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The critical role of PSAC channel in malaria parasite survival is driven home by phenotypic screening under relevant nutrient levels PSAC通道在疟疾寄生虫存活中的关键作用是通过相关营养水平下的表型筛选来实现的
IF 6.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-06-19 DOI: 10.1016/j.chembiol.2025.05.001
Irene Molina , Ryan Mansell , Rui Liang , Benigno Crespo , Margarita Puente , Virginia Franco , Sara Viera , Isabel Camino , Anas Saadeddin , Peter Bellotti , Annie Leung , Sam Henning , Shan Sun , Mikayla Herring , Celia Lopez , Carmen Cuevas , Peter Pogány , Beatriz Urones , Leigh Baxt , Esther Fernández , Lydia Mata-Cantero
Spreading resistance to front-line treatments necessitate the search for new classes of antimalarials. Limitations of standard screening conditions lead us to develop an assay using culture media that more closely reflects nutrient levels in human serum to reveal new therapeutically relevant parasite pathways. Our approach was validated by testing 22k compounds followed by a full 750k compound screen and identified 29 chemotypes with higher activity in nutrient restricted media that were further characterized. Through a combination of chemo-genomics and innovative photocatalytic proximity labeling proteomics, we identified the target of two compounds as the CLAG3 component of the plasmodial surface anion channel (PSAC). Strikingly, every one of the other 29 chemotypes selected was also found to block PSAC activity, highlighting the importance of this nutrient channel for parasite survival under physiological conditions. The effect of PSAC inhibitors in the in vivo humanized mouse model was confirmed.
对一线治疗药物的耐药性不断蔓延,需要寻找新型抗疟药物。标准筛选条件的局限性促使我们开发了一种使用培养基的检测方法,该培养基更接近地反映了人血清中的营养水平,以揭示新的治疗相关的寄生虫途径。我们的方法通过测试22k个化合物和完整的750k个化合物筛选得到验证,并确定了29个在营养受限培养基中具有较高活性的化学型,并进一步进行了表征。通过化学基因组学和创新的光催化接近标记蛋白质组学的结合,我们确定了两个化合物的目标是plasmodial表面阴离子通道(PSAC)的CLAG3组分。引人注目的是,所选择的其他29种化学型中的每一种也被发现阻断PSAC活性,突出了这种营养通道对寄生虫在生理条件下生存的重要性。PSAC抑制剂在人体内小鼠模型中的作用得到了证实。
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引用次数: 0
Charting the development and engineering of CRISPR base editors: lessons and inspirations 绘制CRISPR碱基编辑器的发展和工程:教训和启示
IF 6.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-06-19 DOI: 10.1016/j.chembiol.2025.05.003
Siyuan Zou , Yihong Sun , Weixin Tang
CRISPR base editors (BEs) have introduced a new chapter in precise genome editing. The brief but fruitful history of BE development documents many case studies that not only lay the foundation of base-editing technology but are also instrumental to future protein engineering efforts. In this review, we summarize the development and engineering of various BEs with a focus on recent progress. These include traditional cytosine and adenine base editors (CBEs and ABEs), novel TadA-derived CBEs, transversion BEs, dual BEs, and CRISPR-free BEs. We discuss each aspect of the workflow and highlight the successes and challenges encountered in the engineering process.
CRISPR碱基编辑器(BEs)开启了精确基因组编辑的新篇章。BE发展的短暂而富有成果的历史记录了许多案例研究,这些研究不仅奠定了碱基编辑技术的基础,而且对未来的蛋白质工程工作也有帮助。在这篇综述中,我们总结了各种BEs的开发和工程,并重点介绍了最近的进展。这些包括传统的胞嘧啶和腺嘌呤碱基编辑器(CBEs和abe),新型tada衍生的CBEs,翻转BEs,双重BEs和无crispr的BEs。我们讨论工作流程的每个方面,并强调在工程过程中遇到的成功和挑战。
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引用次数: 0
Integrator: A guardian against RNA-induced chaos 整合者:对抗rna引起的混乱的守护者
IF 6.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-06-19 DOI: 10.1016/j.chembiol.2025.05.009
William Garland , Torben Heick Jensen
In the June 12th issue of Cell, Baluapuri et al.1 report that loss of the Integrator (INT) complex triggers cellular stress by unleashing aberrant transcription, resulting in production of immunogenic double-stranded RNA. Dissecting early and late consequences of INT depletion, the study exemplifies how transcriptional dysregulation can culminate in profound physiological outcomes.
