Search results for "molecular dynamics"
showing 10 items of 1075 documents
Empirical molecular dynamics study of structural, elastic and thermodynamic properties of zinc-blende-like SiGe compound
2004
Abstract A three-body potential coupled with a molecular-dynamics method is used to calculate structural and thermodynamic properties of the hypothetical IV–IV compound SiGe in zinc-blende phase. A good agreement between the calculated and theoretical values of the lattice constant, the bulk modulus and its derivative, and the cohesive energy is obtained. We also compute the elastic constants, Debye temperature, lattice thermal expansion, and the specific heat. We investigate also, the structural properties of SiGe when rock-salt phase appears.
A Definitive Pharmacophore Modelling Study on CDK2 ATP Pocket Binders: Tracing the Path of New Virtual High-Throughput Screenings
2020
Cyclin Dependent Kinases-2 (CDK2) are members of serine/threonine protein kinases family. They play an important role in the regulation events of the eukaryotic cell division cycle, especially during the G1 to S phase transition. Experimental evidence indicate that excessive expression of CDK2s should cause abnormal cell cycle regulation. Therefore, since a long time, CDK2s have been considered potential therapeutic targets for cancer therapy. In this work, onehundred and forty-nine complexes of inhibitors bound in the CDK2-ATP pocket were submitted to short MD simulations (10ns) and free energy calculation. Comparison with experimental data (K<sub>i</sub>, K<sub>d</su…
Comparing molecular dynamics-derived pharmacophore models with docking: A study on CDK-2 inhibitors
2020
Abstract We compared the performance of molecular dynamics (MD)-derived pharmacophore modeling approaches, Common Hit Approach (CHA), and the Molecular dYnamics SHAred PharmacophorE (MYSHAPE) approach, with semi-flexible constrained/unconstrained docking. The aim of this work is to enrich the hit-list of a virtual screening on CDK-2 known inhibitors as a case study. Cyclin-dependent kinases (CDKs) deregulation is associated with cancer growth. CDKs are an attractive target for anticancer agents. MD-derived pharmacophore models have been obtained with LigandScout 4.2.1. Docking analysis has been performed through Glide 7.6. The results highlighted the MYSHAPE approach has a better performanc…
Where Is the Most Hydrophobic Region? Benzopurpurine Self-Assembly at the Calcite–Water Interface
2017
Control of molecular self-assembly at solid–liquid interfaces is challenging due to the complex interplay between molecule–molecule, molecule–surface, molecule–solvent, surface–solvent, and solvent–solvent interactions. Here, we use in-situ dynamic atomic force microscopy to study the self-assembly of Benzopurpurine 4B into oblong islands with a highly ordered inner structure yet incommensurate with the underlying calcite (10.4) surface. Molecular dynamics and free energy calculations provide insights by showing that Benzopurpurine 4B molecules do not anchor to the surface directly but instead assemble on top of the second hydration layer. This seemingly peculiar behavior was then rationali…
Replica-exchange molecular dynamics simulation for supercooled liquids
2000
We investigate to what extend the replica-exchange Monte Carlo method is able to equilibrate a simple liquid in its supercooled state. We find that this method does indeed allow to generate accurately the canonical distribution function even at low temperatures and that its efficiency is about 10-100 times higher than the usual canonical molecular dynamics simulation.
Computer simulation studies of finite-size broadening of solid–liquid interfaces: from hard spheres to nickel
2009
Using Molecular Dynamics (MD) and Monte Carlo (MC) simulations interfacial properties of crystal-fluid interfaces are investigated for the hard sphere system and the one-component metallic system Ni (the latter modeled by a potential of the embedded atom type). Different local order parameters are considered to obtain order parameter profiles for systems where the crystal phase is in coexistence with the fluid phase, separated by interfaces with (100) orientation of the crystal. From these profiles, the mean-squared interfacial width w^2 is extracted as a function of system size. We rationalize the prediction of capillary wave theory that w^2 diverges logarithmically with the lateral size o…
New fitting scheme to obtain effective potential from Car-Parrinello molecular dynamics simulations: Application to silica
2008
A fitting scheme is proposed to obtain effective potentials from Car-Parrinello molecular dynamics (CPMD) simulations. It is used to parameterize a new pair potential for silica. MD simulations with this new potential are done to determine structural and dynamic properties and to compare these properties to those obtained from CPMD and a MD simulation using the so-called BKS potential. The new potential reproduces accurately the liquid structure generated by the CPMD trajectories, the experimental activation energies for the self-diffusion constants and the experimental density of amorphous silica. Also lattice parameters and elastic constants of alpha-quartz are well-reproduced, showing th…
Kinetic and thermodynamic insights into interaction of erlotinib with epidermal growth factor receptor: Surface plasmon resonance and molecular docki…
2020
Abstract Epidermal growth factor receptor (EGFR) plays an important role in cell proliferation at non-small cell lung cancer (NSCLC). Therefore, targeted therapy of cancer via this kind of receptor is highly interested. Small molecule drugs such as erlotinib and gefitinib inhibit EGFR tyrosine kinase and thus suppress cell proliferation. At this paper, erlotinib interaction with EGFR on the cell surface was studied via surface plasmon resonance (SPR) and molecular docking methods. Kinetic parameters indicated that erlotinib affinity toward EGFR was increased through increment of temperature. The thermodynamic analysis showed that van der Waals and hydrogen binding forces play a major role i…
Curvature increases permeability of the plasma membrane for ions, water and the anti-cancer drugs cisplatin and gemcitabine
2019
ABSTRACTIn this work the permeability of a model asymmetric plasma membrane, for ions, water and the anti-cancer drugs cisplatin and gemcitabine is studied by means of all-atom molecular dynamics simulations. It is shown that permeability of the membranes increases from one to three orders of magnitude upon membrane bending depending on the compound and the sign of curvature. Our results show that the membrane curvature is an important factor which should be considered during evaluation of drug translocation.TOC GRAPHICS
Quinoline-Based Molecules Targeting c-Met, EGF, and VEGF Receptors and the Proteins Involved in Related Carcinogenic Pathways
2020
The quinoline ring system has long been known as a versatile nucleus in the design and synthesis of biologically active compounds. Currently, more than one hundred quinoline compounds have been approved in therapy as antimicrobial, local anaesthetic, antipsychotic, and anticancer drugs. In drug discovery, indeed, over the last few years, an increase in the publication of papers and patents about quinoline derivatives possessing antiproliferative properties has been observed. This trend can be justified by the versatility and accessibility of the quinoline scaffold, from which new derivatives can be easily designed and synthesized. Within the numerous quinoline small molecules developed as a…