andrew B Ward and Ian A Wilson and Alexander Bukreyev and Rogier W Sanders and Louis-Philippe Vezina and Tim Beaumont and Marit J van Gils and Véronique Gomord},

doi = {10.1111/pbi.14458},

issn = {1467-7652},

year  = {2025},

date = {2025-01-01},

journal = {Plant Biotechnol J},

volume = {23},

number = {1},

pages = {4--16},

abstract = {Prevention of severe COVID-19 disease by SARS-CoV-2 in high-risk patients, such as immuno-compromised individuals, can be achieved by administration of antibody prophylaxis, but producing antibodies can be costly. Plant expression platforms allow substantial lower production costs compared to traditional bio-manufacturing platforms depending on mammalian cells in bioreactors. In this study, we describe the expression, production and purification of the originally human COVA2-15 antibody in plants. Our plant-produced mAbs demonstrated comparable neutralizing activity with COVA2-15 produced in mammalian cells. Furthermore, they exhibited similar capacity to prevent SARS-CoV-2 infection in a hamster model. To further enhance these biosimilars, we performed three glyco- and protein engineering techniques. First, to increase antibody half-life, we introduced YTE-mutation in the Fc tail; second, optimization of N-linked glycosylation by the addition of a C-terminal ER-retention motif (HDEL), and finally; production of mAb in plant production lines lacking β-1,2-xylosyltransferase and α-1,3-fucosyltransferase activities (FX-KO). These engineered biosimilars exhibited optimized glycosylation, enhanced phagocytosis and NK cell activation capacity compared to conventional plant-produced S15 and M15 biosimilars, in some cases outperforming mammalian cell produced COVA2-15. These engineered antibodies hold great potential for enhancing in vivo efficacy of mAb treatment against COVID-19 and provide a platform for the development of antibodies against other emerging viruses in a cost-effective manner.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39731211,

title = {Structural Immunology of SARS-CoV-2},

author = {Meng Yuan and Ian A Wilson},

doi = {10.1111/imr.13431},

issn = {1600-065X},

year  = {2025},

date = {2025-01-01},

journal = {Immunol Rev},

volume = {329},

number = {1},

pages = {e13431},

abstract = {The SARS-CoV-2 spike (S) protein has undergone significant evolution, enhancing both receptor binding and immune evasion. In this review, we summarize ongoing efforts to develop antibodies targeting various epitopes of the S protein, focusing on their neutralization potency, breadth, and escape mechanisms. Antibodies targeting the receptor-binding site (RBS) typically exhibit high neutralizing potency but are frequently evaded by mutations in SARS-CoV-2 variants. In contrast, antibodies targeting conserved regions, such as the S2 stem helix and fusion peptide, exhibit broader reactivity but generally lower neutralization potency. However, several broadly neutralizing antibodies have demonstrated exceptional efficacy against emerging variants, including the latest omicron subvariants, underscoring the potential of targeting vulnerable sites such as RBS-A and RBS-D/CR3022. We also highlight public classes of antibodies targeting different sites on the S protein. The vulnerable sites targeted by public antibodies present opportunities for germline-targeting vaccine strategies. Overall, developing escape-resistant, potent antibodies and broadly effective vaccines remains crucial for combating future variants. This review emphasizes the importance of identifying key epitopes and utilizing antibody affinity maturation to inform future therapeutic and vaccine design.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39626211,

title = {Discovery of Potent and Selective Pyridone-Based Small Molecule Kinetic Stabilizers of Amyloidogenic Immunoglobulin Light Chains},

author = {Oren L Lederberg and Nicholas L Yan and Julian Sanchez and Wen Ren and Carl Ash and Steven J Wilkens and Huang Qiu and Bo Qin and Virginia H Grant and Alex B Jackman and Robyn L Stanfield and Ian A Wilson and H Michael Petrassi and Derek Rhoades and Jeffery W Kelly},

doi = {10.1021/acs.jmedchem.4c01773},

issn = {1520-4804},

year  = {2024},

date = {2024-12-01},

journal = {J Med Chem},

volume = {67},

number = {23},

pages = {21070--21105},

abstract = {Kinetic stabilization of amyloidogenic immunoglobulin light chains (LCs) through small molecule binding may become the first treatment for the proteinopathy component of light chain amyloidosis (AL). Kinetic stabilizers selectively bind to the native state over the misfolding transition state, slowing denaturation. Prior λ full-length LC dimer (FL LC) kinetic stabilizers exhibited considerable plasma protein binding. We hypothesized that the coumarin "aromatic core" of the stabilizers was responsible for the undesirable plasma protein binding. Here, we describe structure-activity relationship (SAR) data initially focused on replacing the coumarin aromatic core. 2-pyridones proved suitable replacements. We subsequently optimized the "anchor substructure" in the context of 2-pyridones, resulting in potent λ FL LC kinetic stabilizers exhibiting reduced plasma protein binding. The 3-methyl- or 3-ethyl-3-phenylpyrrolidine-2-pyridone scaffold stabilized multiple AL patient-derived λ FL LCs in human plasma. This, coupled with X-ray crystallographic data, indicates that 3-alkyl-3-phenylpyrrolidine-2-pyridone-based stabilizers are promising candidates for treating the proteinopathy component of AL.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39636110,

title = {Differential antigenic imprinting effects between influenza H1N1 hemagglutinin and neuraminidase in a mouse model},

author = {Huibin Lv and Qi Wen Teo and Chang-Chun D Lee and Weiwen Liang and Danbi Choi and Kevin J Mao and Madison R Ardagh and Akshita B Gopal and Arjun Mehta and Matt Szlembarski and Roberto Bruzzone and Ian A Wilson and Nicholas C Wu and Chris K P Mok},

doi = {10.1128/jvi.01695-24},

issn = {1098-5514},

year  = {2024},

date = {2024-12-01},

journal = {J Virol},

pages = {e0169524},

abstract = {Understanding how immune history influences influenza immunity is essential for developing effective vaccines and therapeutic strategies. This study examines the antigenic imprinting of influenza hemagglutinin (HA) and neuraminidase (NA) using a mouse model with sequential infections by H1N1 virus strains exhibiting substantial antigenic differences in HA. In our pre-2009 influenza infection model, we observed that mice with more extensive infection histories produced higher levels of functional NA-inhibiting antibodies (NAI). However, following further infection with the 2009 pandemic H1N1 strain, these mice demonstrated a reduced NAI to the challenged virus. Interestingly, prior exposure to older strains resulted in a lower HA antibody response (neutralization and HAI) to the challenged virus in both pre- and post-2009 scenarios, potentially due to faster viral clearance facilitated by immune memory recall. Overall, our findings reveal distinct trajectories in HA and NA immune responses, suggesting that immune imprinting can differentially impact these proteins based on the extent of antigenic variation in influenza viruses.nnIMPORTANCE: Influenza viruses continue to pose a significant threat to human health, with vaccine effectiveness remaining a persistent challenge. Individual immune history is a crucial factor that can influence antibody responses to subsequent influenza exposures. While many studies have explored how pre-existing antibodies shape the induction of anti-HA antibodies following influenza virus infections or vaccinations, the impact on anti-NA antibodies has been less extensively studied. Using a mouse model, our study demonstrates that within pre-2009 H1N1 strains, an extensive immune history negatively impacted anti-HA antibody responses but enhanced anti-NA antibody responses. However, in response to the 2009 pandemic H1N1 strain, which experienced an antigenic shift, both anti-HA and anti-NA antibody responses were hindered by antibodies from prior pre-2009 H1N1 virus infections. These findings provide important insights into how antigenic imprinting affects both anti-HA and anti-NA antibody responses and underscore the need to consider immune history in developing more effective influenza vaccination strategies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39636969,

title = {A single mutation in bovine influenza H5N1 hemagglutinin switches specificity to human receptors},

author = {Ting-Hui Lin and Xueyong Zhu and Shengyang Wang and Ding Zhang and Ryan McBride and Wenli Yu and Simeon Babarinde and James C Paulson and Ian A Wilson},

doi = {10.1126/science.adt0180},

issn = {1095-9203},

year  = {2024},

date = {2024-12-01},

journal = {Science},

volume = {386},

number = {6726},

pages = {1128--1134},

abstract = {In 2024, several human infections with highly pathogenic clade 2.3.4.4b bovine influenza H5N1 viruses in the United States raised concerns about their capability for bovine-to-human or even human-to-human transmission. In this study, analysis of the hemagglutinin (HA) from the first-reported human-infecting bovine H5N1 virus (A/Texas/37/2024, Texas) revealed avian-type receptor binding preference. Notably, a GlnLeu substitution switched Texas HA binding specificity to human-type receptors, which was enhanced when combined with an AsnLys mutation. Crystal structures of the Texas HA with avian receptor analog LSTa and its GlnLeu mutant with human receptor analog LSTc elucidated the structural basis for this preferential receptor recognition. These findings highlight the need for continuous surveillance of emerging mutations in avian and bovine clade 2.3.4.4b H5N1 viruses.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39550381,

title = {Rational design of uncleaved prefusion-closed trimer vaccines for human respiratory syncytial virus and metapneumovirus},

author = {Yi-Zong Lee and Jerome Han and Yi-Nan Zhang and Garrett Ward and Keegan Braz Gomes and Sarah Auclair and Robyn L Stanfield and Linling He and Ian A Wilson and Jiang Zhu},

doi = {10.1038/s41467-024-54287-x},

issn = {2041-1723},

year  = {2024},

date = {2024-11-01},

journal = {Nat Commun},

volume = {15},

number = {1},

pages = {9939},

abstract = {Respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) cause human respiratory diseases and are major targets for vaccine development. In this study, we design uncleaved prefusion-closed (UFC) trimers for the fusion protein (F) of both viruses by examining mutations critical to F metastability. For RSV, we assess four previous prefusion F designs, including the first and second generations of DS-Cav1, SC-TM, and 847A. We then identify key mutations that can maintain prefusion F in a native-like, closed trimeric form (up to 76%) without introducing any interprotomer disulfide bond. For hMPV, we develop a stable UFC trimer with a truncated F-F linkage and an interprotomer disulfide bond. Dozens of UFC constructs are characterized by negative-stain electron microscopy (nsEM), x-ray crystallography (11 RSV-F structures and one hMPV-F structure), and antigenic profiling. Using an optimized RSV-F UFC trimer as bait, we identify three potent RSV neutralizing antibodies (NAbs) from a phage-displayed human antibody library, with a public NAb lineage targeting sites Ø and V and two cross-pneumovirus NAbs recognizing site III. In mouse immunization, rationally designed RSV-F and hMPV-F UFC trimers induce robust antibody responses with high neutralizing titers. Our study provides a foundation for future prefusion F-based RSV and hMPV vaccine development.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39574610,

