@article{@article{Blanco-Gabella_2025_MG_HBonds,,

title = {Understanding the Role of H-Bonds in the Stability of Molecular Glue-Induced Ternary Complexes},

author = {Patricia Blanco-Gabella and Varbina Ivanova and Álvaro Serrano-Morrás and Julian E. Fuchs and Jordi Juárez-Jiménez},

url = {https://pubs.acs.org/doi/10.1021/acs.jcim.5c02718},

doi = {10.1021/acs.jcim.5c02718},

issn = {1549-9596},

year  = {2026},

date = {2026-01-23},

urldate = {2026-01-23},

journal = {Journal of Chemical Information and Modeling},

abstract = {Protein-protein interaction (PPI) networks play a central role in many biological processes and thus the possibility of modulating them using small molecules offers several biomedical and biotechnological opportunities. Molecular glues (MGs) are small molecules that bind to a PPI interface and stabilize the complex. Oftentimes, MGs present no measurable affinity to at least one of the proteins involved in the ternary complex, and the molecular bases for their action are not completely understood. We previously reported a significant correlation between protein-protein hydrogen bond robustness and the stability of the lenalidomide-induced CRBN-CK1α complex. In this work, we demonstrate that this relationship is not unique for that system, but rather represents a reproducible physicochemical phenomenon underlying the mechanism of action of chemically diverse MGs, including additional IMiDs and Fusicoccin A. Our results shed light into a vaguely understood phenomenon and pave the way for the development of new computational methods that enable the rational design of molecular glues.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{@article{SerranoMorras2025,

title = {A bottom-up approach to find lead compounds in expansive chemical spaces},

author = {Álvaro Serrano-Morrás and Andrea Bertran-Mostazo and Marina Miñarro-Lleonar and Arnau Comajuncosa-Creus and Adrià Cabello and Carme Labranya and Carmen Escudero and Tian V. Tian and Inna Khutorianska and Dmytro S. Radchenko and Yurii S. Moroz and Lucas Defelipe and David Ruiz-Carrillo and Maria Garcia-Alai and Robert Schmidt and Matthias Rarey and Patrick Aloy and Carles Galdeano and Jordi Juárez-Jiménez and Xavier Barril},

url = {https://www.nature.com/articles/s42004-025-01610-2},

doi = {10.1038/s42004-025-01610-2},

issn = {2399-3669},

year  = {2025},

date = {2025-08-01},

urldate = {2025-08-01},

journal = {Communications Chemistry},

volume = {8},

number = {225},

abstract = {Drug discovery starts with the identification of a “hit” compound that, following a long and expensive optimization process, evolves into a drug candidate. Bigger screening collections increase the odds of finding more and better hits. For this reason, large pharmaceutical companies have invested heavily in high-throughput screening (HTS) collections that can contain several million compounds. However, this figure pales in comparison with the emergent on-demand chemical collections, which have recently reached the trillion scale. These chemical collections are potentially transformative for drug discovery, as they could deliver many diverse and high-quality hits, even reaching lead-like starting points. But first, it will be necessary to develop computational tools capable of efficiently navigating such massive virtual collections. To address this challenge, we have conceived an innovative strategy that explores the chemical universe from the bottom up, performing a systematic search on the fragment space (exploration phase), to then mine the most promising areas of on-demand collections (exploitation phase). Using a hierarchy of increasingly sophisticated computational methods to remove false positives, we maximize the success probability and minimize the overall computational cost. A basic implementation of the concept has enabled us to validate the strategy prospectively, allowing the identification of new BRD4 (BD1) binders with potencies comparable to stablished drug candidates.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mi_arro_Lleonar_2023,

title = {Lenalidomide Stabilizes Protein–Protein Complexes by Turning Labile Intermolecular H-Bonds into Robust Interactions},

author = {Marina Miñarro-Lleonar and Andrea Bertran-Mostazo and Jorge Duro and Xavier Barril and Jordi Juárez-Jiménez},

url = {http://dx.doi.org/10.1021/acs.jmedchem.2c01692},

doi = {10.1021/acs.jmedchem.2c01692},

issn = {1520-4804},

year  = {2023},

date = {2023-04-01},

urldate = {2023-04-01},

journal = {Journal of Medicinal Chemistry},

volume = {66},

number = {9},

pages = {6037–6046},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ju_rez_Jim_nez_2020,

title = {Combining Virtual Reality Visualization with Ensemble Molecular Dynamics to Study Complex Protein Conformational Changes},

author = {Jordi Juárez-Jiménez and Philip Tew and Michael O′Connor and Salomé Llabrés and Rebecca Sage and David Glowacki and Julien Michel},

