Structure-based optimization of a non-beta-lactam lead results in inhibitors that do not up-regulate beta-lactamase expression in cell culture

Bacterial expression of beta-lactamases is the most widespread resistance mechanism to beta-lactam antibiotics, such as penicillins and cephalosporins. There is a pressing need for novel, non-beta-lactam inhibitors of these enzymes. One previously discovered novel inhibitor of the beta-lactamase AmpC, compound 1, has several favorable properties: it is chemically dissimilar to beta-lactams and is a noncovalent, competitive inhibitor of the enzyme. However, at 26 microM its activity is modest. Using the X-ray structure of the AmpC/1 complex as a template, 14 analogues were designed and synthesized. The most active of these, compound 10, had a K(i) of 1 microM, 26-fold better than the lead. To understand the origins of this improved activity, the structures of AmpC in complex with compound 10 and an analogue, compound 11, were determined by X-ray crystallography to 1.97 and 1.96 A, respectively. Compound 10 was active in cell culture, reversing resistance to the third generation cephalosporin ceftazidime in bacterial pathogens expressing AmpC. In contrast to beta-lactam-based inhibitors clavulanate and cefoxitin, compound 10 did not up-regulate beta-lactamase expression in cell culture but simply inhibited the enzyme expressed by the resistant bacteria. Its escape from this resistance mechanism derives from its dissimilarity to beta-lactam antibiotics.     

New developments in the synthesis of pyrrolizidinone-based dipeptide isosteres

1,3-Dipolar cycloaddition of acrylamide with the cyclic nitrone derived from proline tert-butyl ester has been employed in the synthesis of bicyclic Gly-(s-cis)Pro isosteres suitably protected for the Fmoc-based solid phase peptide synthesis. (R)-1-Phenylethylamine was introduced as chiral auxiliary to resolve racemic intermediates and obtain enantiopure compounds. Using methacrylamide as dipolarophile, the analogous Ala-Pro mimetics have been prepared in racemic form, whereas the same strategy applied to methyl itaconate failed to give the corresponding Asp-Pro mimetic.     

Physical and Chemical Interaction of Homoconjugated Dienes with Tetracyanoethylene

EDA-complexes of bicyclo[2,2,n]alkadienes (n = 1, 2, 3, 4) ( 1 (n)-series), 1,4-cyclohexadiene ( 2 ) and various other cyclic monoenes, dienes and trienes as donors and tetracyanoethylene (TCNE) as acceptor were investigated. Spectroscopic and thermodynamic constants of the complexes were determined and correlated with the ionisation potentials (I^D) of the hydrocarbon donors obtained from PE. spectroscopy. The nature of the dominant energy contributions to the ground state and the two lowest CT-states of these weak complexes is discussed and structural conclusions are drawn. The role of the complexes in the addition reaction of the hydrocarbon components and TCNE is discussed. The homo Diels-Alder addition product of 1 (2) and TCNE, 9,9,10,10-tetracyanoquadricyclo[2,2,2,0^2,6,2^3,5]decane, and the ‘ene’-addition product of 2 and TCNE, 5-[1′,1′,2′,2′-tetracyanoethyl]-1,3-cyclohexadiene were prepared and characterized. Preliminary results for the mechanistic scheme governing the dehydrogenation of 2 by TCNE are reported.     

Comparisons of NMR spectral quality and success in crystallization demonstrate that NMR and X-ray crystallography are complementary methods for small protein structure determination

X-ray crystallography and NMR spectroscopy provide the only sources of experimental data from which protein structures can be analyzed at high or even atomic resolution. The degree to which these methods complement each other as sources of structural knowledge is a matter of debate; it is often proposed that small proteins yielding high quality, readily analyzed NMR spectra are a subset of those that readily yield strongly diffracting crystals. We have examined the correlation between NMR spectral quality and success in structure determination by X-ray crystallography for 159 prokaryotic and eukaryotic proteins, prescreened to avoid proteins providing polydisperse and/or aggregated samples. This study demonstrates that, across this protein sample set, the quality of a protein's [15N-1H]-heteronuclear correlation (HSQC) spectrum recorded under conditions generally suitable for 3D structure determination by NMR, a key predictor of the ability to determine a structure by NMR, is not correlated with successful crystallization and structure determination by X-ray crystallography. These results, together with similar results of an independent study presented in the accompanying paper (Yee, et al., J. Am. Chem. Soc., accompanying paper), demonstrate that X-ray crystallography and NMR often provide complementary sources of structural data and that both methods are required in order to optimize success for as many targets as possible in large-scale structural proteomics efforts.     

