Julianna Oláh

Does Compound I Vary Significantly between Isoforms of Cytochrome P450

The cytochrome P450 (CYP) enzymes are important in many areas, including pharmaceutical development. Subtle changes in the electronic structure of the active species, Compound I, have been postulated previously to account partly for the experimentally observed differences in reactivity between isoforms. Current predictive models of CYP metabolism typically assume an identical Compound I in all isoforms. Here we present a method to calculate the electronic structure and to estimate the Fe–O bond enthalpy of Compound I, and apply it to several human and bacterial CYP isoforms. Conformational flexibility is accounted for by sampling large numbers of structures from molecular dynamics simulations, which are subsequently optimized with density functional theory (B3LYP) based quantum mechanics/molecular mechanics. The observed differences in Compound I between human isoforms are small: They are generally smaller than the spread of values obtained for the same isoform starting from different initial structures. Hence, it is unlikely that the variation in activity between human isoforms is due to differences in the electronic structure of Compound I. A larger difference in electronic structure is observed between the human isoforms and P450cam and may be explained by the slightly different hydrogen-bonding environment surrounding the cysteinyl sulfur. The presence of substrate in the active site of all isoforms studied appears to cause a slight decrease in the Fe–O bond enthalpy, apparently due to displacement of water out of the active site, suggesting that Compound I is less stable in the presence of substrate.

Understanding the determinants of selectivity in drug metabolism through modeling of dextromethorphan oxidation by cytochrome P450

Cytochrome P450 enzymes play key roles in the metabolism of the majority of drugs. Improved models for prediction of likely metabolites will contribute to drug development. In this work, two possible metabolic routes (aromatic carbon oxidation and O-demethylation) of dextromethorphan are compared using molecular dynamics (MD) simulations and density functional theory (DFT). The DFT results on a small active site model suggest that both reactions might occur competitively. Docking and MD studies of dextromethorphan in the active site of P450 2D6 show that the dextromethorphan is located close to heme oxygen in a geometry apparently consistent with competitive metabolism. In contrast, calculations of the reaction path in a large protein model [using a hybrid quantum mechanical–molecular mechanics (QM/MM) method] show a very strong preference for O-demethylation, in accordance with experimental results. The aromatic carbon oxidation reaction is predicted to have a high activation energy, due to the active site preventing formation of a favorable transition-state structure. Hence, the QM/MM calculations demonstrate a crucial role of many active site residues in determining reactivity of dextromethorphan in P450 2D6. Beyond substrate binding orientation and reactivity of Compound I, successful metabolite predictions must take into account the detailed mechanism of oxidation in the protein. These results demonstrate the potential of QM/MM methods to investigate specificity in drug metabolism.

NO Bonding to Heme Groups: DFT and Correlated ab Initio Calculations

The accuracy of DFT methods for treating NO bonding to heme groups, both with ferric and ferrous iron, is assessed. These systems are shown to be unusually challenging for obtaining accurate binding energies. The hybrid functionals B3LYP and B3PW91 underestimate the bond energy, and the nonhybrid functional BP86 overestimates it as well as predicting the wrong energy ordering for the different spin states of the heme group prior to NO bonding. Large basis set CCSD(T) calculations on model complexes confirm that B3LYP and B3PW91 underestimate the bond strength for NO, by ca. 10 kcal/mol. This is suggested to be due to an underestimate of the medium-range electron correlation associated with metal-ligand pi bonding in this system.