url = {http://dx.doi.org/10.1021/acs.jcim.0c00221},

doi = {10.1021/acs.jcim.0c00221},

issn = {1549-960X},

year  = {2020},

date = {2020-11-01},

urldate = {2020-11-01},

journal = {Journal of Chemical Information and Modeling},

volume = {60},

number = {12},

pages = {6344–6354},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ju_rez_Jim_nez_2020b,

title = {Dynamic design: manipulation of millisecond timescale motions on the energy landscape of cyclophilin A},

author = {Jordi Juárez-Jiménez and Arun A. Gupta and Gogulan Karunanithy and Antonia S. J. S. Mey and Charis Georgiou and Harris Ioannidis and Alessio De Simone and Paul N. Barlow and Alison N. Hulme and Malcolm D. Walkinshaw and Andrew J. Baldwin and Julien Michel},

url = {http://dx.doi.org/10.1039/C9SC04696H},

doi = {10.1039/c9sc04696h},

issn = {2041-6539},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Chemical Science},

volume = {11},

number = {10},

pages = {2670–2680},

publisher = {Royal Society of Chemistry (RSC)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Llabr_s_2016,

title = {Mechanism of the Pseudoirreversible Binding of Amantadine to the M2 Proton Channel},

author = {Salomé Llabrés and Jordi Juárez-Jiménez and Matteo Masetti and Rosana Leiva and Santiago Vázquez and Sabrina Gazzarrini and Anna Moroni and Andrea Cavalli and F. Javier Luque},

url = {http://dx.doi.org/10.1021/jacs.6b07096},

doi = {10.1021/jacs.6b07096},

issn = {1520-5126},

year  = {2016},

date = {2016-11-01},

urldate = {2016-11-01},

journal = {Journal of the American Chemical Society},

volume = {138},

number = {47},

pages = {15345–15358},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ju_rez_Jim_nez_2014,

title = {Assessing the Suitability of the Multilevel Strategy for the Conformational Analysis of Small Ligands},

author = {Jordi Juárez-Jiménez and Xavier Barril and Modesto Orozco and Ramon Pouplana and F. Javier Luque},

url = {http://dx.doi.org/10.1021/jp506779y},

doi = {10.1021/jp506779y},

issn = {1520-5207},

year  = {2014},

date = {2014-10-01},

urldate = {2014-10-01},

journal = {The Journal of Physical Chemistry B},

volume = {119},

number = {3},

pages = {1164–1172},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Viayna_2014,

title = {Synthesis and Multitarget Biological Profiling of a Novel Family of Rhein Derivatives As Disease-Modifying Anti-Alzheimer Agents},

author = {Elisabet Viayna and Irene Sola and Manuela Bartolini and Angela De Simone and Cheril Tapia-Rojas and Felipe G. Serrano and Raimon Sabaté and Jordi Juárez-Jiménez and Belén Pérez and F. Javier Luque and Vincenza Andrisano and M. Victòria Clos and Nibaldo C. Inestrosa and Diego Muñoz-Torrero},

url = {http://dx.doi.org/10.1021/jm401824w},

doi = {10.1021/jm401824w},

issn = {1520-4804},

year  = {2014},

date = {2014-03-01},

urldate = {2014-03-01},

journal = {Journal of Medicinal Chemistry},

volume = {57},

number = {6},

pages = {2549–2567},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{@article{Blanco-Gabella_2025_MG_HBonds,,

title = {Understanding the Role of H-Bonds in the Stability of Molecular Glue-Induced Ternary Complexes},

author = {Patricia Blanco-Gabella and Varbina Ivanova and Álvaro Serrano-Morrás and Julian E. Fuchs and Jordi Juárez-Jiménez},

url = {https://pubs.acs.org/doi/10.1021/acs.jcim.5c02718},

doi = {10.1021/acs.jcim.5c02718},

issn = {1549-9596},

year  = {2026},

date = {2026-01-23},

urldate = {2026-01-23},

journal = {Journal of Chemical Information and Modeling},

abstract = {Protein-protein interaction (PPI) networks play a central role in many biological processes and thus the possibility of modulating them using small molecules offers several biomedical and biotechnological opportunities. Molecular glues (MGs) are small molecules that bind to a PPI interface and stabilize the complex. Oftentimes, MGs present no measurable affinity to at least one of the proteins involved in the ternary complex, and the molecular bases for their action are not completely understood. We previously reported a significant correlation between protein-protein hydrogen bond robustness and the stability of the lenalidomide-induced CRBN-CK1α complex. In this work, we demonstrate that this relationship is not unique for that system, but rather represents a reproducible physicochemical phenomenon underlying the mechanism of action of chemically diverse MGs, including additional IMiDs and Fusicoccin A. Our results shed light into a vaguely understood phenomenon and pave the way for the development of new computational methods that enable the rational design of molecular glues.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Learning Binding Affinities via Fine-Tuning of Protein and Ligand Language Models},

author = {Rohan Gorantla* and Aryo Pradipta Gema and Ian Xi Yang and Álvaro Serrano-Morrás and Benjamin Suutari and Jordi Juárez-Jiménez and Antonia S.J.S. Mey*

