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Corelet™ platform: Precision high throughput screening for targeted drug discovery of biomolecular condensates Corelet™平台:生物分子凝聚物靶向药物发现的精确高通量筛选。
IF 2.7 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-04-01 Epub Date: 2025-02-28 DOI: 10.1016/j.slasd.2025.100224
Aislinn Mayfield , Xin Zhang, Ivan Efremov, Michael G Kauffman, John F Reilly, Bahareh Eftekharzadeh
Biomolecular condensates (BMCs) are crucial for cellular organization and function, and their dysregulation is linked to neurological, oncologic and inflammatory diseases. This highlights the need for advanced investigative tools leading to targeted BMC therapeutics. To address this need, Nereid Therapeutics uses Corelet™ technology and an automated high-throughput screening (HTS) platform to precisely quantify phase separation events and identify BMC modulators for previously undruggable targets. Hundreds of thousands of small molecules have been screened utilizing Corelet technology, yielding small molecule BMC-modulating compounds which serve as the basis for the development of targeted therapies for diseases with high unmet need.
生物分子凝聚体(BMCs)对细胞组织和功能至关重要,其失调与神经、肿瘤和炎症疾病有关。这突出了对先进的研究工具的需求,从而导致靶向BMC治疗。为了满足这一需求,Nereid Therapeutics使用Corelet™技术和自动化高通量筛选(HTS)平台来精确量化相分离事件,并识别以前不可药物靶点的BMC调节剂。利用Corelet技术筛选了成千上万的小分子,产生了小分子bmc调节化合物,这些化合物可作为开发针对高未满足需求疾病的靶向治疗的基础。
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引用次数: 0
Enhancing throughput and robustness of the fibroblast to myofibroblast transition assay 增强成纤维细胞向肌成纤维细胞转化试验的通量和稳健性。
IF 2.7 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-04-01 Epub Date: 2025-03-14 DOI: 10.1016/j.slasd.2025.100226
Elisabeth Bäck , Jessica Bjärkby , Leire Escudero-Ibarz , Stefan Tångefjord , Johan Jirholt , Mei Ding
Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive age-related lung disease with an average survival of 3–5 years post-diagnosis if left untreated. It is characterized by lung fibrosis, inflammation, and destruction of lung architecture, leading to worsening respiratory symptoms and physiological impairment, ultimately culminating in progressive respiratory failure. The development of novel therapeutics for the treatment of IPF represents a significant unmet medical need. Fibroblast to myofibroblast transition (FMT) in response to fibrogenic mediators such as transforming growth factor beta 1 (TGF-β1) has been identified as a key cellular phenotype driving the formation of myofibroblasts and lung fibrosis in IPF. Establishing a robust and high-throughput in vitro human FMT assay is crucial for uncovering new disease targets and for efficiently screening compounds for the advancement of novel therapeutics aimed at targeting myofibroblast activity. However, creating a robust FMT assay suitable for high-throughput drug screening has proven challenging due to the requisite level of automation.
In this study, we focus on evaluating different automation approaches for liquid exchange and compound dosing in the human FMT assay. A semi-automated assay, capable of screening a large number of compounds that inhibit TGF-β1-induced FMT in both Normal Human Lung Fibroblasts (NHLF) and IPF-patient derived Disease Human Lung Fibroblasts (IPF-DHLF), has been successfully developed and optimized. We demonstrate that the optimized FMT assay using liquid handling automation exhibits great assay reproducibility, shows good assay translation using human lung fibroblasts from normal healthy versus IPF-patients, and demonstrates acceptable human primary donor variability. This allows for the standardization of comparisons of compound anti-fibrotic potency across IPF projects.
