Crystal structure and function of the isoniazid target of Mycobacterium tuberculosis.

Resistance to isoniazid in Mycobacterium tuberculosis can be mediated by substitution of alanine for serine 94 in the InhA protein, the drug's primary target. InhA was shown to catalyze the beta-nicotinamide adenine dinucleotide (NADH)-specific reduction of 2-trans-enoyl-acyl carrier protein, an essential step in fatty acid elongation. Kinetic analyses suggested that isoniazid resistance is due to a decreased affinity of the mutant protein for NADH. The three-dimensional structures of wild-type and mutant InhA, refined to 2.2 and 2.7 angstroms, respectively, revealed that drug resistance is directly related to a perturbation in the hydrogen-bonding network that stabilizes NADH binding.

The 1.9 A structure of the branched-chain amino-acid transaminase (IlvE) from Mycobacterium tuberculosis.

Unlike mammals, bacteria encode enzymes that synthesize branched-chain amino acids. The pyridoxal 50-phosphate-dependent transaminase performs the final biosynthetic step in these pathways, converting keto acid precursors into -amino acids. The branched-chain amino-acid transaminase from Mycobacterium tuberculosis (MtIlvE) has been crystallized and its structure has been solved at 1.9 angstrom resolution. The MtIlvE monomer is composed of two domains that interact to form the active site. The biologically active form of IlvE is a homodimer in which each monomer contributes a substrate-specificity loop to the partner molecule. Additional substrate selectivity may be imparted by a conserved N-terminal Phe30 residue, which has previously been observed to shield the active site in the type IV fold homodimer. The active site of MtIlvE contains density corresponding to bound PMP, which is likely to be a consequence of the presence of tryptone in the crystallization medium. Additionally, two cysteine residues are positioned at the dimer interface for disulfide-bond formation under oxidative conditions. It is unknown whether they are involved in any regulatory activities analogous to those of the human mitochondrial branched-chain amino-acid transaminase.

The 1.6 A crystal structure of Mycobacterium smegmatis MshC: the penultimate enzyme in the mycothiol biosynthetic pathway.

Mycobacterium smegmatis MshC catalyzes the ATP-dependent condensation of GlcN-Ins and l-cysteine to form l-Cys-GlcN-Ins, the penultimate step in mycothiol biosynthesis. Attempts to crystallize the native, full-length MshC have been unsuccessful. However, incubation of the enzyme with the cysteinyl adenylate analogue, 5'-O-[N-(l-cysteinyl)-sulfamonyl]adenosine (CSA), followed by a 24-h limited trypsin proteolysis yielded an enzyme preparation that readily crystallized. The three-dimensional structure of MshC with CSA bound in the active site was solved and refined to 1.6 A. The refined structure exhibited electron density corresponding to the entire 47 kDa MshC molecule, with the exception of the KMSKS loop (residues 285-297), a loop previously implicated in the formation of the adenylate in related tRNA synthases. The overall tertiary fold of MshC is similar to that of cysteinyl-tRNA synthetase, with a Rossmann fold catalytic domain. The interaction of the thiolate of CSA with a zinc ion at the base of the active site suggests that the metal ion participates in amino acid binding and discrimination. A number of active site residues were observed to interact with the ligand, suggesting a role in substrate binding and catalysis. Analysis utilizing modeling of the proteolyzed loop and GlcN-Ins docking, as well as the examination of sequence conservation in the active site suggests similarities and differences between cysteinyl-tRNA synthetases and MshC in recognition of the substrates for their respective reactions.

Inhibitors of dihydrodipicolinate reductase, a key enzyme of the diaminopimelate pathway of Mycobacterium tuberculosis.

Tuberculosis (TB) remains a leading cause of infectious disease in the world today and therapies developed over the last forty years are becoming increasingly ineffective against resistant strains of Mycobacterium tuberculosis. In an effort to explore new mechanisms for drug development, we have investigated the enzymes of the diaminopimelate biosynthetic pathway as potential targets. Specifically, dihydrodipicolinate reductase, the essential gene product of dapB, was screened for novel inhibitors. Inhibitors were identified both by a molecular modeling approach which utilized the available crystal structure of the enzyme with an inhibitor bound at the active site as well as by more conventional screening strategies. The resulting compounds contain a number of structural motifs and were all found to be competitive with respect to the DHDP substrate. The K(i) values for the inhibitors range from 10 to 90 microM. The molecular modeling approach was very effective in identifying novel inhibitors of the enzyme. These compounds were obtained at a higher frequency based on the number of compounds analyzed than those inhibitors discovered via conventional screening. However, conventional screening proved beneficial in identifying compounds with greater structural diversity.