title = {Using phage display for rational engineering of a higher affinity humanized 3' phosphohistidine-specific antibody},

author = {Gregory D Martyn and Rajasree Kalagiri and Gianluca Veggiani and Robyn L Stanfield and Indrani Choudhuri and Margaux Sala and Jill Meisenhelder and Chao Chen and Avik Biswas and Ronald M Levy and Dmitry Lyumkis and Ian A Wilson and Tony Hunter and Sachdev S Sidhu},

doi = {10.1101/2024.11.04.621849},

issn = {2692-8205},

year  = {2024},

date = {2024-11-01},

journal = {bioRxiv},

abstract = {Histidine phosphorylation (pHis) is a non-canonical post-translational modification (PTM) that is historically understudied due to a lack of robust reagents that are required for its investigation, such as high affinity pHis-specific antibodies. Engineering pHis-specific antibodies is very challenging due to the labile nature of the phosphoramidate (P-N) bond and the stringent requirements for selective recognition of the two isoforms, 1-phosphohistidine (1-pHis) and 3-phosphohistidine (3-pHis). Here, we present a strategy for  engineering of antibodies for detection of native 3-pHis targets. Specifically, we humanized the rabbit SC44-8 anti-3-pTza (a stable 3-pHis mimetic) mAb into a scaffold (herein referred to as hSC44) that was suitable for phage display. We then constructed six unique Fab phage-displayed libraries using the hSC44 scaffold and selected high affinity 3-pHis binders. Our selection strategy was carefully designed to enrich antibodies that bound 3-pHis with high affinity and had specificity for 3-pHis versus 3-pTza. hSC44.20N32F, the best engineered antibody, has an ~10-fold higher affinity for 3-pHis than the parental hSC44. Eleven new Fab structures, including the first reported antibody-pHis peptide structures were solved by X-ray crystallography. Structural and quantum mechanical calculations provided molecular insights into 3-pHis and 3-pTza discrimination by different hSC44 variants and their affinity increase obtained through  engineering. Furthermore, we demonstrate the utility of these newly developed high-affinity 3-pHis-specific antibodies for recognition of pHis proteins in mammalian cells by immunoblotting and immunofluorescence staining. Overall, our work describes a general method for engineering PTM-specific antibodies and provides a set of novel antibodies for further investigations of the role of 3-pHis in cell biology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39416090,

title = {Reshaping the tumor microenvironment by degrading glycoimmune checkpoints Siglec-7 and -9},

author = {Chao Wang and Yingqin Hou and Jaroslav Zak and Qinheng Zheng and Kelli A McCord and Mengyao Wu and Ding Zhang and Shereen Chung and Yujie Shi and Jinfeng Ye and Yunlong Zhao and Stephanie Hajjar and Ian A Wilson and James C Paulson and John R Teijaro and Xu Zhou and K Barry Sharpless and Matthew S Macauley and Peng Wu},

doi = {10.1101/2024.10.11.617879},

issn = {2692-8205},

year  = {2024},

date = {2024-10-01},

journal = {bioRxiv},

abstract = {Cancer treatment has been rapidly transformed by the development of immune checkpoint inhibitors targeting CTLA-4 and PD-1/PD-L1. However, many patients fail to respond, especially those with an immunosuppressive tumor microenvironment (TME), suggesting the existence of additional immune checkpoints that act through orthogonal mechanisms. Sialic acid-binding immunoglobulin-like lectin (Siglec)-7 and -9 are newly designated glycoimmune checkpoints that are abundantly expressed by tumor-infiltrating myeloid cells. We discovered that T cells express only basal levels of Siglec transcripts; instead, they acquire Siglec-7 and -9 from interacting myeloid cells in the TME via trogocytosis, which impairs their activation and effector function. Mechanistically, Siglec-7 and -9 suppress T cell activity by dephosphorylating T cell receptor (TCR)-related signaling cascades. Using sulfur fluoride exchange (SuFEx) click chemistry, we developed a ligand that binds to Siglec-7 and -9 with high-affinity and exclusive specificity. Using this ligand, we constructed a Siglec-7/9 degrader that targets membrane Siglec-7 and -9 to the lysosome for degradation. Administration of this degrader induced efficient Siglec degradation in both T cells and myeloid cells in the TME. We found that Siglec-7/9 degradation has a negligible effect on macrophage phagocytosis, but significantly enhances T cell anti-tumor immunity. The degrader, particularly when combined with anti-CTLA-4, enhanced macrophage antigen presentation, reshaped the TME, and resulted in long-lasting T cell memory and excellent tumor control in multiple murine tumor models. These findings underscore the need to consider exogenous checkpoints acquired by T cells in the TME when selecting specific checkpoint blockade therapy to enhance T cell immunity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39250525,

title = {Immunization of cows with HIV envelope trimers generates broadly neutralizing antibodies to the V2-apex from the ultralong CDRH3 repertoire},

author = {Pilar X Altman and Gabriel Ozorowski and Robyn L Stanfield and Jeremy Haakenson and Michael Appel and Mara Parren and Wen-Hsin Lee and Huldah Sang and Jordan Woehl and Karen Saye-Francisco and Leigh M Sewall and Collin Joyce and Ge Song and Katelyn Porter and Elise Landais and Raiees Andrabi and Ian A Wilson and Andrew B Ward and Waithaka Mwangi and Vaughn V Smider and Dennis R Burton and Devin Sok},

doi = {10.1371/journal.ppat.1012042},

issn = {1553-7374},

year  = {2024},

date = {2024-09-01},

journal = {PLoS Pathog},

volume = {20},

number = {9},

pages = {e1012042},

abstract = {The generation of broadly neutralizing antibodies (bnAbs) to conserved epitopes on HIV Envelope (Env) is one of the cornerstones of HIV vaccine research. The animal models commonly used for HIV do not reliably produce a potent broadly neutralizing serum antibody response, with the exception of cows. Cows have previously produced a CD4 binding site response by homologous prime and boosting with a native-like Env trimer. In small animal models, other engineered immunogens were shown to focus antibody responses to the bnAb V2-apex region of Env. Here, we immunized two groups of cows (n = 4) with two regimens of V2-apex focusing Env immunogens to investigate whether antibody responses could be generated to the V2-apex on Env. Group 1 was immunized with chimpanzee simian immunodeficiency virus (SIV)-Env trimer that shares its V2-apex with HIV, followed by immunization with C108, a V2-apex focusing immunogen, and finally boosted with a cross-clade native-like trimer cocktail. Group 2 was immunized with HIV C108 Env trimer followed by the same HIV trimer cocktail as Group 1. Longitudinal serum analysis showed that one cow in each group developed serum neutralizing antibody responses to the V2-apex. Eight and 11 bnAbs were isolated from Group 1 and Group 2 cows, respectively, and showed moderate breadth and potency. Potent and broad responses in this study developed much later than previous cow immunizations that elicited CD4bs bnAbs responses and required several different immunogens. All isolated bnAbs were derived from the ultralong CDRH3 repertoire. The finding that cow antibodies can target more than one broadly neutralizing epitope on the HIV surface reveals the generality of elongated structures for the recognition of highly glycosylated proteins. The exclusive isolation of ultralong CDRH3 bnAbs, despite only comprising a small percent of the cow repertoire, suggests these antibodies outcompete the long and short CDRH3 antibodies during the bnAb response.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38935072,

title = {Maturation of germinal center B cells after influenza virus vaccination in humans},

author = {Katherine M McIntire and Hailong Meng and Ting-Hui Lin and Wooseob Kim and Nina E Moore and Julianna Han and Meagan McMahon and Meng Wang and Sameer Kumar Malladi and Bassem M Mohammed and Julian Q Zhou and Aaron J Schmitz and Kenneth B Hoehn and Juan Manuel Carreño and Temima Yellin and Teresa Suessen and William D Middleton and Sharlene A Teefey and Rachel M Presti and Florian Krammer and Jackson S Turner and Andrew B Ward and Ian A Wilson and Steven H Kleinstein and Ali H Ellebedy},

doi = {10.1084/jem.20240668},

issn = {1540-9538},

year  = {2024},

date = {2024-08-01},

journal = {J Exp Med},

volume = {221},

number = {8},

abstract = {Germinal centers (GC) are microanatomical lymphoid structures where affinity-matured memory B cells and long-lived bone marrow plasma cells are primarily generated. It is unclear how the maturation of B cells within the GC impacts the breadth and durability of B cell responses to influenza vaccination in humans. We used fine needle aspiration of draining lymph nodes to longitudinally track antigen-specific GC B cell responses to seasonal influenza vaccination. Antigen-specific GC B cells persisted for at least 13 wk after vaccination in two out of seven individuals. Monoclonal antibodies (mAbs) derived from persisting GC B cell clones exhibit enhanced binding affinity and breadth to influenza hemagglutinin (HA) antigens compared with related GC clonotypes isolated earlier in the response. Structural studies of early and late GC-derived mAbs from one clonal lineage in complex with H1 and H5 HAs revealed an altered binding footprint. Our study shows that inducing sustained GC reactions after influenza vaccination in humans supports the maturation of responding B cells.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39037231,

title = {Exploiting the Affimer platform against influenza A virus},

author = {Oliver Debski-Antoniak and Alex Flynn and David P Klebl and Moisés H Rojas Rechy and Christian Tiede and Ian A Wilson and Stephen P Muench and Darren Tomlinson and Juan Fontana},

doi = {10.1128/mbio.01804-24},

issn = {2150-7511},

year  = {2024},

date = {2024-08-01},

journal = {mBio},

volume = {15},

number = {8},

pages = {e0180424},

abstract = {Influenza A virus (IAV) is well known for its pandemic potential. While current surveillance and vaccination strategies are highly effective, therapeutic approaches are often short-lived due to the high mutation rates of IAV. Recently, monoclonal antibodies (mAbs) have emerged as a promising therapeutic approach, both against current strains and future IAV pandemics. In addition to mAbs, several antibody-like alternatives exist, which aim to improve upon mAbs. Among these, Affimers stand out for their short development time, high expression levels in , and animal-free production. In this study, we utilized the Affimer platform to isolate and produce specific and potent inhibitors of IAV. Using a monomeric version of the IAV trimeric hemagglutinin (HA) fusion protein, we isolated 12 Affimers that inhibit IAV infection . Two of these Affimers were characterized in detail and exhibited nanomolar-binding affinities to the target H3 HA protein, specifically binding to the HA1 head domain. Cryo-electron microscopy (cryo-EM), employing a novel spray approach to prepare cryo-grids, allowed us to image HA-Affimer complexes. Combined with functional assays, we determined that these Affimers inhibit IAV by blocking the interaction of HA with the host-cell receptor, sialic acid. Furthermore, these Affimers inhibited IAV strains closely related to the one used for their isolation. Overall, our results support the use of Affimers as a viable alternative to existing targeted therapies for IAV and highlight their potential as diagnostic reagents.nnIMPORTANCE: Influenza A virus is one of the few viruses that can cause devastating pandemics. Due to the high mutation rates of this virus, annual vaccination is required, and antivirals are short-lived. Monoclonal antibodies present a promising approach to tackle influenza virus infections but are associated with some limitations. To improve on this strategy, we explored the Affimer platform, which are antibody-like proteins made in bacteria. By performing phage-display against a monomeric version of influenza virus fusion protein, an established viral target, we were able to isolate Affimers that inhibit influenza virus infection . We characterized the mechanism of inhibition of the Affimers by using assays targeting different stages of the viral replication cycle. We additionally characterized HA-Affimer complex structure, using a novel approach to prepare samples for cryo-electron microscopy. Overall, these results show that Affimers are a promising tool against influenza virus infection.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39213338,

