Theoretical insights and implications of pH-dependent drug delivery systems using silica and carbon nanotube.

In this paper we have studied the density functional theory of four drugs ibuprofen, alendronate, Sulfasalazine and paracetamol with quartz, propylamine, trimethylamine functionalized quartz and carboxyl modified carbon nanotube. The attractive and repulsive interaction energies between drugs and quartz is obtained at various pH values. The attractive and repulsive energies are well correlated with experimental drug loading and releasing behavior by mesoporous silica nanoparticles. Further, a theoretical model is developed that accounts the electrostatic interaction between silica and drug and the model can predict the drug loading and releasing behavior by silica nanoparticles at various pH values. Sulfasalazine can be taken orally and loaded with trimethyl ammonium functionalized mesoporous silica nanoparticles, which keeps the drug in tact with the carrier in the acidic environment of the stomach and releases it into the neutral or basic medium of the small intestine. Alendronate may be loaded and released from propylamine functionalized mesoporous silica nanoparticles in the ranges of 1-5 and > 8, respectively. Ibuprofen is absorbed in an acidic environment and released in basic conditions for carboxyl modified carbon nanotube. The loading and releasing pH ranges for paracetamol in trimethylammonium functionalized mesoporous silica nanoparticles are 4-8 and >8, respectively. We also convert the pH-dependent variant of the diffusion-controlled Higuchi equation. We have changed the original Higuchi equation to produce the pH-dependent variation by incorporating the Nernst-Planck equation into Flick's first law. The updated equation could be used to forecast when medication particles with varying release times will emerge from a nanoparticles matrix.

A coarse-grained molecular dynamics investigation on spontaneous binding of Aß1-40 fibrils with cholesterol-mixed DPPC bilayers.

Alzheimer's disease is the most common form of dementia. Its aetiology is characterized by the misfolding and aggregation of amyloid-ß (Aß) peptides into ß-sheet-rich Aß oligomers/fibrils. Although multiple experimental studies have suggested that Aß oligomers/fibrils interact with the cell membranes and perturb their structures and dynamics, the molecular mechanism of this interaction is still not fully understood. In the present work, we have performed a total of 120 µs-long simulations to investigate the interaction between trimeric or hexameric Aß1-40 fibrils with either a 100% DPPC bilayer, a 70% DPPC-30% cholesterol bilayer or a 50% DPPC-50% cholesterol bilayer. Our simulation data capture the spontaneous binding of the aqueous Aß1-40 fibrils with the membranes and show that the central hydrophobic amino acid cluster, the lysine residue adjacent to it and the C-terminal hydrophobic residues are all involved in the process. Moreover, our data show that while the Aß1-40 fibril does not bind to the 100% DPPC bilayer, its binding affinity for the membrane increases with the amount of cholesterol. Overall, our data suggest that two clusters of hydrophobic residues and one lysine help Aß1-40 fibrils establish stable interactions with a cholesterol-rich DPPC bilayer. These residues are likely to represent potential target regions for the design of inhibitors, thus opening new avenues in structure-based drug design against Aß oligomer/fibril-membrane interaction.

Acidity constant and DFT-based modelling of pH-responsive alendronate loading and releasing on propylamine-modified silica surface.

