SLAS Discovery最新文献

{"title":"Comparison of two supporting matrices for patient-derived cancer cells in 3D drug sensitivity and resistance testing assay (3D-DSRT)","authors":"Michaela Feodoroff ,&nbsp;Piia Mikkonen ,&nbsp;Laura Turunen ,&nbsp;Antti Hassinen ,&nbsp;Lauri Paasonen ,&nbsp;Lassi Paavolainen ,&nbsp;Swapnil Potdar ,&nbsp;Astrid Murumägi ,&nbsp;Olli Kallioniemi ,&nbsp;Vilja Pietiäinen","doi":"10.1016/j.slasd.2023.03.002","DOIUrl":"10.1016/j.slasd.2023.03.002","url":null,"abstract":"<div><p>Central to the success of functional precision medicine of solid tumors is to perform drug testing of patient-derived cancer cells (PDCs) in tumor-mimicking <em>ex vivo</em> conditions. While high throughput (HT) drug screening methods have been well-established for cells cultured in two-dimensional (2D) format, this approach may have limited value in predicting clinical responses. Here, we describe the results of the optimization of drug sensitivity and resistance testing (DSRT) in three-dimensional (3D) growth supporting matrices in a HT mode (3D-DSRT) using the hepatocyte cell line (HepG2) as an example. Supporting matrices included widely used animal-derived Matrigel and cellulose-based hydrogel, GrowDex, which has earlier been shown to support 3D growth of cell lines and stem cells. Further, the sensitivity of ovarian cancer PDCs, from two patients included in the functional precision medicine study, was tested for 52 drugs in 5 different concentrations using 3D-DSRT.</p><p>Shortly, in the optimized protocol, the PDCs are embedded with matrices and seeded to 384-well plates to allow the formation of the spheroids prior to the addition of drugs in nanoliter volumes with acoustic dispenser. The sensitivity of spheroids to drug treatments is measured with cell viability readout (here, 72 h after addition of drugs). The quality control and data analysis are performed with openly available Breeze software. We show the usability of both matrices in established 3D-DSRT, and report 2D vs 3D growth condition dependent differences in sensitivities of ovarian cancer PDCs to MEK-inhibitors and cytotoxic drugs. This study provides a proof-of-concept for robust and fast screening of drug sensitivities of PDCs in 3D-DSRT, which is important not only for drug discovery but also for personalized <em>ex vivo</em> drug testing in functional precision medicine studies. These findings suggest that comparing results of 2D- and 3D-DSRT is essential for understanding drug mechanisms and for selecting the most effective treatment for the patient.</p></div>","PeriodicalId":21764,"journal":{"name":"SLAS Discovery","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9592481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application of human iPSC-derived macrophages in a miniaturized high-content-imaging-based efferocytosis assay","authors":"Sarah Bitzer ,&nbsp;Mozhgan Dehghan Harati ,&nbsp;Karim C. El Kasmi ,&nbsp;Daniela Schloesser ,&nbsp;Julia Sauer ,&nbsp;Heiko Olbrich ,&nbsp;Michael Schuler ,&nbsp;Florian Gantner ,&nbsp;Ralf Heilker","doi":"10.1016/j.slasd.2023.04.002","DOIUrl":"10.1016/j.slasd.2023.04.002","url":null,"abstract":"<div><p>Macrophages play a pivotal role in drug discovery due to their key regulatory functions in health and disease. Overcoming the limited availability and donor variability of human monocyte-derived macrophages (MDMs), human induced pluripotent stem cell (iPSC)-derived macrophages (IDMs) could provide a promising tool for both disease modeling and drug discovery. To access large numbers of model cells for medium- to high-throughput application purposes, an upscaled protocol was established for differentiation of iPSCs into progenitor cells and subsequent maturation into functional macrophages. These IDM cells resembled MDMs both with respect to surface marker expression and phago- as well as efferocytotic function. A statistically robust high-content-imaging assay was developed to quantify the efferocytosis rate of IDMs and MDMs allowing for measurements both in the 384- and 1536-well microplate format. Validating the applicability of the assay, inhibitors of spleen tyrosine kinase (Syk) were shown to modulate efferocytosis in IDMs and MDMs with comparable pharmacology. The miniaturized cellular assay with the upscaled provision of macrophages opens new routes to pharmaceutical drug discovery in the context of efferocytosis-modulating substances.