<?xml version="1.0" encoding="UTF-8"?><rss version="2.0" xmlns:content="http://purl.org/rss/1.0/modules/content/" xmlns:wfw="http://wellformedweb.org/CommentAPI/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:atom="http://www.w3.org/2005/Atom" xmlns:sy="http://purl.org/rss/1.0/modules/syndication/" xmlns:slash="http://purl.org/rss/1.0/modules/slash/" > <channel> <title>Creative Biolabs PROTAC Blog</title> <atom:link href="https://www.creative-biolabs.com/blog/protac/feed/" rel="self" type="application/rss+xml" /> <link>https://www.creative-biolabs.com/blog/protac</link> <description>PROTAC technology, development service and products</description> <lastBuildDate>Thu, 12 Sep 2024 05:29:15 +0000</lastBuildDate> <language>en-US</language> <sy:updatePeriod> hourly </sy:updatePeriod> <sy:updateFrequency> 1 </sy:updateFrequency> <generator>https://wordpress.org/?v=6.3.1</generator> <image> <url>https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2020/05/cropped-cropped-biolabs.com_-32x32.png</url> <title>Creative Biolabs PROTAC Blog</title> <link>https://www.creative-biolabs.com/blog/protac</link> <width>32</width> <height>32</height> </image> <item> <title>Harnessing PhosTACs for Targeted Protein Dephosphorylation: A New Frontier in Therapeutics</title> <link>https://www.creative-biolabs.com/blog/protac/protac-research/harnessing-phostacs-for-targeted-protein-dephosphorylation-a-new-frontier-in-therapeutics/</link> <dc:creator><![CDATA[biolabs]]></dc:creator> <pubDate>Thu, 12 Sep 2024 05:29:15 +0000</pubDate> <category><![CDATA[PROTAC Research]]></category> <category><![CDATA[FOXO3a]]></category> <category><![CDATA[PDCD4]]></category> <category><![CDATA[PhosTACs]]></category> <category><![CDATA[Protein Phosphorylation]]></category> <guid isPermaLink="false">https://www.creative-biolabs.com/blog/protac/?p=473</guid> <description><![CDATA[Chen, Po-Han, et al. “Modulation of phosphoprotein activity by phosphorylation targeting chimeras (PhosTACs).” ACS chemical biology 16.12 (2021): 2808-2815. In the rapidly evolving field of drug development, targeting protein post-translational modifications (PTMs) has emerged<a class="moretag" href="https://www.creative-biolabs.com/blog/protac/protac-research/harnessing-phostacs-for-targeted-protein-dephosphorylation-a-new-frontier-in-therapeutics/">Read More...</a>]]></description> <content:encoded><![CDATA[<p><span style="font-size: 15px;">Chen, Po-Han, et al. “Modulation of phosphoprotein activity by phosphorylation targeting chimeras (PhosTACs).” <em>ACS chemical biology</em> 16.12 (2021): 2808-2815.</span></p> <p><span style="font-size: 15px;">In the rapidly evolving field of drug development, targeting protein post-translational modifications (PTMs) has emerged as a promising avenue for treating various diseases, particularly cancers. Phosphorylation, a key PTM, plays a critical role in regulating many cellular processes, from cell growth to apoptosis. Dysregulated phosphorylation often leads to diseases, notably cancer and neurodegenerative disorders. Traditionally, therapies have focused on inhibiting kinases to control phosphorylation. However, these kinase inhibitors have limitations, such as drug resistance and off-target effects. A new approach—Phosphorylation Targeting Chimeras (PhosTACs)—is providing a novel way to address these challenges by selectively promoting protein dephosphorylation, offering a powerful alternative to kinase inhibitors.</span></p> <h6><span style="font-size: 15px;"><strong>Understanding Protein Phosphorylation and Dephosphorylation</strong></span></h6> <p><span style="font-size: 15px;">Phosphorylation is a reversible PTM that occurs when a phosphate group is added to proteins, lipids, sugars, or metabolites, influencing their biological function. Kinases are the enzymes responsible for phosphorylation, while phosphatases remove phosphate groups through dephosphorylation. Though there are over 500 protein kinases, only 137 protein phosphatases have been identified, leading to an imbalance in the modulation of phosphorylation across biological systems.</span></p> <p><span style="font-size: 15px;">Hyperphosphorylation, where proteins are excessively phosphorylated, can lead to diseases like Alzheimer’s and cancer. Tau protein hyperphosphorylation in Alzheimer’s disease is linked to microtubule dysfunction, while the retinoblastoma (Rb) tumor suppressor protein becomes inactivated due to hyperphosphorylation in various cancers. Kinase inhibitors, which prevent hyperphosphorylation by blocking kinases, have become widely used therapeutic tools. However, due to the broad roles that kinases play in signaling pathways, inhibiting them often leads to adverse off-target effects and the development of drug resistance.</span></p> <p><span style="font-size: 15px;">In light of these challenges, scientists have turned to phosphatases as a more focused method of regulating phosphorylation. However, global activation of phosphatases can result in unwanted dephosphorylation across numerous pathways, leading to unintended consequences. This has spurred the development of PhosTACs, which selectively recruit phosphatases to specific target proteins for dephosphorylation, providing a more precise approach to control phosphorylation.</span></p> <h6><span style="font-size: 15px;"><strong>What Are PhosTACs?</strong></span></h6> <p><span style="font-size: 15px;">PhosTACs (Phosphorylation Targeting Chimeras) are small, bifunctional molecules designed to promote dephosphorylation by facilitating the proximity between a phosphatase and a target protein. The concept is analogous to <span style="color: #0000ff;"><strong><a style="color: #0000ff;" href="https://www.creative-biolabs.com/protac/protac-molecule-discovery.htm">Proteolysis targeting chimeras</a></strong></span>, which degrade target proteins by recruiting <span style="color: #0000ff;"><strong><a style="color: #0000ff;" href="https://www.creative-biolabs.com/protac/category-e3-ligase-protein-340.htm">E3 ligases</a></strong></span>. Instead of degradation, PhosTACs trigger the removal of phosphate groups from proteins, thus modulating their activity.</span></p> <p><span style="font-size: 15px;">The proof-of-concept for PhosTACs was first demonstrated using the serine/threonine phosphatase PP2A, which regulates a majority of cellular phosphorylation events. PP2A is a holoenzyme consisting of three subunits: a catalytic subunit (PP2A C), a regulatory subunit (PP2A B), and a scaffold subunit (PP2A A). PhosTACs are designed to recruit the PP2A A subunit to the desired protein, enabling dephosphorylation.</span></p> <p><span style="font-size: 15px;"><img decoding="async" fetchpriority="high" class="aligncenter size-full wp-image-474" src="http://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/09/pblog-202409.jpg" alt="" width="865" height="389" srcset="https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/09/pblog-202409.jpg 865w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/09/pblog-202409-300x135.jpg 300w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/09/pblog-202409-768x345.jpg 768w" sizes="(max-width: 865px) 100vw, 865px" /></span></p> <p style="text-align: center;"><span style="font-size: 12px;">Fig.1 Schematic diagram of the mechanism of PhosTACs.<sup>1</sup></span></p> <h6><span style="font-size: 15px;"><strong>PhosTACs in Action: Targeting PDCD4 and FOXO3a</strong></span></h6> <p><span style="font-size: 15px;">The study detailed in the PDF explored the potential of PhosTACs using two tumor suppressor proteins: PDCD4 and FOXO3a. Both proteins are regulated by phosphorylation and play crucial roles in inhibiting oncogenic pathways.</span></p> <ul> <li><span style="font-size: 15px;"><strong>PDCD4 (Programmed Cell Death Protein 4)</strong>: PDCD4 is phosphorylated by Akt and RSK, which leads to its inactivation and degradation. While the exact phosphatase responsible for dephosphorylating PDCD4 had not been previously identified, PhosTACs successfully recruited PP2A A, resulting in the dephosphorylation of PDCD4 at Serine 67 and Serine 457. This marked the first time targeted dephosphorylation of PDCD4 was achieved using a chemical biology approach.</span></li> <li><span style="font-size: 15px;"><strong>FOXO3a (Forkhead Box O3)</strong>: FOXO3a is a transcription factor whose activity is suppressed by phosphorylation, particularly at Serine 318/321, which inhibits its ability to transcribe genes involved in apoptosis and cell cycle regulation. By recruiting PP2A A via PhosTACs, the study demonstrated that FOXO3a phosphorylation was significantly reduced, leading to the reactivation of its transcriptional activity. This shows the potential of PhosTACs to restore tumor suppressor function through targeted dephosphorylation.</span></li> </ul> <h6><span style="font-size: 15px;"><strong>Advantages of PhosTACs Over Traditional Kinase Inhibitors</strong></span></h6> <p><span style="font-size: 15px;">One of the primary advantages of PhosTACs over kinase inhibitors lies in their mechanism of action. Kinase inhibitors typically work through an “occupancy-driven model,” where a small molecule binds to a kinase, preventing it from interacting with its substrates. However, this approach is stoichiometric—one inhibitor molecule can only affect one kinase molecule, and its effect is lost upon dissociation.</span></p> <p><span style="font-size: 15px;">In contrast, PhosTACs function through an “event-driven model,” where a single PhosTAC molecule can induce the dephosphorylation of multiple target proteins by cycling through rounds of recruitment. This makes PhosTACs a potentially more effective tool, especially for conditions requiring prolonged modulation of protein phosphorylation.</span></p> <p><span style="font-size: 15px;">Moreover, selectivity is another advantage of PhosTACs. Kinase inhibitors often have off-target effects due to the conserved ATP-binding sites across different kinases. PhosTACs, by focusing on recruiting phosphatases to specific substrates, reduce the risk of such off-target interactions.</span></p> <h6><span style="font-size: 15px;"><strong>Future Directions</strong></span></h6> <p><span style="font-size: 15px;">While PhosTACs represent a promising new tool in the fight against diseases like cancer and neurodegenerative disorders, many questions remain. For instance, determining the most suitable phosphatases for different target proteins is a key challenge. Additionally, further research is needed to explore how PhosTACs can be used in vivo and whether they can overcome resistance mechanisms seen with kinase inhibitors.</span></p> <p><span style="font-size: 15px;">The development of PhosTACs marks an exciting new frontier in precision medicine, offering the potential for targeted therapies that modulate protein function more selectively and efficiently than ever before. As the field advances, PhosTACs may become a staple in the arsenal of molecular tools used to combat a wide array of diseases.</span></p> <p><span style="font-size: 15px;">Creative Biolabs is known for providing comprehensive services in proteolysis targeting chimeras molecule discovery. We assist with the design, synthesis, and screening of proteolysis targeting chimeras molecules, which are used for targeted protein degradation.</span></p> <p><span style="font-size: 15px;">Browse our services:</span></p> <p><span style="font-size: 15px; color: #0000ff;"><a style="color: #0000ff;" href="/protac/ligand-design-for-target-protein.htm"><strong>Ligand Design for Target Protein</strong></a></span></p> <p><span style="font-size: 15px; color: #0000ff;"><a style="color: #0000ff;" href="/protac/ligand-screening-for-e3-ligase.htm"><strong>Ligand Screening for E3 Ligase</strong></a></span></p> <p><span style="font-size: 15px; color: #0000ff;"><a style="color: #0000ff;" href="/protac/linker-design-and-optimization.htm"><strong>Linker Design and Optimization</strong></a></span></p> <p><span style="font-size: 15px; color: #0000ff;"><a style="color: #0000ff;" href="/protac/protac-structural-modification.htm"><strong>Protein Degraders Structural Modification</strong></a></span></p> <p><span style="font-size: 15px; color: #0000ff;"><a style="color: #0000ff;" href="/protac/custom-peptide-and-compound-synthesis.htm"><strong>Custom Peptide and Compound Synthesis</strong></a></span></p> <p><span style="font-size: 15px;">For more details regarding Creative Biolab’s Protein Degraders service, please feel free to contact us to assist you.</span></p> <p><span style="font-size: 12px;">Reference</span></p> <ol> <li><span style="font-size: 12px;">Chen, Po-Han, et al. “Modulation of phosphoprotein activity by phosphorylation targeting chimeras (PhosTACs).” <em>ACS chemical biology</em>12 (2021): 2808-2815.</span></li> </ol> ]]></content:encoded> </item> <item> <title>Protein-degraders: The New Go-to For Tackling Autoimmune Issues</title> <link>https://www.creative-biolabs.com/blog/protac/protac-research/protein-degraders-the-new-go-to-for-tackling-autoimmune-issues/</link> <dc:creator><![CDATA[biolabs]]></dc:creator> <pubDate>Sat, 24 Aug 2024 06:54:40 +0000</pubDate> <category><![CDATA[PROTAC Research]]></category> <category><![CDATA[BTK inhibitors]]></category> <category><![CDATA[protein targeted degradation chimera]]></category> <category><![CDATA[Protein-degraders]]></category> <guid isPermaLink="false">https://www.creative-biolabs.com/blog/protac/?p=465</guid> <description><![CDATA[Protein targeted degradation chimera is an emerging protein degradation strategy that has been booming in recent years. It was first proposed by Craig Crews et al. in 2001. Its basic principle is<a class="moretag" href="https://www.creative-biolabs.com/blog/protac/protac-research/protein-degraders-the-new-go-to-for-tackling-autoimmune-issues/">Read More...