A computational methodology that couples the acidity (Ka) and density functional theory (DFT) calculations has been developed to explain the pH-dependent drug loading on and releasing from mesoporous silica nanoparticles. The model has been validated by investigating the pH-dependent loading and releasing of a bisphosphonate drug molecule, alendronate, on a propylamine-modified quartz surface (101), a model for functionalized mesoporous silica nanoparticles. The pH-dependent interacting molecular species are the neutral and anionic forms of the drug molecule, silanol group of quartz surface and the functional group in the case of functionalized quartz surface. The interaction energies of all the molecular species of alendronate with silica surface are calculated by using the DFT-based CASTEP method. Five molecular states of alendronate (D0, D-, D2-, D3- and D4-), two for silica surface (S0 and S-) and two for propylamine (P+ and P0) are considered. Ten possible combinations of interactions of alendronate with silica surface and twenty for alendronate and propylamine-functionalized silica surfaces are calculated. The relative probability of interaction of a particular pair of drug and surface combination at a particular pH is weighed by the product of their fractions, the latter is calculated by using the Handerson-Hasselbach equation. The total interaction energies at a particular pH are calculated by summing the possible individual interaction energies. The variation of total interaction energy with pH shows that the functional group of propylamine lowers the interaction energy at lower pH values (1-5), thus favouring adsorption or loading of the drug and increases the interaction energy at higher pH values (pH > 8) and thus favours desorption or release of the drug. This is in agreement with experimental results where it is shown that propylamine-functionalized mesoporous silica nanoparticles load alendronate in the pH range of 1-5 and release at pH = 8. This method can be used to predict the pH-dependent drug loading and releasing of a particular combination of drug and on a particular drug delivery system.

Structure and Function of Alzheimer's Amyloid ßeta Proteins from Monomer to Fibrils: A Mini Review.

Alzheimer's disease is the most common form of dementia, that affects millions of people worldwide. According to the widely accepted amyloid cascade hypothesis, misfolding and aggregation of Aß peptides is the principal cause of Alzheimer's disease. In the present mini-review, we have discussed the different structures of Aß protein from monomer to fibrils and their arrangement in different symmetries. We have highlighted the critical amino acid residue that plays a crucial role in the early stage misfolding of Aß monomers, Aß fibrils arrangement in different symmetries, the elongation process and Aß protein interaction with the membrane. We have further discussed the antibodies that are currently in clinical trial phase III for Alzheimer's disease.

Exploiting Covalent, H-Bonding, and π-π Interactions to Design Antibacterial PDMS Interfaces That Load and Release Salicylic Acid.

Smart antimicrobial surfaces are a powerful tool to prevent bacterial colonization at surfaces. In this work, we report a successful strategy for the functionalization of polydimethylsiloxane (PDMS) surfaces, widely used in medical devices, with salicylic acid (SA), a biocide approved for use in humans. Antimicrobial PDMS surfaces were fabricated via a rational design in which bifunctional silane linker molecules were covalently grafted onto the PDMS via one end, while soft intermolecular interactions with SA were generated at the other end to enable reversible load and release of the biocide. A molecular level understanding of the interface was obtained using attenuated total reflectance Fourier transform infrared, Raman, and X-ray photoelectron spectroscopies, alongside density functional theory calculations. These reveal that the linker molecules dock the SA molecules at the surface via a 1:1 complexation interaction. Furthermore, each 1:1 complex acts as a nucleation point onto which multiple stacks of the biocide are subsequently stabilized via a combination of H-bonding and π-π stacking interactions, thus significantly enhancing SA uptake at the interface. The antimicrobial activity of these surfaces against model Gram-negative and Gram-positive bacteria represented by Escherichia coli, Staphylococcus aureus, and Staphylococcus epidermidis is demonstrated by a log 6 reduction of planktonic bacterial populations and an efficient anti-biofilm activity at the surface.

Unraveling the mechanism of l-gulonate-3-dehydrogenase inhibition by ascorbic acid: Insights from molecular modeling.

l-Gulonate dehydrogenase (GuDH) is a crucial enzyme in the non-phosphorylated sugar metabolism or glucuronate-xylulose (GX) pathway. Some naturally occurring compounds inhibit GuDH. Ascorbic acid is one of such inhibitors for GuDH. However, the exact mechanism by which ascorbic acid inhibits GuDH is still unknown. In this study, we try to investigate GuDH inhibition using computational approaches by generating a model for buffalo GuDH. We used this model to perform blind dockings of ascorbic acid to GuDH. Some docked conformations of ascorbic acid bind near Asp39 and have steric clashes with crystal structure conformation of NADH. To assess the dynamic stability of the GuDH-ascorbic acid complex, we performed six molecular dynamics simulations for GuDH, three each in its free form and in complex with ascorbic acid for 50 ns, to obtain 300 ns of trajectories in total. During the simulations, ascorbic acid interacted with several residues nearby Asp39. As Asp39 is an important residue for NADH binding and specificity, the interaction of ascorbic acid near Asp39 hinders further NADH binding and ultimately affects the enzymatic functioning of GuDH. In this study, we analyze these interactions between ascorbic acid and GuDH. Our analysis reveals novel details on the mechanism of GuDH inhibition by ascorbic acid.