在6月12日出版的《细胞》杂志上,Baluapuri等人报道了Integrator (INT)复合物的缺失通过释放异常转录触发细胞应激,导致免疫原性双链RNA的产生。通过剖析INT耗竭的早期和晚期后果,该研究举例说明了转录失调如何最终导致深刻的生理结果。
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引用次数: 0
A cationic amphiphilic drug synergizes with strobilurin fungicides to control fungal-borne plant diseases 一种阳离子两亲性药物与异比脲类杀菌剂协同作用,控制真菌传播的植物病害
IF 6.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-06-19 DOI: 10.1016/j.chembiol.2025.05.008
Bradley Laflamme , Christopher Blackman , Mackenzie Loranger , Richard Trilles , Kalina Doytchinova-Weil , Stephen S. Scully , J. Miles Blackburn , Anastasia L.G. Kanegesuku , Jennifer L. Roizen , Stephen Bengtson , Lauren E. Brown , John A. Porco , Keiko Yoshioka , Luke Whitesell , Rajagopal Subramaniam , Nicole Robbins , Leah E. Cowen
Fungal phytopathogens are responsible for major losses in agricultural yields annually. While the use of topical fungicides remains key to managing agricultural pathogens, the emergence of drug-resistant strains necessitates identifying additional treatment options. In this study, we performed an in vitro small molecule screen against the devastating cereal pathogen Fusarium graminearum, identifying CMLD009688 as a priority growth inhibitor. Chemical-genetic profiling and subsequent experiments with CMLD009688 revealed that this compound functions as a cationic amphiphilic drug (CAD) and perturbs vacuolar integrity in F. graminearum. CMLD009688 displayed synergy with strobilurin fungicides in limiting F. graminearum growth—likely through both compounds independently affecting vacuolar stability—and a combination treatment of CMLD009688 with the strobilurin pyraclostrobin strongly limited the virulence of both F. graminearum and Botrytis cinerea in distinct models of plant infection. Thus, our findings highlight that cationic amphiphilic molecules show immense promise in helping to protect crops from fungal diseases.
真菌植物病原体是每年农业产量损失的主要原因。虽然局部使用杀菌剂仍然是管理农业病原体的关键,但耐药菌株的出现需要确定其他治疗方案。在这项研究中,我们对破坏性谷物病原菌镰刀菌进行了体外小分子筛选,鉴定出CMLD009688为优先生长抑制剂。CMLD009688的化学遗传学分析和后续实验表明,该化合物具有阳离子两亲性药物(CAD)的功能,并扰乱了F. graminearum的液泡完整性。CMLD009688显示出与strobilurin杀菌剂协同作用,限制了小麦赤霉病菌的生长——可能是通过这两种化合物单独影响液泡稳定性来实现的——CMLD009688与strobilurin pyraclostrobin联合处理,在不同的植物感染模式下,强烈限制了小麦赤霉病菌和灰葡萄孢菌的毒力。因此,我们的研究结果强调,阳离子两亲分子在帮助保护作物免受真菌疾病方面显示出巨大的希望。
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引用次数: 0
Integrative proximal-ubiquitomics profiling for deubiquitinase substrate discovery applied to USP30 应用于USP30去泛素酶底物发现的综合近端泛素组学分析
IF 6.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-05-15 DOI: 10.1016/j.chembiol.2025.04.004
Andreas Damianou , Hannah B.L. Jones , Athina Grigoriou , Mohammed A. Akbor , Edward Jenkins , Philip D. Charles , Iolanda Vendrell , Simon Davis , Benedikt M. Kessler
The growing interest in deubiquitinases (DUBs) as drug targets for modulating critical molecular pathways in disease is fueled by the discovery of their specific cellular roles. A crucial aspect of this fact is the identification of DUB substrates. While mass spectrometry-based proteomic methods can be used to study global changes in cellular ubiquitination following DUB activity perturbation, these datasets often include indirect and downstream ubiquitination events. To enrich for the direct substrates of DUB enzymes, we have developed a proximal-ubiquitome workflow that combines proximity labeling methodology (ascorbate peroxidase-2 [APEX2]) with subsequent ubiquitination enrichment based on the K-ε-GG motif. We applied this technology to identify altered ubiquitination events in the vicinity of the DUB ubiquitin-specific protease 30 (USP30) upon its inhibition. Our findings reveal ubiquitination events previously associated with USP30 on TOMM20 and FKBP8, as well as the candidate substrate LETM1, which is deubiquitinated in a USP30-dependent manner.
