Publications > Maqueda-Zelaya et al

Arch Pharm (Weinheim). 2025 Jan;358(1):e2400614. doi: 10.1002/ardp.202400614. Epub 2024 Nov 27. PubMed 39604268

Identification and study of new NF-κB-inducing kinase ligands derived from the imidazolone scaffold.

Francisco Maqueda-Zelaya¹, Lara Valiño-Rivas², Ana Milián¹, Sara Gutiérrez¹, José Luis Aceña¹, Javier Garcia-Marin³, Mª Dolores Sánchez-Niño¹, Juan J Vaquero³, Alberto Ortiz²

1. Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química "Andrés M. Del Río" (IQAR), Universidad de Alcalá (IRYCIS), Alcalá de Henares, Madrid, Spain.  2. Departamento de Nefrología e Hipertensión, IIS-Fundación Jiménez Díaz UAM, Madrid, Spain.  3. RICORS2040, Madrid, Spain.

Keywords: MAP3K14; NF‐κB‐inducing kinase; NIK; imidazolone; noncanonical pathway

Abstract

Chronic kidney disease (CKD) is a growing health concern, projected to be a major cause of death by 2040, due to an increasing risk of acute kidney injury (AKI). Systems biology-derived data suggest that the unmet need for an orally available drug to treat AKI and improve CKD outcomes may be addressed by targeting kidney inflammation and, specifically, nuclear factor κB-inducing kinase (NIK), a key signaling molecule that activates the noncanonical nuclear factor κB (NF-κB) pathway. We have prepared and identified a small family of imidazolone derivatives that bind NIK and inhibit the noncanonical NF-κB activation pathway. The introduction of heterocyclic substituents in position 2 of the imidazolone core provides compounds with affinity against human NIK. Three candidates, with best affinity profile, were tested in phenotypic experiments of noncanonical NF-κB activation, confirming that the derivative bearing the 4-pyridyl ring can inhibit the processing of NFκB p100 to NFkB2 p52, which is NIK-dependent in cultured kidney tubular cells. Finally, exhaustive docking calculations combined with molecular dynamics studies led us to propose a theoretical binding mode and rationalize affinity measures, in which the aminopyridine motif is a key anchoring point to the hinge region thanks to several hydrogen bonds and the interaction of heterocyclic rings in position 2 with Ser476 and Lys482. Our result will pave the way for the development of potential drug candidates targeting NIK in the context of CKD.

Publications > García-Marín et al

J Comput Aided Mol Des. 2022 Aug;36(8):575-589. doi: 10.1007/s10822-022-00466-1. PubMed 35869378

Insight into the mechanism of molecular recognition between human Integrin-Linked Kinase and Cpd22 and its implication at atomic level.

Javier García-Marín^1, a, Diego Rodríguez-Puyol^2, b, Juan J Vaquero^3, c

1. Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química Andrés M. del Río (IQAR), Universidad de Alcalá (IRYCIS), Alcalá de Henares, 28805, Madrid, Spain.  2. Departamento de Química Biológica y Estructural, Centro de Investigaciones Biológicas, CIB-CSIC, C/Ramiro de Maeztu 9, 28040, Madrid, Spain.  3. Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AX, UK.

a. javier.garciamarin@uah.es  b. javier.garciamarin@uah.es  c. javier.garciamarin@uah.es

Keywords: Cpd22; ILK; Integrin-linked kinase; Molecular dynamics; PELE; Pseudokinase

Abstract

Pseudokinases have received increasing attention over the past decade because of their role in different physiological phenomena. Although pseudokinases lack several active-site residues, thereby hindering their catalytic activity, recent discoveries have shown that these proteins can play a role in intracellular signaling thanks to their non-catalytic functions. Integrin-linked kinase (ILK) was discovered more than two decades ago and was subsequently validated as a promising target for neoplastic diseases. Since then, only a few small-molecule inhibitors have been described, with the V-shaped pyrazole Cpd22 being the most interesting and characterized. However, little is known about its detailed mechanism of action at atomic level. In this study, using a combination of computational chemistry methods including PELE calculations, docking, molecular dynamics and experimental surface plasmon resonance, we were able to prove the direct binding of this molecule to ILK, thus providing the basis of its molecular recognition by the protein and the effect over its architecture. Our breakthroughs show that Cpd22 binding stabilizes the ILK domain by binding to the pseudo-active site in a similar way to the ATP, possibly modulating its scaffolding properties as pseudokinase. Moreover, our results explain the experimental observations obtained during Cpd22 development, thus paving the way to the development of new chemical probes and potential drugs.