title = {Germline-targeting HIV vaccination induces neutralizing antibodies to the CD4 binding site},

author = {Tom G Caniels and Max Medina-Ramìrez and Shiyu Zhang and Sven Kratochvil and Yuejiao Xian and Ja-Hyun Koo and Ronald Derking and Jakob Samsel and Jelle van Schooten and Simone Pecetta and Edward Lamperti and Meng Yuan and María Ríos Carrasco and Iván Del Moral Sánchez and Joel D Allen and Joey H Bouhuijs and Anila Yasmeen and Thomas J Ketas and Jonne L Snitselaar and Tom P L Bijl and Isabel Cuella Martin and Jonathan L Torres and Albert Cupo and Lisa Shirreff and Kenneth Rogers and Rosemarie D Mason and Mario Roederer and Kelli M Greene and Hongmei Gao and Catarina Mendes Silva and Isabel J L Baken and Ming Tian and Frederick W Alt and Bali Pulendran and Michael S Seaman and Max Crispin and Marit J van Gils and David C Montefiori and Adrian B McDermott and François J Villinger and Richard A Koup and John P Moore and Per Johan Klasse and Gabriel Ozorowski and Facundo D Batista and Ian A Wilson and Andrew B Ward and Rogier W Sanders},

doi = {10.1126/sciimmunol.adk9550},

issn = {2470-9468},

year  = {2024},

date = {2024-08-01},

journal = {Sci Immunol},

volume = {9},

number = {98},

pages = {eadk9550},

abstract = {Eliciting potent and broadly neutralizing antibodies (bnAbs) is a major goal in HIV-1 vaccine development. Here, we describe how germline-targeting immunogen BG505 SOSIP germline trimer 1.1 (GT1.1), generated through structure-based design, engages a diverse range of VRC01-class bnAb precursors. A single immunization with GT1.1 expands CD4 binding site (CD4bs)-specific VRC01-class B cells in knock-in mice and drives VRC01-class maturation. In nonhuman primates (NHPs), GT1.1 primes CD4bs-specific neutralizing serum responses. Selected monoclonal antibodies (mAbs) isolated from GT1.1-immunized NHPs neutralize fully glycosylated BG505 virus. Two mAbs, 12C11 and 21N13, neutralize subsets of diverse heterologous neutralization-resistant viruses. High-resolution structures revealed that 21N13 targets the same conserved residues in the CD4bs as VRC01-class and CH235-class bnAbs despite its low sequence similarity (~40%), whereas mAb 12C11 binds predominantly through its heavy chain complementarity-determining region 3. These preclinical data underpin the ongoing evaluation of GT1.1 in a phase 1 clinical trial in healthy volunteers.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38537643b,

title = {Structural and mechanistic insights into disease-associated endolysosomal exonucleases PLD3 and PLD4},

author = {Meng Yuan and Linghang Peng and Deli Huang and Amanda Gavin and Fangkun Luan and Jenny Tran and Ziqi Feng and Xueyong Zhu and Jeanne Matteson and Ian A Wilson and David Nemazee},

doi = {10.1016/j.str.2024.02.019},

issn = {1878-4186},

year  = {2024},

date = {2024-06-01},

journal = {Structure},

volume = {32},

number = {6},

pages = {766--779.e7},

abstract = {Endolysosomal exonucleases PLD3 and PLD4 (phospholipases D3 and D4) are associated with autoinflammatory and autoimmune diseases. We report structures of these enzymes, and the molecular basis of their catalysis. The structures reveal an intra-chain dimer topology forming a basic active site at the interface. Like other PLD superfamily members, PLD3 and PLD4 carry HxKxxxxD/E motifs and participate in phosphodiester-bond cleavage. The enzymes digest ssDNA and ssRNA in a 5'-to-3' manner and are blocked by 5'-phosphorylation. We captured structures in apo, intermediate, and product states and revealed a "link-and-release" two-step catalysis. We also unexpectedly demonstrated phosphatase activity via a covalent 3-phosphohistidine intermediate. PLD4 contains an extra hydrophobic clamp that stabilizes substrate and could affect oligonucleotide substrate preference and product release. Biochemical and structural analysis of disease-associated mutants of PLD3/4 demonstrated reduced enzyme activity or thermostability and the possible basis for disease association. Furthermore, these findings provide insight into therapeutic design.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38816615,

title = {Vaccination induces broadly neutralizing antibody precursors to HIV gp41},

author = {Torben Schiffner and Ivy Phung and Rashmi Ray and Adriana Irimia and Ming Tian and Olivia Swanson and Jeong Hyun Lee and Chang-Chun D Lee and Ester Marina-Zárate and So Yeon Cho and Jiachen Huang and Gabriel Ozorowski and Patrick D Skog and Andreia M Serra and Kimmo Rantalainen and Joel D Allen and Sabyasachi Baboo and Oscar L Rodriguez and Sunny Himansu and Jianfu Zhou and Jonathan Hurtado and Claudia T Flynn and Katherine McKenney and Colin Havenar-Daughton and Swati Saha and Kaitlyn Shields and Steven Schultze and Melissa L Smith and Chi-Hui Liang and Laura Toy and Simone Pecetta and Ying-Cing Lin and Jordan R Willis and Fabian Sesterhenn and Daniel W Kulp and Xiaozhen Hu and Christopher A Cottrell and Xiaoya Zhou and Jennifer Ruiz and Xuesong Wang and Usha Nair and Kathrin H Kirsch and Hwei-Ling Cheng and Jillian Davis and Oleksandr Kalyuzhniy and Alessia Liguori and Jolene K Diedrich and Julia T Ngo and Vanessa Lewis and Nicole Phelps and Ryan D Tingle and Skye Spencer and Erik Georgeson and Yumiko Adachi and Michael Kubitz and Saman Eskandarzadeh and Marc A Elsliger and Rama R Amara and Elise Landais and Bryan Briney and Dennis R Burton and Diane G Carnathan and Guido Silvestri and Corey T Watson and John R Yates and James C Paulson and Max Crispin and Gevorg Grigoryan and Andrew B Ward and Devin Sok and Frederick W Alt and Ian A Wilson and Facundo D Batista and Shane Crotty and William R Schief},

doi = {10.1038/s41590-024-01833-w},

issn = {1529-2916},

year  = {2024},

date = {2024-06-01},

journal = {Nat Immunol},

volume = {25},

number = {6},

pages = {1073--1082},

abstract = {A key barrier to the development of vaccines that induce broadly neutralizing antibodies (bnAbs) against human immunodeficiency virus (HIV) and other viruses of high antigenic diversity is the design of priming immunogens that induce rare bnAb-precursor B cells. The high neutralization breadth of the HIV bnAb 10E8 makes elicitation of 10E8-class bnAbs desirable; however, the recessed epitope within gp41 makes envelope trimers poor priming immunogens and requires that 10E8-class bnAbs possess a long heavy chain complementarity determining region 3 (HCDR3) with a specific binding motif. We developed germline-targeting epitope scaffolds with affinity for 10E8-class precursors and engineered nanoparticles for multivalent display. Scaffolds exhibited epitope structural mimicry and bound bnAb-precursor human naive B cells in ex vivo screens, protein nanoparticles induced bnAb-precursor responses in stringent mouse models and rhesus macaques, and mRNA-encoded nanoparticles triggered similar responses in mice. Thus, germline-targeting epitope scaffold nanoparticles can elicit rare bnAb-precursor B cells with predefined binding specificities and HCDR3 features.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38816616,

title = {Affinity gaps among B cells in germinal centers drive the selection of MPER precursors},

author = {Rashmi Ray and Torben Schiffner and Xuesong Wang and Yu Yan and Kimmo Rantalainen and Chang-Chun David Lee and Shivang Parikh and Raphael A Reyes and Gordon A Dale and Ying-Cing Lin and Simone Pecetta and Sophie Giguere and Olivia Swanson and Sven Kratochvil and Eleonora Melzi and Ivy Phung and Lisa Madungwe and Oleksandr Kalyuzhniy and John Warner and Stephanie R Weldon and Ryan Tingle and Edward Lamperti and Kathrin H Kirsch and Nicole Phelps and Erik Georgeson and Yumiko Adachi and Michael Kubitz and Usha Nair and Shane Crotty and Ian A Wilson and William R Schief and Facundo D Batista},

doi = {10.1038/s41590-024-01844-7},

issn = {1529-2916},

year  = {2024},

date = {2024-06-01},

journal = {Nat Immunol},

volume = {25},

number = {6},

pages = {1083--1096},

abstract = {Current prophylactic human immunodeficiency virus 1 (HIV-1) vaccine research aims to elicit broadly neutralizing antibodies (bnAbs). Membrane-proximal external region (MPER)-targeting bnAbs, such as 10E8, provide exceptionally broad neutralization, but some are autoreactive. Here, we generated humanized B cell antigen receptor knock-in mouse models to test whether a series of germline-targeting immunogens could drive MPER-specific precursors toward bnAbs. We found that recruitment of 10E8 precursors to germinal centers (GCs) required a minimum affinity for germline-targeting immunogens, but the GC residency of MPER precursors was brief due to displacement by higher-affinity endogenous B cell competitors. Higher-affinity germline-targeting immunogens extended the GC residency of MPER precursors, but robust long-term GC residency and maturation were only observed for MPER-HuGL18, an MPER precursor clonotype able to close the affinity gap with endogenous B cell competitors in the GC. Thus, germline-targeting immunogens could induce MPER-targeting antibodies, and B cell residency in the GC may be regulated by a precursor-competitor affinity gap.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38744813,

title = {Functional and antigenic characterization of SARS-CoV-2 spike fusion peptide by deep mutational scanning},

