SLAS Discovery最新文献

{"title":"Corrigendum to “Automation of high-throughput mRNA-seq library preparation: a robust, hands-free and time efficient methodology” [SLAS Discovery, Volume 27 (2022) P140-147/2472-5552]","authors":"","doi":"10.1016/j.slasd.2024.100169","DOIUrl":"10.1016/j.slasd.2024.100169","url":null,"abstract":"","PeriodicalId":21764,"journal":{"name":"SLAS Discovery","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2472555224000315/pdfft?md5=ca0576ce8ee4befca5b23942018c6efb&pid=1-s2.0-S2472555224000315-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141428466","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A robust CETSA data analysis automation workflow for routine screening","authors":"","doi":"10.1016/j.slasd.2024.100172","DOIUrl":"10.1016/j.slasd.2024.100172","url":null,"abstract":"<div><p>The Cellular Thermal Shift Assay (CETSA) enables the study of protein-ligand interactions in a cellular context. It provides valuable information on the binding affinity and specificity of both small and large molecule ligands in a relevant physiological context, hence forming a unique tool in drug discovery. Though high-throughput lab protocols exist for scaling up CETSA, subsequent data analysis and quality control remain laborious and limit experimental throughput. Here, we introduce a scalable and robust data analysis workflow which allows integration of CETSA into routine high throughput screening (HT-CETSA). This new workflow automates data analysis and incorporates quality control (QC), including outlier detection, sample and plate QC, and result triage. We describe the workflow and show its robustness against typical experimental artifacts, show scaling effects, and discuss the impact of data analysis automation by eliminating manual data processing steps.</p></div>","PeriodicalId":21764,"journal":{"name":"SLAS Discovery","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2472555224000340/pdfft?md5=6e5220dfe2b1f933bad2e9c87f5b1177&pid=1-s2.0-S2472555224000340-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141539052","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A high-throughput cell-based screening method for Zika virus protease inhibitor discovery","authors":"","doi":"10.1016/j.slasd.2024.100164","DOIUrl":"10.1016/j.slasd.2024.100164","url":null,"abstract":"<div><p>Zika virus (ZIKV) continues to pose a significant global public health threat, with recurring regional outbreaks and potential for pandemic spread. Despite often being asymptomatic, ZIKV infections can have severe consequences, including neurological disorders and congenital abnormalities. Unfortunately, there are currently no approved vaccines or antiviral drugs for the prevention or treatment of ZIKV. One promising target for drug development is the ZIKV NS2B-NS3 protease due to its crucial role in the virus life cycle. In this study, we established a cell-based ZIKV protease inhibition assay designed for high-throughput screening (HTS). Our assay relies on the ZIKV protease's ability to cleave a cyclised firefly luciferase fused to a natural cleavage sequence between NS2B and NS3 protease within living cells. We evaluated the performance of our assay in HTS setting using the pharmacologic controls (JNJ-40418677 and MK-591) and by screening a Library of Pharmacologically Active Compounds (LOPAC). The results confirmed the feasibility of our assay for compound library screening to identify potential ZIKV protease inhibitors.</p></div>","PeriodicalId":21764,"journal":{"name":"SLAS Discovery","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2472555224000261/pdfft?md5=bf5f1d749131f99bf6ee476dc8d7194b&pid=1-s2.0-S2472555224000261-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141136693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Compound management in a virtual research organization: The cornerstone of a reliable MMV discovery engine","authors":"Anna Adam,&nbsp;Elodie Chenu,&nbsp;Dominique Besson","doi":"10.1016/j.slasd.2024.100168","DOIUrl":"10.1016/j.slasd.2024.100168","url":null,"abstract":"<div><p>Despite the efforts towards malaria eradication, latest estimates show that the number of malaria cases is still rising, and malaria continues to have a devastating impact on people's health and livelihoods particularly in populations located in sub-Saharan Africa ¹. As a Product Development Partnership (PDP), MMV Medicines for Malaria Venture (MMV) plays a crucial role by using public and philanthropic funds to engage the pharmaceutical industry and academic research institutions to discover, develop and deliver the new drugs needed to control and eradicate malaria. MMV Discovery, working with partners, has developed a robust pipeline of molecules and a reliable discovery engine able to support research projects