Hydration of β-cyclodextrin: A molecular dynamics simulation study

We study by molecular dynamics simulations the hydration of -cyclodextrin. Our simulations show that within these barrel-shaped molecules hydrophobicity dominates, while at the top and bottom sides of the barrel interactions with water are mostly hydrophilic in nature. These results agree with crystallographic data at 120 K and, in particular, with the spontaneous hydration process of a cyclodextrin crystal in wet atmosphere. The predicted structure of the hydration shells is discussed and compared with previous molecular mechanics calculations which report an overall hydrophobic behavior. Moreover, the temperature dependence of the hydration process is discussed.     

Binding of biguanides to β-lactoglobulin: molecular-docking and molecular dynamics simulation studies

Biguanides are a class of drugs derived from biguanide and they are the most widely used drugs for diabetes mellitus or pre-diabetes treatment. An investigation of their interaction and a transport protein such as β-lactoglobulin (BLG) at atomic level could be a valuable factor in controlling their transport to biological sites. Molecular-docking and molecular dynamics simulation methods were used to study the interaction of metformin, phenformin and buformin as biguanides and BLG as transport protein. The molecular-docking results revealed that these biguanides bind to BLG and that the BLG affinity for binding the biguanides decreases in the following order: phenformin — buformin — metformin. The docking results also show the hydrophobic interactions to have a significant role in the BLG-biguanides complex stability. Analysis of molecular dynamic simulation trajectories shows that the root mean square deviation of various systems attained equilibrium and fluctuated around the mean value at various times. The time evolution of the radius of gyration and the total solvent-accessible surface of the protein showed that BLG and BLG-biguanide complexes became stable at approximately 2500 ps and that there was not any conformational change in the BLG-biguanide complexes. In addition, the profiles of atomic fluctuations show the rigidity of the ligand-binding site during the simulation.     

Influence of solvent polarity on the separation of leucine enantiomers by β-cyclodextrin: a molecular mechanics and dynamics simulation

The interaction between leucine and β-cyclodextrin with different solvents was studied by molecular mechanics and dynamics simulations. In order to analyse the influence of the solvent polarity on the inclusion complex formation and separation process of leucine enantiomers by β-cyclodextrin, the organic modifiers were characterised by the same value of dielectric constant in the electrostatic contribution to the interaction energy, and a different molecular configuration of amino acids (neutral or zwitterion). The complexes formed in polar solvents were more stable than those in non-polar solvents with the same dielectric constant, because the electrostatic contribution is negative for the former and positive for the latter. The optimized structures obtained for leucine enantiomers and β-cyclodextrin in vacuo are non-inclusion complexes. The solvent polarity contributes to increasing the probability of the presence in an inner position for the guest, whereas the results for non-polar configurations were smaller and distributed in larger areas. The regions where the enantiomers spend more time in the simulation correspond to locations with greater chiral discrimination. d-Leu was the first eluted enantiomer in every case, except for a polar solvent with $\epsilon =26$.     

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.     

Molecular dynamics study of the influence of solvents on the chiral discrimination of alanine enantiomers by β-cyclodextrin

The influence of solvents on the separation of alanine enantiomers using β-cyclodextrin as a chiral selector was studied by means of a molecular dynamics simulation at a constant temperature. The potential energy of the interaction is modelled by the AMBER force field, where different polar and non-polar solvents are represented by the dielectric constant ? and two configurations for the amino acid derived from its electric charge distribution: the AMBER data base or its zwitterion state. The l enantiomer has more positions inside the cavity of a β-cyclodextrin where it is more stable than the d-enantiomer in vacuo and solution, except for solvents such as hydrocarbons in which most positions of the d-alanine inside and outside the cavity are more stable. In all cases, the greatest differences are located near the cavity walls. Molecular dynamics simulations show that Ala is able to form inclusion complexes with β-cyclodextrin in vacuo and in solvents such as hydrocarbons, benzene, acetone, ethanol or water. The chiral discrimination of Ala by β-cyclodextrin is mainly due to the adaptation of the guest to the host in the presence of non-polar agents, whereas the nonbonded interaction is the driving force for zwitterions. The elution order depends on the type of organic modifiers while a reversal of the enantiomeric elution order can be observed in solvents with higher dielectric constants.     

