Chemoinformatics: a Perspective from an Academic Setting in Latin America

Overview

Journal Mol Divers

Date 2017 Dec 6

PMID 29204824

Citations 4

Authors

J Jesus Naveja

C Iluhi Oviedo-Osornio

Nicole N Trujillo-Minero

Jose L Medina-Franco

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

Progress on open chemoinformatic tools for expanding and exploring the chemical space.

Medina-Franco J, Sanchez-Cruz N, Lopez-Lopez E, Diaz-Eufracio B J Comput Aided Mol Des. 2021; 36(5):341-354.

PMID: 34143323 PMC: 8211976. DOI: 10.1007/s10822-021-00399-1.

A general approach for retrosynthetic molecular core analysis.

Naveja J, Pilon-Jimenez B, Bajorath J, Medina-Franco J J Cheminform. 2021; 11(1):61.

PMID: 33430974 PMC: 6760108. DOI: 10.1186/s13321-019-0380-5.

Finding Constellations in Chemical Space Through Core Analysis.

Naveja J, Medina-Franco J Front Chem. 2019; 7:510.

PMID: 31380353 PMC: 6646408. DOI: 10.3389/fchem.2019.00510.

BIOFACQUIM: A Mexican Compound Database of Natural Products.

Pilon-Jimenez B, Saldivar-Gonzalez F, Diaz-Eufracio B, Medina-Franco J Biomolecules. 2019; 9(1).

PMID: 30658522 PMC: 6358837. DOI: 10.3390/biom9010031.

References

Osolodkin D, Radchenko E, Orlov A, Voronkov A, Palyulin V, Zefirov N . Progress in visual representations of chemical space. Expert Opin Drug Discov. 2015; 10(9):959-73. DOI: 10.1517/17460441.2015.1060216. View

Medina-Franco J, Martinez-Mayorga K, Meurice N . Balancing novelty with confined chemical space in modern drug discovery. Expert Opin Drug Discov. 2013; 9(2):151-65. DOI: 10.1517/17460441.2014.872624. View

Mendez-Lucio O, Tran J, Medina-Franco J, Meurice N, Muller M . Toward drug repurposing in epigenetics: olsalazine as a hypomethylating compound active in a cellular context. ChemMedChem. 2014; 9(3):560-5. DOI: 10.1002/cmdc.201300555. View

Law V, Knox C, Djoumbou Y, Jewison T, Guo A, Liu Y . DrugBank 4.0: shedding new light on drug metabolism. Nucleic Acids Res. 2013; 42(Database issue):D1091-7. PMC: 3965102. DOI: 10.1093/nar/gkt1068. View

Gallop M, Barrett R, Dower W, Fodor S, Gordon E . Applications of combinatorial technologies to drug discovery. 1. Background and peptide combinatorial libraries. J Med Chem. 1994; 37(9):1233-51. DOI: 10.1021/jm00035a001. View

Castellano S, Kuck D, Viviano M, Yoo J, Lopez-Vallejo F, Conti P . Synthesis and biochemical evaluation of δ(2)-isoxazoline derivatives as DNA methyltransferase 1 inhibitors. J Med Chem. 2011; 54(21):7663-77. DOI: 10.1021/jm2010404. View

Naveja J, Medina-Franco J . Activity landscape of DNA methyltransferase inhibitors bridges chemoinformatics with epigenetic drug discovery. Expert Opin Drug Discov. 2015; 10(10):1059-70. DOI: 10.1517/17460441.2015.1073257. View

Naveja J, Medina-Franco J . Insights from pharmacological similarity of epigenetic targets in epipolypharmacology. Drug Discov Today. 2017; 23(1):141-150. DOI: 10.1016/j.drudis.2017.10.006. View

Gaulton A, Hersey A, Nowotka M, Bento A, Chambers J, Mendez D . The ChEMBL database in 2017. Nucleic Acids Res. 2016; 45(D1):D945-D954. PMC: 5210557. DOI: 10.1093/nar/gkw1074. View

10.

Medina-Franco J, Giulianotti M, Yu Y, Shen L, Yao L, Singh N . Discovery of a novel protein kinase B inhibitor by structure-based virtual screening. Bioorg Med Chem Lett. 2009; 19(16):4634-8. DOI: 10.1016/j.bmcl.2009.06.078. View

11.

Gasteiger J . Chemoinformatics: Achievements and Challenges, a Personal View. Molecules. 2016; 21(2):151. PMC: 6273366. DOI: 10.3390/molecules21020151. View

12.

Medina-Franco J, Lopez-Vallejo F, Kuck D, Lyko F . Natural products as DNA methyltransferase inhibitors: a computer-aided discovery approach. Mol Divers. 2010; 15(2):293-304. DOI: 10.1007/s11030-010-9262-5. View

13.

Gonzalez-Medina M, Mendez-Lucio O, Medina-Franco J . Activity Landscape Plotter: A Web-Based Application for the Analysis of Structure-Activity Relationships. J Chem Inf Model. 2017; 57(3):397-402. DOI: 10.1021/acs.jcim.6b00776. View

14.

Kuck D, Singh N, Lyko F, Medina-Franco J . Novel and selective DNA methyltransferase inhibitors: Docking-based virtual screening and experimental evaluation. Bioorg Med Chem. 2009; 18(2):822-9. DOI: 10.1016/j.bmc.2009.11.050. View

15.

Naveja J, Medina-Franco J . ChemMaps: Towards an approach for visualizing the chemical space based on adaptive satellite compounds. F1000Res. 2017; 6. PMC: 5538041. DOI: 10.12688/f1000research.12095.2. View

16.

Baell J . Feeling Nature's PAINS: Natural Products, Natural Product Drugs, and Pan Assay Interference Compounds (PAINS). J Nat Prod. 2016; 79(3):616-28. DOI: 10.1021/acs.jnatprod.5b00947. View

17.

Reymond J . The chemical space project. Acc Chem Res. 2015; 48(3):722-30. DOI: 10.1021/ar500432k. View

18.

Maggiora G, Bajorath J . Chemical space networks: a powerful new paradigm for the description of chemical space. J Comput Aided Mol Des. 2014; 28(8):795-802. DOI: 10.1007/s10822-014-9760-0. View

19.

Helal K, Maciejewski M, Gregori-Puigjane E, Glick M, Wassermann A . Public Domain HTS Fingerprints: Design and Evaluation of Compound Bioactivity Profiles from PubChem's Bioassay Repository. J Chem Inf Model. 2016; 56(2):390-8. DOI: 10.1021/acs.jcim.5b00498. View

20.

Guha R, Van Drie J . Structure--activity landscape index: identifying and quantifying activity cliffs. J Chem Inf Model. 2008; 48(3):646-58. DOI: 10.1021/ci7004093. View