TY  - JOUR
A1  - Müller, Patrick
A1  - Meta, Mergim
A1  - Meidner, Jan Laurenz
A1  - Schwickert, Marvin
A1  - Meyr, Jessica
A1  - Schwickert, Kevin
A1  - Kersten, Christian
A1  - Zimmer, Collin
A1  - Hammerschmidt, Stefan Josef
A1  - Frey, Ariane
A1  - Lahu, Albin
A1  - de la Hoz-Rodríguez, Sergio
A1  - Agost-Beltrán, Laura
A1  - Rodríguez, Santiago
A1  - Diemer, Kira
A1  - Neumann, Wilhelm
A1  - Gonzàlez, Florenci V.
A1  - Engels, Bernd
A1  - Schirmeister, Tanja
T1  - Investigation of the compatibility between warheads and peptidomimetic sequences of protease inhibitors — a comprehensive reactivity and selectivity study
JF  - International Journal of Molecular Sciences
N2  - 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.
KW  - covalent inhibitors
KW  - in vitro study
KW  - protease inhibitors
KW  - peptidomimetic sequence
KW  - warhead
KW  - reactivity and selectivity study
Y1  - 2023
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-313596
SN  - 1422-0067
VL  - 24
IS  - 8
ER  - 
TY  - JOUR
A1  - Planes, Maria D.
A1  - Niñoles, Regina
A1  - Rubio, Lourdes
A1  - Bissoli, Gaetano
A1  - Bueso, Eduardo
A1  - García-Sánchez, María J.
A1  - Alejandro, Santiago
A1  - Gonzalez-Guzmán, Miguel
A1  - Hedrich, Rainer
A1  - Rodriguez, Pedro L.
A1  - Fernández, José A.
A1  - Serrano, Ramón
T1  - A mechanism of growth inhibition by abscisic acid in germinating seeds of Arabidopsis thaliana based on inhibition of plasma membrane \(H^+\)-ATPase and decreased cytosolic pH, \(K^+\), and anions
JF  - Journal of Experimental Botany
N2  - The stress hormone abscisic acid (ABA) induces expression of defence genes in many organs, modulates ion homeostasis and metabolism in guard cells, and inhibits germination and seedling growth. Concerning the latter effect, several mutants of Arabidopsis thaliana with improved capability for \(H^+\) efflux (wat1-1D, overexpression of AKT1 and ost2-1D) are less sensitive to inhibition by ABA than the wild type. This suggested that ABA could inhibit \(H^+\) efflux (\(H^+\)-ATPase) and induce cytosolic acidification as a mechanism of growth inhibition. Measurements to test this hypothesis could not be done in germinating seeds and we used roots as the most convenient system. ABA inhibited the root plasma-membrane H+-ATPase measured in vitro (ATP hydrolysis by isolated vesicles) and in vivo (\(H^+\) efflux from seedling roots). This inhibition involved the core ABA signalling elements: PYR/PYL/RCAR ABA receptors, ABA-inhibited protein phosphatases (HAB1), and ABA-activated protein kinases (SnRK2.2 and SnRK2.3). Electrophysiological measurements in root epidermal cells indicated that ABA, acting through the PYR/PYL/RCAR receptors, induced membrane hyperpolarization (due to \(K^+\) efflux through the GORK channel) and cytosolic acidification. This acidification was not observed in the wat1-1D mutant. The mechanism of inhibition of the \(H^+\)-ATPase by ABA and its effects on cytosolic pH and membrane potential in roots were different from those in guard cells. ABA did not affect the in vivo phosphorylation level of the known activating site (penultimate threonine) of (\(H^+\)-ATPase in roots, and SnRK2.2 phosphorylated in vitro the C-terminal regulatory domain of (\(H^+\)-ATPase while the guard-cell kinase SnRK2.6/OST1 did not.
KW  - ABA receptors
KW  - cytosolic pH
KW  - ion channels
KW  - microelectrodes
KW  - protein kinase
KW  - proton efflux
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-121221
VL  - 66
IS  - 3
ER  - 
TY  - JOUR
A1  - Libre, Camille
A1  - Seissler, Tanja
A1  - Guerrero, Santiago
A1  - Batisse, Julien
A1  - Verriez, Cédric
A1  - Stupfler, Benjamin
A1  - Gilmer, Orian
A1  - Cabrera-Rodriguez, Romina
A1  - Weber, Melanie M.
A1  - Valenzuela-Fernandez, Agustin
A1  - Cimarelli, Andrea
A1  - Etienne, Lucie
A1  - Marquet, Roland
A1  - Paillart, Jean-Christophe
T1  - A conserved uORF regulates APOBEC3G translation and is targeted by HIV-1 Vif protein to repress the antiviral factor
JF  - Biomedicines
N2  - The HIV-1 Vif protein is essential for viral fitness and pathogenicity. Vif decreases expression of cellular restriction factors APOBEC3G (A3G), A3F, A3D and A3H, which inhibit HIV-1 replication by inducing hypermutation during reverse transcription. Vif counteracts A3G at several levels (transcription, translation, and protein degradation) that altogether reduce the levels of A3G in cells and prevent its incorporation into viral particles. How Vif affects A3G translation remains unclear. Here, we uncovered the importance of a short conserved uORF (upstream ORF) located within two critical stem-loop structures of the 5′ untranslated region (5′-UTR) of A3G mRNA for this process. A3G translation occurs through a combination of leaky scanning and translation re-initiation and the presence of an intact uORF decreases the extent of global A3G translation under normal conditions. Interestingly, the uORF is also absolutely required for Vif-mediated translation inhibition and redirection of A3G mRNA into stress granules. Overall, we discovered that A3G translation is regulated by a small uORF conserved in the human population and that Vif uses this specific feature to repress its translation.