</a>]]></description> <content:encoded><![CDATA[<p><span style="font-size: 15px;">Protein targeted degradation chimera is an emerging protein degradation strategy that has been booming in recent years. It was first proposed by Craig Crews et al. in 2001. Its basic principle is to use bi-functional small molecules to induce target degradation through the ubiquitin-proteasome system. Protein ubiquitination, thereby achieving target protein degradation. Since ARV-110, the first protein targeted degradation chimera degrader targeting the androgen receptor, entered clinical research in 2019, the <span style="color: #0000ff;"><strong><a style="color: #0000ff;" href="/protac/protac-molecule-discovery.htm">protein targeted degradation chimera</a> </strong></span>field has entered a period of rapid development.</span></p> <p><span style="font-size: 15px;">The BTK protein (Bruton’s tyrosine kinase), a tyrosine kinase and key regulator of the B-cell receptor (BCR) signaling pathway, is overactivated in B-cell lymphoma cells. Previous research by Rao Jue’s team showed that protein targeted degradation chimera technology can achieve effective degradation of wild-type and mutant BTK proteins. Since then, they have also developed a new generation of BTK degrader L18I, which shows better solubility and efficiency in degrading BTK.</span></p> <p><span style="font-size: 15px;">Notably, in addition to B-cell lymphomas, BTK dysfunction also plays an important role in autoimmune diseases. In recent years, BTK inhibitors have been used for the treatment of autoimmune diseases, but due to issues with clinical efficacy and safety, they have experienced both success and failure in clinical trials. Although protein targeted degradation chimera-targeted degradation of BTK exhibits minimal off-target effects, no studies have explored the use of protein targeted degradation chimera degradation of BTK to treat autoimmune diseases.</span></p> <p><span style="font-size: 15px;">On August 6, 2024, Liu Wanli and Rao Xuan of Tsinghua University and Ding Ning of Peking University Cancer Hospital published a research paper titled “PROTAC for Bruton’s tyrosine kinase degradation alleviates inflammation in autoimmune diseases” in the <em>Cell Discovery</em> journal.</span></p> <p><span style="font-size: 15px;">This study shows that the protein targeted degradation chimera degrader L18I, which targets BTK (Bruton’s tyrosine kinase), can effectively treat the autoimmune disease lupus and its severe complication diffuse alveolar hemorrhage (DAH). L18I may become a safer, more effective alternative to immune diseases.</span></p> <p><span style="font-size: 15px;">Given the potential advantages of protein targeted degradation chimera over inhibitors, especially their ability to degrade the entire protein, which may inhibit the entire physiological function of the target protein, in this latest study, the research team explored the <a href="https://www.creative-biolabs.com/protac/ligand-design-for-btk-targeting-protac.htm"><span style="color: #0000ff;"><strong>BTK-targeting protein</strong></span></a> targeted degradation chimera degrader L18I in lupus.</span></p> <p><span style="font-size: 15px;">First, the research team adoptively transferred BM12 splenocytes into C57BL/6 mice to induce lupus-like autoimmune disease. Treatment with L18I began in the second week of induction and continued for two weeks. Ibrutinib is a BTK inhibitor approved by the US FDA for the treatment of B-cell malignancies. It was used as a positive control due to its therapeutic effect in autoimmune diseases.</span></p> <p><span style="font-size: 15px;">The results show that both L18I and ibrutinib can effectively reduce the symptoms of BM12-induced lupus. Specifically, the levels of IgM and IgG autoantibodies, anti-double-stranded DNA, and anti-nuclear antibodies were reduced after treatment. The deposition of antibody immune complexes was also reduced.</span></p> <p><span style="font-size: 15px;"><img decoding="async" class="aligncenter size-full wp-image-466" src="http://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/08/pblog-202407-1.jpg" alt="" width="1286" height="638" srcset="https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/08/pblog-202407-1.jpg 1286w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/08/pblog-202407-1-300x149.jpg 300w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/08/pblog-202407-1-1024x508.jpg 1024w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/08/pblog-202407-1-768x381.jpg 768w" sizes="(max-width: 1286px) 100vw, 1286px" /></span></p> <p style="text-align: center;"><span style="font-size: 12px;">Fig.1 Functional validation of BTK degrader L18I in mouse models.<sup>1</sup></span></p> <p><span style="font-size: 15px;">Diffuse alveolar hemorrhage (DAH) is an extremely serious complication of lupus disease, with a mortality rate of approximately 50%. It manifests as dyspnea and pulmonary infiltrates, mostly accompanied by kidney disease, elevated anti-double-stranded DNA antibodies, and low complementemia. However, commonly used DAH treatment methods have low specificity and have side effects. Therefore, targeted drugs against DAH are urgently needed. The research team speculates that BTK degraders may have a potential role in the treatment of DAH.</span></p> <p><span style="font-size: 15px;">The research team constructed DAH mouse models, which were divided into no DAH, partial DAH, and complete DAH according to lung pathological characteristics, and then treated with different doses of L18I or ibrutinib. L18I significantly reduced the prevalence of DAH compared with the control group, whereas ibrutinib showed only partial effectiveness.</span></p> <p><span style="font-size: 15px;"><img decoding="async" class="aligncenter size-full wp-image-467" src="http://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/08/pblog-202407-2.jpg" alt="" width="1270" height="237" srcset="https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/08/pblog-202407-2.jpg 1270w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/08/pblog-202407-2-300x56.jpg 300w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/08/pblog-202407-2-1024x191.jpg 1024w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/08/pblog-202407-2-768x143.jpg 768w" sizes="(max-width: 1270px) 100vw, 1270px" /></span></p> <p style="text-align: center;"><span style="font-size: 12px;">Fig.2 Representative gross images of lung tissue in mouse models.<sup>1</sup></span></p> <p><span style="font-size: 15px;">For further verification, the DAH score based on HE staining of lung tissue showed that L18I reduced pulmonary hemorrhage and immune cell infiltration, and its effect was more significant than ibrutinib. Consistent with this, lung and spleen weights and total serum IgM levels were reduced after L18I treatment, independent indicators of reduction in DAH syndrome. In addition, L18I also reduced mortality in DAH mice. <img decoding="async" loading="lazy" class="aligncenter size-full wp-image-468" src="http://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/08/pblog-202407-3.jpg" alt="" width="1267" height="218" srcset="https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/08/pblog-202407-3.jpg 1267w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/08/pblog-202407-3-300x52.jpg 300w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/08/pblog-202407-3-1024x176.jpg 1024w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/08/pblog-202407-3-768x132.jpg 768w" sizes="(max-width: 1267px) 100vw, 1267px" /></span></p> <p style="text-align: center;"><span style="font-size: 12px;">Fig.3 Results of H&E staining of tissues in mouse models.<sup>1</sup></span></p> <p><span style="font-size: 15px;">The above experimental results show that L18I shows a certain degree of advantage over ibrutinib in relieving symptoms of the DAH mouse model.</span></p> <p><span style="font-size: 15px;">During the progression of DAH, myeloid CD11b <sup>+</sup> Ly6C <sup>hi</sup>/Ly6C <sup>lo</sup> mononuclear cell infiltration is thought to be proportional to the severity of DAH. This study showed that both L18I and ibrutinib reduced the proportion and number of myeloid CD11b <sup>+</sup> Ly6Chi/Ly6C <sup>lo</sup> monocytes, and the proportion of Ly6C <sup>hi</sup> monocytes in the lung tissue of mice in the L18I treatment group was slightly lower than that of the ibrutinib treatment group, consistent with the degree of pulmonary hemorrhage. In addition, during the progression of DAH, the proportion of B cells and macrophages in the lungs of mice decreased, but it was reversed to a level almost equivalent to that of healthy mice after L18I treatment, while ibrutinib treatment had no such effect.</span></p> <p><span style="font-size: 15px;">The above experimental results show that both L18I and ibrutinib can alleviate the symptoms of DAH in mice, and L18I seems to be more effective than ibrutinib in restoring the normal immune cell microenvironment in the mouse lungs.</span></p> <p><span style="font-size: 15px;">In summary, L18I can not only effectively alleviate the symptoms of lupus by reducing antibody secretion, but also alleviate its serious complication diffuse alveolar hemorrhage (DAH) by reducing the inflammatory response. Considering the multiple side effects of Ibrutinib due to off-target effects and the emergence of new mutations leading to treatment non-response, L18I may become a safer and more effective alternative to BTK inhibitors for the treatment of autoimmune diseases.</span></p> <p><span style="font-size: 12px;">Reference</span></p> <ol> <li><span style="font-size: 12px;">Zhu, Can, et al. “PROTAC for Bruton’s tyrosine kinase degradation alleviates inflammation in autoimmune diseases.” <em>Cell Discovery</em>10.1 (2024): 82.</span></li> </ol> ]]></content:encoded> </item> <item> <title>Can PROTAC Therapy Be a Hope for AIDS Patients?</title> <link>https://www.creative-biolabs.com/blog/protac/protac-research/can-protac-therapy-be-a-hope-for-aids-patients/</link> <dc:creator><![CDATA[biolabs]]></dc:creator> <pubDate>Tue, 23 Jul 2024 07:09:48 +0000</pubDate> <category><![CDATA[PROTAC News]]></category> <category><![CDATA[PROTAC Research]]></category> <category><![CDATA[AIDS]]></category> <category><![CDATA[CRBN]]></category> <category><![CDATA[PROTAC Therapy]]></category> <guid isPermaLink="false">https://www.creative-biolabs.com/blog/protac/?p=458</guid> <description><![CDATA[Nef is an accessory protein encoded by HIV-1, HIV-2, and other primate lentiviruses and is closely related to viral replication, persistent infection, and the development of AIDS. Nef interacts with a variety<a class="moretag" href="https://www.creative-biolabs.com/blog/protac/protac-research/can-protac-therapy-be-a-hope-for-aids-patients/">Read More...</a>]]></description> <content:encoded><![CDATA[<p><span style="font-size: 15px;">Nef is an accessory protein encoded by HIV-1, HIV-2, and other primate lentiviruses and is closely related to viral replication, persistent infection, and the development of AIDS. Nef interacts with a variety of host cell proteins and downregulates cell surface molecules such as CD4, MHC-I, and SERINC5 restriction factors, thereby enhancing viral infectivity and promoting immune evasion. In addition, Nef promotes viral transcription and release by binding to and activating non-receptor protein tyrosine kinases and proteins that regulate the actin cytoskeleton. Studies in non-human primates have shown that Nef is closely related to viral pathogenicity and the development of AIDS. Nef-deficient SIV has poor replication ability in rhesus monkeys and can delay the onset of disease. In addition, in individuals infected with Nef-deficient HIV-1, viral loads can be maintained at low levels even without antiretroviral administration. Nef is an attractive antiretroviral drug target because of its critical role in HIV pathogenesis.</span></p> <p><span style="font-size: 15px;">However, Nef lacks active sites, making it difficult to adopt traditional strategies based on active site binding for drug development. Recently, the team of Professor Thomas E. Smithgall of the University of Pittsburgh published a research paper titled “PROTAC-mediated degradation of HIV-1 Nef efficiently restores cell-surface CD4 and MHC-I expression and blocks HIV-1 replication” in Cell Chemical Biology, innovatively proposed a Nef-targeting PROTAC strategy, and the designed and synthesized Nef-targeting PROTAC demonstrated therapeutic effects beyond traditional antiretroviral drugs.</span></p> <p><span style="font-size: 15px;"><img decoding="async" loading="lazy" class="aligncenter size-full wp-image-459" src="http://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/07/pblog-202407-1.jpg" alt="" width="536" height="254" srcset="https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/07/pblog-202407-1.jpg 536w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/07/pblog-202407-1-300x142.jpg 300w" sizes="(max-width: 536px) 100vw, 536px" /></span></p> <p style="text-align: center;"><span style="font-size: 12px;">Figure 1: Targeted degradation of HIV-1 Nef by CRBN-directed PROTAC.<sup>1</sup></span></p> <p><span style="font-size: 15px;">In this study, the researchers coupled existing hydroxypyrazole Nef-binding compounds with <span style="color: #0000ff;"><strong><a style="color: #0000ff;" href="https://www.creative-biolabs.com/protac/ligand-screening-for-crbn-based-protac.htm">the CRBN/VHL ligand</a></strong></span> of the ubiquitin E3 ligase through a flexible linker to construct a bivalent PROTAC compound library. Through cell-based orthogonal experiments to detect Nef ubiquitination, degradation, and inhibitory functions, we discovered a highly active Nef-targeting PROTAC that directs the CRBN E3 ubiquitin ligase pathway.