Grupo de investigación en Quimioinformática y Nutrición

The activity of the Chemoformative and Nutrition research group focuses on the use of computational tools to (1) predict which natural molecules have a specific bioactivity; (2) find new uses for specific molecules (e.g., valorization of by-products by finding new uses for molecules that are present in them); and (3) find drugs to treat COVID-19 infection.

Working topics:

(1) Finding new pharmacological treatments against COVID-19

• A review of the current landscape of SARS-CoV-2 main protease inhibitors: have we hit the bull’s-eye yet? Macip G, Garcia-Segura P, Mestres-Truyol J, Saldivar-Espinoza B, Pujadas G, Garcia-Vallvé S. Int J Mol Sci. 2022, 23(1), 259; https://doi.org/10.3390/ijms23010259
• Haste makes waste: A critical review of docking-based virtual screening in drug repurposing for SARS-CoV-2 main protease (M-pro) inhibition. Macip G, Garcia-Segura P, Mestres-Truyol J, Saldivar-Espinoza B, Ojeda-Montes MJ, Gimeno A, Cereto-Massagué A, Garcia-Vallvé S, Pujadas G. Med Res Rev. 2021 Oct 26:10.1002/med.21862. do
• Prediction of Novel Inhibitors of the Main Protease (M-pro) of SARS-CoV-2 through Consensus Docking and Drug Reposition. Gimeno A, Mestres-Truyol J, Ojeda-Montes MJ, Macip G, Saldivar-Espinoza B, Cereto-Massagué A, Pujadas G, Garcia-Vallvé S. Int J Mol Sci. 2020 May 27;21(11):3793. doi: 10.3390/ijms21113793

(2) Finding molecules with cosmetic potential

• Identification of Broad-Spectrum MMP Inhibitors by Virtual Screening. Gimeno A, Cuffaro D, Nuti E, Ojeda-Montes MJ, Beltrán-Debón R, Mulero M, Rossello A, Pujadas G, Garcia-Vallvé S. Molecules. 2021 Jul 28;26(15):4553. doi: 10.3390/molecules26154553.
• Understanding the variability of the S1′ pocket to improve matrix metalloproteinase inhibitor selectivity profiles. Gimeno A, Beltrán-Debón R, Mulero M, Pujadas G, Garcia-Vallvé S. Drug Discov Today. 2020 Jan;25(1):38-57. doi: 10.1016/j.drudis.2019.07.013

(3) Finding natural molecules with anti-inflammatory activity

• Anti-Inflammatory and Immunomodulatory Effects of the Grifola frondosa Natural Compound o-Orsellinaldehyde on LPS-Challenged Murine Primary Glial Cells. Roles of NF-κβ and MAPK. Tomas-Hernandez S, Blanco J, Garcia-Vallvé S, Pujadas G, Ojeda-Montes MJ, Gimeno A, Arola L, Minghetti L, Beltrán-Debón R, Mulero M. Pharmaceutics. 2021 May 28;13(6):806. doi: 10.3390/pharmaceutics13060806.
• Anti-inflammatory and Proapoptotic Properties of the Natural Compound o-Orsellinaldehyde. Tomas-Hernandez S, Garcia-Vallvé S, Pujadas G, Valls C, Ojeda-Montes MJ, Gimeno A, Cereto-Massagué A, Roca-Martinez J, Suárez M, Arola L, Blanco J, Mulero M, Beltran-Debón R. J Agric Food Chem. 2018 Oct 24;66(42):10952-10963. doi: 10.1021/acs.jafc.8b00782.
• Identification of human IKK-2 inhibitors of natural origin (part I): modeling of the IKK-2 kinase domain, virtual screening and activity assays. Sala E, Guasch L, Iwaszkiewicz J, Mulero M, Salvadó MJ, Pinent M, Zoete V, Grosdidier A, Garcia-Vallvé S, Michielin O, Pujadas G. PLoS One. 2011 Feb 24;6(2):e16903
• Identification of human IKK-2 inhibitors of natural origin (Part II): in Silico prediction of IKK-2 inhibitors in natural extracts with known anti-inflammatory activity. Sala E, Guasch L, Iwaszkiewicz J, Mulero M, Salvadó MJ, Bladé C, Ceballos M, Valls C, Zoete V, Grosdidier A, Garcia-Vallvé S, Michielin O, Pujadas G. Eur J Med Chem. 2011 Dec;46(12):6098-103.

