pHP-Tethered N-Acyl Carbamate: A Photocage for Nicotinamide

The synthesis of a new photocaged nicotinamide having an N-acyl carbamate linker and a p-hydroxyphenacyl (pHP) chromophore is described. The photophysical and photochemical studies showed an absorption maximum at λ = 330 nm and a quantum yield for release of 11% that are dependent upon both pH and solvent. While the acyl carbamate releases nicotinamide efficiently, a simpler amide linker was inert to photocleavage. This photocaged nicotinamide has significant advantages with respect to quantum yield, absorbance wavelength, rate of release, and solubility that make it the first practical example of a photocaged amide.

Adenoviral L4 33K forms ring-like oligomers and stimulates ATPase activity of IVa2: implications in viral genome packaging

The mechanism of genome packaging in adenoviruses (AdVs) is presumed to be similar to that of dsDNA viruses including herpesviruses and dsDNA phages. First, the empty capsids are assembled after which the viral genome is pushed through a unique vertex by a motor which consists of three minimal components: an ATPase, a small terminase and a portal. Various components of this motor exist as ring-like structures forming a central channel through which the DNA travels during packaging. In AdV, the IVa2 protein is believed to function as a packaging ATPase, however, the equivalents of the small terminase and the portal have not been identified in AdVs. IVa2 interacts with another viral protein late region 4 (L4) 33K which is important for genome packaging. Both IVa2 and 33K are expressed at high levels during the late stage of virus infection. The oligomeric state of IVa2 and 33K was analyzed in virus-infected cells, IVa2 and 33K transfected cells, AdV particles, or as recombinant purified proteins. Electron microscopy of the purified proteins showed ring-like oligomers for both proteins which is consistent with their putative roles as a part of the packaging motor. We found that the ATPase activity of IVa2 is stimulated in the presence of 33K and the AdV genome. Our results suggest that the 33K functions analogous to the small terminase proteins and so will be part of the packaging motor complex.

Developing an antibiotic effective against multi-drug resistant bacteria

The emergence of multi-drug resistant pathogenic bacteria is one of the great challenges to modern medicine. The gram positive cocci Methicillin Resistant Staphylococcus aureus (MRSA) and Vancomycin Resistant Enterococcus faecalis (VRE) are two particularly virulent examples. In vivo studies have shown that the eukaryotic like 'mevalonate' isoprenoid pathway used by these pathogenic cocci is essential to their growth and virulence [1]. Our structures of HMG-CoA reductase (HMGR) from P. mevalonii demonstrated that the bacterial enzymes are structurally distinct from the human enzymes allowing for specific antibacterial activity [2]. High throughput in vitro screening against bacterial HMGR at the Southern Research Center, Birmingham, AL uncovered a lead compound with an IC50 of 80 µM with a competitive mode of action. Our x-ray crystal structures of HMGR from E. faecalis complexed with the lead compound and its variations have informed the synthesis of new inhibitors that have improved the IC50 to 5 µM [3]. Studies of this compound show it to be active against both MRSA and VRE in culture, effective against these bacteria in biofilms, and efficacious in a model system of eukaryotic infection. Structures and kinetics of these compounds will be presented and future directions discussed.

Structural and Functional study of Mevalonate Diphosphate Decarboxylase

Mevalonate diphosphate decarboxylases (MDD) (EC 4.1.1.33) catalyze the Mg2+-dependent decarboxylation of mevalonate 5-diphosphate (MVAPP) by hydrolyzing adenosine triphosphate (ATP) and producing isopentenyl diphosphate (IPP) in the final step of mevalonate pathway. This enzyme is essential in Enterococcus faecalis and other Gram (+) bacteria; therefore, MDD protein is an ideal drug target for the treatment of bacterial infections. We have studied the enzyme kinetics and structures of MDD from Enterococcus faecalis (MDDEF) which causes clinical enterorococcal infections. In the crystal structure of the MDDEF bound with ATP, the catalytically unfavored orientation of the γ-phosphate of ATP implies that conformational changes of MDDEF might occur in order to accommodate the binding of ATP when the MVAPP binds to the active site in advance. A 10-fold decrease of the dissociation constrant (Kd) value of ATPγS has been observed using isothermal titration calorimetry (ITC) when MDDEF is pre-bound with MVAPP. The increase of binding affinity of ATPγS suggests that cooperative binding of ATP to MDDEF can be achieved by the prerequisite binding of MVAPP. Indeed, the crystal structure of MDDEF soaked with the MVAPP shows that one flexible loop that eventually should bind ATP becomes non-flexible and bends toward the active site of MDDEF. Thus, we hypothesize that the binding of the MVAPP to the active site triggers conformational changes of MDDEF which induces the binding of the other substrate, ATP, in its catalytically favored position. Further experiments will be performed for investigating a substrate-binding mechanism for MDDEF and these will serve as platforms for specific drug development in the near future.

