What does I50 mean?

Structural Studies of Inhibitors with Clinically Relevant Influenza Endonuclease Variants

Vital to the treatment of influenza is the use of antivirals such as Oseltamivir (Tamiflu) and Zanamivir (Relenza); however, antiviral resistance is becoming an increasing problem for these therapeutics. The RNA-dependent RNA polymerase acidic N-terminal (PAN) endonuclease, a critical component of influenza viral replication machinery, is an antiviral target that was recently validated with the approval of Baloxavir Marboxil (BXM). Despite its clinical success, BXM has demonstrated susceptibility to resistance mutations, specifically the I38T, E23K, and A36 V mutants of PAN. To better understand the effects of these mutations on BXM resistance and improve the design of more robust therapeutics, this study examines key differences in protein-inhibitor interactions with two inhibitors and the I38T, E23K, and A36 V mutants. Differences in inhibitor binding were evaluated by measuring changes in binding to PAN using two biophysical methods. The binding mode of two distinct inhibitors was determined crystallographically with both wild-type and mutant forms of PAN. Collectively, these studies give some insight into the mechanism of antiviral resistance of these mutants.

Kinetics of the enzyme titration process by reversible modifiers

The effect of reversible modifiers on the initial rate of enzyme catalysed reactions has been investigated in a quasi-equilibrium approximation using the general modifier mechanism of Botts and Morales. It has been shown that, when investigating the dependence of the initial rate on the modifier concentration at a fixed substrate concentration, the kinetics of enzyme titration by reversible modifiers can generally be described using two kinetic constants. Just as the dependence of the initial rate on the substrate concentration (at a fixed modifier concentration) is described using two kinetic constants: the Michaelis constant Km and the limiting rate Vm. Only one constant M50 is needed to describe the kinetics of linear inhibition, and in the case of nonlinear inhibition and activation, along with M50 the constant QM is also needed. Knowing the values of the constants M50 and QM, it is possible to unambiguously determine the modification efficiency, that is, to calculate how many times the initial rate of the enzyme catalysed reaction will change when a certain modifier concentration is added to the incubation medium. The properties of these fundamental constants have been analysed in detail and the dependence of these constants on other parameters of the Botts-Morales model have been shown. Equations describing the dependence of relative reaction rates on the modifier concentration using these kinetic constants are presented. Various ways of linearising these equations for calculating the kinetic constants M50 and QM from experimental data are also presented.

A novel allosteric mechanism in the cysteine peptidase cathepsin K discovered by computational methods

Allosteric modifiers have the potential to fine-tune enzyme activity. Therefore, targeting allosteric sites is gaining increasing recognition as a strategy in drug design. Here we report the use of computational methods for the discovery of the first small-molecule allosteric inhibitor of the collagenolytic cysteine peptidase cathepsin K, a major target for the treatment of osteoporosis. The molecule NSC13345 is identified by high-throughput docking of compound libraries to surface sites on the peptidase that are connected to the active site by an evolutionarily conserved network of residues (protein sector). The crystal structure of the complex shows that NSC13345 binds to a novel allosteric site on cathepsin K. The compound acts as a hyperbolic mixed modifier in the presence of a synthetic substrate, it completely inhibits collagen degradation and has good selectivity for cathepsin K over related enzymes. Altogether, these properties qualify our methodology and NSC13345 as promising candidates for allosteric drug design.

Heat-labile bacterial alkaline phosphatase from a marine Vibrio sp

Psychrophilic organisms have successfully adapted to various low-temperature environments such as cold ocean waters. Catalysts with increased catalytic efficiencies are produced, generally at the expense of thermal stability due to fewer non-covalent stabilizing interactions. A marine bacterial strain producing a particularly heat-labile alkaline phosphatase was selected from a total of 232 strains isolated from North-Atlantic coastal waters. From partial 16S rRNA sequences the strain was characterized as a Vibrio sp. An alkaline phosphatase was purified 151-fold with 54% yield from the culture medium using a single step affinity chromatography procedure on agarose-linked L-histidyldiazobenzylphosphonic acid. The active enzyme was a 55 +/- 6 kDa monomer. The enzyme had optimal activity at pH 10 and was strikingly heat-labile with a half-life of 6 min at 40 degrees C and 30 min at 32 degrees C. This enzyme from Vibrio sp. had a higher turnover number (k(cat)) and higher apparent Michaelis-Menten factor (K(m)) than the enzyme from Escherichia coli, a clear-indication of cold-adaptation. Inorganic phosphate was a competitive inhibitor with a relatively high K(i) value of 1.7 mM. Low affinity for phosphate may contribute to higher turnover rates due to more facile release of product.

