ACS Chemical Biology最新文献_第4页

Mapping the FGF2 Interactome Identifies a Functional Proteoglycan Coreceptor.

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2024-12-20 DOI: 10.1021/acschembio.4c00475

Meg Critcher, Jia Meng Pang, Mia L Huang

引用次数: 0

γ-Secretase Cleaves Bifunctional Fatty Acid-Conjugated Small Molecules with Amide Bonds in Mammalian Cells. γ-分泌酶在哺乳动物细胞中分解带有酰胺键的双功能脂肪酸共轭小分子

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2024-12-20 Epub Date: 2024-11-20 DOI: 10.1021/acschembio.4c00432

Kai Tahara, Akinobu Nakamura, Xiaotong Wang, Keishi Mitamura, Yuki Ichihashi, Keiko Kano, Emi Mishiro-Sato, Kazuhiro Aoki, Yasuteru Urano, Toru Komatsu, Shinya Tsukiji

{"title":"γ-Secretase Cleaves Bifunctional Fatty Acid-Conjugated Small Molecules with Amide Bonds in Mammalian Cells.","authors":"Kai Tahara, Akinobu Nakamura, Xiaotong Wang, Keishi Mitamura, Yuki Ichihashi, Keiko Kano, Emi Mishiro-Sato, Kazuhiro Aoki, Yasuteru Urano, Toru Komatsu, Shinya Tsukiji","doi":"10.1021/acschembio.4c00432","DOIUrl":"10.1021/acschembio.4c00432","url":null,"abstract":"Connecting two small molecules, such as ligands, fluorophores, or lipids, together via a linker with amide bonds is a widely used strategy to generate synthetic bifunctional molecules for various biological and biomedical applications. Such bifunctional molecules have been used in live-cell experiments under the assumption that they should be stable in cells. However, we recently found that a membrane-targeting bifunctional molecule, composed of a lipopeptide and the small-molecule ligand trimethoprim, referred to as mgcTMP, underwent amide-bond cleavage in mammalian cells. In this work, we first identified γ-secretase as the major protease degrading mgcTMP in cells. We next investigated the intracellular degradation of several different types of amide-linked bifunctional compounds and found that N-terminally fatty acid-conjugated small molecules are susceptible to γ-secretase-mediated amide-bond cleavage. In contrast, amide-linked bifunctional molecules composed of two small molecules, such as ligands and hydrophobic groups, which lack lipid modification, did not undergo intracellular degradation. These findings highlight a previously overlooked consideration for the development and application of lipid-based bifunctional molecules in chemical biology research.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"2438-2450"},"PeriodicalIF":3.5,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Expanding the Substrate Selectivity of the Fimsbactin Biosynthetic Adenylation Domain, FbsH. 扩展 Fimsbactin 生物合成腺苷酸化域 FbsH 的底物选择性

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2024-12-20 Epub Date: 2024-11-08 DOI: 10.1021/acschembio.4c00512

Syed Fardin Ahmed, Adam Balutowski, Jinping Yang, Timothy A Wencewicz, Andrew M Gulick

{"title":"Expanding the Substrate Selectivity of the Fimsbactin Biosynthetic Adenylation Domain, FbsH.","authors":"Syed Fardin Ahmed, Adam Balutowski, Jinping Yang, Timothy A Wencewicz, Andrew M Gulick","doi":"10.1021/acschembio.4c00512","DOIUrl":"10.1021/acschembio.4c00512","url":null,"abstract":"Nonribosomal peptide synthetases (NRPSs) produce diverse natural products including siderophores, chelating agents that many pathogenic bacteria produce to survive in low iron conditions. Engineering NRPSs to produce diverse siderophore analogs could lead to the generation of novel antibiotics and imaging agents that take advantage of this unique iron uptake system in bacteria. The highly pathogenic and antibiotic-resistant bacteria Acinetobacter baumannii produces fimsbactin, an unusual branched siderophore with iron-binding catechol groups bound to a serine or threonine side chain. To explore the substrate promiscuity of the assembly line enzymes, we report a structure-guided investigation of the stand-alone aryl adenylation enzyme FbsH. We report structures bound to its native substrate 2,3-dihydroxybenzoic acid (DHB) as well as an inhibitor that mimics the adenylate intermediate. We produced enzyme variants with an expanded binding pocket that are more tolerant for analogs containing a DHB C4 modification. Wild-type and mutant enzymes were then used in an in vitro reconstitution analysis to assess the production of analogs of the final product as well as several early stage intermediates. This analysis shows that some altered substrates progress down the fimsbactin assembly line to the downstream domains. However, analogs from alternate building blocks are produced at lower levels, indicating that selectivity exists in the downstream catalytic domains. These findings expand the substrate scope of producing condensation products between serine and aryl acids and identify the bottlenecks for chemoenzymatic production of fimsbactin analogs.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"2451-2461"},"PeriodicalIF":3.5,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142602145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Repurposing Tolfenamic Acid to Anchor the Uncharacterized Pocket of the PUB Domain for Proteolysis of the Atypical E3 Ligase HOIP. 重新利用鹅膏蕈酸锚定非典型 E3 连接酶 HOIP 的 PUB 结构域未表征口袋的蛋白水解作用。

