tag:blogger.com,1999:blog-73461369661103801182024-03-17T20:02:22.374-07:00Covalent ModifiersA blog highlighting recent publications in the area of covalent modification of proteins, particularly relating to covalent-modifier drugs. @CovalentMod on Twitter, @covalentmod@mstdn.science on Mastodon, and @covalentmod.bsky.social on BlueSkyCNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comBlogger612125tag:blogger.com,1999:blog-7346136966110380118.post-38096925126715466722024-03-13T22:13:00.000-07:002024-03-13T22:13:58.435-07:00An orally bioavailable SARS-CoV-2 main protease inhibitor exhibits improved affinity and reduced sensitivity to mutations<p><span class="ml-1" style="background-color: white; box-sizing: border-box; color: #595959; font-family: roboto, sans-serif; font-size: 17.5px; margin-left: 0.25rem !important;"><span style="box-sizing: border-box;">Michael Westberg <span style="box-sizing: border-box;">et al.</span></span></span></p><p><span class="ml-1" style="background-color: white; box-sizing: border-box; color: #595959; font-family: roboto, sans-serif; font-size: 17.5px; margin-left: 0.25rem !important;"><i style="box-sizing: border-box;">Sci. Transl. Med.</i></span><span class="ml-1" style="background-color: white; box-sizing: border-box; color: #595959; font-family: roboto, sans-serif; font-size: 17.5px; margin-left: 0.25rem !important;"><span style="box-sizing: border-box; font-weight: 900;">16</span>,</span><span class="ml-1" style="background-color: white; box-sizing: border-box; color: #595959; font-family: roboto, sans-serif; font-size: 17.5px; margin-left: 0.25rem !important;">eadi0979</span><span class="ml-1" style="background-color: white; box-sizing: border-box; color: #595959; font-family: roboto, sans-serif; font-size: 17.5px; margin-left: 0.25rem !important;">(2024).</span></p><p><span class="ml-1" style="background-color: white; box-sizing: border-box; color: #595959; font-family: roboto, sans-serif; font-size: 17.5px; margin-left: 0.25rem !important;">DOI:<a href="https://www.science.org/doi/10.1126/scitranslmed.adi0979">10.1126/scitranslmed.adi0979</a></span></p><p>Inhibitors of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro) such as nirmatrelvir (NTV) and ensitrelvir (ETV) have proven effective in reducing the severity of COVID-19, but the presence of resistance-conferring mutations in sequenced viral genomes raises concerns about future drug resistance. Second-generation oral drugs that retain function against these mutants are thus urgently needed. We hypothesized that the covalent hepatitis C virus protease inhibitor boceprevir (BPV) could serve as the basis for orally bioavailable drugs that inhibit SARS-CoV-2 Mpro more efficiently than existing drugs. Performing structure-guided modifications of BPV, we developed a picomolar-affinity inhibitor, ML2006a4, with antiviral activity, oral pharmacokinetics, and therapeutic efficacy similar or superior to those of NTV. A crucial feature of ML2006a4 is a derivatization of the ketoamide reactive group that improves cell permeability and oral bioavailability. Last, ML2006a4 was found to be less sensitive to several mutations that cause resistance to NTV or ETV and occur in the natural SARS-CoV-2 population. Thus, anticipatory design can preemptively address potential resistance mechanisms to expand future treatment options against coronavirus variants.</p><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgjb7l0nYkhaiJAn4bfdvtb5THQeCjxwnG01vOwg2R8y_4VmswaOu9kaFv8dKwgGRdookkYNH5Z3K3dSUov14qUiqm3Gj-fFt76-rL0V9B3NvYWuV_BAR2AB7RTFoksY3NeP_Ax4CakRiJgVFgmizrkXnatH6uRIFAn-04GiYdVRVzkh7yAEq4sauWmIMU/s4299/scitranslmed.adi0979-f3.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="2849" data-original-width="4299" height="212" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgjb7l0nYkhaiJAn4bfdvtb5THQeCjxwnG01vOwg2R8y_4VmswaOu9kaFv8dKwgGRdookkYNH5Z3K3dSUov14qUiqm3Gj-fFt76-rL0V9B3NvYWuV_BAR2AB7RTFoksY3NeP_Ax4CakRiJgVFgmizrkXnatH6uRIFAn-04GiYdVRVzkh7yAEq4sauWmIMU/s320/scitranslmed.adi0979-f3.jpg" width="320" /></a></div><br /><p></p>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-81050705302588169832024-03-06T23:37:00.000-08:002024-03-06T23:37:18.356-08:00Strain-release alkylation of Asp12 enables mutant selective targeting of K-Ras-G12D<p><span style="background-color: white; box-sizing: inherit;"><span style="background-color: transparent;"><span style="color: #222222; font-family: -apple-system, system-ui, Segoe UI, Roboto, Oxygen-Sans, Ubuntu, Cantarell, Helvetica Neue, sans-serif;">Qinheng Zheng, Ziyang Zhang, Keelan Z. Guiley & Kevan M. Shokat</span></span></span></p><p><span style="background-color: white; box-sizing: inherit;"><i style="color: #222222; font-family: -apple-system, "system-ui", "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 20px;">Nat Chem Biol</i></span><span style="background-color: white; color: #222222; font-family: -apple-system, "system-ui", "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 20px;"> <b>2024</b></span></p><p><span style="background-color: white; color: #222222; font-family: -apple-system, "system-ui", "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 20px;"> </span><a href="https://doi.org/10.1038/s41589-024-01565-w" style="font-family: -apple-system, "system-ui", "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 20px;">https://doi.org/10.1038/s41589-024-01565-w</a></p><p>K-Ras is the most commonly mutated oncogene in human cancer. The recently approved non-small cell lung cancer drugs sotorasib and adagrasib covalently capture an acquired cysteine in K-Ras-G12C mutation and lock it in a signaling-incompetent state. However, covalent inhibition of G12D, the most frequent K-Ras mutation particularly prevalent in pancreatic ductal adenocarcinoma, has remained elusive due to the lack of aspartate-targeting chemistry. Here we present a set of malolactone-based electrophiles that exploit ring strain to crosslink K-Ras-G12D at the mutant aspartate to form stable covalent complexes. Structural insights from X-ray crystallography and exploitation of the stereoelectronic requirements for attack of the electrophile allowed development of a substituted malolactone that resisted attack by aqueous buffer but rapidly crosslinked with the aspartate-12 of K-Ras in both GDP and GTP state. The GTP-state targeting allowed effective suppression of downstream signaling, and selective inhibition of K-Ras-G12D-driven cancer cell proliferation in vitro and xenograft growth in mice.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh6ehyWHxYYlsxRGMMN2ctBRAUsUV2Nd-z4l_pzWX_JxZDXPvbY70Nq_ajovsi0wpeGNOL-F0TFITkZXl2cTV_5P2HpHXO33gU1SKk5m6eKet70HAJMYqNalwtAvedD1nGTmw7DrozLCS7pASCSHtCjOjYkd-uN_j1ng1aak7X_t9nR6RZeoGXBOU7tZkE/s1769/41589_2024_1565_Fig1_HTML.webp" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1641" data-original-width="1769" height="297" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh6ehyWHxYYlsxRGMMN2ctBRAUsUV2Nd-z4l_pzWX_JxZDXPvbY70Nq_ajovsi0wpeGNOL-F0TFITkZXl2cTV_5P2HpHXO33gU1SKk5m6eKet70HAJMYqNalwtAvedD1nGTmw7DrozLCS7pASCSHtCjOjYkd-uN_j1ng1aak7X_t9nR6RZeoGXBOU7tZkE/s320/41589_2024_1565_Fig1_HTML.webp" width="320" /></a></div><br /><p><br /></p>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-45731492799359537122024-03-01T07:06:00.000-08:002024-03-01T07:06:26.841-08:00Chemical tools to expand the ligandable proteome: diversity-oriented synthesis-based photoreactive stereoprobes <p>Daisuke Ogasawara, David Konrad, Zher Yin Tan, Kimberly Carey, Jessica Luo, Sang Joon Won, Haoxin Li, Trever Carter, Kristen DeMeester, Evert Njomen, Stuart Schreiber, Ramnik Xavier, Bruno Melillo, Benjamin Cravatt</p><p>bioRxiv 2024.02.27.582206; </p><p>doi: <a href="https://doi.org/10.1101/2024.02.27.582206">https://doi.org/10.1101/2024.02.27.582206</a></p><div>Chemical proteomics enables the global assessment of small molecule-protein interactions in native biological systems and has emerged as a versatile approach for ligand discovery. The range of small molecules explored by chemical proteomics has, however, been limited. Here, we describe a diversity-oriented synthesis (DOS)-inspired library of stereochemically-defined compounds bearing diazirine and alkyne units for UV light-induced covalent modification and click chemistry enrichment of interacting proteins, respectively. We find that these photo-stereoprobes interact in a stereoselective manner with hundreds of proteins from various structural and functional classes in human cells and demonstrate that these interactions can form the basis for high-throughput screening-compatible nanoBRET assays. Integrated phenotypic analysis and chemical proteomics identified photo-stereoprobes that modulate autophagy by engaging the mitochondrial serine protease CLPP. Our findings show the utility of photo-stereoprobes for expanding the ligandable proteome, furnishing target engagement assays, and discovering and characterizing bioactive small molecules by cell-based screening.</div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgAQyG4hbVcJpnC8ZqN-vu0jRRcuOD5GkTufVikeSMiatEAVEBgt2BQnUFqw-BxPQGI5pN4q03UmGiFXQriXCnA3mOVzLOZ3HKJqgC36PLH_ceWn1Z5RA9Vz86fPL3HzuUKNyxYaAtsc3WvNjEJMdIC4iLbPwyNjbRoa94GZ1yecys1w84wpQowX8fWfEU/s1336/Screenshot%202024-03-01%20at%2010.05.57%20AM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1142" data-original-width="1336" height="274" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgAQyG4hbVcJpnC8ZqN-vu0jRRcuOD5GkTufVikeSMiatEAVEBgt2BQnUFqw-BxPQGI5pN4q03UmGiFXQriXCnA3mOVzLOZ3HKJqgC36PLH_ceWn1Z5RA9Vz86fPL3HzuUKNyxYaAtsc3WvNjEJMdIC4iLbPwyNjbRoa94GZ1yecys1w84wpQowX8fWfEU/s320/Screenshot%202024-03-01%20at%2010.05.57%20AM.png" width="320" /></a></div><br /><div><br /></div>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-21506220576768846242024-03-01T06:54:00.000-08:002024-03-01T06:54:01.372-08:00Formaldehyde regulates S-adenosylmethionine biosynthesis and one-carbon metabolism<p>VANHA N. PHAM, KEVIN J. BRUEMMER, JOEL D. W. TOH, EVA J. GE, LOGAN TENNEY, CARL C. WARD, FELIX A. DINGLER, CHRISTOPHER L. MILLINGTON, CARLOS A. GARCIA-PRIETO MIA C. PULOS-HOLMES NICHOLAS T. INGOLIA LUCAS B. PONTEL MANEL ESTELLER KETAN J. PATEL DANIEL K. NOMURA AND CHRISTOPHER J. CHANG </p><p><i>Science</i> <b>2023</b> 382, 6670</p><p>DOI: <a href="http://10.1126/science.abp9201">10.1126/science.abp9201</a></p><p>INTRODUCTION</p><p>One-carbon metabolism manages cellular carbon pools by detoxifying highly reactive carbon species, such as aldehydes, and diverting their carbon toward the biosynthesis of useful products, including amino acids and nucleotides. Formaldehyde (FA) is a major one-carbon unit derived from exogenous environmental exposure and endogenous sources and is quickly scavenged in the cell through enzymatic oxidation to formate and carbon dioxide and/or metabolized through the folate cycle. S-adenosylmethionine (SAM) serves as the primary cellular methyl donor and harbors one-carbon units in a stable and accessible form. The ability to decipher the biochemical interplay between toxic reactive carbon species and stable physiological carbon units is essential for understanding fundamentals of one-carbon metabolism across all kingdoms of life. Especially important is understanding how aberrant carbon imbalances are connected to human diseases such as cancer, liver diseases, and asthma. Although the chronic exposure of toxic aldehydes is correlated to disease states, biological mechanisms of aldehyde signaling and their relation to carbon metabolism remain underexplored.</p><p>RATIONALE</p><p>Owing to its highly electrophilic nature, we hypothesized that FA could act as a one-carbon signal sensed by privileged cysteine sites across the proteome. FA reacts with cysteines on synthetic peptides, and we designed an unbiased, proteome-wide profiling study to systematically identify FA-sensitive cysteine residues. This work builds a biochemical framework for understanding global FA reactivity as a selective posttranslational modification of target proteins and downstream regulatory effects of such modifications.