Hydrogen bond network topology in liquid water and methanol: a graph theory approach

Networks are increasingly recognized as important building blocks of various systems in nature and society. Water is known to possess an extended hydrogen bond network, in which the individual bonds are broken in the sub-picosecond range and still the network structure remains intact. We investigated and compared the topological properties of liquid water and methanol at various temperatures using concepts derived within the framework of graph and network theory (neighbour number and cycle size distribution, the distribution of local cyclic and local bonding coefficients, Laplacian spectra of the network, inverse participation ratio distribution of the eigenvalues and average localization distribution of a node) and compared them to small world and Erdős-Rényi random networks. Various characteristic properties (e.g. the local cyclic and bonding coefficients) of the network in liquid water could be reproduced by small world and/or Erdős-Rényi networks, but the ring size distribution of water is unique and none of the studied graph models could describe it. Using the inverse participation ratio of the Laplacian eigenvectors we characterized the network inhomogeneities found in water and showed that similar phenomena can be observed in Erdős-Rényi and small world graphs. We demonstrated that the topological properties of the hydrogen bond network found in liquid water systematically change with the temperature and that increasing temperature leads to a broader ring size distribution. We applied the studied topological indices to the network of water molecules with four hydrogen bonds, and showed that at low temperature (250 K) these molecules form a percolated or nearly-percolated network, while at ambient or high temperatures only small clusters of four-hydrogen bonded water molecules exist.

Studies on an iron(III)-peroxo porphyrin. Iron(III)-peroxo or iron(II)-superoxo?

We demonstrate that a one electron reduced product of the heme iron dioxygen adduct exists in solution not only as the commonly accepted iron(iii)-peroxo species, but coexists with its isomeric iron(ii)-superoxo form. This unusual reduced metal-superoxide adduct [M(ii)-O(2)(-)] is recently reported as a reactive intermediate in the case of non-heme extradiol dioxygenases and could also be generated by cryoreduction of a heme Fe(II)-O(2) adduct. The existence of iron(ii)-superoxo species in solution is consistent with IR, EPR, mass and Mössbauer spectra. The equilibrium between heme iron(iii)-peroxo and iron(ii)-superoxo forms is supported by density functional theory and explains our previous finding that upon release of coordinated (su)peroxide a corresponding iron(ii) complex remains. These results shed new light on the nature of heme iron(iii)-peroxo species that are key intermediates in the metalloenzyme-catalyzed dioxygen and hydrogen peroxide activation.

Oxazol-2-ylidenes. A new class of stable carbenes?

The investigation of the stability of several imidazol-2-ylidene analogue cyclic carbenes by an isodesmic reaction has revealed that the hitherto unknown oxazol-2-ylidene exhibits only slightly smaller stability than imidazol-2-ylidene, outperforming some of the already synthesized carbenes. Selenazol-2-ylidene also shows significant stability. The contribution of aromaticity to the stabilization has been analysed for the different five-membered ring carbenes, and was found to be relatively small for the oxygen containing systems. Investigation of possible reactivity/decomposition pathways reveals that properly substituted oxazol-2-ylidene is stable against dimerization. The thermodynamically feasible cycloreversion reaction yielding isocyanate and acetylene is prevented by a significant barrier, and furthermore with proper substitution (ring annellation) the ring can be stabilized thermodynamically as well. While in the presence of water a hydrolytic ring opening occurs; this reaction can be hindered if the water content of the reaction mixture is reduced to a few equivalents. This hydrolytic behaviour as well as the electrophilicity and nucleophilicity indices of several known nucleophilic carbenes were compared, revealing that oxazol-2-ylidene exhibits a reduced nucleophilicity with respect to imidazol-2-ylidene, while its electrophilicity is only slightly increased. This unique combination might result in unexpected (organo)catalytic activities, further expanding the colourful applications of NHCs.

Drude-type conductivity of charged sphere colloidal crystals : Density and temperature dependence

We report on extensive measurements in the low-frequency limit of the ac conductivity of colloidal fluids and crystals formed from charged colloidal spheres suspended in de-ionized water. Temperature was varied in a range of 5 degrees C < Theta < 35 degrees C and the particle number density n between 0.2 and 25 microm(-3) for the larger, respectively, 2.75 and 210 microm(-3) for the smaller of two investigated species. At fixed Theta the conductivity increased linearly with increasing n without any significant change at the fluid-solid phase boundary. At fixed n it increased with increasing Theta and the increase was more pronounced for larger n. Lacking a rigorous electrohydrodynamic treatment for counterion-dominated systems we describe our data with a simple model relating to Drudes theory of metal conductivity. The key parameter is an effectively transported particle charge or valence Z(*). All temperature dependencies other than that of Z(*) were taken from literature. Within experimental resolution Z(*) was found to be independent of n irrespective of the suspension structure. Interestingly, Z(*) decreases with temperature in near quantitative agreement with numerical calculations.

