Computational prediction of structure-activity relationships for the binding of aminocyclitols to β-glucocerebrosidase

Glucocerebrosidase (GCase, acid β-Glucosidase) hydrolyzes the sphingolipid glucosylceramide into glucose and ceramide. Mutations in this enzyme lead to a lipid metabolism disorder known as Gaucher disease. The design of competitive inhibitors of GCase is a promising field of research for the design of pharmacological chaperones as new therapeutic agents. Using a series of recently reported molecules with experimental binding affinities for GCase in the nanomolar to micromolar range, we here report an extensive theoretical analysis of their binding mode. On the basis of molecular docking, molecular dynamics, and binding free energy calculations using the linear interaction energy method (LIE), we provide details on the molecular interactions supporting ligand binding in the different families of compounds. The applicability of other computational approaches, such as the COMBINE methodology, is also investigated. The results show the robustness of the standard parametrization of the LIE method, which reproduces the experimental affinities with a mean unsigned error of 0.7 kcal/mol. Several structure-activity relationships are established using the computational models here provided, including the identification of hot spot residues in the binding site. The models derived are envisaged as important tools in ligand-design programs for GCase inhibitors.     

The role of water release from the cyclodextrin cavity in the complexation of benzoyl chlorides by dimethyl-β-cyclodextrin

The influence of temperature on the solvolysis of substituted benzoyl chlorides in the presence of dimethyl-β-cyclodextrin (DM-β-CD) was studied. Based on the influence of the DM-β-CD concentration on chemical reactivity in this process, the cyclodextrin has a catalytic effect on the solvolysis of 4-nitrobenzoyl chloride (4-NO₂) but an inhibitory effect on that of 4-methoxy-(4-MeO), 3-chloro-(3-Cl) and 3-trifluoromethyl-(3-CF₃) benzoyl chlorides. These disparate effects are related to a difference in reaction mechanism; thus, DM-β-CD catalyses associative solvolysis and inhibits dissociative solvolysis. Examining the influence of temperature on the solvolytic process allowed the stoichiometry of the host-guest complexes formed to be established. The formation constants for the complexes of meta-substituted benzoyl chlorides increased with increasing temperature. On the other hand, the equilibrium formation constants for the 1:1 host-guest complexes of para-substituted benzoyl chlorides exhibited the opposite trend. The equilibrium formation constant for 2:1 host-guest complexes for the para-substituted benzoyl chlorides increased with increasing temperature. These differences are ascribed to the release of water from the DM-β-CD cavity during the formation of the host-guest complex.     

Mechanism and Dynamics of the Addition of Lithium Hydride to Acetylene

Reaction ergodography for the addition of lithium hydride to acetylene indicates that the lithium hydride, in both monomeric and dimeric forms, reacts with the acetylene via two similar and competitive pathways. Hence, we have obtained the pseudo-first-order rate constant of this reaction.     

Search for approaches to improving the calculation accuracy of the protein—ligand binding energy by docking

The following reasons limiting the accuracy of calculations of the protein—ligand binding energy by the molecular docking programs are considered: the limited facilities of algorithms of finding a global minimum on a complicated multi-dimensional protein—ligand energy surface, restrictions on the degrees of freedom of a protein—ligand system including docking into a rigid protein, inadequacy of the existing force fields, a lack of taking into account the solvent or too rough allowance for the solvent in the docking procedure, a lack of the local energy optimization in the docking process, an inaccuracy of the construction of models of a target protein and a ligand, simplification of the calculation method of the Gibbs free energy of a molecular system, and limited computer resources for docking of one ligand. A new approach to the development of the new generation of docking programs is proposed. The approach allows one to remove step-by-step the existing simplifications and to increase considerably the accuracy of the whole docking process, including the calculation accuracy of the protein—ligand binding energy. The results of the study are presented and demonstrate the computational feasibility of the assigned docking problem.     

Facile preparation of two tetrols from permethylated α-cyclodextrin and unambiguous NMR analysis

An unprecedented straightforward approach wherein an excess of diisobutylaluminum hydride is able to strip off in reasonable yield (45%) and in a regioselective manner four methyl groups from permethylated α-cyclodextrin, to provide a symmetric tetrol (2) in one chemical step from a commercially available material is described. An asymmetric tetrol (3) was also isolated from the reaction as a minor product (19%). Both compounds are unambiguously characterized by ¹H NMR, ¹³C NMR, COSY, HSQC and HRMS.     