Identification and partial characterization of ectoATPase expressed by immortalized B lymphocytes

EctoATPases are extracellular membrane-bound enzymes that catalyze the hydrolysis of the gamma phosphate from ATP. EctoATPase is expressed by activated and immortalized Epstein-Barr virus-transformed human peripheral blood B lymphocytes and murine B cell hybridomas. By contrast, ectoATPase activity is not expressed on nontransformed human peripheral blood B lymphocytes, murine spleen cells, or murine myeloma cells. The K(m) for ATP for the B cell ectoATPases ranged from 5 to 77 microM; the Vmax ranged from 48 to 129 pmol/ min/10(4) cells. The enzyme required Mg2+ for maximal activity with little dependence on Ca2+. ADP and purine and pyrimidine nucleoside triphosphates were competitive inhibitors of the catalytic reaction. A putative ectoATPase protein has been identified by Western blot analysis of membrane proteins from the immortalized B cells. Under reducing conditions, antiectoATPase antibodies cross-reacted with a 66-kDa protein from murine B cell hybridoma membranes. By contrast a 200-kDa protein from the B cell hybridoma membranes cross-reacted with the antibodies under nonreducing conditions, suggesting a disulfide-linked trimer. The antibodies also cross-reacted with a 66-kDa protein from human B cell membranes under reducing conditions, but did not cross-react with membrane proteins under nonreducing conditions. This suggests that the antibody epitope(s) recognized on the reduced human protein is masked under nonreducing conditions. Thus, this work demonstrates: (1) that ectoATPase may serve as a marker for B cell activation; and (2) mammalian and avian ectoATPases have conserved interspecies immunological epitopes and kinetic properties.

Identification and partial characterization of an ectoATPase expressed by human natural killer cells

An extracellular membrane-associated ectoATPase has been identified on the human natural killer cell line NK3.3. The enzyme is distinct from other classes of ATPases, kinases, and phosphatases. NK3.3 ectoATPase demonstrated a Km for ATP of 41 microM and a Vmax of 0.2 mumol/min and required both Ca2+ and Mg2+ for maximal activity. Purine and pyrimidine nucleotides were competitive inhibitors of the catalytic reaction. Inhibition increased with the addition of increasing negative charge of the phosphate side chain and was also dependent on contributions from the nucleoside. NK3.3 ectoATPase activity was inhibited by reaction with the affinity label [p-(fluorosulfonyl)benzoyl]-5'-adenosine (5'-FSBA), which is shown to modify the enzyme at or near the ATP-binding domain. Photoaffinity labeling of intact NK3.3 cells with [alpha-32P]-8-azidoATP demonstrated an ATP-binding protein of 68-80 kDa unique to NK3.3 cells. A positive correlation was observed between the ability of the various nucleotides to block photoincorporation into the 68-80-kDa protein and their ability to inhibit ectoATPase activity. NK3.3 cells which were made ectoATPase-deficient by reaction with 5'-FSBA demonstrated that this enzyme does not have a major role in the protection of this cytolytic effector cell from the possible lytic effects of extracellular ATP.

Protective effect of oleoyl peptide conjugates against elastolysis by neutrophil elastase and kappa elastin-induced monocyte chemotaxis

Elastin can impair the human neutrophil elastase (HNE) inhibitory capacity of elastase inhibitors. We synthesized oleoyl-alanyl-alanyl-prolyl-valine (Ol-Ala-Ala-Pro-Val-OH) (oleoyl peptide) and the amides (NH2 and NH-C3H7) of this peptide and studied their HNE-inhibitory potencies using succinyl-alanyl-alanyl-alanine-p-nitroanilide (Suc-Ala-Ala-Ala-pNA) or 3H-labeled elastin as substrates, as well as cryostat sections of rabbit skin as an ex vivo substrate. Using Suc-Ala-Ala-Ala-pNA, Ol-Ala-Ala-Pro-Val-OH had an IC50 of 3 microM. When the COOH terminal of the oleoyl peptide was derivatized to amide forms, the compound lost its ability to interact with HNE while keeping its elastin-protecting function: IC50 values for NH2 and NH-C3H7 derivatives were 22 and 17 microM, respectively. Also, the HNE-inhibitory capacity of Ol-Ala-Ala-Pro-Val-OH was only reduced 2-fold by using elastin as a substrate. This decrease was much lower than those determined with other HNE inhibitors of similar potency and could be accounted for by the ability of oleoyl peptide to bind to elastin. Cryostat sections of rabbit skin were also used as an ex vivo substrate for assessing the elastin-protecting property of Ol-Ala-Ala-Pro-Val-OH. Preincubating HNE and oleoyl peptide before application to tissue sections led to an IC50 of 8 microM, close to the value determined with elastin as a substrate. Treatment of sections with oleoyl peptide before adding HNE gave a lower IC50 (4 microM).(ABSTRACT TRUNCATED AT 250 WORDS)

