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1.
Molecules ; 25(6)2020 Mar 13.
Article in English | MEDLINE | ID: mdl-32183087

ABSTRACT

In clinical culture media inoculated with patient samples, selective inhibition of commensal bacteria is essential for accurate diagnosis and effective treatment, as they can mask the presence of pathogenic bacteria. The alanine analogue, 1-aminoethyltetrazole was investigated as a potential alanine racemase inhibitor. For effective uptake and enhanced and selective antibacterial activity, a library of C-terminal 1-aminoethyltetrazole containing di- and oligopeptides were synthesized by solid phase peptide coupling techniques. The investigation of the antimicrobial activity of the synthesised compounds identified several clinically applicable selective inhibitors. These enabled differentiation between the closely related bacteria, Salmonella and Escherichia coli, which can be difficult to discriminate between in a clinical setting. In addition, differentiation between enterococci and other Gram-positive cocci was also seen.


Subject(s)
Alanine Racemase/antagonists & inhibitors , Enzyme Inhibitors/pharmacology , Oligopeptides/chemistry , Oligopeptides/pharmacology , Tetrazoles/chemistry , Alanine Racemase/metabolism , Enzyme Inhibitors/chemistry , Microbial Sensitivity Tests , Oligopeptides/chemical synthesis , Solid-Phase Synthesis Techniques
2.
Pol J Microbiol ; 68(3): 331-341, 2019 Sep.
Article in English | MEDLINE | ID: mdl-31880879

ABSTRACT

Streptococcus iniae is a pathogenic and zoonotic bacteria that impacted high mortality to many fish species as well as capable of causing serious disease to humans. Alanine racemase (Alr, EC 5.1.1.1) is a pyridoxal-5'-phosphate (PLP)-containing homodimeric enzyme that catalyzes the racemization of L-alanine and D-alanine. In this study, we purified alanine racemase from S. iniae that was isolated from an infected Chinese sturgeon (Acipenser sinensis), as well as determined its biochemical characteristics and inhibitors. The alr gene has an open reading frame (ORF) of 1107 bp, encoding a protein of 369 amino acids, which has a molecular mass of 40 kDa. The enzyme has optimal activity at a temperature of 35°C and a pH of 9.5. It belongs to the PLP-dependent enzymes family and is highly specific to L-alanine. S. iniae Alr (SiAlr) could be inhibited by some metal ions, hydroxylamine and dithiothreitol (DTT). The kinetic parameters K m and V max of the enzyme were 33.11 mM, 2426 units/mg for L-alanine, and 14.36 mM, 963.6 units/mg for D-alanine. Finally, the 50% inhibitory concentrations (IC50) values and antibiotic activity of two alanine racemase inhibitors (homogentisic acid and hydroquinone), were determined and found to be effective against both Gram-positive and Gram-negative bacteria employed in this study.Streptococcus iniae is a pathogenic and zoonotic bacteria that impacted high mortality to many fish species as well as capable of causing serious disease to humans. Alanine racemase (Alr, EC 5.1.1.1) is a pyridoxal-5'-phosphate (PLP)-containing homodimeric enzyme that catalyzes the racemization of L-alanine and D-alanine. In this study, we purified alanine racemase from S. iniae that was isolated from an infected Chinese sturgeon (Acipenser sinensis), as well as determined its biochemical characteristics and inhibitors. The alr gene has an open reading frame (ORF) of 1107 bp, encoding a protein of 369 amino acids, which has a molecular mass of 40 kDa. The enzyme has optimal activity at a temperature of 35°C and a pH of 9.5. It belongs to the PLP-dependent enzymes family and is highly specific to L-alanine. S. iniae Alr (SiAlr) could be inhibited by some metal ions, hydroxylamine and dithiothreitol (DTT). The kinetic parameters K m and V max of the enzyme were 33.11 mM, 2426 units/mg for L-alanine, and 14.36 mM, 963.6 units/mg for D-alanine. Finally, the 50% inhibitory concentrations (IC50) values and antibiotic activity of two alanine racemase inhibitors (homogentisic acid and hydroquinone), were determined and found to be effective against both Gram-positive and Gram-negative bacteria employed in this study.


