Publicacions en 2025
Blanco-Gabella, P; Ivanova, V; Serrano-Morrás, A.; Fuchs, J. E.; Juárez-Jiménez, J. Understanding the role of H-bonds in the stability of molecular glue-induced ternary complexes. ChemRxiv, 2025; doi: 10.26434/chemrxiv-2025-wk459.
Serrano-Morrás, A; Bertran-Mostazo, A; Miñarro-Lleonar, M; Comajuncosa-Creus, A; Cabello, A; Labranya, C; Escudero, C; Tian, T; Khutorianska, I; Radchenko, D; Moroz, Y,S; Defelipe, L; Ruiz-Carrillo, D; Garcia-Alai, M, Schmidt, R; Rarey, M; Aloy, P; Galdeano, C; Juárez-Jiménez, J; Barril, X. A novel bottom-up approach to find lead-compounds in billion-sized libraries. ChemRxiv 2025; doi:10.26434/chemrxiv-2025-lph6p
Álvarez-Berbel I, Llabrés S, Domènech O, Busquets MA, Fernàndez-Busquets X, Arce EM, Gavín R., del Río JA, Muñoz-Torrero D, Luque FJ, Sabaté R, Espargaró A, YAT2150: Overcoming limitations of traditional amyloid dyes in aggregation studies, Bioorg. Med. Chem. 2025, 123, 118163
Nadal-Rodriguez, P.; Hartung, F.; Pedrola, M.; Coomar, S.; Diaz-Moreno, A.; Hätälä, A.M.; Rolfes, K.M.; Sánchez-Vera, I.; Gil, J.; Molins, E.; Viayna, A.; Hanzl, A.; Thomä, N.H.; Haarmann-Stemmann, T.; Luque, F.J.; Lavilla, R.;
Ghashghaei, O. A Multicomponent Reaction-Based Platform Opens New Avenues in Aryl Hydrocarbon Receptor Modulation. ACS Cent. Sci. 2025, 11, 629–641
Amaro, R.; Åqvist, J.; Bahar, I.; et al. The need to implement FAIR principles in biomolecular simulations. Nature Methods 2025, 22, 641.
Valdivia, A.; Rocha, M.; Luque, F. J. Mining druggable sites in influenza A hemagglutinin: Binding of the pinanamine-based inhibitor M090. ACS Med. Chem. Lett. 2025, 16, 126.
Cunha, R. D.; Romero-Téllez, S.; Lipparini, F.; Luque, F.J.; Curutchet, C. Extending the MST Model to Large Biomolecular Systems: Parametrization of the ddCOSMO‐MST Continuum Solvation Model. J. Comput. Chem. 2025, 46, e70027.
Pérez-Sanchez, A.; Curutchet, C.; Gonzalez-Lafont, A.; Lluch, J. M. First-principles simulations of the fluorescence modulation of a COX-2-specific fluorogenic probe upon protein dimerization for cancer discrimination. Protein Sci. 2025, 34, e70001.
Rodríguez-Gimeno, A.; Galdeano, C. Drug Discovery approaches to target E3 ligases. ChemBioChem 2025, 26, e202400656
Zinovjev, K.; Curutchet, C. Improved Description of Environment and Vibronic Effects with Electrostatically Embedded ML Potentials. J. Phys. Chem. Lett. 2025, 16, 774–781.
Gonzalo, D.; Cupellini, L.; Curutchet, C. On the breakdown of Förster energy transfer theory due to solvent effects: atomistic simulations unveil distance-dependent dielectric screening in calmodulin. Chem. Sci. 2025, 16, 3693.
Merino-Cacho, L; Barroso-Gomila, O; Pozo-Rodríguez, M; Muratore, V; Guinea-Pérez, C; Serrano-Morrás, A; Pérez, C; Cano-López, S; Urcullu, A; Azkargorta, M; Iloro, I; Galdeano, C; Juárez-Jiménez, J; Mayor, U; Elortza, F; Barrio, R; Sutherland, J D. Cullin-RING ligase BioE3 reveals molecular-glue-induced neosubstrates and rewiring of the endogenous Cereblon ubiquitome. Cell Commun Signal 2025, 23, 101.