Development of carbamate-tethered coumarins as phototriggers for caged nicotinamide

The syntheses of 7-diethylaminocoumarin- or modified DEACM-nicotinamide and 6-bromo-7-methoxycoumarin- or BMCM-nicotinamide have been accomplished by reaction of nicotinoyl isocyanate with the corresponding coumarin allylic alcohol derivatives. The resulting compounds contain an N-acyl O-alkyl carbamate as a new type of linkage for the caging of nicotinamide with a coumarin phototrigger, which undergoes cleavage upon photolysis. Our design of specific caged-nicotinamides was based upon NBO and TD-FT calculations to predict absorption wavelengths and photocleavage potential. This work provides a potentially general method for the caging of amides with coumarin photolabile protecting groups.

Synthesis, photophysical, photochemical, and computational studies of coumarin-labeled nicotinamide derivatives

The syntheses and photophysical/photochemical properties of two amide-tethered coumarin-labeled nicotinamides are described. Photochemical studies of 6-bromo-7-hydroxycoumarin-4-ylmethylnicotinamide (BHC-nicotinamide) revealed an unexpected solvent effect. This result is rationalized by computational studies of the different protonation states using TD-DFT with the M06L/6-311+G** method with implicit and explicit solvation models. Molecular orbital energies responsible for the λ(max) excitation show that the functionalization of the coumarin ring results in a strong red-shift from 330 to 370 nm when the pH of solution is increased from 3.06 to 8.07. From this MO analysis, a model for solvent interactions has been proposed. The BHC-nicotinamide proved to be photochemically stable, which is also interpreted in terms of NBO calculations. The results provide a set of principles for the rational design of either photostable labeling reagents or photolabile cage compounds.

Identification of regions of the tomato gamma-glutamyl kinase that are involved in allosteric regulation by proline

The first step of proline biosynthesis is catalyzed by gamma-glutamyl kinase (GK). To better understand the feedback inhibition properties of GK, we randomly mutagenized a plasmid carrying tomato tomPRO1 cDNA, which encodes proline-sensitive GK. A pool of mutagenized plasmids was transformed into an Escherichia coli GK mutant, and proline-overproducing derivatives were selected on minimal medium containing the toxic proline analog 3,4-dehydro-dl-proline. Thirty-two mutations that conferred 3,4-dehydro-dl-proline resistance were obtained. Thirteen different single amino acid substitutions were identified at nine different residues. The residues were distributed throughout the N-terminal two-thirds of the polypeptide, but 9 mutations affecting 6 residues were in a cluster of 16 residues. GK assays revealed that these amino acid substitutions caused varying degrees of diminished sensitivity to proline feedback inhibition and also resulted in a range of increased proline accumulation in vivo. GK belongs to a family of amino acid kinases, and a predicted three-dimensional model of this enzyme was constructed on the basis of the crystal structures of three related kinases. In the model, residues that were identified as important for allosteric control were located close to each other, suggesting that they may contribute to the structure of a proline binding site. The putative allosteric binding site partially overlaps the dimerization and substrate binding domains, suggesting that the allosteric regulation of GK may involve a direct structural interaction between the proline binding site and the dimerization and catalytic domains.

Three-dimensional structure of a human class II histocompatibility molecule complexed with superantigen

The structure of a bacterial superantigen, Staphylococcus aureus enterotoxin B, bound to a human class II histocompatibility complex molecule (HLA-DR1) has been determined by X-ray crystallography. The superantigen binds as an intact protein outside the conventional peptide antigen-binding site of the class II major histocompatibility complex (MHC) molecule. No large conformational changes occur upon complex formation in either the DR1 or the enterotoxin B molecules. The structure of the complex helps explain how different class II molecules and superantigens associate and suggests a model for ternary complex formation with the T-cell antigen receptor (TCR), in which unconventional TCR-MHC contacts are possible.

Protein-RNA interactions in an icosahedral virus at 3.0 A resolution

Nearly 20 percent of the packaged RNA in bean-pod mottle virus (BPMV) binds to the capsid interior in a symmetric fashion and is clearly visible in the electron density map. The RNA displaying icosahedral symmetry is single-stranded with well-defined polarity and stereochemical properties. Interactions with protein are dominated by nonbonding forces with few specific contacts. The tertiary and quaternary structures of the BPMV capsid proteins are similar to those observed in animal picornaviruses, supporting the close relation between plant comoviruses and animal picornaviruses established by previous biological studies.