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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Vydáno v:Journal of cheminformatics Ročník 12; číslo 1; s. 64 - 25
Hlavní autoři: Saldívar-González, Fernanda I., Huerta-García, C. Sebastian, Medina-Franco, José L.
Médium: Journal Article
Jazyk:angličtina
Vydáno: Cham Springer International Publishing 27.10.2020
BioMed Central Ltd
Springer Nature B.V
BMC
Témata:
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
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Abstract 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.
AbstractList 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.
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.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.
Abstract 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.
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. Keywords: Chemical enumeration, Chemoinformatics, Combinatorial libraries, DOS synthesis, Drug design, Education, KNIME, Python
ArticleNumber 64
Audience Academic
Author Medina-Franco, José L.
Huerta-García, C. Sebastian
Saldívar-González, Fernanda I.
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  surname: Saldívar-González
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  organization: DIFACQUIM Research Group, School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México
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Issue 1
Keywords Combinatorial libraries
DOS synthesis
Education
Drug design
Chemical enumeration
KNIME
Chemoinformatics
Python
Language English
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springer_journals_10_1186_s13321_020_00466_z
PublicationCentury 2000
PublicationDate 2020-10-27
PublicationDateYYYYMMDD 2020-10-27
PublicationDate_xml – month: 10
  year: 2020
  text: 2020-10-27
  day: 27
PublicationDecade 2020
PublicationPlace Cham
PublicationPlace_xml – name: Cham
– name: England
– name: London
PublicationTitle Journal of cheminformatics
PublicationTitleAbbrev J Cheminform
PublicationTitleAlternate J Cheminform
PublicationYear 2020
Publisher Springer International Publishing
BioMed Central Ltd
Springer Nature B.V
BMC
Publisher_xml – name: Springer International Publishing
– name: BioMed Central Ltd
– name: Springer Nature B.V
– name: BMC
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Snippet Virtual compound libraries are increasingly being used in computer-assisted drug discovery applications and have led to numerous successful cases. This paper...
Abstract Virtual compound libraries are increasingly being used in computer-assisted drug discovery applications and have led to numerous successful cases....
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SubjectTerms 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
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Title Chemoinformatics-based enumeration of chemical libraries: a tutorial
URI https://link.springer.com/article/10.1186/s13321-020-00466-z
https://www.ncbi.nlm.nih.gov/pubmed/33372622
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Volume 12
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