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}) })(jQuery); </script> </head> <body class="post-template-default single single-post postid-652 single-format-standard header-image full-width-content genesis-breadcrumbs-visible"><div class="site-container"><header class="site-header"><div class="wrap"><div class="title-area"><p class="site-title"><a href="https://www.thermofisher.com/" title="Thermo Fisher Scientific">Thermo Fisher Scientific</a></p><p class="site-description">Electron and cryo-electron microscopy stories and solutions about the advancement of cellular and structural biology</p></div><div class="widget-area header-widget-area"><section id="block-5" class="widget widget_block"><div class="widget-wrap"> <div class="wp-block-group"><div class="wp-block-group__inner-container is-layout-flow wp-block-group-is-layout-flow"></div></div> </div></section> <section id="block-6" class="widget widget_block"><div class="widget-wrap"> <div class="wp-block-group"><div class="wp-block-group__inner-container is-layout-flow wp-block-group-is-layout-flow"></div></div> </div></section> </div><div class="breadcrumb"><span class="breadcrumb-link-wrap"><a href="https://www.thermofisher.com/blog/?">Accelerating Science</a></span><span class="breadcrumb-link-wrap"><a class="breadcrumb-link" href="https://www.thermofisher.com/blog/atomic-resolution/"><span class="breadcrumb-link-text-wrap">Life in Atomic Resolution</span></a><meta ></span> <span aria-label="breadcrumb separator">/</span> <span class="breadcrumb-link-wrap"><a class="breadcrumb-link" href="https://www.thermofisher.com/blog/atomic-resolution/cryo-electron-microscopy-cryo-em/"><span class="breadcrumb-link-text-wrap">Cryo-Electron Microscopy (Cryo-EM)</span></a><meta ></span> <span aria-label="breadcrumb separator">/</span> <span class="breadcrumb-current-title">Rapid Cryo-EM Epitope Mapping Could Enhance Antibody Drug Discovery</span></div></div></header> <section class="hero-banner" style="background-image:url(https://www.thermofisher.com/blog/atomic-resolution/wp-content/uploads/sites/22/2022/04/Takeda-SARS-image.png)"> </section> <div class="site-inner"><div class="content-sidebar-wrap"><main class="content"><article class="post-652 post type-post status-publish format-standard has-post-thumbnail category-cryo-electron-microscopy-cryo-em category-customer-spotlights category-general tag-cryo-electron-microscopy tag-cryo-em tag-drug-discovery entry" aria-label="Rapid Cryo-EM Epitope Mapping Could Enhance Antibody Drug Discovery"><header class="entry-header"><h1 class="entry-title">Rapid Cryo-EM Epitope Mapping Could Enhance Antibody Drug Discovery</h1> <span class="post-info-author"> By <a href="https://www.thermofisher.com/blog/author/mazdakradjainia/" title="Posts by Mazdak Radjainia" rel="author">Mazdak Radjainia</a> </span> <span class="post-info-date"> 02.24.2022 </span> </header><div class="entry-content"><p>Historically, cryo-electron microscopy (cryo-EM) structure determination required operators to collect one dataset after another. But with the onset of the SARS-CoV-2 pandemic and a subsequent queue of variants continuously impacting our ability to prevent infection with existing solutions, there’s a clear need for faster, more efficient, data collection for the purpose of drug discovery. In collaboration with Takeda Pharmaceuticals and Utrecht University, we demonstrate the power of high-throughput cryo-EM for epitope mapping, including the potential for improved antibody therapeutics.</p> <hr /> <p><a href="https://ter.li/ftyhky"><em>Read our whitepaper: High-throughput cryo-EM epitope mapping of SARS-CoV-2 spike protein antibodies using EPU Multigrid</em></a><em> >></em></p> <hr /> <h2 style="font-size: 100%"><strong>Cryo-EM for rapid epitope mapping</strong></h2> <p>An epitope is a part of a molecule against which an antibody attaches itself.</p> <p>Therapeutic antibodies targeting the SARS-CoV-2 spike protein can play an important role in reducing the burden of the pandemic by protecting vulnerable populations against severe and potentially life-threatening disease.</p> <p>Epitope mapping of large antibody panels allows researchers to identify vulnerable sites on the spike protein, predict and interpret the effect of new mutations, and speed decision-making in selecting antibody combinations that target non-overlapping epitopes. Moreover, structural information about epitopes can help identify liabilities in drug discovery pipelines in response to new emerging variants.