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1.
Bioorg Med Chem Lett ; 16(8): 2283-92, 2006 Apr 15.
Article in English | MEDLINE | ID: mdl-16458512

ABSTRACT

Plasmodium falciparum thioredoxin reductase (PfTrxR: NADPH+Trx(S)2+H+<-->NADP++Trx(SH)2) is a high Mr flavin-dependent TrxR that reduces thioredoxin (Trx) via a CysXXXXCys pair located penultimately to the C-terminal Gly. In this respect, PfTrxR differs significantly from its human counterpart which bears a Cys-Sec redox pair at the same position. PfTrxR is essentially involved in antioxidant defense and redox regulation of the parasite and has been previously validated by knock-out studies as a potential drug target for malaria chemotherapy. Moreover, human TrxR is present in most cancer cells at levels tenfold higher than in normal cells. Here we report the discovery of a series of potent inhibitors of PfTrxR. The three most promising inhibitors, 3(IC50(PfTrxR)=2 microM and IC50(hTrxR)=50 microM), 7(IC50(PfTrxR)=2 microM and IC50(hTrxR)=140 microM), and 11(IC50(PfTrxR)=0.5 microM and IC50(hTrxR)=4 microM) were selective for the parasite enzyme. Detailed mechanistic characterization of the effects of these compounds on the PfTrxR-catalyzed reaction showed clear uncompetitive inhibition with respect to both substrate and cofactor. For the most specific PfTrxR inhibitor 7, an alkylation mechanism study based on a thiol conjugation model was performed. Furthermore, all three compounds were active in the lower micromolar range on the chloroquine-resistant P. falciparum strain K1 in vitro.


Subject(s)
Antimalarials/chemistry , Antimalarials/pharmacology , Plasmodium falciparum/drug effects , Quinoxalines/chemistry , Thioredoxin-Disulfide Reductase/antagonists & inhibitors , Animals , Chloroquine/pharmacology , Dose-Response Relationship, Drug , Drug Resistance , Humans , Inhibitory Concentration 50 , Kinetics , Molecular Structure , Oxidation-Reduction , Plasmodium falciparum/enzymology
2.
Biochemistry ; 40(39): 11698-705, 2001 Oct 02.
Article in English | MEDLINE | ID: mdl-11570870

ABSTRACT

All phosphagen kinases contain a conserved cysteine residue which has been shown by crystallographic studies, on both creatine kinase and arginine kinase, to be located in the active site. There are conflicting reports as to whether this cysteine is essential for catalysis. In this study we have used site-directed mutagenesis to replace Cys282 of human muscle creatine kinase with serine and methionine. In addition, we have replaced Cys282, conserved across all creatine kinases, with alanine. No activity was found with the C282M mutant. The C282S mutant showed significant, albeit greatly reduced, activity in both the forward (creatine phosphorylation) and reverse (MgADP phosphorylation) reactions. The K(m) for creatine was increased approximately 10-fold, but the K(m) for phosphocreatine was relatively unaffected. The V and V/K pH-profiles for the wild-type enzyme were similar to those reported for rabbit muscle creatine kinase, the most widely studied creatine kinase isozyme. However, the V/K(creatine) profile for the C282S mutant was missing a pK of 5.4. This suggests that Cys282 exists as the thiolate anion, and is necessary for the optimal binding of creatine. The low pK of Cys282 was also determined spectrophotometrically and found to be 5.6 +/- 0.1. The S284A mutant was found to have reduced catalytic activity, as well as a 15-fold increase in K(m) for creatine. The pK(a) of Cys282 in this mutant was found to be 6.7 +/- 0.1, indicating that H-bonding to Ser284 is an important, but not the sole, factor contributing to the unusually low pK(a) of Cys282.


Subject(s)
Creatine Kinase/metabolism , Cysteine/metabolism , Muscles/enzymology , Amino Acid Sequence , Animals , Base Sequence , Binding Sites , Creatine Kinase/chemistry , Creatine Kinase/genetics , Creatine Kinase/isolation & purification , Cysteine/chemistry , DNA Primers , Humans , Hydrogen-Ion Concentration , Kinetics , Molecular Sequence Data , Mutagenesis, Site-Directed , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Sequence Homology, Amino Acid , Spectrophotometry, Ultraviolet
3.
Biochemistry ; 40(10): 3056-61, 2001 Mar 13.
Article in English | MEDLINE | ID: mdl-11258919