Development of implantable hydroxypropyl-β-cyclodextrin coated polycaprolactone nanoparticles for the controlled delivery of docetaxel to solid tumors

Treatment of cancer is one of the most challenging problems and conventional therapies are inadequate for targeted, effective and safe therapy. Development of nanoparticle-based drug delivery systems emerge as promising carriers in this field to ensure delivery of anticancer drug to tumor site. The aim of this study was to design hydroxypropyl-β-cyclodextrin (CD) coated nanoparticles using poly(ε-caprolactone) (PCL) and its derivative poly(ethylene glycol)-block-poly(ε-caprolactone) (mePEG-PCL) to be applied as implants to tumor site following surgical operation in cancer patients. CD coated PCL and mePEG-PCL nanospheres were developed to encapsulate poorly soluble chemotherapeutic agent docetaxel (DOC) to improve solubility of drug and to enhance cellular penetration with longer residence time and higher local drug concentration. Nanospheres were prepared according to the nanoprecipitation method and coated with hydroxypropyl-β-cyclodextrin (Cavasol^® W7HP). Cyclodextrin coating was performed for higher drug encapsulation and controlled but complete drug release from nanoparticles. Nanoparticle diameters varied between 60 and 136 nm depending on polymer used for preparation and coating. All nanoparticles have negative surface charge and zeta potential values varied between ?22 and ?37 mV. Encapsulation efficiency of formulations were found to be between 46 and 73 % and CD coated nanoparticles have significantly higher entrapment efficiency. Drug release profiles of nanoparticles were similar to each other and all formulations released encapsulated drug in approximately 12 h. Especially, CD-PCL nanoparticles were found to have highest entrapment efficiency and anticancer efficacy against MCF-7 human breast adenocarcinoma cell lines. Our study proved that polycaprolactone and its PEGylated derivatives can be suitable for development of implantable nanoparticles as a potential drug delivery system of DOC for cancer treatment and a good candidate for further in vivo studies.     

Synthesis of β-cyclodextrin conjugated superparamagnetic iron oxide nanoparticles for selective binding and detection of cholesterol crystals

Water-soluble, β-cyclodextrin conjugated superparamagnetic nanoparticles have been constructed. These particles showed selective binding to cholesterol crystals, which opens the door for the detection of cholesterol crystal-related diseases such as atherosclerosis by magnetic resonance imaging (MRI).     

Synthesis of a Photolabeling Probe for the Study of Antiviral Mechanism of Ribavirin

Ribavirin has been used in urgency to treat SARS patients recently. In order to study its antiviral mechanism by photolabeling approach, we have synthesized and characterized 5-azido-1-β-D-ribofuranosyl-1,2,4-triazole-3-carboxiamide 1 as a photolabeling probe of ribavirin. The azidotriazole nucleoside showed rapid and clean photochemical reaction, suggesting that 1 is a promising probe to study the antiviral mechanism ofribarivin by photolabeling.     

Assemblies of brilliant cresyl violet to DNA in the presence of γ-cyclodextrin

The interactions of brilliant cresyl violet (BCV) with herring sperm DNA in γ-cyclodextrin (γ-CD) supramolecular system were studied by UV-vis absorption spectroscopy and cyclic voltammetry (CV). Both UV-vis absorption and CV data show that the interaction of BCV with DNA depends on the concentration ratio of BCV to DNA (R), the initial concentration of BCV and γ-CD. The binding constants of BCV monomer, (BCV)₂ dimer and (BCV)₂-γ-CD inclusion complex with DNA are 1.64 × 10⁵, 2.56 × 10⁴ and 2.32 × 10³ M⁻¹, respectively. It was observed that γ-CD can affect the interactive mode of BCV with DNA. If R is larger than 0.5, the (BCV)₂-γ-CD inclusion complex will retain intact and bind to DNA via the electrostatic attraction forces. By contrast, when R is smaller than 0.5, the inclusion complex will be partially dissociated and the free BCV monomer is intercalated into the double-helix structure of DNA attributing to the more favorable microenvironment of DNA for the BCV monomer. Our work postulates the importance of the initial concentration of dye and host molecule on the interaction of dye with DNA in living bodies.     