Structure/function studies on enzymes in the diaminopimelate pathway of bacterial cell wall biosynthesis.

Within the past 18 months work has continued on the structure and mechanisms of enzymes involved in the diaminopimelic acid/lysine biosynthetic pathway. A novel structure has been determined for a PLP-independent epimerase, and structures with bound substrates have been solved for two other enzymes. Additionally, new studies have appeared describing the chemical mechanisms of three enzymes in the pathway.

Substrate binding and conformational changes of Clostridium glutamicum diaminopimelate dehydrogenase revealed by hydrogen/deuterium exchange and electrospray mass spectrometry.

C. glutamicum meso-diaminopimelate dehydrogenase is an enzyme of the L-lysine biosynthetic pathway in bacteria. The binding of NADPH and diaminopimelate to the recombinant, overexpressed enzyme has been analyzed using hydrogen/deuterium exchange and electrospray ionization/mass spectrometry. NADPH binding reduces the extent of deuterium exchange, as does the binding of diaminopimelate. Pepsin digestion of the deuterated enzyme and enzyme-substrate complexes coupled with liquid chromatography/mass spectrometry have allowed the identification of eight peptides whose deuterium exchange slows considerably upon the binding of the substrates. These peptides represent regions known or thought to bind NADPH and diaminopimelate. One of these peptides is located at the interdomain hinge region and is proposed to be exchangeable in the "open," catalytically inactive, conformation but nonexchangeable in the "closed," catalytically active conformation formed after NADPH and diaminopimelate binding and domain closure. Furthermore, the dimerization region has been localized by this method, and this study provides an example of detecting protein-protein interface regions using hydrogen/deuterium exchange and electrospray ionization.

The three-dimensional structure of the ternary complex of Corynebacterium glutamicum diaminopimelate dehydrogenase-NADPH-L-2-amino-6-methylene-pimelate.

The three-dimensional (3D) structure of Corynebacterium glutamicum diaminopimelate D-dehydrogenase in a ternary complex with NADPH and L-2-amino-6-methylene-pimelate has been solved and refined to a resolution of 2.1 A. L-2-Amino-6-methylene-pimelate was recently synthesized and shown to be a potent competitive inhibitor (5 microM) vs. meso-diaminopimelate of the Bacillus sphaericus dehydrogenase (Sutherland et al., 1999). Diaminopimelate dehydrogenase catalyzes the reversible NADP+ -dependent oxidation of the D-amino acid stereocenter of mesodiaminopimelate, and is the only enzyme known to catalyze the oxidative deamination of a D-amino acid. The enzyme is involved in the biosynthesis of meso-diaminopimelate and L-lysine from L-aspartate, a biosynthetic pathway of considerable interest because it is essential for growth of certain bacteria. The dehydrogenase is found in a limited number of species of bacteria, as opposed to the alternative succinylase and acetylase pathways that are widely distributed in bacteria and plants. The structure of the ternary complex reported here provides a structural rationale for the nature and potency of the inhibition exhibited by the unsaturated L-2-amino-6-methylene-pimelate against the dehydrogenase. In particular, we compare the present structure with other structures containing either bound substrate, meso-diaminopimelate, or a conformationally restricted isoxazoline inhibitor. We have identified a significant interaction between the alpha-L-amino group of the unsaturated inhibitor and the indole ring of Trp144 that may account for the tight binding of this inhibitor.

Drugs that inhibit mycolic acid biosynthesis in Mycobacterium tuberculosis.

