https://hdl.handle.net/11000/30621 2026-07-26T17:12:25Z 2026-07-26T17:12:25Z Fuentes Baile, Maria García Morales, Pilar Pérez Valenciano, Elizabeth Mata Balaguer, Trinidad Menéndez Gutiérrez, Maria P. de Juan Romero, Camino Rodríguez Lescure, Alvaro Martín Orozco, Elena Mallavia, Ricardo Barberá, Victor M. Saceda, Miguel https://hdl.handle.net/11000/40234 2026-07-21T01:04:23Z 2026-07-20T07:47:24Z

Título : Insights into histone deacetylase inhibitors-induced cell death in cancer cell lines Autor : Fuentes Baile, Maria; García Morales, Pilar; Pérez Valenciano, Elizabeth; Mata Balaguer, Trinidad; Menéndez Gutiérrez, Maria P.; de Juan Romero, Camino; Rodríguez Lescure, Alvaro; Martín Orozco, Elena; Mallavia, Ricardo; Barberá, Victor M.; Saceda, Miguel Resumen : Histone deacetylase inhibitors (HDACis) induce cell death in many chemoresistant cancer models, suggesting their potential as alternative treatments for these malignancies. However, their efficacy in solid tumors remains limited. Therefore, understanding the molecular mechanisms underlying HDACi-induced cell death is essential for developing targeted activators of these pathways, enabling the selective elimination of chemoresistant cancer cells while minimizing the widespread transcriptional effects of HDACis. In this study, we investigated HDACi- induced cell death across models of different cellular origins to determine whether a universal molecular mechanism triggers this process. Our findings demonstrate that HDACi-induced cell death is TP53-independent, resistant to caspase inhibitors, and sensitive to serine protease inhibitors. This form of cell death requires intracellular calcium mobilization to induce mitochondrial depolarization. Using DNA arrays, apoptosis protein arrays, and ELISA assays, combined with siRNA-mediated gene silencing, we identified genes with a causal relationship to TSA-induced cell death. These include dual-specificity phosphatases such as DUSP3 and DUSP10; endoplasmic reticulum stress-related genes such as XBP1, MBTPS1, MBTPS2, and RPS6KA5; and other genes like BAX, AIF, EAF2, NANOS1, and CCNYL1. Our findings reveal novel potential targets for developing antineoplastic agents designed to exploit HDACi-induced cell death pathways, providing a strategy to overcome chemoresistance in cancer therapy.

2026-07-20T07:47:24Z Corell-Escuin, Paula Belmonte-Ballester, Sonia Adhav, Anmol Marina, Alberto Gadea-Salom, Laura Martínez-Gil, Luis Aledavood, Elnaz Fernández-Escamilla, Ana María Gómez Sáez, Ana Gougeard, Nadine Dee, Kieran Murcia, Pablo R. Magos, Eliza Adriana Llena, Carmen Peris-Martínez, Cristina D´Auria, Giuseppe Artacho, Alejandro Mengual-Chuliá, Beatriz López-Labrador, F. Xavier Mira, Alex Ferrer, María Desamparados https://hdl.handle.net/11000/39816 2026-05-01T01:04:04Z 2026-04-30T07:05:43Z

Título : Dermcidin has antiviral activity and protects against influenza Autor : Corell-Escuin, Paula; Belmonte-Ballester, Sonia; Adhav, Anmol; Marina, Alberto; Gadea-Salom, Laura; Martínez-Gil, Luis; Aledavood, Elnaz; Fernández-Escamilla, Ana María; Gómez Sáez, Ana; Gougeard, Nadine; Dee, Kieran; Murcia, Pablo R.; Magos, Eliza Adriana; Llena, Carmen; Peris-Martínez, Cristina; D´Auria, Giuseppe; Artacho, Alejandro; Mengual-Chuliá, Beatriz; López-Labrador, F. Xavier; Mira, Alex; Ferrer, María Desamparados Resumen : Despite the high incidence of influenza virus infections, one-fifth of people infected with influenza remain asymptomatic. The mechanisms associated with this immune resilience are, however, unknown. Here, we show that the human antimicrobial peptide dermcidin has antiviral activity against influenza viruses through binding to hemagglutinin and extends its effect to taxonomically unrelated respiratory viruses such as measles virus and human coronavirus OC43. We show that dermcidin is present in all anatomical regions associated with the entry routes of respiratory viruses, that its levels increase during viral respiratory infections, and that it protects mice against influenza disease. Notably, dermcidin levels were higher in asymptomatic individuals than in susceptible peers, suggesting a role in the onset of disease symptoms. Thus, we show that dermcidin inhibits influenza virus infection in vitro and in vivo, with potential as a human-derived product for the prevention and treatment of respiratory viral infections.

