scholarly journals A small molecule screening to detect potential therapeutic targets in human podocytes

2017 ◽  
Vol 312 (1) ◽  
pp. F157-F171 ◽  
Author(s):  
Eugen Widmeier ◽  
Weizhen Tan ◽  
Merlin Airik ◽  
Friedhelm Hildebrandt
Keyword(s):  
Nephrotic Syndrome ◽  
Small Molecule ◽  
High Throughput ◽  
Therapeutic Targets ◽  
Intermediate Phenotype ◽  
Treatment Modalities ◽  
Glomerular Diseases ◽  
Glomerular Epithelial Cell ◽  
Migration Assay ◽  
Small Molecule Screening

Widmeier E, Tan W, Airik M, Hildebrandt F. A small molecule screening to detect potential therapeutic targets in human podocytes. Am J Physiol Renal Physiol 312: F157–F171, 2017. First published October 19, 2016; doi:10.1152/ajprenal.00386.2016. Steroid-resistant nephrotic syndrome (SRNS) inevitably progresses to end-stage kidney disease, requiring dialysis or transplantation for survival. However, treatment modalities and drug discovery remain limited. Mutations in over 30 genes have been discovered as monogenic causes of SRNS. Most of these genes are predominantly expressed in the glomerular epithelial cell, the podocyte, placing it at the center of the pathogenesis of SRNS. Podocyte migration rate (PMR) represents a relevant intermediate phenotype of disease in monogenic causes of SRNS. We therefore adapted PMR in a high-throughput manner to screen small molecules as potential therapeutic targets for SRNS. We performed a high-throughput drug screening of a National Institutes of Health Clinical Collection (NCC) library ( n = 725 compounds) measuring PMR by videomicroscopy. We used the Woundmaker to perform individual 96-well scratch wounds and screened compounds using a quantitative kinetic live cell imaging migration assay using IncuCyte ZOOM technology. Using a normal distribution for the average PMR in wild-type podocytes with a vehicle control (DMSO), we applied a 90% confidence interval to define “distinct” compounds (5% faster/slower PMR) and found that 12 of 725 compounds (at 10 μM) reduced PMR. Clusters of drugs that alter PMR included actin/tubulin modulators such as the azole class of antifungals and antineoplastic vinca-alkaloids. We hereby identify compounds that alter PMR. The PMR assay provides a new avenue to test therapeutics for nephrotic syndrome. Positive results may reveal novel pathways in the study of glomerular diseases such as SRNS.

scholarly journals High-throughput small molecule screen identifies inhibitors of aberrant chromatin accessibility

2016 ◽  
Vol 113 (11) ◽  
pp. 3018-3023 ◽  
Author(s):  
Samantha G. Pattenden ◽  
Jeremy M. Simon ◽  
Aminah Wali ◽  
Chatura N. Jayakody ◽  
Jacob Troutman ◽  
...  
Keyword(s):  
Small Molecule ◽  
High Throughput ◽  
Histone Deacetylase Inhibitors ◽  
A Priori ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Loss Of Function ◽  
Chromatin Signature ◽  
Biologically Relevant ◽  
Small Molecule Screening

Mutations in chromatin-modifying proteins and transcription factors are commonly associated with a wide variety of cancers. Through gain- or loss-of-function, these mutations may result in characteristic alterations of accessible chromatin, indicative of shifts in the landscape of regulatory elements genome-wide. The identification of compounds that reverse a specific chromatin signature could lead to chemical probes or potential therapies. To explore whether chromatin accessibility could serve as a platform for small molecule screening, we adapted formaldehyde-assisted isolation of regulatory elements (FAIRE), a chemical method to enrich for nucleosome-depleted genomic regions, as a high-throughput, automated assay. After demonstrating the validity and robustness of this approach, we applied this method to screen an epigenetically targeted small molecule library by evaluating regions of aberrant nucleosome depletion mediated by EWSR1-FLI1, the chimeric transcription factor critical for the bone and soft tissue tumor Ewing sarcoma. As a class, histone deacetylase inhibitors were greatly overrepresented among active compounds. These compounds resulted in diminished accessibility at targeted sites by disrupting transcription of EWSR1-FLI1. Capitalizing on precise differences in chromatin accessibility for drug discovery efforts offers significant advantages because it does not depend on the a priori selection of a single molecular target and may detect novel biologically relevant pathways.

scholarly journals Small-molecule metabolome identifies potential therapeutic targets against COVID-19

