Identification of novel bacterial histidine biosynthesis inhibitors using docking, ensemble rescoring, and whole-cell assays.

The rapid spread on multidrug-resistant strains of Staphylococcus aureus requires not just novel treatment options, but the development of faster methods for the identification of new hits for drug development. The exponentially increasing speed of computational methods makes a more extensive use in the early stages of drug discovery attractive if sufficient accuracy can be achieved. Computational target identification using systems-level methods suggested the histidine biosynthesis pathway as an attractive target against S. aureus. Potential inhibitors for the pathway were identified through docking, followed by ensemble rescoring, that is sufficiently accurate to justify immediate testing of the identified compounds by whole-cell assays, avoiding the need for time-consuming and often difficult intermediary enzyme assays. This novel strategy is demonstrated for three key enzymes of the S. aureus histidine biosynthesis pathway, which is predicted to be essential for bacterial biomass productions. Virtual screening of a library of approximately 10(6) compounds identified 49 potential inhibitors of three enzymes of this pathway. Eighteen representative compounds were directly tested on three S. aureus- and two Escherichia coli strains in standard disk inhibition assays. Thirteen compounds are inhibitors of some or all of the S. aureus strains, while 14 compounds weakly inhibit growth in one or both E. coli strains. The high hit rate obtained from a fast virtual screen demonstrates the applicability of this novel strategy to the histidine biosynthesis pathway.

Blueprint for antimicrobial hit discovery targeting metabolic networks.

Advances in genome analysis, network biology, and computational chemistry have the potential to revolutionize drug discovery by combining system-level identification of drug targets with the atomistic modeling of small molecules capable of modulating their activity. To demonstrate the effectiveness of such a discovery pipeline, we deduced common antibiotic targets in Escherichia coli and Staphylococcus aureus by identifying shared tissue-specific or uniformly essential metabolic reactions in their metabolic networks. We then predicted through virtual screening dozens of potential inhibitors for several enzymes of these reactions and showed experimentally that a subset of these inhibited both enzyme activities in vitro and bacterial cell viability. This blueprint is applicable for any sequenced organism with high-quality metabolic reconstruction and suggests a general strategy for strain-specific antiinfective therapy.

Conformational study and enantioselective, regiospecific syntheses of novel aminoxy trans-proline analogues derived from an acylnitroso Diels-Alder cycloaddition.

The cis/trans isomerization of the proline amide bond has many implications in biological processes. The conformations of representative acylnitroso-derived proline analogues derived from cyclopentadiene were shown to exist exclusively as the E or trans conformation in CD2Cl2. The energetically favored conformations were determined using COSMO self-consistent reaction field calculations at the B3LYP/6-31G level of theory in addition to low temperature 1H NMR studies. The syntheses of the acylnitroso-derived peptides utilized two methods to selectively functionalize either of two chemically similar esters in the acylnitroso-derived amino acids. A novel transpeptidation of the amino acid that controlled the absolute stereochemistry in the acylnitroso Diels-Alder cycloaddition took advantage of an activated aminoxy amide linkage to control regiochemistry. Alternatively, an enantioselective and regiospecific enzymatic resolution of a racemic dimethyl ester provided a novel aminoxy acid.

Quantum mechanical study of the ring-closing reaction of the hexatriene radical cation.

The ring-closing reaction of hexatriene radical cation 1(*)(+) to 1,3-cyclohexadiene radical cation 2(*)(+) was studied computationally at the B3LYP/6-31G* and QCISD(T)/6-311G*//QCISD/6-31G* levels of theory. Both, concerted and stepwise mechanisms were initially considered for this reaction. Upon evaluation at the B3LYP level of theory, three of the possible pathways-a concerted C(2)-symmetric via transition structure 3(*)(+) and stepwise C(1)-symmetric pathways involving three-membered ring intermediate 5(*)(+) and four-membered ring intermediate 6(*)(+)-were rejected due to high-energy stationary points along the reaction pathway. The two remaining pathways were found to be of competing energy. The first proceeds through the asymmetric, concerted transition structure 4(*)(+) with an activation barrier E(a) = 16.2 kcal/mol and an overall exothermicity of -23.8 kcal/mol. The second pathway, beginning from the cis,cis,trans rotamer of 1(*)(+), proceeds by a stepwise pathway to the cyclohexadiene product with an overall exothermicity of -18.6 kcal/mol. The activation energy for the rate-determining step in this process, the formation of the intermediate bicyclo[3.1.0]hex-2-ene via transition structure 9(*)(+), was found to be 20.4 kcal/mol. More rigorous calculations of a smaller subsection of the potential energy hypersurface at the QCISD(T)//QCISD level confirmed these findings and emphasized the importance of conformational control of the reactant.

