Quantitative Structure-Epigenetic Activity Relationships

García-Sánchez, Mario Omar; Cruz-Monteagudo, Maykel; Medina-Franco, José L.

doi:10.1007/978-3-319-56850-8_8

Cited by 5 publications

(1 citation statement)

References 106 publications

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“…The functions and a DAD map generated with Activity Landscape Plotter are illustrated with a data set of 88 bromodomain inhibitors (BRDis) and their activity obtained from ChEMBL against isoforms 2, 3, and 4 . In this example, Activity Landscape Plotter performs and outputs 2775 pairwise comparisons which are presented on the DAD map.…”

Section: Resultsmentioning

confidence: 99%

Activity Landscape Plotter: A Web-Based Application for the Analysis of Structure–Activity Relationships

González-Medina

Méndez‐Lucio

Medina-Franco

2017

J. Chem. Inf. Model.

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Activity landscape modeling is a powerful method for the quantitative analysis of structure-activity relationships. This cheminformatics area is in continuous growth, and several quantitative and visual approaches are constantly being developed. However, these approaches often fall into disuse due to their limited access. Herein, we present Activity Landscape Plotter as the first freely available web-based tool to automatically analyze structure-activity relationships of compound data sets. Based on the concept of activity landscape modeling, the online service performs pairwise structure and activity relationships from an input data set supplied by the user. For visual analysis, Activity Landscape Plotter generates Structure-Activity Similarity and Dual-Activity Difference maps. The user can interactively navigate through the maps and export all the pairwise structure-activity information as comma delimited files. Activity Landscape Plotter is freely accessible at https://unam-shiny-difacquim.shinyapps.io/ActLSmaps /.

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Section: Resultsmentioning

confidence: 99%

Activity Landscape Plotter: A Web-Based Application for the Analysis of Structure–Activity Relationships

González-Medina

Méndez‐Lucio

Medina-Franco

2017

J. Chem. Inf. Model.

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The Acid/Base Characterization of Molecules with Epigenetic Activity

Santibáñez‐Morán

Medina‐Franco

2021

ChemMedChem

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The acidic and basic functional groups in a molecule strongly influence its physicochemical properties, affinity for a macromolecule, pharmacokinetics, and toxicity. For instance, basicity has been correlated with molecular promiscuity, hERG blockade, and phospholipidosis. Nonetheless, no systematic characterization of the acid/base profile of epigenomic databases has been reported. This study describes an analysis of the acidic ionization constant distribution of a library of 7820 compounds with reported activity against epigenetic targets. Furthermore, the epigenomics database's acid/base profile was compared to the reference libraries of food chemicals, natural products, and approved drugs. It was found that the acid/base profile of histone lysine demethylase ligands is more similar to previously approved drugs, and histone acetyltransferase ligands have acidic and basic functional groups largely found in food chemicals and natural products; this support the potential of these libraries for finding new epigenetic inhibitors.

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Chemoinformatics: a perspective from an academic setting in Latin America

et al. 2017

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This perspective discusses the current progress of a chemoinformatics group in a major university in Latin America. Three major aspects are discussed in a critical manner: research, education, and collaboration with industry and other public research networks. It is also presented an overview of the progress in applied research and development of research concepts. Efforts to teach chemoinformatics at the undergraduate and graduate levels are discussed. It is addressed how the partnership with industry and other not-for-profit research institutions not only brings additional sources of funding but, more importantly, increases the impact of the multidisciplinary work and offers the students to be exposed to other research environments. We also discuss the main perspectives and challenges that remain to be addressed in these settings.

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Quantitative Structure-Epigenetic Activity Relationships

Cited by 5 publications

References 106 publications

Activity Landscape Plotter: A Web-Based Application for the Analysis of Structure–Activity Relationships

Activity Landscape Plotter: A Web-Based Application for the Analysis of Structure–Activity Relationships

The Acid/Base Characterization of Molecules with Epigenetic Activity

Chemoinformatics: a perspective from an academic setting in Latin America

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