</span></p> <p><span style="font-size: 15px;">SPR assay results show that this type of bivalent PROTAC can induce multiple HIV Nef variants and SIV Nef to form a ternary complex with ubiquitin <span style="color: #0000ff;"><strong><a style="color: #0000ff;" href="https://www.creative-biolabs.com/protac/category-e3-ligase-protein-340.htm">E3 ligase</a></strong></span>, with broad-spectrum activity. Flow cytometry and quantitative western blot analysis experiments showed that Nef-targeted PROTAC can induce Nef degradation, effectively reverse Nef-mediated down-regulation of MHC-I and CD4, and restore receptors that are critical for immune system recognition of HIV-infected cells. Cell surface expression. Furthermore, because there is a significant correlation between Nef’s ability to downregulate MHC-I and the size of viral reservoirs, targeting Nef protein degradation would also help shrink or eliminate viral reservoirs. Further antiviral test results showed that Nef-targeted PROTAC can effectively inhibit Nef-dependent viral replication and reduce infectivity.</span></p> <p><span style="font-size: 15px;">Overall, this study demonstrates the excellent effectiveness of PROTAC in targeting the degradation of HIV-1 Nef protein. By targeting the degradation of Nef, PROTAC not only restores the expression of MHC-I and CD4 on the surface of T cells but also significantly inhibits HIV-1 replication and is expected to enhance host immunity and clear viral reservoirs. This strategy provides new ideas for HIV/AIDS treatment and also shows the strong potential of PROTAC technology in the field of antiviral drug development.</span></p> <p><span style="font-size: 15px;">Here is a simple list of ideal targets for PROTAC<sup>®</sup> technology for your reference.</span></p> <ul> <li><span style="font-size: 15px;"><a href="https://www.creative-biolabs.com/protac/ligand-design-for-nuclear-receptors.htm"><span style="color: #0000ff;"><strong>Targeting nuclear receptors</strong></span></a> (e.g., AR, ER, and RAR)</span></li> <li><span style="font-size: 15px;"><a href="https://www.creative-biolabs.com/protac/ligand-design-for-protein-kinases.htm"><strong><span style="color: #0000ff;">Targeting protein kinases</span></strong></a> (e.g., Akt, BCR, c-Abl, BTK, ALK, CDK9, RIPK2, DAPK1, and PSD-95)</span></li> <li><span style="font-size: 15px;"><a href="https://www.creative-biolabs.com/protac/ligand-design-for-transcriptional-regulators-proteins.htm"><span style="color: #0000ff;"><strong>Targeting transcriptional regulatory proteins</strong></span> </a>(e.g., BRD4, Sirt2, HDAC6, TRIM24, IKZF1/3, and Smad3)</span></li> <li><span style="font-size: 15px;"><a href="https://www.creative-biolabs.com/protac/ligand-design-for-regulatory-proteins.htm"><span style="color: #0000ff;"><strong>Targeting regulatory proteins</strong></span> </a>(e.g., CRABP-I/II, TACC3, AHR, FKBP12, ERRα, and X-protein)</span></li> <li><span style="font-size: 15px;"><a href="https://www.creative-biolabs.com/protac/ligand-design-for-neurodegenerative-related-proteins.htm"><span style="color: #0000ff;"><strong>Targeting neurodegenerative-related proteins</strong></span> </a>(e.g., Huntingtin, Tau, and α-synuclein)</span></li> <li><span style="font-size: 15px;"><a href="https://www.creative-biolabs.com/protac/ligand-design-for-cellular-metabolic-enzymes.htm"><span style="color: #0000ff;"><strong>Targeting cellular metabolic enzymes</strong></span></a> (e.g., MetAP-2 and DHODH)</span></li> </ul> <p><span style="font-size: 12px;">Reference</span></p> <p><span style="font-size: 12px;">Emert-Sedlak, Lori A., et al. “PROTAC-mediated degradation of HIV-1 Nef efficiently restores cell-surface CD4 and MHC-I expression and blocks HIV-1 replication.” <em>Cell Chemical Biology</em> 31.4 (2024): 658-668.</span></p> ]]></content:encoded> </item> <item> <title>Exploring the Impact of E3 Ligase Choice on PROTAC Effectiveness</title> <link>https://www.creative-biolabs.com/blog/protac/protac-reviews/exploring-the-impact-of-e3-ligase-choice-on-protac-effectiveness/</link> <dc:creator><![CDATA[biolabs]]></dc:creator> <pubDate>Fri, 21 Jun 2024 03:00:09 +0000</pubDate> <category><![CDATA[protac reviews]]></category> <category><![CDATA[CRBN]]></category> <category><![CDATA[E3 ligase]]></category> <category><![CDATA[MDM2]]></category> <category><![CDATA[protac]]></category> <category><![CDATA[VHL]]></category> <guid isPermaLink="false">https://www.creative-biolabs.com/blog/protac/?p=453</guid> <description><![CDATA[The field of drug discovery is witnessing a revolutionary shift with the advent of Proteolysis Targeting Chimeras (PROTACs). This innovative therapeutic strategy is redefining how we approach the degradation of proteins, especially<a class="moretag" href="https://www.creative-biolabs.com/blog/protac/protac-reviews/exploring-the-impact-of-e3-ligase-choice-on-protac-effectiveness/">Read More...</a>]]></description> <content:encoded><![CDATA[<p><span style="font-size: 15px;">The field of drug discovery is witnessing a revolutionary shift with the advent of Proteolysis Targeting Chimeras (PROTACs). This innovative therapeutic strategy is redefining how we approach the degradation of proteins, especially protein kinases, which play a pivotal role in cellular signaling and cancer progression. The recent study by Sobierajski, Małolepsza, Pichlak, Gendaszewska-Darmach, and Błażewska published in Drug Discovery Today delves deep into the nuances of PROTAC design, specifically the critical role of E3 ligase selection in the degradation efficacy of protein kinases.</span></p> <h6><span style="font-size: 15px;">Understanding PROTACs</span></h6> <p><span style="font-size: 15px;">PROTACs are bifunctional molecules composed of two active domains: a warhead that binds the protein of interest (POI) and an <span style="color: #0000ff;"><strong><a style="color: #0000ff;" href="/protac/category-e3-ligase-ligand-336.htm">E3 ligase ligand</a></strong></span>, connected by a linker. The successful formation of the ternary complex—comprising the POI, the PROTAC, and the E3 ligase—is crucial for the ubiquitination and subsequent proteasomal degradation of the target protein. The design intricacies of PROTACs, particularly the choice of E3 ligase, significantly influence their therapeutic efficacy and specificity.</span></p> <p><span style="font-size: 15px;"><img decoding="async" loading="lazy" class="aligncenter wp-image-454" src="http://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/06/pblog-202406-1.jpg" alt="" width="387" height="272" srcset="https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/06/pblog-202406-1.jpg 1148w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/06/pblog-202406-1-300x210.jpg 300w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/06/pblog-202406-1-1024x718.jpg 1024w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/06/pblog-202406-1-768x539.jpg 768w" sizes="(max-width: 387px) 100vw, 387px" /></span></p> <p style="text-align: center;"><span style="font-size: 12px;">Fig.1 Mechanism of action of PROTA.<sup>1</sup></span></p> <h6><span style="font-size: 15px;">Importance of E3 Ligase Selection</span></h6> <p><span style="font-size: 15px;">E3 ligases are enzymes that tag proteins with ubiquitin, marking them for degradation by the proteasome. The human genome encodes over 600 E3 ligases, but only a handful have been extensively used in PROTAC design, namely Von-Hippel-Lindau (VHL), cereblon (CRBN), mouse double-minute 2 homolog (MDM2), and inhibitor of apoptosis proteins (IAP). Each E3 ligase brings unique properties to the PROTAC mechanism:</span></p> <p><span style="font-size: 15px;"><a href="/protac/ligand-screening-for-vhl-based-PROTAC.htm"><strong><span style="color: #0000ff;">Von-Hippel-Lindau</span></strong></a> (VHL): VHL is widely expressed and has been a popular choice due to its robust and predictable ubiquitination efficiency. VHL-based PROTACs have shown success in degrading kinases such as BRD4 and BTK.</span></p> <p><span style="font-size: 15px;"><a href="/protac/ligand-screening-for-crbn-based-PROTAC.htm"><span style="color: #0000ff;"><strong>Cereblon</strong></span></a> (CRBN): CRBN is known for its ability to induce the degradation of neosubstrates like IKZF1 and IKZF3, which is beneficial in anticancer strategies. However, CRBN ligands can also lead to off-target effects, necessitating careful design to minimize unwanted interactions.</span></p> <p><span style="font-size: 15px;"><a href="/protac/ligand-screening-for-mdm2-based-PROTAC.htm"><strong><span style="color: #0000ff;">MDM2</span></strong></a>: MDM2 targets the tumor suppressor p53, and its ligands can provide a dual therapeutic approach by both degrading the POI and activating p53 pathways.</span></p> <p><span style="font-size: 15px;"><a href="https://www.creative-biolabs.com/protac/ligand-screening-for-ciap1-based-PROTAC.htm"><strong><span style="color: #0000ff;">IAP</span></strong></a>: IAP ligases have shown potential but are less commonly used due to challenges in identifying suitable ligands.</span></p> <p><span style="font-size: 15px;">The study emphasizes that the degradation efficiency and specificity are not solely dependent on the E3 ligase but also on the linker’s properties, such as its length, rigidity, and polarity. The formation and stability of the ternary complex are influenced by the compatibility between the POI and the chosen E3 ligase, which can vary based on the cellular context and the specific target protein.</span></p> <h6><span style="font-size: 15px;">Recent Developments and Findings</span></h6> <p><span style="font-size: 15px;">CRBN-Based PROTACs: These have been effective in degrading a variety of kinases, but they also show a propensity for degrading off-target proteins, which can be therapeutically advantageous or detrimental depending on the context. For example, CRBN-based PROTACs derived from AKT inhibitors have shown efficacy in targeting PI3K/PTEN mutant cells but not KRAS/BRAF mutant cells.</span></p> <p><span style="font-size: 15px;">VHL-Based PROTACs: These have demonstrated significant promise in degrading kinases such as ERK5 and CDK6. The review notes that VHL ligands tend to form more stable ternary complexes, leading to more efficient degradation of the POI.</span></p> <p><span style="font-size: 15px;">Emerging E3 Ligases: The landscape of E3 ligase ligands is expanding, with new ligases like KEAP1 and DCAF15 being explored for their potential to target previously undruggable proteins.</span></p> <h6><span style="font-size: 15px;">Future Perspectives</span></h6> <p><span style="font-size: 15px;">The choice of E3 ligase is a critical determinant in the design and success of PROTACs. Future research aims to expand the catalog of E3 ligase ligands and understand their unique properties and interactions. There is also a growing interest in developing PROTACs that can target multiple ligases, providing a more versatile and robust degradation mechanism.</span></p> <p><span style="font-size: 15px;">In conclusion, the strategic selection of E3 ligases, combined with precise linker design, holds the key to unlocking the full therapeutic potential of PROTACs. As the field evolves, the ability to harness diverse E3 ligases for targeted protein degradation will undoubtedly lead to more effective and personalized treatments for a wide range of diseases, particularly cancer.</span></p> <p><span style="font-size: 12px;">Reference</span></p> <ol> <li><span style="font-size: 12px;">Sobierajski, Tomasz, et al. “The impact of E3 ligase choice on PROTAC effectiveness in protein kinase degradation.” <em>Drug Discovery Today</em>(2024): 104032.</span></li> </ol> ]]></content:encoded> </item> <item> <title>Linker Matters in PROTAC Design</title> <link>https://www.creative-biolabs.com/blog/protac/uncategorized/linker-matters-in-protac-design/</link> <dc:creator><![CDATA[biolabs]]></dc:creator> <pubDate>Tue, 14 May 2024 08:47:27 +0000</pubDate> <category><![CDATA[protac reviews]]></category> <category><![CDATA[Uncategorized]]></category> <category><![CDATA[PROTAC Design]]></category> <category><![CDATA[PROTAC Linker]]></category> <guid isPermaLink="false">https://www.creative-biolabs.com/blog/protac/?p=446</guid> <description><![CDATA[Proteolysis targeting chimera (PROTAC) technology represents a breakthrough development in the field of drug discovery, utilizing the ubiquitin proteasome system to specifically degrade disease-related proteins. PROTACs are characterized by their unique heterobifunctional<a class="moretag" href="https://www.creative-biolabs.com/blog/protac/uncategorized/linker-matters-in-protac-design/">Read More...</a>]]></description> <content:encoded><![CDATA[<p><span style="font-size: 15px;">Proteolysis targeting chimera (PROTAC) technology represents a breakthrough development in the field of drug discovery, utilizing the ubiquitin proteasome system to specifically degrade disease-related proteins. PROTACs are characterized by their unique heterobifunctional structure, including two functional domains connected via linkers.</span></p> <p><span style="font-size: 15px;">Linker plays a key role in determining the biodegradable efficacy of PROTACs. An advanced and well-designed <strong><span style="color: #0000ff;"><a style="color: #0000ff;" href="/protac/category-linkers-332.htm">PROTAC functional linker</a></span></strong> is under development. Despite this, the correlation between linker characteristics and PROTAC efficacy remains understudied.</span></p> <p><span style="font-size: 15px;">We mainly analyze and discuss the structure types and characteristics of the PROTAC linker, its reasonable design and optimization strategy, and the influence of linker characteristics on the biodegradation efficiency of PROTAC.</span></p> <h6><span style="font-size: 15px;">Structure types and characteristics of PROTAC linker</span></h6> <p><span style="font-size: 15px;">PROTAC linkers can be broadly divided into flexible linkers and relatively rigid linkers.