2021 ◽  
Author(s):  
Sean M.P. Bennet ◽  
Martin Kaufmann ◽  
Kaede Takami ◽  
Calvin Sjaarda ◽  
Katya Douchant ◽  
...  
Keyword(s):  
Small Molecules ◽  
Small Molecule ◽  
Influenza A ◽  
Therapeutic Targets ◽  
Host Cells ◽  
Hydroxybutyric Acid ◽  
Qrt Pcr ◽  
Small Molecule Screening ◽  
Machine Learning Model ◽  
Syncytial Virus

Background: Respiratory viruses are transmitted and acquired via the nasal mucosa, and thereby may influence the nasal metabolome composed of biochemical products produced by both host cells and microbes. Studies of the nasal metabolome demonstrate virus-specific changes that sometimes correlate with viral load and disease severity. Here, we evaluate the nasopharyngeal metabolome of COVID-19 infected individuals and report several small molecules that may be used as potential therapeutic targets. Specimens were tested by qRT-PCR with target primers for three viruses: Influenza A (INFA), respiratory syncytial virus (RSV), and SARS-CoV-2, along with asymptomatic controls. The nasopharyngeal metabolome was characterized using an LC-MS/MS-based small-molecule screening kit capable of quantifying 141 analytes. A machine learning model identified 28 discriminating analytes and correctly categorized patients with a viral infection with an accuracy of 96% (R2=0.771, Q2=0.72). A second model identified 5 analytes to differentiate COVID19-infected patients from those with INFA or RSV with an accuracy of 85% (R2=0.442, Q2=0.301). Specifically, LysoPCaC18:2 concentration was significantly increased in COVID19 patients (P< 0.0001), whereas beta-hydroxybutyric acid, Met SO, succinic acid, and carnosine concentrations were significantly decreased (P< 0.0001). This study demonstrates that COVID19 infection results in a unique NP metabolomic signature with carnosine and LysoPCaC18:2 as potential therapeutic targets.

Abstract A21: High-throughput small molecule screening of genetically diverse glioblastoma stem cells

2012 ◽  
Author(s):  
Garth W. Strohbehn ◽  
Jiangbing Zhou ◽  
Michael Fu ◽  
Toral R. Patel ◽  
Joseph M. Piepmeier ◽  
...  
Keyword(s):  
Stem Cells ◽  
Small Molecule ◽  
High Throughput ◽  
Glioblastoma Stem Cells ◽  
Small Molecule Screening

scholarly journals High-throughput metabolomics used to identify potential therapeutic targets of Guizhi Fuling Wan against endometriosis of cold coagulation and blood stasis

RSC Advances ◽  
2018 ◽  
Vol 8 (34) ◽  
pp. 19238-19250 ◽  
Author(s):  
Xiu-hong Wu ◽  
Chuang Zhao ◽  
Ai-hua Zhang ◽  
Jin-qi Zhang ◽  
Xu Wang ◽  
...  
Keyword(s):  
Small Molecule ◽  
High Throughput ◽  
Comprehensive Evaluation ◽  
Blood Stasis ◽  
Therapeutic Targets ◽  
Endogenous Metabolites ◽  
Cold Coagulation

Metabolomics is an emerging and robust discipline and involves the comprehensive evaluation of small molecule endogenous metabolites and enables the exploration of the pathogenesis of diseases.

scholarly journals Identification and Correction of Additive and Multiplicative Spatial Biases in Experimental High-Throughput Screening

2018 ◽  
Vol 23 (5) ◽  
pp. 448-458
Author(s):  
Bogdan Mazoure ◽  
Iurie Caraus ◽  
Robert Nadon ◽  
Vladimir Makarenkov
Keyword(s):  
Small Molecule ◽  
High Throughput ◽  
High Throughput Screening ◽  
Statistical Procedure ◽  
Microarray Technology ◽  
Spatial Bias ◽  
Small Molecule Screening ◽  
Bias Model ◽  
Different Types ◽  
Multiwell Plates

Data generated by high-throughput screening (HTS) technologies are prone to spatial bias. Traditionally, bias correction methods used in HTS assume either a simple additive or, more recently, a simple multiplicative spatial bias model. These models do not, however, always provide an accurate correction of measurements in wells located at the intersection of rows and columns affected by spatial bias. The measurements in these wells depend on the nature of interaction between the involved biases. Here, we propose two novel additive and two novel multiplicative spatial bias models accounting for different types of bias interactions. We describe a statistical procedure that allows for detecting and removing different types of additive and multiplicative spatial biases from multiwell plates. We show how this procedure can be applied by analyzing data generated by the four HTS technologies (homogeneous, microorganism, cell-based, and gene expression HTS), the three high-content screening (HCS) technologies (area, intensity, and cell-count HCS), and the only small-molecule microarray technology available in the ChemBank small-molecule screening database. The proposed methods are included in the AssayCorrector program, implemented in R, and available on CRAN.

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