特发性肺纤维化(IPF)是一种慢性进行性年龄相关肺部疾病,如果不及时治疗,诊断后平均生存期为3-5年。其特征是肺纤维化、炎症和肺结构破坏,导致呼吸系统症状恶化和生理损害,最终导致进行性呼吸衰竭。治疗IPF的新疗法的发展代表了一个重要的未满足的医疗需求。成纤维细胞向肌成纤维细胞转化(FMT)是对转化生长因子β1 (TGF-β1)等成纤维介质的反应,已被确定为IPF中驱动肌成纤维细胞形成和肺纤维化的关键细胞表型。建立一个强大的、高通量的体外人FMT检测方法对于发现新的疾病靶点和有效筛选化合物以推进针对肌成纤维细胞活性的新疗法至关重要。然而,由于必要的自动化水平,创建一个适用于高通量药物筛选的强大的FMT分析已被证明具有挑战性。在这项研究中,我们着重于评估人类FMT测定中液体交换和化合物给药的不同自动化方法。成功开发并优化了一种半自动化检测方法,能够筛选大量抑制正常人肺成纤维细胞(NHLF)和ipf患者来源的疾病人肺成纤维细胞(IPF-DHLF)中TGF-β1诱导的FMT的化合物。我们证明,使用液体处理自动化的优化FMT分析具有很高的分析重复性,在正常健康的人肺成纤维细胞与ipf患者之间显示了良好的分析翻译,并且显示了可接受的人类原发供体可变性。这允许在IPF项目中比较化合物抗纤维化效力的标准化。
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引用次数: 0
SLAS special issue editorial 2025: Outcomes from antiviral drug discovery for pathogens of pandemic concern SLAS特刊编辑2025:大流行病原体抗病毒药物发现的结果
IF 2.7 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-04-01 Epub Date: 2025-04-08 DOI: 10.1016/j.slasd.2025.100231
Timothy P. Spicer, Louis D. Scampavia
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引用次数: 0
Super-resolution microscopy as a drug discovery tool 超分辨率显微镜作为药物发现工具。
IF 2.7 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-03-01 Epub Date: 2025-01-15 DOI: 10.1016/j.slasd.2025.100209
Lauren Toms, Lorna FitzPatrick, Philip Auckland
At the turn of the century a fundamental resolution barrier in fluorescence microscopy known as the diffraction limit was broken, giving rise to the field of super-resolution microscopy. Subsequent nanoscopic investigation with visible light revolutionised our understanding of how previously unknown molecular features give rise to the emergent behaviour of cells. It transpires that the devil is in these fine molecular details, and essential nanoscale processes were found everywhere researchers chose to look. Now, after nearly two decades, super-resolution microscopy has begun to address previously unmet challenges in the study of human disease and is poised to become a pivotal tool in drug discovery.
在世纪之交,荧光显微镜中被称为衍射极限的基本分辨率障碍被打破,从而产生了超分辨率显微镜领域。随后的可见光纳米研究彻底改变了我们对以前未知的分子特征如何引起细胞涌现行为的理解。事实证明,关键就在这些细微的分子细节中,研究人员在任何地方都能找到必要的纳米尺度过程。现在,经过近二十年,超分辨率显微镜已经开始解决人类疾病研究中以前未遇到的挑战,并准备成为药物发现的关键工具。
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引用次数: 0
Magnetic three-dimensional bioprinting protocol for salivary gland mucoepidermoid carcinoma tumoroid culture 唾液腺黏液表皮样癌类肿瘤培养的磁性三维生物打印方案。
IF 2.7 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-03-01 Epub Date: 2025-01-16 DOI: 10.1016/j.slasd.2025.100217
Jutapak Klangprapan, Joao N. Ferreira
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引用次数: 0
Heterotypic spheroids as a strategy for 3D culture of cryopreserved primary human hepatocytes in stirred-tank systems 异型球体作为在搅拌槽系统中低温保存的人原代肝细胞三维培养的策略。
IF 2.7 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-03-01 Epub Date: 2025-01-11 DOI: 10.1016/j.slasd.2025.100210
Francisca Arez , Lena Preiss , Isabella Ramella Gal , Sofia P. Rebelo , Lassina Badolo , Catarina Brito , Thomas Spangenberg , Paula M. Alves
Primary human hepatocytes (PHHs) are the preferred cell source to address liver function. Despite originating from the native tissue, one of the bottlenecks when using primary material is the donor-to-donor variability. Cryopreserved PHHs offer a high number of cells from the same donor and standardization of cell isolation and cryopreservation procedures, mitigating some of the inter-donor variability. Still, PHHs from different commercial sources present variability in vitro in several parameters, including viability post-thawing, plating capacity, aggregation potential and culture