The use of informatics and automation to remove bottlenecks in drug discovery

Advances in molecular biology and genetics have furnished more targets than could be reasonably progressed, forcing the pharmaceutical industry to invest in increasing chemistry and screening throughput. Combinatorial chemistry, automation and miniaturization are described as the keys to success. Many pharmaceutical companies assisted by the vendor community have risen to the challenges, delivering more functional and reliable robotics; a number of recent developments are described. These, in turn, have highlighted other deficiencies, for example in target selection, integration and scheduling, and assay and reaction optimization. These areas provide the challenges for the future and have already sparked several new initiatives, a number of which are described.

Dual inhibition of human type 4 phosphodiesterase isostates by (R, R)-(+/-)-methyl 3-acetyl-4-[3-(cyclopentyloxy)-4-methoxyphenyl]-3- methyl-1-pyrrolidinecarboxylate

Purified recombinant human type 4 phosphodiesterase B2B (HSPDE4B2B) exists in both a low- and a high-affinity state that bind (R)-rolipram with Kd's of ca. 500 and 1 nM, respectively [Rocque, W. J., Tian, G., Wiseman, J. S., Holmes, W. D., Thompson, I. Z., Willard, D. H., Patel, I. R., Wisely, G. B., Clay, W. C., Kadwell, S. H., Hoffman, C. R., and Luther, M. A. (1997) Biochemistry 36, 14250-14261]. Since the tissue distribution of the two isostates may be significantly different, development of inhibitors that effectively inhibit both forms may be advantageous pharmacologically. In this study, enzyme inhibition and binding of HSPDE4B2B by (R, R)-(+/-)-methyl 3-acetyl-4-[3-(cyclopentyloxy)-4-methoxyphenyl]-3-methyl-1-pyrrolidin ecarboxylate (1), a novel inhibitor of phosphodiesterase 4 (PDE 4), were investigated. Binding experiments demonstrated high-affinity binding of 1 to HSPDE4B2B with a stoichiometry of 1:1. Inhibition of PDE activity showed only a single transition with an observed Ki similar to the apparent Kd determined by the binding experiments. Deletional mutants of HSPDE4B2B, which have been shown to bind (R)-rolipram with low affinity, were shown to interact with 1 with high affinity, indistinguishable from the results obtained with the full-length enzyme. Bound 1 was completely displaced by (R)-rolipram, and the displacement showed a biphasic transition that resembles the biphasic inhibition of HSPDE4B2B by (R)-rolipram. Theoretical analysis of the two transitions exemplified in the interaction of (R)-rolipram with HSPDE4B2B indicated that the two isostates were nonexchangeable. Phosphorylation at serines 487 and 489 on HSPDE4B2B had no effect on the stoichiometry of binding, the affinity for binding, or the inhibition of the enzyme by 1. These data further illustrate the presence of two isostates in PDE 4 as shown previously for (R)-rolipram binding and inhibition. In contrast to (R)-rolipram, where only one of the two isostates of PDE 4 binds with high affinity, 1 is a potent, dual inhibitor of both of the isostates of PDE 4. Kinetic and thermodynamic models describing the interactions between the nonexchangeable isostates of PDE 4 and its ligands are discussed.

Human recombinant phosphodiesterase 4B2B binds (R)-rolipram at a single site with two affinities

The interactions between (R)-rolipram and purified human recombinant low-Km, cAMP-specific phosphodiesterase (HSPDE4B2B) constructs were investigated using biochemical, kinetic, and biophysical approaches. The full-length protein (amino acids 1-564) and an N-terminal truncated protein (amino acids 81-564) exhibited high-affinity (R)-rolipram binding, whereas an N-terminal and C-terminal truncated protein (amino acids 152-528) lacked high-affinity (R)-rolipram binding. The 152-528 and 81-564 proteins had similar Km's and kcat/Km's and differed less than 4-fold compared with the 1-564 protein. (R)-Rolipram inhibition plots were biphasic for the 1-564 and 81-564 proteins and fit to two states, a high-affinity (Ki = 5-10 nM) state and a low-affinity (Ki = 200-400 nM) state, whereas the 152-528 protein fit to a single state (Ki = 350-400 nM). The stoichiometry for high-affinity binding using a filter binding assay was found to be <1 mol of (R)-rolipram per mole of 1-564 or 81-564 protein. Titration microcalorimetric studies revealed both a high-affinity state with a stoichiometry of 0.3 mol of (R)-rolipram per mole of protein and a low-affinity state with a stoichiometry of 0.6 mol of (R)-rolipram per mole of protein for the 81-564 protein. A single low-affinity state with a stoichiometry of 0.9 mol of (R)-rolipram per mole of protein was seen using the 152-528 protein. The data indicate that purified HSPDE4B2B 1-564 and 81-564 proteins contain a single binding site for (R)-rolipram and suggest that the proteins exist in two different states distinguishable by their affinity for (R)-rolipram. Furthermore, the high-affinity binding state of the protein requires amino acid residues at the N-terminus (81-151) of the protein and catalytic domain (152-528), whereas the low-affinity binding state only requires residues in the catalytic domain (152-528). Phosphorylation at residues 487 and 489 of the 81-564 protein does not appear to alter the substrate kinetics or the stoichiometry and binding affinity of (R)-rolipram.

