Prediction of prognosis in patients with left ventricular dysfunction using three-dimensional strain echocardiography and cardiac magnetic resonance imaging.

BACKGROUND: We evaluated three-dimensional speckle tracking echocardiography (3DSTE) strain and cardiac magnetic resonance (CMR) with delayed contrast enhancement (DCE) for the prediction of cardiac events in left ventricular (LV) dysfunction. METHODS: CMR and 3DSTE in 75 patients with ischaemic and 38 with non-ischaemic LV dysfunction were analysed and temporally correlated to cardiac events during 41 ± 9 months of follow-up. RESULTS: Cardiac events occurred in 44 patients, more in patients with ischaemic LV dysfunction. LV ejection fraction (LVEF), global circumferential and global area strain were reduced more in patients with more cardiac events, whereas 3DSTE LV end-systolic volumes and 3DSTE LV masses were larger. However, the area under the curve using receiver-operating characteristic analysis showed modest sensitivity and specificity for all evaluated parameters. Additionally, DCE did not differ significantly between the two groups. Univariate analysis showed ischaemic aetiology of LV dysfunction, LVEF and LV mass by CMR to be predictors of cardiac events with an increased relative risk of 2.4, 1.6 and 1.5, respectively. By multivariate analysis, only myocardial ischaemia and LVEF ≤ 39% were independent predictors of events (p = 0.004 and 0.005, respectively). Subgroup analysis in ischaemic and non-ischaemic patients showed only 3DSTE LV mass in ischaemic patients to have a significant association (p = 0.033) but without an increased relative risk. CONCLUSION: LVEF calculated by 3DSTE or CMR were both good predictors of cardiac events in patients with LV dysfunction. A reduced LVEF ≤ 39% was associated with a 1.6-fold higher probability of a cardiac event. 3DSTE strain measurements and DCE-CMR did not add to the prognostic value of LVEF.

On the efficiency of VBSCF algorithms, a comment on "An efficient algorithm for energy gradients and orbital optimization in valence bond theory".

We comment on the paper [Song et al., J. Comput. Chem. 2009, 30, 399]. and discuss the efficiency of the orbital optimization and gradient evaluation in the Valence Bond Self Consistent Field (VBSCF) method. We note that Song et al. neglect to properly reference Broer et al., who published an algorithm [Broer and Nieuwpoort, Theor. Chim. Acta 1988, 73, 405] to use a Fock matrix to compute a matrix element between two different determinants, which can be used for an orbital optimization. Further, Song et al. publish a misleading comparison with our VBSCF algorithm [Dijkstra and van Lenthe, J. Chem. Phys. 2000, 113, 2100; van Lenthe et al., Mol. Phys. 1991, 73, 1159] to enable them to favorably compare their algorithm with ours. We give detail timings in terms of different orbital types in the calculation and actual timings for the example cases.

Starting SCF calculations by superposition of atomic densities.

We describe the procedure to start an SCF calculation of the general type from a sum of atomic electron densities, as implemented in GAMESS-UK. Although the procedure is well known for closed-shell calculations and was already suggested when the Direct SCF procedure was proposed, the general procedure is less obvious. For instance, there is no need to converge the corresponding closed-shell Hartree-Fock calculation when dealing with an open-shell species. We describe the various choices and illustrate them with test calculations, showing that the procedure is easier, and on average better, than starting from a converged minimal basis calculation and much better than using a bare nucleus Hamiltonian.

Inhibition and substrate recognition--a computational approach applied to HIV protease.

We have developed a computational approach in which an inhibitor's strength is determined from its interaction energy with a limited set of amino acid residues of the inhibited protein. We applied this method to HIV protease. The method uses a consensus structure built from X-ray crystallographic data. All inhibitors are docked into the consensus structure. Given that not every ligand-protein interaction causes inhibition, we implemented a genetic algorithm to determine the relevant set of residues. The algorithm optimizes the q2 between the sum of interaction energies and the observed inhibition constants. The best possible predictive model resulting has a q2 of 0.63. External validation by examining the predictivity for compounds not used in derivation of the model leads to a prediction accuracy between 0.9 and 1.5 log10 unit. Out of 198 residues in the whole protein, the best internally predictive model defines a subset of 20 residues and the best externally predictive model one of 9 residues. These residues are distributed over the subsites of the enzyme. This approach provides insight in which interactions are important for inhibiting HIV protease and it allows for quantitative prediction of inhibitor strength.

Metal-to-ligand electron transfer in diiminopyridine complexes of Mn-Zn. A theoretical study.