ABSTRACT

Creatine kinase (CK) catalyzes the reversible phosphorylation of the guanidine substrate, creatine, by MgATP. Although several X-ray crystal structures of various isoforms of creatine kinase have been published, the detailed catalytic mechanism remains unresolved. A crystal structure of the CK homologue, arginine kinase (AK), complexed with the transition-state analogue (arginine-nitrate-ADP), has revealed two carboxylate amino acid residues (Glu225 and Glu314) within 2.8 A of the proposed transphosphorylation site. These two residues are the putative catalytic groups that may promote nucleophilic attack by the guanidine amino group on the gamma-phosphate of ATP. From primary sequence alignments of arginine kinases and creatine kinases, we have identified two homologous creatine kinase acidic amino acid residues (Glu232 and Asp326), and these were targeted for examination of their potential roles in the CK mechanism. Using site-directed mutagenesis, we have made several substitutions at these two positions. The results indicate that of these two residues the Glu232 is the likely catalytic residue while Asp326 likely performs a role in properly aligning substrates for catalysis.


Subject(s)
Aspartic Acid/genetics , Aspartic Acid/metabolism , Creatine Kinase/genetics , Creatine Kinase/metabolism , Glutamic Acid/genetics , Glutamic Acid/metabolism , Isoenzymes/genetics , Isoenzymes/metabolism , Mutagenesis, Site-Directed , Amino Acid Sequence , Animals , Binding Sites/genetics , Catalysis , Creatine Kinase/isolation & purification , Creatine Kinase, MM Form , Creatinine/analogs & derivatives , Creatinine/metabolism , Humans , Isoenzymes/isolation & purification , Kinetics , Molecular Sequence Data , Muscle, Skeletal/enzymology , Sequence Homology, Amino Acid
4.
Biochemistry ; 39(45): 13862-9, 2000 Nov 14.
Article in English | MEDLINE | ID: mdl-11076527

ABSTRACT

Thiamin diphosphate (ThDP)-dependent enzymes catalyze a range of transformations, such as decarboxylation and ligation. We report a novel spectroscopic assay for detection of some of the ThDP-bound intermediates produced on benzoylformate decarboxylase. Benzoylformate decarboxylase was mixed with its alternate substrate p-nitrobenzoylformic acid on a rapid-scan stopped-flow instrument, resulting in formation of three absorbing species (lambda(max) in parentheses): I(1) (a transient at 620 nm), I(2) (a transient at 400 nm), and I(3) (a stable absorbance with lambda(max) > 730 nm). Analysis of the kinetics of the two transient species supports a model in which a noncovalent complex of the substrate and the enzyme is converted to the first covalent intermediate I(1); the absorbance corresponding to I(1) is probably a charge-transfer band arising from the interaction of the thiamin diphosphate-p-nitrobenzoylformic acid covalent adduct (2-p-nitromandelylThDP) and the enzyme. The rate of disappearance of I(1) parallels the rate of formation of I(2). Chemical models suggest the lambda(max) of I(2) (near 400 nm) to be appropriate to the enamine, a key intermediate in ThDP-dependent reactions resulting from the decarboxylation of the thiamin diphosphate-p-nitrobenzoylformic acid covalent adduct. Therefore, the rate of disappearance of I(1) and/or the appearance of I(2) directly measure the rate of decarboxylation. A relaxation kinetic treatment of the pre-steady-state kinetic data also revealed a hitherto unreported facet of the mechanism, alternating active-sites reactivity. Parallel studies of the His70Ala BFD active-site variant indicate that it cannot form the complex reported by the charge-transfer band (I(1)) at the level of the wild-type protein.


Subject(s)
Carboxy-Lyases/chemistry , Thiamine Pyrophosphate/chemistry , Alanine/genetics , Amino Acid Substitution/genetics , Binding Sites/genetics , Carboxy-Lyases/genetics , Glyoxylates/chemistry , Histidine/genetics , Indicators and Reagents , Kinetics , Mandelic Acids , Nitrobenzoates/chemistry , Spectrophotometry , Substrate Specificity/genetics
5.
Mol Med ; 6(8): 660-9, 2000 Aug.
Article in English | MEDLINE | ID: mdl-11055585

