Journal ArticleDOI
Oil-in-water nanoemulsions comprising Berberine in olive oil: biological activities, binding mechanisms to human serum albumin or holo-transferrin and QMMD simulations.
TLDR
The results of the simulation demonstrated that the Nano-Ber molecules were stabilized on the surface of final aggregates through both hydrophilic and hydrophobic interactions.Abstract:
Berberine is widely used in traditional Iranian medicine to treat diabetes and inflammatory conditions. This study was aimed at developing a method for the preparation of Berberine nanoparticles (N...read more
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Multi-spectroscopic investigation, molecular docking and molecular dynamic simulation of competitive interactions between flavonoids (quercetin and rutin) and sorafenib for binding to human serum albumin.
TL;DR: Serum albumin, the main protein in the plasma acts in the disposition of many drugs and therefore, is a model protein for investigating drug/ligand binding and alteration in the spectrophotometric and molecular docking properties of drug /ligand.
Journal ArticleDOI
Binding and drug displacement study of colchicine and bovine serum albumin in presence of azithromycin using multispectroscopic techniques and molecular dynamic simulation.
Tanveer A. Wani,Ahmed H. Bakheit,Abdulrahman A. Al-Majed,Nojood Altwaijry,Anwar Baquaysh,Ashwaq Aljuraisy,Seema Zargar +6 more
TL;DR: In this paper, the displacement interaction between colchicine and azithromycin on binding to BSA was evaluated using spectroscopic techniques, molecular docking and molecular dynamic simulation studies.
Journal ArticleDOI
Binding of colchicine and ascorbic acid (vitamin C) to bovine serum albumin: An in-vitro interaction study using multispectroscopic, molecular docking and molecular dynamics simulation study
Tanveer A. Wani,Nawaf A. Alsaif,Mohammed M. Alanazi,Ahmed H. Bakheit,Azmat Ali Khan,Seema Zargar +5 more
TL;DR: In this paper, the effect of colchicine on the binding of ascorbic acid (vitamin C) commonly prescribed in viral infections to bovine serum albumin (BSA) was evaluated using fluorescence spectroscopy, absorption spectra, molecular docking, and molecular dynamic simulation.
Journal ArticleDOI
Machine learning-integrated omics for the risk and safety assessment of nanomaterials
TL;DR: In this paper, the authors discuss the potential of combining integrative omics with machine learning in profiling nanomaterial safety and risk assessment and provide guidance for regulatory authorities as well, and they discuss the use of hyphenation of machine learning with biology to provide exclusive insights into the perturbations of delicate biological functions after integration with nano-materials.
Journal ArticleDOI
Targeting virus-host interaction by novel pyrimidine derivative: an in silico approach towards discovery of potential drug against COVID-19.
Jitendra Subhash Rane,Preeti Pandey,Aroni Chatterjee,Rajni Khan,Abhijeet Kumar,Amresh Prakash,Shashikant Ray +6 more
TL;DR: Pyrimidine derivative AP-NP may be explored as an effective inhibitor for hACE2-S complex and in vitro and in vivo studies will strengthen the use of these inhibitors as suitable drug candidates against SARS-COV-2.
References
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Molecular dynamics with coupling to an external bath.
TL;DR: In this paper, a method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling, which can be easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints.
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Use of a Free Radical Method to Evaluate Antioxidant Activity
TL;DR: The antiradical properties of various antioxidants were determined using the free radical 2,2-Diphenyl-1-picrylhydrazyl (DPPH*) in its radical form as discussed by the authors.
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A smooth particle mesh Ewald method
TL;DR: It is demonstrated that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N), which is comparable to that of a simple truncation method of 10 A or less.
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Polymorphic transitions in single crystals: A new molecular dynamics method
Michele Parrinello,A. Rahman +1 more
TL;DR: In this paper, a new Lagrangian formulation is introduced to make molecular dynamics (MD) calculations on systems under the most general externally applied, conditions of stress, which is well suited to the study of structural transformations in solids under external stress and at finite temperature.
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LINCS : A linear constraint solver for molecular simulations
TL;DR: Although the derivation of the algorithm is presented in terms of matrices, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large molecules.