Systematic profiling of taxol and its analogues (taxalogues) binding to β-tubulin and molecular analysis of their effects on microtubule stabilization

Microtubules are highly dynamic polymers of α/β-tubulin that represent major components of the cytoskeleton and have been established as an attractive druggable target of tumors. Taxol, also known as Paclitaxel, is a microtubule-stabilizing agent that binds stoichiometrically to a specific site in β-tubulin, where is out of but nearby the interacting interface of α/β-tubulin complex, to improve the complex stability through an allosterically regulatory mechanism. In this study, the systematic binding profile of taxol and its 22 structurally diverse, medicinally relevant analogues (termed as taxalogues) to the specific site of β-tubulin as well as their effects on the α/β-tubulin complex stability were created and investigated by using structural modeling, dynamics simulation, and energetics analysis. Two helices H1 and H2 of β-tubulin were identified as key hotspots at the α/β-tubulin interface to mediate the binding event of β-tubulin to α-tubulin. Taxalogue binding can trigger a conformational displacement in the H1 and H2 to elicit the stabilization (or destabilization) of α/β-tubulin. However, strong taxalogue binding potency to β-tubulin does not mean effective α/β-tubulin stabilization; there is only an indirect, moderate correlation between them. Cell viability assay revealed that the taxalogue-induced α/β-tubulin stabilization, but not the taxalogue binding, directly influences the antitumor activity of taxalogues. The activity increases in the order: SB-T-1214 < docetaxel < taxol < larotaxel < cisplatin < cabazitaxel.     

Stabilizing effect of cholesterol on the state of β2-adrenergic receptor with a broken ionic lock: a molecular dynamics study

A molecular dynamics simulation of the β₂-adrenergic receptor (β₂AR) embedded in a hydrated lipid bilayer showed that the state with a broken ionic lock (salt bridge) between the arginine residue Arg131 and the glutamic acid residue Glu268 is stabilized in the presence of cholesterol molecules. This should be considered as a transient state to the active state of the receptor.     

Forcefield evaluation and accelerated molecular dynamics simulation of Zn(II) binding to N-terminus of amyloid-β

We report conventional and accelerated molecular dynamics simulation of Zn(II) bound to the N-terminus of amyloid-β. By comparison against NMR data for the experimentally determined binding mode, we find that certain combinations of forcefield and solvent model perform acceptably in describing the size, shape and secondary structure, and that there is no appreciable difference between implicit and explicit solvent models. We therefore used the combination of ff14SB forcefield and GBSA solvent model to compare the result of different binding modes of Zn(II) to the same peptide, using accelerated MD to enhance sampling and comparing the free peptide simulated in the same way. We show that Zn(II) imparts significant rigidity to the peptide, disrupts the secondary structure and pattern of salt bridges seen in the free peptide, and induces closer contact between residues. Free energy surfaces in 1 or 2 dimensions further highlight the effect of metal coordination on peptide’s spatial extent. We also provide evidence that accelerated MD provides improved sampling over conventional MD by visiting as many or more configurations in much shorter simulation times.     

Impact of molecular flexibility on binding strength and self-sorting of chiral π-surfaces

In this work, we have explored for the first time the influence of conformational flexibility of π-core on chiral self-sorting properties of perylene bisimides (PBIs) that are currently one of the most prominent classes of functional dyes. For this purpose, two series of chiral macrocyclic PBIs 3a-c and 4a-c comprising oligoethylene glycol bridges of different lengths at the 1,7 bay positions were synthesized and their atropo-enantiomers (P and M enantiomers) were resolved. Single crystal analysis of atropo-enantiomerically pure (P)-3a not only confirmed the structural integrity of the ethylene glycol bridged macrocycle but also illustrated the formation of π-stacked dimers with left-handed supramolecular helicity. Our detailed studies with the series of highly soluble chiral PBIs 4a-c by 1- and 2-D (1)H NMR techniques, and temperature- and concentration-dependent UV/vis absorption and circular dichroism (CD) spectroscopy revealed that in π-π-stacking dimerization of these PBIs chiral self-recognition (i.e., PP and MM homodimer formation) prevails over self-discrimination (i.e., PM heterodimer formation). Our studies clearly showed that with increasing conformational flexibility of PBI cores imparted by longer bridging units, the binding strength for the dimerization process increases, however, the efficiency for chiral self-recognition decreases. These results are rationalized in terms of an induced-fit mechanism facilitating more planarized π-scaffolds of PBIs containing longer bridging units upon π-π-stacking.     