author = {Ruipeng Lei and Enya Qing and Abby Odle and Meng Yuan and Chaminda D Gunawardene and Timothy J C Tan and Natalie So and Wenhao O Ouyang and Ian A Wilson and Tom Gallagher and Stanley Perlman and Nicholas C Wu and Lok-Yin Roy Wong},

doi = {10.1038/s41467-024-48104-8},

issn = {2041-1723},

year  = {2024},

date = {2024-05-01},

journal = {Nat Commun},

volume = {15},

number = {1},

pages = {4056},

abstract = {The fusion peptide of SARS-CoV-2 spike protein is functionally important for membrane fusion during virus entry and is part of a broadly neutralizing epitope. However, sequence determinants at the fusion peptide and its adjacent regions for pathogenicity and antigenicity remain elusive. In this study, we perform a series of deep mutational scanning (DMS) experiments on an S2 region spanning the fusion peptide of authentic SARS-CoV-2 in different cell lines and in the presence of broadly neutralizing antibodies. We identify mutations at residue 813 of the spike protein that reduced TMPRSS2-mediated entry with decreased virulence. In addition, we show that an F823Y mutation, present in bat betacoronavirus HKU9 spike protein, confers resistance to broadly neutralizing antibodies. Our findings provide mechanistic insights into SARS-CoV-2 pathogenicity and also highlight a potential challenge in developing broadly protective S2-based coronavirus vaccines.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38753503,

title = {Ultrapotent influenza hemagglutinin fusion inhibitors developed through SuFEx-enabled high-throughput medicinal chemistry},

author = {Seiya Kitamura and Ting-Hui Lin and Chang-Chun David Lee and Akihiro Takamura and Rameshwar U Kadam and Ding Zhang and Xueyong Zhu and Lucas Dada and Emiko Nagai and Wenli Yu and Yao Yao and K Barry Sharpless and Ian A Wilson and Dennis W Wolan},

doi = {10.1073/pnas.2310677121},

issn = {1091-6490},

year  = {2024},

date = {2024-05-01},

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

volume = {121},

number = {22},

pages = {e2310677121},

abstract = {Seasonal and pandemic-associated influenza strains cause highly contagious viral respiratory infections that can lead to severe illness and excess mortality. Here, we report on the optimization of our small-molecule inhibitor F0045(S) targeting the influenza hemagglutinin (HA) stem with our Sulfur-Fluoride Exchange (SuFEx) click chemistry-based high-throughput medicinal chemistry (HTMC) strategy. A combination of SuFEx- and amide-based lead molecule diversification and structure-guided design led to identification and validation of ultrapotent influenza fusion inhibitors with subnanomolar EC cellular antiviral activity against several influenza A group 1 strains. X-ray structures of six of these compounds with HA indicate that the appended moieties occupy additional pockets on the HA surface and increase the binding interaction, where the accumulation of several polar interactions also contributes to the improved affinity. The compounds here represent the most potent HA small-molecule inhibitors to date. Our divergent HTMC platform is therefore a powerful, rapid, and cost-effective approach to develop bioactive chemical probes and drug-like candidates against viral targets.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38579013b,

title = {AS03 adjuvant enhances the magnitude, persistence, and clonal breadth of memory B cell responses to a plant-based COVID-19 vaccine in humans},

author = {Lilit Grigoryan and Yupeng Feng and Lorenza Bellusci and Lilin Lai and Bushra Wali and Madison Ellis and Meng Yuan and Prabhu S Arunachalam and Mengyun Hu and Sangeeta Kowli and Sheena Gupta and Sofia Maysel-Auslender and Holden T Maecker and Hady Samaha and Nadine Rouphael and Ian A Wilson and Alberto C Moreno and Mehul S Suthar and Surender Khurana and Stéphane Pillet and Nathalie Charland and Brian J Ward and Bali Pulendran},

doi = {10.1126/sciimmunol.adi8039},

issn = {2470-9468},

year  = {2024},

date = {2024-04-01},

journal = {Sci Immunol},

volume = {9},

number = {94},

pages = {eadi8039},

abstract = {Vaccine adjuvants increase the breadth of serum antibody responses, but whether this is due to the generation of antigen-specific B cell clones with distinct specificities or the maturation of memory B cell clones that produce broadly cross-reactive antibodies is unknown. Here, we longitudinally analyzed immune responses in healthy adults after two-dose vaccination with either a virus-like particle COVID-19 vaccine (CoVLP), CoVLP adjuvanted with AS03 (CoVLP+AS03), or a messenger RNA vaccination (mRNA-1273). CoVLP+AS03 enhanced the magnitude and durability of circulating antibodies and antigen-specific CD4 T cell and memory B cell responses. Antigen-specific CD4 T cells in the CoVLP+AS03 group at day 42 correlated with antigen-specific memory B cells at 6 months. CoVLP+AS03 induced memory B cell responses, which accumulated somatic hypermutations over 6 months, resulting in enhanced neutralization breadth of monoclonal antibodies. Furthermore, the fraction of broadly neutralizing antibodies encoded by memory B cells increased between day 42 and 6 months. These results indicate that AS03 enhances the antigenic breadth of B cell memory at the clonal level and induces progressive maturation of the B cell response.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38582771b,

title = {Triple tandem trimer immunogens for HIV-1 and influenza nucleic acid-based vaccines},

author = {Iván Del Moral-Sánchez and Edmund G Wee and Yuejiao Xian and Wen-Hsin Lee and Joel D Allen and Alba Torrents de la Peña and Rebeca Fróes Rocha and James Ferguson and André N León and Sylvie Koekkoek and Edith E Schermer and Judith A Burger and Sanjeev Kumar and Robby Zwolsman and Mitch Brinkkemper and Aafke Aartse and Dirk Eggink and Julianna Han and Meng Yuan and Max Crispin and Gabriel Ozorowski and Andrew B Ward and Ian A Wilson and Tomáš Hanke and Kwinten Sliepen and Rogier W Sanders},

doi = {10.1038/s41541-024-00862-8},

issn = {2059-0105},

year  = {2024},

date = {2024-04-01},

journal = {NPJ Vaccines},

volume = {9},

number = {1},

pages = {74},

abstract = {Recombinant native-like HIV-1 envelope glycoprotein (Env) trimers are used in candidate vaccines aimed at inducing broadly neutralizing antibodies. While state-of-the-art SOSIP or single-chain Env designs can be expressed as native-like trimers, undesired monomers, dimers and malformed trimers that elicit non-neutralizing antibodies are also formed, implying that these designs could benefit from further modifications for gene-based vaccination approaches. Here, we describe the triple tandem trimer (TTT) design, in which three Env protomers are genetically linked in a single open reading frame and express as native-like trimers. Viral vectored Env TTT induced similar neutralization titers but with a higher proportion of trimer-specific responses. The TTT design was also applied to generate influenza hemagglutinin (HA) trimers without the need for trimerization domains. Additionally, we used TTT to generate well-folded chimeric Env and HA trimers that harbor protomers from three different strains. In summary, the TTT design is a useful platform for the design of HIV-1 Env and influenza HA immunogens for a multitude of vaccination strategies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38579013,

title = {AS03 adjuvant enhances the magnitude, persistence, and clonal breadth of memory B cell responses to a plant-based COVID-19 vaccine in humans},

author = {Lilit Grigoryan and Yupeng Feng and Lorenza Bellusci and Lilin Lai and Bushra Wali and Madison Ellis and Meng Yuan and Prabhu S Arunachalam and Mengyun Hu and Sangeeta Kowli and Sheena Gupta and Sofia Maysel-Auslender and Holden T Maecker and Hady Samaha and Nadine Rouphael and Ian A Wilson and Alberto C Moreno and Mehul S Suthar and Surender Khurana and Stéphane Pillet and Nathalie Charland and Brian J Ward and Bali Pulendran},

doi = {10.1126/sciimmunol.adi8039},

issn = {2470-9468},

year  = {2024},

date = {2024-04-01},

journal = {Sci Immunol},

volume = {9},

number = {94},

pages = {eadi8039},

abstract = {Vaccine adjuvants increase the breadth of serum antibody responses, but whether this is due to the generation of antigen-specific B cell clones with distinct specificities or the maturation of memory B cell clones that produce broadly cross-reactive antibodies is unknown. Here, we longitudinally analyzed immune responses in healthy adults after two-dose vaccination with either a virus-like particle COVID-19 vaccine (CoVLP), CoVLP adjuvanted with AS03 (CoVLP+AS03), or a messenger RNA vaccination (mRNA-1273). CoVLP+AS03 enhanced the magnitude and durability of circulating antibodies and antigen-specific CD4 T cell and memory B cell responses. Antigen-specific CD4 T cells in the CoVLP+AS03 group at day 42 correlated with antigen-specific memory B cells at 6 months. CoVLP+AS03 induced memory B cell responses, which accumulated somatic hypermutations over 6 months, resulting in enhanced neutralization breadth of monoclonal antibodies. Furthermore, the fraction of broadly neutralizing antibodies encoded by memory B cells increased between day 42 and 6 months. These results indicate that AS03 enhances the antigenic breadth of B cell memory at the clonal level and induces progressive maturation of the B cell response.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38582771,

title = {Triple tandem trimer immunogens for HIV-1 and influenza nucleic acid-based vaccines},

author = {Iván Del Moral-Sánchez and Edmund G Wee and Yuejiao Xian and Wen-Hsin Lee and Joel D Allen and Alba Torrents de la Peña and Rebeca Fróes Rocha and James Ferguson and André N León and Sylvie Koekkoek and Edith E Schermer and Judith A Burger and Sanjeev Kumar and Robby Zwolsman and Mitch Brinkkemper and Aafke Aartse and Dirk Eggink and Julianna Han and Meng Yuan and Max Crispin and Gabriel Ozorowski and Andrew B Ward and Ian A Wilson and Tomáš Hanke and Kwinten Sliepen and Rogier W Sanders},

doi = {10.1038/s41541-024-00862-8},

issn = {2059-0105},

year  = {2024},

date = {2024-04-01},

journal = {NPJ Vaccines},

volume = {9},

number = {1},

pages = {74},

abstract = {Recombinant native-like HIV-1 envelope glycoprotein (Env) trimers are used in candidate vaccines aimed at inducing broadly neutralizing antibodies. While state-of-the-art SOSIP or single-chain Env designs can be expressed as native-like trimers, undesired monomers, dimers and malformed trimers that elicit non-neutralizing antibodies are also formed, implying that these designs could benefit from further modifications for gene-based vaccination approaches. Here, we describe the triple tandem trimer (TTT) design, in which three Env protomers are genetically linked in a single open reading frame and express as native-like trimers. Viral vectored Env TTT induced similar neutralization titers but with a higher proportion of trimer-specific responses. The TTT design was also applied to generate influenza hemagglutinin (HA) trimers without the need for trimerization domains. Additionally, we used TTT to generate well-folded chimeric Env and HA trimers that harbor protomers from three different strains. In summary, the TTT design is a useful platform for the design of HIV-1 Env and influenza HA immunogens for a multitude of vaccination strategies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38537643,