ABSTRACT

BACKGROUND: Protozoan parasites of the genus Trypanosoma cause disease in a wide range of mammalian hosts. Trypanosoma brucei brucei, transmitted by tsetse fly to cattle, causes a disease (Nagana) of great economic importance in parts of Africa. T. b. brucei also serves as a model for related Trypanosoma species, which cause human sleeping sickness. MATERIALS AND METHODS: Chalcone and acyl hydrazide derivatives are known to retard the growth of Plasmodium falciparum in vitro and inhibit the malarial cysteine proteinase, falcipain. We tested the effects of these compounds on the growth of bloodstream forms of T. b. brucei in cell culture and in a murine trypanosomiasis model, and investigated their ability to inhibit trypanopain-Tb, the major cysteine proteinase of T. b. brucei. RESULTS: Several related chalcones, acyl hydrazides, and amides killed cultured bloodstream forms of T. b. brucei, with the most effective compound reducing parasite numbers by 50% relative to control populations at a concentration of 240 nM. The most effective inhibitors protected mice from an otherwise lethal T. b. brucei infection in an in vivo model of acute parasite infection. Many of the compounds also inhibited trypanopain-Tb, with the most effective inhibitor having a Ki value of 27 nM. Ki values for trypanopain-Tb inhibition were up to 50- to 100-fold lower than for inhibition of mammalian cathepsin L, suggesting the possibility of selective inhibition of the parasite enzyme. CONCLUSIONS: Chalcones, acyl hydrazides, and amides show promise as antitrypanosomal chemotherapeutic agents, with trypanopain-Tb possibly being one of their in vivo targets.


Subject(s)
Amides/pharmacology , Chalcone/pharmacology , Endopeptidases , Hydrazines/pharmacology , Trypanocidal Agents/pharmacology , Trypanosoma brucei brucei/drug effects , Amides/chemistry , Amides/therapeutic use , Animals , Cathepsin L , Cathepsins/antagonists & inhibitors , Cathepsins/metabolism , Chalcone/chemistry , Chalcone/therapeutic use , Cysteine Endopeptidases/metabolism , Cysteine Proteinase Inhibitors/chemistry , Cysteine Proteinase Inhibitors/pharmacology , Cysteine Proteinase Inhibitors/therapeutic use , Disease Models, Animal , Humans , Hydrazines/chemistry , Hydrazines/therapeutic use , Inhibitory Concentration 50 , Kinetics , Mice , Mice, Inbred BALB C , Molecular Structure , Sheep , Trypanocidal Agents/chemistry , Trypanocidal Agents/therapeutic use , Trypanosoma brucei brucei/enzymology , Trypanosoma brucei brucei/growth & development , Trypanosomiasis/drug therapy , Trypanosomiasis/parasitology
6.
J Protein Chem ; 19(1): 59-66, 2000 Jan.
Article in English | MEDLINE | ID: mdl-10882173

ABSTRACT

We report the expression of the human muscle (CK-MM) and brain (CK-BB) creatine kinases in Escherichia coli. The proteins have been purified to apparent homogeneity and several of their physical and kinetic properties investigated. In the process, we have conclusively verified the correct DNA sequence of the genes encoding the respective isozymes, and determined the correct primary structure and mass of the gene products. Alignment of the primary sequences of these two enzymes shows 81% sequence identity with each other, and no obvious gross structural differences. However, Western blot analyses demonstrated the general lack of antigenic cross-reactivity between these isozymes. Preliminary kinetic analyses show the K(m) and k(cat) values for the creatine and MgATP substrates are similar to values reported for other isozymes from various tissues and organisms. The human muscle and brain CKs do not, however, exhibit the synergism of substrate binding that is observed, for example, in rabbit muscle creatine kinase.


Subject(s)
Brain/enzymology , Creatine Kinase/metabolism , Muscles/enzymology , Amino Acid Sequence , Blotting, Western , Cloning, Molecular , Creatine Kinase/chemistry , Creatine Kinase/genetics , Creatine Kinase/isolation & purification , Escherichia coli/genetics , Humans , Isoenzymes/chemistry , Isoenzymes/genetics , Isoenzymes/isolation & purification , Isoenzymes/metabolism , Kinetics , Molecular Sequence Data , Recombinant Proteins/chemistry , Recombinant Proteins/immunology , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism
7.
Bioorg Chem ; 28(6): 315, 2000 Dec.
Article in English | MEDLINE | ID: mdl-11352468
8.
Proc Natl Acad Sci U S A ; 95(18): 10396-401, 1998 Sep 01.
Article in English | MEDLINE | ID: mdl-9724714

ABSTRACT

Muconate lactonizing enzyme (MLE), a component of the beta-ketoadipate pathway of Pseudomonas putida, is a member of a family of related enzymes (the "enolase superfamily") that catalyze the abstraction of the alpha-proton of a carboxylic acid in the context of different overall reactions. New untwinned crystal forms of MLE were obtained, one of which diffracts to better than 2.0-A resolution. The packing of the octameric enzyme in this crystal form is unusual, because the asymmetric unit contains three subunits. The structure of MLE presented here contains no bound metal ion, but is very similar to a recently determined Mn2+-bound structure. Thus, absence of the metal ion does not perturb the structure of the active site. The structures of enolase, mandelate racemase, and MLE were superimposed. A comparison of metal ligands suggests that enolase may retain some characteristics of the ancestor of this enzyme family. Comparison of other residues involved in catalysis indicates two unusual patterns of conservation: (i) that the position of catalytic atoms remains constant, although the residues that contain them are located at different points in the protein fold; and (ii) that the positions of catalytic residues in the protein scaffold are conserved, whereas their identities and roles in catalysis vary.