KW  - HIV-1
KW  - APOBEC3G
KW  - Vif
KW  - mRNA
KW  - translation
KW  - uORF
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-252147
SN  - 2227-9059
VL  - 10
IS  - 1
ER  - 
TY  - JOUR
A1  - Trafimow, David
A1  - Amrhein, Valentin
A1  - Areshenkoff, Corson N.
A1  - Barrera-Causil, Carlos J.
A1  - Beh, Eric J.
A1  - Bilgiç, Yusuf K.
A1  - Bono, Roser
A1  - Bradley, Michael T.
A1  - Briggs, William M.
A1  - Cepeda-Freyre, Héctor A.
A1  - Chaigneau, Sergio E.
A1  - Ciocca, Daniel R.
A1  - Correa, Juan C.
A1  - Cousineau, Denis
A1  - de Boer, Michiel R.
A1  - Dhar, Subhra S.
A1  - Dolgov, Igor
A1  - Gómez-Benito, Juana
A1  - Grendar, Marian
A1  - Grice, James W.
A1  - Guerrero-Gimenez, Martin E.
A1  - Gutiérrez, Andrés
A1  - Huedo-Medina, Tania B.
A1  - Jaffe, Klaus
A1  - Janyan, Armina
A1  - Karimnezhad, Ali
A1  - Korner-Nievergelt, Fränzi
A1  - Kosugi, Koji
A1  - Lachmair, Martin
A1  - Ledesma, Rubén D.
A1  - Limongi, Roberto
A1  - Liuzza, Marco T.
A1  - Lombardo, Rosaria
A1  - Marks, Michael J.
A1  - Meinlschmidt, Gunther
A1  - Nalborczyk, Ladislas
A1  - Nguyen, Hung T.
A1  - Ospina, Raydonal
A1  - Perezgonzalez, Jose D.
A1  - Pfister, Roland
A1  - Rahona, Juan J.
A1  - Rodríguez-Medina, David A.
A1  - Romão, Xavier
A1  - Ruiz-Fernández, Susana
A1  - Suarez, Isabel
A1  - Tegethoff, Marion
A1  - Tejo, Mauricio
A1  - van de Schoot, Rens
A1  - Vankov, Ivan I.
A1  - Velasco-Forero, Santiago
A1  - Wang, Tonghui
A1  - Yamada, Yuki
A1  - Zoppino, Felipe C. M.
A1  - Marmolejo-Ramos, Fernando
T1  - Manipulating the Alpha Level Cannot Cure Significance Testing
JF  - Frontiers in Psychology
N2  - We argue that making accept/reject decisions on scientific hypotheses, including a recent call for changing the canonical alpha level from p = 0.05 to p = 0.005, is deleterious for the finding of new discoveries and the progress of science. Given that blanket and variable alpha levels both are problematic, it is sensible to dispense with significance testing altogether. There are alternatives that address study design and sample size much more directly than significance testing does; but none of the statistical tools should be taken as the new magic method giving clear-cut mechanical answers. Inference should not be based on single studies at all, but on cumulative evidence from multiple independent studies. When evaluating the strength of the evidence, we should consider, for example, auxiliary assumptions, the strength of the experimental design, and implications for applications. To boil all this down to a binary decision based on a p-value threshold of 0.05, 0.01, 0.005, or anything else, is not acceptable.
KW  - statistical significance
KW  - null hypothesis testing
KW  - p-value
KW  - significance testing
KW  - decision making
Y1  - 2018
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-189973
SN  - 1664-1078
VL  - 9
IS  - 699
ER  - 
TY  - JOUR
A1  - Vazquez-Rodriguez, Saleta
A1  - Vilar, Santiago
A1  - Kachler, Sonja
A1  - Klotz, Karl-Norbert
A1  - Uriarte, Eugenio
A1  - Borges, Fernanda
A1  - Matos, Maria João
T1  - Adenosine receptor ligands: coumarin−chalcone hybrids as modulating agents on the activity of hARs
JF  - Molecules
N2  - Adenosine receptors (ARs) play an important role in neurological and psychiatric disorders such as Alzheimer's disease, Parkinson's disease, epilepsy and schizophrenia. The different subtypes of ARs and the knowledge on their densities and status are important for understanding the mechanisms underlying the pathogenesis of diseases and for developing new therapeutics. Looking for new scaffolds for selective AR ligands, coumarin–chalcone hybrids were synthesized (compounds 1–8) and screened in radioligand binding (hA\(_1\), hA\(_{2A}\) and hA\(_3\)) and adenylyl cyclase (hA\(_{2B}\)) assays in order to evaluate their affinity for the four human AR subtypes (hARs). Coumarin–chalcone hybrid has been established as a new scaffold suitable for the development of potent and selective ligands for hA\(_1\) or hA\(_3\) subtypes. In general, hydroxy-substituted hybrids showed some affinity for the hA\(_1\), while the methoxy counterparts were selective for the hA\(_3\). The most potent hA\(_1\) ligand was compound 7 (K\(_i\) = 17.7 µM), whereas compound 4 was the most potent ligand for hA\(_3\) (K\(_i\) = 2.49 µM). In addition, docking studies with hA\(_1\) and hA\(_3\) homology models were established to analyze the structure–function relationships. Results showed that the different residues located on the protein binding pocket could play an important role in ligand selectivity.
KW  - coumarin
KW  - chalcone
KW  - neurodegenerative diseases
KW  - adenosine receptors
KW  - binding affinity
KW  - docking
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-213165
SN  - 1420-3049
VL  - 25
IS  - 18
ER  -