Search results for "Molecular Dynamic"
showing 10 items of 1090 documents
Design, Synthesis and Biological Evaluation of 7-Chloro-9
2019
Glycogen synthase kinase-3β (GSK-3β) represents a relevant drug target for the treatment of neurodegenerative pathologies including Alzheimer’s disease. We herein report on the optimization of a novel class of GSK-3β inhibitors based on the tofacitinib-derived screen hit 3-((3R,4R)-3-((7-chloro-9H-pyrimido[4,5-b]indol-4-yl)(methyl)amino)-4-methylpiperidin-1-yl)-3-oxopropanenitrile (1). We synthesized a series of 19 novel 7-chloro-9H-pyrimido[4,5-b]indole-based derivatives and studied their structure–activity relationships with focus on the cyanoacetyl piperidine moiety. We unveiled the crucial role of the nitrile group and its importance for the activity of this compound series. A successfu…
Adsorption of the herbicide 4-chloro-2-methylphenoxyacetic acid (MCPA) by goethite.
2014
Interaction between the goethite surface and 4-chloro-2-methylphenoxyacetic acid (MCPA) herbicide was studied using density functional theory (DFT) calculations combined with molecular dynamics (MD). The important step made here lies in the use of a periodic DFT method enabling the study of a mineral surface of different protonation states, in strong contrast with previous molecular modeling studies limited to single protonation state corresponding to the point of zero charge. Different surface OH groups and MCPA proton states were used to mimic the strong effects of pH on the outer- and inner-sphere surface complexes that are theoretically possible, together with their binding energies, an…
A topological isomer of the Au25(SR)18−nanocluster
2020
Energetically low-lying structural isomers of the much-studied thiolate-protected gold cluster Au25(SR)18− are discovered from extensive (80 ns) molecular dynamics (MD) simulations using the reactive molecular force field ReaxFF and confirmed by density functional theory (DFT). A particularly interesting isomer is found, which is topologically connected to the known crystal structure by a low-barrier collective rotation of the icosahedral Au13 core. The isomerization takes place without breaking of any Au–S bonds. The predicted isomer is essentially iso-energetic with the known Au25(SR)18− structure, but has a distinctly different optical spectrum. It has a significantly larger collision cr…
G-quadruplex recognition by DARPIns through epitope/paratope analogy
2022
AbstractWe investigated the mechanisms leading to the specific recognition of Guanine Guadruplex (G4) by DARPins peptides, which can lead to the design of G4s specific sensors. To this end we carried out all-atom molecular dynamic simulations to unravel the interactions between specific nucleic acids, including human-telomeric (h-telo), Bcl-2, and c-Myc, with different peptides, forming a DARPin/G4 complex. By comparing the sequences of DARPin with that of a peptide known for its high affinity for c-Myc, we show that the recognition cannot be ascribed to sequence similarity but, instead, depends on the complementarity between the three-dimensional arrangement of the molecular fragments invo…
Fluorine Scan of Inhibitors of the Cysteine Protease Human Cathepsin L: Dipolar and Quadrupolar Effects in the π-Stacking of Fluorinated Phenyl Rings…
2016
The π-stacking of fluorinated benzene rings on protein backbone amide groups was investigated, using a dual approach comprising enzyme-ligand binding studies complemented by high-level quantum chemical calculations. In the experimental study, the phenyl substituent of triazine nitrile inhibitors of human cathepsin L (hCatL), which stacks onto the peptide amide bond Gly67-Gly68 at the entrance of the S3 pocket, was systematically fluorinated, and differences in inhibitory potency were measured in a fluorimetric assay. Binding affinity is influenced by lipophilicity (clog P), the dipole and quadrupole moments of the fluorinated rings, but also by additional interactions of the introduced fluo…
Experimental investigation and multi-scale modelling of the behavior of mechanically activated metallic powders : from binary systems to High Entropy…
2021
Generally, metal alloys consist of a main element associated with other elements present in smaller quantities such as iron, nickel, aluminum or copper alloys. The precise composition of an alloy is adjusted according to the required performance: high temperature behavior, corrosion resistance, mechanical properties, durability ... In 2004, a Taiwanese scientist, JW Yeh, had the idea of making an alloy base of several elements, at least 5, whose composition in the alloy varies between 5% and 30% at. Yeh invented the high entropy alloy (HEA). Mixed on a microscopic scale, the metals form a remarkably stable solid solution. The explanation is thermodynamic. An alloy is all the more stable as …
Microstructure-process relationship and reactivity at the nanoscale : a molecular dynamics study of Ni, Ni-Al, and Ti-Al metallic systems
2023
The process-microstructure relationship is central in materials science because the microstructure will determine the properties of the materials developed by the processes. In our work, we focused on different metallurgical processes by adopting a description at the atomic scale. This approach allows us to detect the elementary mechanisms that are at the origin of the observed microstructures without having to postulate macroscopic mechanisms or estimate the associated parameters. In this respect, molecular dynamics simulations provide a tool for "in-situ" observation of metallic systems as long as an atomic interaction potential is available. The originality of our approach consists in mo…
Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling
2021
Bacterial phytochrome photoreceptors usually belong to two-component signaling systems which transmit environmental stimuli to a response regulator through a histidine kinase domain. Phytochromes switch between red light-absorbing and far-red light-absorbing states. Despite exhibiting extensive structural responses during this transition, the model bacteriophytochrome from Deinococcus radiodurans (DrBphP) lacks detectable kinase activity. Here, we resolve this long-standing conundrum by comparatively analyzing the interactions and output activities of DrBphP and a bacteriophytochrome from Agrobacterium fabrum (Agp1). Whereas Agp1 acts as a conventional histidine kinase, we identify DrBphP a…
Light-induced Changes in the Dimerization Interface of Bacteriophytochromes
2015
Phytochromes are dimeric photoreceptor proteins that sense red light levels in plants, fungi, and bacteria. The proteins are structurally divided into a light-sensing photosensory module consisting of PAS, GAF, and PHY domains and a signaling output module, which in bacteriophytochromes typically is a histidine kinase (HK) domain. Existing structural data suggest that two dimerization interfaces exist between the GAF and HK domains, but their functional roles remain unclear. Using mutational, biochemical, and computational analyses of the Deinococcus radiodurans phytochrome, we demonstrate that two dimerization interfaces between sister GAF and HK domains stabilize the dimer with approximat…
Interpretation of EXAFS in ReO3using molecular dynamics simulations
2009
Temperature dependent Re L3-edge EXAFS signals from perovskite-type cubic ReO3 have been successfully interpreted using a combination of classical NVT molecular dynamics (MD) and ab initio multiple-scattering approach. The force field model, required for MD simulations, has been determined by fitting the Re-O and O-O pairwise interatomic potentials to a set of experimental data (lattice parameter, elastic constants and bulk modulus) and phonon frequencies, theoretically calculated from the first principles at high symmetry points of the Brillouin zone. The MD simulations reproduce well the anisotropy of thermal vibration for oxygen atoms and confirm a deviation of the mean Re-O-Re angle fro…