title = {Structural and mechanistic insights into disease-associated endolysosomal exonucleases PLD3 and PLD4},

author = {Meng Yuan and Linghang Peng and Deli Huang and Amanda Gavin and Fangkun Luan and Jenny Tran and Ziqi Feng and Xueyong Zhu and Jeanne Matteson and Ian A Wilson and David Nemazee},

doi = {10.1016/j.str.2024.02.019},

issn = {1878-4186},

year  = {2024},

date = {2024-03-01},

journal = {Structure},

abstract = {Endolysosomal exonucleases PLD3 and PLD4 (phospholipases D3 and D4) are associated with autoinflammatory and autoimmune diseases. We report structures of these enzymes, and the molecular basis of their catalysis. The structures reveal an intra-chain dimer topology forming a basic active site at the interface. Like other PLD superfamily members, PLD3 and PLD4 carry HxKxxxxD/E motifs and participate in phosphodiester-bond cleavage. The enzymes digest ssDNA and ssRNA in a 5'-to-3' manner and are blocked by 5'-phosphorylation. We captured structures in apo, intermediate, and product states and revealed a "link-and-release" two-step catalysis. We also unexpectedly demonstrated phosphatase activity via a covalent 3-phosphohistidine intermediate. PLD4 contains an extra hydrophobic clamp that stabilizes substrate and could affect oligonucleotide substrate preference and product release. Biochemical and structural analysis of disease-associated mutants of PLD3/4 demonstrated reduced enzyme activity or thermostability and the possible basis for disease association. Furthermore, these findings provide insight into therapeutic design.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38307019b,

title = {Evolution of human H3N2 influenza virus receptor specificity has substantially expanded the receptor-binding domain site},

author = {Andrew J Thompson and Nicholas C Wu and Angeles Canales and Chika Kikuchi and Xueyong Zhu and Beatriz Fernández de Toro and Francisco J Cañada and Charli Worth and Shengyang Wang and Ryan McBride and Wenjie Peng and Corwin M Nycholat and Jesús Jiménez-Barbero and Ian A Wilson and James C Paulson},

doi = {10.1016/j.chom.2024.01.003},

issn = {1934-6069},

year  = {2024},

date = {2024-02-01},

journal = {Cell Host Microbe},

volume = {32},

number = {2},

pages = {261--275.e4},

abstract = {Hemagglutinins (HAs) from human influenza viruses descend from avian progenitors that bind α2-3-linked sialosides and must adapt to glycans with α2-6-linked sialic acids on human airway cells to transmit within the human population. Since their introduction during the 1968 pandemic, H3N2 viruses have evolved over the past five decades to preferentially recognize human α2-6-sialoside receptors that are elongated through addition of poly-LacNAc. We show that more recent H3N2 viruses now make increasingly complex interactions with elongated receptors while continuously selecting for strains maintaining this phenotype. This change in receptor engagement is accompanied by an extension of the traditional receptor-binding site to include residues in key antigenic sites on the surface of HA trimers. These results help explain the propensity for selection of antigenic variants, leading to vaccine mismatching, when H3N2 viruses are propagated in chicken eggs or cells that do not contain such receptors.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38381847b,

title = {Synthetic development of a broadly neutralizing antibody against snake venom long-chain α-neurotoxins},

author = {Irene S Khalek and R R Senji Laxme and Yen Thi Kim Nguyen and Suyog Khochare and Rohit N Patel and Jordan Woehl and Jessica M Smith and Karen Saye-Francisco and Yoojin Kim and Laetitia Misson Mindrebo and Quoc Tran and Mateusz Kędzior and Evy Boré and Oliver Limbo and Megan Verma and Robyn L Stanfield and Stefanie K Menzies and Stuart Ainsworth and Robert A Harrison and Dennis R Burton and Devin Sok and Ian A Wilson and Nicholas R Casewell and Kartik Sunagar and Joseph G Jardine},

doi = {10.1126/scitranslmed.adk1867},

issn = {1946-6242},

year  = {2024},

date = {2024-02-01},

journal = {Sci Transl Med},

volume = {16},

number = {735},

pages = {eadk1867},

abstract = {Snakebite envenoming is a major global public health concern for which improved therapies are urgently needed. The antigenic diversity present in snake venom toxins from various species presents a considerable challenge to the development of a universal antivenom. Here, we used a synthetic human antibody library to find and develop an antibody that neutralizes long-chain three-finger α-neurotoxins produced by numerous medically relevant snakes. Our antibody bound diverse toxin variants with high affinity, blocked toxin binding to the nicotinic acetylcholine receptor in vitro, and protected mice from lethal venom challenge. Structural analysis of the antibody-toxin complex revealed a binding mode that mimics the receptor-toxin interaction. The overall workflow presented is generalizable for the development of antibodies that target conserved epitopes among antigenically diverse targets, and it offers a promising framework for the creation of a monoclonal antibody-based universal antivenom to treat snakebite envenoming.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38307019,

title = {Evolution of human H3N2 influenza virus receptor specificity has substantially expanded the receptor-binding domain site},

author = {Andrew J Thompson and Nicholas C Wu and Angeles Canales and Chika Kikuchi and Xueyong Zhu and Beatriz Fernández de Toro and Francisco J Cañada and Charli Worth and Shengyang Wang and Ryan McBride and Wenjie Peng and Corwin M Nycholat and Jesús Jiménez-Barbero and Ian A Wilson and James C Paulson},

doi = {10.1016/j.chom.2024.01.003},

issn = {1934-6069},

year  = {2024},

date = {2024-02-01},

journal = {Cell Host Microbe},

volume = {32},

number = {2},

pages = {261--275.e4},

abstract = {Hemagglutinins (HAs) from human influenza viruses descend from avian progenitors that bind α2-3-linked sialosides and must adapt to glycans with α2-6-linked sialic acids on human airway cells to transmit within the human population. Since their introduction during the 1968 pandemic, H3N2 viruses have evolved over the past five decades to preferentially recognize human α2-6-sialoside receptors that are elongated through addition of poly-LacNAc. We show that more recent H3N2 viruses now make increasingly complex interactions with elongated receptors while continuously selecting for strains maintaining this phenotype. This change in receptor engagement is accompanied by an extension of the traditional receptor-binding site to include residues in key antigenic sites on the surface of HA trimers. These results help explain the propensity for selection of antigenic variants, leading to vaccine mismatching, when H3N2 viruses are propagated in chicken eggs or cells that do not contain such receptors.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38381847,

title = {Synthetic development of a broadly neutralizing antibody against snake venom long-chain α-neurotoxins},

author = {Irene S Khalek and R R Senji Laxme and Yen Thi Kim Nguyen and Suyog Khochare and Rohit N Patel and Jordan Woehl and Jessica M Smith and Karen Saye-Francisco and Yoojin Kim and Laetitia Misson Mindrebo and Quoc Tran and Mateusz Kędzior and Evy Boré and Oliver Limbo and Megan Verma and Robyn L Stanfield and Stefanie K Menzies and Stuart Ainsworth and Robert A Harrison and Dennis R Burton and Devin Sok and Ian A Wilson and Nicholas R Casewell and Kartik Sunagar and Joseph G Jardine},

doi = {10.1126/scitranslmed.adk1867},

issn = {1946-6242},

year  = {2024},

date = {2024-02-01},

journal = {Sci Transl Med},

volume = {16},

number = {735},

pages = {eadk1867},

abstract = {Snakebite envenoming is a major global public health concern for which improved therapies are urgently needed. The antigenic diversity present in snake venom toxins from various species presents a considerable challenge to the development of a universal antivenom. Here, we used a synthetic human antibody library to find and develop an antibody that neutralizes long-chain three-finger α-neurotoxins produced by numerous medically relevant snakes. Our antibody bound diverse toxin variants with high affinity, blocked toxin binding to the nicotinic acetylcholine receptor in vitro, and protected mice from lethal venom challenge. Structural analysis of the antibody-toxin complex revealed a binding mode that mimics the receptor-toxin interaction. The overall workflow presented is generalizable for the development of antibodies that target conserved epitopes among antigenically diverse targets, and it offers a promising framework for the creation of a monoclonal antibody-based universal antivenom to treat snakebite envenoming.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37777966,

title = {Widespread impact of immunoglobulin V-gene allelic polymorphisms on antibody reactivity},

author = {Meng Yuan and Ziqi Feng and Huibin Lv and Natalie So and Ivana R Shen and Timothy J C Tan and Qi Wen Teo and Wenhao O Ouyang and Logan Talmage and Ian A Wilson and Nicholas C Wu},

doi = {10.1016/j.celrep.2023.113194},

issn = {2211-1247},

year  = {2023},

date = {2023-10-01},

journal = {Cell Rep},

volume = {42},

number = {10},

pages = {113194},

abstract = {The ability of the human immune system to generate antibodies to any given antigen can be strongly influenced by immunoglobulin V-gene allelic polymorphisms. However, previous studies have provided only limited examples. Therefore, the prevalence of this phenomenon has been unclear. By analyzing >1,000 publicly available antibody-antigen structures, we show that many V-gene allelic polymorphisms in antibody paratopes are determinants for antibody binding activity. Biolayer interferometry experiments further demonstrate that paratope allelic polymorphisms on both heavy and light chains often abolish antibody binding. We also illustrate the importance of minor V-gene allelic polymorphisms with low frequency in several broadly neutralizing antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza virus. Overall, this study not only highlights the pervasive impact of V-gene allelic polymorphisms on antibody binding but also provides mechanistic insights into the variability of antibody repertoires across individuals, which in turn have important implications for vaccine development and antibody discovery.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37841584,

title = {Broad SARS-CoV-2 neutralization by monoclonal and bispecific antibodies derived from a Gamma-infected individual},

author = {Denise Guerra and Tim Beaumont and Laura Radić and Gius Kerster and Karlijn van der Straten and Meng Yuan and Jonathan L Torres and Wen-Hsin Lee and Hejun Liu and Meliawati Poniman and Ilja Bontjer and Judith A Burger and Mathieu Claireaux and Tom G Caniels and Jonne L Snitselaar and Tom P L Bijl and Sabine Kruijer and Gabriel Ozorowski and David Gideonse and Kwinten Sliepen and Andrew B Ward and Dirk Eggink and Godelieve J de Bree and Ian A Wilson and Rogier W Sanders and Marit J van Gils},

