Analysis of the pharmacological properties of clozapine analogues using molecular electrostatic potential surfaces

Molecular electrostatic potential surfaces have been used to study a series of neuroleptic compounds, clozapine and clozapine analogues, with similar structures but two rather different pharmacological profiles. Using the electrostatic potential surfaces, the compounds studied could be assigned to one of two distinct categories corresponding to the two pharmacological classes. The results of this study suggest that the molecular electrostatic potential surfaces may be useful in the a priori prediction of pharmacological properties of untested clozapine analogues.     

Inclusion of solvation free energy with molecular mechanics energy: alanyl dipeptide as a test case.

A combined force field of molecular mechanics and solvation free energy is tested by carrying out energy minimization and molecular dynamics on several conformations of the alanyl dipeptide. Our results are qualitatively consistent with previous experimental and computational studies, in that the addition of solvation energy stabilizes the C5 conformation of the alanyl dipeptide relative to the C7.     

Electrostatic interactions in proteins: Calculations of the electrostatic term of free energy and the electrostatic potential field

The pH-dependence of the electrostatic energy of interactions between titratable groups is calculated for some well studied globular proteins: basic pancreatic trypsin inhibitor, sperm whale myoglobin and tuna cytochrome c. The calculations are carried out using a semi-empirical appraach in terms of the macroscopic model based on the Kirkwood-Tanford theory. The results are discussed in the light of their physicochemical and biological properties. It was found that the pH-dependence of the electrostatic energy correlates with the III–IV transition of cytochrome c. The electrostatic field of the cysteine proteinase inhibitor, cystatin, was calculated in two ways. In the first one, the electrostatic field created by the pH dependent charges of the ionizable groups and peptide dipoles was calculated using the approach proposed. In the second one, the finite-difference method was used. The results obtained by the two methods are in overall agreement. The calculated field was discussed in terms of the binding of cystatin to papain.     

A self-consistent calculation of the free energy and electrostatic potential for a cylindrical polyion

The linearized Poisson-Boltzmann equation is solved for a cylindrical polyion immersed in an ionic solution of specified pH and ionic strength. The boundary condition at the surface of the cylinder is determined self-consistently, so that the only input required is the density of ionizable groups on the cylinder surface and their dissociation characteristics. An expression is also derived for the free energy of the system and it is shown that the degree of dissociation calculated via the self-consistent boundary condition yields the minimum value of the free energy. Calculations are presented for parameters that are relevant to several systems of biological interest and the response of the system to changes in pH and ionic strength is discussed in detail.     

Relation between the molecular electrostatic potential and activity of some FF-MAS related sterol compounds

Follicular Fluid-Meiosis Activating Sterol (FF-MAS) is a compound important for maturation of gametes in mammals. Therefore, it may serve as a lead compound for a novel method of contraception. We studied the Molecular Electrostatic Potential of a series of active and inactive analogues of FF-MAS. We find that double bond configurations required for activity result in a local negative electrostatic potential which is larger as well as more dense compared to those of inactive molecules. We therefore hypothesize that the interaction energy of the double bond system of the MAS compounds with its receptor substantially contributes to the overall interaction energy. This notion is supported by interaction studies of the electrostatic potential originating from the double bonds in crystal structures of cholesterol and four MAS-derived Delta(8,14) structures synthesized and crystallized by us. In addition, we were able to derive a pharmacophore model that relates the local average ESP and its distance to the 3beta-OH oxygen atom to the activity of the molecules.     

Free-energy analysis of protein solvation with all-atom molecular dynamics simulation combined with a theory of solutions

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The use of the electrostatic potential at the molecular surface in recognition interactions: Dibenzo-p-dioxinsand related systems

An ab initio self-consistent-field molecular orbital approach was used to compute the electrostatic potentials of dibenzo-p-dioxin, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), two analogues of the latter, and two isomeric benzoflavones on a three-dimensional molecular surface corresponding to the contour of constant electronic density equal to 0.002 electrons/bohr³. The results are discussed in relation to the biological activities of the respective molecules. It is shown that the electrostatic potential graphically depicted on the molecular surface is well suited for the study of recognition interactions, such as are believed to be involved in the initial receptor-mediated step leading to toxicity in the dibenzo-p-dioxins. The surface potential has the advantage of clearly showing steric features that may play a role in understanding the recognition process being investigated.     

