Publications
Welcome to our research group's publications page. Here, you can explore a selection of our latest research findings and scientific contributions.
Profiling Cysteine Proteases in Neuroinflammatory Cells
Laura Agost-Beltrán, Ania Canseco-Rodríguez, Tanja Schirmeister, Santiago Rodríguez, Ana Sánchez-Pérez, Florenci V. González
ChemMedChem 2024, e202400520.
A new activity-based probe (ABP) for cysteine proteases, FGA139, was designed by attaching a bodipy fluorophore to an irreversible inhibitor's peptide backbone. The probe is synthesized through metathesis and “click” reactions. It profiles activities of cathepsins B, L, and calpain in neurodegenerative cell models, confirming specificity and showing protective effects against oxidative stress and macrophage activation.
Rhodesain inhibitors at the edge of reversibility-irreversibility
Laura Agost-Beltrán, Collin Zimmer, Hans Joachim Räder, Cristian Kernsten, Tanja Schirmeister, Santiago Rodríguez, Florenci V. González
Bioorganic Chemistry 2024, 153, 107830.
A comparative study of Michael acceptor and keto-Michael acceptor inhibitors of the cysteine protease rhodesain has been performed. Five new inhibitors have been prepared bearing the peptide structure of the known cysteine protease inhibitor K11777 and differing on the warhead. For the preparation of the Michael acceptor warhead, a Horner-Wadsworth-Emmons reaction was used. In the synthetic routes of the keto-Michael acceptor warheads, keto-enoate and keto-vinyl sulfone, a metathesis reaction and a radical sulfonylation were the key steps, respectively. Interestingly, keto-Michael acceptors inhibited rhodesain through a dual mode of action, showing reversibility at low inhibitor concentrations and irreversibility at high inhibitor concentrations.
Peptidyl nitroalkene inhibitors of main protease rationalized by computational and crystallographic investigations as antivirals against SARS-CoV-2
Francisco J. Medrano, Sergio de la Hoz-Rodríguez, Sergio Martí, Kemel Arafat, Tanja Schirmeister, Stefan J. Hammerschmidt, Christin Müller, Águeda González-Martínez, Elena Santillana, John Ziebuhr, Antonio Romero, Collin Zimmer, Annabelle Welder, Robert Zimmermann, Alessio Lodola, Katarzyna Swiderek, Vicent Moliner, Florenci V. González
Commun. Chem. 2024, 7, 15.
The coronavirus disease 2019 (COVID-19) pandemic continues to represent a global public health issue. The viral main protease (Mpro) represents one of the most attractive targets for the development of antiviral drugs. Herein we report peptidyl nitroalkenes exhibiting enzyme inhibitory activity against Mpro (Ki: 1–10 μM) good anti-SARS-CoV-2 infection activity in the low micromolar range (EC50: 1–12 μM) without significant toxicity. Additional kinetic studies of compounds FGA145, FGA146 and FGA147 show that all three compounds inhibit cathepsin L, denoting a possible multitarget effect of these compounds in the antiviral activity. Structural analysis shows the binding mode of FGA146 and FGA147 to the active site of the protein. Furthermore, our results illustrate that peptidyl nitroalkenes are effective covalent reversible inhibitors of the Mpro and cathepsin L, and that inhibitors FGA145, FGA146 and FGA147 prevent infection against SARS-CoV-2.
Transcription factors HB21/40/53 trigger inflorescence arrest through abscisic acid accumulation at the end of flowering
Verónica Sánchez-Gerschon, Irene Martínez-Fernández, María R. González-Bermúdez, Sergio de la Hoz-Rodríguez, Florenci V. González, Jorge Lozano-Juste, Cristina Ferrándiz, and Vicente Balanzà
Plant Physiology 2024, 195, 2743.
Flowers, and hence, fruits and seeds, are produced by the activity of the inflorescence meristem after the floral transition. In plants with indeterminate inflorescences, the final number of flowers produced by the inflorescence meristem is determined by the length of the flowering period, which ends with inflorescence arrest. Inflorescence arrest depends on many different factors, such as the presence of seeds, the influence of the environment, or endogenous factors such as phytohormone levels and age, which modulate inflorescence meristem activity. The FRUITFULL-APETALA2 (FUL-AP2) pathway plays a major role in regulating the end of flowering, likely integrating both endogenous cues and those related to seed formation. Among AP2 targets, HOMEOBOX PROTEIN21(HB21) has been identified as a putative mediator of AP2 function in the control of inflorescence arrest. HB21 is a homeodomain leucine zipper transcription factor involved in establishing axillary bud dormancy. Here, we characterized the role of HB21 in the control of the inflorescence arrest at the end of flowering in Arabidopsis (Arabidopsis thaliana). HB21, together with HB40 and HB53, are upregulated in the inflorescence apex at the end of flowering, promoting floral bud arrest. We also show that abscisic acid (ABA) accumulation occurs in the inflorescence apex in an HB-dependent manner. Our work suggests a physiological role of ABA in floral bud arrest at the end of flowering, pointing to ABA as a regulator of inflorescence arrest downstream of the HB21/40/53 genes.