Subject(s)
Alanine Racemase/chemistry , Alanine Racemase/isolation & purification , Bacterial Proteins/chemistry , Bacterial Proteins/isolation & purification , Enzyme Inhibitors/chemistry , Streptococcal Infections/microbiology , Streptococcus iniae/enzymology , Alanine Racemase/antagonists & inhibitors , Alanine Racemase/metabolism , Amino Acid Sequence , Bacterial Proteins/antagonists & inhibitors , Bacterial Proteins/metabolism , Enzyme Stability , Humans , Kinetics , Phylogeny , Sequence Alignment , Streptococcus iniae/chemistry , Substrate Specificity
3.
J Enzyme Inhib Med Chem ; 31(4): 517-26, 2016 Aug.
Article in English | MEDLINE | ID: mdl-26024289

ABSTRACT

Alanine racemase is a fold type III PLP-dependent amino acid racemase enzyme catalysing the conversion of l-alanine to d-alanine utilised by bacterial cell wall for peptidoglycan synthesis. As there are no known homologs in humans, it is considered as an excellent antibacterial drug target. The standard inhibitors of this enzyme include O-carbamyl-d-serine, d-cycloserine, chlorovinyl glycine, alaphosphin, etc. d-Cycloserine is indicated for pulmonary and extra pulmonary tuberculosis but therapeutic use of drug is limited due to its severe toxic effects. Toxic effects due to off-target affinities of cycloserine and other substrate analogs have prompted new research efforts to identify alanine racemase inhibitors that are not substrate analogs. In this review, an updated status of known inhibitors of alanine racemase enzyme has been provided which will serve as a rich source of structural information and will be helpful in generating selective and potent inhibitor of alanine racemase.


Subject(s)
Alanine Racemase/antagonists & inhibitors , Enzyme Inhibitors/pharmacology , Alanine Racemase/metabolism , Animals , Enzyme Inhibitors/chemistry , Humans , Models, Molecular , Molecular Structure
4.
Biochim Biophys Acta ; 1848(1 Pt B): 363-8, 2015 Jan.
Article in English | MEDLINE | ID: mdl-24990251

ABSTRACT

The peptidoglycan of Gram-positive bacteria consists of glycan chains with attached short peptide stems cross-linked to one another by glycyl bridges. The bridge of Staphylococcus aureus has five glycyl units and that of its FemA mutant has one. These long- and short-bridge cross-links create totally different cell-wall architectures. S. aureus and its FemA mutant grown in the presence of an alanine-racemase inhibitor were labeled with d-[1-¹³C]alanine, l-[3-¹³C]alanine, [2-¹³C]glycine, and l-[5-¹9F]lysine to characterize some details of the peptidoglycan tertiary structure. Rotational-echo double-resonance (REDOR) NMR of isolated cell walls was used to measure internuclear distances between ¹³C-labeled alanines and ¹9F-labeled lysine incorporated in the peptidoglycan. The alanyl ¹³C labels in the parent strain were preselected for C{F} and C{P} REDOR measurement by their proximity to the glycine label using ¹³C¹³C spin diffusion. The observed ¹³C¹³C and ¹³C³¹P distances are consistent with a tightly packed architecture containing only parallel stems in a repeating structural motif within the peptidoglycan. Dante selection of d-alanine and l-alanine frequencies followed by ¹³C¹³C spin diffusion rules out scrambling of carbon labels. Cell walls of FemA were also labeled by a combination of d-[1-¹³C]alanine and l-[¹5N]alanine. Proximity of chains was measured by C{N} and N{C} REDOR distances and asymptotic plateaus, and both were consistent with a mixed-geometry model. Binding of an ¹9F-labeled eremomycin analog in the FemA cell wall matches that of binding to the parent-strain cell wall and reveals the proximity of parallel stems in the alternating parallel-perpendicular mixed-geometry model for the FemA peptidoglycan lattice.


Subject(s)
Bacterial Proteins/genetics , Magnetic Resonance Spectroscopy/methods , Mutation , Peptidoglycan/chemistry , Staphylococcus aureus/chemistry , Alanine Racemase/antagonists & inhibitors , Peptidoglycan/biosynthesis
5.
Biochem Pharmacol ; 86(2): 222-30, 2013 Jul 15.
Article in English | MEDLINE | ID: mdl-23680030