Subject(s)
Intramolecular Lyases/chemistry , Phosphopyruvate Hydratase/chemistry , Racemases and Epimerases/chemistry , Binding Sites , Catalysis , Crystallography, X-Ray , Intramolecular Lyases/metabolism , Ligands , Molecular Sequence Data , Phosphopyruvate Hydratase/metabolism , Racemases and Epimerases/metabolism
9.
Biochemistry ; 37(28): 9918-30, 1998 Jul 14.
Article in English | MEDLINE | ID: mdl-9665697

ABSTRACT

The crystal structure of the thiamin diphosphate (ThDP)-dependent enzyme benzoylformate decarboxylase (BFD), the third enzyme in the mandelate pathway of Pseudomonas putida, has been solved by multiple isomorphous replacement at 1.6 A resolution and refined to an R-factor of 15.0% (free R = 18.6%). The structure of BFD has been compared to that of other ThDP-dependent enzymes, including pyruvate decarboxylase. The overall architecture of BFD resembles that of the other family members, and cofactor- and metal-binding residues are well conserved. Surprisingly, there is no conservation of active-site residues not directly bound to the cofactor. The position of functional groups in the active site may be conserved, however. Three classes of metal ions have been identified in the BFD crystal structure: Ca2+ bound to the cofactor in each subunit, Mg2+ on a 2-fold axis of the tetramer, and Ca2+ at a crystal contact. The structure includes a non-proline cis-peptide bond and an unusually long and regular polyproline type II helix that mediates the main contact between tetramers in the crystal. The high-quality electron-density map allowed the correction of errors totaling more than 10% of the amino acid sequence, which had been predicted from the reported sequence of the mdlC gene. Analysis of the BFD structure suggests that requirements for activation of the cofactor, the nature of the reaction intermediates, and architectural considerations relating to the protein fold have been dominant forces in the evolution of ThDP-dependent enzymes.


Subject(s)
Carboxy-Lyases/chemistry , Thiamine Pyrophosphate/chemistry , Amino Acid Sequence , Binding Sites , Calcium/metabolism , Carboxy-Lyases/metabolism , Catalysis , Cations, Divalent , Conserved Sequence , Crystallization , Crystallography, X-Ray , Magnesium/metabolism , Models, Molecular , Molecular Sequence Data , Peptides/chemistry , Protein Conformation , Protein Structure, Secondary , Protein Structure, Tertiary
10.
J Med Chem ; 41(13): 2424-9, 1998 Jun 18.
Article in English | MEDLINE | ID: mdl-9632374

ABSTRACT

We have developed and applied a computational strategy to increase the affinity of fullerene-based inhibitors of the HIV protease. The result is a approximately 50-fold increase in affinity from previously tested fullerene compounds. The strategy is based on the design of derivatives which may potentially increase hydrophobic desolvation upon complex formation, followed by the docking of the hypothetical derivatives into the HIV protease active site and assessment of the model complexes so formed. The model complexes are generated by the program DOCK and then analyzed for desolvated hydrophobic surface. The amount of hydrophobic surface desolvated was compared with a previously tested compound, and if this amount was significantly greater, it was selected as a target. Using this approach, two targets were identified and synthesized, using two different synthetic approaches: a diphenyl C60 alcohol (5) based on a cyclopropyl derivative of Bingel (Chem.Ber. 1993, 126, 1957-1959) and a diisopropyl cyclohexyl C60 alcohol (4a) as synthesized by Ganapathi et al. (J. Org.Chem. 1995, 60, 2954-2955). Both showed tighter binding than the originally tested compound (diphenethylaminosuccinate methano-C60, Ki = 5 microM) with Ki values of 103 and 150 nM, respectively. In addition to demonstrating the utility of this approach, it shows that simple modification of fullerenes can result in high-affinity ligands of the HIV protease, for which they are highly complementary in structure and chemical nature.