2026-04-30T07:05:43Z Ortega del Campo, Sergio Fernández Ballester, Gregorio Joaquín Blanes Mira, Clara Guirado Osorio, Víctor Díaz Martínez, Luis de Ávila, Ana Isabel Soria, María Eugenia Martínez-González, Brenda Villena González, Francisco José Gómez-Maldonado, Josefa Viciana Ramos, María Isabel Clavijo Frutos, Encarnación Santos González, Jesús L. Bastolla, Hugo Perales, Celia Domingo, Esteban Viguera, Enrique Fernández Escamilla, Ana María Grande Pérez, Ana https://hdl.handle.net/11000/39815 2026-04-30T01:03:41Z 2026-04-29T08:09:06Z

Título : Synergistic antiviral effects of structure-guided peptides and a mutagenic base analog on SARS-CoV-2 replication Autor : Ortega del Campo, Sergio; Fernández Ballester, Gregorio Joaquín; Blanes Mira, Clara; Guirado Osorio, Víctor; Díaz Martínez, Luis; de Ávila, Ana Isabel; Soria, María Eugenia; Martínez-González, Brenda; Villena González, Francisco José; Gómez-Maldonado, Josefa; Viciana Ramos, María Isabel; Clavijo Frutos, Encarnación; Santos González, Jesús L.; Bastolla, Hugo; Perales, Celia; Domingo, Esteban; Viguera, Enrique; Fernández Escamilla, Ana María; Grande Pérez, Ana Resumen : The limited durability of vaccine protection and the rapid emergence of SARS-CoV-2 variants highlight the need for antiviral strategies that extend beyond vaccination and conventional small-molecule inhibitors. Here, we explored a dual approach combining structure-guided peptides predicted to interfere with the viral replication complex with lethal mutagenesis to limit SARS-CoV-2 replication. Using the crystallographic interfaces of nsp10 with nsp14 and nsp16, we designed short inhibitory peptides predicted to interact with the viral proofreading and RNA-capping machinery. In parallel, the mutagenic analog 5-fluorouracil was evaluated to determine its effecteffecteffecton SARS-CoV-2 in Vero E6 cells. Peptides P1 and P6 exhibited potent antiviral activity with minimal cytotoxicity, whereas 5-FU reduced specific infectivity without impairing genome replication. Combined treatment with 5-FU and peptide P1 resulted in >104-fold reduction in infectious virus, achieving near-complete loss of infectivity at non-cytotoxic concentrations. Next-generation sequencing revealed that dual treatment increased mutation frequency, altered mutant spectra, and decreased genome stability, consistent with progression toward error catastrophe. Principal component analysis confirmed that combined treatment generated mutant spectra distinct from either monotherapy. These findings are consistent with a dual antiviral strategy in which structure-guided peptides designed to interact with components of the SARS-CoV-2 replication complex act in combination with lethal mutagenesis to produce a synergistic interaction between these two complementary processes. This integrated approach suggests a potential broad-spectrum antiviral strategy with applicability to other coronaviruses.

