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At least 1,063 records · Page 59Linked to original sources
PubMed1999

Cloning of the cDNA encoding phenylalanyl tRNA synthetase regulatory alpha-subunit-like protein whose expression is down-regulated during differentiation.

Hybrid polar compounds (HPCs), such as suberoylanilide hydroxamic acid (SAHA), induce differentiation of transformed cells. Differential display of RNA was used to identify genes whose expression is changed during SAHA-induced differentiation of murine erythroleukemia (MEL) cells. One such cDNA was identified whose mRNA level decreased by 50% after 8h of SAHA treatment as determined by Northern blot analysis. The full-length cDNA (1944bp in length) was cloned by sequencing of an EST clone and rapid amplification of 5' cDNA ends (5'-RACE). The predicted amino acid sequence is 589 amino acids and shares 45% identity with the yeast cytoplasmic phenylalanyl tRNA synthetase (PheRS) regulatory alpha-subunit. Human EST clones which share over 90% identity of predicted amino acid sequence with this cDNA map to chromosome 2 near the paired box homeotic gene 3 (PAX3) locus, a region syngenic to mouse chromosome 1. This is the first report of the cloning of the full-length cDNA for the murine PheRS regulatory alpha-subunit-like protein. The level of PheRS alpha-subunit-like mRNA is regulated during differentiation but not during cell cycle progression.

Amino Acid Sequence↗
PubMed1997

Quantitative colorimetric and gas chromatographic determination of arecaidine propargyl ester.

Arecaidine propargyl ester (APE) is a potent muscarinic agonist often used in pharmacological studies. To date, no sensitive quantitative analytical method for APE has been published. In this study, two methods for the quantitative determination of APE are compared: a colorimetric assay, based on the formation of the corresponding ferric(III)-hydroxamic acid complex, and a direct gas chromatographic method, using arecoline as the internal standard. The latter method was found to be more precise. The utility of the gas chromatographic assay was further demonstrated in a stability study of the drug in the biological fluid aqueous humor of rabbits.

Animals↗
PubMed1994

Oral iron-chelating therapy: the L1 experience.

L1 is the most widely studied oral iron-chelating drug and at present the only one shown to be effective at causing negative iron balance in long-term clinical trials for thalassemia major and other transfusion-dependent refractory anaemias. Because of side-effects, both in experimental animals and in humans, its development as a widely available pharmaceutical agent has been delayed. However, for the large numbers of transfusion-dependent, iron-overloaded patients who do not use DFX because of poor compliance, adverse effects or unavailability of the drug, L1 may be a suitable alternative for iron chelation. However, its use should be restricted to Ethical Committee approved clinical trials. Patients who are capable of using DFX effectively should be encouraged to continue doing so until an oral iron chelator has been fully established for clinical use. It is hoped that 3-hydroxypyrid-4-one analogues of L1 as well as compounds related to pyridoxal isonicotinyl hydrazone, HBED or hydroxamic acid can be found both orally effective and safe for long-term administration. Current and future trials of L1 could address some of the following issues, beside extending present studies on the efficacy and adverse effects of L1: 1. The effect of administering a reduced dose of L1 (< 75 mg/kg per day) on the incidence of adverse effects and on long-term efficacy. 2. The efficacy and adverse effects of L1 at a low dose in patients with non-transfusional iron overload such as thalassaemia intermedia, primary haemochromatosis and congenital haemolytic anaemias. 3. The effect of combining oral L1 with intravenous or subcutaneous DFX on the incidence of adverse effects and efficacy. 4. Elucidation of the mechanisms involved in agranulocytosis and joint toxicity and finding methods to predict for individual susceptibility to these adverse effects and ways of preventing them.

Administration, Oral↗
PubMed2001

Heterocycle-based MMP inhibitors with P2' substituents.

Potent and selective inhibition of matrix metalloproteinases was demonstrated for a series of sulfonamide-based hydroxamic acids. The design of the heterocyclic sulfonamides incorporates a six- or seven-member central ring with a P2' substituent that can be modified. Binding interactions of this substituent at the S2' site are believed to contribute to high inhibitory potency against stromelysin, collagenase-3 and gelatinases A and B, and to provide selectivity against collagenase-1 and matrilysin. An X-ray structure of a stromelysin inhibitor complex was obtained to provide insights into the SAR and selectivity trends observed for the series.