ABSTRACT

The genus Mycobacterium includes non-pathogenic species such as M. smegmatis, and pathogenic species such as M. tuberculosis, the causative agent of tuberculosis (TB). Treatment of TB requires a lengthy regimen of several antibiotics, whose effectiveness has been compromised by the emergence of resistant strains. New antibiotics that can shorten the treatment course and those that have not been compromised by bacterial resistance are needed. In this study, we report that thiadiazolidinones, a relatively little-studied heterocyclic class, inhibit the activity of mycobacterial alanine racemase, an essential enzyme that converts l-alanine to d-alanine for peptidoglycan synthesis. Twelve members of the thiadiazolidinone family were evaluated for inhibition of M. tuberculosis and M. smegmatis alanine racemase activity and bacterial growth. Thiadiazolidinones inhibited M. tuberculosis and M. smegmatis alanine racemases to different extents with 50% inhibitory concentrations (IC50) ranging from <0.03 to 28µM and 23 to >150µM, respectively. The compounds also inhibited the growth of these bacteria, including multidrug resistant strains of M. tuberculosis. The minimal inhibitory concentrations (MIC) for drug-susceptible M. tuberculosis and M. smegmatis ranged from 6.25µg/ml to 100µg/ml, and from 1.56 to 6.25µg/ml for drug-resistant M. tuberculosis. The in vitro activities of thiadiazolidinones suggest that this family of compounds might represent starting points for medicinal chemistry efforts aimed at developing novel antimycobacterial agents.


Subject(s)
Alanine Racemase/antagonists & inhibitors , Mycobacterium smegmatis/drug effects , Mycobacterium tuberculosis/drug effects , Thiadiazoles/pharmacology , Alanine Racemase/chemistry , Alanine Racemase/metabolism , Amino Acid Sequence , Catalysis , Molecular Sequence Data , Mycobacterium smegmatis/enzymology , Mycobacterium tuberculosis/enzymology , Sequence Homology, Amino Acid , Spectrometry, Mass, Electrospray Ionization , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
6.
Biochem Pharmacol ; 83(3): 368-77, 2012 Feb 01.
Article in English | MEDLINE | ID: mdl-22146584

ABSTRACT

Methicillin-resistant Staphylococcus aureus (MRSA) is a human pathogen and a major cause of hospital-acquired infections. New antibacterial agents that have not been compromised by bacterial resistance are needed to treat MRSA-related infections. We chose the S. aureus cell wall synthesis enzyme, alanine racemase (Alr) as the target for a high-throughput screening effort to obtain novel enzyme inhibitors, which inhibit bacterial growth. Among the 'hits' identified was a thiadiazolidinone with chemical properties attractive for lead development. This study evaluated the mode of action, antimicrobial activities, and mammalian cell cytotoxicity of the thiadiazolidinone family in order to assess its potential for development as a therapeutic agent against MRSA. The thiadiazolidones inhibited Alr activity with 50% inhibitory concentrations (IC50) ranging from 0.36 to 6.4 µM, and they appear to inhibit the enzyme irreversibly. The series inhibited the growth of S. aureus, including MRSA strains, with minimal inhibitory concentrations (MICs) ranging from 6.25 to 100 µg/ml. The antimicrobial activity showed selectivity against Gram-positive bacteria and fungi, but not Gram-negative bacteria. The series inhibited human HeLa cell proliferation. Lead development centering on the thiadiazolidinone series would require additional medicinal chemistry efforts to enhance the antibacterial activity and minimize mammalian cell toxicity.


Subject(s)
Alanine Racemase/antagonists & inhibitors , Anti-Bacterial Agents/chemical synthesis , Anti-Bacterial Agents/pharmacology , Methicillin-Resistant Staphylococcus aureus/enzymology , Thiadiazoles/chemistry , Thiadiazoles/pharmacology , Alanine Racemase/metabolism , Anti-Bacterial Agents/administration & dosage , Drug Delivery Systems/methods , HeLa Cells , Humans , Methicillin-Resistant Staphylococcus aureus/drug effects , Microbial Sensitivity Tests , Thiadiazoles/classification
7.
PLoS One ; 6(5): e20374, 2011.
Article in English | MEDLINE | ID: mdl-21637807

ABSTRACT

BACKGROUND: In an effort to discover new drugs to treat tuberculosis (TB) we chose alanine racemase as the target of our drug discovery efforts. In Mycobacterium tuberculosis, the causative agent of TB, alanine racemase plays an essential role in cell wall synthesis as it racemizes L-alanine into D-alanine, a key building block in the biosynthesis of peptidoglycan. Good antimicrobial effects have been achieved by inhibition of this enzyme with suicide substrates, but the clinical utility of this class of inhibitors is limited due to their lack of target specificity and toxicity. Therefore, inhibitors that are not substrate analogs and that act through different mechanisms of enzyme inhibition are necessary for therapeutic development for this drug target. METHODOLOGY/PRINCIPAL FINDINGS: To obtain non-substrate alanine racemase inhibitors, we developed a high-throughput screening platform and screened 53,000 small molecule compounds for enzyme-specific inhibitors. We examined the 'hits' for structural novelty, antimicrobial activity against M. tuberculosis, general cellular cytotoxicity, and mechanism of enzyme inhibition. We identified seventeen novel non-substrate alanine racemase inhibitors that are structurally different than any currently known enzyme inhibitors. Seven of these are active against M. tuberculosis and minimally cytotoxic against mammalian cells. CONCLUSIONS/SIGNIFICANCE: This study highlights the feasibility of obtaining novel alanine racemase inhibitor lead compounds by high-throughput screening for development of new anti-TB agents.