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2024-12-20 Epub Date: 2024-11-08 DOI: 10.1021/acschembio.4c00541

Fumei Zhong, Yu Zhou, Mingqing Liu, Lei Wang, Fudong Li, Jiahai Zhang, Zhiyong Han, Yunyu Shi, Jia Gao, Ke Ruan

{"title":"Repurposing Tolfenamic Acid to Anchor the Uncharacterized Pocket of the PUB Domain for Proteolysis of the Atypical E3 Ligase HOIP.","authors":"Fumei Zhong, Yu Zhou, Mingqing Liu, Lei Wang, Fudong Li, Jiahai Zhang, Zhiyong Han, Yunyu Shi, Jia Gao, Ke Ruan","doi":"10.1021/acschembio.4c00541","DOIUrl":"10.1021/acschembio.4c00541","url":null,"abstract":"The E3 ligase HOIP is vital for the NF-κB pathway and is implicated in cancer and immunity. However, it remains challenging to achieve high selectivity by directly targeting the conserved catalytic RBR domain of HOIP. Herein, we identified four low-molecular-weight compounds that bind to an uncharacterized pocket of the HOIP PUB domain (HOIPPUB). The complex structure facilitated the discovery of the first single-digit micromolar ligand of HOIPPUB, tolfenamic acid, which exhibited over 30-fold selectivity due to the low sequence identity of the uncharacterized pocket of HOIPPUB. Although tolfenamic acid did not block the substrate recognition and linear ubiquitination activity of HOIP, a ligand of the uncharacterized PUB pocket of HOIP (LUPH), by chemical linking pomalidomide with tolfenamic acid, degraded HOIP, reduced NEMO ubiquitination and p65 phosphorylation, and eventually inhibited NF-κB activation and breast cancer cell proliferation. Our work proposes an alternative strategy to target the nonfunctional pocket of the PUB domain with high sequence diversity to promote HOIP degradation, rather than targeting the conserved RBR domain to block the catalytic function of HOIP.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"2469-2476"},"PeriodicalIF":3.5,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142602148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Small Molecule Modulator of the mTORC2 Pathway Discovered from a DEL Library Designed to Bind to Pleckstrin Homology Domains. 从设计与 Pleckstrin 同源结构域结合的 DEL 文库中发现 mTORC2 通路的小分子调节剂。

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2024-12-20 Epub Date: 2024-11-12 DOI: 10.1021/acschembio.4c00597

Arthur Gonse, Jelena Gajić, Jean-Pierre Daguer, Sofia Barluenga, Robbie Loewith, Nicolas Winssinger

{"title":"Small Molecule Modulator of the mTORC2 Pathway Discovered from a DEL Library Designed to Bind to Pleckstrin Homology Domains.","authors":"Arthur Gonse, Jelena Gajić, Jean-Pierre Daguer, Sofia Barluenga, Robbie Loewith, Nicolas Winssinger","doi":"10.1021/acschembio.4c00597","DOIUrl":"10.1021/acschembio.4c00597","url":null,"abstract":"Pleckstrin homology (PH) domains are structural motifs critical for cellular processes, such as signal transduction and cytoskeletal organization. Due to their involvement in various diseases, PH domains are promising therapeutic targets, yet their highly charged and hydrophobic binding sites are not ideal for traditional small drugs. In this study, we designed a DNA-encoded library (DEL) mimicking phospholipids to identify novel modulators targeting PH domains with uncharted chemical properties. Screening against several PH domains led to the discovery of 2DII, a small molecule that selectively binds to mSin1PH. This compound can modulate mTORC2 activity by impairing mTORC2's membrane interactions, resulting in reduced AKT1 phosphorylation. A micromapping via Dexter energy transfer based on 2DII bearing an iridium catalyst (2DII-Ir), along with a biotin-diazirine small molecule was used for target identification by proteomics, which confirmed mSin1 as the primary intracellular target of 2DII, demonstrating its potential for selective mTORC2 pathway modulation. These findings introduce a novel strategy for targeting PH domains and provide a foundation for the development of therapeutic interventions that modulate PH-domain-dependent signaling pathways.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"2502-2514"},"PeriodicalIF":3.5,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multimodal Blood-Based Biomarker Panel Reveals Altered Lysosomal Ionic Content in Alzheimer's Disease.