</p></div>","PeriodicalId":21764,"journal":{"name":"SLAS Discovery","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9973223","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High-throughput approaches to uncover synergistic drug combinations in leukemia","authors":"Emma J. Chory ,&nbsp;Meng Wang ,&nbsp;Michele Ceribelli ,&nbsp;Aleksandra M Michalowska ,&nbsp;Stefan Golas ,&nbsp;Erin Beck ,&nbsp;Carleen Klumpp-Thomas ,&nbsp;Lu Chen ,&nbsp;Crystal McKnight ,&nbsp;Zina Itkin ,&nbsp;Kelli M. Wilson ,&nbsp;David Holland ,&nbsp;Sanjay Divakaran ,&nbsp;James Bradner ,&nbsp;Javed Khan ,&nbsp;Berkley E. Gryder ,&nbsp;Craig J. Thomas ,&nbsp;Benjamin Z. Stanton","doi":"10.1016/j.slasd.2023.04.004","DOIUrl":"10.1016/j.slasd.2023.04.004","url":null,"abstract":"<div><p>We report a comprehensive drug synergy study in acute myeloid leukemia (AML). In this work, we investigate a panel of cell lines spanning both MLL-rearranged and non-rearranged subtypes. The work comprises a resource for the community, with many synergistic drug combinations that could not have been predicted <em>a priori</em>, and open source code for automation and analyses<em>.</em> We base our definitions of drug synergy on the Chou-Talalay method, which is useful for visualizations of synergy experiments in isobolograms, and median-effects plots, among other representations. Our key findings include drug synergies affecting the chromatin state, specifically in the context of regulation of the modification state of histone H3 lysine-27. We report open source high throughput methodology such that multidimensional drug screening can be accomplished with equipment that is accessible to most laboratories. This study will enable preclinical investigation of new drug combinations in a lethal blood cancer, with data analysis and automation workflows freely available to the community.</p></div>","PeriodicalId":21764,"journal":{"name":"SLAS Discovery","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10449086/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10089822","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":"In Vitro three-dimensional (3D) cell culture tools for spheroid and organoid models","authors":"Sang-Yun Lee ,&nbsp;In-Seong Koo ,&nbsp;Hyun Ju Hwang ,&nbsp;Dong Woo Lee","doi":"10.1016/j.slasd.2023.03.006","DOIUrl":"10.1016/j.slasd.2023.03.006","url":null,"abstract":"<div><p>Three-dimensional (3D) cell culture technology has been steadily studied since the 1990′s due to its superior biocompatibility compared to the conventional two-dimensional (2D) cell culture technology, and has recently developed into an organoid culture technology that further improved biocompatibility. Since the 3D culture of human cell lines in artificial scaffolds was demonstrated in the early 90′s, 3D cell culture technology has been actively developed owing to various needs in the areas of disease research, precision medicine, new drug development, and some of these technologies have been commercialized. In particular, 3D cell culture technology is actively being applied and utilized in drug development and cancer-related precision medicine research. Drug development is a long and expensive process that involves multiple steps—from target identification to lead discovery and optimization, preclinical studies, and clinical trials for approval for clinical use. Cancer ranks first among life-threatening diseases owing to intra-tumoral heterogeneity associated with metastasis, recurrence, and treatment resistance, ultimately contributing to treatment failure and adverse prognoses. Therefore, there is an urgent need for the development of efficient drugs using 3D cell culture techniques that can closely mimic <em>in vivo</em> cellular environments and customized tumor models that faithfully represent the tumor heterogeneity of individual patients. This review discusses 3D cell culture technology focusing on research trends, commercialization status, and expected effects developed until recently. We aim to summarize the great potential of 3D cell culture technology and contribute to expanding the base of this technology.</p></div>","PeriodicalId":21764,"journal":{"name":"SLAS Discovery","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9600340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of an enzyme-coupled activity assay for Janus kinase 2 inhibitor screening","authors":"Angelika Pölläniemi ,&nbsp;Anniina Virtanen ,&nbsp;Olli Silvennoinen ,&nbsp;Teemu Haikarainen","doi":"10.1016/j.slasd.2023.05.001","DOIUrl":"10.1016/j.slasd.2023.05.001","url":null,"abstract":"<div><p>JAK2 transmits signals of several important cytokines, such as growth hormone and erythropoietin. The interest toward the therapeutic targeting of JAK2 was boosted in 2005, when the somatic JAK2 V617F mutation, responsible for the majority of myeloproliferative neoplasms (MPNs) was discovered. JAK2 inhibitors have been approved for MPN therapy and they are effective in alleviating symptoms and improving the quality of life of the patients, but they do not lead to molecular remission. This calls for