from screening to candidate nomination, providing access to centers of expertise and evaluating the profile and potential of molecules. To efficiently support this malaria discovery effort, MMV and its partners have established a state-of-the-art compound management network, supporting all discovery activities. This network serves both discovery projects and open innovation initiatives, such as MMV Open, tailoring workflows to align with distinct project objectives. In addition to this, MMV has implemented reliable integrated logistic tools and interfaces. These tools enable the efficient management and tracking of individual not solubilized (dry) samples of project compounds, as well as dedicated, solubilized libraries of compounds designated for primary screens targeting malaria and other neglected diseases.</p></div>","PeriodicalId":21764,"journal":{"name":"SLAS Discovery","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2472555224000303/pdfft?md5=938ea9a32dbd6548b3ddd7c3c0aacd0c&pid=1-s2.0-S2472555224000303-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141312508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a live cell assay for the zinc transporter ZnT8","authors":"Lucia Azzollini ,&nbsp;Dolores Del Prete ,&nbsp;Gernot Wolf ,&nbsp;Christoph Klimek ,&nbsp;Mattia Saggioro ,&nbsp;Fernanda Ricci ,&nbsp;Eirini Christodoulaki ,&nbsp;Tabea Wiedmer ,&nbsp;Alvaro Ingles-Prieto ,&nbsp;Giulio Superti-Furga ,&nbsp;Lia Scarabottolo","doi":"10.1016/j.slasd.2024.100166","DOIUrl":"10.1016/j.slasd.2024.100166","url":null,"abstract":"<div><p>Zinc is an essential trace element that is involved in many biological processes and in cellular homeostasis. In pancreatic β-cells, zinc is crucial for the synthesis, processing, and secretion of insulin, which plays a key role in glucose homeostasis and which deficiency is the cause of diabetes. The accumulation of zinc in pancreatic cells is regulated by the solute carrier transporter SLC30A8 (or Zinc Transporter 8, ZnT8), which transports zinc from cytoplasm in intracellular vesicles. Allelic variants of SLC30A8 gene have been linked to diabetes. Given the physiological intracellular localization of SLC30A8 in pancreatic β-cells and the ubiquitous endogenous expression of other Zinc transporters in different cell lines that could be used as cellular model for SLC30A8 recombinant over-expression, it is challenging to develop a functional assay to measure SLC30A8 activity. To achieve this goal, we have firstly generated a HEK293 cell line stably overexpressing SLC30A8, where the over-expression favors the partial localization of SLC30A8 on the plasma membrane. Then, we used the combination of this cell model, commercial FluoZin-3 cell permeant zinc dye and live cell imaging approach to follow zinc flux across SLC30A8 over-expressed on plasma membrane, thus developing a novel functional imaging- based assay specific for SLC30A8. Our novel approach can be further explored and optimized, paving the way for future small molecule medium-throughput screening.</p></div>","PeriodicalId":21764,"journal":{"name":"SLAS Discovery","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2472555224000285/pdfft?md5=cc84c4d2988c7d8585e18309f5ebba58&pid=1-s2.0-S2472555224000285-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141289026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel thin plate spline methodology to model tissue surfaces and quantify tumor cell invasion in organ-on-chip models","authors":"Elizabeth Elton ,&nbsp;Carly Strelez ,&nbsp;Nolan Ung ,&nbsp;Rachel Perez ,&nbsp;Kimya Ghaffarian ,&nbsp;Danielle Hixon ,&nbsp;Naim Matasci ,&nbsp;Shannon M. Mumenthaler","doi":"10.1016/j.slasd.2024.100163","DOIUrl":"10.1016/j.slasd.2024.100163","url":null,"abstract":"<div><p>Organ-on-chip (OOC) models can be useful tools for cancer drug discovery. Advances in OOC technology have led to the development of more complex assays, yet analysis of these systems does not always account for these advancements, resulting in technical challenges. A challenging task in the analysis of these two-channel microfluidic models is to define the boundary between the channels so objects moving within and between channels can be quantified. We propose a novel imaging-based application of a thin plate spline method – a generalized cubic spline that can be used to model coordinate transformations – to model a tissue boundary and define compartments for quantification of invaded objects, representing the early steps in cancer metastasis. To evaluate its performance, we applied our analytical approach to an adapted OOC developed by Emulate, Inc., utilizing a two-channel system with endothelial cells in the bottom channel and colorectal cancer (CRC) patient-derived organoids (PDOs) in the top channel. Initial