</p> <p>Therefore, in <a href="https://ter.li/ftyhky">collaboration with Takeda Pharmaceuticals and Utrecht University</a>, we set out to determine whether cryo-EM permits rapid epitope mapping for a large antibody panel.</p> <p>Our study launched in the wake of the Omicron variant and subsequent strains, which escape most neutralizing antibodies, as well as the realization that we need additional tools for long-lasting prophylaxis against SARS-COV-2 infections.</p> <h2 style="font-size: 100%"><strong>Newfound speed, quality, and automation of cryo-EM data collection</strong></h2> <p>Robust grid preparation and screening are critical for determining structures from every grid, and successful grid preparation is intimately linked to protein quality and concentration.</p> <p>To evaluate the robustness of our spike protein sample, and to ultimately gauge the suitability of our 12 complexes for structural determination, we used the new automation capabilities of Thermo Scientific <a href="https://ter.li/a3xk9r">EPU Multigrid software</a> on our <a href="https://ter.li/8xcuww">Glacios Cryo-TEM</a>.</p> <p>The twelve screened grids were then subjected to unattended EPU Multigrid data collection using our <a href="https://ter.li/hlgibq">Krios G4 Cryo-TEM</a> equipped with an E-CFEG, <a href="https://ter.li/xlgzmw">Selectris X Energy Filter</a>, and <a href="https://ter.li/1r7ft0">Falcon 4 Direct Electron Detector</a>.</p> <div id="attachment_2165" style="width: 770px" class="wp-caption aligncenter"><img decoding="async" aria-describedby="caption-attachment-2165" class="wp-image-2165 size-large" title="High-throughput cryo-EM epitope mapping of SARS-CoV-2 spike protein antibodies" src="https://www.thermofisher.com/blog/atomic-resolution/wp-content/uploads/sites/22/2022/04/Takeda-UU-WP_blog1-003-1-1024x420.png" alt="High-throughput cryo-EM epitope mapping of SARS-CoV-2 spike protein antibodies" width="760" height="312" /><p id="caption-attachment-2165" class="wp-caption-text">High-throughput cryo-EM epitope mapping of SARS-CoV-2 spike protein antibodies. Spike-Fab complex grids were imaged using Krios G4 cryo-TEM and EPU Multigrid, which resulted in twelve sub 3 Å cryo-EM reconstructions allowing epitope mapping and classification.</p></div> <p>In a single 48 hour-long session, we set EPU Multigrid to collect 1,000 movies per grid, achieving a speed of 250 movies per hour.</p> <p>This workflow enabled us to obtain 12 sub-3-angstrom structures of SARS-CoV-2 spike protein with different complexes and to determine their epitopes. Our results show the significant advances made in speed, quality, and automation of cryo-EM data collection.</p> <p><em>“These exciting results show how state-of-the-art technology, and an optimized sample preparation workflow, can be used to accelerate antibody drug discovery, which is of great importance for COVID-19 and future pandemic threats,” </em>said collaborator Daniel Hurdiss, Assistant Professor at Utrecht University.</p> <p><strong><a href="https://ter.li/ftyhky">Get an in-depth look at this workflow >></a></strong></p> <p>We believe cryo-EM’s high-resolution revolution will soon be followed by a high-throughput revolution, which will improve existing applications through increased efficiency and reduced cost per dataset. It will also extend the range of cryo-EM applications to include fragment-based drug discovery and epitope mapping of large antibody panels.</p> <p>//</p> <p><em>Mazdak </em><em>Radjainia is a Senior Staff Scientist at Thermo Fisher Scientific</em></p>  <div class="jp-relatedposts"> <div class="related-post related-1"> <a href="https://www.thermofisher.com/blog/atomic-resolution/what-is-cryo-em-what-is-cryo-electron-microscopy/"><img width="310" height="274" src="https://www.thermofisher.com/blog/atomic-resolution/wp-content/uploads/sites/22/2024/10/cryoEM-blog-virus-pore4-1920x600_Header-310x274.jpg" class="attachment-grid size-grid wp-post-image" alt="cryoEM-blog-virus pore" decoding="async" /></a> <span class="grid-content"> <h4 class="entry-title"><a href="https://www.thermofisher.com/blog/atomic-resolution/what-is-cryo-em-what-is-cryo-electron-microscopy/">What is cryo-EM?</a></h4> <p>Cryo-EM: cryo electron microscopy Cryo-electron microscopy (... </p> <a 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