Electron–phonon interactions in atomic and molecular devices

Electron–phonon interactions are extremely important for understanding charge transport, inelastic processes, heating, and heat dissipation in nanoscale molecular and atomic devices. In molecular electronics Inelastic Electron Tunneling Spectroscopy (IETS) has recently emerged as one of the premier methods for characterizing molecular-scale junctions and devices. This method provides a distinct chemical fingerprint for identifying molecules within a junction, and has allowed for clear demonstrations of single molecule devices, the effects of electric field on molecular orbitals, the importance of molecular configuration on conductance, as well as information about the charge transport mechanism. In this review we will discuss the use of Point Contact (PC) and IET spectroscopies on molecular and atomic systems, discuss the basic principles involved in inelastic transport for these spectroscopic methods to function, and focus on the experimental techniques involved and the important conclusions drawn from the experiments performed to date.     

Amyloid β fibrils disruption by kolaviron: Molecular docking and extended molecular dynamics simulation studies

Garcinia kola (GK) produces notable effects against neurodegenerative conditions, including experimentally-induced Alzheimer’s disease (AD). These remarkable effects are basically attributable to kolaviron (KV), a bioflavonoid constituent of this seed. Specifically, it has been reported that in AD models, KV produces interesting neuroprotective effects, being able to diminish associated neurotoxicity, via modulation of antioxidative, inflammatory and other disease modifying processes. Intriguingly, the effect of KV on amyloid-beta (Aβ) aggregation and disruption of preformed Aβ fibrils have not been studied. In this study, we have described a thorough computational study on the mechanism of action of KV as an Aβ fibrils disruptor at molecular level. We used comprehensive in silico docking evaluations and extended molecular dynamics simulation to mimic KV/Aβ fibrils system. Results indicate that KV was able to move within the Aβ fibrils, binding with important residues and components in the Aβ peptide identified to be vital for stabilizing preformed fibrils. KV destabilized the assembled Aβ fibrils, indicating the ability KV as a potential anti-amyloidogenic agent. Furthermore, this work highlighted the possibility of identifying new multifunctional phytocompounds as potent AD drugs.     

Des3PI: a fragment-based approach to design cyclic peptides targeting protein–protein interactions

Journal of Computer-Aided Molecular Design - Protein–protein interactions (PPIs) play crucial roles in many cellular processes and their deregulation often leads to cellular dysfunctions. One...     

An in silico approach to design peptide mimetics based on docking and molecular dynamics simulation of EGFR–matuzumab complex

Epidermal growth factor receptor (EGFR) plays an essential role in anticancer therapy. Matuzumab is an antibody for the treatment of colorectal, lung and stomach cancer. Matuzumab binds efficiently to EGFR and blocks its phosphorylation. The recent clinical successes have established application of peptides for cancer treatment. The present contribution introduces an in silico approach to design peptides based on molecular dynamics simulation (MDs) of the matuzumab-EGFR complex in water environment. Moreover, principal component analysis has been used to select multiple conformations of the complex in MDs for designing the peptides. The paratope and epitope in each conformation of the complex were determined, and the alanine scanning was used to identify the hot spots of EGFR conformers. The conformations of the peptides were optimized using PEP-FOLD server and MDs. The selected conformations were analyzed in a docking study to realize the binding site of the EGFR. Finally, pharmokinetics properties of the peptides were calculated. The designed oligopeptides were EWRSYYYWH, YYYWHNEWN, YYYWHNEWS and HNHSRNYGS with a higher affinity to the EGFR relative to the previously reported peptides. The newly designed peptides were investigated for their in vivo toxicities on rats, and all of them were non-toxic.     

Poly(oxyethylene)–cation interactions in aqueous solution: a molecular dynamics study

We have performed molecular dynamics simulations of a poly(oxyethylene) (POE) chain with 15 ethylene oxide units in an aqueous solution in the presence of potassium cations for 1 ns. The effect of the potassium ions on the POE aqueous solution characteristics are examined for the energetics, the hydration, the chain conformation and dynamics, and the solvent structure in comparison to those in the absence of cations. The POE's helical conformation is considerably distorted by complex formations with K⁺, and a significant perturbation of the POE hydration by K⁺ is observed. The competition between the K⁺–water and the K⁺–POE associations is found to be heavily shifted toward the latter. Furthermore, the POE–water pair interaction energy drastically decreases upon addition of K⁺. The observations, along with the decreased chain flexibility, point to the salting-out of POE salt aqueous solutions.     

