Characterization of a complete cycle of acetylcholinesterase catalysis by <Emphasis Type="Italic">ab initio</Emphasis> QM/MM modeling

The reaction mechanism of acetylcholine hydrolysis by acetylcholinesterase, including both acylation and deacylation stages from the enzyme-substrate (ES) to the enzyme-product (EP) molecular complexes, is examined by using an ab initio type quantum mechanical – molecular mechanical (QM/MM) approach. The density functional theory PBE0/aug-6–31+G* method for a fairly large quantum part trapped inside the native protein environment, and the AMBER force field parameters in the molecular mechanical part are employed in computations. All reaction steps, including the formation of the first tetrahedral intermediate (TI1), the acylenzyme (EA) complex, the second tetrahedral intermediate (TI2), and the EP complex, are modeled at the same theoretical level. In agreement with the experimental rate constants, the estimated activation energy barrier of the deacylation stage is slightly higher than that for the acylation phase. The critical role of the non-triad Glu202 amino acid residue in orienting lytic water molecule and in stabilizing the second tetrahedral intermediate at the deacylation stage of the enzymatic process is demonstrated. Figure The computed energy diagram for the reaction path from the enzyme – substrate complex (ES) to the enzyme-product complex (EP).     

Free Energy Calculations of Pharmaceutically Important Properties

When determining the biochemical function of a proposed new drug it is useful to be able to calculate a number of properties which regulate its behaviour. By using the Free Energy Perturbation method incorporated into molecular dynamics, both on its own and in conjunction with quantum mechanical calculations, we have calculated redox potentials, pK_a s, tautomer ratios and partition coefficients on model systems.

This paper reviews the techniques currently being used to perform such calculations and presents the results for a number of different systems. The accuracy with which the properties are determined is most encouraging and suggests that useful calculations on realistic systems are now possible, and will play a major role in drug-design in the future.     

Extension of the GLYCAM06 Biomolecular Force Field to Lipids, Lipid Bilayers and Glycolipids

GLYCAM06 is a generalisable biomolecular force field that is extendible to diverse molecular classes in the spirit of a small-molecule force field. Here we report parameters for lipids, lipid bilayers and glycolipids for use with GLYCAM06. Only three lipid-specific atom types have been introduced, in keeping with the general philosophy of transferable parameter development. Bond stretching, angle bending, and torsional force constants were derived by fitting to quantum mechanical data for a collection of minimal molecular fragments and related small molecules. Partial atomic charges were computed by fitting to ensemble-averaged quantum-computed molecular electrostatic potentials.In addition to reproducing quantum mechanical internal rotational energies and experimental valence geometries for an array of small molecules, condensed-phase simulations employing the new parameters are shown to reproduce the bulk physical properties of a DMPC lipid bilayer. The new parameters allow for molecular dynamics simulations of complex systems containing lipids, lipid bilayers, glycolipids, and carbohydrates, using an internally consistent force field. By combining the AMBER parameters for proteins with the GLYCAM06 parameters, it is also possible to simulate protein-lipid complexes and proteins in biologically relevant membrane-like environments.     

Linear free energy relationship for 4-substituted (o-phenylenediamine)platinum(II) dichloride derivatives using quantum mechanical descriptors

In the present work quantum mechanical methods were used to calculate the rate constants for the first step of the aquation of a set of 4-substituted (o-phenylenediamine)platinum(II) dichloride derivatives containing electron-donating and withdrawing substituents at the 4-position of the aromatic ring. A linear free energy relationship was obtained for log(k(X)/k(H)), k being the rate constant for the first step of hydrolysis, and the electronic Hammett constants sigma(m) and sigma(p). The results showed that electron-donating groups promote the hydrolysis reaction. The quantitative models described here may be useful for the rational design of new, less mutagenic drugs based on platinum complexes.     