</span></p> <p><span style="font-size: 15px;">Flexible linkers are the most widely used type, mainly alkyl linker and polyethylene glycol (PEG) linkers. The flexible linkers that are ubiquitous in <span style="color: #0000ff;"><strong><a style="color: #0000ff;" href="/protac/protac-molecule-discovery.htm">PROTAC designs</a></strong></span> typically use long, flexible structures. However, this design can increase susceptibility to oxidative metabolism in the body.</span></p> <p><span style="font-size: 15px;">In contrast, due to the limitations of synthesis technology in the field of PROTAC, the relatively rigid linker is used less frequently, including a total of 8 types. Among them, naphthenes, especially linkers containing piperazine and piperidine components, are often used because they increase the solubility and stability of ternary complexes. Triazole-based linker is another commonly used rigid linker that uses copper-catalyzed 1,3-dipole cycloaddition reactions with high compatibility and consistent reaction rates with different functional groups due to the advent of click chemistry. Another type of linker, the photocontrolled PROTAC linker, such as the photoswitch PROTAC linker, uses azo fragments instead of alkyl or polyether fragments, which, when exposed to specific wavelengths of light, result in reversible photoisomerization of the resulting PROTACs. This makes it possible to precisely and mutually adjust the biodegradation rate of PROTACs (Figure 1).</span></p> <p><span style="font-size: 15px;"><img decoding="async" loading="lazy" class="aligncenter wp-image-447" src="http://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/05/pblog-202405-1.jpg" alt="" width="291" height="406" /></span></p> <p style="text-align: center;"><span style="font-size: 12px;">Fig. 1 Structural types and characteristics of PROTAC linkers.<sup>1</sup></span></p> <h6><span style="font-size: 15px;">Rational design and optimization strategy of PROTAC linker</span></h6> <p><span style="font-size: 15px;">In general, the design and optimization of PROTAC linkers rely on empirical or computer-aided methods. The general journey of designing and optimizing a PROTAC linker based on experience is as follows:</span></p> <p><span style="font-size: 15px;">First, the researchers designed PROTACs based on experience and then focused on optimizing linkers in four areas:</span></p> <ul> <li><span style="font-size: 15px;">Adjust the linker length to achieve the optimal configuration of a particular PROTAC.</span></li> <li><span style="font-size: 15px;">Modify the type of linker to balance the hydrophilicity and hydrophobicity of PROTACs.</span></li> <li><span style="font-size: 15px;">Modify the flexibility of the linker and junction sites to increase the stability of the ternary complex.</span></li> <li><span style="font-size: 15px;">Design and synthesize multiple PROTACs with different linkers.</span></li> </ul> <p><span style="font-size: 15px;">Whereas, the general process based on computer-aided strategies is:</span></p> <ul> <li><span style="font-size: 15px;">Use crystallography or molecular docking techniques to determine the binding mode of POI to its ligand and E3 to its ligand, respectively.</span></li> <li><span style="font-size: 15px;">Global protein-protein docking simulations were carried out by computational software such as MOE, Rosetta, and PatchDock to obtain model structure sets of poi-ligand and e3-ligand.</span></li> <li><span style="font-size: 15px;">After evaluation using molecular dynamics (MD), analyze protein-protein interactions (PPIs) using a rational model structure and identify proteins that interact proximal to their binding pockets.</span></li> <li><span style="font-size: 15px;">Design different linkers to generate a series of POI-PROTAC-E3 conformations. The structure-activity relationship (SAR) and binding mode of the ternary complex were further analyzed, and the optimal linker was finally obtained.</span></li> </ul> <p><span style="font-size: 15px;">This strategy is widely applicable to the design and optimization of Linker, however, this approach has certain limitations. This approach often requires the synthesis of multiple protacs with various linkers to gain a comprehensive understanding of SAR, which can be time-consuming, laborious, and costly. Another limitation is the accuracy of theoretical predictions, which affects the design of the linker.</span></p> <p><span style="font-size: 15px;">In recent years, the application of artificial intelligence in the design of PROTAC joints has significantly improved the accuracy and efficiency of linker optimization. By leveraging AI strategies, researchers have gained insight into the structure, physics, and chemistry of the PORTAC linker. These insights have been translated into real-world applications, leading to more precise PROTAC linker designs (Figure 2).</span></p> <p><span style="font-size: 15px;"><img decoding="async" loading="lazy" class="aligncenter size-full wp-image-448" src="http://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/05/pblog-202405-2.jpg" alt="" width="535" height="753" srcset="https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/05/pblog-202405-2.jpg 535w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/05/pblog-202405-2-213x300.jpg 213w" sizes="(max-width: 535px) 100vw, 535px" /></span></p> <p style="text-align: center;"><span style="font-size: 12px;">Fig. 2 Appropriate design and optimization strategies for PROTAC linkers.<sup>1</sup></span></p> <h6><span style="font-size: 15px;">Effect on the biodegradation efficiency of PROTACs</span></h6> <p><span style="font-size: 15px;">PROTAC is a heterobifunctional molecule linked by a target protein ligand and an E3 ligase ligand via different linkers, and this structure aids in the establishment of a stable ternary complex, which allows the organism’s 26s proteasome to recognize and degrade the target protein ubiquitination.</span></p> <p><span style="font-size: 15px;">It was found that the properties of linkers play a key role in the stable formation of ternary complexes and the physicochemical and pharmacokinetic properties of PROTACs.</span></p> <p><span style="font-size: 15px;">Firstly, the length of the linker significantly affects the formation of the POI-PROTAC-E3 ternary complex, and the optimal linker length depends on the interaction mode, distance, and spatial structure of the ternary complex. On the other hand, shorter linkers may introduce steric hindrance, disrupt the formation of ternary complexes, and reduce the biodegradation efficiency of PROTACs.</span></p> <p><span style="font-size: 15px;">Secondly, the chemical composition of the linker directly affects the physicochemical properties of PROTACs, which in turn affect the cellular permeability of PROTACs, thereby significantly affecting the biodegradation efficiency of PROTACs.</span></p> <p><span style="font-size: 15px;">Therefore, achieving optimal linker length is critical to generating maximum interaction between POI and E3 ligase, resulting in efficient ubiquitination and biodegradation of POI. On the other hand, the flexibility of the linker is a key factor in determining the biodegradation effect of PROTACs, and a linker with significant conformational flexibility can enhance the interaction between PROTACs, POIs, and <strong><span style="color: #0000ff;"><a style="color: #0000ff;" href="https://www.creative-biolabs.com/protac/category-e3-ligase-protein-340.htm">E3 proteins</a></span></strong>, thereby preventing their stable binding at the fixed interface.</span></p> <p><span style="font-size: 15px;">On the contrary, the introduction of rigid groups in the flexible linker can improve PROTAC rigidity and replicate the original geometry of POI and E3 ligands in PROTACs, resulting in new interactions and improved stability of ternary complexes.</span></p> <p><span style="font-size: 15px;">In addition, the linker’s attachment site to the POI and E3 affects the interaction between the POI and E3. Optimization of the PROTAC linker typically involves identifying the most favorable site for structural derivatization, thus ensuring that maximum binding affinity is preserved. This selection process typically involves analyzing the solvent-exposed region of the POI-ligand or E3-ligand interaction interface, and by introducing an optimal linker in the solvent-exposed region, the protein-protein interaction can be maximized while preserving the original ligand interaction with the POI or E3.</span></p> <p><span style="font-size: 15px;">Given these intricate relationships, it is clear that the linker is a key factor in ensuring greater specificity and targeting efficiency of PROTACs.</span></p> <p><span style="font-size: 15px;">While optimizing the length, group type, flexibility, and junction site of the linker can improve the efficacy of PROTACs, several challenges must be overcome.</span></p> <ul> <li><span style="font-size: 15px;">The complexity and diversity of PROTAC structures hinder the establishment of clear structure-activity relationships. To address this issue, exploring the optimal linker characteristics of specific biodegradable systems can facilitate the rapid identification of more effective PROTACs.</span></li> <li><span style="font-size: 15px;">The physicochemical properties of PROTACs often deviate from the classical drug-like 5 principle, and it is necessary to study the drug similarity rules suitable for PROTACs to minimize the possibility of designing PROTACs with poor pharmacokinetic characteristics.</span></li> <li><span style="font-size: 15px;">Due to their large molecular weight and complex structure, purification and low yield pose challenges to the synthesis and optimization of PROTACs. Therefore, the development of advanced synthesis techniques for PROTACs is essential to obtaining a wider range of structure types.</span></li> <li><span style="font-size: 15px;">The large size of the ternary complex composed of POI-PROTAC-E3 makes the determination of crystal structure difficult. To solve this problem, it is necessary to develop advanced crystallography techniques or more accurate computational simulation methods to gain insights for further optimization.</span></li> </ul> <p><span style="font-size: 15px;">Solving these problems will greatly promote the progress of PROTAC research.</span></p> <p><span style="font-size: 12px;">References</span></p> <ol> <li><span style="font-size: 12px;">Dong, Yawen, et al. “Characteristic roadmap of linker governs the rational design of PROTACs.” <em>Acta Pharmaceutica Sinica B</em>(2024).</span></li> </ol> ]]></content:encoded> </item> <item> <title>New Role Introduced: PDF-Bin, Protein Targeting the Degradation “Dumpcart”</title> <link>https://www.creative-biolabs.com/blog/protac/protac-research/new-role-introduced-pdf-bin-protein-targeting-the-degradation-dumpcart/</link> <dc:creator><![CDATA[biolabs]]></dc:creator> <pubDate>Sun, 21 Apr 2024 09:43:23 +0000</pubDate> <category><![CDATA[PROTAC Research]]></category> <category><![CDATA[ATTEC]]></category> <category><![CDATA[protac]]></category> <guid isPermaLink="false">https://www.creative-biolabs.com/blog/protac/?p=432</guid> <description><![CDATA[Over the past two decades, protein-targeting degradation technologies (TPD), epitomized by PROTAC (proteolysis targeting chimera), have undergone rapid development and are considered one of the most promising breakthrough technologies for tackling difficult-to-drug<a class="moretag" href="https://www.creative-biolabs.com/blog/protac/protac-research/new-role-introduced-pdf-bin-protein-targeting-the-degradation-dumpcart/">Read More...</a>]]></description> <content:encoded><![CDATA[<p><span style="font-size: 15px;">Over the past two decades, protein-targeting degradation technologies (TPD), epitomized by PROTAC (proteolysis targeting chimera), have undergone rapid development and are considered one of the most promising breakthrough technologies for tackling difficult-to-drug targets. Traditional PROTAC technology leverages the catalytic action of E3 ubiquitin ligases to achieve specific degradation of targets via the ubiquitin-proteasome pathway. However, limited by the finite variety of <strong><span style="color: #0000ff;"><a style="color: #0000ff;" href="https://www.creative-biolabs.com/protac/category-e3-ligase-protein-340.htm">available E3 ligases</a></span></strong> and the substrate specificity of the proteasome, recent years have seen the emergence of various lysosome-based TPD strategies. These include LYTAC technology, which targets cell membrane proteins or extracellular proteins, and strategies utilizing autophagy pathways for the degradation of solid aggregates or organelles, such as <strong><span style="color: #0000ff;"><a style="color: #0000ff;" href="https://www.creative-biolabs.com/protac/attec.htm">ATTEC</a></span></strong> (Autophagosome-Tethering Compound) and AUTOTAC. The advent of these technologies has further propelled the development of the TPD field and offered potential therapeutic strategies for a variety of serious diseases.</span></p> <p><span style="font-size: 15px;">With the burgeoning field of “liquid-liquid phase separation,” an increasing number of studies have shown that key proteins in the degradation process can form “degradation condensates” through liquid-liquid phase separation. These condensates act as degradation factories, concentrating degradation-related functional proteins and substrates to be degraded in localized compartments, thereby efficiently executing degradation functions. The most representative of these degradation condensates is the formation of p62 bodies by autophagy receptor protein p62 and polyubiquitin chains. These structures provide anchor points for the attachment and extension of isolation membranes, initiating the subsequent autophagy process (Figure 1). Moreover, p62 also participates in ubiquitin-proteasome pathway-related degradation condensates, serving as a bridge between the proteasome and autophagy pathways. If it were possible to specifically recruit protein targets to these degradation condensates, it might bypass enzymatic catalytic steps (e.g., the catalytic reaction of E3 ubiquitin ligases) and achieve effective degradation by merely bringing them into close spatial proximity.