Enhanced sampling of the molecular potential energy surface using mutually orthogonal latin squares: application to peptide structures

The computational identification of the optimal three-dimensional fold of even a small peptide chain from its sequence, without reference to other known structures, is a complex problem. There have been several attempts at solving this by sampling the potential energy surface of the molecule in a systematic manner. Here we present a new method to carry out the sampling, and to identify low energy conformers of the molecule. The method uses mutually orthogonal Latin squares to select (of the order of) n(2) points from the multidimensional conformation space of size m(n), where n is the number of dimensions (i.e., the number of conformational variables), and m specifies the fineness of the search grid. The sampling is accomplished by first calculating the value of the potential energy function at each one of the selected points. This is followed by analysis of these values of the potential energy to obtain the optimal value for each of the n-variables separately. We show that the set of the n-optimal values obtained in this manner specifies a low energy conformation of the molecule. Repeated application of the method identifies other low energy structures. The computational complexity of this algorithm scales as the fourth power of the size of the molecule. We applied this method to several small peptides, such as the neuropeptide enkephalin, and could identify a set of low energy conformations for each. Many of the structures identified by this method have also been previously identified and characterized by experiment and theory. We also compared the best structures obtained for the tripeptide (Ala)(3) by the present method, with those obtained by an exhaustive grid search, and showed that the algorithm is successful in identifying all the low energy conformers of this molecule.     

Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis

In this report we describe an accurate numerical method for calculating the total electrostatic energy of molecules of arbitrary shape and charge distribution, accounting for both Coulombic and solvent polarization terms. In addition to the solvation energies of individual molecules, the method can be used to calculate the electrostatic energy associated with conformational changes in proteins as well as changes in solvation energy that accompany the binding of charged substrates. The validity of the method is examined by calculating the hydration energies of acetate, methyl ammonium, ammonium, and methanol. The method is then used to study the relationship between the depth of a charge within a protein and its interaction with the solvent. Calculations of the relative electrostatic energies of crystal and misfolded conformations of Themiste dyscritum hemerythrin and the VL domain of an antibody are also presented. The results indicate that electrostatic charge-solvent interactions strongly favor the crystal structures. More generally, it is found that charge-solvent interactions, which are frequently neglected in protein structure analysis, can make large contributions to the total energy of a macromolecular system.     

Free energy surface for rotamers of cis-enol malonaldehyde in aqueous solution studied by molecular dynamics calculations

Two-dimensional free energy surfaces for four rotamers of cis-enol malonaldehyde in water have been investigated by umbrella sampling molecular dynamics (MD) calculations. Biasing potential used in the umbrella sampling calculation was adopted to be the minus of conformational free energy preliminary obtained by the thermodynamic integration MD calculations for the rigid malonaldehyde whose stretching and bending were all fixed. The calculated free energy surface shows that, in water, a rotamer that has an intramolecular hydrogen bond is most stable among the rotamers. This is the same as that in vacuum, while order of relative stability of the other three rotamers is different in water and in vacuum. Inclusion of intramolecular vibrations changed the free energy surface little, i.e. at most 2.6 kJ/mol, which is much smaller than the solvation free energy. Free energy barriers from the most stable intramolecular hydrogen bonded rotamer to the others are lowered by hydration but they are still very high, >50 kJ/mol, such that the malonaldehyde molecule spends most of its time in water taking this conformation. Thus, reaction coordinate for intramolecular proton transfer reaction in water may be constructed assuming this rotamer.     

根据分子连接性指数和基团校正因子预测有机化合物在鱼体中的生物富集因子

研究了２３９种有机化合物的ＢＣＦ预测模型,结果显示根据分子连接性指数（ＭＣＩ）的线性模型不能准确计算及极性化合物的ＢＣＦ,也不适用于超疏水性化合物,在模型中引入基团校正因子后,极性经合物的计算误差明显降低。对数据进行曲线拟合,所得模型的估算精度进一步提高,最终确定以（＾０ｘ＾ｖ）＾２、（＾２ｘ＾ｖ）＾１／２、＾２ｘ、＾３ｘｃ、＾０ｘ＾ｖ及ＯＨ、ＮＨ２、ＮＯ２、ＮＣＯＯ等１０个基团校正团子为参数建立     

Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: a molecular dynamics study