Rapid analysis of NSAIDs binding to β-cyclodextrin using the simultaneous measurement of absorption and circular dichroism with a novel multi-cell low-volume device

One of the relatively recent and most widely used approaches to reduce side effects associated with the use of nonsteroidal anti-inflammatory drugs (NSAIDs) is the complexation of NSAIDs with Cyclodextrins (CyD). So far, CyD interaction with drugs is not well understood. There have been many reports along these lines; however, rarely do these studies exploit the full potential of optical techniques. The purpose of this work is to produce a versatile, compact, low-volume, routine apparatus for the simultaneous measurements of absorbance and circular dichroism (CD) which allows for the concurrent use of three different pathlengths for binding studies of NSAIDs/CyD as a function of pH. A new rotating multi-cell holder which holds four cells was designed and manufactured. The work was achieved using an effective novel method for binding titration employing four separate flow cells connected in series in a flow system involving a titration flask and a pump. The pK _a, binding constants, stoichiometry and structural co-conformations of NSAIDs/β-CyD complexes were elucidated and determined with accuracy. The system proved to be efficient and the analysis time was reduced to less than or equal to one fourth of total analysis time used in one-cell systems, with possible automation for high-throughput analysis.

Thermodynamics of the sorption of organic compounds on polyethylene glycol 400–permethylated β-cyclodextrin stationary phase and its enantioselectivity in gas chromatography

The thermodynamic characteristics of sorption of 24 organic compounds of various classes from the gas phase on the binary stationary phase based on polyethylene glycol 400 and permethylated β-cyclodextrin were determined. The influence of geometrical structure and optical activity of organic compounds on the possibility of forming sorbate–macrocycle complexes was examined. It was found that the studied stationary phase shows the enantioselectivity towards low-polar terpenes under the conditions of gas chromatography.     

Virtual screening using a conformationally flexible target protein: models for ligand binding to p38α MAPK

We have used virtual screening to develop models for the binding of aryl substituted heterocycles to p38α MAPK. Virtual screening was conducted on a number of p38α MAPK crystal structures using a library of 46 known p38α MAPK inhibitors containing a heterocyclic core substituted by pyridine and fluorophenyl rings (structurally related to SB203580) and a set of decoy compounds. Multiple protonation states and tautomers of active and decoy compounds were considered. Each docking model was evaluated using receiver operating characteristic (ROC) curves and enrichment factors. The two best performing single crystal structures were found to be 1BL7 and 2EWA, with enrichment factors of 14.1 and 13.0 at 2 % of the virtual screen respectively. Ensembles of up to four receptors of similar conformations were generated, generally giving good or very good performances with high ROC AUCs and good enrichment. The 1BL7-2EWA ensemble was able to outperform each of its constituent receptors and gave high enrichment factors of 17.3, 12.0, 8.0 at 2, 5 and 10 % respectively, of the virtual screen. A ROC AUC of 0.94 was obtained for this ensemble. This method may be applied to other proteins where there are a large number of inhibitor classes with different binding site conformations.     

Mechanism and Kinetics for the Reaction of NCS and OH Radicals

The mechanism and dynamical properties for the reaction of NCS and OH radicals have been investigated theoretically. The minimum energy paths (MEP) of the reaction were calculated using the density functional theory(DFT) at the B3LYP/6-311 G^** level, and the energies along the MEP were further refined at the QCISD(T)/6-311 G^** level. As a result, the reaction mechanism of the title reaction involves three channels, producing HCS NO and HNC SO products, respectively. Path Ⅰ and path Ⅱ are competitive, with some advantages for path Ⅰ in kinetics. As for path Ⅲ, it looks difficult to react for its high energy barrier. Moreover, the rate constant have been calculated over the temperature range of 8190-2500K using canonical variational transition-state theory (CVT). It was found that the rate constants for both path Ⅰ and path Ⅱ are negatively dependent on temperature, which is similarwith the experimental results for reactions of NCS with NO and NO2, and the variational effect for the rate constant calculation olavs an important role in whole temperature range.     

