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.

Thermal behavior, powder X-ray diffraction, DFT calculations and vibrational spectra of barium bis(pentacyanonitrosylchromate) octahydrate, Ba3[Cr(CN)5NO]2.8H2O(D2O).

The cell parameters of Ba3[Cr(CN)5NO]2.8H2O were determined from powder X-ray diffraction using the autoindexing program TREOR, and refined by the Le Bail methods with the FULLPROF program. An orthorhombic cell was determined with cell parameters a = 15.0324(2) A, b = 12.9542(9) A, and c = 7.5094(5) A. Two possible space groups are consistent with the systematic absences: Pmcb (#55) and P2cb (#32). Infrared spectra are reported for the polycrystalline compound, isotopically normal and partially deuterated, at temperatures ranging between ca. 80 K and 293 K together with the room temperature Raman spectrum. The assignment of the observed bands was accomplished assuming the existence of one type of pentacyanonitrosylchromate ion in the asymmetric unit, as suggested by the single band found in the NO stretching region of the deuterated anion and in the anhydrous compound. TGA-DTA data are also reported and discussed. The assignments are supported by DFT calculations of the normal modes of vibration of the [Cr(CN)5NO](3-) structure, optimized at the same level of theory.

Unfolding of the [Cu2(1,3-bis(9-methyl-1,10-phenanthrolin-2-yl)propane)2]2+ helicate. Coupling of the chlorocarbon dehalogenation to the unfolding process.

A new helical dimeric copper(I) complex [Cu(2)(mphenpr)(2)](ClO(4))(2) where mphenpr is 1,3-bis(9-methyl-1,10-phenanthrolin-2-yl)propane has been prepared and characterized by X-ray crystallography and NMR. In the solid state, the metal centers are 6.42 A apart, and the electronic structure has been investigated with use of density functional theory (DFT) calculations. In solution the dimer equilibrates with a monomeric form [Cu(mphenpr)](ClO(4)), and the mechanism of unfolding of the dimer into monomer has been studied. In the presence of CCl(4), formation of the monomer is coupled to the reductive dehalogenation of the halocarbon. The mechanism of this process has been probed by the study of short-lived potential reaction intermediates using fast kinetic pulse radiolysis techniques and comparisons with DFT calculations. The copper(II) product [Cu(mphenpr)Cl](ClO(4)) and an analogue [Cu(mphenpr)](ClO(4))(2) have been isolated and characterized by X-ray crystallography.

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.

Theoretical investigation on the electronic structure of pentacyano(L)ferrate(II) complexes with NO(+), NO, and NO(-) ligands. Redox interconversion, protonation, and cyanide-releasing reactions.

Reaction pathways for the one- and two-electron reductions of [Fe(CN)(5)NO](2)(-) have been investigated by means of a density functional theory (DFT) approach combined with the polarized continuum model (PCM) of solvation. In addition, UV-vis spectroscopic data were obtained using ZINDO/S calculations including a point-charge model simulation of solvent effects. DFT methodologies have been used to assess the thermodynamical feasibility of protonation and cyanide-release processes for the reduced species. We conclude that [Fe(CN)(5)NO](3)(-) is a stable species in aqueous solution but may release cyanide yielding [Fe(CN)(4)NO](2)(-), consistent with experimental results. On the other hand, the [Fe(CN)(5)NO](4)(-) complex turns out to be unstable in solution, yielding the product of cyanide release, [Fe(CN)(4)NO](3)(-), and/or the protonated HNO complex. All the structural and spectroscopic (IR, UV-vis) predictions for the [Fe(CN)(5)HNO](3)(-) ion are consistent with the scarce but significant experimental evidence of its presence as an intermediate in nitrogen redox interconversion chemistry. Our computed data support an Fe(II)(LS) + NO(+) assignment for [Fe(CN)(5)NO](2)(-), an Fe(II)(LS) + NO assignment for the one-electron reduction product, but an Fe(I)(LS) + NO(+) for the one-electron product after dissociation of an axial cianide, and an Fe(II) + singlet NO(-) for the two-electron reduction species.

Molecular modeling and QSAR analysis of the interaction of flavone derivatives with the benzodiazepine binding site of the GABA(A) receptor complex.

A large number of structurally different classes of ligands, many of them sharing the main characteristics of the benzodiazepine (BDZ) nucleus, are active in the modulation of anxiety, sedation, convulsion, myorelaxation, hypnotic and amnesic states in mammals. These compounds have high affinity for the benzodiazepine binding site (BDZ-bs) of the GABA(A) receptor complex. Since 1989 onwards our laboratories established that some natural flavonoids were ligands for the BDZ-bs which exhibit medium to high affinity in vitro and anxiolytic activity in vivo. Further research resulted in the production of synthetic flavonoid derivatives with increased biochemical and pharmacological activities. The currently accepted receptor/pharmacophore model of the BDZ-bs (Zhang, W.; Koeler, K. F.; Zhang, P.; Cook, J. M. Drug Des. Dev. 1995, 12, 193) accounts for the general requirements that should be met by this receptor for ligand recognition. In this paper we present a model pharmacophore which defines the characteristics for a ligand to be able to interact and bind to a flavone site, in the GABA(A) receptor. closely related to the BDZ-bs. A model of a flavone binding site has already been described (Dekermendjian, K.; Kahnberg, P.; Witt, M. R.; Sterner, O.; Nielsen, M.; Liljerfors, T. J. Med. Chem. 1999, 42, 4343). However, this alternative model is based only on graphic superposition techniques using as template a non-BDZ agonist. In this investigation all the natural and synthetic flavonoids found to be ligands for the BDZ-bs have been compared with the classical BDZ diazepam. A QSAR regression analysis of the parameters that describe the interaction demonstrates the relevance of the electronic effects for the ligand binding, and shows that they are associated with the negatively charged oxygen atom of the carbonyl group of the flavonoids and with the nature of the substituent in position 3'.