Colabind: A Cloud-Based Approach for Prediction of Binding Sites Using Coarse-Grained Simulations with Molecular Probes.

Binding site prediction is a crucial step in understanding protein-ligand and protein-protein interactions (PPIs) with broad implications in drug discovery and bioinformatics. This study introduces Colabind, a robust, versatile, and user-friendly cloud-based approach that employs coarse-grained molecular dynamics simulations in the presence of molecular probes, mimicking fragments of drug-like compounds. Our method has demonstrated high effectiveness when validated across a diverse range of biological targets spanning various protein classes, successfully identifying orthosteric binding sites, as well as known druggable allosteric or PPI sites, in both experimentally determined and AI-predicted protein structures, consistently placing them among the top-ranked sites. Furthermore, we suggest that careful inspection of the identified regions with a high affinity for specific probes can provide valuable insights for the development of pharmacophore hypotheses. The approach is available at https://github.com/porekhov/CG_probeMD.

High-Performance Hydrogen-Selective Pd-Ag Membranes Modified with Pd-Pt Nanoparticles for Use in Steam Reforming Membrane Reactors.

A unique method for synthesizing a surface modifier for metallic hydrogen permeable membranes based on non-classic bimetallic pentagonally structured Pd-Pt nanoparticles was developed. It was found that nanoparticles had unique hollow structures. This significantly reduced the cost of their production due to the economical use of metal. According to the results of electrochemical studies, a synthesized bimetallic Pd-Pt/Pd-Ag modifier showed excellent catalytic activity (up to 60.72 mA cm-2), long-term stability, and resistance to COads poisoning in the alkaline oxidation reaction of methanol. The membrane with the pentagonally structured Pd-Pt/Pd-Ag modifier showed the highest hydrogen permeation flux density, up to 27.3 mmol s-1 m-2. The obtained hydrogen flux density was two times higher than that for membranes with a classic Pdblack/Pd-Ag modifier and an order of magnitude higher than that for an unmodified membrane. Since the rate of transcrystalline hydrogen transfer through a membrane increased, while the speed of transfer through defects remained unchanged, a one and a half times rise in selectivity of the developed Pd-Pt/Pd-Ag membranes was recorded, and it amounted to 3514. The achieved results were due to both the synergistic effect of the combination of Pd and Pt metals in the modifier composition and the large number of available catalytically active centers, which were present as a result of non-classic morphology with high-index facets. The specific faceting, defect structure, and unusual properties provide great opportunities for the application of nanoparticles in the areas of membrane reactors, electrocatalysis, and the petrochemical and hydrogen industries.

Hydrogen Permeability of Composite Pd-Au/Pd-Cu Membranes and Methods for Their Preparation.

Thin Pd-40%Cu films were obtained via the classical melting and rolling method, magnetron sputtering, and modified with nanostructured functional coatings to intensify the process of hydrogen transportation. The films were modified by electrodeposition, according to the classical method of obtaining palladium black and "Pd-Au nanoflowers" with spherical and pentagonal particles, respectively. The experiment results demonstrated the highest catalytic activity (89.47 mA cm-2), good resistance to CO poisoning and long-term stability of Pd-40%Cu films with a pentagonal structured coating. The investigation of the developed membranes in the hydrogen transport processes in the temperature range of 25-300 °C also demonstrated high and stable fluxes of up to 475.28 mmol s-1 m-2 (deposited membranes) and 59.41 mmol s-1 m-2 (dense metal membranes), which were up to 1.5 higher, compared with membrane materials with classic niello. For all-metal modified membranes, the increase in flux was up to sevenfold, compared with a smooth membrane made of pure palladium, and for deposited films, this difference was manyfold. The membrane materials' selectivity was also high, up to 4419. The developed strategy for modifying membrane materials with functional coatings of a fundamentally new complex geometry can shed new light on the development and fabrication of durable and highly selective palladium-based membranes for gas steam reformers.

Experimental validation of proton boron capture therapy for glioma cells.

Proton boron capture therapy (PBCT) has emerged from particle acceleration research for enhancing the biological effectiveness of proton therapy. The mechanism responsible for the dose increase was supposed to be related to proton-boron fusion reactions (11B + p → 3α + 8.7 MeV). There has been some experimental evidence that the biological efficiency of protons is significantly higher for boron-11-containing prostate or breast cancer cells. The aim of this study was to evaluate the sensitizing potential of sodium borocaptate (BSH) under proton irradiation at the Bragg peak of cultured glioma cells. To address this problem, cells of two glioma lines were preincubated with 80 or 160 ppm boron-11, irradiated both at the middle of 200 MeV beam Spread-Out Bragg Peak (SOBP) and at the distal end of the 89.7 MeV beam SOBP and assessed for the viability, as well as their ability to form colonies. Our results clearly show that BSH provides for only a slight, if any, enhancement of the effect of proton radiation on the glioma cells in vitro. In addition, we repeated the experiments using the Du145 prostate cancer cell line, for which an increase in the biological efficiency of proton irradiation in the presence of sodium borocaptate was demonstrated previously. The data presented add new argument against the efficiency of proton boron capture therapy when based solely on direct dose-enhancement effect by the proton capture nuclear reaction, underlining the need to investigate the indirect effects of the secondary alpha irradiation depending on the state and treatment conditions of the irradiated tissue.