Publications > Ortiz

Clin Kidney J. 2021, 15, 372 PubMed 35211298

RICORS2040: the need for collaborative research in chronic kidney disease.

Alberto Ortiz

Keywords: COVID-19; accelerated ageing; burden of disease; chronic kidney disease; decade of the kidney; kidney failure; kidney transplantation; research funding

Abstract

Chronic kidney disease (CKD) is a silent and poorly known killer. The current concept of CKD is relatively young and uptake by the public, physicians and health authorities is not widespread. Physicians still confuse CKD with chronic kidney insufficiency or failure. For the wider public and health authorities, CKD evokes kidney replacement therapy (KRT). In Spain, the prevalence of KRT is 0.13%. Thus health authorities may consider CKD a non-issue: very few persons eventually need KRT and, for those in whom kidneys fail, the problem is 'solved' by dialysis or kidney transplantation. However, KRT is the tip of the iceberg in the burden of CKD. The main burden of CKD is accelerated ageing and premature death. The cut-off points for kidney function and kidney damage indexes that define CKD also mark an increased risk for all-cause premature death. CKD is the most prevalent risk factor for lethal coronavirus disease 2019 (COVID-19) and the factor that most increases the risk of death in COVID-19, after old age. Men and women undergoing KRT still have an annual mortality that is 10- to 100-fold higher than similar-age peers, and life expectancy is shortened by ~40 years for young persons on dialysis and by 15 years for young persons with a functioning kidney graft. CKD is expected to become the fifth greatest global cause of death by 2040 and the second greatest cause of death in Spain before the end of the century, a time when one in four Spaniards will have CKD. However, by 2022, CKD will become the only top-15 global predicted cause of death that is not supported by a dedicated well-funded Centres for Biomedical Research (CIBER) network structure in Spain. Realizing the underestimation of the CKD burden of disease by health authorities, the Decade of the Kidney initiative for 2020-2030 was launched by the American Association of Kidney Patients and the European Kidney Health Alliance. Leading Spanish kidney researchers grouped in the kidney collaborative research network Red de Investigación Renal have now applied for the Redes de Investigación Cooperativa Orientadas a Resultados en Salud (RICORS) call for collaborative research in Spain with the support of the Spanish Society of Nephrology, Federación Nacional de Asociaciones para la Lucha Contra las Enfermedades del Riñón and ONT: RICORS2040 aims to prevent the dire predictions for the global 2040 burden of CKD from becoming true.

Publications > García-Marín et al

ChemMedChem. 2021 Sep 16;16(18):2895-2906. doi: 10.1002/cmdc.202100338. PubMed 34137509

A Computer-Driven Scaffold-Hopping Approach Generating New PTP1B Inhibitors from the Pyrrolo[1,2-a]quinoxaline Core.

Javier García-Marín¹, Mercedes Griera², Ramón Alajarín³, Manuel Rodríguez-Puyol⁴, Diego Rodríguez-Puyol⁵, Juan J Vaquero⁶

1. Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28805, Alcalá de Henares, Spain.  2. Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. Colmenar Viejo, km. 9100, 28034, Madrid, Spain.  3. Instituto de Investigación Química Andrés Manuel del Río (IQAR), Universidad de Alcalá, Alcalá de Henares, Spain.  4. Departamento de Química Biológica y Estructural, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Calle Ramiro de Maeztu 9, 28040, Madrid, Spain.  5. Graphenano Medical Care, S.L., C/Pablo Casals, no. 13, Yecla, Murcia, Spain.  6. Departamento de Biología de Sistemas, Universidad de Alcalá, 28805, Alcalá de Henares, Spain.

Keywords: MM-ISMSA; PTP1B, phosphatase; glucose uptake; molecular dynamics; molecular modelling; pyrrolo[1,2-a]quinoxaline; scaffold hopping

Abstract

Protein tyrosine phosphatase 1B (PTP1B) is a very promising target for the treatment of metabolic disorders such as type II diabetes mellitus. Although it was validated as a promising target for this disease more than 30 years ago, as yet there is no drug in advanced clinical trials, and its biochemical mechanism and functions are still being studied. In the present study, based on our experience generating PTP1B inhibitors, we have developed and implemented a scaffold-hopping approach to vary the pyrrole ring of the pyrrolo[1,2-a]quinoxaline core, supported by extensive computational techniques aimed to explain the molecular interaction with PTP1B. Using a combination of docking, molecular dynamics and end-point free-energy calculations, we have rationally designed a hypothesis for new PTP1B inhibitors, supporting their recognition mechanism at a molecular level. After the design phase, we were able to easily synthesize proposed candidates and their evaluation against PTP1B was found to be in good concordance with our predictions. Moreover, the best candidates exhibited glucose uptake increments in cellulo model, thus confirming their utility for PTP1B inhibition and validating this approach for inhibitors design and molecules thus obtained.