Molecular dynamics (MD) simulations were used to study the stability and solvation of amylose and cellulose fragments. The recently developed gromos carbohydrate force field was further tested by simulating maltose, cellobiose, and maltoheptaose. The MD simulations reproduced fairly well the favorable conformations of disaccharides defined by the torsional angles related with the glycosidic bond and the radius gyration of maltoheptaose. The effects of methylation at different hydroxyl groups on the stability of amylose and cellulose fragments were investigated. The methylations of O-2 and O-3 reduce the stability of a single helix more than methylation at O-6, while the latter reduces the stability of a double helix more. Solvation free-energy differences between the unsubstituted amylose and cellulose fragments and the methylated species were studied using the single-step perturbation method. It was found that methylation at O-2 has the biggest effect, in agreement with experiment.     

Simulating the folding of small proteins by use of the local minimum energy and the free solvation energy yields native-like structures

Assuming that the protein primary sequence contains all information required to fold a protein into its native tertiary structure, we propose a new computational approach to protein folding by distributing the total energy of the macromolecular system along the torsional axes.We further derive a new semiempirical equation to calculate the total energy of a macromolecular system including its free energy of solvation. The energy of solvation makes an important contribution to the stability of biological structures. The segregation of hydrophilic and hydrophobic domains is essential for the formation of micelles, lipid bilayers, and biological membranes, and it is also important for protein folding. The free energy of solvation consists of two components: one derived from interactions between the atoms of the protein, and the second resulting from interactions between the protein and the solvent. The latter component is expressed as a function of the fractional area of protein atoms accessible to the solvent.The protein-folding procedure described in this article consists of two successive steps: a theoretical transition from an ideal α helix to an ideal β sheet is first imposed on the protein conformation, in order to calculate an initial secondary structure. The most stable secondary structure is built from a combination of the lowest energy structures calculated for each amino acid during this transition. An angular molecular dynamics step is then applied to this secondary structure. In this computational step, the total energy of the system consisting of the sum of the torsional energy, the van der Waals energy, the electrostatic energy, and the solvation energy is minimized. This process yields 3-D structures of minimal total energy that are considered to be the most probable native-like structures for the protein.This method therefore requires no prior hypothesis about either the secondary or the tertiary structure of the protein and restricts the input of data to its sequence. The validity of the results is tested by comparing the crystalline and computed structures of four proteins, i.e., the avian and bovine pancreatic polypeptide (36 residues each), uteroglobin (70 residues), and the calcium-binding protein (75 residues); the C_α-C_α maps show significant homologies and the position of secondary structure domains; that of the α helices is particularly close.     

The molecular mechanics program DUPLEX: Computing structures of carcinogen modified DNA by surveying the potential energy surface

The nucleic acids molecular mechanics program DUPLEX has been designed with useful features for surveying the potential energy surface of polynucleotides, especially ones that are modified by polycyclic aromatic carcinogens. The program features helpful strategies for addressing the multiple minimum problem: (1) the reduced variable domain of torsion angle space; (2) search strategies that emphasize large scale searches for smaller subunits, followed by building to larger units by a variety of strategies; (3) the use of penalty functions to aid the minimizer in locating selected structural types in first stage minimizations; penalty functions are released in terminal minimizations to yield final unrestrained minimum energy conformations. Predictive capability is illustrated by DNA modified by activated benzo[a]pyrenes.     

Optimization of ultrasound-assisted aqueous two-phase system extraction of polyphenolic compounds from Aronia melanocarpa pomace by response surface methodology

Aronia melanocarpa berries are abundant in polyphenolic compounds. After juice production, the pomace of pressed berries still contains a substantial amount of polyphenolic compounds. For efficient utilization of A. melanocarpa berries and the enhancement of polyphenolic compound yields in Aronia melanocarpa pomace (AMP), total phenolics (TP) and total flavonoids (TF) from AMP were extracted, using ultrasound-assisted aqueous two-phase system (UAE-ATPS) extraction method. First, the influences of ammonium sulfate concentration, ethanol–water ratio, ultrasonic time, and ultrasonic power on TP and TF yields were investigated. On this basis, process variables such as ammonium sulfate concentration (0.30–0.35?g?mL^?1), ethanol–water ratio (0.6–0.8), ultrasonic time (40–60?min), and ultrasonic power (175–225?W) were further optimized by implementing Box–Benhnken design with response surface methodology. The experimental results showed that optimal extraction conditions of TP from AMP were as follows: ammonium sulfate concentration of 0.324?g?mL^?1, ethanol–water ratio of 0.69, ultrasonic time of 52?min, and ultrasonic power of 200?W. Meanwhile, ammonium sulfate concentration of 0.320?g?mL^?1, ethanol–water ratio of 0.71, ultrasonic time of 50?min, and ultrasonic power of 200?W were determined as optimum extraction conditions of TF in AMP. Experimental validation was performed, where TP and TF yields reached 68.15?±?1.04 and 11.67?±?0.63?mg?g^?1, respectively. Close agreement was found between experimental and predicted values. Overall, the present results demonstrated that ultrasound-assisted aqueous two-phase system extraction method was successfully used to extract total phenolics and flavonoids in A. melanocarpa pomace.     

