scholarly journals A Simple Strategy for Mitigating the Effect of Data Variability on the Identification of Active Chemotypes from High-Throughput Screening Data

2007 ◽  
Vol 12 (2) ◽  
pp. 276-284 ◽  
Author(s):  
Stephen R. Johnson ◽  
Ramesh Padmanabha ◽  
Wayne Vaccaro ◽  
Mark Hermsmeier ◽  
Angela Cacace ◽  
...  
Keyword(s):  
Monte Carlo Simulation ◽  
Monte Carlo ◽  
High Throughput ◽  
High Throughput Screening ◽  
A Priori ◽  
Response Curves ◽  
Simple Strategy ◽  
Data Variability ◽  
The Individual ◽  
Protein Supply

Among the several goals of a high-throughput screening campaign is the identification of as many active chemotypes as possible for further evaluation. Often, however, the number of concentration response curves (e.g., IC50s or Kis) that can be collected following a primary screen is limited by practical constraints such as protein supply, screening workload, and so forth. One possible approach to this dilemma is to cluster the hits from the primary screen and sample only a few compounds from each cluster. This introduces the question as to how many compounds must be selected from a cluster to ensure that an active compound is identified, if it exists at all. This article seeks to address this question using a Monte Carlo simulation in which the dependence of the success of sampling is directly linked to screening data variability. Furthermore, the authors demonstrate that the use of replicated compounds in the screening collection can easily assess this variability and provide a priori guidance to the screener and chemist as to the extent of sampling required to maximize chemotype identification during the triage process. The individual steps of the Monte Carlo simulation provide insight into the correspondence between the percentage inhibition and eventual IC50 curves.

High-Throughput Affinity Selection Mass Spectrometry Using SAMDI-MS to Identify Small-Molecule Binders of the Human Rhinovirus 3C Protease

2021 ◽  
pp. 247255522110232
Author(s):  
Michael D. Scholle ◽  
Doug McLaughlin ◽  
Zachary A. Gurard-Levin
Keyword(s):  
Mass Spectrometry ◽  
Drug Discovery ◽  
High Throughput ◽  
High Throughput Screening ◽  
Human Rhinovirus ◽  
Binding Potential ◽  
Affinity Selection ◽  
Response Curves ◽  
Desorption Ionization ◽  
Self Assembled

Affinity selection mass spectrometry (ASMS) has emerged as a powerful high-throughput screening tool used in drug discovery to identify novel ligands against therapeutic targets. This report describes the first high-throughput screen using a novel self-assembled monolayer desorption ionization (SAMDI)–ASMS methodology to reveal ligands for the human rhinovirus 3C (HRV3C) protease. The approach combines self-assembled monolayers of alkanethiolates on gold with matrix-assisted laser desorption ionization time-of-flight (MALDI TOF) mass spectrometry (MS), a technique termed SAMDI-ASMS. The primary screen of more than 100,000 compounds in pools of 8 compounds per well was completed in less than 8 h, and informs on the binding potential and selectivity of each compound. Initial hits were confirmed in follow-up SAMDI-ASMS experiments in single-concentration and dose–response curves. The ligands identified by SAMDI-ASMS were further validated using differential scanning fluorimetry (DSF) and in functional protease assays against HRV3C and the related SARS-CoV-2 3CLpro enzyme. SAMDI-ASMS offers key benefits for drug discovery over traditional ASMS approaches, including the high-throughput workflow and readout, minimizing compound misbehavior by using smaller compound pools, and up to a 50-fold reduction in reagent consumption. The flexibility of this novel technology opens avenues for high-throughput ASMS assays of any target, thereby accelerating drug discovery for diverse diseases.

Automatic 3D Cell Analysis in High-Throughput Microarray Using Micropillar and Microwell Chips

2015 ◽  
Vol 20 (9) ◽  
pp. 1178-1184 ◽  
Author(s):  
Dong Woo Lee ◽  
Moo-Yeal Lee ◽  
Bosung Ku ◽  
Do-Hyun Nam
Keyword(s):  
Standard Deviation ◽  
High Throughput ◽  
High Throughput Screening ◽  
Doubling Time ◽  
Cultured Cells ◽  
Measurement Methods ◽  
Cell Analysis ◽  
Response Curves ◽  
U251 Cell ◽  
Doubling Times