Publications > Sánchez-Alonso et al

Bioorg Med Chem. 2021 Jul 3; 44:116295.

Pyrrolo[1,2-a]quinoxal-5-inium salts and 4,5-dihydropyrrolo[1,2-a]quinoxalines: Synthesis, activity and computational docking for protein tyrosine phosphatase 1B.

Patricia Sánchez-Alonso¹, Mercedes Griera², Javier García-Marín^1, 3, 4, Manuel Rodríguez-Puyol^5, 6, 7, Ramón Alajarín^{1, 3, 8, a}, Juan J Vaquero^1, 3, 4, Diego Rodríguez-Puyol^5, 6, 7

1. Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain.  2. Graphenano Medical Care, SL, Spain.  3. Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. Colmenar Viejo, km. 9100, 28034 Madrid, Spain.  4. Instituto de Investigación Química Andrés M. del Río (IQAR), Facultad de Farmacia, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain.  5. Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. Colmenar Viejo, km. 9100, 28034 Madrid, Spain.  6. Departamento de Biología de Sistemas, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain.  7. Fundación Renal Iñigo Álvarez de Toledo (FRIAT) y REDinREN del Instituto de Salud Carlos III, Madrid, Spain.  8. Instituto de Investigación Química Andrés M. del Río (IQAR), Facultad de Farmacia, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain. Electronic address:.

a. ramon.alajarin@uah.es

Keywords: 4,5-Dihydropyrrolo[1,2-a]quinoxaline, pyrrolo[1,2-a]quinoxal-5-inium; Diabetes mellitus; Inhibitor; PTP1B; Phosphatase; Selectivity; TC-PTP

Abstract

Protein tyrosine phosphatase (PTP1B) is an interesting therapeutical target for diabetes, obesity, heart disease and cancer. As such, inhibition of PTP1B using orally administered drugs is still being pursued by academia and pharmaceutical companies. The failure of catalytic-site inhibitors led to the focus in this field being switched to allosteric inhibitors. To date, the non-competitive inhibitors that have reached clinical trials target the site formed by the α3/α6/α7 tunnel or the site found in a disordered C-terminal non-catalytic segment. Herein, pyrrolo[1,2-a]quinoxal-5-inium salts and 4,5-dihydropyrrolo[1,2-a]quinoxalines are synthesized from pyrrolo[1,2-a]quinoxalines by alkylation and reduction, respectively. These compounds showed no toxicity in HepG2 cells and exhibited inhibitory activity against PTP1B, with inhibition percentages of between 37% and 53% at 1 μM and activities (IC(50)) of between 0.25 and 1.90 μM. The inhibitory activity against T-cell protein tyrosine phosphatase (TC-TPT) was also assayed, with 4,5-dihydropyrrolo[1,2-a]quinoxalines being found to be slightly more active and selective. Compounds from the two series behave as insulin mimetics since they exhibit enhancement of glucose uptake in C2C12 cells. Computational docking studies provide information about the putative binding mode for both series and the preference for the α3/α6/α7 allosteric tunnel.

Publications > Garcia-Marin et al

ACS Med Chem Lett. 2021 Jul 15;12(11):1656-1662. doi: 10.1021/acsmedchemlett.1c00183. PubMed 34790291

Tripeptides as Integrin-Linked Kinase Modulating Agents Based on a Protein-Protein Interaction with α-Parvin.

Javier Garcia-Marin¹, Mercedes Griera-Merino², Alejandra Matamoros-Recio³, Sergio de Frutos⁴, Manuel Rodríguez-Puyol⁵, Ramón Alajarín¹, Juan J Vaquero⁴, Diego Rodríguez-Puyol²

1. Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, Alcalá de Henares 28805, Spain.  2. Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. Colmenar Viejo, km. 9100, Madrid 28034, Spain.  3. Instituto de Investigación Química Andrés Manuel del Río (IQAR), Universidad de Alcalá, Alcalá de Henares 28805, Spain.  4. Departamento de Biología de Sistemas, Universidad de Alcalá, Alcalá de Henares 28805, Spain.  5. Graphenano Medical Care, S.L, Yecla 30510, Spain.