Relationship of pelvic radiation to intestinal blood flow

Pelvic radiation remains the mainstay in the treatment of many malignancies. Chronic radiation injury represents an obliterative endarteritis. The purpose of our experiment was to investigate the chronic changes in blood flow that occurred in a model of pelvic radiation. Also, we investigated the potential benefits of an elemental diet, sodium meclofenamate, and vitamin A within the radiated large and small bowel. Female Sprague-Dawley rats, 200-250 g, were anesthetized and received 900 rads once a week for 5 weeks for a total of 4500 rads. Group B received sodium meclofenamate, group C elemental diet, and group D vitamin A. Group A received radiation only where control animals (group E) received anesthesia but no radiation. All animals were given treatments during the course of radiation therapy only. Blood flow was determined within the terminal ileum, proximal jejunum, and distal colon 1 week, 5 weeks, 6 months, and 1 year postradiation therapy. Blood flow was determined by strontium-labeled 15-microns microspheres. Results showed that radiation resulted in an increase in blood flow within the terminal ileum at 1 week postradiation of approximately 175% when compared to controls. Blood flow then decreased (59%) when compared to controls at 5 weeks and increased (141%) again at 6 months when compared to controls. No change in blood flow was noted at 1 year postradiation therapy. An elemental diet and sodium meclofenamate prevented these changes in blood flow at each of these times points. No change in blood flow was seen at any of the time points measured within the jejunum or colon.

The effect of epidural analgesia on the return of peristalsis and the length of stay after elective colonic surgery

Epidural analgesia has been shown to improve pulmonary function and analgesia after abdominal surgery. Although epidural analgesia may increase colonic motility, its effect on the clinical outcome following colonic surgery is unclear. Therefore, the purpose of this study was to determine the effect of epidural analgesia on return of peristalsis and length of stay after elective colonic surgery as compared with traditional analgesia. A total of 102 patients undergoing elective colonic surgery (66 left-sided, 36 right) between September 1991 and April 1993 were retrospectively studied. Variables recorded were location of colon anastomosis, type of analgesia, time until return of colonic peristalsis, length of epidural administration, and length of hospital stay. Forty-one patients received epidural and 61 received traditional analgesia. Data was analyzed with a Student's T test (P set < 0.05) and Spearman's correlation coefficient where appropriate. No statistically significant difference was found between epidural and traditional analgesia with regard to return of peristalsis or length of stay. Similarly, when considering the location of the anastomosis (left versus right colon), no statistically significant difference was demonstrated between the two groups. Also, there was no increased incidence in anastomotic leaks or mortality.

The relationship of radon to gastrointestinal malignancies

Radon has known and well-studied carcinogenic effects on pulmonary epithelium. The gastrointestinal tract has potential for radon exposure by swallowed air and/or pulmonary secretions or contaminated drinking water. However, the relationship between radon and gastrointestinal malignancies is poorly documented. Therefore, the purpose of this study was to investigate a potential relationship between radon levels and gastrointestinal malignancies within the Commonwealth of Pennsylvania. In a retrospective analysis, the radon levels as reported by the Department of Environmental Resources for each county in Pennsylvania were compared to the incidence and mortality of gastrointestinal cancer in Pennsylvania by county as reported by the Pennsylvania Tumor Registry from 1985 to 1989. The incidence and mortality of stomach, esophagus, colon, pancreas, and rectal cancer was reported for male, female, and total county population and compared to radon levels for that county. Using the NCSS computer package with P value set at 0.05, a positive correlation was found between radon levels and the incidence of stomach cancer in females, and the mortality of stomach cancer for male, female, and total population. This study suggests a relationship between radon levels and gastric cancer mortality. Further investigation into the role of radon carcinogenesis may be warranted.