Publicacions en 2024
Mendoza-Martínez, C.; Gupta, A.; Llabrés, S.; Barlow, P.; Michel, J. Molecular driving force of a small molecule-induced protein disorder-order transition. ChemRxiv 2024; doi:10.26434/chemrxiv-2024-m15qm
Rivero, P.; Ivanova, V.; Barril, X.; Casampere, M.; Casa, J.; Fabriás, G.; Díaz, Y.; Matheu, M. I. Targeting dihydroceramide desaturase 1 (Des1): Syntheses of ceramide analogues with a rigid scaffold, inhibitory assays, and AlphaFold2-assisted structural insights reveal cyclopropenone PR280 as a potent inhibitor. Bioorg. Chem. 2024, 145, 107233.
Coux, O.; Farras, R.; Abbas, M.; Barrio, R.; Blattner, C.; Brix, K.; Chachami, G.; Chevet, E.; Clague, M. J.; Dantuma, N.; Rankov, A. D.; Galdeano, C.; Giglione, C.; Glickman, M. H.; Lalmanach, G.; Lindon, C.; Matthiesen, R.; Meroni, G.; Pick, E.; Poidevin, L.; Rivas, C.; Rodríguez, M. S.; Sammler, E.; Shiber, A.; Skoulakis, E. M. C.; Stein, M.; Vertegaal, A. C. O. ProteoCure: A European network to fine-tune the proteome. Biochimie 2024, 226, 4.
Bertran-Mostazo, A.; Putriute, G.; Alvarez-Berbel, I.; Busquets, M. A.; Galdeano, C.; Espargaró, A.; Sabaté, R. Proximity-induced pharmacology for amyloid-related diseases. Cells 2024, 13, 449.
Vázquez, G.; Espargaró, A.; Caballero, A. B.; Di Pede-Mattatelli, A.; Busquets, M. A.; Nawrot, D.; Sabaté, R.; Nicolas, E.; Juárez-Jiménez, J.; Gámez, P. A versatile luminescent probe for sensing and monitoring amyloid proteins. Dyes Pigm. 2024, 231, 112348.
Lozano-Baró, E.; Nadal-Rodríguez, P.; Juárez‐Jiménez, J.; Ghashghaei, O.; Lavilla, R. Reaction space charting as a tool in organic chemistry research and development. Adv. Synt. Cat. 2024, 366, 551.
Moyer, A. P.; Ramelot, T. A.; Curti, M.; Eastman, M. A.; Kang, A.; Bera, A. K.; Tejero, R.; Salveson, P. J.; Curutchet, C.; Romero, E.; Montelione, G. T.; Baker, D. Enumerative Discovery of Noncanonical Polypeptide Secondary Structures J. Am. Chem. Soc. 2024, 146, 25501.
Lozano-Baró, E.; Catti, F.; Estarellas, C.; Ghasghaei, O.; Lavilla, R. Drugs from drugs: New Chemical insights into a mature concept. Drug Discov. Today 2024, 29, 104212.
Viayna, A.; Matamoros, P.; Blázquez-Ruano, D.; Zamora, W. J. From canonical to unique: Extension of a lipophilicity scale of aminoacids to non-standard residues. Explor. Drug. Sci. 2024, 2, 389.
Valdivia, A.; Luque, F. J.; Llabrés, S. Binding of cholesterol to the N-terminal domain of the NPC1L1 transporter: Analysis of the epimerization-related binding selectivity and loop mutations. J. Chem. Inf. Model. 2024, 64, 189.
Hermoso-Pinilla, F. J.; Valdivia, A.; Camarasa, M. J.; Ginex, T.; Luque, F. J. Influenza A virus hemagglutinin: From classical fusion inhibitors to proteolysis targeting chimera-based strategies in antiviral drug discovery. Explor. Drug Sci. 2024, 2, 85.
Luque, F. J.; Muñoz-Torrero, D. Acetylcholinesterase: A versatile template to coin potent modulators of multiple therapeutic targets. Acc. Chem. Res. 2024, 57, 450.
