Anisotropic Optical Shock Waves in Isotropic Media with Giant Nonlocal Nonlinearity.

Dispersive shock waves in thermal optical media are nonlinear phenomena whose intrinsic irreversibility is described by time asymmetric quantum mechanics. Recent studies demonstrated that the nonlocal wave breaking evolves in an exponentially decaying dynamics ruled by the reversed harmonic oscillator, namely, the simplest irreversible quantum system in the rigged Hilbert spaces. The generalization of this theory to more complex scenarios is still an open question. In this work, we use a thermal third-order medium with an unprecedented giant Kerr coefficient, the m-cresol/nylon mixed solution, to access an extremely nonlinear, highly nonlocal regime and realize anisotropic shock waves with internal gaps. We compare our experimental observations to results obtained under similar conditions but in hemoglobin solutions from human red blood cells, and found that the gap formation strongly depends on the nonlinearity strength. We prove that a superposition of Gamow vectors in an ad hoc rigged Hilbert space, that is, a tensorial product between the reversed and the standard harmonic oscillators spaces, describes the beam propagation beyond the shock point. The anisotropy turns out from the interaction of trapping and antitrapping potentials. Our work furnishes the description of novel intriguing shock phenomena mediated by extreme nonlinearities.

Electronic halocyclization and radical haloazidation of benzene-linked 1,7-dienes for the synthesis of functionalized 3,1-benzoxazines.

A novel electronic halocyclization and radical haloazidation of benzene-linked 1,7-dienes for the formation of functionalized 3,1-benzoxazines has been achieved by using TMSN3 as an azido source and NBS as a halogen source. This methodology is highlighted by its mild conditions and wide substrate scope, which concomitantly introduces one C-N and two C-halogen bonds into one molecule.

Visible-Light-Induced Trifluoromethylation of Isonitrile-Substituted Methylenecyclopropanes: Facile Access to 6-(Trifluoromethyl)-7,8-Dihydrobenzo[k]phenanthridine Derivatives.

A new visible-light-induced trifluoromethylation of isonitrile-substituted methylenecyclopropanes is developed. A range of substituted 6-(trifluoromethyl)-7,8-dihydrobenzo[k]phenanthridine derivatives are readily furnished by this newly developed tandem reaction with moderate to good yields. This reaction allows the direct formation of two six-membered rings and three new C-C bonds, including the C-CF3 bond, under visible light irradiation.

Palladium-catalyzed cascade cyclization of allylamine-tethered alkylidenecyclopropanes: facile access to iodine/difluoromethylene- and perfluoroalkyl-containing 1-benzazepine scaffolds.

The unprecedented palladium-catalyzed cascade cyclization of allylamine-tethered alkylidenecyclopropanes with an ethyl difluoroiodoacetate or perfluoroalkylated reagent is developed, providing facile access to a variety of synthetically and medicinally valuable iodine/difluoromethylene- and perfluoroalkyl-containing 1-benzazepine frameworks. These reactions exhibited good yields and functional group tolerance via a radical mechanism.

Thermally induced formal [3+2] cyclization of ortho-aminoaryl-tethered alkylidenecyclopropanes: facile synthesis of furoquinoline and thienoquinoline derivatives.

We have developed a facile synthetic method to access furoquinoline and thienoquinoline derivatives via a thermally induced ring-opening and cyclization reaction from ortho-aminoaryl-tethered alkylidenecyclopropanes with the in situ generation of isocyanates or isothiocyanates. These reactions exhibited excellent yields and functional group tolerance under metal-free conditions.

Crystal structure of S-ribosylhomocysteinase (LuxS) in complex with a catalytic 2-ketone intermediate.

S-Ribosylhomocysteinase (LuxS) is an Fe(2+)-dependent metalloenzyme that catalyzes the cleavage of the thioether bond in S-ribosylhomocysteine (SRH) to produce homocysteine (Hcys) and 4,5-dihydroxy-2,3-pentanedione (DPD), the precursor of type II bacterial quorum-sensing molecule. The proposed mechanism involves an initial metal-catalyzed aldose-ketose isomerization reaction, which results in the migration of the ribose carbonyl group from its C1 to C2 position and the formation of a 2-ketone intermediate. A repetition of the isomerization reaction shifts the carbonyl group to the C3 position. Subsequent beta-elimination reaction at the C4 and C5 positions completes the catalytic cycle. In this work, a catalytically inactive mutant (C84A) of Co(2+)-substituted Bacillus subtilis LuxS was cocrystallized with the 2-ketone intermediate and the structure was determined to 1.8 A resolution. The structure reveals that the C2 carbonyl oxygen is directly coordinated with the metal ion, providing strong support for the proposed Lewis acid function of the metal ion during catalysis. Cys-84 and Glu-57 are optimally positioned to act as general acids/bases during the isomerization and elimination reactions. In addition, Ser-6, His-11, and Arg-39 are involved in substrate/ intermediate binding through hydrogen bonding interactions. The above conclusions are further confirmed by site-directed mutagenesis and visible absorption spectroscopic studies.