去泛素酶(DUBs)作为调节疾病关键分子途径的药物靶点的兴趣日益增长,这是由于发现了它们的特定细胞作用。这一事实的一个关键方面是DUB底物的鉴定。虽然基于质谱的蛋白质组学方法可用于研究DUB活性扰动后细胞泛素化的全局变化,但这些数据集通常包括间接和下游泛素化事件。为了对DUB酶的直接底物进行富集,我们开发了一种近端泛素组工作流程,将邻近标记方法(抗坏血酸过氧化物酶-2 [APEX2])与基于K-ε-GG基序的随后泛素化富集相结合。我们应用这项技术来鉴定DUB泛素特异性蛋白酶30 (USP30)抑制后附近泛素化事件的改变。我们的研究结果揭示了先前在TOMM20和FKBP8上与USP30相关的泛素化事件,以及候选底物LETM1,其以USP30依赖的方式去泛素化。
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引用次数: 0
MapID-based quantitative mapping of chemical modifications and expression of human transfer RNA 基于mapid的人转移RNA的化学修饰和表达定量图谱
IF 6.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-05-15 DOI: 10.1016/j.chembiol.2025.04.003
Mitchel L. Tepe , Yitan Chen , Allison Carso , Huiqing Zhou
Detection and quantification of tRNA chemical modifications are critical for understanding their regulatory functions in biology and diseases. However, tRNA-seq–based methods for modification mapping encountered challenges both experimentally (poor processivity of heavily modified tRNAs during reverse transcription or RT) and bioinformatically (frequent reads misalignment to highly similar tRNA genes). Here, we report “MapID-tRNA-seq” where we deployed an evolved reverse transcriptase (RT-1306) into tRNA-seq and developed “MapIDs” that reduce redundancy of the human tRNA genome and explicitly annotate genetic variances. RT-1306 generated robust mutations against m1A and m3C, and RT stops against multiple bulky roadblock modifications. MapID-assisted data processing enabled systematic exclusion of false-positive discoveries of modifications which arise from reads misalignment onto similar genes. We applied MapID-tRNA-seq into mapping m1A, m3C and expression levels of tRNAs in three mammary cell lines, which revealed cell-type dependent modification sites and potential translational regulation of the reduced mitochondrial activities in breast cancer.
tRNA化学修饰的检测和定量对于了解其在生物学和疾病中的调节功能至关重要。然而,基于tRNA-seq的修饰定位方法在实验上(逆转录或RT过程中重度修饰的tRNA的处理能力较差)和生物信息学上(与高度相似的tRNA基因的reads经常错位)都遇到了挑战。在这里,我们报告了“MapID-tRNA-seq”,我们将进化的逆转录酶(RT-1306)部署到tRNA-seq中,并开发了“mapid”,减少了人类tRNA基因组的冗余并明确注释了遗传差异。RT-1306对m1A和m3C产生了强大的突变,RT对多个大的路障修饰停止。mapid辅助的数据处理能够系统地排除由于reads与相似基因不匹配而产生的假阳性修饰发现。我们应用MapID-tRNA-seq对三种乳腺细胞系中trna的m1A、m3C和表达水平进行了定位,揭示了线粒体活性降低在乳腺癌中的细胞型依赖性修饰位点和潜在的翻译调控。
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引用次数: 0
Spatiotemporally resolved GPCR interactome uncovers unique mediators of receptor agonism 时空分辨的GPCR相互作用揭示了受体激动作用的独特介质
IF 6.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-05-15 DOI: 10.1016/j.chembiol.2025.04.006
Maria M. Shchepinova , Rachel Richardson , Jack W. Houghton , Abigail R. Walker , Mohammed A. Safar , Daniel Conole , Aylin C. Hanyaloglu , Edward W. Tate
Cellular signaling by membrane G protein-coupled receptors (GPCRs) is governed by a complex and diverse array of mechanisms. The dynamics of a GPCR interactome, as it evolves over time and space in response to an agonist, provide a unique perspective on pleiotropic signaling decoding and functional selectivity at the cellular level. In this study, we utilized proximity-based APEX2 proteomics to investigate the interaction network of the luteinizing hormone receptor (LHR) on a minute-to-minute timescale. We developed an analytical approach that integrates quantitative multiplexed proteomics with temporal reference profiles, creating a platform to identify the proteomic environment of APEX2-tagged LHR at the nanometer scale. LHR activity is finely regulated spatially, leading to the identification of putative interactors, including the Ras-related GTPase RAP2B, which modulate both receptor signaling and post-endocytic trafficking. This work provides a valuable resource for spatiotemporal nanodomain mapping of LHR interactors across subcellular compartments.