</p><p>RESULTS</p><p>Activity-based protein profiling identified FA modification of privileged cysteine sites across the proteome, including several enzymes responsible for FA metabolism, one-carbon metabolism, and amino acid biosynthesis. We focused on biochemical characterization of a key Cys120 residue on the SAM-generating enzyme S-adenosylmethionine synthase isoform type-1 (MAT1A) that is proximal to the MAT1A active site. FA exposure resulted in inhibition of MAT1A activity in an isoform-specific manner, which led to decreased SAM production. Cellular models containing only the MAT1A isoform displayed a reciprocal decrease in SAM levels with increasing doses of FA exposure. Moreover, an Adh5–/– mouse model of chronic FA elevation also showed SAM deficiency accompanied by lower levels of methylation on select histone methyl sinks. The chronic FA model also resulted in a decrease in methylation of the Mat1a promoter region, resulting in increased MAT1A expression as a compensatory mechanism to maintain available carbon units. We deciphered a compensatory biochemical feedback cycle where FA-dependent SAM deficiency led to an increase in MAT1A expression through genetic and epigenetic mechanisms regulated by FA-dependent transcription factors and DNA promoter hypomethylation, respectively.</p><p>CONCLUSION</p><p>In contrast to the traditional view of FA as an indiscriminate electrophile and toxic metabolite, we show that FA is sensed by specific cysteine sites in the proteome to regulate one-carbon metabolism feedback cycles through SAM biosynthesis. FA reacts with a key cysteine residue on MAT1A to inhibit its activity, resulting in SAM depletion and downstream changes in histone and DNA methylation. Under normal homeostatic conditions, FA is quickly sequestered into the folate cycle for conservation of one-carbon units to maintain balanced SAM biosynthesis. In response to FA overload, reciprocal SAM depletion through isoform-specific MAT1A inhibition results in changes to cellular methylation potential, epigenetic dysregulation, and perturbations in one-carbon metabolism, which in turns leads to compensatory up-regulation of MAT1A expression. This work provides a starting point for further exploration of aldehydes as signaling agents and the nexus between one-carbon metabolism and one-carbon signaling.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEihiyMDL7QTTDiUUbyEdT6K-qdkNmgDVsAVW7kvKxq5E3FrvpUHH3_DAoJTubozDpwqpXoghrpsi0dsNKfKZpcwpVb4wnNMBQT5hSBTm-ZcftWipEWTpwrggoldSzfSLipD6S1hB62m8rKdqHNiKMM61GUbFFVjolv-r2X54cQk_1m_Ur_JJf_uT64Nn7U/s2825/science.abp9201-fa.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1693" data-original-width="2825" height="254" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEihiyMDL7QTTDiUUbyEdT6K-qdkNmgDVsAVW7kvKxq5E3FrvpUHH3_DAoJTubozDpwqpXoghrpsi0dsNKfKZpcwpVb4wnNMBQT5hSBTm-ZcftWipEWTpwrggoldSzfSLipD6S1hB62m8rKdqHNiKMM61GUbFFVjolv-r2X54cQk_1m_Ur_JJf_uT64Nn7U/w424-h254/science.abp9201-fa.jpg" width="424" /></a></div><br /><div><br /></div>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-22255709266216008242024-02-29T09:07:00.000-08:002024-02-29T09:07:46.047-08:00Molecular Bidents with Two Electrophilic Warheads as a New Pharmacological Modality<div style="background-color: white; box-sizing: border-box; font-family: Roboto, arial, sans-serif; font-size: 16px; outline: none;">Zhengnian Li, Jie Jiang, Scott B. Ficarro, Tyler S. Beyett, Ciric To, Isidoro Tavares, Yingde Zhu, Jiaqi Li, Michael J. Eck, Pasi A. Jänne, Jarrod A. Marto, Tinghu Zhang, Jianwei Che, and Nathanael S. Gray</div><div style="background-color: white; box-sizing: border-box; font-family: Roboto, arial, sans-serif; font-size: 16px; outline: none;"><cite style="box-sizing: border-box; outline: none;">ACS Central Science</cite> <span style="box-sizing: border-box; font-weight: bolder; outline: none;">2024</span></div><p><span style="background-color: white; font-family: Roboto, arial, sans-serif; font-size: 16px;">DOI: <a href="https://pubs.acs.org/doi/10.1021/acscentsci.3c01245">10.1021/acscentsci.3c01245</a></span></p><p>A systematic strategy to develop dual-warhead inhibitors is introduced to circumvent the limitations of conventional covalent inhibitors such as vulnerability to mutations of the corresponding nucleophilic residue. Currently, all FDA-approved covalent small molecules feature one electrophile, leaving open a facile route to acquired resistance. We conducted a systematic analysis of human proteins in the protein data bank to reveal ∼400 unique targets amendable to dual covalent inhibitors, which we term “molecular bidents”. We demonstrated this strategy by targeting two kinases: MKK7 and EGFR. The designed compounds, ZNL-8162 and ZNL-0056, are ATP-competitive inhibitors that form two covalent bonds with cysteines and retain potency against single cysteine mutants. Therefore, molecular bidents represent a new pharmacological modality with the potential for improved selectivity, potency, and drug resistance profile.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiejFQ6bhqd6xYY4YjoueJFpsadwTgqUekjbpUaOTHqrtHA-cAD5mmAZ-QMVhR8lUKx0Rmb7xjBXGMvUeuEr4PdmTUTbK8Nrs-ng3cY6uFcCm8rDySpqmj3wmBWFAxLa4pPwRwVaB6JdCyyfYqj0RYYz4nh2aDZNxrNVGag4ezblfXSzjhSd59zvXD0RpU/s1962/images_large_oc3c01245_0002.jpeg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1135" data-original-width="1962" height="283" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiejFQ6bhqd6xYY4YjoueJFpsadwTgqUekjbpUaOTHqrtHA-cAD5mmAZ-QMVhR8lUKx0Rmb7xjBXGMvUeuEr4PdmTUTbK8Nrs-ng3cY6uFcCm8rDySpqmj3wmBWFAxLa4pPwRwVaB6JdCyyfYqj0RYYz4nh2aDZNxrNVGag4ezblfXSzjhSd59zvXD0RpU/w489-h283/images_large_oc3c01245_0002.jpeg" width="489" /></a></div><br /><p></p>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-72906481954498509302024-02-27T23:06:00.000-08:002024-02-27T23:06:54.410-08:00Development of Oxadiazolone Activity-Based Probes Targeting FphE for Specific Detection of Staphylococcus aureus Infections<p><span style="background-color: white; font-family: Roboto, arial, sans-serif; font-size: 16px;">Jeyun Jo, Tulsi Upadhyay, Emily C. Woods, Ki Wan Park, Nichole J. Pedowitz, Joanna Jaworek-Korjakowska, Sijie Wang, Tulio A. Valdez, Matthias Fellner, and Matthew Bogyo</span></p><div style="background-color: white; box-sizing: border-box; font-family: Roboto, arial, sans-serif; font-size: 16px; outline: none;"><cite style="box-sizing: border-box; outline: none;">Journal of the American Chemical Society</cite> <span style="box-sizing: border-box; font-weight: bolder; outline: none;">2024</span></div><span style="background-color: white; font-family: Roboto, arial, sans-serif; font-size: 16px;">DOI: <a href="https://pubs.acs.org/doi/abs/10.1021/jacs.3c13974">10.1021/jacs.3c13974</a></span><div><span style="background-color: white; font-family: Roboto, arial, sans-serif; font-size: 16px;"><br /></span></div><div><span style="background-color: white; font-size: 16px;"><span style="font-family: Roboto, arial, sans-serif;">Staphylococcus aureus (S. aureus) is a major human pathogen that is responsible for a wide range of systemic infections. Since its propensity to form biofilms in vivo poses formidable challenges for both detection and treatment, tools that can be used to specifically image S. aureus biofilms are highly valuable for clinical management. Here, we describe the development of oxadiazolone-based activity-based probes to target the S. aureus-specific serine hydrolase FphE. Because this enzyme lacks homologues in other bacteria, it is an ideal target for selective imaging of S. aureus infections. Using X-ray crystallography, direct cell labeling, and mouse models of infection, we demonstrate that oxadiazolone-based probes enable specific labeling of S. aureus bacteria through the direct covalent modification of the FphE active site serine. These results demonstrate the utility of the oxadizolone electrophile for activity-based probes and validate FphE as a target for the development of imaging contrast agents for the rapid detection of S. aureus infections.</span></span></div><div><span style="background-color: white; font-size: 16px;"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg2a-doJMVyLqrVKFssdCZ2LM4cqxWe6GQzHQF-A8UAfElIwR_FSwQekdYPK06WM2ShMsSPVNeNQknpipnHuL3GrWOp9kLWAk3-WQ58o-Pftzmk9da13o1yAiXHdmsQlKkOmNR7alfcZ9VKtjnYJll456VfHEdcOUbIaezHk9dxEzvYrlaGnfomtbZdZIQ/s500/ja3c13974_0003.webp" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="332" data-original-width="500" height="212" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg2a-doJMVyLqrVKFssdCZ2LM4cqxWe6GQzHQF-A8UAfElIwR_FSwQekdYPK06WM2ShMsSPVNeNQknpipnHuL3GrWOp9kLWAk3-WQ58o-Pftzmk9da13o1yAiXHdmsQlKkOmNR7alfcZ9VKtjnYJll456VfHEdcOUbIaezHk9dxEzvYrlaGnfomtbZdZIQ/s320/ja3c13974_0003.webp" width="320" /></a></div><br /><span style="font-family: Roboto, arial, sans-serif;"><br /></span></span></div>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-1165357779558607592024-02-25T08:11:00.000-08:002024-02-25T08:11:32.611-08:00A covalent compound selectively inhibits RNA demethylase ALKBH5 rather than FTO<p><span class="italic" style="background-color: white; line-height: 1.875em;"><span style="background-color: transparent; font-size: 16px;"><span style="font-family: Source Sans Pro, source-sans-pro, museo_sans300, museo-sans, Arial, sans-serif;">Gan-Qiang Lai, Yali Li, Heping Zhu, Tao Zhang, Jing Gao, Hu Zhou and Cai-Guang Yang </span></span></span></p><p><span class="italic" style="background-color: white; line-height: 1.875em;"><span style="font-family: Source Sans Pro, source-sans-pro, museo_sans300, museo-sans, Arial, sans-serif;"><span style="font-size: 16px;"><i>RSC Chem. Biol.</i></span></span></span><span style="background-color: white; font-family: "Source Sans Pro", source-sans-pro, museo_sans300, museo-sans, Arial, sans-serif; font-size: 16px;">, <b>2024</b>, </span><span style="background-color: white; font-family: "Source Sans Pro", source-sans-pro, museo_sans300, museo-sans, Arial, sans-serif; font-size: 16px;">DOI: </span><a href="https://pubs.rsc.org/en/content/articlelanding/2024/cb/d3cb00230f">10.1039/D3CB00230F</a></p><p>N6-Methyladenosine (m6A) is the most prevalent mRNA modification and is required for gene regulation in eukaryotes. ALKBH5, an m6A demethylase, is a promising target, particularly for anticancer drug discovery. However, the development of selective and potent inhibitors of ALKBH5 rather than FTO remains challenging. Herein, we used a targeted covalent inhibition strategy and identified a covalent inhibitor, TD19, which selectively inhibits ALKBH5 compared with FTO demethylase in protein-based and tumor cell-based assays. TD19 irreversibly modifies the residues C100 and C267, preventing ALKBH5 from binding to m6A-containing RNA. Moreover, TD19 displays good anticancer efficacy in acute myeloid leukemia and glioblastoma multiforme cell lines. Thus, the ALKBH5 inhibitor developed in this study, which selectively targets ALKBH5 compared with FTO, can potentially be used as a probe for investigating the biological functions of RNA demethylase and as a lead compound in anticancer research.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiW3q7eZMxkSMu7_C9Bby4bvMH0x_4aXqtxTEOSk7hZHWiQKII98ZPuttcUHQfcXpgCduoNYu8fQk7qOzTKzxks7bP-R7bqhBOhpHAAK_p7d9xJz2VP4yNrzS0qGM00oEB2VmHO2OAPT8C9ffDAUZbVq0r1Dwuapn7PgNu84SfYGGVebli34xmVyk4A1CA/s980/d3cb00230f-s1_hi-res.