Chemoinformatic Characterization of the Chemical Space and Molecular Diversity of Compound Libraries

Medina‐Franco, José L.

doi:10.1002/9781118618110.ch10

Cited by 10 publications

(8 citation statements)

References 137 publications

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“…This type of deal has been undertaken between two companies working in two different business areas, e.g., human health and crop protection, with each receiving freedom to patent and develop in their own field when interesting molecules originating from the partner are identified. This type of deal involves mainly chemoinformatic and logistic resources in order to select the best complementary chemical space and compounds adding value to the collection of the receiving party . Furthermore, and contrary to the previous consortium model, chemical structures are disclosed from the start and the amount of material to exchange is negotiated.…”

Section: Expanding Diversity For Structure-agnostic Screening Through...mentioning

confidence: 99%

“…This type of deal involves mainly chemoinformatic and logistic resources in order to select the best complementary chemical space and compounds adding value to the collection of the receiving party. 115 Furthermore, and contrary to the previous consortium model, chemical structures are disclosed from the start and the amount of material to exchange is negotiated.…”

Section: Increasing the Size Of Screening Collections Through Compoun...mentioning

confidence: 99%

See 1 more Smart Citation

New Modalities, Technologies, and Partnerships in Probe and Lead Generation: Enabling a Mode-of-Action Centric Paradigm

Valeur

Jimonet

2018

J. Med. Chem.

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With the rise of novel biology and high potential target identification technologies originating from advances in genomics, medicinal chemists are progressively facing targets of increasing complexity and often unprecedented. Novel hit finding technologies, combined with a wider choice of drug modalities, has resulted in a unique repertoire of options to address these challenging targets and to identify suitable starting points for optimization. Furthermore, innovative solutions originating from a range of academic groups and biotech companies require new types of collaborative models to leverage and integrate them in the drug discovery process. This perspective provides a guide for medicinal chemists covering contemporary probe and lead generation approaches and discusses the strengths and limitations of each strategy. Moreover, the expansion of strategies to modulate proteins creates the opportunity of a modality-agnostic and mode-of-action centric hit finding paradigm.

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Section: Expanding Diversity For Structure-agnostic Screening Through...mentioning

confidence: 99%

Section: Increasing the Size Of Screening Collections Through Compoun...mentioning

confidence: 99%

New Modalities, Technologies, and Partnerships in Probe and Lead Generation: Enabling a Mode-of-Action Centric Paradigm

Valeur

Jimonet

2018

J. Med. Chem.

View full text Add to dashboard Cite

show abstract

“…The quantitative information generated helps guide the selection of compound libraries or individual compounds to identify novel lead candidates for biological targets. In particular, diversity analysis helps compare different databases and evaluate the structural novelty of a compound collection [ 113 ]. Free tools such as RDKit [ 23 ], Platform for Unified Molecular Analysis (PUMA) [ 114 ], or the workflows developed in KNIME by Naveja et al [ 115 ] can help in the task of assessing chemical diversity.…”

Section: Post-processing Virtual Librariesmentioning

confidence: 99%

Chemoinformatics-based enumeration of chemical libraries: a tutorial

2020

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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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“…A very useful tool for describing quantitatively the molecular diversity of DOS library compounds in the chemical space is the application of chemoinformatics [56,57,58]. Chemical space, as described by Dobson, is “the total descriptor space that encompasses all the small carbon-based molecules that could in principle be created” [59].…”

Section: Case Study 2: Contribution Of David R Spring To the Discmentioning

confidence: 99%

Diversity-Oriented Synthesis as a Tool for Chemical Genetics

2014

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Chemical genetics is an approach for identifying small molecules with the ability to induce a biological phenotype or to interact with a particular gene product, and it is an emerging tool for lead generation in drug discovery. Accordingly, there is a need for efficient and versatile synthetic processes capable of generating complex and diverse molecular libraries, and Diversity-Oriented Synthesis (DOS) of small molecules is the concept of choice to give access to new chemotypes with high chemical diversity. In this review, the combination of chemical genetics and diversity-oriented synthesis to identify new chemotypes as hit compounds in chemical biology and drug discovery is reported, giving an overview of basic concepts and selected case studies.

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Chemoinformatic Characterization of the Chemical Space and Molecular Diversity of Compound Libraries

Cited by 10 publications

References 137 publications

New Modalities, Technologies, and Partnerships in Probe and Lead Generation: Enabling a Mode-of-Action Centric Paradigm

New Modalities, Technologies, and Partnerships in Probe and Lead Generation: Enabling a Mode-of-Action Centric Paradigm

Chemoinformatics-based enumeration of chemical libraries: a tutorial

Diversity-Oriented Synthesis as a Tool for Chemical Genetics

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