Targeting bacterial virulence: inhibitors of type III secretion in Yersinia

Agents that target bacterial virulence without detrimental effect on bacterial growth are useful chemical probes for studies of virulence and potential candidates for drug development. Several gram-negative pathogens employ type III secretion to evade the innate immune response of the host. Screening of a chemical library with a luciferase reporter gene assay in viable Yersinia pseudotuberculosis furnished several compounds that inhibit the reporter gene signal expressed from the yopE promoter and effector protein secretion at concentrations with no or modest effect on bacterial growth. The selectivity patterns observed for inhibition of various reporter gene strains indicate that the compounds target the type III secretion machinery at different levels. Identification of this set of inhibitors illustrates the approach of utilizing cell-based assays to identify compounds that affect complex bacterial virulence systems.     

Synthesis and single-molecule studies of a well-defined biomimetic modular multidomain polymer using a peptidomimetic beta-sheet module

In the pursuit of advanced biomaterials with combined strength, toughness, and elasticity, a new class of well-defined modular polymers has been synthesized, and their nanomechanical properties have been studied using atomic force microscopy. These polymers are based on a peptidomimetic beta-sheet-based double-closed loop (DCL) module, which was designed to overcome the limitation of the modular polymers we reported previously (J. Am. Chem. Soc. 2004, 126, 2059). Single-molecule force-extension experiments revealed the sequential unfolding of these modules as the polymer is stretched, resulting in more regular sawtooth-patterned curves similar to those seen in titin and other biopolymers. The single-molecule data agreed well with computer modeling, which suggested that hydrogen bonding and pi-stacking are both involved in the formation of small DCL clusters along the polymer chain.     

Role of electron-transfer processes in reactions of diarylcarbenium ions and related quinone methides with nucleophiles

Second-harmonic alternating current voltammetry has been used to determine one-electron reduction potentials of 15 diarylcarbenium ions and 5 structurally analogous quinone methides, which have been employed as reference electrophiles for the development of nucleophilicity scales. A linear correlation (r(2) = 0.993) between the empirical electrophilicity parameters E and the reduction potentials in acetonitrile (E = 14.091E degrees (red) - 0.279) covering a range of 1.64 V (or 158 kJ mol(-)(1)) has been observed. For a large number of nucleophiles, it has been demonstrated that the observed activation free energies of the electrophile-nucleophile combinations are 61-195 kJ mol(-)(1) smaller than the free energy change of electron transfer from nucleophile to electrophile, which definitely excludes outer-sphere electron transfer occurring during these reactions.     

Kinetics of lamellar-to-cubic and intercubic phase transitions of pure and cytochrome c containing monoolein dispersions monitored by time-resolved small-angle X-ray diffraction