The role of preoperative localization in primary hyperparathyroidism

Hyperparathyroidism is being increasingly recognized by the detection of hypercalcemia on routine blood chemistry. Improvement in preoperative localization has been proposed as a way to decrease operative time and decrease morbidity and mortality. The purpose of this study was to retrospectively review the Guthrie Clinic experience of parathyroidectomy with and without preoperative localization. One hundred nineteen patients who presented with primary hyperparathyroidism between 1983 and 1990 were evaluated. There were 27 males and 91 females with an average age of 61. Preoperative localization resulted in a significant decrease in operative time with preoperative localization decreasing operative time from 97 minutes without localization to 70 minutes with localization. Also, complications were less in patients undergoing preoperative localization (5.8% versus 13.9%). Preoperative localization was positively affected by gland size, with larger glands being easier to localized. In conclusion, accurate preoperative localization decreases operative time and decreases complications in this series of patients undergoing exploration for primary hyperparathyroidism. In our institution the thallium technitium scan is most accurate and is the localization procedure of choice.

Secretion of cyclic GMP by cultured epithelial and fibroblast cell lines in response to nitric oxide

LLC-PK1 epithelial cells and RFL-6 fibroblasts secreted both cyclic AMP (cAMP) and cyclic GMP (cGMP) when costimulated with forskolin and 3-morpholinosydnonimine (a chemical nitric oxide generator). Intracellular cAMP levels as high as 1100 and 12,000 pmol/10(6) cells were achieved for the two cell types, respectively. These levels were high enough to reach approximately 50% saturation of the cAMP transporter and inhibited transport of cGMP to an equal extent, suggesting that the two cyclic nucleotides compete for a common transport system. The rates of secretion of cGMP and cAMP from LLC-PK1 cells increased in proportion to their rates of synthesis as concentrations of stimulant were varied, but increased only 25% relative to intracellular concentrations in response to inhibition of phosphodiesterases by 3-isobutylmethylxanthine. It is proposed that secretion of cyclic nucleotides is not simply proportional to the total intracellular pool in these cells, but rather is coupled to synthesis. In support of this model, oxyhemoglobin was used to trap nitric oxide and block activity of guanylate cyclase in cells treated with 3-morpholinosydnonimine. As a result, secretion of cGMP ceased within 1 min, whereas intracellular levels decreased slowly over 60 min. Probenecid [p-(dipropylsulfamoyl)benzoic acid] is a nonselective antagonist of anion transport that inhibited secretion of cAMP in both cell types but, unexpectedly, blocked synthesis of cGMP, and this was reflected in direct inhibition of soluble guanylate cyclase in cell lysates. Two heat-stable, high molecular weight factors that confer sensitivity to probenecid were identified, and these factors increased the sensitivity of guanylate cyclase to nitric acid by an order of magnitude.

Characterization of the peptide substrate specificities of interstitial collagenase and 92-kDa gelatinase. Implications for substrate optimization

The peptide substrate specificities of two matrix metalloproteinases (MMPs), interstitial collagenase (MMP-1), and 92-kDa gelatinase (MMP-9), have been examined. Starting with the parent substrate, Dnp-Pro-Leu-Gly approximately Leu-Trp-Ala-D-Arg-NH2, four separate substrate mixtures were synthesized at subsites P2(Leu) through P2'(Trp). These mixtures contained either naturally occurring L-amino acids, D-amino acids, or either of two distinct sets of miscellaneous amino acids. Combined, these mixtures gave 88 unique substitutions at each position and, over the four subsites, represented 352 potential substrates. Optimal substrates were identified using a combined high performance liquid chromatography/mass spectrometry analysis as previously reported. The results gave an extended profile of the substrate specificities for both MMP-1 and MMP-9 at subsites P2(Leu) through P2'(Trp). Using the data obtained from the mapping, a new peptide substrate, Dnp-Pro-Cha-Abu approximately Smc-His-Ala-D-Arg-NH2 (where Dnp is 2,4-dinitrophenyl, Cha is cyclohexylalanine, Abu is alpha-aminobutyric acid, and Smc is S-methylcysteine) was designed and characterized. This peptide showed a 36-fold improvement in turnover (kcat/Km) versus the parent substrate by interstitial collagenase. In addition, some collagenase subsite specificities described here were found to be different from those previously reported. Experimental data show that the observed selectivity is dependent on the original peptide template employed, which has broader implications for substrate specificity studies.

Methods to prevent colonic injury in pelvic radiation

PURPOSE

Radiation has become an adjunct in the treatment of pelvic malignancies. Attempts to prevent adjacent tissue injury have met with varying degrees of success, and the purpose of this study was to investigate potential radioprotective effects of an elemental diet, sodium meclofenamate, and vitamin A in an animal model of acute and chronic pelvic radiation previously described.

METHODS

Female Sprague-Dawley rats, 200-250 grams, were anesthetized and then received 900 rads of pelvic radiation once per week for five weeks for a total of 4500 rads. Animals were divided into five groups. Treatment groups received radiation and elemental diet, radiation and vitamin A, radiation and sodium meclofenamate. Control animals received anesthesia only and no radiation. Vitamin A was given as a supplement to (662 IU/kg) standard rat chow. Elemental diet was given as a commercially available formula, whereas sodium meclofenamate was given as a postoperative supplement (5 mg/kg/day). All animals were given these treatments during the course of radiation therapy only. Histology of distal colon was measured at one week, five weeks, six months, and one year postradiation therapy. The distal two cm of colon were removed at necropsy and fixed in 10 percent formalin at each of the above time points. Histologic grade was determined by a previously described grading scale.