A series of complexes ML2(x+) (M = Mn-Zn, L = 2,6-bis(iminomethyl)pyridine) was investigated by theoretical methods. Electron transfer from the metal "t(2g)" orbitals to the ligand pi orbitals is reflected in the elongation of ligand C-N bonds and shortening of the C(py)-C(imine) bonds. Using zinc complexes as references, these deformations could be used to quantify the number of electrons transferred. Strong transfer is found in low-spin MnL2(+) (ca. 2 e) and in high-spin MnL2(+) and low-spin MnL2(2+), FeL2(2+), and CoL2(+) (ca. 1 e each). Smaller transfer is found in CoL(2)(2+), and the transfer is insignificant in high-spin MnL2(2+), NiL2(2+), and CuL2(2+). Analysis of the unpaired electron density on the metal (using the Staroverov-Davidson method) shows that the contribution of a biradical description, in which ligand radical anions are antiferromagnetically coupled to the metal center, is significant in most cases. In the case of CoL2(+) and high-spin MnL2(+), where the metal-ligand bond is weakened, it amounts to over 50% of the total transfer.

Ab initio calculations on iron-porphyrin model systems for intermediates in the oxidative cycle of cytochrome P450s.

Geometry optimizations for several spin states of the iron(III)-S-methyl- porphyrin complex, the iron (III)-oxo-S-methyl-porphyrin complex and the respective anions were performed in order to examine models for intermediates in the oxidative cycle of cytochrome P450. The aim of this study was to obtain insights into the ground states of the intermediates of this catalytic cycle and to use the ab initio calculated geometries and charge distributions to suggest better and more realistic parameters for forcefields which are generally used for modeling P450s. The results indicate that the ground states of both the iron(III)-S-methyl-porphyrin complex and the iron(III)-oxo-S-methyl-porphyrin complex are sextet spin states (high spin). The ground states of the anions of both complexes are probably quintet spin states. The fact that experimentally a shift from low spin to high spin is observed upon binding of the substrate suggests that the ab initio calculations for the iron(III)-S-methyl-porphyrin complex in vacuum give a correct representation of the (hydrophobic) substrate-bound state of the active site of P450. The ab initio geometries of the iron-porphyrin complexes are very similar to the experimentally observed geometries, except for the longer iron-sulfur bond in ab initio calculations, which is probably caused by the omission of polarization functions on the sulfur atom during the geometry optimization. The charge distribution in all ab initio calculated complexes can be described by a series of concentric rings of alternating charge, thus allowing a relatively large positive charge on the iron atom. The commonly used forcefields generally underestimate the charge differences between the iron atom and the different parts of the porphyrin moiety or ignore the charges completely. Although forcefield calculations can reproduce the experimental geometry of iron-porphyrin moieties, extension of the forcefields with charges obtained from ab initio calculations should give a better description of the heme moiety in protein modeling and docking experiments.

Lipoxygenase is irreversibly inactivated by the hydroperoxides formed from the enynoic analogues of linoleic acid.

Triple bond analogues of natural fatty acids irreversibly inactivate lipoxygenase during their enzymatic conversion [Nieuwenhuizen, W. F., et al. (1995) Biochemistry 34, 10538-10545]. To gain insight into the mechanism of the irreversible inactivation of soybean lipoxygenase-1, we studied the enzymatic conversion of two linoleic acid analogues, 9(Z)-octadec-9-en-12-ynoic acid (9-ODEYA) and 12(Z)-octadec-12-en-9-ynoic acid (12-ODEYA). During the inactivation process, Fe(III)-lipoxygenase converts 9-ODEYA into three products, i.e. 11-oxooctadec-9-en-12-ynoic acid, racemic 9-hydroxy-10(E)-octadec-10-en-12-ynoic acid, and racemic 9-hydroperoxy-10(E)-octadec-10-en-12-ynoic acid. Fe(II)-lipoxygenase does not convert the inhibitor and is not inactivated by 9-ODEYA. Fe(III)-lipoxygenase converts 12-ODEYA into 13-hydroperoxy-11(Z)-octadec-11-en-9-ynoic acid (34/66 R/S), 13-hydroperoxy11(E)-octadec-11-en-9-ynoic acid (36/64 R/S), 11-hydroperoxyoctadec-12-en-9-ynoic acid (11-HP-12-ODEYA, enantiomeric composition of 33/67), and 11-oxooctadec-12-en-9-ynoic acid (11-oxo-12-ODEYA) during the inactivation process. Also, Fe(II)-lipoxygenase is inactivated by 12-ODEYA. It converts the inhibitor into the same products as Fe(III)-lipoxygenase does, but two additional products are formed, viz. 13-oxo-11(E)-octadec-11-en-9-ynoic acid and 13-oxo-11(Z)-octadec-11-en-9-ynoic acid. The purified reaction products were tested for their lipoxygenase inhibitory activities. The oxo compounds, formed in the reaction of 9-ODEYA and 12-ODEYA, do not inhibit Fe(II)- or Fe(III)-lipoxygenase. The 9- and 13-hydroperoxide products that are formed from 9-ODEYA and 12-ODEYA, respectively, oxidize Fe(II)-lipoxygenase to its Fe(III) state and are weak lipoxygenase inhibitors. 11-HP-12-ODEYA is, however, the most powerful inhibitor and is able to oxidize Fe(II)-lipoxygenase to Fe(III)-lipoxygenase. 11-HP-12-ODEYA is converted into 11-oxo-12-ODEYA by Fe(III)-lipoxygenase. We propose a mechanism for the latter reaction in which Fe(III)-lipoxygenase abstracts the bisallylic hydrogen H-11 from 11-HP-12-ODEYA, yielding a hydroperoxyl radical which is subsequently cleaved into 11-oxo-ODEYA and a hydroxyl radical which may inactivate the enzyme.