“In silico” study of the binding of two novel antagonists to the nociceptin receptor

Antagonists of the nociceptin receptor (NOP) are raising interest for their possible clinical use as antidepressant drugs. Recently, the structure of NOP in complex with some piperidine-based antagonists has been revealed by X-ray crystallography. In this study, a multi-flexible docking (MF-docking) procedure, i.e. docking to multiple receptor conformations extracted by preliminary molecular dynamics trajectories, together with hybrid quantum mechanics/molecular mechanics (QM/MM) simulations have been carried out to provide the binding mode of two novel NOP antagonists, one of them selective (BTRX-246040, formerly named LY-2940094) and one non selective (AT-076), i.e. able to inactivate NOP as well as the classical µ- k- and δ-opioid receptors (MOP KOP and DOP). According to our results, the pivotal role of residue D130^3,32 (upper indexes are Ballesteros–Weinstein notations) is analogous to that enlighten by the already known X-ray structures of opioid receptors: binding of the molecules are predicted to require a slight readjustment of the hydrophobic pocket (residues Y131^3,33, M134^3,36, I219^5,43, Q280^6,52 and V283^6,55) in the orthosteric site of NOP, accommodating either the pyridine–pyrazole (BTRX-246040) or the isoquinoline (AT-076) moiety of the ligand, in turn allowing the protonated piperidine nitrogen to maximize interaction (salt-bridge) with residue D130^3,32 of the NOP, and the aromatic head to be sandwiched in optimal π-stacking between Y131^3,33 and M134^3,36. The QM/MM optimization after the MF-docking procedure has provided the more likely conformations for the binding to the NOP receptor of BTRX-246040 and AT-076, based on different pharmacophores and exhibiting different selectivity profiles. While the high selectivity for NOP of BTRX-246040 can be explained by interactions with NOP specific residues, the lack of selectivity of AT-076 could be associated to its ability to penetrate into the deep hydrophobic pocket of NOP, while retaining a conformation very similar to the one assumed by the antagonist JDTic into the K-opioid receptor. The proposed binding geometries fit better the binding pocket environment providing clues for experimental studies aimed to design selective or multifunctional opioid drugs.     

Durable chiral sensor based on quartz crystal microbalance using self-assembled monolayer of permethylated β-cyclodextrin

A novel chiral sensor based on quartz crystal microbalance (QCM) with a self-assembled monolayer of permethylated β-cyclodextrin as the enantioselective coating has been derived which exhibit improved enantioselectivity and excellent long-term environmental stability when used in gas phase sensing.     

Enhancement of selectivity for producing γ-cyclodextrin

The production of cyclodextrins (CDs) by cyclodextrin-glycosyl-transferase (CGTase) from Bacillus firmus was studied, with respect to the effect of the source of starch upon CD yield and on the selectivity for producing γ-CD. Cyclodextrin production tests were run for 24 h at 50°C, pH 8.0, and 1 mg/L of CGTase, and substrates were maltodextrin or the starches of rice, potato, cassava, and corn hydrolyzed up to D. E. 10. Cornstarch was the best substrate for producing γ-CD. Later, glycyrrhizin (2.5% [w/v]), which forms a stable complex with γ-CD, was added to the cornstarch reaction medium and increased the yield of γ-CD to about four times that produced with only maltodextrin, but the total yield of CDs remained practically unchanged. Therefore, the results showed that the studied CGTase is capable of giving relatively high yield of γ-CD in the presence of glycyrrhizin as complexant and cornstarch as substrate.     

Calorimetry to Evaluate Inclusion Mechanism in the Complexation Between 2-hydroxypropyl-β-cyclodextrin and Barbiturates in Aqueous Solution

Two different types (structures) of inclusion complexes with a 1:1 stoichiometry between barbiturates and 2-hydroxypropyl-β-cyclodextrin (HPCyD) were realized in aqueous solution using isothermal titration calorimetry and molecular dynamics simulation. The first type of complex with a higher association constant was entropy driven and the substituent R ₂ was inserted into the HPCyD cavity by hydrophobic interaction. The barbituric acid ring contributed to the second type of complex, which was characterized by large negative values of ΔH and small positive ΔS reflecting van der Waals interaction and/or hydrogen bonding formation between the hetero atoms in the barbituric acid ring and the secondary hydroxyl groups of HPCyD. This revised version was published online in July 2006 with corrections to the Cover Date.