Substituent effects in pericyclic reactions of radical cations: the ring opening of 3-substituted cyclobutene radical cations

The substituent effects on the ring-opening reaction of cyclobutene radical cations have been studied at the Becke3LYP/6-31G* level of theory. The effect on the reaction energies and activation energies of the concerted and stepwise pathways of electron-donating substituents such as methyl and methoxy as well as electron-withdrawing substituents such as nitrile and carboxaldehyde in the 3-position of the cyclobutene is discussed. The exothermicity of the reaction correlates well with the ability of the substituent to stabilize the 1,3-butadiene radical cation by electron donation or conjugation. The relative stability of the (E) and (Z) isomers of the resulting 1,3-butadiene radical cations depends largely on steric effects. Similarly, steric effects are responsible for the relative energies of the different diastereomeric transition structures. The cyclopropyl carbinyl intermediate of the stepwise pathway resembles the nonclassical carbocation and is stabilized by electron-donating substituents. In the case of electron-donating substituents, this species becomes a minimum on the potential energy hypersurface, whereas unstabilized or destabilized cyclopropyl carbinyl radical cations are not minima on the hypersurface. The stabilization of the cyclopropyl carbinyl radical cation by substituents correlates qualitatively with the Brown-Okamoto substituent parameter sigma+. However, in all cases studied here, the concerted mechanism is the lowest energy pathway.

Computational explorations of vinylcyclopropane-cyclopentene rearrangements and competing diradical stereoisomerizations

The rearrangements and stereoisomerizations of four systems, vinylcyclopropane, 4-tert-butylvinylcyclopropane, 5-methylvinylcyclopropane, and 2,5-dimethylvinylcyclopropane, as well as a variety of deuterated derivatives and 1- and 2-methyl-, methoxy-, difluoro-, and amino-substituted species, were studied by density functional theory calculations using the B3LYP functional and the 6-31G basis set. Energies were evaluated with CASSCF(4, 4)/6-31G single point calculations. The major product is obtained by the si pathway. Structures on this path are essentially pure diradical in character. Higher energy diradical species and intermediates are responsible for the scrambling of the stereochemistry. The stereoselectivity of the reaction is increased by substituents which increase the relative energy of the species involved in competing stereoselectivities. The computed secondary kinetic isotope effects reproduce the experimental values reported in the literature.

Ab initio studies of

Ab initio calculations of the [1,5]-H shift in (3Z)-penta-1,3-diene and other substituted pentadienes and heteroanalogues using the hybrid density functional Becke3LYP with the 6-31G basis set are presented. Electron-donating substituents, such as methoxy in (3Z)-3-methoxypenta-1,3-diene 1, or heteroatoms such as a nitrogen atom in (Z)-ethylidenevinylamine 2, (1Z)-buta-1,3-dienylamine 3, (2Z)-but-2-enylideneamine 4, (Z)-allylidenemethylamine 5, and methylene-(Z)-propenylamine 6 are introduced. The electron-withdrawing fluoride is substituted for the hydrogen atoms in (3Z)-3-fluoropenta-1,3-diene 7, (3Z)-2,4-difluoropenta-1,3-diene 8, (3Z)-1,1',2,3,4,5,5'-heptafluoropenta- 1,3-diene 10, (1E,3E)-1,3,5-trifluoropenta-1,3-diene 11, and (1Z,3E)-1,3,5- trifluoropenta-1,3-diene 13. A detailed analysis of the geometries, energies, and electronic characteristics of the sigmatropic transposition compared to those of the unsubstituted case provides insights into substituent effects of this prototype of pericyclic reaction. The inductive and mesomeric effects of heteroatoms or heterosubstituents are of a great importance and in a continuous balance in the energetics of the transformation. Sterics can also play an important role due to the geometrical constraints of the reaction. As a general trend, decreasing the electron density of the phi system destabilizes the aromatic transition structure and increases the activation energy, and vice versa.

Epoxide formation by ring closure of the cinnamyloxy radical

[formula: see text] The cinnamyloxy and oxiranyl benzyl radicals were generated by photolysis of alkyl 4-nitrobenzenesulfenates. The yet unprecedented epoxide ring formation from a primary alkoxy radical was observed. Experimental evidence supports the fact that the mode of ring opening of the oxiranyl carbinyl radical system is thermodynamically driven. B3LYP/6-31G* calculations indicate that the closed form of the radical is approximately 5 kcal/mol more stable than the open one.

Ion chemistry of anti-o,o dibenzene.

The ion chemistry of anti-o,o'-dibenzene (1) was examined in the gaseous and the condensed phase. From a series of comparative ion cyclotron resonance (ICR) mass spectrometry experiments which involved the interaction of Cu+ with 1, benzene, or mixtures of both, it was demonstrated that 1 can be brought into the gas phase as an intact molecule under the experimental conditions employed. The molecular ions, formally 1*+ and 1*- , were investigated with a four-sector mass spectrometer in metastable-ion decay, collisional activation, charge reversal, and neutralization-reionization experiments. Surprisingly, the expected retrocyclization to yield two benzene molecules was not dominant for the long-lived molecular ions; however, other fragmentations, such as methyl and hydrogen losses, prevailed. In contrast, matrix ionization of 1 in freon (77 K) by gamma-radiation or in argon (12 K) by X-irradiation leads to quantitative retrocyclization to the cationic dimer of benzene, 2*+. Theoretical modeling of the potential-energy surface for the retrocyclization shows that only a small, if any, activation barrier is to be expected for this process. In another series of experiments, metal complexes of 1 were investigated. 1/Cr+ was formed in the ion source and examined by metastable ion decay and collisional activation experiments, which revealed predominant losses of neutral benzene. Nevertheless, comparison with the bis-ligated [(C6H6)2Cr]+ complex provided evidence for the existence of an intact 1/Cr+ under these experimental conditions. No evidence for the existence of 1/Fe+ was obtained, which suggests that iron mediates the rapid retrocyclization of 1/Fe+ into the bis-ligated benzene complex [(C6H6)2Fe]+.