Macrocyclic inhibitors for peptide deformylase: a structure-activity relationship study of the ring size.

Peptide deformylase (PDF) catalyzes the removal of the N-terminal formyl group from newly synthesized polypeptides in eubacteria. Its essential role in bacterial cells but not in mammalian cells makes it an attractive target for antibacterial drug design. We have previously reported an N-formylhydroxylamine-based, metal-chelating macrocyclic PDF inhibitor, in which the P(1)' and P(3)' side chains are covalently joined. In this work, we have carried out a structure-activity relationship study on the size of the macrocycle and found that 15-17-membered macrocycles are optimal for binding to the PDF active site. Unlike the acyclic compounds, which are simple competitive inhibitors, the cyclic compounds all act as slow-binding inhibitors. As compared to their acyclic counterparts, the cyclic inhibitors displayed 20-50-fold higher potency against the PDF active site (K(I) as low as 70 pM), improved selectivity toward PDF, and improved the metabolic stability in rat plasma. Some of the macrocyclic inhibitors had potent, broad spectrum antibacterial activity against clinically significant Gram-positive and Gram-negative pathogens. These results suggest that the macrocyclic scaffold provides an excellent lead for the development of a new class of antibiotics.

Slow-binding inhibition of peptide deformylase by cyclic peptidomimetics as revealed by a new spectrophotometric assay.

A new spectrophotometric/fluorimetric assay for peptide deformylase (PDF) has been developed by coupling the PDF reaction with that of dipeptidyl peptidase I (DPPI) and using N-formyl-Met-Lys-AMC as substrate. Removal of the N-terminal formyl group by PDF renders the dipeptide an efficient substrate of DPPI, which subsequently removes the dipeptidyl units to release 7-amino-4-methylcoumarin as the chromophore/fluorophore. The PDF reaction is conveniently monitored on a UV-Vis spectrophotometer or a fluorimeter in a continuous fashion. The utility of the assay was demonstrated by determining the catalytic activity of PDF and the inhibition constants of PDF inhibitors. These studies revealed the slow-binding behavior of a previously reported macrocyclic PDF inhibitor. This method offers several advantages over the existing PDF assays and should be particularly useful for screening PDF inhibitors in the continuous fashion.

Peptidyl hydroxamic acids as methionine aminopeptidase inhibitors.

A new class of methionine aminopeptidase (MetAP) inhibitors, which contain an internal hydroxamate (N-acyl-N-alkylhydroxylamine) core as the metal-chelating group, has been designed, synthesized, and tested. The compounds exhibited reversible, competitive inhibition against Escherichia coli MetAP as well as human MetAP-1 and MetAP-2. The most potent inhibitor had a K(i) value of 2.5 microM and >20-fold selectivity toward E. coli MAP.

Catalytic mechanism of S-ribosylhomocysteinase (LuxS): direct observation of ketone intermediates by 13C NMR spectroscopy.

S-Ribosylhomocysteinase (LuxS) catalyzes the cleavage of the thioether linkage of S-ribosylhomocysteine (SRH) to produce l-homocysteine and 4,5-dihydroxy-2,3-pentanedione (DHPD). This is a key step in the biosynthetic pathway of the type II autoinducer (AI-2) in both Gram-positive and Gram-negative bacteria. Previous studies demonstrated that LuxS contains a catalytically essential Fe2+ ion. The catalytic mechanism of LuxS was investigated using 2- and 3-13C-labeled SRH as substrate and 13C NMR spectroscopy. These studies revealed the presence of 2- and 3-keto intermediates in the catalytic pathway. The 2-keto intermediate was chemically synthesized, and its chemical and kinetic competence was demonstrated. The results support a catalytic mechanism in which the metal ion catalyzes an internal redox reaction, shifting the carbonyl group from the C-1 position to the C-3 position. Subsequent beta-elimination at the C-4 and C-5 positions releases homocysteine as a free thiol. The results also suggest that Cys-84 and Glu-57 are the possible general acids/bases for proton transfer during catalysis and that the keto intermediates are released from the enzyme active site before rebinding and completion of the reaction.

Structure-based design of a macrocyclic inhibitor for peptide deformylase.