</span></p> <p><span style="font-size: 15px;"><img decoding="async" loading="lazy" class="aligncenter wp-image-433" src="http://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/04/pblog-202404-1.jpg" alt="" width="393" height="232" srcset="https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/04/pblog-202404-1.jpg 1269w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/04/pblog-202404-1-300x177.jpg 300w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/04/pblog-202404-1-1024x604.jpg 1024w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/04/pblog-202404-1-768x453.jpg 768w" sizes="(max-width: 393px) 100vw, 393px" /></span></p> <p style="text-align: center;"><span style="font-size: 12px;">Figure 1. Autophagy degradation process mediated by p62 degradation condensate</span></p> <p><span style="font-size: 15px;">Recently, the research group of Li Pilong and Li Zengpeng of the third Institute of Oceanography of the Ministry of Natural Resources published a cooperative research paper on an integrated targeted protein degradation platform in Cell Research. The paper reports a novel protein-targeting degradation technology named PDF-Bin. The core component of this technology is a bispecific antibody capable of simultaneously binding to the p62 protein and the target protein. It can specifically recruit the target protein to p62 degradation condensates, thereby achieving targeted degradation functionality (see Figure 2).</span></p> <p><span style="font-size: 15px;"><img decoding="async" loading="lazy" class="aligncenter wp-image-434" src="http://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/04/pblog-202404-2.jpg" alt="" width="441" height="133" /></span></p> <p style="text-align: center;"><span style="font-size: 12px;">Figure 2. A schematic diagram of PDF-Bin</span></p> <p><span style="font-size: 15px;">PDF-Bin is named after P62 degradation factory based on a bispecific antibody, comprising an antibody that specifically binds to p62 (Pn), an antibody that specifically binds to the target protein, and a <strong><span style="color: #0000ff;"><a style="color: #0000ff;" href="https://www.creative-biolabs.com/protac/category-linkers-332.htm">flexible linker</a></span></strong> connecting them. To obtain p62-specific antibody, researchers utilized phage display technology combined with colocalization analysis through microscopy, resulting in the identification of three antibody specifically binding to p62 (A1E, D9A, and E12C). PDF-Bin constructs created by fusing these three Pns with an EGFP-tagged antibody Gn (A1E-Gn, D9A-Gn, and E12C-Gn) all demonstrated effective degradation of EGFP-TDP43 protein.</span></p> <p><span style="font-size: 15px;">Subsequently, the researchers tested the degradation capability of A1E-Gn against a series of targets fused with the EGFP tag. The results showed that A1E-Gn could degrade target proteins located in the nucleus, cytoplasm, cell membrane, and those forming solid aggregates, proving that PDF-Bin has a broad range of applications.</span></p> <p><span style="font-size: 15px;">To further explore the properties of PDF-Bin, the researchers constructed respective PDF-Bin fusion proteins targeting EGFP-TDP43 and the endogenous STAT3. Surprisingly, the degradation of EGFP-TDP43 by PDF-Bin depended on the proteasome pathway, while the degradation of STAT3 was mediated through the autophagy-lysosome pathway. This result suggests that PDF-Bin selects the most suitable degradation pathway based on the inherent characteristics of the target protein, thus achieving more efficient degradation (see Figure 3).</span></p> <p><span style="font-size: 15px;"><img decoding="async" loading="lazy" class="aligncenter wp-image-435" src="http://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/04/pblog-202404-3.jpg" alt="" width="390" height="386" srcset="https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/04/pblog-202404-3.jpg 831w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/04/pblog-202404-3-300x297.jpg 300w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/04/pblog-202404-3-768x761.jpg 768w" sizes="(max-width: 390px) 100vw, 390px" /></span></p> <p style="text-align: center;"><span style="font-size: 12px;">Figure 3. A schematic diagram of PDF-Bin degradation mechanism</span></p> <p><span style="font-size: 15px;">Lastly, the researchers preliminarily explored the therapeutic potential of PDF-Bin. STAT3, a classic target in cancer therapy, is widely activated in various cancers and regulates the proliferation and differentiation of cancer cells. By specifically degrading STAT3 protein in non-small cell lung cancer cell lines using PDF-Bin, tumor cell proliferation and migration were effectively inhibited, offering new strategies for the development of novel anti-tumor drugs.</span></p> <p><span style="font-size: 15px;">In summary, this study developed a protein-targeting degradation strategy based on bispecific antibodies. It is effective in degrading target proteins across various subcellular localizations and different mobilities. Additionally, it integrates the ubiquitin-proteasome and autophagy-lysosome pathways, autonomously selecting the optimal degradation pathway based on the characteristics of the target protein.</span></p> <p><span style="font-size: 12px;">Reference:</span></p> <p><span style="font-size: 12px;">Jia, Wen, <em>et al</em>. “An all-in-one targeted protein degradation platform guided by degradation condensates-bridging bi-specific nanobodies.” <em>Cell Research</em> (2024): 1-4.</span></p> ]]></content:encoded> </item> <item> <title>Extracellular Protein Targeted Degradation (eTPD): Six Drug Discovery Modalities</title> <link>https://www.creative-biolabs.com/blog/protac/protac-reviews/extracellular-protein-targeted-degradation-etpd-six-drug-discovery-modalities/</link> <dc:creator><![CDATA[biolabs]]></dc:creator> <pubDate>Mon, 18 Mar 2024 06:46:53 +0000</pubDate> <category><![CDATA[protac reviews]]></category> <category><![CDATA[eTPD]]></category> <category><![CDATA[iTPD]]></category> <guid isPermaLink="false">https://www.creative-biolabs.com/blog/protac/?p=421</guid> <description><![CDATA[Targeted protein degradation (TPD) has emerged over the past decade as a major novel drug modality for the removal of intracellular proteins with bispecific small molecules that recruit proteins of interest (POIs)<a class="moretag" href="https://www.creative-biolabs.com/blog/protac/protac-reviews/extracellular-protein-targeted-degradation-etpd-six-drug-discovery-modalities/">Read More...</a>]]></description> <content:encoded><![CDATA[<p><span style="font-size: 15px;">Targeted protein degradation (TPD) has emerged over the past decade as a major novel drug modality for the removal of intracellular proteins with bispecific small molecules that recruit proteins of interest (POIs) to E3 ligases for degradation in the proteasome. Unlike traditional mass-occupancy-based drugs, intracellular TPD (iTPD) eliminates the target and catalyzes action, so it can be more effective and sustained with lower dosage requirements.</span></p> <p><span style="font-size: 15px;">Recently, this approach has been extended to the extracellular proteome, including secreted proteins and membrane proteins. Extracellular protein-targeted degradation (eTPD) utilizes bispecific antibodies, conjugates, or small molecules to transport extracellular POIs to lysosomes for degradation. Here, we highlight the latest advances in eTPDs, including degradation systems, targets, molecular design, and parameters to advance them. Almost any protein, intracellular or extracellular, can now be treated with TPD in principle.</span></p> <h6><span style="font-size: 15px;">1. Intracellular protein-targeted degradation (iTPD): PROTACs and molecular glues</span></h6> <p><span style="font-size: 15px;">In recent years, intracellular targeted protein degradation (iTPD) has emerged as an important new model for small molecule drugs (Figure 1). At present, two classes of such molecules have been developed. The first type is <span style="color: #0000ff;"><strong><a style="color: #0000ff;" href="https://www.creative-biolabs.com/protac/protac-molecule-discovery.htm">proteolysis-targeting chimeras</a></strong></span> (PROTACs), which are large bispecific small molecules conjugated by a linker. They induce POI ubiquitination and the tagged disease causing protein will be ultimately degraded by the proteasome in the cytoplasm. The second type is known as molecular glue, which enhances the interaction between E3 ligase and POI, leading to its ubiquitination and proteasomal degradation. iTPD offers significant advantages over traditional “mass drive” based inhibitors. First, PROTACs, or molecular glues, can theoretically bind anywhere on a POI, whereas inhibitors often require binding to active or allosteric sites. Second, the degradation of the target removes the entire protein, including its scaffold function, so the therapeutic activity of the drug should last longer and more closely follow the results of knockout experiments. Third, these molecules are catalytic and not stoichiometric, as in classical pharmacological inhibitors, so the same therapeutic effect can be achieved at low doses. There are currently more than two dozen clinical trials involving PROTACs and molecular glues, some of which have entered Phase II and Phase III studies.</span></p> <p><span style="font-size: 15px;"><img decoding="async" loading="lazy" class="aligncenter wp-image-422" src="http://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/03/pblog-202403-1.jpg" alt="" width="403" height="229" srcset="https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/03/pblog-202403-1.jpg 560w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/03/pblog-202403-1-300x170.jpg 300w" sizes="(max-width: 403px) 100vw, 403px" /></span></p> <p style="text-align: center;"><span style="font-size: 12px;">Fig. 1 General mechanisms of intracellular targeted protein degradation pathways<sup>1</sup></span></p> <h6><span style="font-size: 15px;">2. Extracellular Protein Targeted Degradation (eTPD): An Emerging Drug Modality</span></h6> <p><span style="font-size: 15px;">The iTPD of the cytosolic protein has stimulated research into the extracellular proteome in biology and chemistry, known as extracellular TPD (eTPD). In addition to the location of the target POI, there are at least three significant differences between iTPD and eTPD (Figure 2).</span></p> <p><span style="font-size: 15px;">First, cells recycle proteins through two main pathways: the proteasomal and lysosomal pathways. iTPD is almost entirely dependent on the proteasome pathway, which is commonly used to process intracellular proteins. eTPD involves bispecific biologics or small molecules that recruit membrane-bound or secreted POIs to membrane-bound circulating receptors and deliver POIs to lysosomes, which are typical pathways for extracellular protein degradation.</span></p> <p><span style="font-size: 15px;">Second, these two proteolytic disruption modes have different kinetics and use different proteases. iTPD is faster—usually within a few minutes to a few hours because all the components are inside the cell. In contrast, the rate of eTPD is generally slower, typically 6–48 hours, as it involves vesicle transport from the membrane through early and late endosomes, and eventually fusion with lysosomes, leading to protein degradation.</span></p> <p><span style="font-size: 15px;">Third, almost all iTPD systems use only a few E3 ligases, mainly CRBN or VHL, which present challenges in finding E3 ligase conjugates. Both ligases are widely expressed in tissues, which limits tissue-selective targeting. In contrast, eTPD can use a variety of degradation systems, which allows for more specific tissue selectivity.</span></p> <p><span style="font-size: 15px;">Finally, the pharmacokinetics of antibodies are very long compared to typical small molecules, so they are administered less frequently.</span></p> <p><span style="font-size: 15px;">Therefore, eTPD represents an emerging new paradigm for biologics development.</span></p> <p><span style="font-size: 15px;"><img decoding="async" loading="lazy" class="aligncenter wp-image-423" src="http://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/03/pblog-202403-2.jpg" alt="" width="337" height="214" srcset="https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/03/pblog-202403-2.jpg 589w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/03/pblog-202403-2-300x190.jpg 300w" sizes="(max-width: 337px) 100vw, 337px" /></span></p> <p style="text-align: center;"><span style="font-size: 12px;">Fig. 2 General mechanisms of extracellular targeted protein degradation pathways<sup>1</sup></span></p> <h6><span style="font-size: 15px;">3. Six different strategies for eTPD</span></h6> <p><span style="font-size: 15px;">At present, there are six different methods and strategies for eTPD, including eTPD—a clearance antibody that degrades soluble POI, eTPD—a circulating receptor eTPD based on glycans, eTPD based on transmembrane E3 ligase targeting membrane proteins, eTPD based on cytokines, eTPD based on integrin, and eTPD that degrades membrane proteins from the inside.</span></p> <ul> <li><span style="font-size: 15px;">Clearance antibody eTPD that degrades soluble POI</span></li> </ul> <p><span style="font-size: 15px;">The Fc region of the antibody has an important function for antibody circulation and immune cell activation. Nascent Fc receptors (FcRns) are responsible for recovering antibodies internalized into endosomes, sending them back outside the cell before they reach lysosomal degradation, and enhanced binding of antibodies to FcRn can extend their half-life in human serum to 21 days.