Area-based and intensity-based 3D cell viability measurement methods are compared in high-throughput screening in order to analyze their effects on the assay results (doubling time and IC50) and their repeatability. Many other 3D cell-based high-throughput screening platforms had been previously introduced, but these had not clearly addressed the effects of the two methods on the assay results and assay repeatability. In this study, the optimal way to analyze 3D cultured cells is achieved by comparing day-to-day data of doubling times and IC50 values obtained from the two methods. In experiments, the U251 cell line is grown in chips. The doubling time, based on the area of the 3D cells, was 27.8 ± 1.8 h (standard deviation: 6.6%) and 27.8 ± 3.8 h (standard deviation: 13.7%) based on the intensity of the 3D cells. The doubling time calculated by area shows a smaller standard deviation than one calculated by intensity. IC50 values calculated by both methods are very similar. The standard deviations of IC50 values for the two methods were within ±3-fold. The IC50 variations of the 12 compounds were similar regardless of the viability measurement methods and were highly related to the shape of the dose–response curves.

Electricity supplier selection by a household in the Czech Republic in 2017 and 2018 – Monte Carlo simulation approach

2019 ◽  
Author(s):  
Martina Kuncova
Keyword(s):  
Monte Carlo Simulation ◽  
Monte Carlo ◽  
Czech Republic ◽  
Electricity Market ◽  
Electricity Consumption ◽  
Point Of View ◽  
The Czech Republic ◽  
Extra Effort ◽  
The Individual ◽  
Monte Carlo Simulation Model

The situation on the electricity retail market in the Czech Republic is not clear because of the number of suppliers and its products. Although the information about the prices for the electricity consumption for households is available on the web and each household can change the supplier nearly with no extra effort and cost, households are still often not familiar with the individual price items of the products. In this article the analysis of the Czech electricity market from the distribution rate D25d point of view is made for the years 2017-2018 when the household annual consumption is simulated via Monte Carlo simulation model. The aim of this paper is to select such a supplier and product that minimizes the total costs of the electricity for a household for the selected distribution rate and compare it with the results from the previous years.

scholarly journals Determining patient abdomen thickness from a single digital radiograph with a computational model: clinical results from a proof of concept study

2020 ◽  
Vol 93 (1111) ◽  
pp. 20200010
Author(s):  
Mark Worrall ◽  
Sarah Vinnicombe ◽  
David Sutton
Keyword(s):  
Monte Carlo Simulation ◽  
Monte Carlo ◽  
Computational Model ◽  
A Priori ◽  
Clinical Results ◽  
A Priori Knowledge ◽  
Proof Of Concept ◽  
Radiographic Image ◽  
X Ray ◽  
Digital Radiograph

Objective: A computational model has been created to estimate the abdominal thickness of a patient following an X-ray examination; its intended application is assisting with patient dose audit of paediatric X-ray examinations. This work evaluates the accuracy of the computational model in a clinical setting for adult patients undergoing anteroposterior (AP) abdomen X-ray examinations. Methods: The model estimates patient thickness using the radiographic image, the exposure factors with which the image was acquired, a priori knowledge of the characteristics of the X-ray unit and detector and the results of extensive Monte Carlo simulation of patient examinations. For 20 patients undergoing AP abdominal X-ray examinations, the model was used to estimate the patient thickness; these estimates were compared against a direct measurement made at the time of the examination. Results: Estimates of patient thickness made using the model were on average within ±5.8% of the measured thickness. Conclusion: The model can be used to accurately estimate the thickness of a patient undergoing an AP abdominal X-ray examination where the patient’s size falls within the range of the size of patients used to create the computational model. Advances in knowledge: This work demonstrates that it is possible to accurately estimate the AP abdominal thickness of an adult patient using the digital X-ray image and a computational model.

scholarly journals Homogeneous Cell- and Bead-Based Assays for High Throughput Screening Using Fluorometric Microvolume Assay Technology

1999 ◽  
Vol 4 (4) ◽  
pp. 193-204 ◽  
Author(s):  
Sheri Miraglia ◽  
Elana E. Swartzman ◽  
Julia Mellentin-Michelotti ◽  
Lolita Evangelista ◽  
Christopher Smith ◽  
...  
Keyword(s):  
Ligand Binding ◽  
High Throughput ◽  
High Throughput Screening ◽  
Laser Scanner ◽  
Peptide Ligand ◽  
Binding Assays ◽  
Using Data ◽  
Immunological Assays ◽  
The Individual ◽  
Homogeneous Assays