Binding of novel fullerene inhibitors to HIV-1 protease: insight through molecular dynamics and molecular mechanics Poisson–Boltzmann surface area calculations

The objectives of this study include the design of a series of novel fullerene-based inhibitors for HIV-1 protease (HIV-1 PR), by employing two strategies that can also be applied to the design of inhibitors for any other target. Additionally, the interactions which contribute to the observed exceptionally high binding free energies were analyzed. In particular, we investigated: (1) hydrogen bonding (H-bond) interactions between specific fullerene derivatives and the protease, (2) the regions of HIV-1 PR that play a significant role in binding, (3) protease changes upon binding and (4) various contributions to the binding free energy, in order to identify the most significant of them. This study has been performed by employing a docking technique, two 3D-QSAR models, molecular dynamics (MD) simulations and the molecular mechanics Poisson–Boltzmann surface area (MM–PBSA) method. Our computed binding free energies are in satisfactory agreement with the experimental results. The suitability of specific fullerene derivatives as drug candidates was further enhanced, after ADMET (absorption, distribution, metabolism, excretion and toxicity) properties have been estimated to be promising. The outcomes of this study revealed important protein–ligand interaction patterns that may lead towards the development of novel, potent HIV-1 PR inhibitors.     

Identification of good and bad fragments of tricyclic triazinone analogues as potential PKC-θ inhibitors through SMILES–based QSAR and molecular docking

Structural Chemistry - Based on the mechanism of action of PKC-θ, the inhibition of this enzyme is considered a potential target for the treatment of autoimmune diseases such as rheumatoid...     

Identification of novel PI3Kδ inhibitors by docking,ADMET prediction and molecular dynamics simulations

BackgroundPhosphoinositide-3-kinase Delta (PI3Kδ) plays a key role in B-cell signal transduction and inhibition of PI3Kδ is confirmed to have clinical benefit in certain types of activation of B-cell malignancies. Virtual screening techniques have been used to discover new molecules for developing novel PI3Kδ inhibitors with little side effects.MethodComputer aided drug design method were used to rapidly screen optimal PI3Kδ inhibitors from the Asinex database. Virtual screening based molecular docking was performed to find novel and potential lead compound targeting PI3Kδ, at first. Subsequently, drug likeness studies were carried out on the retrieved hits to evaluate and analyze their drug like properties such as absorption, distribution, metabolism, excretion, and toxicity (ADMET) for toxicity prediction. Three least toxic compounds were selected for the molecular dynamics (MD) simulations for 30 ns in order to validate its stability inside the active site of PI3Kδ receptor.ResultsBased on the present in silico analysis, two molecules have been identified which occupied the same binding pocket confirming the selection of active site. ASN 16296138 (Glide score: −12.175 kcal/mol, cdocker binding energy: −42.975 kcal/mol and ΔG_bind value: −90.457 kcal/mol) and BAS 00227397 (Glide score: −10.988 kcal/mol, cdocker binding energy: −39.3376 kcal/mol and ΔG_bind value: −81.953 kcal/mol) showed docking affinities comparatively much stronger than those of already reported known inhibitors against PI3Kδ. These two ligand’s behaviors also showed consistency during the simulation of protein-ligand complexes for 30000 ps respectively, which is indicative of its stability in the receptor pocket.ConclusionCompound ASN 16296138 and BAS 00227397 are potential candidates for experimental validation of biological activity against PI3Kδ in future drug discovery studies. This study smoothes the path for the development of novel leads with improved binding properties, high drug likeness, and low toxicity to humans for the treatment of cancer.     

Imidazole-containing farnesyltransferase inhibitors: 3D quantitative structure–activity relationships and molecular docking

One of the most promising anticancer and recent antimalarial targets is the heterodimeric zinc-containing protein farnesyltransferase (FT). In this work, we studied a highly diverse series of 192 Abbott-initiated imidazole-containing compounds and their FT inhibitory activities using 3D-QSAR and docking, in order to gain understanding of the interaction of these inhibitors with FT to aid development of a rational strategy for further lead optimization. We report several highly significant and predictive CoMFA and CoMSIA models. The best model, composed of CoMFA steric and electrostatic fields combined with CoMSIA hydrophobic and H-bond acceptor fields, had r ² = 0.878, q ² = 0.630, and r _pred² = 0.614. Docking studies on the statistical outliers revealed that some of them had a different binding mode in the FT active site based on steric bulk and available active site space, explaining why the predicted activities differed from the experimental activities. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Studying protein–protein affinity and immobilized ligand–protein affinity interactions using MS-based methods