Collagenases↗
PubMed2001

Design and synthesis of a novel class of histone deacetylase inhibitors.

Histone deacetylase inhibitors (HDACs) have emerged as a novel class of antiproliferative agents. Utilizing structure-based design, the synthesis of a series of sulfonamide hydroxamic acids is described. Further optimization of this series by substitution of the terminal aromatic ring yielded HDAC inhibitors with good in vitro and in vivo activities.

Cell Division↗
PubMed2003

Synthesis and biological activity of piperazine-based dual MMP-13 and TNF-alpha converting enzyme inhibitors.

A series of novel MMP-13 and TNF-alpha converting enzyme inhibitors based on piperazine 2-hydroxamic acid scaffolds are described. The TACE, MMP-1 and MMP-13 activity of these inhibitors as well as the effect of substitution of the piperazine nitrogen and the P-1' benzyloxy tailpiece is discussed. Moderate in vivo activity is observed with several members of this group.

ADAM Proteins↗
PubMed2000

Antimicrobial effects of novel siderophores linked to beta-lactam antibiotics.

As a strategy to increase the penetration of antibiotic drugs through the outer membrane of gram-negative pathogens, facilitated transport through siderophore receptors has been frequently exploited. Hydroxamic acids, catechols, or very close isosteres of catechols, which are mimics of naturally occurring siderophores, have been used successfully as covalently linked escorting moieties, but a much wider diversity of iron binding motifs exists. This observation, coupled to the relative lack of specificity of siderophore receptors, prompted us to initiate a program to identify novel, noncatechol siderophoric structures. We screened over 300 compounds for their ability to (1) support growth in low iron medium of a Pseudomonas aeruginosa siderophore biosynthesis deletion mutant, or (2) compete with a bactericidal siderophore-antibiotic conjugate for siderophore receptor access. From these assays we identified a set of small molecules that fulfilled one or both of these criteria. We then synthesized these compounds with functional groups suitable for attachment to both monobactam and cephalosporin core structures. Siderophore-beta-lactam conjugates then were tested against a panel of Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus strains. Although several of the resultant chimeric compounds had antimicrobial activity approaching that of ceftazidime, and most compounds demonstrated very potent activity against their cellular targets, only a single compound was obtained that had enhanced, siderophore-mediated antibacterial activity. Results with tonB mutants frequently showed increased rather than decreased susceptibilities. suggesting that multiple factors influenced the intracellular concentration of the drugs.

Anti-Bacterial Agents↗
PubMed2003

Development of a liquid chromatography-electrospray-tandem mass spectrometry method for the quantitative determination of benzoxazinone derivatives in plants.

A new method for the quantification of benzoxazinone derivatives in extracts of wheat foliage and root samples using liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS-MS) is described. Using this method, the characterization, separation, and quantitative detection of a mixture of six naturally occurring 1,4-benzoxazin-3(4H)-one derivatives, including the hydroxamic acids (DIMBOA, DIBOA), lactams (HBOA, and HMBOA), benzoxazilinones (BOA, MBOA), and two synthetic methoxylated variations of DIBOA and HBOA, was achieved. The application of a novel, highly modified reversed-phase LC column, the dodecyl (C12) TMS end-capped Synergi MAX-RP, enhanced the on-line chromatographic separation through improvements to component resolution, analyte stability and peak shape and also to the column lifetime. The complete ESI-MS-MS precursor-product ion fragmentation pathways for the benzoxazinone derivatives are described for the first time and used to deduce a generic fragmentation pattern for the compound class. Characteristic transitions for the benzoxazinones were thus used in the developed analytical method enabling reliable quantification with simultaneous screening for other potentially present derivatives, while eliminating interferences from other coeluting contaminants from the complex plant extract matrix. Quantitative analysis was done in the multiple reaction monitoring mode, using two specific combinations of a precursor-product ion transitions for each compound. The ESI-MS-MS detection method offered improvements to the sensitivity and selectivity, as compared with previously applied LC methods, with detection limits down to 0.002-0.023 ng/microL. The developed method was demonstrated by analyzing foliages and roots of six different wheat cultivars using pressurized liquid extraction-solid-phase extraction cleanup-LC-ESI-MS-MS. The analytes were detected in the range of 0.7-207 microg/g of dry weight.