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="375" data-original-width="980" height="152" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiW3q7eZMxkSMu7_C9Bby4bvMH0x_4aXqtxTEOSk7hZHWiQKII98ZPuttcUHQfcXpgCduoNYu8fQk7qOzTKzxks7bP-R7bqhBOhpHAAK_p7d9xJz2VP4yNrzS0qGM00oEB2VmHO2OAPT8C9ffDAUZbVq0r1Dwuapn7PgNu84SfYGGVebli34xmVyk4A1CA/w399-h152/d3cb00230f-s1_hi-res.gif" width="399" /></a></div><br /><p><br /></p>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-52969473232699741462024-02-18T21:26:00.000-08:002024-02-18T21:26:19.827-08:00Discovery of 6-Formylpyridyl Urea Derivatives as Potent Reversible-Covalent Fibroblast Growth Factor Receptor 4 Inhibitors with Improved Anti-Hepatocellular Carcinoma Activity<div style="background-color: white; box-sizing: border-box; font-family: Roboto, arial, sans-serif; font-size: 16px; outline: none;">Fang Yang, Qianmeng Lin, Xiaojuan Song, Huisi Huang, Xiaojuan Chen, Jianwen Tan, Yun Li, Yang Zhou, Zhengchao Tu, Hongli Du, Zhi-min Zhang, Raquel Ortega, Xiaojing Lin, Adam V. Patterson, Jeff B. Smaill, Yongheng Chen, and Xiaoyun Lu</div><div style="background-color: white; box-sizing: border-box; font-family: Roboto, arial, sans-serif; font-size: 16px; outline: none;"><cite style="box-sizing: border-box; outline: none;">Journal of Medicinal Chemistry</cite> <span style="box-sizing: border-box; font-weight: bolder; outline: none;">2024</span></div><p><span style="background-color: white; font-family: Roboto, arial, sans-serif; font-size: 16px;">DOI: <a href="https://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.3c01810">10.1021/acs.jmedchem.3c01810</a></span></p><p>Fibroblast growth factor receptor 4 (FGFR4) has been considered as a potential anticancer target due to FGF19/FGFR4 mediated aberrant signaling in hepatocellular carcinoma (HCC). Several FGFR4 inhibitors have been reported, but none have gained approval. Herein, a series of 5-formyl-pyrrolo[3,2-b]pyridine-3-carboxamides and a series of 6-formylpyridyl ureas were characterized as selective reversible-covalent FGFR4 inhibitors. The representative 6-formylpyridyl urea 8z exhibited excellent potency against FGFR4WT, FGFR4V550L, and FGFR4V550M with IC50 values of 16.3, 12.6, and 57.3 nM, respectively. It also potently suppressed proliferation of Ba/F3 cells driven by FGFR4WT, FGFR4V550L, and FGFR4V550M, and FGFR4-dependent Hep3B and Huh7 HCC cells, with IC50 values of 1.2, 13.5, 64.5, 15.0, and 20.4 nM, respectively. Furthermore, 8z displayed desirable microsomal stability and significant in vivo efficacy in the Huh7 HCC cancer xenograft model in nude mice. The study provides a promising new lead for anticancer drug discovery directed toward overcoming FGFR4 gatekeeper mutation mediated resistance in HCC patients.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgNw4LlwUf-Ia7FB8nrLH6PSbR3hojmNQ6HRkVlTQzvNh0Z48HhMs8wTP8BvZkT3SJhk1wj3ncPi-VdxZ6OOGOQQdVNfw80QBDp3lkETIc1pCN1NED7UKMTALY5G0LlhsiondSVdZSSdXgtcnnbAN2qxugdsCMkFoZM5eTJYmkOcWu_YpXkh8-dt3mt9Kw/s1434/images_large_jm3c01810_0019.jpeg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="558" data-original-width="1434" height="176" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgNw4LlwUf-Ia7FB8nrLH6PSbR3hojmNQ6HRkVlTQzvNh0Z48HhMs8wTP8BvZkT3SJhk1wj3ncPi-VdxZ6OOGOQQdVNfw80QBDp3lkETIc1pCN1NED7UKMTALY5G0LlhsiondSVdZSSdXgtcnnbAN2qxugdsCMkFoZM5eTJYmkOcWu_YpXkh8-dt3mt9Kw/w452-h176/images_large_jm3c01810_0019.jpeg" width="452" /></a></div><br /><p><br /></p>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-77100885332575572942024-02-16T12:23:00.000-08:002024-02-16T12:23:48.581-08:00Structure-based design of a phosphotyrosine-masked covalent ligand targeting the E3 ligase SOCS2<p><i style="background-color: white; box-sizing: inherit; color: #222222; font-family: -apple-system, "system-ui", "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 20px;"></i></p><p><span style="color: #222222; font-family: -apple-system, system-ui, Segoe UI, Roboto, Oxygen-Sans, Ubuntu, Cantarell, Helvetica Neue, sans-serif;">Sarath Ramachandran, Nikolai Makukhin, Kevin Haubrich, Manjula Nagala, Beth Forrester, Dylan M. Lynch, Ryan Casement, Andrea Testa, Elvira Bruno, Rosaria Gitto & Alessio Ciulli </span></p><p><i style="background-color: white; box-sizing: inherit; color: #222222; font-family: -apple-system, "system-ui", "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 20px;">Nat Commun</i><span style="background-color: white; color: #222222; font-family: -apple-system, "system-ui", "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 20px;"> </span><span style="background-color: white; box-sizing: inherit; color: #222222; font-family: -apple-system, "system-ui", "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 20px; font-weight: bolder;">14</span><span style="background-color: white; color: #222222; font-family: -apple-system, "system-ui", "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 20px;">, 6345 (2023). </span></p><p><span style="background-color: white; color: #222222; font-family: -apple-system, "system-ui", "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 20px;"><a href="https://doi.org/10.1038/s41467-023-41894-3">https://doi.org/10.1038/s41467-023-41894-3</a></span></p><p>The Src homology 2 (SH2) domain recognizes phosphotyrosine (pY) post translational modifications in partner proteins to trigger downstream signaling. Drug discovery efforts targeting the SH2 domains have long been stymied by the poor drug-like properties of phosphate and its mimetics. Here, we use structure-based design to target the SH2 domain of the E3 ligase suppressor of cytokine signaling 2 (SOCS2). Starting from the highly ligand-efficient pY amino acid, a fragment growing approach reveals covalent modification of Cys111 in a co-crystal structure, which we leverage to rationally design a cysteine-directed electrophilic covalent inhibitor MN551. We report the prodrug MN714 containing a pivaloyloxymethyl (POM) protecting group and evidence its cell permeability and capping group unmasking using cellular target engagement and in-cell 19F NMR spectroscopy. Covalent engagement at Cys111 competitively blocks recruitment of cellular SOCS2 protein to its native substrate. The qualified inhibitors of SOCS2 could find attractive applications as chemical probes to understand the biology of SOCS2 and its CRL5 complex, and as E3 ligase handles in proteolysis targeting chimera (PROTACs) to induce targeted protein degradation.</p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEh-28do7N-fw_glgt7y8bppabjocHtf8ncXfw0YiLfclHonNytXZO9nSfhUpQ_k7ImkM2JjdvMr1yfptUsrRQVZc5oAyNX1oyfPGmOKeCdlXu8evdgCKSwfxyzmFyFN-uUY29M31HAKdhtx3z9MgW0HiW6x-bFShIvBj6jwqD_tQsL-y9rxWQ6QKsVBV6k" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="1740" data-original-width="2001" height="297" src="https://blogger.googleusercontent.com/img/a/AVvXsEh-28do7N-fw_glgt7y8bppabjocHtf8ncXfw0YiLfclHonNytXZO9nSfhUpQ_k7ImkM2JjdvMr1yfptUsrRQVZc5oAyNX1oyfPGmOKeCdlXu8evdgCKSwfxyzmFyFN-uUY29M31HAKdhtx3z9MgW0HiW6x-bFShIvBj6jwqD_tQsL-y9rxWQ6QKsVBV6k=w342-h297" width="342" /></a></div><br /><br /><p></p>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-68351368406353891502024-02-15T20:13:00.000-08:002024-02-15T20:13:24.419-08:00Development of a Covalent Small Molecule Downmodulator for the Transcription Factor Brachyury<p>Davis H. Chase, Adrian M. Bebenek, Pengju Nie, Saul Jaime-Figueroa, Arseniy Butrin, Danielle A. Castro, John Hines, Brian M. Linhares, Craig M. Crews</p><p><i style="background-color: white; box-sizing: border-box; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;">Angew. Chem. Int. Ed.</i><span style="background-color: white; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;"> </span><span style="background-color: white; box-sizing: border-box; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px; font-weight: bolder;">2024</span><span style="background-color: white; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;">, e202316496.</span></p><p><a href="https://doi.org/10.1002/anie.202316496">https://doi.org/10.1002/anie.202316496</a></p><p>Brachyury is an oncogenic transcription factor whose overexpression drives chordoma growth. The downmodulation of brachyury in chordoma cells has demonstrated therapeutic potential, however, as a transcription factor it is classically deemed “undruggable”. Given that direct pharmacological intervention against brachyury has proven difficult, attempts at intervention have instead targeted upstream kinases. Recently, afatinib, an FDA-approved kinase inhibitor, has been shown to modulate brachyury levels in multiple chordoma cell lines. Herein, we use afatinib as a lead to undertake a structure-based drug design approach, aided by mass-spectrometry and x-ray crystallography, to develop DHC-156, a small molecule that more selectively binds brachyury and downmodulates it as potently as afatinib. We eliminated kinase-inhibition from this novel scaffold while demonstrating that DHC-156 induces the post-translational downmodulation of brachyury that results in an irreversible impairment of chordoma tumor cell growth. In doing so, we demonstrate the feasibility of direct brachyury modulation, which may further be developed into more potent tool compounds and therapies.</p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEhDpnN9g-ToLWXnhpLUuEACcMRPGDVAZ1b8jh_1R3F6EMRTqeULJZn2VKvF_h1ejQ-6Y7Nc_j5mjKHw5eBqEwXfvQt-sk4bAkMKFkagmNCqDKyPYJI4kr2OVO7yC0GGjhI3RAJLwseP3KiRE74juxVkUa1AaLzNimsOe-YptrzzTL58y9GsA5tRPTyYaLA" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="1104" data-original-width="1158" height="240" src="https://blogger.googleusercontent.com/img/a/AVvXsEhDpnN9g-ToLWXnhpLUuEACcMRPGDVAZ1b8jh_1R3F6EMRTqeULJZn2VKvF_h1ejQ-6Y7Nc_j5mjKHw5eBqEwXfvQt-sk4bAkMKFkagmNCqDKyPYJI4kr2OVO7yC0GGjhI3RAJLwseP3KiRE74juxVkUa1AaLzNimsOe-YptrzzTL58y9GsA5tRPTyYaLA" width="252" /></a></div><br /><br /><p></p>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-68168593158162869972024-02-07T08:51:00.000-08:002024-02-07T08:51:13.846-08:00Mixed Alkyl/Aryl Phosphonates Identify Metabolic Serine Hydrolases as Antimalarial Targets<p>John M. Bennett, Sunil K. Narwal, Stephanie Kabeche, Daniel Abegg, Fiona Hackett, Tomas Yeo, Veronica L. Li, Ryan K. Muir, Franco F. Faucher, Scott Lovell, Michael J. Blackman, Alexander Adibekian, Ellen Yeh, David A. Fidock, Matthew Bogyo</p><p><i>bioRxiv</i> 2024.01.11.575224; doi: <a href="https://doi.org/10.1101/2024.01.11.575224">https://doi.org/10.1101/2024.01.11.575224</a></p><div>Malaria, caused by Plasmodium falciparum, remains a significant health burden. A barrier for developing anti-malarial drugs is the ability of the parasite to rapidly generate resistance. We demonstrated that Salinipostin A (SalA), a natural product, kills parasites by inhibiting multiple lipid metabolizing serine hydrolases, a mechanism with a low propensity for resistance. Given the difficulty of employing natural products as therapeutic agents, we synthesized a library of lipidic mixed alkyl/aryl phosphonates as bioisosteres of SalA. Two constitutional isomers exhibited divergent anti-parasitic potencies which enabled identification of therapeutically relevant targets. We also confirm that this compound kills parasites through a mechanism that is distinct from both SalA and the pan-lipase inhibitor, Orlistat. Like SalA, our compound induces only weak resistance, attributable to mutations in a single protein involved in multidrug resistance. These data suggest that mixed alkyl/aryl phosphonates are a promising, synthetically tractable anti-malarials with a low-propensity to induce resistance.