the discovery of new compounds for JAK2-targeted therapeutic approaches. Here we describe the development of a fluorescence-based activity assay for the screening of versatile inhibitor types against JAK2. The assay was utilized to screen a diverse set of small molecule weight natural products and the assay performance was compared to that of differential scanning fluorimetry. We identified 37 hits and further analysis of the most potent hits revealed that most of them displayed non-ATP competitive binding modes. The hits were profiled against other JAK family members and showed distinctive selectivity profiles. The developed assay is consistent, simple and inexpensive to use, and can be utilized for inhibitor screening of diverse compound classes against all JAK family members.</p></div>","PeriodicalId":21764,"journal":{"name":"SLAS Discovery","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9598842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fragment-based drug discovery of small molecule ligands for the human chemokine CCL28","authors":"Angela L. Zhou ,&nbsp;Davin R. Jensen ,&nbsp;Francis C. Peterson ,&nbsp;Monica A. Thomas ,&nbsp;Roman R. Schlimgen ,&nbsp;Michael B. Dwinell ,&nbsp;Brian C. Smith ,&nbsp;Brian F. Volkman","doi":"10.1016/j.slasd.2023.02.004","DOIUrl":"10.1016/j.slasd.2023.02.004","url":null,"abstract":"<div><p>The mucosal chemokine CCL28 is a promising target for immunotherapy drug development due to its elevated expression level in epithelial cells and critical role in creating and maintaining an immunosuppressive tumor microenvironment. Using sulfotyrosine as a probe, NMR chemical shift mapping identified a potential receptor-binding hotspot on the human CCL28 surface. CCL28 was screened against 2,678 commercially available chemical fragments by 2D NMR, yielding thirteen verified hits. Computational docking predicted that two fragments could occupy adjoining subsites within the sulfotyrosine recognition cleft. Dual NMR titrations confirmed their ability to bind CCL28 simultaneously, thereby validating an initial fragment pair for linking and merging strategies to design high-potency CCL28 inhibitors.</p></div>","PeriodicalId":21764,"journal":{"name":"SLAS Discovery","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10339762/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10153938","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":"High throughput assay for compounds that boost BDNF expression in neurons","authors":"Guey-Ying Liao ,&nbsp;Haifei Xu ,&nbsp;Justin Shumate ,&nbsp;Louis Scampavia ,&nbsp;Timothy Spicer ,&nbsp;Baoji Xu","doi":"10.1016/j.slasd.2023.02.005","DOIUrl":"10.1016/j.slasd.2023.02.005","url":null,"abstract":"<div><p>Deficiencies in brain-derived neurotrophic factor (BDNF) have been linked to several brain disorders, making compounds that can boost neuronal BDNF synthesis attractive as potential therapeutics. However, a sensitive and quantitative BDNF assay for high-throughput screening (HTS) is still missing. Here we report the generation of a new mouse <em>Bdnf</em> allele, <em>Bdnf^NLuc</em>, in which the sequence encoding nano luciferase (NLuc) is inserted into the <em>Bdnf</em> locus immediately before the stop codon so that the allele will produce a BDNF-NLuc fusion protein. BDNF-NLuc protein appears to function like BDNF as <em>Bdnf^NLuc/NLuc</em> homozygous mice grew and behaved almost normally. We were able to establish and optimize cultures of cortical and hippocampal <em>Bdnf^NLuc/+</em> neurons isolated from mouse embryos in 384-well plates. We used the cultures as a phenotypic assay to detect the ability of 10 mM KCl to stimulate BDNF synthesis and achieved a reproducible Z′ factor &gt; 0.50 for the assay, a measure considered suitable for HTS. We successfully scaled up the assay to screen the 1280-compound LOPAC library (Library of Pharmacologically Active Compounds). The screen identified several BDNF-boosting compounds, one of which is Bay K8644, a L-type voltage-gated calcium channel (L-VGCC) agonist, which was previously shown to stimulate BDNF synthesis. These results indicate that our phenotypic neuronal assay is ready for HTS to identify novel BDNF-boosting compounds.