Much of drug discovery today is predicated on the concept of selective targeting of particular bioactive macromolecules by low-molecular-mass drugs. The binding of drugs to their macromolecular targets is therefore seen as paramount for pharmacological activity. In vitro assessment of drug-target interactions is classically quantified in terms of binding parameters such as IC(50) or K(d). This article presents an alternative perspective on drug optimization in terms of drug-target binary complex residence time, as quantified by the dissociative half-life of the drug-target binary complex. We describe the potential advantages of long residence time in terms of duration of pharmacological effect and target selectivity.

Drug–target residence time and its implications for lead optimization

Aminoglycoside Modifying Enzymes

Bacterial resistance to inorganic and organic mercury compounds (HgR) is one of the most widely observed phenotypes in eubacteria. Loci conferring HgR in Gram-positive or Gram-negative bacteria typically have at minimum a mercuric reductase enzyme (MerA) that reduces reactive ionic Hg(II) to volatile, relatively inert, monoatomic Hg(0) vapor and a membrane-bound protein (MerT) for uptake of Hg(II) arranged in an operon under control of MerR, a novel metal-responsive regulator. Many HgR loci encode an additional enzyme, MerB, that degrades organomercurials by protonolysis, and one or more additional proteins apparently involved in transport. Genes conferring HgR occur on chromosomes, plasmids, and transposons and their operon arrangements can be quite diverse, frequently involving duplications of the above noted structural genes, several of which are modular themselves. How this very mobile and plastic suite of proteins protects host cells from this pervasive toxic metal, what roles it has in the biogeochemical cycling of Hg, and how it has been employed in ameliorating environmental contamination are the subjects of this review.

Bacterial mercury resistance from atoms to ecosystems

The Behavior and Significance of Slow-Binding Enzyme Inhibitors

Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate.

The kinetics of reversible tight-binding inhibition.

Investigations have been made of the slow, tight-binding inhibition by methotrexate of the reaction catalyzed by dihydrofolate reductase from Streptococcus faecium A. Quantitative analysis has shown that progress curve data are in accord with a mechanism that involves the rapid formation of an enzyme-NADPH-methotrexate complex that subsequently undergoes a relatively slow, reversible isomerization reaction. From the Ki value for the dissociation of methotrexate from the E-NADPH-methotrexate complex (23 nM) and values of 5.1 and 0.013 min-1 for the forward and reverse rate constants of the isomerization reaction, the overall inhibition constant for methotrexate was calculated to be 58 pM. The formation of an enzyme-methotrexate complex was demonstrated by means of fluorescence quenching, and a value of 0.36 muM was determined for its dissociation constant. The same technique was used to determine dissociation constants for the reaction of methotrexate with the E-NADP and E-NADPH complexes. The results indicate that in the presence of either NADPH or NADP there is enhancement of the binding of methotrexate to the enzyme. It is proposed that methotrexate behaves as a pseudosubstrate for dihydrofolate reductase.

Methotrexate, a high-affinity pseudosubstrate of dihydrofolate reductase.

Mercuric reductase from R-plasmid NR1: characterization and mechanistic study

Gentamicin acetyltransferase I will catalyze acyl transfer from chloroacetylcoenzyme A to form 3-N-chloroacetylgentamicin. This product can be linked to coenzyme A to form a multisubstrate analog by nucleophilic displacement of the chlorine by the sulfur of coenzyme A. The analog can be purified by selective binding to cationic and anionic ion exchange resins. Kinetic analysis of a time-dependent onset and reversal of inhibition of gentamicin acetyltransferase I by the purified multisubstrate analog yields an inhibition constant of 5-20×10-10M. The inhibitor does not potentiate antibiotic activity against resistant Escherichia coli. Nevertheless, the effectiveness of the tight-binding between the enzyme and the multisubstrate analog demonstrates that inhibitors of resistance can be designed and prepared by specific enzymatic synthesis.

Synthesis of a tight-binding, multisubstrate analog inhibitor of gentamicin acetyltransferase I.

Gentamicin acetyltransferase I is induced 13-fold in R factor resistant Escherichia coli by high concentrations (1 mg/ml) of gentamicin in the growth medium. The enzyme is maximally released from bacteria by osmotic shock in late-log phase, unlike previously studied periplasmic enzymes. Streptomycin sulfate and ammonium sulfate precipitations of shockate followed by affinity and ion-exchange chromatography recover 51% of the induced enzyme with a 360-fold increase in purity (12% of 4400-fold, uninduced). The purified enzyme appears homogeneous by six criteria, the first aminoglycoside inactivating enzyme so purified. Sodium dodecyl sulfate electrophoresis, amino acid analysis, and sedimentation analyses indicate a tetrameric protein of 63000 molecular weight. The protein does not contain tryptophan. Kinetic analyses yield apparent values of: Vmax = 3.4 +/- 0.2 mumol per min mg at pH 8 (optimum), Km (acetyl-CoA) = 3.9 +/- 0.2 muM, Km (gentamicin Cla) = 0.3 +/- 0.08 muM, KI (gentamicin substrate inhibition) = 160 +/- 29 muM. The activity of the enzyme is stable to a variety of conditions, including lyophilization and prolonged storage, and can be monitored by two convenient spectrophotometric assays.

Jeffrey W. Williams

Papers

The kinetics of reversible tight-binding inhibition.

Methotrexate, a high-affinity pseudosubstrate of dihydrofolate reductase.

Mercuric reductase from R-plasmid NR1: characterization and mechanistic study

Synthesis of a tight-binding, multisubstrate analog inhibitor of gentamicin acetyltransferase I.

Purification and properties of gentamicin acetyltransferase I.