Chromatography, Liquid↗
PubMed1995

Cleavage processing of angiotensin-converting enzyme by a membrane-associated metalloprotease.

Angiotensin-converting enzyme (ACE) is synthesized as a type 1 ectoprotein. It is released from the cell surface by a proteolytic cleavage-secretion process which is enhanced by treatment of the cells with phorbol esters. Here, we report the development of an in vitro cell-free assay system for the cleavage-secretion, its characterization, and the identification of a potent inhibitor of this process. Membranes prepared from ACE89 cells secreted the testicular isozyme of ACE (ACET) in a temperature- and time-dependent fashion. As expected, the in vitro secreted ACET lacked the membrane-anchoring carboxy-terminal tail of the cell-associated ACET. The in vitro secretase activity was resistant to high salt extraction and to inhibitors of serine, chymotrypsin, trypsin, cysteine, aspartate, and elastase type proteases. However, the activity was sensitive to metal ion chelators and to a synthetic hydroxamic acid derivative, compound 3, a known inhibitor of certain metalloproteases. Compound 3 very efficiently blocked both basal and phorbol ester-stimulated ACET secretion by ACE89 cells. The inhibition was rapid, dose-dependent, and reversible, and ACET synthesis, glycosylation, and transport were not affected. Cleavage-secretion of ACET in transiently transfected HeLa cells was also inhibited by compound 3. Finally, in vitro cleavage-secretion of the other isozyme of ACE, ACEP, by membranes isolated from rabbit lungs was strongly inhibited by compound 3. These results indicate that the cleavage-secretion of both isozymes of ACE is carried out by an integral membrane metalloprotease which is specifically inhibited by compound 3.

Amino Acid Sequence↗
PubMed1983

Structural analysis of the inhibition of thermolysin by an active-site-directed irreversible inhibitor.

The mode of binding of the irreversible thermolysin inhibitor ClCH2CO-DL-(N-OH)Leu-OCH3 [Rasnick, D., & Powers, J.C. (1978) Biochemistry 17, 4363-4369] has been determined by X-ray crystallography at a resolution of 2.3 A and the structure of the covalent complex refined to give a crystallographic residual of 17.0%. This is the first such structural study of an active-site-directed covalent complex of a zinc protease. As anticipated by Rasnick and Powers, the inhibitor alkylates Glu-143 in the thermolysin active site, and the hydroxamic acid moiety coordinates the zinc ion. The formation of the covalent complex is associated with a significant shift in a segment of the polypeptide backbone in the vicinity of the active site. This conformational adjustment appears to be necessary to relieve steric hindrance which would otherwise prevent alkylation of Glu-143. It is suggested that this steric hindrance, which occurs for thermolysin but would not be expected for carboxypeptidase A, accounts for the previously inexplicable difference in reactivity of these two metalloproteases toward N-haloacetyl amino acids. The relevance of this steric hindrance to the mechanism of catalysis is discussed. In agreement with previous results [Kester, W. R., & Matthews, B. W. (1977) Biochemistry 16, 2506-2516], it appears that steric hindrance prevents the direct attack of Glu-143 on the carbonyl carbon of an extended substrate, therefore ruling out the anhydride pathway in thermolysin-catalyzed hydrolysis of polypeptide substrates and their ester analogues.

Binding Sites↗
PubMed1985

Clostridium histolyticum collagenase: development of new thio ester, fluorogenic, and depsipeptide substrates and new inhibitors.

