AntiMalarial Mode of Action (AMMA) Database: Data Selection, Verification and Chemical Space Analysis

Molecular Informatics
Pavel SidorovAlexandre Varnek

Abstract

This paper presents the effort of collecting and curating a data set of 15461 molecules tested against the malaria parasite, with robust activity and mode of action annotations. The set is compiled from in-house experimental data and the public ChEMBL database subsets. We illustrate the usefulness of the dataset by building QSAR models for antimalarial activity and QSPR models for modes of actions, as well as by the analysis of the chemical space with the Generative Topographic Mapping method. The GTM models perform well in prediction of both activity and mode of actions, on par with the classical SVM methods. The visualization of obtained maps helps to understand the distribution of molecules corresponding to different modes of action: molecules with similar targets are located close to each other on the map. Therefore, this analysis may suggest new modes of action for non-annotated or even annotated compounds. In perspective, this can be used as a tool for prediction of both antimalarial activity and target for novel, untested compounds.

References

Feb 14, 1997·Journal of Medicinal Chemistry·P M O'NeillB K Park
Jul 12, 2002·Bioorganic & Medicinal Chemistry·Feng ChengKaixian Chen
Oct 16, 2002·Journal of Chemical Information and Computer Sciences·Apurba K BhattacharjeeWilbur K Milhous
Jan 28, 2004·Acta Tropica·Thierry Joët, Sanjeev Krishna
Sep 1, 2004·European Journal of Medicinal Chemistry·C X XueB T Fan
Feb 25, 2005·Bioorganic & Medicinal Chemistry·V Raja SolomonS B Katti
Nov 18, 2005·Journal of Computer-aided Molecular Design·A VarnekV P Solov'ev
Jan 24, 2006·Journal of Chemical Information and Modeling·Manish K Gupta, Yenamandra S Prabhakar
Jan 24, 2006·Bioorganic & Medicinal Chemistry·Alan R KatritzkyMati Karelson
Mar 11, 2008·Revista Do Instituto De Medicina Tropical De São Paulo·Pedro Alves da Silva Autreto, Francisco Carlos Lavarda
Jun 27, 2008·Proceedings of the National Academy of Sciences of the United States of America·David PlouffeElizabeth A Winzeler
Jul 9, 2008·Journal of Enzyme Inhibition and Medicinal Chemistry·Shreekant DeshpandeYenamandra S Prabhakar
Jul 14, 2009·Parasitology Research·Markus Jensen, Heinz Mehlhorn
Nov 13, 2009·Malaria Journal·Nicholas J WhiteNicholas P J Day
Mar 26, 2010·Infectious Disorders Drug Targets·Margaret A Phillips, Pradipsinh K Rathod
May 21, 2010·Nature·Francisco-Javier GamoJose F Garcia-Bustos
May 21, 2010·Nature·W Armand GuiguemdeR Kiplin Guy
Jun 24, 2010·Current Opinion in Chemical Biology·Victoria BartonPaul M O'Neill
Jul 21, 2010·Current Pharmaceutical Design·Isela GarcíaGenerosa Gómez
Sep 29, 2011·Nucleic Acids Research·Anna GaultonJohn P Overington
Dec 21, 2012·Journal of Chemical Information and Modeling·Liying ZhangAlexander Tropsha
Jun 27, 2013·PloS One·Thomas SpangenbergPaul Willis
Oct 23, 2013·PLoS Computational Biology·Andreas Spitzmüller, Jordi Mestres
Dec 1, 2012·International Journal for Parasitology. Drugs and Drug Resistance·Philipp LudinPascal Mäser
Mar 10, 2011·ACS Medicinal Chemistry Letters·Mathias Wawer, Jürgen Bajorath
Sep 23, 2014·Journal of Molecular Graphics & Modelling·Luana Janaína de Campos, Eduardo Borges de Melo
Nov 26, 2014·Journal of Chemical Information and Modeling·Héléna A GasparAlexandre Varnek
Nov 5, 2015·Trends in Parasitology·Hagai Ginsburg, Alyaa M Abdel-Haleem
Nov 14, 2015·Journal of Computer-aided Molecular Design·Pavel SidorovDragos Horvath
Jul 2, 2016·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Birgit ViiraElisabeth Davioud-Charvet
Jul 14, 2016·Journal of Chemical Information and Modeling·Kyrylo KlimenkoAlexandre Varnek
Jul 12, 2010·Molecular Informatics·Alexander Tropsha
Apr 15, 2017·Journal of Chemical Information and Modeling·Shilva KayasthaAlexandre Varnek

❮ Previous
Next ❯

Citations

Jan 28, 2019·European Journal of Medicinal Chemistry·Iuri CasciucAlexandre Varnek
Dec 21, 2018·Journal of Chemical Information and Modeling·Iuri CasciucAlexandre Varnek

❮ Previous
Next ❯

Related Concepts

Related Feeds

Antimalarial Agents (ASM)

Antimalarial agents, also known as antimalarials, are designed to prevent or cure malaria. Discover the latest research on antimalarial agents here.

Antimalarial Agents

Antimalarial agents, also known as antimalarials, are designed to prevent or cure malaria. Discover the latest research on antimalarial agents here.

© 2022 Meta ULC. All rights reserved