Subject(s)
Carbon/chemistry , Carbon/metabolism , HIV Protease Inhibitors/chemistry , HIV Protease Inhibitors/metabolism , HIV Protease/metabolism , Binding Sites , Drug Design , HIV Protease Inhibitors/chemical synthesis , Models, Molecular , Molecular Conformation , Recombinant Proteins/metabolism , Stereoisomerism
11.
Proc Natl Acad Sci U S A ; 95(7): 3362-5, 1998 Mar 31.
Article in English | MEDLINE | ID: mdl-9520370

ABSTRACT

Phenylglyoxal is an arginine-specific reagent that inactivates creatine kinase (CK). Previous results suggest that modification of the dimeric enzyme at a single arginine residue per subunit causes complete inactivation accompanied by the loss of nucleotide binding; the actual site of modification was not identified. Here, high-resolution tandem mass spectrometry (MS/MS) was used to identify three phenylglyoxal-modified Arg residues in monomeric rabbit muscle CK. Electrospray ionizaton Fourier-transform MS of the phenylglyoxal-modified CK that had lost approximately 80% activity identified three species: unmodified, once-modified (+116 Da), and twice-modified (+232 Da) enzyme in a ratio of approximately 1:4:1. MS/MS restricts the derivatized sites to P122-P212 and P283-V332, whereas MS of Lys-C digestions revealed two modified peptides, A266-K297 and G116-K137. The only Arg in A266-K297 is Arg-291 (invariant), whereas MS/MS of modified G116-K137 shows that two of the three sites Arg-129, Arg-131, or Arg-134 (all invariant) can contain the modification. The recently reported x-ray crystal structure for the octameric chicken mitochondrial CK indicates that its nucleotide triphosphate-binding site indeed contains the equivalent of R291, R129, and R131 reported here to be at the active site of rabbit muscle CK.


Subject(s)
Arginine/chemistry , Creatine Kinase/chemistry , Nucleotides/metabolism , Animals , Arginine/metabolism , Binding Sites , Creatine Kinase/metabolism , Energy Metabolism , Mass Spectrometry , Muscle, Skeletal/metabolism , Nucleotides/chemistry , Rabbits
12.
Exp Parasitol ; 87(3): 212-21, 1997 Nov.
Article in English | MEDLINE | ID: mdl-9371086

ABSTRACT

The crystal structures of papain, cruzain, and human liver cathepsin B were used to build homology-based enzyme models of a cathepsin L-like cysteine protease (cpL) and a cathepsin B-like cysteine protease (cpB) from the protozoan parasite Leishmania major. Although structurally a member of the cathepsin B subfamily, the L. major cpB is not able to cleave synthetic substrates having an arginine in position P2. This biochemical property correlates with the prediction of a glycine instead of a glutamic acid at position 205 (papain numbering). The modeled active sites of the L. major cpB and cpL were used to screen the Available Chemicals Directory (a database of about 150,000 commercially available compounds) for potential cysteine protease inhibitors, using DOCK3.5. Based on both steric and force field considerations, 69 compounds were selected. Of these, 18 showed IC50's between 50 and 100 microM and 3 had IC50's below 50 microM. A secondary library of compounds, originally derived from a structural screen against the homologous protease of Plasmodium falciparum (falcipain), and subsequently expanded by combinatorial chemistry, was also screened. Three inhibitors were identified which were not only effective against the L. major protease but also inhibited parasite growth at 5-50 microM.


Subject(s)
Cysteine Endopeptidases/chemistry , Cysteine Proteinase Inhibitors/pharmacology , Endopeptidases , Leishmania major/enzymology , Trypanocidal Agents/pharmacology , Animals , Azo Compounds/pharmacology , Binding Sites , Cathepsin B/drug effects , Cathepsin L , Cathepsins/drug effects , Computer Simulation , Cysteine Endopeptidases/drug effects , Drug Design , Drug Evaluation, Preclinical , Folic Acid/analogs & derivatives , Folic Acid/pharmacology , Hydrazines/pharmacology , Models, Molecular , Sequence Alignment , Succinimides/pharmacology , Sulfuric Acid Esters/pharmacology , Trypanocidal Agents/chemistry
14.
Biochemistry ; 35(51): 16489-501, 1996 Dec 24.
Article in English | MEDLINE | ID: mdl-8987982