Ginex, T.; Vázquez, J.; Estarellas, C.; Luque, F. J. Quantum mechanical-based strategies in drug discovery: Finding the pace to new challenges in drug design. Curr Opin. Struct. Biol. 2024, 87, 102870.
Vázquez, J.; García, R.; Linares, P.; Luque, F. J.; Herrero, E. On the relevance of query definition in the performance of 3D ligand-based virtual screening. J. Comput. Aided. Mol. Des. 2024, 38, 18.
Publicacions en 2023
Rudinskiy, M.; Pons-Vizcarra, M.; Solda, T.; Fregno, I.; Bergmann, T. J.; Ruano, A.; Delgado, A.; Morales, S.; Barril, X.; Cubero, E.; García-Collazo, A. M.; Pérez- Carmona, N.; Molinari, M. Validation of a highly sensitive HaloTag-based assay to evaluate the potency of a novel class of allosteric β-Galactosidase correctors. PLoS One 2023, 18, e0294437.
Guzman, B.; Perez, N.; Garcia, A.M.; Cubero, E.; Barril, X.; Bellotto, M.; Morales, S.; Ruano, A.; Delgado, A.; Poletto, C.; Forloni, G.; Maj, R. GT-02287, a brain-penetrant structurally targeted allosteric regulator for glucocerebrosidase show evidence of pharmacological efficacy in models of Parkinson’s disease. Parkinsonism Relat. Disord. 2023, 113, 105512.
Edo-Osagie, A.; Serillon, D.; Ruani, F.; Barril, X.; Gourlaouen, C.; Armaroli, N.; Ventura, B.; de Rouville, H.-P- J.; Heitz, V. Multi-responsive eight-State bis (acridinium-Zn (II) porphyrin) receptor. J. Am. Chem. Soc. 2023, 145, 10691.
Guzman, B.; Pérez, N.; Garcia-Collazo, A.M.; Cubero, E.; Barril, X.; Bellotto, M.; Taylor, J. A structurally targeted allosteric regulator of GCase restores enzyme activity, reduces microgliosis, and improves fine locomotor skills in the CBE model of neuronopathic Gaucher disease. Mol. Gen. Metab. 2023, 138, 107133.
Curti, M.; Maffeis, V.; Duarte, L. G. T. A.; Shareef, S.; Hallado, L. X.; Curutchet, C.; Romero, E. Engineering excitonically coupled dimers in an artificial protein for light harvesting via computational modeling. Prot. Sci. 2023, 32, e4579.
Souza, J. R.; Curutchet, C.; Aoto, Y. A.; Homem-De-Mello, P. Benchmarking DFT functionals for photophysics of pyranoflavylium cations. J. Mol. Graph. Model. 2023, 122, 108460.
Nottoli, M.; Bondanza, M.; Mazzeo, P.; Cupellini, L.; Curutchet, C.; Loco, D.; Lagardère, L.; Piquemal, J-P.; Mennucci, B.; Lipparini, F. QM/AMOEBA description of properties and dynamics of embedded molecules. WIRES Comput. Mol. Sci. 2023, 13, e1674.
Ozaydin, B.; Curutchet, C. Unraveling the role of thermal fluctuations on the exciton structure of the cryptophyte PC612 and PC645 photosynthetic antenna complexes. Front. Mol. Biosci. 2023, 18, 1268278.
Miñarro-Lleonar, M.; Bertran-Mostazo, A.; Duro, J.; Barril, X.; Juárez-Jiménez, J. Lenalidomide stabilizes protein–protein complexes by turning labile intermolecular H-bonds into robust interactions. J. Med. Chem. 2023, 66, 6037.