RESULTS

Results showed a qualitative radiation injury that could be documented at one and five weeks postradiation. Elemental diet, vitamin A, and sodium meclofenamate prevented histologic changes that occurred at these time points. No difference in histologic grade was seen between any groups at six months and one year postradiation therapy.

CONCLUSION

In summary, our model of pelvic radiation produces a definable radiation injury within the colon at one and five weeks postradiation. Use of elemental diet, vitamin A, and sodium meclofenamate prevented these changes.

Isotope effects and alternative substrate reactivities for tryptophan 2,3-dioxygenase

Tryptophan 2,3-dioxygenase (EC 1.13.1.12) is a hemoprotein which catalyzes the first step in the oxidative degradation of tryptophan. The reaction is believed to proceed by addition of O2 across the 2,3-bond of the indole ring, followed by decomposition of the resultant dioxetane to give N-formylkynurenine. A primary D2O isotope effect of 4.4 on Vmax/Km was observed at the pH optimum, pH 7.0. This implies that abstraction of the indole proton is at least partially rate-determining. An inverse secondary isotope effect of 0.96 was observed for L-[2-3H]tryptophan at this pH. The secondary isotope effect signals the formation of the C-O bond at C-2. As the rate of proton abstraction increased with increasing pH, the D2O isotope effect decreased to 1.2 at pH 8.5 and the secondary isotope effect increased to 0.92. The rate-determining steps therefore change with increasing pH, and bond formation at C-2 becomes more rate-limiting. The secondary isotope effect did not change significantly with varying O2 concentration so that substrate binding is primarily ordered with O2 binding first. The specificity of the enzyme towards substituted tryptophans shows that substitution of the phenyl ring of the indole is sterically unfavorable. Steric hindrance is highest at the 4- and 7-positions, while the 5- and 6-positions are less sensitive. 6-Fluoro-L-tryptophan was more reactive than tryptophan, and the increased reactivity can be explained by an electronic effect that enhances of the rate of C-O bond formation at C-2.

Determination of endothelin by an immobilized receptor assay utilizing a 96-well format

Bovine cerebellar membranes immobilized on 96-well microtiter plates provide receptors for 125I-labeled endothelin-1 as the basis for a competitive binding assay. Adsorption of the membranes to a surface does not significantly alter the ligand-receptor interaction and reduces non-specific binding to 3-7% of total binding compared to 10-20% for a filtration technique. Considerable savings in reagents are realized since assays can be performed in 100 microliter volumes with only 10-20 micrograms of membrane protein. The 96-well format allows the rapid quantitation of large numbers of samples, and the assay is especially attractive in that it utilizes readily available reagents and equipment without the need for specific antibodies. The endothelin-receptor-based assay may be used to measure conversion of big endothelin-1 to endothelin-1 in aqueous assays. Since the presence of serum does not affect this method, tissue culture medium may be directly analyzed for endothelin production by cultured cells. All three isoforms of endothelin are detected, and the specificity of the receptor is retained since fragments and precursor forms of endothelin are not recognized. In cases where multiple endothelin isoforms may be present or where specificity of binding is in question, this assay may be used in conjunction with high pressure liquid chromatography to distinguish active peptides.

Metabolism of 11-deoxycorticosterone by hamster adrenal mitochondria

Metabolism of 11-deoxycorticosterone (DOC) by hamster adrenal mitochondria gives 19-hydroxy-DOC and corticosterone (via 11-hydroxylation) in approximately equal yields. The ratio of 19- to 11-hydroxylation was invariant with changes in concentration of substrate or a competitive inhibitor. It is most likely, therefore, that a single 11,19-hydroxylase catalyzes both oxidations. Both primary products are further oxidized to the corresponding carbonyl analogs, 19-oxo-DOC and 11-dehydrocorticosterone, at rates that are approx. 20% of their rates of formation. The oxidation of 11-dehydrocorticosterone is catalyzed by a dehydrogenase utilizing either NAD or NADP while the oxidation of 19-hydroxy-DOC is catalyzed by an oxidase requiring NADPH. The 11-dehydrocorticosterone is stable in this enzyme preparation while 19-oxo-DOC is metabolized to two additional products, which are tentatively identified as 19-oic-DOC and 19-norcorticosterone. 19-nor-DOC was found to be hydroxylated at a rate that is 20% faster than the rate for DOC under the same conditions. It is therefore possible that 19-norcorticosterone can arise from 19-oic-DOC via decarboxylation to 19-nor-DOC and subsequent 11-hydroxylation, but the kinetics of its formation suggest that it may actually be formed directly from 19-oxo-DOC without free intermediates. 4-Androstene-3,17-dione and 17-hydroxy-DOC were also substrates for this 11,19-hydroxylase, but 18-hydroxy-DOC was not. Maintenance of hamsters on a low sodium diet had no effect on the metabolism of DOC by the isolated adrenal mitochondria.