Binding of 12-Crown-4 with Alzheimer's Aß40 and Aß42 Monomers and Its Effect on Their Conformation: Insight from Molecular Dynamics Simulations.

Alzheimer's disease is the most common form of dementia and is considered to be caused by the conformational change of Aß monomers, from their native monomeric states, to form Aß oligomers/aggregates in the brain. Turn formation in Aß monomer has been suggested to be the nucleation step for Aß misfolding. In the present work, we have performed a series of all-atom molecular dynamics simulations, a total time of 11.4 µs, to elucidate factor that contributes for early stage misfolding of Aß40 and Aß42 monomers and reveals the binding modes of 12-crown-4 on Aß40 and Aß42 monomer and effect of its binding on structural stability. Our simulation data revealed that the region around Val24-Lys28 is most prevalent for turn formation and a gain of water molecules around Lys28 side chains occurs at the same time as a significant gain in conformational entropy of the side chain. The initiation steps lead a greater number of water molecules available and enhancement of the conformational entropy of the backbone atoms; this leads to greater probability of breaking Lys28 backbone intrapeptide H-bonds, and consequently turns formation. Simulations of Aß40 and Aß42 monomers with 12-crown-4 showed that the molecule is highly specific toward positively charged Lys16, Lys28 residues, and N-terminal Asp1. Lys16 and Asp1 have been previously reported to make Aß peptide toxic. Our secondary structure analysis revealed that in the absence of 12-crown-4 there was a ß-sheet formed in the Aß40 peptide. In case of Aß42 monomer, in the absence of 12-crown-4, we observed that the second helix region converted into a coil and turn; however, in the presence of 12-crown-4 it remained stable. Observed pharmacophore features of, 12-crown-4 will not only help in designing new candidate drug molecules, which are specific to Aß peptides but could also be used to design new imaging probe molecules, which could be used for labeling Aß peptide.

12-Crown-4 Ether Disrupts the Patient Brain-Derived Amyloid-ß-Fibril Trimer: Insight from All-Atom Molecular Dynamics Simulations.

Recent experimental data elucidated that 12-crown-4 ether molecule can disrupt Aß40 fibrils but the mechanism of disruption remains elusive. We have performed a series of all-atom molecular dynamics simulations to study the molecular mechanism of Aß40 fibril disruption by 12-crown-4. In the present study we have used the Aß40 fibril trimer as it is the smallest unit that maintains a stable U-shaped structure, and serves as the nucleus to form larger fibrils. Our study reveals that 12-crown-4 ether can enter into the hydrophobic core region and form competitive, hydrophobic interactions with key hydrophobic residues; these interactions break the intersheet hydrophobic interactions and lead to the opening of the U-shaped topology and a loss of ß-sheet structure. Furthermore, we observed periods of time when 12-crown-4 was in the hydrophobic core and periods of time when it interacted with Lys28 (chain C), a "tug of war"; the 12-crown-4 binding with Lys28 destabilizes the salt-bridge between Asp23 and Lys28. In addition to the two aforementioned binding modes, the 12-crown-4 binds with Lys16, which is known to form a salt-bridge with Glu22 in antiparallel arranged Aß fibrils. Our results are in good agreement with experimental results and suggest that molecules that have the ability to interact with both the hydrophobic core region and positively charged residues could serve as potential inhibitors of Aß fibrils.