Zamora, W. J.; Viayna, A.; Pinheiro, S.; Curutchet, C.; Bisbal, L.; Ruiz, R.; Ràfols, C.; Luque, F. J. Prediction of toluene/water partition coefficients in the SAMPL9 blind challenge: Assessment of machine learning and IEF-PCM/MST continuum solvation models. Phys. Chem. Chem. Phys. 2023, 25, 17952
Jiang, X.; Li, J.; Viayna, A.; Luque, F. J.; Woodson, M.; Jing, L.; Gao, S.; Zhao, F.; Xie, M.; Toth, K.; Tavis, J.; Tollefson, A. E.; Liu, X.; Zhan, P. Identification of novel 1, 2, 3-triazole isatin derivatives as potent SARS-CoV-2 3CLpro inhibitors via click-chemistry-based rapid screening. RSC Med. Chem. 2023, 14, 2068.
de Candia, M.; Titov, A. A.; Viayna, A.; Kulikova, L. N.; Purgatorio, R.; Piergiovanni, B.; Niso, M.; Catto, M.; Voskressensky, L. G.; Luque, F. J.; Altomare, C. D. In-vitro and in-silico studies of annelated 1, 4, 7, 8-tetrahydroazocine ester derivatives as nanomolar selective inhibitors of human butyrylcholinesterase. Chem. Biol. Interact. 2023, 386, 110741.
Pesce, A.; Barmpidi, K.; Dewilde, S.; Estarellas, C.; Moens, L.; Bolognesi, M.; Luque, F. J.; Nardini, M. Structural and dynamic characterization of the hexa-coordinated globin from Spisula solidissima. J. Inorg. Biochem. 2023, 246, 112289.
Vázquez, J.; Ginex, T.; Herrero, E.; Morisseau, C.; Hammock, B.; Luque, F.J. Screening and biological evaluation of soluble epoxide hydrolase inhibitors: Assessing the role of hydrophobicity in the pharmacophore-guided search of novel hits. J. Chem. Inf. Model. 2023, 63, 3209.
Publicacions en 2022
Mendoza-Martínez, C.; Papadourakis, M.; Llabrés, S.; Gupta, A. A.; Barlow, P. N.; Michel, J. Energetics of a protein disorder-order transition in small molecule recognition. Chem. Sci. 2022, 13, 5220.
Morgillo, C. M.; Lupia, A.; Deplano, A.; Pirone, L.; Fiorillo, B.; Pedone, E.; Luque, F. J.; Onnis, V.; Moraca, F.; Catalanotti, B. Molecular Basis for Non-Covalent, Non-Competitive FAAH Inhibition. Int. J. Mol. Sci. 2022, 23, 15502.
Basagni, F.; Naldi, M.; Ginex, T.; Luque, F. J.; Fagiani, F.; Lanni, C.; Iurlo, M.; Marcaccio, M.; Minarini, A.; Bartolini, M.; Rosini, M. Inhibition of β-Amyloid Aggregation in Alzheimer’s Disease: The Key Role of (Pro) electrophilic Warheads. ACS Med. Chem. Lett. 2022, 13, 1812.
Álvarez-Berbel, I.; Espargaró, A.; Viayna, A.; Caballero, A. B.; Busquets, M. A.; Gámez, P.; Luque, F. J.; Sabaté, R. Three to Tango: Inhibitory Effect of Quercetin and Apigenin on Acetylcholinesterase, Amyloid-β Aggregation and Acetylcholinesterase-Amyloid Interaction. Pharmaceutics 2022, 14, 2342.
Basagni, F.; Naldi, M.; Ginex, T.; Luque, F. J.; Fagiani, F.; Lanni, C.; Iurlo, M.; Marcaccio, M.; Minarini, A.; Bartolini, M.; Rosini, M. Inhibition of β-Amyloid Aggregation in Alzheimer’s Disease: The Key Role of (Pro) electrophilic Warheads. ACS Med. Chem. Lett. 2022, 13, 1812.
Álvarez-Berbel, I.; Espargaró, A.; Viayna, A.; Caballero, A. B.; Busquets, M. A.; Gámez, P.; Luque, F. J.; Sabaté, R. Three to Tango: Inhibitory Effect of Quercetin and Apigenin on Acetylcholinesterase, Amyloid-β Aggregation and Acetylcholinesterase-Amyloid Interaction. Pharmaceutics 2022, 14, 2342.
Corro-Morón, M.; Granell, A.; Ivanova, V.; Domingo, E.; Beltrán-Debón, R.; Barril, X.; Sanz, M.-J.; Matheu, M. I.; Castillón, S.; Díaz, Y. Revealing 2-Dimethylhydrazino-2-Alkyl Alkynyl Sphingosine Derivatives as Sphingosine Kinase 2 Inhibitors: Some Hints on the Structural Basis for Selective Inhibition. Bioorg. Chem. 2022, 121, 105668.
