{"id":151,"date":"2024-01-28T22:43:40","date_gmt":"2024-01-28T22:43:40","guid":{"rendered":"https:\/\/www.ub.edu\/cmd_lab\/?page_id=151"},"modified":"2024-02-23T15:06:32","modified_gmt":"2024-02-23T15:06:32","slug":"publications","status":"publish","type":"page","link":"https:\/\/www.ub.edu\/cmd_lab\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"

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Highlights<\/strong><\/h3>\n
<\/a><\/form>
\"Understanding<\/td>

Blanco-Gabella, Patricia; Ivanova, Varbina; Serrano-Morr\u00e1s, \u00c1lvaro; Fuchs, Julian E.; Ju\u00e1rez-Jim\u00e9nez, Jordi<\/p>

Understanding the Role of H-Bonds in the Stability of Molecular Glue-Induced Ternary Complexes<\/a> (Journal Article<\/span>)<\/p>

In: <\/span>Journal of Chemical Information and Modeling, <\/span>2026<\/span>, ISSN: 1549-9596<\/span>.<\/p>

(Abstract<\/a><\/span> | Links<\/a><\/span> | BibTeX<\/a><\/span>)<\/p>

@article{@article{Blanco-Gabella_2025_MG_HBonds,,
\r\ntitle = {Understanding the Role of H-Bonds in the Stability of Molecular Glue-Induced Ternary Complexes},
\r\nauthor = {Patricia Blanco-Gabella and Varbina Ivanova and \u00c1lvaro Serrano-Morr\u00e1s and Julian E. Fuchs and Jordi Ju\u00e1rez-Jim\u00e9nez},
\r\nurl = {https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.5c02718},
\r\ndoi = {10.1021\/acs.jcim.5c02718},
\r\nissn = {1549-9596},
\r\nyear  = {2026},
\r\ndate = {2026-01-23},
\r\nurldate = {2026-01-23},
\r\njournal = {Journal of Chemical Information and Modeling},
\r\nabstract = {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-CK1\u03b1 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.},
\r\nkeywords = {},
\r\npubstate = {published},
\r\ntppubtype = {article}
\r\n}
\r\n<\/pre><\/div>
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\"A<\/td>

Serrano-Morr\u00e1s, \u00c1lvaro; Bertran-Mostazo, Andrea; Mi\u00f1arro-Lleonar, Marina; Comajuncosa-Creus, Arnau; Cabello, Adri\u00e0; Labranya, Carme; Escudero, Carmen; Tian, Tian V.; Khutorianska, Inna; Radchenko, Dmytro S.; Moroz, Yurii S.; Defelipe, Lucas; Ruiz-Carrillo, David; Garcia-Alai, Maria; Schmidt, Robert; Rarey, Matthias; Aloy, Patrick; Galdeano, Carles; Ju\u00e1rez-Jim\u00e9nez, Jordi; Barril, Xavier<\/p>

A bottom-up approach to find lead compounds in expansive chemical spaces<\/a> (Journal Article<\/span>)<\/p>

In: <\/span>Communications Chemistry, <\/span>vol. 8, <\/span>no. 225, <\/span>2025<\/span>, ISSN: 2399-3669<\/span>.<\/p>

(Abstract<\/a><\/span> | Links<\/a><\/span> | BibTeX<\/a><\/span>)<\/p>

@article{@article{SerranoMorras2025,
\r\ntitle = {A bottom-up approach to find lead compounds in expansive chemical spaces},
\r\nauthor = {\u00c1lvaro Serrano-Morr\u00e1s and Andrea Bertran-Mostazo and Marina Mi\u00f1arro-Lleonar and Arnau Comajuncosa-Creus and Adri\u00e0 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 Ju\u00e1rez-Jim\u00e9nez and Xavier Barril},
\r\nurl = {https:\/\/www.nature.com\/articles\/s42004-025-01610-2},
\r\ndoi = {10.1038\/s42004-025-01610-2},
\r\nissn = {2399-3669},
\r\nyear  = {2025},
\r\ndate = {2025-08-01},
\r\nurldate = {2025-08-01},
\r\njournal = {Communications Chemistry},
\r\nvolume = {8},
\r\nnumber = {225},
\r\nabstract = {Drug discovery starts with the identification of a \u201chit\u201d 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.},
\r\nkeywords = {},
\r\npubstate = {published},
\r\ntppubtype = {article}
\r\n}
\r\n<\/pre><\/div>
Close<\/a><\/p><\/div>
Drug discovery starts with the identification of a \u201chit\u201d 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.<\/div>
Close<\/a><\/p><\/div>
\"Lenalidomide<\/td>

Mi\u00f1arro-Lleonar, Marina; Bertran-Mostazo, Andrea; Duro, Jorge; Barril, Xavier; Ju\u00e1rez-Jim\u00e9nez, Jordi<\/p>

Lenalidomide Stabilizes Protein\u2013Protein Complexes by Turning Labile Intermolecular H-Bonds into Robust Interactions<\/a> (Journal Article<\/span>)<\/p>

In: <\/span>Journal of Medicinal Chemistry, <\/span>vol. 66, <\/span>no. 9, <\/span>pp. 6037\u20136046, <\/span>2023<\/span>, ISSN: 1520-4804<\/span>.<\/p>

(Links<\/a><\/span> | BibTeX<\/a><\/span>)<\/p>

\"Combining<\/td>

Ju\u00e1rez-Jim\u00e9nez, Jordi; Tew, Philip; O\u2032Connor, Michael; Llabr\u00e9s, Salom\u00e9; Sage, Rebecca; Glowacki, David; Michel, Julien<\/p>

