Atomically accurate de novo design of single-domain antibodies

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 18, 2024

Despite the central role that antibodies play in modern medicine, there is currently no way to rationally design novel bind a specific epitope on target. Instead, antibody discovery involves time-consuming immunization of an animal or library screening approaches. Here we demonstrate fine-tuned RFdiffusion network capable designing de novo variable heavy chains (VHH's) user-specified epitopes. We experimentally confirm binders four disease-relevant epitopes, and cryo-EM structure designed VHH bound influenza hemagglutinin nearly identical model both configuration CDR loops overall binding pose.

Language: Английский

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Bringing immunofocusing into focus

npj Vaccines, Journal Year: 2024, Volume and Issue: 9(1)

Published: Jan. 9, 2024

Abstract Immunofocusing is a strategy to create immunogens that redirect humoral immune responses towards targeted epitope and away from non-desirable epitopes. methods often aim develop “universal” vaccines provide broad protection against highly variant viruses such as influenza virus, human immunodeficiency virus (HIV-1), most recently, severe acute respiratory syndrome coronavirus (SARS-CoV-2). We use existing examples illustrate five main immunofocusing strategies—cross-strain boosting, mosaic display, protein dissection, scaffolding, masking. also discuss obstacles for like imprinting. A thorough understanding, advancement, application of the we outline here will enable design high-resolution protect future viral outbreaks.

Language: Английский

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Contextualising the developability risk of antibodies with lambda light chains using enhanced therapeutic antibody profiling

Communications Biology, Journal Year: 2024, Volume and Issue: 7(1)

Published: Jan. 8, 2024

Abstract Antibodies with lambda light chains ( λ -antibodies) are generally considered to be less developable than those kappa κ -antibodies). Though this hypothesis has not been formally established, it led substantial systematic biases in drug discovery pipelines and thus contributed dominance amongst clinical-stage therapeutics. However, the identification of increasing numbers epitopes preferentially engaged by -antibodies shows there is a functional cost neglecting consider them as potential lead candidates. Here, we update our Therapeutic Antibody Profiler (TAP) tool use latest data machine learning-based structure prediction, apply evaluate developability risk profiles for based on their surface physicochemical properties. We find that while human average have higher issues -antibodies, sizeable proportion assigned lower-risk TAP should represent more tractable candidates therapeutic development. Through comparative analysis low- high-risk populations, highlight opportunities strategic design suggests would enrich -antibodies. Overall, provide context differing - enabling rational approach incorporate diversity into initial pool immunotherapeutic

Language: Английский

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Broadly neutralizing antibodies targeting pandemic GII.4 variants or seven GII genotypes of human norovirus

Science Translational Medicine, Journal Year: 2025, Volume and Issue: 17(788)

Published: March 5, 2025

Human norovirus causes more than 700 million illnesses annually. Extensive genetic diversity and a paucity of information on conserved neutralizing epitopes pose major obstacles to the design broadly protective immunogens. Here, we used high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS)-driven proteomics quantitatively characterize circulating serum IgG repertoire before after immunization with an experimental monovalent GII.4 VP1 capsid-encoding adenoviral vaccine. Two participants were specifically selected basis breadth neutralization responses either across variants (participant A) or GII genotypes B). In participant A, vaccination back-boosted highly abundant antibody clonotypes targeting among rapidly evolving spanning from strain identified in 1987 2019. B, recall response consisting monoclonal antibodies remarkable cross-GII ligand-binding blockade (blocking ≥ seven genotypes) virus breadth. The cocrystal structure one these antibodies, VX22, complex capsid protruding (P) domain revealed epitope (residues 479 484 509 513) within two lateral loops P1 subdomain. Antibody evolutionary trajectory analysis further that VX22 had originally evolved early heterologous infection, likely by GII.12 strain. Together, our study demonstrates human broad potency can be boosted vector-based vaccine, findings may guide immunogens for vaccines.

Language: Английский

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Convergent and clonotype-enriched mutations in the light chain drive affinity maturation of a public antibody

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: March 11, 2025

SUMMARY Public antibodies that recognize conserved epitopes are critical for vaccine development, and identifying somatic hypermutations (SHMs) enhance antigen affinity in these public responses is key to guiding design better protection. We propose affinity-enhancing SHMs selectively enriched antibody clonotypes, surpassing the background frequency seen carrying same V genes, but with different epitope specificities. Employing a human IGHV4-59 / IGKV3-20 as model, we compare SHM signatures also using recognizing other epitopes. Critically, this comparison identified clonotype-enriched mutations light chain. Our analyses show SHMs, combination, binding previously uncharacterized viral epitope, it increasing after multiple vaccinations. findings offer framework based on convergence clonotype-enrichment can help guide aimed elicit antibodies. Graphical Abstract Highlights Clonotype-enriched chain of antibody, M15 These targets undescribed, Serum levels targeting increase repeated vaccinations