细胞膜G蛋白偶联受体(gpcr)的细胞信号传导是由一系列复杂多样的机制控制的。GPCR相互作用组响应激动剂随时间和空间的演变,为细胞水平上的多效性信号解码和功能选择性提供了独特的视角。在这项研究中,我们利用基于接近度的APEX2蛋白质组学研究了黄体生成素受体(LHR)在分钟到分钟时间尺度上的相互作用网络。我们开发了一种将定量多路蛋白质组学与时间参考谱相结合的分析方法,创建了一个在纳米尺度上识别apex2标记的LHR蛋白质组学环境的平台。LHR活性在空间上受到精细调节,从而确定了可能的相互作用因子,包括ras相关的GTPase RAP2B,它可以调节受体信号传导和内吞后转运。这项工作为跨亚细胞区室的LHR相互作用的时空纳米域映射提供了宝贵的资源。
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引用次数: 0
Microbiota mechanisms in cancer progression and therapy 微生物群在癌症进展和治疗中的机制
IF 6.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-05-15 DOI: 10.1016/j.chembiol.2025.04.005
Xing Zhang , Kyong Tkhe Fam , Tingting Dai , Howard C. Hang
The composition of the microbiota in patients has been shown to correlate with cancer progression and response to therapy, highlighting unique opportunities to improve patient outcomes. In this review, we discuss the challenges and advancements in understanding the chemical mechanisms of specific microbiota species, pathways, and molecules involved in cancer progression and treatment. We also describe the modulation of cancer and immunotherapy by the microbiota, along with approaches for investigating microbiota enzymes and metabolites. Elucidating these specific microbiota mechanisms and molecules should offer new opportunities for developing enhanced diagnostics and therapeutics to improve outcomes for cancer patients. Nonetheless, many microbiota mechanisms remain to be determined and require innovative chemical genetic approaches.
患者体内微生物群的组成已被证明与癌症进展和对治疗的反应相关,突出了改善患者预后的独特机会。在这篇综述中,我们讨论了在理解癌症进展和治疗中涉及的特定微生物群、途径和分子的化学机制方面的挑战和进展。我们还描述了微生物群对癌症和免疫治疗的调节,以及研究微生物群酶和代谢物的方法。阐明这些特定的微生物群机制和分子将为开发增强的诊断和治疗方法提供新的机会,以改善癌症患者的预后。尽管如此,许多微生物群机制仍有待确定,需要创新的化学遗传方法。
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引用次数: 0
Meet the Cell Chemical Biology author and newest advisory board member: Marcus Conrad 认识一下《细胞化学生物学》的作者和最新的顾问委员会成员:马库斯·康拉德
IF 6.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-05-15 DOI: 10.1016/j.chembiol.2025.04.011
Marcus Conrad
In an interview with Dr. Mishtu Dey, the editor-in-chief of Cell Chemical Biology, Prof. Marcus Conrad, a new advisory board member and lead author of the paper entitled “N-acetyl-L-cysteine averts ferroptosis by fostering glutathione peroxidase 4,” shares his perspective on his research area, opportunities in the chemical biology field, and his plans to meaningfully contribute in this new position.
在接受《细胞化学生物学》杂志主编Mishtu Dey博士的采访时,新顾问委员会成员、论文《n-乙酰- l-半胱氨酸通过培养谷胱甘肽过氧化物酶4来避免铁凋亡》的主要作者Marcus Conrad教授分享了他对自己的研究领域、化学生物学领域的机遇以及他在这个新职位上做出有意义贡献的计划。
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引用次数: 0
Meet the authors: Xing Zhang, Kyong Fam, Tingting Dai, and Howard Hang 见见作者:张星、法京、戴婷婷和杭霍华德
IF 6.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-05-15 DOI: 10.1016/j.chembiol.2025.04.010
Xing Zhang, Kyong Fam, Tingting Dai, Howard Hang
In an interview with Dr. Mishtu Dey, the editor-in-chief of Cell Chemical Biology, the authors of the Review article entitled “Microbiota mechanisms in cancer progression and therapy” share their perspectives on their field and lives as scientists.
在接受《细胞化学生物学》杂志主编Mishtu Dey博士的采访时,这篇题为“微生物群在癌症进展和治疗中的机制”的评论文章的作者分享了他们作为科学家对自己领域和生活的看法。
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引用次数: 0
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Cell Chemical Biology
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