Purification of plasmid DNA with polymer-salt aqueous two-phase system: optimization using response surface methodology

An experimental design was used to optimize plasmid purification from an alkaline lysate of Escherichia coli cells using PEG-sodium citrate aqueous two-phase systems (ATPS), and to evaluate the influence of pH, PEG molecular weight, tie line length, phase volume ratio, and lysate load. To build the mathematical model and minimize the number of experiments for the design parameters, response surface methodology (RMS) with an orthogonal rotatable central composite design was defined based on the conditions found for the highest purification by preliminary tests. The adequacy of the calculated models for the plasmid recovery and remaining RNA were confirmed by means of variance analysis and additional experiments. Analysis of contours of constant response as a function of pH, PEG molecular weight, tie line length, and cell lysate load for three different phase volume ratios revealed different effects of these five factors on the studied parameters. Plasmid recovery of 99% was predicted for a system with PEG 400, pH 6.9, tie line length of 38.7%, phase volume ratio of 1.5, and lysate load of 10% (v/v). Under these conditions the predicted RNA removal was 68%.     

Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces

Protein-DNA interactions play an essential role in the genetic activities of life. Many structures of protein-DNA complexes are already known, but the common rules on how and where proteins bind to DNA have not emerged. Many attempts have been made to predict protein-DNA interactions using structural information, but the success rate is still about 80%. We analyzed 63 protein-DNA complexes by focusing our attention on the shape of the molecular surface of the protein and DNA, along with the electrostatic potential on the surface, and constructed a new statistical evaluation function to make predictions of DNA interaction sites on protein molecular surfaces. The shape of the molecular surface was described by a combination of local and global average curvature, which are intended to describe the small convex and concave and the large-scale concave curvatures of the protein surface preferentially appearing at DNA-binding sites. Using these structural features, along with the electrostatic potential obtained by solving the Poisson-Boltzmann equation numerically, we have developed prediction schemes with 86% and 96% accuracy for DNA-binding and non-DNA-binding proteins, respectively.     

Calculation of the relative binding free energy of 2'GMP and 2'AMP to ribonuclease T1 using molecular dynamics/free energy perturbation approaches

We present a calculation of the relative changes in binding free energy between the complex of ribonuclease T1 (RNase Tr) with its inhibitor 2'-guanosine monophosphate (2'GMP) and that of RNase T1-2'-adenosine monophosphate (2'AMP) by means of a thermodynamic perturbation method implemented with molecular dynamics. Using the available crystal structure of the RNase T1-2'GMP complex, the structure of the RNase T1-2'AMP complex was obtained as a final structure of the perturbation calculation. The calculated difference in the free energy of binding (delta delta Gbind) was 2.76 kcal/mol. This compares well with the experimental value of 3.07 kcal/mol. The encouraging agreement in delta delta Gbind suggests that the interactions of inhibitors with the enzyme are reasonably represented. Energy component analyses of the two complexes reveal that the active site of RNase T1 electrostatically stabilizes the binding of 2'GMP more than that of 2'AMP by 44 kcal/mol, while the van der Waals' interactions are similar in the two complexes. The analyses suggest that the mutation from Glu46 to Gln may lead to a preference of RNase T1 for adenine in contrast to the guanine preference of the wild-type enzyme. Although the molecular dynamics equilibration moves the atoms of the RNase T1-2'GMP system about 0.9 A from their X-ray positions and the mutation of the G to A in the active site increases the deviation from the X-ray structure, the mutation of the A back to G reduces the deviation. This and the agreement found for delta delta Gbind suggest that the molecular dynamics/free energy perturbation method will be useful for both energetic and structural analysis of protein-ligand interactions.