A new series of thio ester, depsipeptide, and peptide substrates have been synthesized for the bacterial enzyme Clostridium histolyticum collagenase. The hydrolysis of the depsipeptide substrate was followed on a pH stat, and thio ester hydrolysis was measured by inclusion of the chromogenic thiol reagent 4,4'-dithiopyridine in the assay mixture. The best thio ester substrate, Boc-Abz-Gly-Pro-Leu-SCH2CO-Pro-Nba, had a kcat/KM of 63 000 M-1 s-1, while several shorter thio ester sequences were inactive as substrates. In general, the peptide analogues of all the reactive thio ester substrates were shown to be hydrolyzed 5-10 times faster by collagenase. In one case (Z-Gly-Pro-Leu-Gly-Pro-NH2) where a comparison was made, the peptide substrate was respectively 8- and 106-fold more readily hydrolyzed than the corresponding thio ester and ester substrates. Cleavages of the two fluorescence-quench substrates Abz-Gly-Pro-Leu-Gly-Pro-Nba and Abz-Gly-Pro-Leu-SCH2CO-Pro-Nba could be easily followed fluorogenically since a 5-10-fold increase in fluorescence occurred upon hydrolysis. The fluorescent peptide substrate is the best synthetic substrate known for C. histolyticum collagenase with a kcat/KM value of 490 000 M-1 s-1. A series of new reversible inhibitors were developed by the attachment of zinc ligating groups (hydroxamic acid, carboxymethyl, and thiol) to various peptide sequences specific for C. histolyticum collagenase. The shorter peptides designed to bind to either the P3-P1 or P1'-P3' subsites were poor to moderate inhibitors. The thiol HSCH2CH2CO-Pro-Nba had the lowest K1 (0.02 mM).(ABSTRACT TRUNCATED AT 250 WORDS)

Clostridium↗
PubMed1989

1H NMR studies of aliphatic ligand binding to human plasminogen kringle 4.

A detailed 1H NMR analysis of ligand binding to the human plasminogen kringle 4 domain has been carried out at 300 MHz. The ligands that were investigated are N alpha-acetyl-L-lysine, L-lysine methyl ester, N alpha-acetyl-L-lysine methyl ester, L-lysine hydroxamic acid, trans-(aminomethyl)cyclohexanecarboxylic acid (AMCHA), and 4-(aminomethyl)bicyclo[2.2.2]octane-1-carboxylic acid (AMBOC). Specific ligand-binding effects were detected via two-dimensional COSY experiments. The side chains that are the most perturbed by ligand presence are those from Trp62, Phe64, and Trp72. Ligand-kringle saturation transfer (Overhauser) experiments show that the aromatic rings from these three residues, especially Trp72, are in direct contact with the ligand. These results add support to a previously reported model of the kringle 4 lysine-binding site [Ramesh, V., Petros, A. M., Llinás, M., Tulinsky, A., & Park, C. H. (1987) J. Mol. Biol. 198, 481-498] by which these aromatic groups are assigned a key role in establishing hydrophobic interactions with the ligand molecule. Equilibrium association constants (Ka) and kinetic rate constants (kon, koff) were determined for the binding of the various linear and cyclic ligands to kringle 4. We find that those ligands whose carboxylate function is blocked bind significantly weaker (Ka approximately less than 2 mM-1) than the corresponding analogues where the anionic center is present (Ka approximately greater than 20 mM-1), which underscores the relevance of the polar group in stabilizing the interaction with the kringle 4 binding site.(ABSTRACT TRUNCATED AT 250 WORDS)

Histidine↗
PubMed2006

Catalytic activity and inhibition of human histone deacetylase 8 is dependent on the identity of the active site metal ion.

Histone deacetylases play a key role in regulating transcription and other cellular processes by catalyzing the hydrolysis of epsilon-acetyl-lysine residues. For this reason, inhibitors of histone deacetylases are potential targets for the treatment of cancer. A subset of these enzymes has previously been shown to require divalent metal ions for catalysis. Here we demonstrate that histone deacetylase 8 (HDAC8) is catalytically active with a number of divalent metal ions in a 1:1 stoichiometry with the following order of specific activity: Co(II) > Fe(II) > Zn(II) > Ni(II). The identity of the catalytic metal ion influences both the affinity of the HDAC inhibitor suberoylanilide hydroxamic acid (SAHA) and the Michaelis constant, with Fe(II)- and Co(II)-HDAC8 having K(M) values that are over 5-fold lower than that of Zn(II)-HDAC8. These data suggest that Fe(II), rather than Zn(II), may be the in vivo catalytic metal. In further support of this hypothesis, recombinant HDAC8 purified from E. coli contains 8-fold more iron than zinc before dialysis, and the HDAC8 activity in cell lysates is oxygen-sensitive. Identification of the in vivo metal ion of HDAC8 is essential for understanding the biological function and regulation of HDAC8 and for the development of improved inhibitors of this class of enzymes.