Pattern recognition based on color-coded quantum mechanical surfaces for molecular alignment

A pattern recognition algorithm for the alignment of drug-like molecules has been implemented. The method is based on the calculation of quantum mechanical derived local properties defined on a molecular surface. This approach has been shown to be very useful in attempting to derive generalized, non-atom based representations of molecular structure. The visualization of these surfaces is described together with details of the methodology developed for their use in molecular overlay and similarity calculations. In addition, this paper also introduces an additional local property, the local curvature (C _L), which can be used together with the quantum mechanical properties to describe the local shape. The method is exemplified using some problems representing common tasks encountered in molecular similarity. Figure Molecular surfaces for Lorazepam (left) and Diazepam (right)     

Correlating Cellulose Derivative Intrinsic Viscosity with Mechanical Susceptibility of Swollen Hydrophilic Matrix Tablets

Hydrophilic matrix tablets are prone to mechanical stress while passing through the gastrointestinal tract, which may result in inappropriate drug-release characteristics. Intrinsic viscosity is a physical polymer property that can be directly compared across various types and grades of polymers and correlated with the mechanical susceptibility of swollen matrix tablets. Five tablet formulations containing different HPMC and HPC polymers were prepared and analyzed using an in vitro glass bead manipulation test. The dissolution rate results were modeled using the Korsmeyer-Peppas equation and a correlation was found between the fit constants k and n, goodness-of-fit measure parameters, and intrinsic viscosity. Moreover, the dissolution profiles were used to calculate the degree of mechanical susceptibility for each formulation, defined as the ratio of the average dissolution rate after manipulation and the initial dissolution rate before manipulation. It was confirmed that an increased intrinsic viscosity polymer value resulted in a decrease in mechanical susceptibility. Considering this, two simple rules were defined for designing robust matrix tablets with respect to mechanical stresses.     

A biphasic nature of the bleomycin-mediated degradation of DNA

The bleomycin-mediated digestion of DNA in the presence of ferrous ion, molecular oxygen, and dithiothreitol is characterized by a fast initial reaction, which is followed by a much slower process. The fast degradation is due to the fast activation of the bleomycin-Fe(II) complex and the subsequent fast reaction of the activated complex with DNA. The rate determining step for the slow process is reactivation of the bleomycin-Fe(III) complex. The apparent rate constants for both reactions increase with increasing ionic strength. The latter, unusual results are interpreted in terms of inhibition of bleomycin turnover by binding of cationic species with DNA at low ionic strength.     

COBRAMM 2.0 — A software interface for tailoring molecular electronic structure calculations and running nanoscale (QM/MM) simulations

We present a new version of the simulation software COBRAMM, a program package interfacing widely known commercial and academic software for molecular modeling. It allows a problem-driven tailoring of computational chemistry simulations with effortless ground and excited-state electronic structure computations. Calculations can be executed within a pure QM or combined quantum mechanical/molecular mechanical (QM/MM) framework, bridging from the atomistic to the nanoscale. The user can perform all necessary steps to simulate ground state and photoreactions in vacuum, complex biopolymer, or solvent environments. Starting from ground-state optimization, reaction path computations, initial conditions sampling, spectroscopy simulation, and photodynamics with deactivation events, COBRAMM is designed to assist in characterization and analysis of complex molecular materials and their properties. Interpretation of recorded spectra range from steady-state to time-resolved measurements. Various tools help the user to set up the system of interest and analyze the results.     

Development of a Mini-Tablet of Co-Grinded Prednisone–Neusilin Complex for Pediatric Use

The purpose of this study is to enhance the dissolution rate of prednisone by co-grinding with Neusilin to form a complex that can be incorporated into a mini-tablet formulation for pediatrics. Prednisone–Neusilin complex was co-grinded at various ratios (1:1, 1:3, 1:5, and 1:7). The physicochemical properties of the complex were characterized by various analytical techniques including: differential scanning calorimetry (DSC), X-ray powder diffraction (XRPD), scanning electron microscope (SEM), particle size, surface area, solubility, and dissolution rate. The co-grinded prednisone–Neusilin complex (1:7) was blended with other excipients and was formulated into a 2-mm diameter mini-tablet. The mini-tablets were further evaluated for thickness, weight, content uniformity, and dissolution rate. To improve taste masking and stability, mini-tablets were coated by dip coating with Eudragit® EPO solution. DSC and XRPD results showed that prednisone was transformed from crystalline state into amorphous state after co-grinding with Neusilin. Particle size, surface area, and SEM results confirmed that prednisone was adsorbed to Neusilin’s surface. Co-grinded prednisone–Neusilin complex (1:7) had a solubility of 0.24 mg/mL and 90% dissolved within 20 min as compared to crystalline prednisone which had a solubility of 0.117 mg/mL and 30% dissolved within 20 min. The mini-tablets containing co-grinded prednisone–Neusilin complex (1:7) exhibited acceptable physicochemical and mechanical properties including dissolution rate enhancement. These mini-tablets were successfully dip coated in Eudragit® EPO solution to mask the taste of the drug during swallowing. This work illustrates the potential use of co-grinded prednisone–Neusilin to enhance solubility and dissolution rate as well as incorporation into a mini-tablet formulation for pediatric use.Key words: mini-tablet, Neusilin, pediatric, prednisone, solubility     