},

url = {https://pubs.acs.org/doi/10.1021/acs.jcim.5c02063},

doi = {10.1021/acs.jcim.5c02063},

issn = { 1549-960X},

year  = {2025},

date = {2025-10-31},

urldate = {2025-10-31},

journal = {Journal of Chemical Information and Modeling},

volume = {ASAP},

abstract = {Accurate in silico prediction of protein–ligand binding affinity is essential for efficient hit identification in large molecular libraries. Commonly used structure-based methods such as docking often fail to rank compounds effectively, and free energy-based approaches, while accurate, are too computationally intensive for large-scale screening. Existing deep learning models struggle to generalize to new targets or drugs, and current evaluation methods often do not accurately reflect real-world performance. We introduce BALM, a deep learning framework that predicts binding affinity using pretrained protein and ligand language models. We also propose improved evaluation strategies with diverse data sets and metrics to assess model performance to new targets better. Using a curated version of BindingDB, BALM shows generalization to unseen drugs, scaffolds, and targets. In few-shot learning scenarios for targets such as USP7 and Mpro, it outperforms traditional machine learning and docking methods, including AutoDock Vina. Adoption of our target-based evaluation methods will allow a more stringent evaluation of machine learning-based scoring tools. Our binding affinity prediction framework shows good performance, is computationally efficient, and is highly adaptable within this evaluation setting, making it practical for early-stage drug discovery screening.



},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{@article{SerranoMorras2025,

title = {A bottom-up approach to find lead compounds in expansive chemical spaces},

author = {Álvaro Serrano-Morrás and Andrea Bertran-Mostazo and Marina Miñarro-Lleonar and Arnau Comajuncosa-Creus and Adrià Cabello and Carme Labranya and Carmen Escudero and Tian V. Tian and Inna Khutorianska and Dmytro S. Radchenko and Yurii S. Moroz and Lucas Defelipe and David Ruiz-Carrillo and Maria Garcia-Alai and Robert Schmidt and Matthias Rarey and Patrick Aloy and Carles Galdeano and Jordi Juárez-Jiménez and Xavier Barril},

url = {https://www.nature.com/articles/s42004-025-01610-2},

doi = {10.1038/s42004-025-01610-2},

issn = {2399-3669},

year  = {2025},

date = {2025-08-01},

urldate = {2025-08-01},

journal = {Communications Chemistry},

volume = {8},

number = {225},

abstract = {Drug discovery starts with the identification of a “hit” compound that, following a long and expensive optimization process, evolves into a drug candidate. Bigger screening collections increase the odds of finding more and better hits. For this reason, large pharmaceutical companies have invested heavily in high-throughput screening (HTS) collections that can contain several million compounds. However, this figure pales in comparison with the emergent on-demand chemical collections, which have recently reached the trillion scale. These chemical collections are potentially transformative for drug discovery, as they could deliver many diverse and high-quality hits, even reaching lead-like starting points. But first, it will be necessary to develop computational tools capable of efficiently navigating such massive virtual collections. To address this challenge, we have conceived an innovative strategy that explores the chemical universe from the bottom up, performing a systematic search on the fragment space (exploration phase), to then mine the most promising areas of on-demand collections (exploitation phase). Using a hierarchy of increasingly sophisticated computational methods to remove false positives, we maximize the success probability and minimize the overall computational cost. A basic implementation of the concept has enabled us to validate the strategy prospectively, allowing the identification of new BRD4 (BD1) binders with potencies comparable to stablished drug candidates.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Cullin-RING ligase BioE3 reveals molecular-glue-induced neosubstrates and rewiring of the endogenous Cereblon ubiquitome},

author = {Laura Merino-Cacho and Orhi Barroso-Gomila and Mónica Pozo-Rodríguez and Veronica Muratore and Claudia Guinea-Pérez and Álvaro Serrano and Coralia Pérez and Sandra Cano-López and Ainhoa Urcullu and Mikel Azkargorta and Ibon Iloro and Carles Galdeano and Jordi Juárez-Jiménez and Ugo Mayor and Felix Elortza and Rosa Barrio and James D Sutherland},

