John S. Blanchard

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 drugs 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.

Meropenem-Clavulanate Is Effective Against Extensively Drug-Resistant Mycobacterium tuberculosis

β-lactam antibiotics are ineffective against Mycobacterium tuberculosis, being rapidly hydrolyzed by the chromosomally encoded blaC gene product. The carbapenem class of β-lactams are very poor substrates for BlaC, allowing us to determine the three-dimensional structure of the covalent BlaC-meropenem covalent complex at 1.8 angstrom resolution. When meropenem was combined with the β-lactamase inhibitor clavulanate, potent activity against laboratory strains of M. tuberculosis was observed [minimum inhibitory concentration (MICmeropenem) less than 1 microgram per milliliter], and sterilization of aerobically grown cultures was observed within 14 days. In addition, this combination exhibited inhibitory activity against anaerobically grown cultures that mimic the “persistent” state and inhibited the growth of 13 extensively drug-resistant strains of M. tuberculosis at the same levels seen for drug-susceptible strains. Meropenem and clavulanate are Food and Drug Administration–approved drugs and could potentially be used to treat patients with currently untreatable disease.

Flavoprotein Disulfide Reductases: Advances in Chemistry and Function

The flavoprotein disulfide reductases represent a family of enzymes that show high sequence and structural homology. They catalyze the pyridine-nucleotide-dependent reduction of a variety of substrates, including disulfide-bonded substrates (lipoamide dehydrogenase, glutathione reductase and functional homologues, thioredoxin reductase, and alkylhydroperoxide reductase), mercuric ion (mercuric ion reductase), hydrogen peroxide (NADH peroxidase), molecular oxygen (NADH oxidase), and the reductive cleavage of a carbonyl-activated carbon-sulfur bond followed by carboxylation (2-ketopropyl-coenzyme-M carboxylase?oxidoreductase). They use at least one nonflavin redox center to transfer electrons from reduced pyridine nucleotide to their substrate through flavin adenine dinucleotide. The nature of the nonflavin redox center located adjacent to the flavin varies and three types have been identified: an enzymic disulfide (most commonly), an enzymic cysteine sulfenic acid (NADH peroxidase and NADH oxidase), and a mixed Cys-S-S-CoA disulfide (coenzyme A disulfide reductase). Selection of the particular nonflavin redox center and utilization of a second, or even a third, nonflavin redox center in some cases presumably represents the most efficient strategy for reduction of the individual substrate.

BUFFERS: PRINCIPLES AND PRACTICE

Publisher Summary The chapter discusses buffers, its principles, selection, preparation, and practice. It has become important to find buffers to stabilize hydrogen ion concentrations while not interfering with the function of the enzyme being studied. The development of a series of N-substituted taurine and glycine buffers has provided buffers in the physiologically relevant range (6.1–10.4) of most enzymes, which have limited side effects with most enzymes. These buffers are nontoxic to cells at 50 mM concentrations and in some cases much higher. Many factors must be considered while choosing a buffer. When studying an enzyme one must consider the pH optimum of the enzyme, nonspecific buffer effects on the enzyme, and interactions with substrates or metals. Determining the pH optimum of a protein is a first step in determining the best buffer to employ. Volatile buffers are useful in electrophoresis, ion-exchange chromatography, and digestion of proteins followed by separation of peptides or amino acids. There may be occasions where a single buffer system is desired that can span a wide pH range of perhaps 5 or more pH units. One method would be a mixture of buffers that sufficiently covers the pH range of interest. This may lead to nonspecific buffer interactions, for which corrections must be made. Another common approach is to use a series of structurally related buffers that have evenly spaced pK values such that each pK is separated by approximately ±1 pH unit.

[4] Buffers: Principles and practice

Publisher Summary Biochemical processes can be severely affected by minute changes in hydrogen ion concentrations. At the same time, many protons may be consumed or released during an enzymatic reaction. It has become increasingly important to find buffers to stabilize hydrogen ion concentrations while not interfering with the function of the enzyme being examined. The quality of a buffer is dependent on its buffering capacity and its ability to maintain a stable pH upon dilution or addition of neutral salts. There are many factors that must be considered when choosing a buffer. When studying an enzyme, the pH optimum of the enzyme, nonspecific buffer effects on the enzyme, and interactions with substrates or metals must be considered. When purifying a protein, cost becomes an important consideration, as does the compatibility of the buffer with different purification techniques. The good buffers have been shown to be relatively free of side effects. However, inorganic buffers do have a high potential for specific buffer effects. Many enzymes are inhibited by phosphate buffer, including carboxypeptidase, urease, as well as many kinases and dehydrogenases.

Mechanisms of Isoniazid Resistance in Mycobacterium tuberculosis: Enzymatic Characterization of Enoyl Reductase Mutants Identified in Isoniazid-Resistant Clinical Isolates

Mutants in the structural gene of the inhA-encoded NADH-dependent 2-trans enoyl-acyl carrier protein reductase were identified from isoniazid-resistant clinical isolates of Mycobacterium tuberculosis. Recombinant InhA proteins with defined single amino acid replacements were expressed in Escherichia coli and purified to homogeneity. Steady-state kinetic parameters for wild type (WT) and I16T, I21V, I47T, and I95P mutants of the enoyl reductase were measured spectrophotometrically. NADH binding to WT and I16T, I21V, I47T, S94A, and I95P mutant reductases were determined by fluorescence spectroscopy and demonstrated that all mutant enzymes had reduced NADH affinity and that NADH binding to all mutants was cooperative as compared with the hyperbolic binding of NADH to the WT enzyme. Since KatG-produced electrophilic derivatives of isoniazid have been suggested to inactivate the enoyl reductase-NADH complex, the kinetics of inactivation for the WT and I21V and I95P mutants was determined. Both mutations resulted in significantly increased values for the apparent first-order rate constant of inactivation.