Identification of novel selective MMP-9 inhibitors as potential anti-metastatic lead using structure-based hierarchical virtual screening and molecular dynamics simulation.

MMP-9 is an attractive target for the development of new anticancer drugs. In the current study, pharmacophore modeling was employed using two highly active and selective gelatinase inhibitors obtained from two X-ray crystal structures (PDB IDs: and ) to identify novel selective MMP-9 inhibitors. The derived model was refined manually and also validated by the GH scoring method. The refined pharmacophore model, ADRR, was able to retrieve 86% of actives with a GH score of 0.774, indicating that the model was capable of retrieving the active MMP-9 inhibitors. ADRR was used to screen 2 838 166 unique structures. Hit filtration was carried out using a fitness score >1.5 and drug-likeness properties. Hierarchical clustering generates 33 clusters based on diversity. A total of 33 molecules were obtained and these molecules were taken for cross-docking studies with 5 subtype MMPs. Among 33 tested, 2 molecules, P10A-0000088030 (Lig-1) and P10A-0001383812 (Lig-2), were found to have the highest docking scores (-8.59 kcal mol(-1) and -8.27 kcal mol(-1)) towards MMP-9 compared with the other MMPs. Further MM-GBSA analysis was performed for two hits with 5 subtype MMPs to reveal the essential features that contribute to selectivity. The results showed that van der Waals contributions play a central role in determining the selectivity of MMP-9 inhibitors. Molecular dynamics studies were carried out for total time of 330 ns to assess the stability of ligands at the active site. MD analysis showed that binding of Lig-1 with MMP-9 is stable compared to that with Lig-2. Hence, we suggest the Lig-1 compound as a good lead in designing novel potent inhibitors of MMP-9.

Synthesis, characterization, antiproliferative and molecular docking study of new half sandwich Ir(III), Rh(III) and Ru(II) complexes.

The new carbazole N,N' ligand containing [(η(5)-C5Me5)MCl(L)]PF6, (M=Ir (1) and Rh (2)) and [(η(6)-C6H6)RuCl(L)]PF6 (3) (C5Me5=pentamethylcyclopentadienyl, L=9-ethyl-N-(pyridine-2-yl methylene)-9H-carbazole-3-amine) complexes has been synthesized and characterized by (1)H NMR, (13)C NMR, 2D NMR, melting point analysis, electronic absorption, infrared spectroscopy, HR-Mass spectroscopy and elemental analyses. The crystal structure of the [(η(5)-C5Me5)RhCl(L)]PF6 has been confirmed by single crystal XRD. The anticancer study of the synthesized complexes 1-3 clearly showed a potent inhibitor of human breast cancer cells (MCF-7) under in vitro conditions. The inhibitory concentrations (IC50) of the complexes 1-3 were determined at low (5, 6 and 8µM) concentration against the MCF-7 human breast cancer cell line. Further cytotoxic, cell cycle and nuclear studies confirmed that the novel half sandwich Ir(III), Rh(III) and Ru(II) complexes could be effective against MCF-7 human breast cancer cell proliferation. Moreover the results indicate that anticancer in vitro activity of complexes 1-3 falls in the order of 1>2>3. A molecular docking study of the complexes 1-3 showed the nature of binding energy, H-bond and hydrophobic interactions with the cyclooxygenase-2 (COX-2) receptor.

Molecular interaction of selected phytochemicals under the charged environment of Plasmodium falciparum chloroquine resistance transporter (PfCRT) model.