We investigated the effect of incorporation of a small aqueous peripheral membrane protein (cyt c) into the three-dimensional periodic nanochannel structures formed by the lipid monoolein (MO) on its rich phase behavior as a function of temperature, pressure, and protein concentration using synchrotron X-ray small-angle diffraction. By simultaneous use of the pressure-jump relaxation technique and time-resolved synchrotron X-ray diffraction, we also studied the kinetics of various lipid mesophase transformations of the system for understanding the mechanistic pathways of their formation influenced by the protein-lipid interactions. Cyt c incorporated into the bicontinuous cubic phase Ia3d of MO has a significant effect on the lipid structure and the pressure stability of the system already at low protein concentrations. Concentrations higher than 0.2 wt % of cyt c led to an increase in interfacial curvature due to interaction of the protein with the lipid headgroups. This promotes the formation of a new, probably partially micellar cubic phase of crystallographic space group P4(3)32. Upon pressurization, the P4(3)32 phase undergoes a phase transition to a cubic Pn3m phase with smaller partial specific volume. Increase in protein concentration increases the pressure stability of the P4(3)32 phase. The formation of this phase from the cubic phase Pn3m is a slow process taking many seconds and having a time lag in the beginning. It seems to occur as a two-state process without ordered intermediate states. At temperatures above 60 degrees C, the P4(3)32 phase is unable to accommodate the unfolded protein and transforms to a bicontinuous cubic Ia3d phase. Time-resolved small-angle X-ray scattering studies show that the L(alpha) --> Ia3d transition in pure MO dispersions under limited hydration conditions occurs within a time interval of 1 s at 35 degrees C preceded by a lag phase of 1.5 s. The Ia3d cubic phase initially forms with a much larger lattice constant due to hydration and experiences an initially lower curvature that relaxes within about 1 s. Interestingly, no other cubic phases are involved as intermediates in the transition, i.e., the gyroid cubic phase is able to form directly from the L(alpha) phase. The mechanism behind the L(alpha) --> Ia3d transition in pure MO dispersions has been discussed within the framework of recent stalk models for membrane fusion. In the presence of cyt c, the L(alpha) --> Ia3d transition is much slower. The rather long relaxation times of the order of seconds are probably due to a kinetic trapping of the system and limitation by the transport and redistribution of water and lipid in the evolving new lipid phases. We also studied the transition from the pure lamellar L(alpha) phase to the Ia3d-P4(3)32 two phase region and observed a rather complex transition behavior with transient lamellar and cubic intermediate states.     

Action spectroscopy and temperature diagnostics of H+ 3 by chemical probing

Infrared absorption spectroscopy of few hundred H+(3) ions trapped in a 22-pole ion trap is presented using chemical probing as a sensitive detection technique down to the single ion level. By exciting selected overtone transitions of the (v(1)=0,v(2) (l)=3(1))<--(0,0(0)) vibrational band using an external cavity diode laser an accurate diagnostics measurement of the effective translational and rotational temperatures of the trapped ions was performed. The absolute accuracy of the measured transition frequencies was improved by a factor of four compared to previous plasma spectroscopy measurements using velocity modulation [Ventrudo et al., J. Chem. Phys. 100, 6263 (1994)]. The observed buffer gas cooling conditions in the ion trap indicate how to cool trapped H+(3) ions into the lowest ortho and para rotational states. Future experiments will utilize such an internally cold ion ensemble for state-selected dissociative recombination experiments at the heavy ion storage ring Test Storage Ring (TSR).     

Transformation of acridines and azepines into the corresponding 3-oxo-heterocycles by means of hypervalent aromatic iodine compounds

Summary The acridines3,5, and6, as well as the dibenzo[b,f]-azepine4 were converted into the 3-oxo-derivatives7–10 using hypervalent iodine compounds (iodosylbenzene and bis-(trifluoroacetoxy)iodopentafluorobenzene).

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Oxidation von Acridinen und Azepinen in ihre 3-Oxoderivate mit Hilfe von hypervalenten aromatischen Jodverbindungen (Kurze Mitt.)

Zusammenfassung Die Acridine3,5 und6 sowie das Dibenzo[b,f]azepin4 wurden mit Hilfe der beiden hypervalenten Jod-Verbindungen Jodosobenzol (1) und Bis-trifluoroacetoxyiodbenzol (2) zu den entsprechenden 3-Acridinonen7,9 und10 sowie zum Dibenzoazepin-3-on8 oxidiert.

     

Purine analog inhibitors of xanthine oxidase - structure activity relationships and proposed binding of the molybdenum cofactor