Combining Virtual Reality Visualization with Ensemble Molecular Dynamics to Study Complex Protein Conformational Changes<\/a> (Journal Article<\/span>)<\/p>

In: <\/span>Journal of Chemical Information and Modeling, <\/span>vol. 60, <\/span>no. 12, <\/span>pp. 6344\u20136354, <\/span>2020<\/span>, ISSN: 1549-960X<\/span>.<\/p>

(Links<\/a><\/span> | BibTeX<\/a><\/span>)<\/p>

\"Dynamic<\/td>

Ju\u00e1rez-Jim\u00e9nez, Jordi; Gupta, Arun A.; Karunanithy, Gogulan; Mey, Antonia S. J. S.; Georgiou, Charis; Ioannidis, Harris; Simone, Alessio De; Barlow, Paul N.; Hulme, Alison N.; Walkinshaw, Malcolm D.; Baldwin, Andrew J.; Michel, Julien<\/p>

Dynamic design: manipulation of millisecond timescale motions on the energy landscape of cyclophilin A<\/a> (Journal Article<\/span>)<\/p>

In: <\/span>Chemical Science, <\/span>vol. 11, <\/span>no. 10, <\/span>pp. 2670\u20132680, <\/span>2020<\/span>, ISSN: 2041-6539<\/span>.<\/p>

(Links<\/a><\/span> | BibTeX<\/a><\/span>)<\/p>

\"Mechanism<\/td>

Llabr\u00e9s, Salom\u00e9; Ju\u00e1rez-Jim\u00e9nez, Jordi; Masetti, Matteo; Leiva, Rosana; V\u00e1zquez, Santiago; Gazzarrini, Sabrina; Moroni, Anna; Cavalli, Andrea; Luque, F. Javier<\/p>

Mechanism of the Pseudoirreversible Binding of Amantadine to the M2 Proton Channel<\/a> (Journal Article<\/span>)<\/p>

In: <\/span>Journal of the American Chemical Society, <\/span>vol. 138, <\/span>no. 47, <\/span>pp. 15345\u201315358, <\/span>2016<\/span>, ISSN: 1520-5126<\/span>.<\/p>

(Links<\/a><\/span> | BibTeX<\/a><\/span>)<\/p>

\"Assessing<\/td>

Ju\u00e1rez-Jim\u00e9nez, Jordi; Barril, Xavier; Orozco, Modesto; Pouplana, Ramon; Luque, F. Javier<\/p>

Assessing the Suitability of the Multilevel Strategy for the Conformational Analysis of Small Ligands<\/a> (Journal Article<\/span>)<\/p>

In: <\/span>The Journal of Physical Chemistry B, <\/span>vol. 119, <\/span>no. 3, <\/span>pp. 1164\u20131172, <\/span>2014<\/span>, ISSN: 1520-5207<\/span>.<\/p>

(Links<\/a><\/span> | BibTeX<\/a><\/span>)<\/p>

\"Synthesis<\/td>

Viayna, Elisabet; Sola, Irene; Bartolini, Manuela; Simone, Angela De; Tapia-Rojas, Cheril; Serrano, Felipe G.; Sabat\u00e9, Raimon; Ju\u00e1rez-Jim\u00e9nez, Jordi; P\u00e9rez, Bel\u00e9n; Luque, F. Javier; Andrisano, Vincenza; Clos, M. Vict\u00f2ria; Inestrosa, Nibaldo C.; Mu\u00f1oz-Torrero, Diego<\/p>

Synthesis and Multitarget Biological Profiling of a Novel Family of Rhein Derivatives As Disease-Modifying Anti-Alzheimer Agents<\/a> (Journal Article<\/span>)<\/p>

In: <\/span>Journal of Medicinal Chemistry, <\/span>vol. 57, <\/span>no. 6, <\/span>pp. 2549\u20132567, <\/span>2014<\/span>, ISSN: 1520-4804<\/span>.<\/p>

(Links<\/a><\/span> | BibTeX<\/a><\/span>)<\/p>

@article{Viayna_2014,
\r\ntitle = {Synthesis and Multitarget Biological Profiling of a Novel Family of Rhein Derivatives As Disease-Modifying Anti-Alzheimer Agents},
\r\nauthor = {Elisabet Viayna and Irene Sola and Manuela Bartolini and Angela De Simone and Cheril Tapia-Rojas and Felipe G. Serrano and Raimon Sabat\u00e9 and Jordi Ju\u00e1rez-Jim\u00e9nez and Bel\u00e9n P\u00e9rez and F. Javier Luque and Vincenza Andrisano and M. Vict\u00f2ria Clos and Nibaldo C. Inestrosa and Diego Mu\u00f1oz-Torrero},
\r\nurl = {http:\/\/dx.doi.org\/10.1021\/jm401824w},
\r\ndoi = {10.1021\/jm401824w},
\r\nissn = {1520-4804},
\r\nyear  = {2014},
\r\ndate = {2014-03-01},
\r\nurldate = {2014-03-01},
\r\njournal = {Journal of Medicinal Chemistry},
\r\nvolume = {57},
\r\nnumber = {6},
\r\npages = {2549\u20132567},
\r\npublisher = {American Chemical Society (ACS)},
\r\nkeywords = {},
\r\npubstate = {published},
\r\ntppubtype = {article}
\r\n}
\r\n<\/pre><\/div>
Close<\/a><\/p><\/div>