url = {https://link.springer.com/article/10.1186/s12964-025-02091-5},

doi = {https://doi.org/10.1186/s12964-025-02091-5},

issn = {1478-811X},

year  = {2025},

date = {2025-02-19},

urldate = {2025-02-19},

journal = {Cell Communication and Signaling},

volume = {23},

number = {1},

pages = {101},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {A versatile luminescent probe for sensing and monitoring amyloid proteins},

author = {Guillem Vázquez and Alba Espargaró and Ana B. Caballero and Ania {Di Pede}-Mattatelli and M. Antònia Busquets and Daria Nawrot and Raimon Sabaté and Ernesto Nicolás and Jordi Juárez-Jiménez and Patrick Gamez},

url = {https://www.sciencedirect.com/science/article/pii/S0143720824004133},

doi = {https://doi.org/10.1016/j.dyepig.2024.112348},

issn = {0143-7208},

year  = {2024},

date = {2024-12-01},

urldate = {2024-12-01},

journal = {Dyes and Pigments},

volume = {231},

pages = {112348},

abstract = {A modified lysine residue containing an environment-sensitive moiety was prepared through a straightforward synthesis, and its fluorescent properties were examined. The new fluorescent sensor, DMN-BocK, can monitor amyloid aggregation processes associated with neurodegenerative diseases such as Alzheimer's or Parkinson's. DMN-BocK offers advantages over classical amyloid-specific dyes like Thioflavins or Congo Red because it is (1) available to detect a broader range of amyloid structures; (2) useful both in vitro and in cellulo; (3) capable of differentiating amyloid structures, providing information on the binding site microenvironment; and (4) a synthon than can be incorporated into protein sequences to gain further structural information. Our findings suggest that DMN-based amino-acid probes have a strong potential to become a sensor of choice for in vitro and in cellulo studies of amyloid aggregation in drug discovery assays.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Reaction Space Charting as a Tool in Organic Chemistry Research and Development},

author = {Eloy Lozano-Baró and Pau Nadal-Rodríguez and Jordi Juárez-Jiménez and Ouldouz Ghashghaei and Rodolfo Lavilla

},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adsc.202301205},

doi = { https://doi.org/10.1002/adsc.202301205},

year  = {2024},

date = {2024-01-17},

urldate = {2024-01-17},

journal = {Advanced Synthesis & Catalysis},

volume = {366},

number = {4},

pages = {551-573},

abstract = {The chemical and reaction spaces are incredibly vast and special procedures are required to study them. Their complex and multiparametric nature encompass myriads of compounds and interactions and endless modifications involving the distinct impact of relevant variables (temperature, solvent, stoichiometry, etc.). This often calls for the design, collection, and analysis/interpretation of large datasets. Reaction charting, the systematic scanning, description, analysis, and guided modifications of a given process, stands as the most promising approach. It offers fast and accurate solutions as well as expanding the knowledge about the systems. This deeper understanding enables reliable predictions, improvement of the productivity (yields, scope), eventually leading to sustainable, economic, and safe applications. The present review introduces the topic, analyzing selected examples and recent advancements in different organic chemistry-related fields. The covered methodologies range from classical experimentation modifying one factor at a time, to Design of Experiments and more modern computational approaches involving Machine Learning and Artificial Intelligence. In this way, the impact of charting in process development, biological and medicinal chemistry, catalysis, reaction discovery and computational methods is accounted. Finally, the conclusion/outlook section gives a general appraisal and a prospect on the future implementation of the methodology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mi_arro_Lleonar_2023,

title = {Lenalidomide Stabilizes Protein–Protein Complexes by Turning Labile Intermolecular H-Bonds into Robust Interactions},

author = {Marina Miñarro-Lleonar and Andrea Bertran-Mostazo and Jorge Duro and Xavier Barril and Jordi Juárez-Jiménez},

url = {http://dx.doi.org/10.1021/acs.jmedchem.2c01692},

doi = {10.1021/acs.jmedchem.2c01692},

issn = {1520-4804},

year  = {2023},

date = {2023-04-01},

urldate = {2023-04-01},

journal = {Journal of Medicinal Chemistry},

volume = {66},

number = {9},

pages = {6037–6046},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Scott_2022,

title = {A fluorogenic probe for granzyme B enables in-biopsy evaluation and screening of response to anticancer immunotherapies},

author = {Jamie I. Scott and Lorena Mendive-Tapia and Doireann Gordon and Nicole D. Barth and Emily J. Thompson and Zhiming Cheng and David Taggart and Takanori Kitamura and Alberto Bravo-Blas and Edward W. Roberts and Jordi Juarez-Jimenez and Julien Michel and Berber Piet and I. Jolanda Vries and Martijn Verdoes and John Dawson and Neil O. Carragher and Richard A. O’ Connor and Ahsan R. Akram and Margaret Frame and Alan Serrels and Marc Vendrell},