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2024-12-19 DOI: 10.1021/acschembio.4c00602

Senthilkumar Deivasigamani, Shareefa Thekkan, Hernando M Vergara, Owen Conolly, Mali Cosden, Thienlong Phan, Sean Smith, Jacob Marcus, Jason Uslaner, Dhivya Venkat, Robert E Drolet, Yamuna Krishnan, Souvik Modi

{"title":"Multimodal Blood-Based Biomarker Panel Reveals Altered Lysosomal Ionic Content in Alzheimer's Disease.","authors":"Senthilkumar Deivasigamani, Shareefa Thekkan, Hernando M Vergara, Owen Conolly, Mali Cosden, Thienlong Phan, Sean Smith, Jacob Marcus, Jason Uslaner, Dhivya Venkat, Robert E Drolet, Yamuna Krishnan, Souvik Modi","doi":"10.1021/acschembio.4c00602","DOIUrl":"https://doi.org/10.1021/acschembio.4c00602","url":null,"abstract":"Lysosomal storage disorders (LSDs) and adult neurodegenerative disorders like Alzheimer's disease (AD) share various clinical and pathophysiological features. LSDs are characterized by impaired lysosomal activity caused by mutations in key proteins and enzymes. While lysosomal dysfunction is also linked to AD pathogenesis, its precise role in disease onset or progression remains unclear. Lysosomal ionic homeostasis is recognized as a key feature of many LSDs, but it has not been clinically linked with AD pathology. Thus, investigating whether this regulation is disrupted in AD is important, as it could lead to new therapeutic targets and biomarkers for this multifactorial disease. Here, using two-ion mapping (2-IM) technology, we quantitatively profiled lysosomal pH and Ca2+ in blood-derived monocytes from AD patients and age-matched controls and correlated lysosome ionicity with age and key markers of AD pathology, namely, amyloid deposits, tauopathy, neurodegeneration, and inflammation. Together, the data show that the ionic milieu of lysosomes is dysregulated in monocytes of AD patients and correlates with key plasma biomarkers of AD. Using a machine learning model based on the above parameters, we describe a proof-of-concept combinatorial biomarker platform that accurately distinguishes between patients with AD and control participants with an area under the curve of >96%. Our study introduces a convenient, noninvasive platform with the potential to diagnose Alzheimer's disease based on fluid, cellular, and molecular biomarkers. Further, these findings highlight the potential for investigating therapeutic mechanisms capable of restoring lysosome ionic homeostasis to ameliorate AD.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142851637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Painting Cell-Cell Interactions by Horseradish Peroxidase and Endogenously Generated Hydrogen Peroxide.

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2024-12-18 DOI: 10.1021/acschembio.4c00419

Youngjoon Cho, Inyoung Jeong, Kwang-Eun Kim, Hyun-Woo Rhee

{"title":"Painting Cell-Cell Interactions by Horseradish Peroxidase and Endogenously Generated Hydrogen Peroxide.","authors":"Youngjoon Cho, Inyoung Jeong, Kwang-Eun Kim, Hyun-Woo Rhee","doi":"10.1021/acschembio.4c00419","DOIUrl":"https://doi.org/10.1021/acschembio.4c00419","url":null,"abstract":"Cell-cell interactions are fundamental in biology for maintaining physiological conditions with direct contact being the most straightforward mode of interaction. Recent advancements have led to the development of various chemical tools for detecting or identifying these interactions. However, the use of exogenous cues, such as toxic reagents, bulky probes, and light irradiation, can disrupt normal cell physiology. For example, the toxicity of hydrogen peroxide (H2O2) limits the applications of peroxidases in the proximity labeling field. In this study, we aimed to address this limitation by demonstrating that membrane-localized horseradish peroxidase (HRP-TM) efficiently utilizes endogenously generated extracellular H2O2. By harnessing endogenous H2O2, we observed that HRP-TM-expressing cells can effectively label contacting cells without the need for exogenous H2O2 treatment. Furthermore, we confirmed that HRP-TM labels proximal cells in an interaction-dependent manner. These findings offer a novel approach for studying cell-cell interactions under more physiological conditions without the confounding effects of exogenous stimuli. Our study contributes to elucidating cell-cell interaction networks in various model organisms, providing valuable insights into the dynamic interplay between cells in their native network.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Development of a Class A/B Hybrid GPCR System for the Proximity-Assisted Screening of GPCR Ligands.