doi = {10.1016/j.isci.2023.108009},

issn = {2589-0042},

year  = {2023},

date = {2023-10-01},

journal = {iScience},

volume = {26},

number = {10},

pages = {108009},

abstract = {The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has remained a medical threat due to the evolution of multiple variants that acquire resistance to vaccines and prior infection. Therefore, it is imperative to discover monoclonal antibodies (mAbs) that neutralize a broad range of SARS-CoV-2 variants. A stabilized spike glycoprotein was used to enrich antigen-specific B cells from an individual with a primary Gamma variant infection. Five mAbs selected from those B cells showed considerable neutralizing potency against multiple variants, with COVA309-35 being the most potent against the autologous virus, as well as Omicron BA.1 and BA.2, and COVA309-22 having binding and neutralization activity against Omicron BA.4/5, BQ.1.1, and XBB.1. When combining the COVA309 mAbs as cocktails or bispecific antibodies, the breadth and potency were improved. In addition, the mechanism of cross-neutralization of the COVA309 mAbs was elucidated by structural analysis. Altogether these data indicate that a Gamma-infected individual can develop broadly neutralizing antibodies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37703367,

title = {Chimeric hemagglutinin split vaccines elicit broadly cross-reactive antibodies and protection against group 2 influenza viruses in mice},

author = {Eduard Puente-Massaguer and Kirill Vasilev and Annika Beyer and Madhumathi Loganathan and Benjamin Francis and Michael J Scherm and Guha Asthagiri Arunkumar and Irene González-Domínguez and Xueyong Zhu and Ian A Wilson and Lynda Coughlan and Weina Sun and Peter Palese and Florian Krammer},

doi = {10.1126/sciadv.adi4753},

issn = {2375-2548},

year  = {2023},

date = {2023-09-01},

journal = {Sci Adv},

volume = {9},

number = {37},

pages = {eadi4753},

abstract = {Seasonal influenza virus vaccines are effective when they are well matched to circulating strains. Because of antigenic drift/change in the immunodominant hemagglutinin (HA) head domain, annual vaccine reformulations are necessary to maintain a match with circulating strains. In addition, seasonal vaccines provide little to no protection against newly emerging pandemic strains. Sequential vaccination with chimeric HA (cHA) constructs has been proven to direct the immune response toward the immunosubdominant but more conserved HA stalk domain. In this study, we show that immunization with group 2 cHA split vaccines in combination with the CpG 1018 adjuvant elicits broadly cross-reactive antibodies against all group 2 HAs, as well as systemic and local antigen-specific T cell responses. Antibodies elicited after sequential vaccination are directed to conserved regions of the HA such as the stalk and the trimer interface and also to the N2 neuraminidase (NA). Immunized mice were fully protected from challenge with a broad panel of influenza A viruses.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37722054,

title = {The smallest functional antibody fragment: Ultralong CDR H3 antibody knob regions potently neutralize SARS-CoV-2},

author = {Ruiqi Huang and Gabrielle Warner Jenkins and Yunjeong Kim and Robyn L Stanfield and Amrinder Singh and Maria Martinez-Yamout and Gerard J Kroon and Jonathan L Torres and Abigail M Jackson and Abigail Kelley and Namir Shaabani and Baisen Zeng and Michael Bacica and Wen Chen and Christopher Warner and Jasmina Radoicic and Joongho Joh and Krishani Dinali Perera and Huldah Sang and Tae Kim and Jianxiu Yao and Fangzhu Zhao and Devin Sok and Dennis R Burton and Jeff Allen and William Harriman and Waithaka Mwangi and Donghoon Chung and John R Teijaro and Andrew B Ward and H Jane Dyson and Peter E Wright and Ian A Wilson and Kyeong-Ok Chang and Duncan McGregor and Vaughn V Smider},

doi = {10.1073/pnas.2303455120},

issn = {1091-6490},

year  = {2023},

date = {2023-09-01},

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

volume = {120},

number = {39},

pages = {e2303455120},

abstract = {Cows produce antibodies with a disulfide-bonded antigen-binding domain embedded within ultralong heavy chain third complementarity determining regions. This "knob" domain is analogous to natural cysteine-rich peptides such as knottins in that it is small and stable but can accommodate diverse loops and disulfide bonding patterns. We immunized cattle with SARS-CoV-2 spike and found ultralong CDR H3 antibodies that could neutralize several viral variants at picomolar IC potencies in vitro and could protect from disease in vivo. The independent CDR H3 peptide knobs were expressed and maintained the properties of the parent antibodies. The knob interaction with SARS-CoV-2 spike was revealed by electron microscopy, X-ray crystallography, NMR spectroscopy, and mass spectrometry and established ultralong CDR H3-derived knobs as the smallest known recombinant independent antigen-binding fragment. Unlike other vertebrate antibody fragments, these knobs are not reliant on the immunoglobulin domain and have potential as a new class of therapeutics.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37279624,

title = {Pharmacological stabilization of the native state of full-length immunoglobulin light chains to treat light chain amyloidosis},

author = {Nicholas L Yan and Gareth J Morgan and H Michael Petrassi and Ian A Wilson and Jeffery W Kelly},

doi = {10.1016/j.cbpa.2023.102319},

issn = {1879-0402},

year  = {2023},

date = {2023-08-01},

journal = {Curr Opin Chem Biol},

volume = {75},

pages = {102319},

abstract = {Immunoglobulin light chain amyloidosis (AL) is a cancer of plasma cells that secrete unstable full-length immunoglobulin light chains. These light chains misfold and aggregate, often with aberrant endoproteolysis, leading to organ toxicity. AL is currently treated by pharmacological elimination of the clonal plasma cells. Since it remains difficult to completely kill these cells in the majority of patients, we seek a complementary drug that inhibits light chain aggregation, which should diminish organ toxicity. We discovered a small-molecule binding site on full-length immunoglobulin light chains by structurally characterizing hit stabilizers emerging from a high-throughput screen seeking small molecules that protect full-length light chains from conformational excursion-linked endoproteolysis. The x-ray crystallographic characterization of 7 structurally distinct hit native-state stabilizers provided a structure-based blueprint, reviewed herein, to design more potent stabilizers. This approach enabled us to transform hits with micromolar affinity into stabilizers with nanomolar dissociation constants that potently prevent light chain aggregation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37506693,

title = {Human anti-N1 monoclonal antibodies elicited by pandemic H1N1 virus infection broadly inhibit HxN1 viruses in vitro and in vivo},

author = {Lena Hansen and Meagan McMahon and Hannah L Turner and Xueyong Zhu and Jackson S Turner and Gabriel Ozorowski and Daniel Stadlbauer and Juha Vahokoski and Aaron J Schmitz and Amena A Rizk and Wafaa B Alsoussi and Shirin Strohmeier and Wenli Yu and José Alberto Choreño-Parra and Luis Jiménez-Alvarez and Alfredo Cruz-Lagunas and Joaquín Zúñiga and Philip A Mudd and Rebecca J Cox and Ian A Wilson and Andrew B Ward and Ali H Ellebedy and Florian Krammer},

doi = {10.1016/j.immuni.2023.07.004},

issn = {1097-4180},

year  = {2023},

date = {2023-08-01},

journal = {Immunity},

volume = {56},

number = {8},

pages = {1927--1938.e8},

abstract = {Neuraminidase (NA) is one of the two influenza virus surface glycoproteins, and antibodies that target it are an independent correlate of protection. However, our current understanding of NA antigenicity is incomplete. Here, we describe human monoclonal antibodies (mAbs) from a patient with a pandemic H1N1 virus infection in 2009. Two mAbs exhibited broad reactivity and inhibited NA enzyme activity of seasonal H1N1 viruses circulating before and after 2009, as well as viruses with avian or swine N1s. The mAbs provided robust protection from lethal challenge with human H1N1 and avian H5N1 viruses in mice, and both target an epitope on the lateral face of NA. In summary, we identified two broadly protective NA antibodies that share a novel epitope, inhibited NA activity, and provide protection against virus challenge in mice. Our work reaffirms that NA should be included as a target in future broadly protective or universal influenza virus vaccines.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37534714,

title = {An Engineered Human-Antibody Fragment with Fentanyl Pan-Specificity That Reverses Carfentanil-Induced Respiratory Depression},

author = {Lisa M Eubanks and Tossapol Pholcharee and David Oyen and Yoshihiro Natori and Bin Zhou and Ian A Wilson and Kim D Janda},

doi = {10.1021/acschemneuro.3c00455},

issn = {1948-7193},

year  = {2023},

date = {2023-08-01},

journal = {ACS Chem Neurosci},

volume = {14},

number = {16},

pages = {2849--2856},

abstract = {The opioid overdose crisis primarily driven by potent synthetic opioids resulted in more than 500,000 deaths in the US over the last 20 years. Though naloxone, a short-acting medication, remains the primary treatment option for temporarily reversing opioid overdose effects, alternative countermeasures are needed. Monoclonal antibodies present a versatile therapeutic opportunity that can be tailored to synthetic opioids and help prevent post-treatment renarcotization. The ultrapotent analog carfentanil is especially concerning due to its unique pharmacological properties. With this in mind, we generated a fully human antibody through a drug-specific B cell sorting strategy with a combination of carfentanil and fentanyl probes. The resulting pan-specific antibody was further optimized through scFv phage display, producing C10-S66K. This monoclonal antibody displays high affinity to carfentanil, fentanyl, and other analogs and reversed carfentanil-induced respiratory depression. Additionally, X-ray crystal structures with carfentanil and fentanyl bound provided structural insight into key drug:antibody interactions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37582161,

title = {Broadening a SARS-CoV-1-neutralizing antibody for potent SARS-CoV-2 neutralization through directed evolution},

author = {Fangzhu Zhao and Meng Yuan and Celina Keating and Namir Shaabani and Oliver Limbo and Collin Joyce and Jordan Woehl and Shawn Barman and Alison Burns and Quoc Tran and Xueyong Zhu and Michael Ricciardi and Linghang Peng and Jessica Smith and Deli Huang and Bryan Briney and Devin Sok and David Nemazee and John R Teijaro and Ian A Wilson and Dennis R Burton and Joseph G Jardine},