</span></p> <p><span style="font-size: 15px;">The “scavenging antibody” is designed so that FcRn delivers POI to acidic endosomes in a pH-switchable manner, releasing POI for lysosomal degradation (Figure 3a). This is inspired by the natural circulating mechanism of low-density lipoprotein (LDL) uptake, which binds to the LDL receptor and is released into endosomes at low pH for lysosomal degradation. Tocilizumab (Tcz), a humanized antibody approved for the treatment of rheumatoid arthritis, binds pH-dependently to the IL-6 receptor (IL-6R). By redesigning Tcz as a clearing antibody, its affinity for FcRn was increased by utilizing a known mutation, and then by mutations in the complementary deterministic region CDRs, the affinity for IL-6 was reduced by approximately 20-fold at pH 6.0 while maintaining affinity at pH 7.4. The modified antibody can deliver IL-6R to the lysosome while maintaining attachment to FcRn and cycling back to the plasma membrane to collect more IL-6. pH-switchable Tocilizumab was approved in 2020 for the treatment of neuromyelitis optica spectrum disorder, representing the first approved antibody in eTPD.</span></p> <ul> <li><span style="font-size: 15px;">Glycan-based circulating receptor eTPD</span></li> </ul> <p><span style="font-size: 15px;">The use of glycan-targeted recycling receptors, such as cationic independent mannose 6-phosphate receptor (CI-M6PR) or sialic acid glycoprotein receptor (ASGPR), can promote lysosomal degradation of membranes and soluble POIs (Figure 3b). One approach, known as lysosome-targeted chimerism (LYTAC), involves the bioconjugation of multiple glycan ligands of CI-M6PR to antibodies targeting POIs, and the LYTAC-POI complex binds to CI-M6PR and is internalized, resulting in the degradation of POIs in lysosomes. Another approach, known as Bifunctional Small Molecules of MoDE or ASGPR-Targeting Chimeras (ATACs), is being used to develop a similar ASGPR-based approach.</span></p> <p><span style="font-size: 15px;">CI-M6PR is a 300 kDa dimer type I receptor, a pH switchable receptor that binds to ligands at neutral pH and is released in acidic endosomes before fusion with lysosomes. CI-M6PR has been used to shuttle M6P-carrying exogenous lysosomal enzymes to lysosomes for the treatment of lysosomal diseases. ASGPR is predominantly highly expressed on hepatocytes and rapidly clears non-sialylated glycoproteins. In conclusion, glycan-based eTPD degradation methods mainly utilize ASGPR or CI-M6PR.</span></p> <ul> <li><span style="font-size: 15px;">eTPD based on transmembrane E3 ligase targeting membrane proteins</span></li> </ul> <p><span style="font-size: 15px;">In addition to the 600–700 intracellular members of E3 ligases, there is a family of E3 ligases containing transmembrane domains with about 30 members. Target proteins can be degraded using bispecific antibodies targeting this family member and POI, known as antibody-based protein degradation-targeting chimeras (AbTACs), protein degradation-targeting antibodies (PROTABs), or receptor elimination (REULR) recruited by E3 ubiquitin ligase (Figure 3c). In one study, an AbTAC of PD-L1 was constructed, with the POI arm selecting the Fab domain of atezolizumab bound to PD-L1 and the degradation arm using the Fab of the RNF43 extracellular domain. Atz-AbTAC adopted the classical KICH mode. Atz AbTAC induced the degradation of PD-L1 with a DC50 of 3.4 nM, a 24-hour maximum degradation (Dmax) of approximately 63%, and whole-cell proteomics showed no significant overall changes in the cellular proteome and no significant cytotoxicity.</span></p> <p><span style="font-size: 15px;">In conclusion, it has been shown that bispecific molecules (AbTACs, PROTABs, and REULRs) with members of the transmembrane E3 ubiquitin ligase family can co-selectively degrade some important membrane proteins for therapeutic purposes.</span></p> <ul> <li><span style="font-size: 15px;">eTPDs based on cytokine-targeting membrane proteins</span></li> </ul> <p><span style="font-size: 15px;">It is well known that many cytokines can be absorbed and degraded by their receptors by shuttling to lysosomes. This provides another opportunity to harness the endogenous mechanism of eTPD in a method called cytokine receptor-targeting chimera (KineTAC) (Figure 3d). KineTACs bind to natural cytokines or growth factors with one arm, while the other arm binds exclusively to POIs. This allows it to work against membrane-bound and soluble proteins for efficient and specific protein degradation.</span></p> <p><span style="font-size: 15px;">Like AbTAC, KineTAC can degrade a wide range of membrane proteins in a wide range of cell types. And similar to LYTAC, they can also degrade soluble proteins because cycling is not dependent on ubiquitination. In addition, the transcription level of POI can be significantly higher than that of degradants and can still be efficiently degraded.</span></p> <ul> <li><span style="font-size: 15px;">Integrin-based eTPD</span></li> </ul> <p><span style="font-size: 15px;">Inspired by the targeted delivery of anticancer drugs using integrin αVβ3, eTPD introduces an integrin-based degradation system (Figure 3e). It involves the use of bispecific antibodies that bind specifically to integrins with one arm and the other to POIs. Directs POIs to lysosomes for degradation while harnessing the cycling capacity of integrins to enhance target localization and efficiency.</span></p> <p><span style="font-size: 15px;">As proof of principle, the biotin-binding protein NeutrAvidin was targeted using an integrin αVβ3-binding biotin chimera. This molecule contains a cyclic RGD motif (cRGD) covalently linked to biotin, which successfully internalizes NeutrAvidin in A549 cells within 20 h. Overall, this integrin-based degradation system shows exciting potential for tumor-selective degradation of membranes or soluble proteins.</span></p> <ul> <li><span style="font-size: 15px;">Degradation of membrane proteins from the inside of eTPD</span></li> </ul> <p><span style="font-size: 15px;">Receptor tyrosine kinase (<span style="color: #0000ff;"><strong><a style="color: #0000ff;" href="https://www.creative-biolabs.com/protac/ligand-design-for-alk-targeting-protac.htm">RTK</a></strong></span>) has been studied for PROTAC targeting, which contains a canonical E3 ligase conjugate of CRBN or VHL linked to various RTK inhibitors (Figure 3f). This PROTAC binds in part to the intracellular kinase domain of the receptor tyrosine kinase (RTK), while the other part binds to the E3 ligase. As a result, the receptor tyrosine kinase is ubiquitinated, and the receptor tyrosine kinase is degraded in the proteasome. In summary, the use of PROTACs conjugated to VHL or CRBN can degrade RTKs internally. Although this approach is still in its infancy, PROTACs using intracellular domains targeting membrane proteins have shown promising applications.</span></p> <p> </p> <p><span style="font-size: 15px;"><img decoding="async" loading="lazy" class="aligncenter wp-image-424" src="http://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/03/pblog-202403-3.jpg" alt="" width="253" height="252" srcset="https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/03/pblog-202403-3.jpg 824w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/03/pblog-202403-3-300x300.jpg 300w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/03/pblog-202403-3-150x150.jpg 150w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/03/pblog-202403-3-768x765.jpg 768w" sizes="(max-width: 253px) 100vw, 253px" /></span></p> <p style="text-align: center;"><span style="font-size: 12px;">Fig. 3 Six different methods for degrading extracellular proteins<sup>1</sup></span></p> <p><span style="font-size: 15px;">The eTPD field is in its infancy and is rapidly following the development of the iTPD field, with various designs and methods currently being studied. However, there are still many important issues to be solved in the field of eTPD.</span></p> <p><span style="font-size: 15px;">References:</span></p> <ol> <li><span style="font-size: 15px;">Wells, James A., and Kaan Kumru. “Extracellular targeted protein degradation: an emerging modality for drug discovery.” Nature Reviews Drug Discovery 23.2 (2024): 126-140.</span></li> </ol> ]]></content:encoded> </item> <item> <title>Review: Molecular Glue vs. PROTAC</title> <link>https://www.creative-biolabs.com/blog/protac/protac-reviews/review-molecular-glue-vs-protac/</link> <dc:creator><![CDATA[biolabs]]></dc:creator> <pubDate>Sat, 24 Feb 2024 03:00:28 +0000</pubDate> <category><![CDATA[protac reviews]]></category> <category><![CDATA[Molecular Glue]]></category> <category><![CDATA[protac]]></category> <guid isPermaLink="false">https://www.creative-biolabs.com/blog/protac/?p=406</guid> <description><![CDATA[Targeted protein degradation (TPD) primarily degrades target proteins through the ubiquitin-proteasome and lysosome, and according to the specific mechanism of action, it can be further subdivided into nearly 10 different technical routes,<a class="moretag" href="https://www.creative-biolabs.com/blog/protac/protac-reviews/review-molecular-glue-vs-protac/">Read More...</a>]]></description> <content:encoded><![CDATA[<p><span style="font-size: 15px;">Targeted protein degradation (TPD) primarily degrades target proteins through the ubiquitin-proteasome and lysosome, and according to the specific mechanism of action, it can be further subdivided into nearly 10 different technical routes, among which the fastest developing are molecular glue and<span style="color: #0000ff;"><a style="color: #0000ff;" href="/protac/protac-molecule-discovery.htm"> <strong>PROTAC technology</strong></a></span>.</span></p> <p><span style="font-size: 15px;">The molecular glue of BMS has reached an annual sales volume of 12.891 billion US dollars, while Arvinas’ PROTAC molecule ARV-471 has already initiated phase III clinical trials. Targeted degradation based on lysosomes has a shorter development time and is still in the pre-clinical stage.</span></p> <p><span style="font-size: 15px;">Under the current drug development situation where conventional target development is exhausted and it is difficult to find new targets, TPD technology provides a new pathway for drug development, greatly broadening the range of target proteins and is expected to be one of the most promising technologies for the future.</span></p> <h6>1. Differences between PROTAC and molecular glue</h6> <p><span style="font-size: 15px;">Proteolysis Targeting Chimeras (PROTACs) and molecular glues are two rapidly developing technologies for targeted protein degradation in recent years. They achieve protein degradation in disease treatment through different mechanisms, and both have the potential to change traditional drug development methods.</span></p> <p><span style="font-size: 15px;">① Different Structures: PROTACs generally consist of three parts: a target protein ligand, a linker, and an E3 ubiquitin ligase ligand. This structural design enables PROTAC molecules to simultaneously connect with the target protein and E3. Molecular glues, on the other hand, are usually single, small molecules. They promote interactions between them by altering the conformation of the target protein or E3 ubiquitin ligase, without the need for specific linkers or high-affinity ligands for the target protein (Figure 1).</span></p> <p><span style="font-size: 15px;">② Different Mechanisms: The main difference between PROTACs and molecular glues lies in their mechanisms of action. PROTACs induce target protein degradation by linking the target protein to the E3 ligase ligand, allowing the ubiquitin attached to the target protein to enter the proteasome for degradation. This method can thoroughly eliminate pathological proteins, thereby offsetting their disease activity. However, molecular glues form a stable complex by stably interacting with the pathological protein, thereby inhibiting its activity or degrading the target protein.</span></p> <p><span style="font-size: 15px;">③ Different Efficiencies: PROTAC can achieve selective degradation of target proteins, and its efficacy depends on the affinity between PROTAC and the target protein and E3 ligase. Unlike traditional enzyme inhibitors or receptor blockers, PROTAC not only inhibits protein function but also reduces protein quantity. Molecular glues can also promote the degradation of target proteins. Since this is achieved by directly binding the target protein with the E3 ligase, its efficiency depends on the affinity between the molecular glue, the target protein, and the E3 ligase (Table 1).