Multiscale Modeling for Host-Guest Chemistry of Dendrimers in Solution

Kim, Seung Ha; Lamm, Monica H.

doi:10.3390/polym4010463

Cited by 14 publications

(15 citation statements)

References 95 publications

(159 reference statements)

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“…When the experimental approaches such as small angle neutron scattering (SANS), 49 X-ray, 50 nuclear magnetic resonance (NMR), [51][52][53] and fluorescence resonance energy transfer (FRET) 54 are used to understand the structure and the effective interaction of dendrimers with other molecules, computer simulation techniques have also been proved to be very effective in elucidating these properties of dendrimers or dendrimer-bioagent/biomolecule complexes. [55][56][57][58] Due to the rapid development of the computational algorithms and available computational resources, computer simulations can achieve various length and time scales on the basis of the potential function (force field) and coarse-grained (CG) degree of models. The scope of this review is limited to the theoretical and computational studies of dendrimers and their interactions with drugs, linear PEs, lipid membranes, and proteins.…”

Section: Introductionmentioning

confidence: 99%

Theoretical and computational studies of dendrimers as delivery vectors

2013

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It is a great challenge for nanomedicine to develop novel dendrimers with maximum therapeutic potential and minimum side-effects for drug and gene delivery. As delivery vectors, dendrimers must overcome lots of barriers before delivering the bio-agents to the target in the cell. Extensive experimental investigations have been carried out to elucidate the physical and chemical properties of dendrimers and explore their behaviors when interacting with biomolecules, such as gene materials, proteins, and lipid membranes. As a supplement of the experimental techniques, it has been proved that computer simulations could facilitate the progress in understanding the delivery process of bioactive molecules. The structures of dendrimers in dilute solutions have been intensively investigated by monomer-resolved simulations, coarse-grained simulations, and atom-resolved simulations. Atomistic simulations have manifested that the hydrophobic interactions, hydrogen-bond interactions, and electrostatic attraction play critical roles in the formation of dendrimer-drug complexes. Multiscale simulations and statistical field theories have uncovered some physical mechanisms involved in the dendrimer-based gene delivery systems. This review will focus on the current status and perspective of theoretical and computational contributions in this field in recent years. (275 references).

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Section: Introductionmentioning

confidence: 99%

Theoretical and computational studies of dendrimers as delivery vectors

2013

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“…TA binding studiescomputational approach Computational methods have been widely used for complementing and/or conrming experimental data on the host-guest interactions of dendrimers with different target molecules. A comprehensive review in this eld has been recently published by Lamm et al 42 In order to gain a deeper understanding of the interactions between dendrimers and TA molecules and the mechanisms underlying the entrapment we carried out molecular dynamics simulations of TA-dendrimer systems. Several scripts were implemented for the analysis of the data obtained from the molecular simulations.…”

Section: Ta Binding Studies Using Wine Samplesmentioning

confidence: 99%

pH-dependent nano-capturing of tartaric acid using dendrimers

et al. 2014

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The ability of dendrimers to bind to various target molecules through non-covalent interactions was used to capture water soluble organic reagents, such as tartaric acid (TA), from different matrices, i.e. aqueous solutions and wine samples. The influence of the pH, dendrimer type, generation and feeding concentration on the host-guest complexation of TA was investigated. The maximum binding capacity of TA in aqueous solutions was achieved by amine end-capped dendrimers at pH 5. At extreme pH values of 2 and 11, the binding of TA dropped strikingly, demonstrating the pH-dependency underlying the host-guest interactions. The linear correlation between the maximum binding capacity of TA at pH 5 and the number of primary amine groups on the surface of PAMAM and PPI dendrimers strongly indicated that host-guest complex formation between TA and dendrimers is largely dependent on electrostatic interactions. Molecular simulations confirmed the predominant electrostatic nature of the interactions between TA and the amine end-capped dendrimers and also provided important information on the spatial distribution of TA within the PAMAM G5 dendrimer. All these results designate dendrimers as potential nano-capturing systems for the removal/recovery of TA from complex matrices such as wine, industrial waste or fruit juices.

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“…Molecular modelling has been increasingly used to rationally design dendrimers for biomedical applications with special focus on studying their structure and dynamic response to environment stimulus (e.g. pH change) as well as interactions of dendrimers with other molecules [23,[25][26][27][28]. Modelling studies of dendrimers have been conducted using different force fields developed for proteins and small molecules, including CHARMM [29], AMBER [30], CVFF [31], Dreiding [32], GROMOS [33], COMPAS [34] and OPLS [35].…”

Section: Introductionmentioning

confidence: 99%

Practical computational toolkits for dendrimers and dendrons structure design

Martinho

Silva

Florindo

et al. 2017

J Comput Aided Mol Des

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Dendrimers and dendrons offer an excellent platform for developing novel drug delivery systems and medicines. The rational design and further development of these repetitively branched systems are restricted by difficulties in scalable synthesis and structural determination, which can be overcome by judicious use of molecular modelling and molecular simulations. A major difficulty to utilise in silico studies to design dendrimers lies in the laborious generation of their structures. Current modelling tools utilise automated assembly of simpler dendrimers or the inefficient manual assembly of monomer precursors to generate more complicated dendrimer structures. Herein we describe two novel graphical user interface toolkits written in Python that provide an improved degree of automation for rapid assembly of dendrimers and generation of their 2D and 3D structures. Our first toolkit uses the RDkit library, SMILES nomenclature of monomers and SMARTS reaction nomenclature to generate SMILES and mol files of dendrimers without 3D coordinates. These files are used for simple graphical representations and storing their structures in databases. The second toolkit assembles complex topology dendrimers from monomers to construct 3D dendrimer structures to be used as starting points for simulation using existing and widely available software and force fields. Both tools were validated for ease-of-use to prototype dendrimer structure and the second toolkit was especially relevant for dendrimers of high complexity and size.

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Multiscale Modeling for Host-Guest Chemistry of Dendrimers in Solution

Cited by 14 publications

References 95 publications

Theoretical and computational studies of dendrimers as delivery vectors

Theoretical and computational studies of dendrimers as delivery vectors

pH-dependent nano-capturing of tartaric acid using dendrimers

Practical computational toolkits for dendrimers and dendrons structure design

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