{"id":4836,"date":"2025-12-02T11:48:32","date_gmt":"2025-12-02T11:48:32","guid":{"rendered":"https:\/\/www.sygnaturediscovery.com\/?post_type=case-study&#038;p=4836"},"modified":"2026-02-10T21:19:13","modified_gmt":"2026-02-10T21:19:13","slug":"targeted-protein-degradation-insights-into-a-vhl-compound-structure","status":"publish","type":"case-study","link":"https:\/\/www.sygnaturediscovery.com\/fr\/case-study\/targeted-protein-degradation-insights-into-a-vhl-compound-structure\/","title":{"rendered":"Targeted protein degradation: insights into a VHL-compound structure"},"content":{"rendered":"\n<h3 class=\"wp-block-heading fusion-responsive-typography-calculated has-dark-blue-500-color has-text-color has-link-color has-text-2-xl-font-size wp-elements-a6ce3bf8974c6f6f2269535abc734684\">Introduction<\/h3>\n\n\n\n<p><a href=\"https:\/\/www.sygnaturediscovery.com\/fr\/modalites\/degradation-ciblee-des-proteines\/\" type=\"page\" id=\"7231\" target=\"_blank\" rel=\"noreferrer noopener\">Targeted protein degradation (TPD)<\/a>\u00a0is an emerging therapeutic strategy that hijacks the cell\u2019s ubiquitin\u2013proteasome system to selectively degrade proteins. In this process, ubiquitin tags are attached to lysine residues on target proteins, marking them for destruction. A key player in this cascade is the E3 ligase, which recognizes substrates, polyubiquitinates them, and directs them to the proteasome.<\/p>\n\n\n\n<p>This mechanism can be exploited using bifunctional molecules called proteolysis-targeting chimeras (PROTACs). These molecules simultaneously bind an E3 ligase and a target protein, connected by a linker. Humans have over 600 E3 ligases, but VHL (von Hippel\u2013Lindau) and Cereblon are the most widely used due to their well-characterized binding sites.<\/p>\n\n\n\n<p>At Sygnature Discovery, we have already established production of both VHL and Cereblon which are active in SPR. With VHL-ligand-based PROTACs rapidly advancing\u2014frontrunners now in Phase III trials\u2014the field is full of potential to develop novel therapies across diverse targets. In this blog, we showcase how leveraging our expertise in functional VHL protein production has propelled us to go a step further in TPD.<\/p>\n\n\n\n<h3 class=\"wp-block-heading fusion-responsive-typography-calculated has-dark-blue-500-color has-text-color has-link-color has-text-2-xl-font-size wp-elements-1db4d8d70e602807ae6de776533e55fb\">Structural insights for rational PROTAC design<\/h3>\n\n\n\n<p>Within a PROTAC, the binding moieties for the E3 ligase and target protein are critical for substrate recognition, but the linker is equally important. It determines the spatial arrangement and flexibility between the two complexes, ensuring lysine residues remain accessible for polyubiquitination. The linker also influences the PROTAC\u2019s physicochemical and pharmacokinetic properties.<\/p>\n\n\n\n<p>Structural data from ternary complexes (E3 ligase\u2013PROTAC\u2013target) provide valuable mechanistic insights that can guide iterative design for improved efficacy. Similarly, structures of binary complexes (PROTAC bound to either the E3 ligase or target) help optimize binding interactions and linker positioning.<\/p>\n\n\n\n<h3 class=\"wp-block-heading fusion-responsive-typography-calculated has-dark-blue-500-color has-text-color has-link-color has-text-2-xl-font-size wp-elements-e1070527a8c048a4381f046db2c86397\">VHL and the VCB complex: A widely used tool<\/h3>\n\n\n\n<p>VHL functions within a multi-subunit complex that recruits substrates such as hypoxia-inducible factor (HIF) for ubiquitination and degradation. Together with adaptor proteins Elongin B and Elongin C, VHL forms the VCB complex, a minimal yet powerful tool for TPD development.