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The aim of the study reported here was to develop a regression equation for predicting oral clearance of various kinds of drugs in humans using experimental data from rats and dogs and molecular structural parameters. The data concerning the oral clearance of 87 drugs from rats, dogs, and humans were obtained from literature. The compounds have various structures, pharmacological activities, and pharmacokinetic characteristics. In addition, the molecular weight, calculated partition coefficient (c log P), and the number of hydrogen bond acceptors were used as possible descriptors related to oral clearance in human. Multivariate regression analyses, multiple linear regression analysis, and the partial least squares (PLS) method were used to predict oral clearance in human, and the predictive performances of these techniques were compared by allometric approaches, which have been used in interspecies scaling. Interaction terms were also introduced into the regression analysis to evaluate the nonlinear relationship. For the data set used in this study, the PLS model with the tertiary term descriptors gave the best predictive performance, and the value of the squared cross-validated correlation coefficient (q(2)) was 0.694. This PLS model, using animal oral clearance data for only two species and easily calculated molecular structural parameters, can generally predict oral clearance in human better than the allometric approaches. In addition, the molecular structural parameters and the interaction term descriptors were useful for predicting oral clearance in human by PLS. Another advantage of this PLS model is that it can be applied to drugs with various characteristics.
Several Ni(II) complexes derived from (S)-o-N-(N-benzylprolyl)aminobenzophenone ((S)-BBP) and amino acids of general formula [Ni((S)-BBP-L-(or D-)-aa)] were prepared. The crystal and molecular structures of [Ni((S)-BBP-Gly)], [Ni((S)-BBP-L-Ser)] and [Ni((S)-BBP-L-aaIm)](aaIm =L-2-amino-3-(imidazol-1-yl)propanoate were determined by X-ray diffraction analysis. In the three complexes the nickel atoms display a square-planar coordination and the overall structure around the metal indicates that the entire Schiff-base ligands form quite rigid frameworks. Molecular mechanics calculations were carried out for complexes [Ni((S)-BBP-Gly)], [Ni((S)-BBP-Ser)] and [Ni((S)-BBP-aaIm)] containing either the L- or D-amino acid forms, and the factors controlling the stereoselectivity are discussed. Several other [Ni((S)-BBP-L-aa)] complexes are also prepared and their circular dichroism spectra in solution and of the solids dispersed in KBr disks are measured and discussed. In agreement with other studies in solution with similar [Ni((S)-BBP-aa)] complexes, the Cotton effects for the bands with lambda(max) at 520--530 nm are positive when the amino acids have the L-configuration at the alpha-carbon. The same is observed in this work for the solid-state CD spectra of all compounds.
From the experimental crystal structure and ab initio calculations on resveratrol and its derivatives, structural features of mechanistic importance are described. The molecular structure reveals the relative coplanarity of the trans-stilbene skeleton, and the molecular packing in the solid state shows an extensive hydrogen bond network that elucidates the flip-flop motion of the three hydroxyl groups that alternately form and break H bonds with each of the neighboring phenolic oxygens. The dynamic behavior provoked by the alternation of hydrogen bond formation and breaking can result in the ready mobility of up to three hydrogen atoms per resveratrol molecule that can be transferred to reactive oxidants that are rich in electron density. In addition, theoretical studies confirm the planarity of resveratrol as well as for half of the molecule of a condensation dimeric derivative of resveratrol, trans-sigma-viniferin. Furthermore, these studies show the p-4'-OH group to be more acidic compared to the other two m-OH groups. These features correlate with the biological activity of resveratrol as an antioxidant and support earlier studies showing H-atom transfer to be the dominant mechanism by which phenolic antioxidants intercept free radicals.
Sonochemical bleaching of monoazo dyes was investigated by irradiating 30 microM solutions of two "aryl-azo-naphthol" type model dyes in acidic, neutral and basic conditions using a 300 kHz emitter. It was found that the rate of bleaching in all cases was first order with respect to the maximum absorption of the dye in the visible band, and accelerated with increased acidity. The inhibition observed at alkaline conditions was attributed to the formation of anionic dye structures and their competition with the dye and its intermediate oxidation products for hydroxyl radicals, which are the major precursors of azo dye oxidation in sonicated water. Decolorization of the dyes was also related to the size of the molecule and the type or position of substituents about azo bonds. Comparison of color decay rates at similar conditions showed that the dye with a simple structure, low molecular mass and one ortho-substituent (hydroxyl) about the azo bond bleached considerably faster than the one having a more complicated structure (higher mass) and an additional o-substituent to the azo bond other than the OH group.