longevity. Here we combine stirred-tank culture systems, which allow robust aggregation processes, and co-culture approaches with the HepaRG cell line to generate spheroids from cryopreserved PHHs. By employing small-scale stirred-tank culture systems we could cope with the scarce availability and high cost of primary material. In the optimized co-culture conditions we could generate PHH:HepaRG spheroids from 12 donors acquired from 4 different commercial sources. All PHHs showed similar aggregation profiles, forming small compact heterotypic spheroids as early as 3 days in co-culture and were maintained for at least 5 weeks in culture. The heterotypic spheroids maintained the hepatocyte polarization and identity and showed metabolization capacity for 5 main phase I metabolizing enzymes, namely CYP3A4, CYP2C9, CYP1A2, CYP2D6, and CYP2C8. Moreover, the heterotypic spheroids showed the capacity to metabolize a novel compound under clinical development, showing their potential to be employed in drug discovery applications.
Overall, we present a robust aggregation strategy for cryopreserved PHHs from different suppliers, applicable for pharmacological and toxicological in vitro research.
原代人肝细胞(PHHs)是解决肝功能的首选细胞来源。尽管来源于原生组织,但使用原生材料的瓶颈之一是供体与供体之间的差异。低温保存的phh提供了来自同一供体的大量细胞,并且标准化了细胞分离和低温保存程序,减轻了一些供体间的差异。尽管如此,来自不同商业来源的phh在体外的几个参数上存在差异,包括解冻后的活力、镀敷能力、聚集潜力和培养寿命。在这里,我们结合了搅拌罐培养系统,它允许强大的聚集过程,以及HepaRG细胞系的共培养方法,从冷冻保存的phh中产生球体。采用小型搅拌槽培养系统可以解决原料稀缺和成本高的问题。在优化的共培养条件下,我们可以从4个不同的商业来源获得的12个供体中产生PHH:HepaRG球体。所有phh均表现出相似的聚集特征,早在共培养的第3天就形成了紧凑的小异型球体,并在培养中维持了至少5周。异型球体维持了肝细胞的极化和特性,并表现出对CYP3A4、CYP2C9、CYP1A2、CYP2D6和CYP2C8这5种主要I期代谢酶的代谢能力。此外,异型球体在临床开发中显示出代谢新化合物的能力,显示出它们在药物发现应用中的潜力。总的来说,我们提出了一种强大的聚合策略,适用于来自不同供应商的冷冻保存phh,用于体外药理学和毒理学研究。
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引用次数: 0
Novel high-content and open-source image analysis tools for profiling mitochondrial morphology in neurological cell models 用于分析神经细胞模型中线粒体形态的新型高含量和开源图像分析工具。
IF 2.7 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-03-01 Epub Date: 2025-01-06 DOI: 10.1016/j.slasd.2025.100208
Marcus Y. Chin , David A. Joy , Madhuja Samaddar, Anil Rana, Johann Chow, Takashi Miyamoto, Meredith Calvert
Mitochondria undergo dynamic morphological changes depending on cellular cues, stress, genetic factors, or disease. The structural complexity and disease-relevance of mitochondria have stimulated efforts to generate image analysis tools for describing mitochondrial morphology for therapeutic development. Using high-content analysis, we measured multiple morphological parameters and employed unbiased feature clustering to identify the most robust pair of texture metrics that described mitochondrial state. Here, we introduce a novel image analysis pipeline to enable rapid and accurate profiling of mitochondrial morphology in various cell types and pharmacological perturbations. We applied a high-content adapted implementation of our tool, MitoProfilerHC, to quantify mitochondrial morphology changes in i) a mammalian cell dose response study and ii) compartment-specific drug effects in primary neurons. Next, we expanded the usability of our pipeline by using napari, a Python-powered image analysis tool, to build an open-source version of MitoProfiler and validated its performance and applicability. In conclusion, we introduce MitoProfiler as both a high-content-based and an open-source method to accurately quantify mitochondrial morphology in cells, which we anticipate to greatly facilitate mechanistic discoveries in mitochondrial biology and disease.