Phytochemicals of Catharanthus roseus Linn. and Tylophora indica have been known for their inhibition of malarial parasite, Plasmodium falciparum in cell culture. Resistance to chloroquine (CQ), a widely used antimalarial drug, is due to the CQ resistance transporter (CRT) system. The present study deals with computational modeling of Plasmodium falciparum chloroquine resistance transporter (PfCRT) protein and development of charged environment to mimic a condition of resistance. The model of PfCRT was developed using Protein homology/analogy engine (PHYRE ver 0.2) and was validated based on the results obtained using PSI-PRED. Subsequently, molecular interactions of selected phytochemicals extracted from C. roseus Linn. and T. indica were studied using multiple-iterated genetic algorithm-based docking protocol in order to investigate the translocation of these legends across the PfCRT protein. Further, molecular dynamics studies exhibiting interaction energy estimates of these compounds within the active site of the protein showed that compounds are more selective toward PfCRT. Clusters of conformations with the free energy of binding were estimated which clearly demonstrated the potential channel and by this means the translocation across the PfCRT is anticipated.

Molecular dynamics simulation and conformational analysis of some catalytically active peptides.

The design of stable and inexpensive artificial enzymes with potent catalytic activity is a growing field in peptide science. The first step in this design process is to understand the key factors that can affect the conformational preference of an enzyme and correlate them with its catalytic activity. In this work, molecular dynamics simulations in explicit water of two catalytically active peptides (peptide 1: Fmoc-Phe1-Phe2-His-CONH2; peptide 2: Fmoc-Phe1-Phe2-Arg-CONH2) were performed at temperatures of 300, 400, and 500 K. Conformational analysis of these peptides using Ramachandran plots identified the secondary structures of the amino acid residues involved (Phe1, Phe2, His, Arg) and confirmed their conformational flexibility in solution. Furthermore, Ramachandran maps revealed the intrinsic preference of the constituent residues of these compounds for a helical conformation. Long-range interaction distances and radius of gyration (R g) values obtained during 20 ns MD simulations confirmed their tendency to form folded conformations. Results showed a decrease in side-chain (Phe1, Phe2, His ring, and Arg) contacts as the temperature was raised from 300 to 400 K and then to 500 K. Finally, the radial distribution functions (RDF) of the water molecules around the nitrogen atoms in the catalytically active His and Arg residues of peptide 1 and peptide 2 revealed that the strongest water-peptide interaction occurred with the arginine nitrogen atoms in peptide 2. Our results highlight differences in the secondary structures of the two peptides that can be explained by the different arrangement of water molecules around the nitrogen atoms of Arg in peptide 2 as compared to the arrangement of water molecules around the nitrogen atoms of His in peptide 1. The results of this work thus provide detailed insight into peptide conformations which can be exploited in the future design of peptide analogs.

A critical survey of average distances between catalytic carboxyl groups in glycoside hydrolases.

Published X-ray crystallographic structures for glycoside hydrolases (GHs) from 39 different families are surveyed according to some rigorous selection criteria, and the distances separating 208 pairs of catalytic carboxyl groups (20 α-retaining, 87 ß-retaining, 38 α-inverting, and 63 ß-inverting) are analyzed. First, the average of all four inter-carboxyl O…O distances for each pair is determined; second, the mean of all the pair-averages within each GH family is determined; third, means are determined for groups of GH families. No significant differences are found for free structures compared with those complexed with a ligand in the active site of the enzyme, nor for α-GHs as compared with ß-GHs. The mean and standard deviation (1σ) of the unimodal distribution of average O…O distances for all families of inverting GHs is 8 ± 2Å, with a very wide range from 5Å (GH82) to nearly 13Å (GH46). The distribution of average O…O distances for all families of retaining GHs appears to be bimodal: the means and standard deviations of the two groups are 4.8 ± 0.3Å and 6.4 ± 0.6Å. These average values are more representative, and more likely to be meaningful, than the often-quoted literature values, which are based on a very small sample of structures. The newly-updated average values proposed here may alter perceptions about what separations between catalytic residues are "normal" or "abnormal" for GHs.

Adsorption of arginine-glycine-aspartate tripeptide onto negatively charged rutile (110) mediated by cations: the effect of surface hydroxylation.

