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Identification of novel 3-dehydroquinate dehydratase (DHQD) inhibitors for anti-tuberculosis activity: insights from virtual screening, molecular docking, and dynamics simulations.
In Silico Pharmacol
January 2025
Molecular Biophysics and Structural Biology (MBSB) Group, Department of Biochemistry, University of Johannesburg, Auckland Park Kingsway Campus, Johannesburg, 2006 South Africa.
Tuberculosis (TB) remains a pressing global health concern, causing substantial mortality and morbidity despite existing drugs and vaccines. The escalating challenge of drug-resistant TB underscores the critical need for novel medications. This study focuses on the enzyme 3-hydroquinate dehydratase (DHQD) in the shikimate pathway of (Mtb), essential for Mtb growth.
View Article and Find Full Text PDFDetectEV: A functional enzymatic assay to assess integrity and bioactivity of extracellular vesicles.
J Extracell Vesicles
January 2025
Cell-Tech HUB and Institute for Research and Biomedical Innovation (IRIB), National Research Council of Italy (CNR), Palermo, Italy.
The application of extracellular vesicles (EVs) as therapeutics or nanocarriers in cell-free therapies necessitates meticulous evaluations of different features, including their identity, bioactivity, batch-to-batch reproducibility, and stability. Given the inherent heterogeneity in EV preparations, this assessment demands sensitive functional assays to provide key quality control metrics, complementing established methods to ensure that EV preparations meet the required functionality and quality standards. Here, we introduce the detectEV assay, an enzymatic-based approach for assessing EV luminal cargo bioactivity and membrane integrity.
View Article and Find Full Text PDFDynamic collateral sensitivity profiles highlight opportunities and challenges for optimizing antibiotic treatments.
PLoS Biol
January 2025
Department of Biophysics, University of Michigan, Ann Arbor, Michigan, United States of America.
As failure rates for traditional antimicrobial therapies escalate, recent focus has shifted to evolution-based therapies to slow resistance. Collateral sensitivity-the increased susceptibility to one drug associated with evolved resistance to a different drug-offers a potentially exploitable evolutionary constraint, but the manner in which collateral effects emerge over time is not well understood. Here, we use laboratory evolution in the opportunistic pathogen Enterococcus faecalis to phenotypically characterize collateral profiles through evolutionary time.
View Article and Find Full Text PDFAdaptive sampling-based structural prediction reveals opening of a GABA receptor through the αβ interface.
Sci Adv
January 2025
SciLifeLab, Department of Applied Physics, KTH Royal Institute of Technology, Tomtebodävagen 23, Solna, 17165 Stockholm, Sweden.
γ-Aminobutyric acid type A (GABA) receptors are ligand-gated ion channels in the central nervous system with largely inhibitory function. Despite being a target for drugs including general anesthetics and benzodiazepines, experimental structures have yet to capture an open state of classical synaptic α1β2γ2 GABA receptors. Here, we use a goal-oriented adaptive sampling strategy in molecular dynamics simulations followed by Markov state modeling to capture an energetically stable putative open state of the receptor.
View Article and Find Full Text PDFNon-Invasive Nanometer Resolution Assessment of Cell-Soft Hydrogel System Mechanical Properties by Scanning Ion Conductance Microscopy.
Int J Mol Sci
December 2024
Department of Physics, M.V. Lomonosov Moscow State University, 1/2 Leninskie Gory, 119991 Moscow, Russia.
Biomimetic hydrogels have garnered increased interest due to their considerable potential for use in various fields, such as tissue engineering, 3D cell cultivation, and drug delivery. The primary challenge for applying hydrogels in tissue engineering is accurately evaluating their mechanical characteristics. In this context, we propose a method using scanning ion conductance microscopy (SICM) to determine the rigidity of living human breast cancer cells MCF-7 cells grown on a soft, self-assembled Fmoc-FF peptide hydrogel.
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