doi = {10.1126/scisignal.abk3516},

issn = {1937-9145},

year  = {2023},

date = {2023-08-01},

journal = {Sci Signal},

volume = {16},

number = {798},

pages = {eabk3516},

abstract = {The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the need for strategies to rapidly develop neutralizing monoclonal antibodies that can function as prophylactic and therapeutic agents and to help guide vaccine design. Here, we demonstrate that engineering approaches can be used to refocus an existing antibody that neutralizes one virus but not a related virus. Through a rapid affinity maturation strategy, we engineered CR3022, a SARS-CoV-1-neutralizing antibody, to bind to the receptor binding domain of SARS-CoV-2 with >1000-fold increased affinity. The engineered CR3022 neutralized SARS-CoV-2 and provided prophylactic protection from viral challenge in a small animal model of SARS-CoV-2 infection. Deep sequencing throughout the engineering process paired with crystallographic analysis of engineered CR3022 elucidated the molecular mechanisms by which the antibody can accommodate sequence differences in the epitopes between SARS-CoV-1 and SARS-CoV-2. This workflow provides a blueprint for the rapid broadening of neutralization of an antibody from one virus to closely related but resistant viruses.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37419097,

title = {Major classes of neutralizing antibodies evaded by the SARS-CoV-2 Omicron variant},

author = {Meng Yuan and Ian A Wilson},

doi = {10.1016/j.str.2023.06.005},

issn = {1878-4186},

year  = {2023},

date = {2023-07-01},

journal = {Structure},

volume = {31},

number = {7},

pages = {755--757},

abstract = {Understanding how SARS-CoV-2 evades neutralizing antibodies is crucial for the development of therapeutic antibodies and universal vaccines. In this issue of Structure, Patel et al. elucidate mechanisms of SARS-CoV-2 escape from two major antibody classes. Cryoelectron microscopy (cryo-EM) structures of these antibodies with the SARS-CoV-2 spike formed the basis of their findings.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37507365,

title = {Affinity-matured homotypic interactions induce spectrum of PfCSP structures that influence protection from malaria infection},

author = {Gregory M Martin and Jonathan L Torres and Tossapol Pholcharee and David Oyen and Yevel Flores-Garcia and Grace Gibson and Re'em Moskovitz and Nathan Beutler and Diana D Jung and Jeffrey Copps and Wen-Hsin Lee and Gonzalo Gonzalez-Paez and Daniel Emerling and Randall S MacGill and Emily Locke and C Richter King and Fidel Zavala and Ian A Wilson and Andrew B Ward},

doi = {10.1038/s41467-023-40151-x},

issn = {2041-1723},

year  = {2023},

date = {2023-07-01},

journal = {Nat Commun},

volume = {14},

number = {1},

pages = {4546},

abstract = {The generation of high-quality antibody responses to Plasmodium falciparum (Pf) circumsporozoite protein (PfCSP), the primary surface antigen of Pf sporozoites, is paramount to the development of an effective malaria vaccine. Here we present an in-depth structural and functional analysis of a panel of potent antibodies encoded by the immunoglobulin heavy chain variable (IGHV) gene IGHV3-33, which is among the most prevalent and potent antibody families induced in the anti-PfCSP immune response and targets the Asn-Ala-Asn-Pro (NANP) repeat region. Cryo-electron microscopy (cryo-EM) reveals a remarkable spectrum of helical antibody-PfCSP structures stabilized by homotypic interactions between tightly packed fragments antigen binding (Fabs), many of which correlate with somatic hypermutation. We demonstrate a key role of these mutated homotypic contacts for high avidity binding to PfCSP and in protection from Pf malaria infection. Together, these data emphasize the importance of anti-homotypic affinity maturation in the frequent selection of IGHV3-33 antibodies and highlight key features underlying the potent protection of this antibody family.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37276407,

title = {Fully synthetic platform to rapidly generate tetravalent bispecific nanobody-based immunoglobulins},

author = {Laetitia Misson Mindrebo and Hejun Liu and Gabriel Ozorowski and Quoc Tran and Jordan Woehl and Irene Khalek and Jessica M Smith and Shawn Barman and Fangzhu Zhao and Celina Keating and Oliver Limbo and Megan Verma and Jingjia Liu and Robyn L Stanfield and Xueyong Zhu and Hannah L Turner and Devin Sok and Po-Ssu Huang and Dennis R Burton and Andrew B Ward and Ian A Wilson and Joseph G Jardine},

doi = {10.1073/pnas.2216612120},

issn = {1091-6490},

year  = {2023},

date = {2023-06-01},

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

volume = {120},

number = {24},

pages = {e2216612120},

abstract = {Nanobodies bind a target antigen with a kinetic profile similar to a conventional antibody, but exist as a single heavy chain domain that can be readily multimerized to engage antigen via multiple interactions. Presently, most nanobodies are produced by immunizing camelids; however, platforms for animal-free production are growing in popularity. Here, we describe the development of a fully synthetic nanobody library based on an engineered human V3-23 variable gene and a multispecific antibody-like format designed for biparatopic target engagement. To validate our library, we selected nanobodies against the SARS-CoV-2 receptor-binding domain and employed an on-yeast epitope binning strategy to rapidly map the specificities of the selected nanobodies. We then generated antibody-like molecules by replacing the V and V domains of a conventional antibody with two different nanobodies, designed as a molecular clamp to engage the receptor-binding domain biparatopically. The resulting bispecific tetra-nanobody immunoglobulins neutralized diverse SARS-CoV-2 variants with potencies similar to antibodies isolated from convalescent donors. Subsequent biochemical analyses confirmed the accuracy of the on-yeast epitope binning and structures of both individual nanobodies, and a tetra-nanobody immunoglobulin revealed that the intended mode of interaction had been achieved. This overall workflow is applicable to nearly any protein target and provides a blueprint for a modular workflow for the development of multispecific molecules.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37384622,

title = {Antigen pressure from two founder viruses induces multiple insertions at a single antibody position to generate broadly neutralizing HIV antibodies},

author = {Collin Joyce and Sasha Murrell and Ben Murrell and Oluwarotimi Omorodion and Lorena S Ver and Nancy Carrico and Raiza Bastidas and Rebecca Nedellec and Michael Bick and Jordan Woehl and Fangzhu Zhao and Alison Burns and Shawn Barman and Michael Appel and Alejandra Ramos and Lalinda Wickramasinghe and Kemal Eren and Thomas Vollbrecht and Davey M Smith and Sergei L Kosakovsky Pond and Ryan McBride and Charli Worth and Facundo Batista and Devin Sok and  and Pascal Poignard and Bryan Briney and Ian A Wilson and Elise Landais and Dennis R Burton},

doi = {10.1371/journal.ppat.1011416},

issn = {1553-7374},

year  = {2023},

date = {2023-06-01},

journal = {PLoS Pathog},

volume = {19},

number = {6},

pages = {e1011416},

abstract = {Vaccination strategies aimed at maturing broadly neutralizing antibodies (bnAbs) from naïve precursors are hindered by unusual features that characterize these Abs, including insertions and deletions (indels). Longitudinal studies of natural HIV infection cases shed light on the complex processes underlying bnAb development and have suggested a role for superinfection as a potential enhancer of neutralization breadth. Here we describe the development of a potent bnAb lineage that was elicited by two founder viruses to inform vaccine design. The V3-glycan targeting bnAb lineage (PC39-1) was isolated from subtype C-infected IAVI Protocol C elite neutralizer, donor PC39, and is defined by the presence of multiple independent insertions in CDRH1 that range from 1-11 amino acids in length. Memory B cell members of this lineage are predominantly atypical in phenotype yet also span the class-switched and antibody-secreting cell compartments. Development of neutralization breadth occurred concomitantly with extensive recombination between founder viruses before each virus separated into two distinct population "arms" that evolved independently to escape the PC39-1 lineage. Ab crystal structures show an extended CDRH1 that can help stabilize the CDRH3. Overall, these findings suggest that early exposure of the humoral system to multiple related Env molecules could promote the induction of bnAbs by focusing Ab responses to conserved epitopes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37163615,

title = {Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine},

author = {Yupeng Feng and Meng Yuan and John M Powers and Mengyun Hu and Jennifer E Munt and Prabhu S Arunachalam and Sarah R Leist and Lorenza Bellusci and JungHyun Kim and Kaitlin R Sprouse and Lily E Adams and Sumana Sundaramurthy and Xueyong Zhu and Lisa M Shirreff and Michael L Mallory and Trevor D Scobey and Alberto Moreno and Derek T O'Hagan and Harry Kleanthous and Francois J Villinger and David Veesler and Neil P King and Mehul S Suthar and Surender Khurana and Ralph S Baric and Ian A Wilson and Bali Pulendran},

doi = {10.1126/scitranslmed.adg7404},

issn = {1946-6242},

year  = {2023},

date = {2023-05-01},

journal = {Sci Transl Med},

volume = {15},

number = {695},

pages = {eadg7404},

abstract = {The rapid emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that evade immunity elicited by vaccination has placed an imperative on the development of countermeasures that provide broad protection against SARS-CoV-2 and related sarbecoviruses. Here, we identified extremely potent monoclonal antibodies (mAbs) that neutralized multiple sarbecoviruses from macaques vaccinated with AS03-adjuvanted monovalent subunit vaccines. Longitudinal analysis revealed progressive accumulation of somatic mutation in the immunoglobulin genes of antigen-specific memory B cells (MBCs) for at least 1 year after primary vaccination. Antibodies generated from these antigen-specific MBCs at 5 to 12 months after vaccination displayed greater potency and breadth relative to those identified at 1.4 months. Fifteen of the 338 (about 4.4%) antibodies isolated at 1.4 to 6 months after the primary vaccination showed potency against SARS-CoV-2 BA.1, despite the absence of serum BA.1 neutralization. 25F9 and 20A7 neutralized authentic clade 1 sarbecoviruses (SARS-CoV, WIV-1, SHC014, SARS-CoV-2 D614G, BA.1, and Pangolin-GD) and vesicular stomatitis virus-pseudotyped clade 3 sarbecoviruses (BtKY72 and PRD-0038). 20A7 and 27A12 showed potent neutralization against all SARS-CoV-2 variants and multiple Omicron sublineages, including BA.1, BA.2, BA.3, BA.4/5, BQ.1, BQ.1.1, and XBB. Crystallography studies revealed the molecular basis of broad and potent neutralization through targeting conserved sites within the RBD. Prophylactic protection of 25F9, 20A7, and 27A12 was confirmed in mice, and administration of 25F9 particularly provided complete protection against SARS-CoV-2, BA.1, SARS-CoV, and SHC014 challenge. These data underscore the extremely potent and broad activity of these mAbs against sarbecoviruses.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37198165,

title = {Structural basis of epitope selectivity and potent protection from malaria by PfCSP antibody L9},

author = {Gregory M Martin and Monica L Fernández-Quintero and Wen-Hsin Lee and Tossapol Pholcharee and Lisa Eshun-Wilson and Klaus R Liedl and Marie Pancera and Robert A Seder and Ian A Wilson and Andrew B Ward},