Tablet formulation containing meloxicam and beta-cyclodextrin: mechanical characterization and bioavailability evaluation

The purpose of this research was to evaluate beta-cyclodextrin (beta-CD) as a vehicle, either singly or in blends with lactose (spray-dried or monohydrate), for preparing a meloxicam tablet. Aqueous solubility of meloxicam in presence of beta-CD was investigated. The tablets were prepared by direct compression and wet granulation techniques. The powder blends and the granules were evaluated for angle of repose, bulk density, compressibility index, total porosity, and drug content. The tablets were subjected to thickness, diameter, weight variation test, drug content, hardness, friability, disintegration time, and in vitro dissolution studies. The effect of beta-CD on the bioavailability of meloxicam was also investigated in human volunteers using a balanced 2-way crossover study. Phase-solubility studies indicated an A(L)-type diagram with inclusion complex of 1:1 molar ratio. The powder blends and granules of all formulations showed satisfactory flow properties, compressibility, and drug content. All tablet formulations prepared by direct compression or wet granulation showed acceptable mechanical properties. The dissolution rate of meloxicam was significantly enhanced by inclusion of beta-CD in the formulations up to 30%. The mean pharmacokinetic parameters (C(max), K(e), and area under the curve [AUC](0-infinity)) were significantly increased in presence of beta-CD. These results suggest that beta-CD would facilitate the preparation of meloxicam tablets with acceptable mechanical properties using the direct compression technique as there is no important difference between tablets prepared by direct compression and those prepared by wet granulation. Also, beta-CD is particularly useful for improving the oral bioavailablity of meloxicam.     

Calculation of chromophore excited state energy shifts in response to molecular dynamics of pigment-protein complexes

The absorption and energy transfer properties of photosynthetic pigments are strongly influenced by their local environment or “site.” Local electrostatic fields vary in time with protein and chromophore molecular movement and thus transiently influence the excited state transition properties of individual chromophores. Site-specific information is experimentally inaccessible in many light-harvesting pigment–proteins due to multiple chromophores with overlapping spectra. Full quantum mechanical calculations of each chromophores excited state properties are too computationally demanding to efficiently calculate the changing excitation energies along a molecular dynamics trajectory in a pigment–protein complex. A simplified calculation of electrostatic interactions with each chromophores ground to excited state transition, the so-called charge density coupling (CDC) for site energy, CDC, has previously been developed to address this problem. We compared CDC to more rigorous quantum chemical calculations to determine its accuracy in computing excited state energy shifts and their fluctuations within a molecular dynamics simulation of the bacteriochlorophyll containing light-harvesting Fenna–Mathews–Olson (FMO) protein. In most cases CDC calculations differed from quantum mechanical (QM) calculations in predicting both excited state energy and its fluctuations. The discrepancies arose from the inability of CDC to account for the differing effects of charge on ground and excited state electron orbitals. Results of our study show that QM calculations are indispensible for site energy computations and the quantification of contributions from different parts of the system to the overall site energy shift. We suggest an extension of QM/MM methodology of site energy shift calculations capable of accounting for long-range electrostatic potential contributions from the whole system, including solvent and ions.     

Structures of TraI in solution

Cobalt and potassium are biologically important metal elements that are present in a large array of proteins. Cobalt is mostly found in vivo associated with a corrin ring, which represents the core of the vitamin B₁₂ molecule. Potassium is the most abundant metal in the cytosol, and it plays a crucial role in maintaining membrane potential as well as correct protein function. Here, we report a thorough analysis of the geometric properties of cobalt and potassium coordination spheres that was performed with high resolution on a representative set of structures from the Protein Data Bank and complemented by quantum mechanical calculations realized at the DFT level of theory (B3LYP/ SDD) on mononuclear model systems. The results allowed us to draw interesting conclusions on the structural characteristics of both Co and K centers, and to evaluate the importance of effects such as their association energies and intrinsic thermodynamic stabilities. Overall, the results obtained provide useful data for enhancing the atomic models normally applied in theoretical and computational studies of Co or K proteins performed at the quantum mechanical level, and for developing molecular mechanical parameters for treating Co or K coordination spheres in molecular mechanics or molecular dynamics studies.