Role of mast cell chymase in the extracellular processing of big-endothelin-1 to endothelin-1 in the perfused rat lung

Previous studies of endothelin-1 (ET) synthesis have shown that some cultured endothelial cells secrete an intermediate product, big-endothelin-1 (bigET), suggesting that the processing of secreted bigET to ET may be physiologically significant. In this study, two pertinent ET converting enzyme activities, mast cell chymase I (EC 3.4.21.39) and a phosphoramidon-sensitive, neutral metalloprotease, were identified in a rat lung particulate fraction. We perfused rat lungs with bigET and chymostatin or phosphoramidon to study the relevance of these two proteases to the processing of extracellular bigET in vivo. Addition of compound 48/80 (a compound which activates mast cells, causing degranulation and release of chymase) to the perfusion buffer greatly increased hydrolysis of exogenously added bigET to ET. ET formation was inhibited completely by 32 microM chymostatin, whereas inhibition by 50 microM phosphoramidon was incomplete and variable. Perfusate histamine levels were used to monitor the extent of mast cell degranulation, and inhibition of ET production by phosphoramidon was attributed to inhibition of degranulation, per se. There was a direct correlation between perfusate ET and histamine levels in both control and phosphoramidon-treated (but not chymostatin-treated) lungs. Our results suggest that chymase from lung mast cells is capable of physiologically relevant extracellular processing by bigET to ET in the perfused rat lung.

Evidence against a role for aspartyl proteases in intracellular processing of big endothelin

CPAE endothelial cells were cultured in the presence of pepstatin, NH4Cl, or chloroquine in order to assess their effects on the secretion of endothelin-1 (ET-1). The first of these is an inhibitor of aspartyl proteases and the last two are known to neutralize acidic intracellular compartments. The pepstatin was encapsulated into liposomes to aid in its uptake, and uptake was confirmed by measuring the residual aspartyl protease activity in washed, lysed cells. Pepstatin had no effect (less than 5%) on the secretion of ET-1, 25 mM NH4Cl decreased secretion by 30-47%, and 25 microM chloroquine increased secretion by 37-79%. In contrast, each of these reagents is known to inhibit lysosomal degradation of intracellular proteins by 75-90%. Additionally, big ET was shown to be a very poor substrate, in terms of kcat/Km values, for aspartyl proteases. The rate constants were less than 10(4) M-1 s-1, which is approximately 1% of the value for the best substrates. The data, therefore, do not support a role for aspartyl proteases in the formation of ET-1. Similar to chloroquine, 0.5 microM monensin increased the secretion of ET-1 by 40-60%. Both of these reagents have previously been shown to increase the rate of constitutive secretion of peptides by affecting their partitioning between packaging into storage granules and constitutive secretion. The results would therefore provide supportive evidence for the existence of a storage form of ET-1 in endothelial cells.

A radiometric kynurenine monooxygenase assay

Kynurenine 3-monooxygenase is a flavin-dependent monooxygenase that catalyzes the oxidation of L-kynurenine to 3-hydroxy-L-kynurenine in the kynurenine pathway of tryptophan metabolism. The enzyme requires NADH or NADPH as a cofactor. A discontinuous assay that utilizes L-[3H]kynurenine as substrate is described. The assay offers high precision and a wide range of accessible substrate and cofactor concentrations. The assay was used to measure kinetic isotope effects and the stereospecificity of oxidation of the cofactor. Hydride is transferred from the A-side (pro-R) of NADH and NADPH since primary deuterium isotope effects were observed for both cofactors when they were deuterated on the A-side but not on the B-side. The large isotope effect on Vmax/Km for NADH is sensitive to the concentration of kynurenine, which indicates that NADH can bind before kynurenine.

Inhibition of 5-lipoxygenase by substituted 3,4-dihydro-2H-1,4-thiazines

A series of substituted 3,4-dihydro-2H-1,4-thiazines inhibit 5-lipoxygenase from rat leukocytes and exhibit submicromolar IC50 values. A novel synthesis of these compounds was developed based on the formation of hydroxymethyleneamine 13 and its cyclization to the title compounds. The dihydrothiazines have low oxidation potentials, typically E1/2 is near 0.3 V, and a representative compound reduces Fe(III)(phen)3, with k = 10(5) M-1s-1. We propose that these lipophilic compounds bind to 5-lipoxygenase and reduce the iron in the active site, thus inactivating the enzyme.