Analysis of gadobenate dimeglumine by capillary zone electrophoresis coupled with electrospray-mass spectrometry

Highly reliable and accurate analytical methods are needed for the determination of magnetic resonance imaging (MRI) contrast agents in complex matrices of clinical interest. We demonstrate the reliability of capillary zone electrophoresis (CZE) coupled with electrospray ionization-mass spectrometry (ESI-MS) for the analysis of MultiHance (gadobenate dimeglumine), a gadolinium-based MRI agent. A sheath liquid interface connected the CE system with an electrospray mass spectrometer equipped with an ion-trap analyzer. CZE with ultraviolet (CZE-UV) and with mass detection (CZE-MS) were compared by analyzing gadobenate dimeglumine and the free ligand diluted in water and in biological fluids (i.e., human serum and urine). The optimization of some relevant CZE-MS parameters was accomplished, like CE buffer composition, sheath liquid composition and flow, and type and length of the separation capillary. CZE-UV was highly influenced by the biological sample components, which hindered a reliable quantification of both gadobenate and free ligand in serum and urine. In CZE-MS, on the other hand, the electrophoretic runs turned out to be independent of the clinical matrices, due to the informative potential and to the selectivity of MS detection.     

Chemical waves and pattern formation in the 1,2-dipalmitoyl-sn-glycero-3-phosphocholine/water lamellar system

The present work deals with the spatially extended oscillatory Belousov Zhabotinsky reaction-diffusion system carried out in an anisotropic environment of phosphatidylcholines/water binary system, which presents layered aqueous domains separated by lipid bilayers. We report the occurrence of stable Turing patterns, spiral waves, and other exotic structures in phospholipids bilayers that are generally used as a models for cell plasma membranes.     

Synthesis of Glycosylrifamycins,a new type of semisynthetic rifamycins

Glycosylrifamycins, a new type of semisynthetic rifamycin derivatives, can be easily obtained by reaction of 3-(2-aminoethylthio)rifamycin SV ( 2 ) with a glycosyl compound carrying a coupling group, such as isothicyanate or carboxy. We prepared O-acetylated and free glucopyranosyl and arabinopyranosyl derivatives of rifamycin S and SV (see 3–10 ). Additionally, derivatives with D -saccharo-1,4-lactone and with shikimic acid were obtained (see 11–15 ). Glycosylrifamycins show an interesting inhibitory power on Gram-positive bacteria (Table).     

Oxidation of propene over various doped tungsten oxides

The oxidation of propene was studied on several tungsten oxides which contained small amounts of Ti, Ta, Nb and Sn. Only the Sn-containing specimen was found to be selective in the conversion of propene to acrolein. The catalytic results are correlated with crystal structures determined by electron microscopy.

---

, Ti, Ta, Nb Sn. , , Sn, . , .

     

Discriminating the helical forms of peptides by NMR and molecular dynamics simulation

The HNCO NMR pulse sequence was applied to three selectively labeled (15)N and (13)C isotopic homologues of the peptide Ac-WAAAH(AAARA)(3)A-NH(2) to probe directly for hydrogen bonds between residues 8 and 11 (characteristic of a 3(10)-helix), 8 and 12 (alpha-helix), and 8 and 13 (pi-helix). The experiments demonstrate conclusively, and in agreement with circular dichroism studies, that the center of the peptide is alpha-helical; there is no discernible 3(10)- or pi-helix at these specific positions. Molecular dynamics simulations of the preceding peptide and Ac-(AAAAK)(3)A-NH(2) in water using the potential energy parameter set CHARMM22/CMAP correctly yield an alpha-helix, in contrast to simulations with the set CHARMM22, which result in a pi-helix.