application and visualization of this method revealed boundary variations due to microscope stage tilt and ridge and valley-like contours in the endothelial tissue surface. The method was functionalized into a reproducible analytical process and web tool – the Chip Invasion and Contour Analysis (ChICA) – to model the endothelial surface and quantify invading tumor cells across multiple chips. To illustrate applicability of the analytical method, we applied the tool to CRC organoid-chips seeded with two different endothelial cell types and measured distinct variations in endothelial surfaces and tumor cell invasion dynamics. Since ChICA utilizes only positional data output from imaging software, the method is applicable to and agnostic of the imaging tool and image analysis system used. The novel thin plate spline method developed in ChICA can account for variation introduced in OOC manufacturing or during the experimental workflow, can quickly and accurately measure tumor cell invasion, and can be used to explore biological mechanisms in drug discovery.</p></div>","PeriodicalId":21764,"journal":{"name":"SLAS Discovery","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S247255522400025X/pdfft?md5=1d111c27c601b575d3944e3576f55d04&pid=1-s2.0-S247255522400025X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141138799","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development and validation of a generic methyltransferase enzymatic assay based on an SAH riboswitch","authors":"Ha Pham ,&nbsp;Meera Kumar ,&nbsp;Anibal Ramos Martinez ,&nbsp;Mahbbat Ali ,&nbsp;Robert G. Lowery","doi":"10.1016/j.slasd.2024.100161","DOIUrl":"10.1016/j.slasd.2024.100161","url":null,"abstract":"<div><p>Methylation of proteins and nucleic acids plays a fundamental role in epigenetic regulation, and discovery of methyltransferase (MT) inhibitors is an area of intense activity. Because of the diversity of MTs and their products, assay methods that detect <em>S</em>-adenosylhomocysteine (SAH) – the invariant product of <em>S</em>-adenosylmethionine (SAM)-dependent methylation reactions - offer some advantages over methods that detect specific methylation events. However, direct, homogenous detection of SAH requires a reagent capable of discriminating between SAH and SAM, which differ by a single methyl group. Moreover, MTs are slow enzymes and many have submicromolar affinities for SAM; these properties translate to a need for detection of SAH at low nanomolar concentrations in the presence of excess SAM. To meet these needs, we leveraged the exquisite molecular recognition properties of a naturally occurring SAH-sensing RNA aptamer, or riboswitch. By splitting the riboswitch into two fragments, such that SAH binding induces assembly of a trimeric complex, we engineered sensors that transduce binding of SAH into positive fluorescence polarization (FP) and time resolved Förster resonance energy transfer (TR-FRET) signals. The split riboswitch configuration, called the AptaFluor™ SAH Methyltransferase Assay, allows robust detection of SAH (Z’ &gt; 0.7) at concentrations below 10 nM, with overnight signal stability in the presence of typical MT assay components. The AptaFluor assay tolerates diverse MT substrates, including histones, nucleosomes, DNA and RNA, and we demonstrated its utility as a robust, enzymatic assay method for several methyltransferases with SAM K_m values &lt; 1 µM. The assay was validated for HTS by performing a pilot screen of 1,280 compounds against the SARS-CoV-2 RNA capping enzyme, nsp14. By enabling direct, homogenous detection of SAH at low nanomolar concentrations, the AptaFluor assay provides a universal platform for screening and profiling MTs at physiologically relevant SAM concentrations.</p></div>","PeriodicalId":21764,"journal":{"name":"SLAS Discovery","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2472555224000236/pdfft?md5=fc3163f869c64a2c1aec56e9077589d4&pid=1-s2.0-S2472555224000236-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141094784","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterisation of high throughput screening outputs for small molecule degrader discovery","authors":"Lillie E. Bell ,&nbsp;Catherine Bardelle ,&nbsp;Martin J Packer ,&nbsp;Johanna Kastl ,&nbsp;Geoffrey A. Holdgate ,&nbsp;Gareth Davies","doi":"10.1016/j.slasd.2024.100162","DOIUrl":"10.1016/j.slasd.2024.100162","url":null,"abstract":"<div><p>Targeted protein degradation is an important mechanism carried out by the cellular machinery, one that is gaining momentum as an exploitable strategy for the development of drug-like compounds. Molecules which are able to induce proximity between elusive therapeutic targets of interest and E3 ligases which subsequently leads to proteasomal degradation of the target are beginning to decrease the percentage of the human proteome described as undruggable. Therefore, having the ability to screen for, and understand the mechanism of, such molecules is becoming an increasingly attractive scientific focus. We have established a number of cascade experiments including cell-based assays and orthogonal triage steps to provide annotation to the selectivity and mechanism of action for compounds identified as putative degraders from a primary high throughput screen against a high value oncology target. We will describe our current position, using PROTACs as proof-of-concept, on the analysis of these novel outputs and highlight challenges encountered.