Chemical and quantum mechanical studies of the free radical C-C bond formation in the lipoxygenase-catalyzed dimerisation of octodeca-9,12-diynoic acid.

Triple bond analogues of poly-unsaturated fatty acids are well-known inactivators of lipoxygenases. In an earlier study we proposed that, since 11-oxo-octadeca-9,12-diynoic acid (11-oxo-ODYA) is the only oxygenated product formed during the irreversible inactivation of soybean lipoxygenase-1, the inactivation should proceed via a C11 centered octadeca-9,12-diynoic acid radical (ODYA radical). In the present study we investigated the lipoxygenase-catalysed formation of the ODYA radical. In the reaction of lipoxygenase with ODYA in the absence of dioxygen and in the presence of 13(S)-hydroperoxy-octadeca-9Z, 11E-dienoic acid (13-HPOD), free ODYA radicals were formed which resulted in the formation of three dimeric ODYA products in which one ODYA moiety is linked via its C9 (12%), C11 (72%) or C13 (16%) to the C11 methylene of the other ODYA moiety. With the ab initio Hartree-Fock method, using the 2,5-heptadiynyl radical as a model compound, the electron spin in the ODYA radical was calculated to be located for 12.0, 75.0 and 12.0% on carbon atoms C9, C11 and C13 of the ODYA radical, respectively. The ODYA-ODYA dimer formation could thus be explained on the basis of the electron spin distribution in the ODYA radical. The dimer formation, i. e. reaction of an ODYA radical with an ODYA molecule was compared with the reaction of the ODYA radical with dioxygen. On the basis of this comparison it is concluded that a) the ODYA dimer formation occurs at the carbon atom with the highest electron spin population; b) ODYA dimer formation is predominantly a kinetically determined process; c) the electron spin distribution in the ODYA radical can be used to predict the composition of the dimer mixture; and d) the regiospecific oxygen addition in the formation of 11-oxo-ODYA is enzymatically controlled.

The agonistic binding site at the histamine H2 receptor. I. Theoretical investigations of histamine binding to an oligopeptide mimicking a part of the fifth transmembrane alpha-helix.

Mutation studies on the histamine H2 receptor were reported by Gantz et al. [J. Biol. Chem., 267 (1992) 20840], which indicate that both the mutation of the fifth transmembrane Asp186 (to Ala186) alone or in combination with Thr190 (to Ala190) maintained, albeit partially, the cAMP response to histamine. Recently, we have shown that histamine binds to the histamine H2 receptor as a monocation in its proximal tautomeric form, and, moreover, we suggested that a proton is donated from the receptor towards the tele-position of the agonist, thereby triggering the biological effect [Nederkoorn et al., J. Mol. Graph., 12 (1994) 242; Eriks et al., Mol. Pharmacol., 44 (1993) 886]. These findings result in a close resemblance with the catalytic triad (consisting of Ser, His and Asp) found in serine proteases. Thr190 resembles a triad's serine residue closely, and could also act as a proton donor. However, the mutation of Thr190 to Ala190-the latter is unable to function as a proton donor-does not completely abolish the agonistic cAMP response. At the fifth transmembrane alpha-helix of the histamine H2 receptor near the extracellular surface, another amino acid is present, i.e. Tyr182, which could act as a proton donor. Furthermore, Tyr182 lies within the proximity of Asp186, so an alternative couple of amino acids, Tyr182 and Asp186, could constitute the histamine binding site at the fifth alpha-helix instead of the (mutated) couple Asp186 and Thr190. In the first part of our present study, this hypothesis is investigated with the aid of an oligopeptide with an alpha-helical backbone, which represents a part of the fifth transmembrane helix. Both molecular mechanics and ab initio data lead to the conclusion that the Tyr182/Asp186 couple is most likely to act as the binding site for the imidazole ring present in histamine.

