scholarly journals Nanomaterials Interaction with Cell Membranes: Computer Simulation Studies

Author(s):  
Alexey A. Tsukanov ◽  
Olga Vasiljeva

AbstractThis chapter provides a brief review of computer simulation studies on the interaction of nanomaterialswith biomembranes. The interest in this area is governed by the variety of possible biomedical applications of nanoparticles and nanomaterials as well as by the importance of understanding their possible cytotoxicity. Molecular dynamics is a flexible and versatile computer simulation tool, which allows us to research the molecular level mechanisms of nanomaterials interaction with cell or bacterial membrane, predicting in silico their behavior and estimating physicochemical properties. In particular, based on the molecular dynamics simulations, a bio-action mechanism of two-dimensional aluminum hydroxide nanostructures, termed aloohene, was discovered by the research team led by Professor S. G. Psakhie, accounting for its anticancer and antimicrobial properties. Here we review three groups of nanomaterials (NMs) based on their structure: nanoparticles (globular, non-elongated), (quasi)one-dimensional NMs (nanotube, nanofiber, nanorod) and two-dimensional NMs (nanosheet, nanolayer, nanocoated substrate). Analysis of the available in silico studies, thus can enable us a better understanding of how the geometry and surface properties of NMs govern the mechanisms of their interaction with cell or bacterial membranes.

2002 ◽  
Vol 731 ◽  
Author(s):  
Romulo Ochoa ◽  
Michael Arief ◽  
Joseph H. Simmons

AbstractWe conduct molecular dynamics computer simulations of fracture in silica glass using the van Beest, Kramer, and van Santen model. Stress is applied by uniaxial strain at different pulling rates. Comparisons with previous fracture simulations of silica that used the Soules force function are presented. We find that in both models stress is relieved by rotation of the (SiO4)-2 tetrahedrons, increasing Si-O-Si bonding angles, and only small changes in the tetrahedron dimensions and O-Si-O angles.


2021 ◽  
Vol 22 (11) ◽  
pp. 6028
Author(s):  
Simone Mulliri ◽  
Aatto Laaksonen ◽  
Pietro Spanu ◽  
Riccardo Farris ◽  
Matteo Farci ◽  
...  

Herein we describe a combined experimental and in silico study of the interaction of a series of pyrazolo[1,2-a]benzo[1,2,3,4]tetrazin-3-one derivatives (PBTs) with parallel G-quadruplex (GQ) DNA aimed at correlating their previously reported anticancer activities and the stabilizing effects observed by us on c-myc oncogene promoter GQ structure. Circular dichroism (CD) melting experiments were performed to characterize the effect of the studied PBTs on the GQ thermal stability. CD measurements indicate that two out of the eight compounds under investigation induced a slight stabilizing effect (2–4 °C) on GQ depending on the nature and position of the substituents. Molecular docking results allowed us to verify the modes of interaction of the ligands with the GQ and estimate the binding affinities. The highest binding affinity was observed for ligands with the experimental melting temperatures (Tms). However, both stabilizing and destabilizing ligands showed similar scores, whilst Molecular Dynamics (MD) simulations, performed across a wide range of temperatures on the GQ in water solution, either unliganded or complexed with two model PBT ligands with the opposite effect on the Tms, consistently confirmed their stabilizing or destabilizing ability ascertained by CD. Clues about a relation between the reported anticancer activity of some PBTs and their ability to stabilize the GQ structure of c-myc emerged from our study. Furthermore, Molecular Dynamics simulations at high temperatures are herein proposed for the first time as a means to verify the stabilizing or destabilizing effect of ligands on the GQ, also disclosing predictive potential in GQ-targeting drug discovery.


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