</span></p> <p><img decoding="async" loading="lazy" class="aligncenter wp-image-407" src="http://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/02/pblog-202402-01.jpg" alt="" width="280" height="203" srcset="https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/02/pblog-202402-01.jpg 577w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/02/pblog-202402-01-300x217.jpg 300w" sizes="(max-width: 280px) 100vw, 280px" /></p> <p style="text-align: center;"><span style="font-size: 12px;">Fig.1 Mode of action and structural features of molecular glue and PROTAC</span></p> <table style="width: 100%; border-style: solid; border-color: #575757;"> <tbody> <tr> <td style="width: 24.3377%; border-style: solid; border-color: #575757;"></td> <td style="width: 43.3775%; border-style: solid; border-color: #575757;"><strong>Molecular glue</strong></td> <td style="width: 32.1192%; border-style: solid; border-color: #575757;"><strong>PROTAC</strong></td> </tr> <tr> <td style="width: 24.3377%; border-style: solid; border-color: #575757;">Mechanism</td> <td style="width: 43.3775%; border-style: solid; border-color: #575757;">Inducing PPI by binding to the E3 enzyme or target protein</td> <td style="width: 32.1192%; border-style: solid; border-color: #575757;">Binding target and E3 enzyme</td> </tr> <tr> <td style="width: 24.3377%; border-style: solid; border-color: #575757;">Target protein (POI)</td> <td style="width: 43.3775%; border-style: solid; border-color: #575757;">Undetermined</td> <td style="width: 32.1192%; border-style: solid; border-color: #575757;">Predictable</td> </tr> <tr> <td style="width: 24.3377%; border-style: solid; border-color: #575757;">Discovery strategy</td> <td style="width: 43.3775%; border-style: solid; border-color: #575757;">Discovered by chance in history</td> <td style="width: 32.1192%; border-style: solid; border-color: #575757;">Reasonable design</td> </tr> <tr> <td style="width: 24.3377%; border-style: solid; border-color: #575757;">Feature</td> <td style="width: 43.3775%; border-style: solid; border-color: #575757;">Unit price</td> <td style="width: 32.1192%; border-style: solid; border-color: #575757;">Divalent</td> </tr> <tr> <td style="width: 24.3377%; border-style: solid; border-color: #575757;">Linker</td> <td style="width: 43.3775%; border-style: solid; border-color: #575757;">No need to connect sub</td> <td style="width: 32.1192%; border-style: solid; border-color: #575757;">Connection required</td> </tr> <tr> <td style="width: 24.3377%; border-style: solid; border-color: #575757;">Molecular weight</td> <td style="width: 43.3775%; border-style: solid; border-color: #575757;">Low</td> <td style="width: 32.1192%; border-style: solid; border-color: #575757;">high</td> </tr> <tr> <td style="width: 24.3377%; border-style: solid; border-color: #575757;">Lipinski’s Five Rules</td> <td style="width: 43.3775%; border-style: solid; border-color: #575757;">Accord with</td> <td style="width: 32.1192%; border-style: solid; border-color: #575757;">Not compliant</td> </tr> <tr> <td style="width: 24.3377%; border-style: solid; border-color: #575757;">Target protein binding pocket</td> <td style="width: 43.3775%; border-style: solid; border-color: #575757;">Non essential</td> <td style="width: 32.1192%; border-style: solid; border-color: #575757;">Required</td> </tr> <tr> <td style="width: 24.3377%; border-style: solid; border-color: #575757;">Affinity</td> <td style="width: 43.3775%; border-style: solid; border-color: #575757;">The affinity for the E3 enzyme and POI is not very strong.</td> <td style="width: 32.1192%; border-style: solid; border-color: #575757;">Strong affinity for the E3 enzyme and POI</td> </tr> </tbody> </table> <p style="text-align: center;"><span style="font-size: 12px;">Table 1: The difference between molecular glue and PROTAC</span></p> <h6>2. The Cutting-Edge Advances of PROTACs and Molecular Glues</h6> <p><span style="font-size: 15px;">To date, PROTACs have been successfully used in the research of various types of protein-related diseases, showing strong therapeutic effects in clinical trials. For example, there’s ARV-471 which targets estrogen receptors, and MT-802 which targets BTK. However, there are currently no PROTAC drugs approved worldwide.</span></p> <p><span style="font-size: 15px;">With Arvinas’ two candidate molecules, ARV-110 and ARV-471, taking the lead in obtaining positive clinical data, this field has experienced robust growth in recent years. Currently, several PROTAC drugs have entered the clinical stage, with targets including AR, ER, BCL-XL, IKZF1/3, STAT3, BTK, TRK, BRD9, etc.</span></p> <table style="width: 100%; border-style: solid; border-color: #575757;"> <tbody> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;"><strong>PROTAC</strong></td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144"><strong>Target points</strong></td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274"><strong>Indications</strong></td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;"><strong>Research stage</strong></td> </tr> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;">ARV-471</td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144"><span style="color: #0000ff;"><strong><a style="color: #0000ff;" href="/protac/ligand-design-for-estrogen-receptor-er-targeting-PROTAC.htm">Estrogen receptor</a> </strong></span>(ER)</td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274">Breast cancer (ER+/HER2 BreakCancer)</td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;">Phase III</td> </tr> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;">ARV-110</td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144"><strong><span style="color: #0000ff;"><a style="color: #0000ff;" href="/protac/ligand-design-for-androgen-receptor-ar-targeting-PROTAC.htm">Androgen receptor</a></span></strong> (AR)</td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274">Metastatic castration resistant prostate cancer (mCRPC)</td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;">Phase II</td> </tr> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;">ARV-766</td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144">Androgen receptor (AR)</td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274">Metastatic castration resistant prostate cancer (mCRPC)</td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;">Phase II</td> </tr> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;">KT-474</td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144">Interleukin-1 receptor associated kinase 4 (IRAK4)</td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274">Allergic dermatitis, purulent sweat gland inflammation, rheumatoid arthritis</td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;">Phase II</td> </tr> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;">LNK01001</td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144">–</td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274">Rheumatoid arthritis, atopic dermatitis, ankylosing spondylitis</td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;">Phase II</td> </tr> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;">GT20029</td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144">AR</td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274">Androgenic alopecia</td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;">Phase II</td> </tr> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;">CFT7455</td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144"><strong><span style="color: #0000ff;"><a style="color: #0000ff;" href="protac/ligand-design-for-ikzf1-3-targeting-PROTAC.htm">IKZF1/3</a></span></strong></td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274">Recurrent/refractory non Hodgkin’s lymphoma or multiple myeloma</td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;">PhaseI/I</td> </tr> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;">CFT1946</td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144">BRAFV600</td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274">BRAFV600 mutated solid tumor</td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;">PhaseI/I</td> </tr> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;">NX-2127</td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144">BTK+IKZF</td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274">B-cell malignant tumor</td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;">Phase I</td> </tr> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;">NX-5948</td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144"><strong><span style="color: #0000ff;"><a style="color: #0000ff;" href="/protac/ligand-design-for-btk-targeting-PROTAC.htm">BTK</a></span></strong></td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274">B-cell malignant tumors and autoimmune diseases</td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;">Phase I</td> </tr> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;">LNK01002</td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144">–</td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274">Hematological tumors</td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;">Phase I</td> </tr> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;">LNK01003</td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144">–</td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274">Immunity and inflammation</td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;">Phase I</td> </tr> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;">HSK29116</td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144">BTK</td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274">B-cell malignant tumor</td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;">Phase I</td> </tr> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;">MZ-001</td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144">BTK</td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274">B-cell malignant tumors and autoimmune diseases</td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;">IND declaration</td> </tr> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;">HP518</td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144">AR</td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274">MCRPC with standard treatment failure</td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;">IND declaration</td> </tr> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;">CFT8919</td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144">EGFR L858R</td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274">Non small cell lung cancer (NSCLC) with drug-resistant EGFR mutations</td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;">Preclinical</td> </tr> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;">CFT8634</td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144">BRD9</td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274">Synovial sarcoma and solid tumors with smarcb1 deficiency</td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;">Precision</td> </tr> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;">KYM-001</td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144">KYM-001</td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274">MYD88 gene mutation in B-cell lymphoma</td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;">Precision</td> </tr> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;">CG416</td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144">Neurotrophic factor receptor tyrosine kinase (TRK)</td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274">–</td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;">Preclinical</td> </tr> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;">CG428</td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144">TRK</td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274">–</td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;">Precision</td> </tr> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;">CG001419</td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144">TRK</td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274">–</td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;">Precision</td> </tr> <tr> <td style="width: 13.0795%; border-style: solid; border-color: #575757;">HC-X029</td> <td style="width: 25.6623%; border-style: solid; border-color: #575757;" width="144">AR sv</td> <td style="width: 47.1854%; border-style: solid; border-color: #575757;" width="274">End line treatment for mCRPC with failed standard treatment</td> <td style="width: 14.0728%; border-style: solid; border-color: #575757;">Precision</td> </tr> </tbody> </table> <p style="text-align: center;"><span style="font-size: 12px;">Table 2: PROTACs currently in the clinical stage</span></p> <p><span style="font-size: 15px;">In contrast, molecular glues as a relatively new therapy, are less researched and developed but have already demonstrated therapeutic potential in certain specific instances. The molecular glues that have been approved for clinical use are primarily immunomodulators, such as Thalidomide, Lenalidomide, and Pomalidomide, used to treat conditions such as multiple myeloma and myelodysplastic syndromes. The molecular weights of these three molecular glue degraders are all below 300 Da, and they all degrade target proteins, including the transcription factor IKZF1/3, by recruiting the E3 ubiquitin ligase CRBN. In addition, thalidomide analogs are often used as ligands for CRBN in many PROTAC molecules. For example, the E3 ligase ligand in the phase III clinical drug ARV-471 is (R)-thalidomide.</span></p> <h6>3. Future Development Trend of PROTAC and Molecular Glue</h6> <p><span style="font-size: 15px;">Although there are currently no PROTAC drugs on the market, several drugs that have preliminary human clinical data have been proven to significantly degrade intracellular proteins with good therapeutic effects. However, confirming efficacy is a slow process, and more extensive sample data needs to be gathered to verify its validity. Due to its unique mechanism of action, PROTAC technology is attracting more and more biopharmaceutical innovators and entrepreneurs to compete on this new track. Over the course of more than 20 years of development, PROTAC has broken through the widely accepted drug development rules, opening a new chapter for drug development in its continuous exploration and advancement. It is expected that PROTAC technology will have a wider application in future drug research and development. Meanwhile, with technological enhancements, the design and preparation process of PROTAC will become more precise and controllable.</span></p> <p><span style="font-size: 15px;">Currently, more than 600 types of E3 ligases have been reported, but only five have been used for molecular glue-mediated degradation, namely CRBN, DDB1, β-TrCP, DCAF15, and SIAH1. The E3 ligase library still has immense potential waiting to be explored. Identifying new E3 ligase ligands helps expand our degradable target proteins. Moreover, the chemical space of molecular glue drug molecules also merits further exploration. The majority of molecular glues reported to date still share a high degree of similarity with thalidomide and its derivatives. Certainly, this poses a significant challenge for drug developers who need to deepen their understanding of protein-protein interaction interfaces and create more rational structure-guided molecular glue designs, pushing molecular glues into clinical use and aiding in the treatment of more diseases.