</p></div>","PeriodicalId":21764,"journal":{"name":"SLAS Discovery","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2472555224000248/pdfft?md5=dc288a87ff98b6fd26cc25724269aadb&pid=1-s2.0-S2472555224000248-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141140527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Creating a more strategic small molecule biophysical hit characterization workflow","authors":"Christopher Fotsch ,&nbsp;Debaleena Basu ,&nbsp;Ryan Case ,&nbsp;Qing Chen ,&nbsp;Pratibha C. Koneru ,&nbsp;Mei-Chu Lo ,&nbsp;Rachel Ngo ,&nbsp;Pooja Sharma ,&nbsp;Amit Vaish ,&nbsp;Xiang Yi ,&nbsp;Stephan G. Zech ,&nbsp;Peter Hodder","doi":"10.1016/j.slasd.2024.100159","DOIUrl":"10.1016/j.slasd.2024.100159","url":null,"abstract":"<div><p>To confirm target engagement of hits from our high-throughput screening efforts, we ran biophysical assays on several hundreds of hits from 15 different high-throughput screening campaigns. Analyzing the biophysical assay results from these screening campaigns led us to conclude that we could be more strategic in our biophysical analysis of hits by first confirming activity in a thermal shift assay (TSA) and then confirming activity in either a surface plasmon resonance (SPR) assay or a temperature-related intensity change (TRIC) assay. To understand how this new workflow shapes the quality of the final hits, we compared TSA/SPR or TSA/TRIC confirmed and unconfirmed hits to one another using four measures of compound quality: quantitative estimate of drug-likeness (QED), Pan-Assay Interference Compounds (PAINS), promiscuity, and aqueous solubility. In general, we found that the biophysically confirmed hits performed better in the compound quality metrics than the unconfirmed hits, demonstrating that our workflow not only confirmed target engagement of the hits but also enriched for higher quality hits.</p></div>","PeriodicalId":21764,"journal":{"name":"SLAS Discovery","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2472555224000212/pdfft?md5=389ec9b1863fb13b54ef5a3823355f2d&pid=1-s2.0-S2472555224000212-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140900579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhancing scaffold-free spheroid models: 3D cell bioprinting method for metastatic HSC3–Oral squamous carcinoma cell line","authors":"Taís Bacelar Sacramento de Araújo ,&nbsp;Raphael Luís Rocha Nogueira ,&nbsp;Leonardo de Oliveira Siquara da Rocha ,&nbsp;Iasmin Nogueira Bastos ,&nbsp;Rosane Borges Dias ,&nbsp;Bruno Solano De Freitas Souza ,&nbsp;Daniel William Lambert ,&nbsp;Ricardo D. Coletta ,&nbsp;Viviane Aline Oliveira Silva ,&nbsp;Clarissa A. Gurgel Rocha","doi":"10.1016/j.slasd.2024.100158","DOIUrl":"https://doi.org/10.1016/j.slasd.2024.100158","url":null,"abstract":"<div><p>3D <em>in vitro</em> systems offer advantages over the shortcomings of two-dimensional models by simulating the morphological and functional features of <em>in vivo</em>-like environments, such as cell-cell and cell-extracellular matrix interactions, as well as the co-culture of different cell types. Nevertheless, these systems present technical challenges that limit their potential in cancer research requiring cell line- and culture-dependent standardization. This protocol details the use of a magnetic 3D bioprinting method and other associated techniques (cytotoxicity assay and histological analysis) using oral squamous cell carcinoma cell line, HSC3, which offer advantages compared to existing widely used approaches. This protocol is particularly timely, as it validates magnetic bioprinting as a method for the rapid deployment of 3D cultures as a tool for compound screening and development of heterotypic cultures such as co-culture of oral squamous cell carcinoma cells with cancer-associated fibroblasts (HSC3/CAFs).</p></div>","PeriodicalId":21764,"journal":{"name":"SLAS Discovery","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2472555224000200/pdfft?md5=65af641e1cc59f0ba7520fa27146fec1&pid=1-s2.0-S2472555224000200-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140924481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}