</div><div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEiEcbTD1GT1yUxVF3wM5pc322Rpu6k2Z5CAu6xR8gPdajKcKl0uKgbET5S8ni8bsEJACeLDVv0dJGgieJSJlwscYmQ9Ip4-6_QuoWGud5YFppgbTB0LRzJPStCh9fS9kIizpaV_UzyX1cTJ7j-l1AhI29EUF-YkEBWjRSCvrsR2AgGyGd0hbWxTkgKCKY0" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="1246" data-original-width="1070" height="240" src="https://blogger.googleusercontent.com/img/a/AVvXsEiEcbTD1GT1yUxVF3wM5pc322Rpu6k2Z5CAu6xR8gPdajKcKl0uKgbET5S8ni8bsEJACeLDVv0dJGgieJSJlwscYmQ9Ip4-6_QuoWGud5YFppgbTB0LRzJPStCh9fS9kIizpaV_UzyX1cTJ7j-l1AhI29EUF-YkEBWjRSCvrsR2AgGyGd0hbWxTkgKCKY0" width="206" /></a></div><br /><br /></div>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-50403077731966383452024-02-06T20:07:00.000-08:002024-02-06T20:07:49.500-08:00Landscape of In Silico Tools for Modeling Covalent Modification of Proteins: A Review on Computational Covalent Drug Discovery<div style="background-color: white; box-sizing: border-box; display: inline !important; font-family: Roboto, arial, sans-serif; font-size: 16px; outline: none; text-align: left;">Md Nazmul Hasan, Manisha Ray, and Arjun Saha</div><div style="background-color: white; box-sizing: border-box; font-family: Roboto, arial, sans-serif; font-size: 16px; outline: none; text-align: left;"><cite style="box-sizing: border-box; outline: none;">The Journal of Physical Chemistry B</cite> <span style="box-sizing: border-box; font-weight: bolder; outline: none;">2023</span> <em style="box-sizing: border-box; outline: none;">127</em> (45), 9663-9684</div><div style="background-color: white; box-sizing: border-box; font-family: Roboto, arial, sans-serif; font-size: 16px; outline: none; text-align: left;"><br /></div><span style="background-color: white; font-family: Roboto, arial, sans-serif; font-size: 16px;">DOI: <a href="https://doi.org/10.1021/acs.jpcb.3c04710">10.1021/acs.jpcb.3c04710</a></span><div><span style="background-color: white; font-family: Roboto, arial, sans-serif; font-size: 16px;"><br /></span></div><div><span style="background-color: white; font-size: 16px;"><span style="font-family: Roboto, arial, sans-serif;">Covalent drug discovery has been a challenging research area given the struggle of finding a sweet balance between selectivity and reactivity for these drugs, the lack of which often leads to off-target activities and hence undesirable side effects. However, there has been a resurgence in covalent drug design following the success of several covalent drugs such as boceprevir (2011), ibrutinib (2013), neratinib (2017), dacomitinib (2018), zanubrutinib (2019), and many others. Design of covalent drugs includes many crucial factors, where “evaluation of the binding affinity” and “a detailed mechanistic understanding on covalent inhibition” are at the top of the list. Well-defined experimental techniques are available to elucidate these factors; however, often they are expensive and/or time-consuming and hence not suitable for high throughput screens. Recent developments in in silico methods provide promise in this direction. In this report, we review a set of recent publications that focused on developing and/or implementing novel in silico techniques in “Computational Covalent Drug Discovery (CCDD)”. We also discuss the advantages and disadvantages of these approaches along with what improvements are required to make it a great tool in medicinal chemistry in the near future.</span></span></div><div><span style="background-color: white; font-size: 16px;"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg-VshUHVCVtAI0LPAXr3JgaMg9iH1kTL0x8ETqkF-rIAqQ5XuxBCNSMHcjSFncIq5voSL_AB49P3WT_psEajgbS41gPDU1UNmJIB_gWKnjCvgmYEiStR-LfZOs7_zQS6_X-OofB7ZV5zg-t7E1p_-DPiMZliaFJstxDpgcGVHYVJESQBJszJo3Xxanc7A/s956/images_large_jp3c04710_0018.jpeg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="562" data-original-width="956" height="226" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg-VshUHVCVtAI0LPAXr3JgaMg9iH1kTL0x8ETqkF-rIAqQ5XuxBCNSMHcjSFncIq5voSL_AB49P3WT_psEajgbS41gPDU1UNmJIB_gWKnjCvgmYEiStR-LfZOs7_zQS6_X-OofB7ZV5zg-t7E1p_-DPiMZliaFJstxDpgcGVHYVJESQBJszJo3Xxanc7A/w384-h226/images_large_jp3c04710_0018.jpeg" width="384" /></a></div><br /><span style="font-family: Roboto, arial, sans-serif;"><br /></span></span></div>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-17165586608576335152024-02-06T13:36:00.000-08:002024-02-06T13:36:33.968-08:00Discovery of lirafugratinib (RLY-4008), a highly selective irreversible small-molecule inhibitor of FGFR2<div class="csl-bib-body" style="line-height: 1.35;"><div class="csl-entry" style="clear: left;">Schönherr, H.; Ayaz, P.; Taylor, A. M.; Casaletto, J. B.; Touré, B. B.; Moustakas, D. T.; Hudson, B. M.; Valverde, R.; Zhao, S.; O’Hearn, P. J.; Foster, L.; Sharon, D. A.; Garfinkle, S.; Giordanetto, F.; Lescarbeau, A.; Kurukulasuriya, R.; Gerami-Moayed, N.; Maglic, D.; Bruderek, K.; Naik, G.; Gunaydin, H.; Mader, M. M.; Boezio, A. A.; McLean, T. H.; Chen, R.; Wang, Y.; Shaw, D. E.; Watters, J.; Bergstrom, D. A.</div><div class="csl-entry" style="clear: left;"><br /></div><div class="csl-entry" style="clear: left;"><i>Proceedings of the National Academy of Sciences </i><b>2024</b>, <i>121</i> (6), e2317756121. <a href="https://doi.org/10.1073/pnas.2317756121">https://doi.org/10.1073/pnas.2317756121</a>.</div></div><p>Fibroblast growth factor receptor (FGFR) kinase inhibitors have been shown to be effective in the treatment of intrahepatic cholangiocarcinoma and other advanced solid tumors harboring FGFR2 alterations, but the toxicity of these drugs frequently leads to dose reduction or interruption of treatment such that maximum efficacy cannot be achieved. The most common adverse effects are hyperphosphatemia caused by FGFR1 inhibition and diarrhea due to FGFR4 inhibition, as current therapies are not selective among the FGFRs. Designing selective inhibitors has proved difficult with conventional approaches because the orthosteric sites of FGFR family members are observed to be highly similar in X-ray structures. In this study, aided by analysis of protein dynamics, we designed a selective, covalent FGFR2 inhibitor. In a key initial step, analysis of long-timescale molecular dynamics simulations of the FGFR1 and FGFR2 kinase domains allowed us to identify differential motion in their P-loops, which are located adjacent to the orthosteric site. Using this insight, we were able to design orthosteric binders that selectively and covalently engage the P-loop of FGFR2. Our drug discovery efforts culminated in the development of lirafugratinib (RLY-4008), a covalent inhibitor of FGFR2 that shows substantial selectivity over FGFR1 (~250-fold) and FGFR4 (~5,000-fold) in vitro, causes tumor regression in multiple FGFR2-altered human xenograft models, and was recently demonstrated to be efficacious in the clinic at doses that do not induce clinically significant hyperphosphatemia or diarrhea.</p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEirPNNfoDQ0-9lLo34yRI2QmF1zmmuUKzs0WoXQVkbyonysm1bmfdGn6pvgFY_EBHc5PrV_SsDhMstcNuhid-FtHlG-AXlMCv5gUpEsGXfvlju00ehDgwCZU2ewJpWzik7WOeenSJkpTnxkzjCclGuiruzt6AzzA0p6No6H7vfkhzQlTP729BqeZmXKKvI" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="1948" data-original-width="1719" height="240" src="https://blogger.googleusercontent.com/img/a/AVvXsEirPNNfoDQ0-9lLo34yRI2QmF1zmmuUKzs0WoXQVkbyonysm1bmfdGn6pvgFY_EBHc5PrV_SsDhMstcNuhid-FtHlG-AXlMCv5gUpEsGXfvlju00ehDgwCZU2ewJpWzik7WOeenSJkpTnxkzjCclGuiruzt6AzzA0p6No6H7vfkhzQlTP729BqeZmXKKvI" width="212" /></a></div><br /><br /><p></p>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-20696464822544135502024-02-06T13:11:00.000-08:002024-02-06T13:11:39.316-08:00ZNL0325, a Pyrazolopyrimidine-Based Covalent Probe, Demonstrates an Alternative Binding Mode for Kinases<span style="background-color: white; font-family: Roboto, arial, sans-serif; font-size: 16px;">Zhengnian Li, Wenchao Lu, Tyler S. Beyett, Scott B. Ficarro, Jie Jiang, Jason Tse, Audrey Yong-Ju Kim, Jarrod A. Marto, Jianwei Che, Pasi A. Jänne, Michael J. Eck, Tinghu Zhang, and Nathanael S. Gray</span><div><span style="font-family: Roboto, arial, sans-serif;"><br /></span><cite style="background-color: white; box-sizing: border-box; font-family: Roboto, arial, sans-serif; font-size: 16px; outline: none;">Journal of Medicinal Chemistry</cite><span style="background-color: white; font-family: Roboto, arial, sans-serif; font-size: 16px;"> <b>2024-5</b></span><br /><span style="background-color: white; font-family: Roboto, arial, sans-serif; font-size: 16px;">DOI: <a href="https://pubs.acs.org/doi/full/10.1021/acs.jmedchem.3c01891">10.1021/acs.jmedchem.3c01891</a></span><br /><p style="text-align: left;">The pyrazolopyrimidine (PP) heterocycle is a versatile and widely deployed core scaffold for the development of kinase inhibitors. Typically, a 4-amino-substituted pyrazolopyrimidine binds in the ATP-binding pocket in a conformation analogous to the 6-aminopurine of ATP. Here, we report the discovery of ZNL0325 which exhibits a flipped binding mode where the C3 position is oriented toward the ribose binding pocket. ZNL0325 and its analogues feature an acrylamide side chain at the C3 position which is capable of forming a covalent bond with multiple kinases that possess a cysteine at the αD-1 position including BTK, EGFR, BLK, and JAK3. These findings suggest that the ability to form a covalent bond can override the preferred noncovalent binding conformation of the heterocyclic core and provides an opportunity to create structurally distinct covalent kinase inhibitors.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEiKowO5ijj7E8LIVDimTM0ikuNtHkf7NYO4HjvDf8gHgBNLzYOmFYxUZByttuX9OneRb8SN-Lcb8PKwno1C7KcwsHNs3fZ-sBe_Pq1qqeZa9z8Sr4Di_vLzqe-bkyLvme1a8wvxvRU__SgGAPhxnwCTABdNpTrrXEWIrvAsepqhdXyV0fr1GMoKZoFYi9c" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="891" data-original-width="1750" height="163" src="https://blogger.googleusercontent.com/img/a/AVvXsEiKowO5ijj7E8LIVDimTM0ikuNtHkf7NYO4HjvDf8gHgBNLzYOmFYxUZByttuX9OneRb8SN-Lcb8PKwno1C7KcwsHNs3fZ-sBe_Pq1qqeZa9z8Sr4Di_vLzqe-bkyLvme1a8wvxvRU__SgGAPhxnwCTABdNpTrrXEWIrvAsepqhdXyV0fr1GMoKZoFYi9c" width="320" /></a></div><br /><p></p></div>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-85861477327429385792024-02-02T14:02:00.000-08:002024-02-02T14:02:31.756-08:00Exploiting the Cullin E3 Ligase Adaptor Protein SKP1 for Targeted Protein Degradation<div style="background-color: white; box-sizing: border-box; font-family: Roboto, arial, sans-serif; font-size: 16px; outline: none;">Seong Ho Hong, Anand Divakaran, Akane Osa, Oscar W. Huang, Ingrid E. Wertz, and Daniel K. Nomura</div><div style="background-color: white; box-sizing: border-box; font-family: Roboto, arial, sans-serif; font-size: 16px; outline: none;"><cite style="box-sizing: border-box; outline: none;">ACS Chemical Biology</cite> <span style="box-sizing: border-box; font-weight: bolder; outline: none;">2024</span></div><div style="background-color: white; box-sizing: border-box; font-family: Roboto, arial, sans-serif; font-size: 16px; outline: none;"><span style="box-sizing: border-box; font-weight: bolder; outline: none;"><span style="font-weight: 400;">DOI: </span></span><a href="https://doi.org/10.1021/acschembio.3c00642" style="box-sizing: border-box; color: #95989a; font-size: 12px; outline: none 0px; text-decoration-line: none; transition: color 0.3s ease 0s;" title="DOI URL">https://doi.org/10.1021/acschembio.3c0064</a></div><div style="background-color: white; box-sizing: border-box; font-family: Roboto, arial, sans-serif; font-size: 16px; outline: none;"><br /></div><p>Targeted protein degradation with proteolysis targeting chimeras (PROTACs) is a powerful therapeutic modality for eliminating disease-causing proteins through targeted ubiquitination and proteasome-mediated degradation. Most PROTACs have exploited substrate receptors of Cullin-RING E3 ubiquitin ligases such as cereblon and VHL. Whether core, shared, and essential components of the Cullin-RING E3 ubiquitin ligase complex can be used for PROTAC applications remains less explored. Here, we discovered a cysteine-reactive covalent recruiter EN884 against the SKP1 adapter protein of the SKP1-CUL1-F-box containing the SCF complex. We further showed that this recruiter can be used in PROTAC applications to degrade neo-substrate proteins such as BRD4 and the androgen receptor in a SKP1- and proteasome-dependent manner. Our studies demonstrate that core and essential adapter proteins within the Cullin-RING E3 ubiquitin ligase complex can be exploited for targeted protein degradation applications and that covalent chemoproteomic strategies can enable recruiter discovery against these targets.</p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEisLayjOuEoKnM1Gi5kXsZUimgGAEG1cdXYYdRa2PYxNQ2-LnhOetYLsg38FzlnMNWHYUI8uP_PqwahQQQhr2vgOSLBPHRMq0tUzpIKyi02iWx6zoHWfIEbjRV2OrQ8YOBW64XC26TCkp3WORjmrzWolT5hNLu-__-WcRaoaEw8MSFu_oFCDrPndpaJvLI" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="491" data-original-width="996" height="197" src="https://blogger.googleusercontent.com/img/a/AVvXsEisLayjOuEoKnM1Gi5kXsZUimgGAEG1cdXYYdRa2PYxNQ2-LnhOetYLsg38FzlnMNWHYUI8uP_PqwahQQQhr2vgOSLBPHRMq0tUzpIKyi02iWx6zoHWfIEbjRV2OrQ8YOBW64XC26TCkp3WORjmrzWolT5hNLu-__-WcRaoaEw8MSFu_oFCDrPndpaJvLI=w398-h197" width="398" /></a></div><br /><br /><p></p>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-42345013590338136552024-02-01T21:41:00.000-08:002024-02-01T21:41:46.659-08:00Kinase-impaired BTK mutations are susceptible to clinical-stage BTK and IKZF1/3 degrader NX-2127<div class="d-inline" style="background-color: white; box-sizing: border-box; color: #595959; display: inline !important; font-family: roboto, sans-serif; font-size: 17.5px;"><ul class="list-inline d-inline" style="box-sizing: border-box; display: inline !important; list-style: none; margin: 0px; padding-left: 0px;" title="list of authors"><li class="list-inline-item" style="box-sizing: border-box; display: inline-block;"><span class="hlFld-ContribAuthor" style="box-sizing: border-box;">Skye Montoya <em style="box-sizing: border-box;">et al.