Publications

2025

• Garcia-Segura P, Llop-Peiró A, Novau-Ferré N, Mestres-Truyol J, Saldivar-Espinoza B, Pujadas G, Garcia-Vallvé S. SARS-CoV-2 main protease (M-pro) mutational profiling: An insight into mutation coldspots. Comput Biol Med. 2025. 184:109344. doi: 10.1016/j.compbiomed.2024.109344.

2024

• Llop-Peiró A, Macip G, Garcia-Vallvé S, Pujadas G. Are protein-ligand docking programs good enough to predict experimental poses of noncovalent ligands bound to the SARS-CoV-2 main protease? Drug Discov Today. 2024 Oct;29(10):104137. doi: 10.1016/j.drudis.2024.104137

• Llop-Peiró A, Pujadas G, Gimeno A, Garcia-Vallvé S. PDB-CAT: A User-Friendly Tool to Classify and Analyze PDB Protein-Ligand Complexes. ChemRxiv. 2024; doi:10.26434/chemrxiv-2024-54073

• Llop-Peiró A, Pujadas G, Garcia-Vallvé S. Challenges in distinguishing functional proteins from polyproteins in databases: implications for drug discovery. Brief Bioinform. 2024 Jan 22;25(2):bbae012. doi: 10.1093/bib/bbae012.

2023

• Cuffaro D, Gimeno A, Bernardoni BL, Di Leo R, Pujadas G, Garcia-Vallvé S, Nencetti S, Rossello A, Nuti E. Identification of N-Acyl Hydrazones as New Non-Zinc-Binding MMP-13 Inhibitors by Structure-Based Virtual Screening Studies and Chemical Optimization. Int J Mol Sci. 2023 Jul 4;24(13):11098. doi: 10.3390/ijms241311098

• Saldivar-Espinoza B, Garcia-Segura P, Novau-Ferré N, Macip G, Martínez R, Puigbò P, Cereto-Massagué A, Pujadas G, Garcia-Vallve S. The Mutational Landscape of SARS-CoV-2. Int J Mol Sci. 2023 May 22;24(10):9072. doi: 10.3390/ijms24109072

• Fadlallah S, Julià C, García-Vallvé S, Pujadas G, Serratosa F. Drug Potency Prediction of SARS-CoV-2 Main Protease Inhibitors Based on a Graph Generative Model. Int J Mol Sci. 2023 May 15;24(10):8779. doi: 10.3390/ijms24108779

2022

• Saldivar-Espinoza B, Macip G, Garcia-Segura P, Mestres-Truyol J, Puigbo P, Cereto-Massague A, Pujadas G, Garcia-Vallve S. Prediction of Recurrent Mutations in SARS-CoV-2 Using Artificial Neural Networks. Int. J. Mol. Sci. 2022, 23(23), 14683; https://doi.org/10.3390/ijms232314683

• Saldivar-Espinoza B, Macip G, Pujadas G, Garcia-Vallve S. Could nucleocapsid be a next-generation COVID-19 vaccine candidate? Int J Infect Dis. 2022 Nov 5;125:231-232. doi: 10.1016/j.ijid.2022.11.002.

• Macip G, Garcia-Segura P, Mestres-Truyol J, Saldivar-Espinoza B, Pujadas G, Garcia-Vallvé S. A Review of the Current Landscape of SARS-CoV-2 Main Protease Inhibitors: Have We Hit the Bullseye Yet? Int. J. Mol. Sci. 2022, 23, 259. https://doi.org/10.3390/ijms23010259

• Macip G, Garcia-Segura P, Mestres-Truyol J, Saldivar-Espinoza B, Ojeda-Montes MJ, Gimeno A, Cereto-Massagué A, Garcia-Vallvé S, Pujadas G. Haste makes waste: A critical review of docking-based virtual screening in drug repurposing for SARS-CoV-2 main protease (M-pro) inhibition. Med Res Rev. 2021 Oct 26. doi: 10.1002/med.21862

2021

• Gimeno A, Cuffaro D, Nuti E, Ojeda-Montes MJ, Beltrán-Debón R, Mulero M, Rossello A, Pujadas G, Garcia-Vallvé S. Identification of Broad-Spectrum MMP Inhibitors by Virtual Screening. Molecules. 2021 Jul 28;26(15):4553. doi: 10.3390/molecules26154553.

• Tomas-Hernandez S, Blanco J, Garcia-Vallvé S, Pujadas G, Ojeda-Montes MJ, Gimeno A, Arola L, Minghetti L, Beltrán-Debón R, Mulero M. 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. Pharmaceutics. 2021 May 28;13(6):806. doi: 10.3390/pharmaceutics13060806.

2020

2019

• 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. Mining large databases to find new leads with low similarity to known actives: application to find new DPP-IV inhibitors. Future Med Chem. 2019 Jun;11(12):1387-1401. doi: 10.4155/fmc-2018-0597.

• Gimeno A, Ojeda-Montes MJ, Tomás-Hernández S, Cereto-Massagué A, Beltrán-Debón R, Mulero M, Pujadas G, Garcia-Vallvé S. The Light and Dark Sides of Virtual Screening: What Is There to Know? Int J Mol Sci. 2019 Mar 19;20(6). pii: E1375. doi: 10.3390/ijms20061375.

