Chemoinformatics-based enumeration of chemical libraries: a tutorial

Virtual compound libraries are increasingly being used in computer-assisted drug discovery applications and have led to numerous successful cases. This paper aims to examine the fundamental concepts of library design and describe how to enumerate virtual libraries using open source tools. To exempli...

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Bibliographic Details
Published in:Journal of cheminformatics Vol. 12; no. 1; pp. 64 - 25
Main Authors: Saldívar-González, Fernanda I., Huerta-García, C. Sebastian, Medina-Franco, José L.
Format: Journal Article
Language:English
Published: Cham Springer International Publishing 27.10.2020
BioMed Central Ltd
Springer Nature B.V
BMC
Subjects:
Acetylcholinesterase
Applications
Challenges
Chemical enumeration
Chemical reactions
Chemistry
Chemistry and Materials Science
Chemists
Chemoinformatics
Combinatorial analysis
Combinatorial libraries
Computational Biology/Bioinformatics
Computer Applications in Chemistry
Digital libraries
Documentation and Information in Chemistry
DOS synthesis
Drug design
Drug discovery
Education
Educational
Enumeration
Enzyme inhibitors
In Silico Structure Generation: Recent Developments
Lactams
Reagents
Theoretical and Computational Chemistry
Virtual libraries
Combinatorial libraries
DOS synthesis
Education
Drug design
Chemical enumeration
KNIME
Chemoinformatics
Python
ISSN:1758-2946, 1758-2946
Online Access:Get full text
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Summary:Virtual compound libraries are increasingly being used in computer-assisted drug discovery applications and have led to numerous successful cases. This paper aims to examine the fundamental concepts of library design and describe how to enumerate virtual libraries using open source tools. To exemplify the enumeration of chemical libraries, we emphasize the use of pre-validated or reported reactions and accessible chemical reagents. This tutorial shows a step-by-step procedure for anyone interested in designing and building chemical libraries with or without chemoinformatics experience. The aim is to explore various methodologies proposed by synthetic organic chemists and explore affordable chemical space using open-access chemoinformatics tools. As part of the tutorial, we discuss three examples of design: a Diversity-Oriented-Synthesis library based on lactams, a bis-heterocyclic combinatorial library, and a set of target-oriented molecules: isoindolinone based compounds as potential acetylcholinesterase inhibitors. This manuscript also seeks to contribute to the critical task of teaching and learning chemoinformatics.
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ISSN:1758-2946
1758-2946
DOI:10.1186/s13321-020-00466-z