Aminoglycoside 2′-N-acetyltransferase from Mycobacterium tuberculosis in complex with coenzyme A and aminoglycoside substrates

AAC(2′)-Ic catalyzes the coenzyme A (CoA)-dependent acetylation of the 2′ hydroxyl or amino group of a broad spectrum of aminoglycosides. The crystal structure of the AAC(2′)-Ic from Mycobacterium tuberculosis has been determined in the apo enzyme form and in ternary complexes with CoA and either tobramycin, kanamycin A or ribostamycin, representing the first structures of an aminoglycoside acetyltransferase bound to a drug. The overall fold of AAC(2′)-Ic places it in the GCN5-related N-acetyltransferase (GNAT) superfamily. Although the physiological function of AAC(2′)-Ic is uncertain, a structural analysis of these high-affinity aminoglycoside complexes suggests that the enzyme may acetylate a key biosynthetic intermediate of mycothiol, the major reducing agent in mycobacteria, and participate in the regulation of cellular redox potential.

Mycobacterium Tuberculosis Dihydrofolate Reductase is a Target for Isoniazid

Isoniazid is a key drug used in the treatment of tuberculosis. Isoniazid is a pro-drug, which, after activation by the katG-encoded catalase peroxidase, reacts nonenzymatically with NAD+ and NADP+ to generate several isonicotinoyl adducts of these pyridine nucleotides. One of these, the acyclic 4S isomer of isoniazid-NAD, targets the inhA-encoded enoyl-ACP reductase, an enzyme essential for mycolic acid biosynthesis in Mycobacterium tuberculosis. Here we show that the acyclic 4R isomer of isoniazid-NADP inhibits the M. tuberculosis dihydrofolate reductase (DHFR), an enzyme essential for nucleic acid synthesis. This biologically relevant form of the isoniazid adduct is a subnanomolar bisubstrate inhibitor of M. tuberculosis DHFR. Expression of M. tuberculosis DHFR in Mycobacterium smegmatis mc2155 protects cells against growth inhibition by isoniazid by sequestering the drug. Thus, M. tuberculosis DHFR is the first new target for isoniazid identified in the last decade.

Purification and Characterization of the Mycobacterium smegmatis Catalase-Peroxidase Involved in Isoniazid Activation

The unique antitubercular activity of isoniazid requires that the drug be oxidized by the katG-encoded mycobacterial catalase-peroxidase to an activated drug form. In order to quantitatively assess the catalytic capabilities of the enzyme, the native catalase-peroxidase from Mycobacterium smegmatis was purified over 200-fold to homogeneity. The enzyme was shown to exhibit both catalase and peroxidase activities, and in the presence of either hydrogen peroxide or t-butyl peroxide, was found to catalyze the oxidation of the reduced pyridine nucleotides, NADH and NADPH, as well as artificial peroxidase substrates, at rates between 2.7 and 20 s. The homogeneous enzyme exhibited a visible absorbance spectrum typical of ferric heme-containing catalase-peroxidases, with a Soret maximum at 406 nm. Low temperature (10 K) electron paramagnetic resonance spectra in the presence of ethylene glycol revealed a high spin Fe(III) signal with g values of 5.9 and 5.6. The enzyme was very slowly (t = 20 min) reduced by dithionite, and the reduced form showed typical spectral changes when either KCN or CO were subsequently added. The M. smegmatis catalase-peroxidase was found to contain 2 heme molecules per tetramer, which were identified as iron protoporphyrin IX by the pyridine hemochromogen assay. The peroxidatic activity was inhibited by KCN, NaN, isoniazid (isonicotinic acid hydrazide), and its isomer, nicotinic acid hydrazide, but not by 3-amino-1,2,4-triazole. The role of mycobacterial catalase-peroxidases in the oxidative activation of the antitubercular prodrug isoniazid is discussed.

Structural and Enzymatic Analysis of MshA from Corynebacterium glutamicum: SUBSTRATE-ASSISTED CATALYSIS

The glycosyltransferase termed MshA catalyzes the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to 1-l-myo-inositol-1-phosphate in the first committed step of mycothiol biosynthesis. The structure of MshA from Corynebacterium glutamicum was determined both in the absence of substrates and in a complex with UDP and 1-l-myo-inositol-1-phosphate. MshA belongs to the GT-B structural family whose members have a two-domain structure with both domains exhibiting a Rossman-type fold. Binding of the donor sugar to the C-terminal domain produces a 97° rotational reorientation of the N-terminal domain relative to the C-terminal domain, clamping down on UDP and generating the binding site for 1-l-myo-inositol-1-phosphate. The structure highlights the residues important in binding of UDP-N-acetylglucosamine and 1-l-myo-inositol-1-phosphate. Molecular models of the ternary complex suggest a mechanism in which the β-phosphate of the substrate, UDP-N-acetylglucosamine, promotes the nucleophilic attack of the 3-hydroxyl group of 1-l-myo-inositol-1-phosphate while at the same time promoting the cleavage of the sugar nucleotide bond.