Identify promising IKK-β inhibitors: A docking-based 3D-QSAR study combining molecular design and molecular dynamics simulation

Inhibitor of nuclear factor kappa B kinase subunit beta (IKK-β), a specific regulator of nuclear factor-κB (NF-κB), is considered a valid target to design novel drugs to treat rheumatoid arthritis, glomerulonephritis and various cancers. In this study, in order to design and then identify promising compounds targeting IKK-β, a series of reported IKK-β inhibitors were used to develop 3D-QSAR models. Docking-based and minimization-based poses were generated for model construction. CoMSIA model #8 based on docking poses was selected due to its satisfactory internal and external validation results and the sufficient information delivery capability. After a contour map analysis, 41 new designs were depicted based on a graphical design scheme and 25 of them were assessed as eligible for screening. Compound 21MX007 has aroused our attention for its both competitive QSAR-prediction and docking-scoring result. Detailed docking interactions of 21MX007-protein complex were investigated via a deep analysis of docking results and a comparative molecular dynamics simulation. Strong interactions and an extra hydrogen bond which echoes the H-bond requirements of substituent acquired from the design scheme were observed. From MD analysis, 21MX007-protein system was tested. The system was proved to have good stability in terms of a downward trend of RMSD and Rg values and a continuous and stable H-bond interaction and a lower average binding free energy. Thus, compound 21MX007 was successfully identified as a promising IKK-β inhibitor.     

Molecular dynamics simulation study on zwitterionic structure to maintain the normal conformations of Glutathione

Molecular dynamics simulations were applied to normal conformational Glutathione (GSH) and GSH over zwitterionic and hydrophobic surfaces respectively. Conformational analysis of GSH during the simulation time on RMSD, conformational flexibility and dihedral distribution were performed. The re- sults showed that zwitterionic structure maintains the normal conformations of GSH to a better extent, which should be a first good proof of the hypothesis of "maintain of normal structure".     

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.     

Effect of pH and α-, β- and γ-cyclodextrin on the spectral properties of etoricoxib: spectroscopic and molecular dynamics study

The spectral properties of etoricoxib (ETR) at pH 2.0, 6.0 and 10.0 in the presence of cyclodextrins (CDs) were investigated. The absorption spectrum of ETR in acidic medium exhibited two bands centered at 236 and 273 nm, while in basic medium it exhibited two bands centered at 236 and 285 nm. No change in the spectrum was observed in the presence of CDs. The fluorescence emission spectra of ETR in acidic and basic media exhibited one band at 380 nm and another one at 484 nm. The emission band at 484 nm was enhanced when ETR was complexed with β-CD and γ-CD at pH 2.0, 6.0 and 10.0, while the band at 380 nm was enhanced selectively when ETR was complexed with α-CD at pH 2.0. Molecular dynamics simulations computations revealed that at pH 2.0, the sulfonyl moiety of H₂ETR²⁺ is preferentially included within the α-CD cavity, which is believed to cause the enhancement of the band at 380 nm. Moreover, at pH 6.0 and 10.0, the enhancement of the band at 484 nm was related to the inclusion of the chloropyridinyl and methylpyridinyl groups of the bipyridine moiety of HETR⁺ and ETR within β-CD and γ-CD cavities. Benesi–Hildebrand analysis showed that the ETR/β-CD complex adopts a 1:1 stoichiometry with association constant of K ₁₁?=?64.8 at pH 2.0, K ₁₁?=?105.4 at pH 6.0 and K ₁₁?=?520.5 at pH 10.0.     