Abstract

Integrin-linked kinase (ILK) has emerged as a controversial pseudokinase protein that plays a crucial role in the signaling process initiated by integrin-mediated signaling. However, ILK also exhibits a scaffolding protein function inside cells, controlling cytoskeletal dynamics, and has been related to non-neoplastic diseases such as chronic kidney disease (CKD). Although this protein always acts as a heterotrimeric complex bound to PINCH and parvin adaptor proteins, the role of parvin proteins is currently not well understood. Using in silico approaches for the design, we have generated and prepared a set of new tripeptides mimicking an α-parvin segment. These derivatives exhibit activity in phenotypic assays in an ILK-dependent manner without altering kinase activity, thus allowing the generation of new chemical probes and drug candidates with interesting ILK-modulating activities.

Publications > Miguel et al

Nefrologia. 2020, 40, 491

The pHLIP system as a vehicle for microRNAs in the kidney.

Verónica Miguel^1, a, Carlos Rey², José Luis Aceña³, Francisco Maqueda³, Carlos Fernández-Hernando⁴, Diego Rodríguez-Puyol⁵, Juan J Vaquero³, Santiago Lamas²

1. Programa de Procesos Fisiológicos y Patológicos, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, España. Electronic address:.  2. Programa de Procesos Fisiológicos y Patológicos, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, España.  3. Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química Andrés M. del Río (IQAR), Universidad de Alcalá, IRYCIS, Alcalá de Henares, Madrid, España.  4. Integrative Cell Signaling and Neurobiology of Metabolism Program, Department of Comparative Medicine and Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, Estados Unidos.  5. Department of Medicine and Medical Specialties, Research Foundation of the University Hospital Príncipe de Asturias, IRYCIS, Alcalá University, Alcalá de Henares, Madrid, España.

a. vmiguel@cbm.csic.es

Palabras clave: Fibrosis renal; PNA; PNAs; Renal fibrosis; miRNA; miRNAs; pHLIP

Resumen

MicroRNAs (miRNAs) are small endogenous RNAs that regulate gene expression through post-transcriptional repression of their target messenger RNAs. A study of changes in expression of certain miRNAs in the kidney has supplied evidence on their pathogenic role and therapeutic potential in nephrology. This review proposes a nanotechnology approach based on the binding of analogs or inhibitors of miRNAs formed by peptide nucleic acids (PNAs) to peptides with a transmembrane structure sensitive to a low pH, called pHLIPs (pH %@5Blow%@5D insertion peptides). The review draws on the concept that an acidic pH in the microenvironment of the renal tubule may facilitate concentration and distribution of the pHLIP-PNA complex in this organ. In this context, we have demonstrated for the first time that targeted administration of miR-33 inhibitors with the pHLIP system effectively prevents the development of renal fibrosis, thus opening up this technology to new strategies for diagnosis and treatment of kidney diseases.

Publications > Valino-Rivas et al

Trends Mol Med. 2019, 25, 341 PubMed 30926358

NIK as a Druggable Mediator of Tissue Injury.

Lara Valino-Rivas¹, Juan Jose Vaquero², David Sucunza², Sara Gutierrez², Ana B Sanz¹, Manuel Fresno³, Alberto Ortiz^1, 4, a, Maria Dolores Sanchez-Nino^1, 4, a

1. Department of Nephrology and Hypertension, Instituto de Investigacion Sanitaria (IIS) Fundacion Jimenez Diaz, School of Medicine, Universidad Autonoma de Madrid (UAM), Red de Investigacion Renal (REDINREN), and Fundacion Renal Inigo Alvarez de Toledo (FRIAT), Madrid, Spain.  2. Departamento de Quimica Organica y Quimica Inorganica, Universidad de Alcala and REDINREN, Madrid, Spain.  3. Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas de la UAM, Madrid, Spain.  4. These authors contributed equally. Electronic address:.

a. aortiz@fjd.es  a. mdsanchez@fjd.es

Keywords: *MAP3K14; *NIK; *TWEAK; *acute kidney injury; *apoptosis; *autoimmunity; *cell death; *chronic kidney disease; *cirrhosis; *diabetes; *epigenetic; *esteatohepatitis; *hepatitis; *inflammation; *mantle lymphoma; *myeloid leukemia; *osteoporosis; *sarcopenia; *verteporfin