The specificity of two proteinases that cleave adjacent to arginine, C1 esterase and acrosin, for peptide p-nitroanilide substrates

Relative values of Vmax/Km for hydrolysis of 40 peptide p-nitroanilides catalyzed by human Cl-s and human acrosin are reported. For Cl-s, Ac-Lys(gamma Cbz)-Gly-Arg is the optimum sequence, but 25% of the substrates have (Vmax/Km)rel greater than 0.25 compared to this sequence. The best acrosin substrate tested has the sequence Tos-Gly-Pro-Arg, although (Vmax/Km)rel greater than 0.15 for more than half of the substrates. Proline at P2 is preferred by acrosin. Both enzymes prefer arginine at P1 greater than or equal to 3-fold over lysine and will not accept citrulline. In addition, occupancy of site S3 may yield an increase in Vmax/Km of greater than or equal to 10-fold with either enzyme, but many residues are accepted at S2, S3 and S4. Thus, an acrosin assay using Tos-Gly-Pro-Arg p-nitroanilide as a substrate is more than 20-times as sensitive as existing assays with blocked arginine derivatives.

Alpha-secondary isotope effects in the lipoxygenase reaction

Isotope effects for the oxidation of [5,6,8,9,11,12,14,15-3H]arachidonic acid catalyzed by soybean lipoxygenase and by 5-lipoxygenase were measured. This labeling pattern represents substitution at each of the vinylic hydrogens of the substrate. The observed isotope effect for soybean lipoxygenase was 1.16 +/- 0.02 and for 5-lipoxygenase was 1.11 +/- 0.05. These isotope effects are inconsistent with any change in hybridization (sp2 to sp3) at the vinylic carbons prior to or during the rate-determining step and are concluded to be most consistent with the formation of a carbanion-like intermediate or transition state. In contrast, the oxidation of arachidonic acid by Ce(IV), which is thought to proceed via a cation radical intermediate, exhibited at most a small isotope effect (1.02 +/- 0.01). The reduction potential for the cation radical formed from arachidonic acid in this reaction is estimated to be 2.7 V vs NHE by comparison of the rates of oxidation of arachidonic acid and cyclohexene by Ce(IV). This is similar to the potential for the cation radical of 2-butene. No isotope effect (1.00 +/- 0.03) was observed in the 5-lipoxygenase reaction for conversion of the initially formed product 5-hydroperoxyeicosatetraenoic acid to the epoxide leukotriene A4. From this it is concluded that there is little carbon-oxygen bond formation prior to or during the rate-determining step for epoxide formation.

An assay for dihydroorotase using high-performance liquid chromatography with radioactivity detection

An assay for measuring dihydroorotase activity was devised. Radiolabeled substrate and product were separated by high-performance liquid chromatography using a reverse-phase column with ion-pairing, and the radioactivity was quantitated by flow detection.

Inhibition of the proteolysis of rat erythrocyte membrane proteins by a synthetic inhibitor of calpain

A synthetic inhibitor of calpain protects rat erythrocyte membrane-associated cytoskeletal proteins from proteolytic degradation (IC50 = 1 microM) which occurs when the cells are rendered permeable to Ca++. Leupeptin, a naturally occurring inhibitor of the enzyme, does not afford any protection at concentrations up to 100 microM.

Activity of soybean lipoxygenase in the absence of lipid hydroperoxide

Soybean lipoxygenase was assayed under conditions such that the concentration of the enzyme was in excess of the concentration of the substrate, arachidonic acid. Under these conditions, the concentration of lipid hydroperoxides present as contaminants in the substrate was negligible relative to the enzyme concentration, and the concentration of lipid hydroperoxide product could be determined accurately. The ferric form of the enzyme was observed to be fully active and to catalyze the oxidation of arachidonic acid at a near-diffusion-controlled rate, 1.4 X 10(7) M-1 s-1 at 0 degree C, at concentrations of lipid hydroperoxides as low as 5% of the enzyme concentration. From this, it can be concluded that the higher oxidation states that would be accessible by oxidation of Fe(III) by hydroperoxide are not required for catalysis by soybean lipoxygenase. Surprisingly, the activation of the ferrous form of the enzyme was also observed at insignificantly low lipid hydroperoxide concentrations. This activation presumably involves oxidation of the ferrous to the ferric form of the enzyme and must be more facile than has hitherto been reported. This result may rationalize previous reports that the ferrous and the ferric forms of the enzyme are both active.