ABSTRACT

We have discovered a superfamily of enzymes related by their ability to catalyze the abstraction of the alpha-proton of a carboxylic acid to form an enolic intermediate. Although each reaction catalyzed by these enzymes is initiated by this common step, their overall reactions (including racemization, beta-elimination of water, beta-elimination of ammonia, and cycloisomerization) as well as the stereochemical consequences (syn vs anti) of the beta-elimination reactions are diverse. Analysis of sequence and structural similarities among these proteins suggests that all of their chemical reactions are mediated by a common active site architecture modified through evolution to allow the enolic intermediates to partition to different products in their respective active sites via different overall mechanisms. All of these enzymes retain the ability to catalyze the thermodynamically difficult step of proton abstraction. These homologous proteins, designated the "enolase superfamily", include enolase as well as more metabolically specialized enzymes: mandelate racemase, galactonate dehydratase, glucarate dehydratase, muconate-lactonizing enzymes, N-acylamino acid racemase, beta-methylaspartate ammonia-lyase, and o-succinylbenzoate synthase. Comparative analysis of structure-function relationships within the superfamily suggests that carboxyphosphonoenolpyruvate synthase, another member of the superfamily, does not catalyze the reaction proposed in the literature but catalyzes an enolase-like reaction instead. The established and deduced structure-function relationships in the superfamily allow the prediction that other apparent members of the family for which no catalytic functions have yet been assigned will also perform chemistry involving abstraction of the alpha-protons of carboxylic acids.


Subject(s)
Carboxylic Acids/metabolism , Intramolecular Lyases , Phosphopyruvate Hydratase/metabolism , Amino Acid Sequence , Ammonia-Lyases/chemistry , Ammonia-Lyases/genetics , Ammonia-Lyases/metabolism , Binding Sites , Carboxylic Acids/chemistry , Catalysis , Evolution, Molecular , Humans , Isomerases/chemistry , Isomerases/genetics , Isomerases/metabolism , Metals/chemistry , Models, Molecular , Molecular Sequence Data , Molecular Structure , Phosphopyruvate Hydratase/chemistry , Phosphopyruvate Hydratase/genetics , Protein Conformation , Protein Structure, Secondary , Protons , Racemases and Epimerases/chemistry , Racemases and Epimerases/genetics , Racemases and Epimerases/metabolism , Sequence Homology, Amino Acid , Stereoisomerism
16.
Bioorg Med Chem ; 4(9): 1421-7, 1996 Sep.
Article in English | MEDLINE | ID: mdl-8894100

ABSTRACT

To streamline the preclinical phase of pharmaceutical development, we have explored the utility of structural data on the molecular target and synergy between computational and medicinal chemistry. We have concentrated on parasitic infectious diseases with a particular emphasis on the development of specific noncovalent inhibitors of proteases that play a key role in the parasites' life cycles. Frequently, the structure of the enzyme target of pharmaceutical interest is not available. In this setting we have modeled the structure of the relevant enzyme by virtue of its sequence similarity with proteins of known structure. For example, we have constructed a homology-based model of falcipain, the trophozoite cysteine protease, and used the computational ligand identification algorithm DOCK to identify in compuo enzyme inhibitors including oxalic bis(2-hydroxy-1-naphthyl-methylene)hydrazide (1) [Ring, C. S.; Sun, E.; McKerow, J. H.; Lee, G.; Rosenthal, P. J., Kuntz, I. D.; Cohen, F. E., Proc. Natl Acad. Sci. U.S.A. 1993, 90, 3583]. Compound 1 inhibits falcipain (IC50 6 microM) and the organism in vitro as judged by hypoxanthine uptake (IC50 7 microM). Following this lead, to date, we have identified potent bis arylacylhydrazides (IC50 150 nM) and chalcones (IC50 200 nM) that are active against both chloroquine-sensitive and chloroquine-resistant strains of malaria. In a second example, cruzain, the crystallographically determined structure of a papain-like cysteine protease, resolved to 2.35 A, was available. Aided by DOCK, we have identified a family of bis-arylacylhydrazides that are potent inhibitors of cruzain (IC50 600 microM). These compounds represent useful leads for pharmaceutical development over strict enzyme inhibition criteria in a structure-based design program.