Classical molecular dynamics (MD) simulations were employed to investigate the adsorption behaviors of arginine-glycine-aspartate (RGD) tripeptide onto the negatively charged hydroxylated/nonhydroxylated rutile (110) surfaces, mediated by biologically important cations (Na+ or Ca2+). The simulation results indicate that the inherent nature of the cation determines its binding strength, thereby regulating the adsorption geometry of the peptide. The sparse hydroxyl groups on the nonhydroxylated rutile diminish the probability of H-bond formation between RGD and the surface, resulting in an early desorption of the peptide even with a mediating Na+ ion. In contrast, the negatively charged aspartate (Asp) side chain is bridged to the negatively charged hydroxylated rutile by an inner-sphere Na+ ion, in coordination with the Asp-rutile hydrogen bonds at the anchoring sites. The inner- and outer-sphere Ca2+ ions are demonstrated to be capable of "trapping" RGD on both hydroxylated and nonhydroxylated rutile, in the absence of hydrogen bonds with the surface. The strongly bound inner-sphere mediating Ca2+ ion exerts a "gluing" effect on the Asp side chain, producing a tightly packed RGD-rutile complex, whereas a less localized distribution density of the outer-sphere mediating Ca2+ ion results in a higher mobility of the Asp side chain. The intramolecular interaction is suggested to facilitate the structural stability of RGD adsorbed on the negative rutile in a "horseshoe" configuration.

Modeling the interaction between integrin-binding peptide (RGD) and rutile surface: the effect of cation mediation on Asp adsorption.

The binding of a negatively charged residue, aspartic acid (Asp) in tripeptide arginine-glycine-aspartic acid, onto a negatively charged hydroxylated rutile (110) surface in aqueous solution, containing divalent (Mg(2+), Ca(2+), or Sr(2+)) or monovalent (Na(+), K(+), or Rb(+)) cations, was studied by molecular dynamics (MD) simulations. The results indicate that ionic radii and charges will significantly affect the hydration, adsorption geometry, and distance of cations from the rutile surface, thereby regulating the Asp/rutile binding mode. The adsorption strength of monovalent cations on the rutile surface in the order Na(+) > K(+) > Rb(+) shows a "reverse" lyotropic trend, while the divalent cations on the same surface exhibit a "regular" lyotropic behavior with decreasing crystallographic radii (the adsorption strength of divalent cations: Sr(2+) > Ca(2+) > Mg(2+)). The Asp side chain in NaCl, KCl, and RbCl solutions remains stably H-bonded to the surface hydroxyls and the inner-sphere adsorbed compensating monovalent cations act as a bridge between the COO(-) group and the rutile, helping to "trap" the negatively charged Asp side chain on the negatively charged surface. In contrast, the mediating divalent cations actively participate in linking the COO(-) group to the rutile surface; thus the Asp side chain can remain stably on the rutile (110) surface, even if it is not involved in any hydrogen bonds with the surface hydroxyls. Inner- and outer-sphere geometries are all possible mediation modes for divalent cations in bridging the peptide to the rutile surface.

Interplay of sequence, conformation, and binding at the Peptide-titania interface as mediated by water.

The initial stages of the adsorption of a hexapeptide at the aqueous titania interface are modeled using atomistic molecular dynamics simulations. This hexapeptide has been identified by experiment [Sano, K. I.; Shiba, K. J. Am. Chem. Soc. 2003, 125, 14234] to bind to Ti particles. We explore the current hypothesis presented by these authors that binding at this peptide-titania interface is the result of electrostatic interactions and find that contact with the surface appears to take place via a pair of oppositely charged groups in the peptide. Our data indicate that the peptide may initially recognize the water layers at the interface, not the titania surface itself, via these charged groups. We also report results of simulations for hexapeptide sequences with selected single-point mutations for alanine and compare these behaviors with those suggested from observed binding affinities from existing alanine scan experiments. Our results indicate that factors in addition to electrostatics also contribute, with the structural rigidity conferred by proline suggested to play a significant role. Finally, our findings suggest that intrapeptide interaction may provide mechanisms for surface detachment that could be detrimental to binding at the interface.