Specificity of an HPETE peroxidase from rat PMN

The 15,000xg supernatant of sonicated rat PMN contains 5-lipoxygenase that converts arachidonic acid to 5-hydroperoxyeicosatetraenoic acid (5-HPETE) and leukotriene A4 and an HPETE peroxidase that catalyzes reduction of the 5-HPETE. The specificity of this HPETE peroxidase for peroxides, reducing agents, and inhibitors has been characterized to distinguish this enzyme from other peroxidase activities. In addition to 5-HPETE, the HPETE peroxidase will catalyze reduction of 15-hydroperoxyeicosatetraenoic acid, 13-hydroperoxyoctadecadienoic acid, and 15-hydroperoxy-8,11,13-eicosatrienoic acid, but not cumene or t-butylhydroperoxides. The HPETE peroxidase accepted 5 of 11 thiols tested as reducing agents. However, glutathione is greater than 15 times more effective than any other thiol tested. Other reducing agents, ascorbate, NADH, NADPH, phenol, p-cresol, and homovanillic acid, were not accepted by HPETE peroxidase. This enzyme is not inhibited by 10 mM KCN, 2 mM aspirin, 2 mM salicylic acid, or 0.5 mM indomethacin. When 5-[14C]HPETE is generated from [14C]arachidonic acid in the presence of unlabeled 5-HPETE and the HPETE peroxidase, the 5-[14C]HETE produced is of much lower specific activity than the [14C]arachidonic acid. This indicates that the 5-[14C]HPETE leaves the active site of 5-lipoxygenase and mixes with the unlabeled 5-HPETE in solution prior to reduction and is a kinetic demonstration that 5-lipoxygenase has no peroxidase activity. Specificity for peroxides, reducing agents, and inhibitors differentiates HPETE peroxidase from glutathione peroxidase, phospholipid-hydroperoxide glutathione peroxidase, a 12-HPETE peroxidase, and heme peroxidases. The HPETE peroxidase could be a glutathione S-transferase selective for fatty acid hydroperoxides.

Inhibition of Escherichia coli growth and diaminopimelic acid epimerase by 3-chlorodiaminopimelic acid

The diaminopimelic acid (DAP) analog, 3-chloro-DAP, was synthesized and tested as the racemic acid for antibacterial activity and for inhibition of DAP epimerase. 3-Chloro-DAP was a potent inhibitor of DAP epimerase purified from Escherichia coli (Ki = 200 nM), and it is argued that 3-chloro-DAP is converted to a tight-binding transition state analog at the active site of this enzyme. Furthermore, 3-chloro-DAP inhibited growth of two E. coli mutants. In one of the mutants known for supersusceptibility to beta-lactams, inhibition was not seen until the mid-log phase of growth, while in the other mutant, a DAP auxotroph, inhibition occurred much earlier. Growth inhibition was reversed by DAP in both strains. In the auxotroph, the reversal was specific for meso-DAP, indicating that DAP epimerase was the target for 3-chloro-DAP. Thus we suggest a novel mechanism of bacterial growth inhibition which depends on DAP epimerase inhibition by a DAP analog.

Ketones as electrophilic substrates of lipoxygenase

The rate-limiting step of the lipoxygenase reaction involves the abstraction of a hydrogen from the methylene carbon of a 1,4-diene. One possibility for the mechanism of the enzyme is the abstraction of this hydrogen as a proton to generate a carbanionic intermediate or transition state. In order to investigate this possibility, 5-, 8-, 12-, and 15-hydroxy-eicosatetraenoic acid were oxidized to the corresponding ketones and these ketones were assayed as substrates of the 5-, 12-, and 15-lipoxygenases from rat neutrophils, rat platelets, and soybeans, respectively. The ketones were in no case better substrates than arachidonic acid and in some cases the hydroxyeicosatetraenoic acids were equally active as the corresponding ketones. Since no increased rate of oxidation for these electrophilic substrates was observed, it is concluded that no transition state with carbanionic character is generated in the rate-determining step of the lipoxygenase reaction.

Kinetics of leukotriene A4 synthesis by 5-lipoxygenase from rat polymorphonuclear leukocytes

When arachidonic acid is added to lysates of rat polymorphonuclear leukocytes, it is oxidized to (5S)-hydroperoxy-6(E),8(Z),11(Z),14(Z)-eicosatetraenoic acid (5-HPETE). The 5-HPETE then partitions between reduction to the 5-hydroxyeicosanoid and conversion to leukotriene A4 (LTA4). Both steps in the formation of LTA4 are catalyzed by the enzyme 5-lipoxygenase. When [3H]arachidonic acid and unlabeled 5-HPETE were incubated together with 5-lipoxygenase, approximately 20% of the arachidonic acid oxidized at low enzyme concentrations was converted to LTA4 without reduction of the specific radioactivity of the LTA4 by the unlabeled 5-HPETE. A significant fraction of the [3H]-5-HPETE intermediate that is formed from arachidonic acid must therefore be converted directly to LTA4 without dissociation of the intermediate from the enzyme. This result predicts that even in the presence of high levels of peroxidase activity, which will trap any free 5-HPETE by reduction, the minimum efficiency of conversion of 5-HPETE to LTA4 will be approximately 20%, and this prediction was confirmed. 5-HPETE was found to be a competitive substrate relative to arachidonic acid, so that it is likely that the two substrates share a common active site.