This review discusses the most important current methods employing mass spectrometry (MS) analysis for the study of protein affinity interactions. The methods are discussed in depth with particular reference to MS-based approaches for analyzing protein–protein and protein–immobilized ligand interactions, analyzed either directly or indirectly. First, we introduce MS methods for the study of intact protein complexes in the gas phase. Next, pull-down methods for affinity-based analysis of protein–protein and protein–immobilized ligand interactions are discussed. Presently, this field of research is often called interactomics or interaction proteomics. A slightly different approach that will be discussed, chemical proteomics, allows one to analyze selectivity profiles of ligands for multiple drug targets and off-targets. Additionally, of particular interest is the use of surface plasmon resonance technologies coupled with MS for the study of protein interactions. The review addresses the principle of each of the methods with a focus on recent developments and the applicability to lead compound generation in drug discovery as well as the elucidation of protein interactions involved in cellular processes. The review focuses on the analysis of bioaffinity interactions of proteins with other proteins and with ligands, where the proteins are considered as the bioactives analyzed by MS.     

Molecular dynamics assessment of doxorubicin–carbon nanotubes molecular interactions for the design of drug delivery systems

Carbon nanotubes (CNTs) constitute an interesting material for nanomedicine applications because of their unique properties, especially their ability to penetrate membranes, to transport drugs specifically and to be easily functionalized. In this work, the energies of the intermolecular interactions of single-walled CNTs and the anticancer drug doxorubicin (DOX) were determined using the AMBER 12 molecular dynamics MM/PBSA and MM/GBSA methods with the aim of better understanding how the structural parameters of the nanotube can improve the interactions with the drug and to determine which structural parameters are more important for increasing the stability of the complexes formed between the CNTs and DOX. The armchair, zigzag, and chiral nanotubes were finite hydrogen-terminated open tubes, and the DOX was encapsulated inside the tube or adsorbed on the nanotube surface. Pentagon/heptagon bumpy defects and polyethylene glycol (PEG) nanotube functionalization were also studied. The best interaction occurred when the drug was located inside the cavity of the nanotube. Armchair and zigzag nanotubes doped with nitrogen, favored interaction with the drug, whereas chiral nanotubes exhibited better drug interactions when having bumpy defects. The π-π stacking and N-H…π electrostatic interactions were important components of the attractive drug-nanotube forces, enabling significant flattening of the nanotube to favor a dual strong interaction with the encapsulated drug, with DOX–CNT equilibrium distances of 3.1–3.9 Å. These results can contribute to the modeling of new drug-nanotube delivery systems.

     

Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations

Aggregation of amyloid-β (Aβ) peptides correlates with the pathology of Alzheimer's disease. However, the inter-molecular interactions between Aβ protofibril remain elusive. Herein, molecular mechanics Poisson-Boltzmann surface area analysis based on all-atom molecular dynamics simulations was performed to study the inter-molecular interactions in Aβ(17-42) protofibril. It is found that the nonpolar interactions are the important forces to stabilize the Aβ(17-42) protofibril, while electrostatic interactions play a minor role. Through free energy decomposition, 18 residues of the Aβ(17-42) are identified to provide interaction energy lower than -2.5 kcal/mol. The nonpolar interactions are mainly provided by the main chain of the peptide and the side chains of nine hydrophobic residues (Leu17, Phe19, Phe20, Leu32, Leu34, Met35, Val36, Val40, and Ile41). However, the electrostatic interactions are mainly supplied by the main chains of six hydrophobic residues (Phe19, Phe20, Val24, Met35, Val36, and Val40) and the side chains of the charged residues (Glu22, Asp23, and Lys28). In the electrostatic interactions, the overwhelming majority of hydrogen bonds involve the main chains of Aβ as well as the guanidinium group of the charged side chain of Lys28. The work has thus elucidated the molecular mechanism of the inter-molecular interactions between Aβ monomers in Aβ(17-42) protofibril, and the findings are considered critical for exploring effective agents for the inhibition of Aβ aggregation.     