线粒体经历动态形态变化取决于细胞线索,压力,遗传因素,或疾病。线粒体的结构复杂性和疾病相关性促使人们努力生成图像分析工具,用于描述治疗开发的线粒体形态。通过高含量分析,我们测量了多个形态参数,并采用无偏特征聚类来识别描述线粒体状态的最稳健的纹理指标对。在这里,我们引入了一种新的图像分析管道,可以快速准确地分析各种细胞类型和药理扰动下的线粒体形态。我们应用了我们的工具MitoProfilerHC的高含量适应性实现,量化了i)哺乳动物细胞剂量反应研究和ii)初级神经元中室特异性药物效应的线粒体形态学变化。接下来,我们通过使用napari(一个python驱动的图像分析工具)来扩展管道的可用性,构建开源版本的MitoProfiler,并验证其性能和适用性。总之,我们介绍MitoProfiler作为一种基于高含量和开源的方法来准确量化细胞中的线粒体形态,我们预计这将极大地促进线粒体生物学和疾病的机制发现。
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引用次数: 0
Design, synthesis, and screening of an RNA optimized fluorinated fragment library RNA优化氟化片段文库的设计、合成和筛选
IF 2.7 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-03-01 Epub Date: 2025-01-17 DOI: 10.1016/j.slasd.2025.100215
Kasper P. Lundquist , Isabella Romeo , Raffaele B. Puglielli , Maëlle Pestalozzi , Marie L. Gram , Emily S. Hudson , Ofri Levi , Yoav S. Arava , Charlotte H. Gotfredsen , Mads H. Clausen
Fragment-based screening is an efficient method for early-stage drug discovery. In this study, we aimed to create a fragment library optimized for producing high hit rates against RNA targets. RNA has historically been an underexplored target, but recent research suggests potential for optimizing small molecule libraries for RNA binding. We extended this concept to fragment libraries to produce an RNA optimized fluorinated fragment library. We then screened this library, alongside two non-RNA optimized fragment libraries, against three RNA targets: the human cytoplasmic A-site and the S. cerevisiae tRNAAsp anticodon stem loop with and without nucleobase modifications. The screens yielded 24, 31, and 20 hits against the respective targets. Importantly, statistical analysis confirmed a significant overrepresentation of hits in our RNA optimized library. Based on these findings, we propose guidelines for developing RNA optimized fragment libraries. We hope the guidelines will help expediting fragment-based ligand discovery for RNA targets and contribute to presenting RNA as a promising target in drug discovery.