<\/p>\n\n\n\n<p>Following the determination of the VCB\u2013HIF structure in 2002, significant efforts focused on designing small molecules that mimic HIF\u2019s binding interface on VHL. Among these, the VH032 scaffold, particularly with a left-hand-side (LHS) amide exit vector, remains the most widely used VHL-binding moiety in degrader development\u00a0<strong>(Figure 1).<\/strong><\/p>\n\n\n\n<div style=\"height:72px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<figure class=\"wp-block-image alignfull size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"622\" height=\"378\" src=\"https:\/\/www.sygnaturediscovery.com\/wp-content\/uploads\/2025\/12\/VH032-scaffold.webp\" alt=\"\" class=\"wp-image-4840\" srcset=\"https:\/\/www.sygnaturediscovery.com\/wp-content\/uploads\/2025\/12\/VH032-scaffold.webp 622w, https:\/\/www.sygnaturediscovery.com\/wp-content\/uploads\/2025\/12\/VH032-scaffold-300x182.webp 300w, https:\/\/www.sygnaturediscovery.com\/wp-content\/uploads\/2025\/12\/VH032-scaffold-592x360.webp 592w\" sizes=\"(max-width: 622px) 100vw, 622px\"><figcaption class=\"wp-element-caption\"><em><strong>Figure 1.<\/strong>\u00a0VH032 scaffold with different exit vector positions.<\/em><\/figcaption><\/figure>\n\n\n\n<div style=\"height:56px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h3 class=\"wp-block-heading fusion-responsive-typography-calculated has-dark-blue-500-color has-text-color has-link-color has-text-2-xl-font-size wp-elements-55af50e7e248fda832cbbb3635921efa\">Structure determination of VCB-VH032 complex<\/h3>\n\n\n\n<p>Building upon our expertise in production of highly active, homogenous\u00a0<a href=\"https:\/\/peakproteins.com\/portfolio-items\/production-of-active-vhl-and-analysis-by-spr\/\" target=\"_blank\" rel=\"noreferrer noopener\">VCB complex in-house<\/a>, our team successfully determined the X-ray crystal structure of the VCB complex bound to the tool compound VH032 at 2.3 \u00c5 resolution\u00a0<strong>(Figure 2a)<\/strong>. The heterotrimeric VCB complex crystallized under conditions optimized from literature and broad screening. The resulting crystals contained two heterotrimers per asymmetric unit, each with VH032 bound to VHL.<\/p>\n\n\n\n<div style=\"height:56px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<figure class=\"wp-block-image alignfull size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"1415\" height=\"584\" src=\"https:\/\/www.sygnaturediscovery.com\/wp-content\/uploads\/2025\/12\/BCB-VH032-structure.webp\" alt=\"\" class=\"wp-image-4847\" srcset=\"https:\/\/www.sygnaturediscovery.com\/wp-content\/uploads\/2025\/12\/BCB-VH032-structure.webp 1415w, https:\/\/www.sygnaturediscovery.com\/wp-content\/uploads\/2025\/12\/BCB-VH032-structure-300x124.webp 300w, https:\/\/www.sygnaturediscovery.com\/wp-content\/uploads\/2025\/12\/BCB-VH032-structure-1024x423.webp 1024w, https:\/\/www.sygnaturediscovery.com\/wp-content\/uploads\/2025\/12\/BCB-VH032-structure-768x317.webp 768w, https:\/\/www.sygnaturediscovery.com\/wp-content\/uploads\/2025\/12\/BCB-VH032-structure-640x264.webp 640w\" sizes=\"(max-width: 1415px) 100vw, 1415px\"><figcaption class=\"wp-element-caption\"><em><strong>Figure 2.<\/strong>\u00a0Structure of VCB-VH032 complex.<\/em><br><em><strong>(a)<\/strong>\u00a0Our in-house structure showing VHL (blue), Elongin C (purple), Elongin B (cyan), and VH032 (orange).<strong>\u00a0(b)<\/strong>\u00a0Overlay with VCB\u2013753b\u2013BCL-2 complex (PDB 8FY0) reveals excellent alignment of VCB and the VH032 scaffold.