New insights into the bioactivity of SiO2–CaO and SiO2–CaO–P2O5 sol–gel glasses by molecular dynamics simulations

The structures of binary xCaO · (100 ? x)SiO₂ glasses with x = 10, 20 and 30 mol-% and ternary (20 ? x)CaO · xP₂O₅ · 80SiO₂ glasses with x = 3, 10, 15, 17 and 20 mol-% have been studied by means of classical molecular dynamics simulations using both the melt-quenched and the sol–gel protocols. The structural picture derived correlates the bioactive behaviour to the combined effects of the connectivity of the extended silicate network and to the tendency to form (or not to form) non-homogeneous domains. In this context, a mathematical relationship that relates the Ca/P ratio in the Ca phosphate micro-segregation zones to the P₂O₅ content in ternary glasses has been developed and this has been used to fine-tuning the optimum amount of P in a glass for its highest in vitro bioactivity. The composition with optimal Ca/P ratio, 80Si–14.8Ca–5.2P, has been synthesized and the results of bioactivity tests have confirmed the prediction.     

Modeling the molecular dynamics of cytochrome C in aqueous and water–methanol environment

One-microsecond molecular dynamics of horse heart cytochrome C was modeled in aqueous and water–methanol environment. It was shown that the coordination bond between Met-80 sulfur and heme iron is broken in water– methanol solution.     

Investigating the imidazolium–anion interaction through the anion-templated construction of interpenetrated and interlocked assemblies

The interaction between imidazolium cations and coordinating anions is investigated through the anion‐templated assembly of interpenetrated and interlocked structures. The orientation of the imidazolium motif with respect to anion binding, and hence the hydrogen bond donor arrangement, was varied in acyclic receptors, interpenetrated assemblies, and the first mono‐imidazolium interlocked systems. Their anion recognition properties and co‐conformations were studied by solution‐phase ¹H NMR investigations, solid‐state structures, molecular dynamics simulations, and density functional theory calculations. Our findings suggest that the imidazolium‐anion binding interaction is dominated by electrostatics with hydrogen‐bonding contributions having weak orientational dependence.     

The study of cell wall structure and cellulose–cellulase interactions through fluorescence microscopy

The efficient decomposition of biomass into carbohydrates for the sustainable generation of biofuels has become the focus of much research. Yet, limited understanding exists on how the enzymes that catalyze the biochemical conversion of biomass, such as cellulases, interact with cellulose microfibrils and how cellulose structure is changed by cellulolytic enzymes. This has spurred the application of high-resolution imaging techniques, such as atomic force microscopy or fluorescence microscopy, to visualize the biomolecular interactions and structural changes that occur at the micro/nanoscale. In particular, fluorescence microscopy offers advantages such as high sensitivity and the ability to monitor species under biologically relevant conditions. Furthermore, the introduction of techniques, such as single molecule or super-resolution fluorescence microscopy, has allowed imaging biomolecules and macromolecular structures with near molecular resolution. These advantages make fluorescence microscopy ideally suited for the study of cell wall structure and cellulose–cellulase interactions. The application of fluorescence microscopy has already yielded key insights into the arrangement of structural polysaccharides in the plant cell wall, the reversibility and binding kinetics of cellulases, their molecular motion on crystalline cellulose, and the structural changes that occur as cellulose is depolymerized by cellulases. Yet, the application of fluorescence to study cellulose–cellulase interactions remains limited. This review aims at (1) providing an overview of fluorescence microscopy techniques suitable for the study of cellulose–cellulase interactions; (2) the applications of these techniques to date and the key insights obtained; and (3) the opportunities for future studies of the interaction of cell wall degrading enzymes with cellulosic materials.     

Layer-by-layer construction of protein architectures through avidin–biotin and lectin–sugar interactions for biosensor applications

In this review, the preparation and properties of protein architectures constructed by layer-by-layer (LbL) deposition through avidin–biotin and concanavalin A (Con A)–sugar interactions are discussed in relation to their use for optical and electrochemical biosensors. LbL films can be constructed through the alternate deposition of avidin and biotin-labeled enzymes on the surfaces of optical probes and electrodes. The enzymes retain their catalytic activity, resulting in the formation of optical and electrochemical biosensors. Alternatively, Con A can be used to construct enzyme-containing LbL films and microcapsules using sugar-labeled enzymes. Some enzymes such as glucose oxidase and horseradish peroxidase can be used for this purpose without labeling with sugar, because these enzymes contain intrinsic hydrocarbon chains on their molecular surfaces. The Con A/enzyme LbL architectures were successfully used to develop biosensors sensitive to specific substrates of the enzyme. In addition, Con A-based films can be used for the optical and electrochemical detection of sugars.