基于片段的筛选是早期药物发现的有效方法。在这项研究中,我们的目标是创建一个片段文库,以优化对RNA靶标的高命中率。RNA在历史上一直是一个未被充分开发的目标,但最近的研究表明,优化RNA结合的小分子文库具有潜力。我们将这一概念扩展到片段库,以产生RNA优化的氟化片段库。然后,我们筛选了这个文库,以及两个非RNA优化片段文库,针对三个RNA靶标:人类细胞质a位点和酿酒葡萄球菌tRNAAsp反密码子干环,有和没有核碱基修饰。屏幕分别对各自的目标进行了24次、31次和20次命中。重要的是,统计分析证实了在我们的RNA优化文库中有显著的高命中率。基于这些发现,我们提出了开发RNA优化片段文库的指导方针。我们希望该指南将有助于加快基于片段的RNA靶点配体的发现,并有助于将RNA作为药物发现的有希望的靶点。
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引用次数: 0
A high throughput assay for phosphoribosylformylglycinamidine synthase 磷酸核糖基甲酰基甘氨酸合成酶的高通量测定。
IF 2.7 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-03-01 Epub Date: 2025-01-15 DOI: 10.1016/j.slasd.2025.100212
Nandini Sharma , Yuka Otsuka , Louis Scampavia , Timothy P. Spicer , Jarrod B. French
Metabolic reprogramming of purine biosynthesis is a hallmark of cancer metabolism and represents a critical vulnerability. The enzyme phosphoribosylformylglycinamidine synthase (PFAS) catalyzes the fourth step in de novo purine biosynthesis and has been demonstrated to be prognostic for survival of liver cancer. Despite the importance of this protein as a drug target, there are no known specific inhibitors of PFAS activity. Here, we describe a new continuous, spectrophotometric assay for the synthase domain of PFAS that is amenable to high-throughput screening (HTS). This mechanism-based fluorescent assay makes use of the acid phosphatase substrate, 6,8-difluoro-4-methylumbelliferyl phosphate (DiFMUP). PFAS catalyzes the turnover of DiFMUP with a KM of 108 ± 7 µM. After optimization and miniaturization of the assay for 1,536-well format, we conducted a pilot HTS using the LOPAC1280 library. The assay performed extremely well, with an average Z′ of 0.94 ± 0.02, average signal to noise of 5.01 ± 0.06, excellent inter plate correlation, and a hit rate of 1.18 %. This assay provides a critically needed tool to advance the study of PFAS enzymology and will be foundational for the discovery of small molecule inhibitors both as functional probes and for the basis of new drug development.
嘌呤生物合成的代谢重编程是癌症代谢的一个标志,代表了一个关键的脆弱性。磷酸核糖基甲酰基甘氨酸合成酶(PFAS)催化嘌呤新生生物合成的第四步,并已被证明是肝癌生存的预后因素。尽管这种蛋白作为药物靶点很重要,但目前还没有已知的特异性PFAS活性抑制剂。在这里,我们描述了一种新的连续分光光度法测定PFAS合成酶结构域,适用于高通量筛选(HTS)。这种基于机制的荧光分析利用了酸性磷酸酶底物,6,8-二氟-4-甲基伞花酰磷酸(DiFMUP)。PFAS催化DiFMUP的周转,KM为108±7µM。在优化和小型化1536孔格式的分析后,我们使用LOPAC1280文库进行了试点HTS。该方法的检测效果非常好,平均Z´为0.94±0.02,平均信噪比为5.01±0.06,板间相关性良好,准确率为1.18%。该分析为推进PFAS酶学研究提供了一个急需的工具,并将为发现小分子抑制剂作为功能探针和新药开发的基础奠定基础。
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引用次数: 0
Single-plate kinome screening in live-cells to enable highly cost-efficient kinase inhibitor profiling 活细胞单片激酶组筛选,使高成本效益的激酶抑制剂分析。
IF 2.7 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-03-01 Epub Date: 2025-01-16 DOI: 10.1016/j.slasd.2025.100214
Martin P. Schwalm , Stefan Knapp
Cancer research, cancer treatment, and the field of chemical biology are examples which heavily rely on the discovery of selective kinase inhibitors. While determining on-target potency is often feasible for most laboratories, the equally critical but frequently neglected selectivity screening remains less accessible to the broader scientific community. This limitation can stem from various factors, such as the unavailability of a large number of purified kinases or the costs associated with commercial screening systems. To address these challenges and enable a wider range of scientists, this protocol leverages a commercial kinome selectivity screen to facilitate a low-cost, two-day, single-plate selectivity screen against 192 kinases.
癌症研究、癌症治疗和化学生物学领域都是严重依赖于选择性激酶抑制剂发现的例子。虽然确定靶效价对大多数实验室来说通常是可行的,但同样重要但经常被忽视的选择性筛选仍然很少被广泛的科学界所接受。这种限制可能源于各种因素,例如无法获得大量纯化的激酶或与商业筛选系统相关的成本。为了应对这些挑战,并使更广泛的科学家,该方案利用商业激酶组选择性筛选来促进低成本,两天,针对192个激酶的单板选择性筛选。
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引用次数: 0
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SLAS Discovery
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