Tuberculosis resurged in the late 1980s and now kills more than 2 million people a year. The reemergence of tuberculosis as a potential public health threat, the high susceptibility of human immunodeficiency virus-infected persons to the disease, and the proliferation of multi-drug-resistant (MDR) strains have created much scientific interest in developing new antimycobacterial agents to both treat Mycobacterium tuberculosis strains resistant to existing drugs, and shorten the duration of short-course treatment to improve patient compliance. Bacterial cell-wall biosynthesis is a proven target for new antibacterial drugs. Mycolic acids, which are key components of the mycobacterial cell wall, are alpha-alkyl, beta-hydroxy fatty acids, with a species-dependent saturated "short" arm of 20-26 carbon atoms and a "long" meromycolic acid arm of 50-60 carbon atoms. The latter arm is functionalized at regular intervals by cyclopropyl, alpha-methyl ketone, or alpha-methyl methylethers groups. The mycolic acid biosynthetic pathway has been proposed to involve five distinct stages: (i) synthesis of C20 to C26 straight-chain saturated fatty acids to provide the alpha-alkyl branch; (ii) synthesis of the meromycolic acid chain to provide the main carbon backbone, (iii) modification of this backbone to introduce other functional groups; (iv) the final Claisen-type condensation step followed by reduction; and (v) various mycolyltransferase processes to cellular lipids. The drugs shown to inhibit mycolic acid biosynthesis are isoniazid, ethionamide, isoxyl, thiolactomycin, and triclosan. In addition, pyrazinamide was shown to inhibit fatty acid synthase type I which, in turn, provides precursors for fatty acid elongation to long-chain mycolic acids by fatty acid synthase II. Here we review the biosynthesis of mycolic acids and the mechanism of action of antimicrobial agents that act upon this pathway. In addition, we describe molecular modeling studies on InhA, the bona-fide target for isoniazid, which should improve our understanding of the amino acid residues involved in the enzyme's mechanism of action and, accordingly, provide a rational approach to the design of new drugs.

Vinylogous amide analogues of diaminopimelic acid (DAP) as inhibitors of enzymes involved in bacterial lysine biosynthesis.

[reaction: see text] Vinylogous amides 5 and 6 have been synthesized from L-propargyl glycine and tested against diaminopimelate (DAP) enzymes involved in bacterial lysine biosynthesis. Both are reversible inhibitors of DAP D-dehydrogenase and DAP epimerase with IC(50) values in the 500 microM range. Compound 5 shows competitive inhibition against the L-dihydrodipicolinate (DHDP) reductase with a K(i) value of 32 microM, which is comparable to the planar dipicolinate 16 (K(i) = 26 microM), the best known inhibitor of the enzyme.

Enterococcus faecalis glutathione reductase: purification, characterization and expression under normal and hyperbaric O2 conditions.

Glutathione reductase is found ubiquitously in eukaryotes and Gram-negative bacteria, and plays a significant role in bacterial defense against oxidative stress. Glutathione reductase from the Gram-positive bacterium Enterococcus faecalis was purified to homogeneity using anion exchange, hydrophobic interaction, and affinity chromatography. The homogeneous 49-kDa enzyme contained 1 mol bound FAD per subunit. The determined N-terminal amino acid sequence of the E. faecalis enzyme displays significant identity with glutathione reductases from other Gram-negative and Gram-positive bacteria, as well as yeast and human erythrocyte reductases. The kinetic mechanism is ping-pong, and the determined kinetic parameters exhibited by the E. faecalis glutathione reductase are similar to those found for glutathione reductases from yeast, Escherichia coli, and human erythrocyte. A two-fold increased expression of glutathione reductase activity and a three-fold induction of glutathione peroxidase activity were observed under hyperbaric O2 growth conditions without a corresponding change in the total glutathione and soluble thiol content. The difference in the expression of the enzyme, and its cognate substrate's intracellular concentration, under these conditions suggest that the gene encoding glutathione reductase is responsive to oxygen concentration, but that the genes encoding the glutathione synthesizing enzymes are not linked to an oxygen-sensitive promoter.

The effects of in vivo inactivation of GABA-transaminase and glutamic acid decarboxylase on levels of GABA in the rat retina.

Gabaculine and gamma-vinyl GABA (GVG) are specific enzyme-activated irreversible inhibitors of GABA-transaminase (GABA-T). gamma-Acetylenic GABA (GAG) irreversibly inhibits both GABA-T and glutamic acid decarboxylase (GAD). Subcutaneous injection of any of those compounds rapidly elevated levels of GABA in the retinae of rats. After injection of 10 mg/kg gabaculine, levels of retinal GABA climbed 5-fold in 4 h, and peaked 16 h after injection at levels approximately 7 times those from water-injected control rats. They remained significantly elevated compared to control levels for at least 6 days after injection. The postgabaculine increase in levels of retinal GABA was linear with time between 0.5 and 4 h after injection. In contrast, retinal GABA levels peaked at less than 3 times control levels within 8 h of injection of 50 mg/kg GAG and returned to baseline levels within 4 days. GAG, upon coadministration with gabaculine, significantly attenuated the postgabaculine rise in levels of GABA in retinae. Neither the rate of rise, nor the maximum levels, of retinal GABA was so great after injection of GAG plus gabaculine, compared to those after injection of gabaculine alone. The degree to which postgabaculine GABA accumulation was inhibited in the retina by 50 mg/kg GAG closely corresponded with the extent to which that dose of GAG inactivated retinal GAD activity. The results of this study extend previous reports from this laboratory that systemically administered gabaculine, GVG and GAG all inactivate target enzymes more potently in retina than in other brain regions.(ABSTRACT TRUNCATED AT 250 WORDS)