Subject(s)
Drug Design , Parasites/enzymology , Protease Inhibitors/chemistry , Aldehydes , Animals , Crystallography, X-Ray , Hydrazines , Magnetic Resonance Spectroscopy , Models, Molecular , Plasmodium falciparum/enzymology , Protein Conformation , Structure-Activity Relationship , Trypanosoma cruzi/enzymology
17.
Biochemistry ; 35(24): 7895-902, 1996 Jun 18.
Article in English | MEDLINE | ID: mdl-8672491

ABSTRACT

Creatine kinase (CK; EC 2.7.3.2) catalyzes the reversible conversion of creatine and MgATP to phosphocreatine and MgADP. In the absence of an X-ray crystal structure, we have used the sequence homology of creatine kinases and other guanidino kinases from a variety of sources to identify the conserved histidine residues in rabbit muscle CK, as well as to try to pinpoint a reactive histidine that has been implicated in the active site. This residue has been proposed to act as a general acid/base catalyst assisting in the phosphoryl transfer mechanism [Cook et al. (1981) Biochemistry 20, 1204-1210]. There are 17 histidine residues in rabbit muscle CK, and of these, only five have been conserved in all guanidino kinase sequences published to date [Mühlebach et al. (1994) Mol. Cell. Biochem. 133, 245-62]. In rabbit muscle CK, these residues are H96, H105, H190, H233, and H295. We have carried out site-specific mutagenesis of these five histidine residues, replacing each with an asparagine. Each of these mutants exhibited enzymatic activity but to varying degrees. The H105N, H190N, and H233N mutants displayed specific activities similar to that of the wild-type enzyme. H96N has high activity, but appears to be quite unstable, losing catalytic activity upon cell lysis by sonication and/or chromatographic steps involved in purification. H295N shows a significantly reduced catalytic activity relative to the native enzyme, due to marked decreases in kcat and the affinities for both substrates. Each of the five mutants is inactivated by diethyl pyrocarbonate (DEP), and inactivation is reversible upon incubation with hydroxylamine. However, only H295N shows a dramatically reduced rate of inactivation relative to native CK, consistent with H295 being the residue modified by DEP in the native enzyme. These intriguing results indicate that four of the conserved histidines (H96, H105, H295, and H233) are not essential for activity, and while H295 may be at the active site of CK, it is unlikely to play the role of a general acid/base catalyst.


Subject(s)
Creatine Kinase/chemistry , Creatine Kinase/metabolism , Histidine , Muscle, Skeletal/enzymology , Protein Conformation , Amino Acid Sequence , Animals , Cloning, Molecular , Conserved Sequence , Creatine Kinase/isolation & purification , Diethyl Pyrocarbonate/pharmacology , Dithionitrobenzoic Acid/pharmacology , Escherichia coli , Hot Temperature , Hydroxylamine , Hydroxylamines/pharmacology , Kinetics , Molecular Sequence Data , Mutagenesis, Site-Directed , Protein Denaturation , Rabbits , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Sequence Homology, Amino Acid , Thermodynamics
19.
Biochemistry ; 35(18): 5662-9, 1996 May 07.
Article in English | MEDLINE | ID: mdl-8639525

ABSTRACT

On the basis of the available high-resolution structures of mandelate racemase (MR) from Pseudomonas putida [Landro, J.A., Gerlt, J.A., Kozarich, J.W., Koo, C.W., Shah, V.J., Kenyon, G.L., Neidhart, D.J., Fujita, J., & Petsko, G.A. (1994) Biochemistry 33, 635-643], Lys 166 and His 297 are positioned appropriately to participate in catalysis as acid/base catalysts, with Lys 166 participating as the (S)-specific acid/base catalyst and His 297 participating as the (R)-specific acid/base catalyst. The dependence of kcat on pH for the racemization of both (R)- and (S)-mandelates suggests that the pKaS of the conjugate acids of Lys 166 and His 297 are both approximately 6.4 [Landro, J.A., Kallarakal, A.T., Ransom, S.C., Gerlt, J.A., Kozarich, J.W., Neidhart, D.J., Kenyon, G.L. (1991) Biochemistry 30, 9274-9281; Kallarakal, A.T., Mitra, B., Kozarich, J.W., Gerlt, J.A., Clifton, J.R., Petsko, G.A., & Kenyon, G.L. (1995) Biochemistry 34, 2788-2797]. Both acid/base catalysts are in close proximity to and approximately equidistant to the epsilon-ammonium group of Lys 164 and the essential Mg2+. The positive electrostatic potential provided by these cationic groups might be expected to increase the acidities of the cationic conjugate acids of the acid/base catalysts, thereby explaining the depressed pKa of Lys 166 but not the "normal" pKa of His 297. Asp 270 is hydrogen bonded of N delta of His 297 and, therefore, may allow the pKa of His 297 to be normal. In this paper we report the structural and mechanistic properties of the mutant in which Asp 270 is replaced with asparagine (D270N). The structure of D270N with (S)-atrolactate bound in the active site reveals no geometric alterations in the active site when compared to the structure of wild-type MR complexed with (S)-atrolactate, with the exception that the side chain of His 297 is tilted and displaced approximately 0.5 A away from Asn 270 and toward the (S)-atrolactate. The kcatS for both (R)- and (S)-mandelates are reduced approximately 10(4)-fold. In accord with the proposal that Asp 270 influences the pKa of His 297, in the (R)- to (S)-direction no ascending limb is detected in the dependence of kcat of pH; instead, kcat decreases from a low pH plateau as described by a pKa of 10. In the (S)- to (R)-direction the dependence of kcat of pH is a bell-shaped curve that is described by pKaS of 6.4 and 10. In analogy to the previously reported properties of the H297N mutant [Landro, J.A., Kallarakal, A.T., Ransom, S.C., Gerlt, J.A., Kozarich, J.W., Neidhart, D.J., & Kenyon, G.L. (1991) Biochemistry 30, 9274-9281], D270N catalyzes both the facile exchange of the alpha-proton of (S)- but not (R)-mandelate with solvent and the stereospecific elimination of bromide ion from (S)-p-(bromomethyl)mandalate. These observations suggest that His 297 and Asp 270 function as a catalytic dyad, with Asp 270 being at least partially responsible for the normal pKa of His 297 in wild-type MR.