Base Sequence↗
PubMed1997

Kinetic characterization of the serralysins: a divergent catalytic mechanism pertaining to astacin-type metalloproteases.

Substrates HO2CCH2CH2CO- and HOCH2CHOHCHOHCO-Phe-Leu-Ala-5-nitro-2-pyridinamide are cleaved efficiently at the acylarenamide linkage, with a convenient spectrophotometric assay, by the Serratia and Pseudomonas approximately 50-kDa extracellular metalloproteases (serralysins). The pH range of catalytic activity extends uniformly from 4 to greater than 10 (k(cat)/Km approximately 10(3) s(-1) M(-1), similar profile for k(cat)). Substrate analogue hydroxamic acid Cbz-Leu-Ala-NHOH competitively inhibits serralysin (Ki 0.04 mM), with a pH dependence indicating that either a displaced metal-bound H2O or a similarly motile enzymic phenol residue (Tyr216) that is crystallographically found ligated to the active-site Zn2+ of the uncomplexed enzyme must have a pKa of approximately 5. A chemical catalytic mechanism of proteolysis consistent with the kinetic data is proposed, in which Tyr216-ArO-, in the course of being released from the active-site metal ion, deprotonates a water molecule attacking the Zn2+-activated substrate linkage, leading to a metal-coordinated tetrahedral oxyanion adduct that subsequently fragments.

Binding Sites↗
PubMed2002

Redox-active metal-containing nucleotides: synthesis, tunability, and enzymatic incorporation into DNA.

Novel redox-active DNA labeling tags with tunable electrochemical potentials are modularly synthesized using (a) bis-substituted Ru2+ or Os2+ precursors (R2bpy)2ML2, (b) substituted 2,4-pentanediones or hydroxamic acids bearing a functionalized linker, and (c) modified nucleotides. DNA polymerase efficiently incorporates the metal-containing nucleotide triphosphate into DNA oligonucleotides.

2,2'-Dipyridyl↗
PubMed2002

Impact of mobility on structure-based drug design for the MMPs.

Structure-based approaches for drug design generally do not incorporate solvent effects and dynamic information to predict inhibitor-binding affinity because of practical limitations. The matrix metalloproteinases (MMPs) have previously been demonstrated to exhibit significant mobility in their active sites. This dynamic characteristic significantly complicates the drug design process based on static structures, which was clearly observed for a class of hydroxamic acids containing a butynyl moiety. Compound 1 was expected to be selective against MMP-1 based on predicted steric clashes between the butynyl P1' group and the S1' pocket, but the observation of complex inhibitor dynamics in the NMR structure of MMP-1:1 provides an explanation for the low nanomolar binding to MMP-1.

Binding Sites↗
PubMed2006

Effect of 6-methoxybenzoxazolin-2-one (MBOA) on the reproduction rate of the grain aphid (Sitobion avenae F.).

Partial host-plant resistance could make a substantial contribution to reducing the damage caused by economically important grain aphids and, therefore, to reduced insecticide use. Naturally occurring hydroxamic acids, in particular 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA), have been shown to be involved in the resistance of cereals to insects. DIMBOA is unstable in aqueous solutions and has been reported to decompose to 6-methoxybenzoxazolin-2-one (MBOA). MBOA was tested on grain aphids living on artificial diet incorporated with MBOA. From 0 to 0.1 mM, the intrinsic rate of increase (rm) increased. From 0.1 to 0.3 it decreased by 73%. The rm was calculated to be 0 at 1.0 mM. Consequently, even low concentrations of MBOA may reduce the aphid multiplication to a level below the economic damage threshold. Therefore, it is possible to breed wheat varieties with a sufficiently high content of DIMBOA to decrease grain aphid populations.

Animals↗