Quantum chemistry as a tool in bioenergetics

Recent developments of quantum chemical methods have made it possible to tackle crucial questions in bioenergetics. The most important systems, cytochrome c oxidase in cellular respiration and photosystem II (PSII) in photosynthesis will here be used as examples to illustrate the power of the quantum chemical tools. One main contribution from quantum chemistry is to put mechanistic suggestions onto an energy scale. Accordingly, free energy profiles can be constructed both for reduction of molecular oxygen in cytochrome c oxidase and water oxidation in PSII, including O-O bond cleavage and formation, and also proton pumping in cytochrome c oxidase. For the construction of the energy diagrams, the computational results sometimes have to be combined with experimental information, such as reduction potentials and rate constants for individual steps in the reactions.     

Effects of hydration on scale factors for ab initio force constants. IV. trans and cis N-methylacetamide

Scaled quantum mechanical force fields have been calculated using the 4-31G basis for trans and cis conformers of both isolated and water-solvated N-methylacetamide (NMA). (1) A single set of scale factors for isolated NMA yields relatively correct predictions of the shifts in vibrational frequencies between the trans and cis conformers. This is also true of a single set of scale factors for trans and cis NMA in water. The total standard deviation between measured and calculated frequencies for trans NMA in both isolated and solvated states is 6 cm^?1. This implies that it should be possible to use a single set of scale factors to accurately predict the vibrational spectra of a peptide in a variety of conformational states. (2) The computationally predicted effect of hydration on force constants for the supermolecule NMA · nH₂O are generally consistent with the experimentally measured effects of hydration on scale factors. These results indicate that supermolecule calculations can be useful in predicting the effects of hydration on spectra. (3) Three types of scale factors are calculated as follows: (a) first from ab initio calculations on an isolated molecule using frequencies measured from isolated molecules; (b) second from calculations on an isolated molecule using frequencies measured from water-solvated or otherwise hydrogen-bonded molecules; (c) and third from supermolecule calculations on a molecule hydrogen-bonded to water, using frequencies measured from water-solvated molecules. (4) The third type of scale factors are similar to the first type, for confidently measured modes, even though some of the force constants are very different. This suggests that one set of scale factors may be transferable to both isolated and hydrogen-bonded molecules, and that the simple representation of hydration used here may be a useful approximation. The second type of scale factors yield accurate frequencies, but they may not be generally transferable.     

Study on mechanical properties of polyethylene with chain branching in atomic scale by molecular dynamics simulation

The effects of length and content of chain branching on the mechanical properties of polyethylene (PE) in atomic scale were examined by molecular dynamics (MD) simulations. Methyl-, ethyl- and butyl-groups were adopted as branched chains to distribute along PE backbones. Plastic flow deformation was captured by providing a uniaxial tensile loading at a given strain rate, which shows the characteristic of rate dependence. Current results are in reasonable agreements with existing experimental data. The statistical results show that the longer length of chain branching induces lower equilibrium density and higher yield strength of branched PE. In addition, higher content of chain branching brings higher equilibrium density and lower yield strength of branched PE. It is assumed that the distribution of dihedral angles influences the deformation of PE definitely. The non-bond interactions contribute to the load-bearing capacity of PE largely. Branched PE shows big differences on mechanical behaviours comparing with the linear one. Chain branching distribution also greatly affects the performance of PE, which needs a further discussion.     

Alkaline phosphatase inhibition by vanadyl-beta-diketone complexes: electron density effects

A series of systematically modified vanadyl-beta-diketone complexes, VO(beta-diketone)(2), bearing substituent groups with different electron inductive properties were synthesized and evaluated as inhibitors against calf-intestine alkaline phosphatase (APase). A combination of biochemical and quantum mechanical techniques were employed to identify structure-activity relationships relevant for rational design of phosphatase inhibitors. Kinetic parameters and activation free energy, enthalpy, and entropy for calf-intestine APase-catalyzed dephosphorylation of para-nitrophenylphosphate were also determined along with the inhibition constants (K(i)) for the VO(beta-diketone)(2) complexes. Increased positive charge on the vanadyl group increases the inhibition potency of the complex while the absence of an available coordination site on the complex decreases its inhibition potency. These findings correlate well with the results of ab initio electron density calculations for the complexes.     

