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Pooled CRISPR-Based Genetic Screens in Mammalian Cells
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A reliable computational workflow for the selection of optimal screening libraries.

Yocheved Gilad1, Katalin Nadassy2, Hanoch Senderowitz1

  • 1Department of Chemistry, Bar-Ilan University, Ramat-Gan, 52900 Israel.

Journal of Cheminformatics
|December 23, 2015
PubMed
Summary

Selecting the best screening libraries for drug discovery is challenging. We developed a novel workflow to rationally assess and select project-specific compound libraries based on quality and diversity metrics.

Keywords:
DiversityFingerprintsLibrary selectionQSARScreening librariesSimilarity

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Area of Science:

  • * Drug discovery and development
  • * Cheminformatics and computational chemistry
  • * Medicinal chemistry

Background:

  • * High-throughput screening (HTS) campaigns are crucial in drug discovery.
  • * The quality of compound libraries directly impacts screening success.
  • * Selecting optimal screening libraries from various vendors is a significant challenge.

Purpose of the Study:

  • * To develop a novel workflow for the rational selection of project-specific screening libraries.
  • * To provide a systematic approach for evaluating and comparing different compound collections.
  • * To aid in optimizing drug discovery pipelines by ensuring high-quality library selection.

Main Methods:

  • * A multi-step workflow including data curation, ADME/T profiling, promiscuity assessment, diversity analysis, and similarity matching.
  • * Implementation of Lipinski's and Veber's rules, and a validated blood-brain barrier permeation model.
  • * Identification and application of optimal diversity and similarity descriptors using established databases (Drug Bank, CMC, CHEMBL).

Main Results:

  • * The workflow was applied to analyze nine common screening libraries from six vendors, assessing their quality.
  • * Detailed analysis reports were generated for each library, highlighting strengths and weaknesses.
  • * A consensus approach was developed to provide a single score for library selection under various scenarios.

Conclusions:

  • * A validated workflow for rational screening library selection has been developed and tested.
  • * The workflow is adaptable and reproducible, suitable for computational groups.
  • * Routine use in laboratory projects consistently yields well-balanced compound libraries.