<\/em><\/figcaption><\/figure>\n\n\n\n<div style=\"height:56px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<p>A comparison of our in-house VCB-VH032 structure with a published crystal structure of VCB bound to a VH032-based PROTAC in complex with BCL-2 shows excellent superimposition\u00a0<strong>(Figure 2b)<\/strong>. This not only confirms the integrity of our VCB complex but also allows us to test the DMSO tolerance of crystals- opening avenues for soaking or co-crystallization with additional ligands.<\/p>\n\n\n\n<div style=\"height:56px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<div class=\"wp-block-group has-orange-gradient-gradient-background has-background is-content-justification-center is-nowrap is-layout-flex wp-container-core-group-is-layout-775de51a wp-block-group-is-layout-flex\" style=\"border-radius:2em;margin-top:0;margin-bottom:0\" allowchildrentofillwidth=\"\" overflow=\"\" flexwrap=\"\"><section class=\"Pegasus__Container w-full   relative h-fit  text-content-dark mobile-stacking-standard is-layout-flow wp-block-pegasus-container-is-layout-flow\" style=\"  padding-right:var(--wp--preset--spacing--50);padding-left:var(--wp--preset--spacing--50);padding-top:var(--wp--preset--spacing--40);padding-bottom:var(--wp--preset--spacing--40); border-radius:1.5rem;\">\n\t        \n\t\n\t\t\t\t\t\t\n\t\t        \t\t\n\t\t\t\t\t\t\t\n\t\t\t<div class=\"inner relative h-full is-flex-layout flex flex-col justify-start  w-full\">\n\n<div class=\"wp-block-group children-fill-width has-global-padding is-layout-constrained wp-block-group-is-layout-constrained\" style=\"border-radius:1.5rem\" overflow=\"\" flexwrap=\"\">\n<div class=\"wp-block-group alignwide is-vertical is-content-justification-left is-layout-flex wp-container-core-group-is-layout-7b15fec5 wp-block-group-is-layout-flex\" style=\"padding-top:var(--wp--preset--spacing--20);padding-bottom:var(--wp--preset--spacing--20)\" allowchildrentofillwidth=\"\" overflow=\"\" flexwrap=\"\">\n<h2 class=\"wp-block-heading has-text-3-xl-font-size\">How Sygnature can help your degrader projects<\/h2>\n\n\n\n<div style=\"height:0px\" aria-hidden=\"true\" class=\"wp-block-spacer wp-container-content-93ed7744\"><\/div>\n\n\n\n<p class=\"has-text-lg-font-size\">If you would like to learn more about our protein services or other services, please\u00a0<a href=\"mailto:info@peakproteins.com\">get in touch<\/a>.<\/p>\n\n\n\n<div style=\"height:0px\" aria-hidden=\"true\" class=\"wp-block-spacer wp-container-content-93ed7744\"><\/div>\n\n\n\n<div class=\"wp-block-buttons is-layout-flex wp-block-buttons-is-layout-flex\">\n<div class=\"wp-block-button\" modaltype=\"\"><a class=\"wp-block-button__link wp-element-button\" href=\"https:\/\/www.sygnaturediscovery.com\/fr\/contact\/\">Get in touch<\/a><\/div>\n<\/div>\n<\/div>\n<\/div>\n\n<\/div>\n\t\t\n\t        <\/section>\n<\/div>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>The concept of Targeted Protein Degradation (TPD) covers all techniques that exploit the natural mechanisms of cellular degradation to target a disease-causing protein for destruction.\u00a0<\/p>\n","protected":false},"featured_media":0,"template":"","category":[770,686,680,704,743],"resource_tag":[],"class_list":["post-4836","case-study","type-case-study","status-publish","hentry","category-crystallography","category-modalities","category-protein-and-structure","category-structural-biology","category-tpd"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.4 - 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