Avila-Barrientos, L. P.; Cofas-Vargas, L. F.; Agüero-Chapin, G.; Hernández-García, E.; Ruiz-Carmona, S.; Valdez-Cruz, N. A.; Trujillo-Roldán, M.; Weber, J.; Ruiz-Blanco, Y. B.; Barril, X.; García-Hernández, E. Computational Design of Inhibitors Targeting the Catalytic β Subunit of Escherichia Coli FO F1-ATP Synthase. Antibiotics 2022, 11, 1.
Miñarro-Lleonar, M.; Ruiz-Carmona, S.; Alvarez-Garcia, D.; Schmidtke, P.; Barril, X. Development of an Automatic Pipeline for Participation in the CELPP Challenge. Int. J. Mol. Sci. 2022, 23, 4756.
Alvarez-Garcia, D.; Schmidtke, P.; Cubero, E.; Barril, X. Extracting Atomic Contributions to Binding Free Energy Using Molecular Dynamics Simulations with Mixed Solvents (MDmix). Curr. Drug Discov. Technol. 2022, 19, 62.
Burastero, O.; Defelipe, L. A.; Gola, G.; Tateosian, N. L.; Lopez, E. D.; Martinena, C. B.; Arcon, J. P.; Traian, M. D.; Wetzler, D. E.; Bento, I.; Barril, X.; Ramirez, J.; Marti, M. A.; Garcia-Alai, M. M.; Turjanski, A. G. Cosolvent Sites-Based Discovery of Mycobacterium Tuberculosis Protein Kinase G Inhibitors. J. Med. Chem. 2022, 65, 9691.
Cunha, R. D.; Ferreira, L. J.; Orestes, E.; Coutinho-Neto, M. D.; de Almeida, J. M.; Carvalho, R. M.; Maciel, C. D.; Curutchet, C.; Homem-de-Mello, P. Naphthenic acids aggregation: The role of salinity. Computation 2022, 10, 170.
Codony, S.; Pont, C.; Griñan-Ferré, C.; et. al. Discovery and in vivo proof of concept of a highly potent dual inhibitor of soluble epoxide hydrolase and acetylcholinesterase for the treatment of Alzheimer’s disease. J. Med. Chem. 2022, 65, 6, 4909.
Scott, J. I.; Mendive-Tapia, L.; Gordon, D.; et. al. A fluorogenic probe for granzyme B enables in-biopsy evaluation and screening of response to anticancer immunotherapies. Nat. Commun. 2022, 13, 2366.
Aledavood, E.; Gheeraert, A.; Forte, A.; Vuillon, L.; Rivalta, I.; Luque, F. J.; Estarellas, C. Elucidating the activation mechanism of AMPK by direct pan-activator PF-739. Front. Mol. Biosci., 2022, 8, 760026.
Aledavood, E.; Selmi, B.; Estarellas, C.; Masetti, M.; Luque, F. J. From acid activation mechanisms of proton conduction to design of inhibitors of the M2 proton channel of influenza A virus. Front. Mol. Biosci., 2022, 8, 796229.
Sanz-Gomez, M.; Aledavood, E.; Beroiz-Salaverri, M.; Lagartera, L.; Vega-Martin, E.; Gil-Ortega, M.; Cumella, J.; Perez, C.; Luque, F. J.; Estarellas, C.; Fernandez-Alfonso, M. S.; Castro, A. Novel indolic AMPK modulators induce vasodilatation through activation of the AMPK-eNOS-NO pathway. Sci. Rep., 2022, 12, 4225.
Borsatto, A.; Akkad, O.; Galdadas, I.; Ma, S. M.; Damfo, S.; Haider, S.; Kozielski, F.; Estarellas, C.; Gervasio, F. L. Revealing druggable cryptic pockets in the Nsp1 of SARS-CoV-2 and other beta-coronaviruses by simulations and crystallography. Elife, 2022, 11, e81167.