doi = {10.1038/s41467-023-38509-2},

issn = {2041-1723},

year  = {2023},

date = {2023-05-01},

journal = {Nat Commun},

volume = {14},

number = {1},

pages = {2815},

abstract = {A primary objective in malaria vaccine design is the generation of high-quality antibody responses against the circumsporozoite protein of the malaria parasite, Plasmodium falciparum (PfCSP). To enable rational antigen design, we solved a cryo-EM structure of the highly potent anti-PfCSP antibody L9 in complex with recombinant PfCSP. We found that L9 Fab binds multivalently to the minor (NPNV) repeat domain, which is stabilized by a unique set of affinity-matured homotypic, antibody-antibody contacts. Molecular dynamics simulations revealed a critical role of the L9 light chain in integrity of the homotypic interface, which likely impacts PfCSP affinity and protective efficacy. These findings reveal the molecular mechanism of the unique NPNV selectivity of L9 and emphasize the importance of anti-homotypic affinity maturation in protective immunity against P. falciparum.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36862518,

title = {Site of vulnerability on SARS-CoV-2 spike induces broadly protective antibody against antigenically distinct Omicron subvariants},

author = {Siriruk Changrob and Peter J Halfmann and Hejun Liu and Jonathan L Torres and Joshua J C McGrath and Gabriel Ozorowski and Lei Li and G Dewey Wilbanks and Makoto Kuroda and Tadashi Maemura and Min Huang and Nai-Ying Zheng and Hannah L Turner and Steven A Erickson and Yanbin Fu and Atsuhiro Yasuhara and Gagandeep Singh and Brian Monahan and Jacob Mauldin and Komal Srivastava and Viviana Simon and Florian Krammer and D Noah Sather and Andrew B Ward and Ian A Wilson and Yoshihiro Kawaoka and Patrick C Wilson},

doi = {10.1172/JCI166844},

issn = {1558-8238},

year  = {2023},

date = {2023-04-01},

journal = {J Clin Invest},

volume = {133},

number = {8},

abstract = {The rapid evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants has emphasized the need to identify antibodies with broad neutralizing capabilities to inform future monoclonal therapies and vaccination strategies. Herein, we identified S728-1157, a broadly neutralizing antibody (bnAb) targeting the receptor-binding site (RBS) that was derived from an individual previously infected with WT SARS-CoV-2 prior to the spread of variants of concern (VOCs). S728-1157 demonstrated broad cross-neutralization of all dominant variants, including D614G, Beta, Delta, Kappa, Mu, and Omicron (BA.1/BA.2/BA.2.75/BA.4/BA.5/BL.1/XBB). Furthermore, S728-1157 protected hamsters against in vivo challenges with WT, Delta, and BA.1 viruses. Structural analysis showed that this antibody targets a class 1/RBS-A epitope in the receptor binding domain via multiple hydrophobic and polar interactions with its heavy chain complementarity determining region 3 (CDR-H3), in addition to common motifs in CDR-H1/CDR-H2 of class 1/RBS-A antibodies. Importantly, this epitope was more readily accessible in the open and prefusion state, or in the hexaproline (6P)-stabilized spike constructs, as compared with diproline (2P) constructs. Overall, S728-1157 demonstrates broad therapeutic potential and may inform target-driven vaccine designs against future SARS-CoV-2 variants.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37031217,

title = {Single-component multilayered self-assembling protein nanoparticles presenting glycan-trimmed uncleaved prefusion optimized envelope trimmers as HIV-1 vaccine candidates},

author = {Yi-Nan Zhang and Jennifer Paynter and Aleksandar Antanasijevic and Joel D Allen and Mor Eldad and Yi-Zong Lee and Jeffrey Copps and Maddy L Newby and Linling He and Deborah Chavez and Pat Frost and Anna Goodroe and John Dutton and Robert Lanford and Christopher Chen and Ian A Wilson and Max Crispin and Andrew B Ward and Jiang Zhu},

doi = {10.1038/s41467-023-37742-z},

issn = {2041-1723},

year  = {2023},

date = {2023-04-01},

journal = {Nat Commun},

volume = {14},

number = {1},

pages = {1985},

abstract = {Uncleaved prefusion-optimized (UFO) design can stabilize diverse HIV-1 envelope glycoproteins (Envs). Single-component, self-assembling protein nanoparticles (1c-SApNP) can display 8 or 20 native-like Env trimers as vaccine candidates. We characterize the biophysical, structural, and antigenic properties of 1c-SApNPs that present the BG505 UFO trimer with wildtype and modified glycans. For 1c-SApNPs, glycan trimming improves recognition of the CD4 binding site without affecting broadly neutralizing antibodies (bNAbs) to major glycan epitopes. In mice, rabbits, and nonhuman primates, glycan trimming increases the frequency of vaccine responders (FVR) and steers antibody responses away from immunodominant glycan holes and glycan patches. The mechanism of vaccine-induced immunity is examined in mice. Compared with the UFO trimer, the multilayered E2p and I3-01v9 1c-SApNPs show 420 times longer retention in lymph node follicles, 20-32 times greater presentation on follicular dendritic cell dendrites, and up-to-4 times stronger germinal center reactions. These findings can inform future HIV-1 vaccine development.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37037866,

title = {High-throughput identification of prefusion-stabilizing mutations in SARS-CoV-2 spike},

author = {Timothy J C Tan and Zongjun Mou and Ruipeng Lei and Wenhao O Ouyang and Meng Yuan and Ge Song and Raiees Andrabi and Ian A Wilson and Collin Kieffer and Xinghong Dai and Kenneth A Matreyek and Nicholas C Wu},

doi = {10.1038/s41467-023-37786-1},

issn = {2041-1723},

year  = {2023},

date = {2023-04-01},

journal = {Nat Commun},

volume = {14},

number = {1},

pages = {2003},

abstract = {Designing prefusion-stabilized SARS-CoV-2 spike is critical for the effectiveness of COVID-19 vaccines. All COVID-19 vaccines in the US encode spike with K986P/V987P mutations to stabilize its prefusion conformation. However, contemporary methods on engineering prefusion-stabilized spike immunogens involve tedious experimental work and heavily rely on structural information. Here, we establish a systematic and unbiased method of identifying mutations that concomitantly improve expression and stabilize the prefusion conformation of the SARS-CoV-2 spike. Our method integrates a fluorescence-based fusion assay, mammalian cell display technology, and deep mutational scanning. As a proof-of-concept, we apply this method to a region in the S2 domain that includes the first heptad repeat and central helix. Our results reveal that besides K986P and V987P, several mutations simultaneously improve expression and significantly lower the fusogenicity of the spike. As prefusion stabilization is a common challenge for viral immunogen design, this work will help accelerate vaccine development against different viruses.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37044090,

title = {Germline-targeting HIV-1 Env vaccination induces VRC01-class antibodies with rare insertions},

author = {Tom G Caniels and Max Medina-Ramírez and Jinsong Zhang and Anita Sarkar and Sonu Kumar and Alex LaBranche and Ronald Derking and Joel D Allen and Jonne L Snitselaar and Joan Capella-Pujol and Iván Del Moral Sánchez and Anila Yasmeen and Marilyn Diaz and Yoann Aldon and Tom P L Bijl and Sravani Venkatayogi and Joshua S Martin Beem and Amanda Newman and Chuancang Jiang and Wen-Hsin Lee and Maarten Pater and Judith A Burger and Mariëlle J van Breemen and Steven W de Taeye and Kimmo Rantalainen and Celia LaBranche and Kevin O Saunders and David Montefiori and Gabriel Ozorowski and Andrew B Ward and Max Crispin and John P Moore and Per Johan Klasse and Barton F Haynes and Ian A Wilson and Kevin Wiehe and Laurent Verkoczy and Rogier W Sanders},

doi = {10.1016/j.xcrm.2023.101003},

issn = {2666-3791},

year  = {2023},

date = {2023-04-01},

journal = {Cell Rep Med},

volume = {4},

number = {4},

pages = {101003},

abstract = {Targeting germline (gl-) precursors of broadly neutralizing antibodies (bNAbs) is acknowledged as an important strategy for HIV-1 vaccines. The VRC01-class of bNAbs is attractive because of its distinct genetic signature. However, VRC01-class bNAbs often require extensive somatic hypermutation, including rare insertions and deletions. We describe a BG505 SOSIP trimer, termed GT1.2, to optimize binding to gl-CH31, the unmutated common precursor of the CH30-34 bNAb lineage that acquired a large CDRH1 insertion. The GT1.2 trimer activates gl-CH31 naive B cells in knock-in mice, and B cell responses could be matured by selected boosting immunogens to generate cross-reactive Ab responses. Next-generation B cell sequencing reveals selection for VRC01-class mutations, including insertions in CDRH1 and FWR3 at positions identical to VRC01-class bNAbs, as well as CDRL1 deletions and/or glycine substitutions to accommodate the N276 glycan. These results provide proof of concept for vaccine-induced affinity maturation of B cell lineages that require rare insertions and deletions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36175661,

title = {Targeted protein S-nitrosylation of ACE2 inhibits SARS-CoV-2 infection},

author = {Chang-Ki Oh and Tomohiro Nakamura and Nathan Beutler and Xu Zhang and Juan Piña-Crespo and Maria Talantova and Swagata Ghatak and Dorit Trudler and Lauren N Carnevale and Scott R McKercher and Malina A Bakowski and Jolene K Diedrich and Amanda J Roberts and Ashley K Woods and Victor Chi and Anil K Gupta and Mia A Rosenfeld and Fiona L Kearns and Lorenzo Casalino and Namir Shaabani and Hejun Liu and Ian A Wilson and Rommie E Amaro and Dennis R Burton and John R Yates and Cyrus Becker and Thomas F Rogers and Arnab K Chatterjee and Stuart A Lipton},

doi = {10.1038/s41589-022-01149-6},

issn = {1552-4469},

year  = {2023},

date = {2023-03-01},

journal = {Nat Chem Biol},

volume = {19},

number = {3},

pages = {275--283},

abstract = {Prevention of infection and propagation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a high priority in the Coronavirus Disease 2019 (COVID-19) pandemic. Here we describe S-nitrosylation of multiple proteins involved in SARS-CoV-2 infection, including angiotensin-converting enzyme 2 (ACE2), the receptor for viral entry. This reaction prevents binding of ACE2 to the SARS-CoV-2 spike protein, thereby inhibiting viral entry, infectivity and cytotoxicity. Aminoadamantane compounds also inhibit coronavirus ion channels formed by envelope (E) protein. Accordingly, we developed dual-mechanism aminoadamantane nitrate compounds that inhibit viral entry and, thus, the spread of infection by S-nitrosylating ACE2 via targeted delivery of the drug after E protein channel blockade. These non-toxic compounds are active in vitro and in vivo in the Syrian hamster COVID-19 model and, thus, provide a novel avenue to pursue therapy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}