The task of computing molecular structure from combinations of experimental and theoretical constraints is expensive because of the large number of estimated parameters (the 3D coordinates of each atom) and the rugged landscape of many objective functions. For large molecular ensembles with multiple protein and nucleic acid components, the problem of maintaining tractability in structural computations becomes critical. A well-known strategy for solving difficult problems is divide-and-conquer. For molecular computations, there are two ways in which problems can be divided: (1) using the natural hierarchy within biological macromolecules (taking advantage of primary sequence, secondary structural subunits and tertiary structural motifs, when they are known); and (2) using the hierarchy that results from analyzing the distribution of structural constraints (providing information about which substructures are constrained to one another). In this paper, we show that these two hierarchies can be complementary and can provide information for efficient decomposition of structural computations. We demonstrate five methods for building such hierarchies--two automated heuristics that use both natural and empirical hierarchies, one knowledge-based process using both hierarchies, one method based on the natural hierarchy alone, and for completeness one random hierarchy oblivious to auxiliary information--and apply them to a data set for the procaryotic 30S ribosomal subunit using our probabilistic least squares structure estimation algorithm. We show that the three methods that combine natural hierarchies with empirical hierarchies create decompositions which increase the efficiency of computations by as much as 50-fold. There is only half this gain when using the natural decomposition alone, while the random hierarchy suggests that a speedup of about five can be expected just by virtue of having a decomposition. Although the knowledge-based method performs marginally better, the automatic heuristics are easier to use, scale more reliably to larger problems, and can match the performance of knowledge-based methods if provided with basic structural information.
The molecular structure of the formal iron(IV) porphyrinate derivative, [[Fe(TTP)]2N]SbCl6 (TTP = tetratolylporphyrinate), is reported. The structural parameters are compared to the previously reported species [Fe(TPP)]2N, in which the iron oxidation state is +3.5. Both the equatorial and axial bond distances in [[Fe(TTP)]2N]SbCl6 are slightly shortened and consistent with an increased formal charge on iron. The value for the axial Fe-N distance is 1.6280(7) A, and the average value of the equatorial Fe-Np distances is 1.979(5) A. The Mössbauer isomer shift decreases upon oxidation, again consistent with an increase in formal charge. Values for the isomer shift at room temperature are -0.13 mm/s for [[Fe(TTP)]2N]SbCl6 and 0.04 mm/s for [Fe(TTP)]2N. Crystal data for [[Fe(TTP)]2N]SbCl6 are as follows: orthorhombic, space group Fddd, Z = 8, a = 23.689(2) A, b = 31.056(3) A, c = 22.7788(18) A.
In this work, a hierarchic system of QSAR models from 1D to 4D is considered on the basis of the simplex representation of molecular structure (SiRMS). The essence of this system is that the QSAR problem is solved sequentially in a series of the improved models of the description of molecular structure. Thus, at each subsequent stage of a hierarchic system, the QSAR problem is not solved ab ovo, but rather the information obtained from the previous step is used. Actually, we deal with a system of solutions defined more exactly. In the SiRMS approach, a molecule is represented as a system of different simplex descriptors (tetratomic fragments with fixed composition, structure, chirality and symmetry). The level of simplex-descriptor detail increases consecutively from 1D to 4D representations of molecular structure. It enables us to determine the fragments of structure that promote or interfere with the given biological activity easily. Molecular design of compounds with a given level of activity is possible on the basis of SiRMS. The efficiency of the method is demonstrated for the example of the analysis of substituted piperazines affinity for the 5-HT1A receptor.
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A short account is presented of the method of measuring molecular masses (M(r)) of pure biological samples by electrospray ionisation mass spectrometry. It is demonstrated that the technique yields M(r) values with an effective accuracy equal to or better than 0.008% of the calculated M(r), provided that the correct molecular structure is employed in the calculation. It is therefore recommended that this method of measuring M(r)'s should be considered to form an essential part of all studies aimed at elucidating the molecular structure of purified biological macromolecules or for confirming the identity of labelled samples of such molecules.
To elucidate critical genetic elements in the development of hepatocellular carcinoma associated with hepatitis B virus DNA integration, a single integrant in hepatocellular carcinoma cells and one species of multiple integrants in hepatocytes, both obtained from the same patient, were compared structurally using molecular cloning techniques. Both hepatitis B virus integrants showed similar inverted repeat sequences consisting of two defective virus genomes. The recombination of viral DNAs seemed to be mediated by short regions of base homology near the direct repeat 1 and at other regions of the virus genomes in both integrants. The virus component in the junction with host DNAs was the cohesive end region in each identical end of the viral integrant in hepatocellular carcinoma cells and in one end of the viral integrant in hepatocytes. The structure of the integrant in hepatocellular carcinoma cells was characterized by an inverted, duplicated conformation composed not only of integrated virus genomes but also of flanking cellular sequences. It was shown to be the so-called "alpha dimer" of satellite DNA. In contrast, the flanking, nonreiterated cellular DNA in the hepatocyte-derived clone did not show discernible rearrangement. These findings suggest that a common mechanism underlies the integration of hepatitis B virus DNA so that a similar organization of inverted repeat genomes is found in hepatocellular carcinoma cells and in hepatocytes. The unstable nature of cellular DNA where DNA integration occurs may be important in generating chromosome alterations found in hepatocellular carcinoma.