(4) Finding molecules with anti-diabetic activity

• Mining large databases to find new leads with low similarity to known actives: application to find new DPP-IV inhibitors. Ojeda-Montes MJ, Casanova-Martí À, Gimeno A, Tomás-Hernández S, Cereto-Massagué A, Wolber G, Beltrán-Debón R, Valls C, Mulero M, Pinent M, Pujadas G, Garcia-Vallvé S. Future Med Chem. 2019 Jun;11(12):1387-1401. doi: 10.4155/fmc-2018-0597.
• Activity and selectivity cliffs for DPP-IV inhibitors: Lessons we can learn from SAR studies and their application to virtual screening. Ojeda-Montes MJ, Gimeno A, Tomas-Hernández S, Cereto-Massagué A, Beltrán-Debón R, Valls C, Mulero M, Pujadas G, Garcia-Vallvé S. Med Res Rev. 2018 Sep;38(6):1874-1915. doi: 10.1002/med.21499.
• Ephedrine as a lead compound for the development of new DPP-IV inhibitors. Ojeda-Montes MJ, Ardid-Ruiz A, Tomás-Hernández S, Gimeno A, Cereto-Massagué A, Beltrán-Debón R, Mulero M, Garcia-Vallvé S, Pujadas G, Valls C. Future Med Chem. 2017 Dec;9(18):2129-2146. doi: 10.4155/fmc-2017-0080.
• Discovery of Natural Products that Modulate the Activity of PPARgamma: A Source for New Antidiabetics. Garcia-Vallve S, Guasch L, Mulero M. Foodinformatics Applications of Chemical Information to Food Chemistry, 151-176. Editors: Karina Martinez-Mayorga and José Luis Medina-Franco. Springer 2014
• DPP-IV, An Important Target for Antidiabetic Functional Food Design. Ojeda MJ, Cereto-Massagué A, Valls C, Pujadas G. Foodinformatics Applications of Chemical Information to Food Chemistry, 177-212. Editors: Karina Martinez-Mayorga and José Luis Medina-Franco. Springer 2014
• Peroxisome Proliferator-Activated Receptor γ (PPARγ) and Ligand Choreography: Newcomers Take the Stage. Garcia-Vallvé S, Guasch L, Tomas-Hernández S, del Bas JM, Ollendorff V, Arola L, Pujadas G, Mulero M. J Med Chem. 2015 Jul 23;58(14):5381-94. doi: 10.1021/jm501155f.
• Identification of novel human dipeptidyl peptidase-IV inhibitors of natural origin (part I): virtual screening and activity assays. Guasch L, Ojeda MJ, González-Abuín N, Sala E, Cereto-Massagué A, Mulero M, Valls C, Pinent M, Ardévol A, Garcia-Vallvé S, Pujadas G. PLoS One. 2012;7(9):e44971
• Identification of novel human dipeptidyl peptidase-IV inhibitors of natural origin (Part II): in silico prediction in antidiabetic extracts. Guasch L, Sala E, Ojeda MJ, Valls C, Bladé C, Mulero M, Blay M, Ardévol A, Garcia-Vallvé S, Pujadas G. PLoS One. 2012;7(9):e44972
• Identification of PPARgamma partial agonists of natural origin (I): development of a virtual screening procedure and in vitro validation. Guasch L, Sala E, Castell-Auví A, Cedó L, Liedl KR, Wolber G, Muehlbacher M, Mulero M, Pinent M, Ardévol A, Valls C, Pujadas G, Garcia-Vallvé S. PLoS One. 2012;7(11):e50816
• Identification of PPARgamma partial agonists of natural origin (II): in silico prediction in natural extracts with known antidiabetic activity. Guasch L, Sala E, Mulero M, Valls C, Salvadó MJ, Pujadas G, Garcia-Vallvé S. PLoS One. 2013;8(2):e55889.
• Development of docking-based 3D-QSAR models for PPARgamma full agonists. Guasch L, Sala E, Valls C, Mulero M, Pujadas G, Garcia-Vallvé S. J Mol Graph Model. 2012 Jun;36:1-9. doi: 10.1016/j.jmgm.2012.03.001.
• Structural insights for the design of new PPARgamma partial agonists with high binding affinity and low transactivation activity. Guasch L, Sala E, Valls C, Blay M, Mulero M, Arola L, Pujadas G, Garcia-Vallvé S. J Comput Aided Mol Des. 2011 Aug;25(8):717-28. doi: 10.1007/s10822-011-9446-9.

(5) Finding natural molecules with anti-obesity activity

• Combined Ligand- and Receptor-Based Virtual Screening Methodology to Identify Structurally Diverse Protein Tyrosine Phosphatase 1B Inhibitors. Gimeno A, Ardid-Ruiz A, Ojeda-Montes MJ, Tomás-Hernández S, Cereto-Massagué A, Beltrán-Debón R, Mulero M, Valls C, Aragonès G, Suárez M, Pujadas G, Garcia-Vallvé S. ChemMedChem. 2018 Sep 19;13(18):1939-1948. doi: 10.1002/cmdc.201800267.

(6) Development of methodologies/computational tools for improving the prediction of the bioactivity of small molecules

• DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets. Cereto-Massagué A, Guasch L, Valls C, Mulero M, Pujadas G, Garcia-Vallvé S. Bioinformatics. 2012 Jun 15;28(12):1661-2
• The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites. Cereto-Massagué A, Ojeda MJ, Joosten RP, Valls C, Mulero M, Salvado MJ, Arola-Arnal A, Arola L, Garcia-Vallvé S, Pujadas G. J Cheminform. 2013 Jul 29;5(1):36. doi: 10.1186/1758-2946-5-36.

(7) Development of methodologies/computational tools for predicting new uses for existing drugs or molecules that are abundant in by-products of natural origin

• Molecular fingerprint similarity search in virtual screening. Cereto-Massagué A, Ojeda MJ, Valls C, Mulero M, Garcia-Vallvé S, Pujadas G. Methods. 2015 Jan;71:58-63.
• Tools for in silico target fishing. Cereto-Massagué A, Ojeda MJ, Valls C, Mulero M, Pujadas G, Garcia-Vallve S. Methods. 2015 Jan;71:98-103.