url = {http://dx.doi.org/10.1038/s41467-022-29691-w},

doi = {10.1038/s41467-022-29691-w},

issn = {2041-1723},

year  = {2022},

date = {2022-05-01},

journal = {Nature Communications},

volume = {13},

number = {1},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Codony_2022,

title = {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},

author = {Sandra Codony and Caterina Pont and Christian Griñán-Ferré and Ania Di Pede-Mattatelli and Carla Calvó-Tusell and Ferran Feixas and Sílvia Osuna and Júlia Jarné-Ferrer and Marina Naldi and Manuela Bartolini and María Isabel Loza and José Brea and Belén Pérez and Clara Bartra and Coral Sanfeliu and Jordi Juárez-Jiménez and Christophe Morisseau and Bruce D. Hammock and Mercè Pallàs and Santiago Vázquez and Diego Muñoz-Torrero},

url = {http://dx.doi.org/10.1021/acs.jmedchem.1c02150},

doi = {10.1021/acs.jmedchem.1c02150},

issn = {1520-4804},

year  = {2022},

date = {2022-03-01},

journal = {Journal of Medicinal Chemistry},

volume = {65},

number = {6},

pages = {4909–4925},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kowalczyk_2021,

title = {Dual Effect of Prussian Blue Nanoparticles on Aβ40 Aggregation: β-Sheet Fibril Reduction and Copper Dyshomeostasis Regulation},

author = {Joanna Kowalczyk and Ettore Grapsi and Alba Espargaró and Ana B. Caballero and Jordi Juárez-Jiménez and Maria A. Busquets and Patrick Gamez and Raimon Sabate and Joan Estelrich},

url = {http://dx.doi.org/10.1021/acs.biomac.0c01290},

doi = {10.1021/acs.biomac.0c01290},

issn = {1526-4602},

year  = {2021},

date = {2021-01-01},

journal = {Biomacromolecules},

volume = {22},

number = {2},

pages = {430–440},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ju_rez_Jim_nez_2020,

title = {Combining Virtual Reality Visualization with Ensemble Molecular Dynamics to Study Complex Protein Conformational Changes},

author = {Jordi Juárez-Jiménez and Philip Tew and Michael O′Connor and Salomé Llabrés and Rebecca Sage and David Glowacki and Julien Michel},

url = {http://dx.doi.org/10.1021/acs.jcim.0c00221},

doi = {10.1021/acs.jcim.0c00221},

issn = {1549-960X},

year  = {2020},

date = {2020-11-01},

urldate = {2020-11-01},

journal = {Journal of Chemical Information and Modeling},

volume = {60},

number = {12},

pages = {6344–6354},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kuzmanic_2020,

title = {Investigating Cryptic Binding Sites by Molecular Dynamics Simulations},

author = {Antonija Kuzmanic and Gregory R. Bowman and Jordi Juarez-Jimenez and Julien Michel and Francesco L. Gervasio},

url = {http://dx.doi.org/10.1021/acs.accounts.9b00613},

doi = {10.1021/acs.accounts.9b00613},

issn = {1520-4898},

year  = {2020},

date = {2020-03-01},

journal = {Accounts of Chemical Research},

volume = {53},

number = {3},

pages = {654–661},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ju_rez_Jim_nez_2020b,

title = {Dynamic design: manipulation of millisecond timescale motions on the energy landscape of cyclophilin A},

author = {Jordi Juárez-Jiménez and Arun A. Gupta and Gogulan Karunanithy and Antonia S. J. S. Mey and Charis Georgiou and Harris Ioannidis and Alessio De Simone and Paul N. Barlow and Alison N. Hulme and Malcolm D. Walkinshaw and Andrew J. Baldwin and Julien Michel},

url = {http://dx.doi.org/10.1039/C9SC04696H},

doi = {10.1039/c9sc04696h},

issn = {2041-6539},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Chemical Science},

volume = {11},

number = {10},

pages = {2670–2680},

publisher = {Royal Society of Chemistry (RSC)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{De_Simone_2019,

title = {A computationally designed binding mode flip leads to a novel class of potent tri-vector cyclophilin inhibitors},

author = {Alessio De Simone and Charis Georgiou and Harris Ioannidis and Arun A. Gupta and Jordi Juárez-Jiménez and Dahlia Doughty-Shenton and Elizabeth A. Blackburn and Martin A. Wear and Jonathan P. Richards and Paul N. Barlow and Neil Carragher and Malcolm D. Walkinshaw and Alison N. Hulme and Julien Michel},