</span></p> <p><span style="font-size: 12px;">Reference:</span></p> <p><span style="font-size: 12px;">Dong G, Ding Y, He S, et al. Molecular glues for targeted protein degradation: from serendipity to rational discovery[J]. Journal of medicinal chemistry, 2021, 64(15): 10606-10620.</span></p> ]]></content:encoded> </item> <item> <title>A New PROTAC Targeting the METTL3-METTL14 Complex Has Arrived!</title> <link>https://www.creative-biolabs.com/blog/protac/uncategorized/a-new-protac-targeting-the-mettl3-mettl14-complex-has-arrived/</link> <dc:creator><![CDATA[biolabs]]></dc:creator> <pubDate>Mon, 29 Jan 2024 01:41:40 +0000</pubDate> <category><![CDATA[Uncategorized]]></category> <category><![CDATA[METTL3-METTL14]]></category> <category><![CDATA[protac]]></category> <guid isPermaLink="false">https://www.creative-biolabs.com/blog/protac/?p=372</guid> <description><![CDATA[N 6-methyladenosine (m6A) methylation is the most abundant type of RNA modification, primarily catalyzed by the METTL3-METTL14 methyltransferase complex (MTC). This complex includes the core catalytic proteins METTL3 and METTL14, as well<a class="moretag" href="https://www.creative-biolabs.com/blog/protac/uncategorized/a-new-protac-targeting-the-mettl3-mettl14-complex-has-arrived/">Read More...</a>]]></description> <content:encoded><![CDATA[<p><span style="font-size: 15px;">N 6-methyladenosine (m6A) methylation is the most abundant type of RNA modification, primarily catalyzed by the METTL3-METTL14 methyltransferase complex (MTC). This complex includes the core catalytic proteins METTL3 and METTL14, as well as several regulatory proteins, including WTAP, VIRMA, HAKAI, ZC3H13, and RBM15. METTL3 is the sole catalytic component, while METTL14 primarily maintains the integrity of the complex and promotes the binding of substrate RNA.</span></p> <p><span style="font-size: 15px;">The methyltransferase complex is associated with various diseases, including cancer, cardiovascular disease, and neurological disorders. As the core catalytic subunit of MTC, METTL3 is overexpressed in various types of cancer, such as hematological malignancies, lung cancer, and liver cancer, and is considered a key oncogenic driver in malignant myeloid hematopoietic cells. Studies have revealed that METTL3 sustains the leukemic state of acute myeloid leukemia (AML) by catalyzing the methylation of mRNA encoding oncogenic transcription factors. Inducible loss of METTL3 has been shown to lead to cell cycle arrest and impaired differentiation and growth in AML cells. In addition, METTL14 is also overexpressed in AML cells and promotes leukemia occurrence by regulating MYB and MYC through m6A modification.</span></p> <p><span style="font-size: 15px;">Given the pivotal role of the METTL3-METTL14 complex in tumorigenesis, the development of specific METTL3-METTL14 inhibitors is an emerging and promising research area. Up to now, only a few inhibitors targeting the catalytic activity of the METTL3-METTL14 complex, such as UZH2 and STM2457, have been developed, which are SAM-competitive inhibitors of METTL3. STM2457 has exhibited potent anti-leukemic potential in AML cell lines without noticeably affecting normal hematopoiesis. These findings suggest that the METTL3-METTL14 complex is an appealing target for cancer therapy, especially for AML. However, there is a lack of research on METTL3 inhibitors targeting its catalytic activity.</span></p> <p><span style="font-size: 15px;">Recently, researchers from the Shanghai Institute of Materia Medica have developed a selective <span style="color: #0000ff;"><strong><a style="color: #0000ff;" href="/protac/protac-molecule-discovery.htm">proteolysis-targeting chimera (PROTAC) </a></strong></span>for the METTL3-METTL14 complex, WD6305.</span></p> <p><span style="font-size: 15px;"><strong>Other metabolic enzymes targeting PROTACs</strong></span></p> <ul> <li><span style="font-size: 15px; color: #0000ff;"><a style="color: #0000ff;" href="https://www.creative-biolabs.com/protac/ligand-design-for-metap-2-targeting-PROTAC.htm"><strong>MetAP-2-targeting PROTAC®</strong></a></span></li> <li><span style="font-size: 15px; color: #0000ff;"><a style="color: #0000ff;" href="https://www.creative-biolabs.com/protac/ligand-design-for-dhodh-targeting-PROTAC.htm"><strong>DHODH-targeting PROTAC®</strong></a></span></li> </ul> <p><span style="font-size: 15px;">Their study results show that WD6305 more effectively inhibits m6A modification and AML cell proliferation compared to its parent inhibitor, UZH2, and promotes cell apoptosis. Furthermore, they found that WD6305 affects several signaling pathways associated with the development and proliferation of AML. These findings indicate that targeted degradation of the METTL3-METTL14 complex is a promising AML treatment strategy (Figure 1).</span></p> <p><img decoding="async" loading="lazy" class="aligncenter size-full wp-image-394" src="http://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/01/p202401-1-1.jpg" alt="" width="375" height="375" /></p> <p style="text-align: center;"><span style="font-size: 12px;">Figure 1. Schematic diagram of METTL3-METTL14 complex PROTAC action. (Du W, 2024)</span></p> <p><span style="font-size: 15px;">In this study, the researchers attempted to develop an efficient therapeutic tool to disrupt the stability of METTL3 and/or METTL14. Using UZH2, a METTL3 inhibitor, as a binding ligand, they designed and synthesized a series of METL3-targeting PROTAC molecules. The researchers then utilized Western Bolt to investigate the degradation capabilities of these compounds in MonoMac-6 cells, an AML cell line expressing METTL3. The experimental results indicated that compound 9 (WD6305) had the strongest degradation ability (Figure 2). Following this, the researchers selected WD6305, the compound that exhibited the most efficient degradation, to further characterize its degradation efficiency on METTL3. Western blot and proteomics analyses revealed that WD6305 reduced the levels of the METTL3 and METTL14 proteins in a dose-dependent and selective manner in MonoMac-6 cells (Figure 3). The entirety of these research findings verified that WD6305 is an efficient, selective, fast-acting, and enduring degrader of METTL3 and effectively removes the METTL3-METTL14 complex.</span></p> <p><img decoding="async" loading="lazy" class="aligncenter size-full wp-image-395" src="http://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/01/p202401-2-1.jpg" alt="" width="497" height="442" srcset="https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/01/p202401-2-1.jpg 497w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/01/p202401-2-1-300x267.jpg 300w" sizes="(max-width: 497px) 100vw, 497px" /></p> <p style="text-align: center;"><span style="font-size: 12px;">Figure 2. Degradation profiling of METTL3-based degrader (Du W, 2024)</span></p> <p><span style="font-size: 15px;">Next, the researchers confirmed the mechanism by which WD6305 degrades the METTL3-METTL14 complex. The study demonstrated that WD6305 degrades the METTL3-METTL14 complex via the ubiquitin-proteasome system. Lastly, the researchers assessed the anti-leukemic potential of WD6305 in several AML cell lines, including Mono-Mac-6 and MOLM-16. The study results show that WD6305 displayed stronger anti-proliferative activity and could more effectively induce apoptosis in Mono-Mac-6 cells than UZH2 (Figure 3). These findings suggest that, compared to its parent METTL3 inhibitor, WD6305 has superior anti-leukemic activity.</span></p> <p><img decoding="async" loading="lazy" class="aligncenter size-full wp-image-396" src="http://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/01/p202401-3-1.jpg" alt="" width="499" height="517" srcset="https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/01/p202401-3-1.jpg 499w, https://www.creative-biolabs.com/blog/protac/wp-content/uploads/sites/4/2024/01/p202401-3-1-290x300.jpg 290w" sizes="(max-width: 499px) 100vw, 499px" /></p> <p style="text-align: center;"><span style="font-size: 12px;">Figure 3. Mechanism of degradation of the METTL3-METTL14 complex (Du W, 2024)</span></p> <p><span style="font-size: 15px;">This study confirmed that WD6305 is a potent and selective PROTAC degrader for the METTL3-METTL14 complex. WD6305 inhibits m6A modification and AML cell proliferation and induces apoptosis more effectively than its parent inhibitor. In addition, WD6305 impacts multiple signaling pathways associated with AML development and proliferation. The study reveals PROTAC degradation of the METTL3-METTL14 complex as a potential anti-leukemia strategy and offers an ideal chemical tool for further understanding the function of the METTL3-METTL14 protein.</span></p> <p><span style="font-size: 12px;">Reference</span></p> <p><span style="font-size: 12px;">Du W, Huang Y, Chen X, et al. Discovery of a PROTAC degrader for METTL3-METTL14 complex[J]. Cell Chemical Biology, 2024.</span></p> ]]></content:encoded> </item> <item> <title>Researchers Have Made New Advances in the Field of Protein Degradation</title> <link>https://www.creative-biolabs.com/blog/protac/protac-research/researchers-have-made-new-advances-in-the-field-of-protein-degradation/</link> <dc:creator><![CDATA[biolabs]]></dc:creator> <pubDate>Fri, 22 Dec 2023 03:45:21 +0000</pubDate> <category><![CDATA[PROTAC Research]]></category> <category><![CDATA[LipoSM-PROTAC]]></category> <category><![CDATA[PROTAC Delivery]]></category> <category><![CDATA[Protein Research]]></category> <guid isPermaLink="false">https://www.creative-biolabs.com/blog/protac/?p=366</guid> <description><![CDATA[ROTAC technology has advantages such as targeting non-druggable targets, high catalytic activity, and overcoming drug resistance, making it a new strategy in drug development. Traditional PROTAC design and synthesis require a significant<a class="moretag" href="https://www.creative-biolabs.com/blog/protac/protac-research/researchers-have-made-new-advances-in-the-field-of-protein-degradation/">Read More...</a>]]></description> <content:encoded><![CDATA[<p><span style="font-size: 15px;">ROTAC technology has advantages such as targeting non-druggable targets, high catalytic activity, and overcoming drug resistance, making it a new strategy in drug development. Traditional PROTAC design and synthesis require a significant amount of time and resources, limiting its application in drug development. To address these limitations, researchers have actively explored the development of more specific and potent <span style="color: #0000ff;"><strong><a style="color: #0000ff;" href="/protac/protac-molecule-discovery.htm">PROTAC molecules</a></strong></span>. In this situation, the research group led by Li Zigang and Yin Feng proposed a novel Split-and-Mix nanoscale self-regulating platform (SM-PROTAC), which offers advantages such as easy screening of input assembly molecules, adjustable assembly molecule ratios, high universality, and time savings. However, the effective degradation concentration of peptide-based SM-PROTAC is relatively high.</span></p> <p><span style="font-size: 15px;">To find a more suitable system for the SM concept, the research group developed a new lipid-based Split-and-Mix nanoscale self-regulating platform (LipoSM-PROTAC). Validation in the biological field revealed that its effective concentration is 50–100 times lower than that of peptide-based SM-PROTAC. It also possesses characteristics of folate-selective delivery, enabling precise targeting of specific cell lines, demonstrating excellent biosafety, and holding significant clinical translation potential. It is widely applicable in various biological application areas. The research results, titled “Selective Protein of Interest (POI) degradation through split-and-mix liposome PROTAC approach”, were published in the <em>Journal of the American Chemical Society</em> and were selected as the cover article.</span></p> <p><span style="font-size: 15px;">In this study, the researchers introduce a unique method that involves split-and-mix liposomes for PROTAC delivery. Liposomes, which are lipid-based vesicles, are used as carriers for delivering PROTAC molecules to the target cells. The split-and-mix strategy enhances the selectivity of protein degradation by allowing the assembly of liposomes with specific recognition elements tailored for the POI.</span></p> <p><span style="font-size: 15px;">The research aims to achieve selective and efficient protein degradation, a critical aspect in therapeutic interventions for various diseases, including cancer. The utilization of liposomes as carriers offers advantages in terms of drug delivery, and the split-and-mix strategy provides a customizable and precise approach to tailor PROTAC delivery for specific protein targets.</span></p> <p><span style="font-size: 15px;">The research group is currently conducting <em>in vivo</em> studies based on the LipoSM-PROTAC platform. Simultaneously, they are actively searching for more effective SM carriers, such as polylactic acid (PLA) and dendrimers, in the hope of developing carrier molecules that are more potent and clinically translatable. The research group’s investigations are not limited to protein degradation through the proteasome. They are continuously developing various biodegrading agents, such as Lytac, Ribotac, and Autotac, to achieve effective degradation of a variety of target molecules.</span></p> <p><span style="font-size: 15px;">In summary, the Li Zigang and Yin Feng research group will continue to explore applications in various fields based on the SM system, bringing more innovation and breakthroughs to the field of biomedicine.</span></p> ]]></content:encoded> </item> </channel> </rss>