Structure change of β-hairpin induced by turn optimization: an enhanced sampling molecular dynamics simulation study

Our previous study showed that for the tested polypeptides which have similar β-hairpin structures but different sequences, their folding free energy pathways are dominantly determined by the turn conformational propensity. In this study, we study how the turn conformational propensity affects the structure of hairpins. The folding of two mutants of GB1p peptide (GB1m2 and GB1m3), which have the optimized turn sequence ((6)DDATK(11)T?→?(6)NPATG(11)K) with native structures unsolved, were simulated using integrated tempering sampling molecular dynamics simulations and the predicted stable structures were compared to wild-type GB1p. It was observed that the turn optimization of GB1p generates a more favored 5-residue type I(') turn in addition to the 6-residue type I turn in wild-type GB1p. As a result two distinctly different hairpin structures are formed corresponding to the "misfolded" (M) and the "folded" (F) states. M state is a one-residue-shifted asymmetric β-hairpin structure whereas F state has the similar symmetric hairpin structure as wild-type GB1p. The formation of the favored type I(') turn has a small free energy barrier and leads to the shifted β-hairpin structure, following the modified "zipping" model. The presence of disfavored type I turn structure makes the folding of a β-hairpin consistent with the "hydrophobic-core-centric" model. On the other hand, the folding simulations on other two GB1p mutants (GB1r1 and GBr2), which have the position of the hydrophobic core cluster further away from the turn compared to wild-type GB1p, showed that moving the hydrophobic core cluster away from the turn region destabilizes but does not change the hairpin structure. Therefore, the present study showed that the turn conformational propensity is a key factor in affecting not only the folding pathways but also the stable structure of β-hairpins, and the turn conformational change induced by the turn optimization leads to significant changes of β-hairpin structure.     

A molecular simulation study of the distribution of cation in zeolites

NVT Monte Carlo simulations are first used to describe the distribution of Na cations in Faujasite for several Si/Al ratios. These calculations were performed by combining two different sets of potential parameters combined with both T-atoms and explicit Si,Al models. Grand Canonical Monte Carlo simulations are then employed to investigate the influence of water adsorption on the distribution of cations in the case of a Faujasite sample with 56 cations (NaY56). These simulations data are compared to available experimental data and the influence of the choice of the forcefield for describing the cation/zeolite interaction on these results is discussed.     

Exploring the binding mechanism of thioflavin-T to the β-amyloid peptide by blind docking method

Using blind dock method,we find that thioflavin-T(ThT) can bind to both monomers and fibrils of the full-length β-amyloid peptide(Aβ1-42) and has a higher binding affinity to the fibrils.It is shown that the hydrophobic interaction between the ligand(ThT) and substrate(Aβ1-42) are stronger than hydrogen bonds.Furthermore,ThT tends to be located near the C-terminus of Aβ monomer through hydrophobic and electrostatic interactions,while it tends to contact the residues Met35 and Gly27 of the fibril surface mainly through hydrophobic interaction.Finally,according to the docking results and ThT fluorescence assay,a kinetic equation is proposed to deduce the aggregation rate coefficient of Aβ1-42.     

A single-molecule study of the inhibition effect of Naringenin on transforming growth factor-β ligand-receptor binding

With single-molecule fluorescence imaging and single-molecule force measurement, we have found that the natural compound Naringenin exerts an inhibition effect on TGF-β ligand-receptor interaction, the initial step of TGF-β signaling.     

Effect of concentration on surfactant micelle shapes —A molecular dynamics study

Many aspects of the behavior of surfactants have not been well understood due to the coupling of many different mechanisms. Computer simulation is, therefore, attractive in the sense that it can explore the effect of different mechanisms separately. In this paper, the shapes, structures and sizes of sodium dodecylbenzenesulfonate (SDBS) micelles under different concentrations in an oil/water mixture were studied via molecular dynamics (MD) simulations using a simplified atomistic model which basically maintains the hydrophile and lipophile properties of the surfactant molecules. Above the critical micellar concentration (cmc), surfactant molecules aggregate spontaneously to form a wide variety of assemblies, from spherical to rodlike, wormlike and bilayer micelles. Changes in their ratios of the principle moments of inertia (g₁/g₃, g₂/g₃) indicated the transition of micelle shapes at different concentrations. The aggregation number of micelle is found to have a power-law dependence on surfactant concentration.