2026-04-29T08:09:06Z Madruga, Enrique García-Rubia, Alfonso Sánchez-Núñez, Carlos Martínez-González, Loreto Fernández-Escamilla, Ana María Lastres-Becker, Isabel Gil, Carmen Martínez, Ana https://hdl.handle.net/11000/39585 2026-03-26T02:06:57Z 2026-03-25T13:47:05Z

Título : Brain Permeable SGK1 Inhibitors: A Promising Therapeutic Strategy for Neurodegenerative Diseases Autor : Madruga, Enrique; García-Rubia, Alfonso; Sánchez-Núñez, Carlos; Martínez-González, Loreto; Fernández-Escamilla, Ana María; Lastres-Becker, Isabel; Gil, Carmen; Martínez, Ana Resumen : A major challenge in modern medicine is developing new therapies for aging-related diseases such as neurodegenerative disorders, whose prevalence increases with longer life expectancy. Although kinase inhibitors have achieved clinical success, their development for central nervous system (CNS) disorders remains limited due to the complexity of kinase networks and poor blood− brain barrier (BBB) permeability. Serum/glucocorticoid-regulated kinase 1 (SGK1) participates in multiple signaling pathways but remains an underexplored target in neurodegeneration. Following a mixed ligand- and structure-based virtual screening, we have previously identified a brain-penetrant SGK1 inhibitor. A medicinal chemistry program based on hit expansion and optimization for BBB permeability reported here has generated a new family of SGK1 inhibitors as chemical probes that enable the investigation of SGK1’s role in neurological disorders and serve as promising starting points for drug development. These findings highlight SGK1 as a potential therapeutic target for neurodegenerative diseases, such as Alzheimer’s disease.

2026-03-25T13:47:05Z Cianferoni, Damiano Vizarraga, David Fernández-Escamilla, Ana Mª Fita, Ignacio Hamdani, Rahma Reche, Raul Delgado, Javier Serrano, Luis https://hdl.handle.net/11000/39409 2026-02-24T02:08:47Z 2026-02-23T17:35:32Z

Título : Artificial intelligence and first-principle methods in protein redesign: A marriage of convenience? Autor : Cianferoni, Damiano; Vizarraga, David; Fernández-Escamilla, Ana Mª; Fita, Ignacio; Hamdani, Rahma; Reche, Raul; Delgado, Javier; Serrano, Luis Resumen : Since AlphaFold2’s rise, many deep learning methods for protein design have emerged. Here, we validate widely used and recognized tools, compare them with first-principle methods, and explore their combinations, focusing on their effectiveness in protein redesign and potential for therapeutic repurposing. We address two challenges: evaluating tools and combinations ability to detect the effects of multiple concurrent mutations in protein variants, and leveraging large-scale datasets to compare modelingfree methods, namely force fields, which handle point mutations well with limited backbone rearrangement, and inverse folding tools, which excel at native sequence recovery but may struggle with non-natural proteins. Debuting TriCombine, a tool that identifies residue triangles in input structures, matches them to a structural database, and scores mutants based on substitution frequencies, we shortlisted candidates, modeled them with FoldX, and generated 16 SH3 mutants carrying up to 9 concurrent substitutions. The dataset was expanded to include 36 mutants and 11 crystal structures (7 newly solved), along with a parallel set of multiple non-concurrent mutants from three additional proteins. For broader validation, we analyzed 160,000 four-site GB1 mutants and 163,555 (single and double) variants across 179 natural and de novo domains. We show that combining AIbased modeling tools with force field scoring functions yields the most reliable results. Inverse folding tools perform very well but lose accuracy on less-represented proteins. First-principle force fields like FoldX remain the most accurate for point mutations. All methods perform worse when applied to unsolved de novo models, underscoring the need for hybrid strategies in robust protein design.

2026-02-23T17:35:32Z Espinosa-Urgel, Manuel Serrano, Luis Ramos, Juan Luis Fernández-Escamilla, Ana Mª https://hdl.handle.net/11000/39408 2026-02-24T02:08:46Z 2026-02-23T17:14:17Z

Título : Engineering Biological Approaches for Detection of Toxic Compounds: A New Microbial Biosensor Based on the Pseudomonas putida TtgR Repressor Autor : Espinosa-Urgel, Manuel; Serrano, Luis; Ramos, Juan Luis; Fernández-Escamilla, Ana Mª Resumen : Environmental contamination by toxic organic compounds and antimicrobials is one of the causes for the recent surge of multidrug-resistant pathogenic bacteria. Monitoring contamination is therefore the first step in containment of antimicrobial resistance and requires the development of simple, sensitive, and quantitative tools that detect a broad spectrum of toxic compounds. In this study, we have engineered a new microbial biosensor based on the ttgR-regulated promoter that controls expression of the TtgABC extrusion efflux pump of Pseudomonas putida, coupled to a gfp reporter. The system was introduced in P. putida DOT-T1E, a strain characterized by its ability to survive in the presence of high concentrations of diverse toxic organic compounds. This whole-cell biosensor is capable to detect a wide range of structurally diverse antibiotics, as well as compounds such as toluene or flavonoids.