url = {http://dx.doi.org/10.1039/C8SC03831G},

doi = {10.1039/c8sc03831g},

issn = {2041-6539},

year  = {2019},

date = {2019-01-01},

journal = {Chemical Science},

volume = {10},

number = {2},

pages = {542–547},

publisher = {Royal Society of Chemistry (RSC)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Alencar_2018,

title = {First homology model of Plasmodium falciparum glucose-6-phosphate dehydrogenase: Discovery of selective substrate analog-based inhibitors as novel antimalarial agents},

author = {Nelson Alencar and Irene Sola and María Linares and Jordi Juárez-Jiménez and Caterina Pont and Antonio Viayna and David Vílchez and Cristina Sampedro and Paloma Abad and Susana Pérez-Benavente and Jerónimo Lameira and José M. Bautista and Diego Muñoz-Torrero and F. Javier Luque},

url = {http://dx.doi.org/10.1016/j.ejmech.2018.01.044},

doi = {10.1016/j.ejmech.2018.01.044},

issn = {0223-5234},

year  = {2018},

date = {2018-02-01},

journal = {European Journal of Medicinal Chemistry},

volume = {146},

pages = {108–122},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mey_2017,

title = {Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations},

author = {Antonia S. J. S. Mey and Jordi Juárez Jiménez and Julien Michel},

url = {http://dx.doi.org/10.1007/s10822-017-0083-9},

doi = {10.1007/s10822-017-0083-9},

issn = {1573-4951},

year  = {2017},

date = {2017-11-01},

journal = {Journal of Computer-Aided Molecular Design},

volume = {32},

number = {1},

pages = {199–210},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Llona_Minguez_2017,

title = {Tetrahydrobenzothiophene carboxamides: Beyond the kinase domain and into the fatty acid realm},

author = {Sabin Llona-Minguez and Shabnam Fayezi and Alireza Alihemmati and Jordi Juárez-Jiménez and F. Javier Piedrafita and Thomas Helleday},

url = {http://dx.doi.org/10.1016/j.bmcl.2017.08.006},

doi = {10.1016/j.bmcl.2017.08.006},

issn = {0960-894X},

year  = {2017},

date = {2017-09-01},

journal = {Bioorganic & Medicinal Chemistry Letters},

volume = {27},

number = {18},

pages = {4462–4466},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Di_Pietro_2017,

title = {Unveiling a novel transient druggable pocket in BACE-1 through molecular simulations: Conformational analysis and binding mode of multisite inhibitors},

author = {Ornella Di Pietro and Jordi Juárez-Jiménez and Diego Muñoz-Torrero and Charles A. Laughton and F. Javier Luque},

editor = {Chandra Verma},

url = {http://dx.doi.org/10.1371/journal.pone.0177683},

doi = {10.1371/journal.pone.0177683},

issn = {1932-6203},

year  = {2017},

date = {2017-05-01},

journal = {PLOS ONE},

volume = {12},

number = {5},

pages = {e0177683},

publisher = {Public Library of Science (PLoS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Delcanale_2017,

title = {Tuning the local solvent composition at a drug carrier surface: the effect of dimethyl sulfoxide/water mixture on the photofunctional properties of hypericin–β-lactoglobulin complexes},

author = {P. Delcanale and B. Rodríguez-Amigo and J. Juárez-Jiménez and F. J. Luque and S. Abbruzzetti and M. Agut and S. Nonell and C. Viappiani},

url = {http://dx.doi.org/10.1039/C7TB00081B},

doi = {10.1039/c7tb00081b},

issn = {2050-7518},

year  = {2017},

date = {2017-01-01},

journal = {Journal of Materials Chemistry B},

volume = {5},

number = {8},

pages = {1633–1641},

publisher = {Royal Society of Chemistry (RSC)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Llabr_s_2016,

title = {Mechanism of the Pseudoirreversible Binding of Amantadine to the M2 Proton Channel},

author = {Salomé Llabrés and Jordi Juárez-Jiménez and Matteo Masetti and Rosana Leiva and Santiago Vázquez and Sabrina Gazzarrini and Anna Moroni and Andrea Cavalli and F. Javier Luque},

url = {http://dx.doi.org/10.1021/jacs.6b07096},

doi = {10.1021/jacs.6b07096},

issn = {1520-5126},

year  = {2016},

date = {2016-11-01},

urldate = {2016-11-01},

journal = {Journal of the American Chemical Society},

volume = {138},

number = {47},

pages = {15345–15358},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Di_Pietro_2016,

title = {Design, synthesis and biological evaluation of N-methyl-N-[(1,2,3-triazol-4-yl)alkyl]propargylamines as novel monoamine oxidase B inhibitors},