Impact of the Warhead of Dipeptidyl Keto Michael Acceptors on the inhibition Mechanism of Cysteine Protease Cathepsin L
Adrián Fernández-de-la-Pradilla, Santiago Royo, Tanja Schirmeister, Fabian Barthels, Katarzyna Swiderek, Florenci V. González, Vicent Moliner
ACS Catalysis 2023, 13, 13354-13368.
Cathepsin L (CatL) is a lysosomal cysteine protease whose activity has been related to several human pathologies. However, although preclinical trials using CatL inhibitors were promising, clinical trials have been unsuccessful up to now. We are presenting a study of two designed dipeptidyl keto Michael acceptor potential inhibitors of CatL with either a keto vinyl ester or a keto vinyl sulfone (KVS) warhead. The compounds were synthesized and experimentally assayed in vitro, and their inhibition molecular mechanism was explored based on molecular dynamics simulations at the density functional theory/molecular mechanics level. The results confirm that both compounds inhibit CatL in the nanomolar range and show a time-dependent inhibition. Interestingly, despite both presenting almost equivalent equilibrium constants for the reversible formation of the noncovalent enzyme/inhibitor complex, differences are observed in the chemical step corresponding to the enzyme–inhibitor covalent bond formation, results that are mirrored by the computer simulations. Theoretically determined kinetic and thermodynamic results, which are in very good agreement with the experiments, afford a detailed explanation of the relevance of the different structural features of both compounds having a significant impact on enzyme inhibition. The unprecedented binding interactions of both inhibitors in the P1′ site of CatL represent valuable information for the design of inhibitors. In particular, the peptidyl KVS can be used as a starting lead compound in the development of drugs with medical applications for the treatment of cancerous pathologies since sulfone warheads have previously shown promising cell stability compared to other functions such as carboxylic esters. Future improvements can be guided by the atomistic description of the enzyme–inhibitor interactions established along the inhibition reaction derived from computer simulations.
Investigation of the Compatibility between Warheads and Peptidomimetic Sequences of Protease Inhibitors - A Comprehensive Reactivity and Selectivity Study
Patrick Müller, Mergim Meta, Jan Laurenz Meidner, Marvin Schwickert, Jessica Meyr, Kevin Schwickert, Christian Kersten, Collin Zimmer, Stefan Josef Hammerschmidt, Ariane Frey, Albin Lahu, Sergio de la Hoz-Rodríguez, Laura Agost-Beltrán, Santiago Rodríguez, Kira Diemer, Wilhelm Neumann, Florenci V. González, Bernd Engels, Tanja Schirmeister
Internacional Journal of Molecular Sciences 2023, 24(8), 7226.
Covalent peptidomimetic protease inhibitors have gained a lot of attention in drug development in recent years. They are designed to covalently bind the catalytically active amino acids through electrophilic groups called warheads. Covalent inhibition has an advantage in terms of pharmacodynamic properties but can also bear toxicity risks due to non-selective off-target protein binding. Therefore, the right combination of a reactive warhead with a well-suited peptidomimetic sequence is of great importance. Herein, the selectivities of well-known warheads combined with peptidomimetic sequences suited for five different proteases were investigated, highlighting the impact of both structure parts (warhead and peptidomimetic sequence) for affinity and selectivity. Molecular docking gave insights into the predicted binding modes of the inhibitors inside the binding pockets of the different enzymes. Moreover, the warheads were investigated by NMR and LC-MS reactivity assays against serine/threonine and cysteine nucleophile models, as well as by quantum mechanics simulations.
Covalent peptidomimetic protease inhibitors have gained a lot of attention in drug development in recent years. They are designed to covalently bind the catalytically active amino acids through electrophilic groups called warheads. Covalent inhibition has an advantage in terms of pharmacodynamic properties but can also bear toxicity risks due to non-selective off-target protein binding. Therefore, the right combination of a reactive warhead with a well-suited peptidomimetic sequence is of great importance. Herein, the selectivities of well-known warheads combined with peptidomimetic sequences suited for five different proteases were investigated, highlighting the impact of both structure parts (warhead and peptidomimetic sequence) for affinity and selectivity. Molecular docking gave insights into the predicted binding modes of the inhibitors inside the binding pockets of the different enzymes. Moreover, the warheads were investigated by NMR and LC-MS reactivity assays against serine/threonine and cysteine nucleophile models, as well as by quantum mechanics simulations.