A kinetic study of the inhibition of yeast AMP deaminase by polyphosphate

Inorganic pyrophosphate and polyphosphates have acted as potent inhibitors of purified AMP deaminase (EC 3.5.4.6) from yeast: the activity fell to a definite limit with the increase in the concentration of the inhibitor. The effect of polyphosphate was largely on the maximal velocity of the enzyme with some decrease in affinity. The cooperative effect of AMP, analyzed in terms of a Hill coefficient, remained at 2 in the absence and presence of polyphosphate. Binding of polyphosphate to the enzyme showed no cooperativity. The inhibition of AMP deaminase by polyphosphate can be qualitatively and quantitatively accounted for by the partial mixed-type inhibition mechanism. Both the Ki value for the inhibitor and the breakdown rate of the enzyme-substrate-inhibitor complex are dependent on the chain length of polyphosphate, suggesting that the breakdown rate of the enzyme-substrate-inhibitor complex is regulated by binding of polyphosphate to a specific inhibitory site.

Metal ion inactivation and chelator stimulation of Streptococcus mitis arginine aminopeptidase

Activation of Streptococcus mitis (ATTC 9811) arginine aminopeptidase resulted in removal of the metal(s) from the enzyme molecule, and the action of the heavy metal ion in the inactivation process was shown to involve formation of a chelate complex between the enzyme molecule and metal or oxidation of functional group(s) on the enzyme surface. The enzyme also underwent activation by bovine serum albumin, amino acids, phosphate, and citric acid, which are probable physiological chelators.

Endothelial binding sites for heparin. Specificity and role in heparin neutralization

The specificity of endothelial binding sites for heparin was investigated with heparin fractions and fragments differing in their Mr, charge density and affinity for antithrombin III, as well as with heparinoids and other anionic polyelectrolytes (polystyrene sulphonates). The affinity for endothelial cells was estimated by determining I50 values in competition experiments with 125I-heparin. We found that affinity for endothelial cells increases as a function of Mr and charge density (degree of sulphation). Binding sites are not specific receptors for heparin. Other anionic polyelectrolytes, such as pentosan polysulphates and polystyrene sulphonates, competed with heparin for binding to endothelial cells. Fractions of standard heparin with high affinity for antithrombin III also had greater affinity for endothelium. However, these two properties of heparin (affinity for antithrombin III and affinity for endothelial cells) could be dissociated. Oversulphated heparins and oversulphated low-Mr heparin fragments had lower anticoagulant activity and higher affinity for endothelial cells than did their parent compounds. Synthetic pentasaccharides, bearing the minimal sequence for binding to antithrombin III, did not bind to endothelial cells. Binding to endothelial cells involved partial neutralization of heparin. Bound heparin exhibited only 5% and 7% of antifactor IIa and antifactor Xa specific activity, respectively. In the presence of 200 nM-antithrombin III, and in the absence of free heparin, a limited fraction (approx. 30%) of bound heparin was displaced from endothelial cells during a 1 h incubation period. These data suggested that a fraction of surface-bound heparin could represent a pool of anticoagulant.

Binding and endocytosis of heparin by human endothelial cells in culture

Binding of heparin and low molecular weight heparin fragments (CY 222, Mr range 1500-8000) to human vascular endothelial cells was studied. Primary culture of human umbilical vein endothelial cells and either 125I or 3H-labeled heparin or [125I]CY 222 were used. Slow, saturable and specific binding was found. No other tested glycosaminoglycan, excepting a highly sulfated heparan fraction, was able to compete for heparin binding. Two groups of binding sites for [3H]heparin could be distinguished: one with high affinity (Kd = 0.12 microM) and another with lower affinity (Kd = 1.37 microM) and a relative large capacity of binding (1.16 X 10(7) molecules/cell) was calculated. The Kd for unlabeled heparin, as calculated from competition experiments, was 0.23 microM. Much lower affinity was calculated for unlabeled low molecular weight heparin fragments CY 222 (Kd = 4.3 microM) from competition experiments with [125I]CY 222. The binding reversibility was only partial for unfractionated heparin. Even by chasing with unlabeled compound, a fraction of 25-30% was not dissociable from endothelial cells. This fraction was much lower if incubation was carried out at 4 degrees C. The addition of basic proteins (histones) to the incubation medium greatly enhanced the undissociable binding at 37 degrees C, but not at 4 degrees C. The undissociable fraction of heparin was not available to degradation by purified microbial heparinase. These results suggest that a fraction of bound heparin is internalized by the vascular endothelium.