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Identication, analysis and prediction of frequent hitters from high-throughput screening

Barozet, Amelie (2016) BINP31 20152
Degree Projects in Bioinformatics
Abstract
High-throughput screening is one of the most extensively used methods for the identification of molecules of interest during early stages of drug development projects. It is however subject to many artifacts due to various mechanisms. Aggregation and redox cycling are examples of mechanisms of unspecific inhibition that make a large number of compounds appear as active in several high throughput screens that target distinct proteins. Pursuing such compounds (called frequent hitters) is very likely to lead to a dead-end. Understanding the importance of unspecific mechanisms of inhibition as well as identifying the corresponding compounds may thus save drug researchers a lot of time and resources. In a first part, we report an analysis of... (More)
High-throughput screening is one of the most extensively used methods for the identification of molecules of interest during early stages of drug development projects. It is however subject to many artifacts due to various mechanisms. Aggregation and redox cycling are examples of mechanisms of unspecific inhibition that make a large number of compounds appear as active in several high throughput screens that target distinct proteins. Pursuing such compounds (called frequent hitters) is very likely to lead to a dead-end. Understanding the importance of unspecific mechanisms of inhibition as well as identifying the corresponding compounds may thus save drug researchers a lot of time and resources. In a first part, we report an analysis of the behavior of literature-reported aggregating compounds in recent internal high throughput screens. We show that aggregation is not a major issue in in-house screens at AstraZeneca. In a second part, we describe an in silico method that successfully identifies fragments which contribute to the redox cycling properties of compounds containing them. (Less)
Popular Abstract
Problematic compounds in high-throughput screening libraries


Drug development projects usually start with identifying a molecular target related to a disease and with finding an inhibitor, that is a compound which can prevent the action of that molecular target. Nowadays, the preferred way to look for inhibitors is high-throughput screening (HTS). This consists in measuring in an automated way the effects of individual compounds against a target. Such automation enables the testing of many compounds at a fast speed. Unfortunately, some compounds can alter the measurement and appear as having an effect when they do not, and some others can inhibit many targets in a non specific fashion. Such compounds are not interesting starting... (More)
Problematic compounds in high-throughput screening libraries


Drug development projects usually start with identifying a molecular target related to a disease and with finding an inhibitor, that is a compound which can prevent the action of that molecular target. Nowadays, the preferred way to look for inhibitors is high-throughput screening (HTS). This consists in measuring in an automated way the effects of individual compounds against a target. Such automation enables the testing of many compounds at a fast speed. Unfortunately, some compounds can alter the measurement and appear as having an effect when they do not, and some others can inhibit many targets in a non specific fashion. Such compounds are not interesting starting points and it is important to be able to understand their effect and identify them. Aggregation and redox cycling are two mechanisms that lead to unspecific inhibition of the target. In this thesis we analyze the compounds that act through these mechanisms.

Aggregation

Some compounds are able to form large aggregates that isolate the targets, thereby inhibiting them. A recent publication reported a list of aggregators and we analyzed historical HTS data to verify whether those compounds were indeed problematic. We compared results from historical screens for these compounds and for other compounds in the screening library, in order to determine if the reported aggregators were really found active more often than other compounds.

Results showed that aggregation is not a major problem in HTS: in recent screens, precautions were taken to limit its effect and very few reported compounds were problematic. Still, the analysis identified around 270 compounds that should not be tested in the future.

Redox Cycling

Redox cycling consists in a cascade of electron exchanges which results in the chemical modification of susceptible targets only. For each compound, we therefore compared the number of times it was found to have an effect on these targets compared to the number of times it was tested, and we did the same for other non susceptible targets. Compounds that are particularly active against susceptible targets but not against other targets are likely to be redox cycling compounds.

Results identified molecular fragments that could give redox cycling properties to compounds, indicating compounds that should be removed when a redox-susceptible screen is run. These results were confirmed experimentally. This analysis was also used to estimate the reliability of three different screens aimed at identifying redox cycling compounds.


Supervisor: Ola Engkvist (Computational Chemistry, AstraZeneca R&D Gothenburg)
MasterĀ“s Degree Project 45 credits in Bioinformatics 2015-2016
Department of Biology, Lund University (Less)
Please use this url to cite or link to this publication:
author
Barozet, Amelie
supervisor
organization
course
BINP31 20152
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
8863601
date added to LUP
2016-03-18 15:35:36
date last changed
2016-03-21 10:55:18
@misc{8863601,
  abstract     = {High-throughput screening is one of the most extensively used methods for the identification of molecules of interest during early stages of drug development projects. It is however subject to many artifacts due to various mechanisms. Aggregation and redox cycling are examples of mechanisms of unspecific inhibition that make a large number of compounds appear as active in several high throughput screens that target distinct proteins. Pursuing such compounds (called frequent hitters) is very likely to lead to a dead-end. Understanding the importance of unspecific mechanisms of inhibition as well as identifying the corresponding compounds may thus save drug researchers a lot of time and resources. In a first part, we report an analysis of the behavior of literature-reported aggregating compounds in recent internal high throughput screens. We show that aggregation is not a major issue in in-house screens at AstraZeneca. In a second part, we describe an in silico method that successfully identifies fragments which contribute to the redox cycling properties of compounds containing them.},
  author       = {Barozet, Amelie},
  language     = {eng},
  note         = {Student Paper},
  title        = {Identication, analysis and prediction of frequent hitters from high-throughput screening},
  year         = {2016},
}