2018

• 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. Anti-inflammatory and Proapoptotic Properties of the Natural Compound o-Orsellinaldehyde. J Agric Food Chem. 2018 Oct 24;66(42):10952-10963. doi: 10.1021/acs.jafc.8b00782.
• 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. Combined ligand- and receptor-based virtual screening methodology to identify structurally diverse PTP1B inhibitors. ChemMedChem. 2018 Sep 19;13(18):1939-1948. doi: 10.1002/cmdc.201800267.
• Ojeda-Montes MJ, Gimeno A, Tomas-Hernández S, Cereto-Massagué A, Beltrán-Debón R, Valls C, Mulero M, Pujadas G, Garcia-Vallvé S. Activity and selectivity cliffs for DPP-IV inhibitors: Lessons we can learn from SAR studies and their application to virtual screening. Med Res Rev. 2018 Sep;38(6):1874-1915. doi: 10.1002/med.21499.
• Tomas-Hernández S, Blanco J, Rojas C, Roca-Martínez J, Ojeda-Montes MJ, Beltrán-Debón R, Garcia-Vallve S, Pujadas G, Arola L, Mulero M. Resveratrol Potently Counteracts Quercetin Starvation-Induced Autophagy and Sensitizes HepG2 Cancer Cells to Apoptosis. Mol Nutr Food Res. 2018 Mar;62(5). doi: 10.1002/mnfr.201700610.

2017

• 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. Ephedrine as a lead compound for the development of new DPP-IV inhibitors. Future Med Chem. 2017 Nov 27; 9(18):2129-2146. doi: 10.4155/fmc-2017-0080.

2015

• Garcia-Vallvé S, Guasch L, Tomas-Hernández S, Del Bas JM, Ollendorff V, Arola L, Pujadas G, Mulero M. Peroxisome Proliferator-Activated Receptor γ (PPARγ) and Ligand Choreography: Newcomers Take the Stage. J Med Chem. 2015 Jul 23;58(14):5381-94. doi: 10.1021/jm501155f. 
• Cereto-Massagué A, Ojeda MJ, Valls C, Mulero M, Pujadas G, Garcia-Vallve S. Tools for in silico target fishing. Methods. 2015 Jan;71:98-103. doi: 10.1016/j.ymeth.2014.09.006.
• Cereto-Massagué A, Ojeda MJ, Valls C, Mulero M, Garcia-Vallvé S, Pujadas G. Molecular fingerprint similarity search in virtual screening. Methods. 2015 Jan;71:58-63. doi: 10.1016/j.ymeth.2014.08.005

2014

• Rojas C, Pan-Castillo B, Valls C, Pujadas G, Garcia-Vallve S, Arola L, Mulero M. Resveratrol enhances palmitate-induced ER stress and apoptosis in cancer cells. PLoS One. 2014 Dec 1;9(12):e113929. doi: 10.1371/journal.pone.0113929. eCollection 2014.

2013

• Cereto-Massagué A, Ojeda MJ, Joosten RP, Valls C, Mulero M, Salvado MJ, Arola-Arnal A, Arola L, Garcia-Vallvé S, Pujadas G. The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites. J Cheminform. 2013 Jul 29;5(1):36. doi: 10.1186/1758-2946-5-36.
• Pallarès V, Fernández-Iglesias A, Cedó L, Castell-Auví A, Pinent M, Ardévol A, Salvadó MJ, Garcia-Vallvé S, Blay M. Grape seed procyanidin extract reduces the endotoxic effects induced by lipopolysaccharide in rats. Free Radic Biol Med. 2013 Jul;60:107-14. doi: 10.1016/j.freeradbiomed.2013.02.007.
• Guasch L, Sala E, Mulero M, Valls C, Salvadó MJ, Pujadas G, Garcia-Vallvé S. Identification of PPARgamma partial agonists of natural origin (II): in silico prediction in natural extracts with known antidiabetic activity. PLoS One. 2013;8(2):e55889. doi: 10.1371/journal.pone.0055889.

