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Enhancing HDAC Inhibitor Screening: Addressing Zinc Parameterization and Ligand Protonation in Docking Studies.
Int J Mol Sci
January 2025
Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy.
Precise binding free-energy predictions for ligands targeting metalloproteins, especially zinc-containing histone deacetylase (HDAC) enzymes, require specialized computational approaches due to the unique interactions at metal-binding sites. This study evaluates a docking algorithm optimized for zinc coordination to determine whether it could accurately differentiate between protonated and deprotonated states of hydroxamic acid ligands, a key functional group in HDAC inhibitors (HDACi). By systematically analyzing both protonation states, we sought to identify which state produces docking poses and binding energy estimates most closely aligned with experimental values.
View Article and Find Full Text PDFAn Addendum to the Chemiosmotic Theory of Mitochondrial Activity: The Role of RNA as a Proton Sink.
Biomolecules
January 2025
School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.
Mitochondrial ATP synthesis is driven by harnessing the electrochemical gradient of protons (proton motive force) across the mitochondrial inner membrane via the process of chemiosmosis. While there is consensus that the proton gradient is generated by components of the electron transport chain, the mechanism by which protons are supplied to ATP synthase remains controversial. As opposed to a global coupling model whereby protons diffuse into the intermembrane space, a localised coupling model predicts that protons remain closely associated with the lipid membrane prior to interaction with ATP synthase.
View Article and Find Full Text PDFZIF-8-Embedded Cation-Exchange Membranes with Improved Monovalent Ion Selectivity for Capacitive Deionization.
Membranes (Basel)
January 2025
Department of Green Chemical Engineering, College of Engineering, Sangmyung University, Cheonan 31066, Republic of Korea.
Membrane capacitive deionization (MCDI) is an electrochemical ion separation process that combines ion-exchange membranes (IEMs) with porous carbon electrodes to enhance desalination efficiency and address the limitations of conventional capacitive deionization (CDI). In this study, a cation-exchange membrane (CEM) embedded with a metal-organic framework (MOF) was developed to effectively separate monovalent and multivalent cations in influent solutions via MCDI. To fabricate CEMs with high monovalent ion selectivity, ZIF-8 was incorporated into sulfonated poly(2,6-dimethyl-1,4-phenylene oxide) (SPPO) at various weight ratios.
View Article and Find Full Text PDFInjectable Biocompatible Zeolite Nanocrystals for Enhanced Tumor Oxygenation and MRI Imaging.
ACS Appl Mater Interfaces
January 2025
Université de Caen Normandie, ENSICAEN, CNRS, LCS, 14000 Caen, France.
Tumor hypoxia significantly limits the effectiveness of radiotherapy, as oxygen is crucial for producing cancer-killing reactive oxygen species. To address this, we synthesized nanosized faujasite (PBS-Na-FAU) zeolite crystals using clinical-grade phosphate-buffered saline (PBS) as the solvent, ensuring preserved crystallinity, microporous volume, and colloidal stability. The zeolite nanocrystals showed enhanced safety profiles and , and studies showed no apparent toxicity to animals.
View Article and Find Full Text PDFIon permeability profiles of renal paracellular channel-forming claudins.
Acta Physiol (Oxf)
February 2025
Clinical Physiology/Nutritional Medicine, Medical Department, Division of Gastroenterology, Infectiology, Rheumatology, Charité-Universitätsmedizin Berlin, Berlin, Germany.
Aim: Members of the claudin protein family are the major constituents of tight junction strands and determine the permeability properties of the paracellular pathway. In the kidney, each nephron segment expresses a distinct subset of claudins that form either barriers against paracellular solute transport or charge- and size-selective paracellular channels. It was the aim of the present study to determine and compare the permeation properties of these renal paracellular ion channel-forming claudins.
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