</p></div>","PeriodicalId":21764,"journal":{"name":"SLAS Discovery","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9356229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Using chemical and biological data to predict drug toxicity","authors":"Anika Liu ,&nbsp;Srijit Seal ,&nbsp;Hongbin Yang ,&nbsp;Andreas Bender","doi":"10.1016/j.slasd.2022.12.003","DOIUrl":"10.1016/j.slasd.2022.12.003","url":null,"abstract":"<div><p>Various sources of information can be used to better understand and predict compound activity and safety-related endpoints, including biological data such as gene expression and cell morphology. In this review, we first introduce types of chemical, <em>in vitro</em> and <em>in vivo</em> information that can be used to describe compounds and adverse effects. We then explore how compound descriptors based on chemical structure or biological perturbation response can be used to predict safety-related endpoints, and how especially biological data can help us to better understand adverse effects mechanistically. Overall, the described applications demonstrate how large-scale biological information presents new opportunities to anticipate and understand the biological effects of compounds, and how this can support predictive toxicology and drug discovery projects.</p></div>","PeriodicalId":21764,"journal":{"name":"SLAS Discovery","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9350503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High throughput screening for drugs that inhibit 3C-like protease in SARS-CoV-2","authors":"Emery Smith ,&nbsp;Meredith E. Davis-Gardner ,&nbsp;Ruben D. Garcia-Ordonez ,&nbsp;Tu-Trinh Nguyen ,&nbsp;Mitchell Hull ,&nbsp;Emily Chen ,&nbsp;Xuerong Yu ,&nbsp;Thomas D. Bannister ,&nbsp;Pierre Baillargeon ,&nbsp;Louis Scampavia ,&nbsp;Patrick Griffin ,&nbsp;Michael Farzan ,&nbsp;Timothy P. Spicer","doi":"10.1016/j.slasd.2023.01.001","DOIUrl":"10.1016/j.slasd.2023.01.001","url":null,"abstract":"<div><p>The SARS coronavirus 2 (SARS-CoV-2) pandemic remains a major problem in many parts of the world and infection rates remain at extremely high levels. This high prevalence drives the continued emergence of new variants, and possibly ones that are more vaccine-resistant and that can drive infections even in highly vaccinated populations. The high rate of variant evolution makes clear the need for new therapeutics that can be clinically applied to minimize or eliminate the effects of COVID-19. With a hurdle of 10 years, on average, for first in class small molecule therapeutics to achieve FDA approval, the fastest way to identify therapeutics is by drug repurposing. To this end, we developed a high throughput cell-based screen that incorporates the essential viral 3C-like protease and its peptide cleavage site into a luciferase complementation assay to evaluate the efficacy of known drugs encompassing approximately 15,000 clinical-stage or FDA-approved small molecules. Confirmed inhibitors were also tested to determine their cytotoxic properties. Medicinal chemistry efforts to optimize the hits identified Tranilast as a potential lead. Here, we report the rapid screening and identification of potentially relevant drugs that exhibit selective inhibition of the SARS-CoV-2 viral 3C-like protease.</p></div>","PeriodicalId":21764,"journal":{"name":"SLAS Discovery","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9839384/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9448729","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":"High-content phenotypic screen to identify small molecule enhancers of Parkin-dependent ubiquitination and mitophagy","authors":"Roberta Tufi ,&nbsp;Emily H. Clark ,&nbsp;Tamaki Hoshikawa,&nbsp;Christiana Tsagkaraki,&nbsp;Jack Stanley,&nbsp;Kunitoshi Takeda,&nbsp;James M. Staddon,&nbsp;Thomas Briston","doi":"10.1016/j.slasd.2022.12.004","DOIUrl":"10.1016/j.slasd.2022.12.004","url":null,"abstract":"<div><p>Mitochondrial dysfunction and aberrant mitochondrial homeostasis are key aspects of Parkinson's disease (PD) pathophysiology. Mutations in PINK1 and Parkin proteins lead to autosomal recessive PD, suggesting that defective mitochondrial clearance via mitophagy is key in PD etiology. Accelerating the identification and/or removal of dysfunctional mitochondria could therefore provide a disease-modifying approach to treatment. To that end, we performed a high-content phenotypic screen (HCS) of ∼125,000 small molecules to identify compounds that positively modulate mitochondrial accumulation of the PINK1-Parkin-dependent mitophagy initiation marker p-Ser65-Ub in Parkin haploinsufficiency (Parkin ^+/R275W) human fibroblasts. Following confirmatory counter-screening and orthogonal assays, we selected compounds of interest that enhance mitophagy-related biochemical and functional endpoints in patient-derived fibroblasts. Identification of inhibitors of the ubiquitin-specific peptidase and negative regulator of mitophagy USP30 within our hits further validated our approach. The compounds identified in this work provide a novel starting point for further investigation and optimization.</p></div>","PeriodicalId":21764,"journal":{"name":"SLAS Discovery","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9349728","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}