Modeling Antibacterial Activity with Machine Learning and Fusion of Chemical Structure Information with Microorganism Metabolic Networks

Journal of Chemical Information and Modeling
Deyani Nocedo-MenaHumberto González-Díaz

Abstract

Predicting the activity of new chemical compounds over pathogenic microorganisms with different metabolic reaction networks (MRN s) is an important goal due to the different susceptibility to antibiotics. The ChEMBL database contains >160 000 outcomes of preclinical assays of antimicrobial activity for 55 931 compounds with >365 parameters of activity (MIC, IC50, etc.) and >90 bacteria strains of >25 bacterial species. In addition, the Leong and Barabàsi data set includes >40 MRNs of microorganisms. However, there are no models able to predict antibacterial activity for multiple assays considering both drug and MRN structures at the same time. In this work, we combined perturbation theory, machine learning, and information fusion techniques to develop the first PTMLIF model. The best linear model found presented values of specificity = 90.31/90.40 and sensitivity = 88.14/88.07 in training/validation series. We carried out a comparison to nonlinear artificial neural network (ANN) techniques and previous models from the literature. Next, we illustrated the practical use of the model with an experimental case of study. We reported for the first time the isolation and characterization of terpenes from the plant Cissus incisa. The a...Continue Reading

References

Jul 7, 1995·Journal of Ethnopharmacology·S C HessR A Yunes
Jun 5, 1998·Journal of Chemical Information and Computer Sciences·R García-Domenech, J V de Julián-Ortiz
Oct 18, 2000·Nature·H JeongA L Barabási
Mar 30, 2001·Journal of Chemical Information and Computer Sciences·R K MishraJ Galvez
Jul 23, 2002·Journal of Chemical Information and Computer Sciences·Mark T D CroninGerrit Schüürmann
Jan 25, 2003·Journal of Molecular Graphics & Modelling·Miguel Murcia-SolerPiedad Medina-Casamayor
Jul 23, 2003·Bioorganic & Medicinal Chemistry Letters·S Mut-RondaG M Antón-Fos
Feb 19, 2004·Journal of Agricultural and Food Chemistry·Yong-Suk Kim, Dong-Hwa Shin
Mar 23, 2004·Journal of Chemical Information and Computer Sciences·Enrique MolinaEugenio Uriarte
May 25, 2004·Journal of Chemical Information and Computer Sciences·Miguel Murcia-SolerAngel Villanueva-Pareja
Sep 28, 2005·Organic & Biomolecular Chemistry·Florence O McCarthyAnita R Maguire
Dec 17, 2009·Bioorganic & Medicinal Chemistry Letters·Dharmendra SaikiaArvind S Negi
Oct 18, 2011·European Journal of Medicinal Chemistry·Yovani Marrero-PonceAlexander D Crawford
Feb 5, 2013·European Journal of Pharmaceutical Sciences : Official Journal of the European Federation for Pharmaceutical Sciences·Alejandro Speck-PlancheM Natália D S Cordeiro
Mar 3, 2015·Progress in Medicinal Chemistry·Pamela Brown, Michael J Dawson
Mar 10, 2015·Combinatorial Chemistry & High Throughput Screening·Alejandro Speck-Planche, Maria N D S Cordeiro
May 20, 2015·Bioorganic & Medicinal Chemistry Letters·Lu ChenZhizhen Zhang
Oct 1, 2014·Pharmacognosy Research·Aliyu M MusaMohammed A Ibrahim
Mar 10, 2016·Journal of Chemical Information and Modeling·Alejandro Speck-PlancheM N D S Cordeiro
Nov 20, 2016·Journal of Computational Chemistry·Fahimeh GhasemiAlireza Mehri Dehnavi
Aug 19, 2017·ACS Infectious Diseases·Kamaleddin Haj Mohammad Ebrahim Tehrani, Nathaniel I Martin
Sep 19, 2017·Journal of Proteome Research·Saúl G Martínez-ArzateHumbert González-Díaz
Dec 11, 2017·Current Opinion in Biotechnology·Laura J Dunphy, Jason A Papin
Dec 26, 2017·The Lancet Infectious Diseases·Evelina TacconelliUNKNOWN WHO Pathogens Priority List Working Group
Feb 22, 2018·ACS Infectious Diseases·Tania J LupoliBen Gold
Mar 21, 2018·ACS Infectious Diseases·Jacqueline M Zaengle-BaroneKatherine J Franz
Jun 25, 2018·Drug Discovery Today·Fahimeh GhasemiHoracio Pérez-Sánchez
Sep 22, 2018·ACS Combinatorial Science·Harbil BediagaHumbert González-Díaz

❮ Previous
Next ❯

Citations

Nov 23, 2019·Current Topics in Medicinal Chemistry·Deyani Nocedo-MenaMaría Del Rayo Camacho-Corona
Jun 5, 2020·Expert Opinion on Drug Discovery·Riccardo ZanniJorge Galvez
Sep 25, 2020·SAR and QSAR in Environmental Research·V V KleandrovaA Speck-Planche
Jun 10, 2020·Current Topics in Medicinal Chemistry·Valeria V Kleandrova, Alejandro Speck-Planche
Nov 24, 2020·Future Medicinal Chemistry·Valeria V Kleandrova, Alejandro Speck-Planche
Jan 8, 2021·Nanoscale·Bernabé Ortega-Tenezaca, Humberto González-Díaz
Apr 21, 2020·European Journal of Medicinal Chemistry·Siva S PandaAhmed Samir
Sep 18, 2020·Current Topics in Medicinal Chemistry·Bernabe Ortega-TenezacaHumbert González-Díaz
Aug 21, 2019·Molecular Pharmaceutics·Emilia Vásquez-DomínguezHumbert González-Díaz
Sep 14, 2019·Journal of Chemical Information and Modeling·José Pérez-Parras ToledanoGonzalo Cerruela-García
Aug 28, 2021·Antibiotics·Valeria V KleandrovaAlejandro Speck-Planche
Dec 11, 2021·International Journal of Molecular Sciences·Viviana Quevedo-TumailliHumberto González-Díaz

❮ Previous
Next ❯

Related Concepts

Related Feeds

Carbapenems (ASM)

Carbapenems are members of the beta lactam class of antibiotics and are used for the treatment of severe or high-risk bacterial infections. Discover the latest research on carbapenems here.

Carbapenems

Carbapenems are members of the beta lactam class of antibiotics and are used for the treatment of severe or high-risk bacterial infections. Discover the latest research on carbapenems here.

Acinetobacter Infections

Acinetobacter infections have become common in hospitalized patients, especially in the intensive care unit setting and are difficult to treat due to their propensity to develop antimicrobial drug resistance. Discover the latest research on Acinetobacter Infections here.