2026-02-23T17:14:17Z Espinosa-Urgel, Manuel Serrano, Luis Ramos, Juan Luis Fernández-Escamilla, Ana Mª https://hdl.handle.net/11000/39333 2026-02-17T02:08:18Z 2026-02-16T17:03:17Z

Título : Engineering Biological Approaches for Detection of Toxic Compounds: A New Microbial Biosensor Based on the Pseudomonas putida TtgR Repressor Autor : Espinosa-Urgel, Manuel; Serrano, Luis; Ramos, Juan Luis; Fernández-Escamilla, Ana Mª Resumen : Environmental contamination by toxic organic compounds and antimicrobials is one of the causes for the recent surge of multidrug-resistant pathogenic bacteria. Monitoring contamination is therefore the first step in containment of antimicrobial resistance and requires the development of simple, sensitive, and quantitative tools that detect a broad spectrum of toxic compounds. In this study, we have engineered a new microbial biosensor based on the ttgR-regulated promoter that controls expression of the TtgABC extrusion efflux pump of Pseudomonas putida, coupled to a gfp reporter. The system was introduced in P. putida DOT-T1E, a strain characterized by its ability to survive in the presence of high concentrations of diverse toxic organic compounds. This whole-cell biosensor is capable to detect a wide range of structurally diverse antibiotics, as well as compounds such as toluene or flavonoids.

2026-02-16T17:03:17Z Cañadas-Garre, Marisa Fernández-Escamilla, Ana Mª Fernández-Ballester, Gregorio Becerra-Massare, Patricia García-Calvente, Carlos Ramos, Juan Luis Llamas-Elvira, José Manuel https://hdl.handle.net/11000/39332 2026-02-17T02:08:17Z 2026-02-16T16:53:51Z

Título : Novel BRAFI599Ins Mutation Identified in a Follicular Variant of Papillary Thyroid Carcinoma: A Molecular Modeling Approach Autor : Cañadas-Garre, Marisa; Fernández-Escamilla, Ana Mª; Fernández-Ballester, Gregorio; Becerra-Massare, Patricia; García-Calvente, Carlos; Ramos, Juan Luis; Llamas-Elvira, José Manuel Resumen : Objective: BRAF mutations are the most common genetic alteration found in papillary thyroid carcinoma (PTC). Approximately, 90% correspond to BRAFV600E, although other less common BRAF mutations have been described. The aim of this study was to describe a new mutation on BRAF gene discovered on the previous thyroid cytology of a patient diagnosed with a follicular variant of PTC (FV-PTC). Methods: The mutation was identified by independent cloning of the 2 alleles and direct sequencing in the previous cytology and tumor tissue samples from a patient diagnosed with FV-PTC. To elucidate the effect of the mutation on the structure and hence on the activating mechanism of the protein, the structures of BRAFI599Ins, BRAFT599Ins, BRAFV599Ins and BRAFV600E were modeled by using the reconstructed wild-type BRAF (BRAFWT) crystal structure. Results: The novel mutation in BRAF consisted in the in-frame insertion of 3 nucleotides (TAA) after nucleotide 1795, resulting in the incorporation of an extra isoleucine residue at position 599 (BRAFI599Ins) of the protein. The structural comparison of BRAFI599Ins, BRAFT599Ins, BRAFV599Ins with BRAFWT, and BRAFV600E models revealed that the overall shape of the kinase was conserved in the protein produced by this novel mutation, except for the displacement of the activation loop (A-loop), as a direct consequence of the increase in loop size, and the exposition of 1 of the 2 residues involved in BRAF activation (T599), probably facilitating its phosphorylation. Conclusion: BRAFI599Ins mutation constitutes a new BRAF mutation affecting the length of the A-loop, which most likely facilitates BRAF activation by altering the A-loop conformation.