</em></span></li> <br /></ul></div><span class="ml-1" style="background-color: white; box-sizing: border-box; color: #595959; font-family: roboto, sans-serif; font-size: 17.5px; margin-left: 0.25rem !important;"><i style="box-sizing: border-box;">Science</i></span><span class="ml-1" style="background-color: white; box-sizing: border-box; color: #595959; font-family: roboto, sans-serif; font-size: 17.5px; margin-left: 0.25rem !important;"><span style="box-sizing: border-box; font-weight: 900;">383</span>,</span><span class="ml-1" style="background-color: white; box-sizing: border-box; color: #595959; font-family: roboto, sans-serif; font-size: 17.5px; margin-left: 0.25rem !important;">eadi5798</span><span class="ml-1" style="background-color: white; box-sizing: border-box; color: #595959; font-family: roboto, sans-serif; font-size: 17.5px; margin-left: 0.25rem !important;">(2024).</span><div><p> DOI: <a href="http://doi.org/10.1126/science.adi5798">10.1126/science.adi5798</a></p><h2 property="name" style="box-sizing: border-box; color: #1a1a1a; font-family: var(--font-family-sans-serif); letter-spacing: 0.02em; line-height: 1.25; margin: 1rem 0px 1.5rem;"><span style="font-size: medium;">Structured Abstract</span></h2><section id="abs-sec-1" style="box-sizing: border-box; color: #333333; font-family: "PT Serif", serif;"><h3 style="box-sizing: border-box; color: #1a1a1a; font-family: var(--font-family-sans-serif); line-height: 1.25; margin: 1rem 0px;"><span style="font-size: medium;">INTRODUCTION</span></h3><div role="paragraph" style="box-sizing: border-box; margin: 1rem 0px 0px;"><span style="font-size: medium;">Bruton’s tyrosine kinase (BTK) is a nonreceptor kinase in the B cell receptor (BCR) signaling cascade critical for B cell survival. As such, chronic lymphocytic leukemia (CLL) and other B cell cancers are sensitive to inhibition of BTK. Covalent and noncovalent inhibitors of BTK have revolutionized the treatment of these cancers. Therefore, understanding mechanisms by which acquired mutations in BTK confer drug resistance and developing new therapies to overcome resistance are critically important.</span></div></section><section id="abs-sec-2" style="box-sizing: border-box; color: #333333; font-family: "PT Serif", serif;"><h3 style="box-sizing: border-box; color: #1a1a1a; font-family: var(--font-family-sans-serif); line-height: 1.25; margin: 1rem 0px;"><span style="font-size: medium;">RATIONALE</span></h3><div role="paragraph" style="box-sizing: border-box; margin: 1rem 0px 0px;"><span style="font-size: medium;">We recently discovered BTK mutations that confer resistance across covalent and noncovalent BTK inhibitors. In this study, we found that a group of these mutants impair BTK kinase activity despite still enabling downstream BCR signaling. We therefore set out to understand the nonenzymatic functions of BTK and explored targeted protein degradation to overcome the oncogenic scaffold function of mutant BTK. This effort included evaluation of BTK degradation in patients with CLL treated in a phase 1 clinical trial of NX-2127, a first-in-class BTK degrader (NCT04830137).</span></div></section><section id="abs-sec-3" style="box-sizing: border-box; color: #333333; font-family: "PT Serif", serif;"><h3 style="box-sizing: border-box; color: #1a1a1a; font-family: var(--font-family-sans-serif); line-height: 1.25; margin: 1rem 0px;"><span style="font-size: medium;">RESULTS</span></h3><div role="paragraph" style="box-sizing: border-box; margin: 1rem 0px 0px;"><span style="font-size: medium;">BTK enzymatic activity assays revealed that drug resistance mutations in BTK fall into two distinct groups: kinase proficient and kinase impaired. Immunoprecipitation mass spectrometry of kinase-impaired BTK L528W (Leu<span style="box-sizing: border-box; line-height: 0; position: relative; top: -0.5em; vertical-align: baseline;">528</span>→Trp) revealed a scaffold function of BTK with downstream signaling and survival dependent on surrogate kinases that bind to kinase-impaired BTK proteoforms. To target the nonenzymatic functions of BTK, we developed NX-2127, a heterobifunctional molecule that engages the ubiquitin-proteasome system to simultaneously bind both BTK and the cereblon E3 ubiquitin ligase complex, inducing polyubiquitination and proteasome-dependent degradation of IKZF1/3 and all recurrent drug-resistant forms of mutant BTK. The activity of NX-2127 on BTK degradation was further demonstrated in patients with CLL treated in a phase 1 clinical trial of NX-2127, where >80% BTK degradation was achieved and clinical responses were also seen in 79% of evaluable patients, independent of mutant BTK genotypes.</span></div></section><section id="abs-sec-4" style="box-sizing: border-box; color: #333333; font-family: "PT Serif", serif;"><h3 style="box-sizing: border-box; color: #1a1a1a; font-family: var(--font-family-sans-serif); line-height: 1.25; margin: 1rem 0px;"><span style="font-size: medium;">CONCLUSION</span></h3><div role="paragraph" style="box-sizing: border-box; margin: 1rem 0px 1.75rem;"><span style="font-size: medium;">We identified that BTK inhibitor resistance mutations fall into two distinct functional categories. Kinase-impaired BTK mutants disable BTK kinase activity while promoting physical interactions with other kinases to sustain downstream BCR signaling. This scaffold function of BTK was disrupted by NX-2127, a potent BTK degrader, which showed promising responses for patients with relapsed and refractory CLL, independently of mutant BTK functional category.</span></div><div role="paragraph" style="box-sizing: border-box; font-size: 22.5px; margin: 1rem 0px 1.75rem;"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEj0GvIQ8P5aLEX9XHVDGmAOC_0ZnwiYqiqJTxaHhYvGJLYrQ-cuFohS9ydA3iDlhL7OwQxOgesYjjydtyMgw1Tm7f_jy4kpa7yxCSN6bTtsnMS262cKnY-2UmtF_wSDEyRAZugyJwCCMe12GKj-8T4GTuZWK8dT9VMPfk5ditkDdkWyzIv67ZfGLrTuHcg" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="2777" data-original-width="2845" height="240" src="https://blogger.googleusercontent.com/img/a/AVvXsEj0GvIQ8P5aLEX9XHVDGmAOC_0ZnwiYqiqJTxaHhYvGJLYrQ-cuFohS9ydA3iDlhL7OwQxOgesYjjydtyMgw1Tm7f_jy4kpa7yxCSN6bTtsnMS262cKnY-2UmtF_wSDEyRAZugyJwCCMe12GKj-8T4GTuZWK8dT9VMPfk5ditkDdkWyzIv67ZfGLrTuHcg" width="246" /></a></div><br /><br /></div></section></div>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-5254804245626629442024-02-01T09:12:00.000-08:002024-02-01T09:12:08.669-08:00Location-agnostic site-specific protein bioconjugation via Baylis Hillman adducts<p><span style="background-color: white; color: #222222; font-family: -apple-system, "system-ui", "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 20px;">Mir, M.H., Parmar, S., Singh, C. </span><i style="background-color: white; box-sizing: inherit; color: #222222; font-family: -apple-system, "system-ui", "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 20px;">et al.</i></p><p><span style="background-color: white; color: #222222; font-family: -apple-system, "system-ui", "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 20px;"> </span><i style="background-color: white; box-sizing: inherit; color: #222222; font-family: -apple-system, "system-ui", "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 20px;">Nat Commun</i><span style="background-color: white; color: #222222; font-family: -apple-system, "system-ui", "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 20px;"> </span><span style="background-color: white; box-sizing: inherit; color: #222222; font-family: -apple-system, "system-ui", "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 20px; font-weight: bolder;">15</span><span style="background-color: white; color: #222222; font-family: -apple-system, "system-ui", "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 20px;">, 859 (2024). </span></p><p><span style="background-color: white; color: #222222; font-family: -apple-system, "system-ui", "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 20px;"><a href="https://doi.org/10.1038/s41467-024-45124-2">https://doi.org/10.1038/s41467-024-45124-2</a></span></p><div style="text-align: left;"><span style="background-color: white; color: #222222; font-family: Harding, Palatino, serif; font-size: 22.5px;">Proteins labelled site-specifically with small molecules are valuable assets for chemical biology and drug development. The unique reactivity profile of the 1,2-aminothiol moiety of </span><i style="background-color: white; box-sizing: inherit; color: #222222; font-family: Harding, Palatino, serif; font-size: 22.5px;">N</i><span style="background-color: white; color: #222222; font-family: Harding, Palatino, serif; font-size: 22.5px;">-terminal cysteines (</span><i style="background-color: white; box-sizing: inherit; color: #222222; font-family: Harding, Palatino, serif; font-size: 22.5px;">N</i><span style="background-color: white; color: #222222; font-family: Harding, Palatino, serif; font-size: 22.5px;">-Cys) of proteins renders it highly attractive for regioselective protein labelling. Herein, we report an ultrafast </span><i style="background-color: white; box-sizing: inherit; color: #222222; font-family: Harding, Palatino, serif; font-size: 22.5px;">Z</i><span style="background-color: white; color: #222222; font-family: Harding, Palatino, serif; font-size: 22.5px;">-selective reaction between isatin-derived Baylis Hillman adducts and 1,2-aminothiols to form a bis-heterocyclic scaffold, and employ it for stable protein bioconjugation under both in vitro and live-cell conditions. We refer to our protein bioconjugation technology as </span><u style="background-color: white; box-sizing: inherit; color: #222222; font-family: Harding, Palatino, serif; font-size: 22.5px;">B</u><span style="background-color: white; color: #222222; font-family: Harding, Palatino, serif; font-size: 22.5px;">aylis </span><u style="background-color: white; box-sizing: inherit; color: #222222; font-family: Harding, Palatino, serif; font-size: 22.5px;">H</u><span style="background-color: white; color: #222222; font-family: Harding, Palatino, serif; font-size: 22.5px;">illman </span><u style="background-color: white; box-sizing: inherit; color: #222222; font-family: Harding, Palatino, serif; font-size: 22.5px;">o</u><span style="background-color: white; color: #222222; font-family: Harding, Palatino, serif; font-size: 22.5px;">rchestrated </span><u style="background-color: white; box-sizing: inherit; color: #222222; font-family: Harding, Palatino, serif; font-size: 22.5px;">p</u><span style="background-color: white; color: #222222; font-family: Harding, Palatino, serif; font-size: 22.5px;">rotein </span><u style="background-color: white; box-sizing: inherit; color: #222222; font-family: Harding, Palatino, serif; font-size: 22.5px;">a</u><span style="background-color: white; color: #222222; font-family: Harding, Palatino, serif; font-size: 22.5px;">minothiol </span><u style="background-color: white; box-sizing: inherit; color: #222222; font-family: Harding, Palatino, serif; font-size: 22.5px;">l</u><span style="background-color: white; color: #222222; font-family: Harding, Palatino, serif; font-size: 22.5px;">abelling (BHoPAL). Furthermore, we report a lipoic acid ligase-based technology for introducing the 1,2-aminothiol moiety at any desired site within proteins, rendering BHoPAL location-agnostic (not limited to </span><i style="background-color: white; box-sizing: inherit; color: #222222; font-family: Harding, Palatino, serif; font-size: 22.5px;">N</i><span style="background-color: white; color: #222222; font-family: Harding, Palatino, serif; font-size: 22.5px;">-Cys). By using this approach in tandem with BHoPAL, we generate dually labelled protein bioconjugates appended with different labels at two distinct specific sites on a single protein molecule. Taken together, the protein bioconjugation toolkit that we disclose herein will contribute towards the generation of both mono and multi-labelled protein-small molecule bioconjugates for applications as diverse as biophysical assays, cellular imaging, and the production of therapeutic protein–drug conjugates. In addition to protein bioconjugation, the bis-heterocyclic scaffold we report herein will find applications in synthetic and medicinal chemistry.