A number of new hypoxanthine analogs have been prepared as substrate inhibitors of xanthine oxidase. Most noteworthy inhibitory new hypoxanthine analogs are 3-(m-tolyl)pyrazolo[1,5-a]pyrimidin-7-one ( 47 ), ID₅₀ 0.06 μM and 3-phenylpyrazolo[1,5-a]pyrimidin-7-one ( 46 ), ID₅₀ 0.40 μM. 5-(p-Chlorophenyl)pyrazolo[1,5-a]pyrimidin-7-one ( 63 ) and the corresponding 5-nitrophenyl derivative 64 exhibited an ID₅₀ of 0.21 and 0.23 μM, respectively. 7-Phenylpyrazolo[1,5-a]-s-triazin-4-one ( 40 ) is shown to exhibit an ID₅₀ of 0.047 μM. The structure-activity relationships of these new phenyl substituted hypoxanthine analogs are discussed and compared with the xanthine analogs 3-m-tolyl- and 3-phenyl-7-hydroxypyrazolo[1,5-a]pyrimidin-5-ones ( 90 ) and ( 91 ), previously reported from our laboratory to have ID₅₀ of 0.025 and 0.038 μM, respectively. The presence of the phenyl and substitutedphenyl groups contribute directly to the substrate binding of these potent inhibitors. This work presents an updated study of structure-activity relationships and binding to xanthine oxidase. In view of the recent elucidation of the pterin cofactor and the proposed binding of this factor to the molybdenum ion in xanthine oxidase, a detailed mechanism of xanthine oxidase oxidation of hypoxanthine and xanthine is proposed. Three types of substrate binding are viewed for xanthine oxidase. The binding of xanthine to xanthine oxidase is termed Type I binding. The binding of hypoxanthine is termed Type II binding and the specific binding of alloxanthine is assigned as Type III binding. These three types of substrate binding are analyzed relative to the most potent compounds known to inhibit xanthine oxidase and these inhibitors have been classified as to the type of inhibitor binding most likely to be associated with specific enzyme inhibition. The structural requirements for each type of binding can be clearly seen to correlate with the inhibitory activity observed. The chemical syntheses of the new 3-phenyl- and 3-substituted phenylpyrazolo[1,5-a]pyrimidines with various substituents are reported. The syntheses of various 8-phenyl-2-substituted pyrazolo-[1,5-a]-s-triazines, certain s-triazolo[1,5-a]-s-triazines and s-triazolo[1,5-a]pyrimidine derivatives prepared in connection with the present study are also described.     

Synthesis of 4,6-disubstituted-7-β-D-ribofuranosyl- and arabinofuranosylpyrazolo[3,4-d]pyrimidines and certain related ribonucleosides

Several disubstituted pyrazolo[3,4-d]pyrimidine, pyrazolo[1,5-a]pyrimidine and thiazolo[4,5-d]pyrimidine ribonucleosides have been prepared as congeners of uridine and cytidine. Glycosylation of the trimethylsilyl (TMS) derivative of pyrazolo[3,4-d]pyrimidine-4,6(1H,5H,7H)-dione ( 4 ) with 1-O-acetyl-2,3,5-tri-O-benzoyl-D-ribofuranose ( 5 ) in the presence of TMS triflate afforded 7-(2,3,5-tri-O-benzoyl-β-D-ribofuranosyl)pyrazolo-[3,4-d]pyrimidine-4,6(1H,5H)-dione ( 6 ). Debenzoylation of 6 gave the uridine analog 7-β-D-ribofuranosylpyrazolo[3,4-d]pyrimidine-4,6(1H,5H)-dione ( 3 ), identical with 7-ribofuranosyloxoallopurinol reported earlier. Thiation of 6 gave 7 , which on debenzoylation afforded 7-β-D-ribofuranosyl-6-oxopyrazolo[3,4-d]pyrimidine-4(1H,5H)-thione ( 8 ). Ammonolysis of 7 at elevated temperature gave a low yield of the cytidine analog 4-amino-7-β-D-ribofuranosylpyrazolo[3,4-d]pyrimidin-6(1H)-one ( 11 ). Chlorination of 6 , followed by ammonolysis, furnished an alternate route to 11 . A similar glycosylation of TMS-4 with 2,3,5-tri-O-benzyl-α-D-arabinofuranosyl chloride ( 12 ) gave mainly the N7-glycosylated product 13 , which on debenzylation provided 7-β-D-arabinofuranosylpyrazolo[3,4-d]pyrimidine-4,6(1H,5H)-dione ( 14 ). 4-Amino-7-β-D-arabinofuranosyl-pyrazolo[3,4-d]pyrimidin-6(1H)-one ( 19 ) was prepared from 13 via the C4-pyridinium chloride intermediate 17 . Condensation of the TMS derivatives of 7-hydroxy- ( 20 ) or 7-aminopyrazolo[1,5-a]pyrimidin-5(4H)-one ( 23 ) with 5 in the presence of TMS triflate gave the corresponding blocked nucleosides 21 and 24 , respectively, which on deprotection afforded 7-hydroxy- 22 and 7-amino-4-β-D-ribofuranosylpyrazolo[1,5-a]pyrimidin-5-one ( 25 ), respectively. Similarly, starting either from 2-chloro ( 26 ) or 2-aminothiazolo[4,5-d]pyrimidine-5,7-(4H,6H)-dione ( 29 ), 2-amino-4-β-D-ribofuranosylthiazolo[4,5-d]pyrimidine-5,7(6H)-dione ( 28 ) has been prepared. The structure of 25 was confirmed by single crystal X-ray diffraction studies.     