author = {Ornella Di Pietro and Nelson Alencar and Gerard Esteban and Elisabet Viayna and Natalia Szałaj and Javier Vázquez and Jordi Juárez-Jiménez and Irene Sola and Belén Pérez and Montse Solé and Mercedes Unzeta and Diego Muñoz-Torrero and F. Javier Luque},

url = {http://dx.doi.org/10.1016/j.bmc.2016.06.045},

doi = {10.1016/j.bmc.2016.06.045},

issn = {0968-0896},

year  = {2016},

date = {2016-10-01},

journal = {Bioorganic & Medicinal Chemistry},

volume = {24},

number = {20},

pages = {4835–4854},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mey_2016,

title = {Blinded predictions of binding modes and energies of HSP90-α ligands for the 2015 D3R grand challenge},

author = {Antonia S. J. S. Mey and Jordi Juárez-Jiménez and Alexis Hennessy and Julien Michel},

url = {http://dx.doi.org/10.1016/j.bmc.2016.07.044},

doi = {10.1016/j.bmc.2016.07.044},

issn = {0968-0896},

year  = {2016},

date = {2016-10-01},

journal = {Bioorganic & Medicinal Chemistry},

volume = {24},

number = {20},

pages = {4890–4899},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Rey_Carrizo_2015,

title = {New polycyclic dual inhibitors of the wild type and the V27A mutant M2 channel of the influenza A virus with unexpected binding mode},

author = {Matias Rey-Carrizo and Sabrina Gazzarrini and Salomé Llabrés and Marta Frigolé-Vivas and Jordi Juárez-Jiménez and Mercè Font-Bardia and Lieve Naesens and Anna Moroni and F. Javier Luque and Santiago Vázquez},

url = {http://dx.doi.org/10.1016/j.ejmech.2015.04.030},

doi = {10.1016/j.ejmech.2015.04.030},

issn = {0223-5234},

year  = {2015},

date = {2015-05-01},

journal = {European Journal of Medicinal Chemistry},

volume = {96},

pages = {318–329},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Rodr_guez_Amigo_2015,

title = {The complex of hypericin with β-lactoglobulin has antimicrobial activity with potential applications in dairy industry},

author = {Beatriz Rodríguez-Amigo and Pietro Delcanale and Gabriel Rotger and Jordi Juárez-Jiménez and Stefania Abbruzzetti and Andrea Summer and Montserrat Agut and F. Javier Luque and Santi Nonell and Cristiano Viappiani},

url = {http://dx.doi.org/10.3168/jds.2014-8691},

doi = {10.3168/jds.2014-8691},

issn = {0022-0302},

year  = {2015},

date = {2015-01-01},

journal = {Journal of Dairy Science},

volume = {98},

number = {1},

pages = {89–94},

publisher = {American Dairy Science Association},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ju_rez_Jim_nez_2014,

title = {Assessing the Suitability of the Multilevel Strategy for the Conformational Analysis of Small Ligands},

author = {Jordi Juárez-Jiménez and Xavier Barril and Modesto Orozco and Ramon Pouplana and F. Javier Luque},

url = {http://dx.doi.org/10.1021/jp506779y},

doi = {10.1021/jp506779y},

issn = {1520-5207},

year  = {2014},

date = {2014-10-01},

urldate = {2014-10-01},

journal = {The Journal of Physical Chemistry B},

volume = {119},

number = {3},

pages = {1164–1172},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Di_Pietro_2014,

title = {Tetrahydrobenzo[h][1,6]naphthyridine-6-chlorotacrine hybrids as a new family of anti-Alzheimer agents targeting β-amyloid, tau, and cholinesterase pathologies},

author = {Ornella Di Pietro and F. Javier Pérez-Areales and Jordi Juárez-Jiménez and Alba Espargaró and M. Victòria Clos and Belén Pérez and Rodolfo Lavilla and Raimon Sabaté and F. Javier Luque and Diego Muñoz-Torrero},

url = {http://dx.doi.org/10.1016/j.ejmech.2014.07.021},

doi = {10.1016/j.ejmech.2014.07.021},

issn = {0223-5234},

year  = {2014},

date = {2014-09-01},

journal = {European Journal of Medicinal Chemistry},

volume = {84},

pages = {107–117},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Rey_Carrizo_2014,

title = {Easily Accessible Polycyclic Amines that Inhibit the Wild-Type and Amantadine-Resistant Mutants of the M2 Channel of Influenza A Virus},

author = {Matias Rey-Carrizo and Marta Barniol-Xicota and Chunlong Ma and Marta Frigolé-Vivas and Eva Torres and Lieve Naesens and Salomé Llabrés and Jordi Juárez-Jiménez and Francisco J. Luque and William F. DeGrado and Robert A. Lamb and Lawrence H. Pinto and Santiago Vázquez},