</span></div><p><span style="background-color: white; color: #222222; font-family: Harding, Palatino, serif; font-size: 22.5px;"></span></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEh-Hn6YAYDeK5Ij2U6AI_zx70CjkaCBo-ZYGgZQrxxebLuGcbo4R8V1rjLJaJX_OwHDo9xACnlfMtIx6QlqlcFGApifkJEAjoWw6yz-UOY7Z6HbO6m5MNrPKFb72z-tvzvaUaZ_TE8z6ipJ-PexCG2KVDPnCSyZs1SzVYwPXspBJodr2LCjAX_1S8YxSiE" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="1040" data-original-width="1941" height="252" src="https://blogger.googleusercontent.com/img/a/AVvXsEh-Hn6YAYDeK5Ij2U6AI_zx70CjkaCBo-ZYGgZQrxxebLuGcbo4R8V1rjLJaJX_OwHDo9xACnlfMtIx6QlqlcFGApifkJEAjoWw6yz-UOY7Z6HbO6m5MNrPKFb72z-tvzvaUaZ_TE8z6ipJ-PexCG2KVDPnCSyZs1SzVYwPXspBJodr2LCjAX_1S8YxSiE=w472-h252" width="472" /></a></div><br /><br /><p></p>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-52464728265313434192024-01-30T08:35:00.000-08:002024-01-30T08:35:03.723-08:00Peptide-Based Covalent Inhibitors Bearing Mild Electrophiles to Target a Conserved His Residue of the Bacterial Sliding Clamp<p> <span style="background-color: white; font-family: Roboto, arial, sans-serif; font-size: 16px;">Guillaume Compain, Clément Monsarrat, Julie Blagojevic, Karl Brillet, Philippe Dumas, Philippe Hammann, Lauriane Kuhn, Isabelle Martiel, Sylvain Engilberge, Vincent Oliéric, Philippe Wolff, Dominique Y. Burnouf, Jérôme Wagner, and Gilles Guichard</span></p><div style="background-color: white; box-sizing: border-box; font-family: Roboto, arial, sans-serif; font-size: 16px; outline: none;"><cite style="box-sizing: border-box; outline: none;">JACS Au</cite> <span style="box-sizing: border-box; font-weight: bolder; outline: none;">2024</span></div><span style="background-color: white; font-family: Roboto, arial, sans-serif; font-size: 16px;">DOI: <a href="https://pubs.acs.org/doi/10.1021/jacsau.3c00572">10.1021/jacsau.3c00572</a></span><div><span style="background-color: white; font-family: Roboto, arial, sans-serif; font-size: 16px;"><br /></span></div><div><span style="background-color: white; font-size: 16px;"><span style="font-family: Roboto, arial, sans-serif;">Peptide-based covalent inhibitors targeted to nucleophilic protein residues have recently emerged as new modalities to target protein–protein interactions (PPIs) as they may provide some benefits over more classic competitive inhibitors. Covalent inhibitors are generally targeted to cysteine, the most intrinsically reactive amino acid residue, and to lysine, which is more abundant at the surface of proteins but much less frequently to histidine. Herein, we report the structure-guided design of targeted covalent inhibitors (TCIs) able to bind covalently and selectively to the bacterial sliding clamp (SC), by reacting with a well-conserved histidine residue located on the edge of the peptide-binding pocket. SC is an essential component of the bacterial DNA replication machinery, identified as a promising target for the development of new antibacterial compounds. Thermodynamic and kinetic analyses of ligands bearing different mild electrophilic warheads confirmed the higher efficiency of the chloroacetamide compared to Michael acceptors. Two high-resolution X-ray structures of covalent inhibitor–SC adducts were obtained, revealing the canonical orientation of the ligand and details of covalent bond formation with histidine. Proteomic studies were consistent with a selective SC engagement by the chloroacetamide-based TCI. Finally, the TCI of SC was substantially more active than the parent noncovalent inhibitor in an in vitro SC-dependent DNA synthesis assay, validating the potential of the approach to design covalent inhibitors of protein–protein interactions targeted to histidine.</span></span></div><div><span style="background-color: white; font-size: 16px;"><span style="font-family: Roboto, arial, sans-serif;"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEiJBlcpVqmpiSVrjRjb41LSz53_1Tej48y7dXPWvAynouzuqoEKrBgGqsISIQKA3CL995VWehC749XPll1x_h2RI22ROOFtV9W2p_WPYRcq_GoXwxLXeM0C3JKFbdt293eifBrIDnmGzynlGAYl4r41nBNb0iJzLqXcPcJEYAJFao9TTA0sizITTFMIe5o" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="508" data-original-width="996" height="227" src="https://blogger.googleusercontent.com/img/a/AVvXsEiJBlcpVqmpiSVrjRjb41LSz53_1Tej48y7dXPWvAynouzuqoEKrBgGqsISIQKA3CL995VWehC749XPll1x_h2RI22ROOFtV9W2p_WPYRcq_GoXwxLXeM0C3JKFbdt293eifBrIDnmGzynlGAYl4r41nBNb0iJzLqXcPcJEYAJFao9TTA0sizITTFMIe5o=w447-h227" width="447" /></a></div><br /><br /></span></span></div>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-65463242337120950962024-01-29T20:59:00.000-08:002024-01-29T20:59:27.924-08:00Novel Covalent Probe Selectively Targeting Glutathione Peroxidase 4 In Vivo: Potential Applications in Pancreatic Cancer Therapy<div style="background-color: white; box-sizing: border-box; font-family: Roboto, arial, sans-serif; font-size: 16px; outline: none;">Zifeng Tang, Jie Li, Lijie Peng, Fang Xu, Yi Tan, Xiaoqiang He, Chengjun Zhu, Zhi-Min Zhang, Zhang Zhang, Pinghua Sun, Ke Ding, and Zhengqiu Li</div><div style="background-color: white; box-sizing: border-box; font-family: Roboto, arial, sans-serif; font-size: 16px; outline: none;"><cite style="box-sizing: border-box; outline: none;">Journal of Medicinal Chemistry</cite> <span style="box-sizing: border-box; font-weight: bolder; outline: none;">2024</span></div><p><span style="background-color: white; font-family: Roboto, arial, sans-serif; font-size: 16px;">DOI: <a href="https://pubs.acs.org/doi/10.1021/acs.jmedchem.3c01608">10.1021/acs.jmedchem.3c01608</a></span></p><p>Glutathione peroxidase 4 (GPX4) emerges as a promising target for the treatment of therapy-resistant cancer through ferroptosis. Thus, there is a broad interest in the development of GPX4 inhibitors. However, a majority of reported GPX4 inhibitors utilize chloroacetamide as a reactive electrophilic warhead, and the selectivity and pharmacokinetic properties still need to be improved. Herein, we developed a compound library based on a novel electrophilic warhead, the sulfonyl ynamide, and executed phenotypic screening against pancreatic cancer cell lines. Notably, one compound A16 exhibiting potent cell toxicity was identified. Further chemical proteomics investigations have demonstrated that A16 specifically targets GPX4 under both in situ and in vivo conditions, inducing ferroptosis. Importantly, A16 exhibited superior selectivity and potency compared to reported GPX4 inhibitors, ML210 and ML162. This provides the structural diversity of tool probes for unraveling the fundamental biology of GPX4 and exploring the therapeutic potential of pancreatic cancer via ferroptosis induction.</p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEirN5T20jEP3GSIbX4YZFz1FaArfkpSxCJnHAE85xdSLmhsfIpejTd-NmTqgwsXEmq4ToovSvxSsxFD5EeryXU2EuWFG5I8V5-6BHjeN_SwTn_0grANFpjSi-QwrPyU2zrd_6N7NdQMG-m8C5zFgxuzjnQJb93F5fLdWRNQRRB6t2phKM6wMG5w9MHljBY" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="220" data-original-width="996" height="71" src="https://blogger.googleusercontent.com/img/a/AVvXsEirN5T20jEP3GSIbX4YZFz1FaArfkpSxCJnHAE85xdSLmhsfIpejTd-NmTqgwsXEmq4ToovSvxSsxFD5EeryXU2EuWFG5I8V5-6BHjeN_SwTn_0grANFpjSi-QwrPyU2zrd_6N7NdQMG-m8C5zFgxuzjnQJb93F5fLdWRNQRRB6t2phKM6wMG5w9MHljBY" width="320" /></a></div><br /><br /><p></p>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-87530629253424006762024-01-29T08:56:00.000-08:002024-01-29T08:56:37.642-08:00Peptide–Drug Conjugates: An Emerging Direction for the Next Generation of Peptide Therapeutics<p> <span style="background-color: white; font-family: Roboto, arial, sans-serif; font-size: 16px;">Trevor T. Dean, Juliet Jelú-Reyes, A’Lester C. Allen, and Terry W. Moore</span></p><div style="background-color: white; box-sizing: border-box; font-family: Roboto, arial, sans-serif; font-size: 16px; outline: none;"><cite style="box-sizing: border-box; outline: none;">Journal of Medicinal Chemistry</cite> <span style="box-sizing: border-box; font-weight: bolder; outline: none;">2024</span></div><span style="background-color: white; font-family: Roboto, arial, sans-serif; font-size: 16px;">DOI: <a href="http://10.1021/acs.jmedchem.3c01835">10.1021/acs.jmedchem.3c01835</a></span><div><span style="font-family: Roboto, arial, sans-serif;"><span style="font-size: 16px;"><br /></span></span><div><span style="background-color: white; font-size: 16px;"><span style="font-family: Roboto, arial, sans-serif;">Building on recent advances in peptide science, medicinal chemists have developed a hybrid class of bioconjugates, called peptide–drug conjugates, that demonstrate improved efficacy compared to peptides and small molecules independently. In this Perspective, we discuss how the conjugation of synergistic peptides and small molecules can be used to overcome complex disease states and resistance mechanisms that have eluded contemporary therapies because of their multi-component activity. We highlight how peptide–drug conjugates display a multi-factor therapeutic mechanism similar to that of antibody–drug conjugates but also demonstrate improved therapeutic properties such as less-severe off-target effects and conjugation strategies with greater site-specificity. The many considerations that go into peptide–drug conjugate design and optimization, such as peptide/small-molecule pairing and chemo-selective chemistries, are discussed. We also examine several peptide–drug conjugate series that demonstrate notable activity toward complex disease states such as neurodegenerative disorders and inflammation, as well as viral and bacterial targets with established resistance mechanisms.</span></span></div></div><div><span style="background-color: white; font-size: 16px;"><span style="font-family: Roboto, arial, sans-serif;"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEhlLaam8uAX722267Qu3vOhPl2xs6ifpbF9bXxj3V68lTFVasxA9TgiUz9ttpXaUCXIqYISd6P8ncOi5NQLMO6sc0S0bI_VRTN11lxHzfymTiKCpONF6l0_xIt_rfg3mXPc5_6foIzDY0s-3D1gTHnqlIqJTFquWAXEMmcX9sf_0zRpY5qNPLi_bYSe9J8" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="1286" data-original-width="1323" height="240" src="https://blogger.googleusercontent.com/img/a/AVvXsEhlLaam8uAX722267Qu3vOhPl2xs6ifpbF9bXxj3V68lTFVasxA9TgiUz9ttpXaUCXIqYISd6P8ncOi5NQLMO6sc0S0bI_VRTN11lxHzfymTiKCpONF6l0_xIt_rfg3mXPc5_6foIzDY0s-3D1gTHnqlIqJTFquWAXEMmcX9sf_0zRpY5qNPLi_bYSe9J8" width="247" /></a></div><br /><br /></span></span></div>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-79878141317073735432024-01-28T17:30:00.000-08:002024-01-28T17:30:07.949-08:00Covalent Hits and Where to Find Them<p>Simon C.C. Lucas, J. Henry Blackwell, Sarah H. Hewitt, Hannah Semple, Benjamin C. Whitehurst, Hua Xu,</p><div>SLAS Discovery, 2024</div><p><span class="anchor-text" style="border-bottom: 2px solid rgb(235, 101, 0); box-sizing: border-box; margin: 0px; padding: 0px; transition: border-bottom-color 0.3s ease 0s;"><a href="https://doi.org/10.1016/j.slasd.2024.01.003">https://doi.org/10.1016/j.slasd.2024.01.003</a></span></p><p>Covalent hits for drug discovery campaigns are neither fantastic beasts nor mythical creatures, they can be routinely identified through electrophile-first screening campaigns using a suite of different techniques. These include biophysical and biochemical methods, cellular approaches, and DNA-encoded libraries. Employing best practice, however, is critical to success. The purpose of this review is to look at state of the art covalent hit identification, how to identify hits from a covalent library and how to select compounds for medicinal chemistry programmes.