Comment on: "Disentangling density and temperature effects in the viscous slowing down of glass forming liquids" [J. Chem. Phys. 120, 6135 (2004)

Recently, Tarjus et al. [G. Tarjus, D. Kivelson, S. Mossa, and C. Alba-Simionesco, J. Chem. Phys. 120, 6135 (2004)] concluded from a review of data for a variety of glass formers that the supercooled dynamics are almost invariably dominated by temperature T, rather than by density rho. By including additional published data into such a compilation, we show that for van der Waals molecular liquids, the dynamics near T(g) are in fact governed as much by density as by temperature. Moreover, relaxation times measured at various temperatures and pressures can be superimposed by plotting as a function rho(gamma)/T. This scaling form can arise from an assumed inverse power law for the intermolecular repulsive potential, with gamma a material constant. (c) 2004 American Institute of Physics.     

Synthesis of imidazo[4,5-d]pyridazine nucleosides related to inosine

Several imidazo[4,5-d]pyridazine nucleosides which are structurally similar to inosine were synthesized. Anhydrous stannic chloride-catalyzed condensation of persilylated imidazo[4,5-d]-pyridazin-4(5H)one (1) and imidazo[4,5-d]pyridazine-4,7(5H,6H)dione ( 16 ) with 1-O-acetyl-2,3,5-tri-O-benzoyl-β-D-ribofuranose ( 3 ) provided (after sodium methoxide deblocking) 6-β-D-ribo furanosylimidazo[4,5-d]pyridazin-4(5H)one (5) and 3,6-di-(β-D-ribofuranosyI)imidazo[4,5-d]pyridazin-4-one ( 7 ); and 1-(β-D-ribofuranosyl)imidazo[4,5-d]pyridazine-4,7(5H,6H)dione ( 19 ) and 1,5 or 6-di-(β-D-ribofuranosyl)imidazo[4,5-d ]pyridazine-4,7(5H or 6H)dione ( 21 ), respeeitvely. 4,7-Diehloro-1-β-D-ribofuranosylimidazo[4,5-d]pyridazine ( 12 ) and dimethyl 1-β-D-ribofuranosylimidazole-4,5-dicarboxylate ( 26 ), both prepared from stannic chloride-catalyzed ribosylations of the corresponding heterocycles, were converted in several steps to 3-β-D-ribo-furanosy limidazo[4,5-d]pyridazin-4(5H)one ( 14 ) and nucleosidc 19 , respectively. Acid-catalyzed isopropylidenation of mesomeric betaine 7 or nuclcoside 14 provided 3-(2,3-isopropylidene-β-D-ribofuranosyl)imidazo[4,5-d]pyrizin-4(5H)one ( 31 ). 1-β-D-Ribofuranosylimidazo[4,5-d]-pyridazine ( 29 ) was obtained in several steps from nueleoside 12 . The structure of the nucleosides was established by the use of carbon-13 and proton nmr.