High throughput drug screening has become a critical component of the drug discovery process. The screening of libraries containing hundreds of thousands of compounds has resulted in a requirement for assays and instrumentation that are amenable to nonradioactive formats and that can be miniaturized. Homogeneous assays that minimize upstream automation of the individual assays are also preferable. Fluorometric microvolume assay technology (FMAT) is a fluorescence-based platform for the development of nonradioactive cell- and bead-based assays for HTS. This technology is plate format-independent, and while it was designed specifically for homogeneous ligand binding and immunological assays, it is amenable to any assay utilizing a fluorescent cell or bead. The instrument fits on a standard laboratory bench and consists of a laser scanner that generates a 1 mm2 digitized image of a 100-μm deep section of the bottom of a microwell plate. The instrument is directly compatible with a Zymark Twister™ (Zymark Corp., Hopkinton, MA) for robotic loading of the scanner and unattended operation in HTS mode. Fluorescent cells or beads at the bottom of the well are detected as localized areas of concentrated fluorescence using data processing. Unbound flurophore comprising the background signal is ignored, allowing for the development of a wide variety of homogeneous assays. The use of FMAT for peptide ligand binding assays, immunofluorescence, apoptosis and cytotoxicity, and bead-based immunocapture assays is described here, along with a general overview of the instrument and software.

Intensity and resolution effects in converging multichannel collimators for SANS by Monte Carlo simulation

2003 ◽  
Vol 36 (5) ◽  
pp. 1262-1265 ◽  
Author(s):  
A. N. Falcão ◽  
F. M. A. Margaça ◽  
F. G. Carvalho
Keyword(s):  
Computer Simulation ◽  
Monte Carlo Simulation ◽  
Monte Carlo ◽  
Neutron Beam ◽  
Incident Neutron ◽  
Beam Direction ◽  
Channel Axis ◽  
Monte Carlo Computer Simulation ◽  
The Individual ◽  
Incident Neutron Beam

A study of the contribution of the individual channels of a converging multichannel collimator to the operation of the device is carried out by means of a Monte Carlo computer simulation. The simulation shows that the coupling between the divergence of the incident neutron beam and the inclination of the individual CMC channel axis relative to the beam direction modulates the channel performance as far as intensity and resolution of the transmitted neutrons are concerned. While this does not impair in any significant way the usefulness of the device, the results are helpful to the designer.

scholarly journals Systematic Identification of Antiprion Drugs by High-Throughput Screening Based on Scanning for Intensely Fluorescent Targets

2005 ◽  
Vol 79 (12) ◽  
pp. 7785-7791 ◽  
Author(s):  
Uwe Bertsch ◽  
Konstanze F. Winklhofer ◽  
Thomas Hirschberger ◽  
Jan Bieschke ◽  
Petra Weber ◽  
...  
Keyword(s):  
High Throughput ◽  
Conformational Changes ◽  
High Throughput Screening ◽  
Prion Diseases ◽  
Inhibitory Effect ◽  
Helical Conformation ◽  
Response Curves ◽  
Vitro Assay ◽  
Systematic Identification

ABSTRACT Conformational changes and aggregation of specific proteins are hallmarks of a number of diseases, like Alzheimer's disease, Parkinson's disease, and prion diseases. In the case of prion diseases, the prion protein (PrP), a neuronal glycoprotein, undergoes a conformational change from the normal, mainly alpha-helical conformation to a disease-associated, mainly beta-sheeted scrapie isoform (PrPSc), which forms amyloid aggregates. This conversion, which is crucial for disease progression, depends on direct PrPC/PrPSc interaction. We developed a high-throughput assay based on scanning for intensely fluorescent targets (SIFT) for the identification of drugs which interfere with this interaction at the molecular level. Screening of a library of 10,000 drug-like compounds yielded 256 primary hits, 80 of which were confirmed by dose response curves with half-maximal inhibitory effects ranging from 0.3 to 60 μM. Among these, six compounds displayed an inhibitory effect on PrPSc propagation in scrapie-infected N2a cells. Four of these candidate drugs share an N′-benzylidene-benzohydrazide core structure. Thus, the combination of high-throughput in vitro assay with the established cell culture system provides a rapid and efficient method to identify new antiprion drugs, which corroborates that interaction of PrPC and PrPSc is a crucial molecular step in the propagation of prions. Moreover, SIFT-based screening may facilitate the search for drugs against other diseases linked to protein aggregation.

Sign in / Sign up

Export Citation Format

Share Document