Abstract

NF-kappaB-inducing kinase (NIK, MAP3K14) is best known as the apical kinase that triggers non-canonical NF-kappaB activation and by its role in the immune system. Recent data indicate a role for NIK expressed by non-lymphoid cells in cancer, kidney disease, liver injury, glucose homeostasis, osteosarcopenia, vascular calcification, hematopoiesis, and endothelial function. The spectrum of NIK-associated disease now ranges from immunodeficiency (when NIK is defective) to autoimmunity, cancer, sterile inflammation, fibrosis, and metabolic disease when NIK is overactive. The development of novel small-molecule NIK inhibitors has paved the way to test NIK targeting to treat disease in vivo, and may eventually lead to NIK targeting in the clinic. In addition, NIK activators are being explored for specific conditions such as myeloid leukemia.

Publications > article

Nefrologia 2019, 39, 568 PubMed 31196660

MAP3K kinases and kidney injury.

Leticia Cuarental, David Sucunza, Lara Valino-Rivas, Beatriz Fernandez-Fernandez, Ana Belen Sanz, Alberto Ortiz, Juan Jose Vaquero, Maria Dolores Sanchez-Nino

Palabras clave: *ASK1; *Acute kidney injury; *Diabetic kidney disease; *Enfermedad renal cronica; *Enfermedad renal diabetica; *Kidney; *MAP3K kinases; *MAP3K quinasas; *MAP3K14; *NF-kappaB; *NIK; *Rinon; *Selonsertib; *TWEAK

Resumen

Mitogen-activated protein kinases (MAP kinases) are functionally connected kinases that regulate key cellular process involved in kidney disease such as all survival, death, differentiation and proliferation. The typical MAP kinase module is composed by a cascade of three kinases: a MAP kinase kinase kinase (MAP3K) that phosphorylates and activates a MAP kinase kinase (MAP2K) which phosphorylates a MAP kinase (MAPK). While the role of MAPKs such as ERK, p38 and JNK has been well characterized in experimental kidney injury, much less is known about the apical kinases in the cascade, the MAP3Ks. There are 24 characterized MAP3K (MAP3K1 to MAP3K21 plus RAF1, BRAF and ARAF). We now review current knowledge on the involvement of MAP3K in non-malignant kidney disease and the therapeutic tools available. There is in vivo interventional evidence clearly supporting a role for MAP3K5 (ASK1) and MAP3K14 (NIK) in the pathogenesis of experimental kidney disease. Indeed, the ASK1 inhibitor Selonsertib has undergone clinical trials for diabetic kidney disease. Additionally, although MAP3K7 (MEKK7, TAK1) is required for kidney development, acutely targeting MAP3K7 protected from acute and chronic kidney injury; and targeting MAP3K8 (TPL2/Cot) protected from acute kidney injury. By contrast MAP3K15 (ASK3) may protect from hypertension and BRAF inhibitors in clinical use may induced acute kidney injury and nephrotic syndrome. Given their role as upstream regulators of intracellular signaling, MAP3K are potential therapeutic targets in kidney injury, as demonstrated for some of them. However, the role of most MAP3K in kidney disease remains unexplored.

Publications > Gutierrez et al

Eur J Med Chem. 2018, 157, 946 PubMed 30165342

Discovery of potent calpain inhibitors based on the azolo-imidazolidenone.

Sara Gutierrez¹, Maria Moron¹, Mercedes Griera², David Sucunza¹, Laura Calleros², Andrea Garcia-Jerez², Claire Coderch³, Francisco J Hermoso³, Carolina Burgos¹, Manuel Rodriguez-Puyol², Beatriz de Pascual-Teresa³, Maria L Diez-Marques², Antonio Jimenez², Miguel Toro-Londono², Diego Rodriguez-Puyol⁴, Juan J Vaquero¹

1. Departamento de Quimica Organica y Quimica Inorganica, Universidad de Alcala.  2. Departamento de Biologia de Sistemas, Universidad de Alcala, 28871, Alcala de.  3. Departamento de Quimica y Bioquimica, Facultad de Farmacia, Universidad San.  4. Research Unit and Nephrology Section, Hospital Principe de Asturias and.

Keywords: Azolo-imidazolidenone; Blockade of apoptosis; Calpain inhibitors; SAR; Uncompetitive inhibition

Abstract

A series of new azolopyrimidine-peptide hybrids and indolomethylideneimidazolones