Browsing Bergen Open Research Archive by Author "Brenk, Ruth"
Now showing items 1-12 of 12
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Crystal structure of Pseudomonas aeruginosa FabB C161A, a template for structure-based design for new antibiotics
Yadrykhinsky, Vladyslav; Georgiou, Charis; Brenk, Ruth (Journal article; Peer reviewed, 2022)Background: FabB (3-oxoacyl-[acyl-carrier-protein] synthase 1) is part of the fatty acid synthesis II pathway found in bacteria and a potential target for antibiotics. The enzyme catalyses the Claisen condensation of ... -
DrugPred_RNA—A Tool for Structure-Based Druggability Predictions for RNA Binding Sites
Rekand, Illimar Hugo; Brenk, Ruth (Journal article; Peer reviewed, 2021)RNA is an emerging target for drug discovery. However, like for proteins, not all RNA binding sites are equally suited to be addressed with conventional drug-like ligands. To this end, we have developed the structure-based ... -
An Experimental Toolbox for Structure-Based Hit Discovery for P. aeruginosa FabF, a Promising Target for Antibiotics
Espeland, Ludvik Olai; Georgiou, Charis; Klein, Raphael; Bhukya, Hemalatha; Haug, Bengt Erik; Underhaug, Jarl; Mainkar, Prathama S.; Brenk, Ruth (Journal article; Peer reviewed, 2021)FabF (3-oxoacyl-[acyl-carrier-protein] synthase 2), which catalyses the rate limiting condensation reaction in the fatty acid synthesis II pathway, is an attractive target for new antibiotics. Here, we focus on FabF from ... -
Fragment screening using biolayer interferometry reveals ligands targeting the SHP-motif binding site of the AAA+ ATPase p97
Bothe, Sebastian; Hänzelmann, Petra; Böhler, Stephan; Kehrein, Josef; Zehe, Markus; Wiedemann, Christoph; Hellmich, Ute A.; Brenk, Ruth; Schindelin, Hermann; Sotriffer, Christoph (Journal article; Peer reviewed, 2022)Biosensor techniques have become increasingly important for fragment-based drug discovery during the last years. The AAA+ ATPase p97 is an essential protein with key roles in protein homeostasis and a possible target for ... -
How To Design Selective Ligands for Highly Conserved Binding Sites: A Case Study Using N-Myristoyltransferases as a Model System
Kersten, Christian; Fleischer, Edmond; Kehrein, Josef; Borek, Christoph; Jaenicke, Elmar; Sotriffer, Christoph; Brenk, Ruth (Peer reviewed; Journal article, 2020)A model system of two related enzymes with conserved binding sites, namely N-myristoyltransferase from two different organisms, was studied to decipher the driving forces that lead to selective inhibition in such cases. ... -
Identification of a potential allosteric site of Golgi α-mannosidase II using computer-aided drug design
Irsheid, Lina; Wehler, Thomas; Borek, Christoph; Kiefer, Werner; Brenk, Ruth; Ortiz-Soto, Maria Elena; Seibel, Jurgen; Schirmeister, Tanja (Peer reviewed; Journal article, 2019-05-08)Golgi α-mannosidase II (GMII) is a glycoside hydrolase playing a crucial role in the N-glycosylation pathway. In various tumour cell lines, the distribution of N-linked sugars on the cell surface is modified and correlates ... -
In silico identification and experimental validation of hits active against KPC-2 β-lactamase
Klein, Raphael; Linciano, Pasquale; Celenza, Guiseppe; Bellio, Pierangelo; Papaioannou, Sofia; Blazques, Jesus; Cendron, Laura; Brenk, Ruth; Tondi, Donatella (Peer reviewed; Journal article, 2018-11-29)Bacterial resistance has become a worldwide concern, particularly after the emergence of resistant strains overproducing carbapenemases. Among these, the KPC-2 carbapenemase represents a significant clinical challenge, ... -
Investigating Polypharmacology through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3
Gartan, Parveen; Khorsand, Fahimeh; Mizar, Pushpak; Vahokoski, Juha; Cervantes, Luis F.; Haug, Bengt Erik; Brenk, Ruth; Brooks, Charles L.; Reuter, Nathalie (Journal article; Peer reviewed, 2024)Using a combination of multisite λ−dynamics (MSλD) together with in vitro IC50 assays, we evaluated the polypharmacological potential of a scaffold currently in clinical trials for inhibition of human neutrophil elastase ... -
Riboswitches as Drug Targets for Antibiotics
Panchal, Vipul Navinchandra; Brenk, Ruth (Journal article; Peer reviewed, 2021)Riboswitches reside in the untranslated region of RNA and regulate genes involved in the biosynthesis of essential metabolites through binding of small molecules. Since their discovery at the beginning of this century, ... -
RNA-binding is an ancient trait of the Annexin family
Patil, Sudarshan; Panchal, Vipul Navinchandra; Røstbø, Trude Kvalnes; Romanyuk, Sofya; Hollås, Hanne; Brenk, Ruth; Grindheim, Ann Kari; Vedeler, Anni (Journal article; Peer reviewed, 2023)Introduction: The regulation of intracellular functions in mammalian cells involves close coordination of cellular processes. During recent years it has become evident that the sorting, trafficking and distribution of ... -
Targeting the Class A Carbapenemase GES-5 via Virtual Screening
Klein, Raphael; Cendron, Laura; Montanari, Maria; Bellio, Pierangelo; Celenza, Giuseppe; Maso, Lorenzo; Tondi, Donatella; Brenk, Ruth (Journal article; Peer reviewed, 2020)The worldwide spread of β-lactamases able to hydrolyze last resort carbapenems contributes to the antibiotic resistance problem and menaces the successful antimicrobial treatment of clinically relevant pathogens. Class A ... -
To hit or not to hit, that is the question -genome-wide structure-based druggability predictions for pseudomonas aeruginosa proteins
Sarkar, Aurijit; Brenk, Ruth (Peer reviewed; Journal article, 2015-09-11)Pseudomonas aeruginosa is a Gram-negative bacterium known to cause opportunistic infections in immune-compromised or immunosuppressed individuals that often prove fatal. New drugs to combat this organism are therefore ...