</p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEiivBys3r_1GNcedZSx05aIr9AJqLGtDN4LjDRo0fygdwVtjohSKKR4IPMMuuR_ts9QCHA4KWBMdIvG8sYcYkswNQR6mj-4GYHVnULuAhWjSm--Bcis8Pw5715FvrAKlATg0x5bbLwdbk6whM_XGm1i7bnQIA0eVSq3e0fnZw-faGbAyA6Co00vkvJZOAE" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="392" data-original-width="715" height="175" src="https://blogger.googleusercontent.com/img/a/AVvXsEiivBys3r_1GNcedZSx05aIr9AJqLGtDN4LjDRo0fygdwVtjohSKKR4IPMMuuR_ts9QCHA4KWBMdIvG8sYcYkswNQR6mj-4GYHVnULuAhWjSm--Bcis8Pw5715FvrAKlATg0x5bbLwdbk6whM_XGm1i7bnQIA0eVSq3e0fnZw-faGbAyA6Co00vkvJZOAE" width="320" /></a></div><br /><br /><p></p>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-35770838902326742692024-01-27T21:42:00.000-08:002024-01-27T21:42:04.486-08:00Phenotypic screening of covalent compound libraries identifies chloromethyl ketone antibiotics and MiaA as a new target<div class="highwire-cite-authors" style="-webkit-font-smoothing: antialiased; border: 0px; color: #333333; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-size: 1.05rem; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: 1.25; margin: 5px 0px 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="highwire-citation-authors" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-size: 1.05rem; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="highwire-citation-author first" data-delta="0" style="-webkit-font-smoothing: antialiased; border: 0px; font: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Yizhen</span> <span class="nlm-surname" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Jin</span></span>, <span class="highwire-citation-author" data-delta="1" style="-webkit-font-smoothing: antialiased; border: 0px; font: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Sadhan</span> <span class="nlm-surname" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Jana</span></span>, <span class="highwire-citation-author" data-delta="2" style="-webkit-font-smoothing: antialiased; border: 0px; font: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Mikail E.</span> <span class="nlm-surname" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Abbasov</span></span>, <span class="highwire-citation-author" data-delta="3" style="-webkit-font-smoothing: antialiased; border: 0px; font: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Hening</span> <span class="nlm-surname" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Lin</span></span></span></div><div class="highwire-cite-metadata" style="-webkit-font-smoothing: antialiased; border: 0px; color: #333333; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-size: 0.82rem; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: 1.25; margin: 5px 0px 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="highwire-cite-metadata-journal highwire-cite-metadata" style="-webkit-font-smoothing: antialiased; background-color: whitesmoke; border: 0px; font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-size: 1.05rem; font-stretch: inherit; font-variant-alternates: inherit; font-variant-east-asian: inherit; font-variant-numeric: inherit; font-variant-position: inherit; font-variation-settings: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">bioRxiv </span><span class="highwire-cite-metadata-pages highwire-cite-metadata" style="-webkit-font-smoothing: antialiased; background-color: whitesmoke; border: 0px; font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-size: 1.05rem; font-stretch: inherit; font-variant-alternates: inherit; font-variant-east-asian: inherit; font-variant-numeric: inherit; font-variant-position: inherit; font-variation-settings: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">2024.01.22.576576; </span></div><div class="highwire-cite-metadata" style="-webkit-font-smoothing: antialiased; border: 0px; color: #333333; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-size: 0.82rem; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: 1.25; margin: 5px 0px 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="highwire-cite-metadata-doi highwire-cite-metadata" style="-webkit-font-smoothing: antialiased; background-color: whitesmoke; border: 0px; font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-size: 1.05rem; font-stretch: inherit; font-variant-alternates: inherit; font-variant-east-asian: inherit; font-variant-numeric: inherit; font-variant-position: inherit; font-variation-settings: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="doi_label" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-size: 1.05rem; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">doi:</span> <a href="https://doi.org/10.1101/2024.01.22.576576">https://doi.org/10.1101/2024.01.22.576576</a></span></div><p>The emerging antibiotic resistance requires the development of new antibiotics working on novel bacterial targets. Here, we reported an antibiotic discovery workflow by combining the cysteine-reactive compound library phenotypic screening with activity-based protein profiling, which enables the rapid identification of lead compounds as well as new druggable targets in pathogens. Compounds featuring chloromethyl ketone scaffolds exhibited a notably high hit rate against both gram-negative and gram-positive bacterial strains, but not the more commonly used warheads such as acrylamide or chloroacetamide. Target identification of the lead compound, 10-F05, revealed that its primary targets in S. flexneri are FabH Cys112 and MiaA Cys273. We validated the target relevance through biochemical and genetic interactions. Mechanistic studies revealed modification of MiaA by 10-F05 impair substrate tRNA binding, leading to decreased bacterial stress resistance and virulence. Our findings underscore chloromethyl ketone as a novel antibacterial warhead in covalent antibiotic design. The study showcases that combining covalent compound library phenotypic screening with chemoproteomics is an efficient way to identify new drug targets as well as lead compounds, with the potential to open new research directions in drug discovery and chemical biology.</p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEjba5QJMxHNHD-OEagbDAHU7vnUwu2Tvz5QnyQ-JEJe4JvR706RyZ_Qv-cc_fy4z9Hl5_yjgvE7tpAKx4KBfy0hzGdR2Y5b2A1KSDRUIO6TvLIaJLRUkoU3WlS3ALS_0vz9JR8JPIR3Rz7PWvDZPTYXHWECYdf6-PGNEGufqY2tlraJqiAInQREWbbmTyg" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="772" data-original-width="1280" height="193" src="https://blogger.googleusercontent.com/img/a/AVvXsEjba5QJMxHNHD-OEagbDAHU7vnUwu2Tvz5QnyQ-JEJe4JvR706RyZ_Qv-cc_fy4z9Hl5_yjgvE7tpAKx4KBfy0hzGdR2Y5b2A1KSDRUIO6TvLIaJLRUkoU3WlS3ALS_0vz9JR8JPIR3Rz7PWvDZPTYXHWECYdf6-PGNEGufqY2tlraJqiAInQREWbbmTyg" width="320" /></a></div><br /><br /><p></p>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-31151460211716352024-01-25T08:23:00.000-08:002024-01-25T08:23:42.843-08:00Global Reactivity Profiling of the Catalytic Lysine in Human Kinome for Covalent Inhibitor Development<p><span class="author" style="background-color: white; box-sizing: border-box; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;">Guanghui Tang</span><span style="background-color: white; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;">, </span><span class="author" style="background-color: white; box-sizing: border-box; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;"><text style="box-sizing: border-box;"></text>Wei Wang</span><span style="background-color: white; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;">, </span><span class="author" style="background-color: white; box-sizing: border-box; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;"><text style="box-sizing: border-box;"></text>Chengjun Zhu</span><span style="background-color: white; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;">, </span><span class="author" style="background-color: white; box-sizing: border-box; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;"><text style="box-sizing: border-box;"></text>Huisi Huang</span><span style="background-color: white; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;">, </span><span class="author" style="background-color: white; box-sizing: border-box; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;"><text style="box-sizing: border-box;"></text>Peng Chen</span><span style="background-color: white; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;">, </span><span class="author" style="background-color: white; box-sizing: border-box; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;"><text style="box-sizing: border-box;"></text>Xuan Wang</span><span style="background-color: white; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;">, </span><span class="author" style="background-color: white; box-sizing: border-box; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;"><text style="box-sizing: border-box;"></text>Manyi Xu</span><span style="background-color: white; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;">, </span><span class="author" style="background-color: white; box-sizing: border-box; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;"><text style="box-sizing: border-box;"></text>Jie Sun</span><span style="background-color: white; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;">, </span><span class="author" style="background-color: white; box-sizing: border-box; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;"><text style="box-sizing: border-box;"></text>Chong-Jing Zhang</span><span style="background-color: white; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;">, </span><span class="author" style="background-color: white; box-sizing: border-box; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;"><text style="box-sizing: border-box;"></text>Qicai Xiao</span><span style="background-color: white; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;">, </span><span class="author" style="background-color: white; box-sizing: border-box; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;"><text style="box-sizing: border-box;"></text>Liqian Gao</span><span style="background-color: white; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;">, </span><span class="author" style="background-color: white; box-sizing: border-box; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;"><text style="box-sizing: border-box;"></text>Zhi-Min Zhang</span><span style="background-color: white; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;">, </span><span class="author" style="background-color: white; box-sizing: border-box; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;"><text style="box-sizing: border-box;"></text>Shao Q. Yao</span><span style="background-color: white; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;">, </span></p><p><i style="background-color: white; box-sizing: border-box; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;">Angew. Chem. Int. Ed.</i><span style="background-color: white; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;"> </span><span style="background-color: white; box-sizing: border-box; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px; font-weight: bolder;">2024</span><span style="background-color: white; color: #1c1d1e; font-family: "Open Sans", icomoon, sans-serif; font-size: 17.5px;">, e202316394.</span></p><p><span style="background-color: white; font-size: 17.5px;"><span style="color: #1c1d1e; font-family: Open Sans, icomoon, sans-serif;"><a href="https://doi.org/10.1002/anie.202316394">https://doi.org/10.1002/anie.202316394</a></span></span></p><p><span style="background-color: white; font-family: "Open Sans", icomoon, sans-serif; font-size: 20px;">Advances in targeted covalent inhibitors (TCIs) have been made by using lysine-reactive chemistries. Few aminophiles possessing balanced reactivity/stability for the development of cell-active TCIs are however available. We report herein lysine-reactive activity-based probes (ABPs; 2-14) based on the chemistry of aryl fluorosulfates (ArOSO2F) capable of global reactivity profiling of the catalytic lysine in human kinome from mammalian cells. We concurrently developed reversible covalent ABPs (15/16) by installing salicylaldehydes (SA) onto a promiscuous kinase-binding scaffold. The stability and amine reactivity of these probes exhibited a broad range of tunability. X-ray crystallography and mass spectrometry (MS) confirmed the successful covalent engagement between ArOSO2F on 9 and the catalytic lysine of SRC kinase. Chemoproteomic studies enabled the profiling of >300 endogenous kinases, thus providing a global landscape of ligandable catalytic lysines of the kinome. By further introducing these aminophiles into VX-680 (a noncovalent inhibitor of AURKA kinase), we generated novel lysine-reactive TCIs that exhibited excellent in vitro potency and reasonable cellular activities with prolonged residence time. Our work serves as a general guide for the development of lysine-reactive ArOSO2F-based TCIs.