Glutathione peroxidase is neither required nor kinetically competent for conversion of 5-HPETE to 5-HETE in rat PMN lysates

In the 5-lipoxygenase pathway for arachidonic acid metabolism, reduction of 5-hydroperoxyeicosatetraenoic acid (5-HPETE) to 5-hydroxyeicosatetraenoic acid (5-HETE) is catalyzed by an activity different from glutathione peroxidase. Glutathione peroxidase here refers to the nonspecific peroxidase that catalyzes the reduction by glutathione of cumene hydroperoxide and a variety of other peroxides including 5-HPETE. This enzyme is inhibited by mercaptosuccinic acid. Preparations of the 15,000xg supernatant from lysed rat peritoneal polymorphonuclear leukocytes were the source of these activities. Thus, when glutathione peroxidase is inhibited to less than 0.5% of its normal activity by mercaptosuccinic acid, 5-HPETE is reduced as efficiently as in the absence of mercaptosuccinate. In lysate preparations from which endogenous glutathione has been removed, reduction of 5-HPETE is still observed but only in the presence of added reducing agents, e.g., 0.2 mM glutathione. When endogenous glutathione peroxidase is not inhibited, reduction of 5-HPETE occurs at a rate greater than 15-fold faster than can be accounted for by this activity. We conclude, therefore, that the glutathione peroxidase in rat PMNs is not kinetically competent to account for reduction of 5-HPETE. There is a distinct peroxidase that catalyzes this reaction. The 5-HPETE peroxidase can utilize glutathione as reducing agent but is not inhibited by mercaptosuccinate, and additional results indicate that it is inactivated during turnover.

5-lipoxygenase from rat PMN lysate

The products of arachidonic acid metabolism in the 15,000xg supernatant of sonicated rat PMN are described. Only products derived from 5-lipoxygenase are observed. These products are 5-HETE and products derived from hydrolysis of LTA4, particularly LTB4. Some minor products derived from decomposition of 5-HPETE are also observed. The dependence of the activity of 5-lipoxygenase on enzyme and on substrate concentrations is presented and discussed in terms of a kinetic model that includes enzyme inactivation during turnover and substrate inhibition. The 5-lipoxygenase activity is stimulated by Ca++ and ATP.

Purification and properties of diaminopimelic acid epimerase from Escherichia coli

Diaminopimelic acid epimerase was purified from Escherichia coli. The enzyme is a monomer of Mr = 34,000. Diaminopimelic acid epimerase is not a pyridoxal phosphate-dependent enzyme: there is no evidence for pyridoxal phosphate in the ultraviolet spectrum of the purified enzyme, and the epimerase is not inactivated by carbonyl reagents such as hydroxylamine and sodium borohydride. Exchange of the alpha-protons of the substrates, DL- and LL-diaminopimelic acid, with solvent accompanies epimerization; and exchange of 3H from solvent into diaminopimelic acid gives 3H primarily (80-90%) in the product isomer, regardless of whether the DL- or LL-isomer is substrate. From these results it is concluded that the epimerase utilizes a two-base mechanism for proton translocation. In these major aspects of its mechanism, diaminopimelic acid epimerase resembles proline racemase. It is argued that the relative values of the isotope fractionation factors for the two proton acceptor sites on the enzyme can be estimated from the isotope effects for the DL- and LL-isomers of diaminopimelic acid. The observed difference in the isotope effects predicts that one, but not both, of the proton acceptor sites is a thiol, and it is demonstrated that diaminopimelic acid epimerase has a single thiol which is necessary for activity and which reacts with iodoacetamide.

Mechanism of inhibition of horseradish peroxidase by cyclopropanone hydrate

Cyclopropanone hydrate irreversibly inactivates horseradish peroxidase in a time-dependent manner in the presence of oxidizing agent, hydrogen peroxide. The inhibition reaction is a second order reaction of cyclopropanone hydrate with compound I, the 2 electron-oxidized form of peroxidase, and results in covalent modification of the heme cofactor. A new propionic acid side chain is substituted for one of the methine protons of the heme. A mechanism for inhibition is proposed to involve oxidative ring opening of cyclopropanone hydrate to give the primary free radical of propionic acid, which subsequently alkylates the heme. An isoporphyrin pi cation intermediate is predicted by this mechanism, and this intermediate has been detected spectroscopically.