2026-02-16T16:53:51Z Fernández Escamilla, Ana María https://hdl.handle.net/11000/39323 2026-02-17T02:08:15Z 2026-02-16T11:49:18Z

Título : Exploring new findings on amyloidosis Autor : Fernández Escamilla, Ana María

2026-02-16T11:49:18Z Ramos, Juan Luis Daniels, Craig Krell, Tino Duque, Estrella Godoy, Patricia de la Torre, Jesús Fernández-Escamilla, Ana Mª Daddaoua, Abdelali Navarro-Avilés, Gloria Fillet, Sandy Pini, Cecilia Molina-Henares, María Antonia Lacal, Jesús Busch, Andreas Silva-Jiménez, Hortencia Rodríguez, Sara Molina, Lázaro Bursakov, Sergey A. Roca, Amalia Segura, Ana https://hdl.handle.net/11000/39315 2026-02-14T02:07:05Z 2026-02-13T19:14:44Z

Título : 8.3 Molecular Responses to Solvent Stress: Strategies for Living in Unpalatable Substrates Autor : Ramos, Juan Luis; Daniels, Craig; Krell, Tino; Duque, Estrella; Godoy, Patricia; de la Torre, Jesús; Fernández-Escamilla, Ana Mª; Daddaoua, Abdelali; Navarro-Avilés, Gloria; Fillet, Sandy; Pini, Cecilia; Molina-Henares, María Antonia; Lacal, Jesús; Busch, Andreas; Silva-Jiménez, Hortencia; Rodríguez, Sara; Molina, Lázaro; Bursakov, Sergey A.; Roca, Amalia; Segura, Ana Resumen : This review article covers some general conclusions reached in research studies with respect to a number of solvent-tolerant Pseudomonas strains. The seminal observation was performed by Inoue and Korikoshi 1989 when they described in Nature a bacterium, belonging to the genus Pseudomonas, which was able to thrive in the presence of high concentrations of toluene. This property of extreme tolerance to solvents makes this Pseudomonas strain the first extremophile identified as able to survive in the presence of highly toxic solvents. Following this seminal observation, other solvent-tolerant strains, such as Pseudomonas putida DOT-T1E, S12, GM1, and MTB6, were described as able to grow in the presence of highly toxic solvents such as p-xylene (log Pow 3.15), styrene (log Pow 3.0), octanol (log Pow 2.92), and toluene (log Pow 2.69) (Aono et al. 1992; Cruden et al. 1992; Huertas et al. 2000; Isken and de Bont 1996; Kim et al. 1998; Ramos et al. 1995; Weber et al. 1994). These microbes can reach high cell densities in culture medium in the presence of 0.3% (v/v) of the mentioned solvents, a concentration that kills most of the microbes we work with in our laboratories. This solvent-tolerant trait allows us to consider this set of Pseudomonas strains as extremophiles. Normally solvent toxicity is due to these chemicals dissolving in the cell membranes, disorganizing them and altering the electron flow. They also prevent ATP synthesis and irrevocably provoke cell death. Currently, there is an inherent interest in deciphering the basis for survival and growth of extremophile microbes in such harsh conditions, particularly for the exploitation of these microbes in the bioremediation of heavily-polluted sites and in the biotransformation of water-insoluble compounds into added-value products. The growing interest in biodegradation derives from the fact that many pollutants are toxic above a certain threshold, killing many living organisms. The use of solvent-tolerant microorganisms, provided with an arsenal of enzymes to deal with pollutants, represents a powerful tool for in situ pollutant removal. In the case of biotransformation, many substrates of interest are poorly soluble in water and the use of a double-phase system, made of water and an organic solvent for the production of high added-value chemicals is of great interest in green chemistry. Among some examples we can cite the use of solvent-tolerant microorganisms to produce catechols or to carry out biotransformation of aromatic hydrocarbons including nitro substituted ones (Ju and Parales 2006; Neumann et al. 2005, 2006; Ramos-Gonza´lez et al. 2003; Ruhl et al. 2009; Rojas et al. 2004; Verhoef et al. 2009; Wierckx et al. 2005). Notas: Editor: Koki Horikoshi

2026-02-13T19:14:44Z