2012

• 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. Identification of PPARgamma partial agonists of natural origin (I): development of a virtual screening procedure and in vitro validation. PLoS One. 2012;7(11):e50816. doi: 10.1371/journal.pone.0050816.
• Guerrero L, Castillo J, Quiñones M, Garcia-Vallvé S, Arola L, Pujadas G, Muguerza B. Inhibition of angiotensin-converting enzyme activity by flavonoids: structure-activity relationship studies. PLoS One. 2012;7(11):e49493. doi:10.1371/journal.pone.0049493.
• Guasch L, Sala E, Ojeda MJ, Valls C, Bladé C, Mulero M, Blay M, Ardévol A, Garcia-Vallvé S, Pujadas G. Identification of novel human dipeptidyl peptidase-IV inhibitors of natural origin (Part II): in silico prediction in antidiabetic extracts. PLoS One. 2012;7(9):e44972. doi: 10.1371/journal.pone.0044972.
• 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. Identification of novel human dipeptidyl peptidase-IV inhibitors of natural origin (part I): virtual screening and activity assays. PLoS One. 2012;7(9):e44971. doi: 10.1371/journal.pone.0044971.
• González-Abuín N, Martínez-Micaelo N, Blay M, Pujadas G, Garcia-Vallvé S, Pinent M, Ardévol A. Grape seed-derived procyanidins decrease dipeptidyl-peptidase 4 activity and expression. J Agric Food Chem. 2012 Sep 12;60(36):9055-61. doi: 10.1021/jf3010349.
• Valls C, Rojas C, Pujadas G, Garcia-Vallve S, Mulero M. Characterization of the activity and stability of amylase from saliva and detergent: laboratory practicals for studying the activity and stability of amylase from saliva and various commercial detergents. Biochem Mol Biol Educ. 2012 Jul;40(4):254-65. doi: 10.1002/bmb.20612.
• Cereto-Massagué A, Guasch L, Valls C, Mulero M, Pujadas G, Garcia-Vallvé S. DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets. Bioinformatics. 2012 Jun 15;28(12):1661-2. doi:10.1093/bioinformatics/bts249.
• Guasch L, Sala E, Valls C, Mulero M, Pujadas G, Garcia-Vallvé S. Development of docking-based 3D-QSAR models for PPARgamma full agonists. J Mol Graph Model. 2012 Jun;36:1-9. doi: 10.1016/j.jmgm.2012.03.001.
• Castell-Auví A, Cedó L, Pallarès V, Blay MT, Pinent M, Motilva MJ, Garcia-Vallvé S, Pujadas G, Maechler P, Ardévol A. Procyanidins modify insulinemia by affecting insulin production and degradation. J Nutr Biochem. 2012 Dec;23(12):1565-72. doi: 10.1016/j.jnutbio.2011.10.010.
• Quesada H, Díaz S, Pajuelo D, Fernández-Iglesias A, Garcia-Vallvé S, Pujadas G, Salvadó MJ, Arola L, Bladé C. The lipid-lowering effect of dietary proanthocyanidins in rats involves both chylomicron-rich and VLDL-rich fractions. Br J Nutr. 2012 Jul;108(2):208-17. doi: 10.1017/S0007114511005472.

2011

• 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. 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. Eur J Med Chem. 2011 Dec;46(12):6098-103. doi:10.1016/j.ejmech.2011.09.022.
• Valls C, Pujadas G, Garcia-Vallve S, Mulero M. Characterization of the protease activity of detergents: laboratory practicals for studying the protease profile and activity of various commercial detergents. Biochem Mol Biol Educ. 2011 Jul;39(4):280-90. doi: 10.1002/bmb.20488.
• Guasch L, Sala E, Valls C, Blay M, Mulero M, Arola L, Pujadas G, Garcia-Vallvé S. Structural insights for the design of new PPARgamma partial agonists with high binding affinity and low transactivation activity. J Comput Aided Mol Des. 2011 Aug;25(8):717-28. doi: 10.1007/s10822-011-9446-9.
• Sala E, Guasch L, Iwaszkiewicz J, Mulero M, Salvadó MJ, Pinent M, Zoete V, Grosdidier A, Garcia-Vallvé S, Michielin O, Pujadas G. Identification of human IKK-2 inhibitors of natural origin (part I): modeling of the IKK-2 kinase domain, virtual screening and activity assays. PLoS One. 2011 Feb 24;6(2):e16903. doi:10.1371/journal.pone.0016903.

BOOK CHAPTERS

• Macip G, Mestres-Truyol J, Garcia-Segura P, Saldivar-Espinoza B, Garcia-Vallve S., Pujadas G. Mining for Vioactive Molecules in Open Databases. In: Open Access Databases and Datasets for Drug Discovery (eds A Daina, MT. Przewosny, V. Zoete).Book series: Methods and Principles in Medicinal Chemistry Vol. 83. Wiley-VCH (Verlag). November 2023. 978-3-527-34839-8 (ISBN)
• Kukhtar, D., Mulero, M., Beltrán-Debón, R., Valls, C., Pujadas, G. and Garcia-Vallve, S.  Multiple Peroxisome Proliferator-Activated Receptor-Based Ligands. In: Drug Selectivity: An Evolving Concept in Medicinal Chemistry (eds N. Handler and H. Buschmann), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. 2017 doi: 10.1002/9783527674381.ch14
• García-Vallve S, Guasch L, Mulero M. Discovery of Natural Products that Modulate the Activity of PPARgamma: A Source for New Antidiabetics. In: Foodinformatics. Applications of Chemical Information to Food Chemistry. Martinez-Mayorga, Karina, Medina-Franco, José Luis (Eds.), pp 151-176. Springer, 2014. ISBN 978-3-319-10226-9
• Pujadas G, Ojeda MJ, Cereto-Massagué A, Valls C. DPP-IV, An Important Target for Antidiabetic Functional Food Design. In: Foodinformatics. Applications of Chemical Information to Food Chemistry. Martinez-Mayorga, Karina, Medina-Franco, José Luis (Eds.), pp 177-212. Springer, 2014. ISBN 978-3-319-10226-9