The structure, conformation, molecular geometry and the mode of packing of 7-tert-butyl-N-methyl-2,4-diphenyl-3-azabicyclo[3.3.1]nonane (C(25)H(33)N; MTABN), N-acetyl-2,4-diphenyl-3-azabicyclo[3.3.1]nonane (C(22)H(25)NO; AABN) and N-methyl-2,4-bis(2-methylphenyl)-3-azabicyclo[3.3.1]nonan-9-ol (C(23)H(29)NO; MHABN) are presented. The compounds MTABN and MHABN crystallize in monoclinic space groups, whereas AABN is orthorhombic. In each of the three structures, the bicyclic ring system adopts a chair-chair conformation and the phenyl rings are in equatorial orientation with respect to the piperidine ring. In AABN, apart from the van der Waals forces, weak intermolecular C-H.O type interactions are involved in the packing.
A molecular structural criterion of ligand selectivity for the 5-HT2 versus 5-HT1C receptor was hypothesized on the basis of radioligand binding data. Despite the large number of compounds which have been tested at both receptors, analysis of published data led to the identification of only five agents which are greater than 10-fold selective for the 5-HT2 versus the 5-HT1C receptor. Comparison of the two-dimensional structures revealed that, although these five compounds represent three distinct structural classes, they share a common structural feature located in the region hypothesized to be involved in receptor binding: a carbonyl or carboxyl oxygen interposed spatially between an aromatic ring and nitrogen atom. This structural feature was used to predict the relative selectivity of compounds that had not previously been analyzed at both the 5-HT2 and 5-HT1C receptors. All six drugs tested which contain the identified reactive carbonyl or carboxyl group were found to be selective for the 5-HT2 versus the 5-HT1C receptor with selectivity ratios ranging from 26 to 380. By contrast, three agents which are structurally similar but do not contain the reactive carbonyl or carboxyl group displayed equally high affinity for both receptor binding sites. Since the physiological roles of the 5-HT2 and 5-HT1C receptor are markedly different, it would be of potential clinical and scientific value to utilize this molecular structural feature to further identify chemical compounds which would selectively interact with only one of the two receptors.
Dilated cardiomyopathy is characterized by decreased contractile function and loss of myofibril organization. Previously unexplored structural and molecular events that precede and initiate dilation can now be studied in tropomodulin-overexpressing transgenic (TOT) mice exhibiting progressive dilated cardiomyopathy. Onset of dilation did not correspond to a change in transgene expression levels, which were more than threefold above normal at birth and remained elevated throughout postnatal life. Similarly, mitogen-activated protein kinase activation (p38, ERK1/ERK2, JNK1/JNK2) was not associated with dilation. In contrast, calcineurin was activated before dilation, presumably due to doubling of intracellular diastolic calcium levels in TOT cardiomyocytes. Amplitude of systolic calcium transients was greatly increased as well, demonstrating the novel and unique calcium handling profile of TOT cardiomyocytes. Loss of myofibril organization was not apparent by confocal microscopy until over 1 week after birth, although neonatal sarcomeric abnormalities were revealed by ultrastructural analysis. Rapid postnatal increases in heart:body weight ratio at 1.5 weeks were followed by two waves of mortality between 2 and 3 weeks after birth coincident with maturational stress. Ultimately, TOT pathogenesis is a compensatory response to altered sarcomeric structure driven by calcineurin activation within days after birth, making TOTs an excellent paradigm for studying the role of calcium overload in dilated cardiomyopathy.
We have equipped our graphics library with efficient functions so that a molecular structure viewer program can provide both portability and high-throughput rendering without hardware acceleration. The library renders graphics primitives into off-screen image memory with novel functions such as a point list for the vertices of three-dimensional graphical primitives, scan conversions of sphere and cylinder primitives, and z-buffered bit-block transfer. A molecular structure viewer program was implemented with the graphics library, giving reasonable rendering performance on conventional UNIX workstations with the X-Window system. The use of dynamic linking also lends a flexible extension facility to this software system. An advanced polygon renderer can be provided as an plug-in style extension module as well as other functional modules that are specific to the application program. The design of our graphics library is not only effective in molecular graphics but is also applicable for general three-dimensional graphics software systems.
Abnormal conduction is fundamental to the pathogenesis of both atrial fibrillation and ventricular tachycardia/fibrillation. Normal atrial and ventricular myocytes express different combinations of multiple gap junction channel proteins and are interconnected by gap junctions in markedly different spatial distributions. These observations suggest that the disparate anisotropic conduction properties of atrial and ventricular muscle are determined, in part, by both structural and molecular features of gap junctions. Alterations in gap junctional coupling likely contribute to conduction abnormalities underlying reentrant atrial or ventricular arrhythmias.
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