Subject(s)
Point Mutation , Racemases and Epimerases/chemistry , Racemases and Epimerases/genetics , Base Sequence , Binding Sites/genetics , Catalysis , DNA, Bacterial/genetics , Hydrogen-Ion Concentration , Kinetics , Mandelic Acids/chemistry , Mandelic Acids/metabolism , Models, Molecular , Molecular Sequence Data , Molecular Structure , Mutagenesis, Site-Directed , Pseudomonas putida/enzymology , Pseudomonas putida/genetics , Racemases and Epimerases/metabolism , Solvents , Stereoisomerism
20.
Biochemistry ; 35(1): 41-6, 1996 Jan 09.
Article in English | MEDLINE | ID: mdl-8555196

ABSTRACT

Acetoacetate decarboxylase from Clostridium acetobutylicum (AAD) catalyzes the decarboxylation of acetoacetate via a Schiff base intermediate [Hamilton, G. A., & Westheimer, F. H. (1959) J. Am. Chem. Soc. 81, 6332; Fridovich, I., & Westheimer F. H. (1962) J. Am. Chem. Soc. 84, 3208]. The pKa of the active-site lysine (Lys 115) is 6.0, 4.5 pKa units less than the pKa of lysine in solution [Kokesh, F. C., & Westheimer, F. H. (1971) J. Am. Chem. Soc. 93, 7270; Frey, P. A., Kokesh, F. C., & Westheimer, F. H. (1971) J. Am. Chem. Soc. 93, 7266; Schmidt, D. E., Jr., & Westheimer, F. H. (1971) Biochemistry 10, 1249]. Westheimer and co-workers hypothesized that the pKa of Lys 115 is decreased by its spatial proximity to the epsilon-ammonium group of Lys 116. We have investigated this proposal by studying site-directed mutants of Lys 115 and Lys 116. Two substitutions for Lys 115 (K115C and K115Q) were both catalytically inactive at pH 5.95, the pH optimum of wild type AAD, demonstrating the importance of this residue in catalysis. Activity could be restored to K115C by aminoethylation with 2-bromoethyl-ammonium bromide (2-BEAB). Substitutions for Lys 116 (K116C, K116N, and K116R) had reduced but significant activities at pH 5.95. The effects of Lys 116 on the pKa of Lys 115 in the mutant AADs were evaluated following imine formation with 5-nitrosalicylaldehyde and reduction with NaBH4. Whereas the pKa of Lys 115 in K116R is similar to that observed for wild type AAD, the pKaS of Lys 115 in K116C and K116N were elevated to > 9.2. Alkylation of Cys 116 in K116C with 2-BEAB resulted in both significant activation and restoration of the pKa of Lys 115 to 5.9. These data support Westheimer's hypothesis that the pKa of the Schiff base-forming Lys 115 is decreased by its spatial proximity to the epsilon-ammonium group of Lys 116.


Subject(s)
Carboxy-Lyases/chemistry , Carboxy-Lyases/metabolism , Clostridium/enzymology , Lysine , Amino Acid Sequence , Base Sequence , Binding Sites , Carboxy-Lyases/isolation & purification , Chromatography, High Pressure Liquid , Chromatography, Ion Exchange , DNA Primers , Kinetics , Molecular Sequence Data , Mutagenesis, Site-Directed , Peptide Fragments/chemistry , Peptide Fragments/isolation & purification , Point Mutation , Polymerase Chain Reaction , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Schiff Bases , Spectrophotometry
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