Evolutionary and mechanistic insights into substrate and product accommodation of CTP:phosphocholine cytidylyltransferase from Plasmodium falciparum

The enzyme CTP:phosphocholine cytidylyltransferase (CCT) is essential in the lipid biosynthesis of Plasmodia (Haemosporida), presenting a promising antimalarial target. Here, we identified two independent gene duplication events of CCT within Apicomplexa and characterized a truncated construct of Plasmodium falciparum CCT that forms a dimer resembling the molecular architecture of CCT enzymes from other sources. Based on biophysical and enzyme kinetics methods, our data show that the CDP‐choline product of the CCT enzymatic reaction binds to the enzyme considerably stronger than either substrate (CTP or choline phosphate). Interestingly, in the presence of Mg2+, considered to be a cofactor of the enzyme, the binding of the CTP substrate is attenuated by a factor of 5. The weaker binding of CTP:Mg2+, similarly to the related enzyme family of aminoacyl tRNA synthetases, suggests that, with lack of Mg2+, positively charged side chain(s) of CCT may contribute to CTP accommodation. Thermodynamic investigations by isothermal titration calorimetry and fluorescent spectroscopy studies indicate that accommodation of the choline phosphate moiety in the CCT active site is different when it appears on its own as one of the substrates or when it is linked to the CDP‐choline product. A tryptophan residue within the active site is identified as a useful internal fluorescence sensor of enzyme–ligand binding. Results indicate that the catalytic mechanism of Plasmodium falciparum CCT may involve conformational changes affecting the choline subsite of the enzyme.

Direct hydride shift mechanism and stereoselectivity of P450nor confirmed by QM/MM calculations.

Nitric oxide reductase (P450(nor)) found in Fusarium oxysporum catalyzes the reduction of nitric oxide to N(2)O in a multistep process. The reducing agent, NADH, is bound in the distal pocket of the enzyme, and direct hydride transfer occurs from NADH to the nitric oxide bound heme enzyme, forming intermediate I. Here we studied the possibility of hydride transfer from NADH to both the nitrogen and oxygen of the heme-bound nitric oxide, using quantum chemical and combined quantum mechanics/molecular mechanics (QM/MM) calculations, on two different protein models, representing both possible stereochemistries, a syn- and an anti-NADH arrangement. All calculations clearly favor hydride transfer to the nitrogen of nitric oxide, and the QM-only barrier and kinetic isotope effects are good agreement with the experimental values of intermediate I formation. We obtained higher barriers in the QM/MM calculations for both pathways, but hydride transfer to the nitrogen of nitric oxide is still clearly favored. The barriers obtained for the syn, Pro-R conformation of NADH are lower and show significantly less variation than the barriers obtained in the case of anti conformation. The effect of basis set and wide range of functionals on the obtained results are also discussed.

Relationship between stability and dimerization ability of silylenes

Abstract Isodesmic reaction energies and dimerization energies were calculated for several silylenes using B3LYP/6-31G(D) and MP2/6-311+G(2D) quantum chemical methods. Two different dimerization routes, the disilene formation and the four-membered bridge structure, were considered. The dimerization energy for disilene formation correlates excellently with the stabilization energy and the singlet–triplet energy separation of the silylenes. No correlation, however, has been found between the dimerization energy of the bridged dimer formation and the isodesmic reaction energy or the singlet–triplet energy separation of silylenes.