Metabolite predictions for para-substituted anisoles based on ab initio complete active space self-consistent field calculations.

The cytochrome P450 mediated oxidative metabolism of a series of para-substituted anisoles has been examined using ab initio CASSCF (complete active space self-consistent field) calculations. On the basis of these calculations, oxidative metabolites were rationalized using the concept of hydrogen atom abstraction, spin delocalization, and hydroxyl radical recombination, which is believed to govern part of the oxidation and oxygenation reactions catalyzed by cytochrome P450. Spin distributions and energy differences between substrates, metabolic intermediates, and products were calculated. A comparison of the predictions with recent experimental findings from other laboratories supports the applicability of the currently used computational model for predicting qualitatively the oxidative metabolism by cytochrome P450.

Mechanisms of activation of phenacetin to reactive metabolites by cytochrome P-450: a theoretical study involving radical intermediates.

The cytochrome P-450-mediated activation of phenacetin (PHEN) to reactive intermediates by two hypothetical mechanisms has been studied by use of SV 6-31G ab initio energy and spin distribution calculations. In our calculations, the cytochrome P-450 enzyme system has been substituted by a singlet oxygen atom in order to reduce the computational efforts and to fulfill the requirements as to spin conservation. Both mechanisms are based on the currently increasingly accepted view that radical intermediates, formed via sequential one-electron steps, play a crucial role in the metabolic activation of substrates by cytochrome P-450. The first pathway is proposed to involve an initial abstraction of an electron and a proton from the alpha-methylene carbon atom in the ethoxy side chain and can explain the O-deethylation products paracetamol and acetaldehyde. In the second pathway, an initial abstraction of an electron and a proton from the nitrogen atom in the acetylamino side chain is proposed. The calculated spin densities of the formed nitrogen radical indicate that the unpaired electron is primarily localized at the nitrogen atom and to a smaller extent at the ortho- and paracarbon atoms relative to the acetylamino group. Radical recombination reactions between a hydroxyl radical and the spin delocalization-radicalized reactive centers of the nitrogen radical can explain the formation of the metabolites N-hydroxy-PHEN, 2-hydroxy-PHEN, and the arylating metabolite N-acetyl-p-benzoquinone imine (NAPQI), which forms a 3-(S-glutathionyl)paracetamol conjugate in the presence of glutathione. NAPQI is proposed to be formed via intermediate formation of a hemiketal. Proposals are made for the decomposition of this hemiketal into NAPQI that are consistent with currently available experimental data on 14C- and 18O-labeled PHEN.

A theoretical study on the metabolic activation of paracetamol by cytochrome P-450: indications for a uniform oxidation mechanism.

The cytochrome P-450 mediated activation of paracetamol (PAR) to the reactive electrophilic intermediate N-acetyl-p-benzoquinone imine (NAPQI) has been studied by use of SV 6-31G ab initio energy calculations and spin distributions. A simplified model for cytochrome P-450 has been used by substituting the proposed biologically active ferric-oxene state of cytochrome P-450 by a singlet oxygen atom. The results indicate that an initial hydrogen abstraction from the phenolic hydroxyl group is favored by 30.1 kcal/mol over an initial hydrogen abstraction from the acetylamino nitrogen atom. Metabolic activation of PAR via primary formation of a phenoxy radical seems the most likely mechanism. The calculated ab initio spin densities indicate that the radical formed by hydrogen abstraction from the phenolic hydroxyl group stays predominantly localized at the phenolic oxygen. A second hydrogen abstraction from the acetylamino nitrogen atom, giving rise to the reactive intermediate NAPQI, is then favored in terms of energy differences. The unpaired electron of the phenoxy radical was found to delocalize only to a small extent toward the carbon atoms at the ortho and para positions relative to the hydroxyl-containing ring carbon, but nevertheless a recombination reaction between a hydroxyl radical and these radicalized carbon atoms at the ortho or para positions could explain the formation of the minor metabolites 3-hydroxy-PAR and p-benzoquinone plus acetamide.