url = {http://dx.doi.org/10.1021/jm5005804},

doi = {10.1021/jm5005804},

issn = {1520-4804},

year  = {2014},

date = {2014-06-01},

journal = {Journal of Medicinal Chemistry},

volume = {57},

number = {13},

pages = {5738–5747},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Viayna_2014,

title = {Synthesis and Multitarget Biological Profiling of a Novel Family of Rhein Derivatives As Disease-Modifying Anti-Alzheimer Agents},

author = {Elisabet Viayna and Irene Sola and Manuela Bartolini and Angela De Simone and Cheril Tapia-Rojas and Felipe G. Serrano and Raimon Sabaté and Jordi Juárez-Jiménez and Belén Pérez and F. Javier Luque and Vincenza Andrisano and M. Victòria Clos and Nibaldo C. Inestrosa and Diego Muñoz-Torrero},

url = {http://dx.doi.org/10.1021/jm401824w},

doi = {10.1021/jm401824w},

issn = {1520-4804},

year  = {2014},

date = {2014-03-01},

urldate = {2014-03-01},

journal = {Journal of Medicinal Chemistry},

volume = {57},

number = {6},

pages = {2549–2567},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ju_rez_Jim_nez_2014b,

title = {Exploring the structural basis of the selective inhibition of monoamine oxidase A by dicarbonitrile aminoheterocycles: Role of Asn181 and Ile335 validated by spectroscopic and computational studies},

author = {Jordi Juárez-Jiménez and Eduarda Mendes and Carles Galdeano and Carla Martins and Daniel B. Silva and José Marco-Contelles and Maria Carmo Carreiras and F. Javier Luque and Rona R. Ramsay},

url = {http://dx.doi.org/10.1016/j.bbapap.2013.11.003},

doi = {10.1016/j.bbapap.2013.11.003},

issn = {1570-9639},

year  = {2014},

date = {2014-02-01},

journal = {Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics},

volume = {1844},

number = {2},

pages = {389–397},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Di_Pietro_2014b,

title = {1,2,3,4-Tetrahydrobenzo[h][1,6]naphthyridines as a new family of potent peripheral-to-midgorge-site inhibitors of acetylcholinesterase: Synthesis, pharmacological evaluation and mechanistic studies},

author = {Ornella Di Pietro and Elisabet Viayna and Esther Vicente-García and Manuela Bartolini and Rosario Ramón and Jordi Juárez-Jiménez and M. Victòria Clos and Belén Pérez and Vincenza Andrisano and F. Javier Luque and Rodolfo Lavilla and Diego Muñoz-Torrero},

url = {http://dx.doi.org/10.1016/j.ejmech.2013.12.008},

doi = {10.1016/j.ejmech.2013.12.008},

issn = {0223-5234},

year  = {2014},

date = {2014-02-01},

journal = {European Journal of Medicinal Chemistry},

volume = {73},

pages = {141–152},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bolea_2011,

title = {Synthesis, Biological Evaluation, and Molecular Modeling of Donepezil and N-[(5-(Benzyloxy)-1-methyl-1H-indol-2-yl)methyl]-N-methylprop-2-yn-1-amine Hybrids as New Multipotent Cholinesterase/Monoamine Oxidase Inhibitors for the Treatment of Alzheimer’s Disease},

author = {Irene Bolea and Jordi Juárez-Jiménez and Cristóbal Rı́os and Mourad Chioua and Ramón Pouplana and F. Javier Luque and Mercedes Unzeta and José Marco-Contelles and Abdelouahid Samadi},

url = {http://dx.doi.org/10.1021/jm200853t},

doi = {10.1021/jm200853t},

issn = {1520-4804},

year  = {2011},

date = {2011-11-01},

urldate = {2011-11-01},

journal = {Journal of Medicinal Chemistry},

volume = {54},

number = {24},

pages = {8251–8270},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Duque_2011,

title = {Exploring the Size Limit of Templates for Inhibitors of the M2 Ion Channel of Influenza A Virus},

author = {María D. Duque and Chunlong Ma and Eva Torres and Jun Wang and Lieve Naesens and Jordi Juárez-Jiménez and Pelayo Camps and F. Javier Luque and William F. DeGrado and Robert A. Lamb and Lawrence H. Pinto and Santiago Vázquez},

url = {http://dx.doi.org/10.1021/jm101334y},

doi = {10.1021/jm101334y},

issn = {1520-4804},

year  = {2011},

date = {2011-04-01},

journal = {Journal of Medicinal Chemistry},

volume = {54},

number = {8},

pages = {2646–2657},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}