</span></p><p><span style="background-color: white; font-size: 17.5px;"><span style="color: #1c1d1e; font-family: Open Sans, icomoon, sans-serif;"></span></span></p><div class="separator" style="clear: both; text-align: center;"><span style="color: #1c1d1e; font-family: Open Sans, icomoon, sans-serif;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEgt42-g4UF21ZdjQJe9zN0_YKAv7PTAXuQDRvmJAM5AL_58h1UNkxY_sVZORTg8fE1tSA-MtEEb_PcA4NpRq2LYGqCx6b3l4e7fVs9eDTv2Ug6AXD1969pCQkyPBpTSptM3bTY1jncGO6bAQglEcpLJBw_OEKQOMtTqk7gJ7iljEhiSBuEc4HsPXd2_2zE" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="1258" data-original-width="2256" height="178" src="https://blogger.googleusercontent.com/img/a/AVvXsEgt42-g4UF21ZdjQJe9zN0_YKAv7PTAXuQDRvmJAM5AL_58h1UNkxY_sVZORTg8fE1tSA-MtEEb_PcA4NpRq2LYGqCx6b3l4e7fVs9eDTv2Ug6AXD1969pCQkyPBpTSptM3bTY1jncGO6bAQglEcpLJBw_OEKQOMtTqk7gJ7iljEhiSBuEc4HsPXd2_2zE" width="320" /></a></span></div><span style="color: #1c1d1e; font-family: Open Sans, icomoon, sans-serif;"><br /><br /></span><p></p>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-25138953106084310822024-01-24T20:56:00.000-08:002024-01-24T20:56:08.842-08:00Silicon-Containing Thiol-Specific Bioconjugating Reagent<p>Zhenguo Zhang, Lanyang Li, Hailun Xu, Chi-Lik Ken Lee, Zhenhua Jia, and Teck-Peng Loh</p><p><i>Journal of the American Chemical Society </i>2024 146 (3), 1776-1782</p><p>DOI: <a href="http://10.1021/jacs.3c12050">10.1021/jacs.3c12050</a></p><p>A new bioconjugation reagent containing silicon has been developed for the selective reaction with thiols. The inclusion of silicon significantly improves chemoselectivity and suppresses retro processes, thereby exceeding the capabilities of traditional reagents. The method is versatile and compatible with a broad range of thiols and unsaturated carbonyl compounds and yields moderate to high results. These reactions can be conducted under biocompatible conditions, thereby making them suitable for protein bioconjugation. The resulting conjugates display good stability in the presence of various biomolecules, which suggests their potential application for the synthesis of antibody–drug conjugates. Furthermore, the presence of a silicon moiety within the conjugated products opens up new avenues for drug release and bridging inorganics with other disciplines. This new class of silicon-containing thiol-specific bioconjugation reagents has significant implications for researchers working in bioanalytical science and medicinal chemistry and leads to innovative opportunities for advancing the field of bioconjugation research and medicinal chemistry.</p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEgdwQHuH51HbGErAy2PZ8UDSrqRFX2fPtzp-uqwlduwWadjzYeRe2rFvEWRPJVcXDnuviZBa6yuctOU-GDZHI3J8904dA__7NqixEd1gL28Agh9COKT9l0DWJ_go1Sqgsu4C3s3LlEOv63ZDPW0-iKqZXTeb_aiY_Cj8x1lmVYQimXlZr08BT1REx-PGX8" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="532" data-original-width="988" height="172" src="https://blogger.googleusercontent.com/img/a/AVvXsEgdwQHuH51HbGErAy2PZ8UDSrqRFX2fPtzp-uqwlduwWadjzYeRe2rFvEWRPJVcXDnuviZBa6yuctOU-GDZHI3J8904dA__7NqixEd1gL28Agh9COKT9l0DWJ_go1Sqgsu4C3s3LlEOv63ZDPW0-iKqZXTeb_aiY_Cj8x1lmVYQimXlZr08BT1REx-PGX8" width="320" /></a></div><br /><br /><p></p>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.comtag:blogger.com,1999:blog-7346136966110380118.post-11714356055559033572024-01-20T17:56:00.000-08:002024-01-20T17:56:32.315-08:00Expanding the ligandable proteome by paralog hopping with covalent probes<div class="highwire-cite-authors" style="-webkit-font-smoothing: antialiased; border: 0px; color: #333333; font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-variant-alternates: inherit; font-variant-east-asian: inherit; font-variant-numeric: inherit; font-variant-position: inherit; font-variation-settings: inherit; line-height: 1.25; margin: 5px 0px 0px; outline: 0px; padding: 0px; text-align: left; vertical-align: baseline;"><span class="highwire-citation-authors" style="-webkit-font-smoothing: antialiased; background-color: white; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="highwire-citation-author first" data-delta="0" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Yuanjin</span> <span class="nlm-surname" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Zhang</span></span>, <span class="highwire-citation-author" data-delta="1" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Zhonglin</span> <span class="nlm-surname" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Liu</span></span>, <span class="highwire-citation-author" data-delta="2" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Marsha</span> <span class="nlm-surname" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Hirschi</span></span>, <span class="highwire-citation-author" data-delta="3" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Oleg</span> <span class="nlm-surname" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Brodsky</span></span>, <span class="highwire-citation-author" data-delta="4" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Eric</span> <span class="nlm-surname" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Johnson</span></span>, <span class="highwire-citation-author" data-delta="5" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Sang Joon</span> <span class="nlm-surname" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Won</span></span>, <span class="highwire-citation-author" data-delta="6" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Asako</span> <span class="nlm-surname" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Nagata</span></span>, <span class="highwire-citation-author" data-delta="7" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Matthew D</span> <span class="nlm-surname" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Petroski</span></span>, <span class="highwire-citation-author" data-delta="8" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Jaimeen D</span> <span class="nlm-surname" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Majmudar</span></span>, <span class="highwire-citation-author" data-delta="9" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Sherry</span> <span class="nlm-surname" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Niessen</span></span>, <span class="highwire-citation-author" data-delta="10" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Todd</span> <span class="nlm-surname" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">VanArsdale</span></span>, <span class="highwire-citation-author" data-delta="11" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Adam M</span> <span class="nlm-surname" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Gilbert</span></span>, <span class="highwire-citation-author" data-delta="12" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Matthew M</span> <span class="nlm-surname" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Hayward</span></span>, <span class="highwire-citation-author" data-delta="13" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Al E</span> <span class="nlm-surname" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Stewart</span></span>, <span class="highwire-citation-author" data-delta="14" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Andrew R</span> <span class="nlm-surname" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Nager</span></span>, <span class="highwire-citation-author" data-delta="15" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Bruno</span> <span class="nlm-surname" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Melillo</span></span>, <span class="highwire-citation-author" data-delta="16" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Benjamin F</span> <span class="nlm-surname" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: GillSansRegular, "Gill Sans MT", "Gill Sans", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Cravatt</span></span></span></div><div class="highwire-cite-metadata" style="-webkit-font-smoothing: antialiased; border: 0px; color: #333333; font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-variant-alternates: inherit; font-variant-east-asian: inherit; font-variant-numeric: inherit; font-variant-position: inherit; font-variation-settings: inherit; line-height: 1.25; margin: 5px 0px 0px; outline: 0px; padding: 0px; text-align: left; vertical-align: baseline;"><span style="background-color: white;"><span class="highwire-cite-metadata-journal highwire-cite-metadata" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">bioRxiv </span><span class="highwire-cite-metadata-pages highwire-cite-metadata" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">2024.01.18.576274; </span></span></div><div class="highwire-cite-metadata" style="-webkit-font-smoothing: antialiased; border: 0px; color: #333333; font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-variant-alternates: inherit; font-variant-east-asian: inherit; font-variant-numeric: inherit; font-variant-position: inherit; font-variation-settings: inherit; line-height: 1.25; margin: 5px 0px 0px; outline: 0px; padding: 0px; text-align: left; vertical-align: baseline;"><span class="highwire-cite-metadata-doi highwire-cite-metadata" style="-webkit-font-smoothing: antialiased; background-color: white; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="doi_label" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-feature-settings: inherit; font-kerning: inherit; font-optical-sizing: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-variation-settings: inherit; font-weight: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">doi:</span> <a href="https://doi.org/10.1101/2024.01.18.576274">https://doi.org/10.1101/2024.01.18.576274</a></span></div><p><span style="background-color: white; color: #191919; font-family: "Lucida Sans", Helvetica, Arial, sans-serif;">More than half of the ~20,000 protein-encoding human genes have at least one paralog. Chemical proteomics has uncovered many electrophile-sensitive cysteines that are exclusive to a subset of paralogous proteins. Here, we explore whether such covalent compound-cysteine interactions can be used to discover ligandable pockets in paralogs that lack the cysteine. Leveraging the covalent ligandability of C109 in the cyclin CCNE2, we mutated the corresponding residue in paralog CCNE1 to cysteine (N112C) and found through activity-based protein profiling (ABPP) that this mutant reacts stereoselectively and site-specifically with tryptoline acrylamides. We then converted the tryptoline acrylamide-N112C-CCNE1 interaction into a NanoBRET-ABPP assay capable of identifying compounds that reversibly inhibit both N112C- and WT-CCNE1:CDK2 complexes. X-ray crystallography revealed a cryptic allosteric pocket at the CCNE1:CDK2 interface adjacent to N112 that binds the reversible inhibitors. Our findings thus provide a roadmap for leveraging electrophile-cysteine interactions to extend the ligandability of the proteome beyond covalent chemistry.</span></p><p><span style="background-color: white; color: #191919; font-family: "Lucida Sans", Helvetica, Arial, sans-serif;"></span></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEhgQ3ywat_6tRygc_3hV_ANQjgrlAtm3wOAT2ueY7i0RpAIbponxkhe7tJSzL0xdHj6cdCc43WI1KF8atjmSe5gGcovZkLTh5LaVNcnMaTYOuETRfih0MVTtWcQQHhiSzYMNn28JCXc55qwvu1NBiNZD-J7xsdBtQKojovSwni_ZwVOpdS2X0sh3OWyuNs" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="748" data-original-width="1302" height="184" src="https://blogger.googleusercontent.com/img/a/AVvXsEhgQ3ywat_6tRygc_3hV_ANQjgrlAtm3wOAT2ueY7i0RpAIbponxkhe7tJSzL0xdHj6cdCc43WI1KF8atjmSe5gGcovZkLTh5LaVNcnMaTYOuETRfih0MVTtWcQQHhiSzYMNn28JCXc55qwvu1NBiNZD-J7xsdBtQKojovSwni_ZwVOpdS2X0sh3OWyuNs" width="320" /></a></div><br /><br /><p></p>CNRhttp://www.blogger.com/profile/10393580353823043051noreply@blogger.com