Language: Английский

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The Patent and Literature Antibody Database (PLAbDab): an evolving reference set of functionally diverse, literature-annotated antibody sequences and structures

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 52(D1), P. D545 - D551

Published: Nov. 16, 2023

Abstract Antibodies are key proteins of the adaptive immune system, and there exists a large body academic literature patents dedicated to their study concomitant conversion into therapeutics, diagnostics, or reagents. These documents often contain extensive functional characterisations sets antibodies they describe. However, leveraging these heterogeneous reports, for example offer insights properties query interest, is currently challenging as no central repository through which this wide corpus can be mined by sequence structure. Here, we present PLAbDab (the Patent Literature Antibody Database), self-updating containing over 150,000 paired antibody sequences 3D structural models, 65 000 unique. We describe methods used extract, filter, pair, model in PLAbDab, showcase how searched sequence, structure, keyword. uses include annotating with potential antigen information from similar entries, analysing models existing identify modifications that could improve properties, facilitating compilation bespoke datasets sequences/structures bind specific antigen. freely available via Github (https://github.com/oxpig/PLAbDab) searchable webserver (https://opig.stats.ox.ac.uk/webapps/plabdab/).

Language: Английский

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Innovations and trends in antibody repertoire analysis

Current Opinion in Biotechnology, Journal Year: 2024, Volume and Issue: 86, P. 103082 - 103082

Published: March 1, 2024

Language: Английский

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The Observed T cell receptor Space database enables paired-chain repertoire mining, coherence analysis and language modelling

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 21, 2024

T cell activation is governed through receptors (TCRs), heterodimers of two sequence-variable chains (often an alpha [ α ] and beta β chain) that recognise linear antigen fragments presented on the surfaces. Early sequencing technologies limited study immune repertoire TCRs to unpaired transcripts, leading extensive analysis -chain data alone as its greater sequence diversity suggested it should dominate recognition. Over time, structural has revealed both contribute binding most antigens highthroughput single-cell handling have been increasingly applied obtain samples complete TCR variable region sequences from repertoires. Despite this, there currently no repository dedicated curation publicly available paired data. We addressed this gap by creating Observed receptor Space (OTS) database, a source consistently processed annotated, full-length, paired-chain 50 studies at least 75 individuals. Currently, OTS contains 5.35M redundant (1.63M nonredundant) predominantly human and, based recent availability trends, will grow rapidly. perform initial OTS, identification pairing biases, public TCRs, distinct chain coherence patterns relative antibodies. also harness build language model, providing embedding representations method for residue in-filling conditional partner chain. be updated maintained central community resource freely downloadable web application https://opig.stats.ox.ac.uk/webapps/ots .

Language: Английский

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Improved computational epitope profiling using structural models identifies a broader diversity of antibodies that bind to the same epitope

Frontiers in Molecular Biosciences, Journal Year: 2023, Volume and Issue: 10

Published: Sept. 18, 2023

The function of an antibody is intrinsically linked to the epitope it engages. Clonal clustering methods, based on sequence identity, are commonly used group antibodies that will bind same epitope. However, such methods neglect fact with highly diverse sequences can exhibit similar binding site geometries and engage common epitopes. In a previous study, we described SPACE1, method structurally clustered in order predict their This methodology was limited by inaccuracies incomplete coverage template-based modeling. addition, only benchmarked at level domain-consistency one virus class. Here, present SPACE2, which uses latest machine learning-based structure prediction technology combined novel protocol, benchmark data have epitope-level resolution. On six sets antigen-specific antibodies, demonstrate SPACE2 accurately clusters epitopes achieves far higher dataset than clonal SPACE1. Furthermore, show functionally consistent structural identified even more sequence, genetic lineage, species origin those found These results reiterate improve our ability identify epitope, adding information sequence-based especially datasets from sources. openly available GitHub (https://github.com/oxpig/SPACE2).

Language: Английский

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Structural trends in antibody-antigen binding interfaces: a computational analysis of 1833 experimentally determined 3D structures

Computational and Structural Biotechnology Journal, Journal Year: 2023, Volume and Issue: 23, P. 199 - 211

Published: Dec. 4, 2023

Antibodies are attractive therapeutic candidates due to their ability bind cognate antigens with high affinity and specificity. Still, the underlying molecular rules governing antibody-antigen interface remain poorly understood, making in silico antibody design inherently difficult keeping discovery of novel antibodies a costly laborious process. This study investigates characteristics binding interfaces through computational analysis more than 850,000 atom-atom contacts from largest reported set complexes 1833 nonredundant, experimentally determined structures. The compares conventional single-domain (sdAbs) targeting both protein- peptide antigens. We find clear patterns number amino acid frequencies paratope. direct comparison sdAbs helps elucidate mechanisms employed by compensate for smaller size fact that they harbor only half complementarity-determining regions compared antibodies. Furthermore, we pinpoint hotspot residues often found at these positions. These findings have potential applications engineering improved libraries.

Language: Английский

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