Enzymatic synthesis of UDP-(3-deoxy-3-fluoro)-D-galactose and UDP-(2-deoxy-2-fluoro)-D-galactose and substrate activity with UDP-galactopyranose mutase.

The novel UDP-sugar uridine 5'-(3-deoxy-3-fluoro-D-galactopyranosyl diphosphate) (1) and UDP-(2-deoxy-2-fluoro)-D-galactose (2) have been prepared enzymatically and tested as substrate analogues for the enzyme UDP-galactopyranose mutase (UDP-Galp mutase EC 5.4.99.9). Turnover of both 1 and 2 by UDP-Galp mutase was observed by HPLC and 19F NMR. The HPLC elution profile and 19F chemical shift of the products are consistent with the formation of the predicted furanose forms of 1 and 2. The Km values for compounds 1 and 2 were similar to those of the natural substrate UDP-Galp (0.26 mM for 1, 0.2 mM for 2, and 0.6 mM for UDP-Galp), but the values for kcat were substantially different (1.6/min for 1, 0.02/min for 2, and 1364/min for UDP-Galp). A correlation was also observed between the equilibrium yield of product formed during turnover of UDP-sugar by UDP-Galp mutase (UDP-Galp, compound 1 or compound 2), and the amount of furanose present for the free sugar at thermal equilibrium in aqueous solution, using 1H and 19F NMR spectroscopy. The implications of these results to the mechanism of the unusual enzymatic reaction are discussed.

Structures of D-threo-2,5-hexodiulose 1-phosphate and D-threo-2,5-hexodiulose 1,6-bisphosphate (5-keto-D-fructose mono- and bis-phosphate) in solution by 13C-N.M.R. spectroscopy.

The mono- (2) and bis-phosphate (3) derivatives of D-threo-2,5-hexodiulose (1) (5-keto-D-fructose) were synthesized enzymically and purified by anion-exchange chromatography. The proportions, sizes of ring, and anomeric configurations were determined by F.t. 31P- and 13C-n.m.r. spectroscopy. Compound 2 was found to exist preponderantly (70-78%) in the beta-pyranose form with the remainder existing in the 2R,5R-furanose form. Compound 3 assumes two different furanose forms in solution, one (77-84%) being the 2R,5R-furanose form and the other the 2S,5R-furanose form.

Illiteracy among Medicaid recipients and its relationship to health care costs.

Poor literacy is associated with poor health status, but whether illiteracy is also linked to higher medical care costs is unclear. We characterized the literacy skills of 402 randomly selected adult Medicaid enrollees to determine if there was an association between literacy skills and health care costs. Each subject's literacy skills were measured with a bilingual (English/Spanish) reading-assessment instrument. We also reviewed each subject's health care costs over the same one-year period. The mean reading level of this Medicaid population was at grade 5.6. Mean annual health care costs were $4,574 per person. There was no significant relationship between literacy and health care costs. While there are compelling reasons to improve poor reading skills among Medicaid enrollees, illiteracy in this population does not appear to contribute to the high cost of providing government-sponsored care.

Preliminary investigation of transfer between single-word decoding ability and contextual reading comprehension by poor readers in grade six.

The study sought to investigate transfer between single-word decoding skill and contextual reading comprehension using 60 sixth grade pupils classified as 30 poor and 30 very poor readers. There were two training groups, content-specific and non-content-specific. One group received single-word decoding training, which led to decoding mastery of all words to be read in narrative prose passages and the accompanying literal and inferential comprehension questions. The other group learned to identify and pronounce words, equal in difficulty and number to those of the content-specific group but never a part of the passages and questions for the study. Pupils given content-specific training answered significantly more literal and inferential questions correctly than did those given non-content-specific training. It is suggested that there is transfer between single-word decoding skill and contextual, literal and inferential comprehension.