A macrocyclic, peptidomimetic inhibitor of peptide deformylase was designed by covalently cross-linking the P1' and P3' side chains. The macrocycle, which contains an N-formylhydroxylamine side chain as the metal-chelating group, was synthesized from a diene precursor via olefin metathesis using Grubbs's catalyst. The cyclic inhibitor showed potent inhibitory activity toward Escherichia coli deformylase (K(I) = 0.67 nM) and antibacterial activity against both Gram-positive and Gram-negative bacteria (MIC = 0.7-12 microg/mL).

Characterization of a human peptide deformylase: implications for antibacterial drug design.

Ribosomal protein synthesis in eubacteria and eukaryotic organelles initiates with an N-formylmethionyl-tRNA(i), resulting in N-terminal formylation of all nascent polypeptides. Peptide deformylase (PDF) catalyzes the subsequent removal of the N-terminal formyl group from the majority of bacterial proteins. Deformylation was for a long time thought to be a feature unique to the prokaryotes, making PDF an attractive target for designing novel antibiotics. However, recent genomic sequencing has revealed PDF-like sequences in many eukaryotes, including man. In this work, the cDNA encoding Homo sapiens PDF (HsPDF) has been cloned and a truncated form that lacks the N-terminal 58-amino-acid targeting sequence was overexpressed in Escherichia coli. The recombinant, Co(2+)-substituted protein is catalytically active in deformylating N-formylated peptides, shares many of the properties of bacterial PDF, and is strongly inhibited by specific PDF inhibitors. Expression of HsPDF fused to the enhanced green fluorescence protein in human embryonic kidney cells revealed its location in the mitochondrion. However, HsPDF is much less active than its bacterial counterpart, providing a possible explanation for the apparent lack of deformylation in the mammalian mitochondria. The lower catalytic activity is at least partially due to mutation of a highly conserved residue (Leu-91 in E. coli PDF) in mammalian PDF. PDF inhibitors had no detectable effect on two different human cell lines. These results suggest that HsPDF is likely an evolutional remnant without any functional role in protein formylation/deformylation and validates PDF as an excellent target for antibacterial drug design.

S-Ribosylhomocysteinase (LuxS) is a mononuclear iron protein.

S-Ribosylhomocysteinase (LuxS) catalyzes the cleavage of the thioether linkage of S-ribosylhomocysteine (SRH) to produce L-homocysteine and 4,5-dihydroxy-2,3-pentanedione (DHPD). This is a key step in the biosynthetic pathway of the type II autoinducer (AI-2) in both Gram-positive and Gram-negative bacteria. Previous studies demonstrated that LuxS contains a divalent metal cofactor, which has been proposed to be a Zn(2+) ion. To gain insight into the catalytic mechanism of this unusual reaction and the function of the metal cofactor, we developed an efficient expression and purification system to produce LuxS enriched in either Fe(2+), Co(2+), or Zn(2+). Comparison of the catalytic properties and stability of the metal-substituted LuxS with those of the native enzyme revealed that the native metal ion is Fe(2+). The electronic absorption spectrum of the Co(II)-substituted LuxS underwent dramatic catalysis-dependent changes, suggesting the direct involvement of the metal ion in catalysis. Site-directed mutagenesis studies showed that Glu-57 and Cys-84 are essential for catalysis, most likely acting as general acids/bases. Reaction in D(2)O resulted in the incorporation of deuterium at the C-1, C-2, and C-5 positions of the diketone product. These data suggest a catalytic mechanism in which the metal ion catalyzes an intramolecular redox reaction, shifting the carbonyl group from the C-1 position to the C-3 position of the ribose. Subsequent beta-elimination at the C-4 and C-5 positions releases homocysteine as a free thiol.

Glycoside-clustering round calixarenes toward the development of multivalent ligands. Synthesis and conformational analysis of Calix[4]arene O- and C-glycoconjugates.

Bis- and tetra-O- and C-glycosyl calixarenes (calixsugars) have been prepared by tethering carbohydrate moieties to a tetrapropoxycalix[4]arene scaffold through alkyl chains. Two methodologies have been employed. One consisted of the stereoselective multiple glycosylation of upper rim calix[4]arene polyols leading to calix-O-glycosides; the other involved a multiple Wittig olefination of upper rim calix[4]arene-derived polyaldehydes by the use of sugar phosphoranes and reduction of the alkene double bonds affording calix-C-glycosides. The NMR spectra and NOE experiments of bis-glycosylated products indicate that compounds bearing sugar-protected residues exist preferentially in solution in a flattened cone arrangement (far conformation) whereas deprotected derivatives adopt a close conformation. Calculations by molecular mechanics of the latter compounds point to a close conformation as well in gas phase.