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2024-12-16 DOI: 10.1021/acschembio.4c00658

Monika T Gnatzy, Steffen Hartmann, Felix Hausch

{"title":"Development of a Class A/B Hybrid GPCR System for the Proximity-Assisted Screening of GPCR Ligands.","authors":"Monika T Gnatzy, Steffen Hartmann, Felix Hausch","doi":"10.1021/acschembio.4c00658","DOIUrl":"https://doi.org/10.1021/acschembio.4c00658","url":null,"abstract":"Class A G protein-coupled receptors (GPCRs) are key mediators in numerous signaling pathways and important drug targets for several diseases. A major shortcoming in GPCR ligand screening is the detection limit for weak binding molecules, which is especially critical for poorly druggable GPCRs. Here, we present a proximity-based screening system for class A GPCRs, which adopts the natural two-step activation mechanism of class B GPCRs. In this approach, class A/B chimeras with the extracellular domain of the class B receptor CRF1R grafted to the transmembrane domain of target class A receptors are stimulated with hybrid ligands. These ligands contain a high-affinity peptide derived from CRF, which recruits the hybrid ligands to the engineered target GPCR, dramatically increasing the local concentration of the test substances. We exemplified this method for neurotensin receptor 1 (NTR1) and endothelin receptor B (ETB), two important class A GPCR drug targets for pulmonary arterial hypertension or psychological disorders and neurodegenerative diseases. We observed >20× activity enhancement by the directed proximity approach, enabling the detection of weakly activating sequences that would have otherwise remained undetected. Our approach allows to probe GPCR activation in the membrane of living cells and may be especially useful for GPCRs for which it has been difficult to generate small drug-like molecules.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833152","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Impact of Sugar Conformation on the Single-Stranded DNA Selectivity of APOBEC3A and APOBEC3B Enzymes. 糖构象对 APOBEC3A 和 APOBEC3B 酶单链 DNA 选择性的影响

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2024-12-16 DOI: 10.1021/acschembio.4c00540

Mackenzie K Wyllie, Clare K Morris, Nicholas H Moeller, Henry A M Schares, Ramkumar Moorthy, Christopher A Belica, Michael J Grillo, Özlem Demir, Alex M Ayoub, Michael A Carpenter, Hideki Aihara, Reuben S Harris, Rommie E Amaro, Daniel A Harki

{"title":"The Impact of Sugar Conformation on the Single-Stranded DNA Selectivity of APOBEC3A and APOBEC3B Enzymes.","authors":"Mackenzie K Wyllie, Clare K Morris, Nicholas H Moeller, Henry A M Schares, Ramkumar Moorthy, Christopher A Belica, Michael J Grillo, Özlem Demir, Alex M Ayoub, Michael A Carpenter, Hideki Aihara, Reuben S Harris, Rommie E Amaro, Daniel A Harki","doi":"10.1021/acschembio.4c00540","DOIUrl":"https://doi.org/10.1021/acschembio.4c00540","url":null,"abstract":"The APOBEC3 family of polynucleotide cytidine deaminases has diverse roles as viral restriction factors and oncogenic mutators. These enzymes convert cytidine to uridine in single-stranded (ss)DNA, inducing genomic mutations that promote drug resistance and tumor heterogeneity. Of the seven human APOBEC3 members, APOBEC3A (A3A) and APOBEC3B (A3B) are most implicated in driving pro-tumorigenic mutations. How these enzymes engage and selectively deaminate ssDNA over RNA is not well understood. We previously conducted molecular dynamics (MD) simulations that support the role of sugar conformation as a key molecular determinant in nucleic acid recognition by A3B. We hypothesize that A3A and A3B selectively deaminate substrates in the 2'-endo (DNA) conformation and show reduced activity for 3'-endo (RNA) conformation substrates. Consequently, we have characterized A3A- and A3B-binding and deaminase activity with chimeric oligonucleotides containing cytidine analogues that promote either the 2'-endo or 3'-endo conformation. Using fluorescence polarization and gel-based deamination assays, we determined that sugar conformation preferentially impacts the ability of these enzymes to deaminate substrates and less so binding to substrates. Using MD simulations, we identify specific active site interactions that promote selectivity based on the 2'-endo conformation. These findings help inform the biological functions of A3A and A3B in providing antiviral innate immunity and pathogenic functions in cancer.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142826638","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Bioluminescent Probes for the Detection of Superoxide and Nitric Oxide.

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2024-12-16 DOI: 10.1021/acschembio.4c00551

Matthew A Larsen, Mike Valley, Natasha Karassina, Hui Wang, Wenhui Zhou, Jolanta Vidugiriene

引用次数: 0