Kinetic studies on human lactate dehydrogenase isoenzyme-catalyzed lactate-to-pyruvate reaction

In order to evaluate the functional differences that may exist in human lactate dehydrogenase (LDH) isoenzymes widely used for clinical examination the kinetic and thermodynamic properties of the lactate to pyruvate reaction that they catalize were examined. Small but significant differences in the kinetic properties of the three isoenzymes were observed. The difference in the rate constants might affect the activity measurement of the individual isoenzyme as the initial velocity for the L-P reaction catalyzed will not be the same for an equal amount of enzyme. Equilibrium constants for the overall reaction in the presence and absence of pyruvate have been determined. On the basis of transition-state theory, the standard enthalpy and free-energy changes for formation of ternary activated complex were positive, while the standard entropy change was negative. Although the standard free-energy change was the same for activation by the three isoenzymes, the enthalpy and entropy changes for the LDH-3-catalyzed reaction were different from the respective values for others. A large positive value for the free-energy change and a negative value for the entropy change indicated unfavorable production of the activated complex (K _infeq. ^sup╪ =1.89×10^-16). The enzyme appears to stabilize and retain the activated complex until it dissociates into the products.     

Kinetic analysis of site-specific photoaptamer-protein cross-linking

ssDNA oligonucleotides containing bromodeoxyuridine, BrdU-photoaptamers, are rapidly emerging as specific protein capture reagents in protein microarray technologies. A mathematical model for the kinetic analysis of photoaptamer-protein photocross-linking reactions is presented. The model is based on specific aptamer/protein binding followed by laser excitation that can lead to either covalent cross-linking of the photoaptamer and protein in the complex or irreversible photodamage to the aptamer. Two distinct kinetic regimes, (1) frozen and (2) rapid equilibrium, are developed analytically to model binding kinetics between laser pulses. The models are used to characterize the photocross-linking between three photoaptamers and their cognate protein targets; photoaptamers 0650 and 0615 cross-link human basic fibroblast growth factor and 0518 cross-links HIV MN envelope glycoprotein. Data for cross-linking reaction yields as a function of both laser energy dose and target protein concentration are analyzed for affinity constants and cross-link reaction rates. The binding dissociation constants derived from the cross-linking data are in good accord with independent measurements; the rapid equilibrium model appears to produce results more consistent with the experimental observations, although there is significant overlap between the two models for most conditions explored here. The rate of photodamage for 0615 and 0518 is 3.5 and 2.5 times that of the specific cross-link, giving low maximum reaction yields of approximately 20% and approximately 30%, whereas 0650 cross-links with a rate over five times higher than its photodamage rate and has a maximum reaction yield exceeding 80%. Quantum yields for the three systems are estimated from the data; photoaptamer 0650 has a reasonably high quantum yield of approximately 0.2 for protein cross-linking, while 0518 and 0615 have quantum yields of 0.07 and 0.02. The work presented here provides a useful set of metrics that allow for refinement of photoaptamer properties.     

Flash photolysis studies on the CO complexes of ferrous cytochrome P-450scc and cytochrome P-45011 beta. Effects of steroid binding on the photochemical and ligand binding properties

Upon irradiation by a light flash (100-J), the carbon monoxide complex of cytochrome P-450scc was fully photodissociated in both the presence and absence of cholesterol, while less than 20% of the CO complex was photodissociable with those of deoxycorticosterone-bound and -free forms of cytochrome P-45011 beta. When the quantum yield of the reaction was measured for each photodissociable portion, the values were 0.5 and 1.0 for the substrate-free and -bound forms of cytochrome P-450scc, and 0.03 and 0.8 for the substrate-free and -bound forms of cytochrome P-45011 beta, respectively. Thus, CO complexes of these enzymes become more photosensitive upon binding with the specific substrates. Steroid binding also affected kinetic constants of reactions between the ferrous enzymes and CO. The rate constants for the CO recombination at 15 degrees C were 2.7 X 10(6) and 2.3 X 10(5) M-1 s-1 for the substrate-free and -bound forms of cytochrome P-450scc, and were 7.0 X 10(5) and 5.4 X 10(3) M-1 s-1 for the substrate-free and -bound forms of cytochrome P-45011 beta, respectively. The rate constants for the CO dissociation also decreased upon the steroid bindings. The products of the enzyme reactions, pregnenolone and corticosterone, had similar effects on the kinetic constants. From these findings, we postulate that the binding of a steroid to the substrate site of each enzyme alters the bonding character of CO with the heme-iron, thereby affecting both photochemical and kinetic properties of the CO complex. The nature of the photoindissociable portion of the CO complex of cytochrome P-45011 beta is also discussed.