Subject(s)
Alanine Racemase/antagonists & inhibitors , Anti-Infective Agents/pharmacology , Enzyme Inhibitors/classification , Enzyme Inhibitors/pharmacology , High-Throughput Screening Assays/methods , Mycobacterium tuberculosis/drug effects , Alanine Dehydrogenase/metabolism , Alanine Racemase/chemistry , Alanine Racemase/metabolism , Alanine Racemase/pharmacology , Anti-Infective Agents/analysis , Anti-Infective Agents/chemistry , Anti-Infective Agents/classification , Cell Death/drug effects , Enzyme Inhibitors/analysis , Enzyme Inhibitors/chemistry , HeLa Cells , Humans , Inhibitory Concentration 50 , Kinetics , Mass Spectrometry , Microbial Sensitivity Tests , Substrate Specificity/drug effects
8.
Anal Biochem ; 396(1): 1-7, 2010 Jan 01.
Article in English | MEDLINE | ID: mdl-19748470

ABSTRACT

Bacterial cell wall biosynthesis is the target of several antibacterial agents and is also of interest as a target for future antibacterial agent development. Given the now widespread availability of liquid chromatography-tandem mass spectrometry (LC-MS/MS) instruments, the development of LC-MS/MS assays for cell wall biosynthesis intermediates would fill a needed gap in the analytical methodology available for antibacterial agent discovery and characterization. An LC-MS/MS assay for several early cell wall intermediates-L-Ala, D-Ala, and D-Ala-D-Ala-has been developed. This method relies on derivatization of bacterial extracts with Marfey's reagent. Marfey's reagent adducts of L-Ala and D-Ala were cleanly separated chromatographically, allowing Marfey's adducts of D-Ala and L-Ala to be separated prior to mass spectrometry (MS) detection and quantitation. The Marfey's adduct of D-Ala-D-Ala was also readily detectable using this same approach. This method shows good linearity (R(2)>0.99), with a lower limit of quantitation of 1 pmol. This assay was demonstrated for characterization of the in vivo effect of cycloserine on Escherichia coli. Cycloserine resulted in a dramatic lowering of both D-Ala and D-Ala-D-Ala levels. Ampicillin had little effect on levels of these three metabolites, consistent with the actions of ampicillin on the later stages of cell wall biosynthesis. These observations indicate that cycloserine inhibits alanine racemase production of D-Ala in E. coli and demonstrates the utility of this assay in directly assessing D-Ala branch targeted antibacterial agents.


Subject(s)
Alanine Racemase/antagonists & inhibitors , Alanine/analogs & derivatives , Alanine/analysis , Cycloserine/pharmacology , Dinitrobenzenes/metabolism , Dipeptides/analysis , Escherichia coli/enzymology , Tandem Mass Spectrometry/methods , Alanine/metabolism , Alanine Racemase/metabolism , Biological Assay , Cell Wall/drug effects , Cell Wall/metabolism , Chromatography, Liquid , Escherichia coli/drug effects , Reference Standards , Reproducibility of Results , Substrate Specificity
9.
BMB Rep ; 42(1): 47-52, 2009 Jan 31.
Article in English | MEDLINE | ID: mdl-19192393

ABSTRACT

Alanine racemase catalyzes the interconversion of L-alanine and D-alanine and plays a crucial role in spore germination and cell wall biosynthesis. In this study, alanine racemase produced by Bacillus anthracis was expressed and purified as a monomer in Escherichia coli and the importance of lysine 41 in the cofactor binding octapeptide and tyrosine 270 in catalysis was evaluated. The native enzyme exhibited an apparent K(m) of 3 mM for L-alanine, and a V(max) of 295 micromoles/min/mg, with the optimum activity occurring at 37 degrees C and a pH of 8-9. The activity observed in the absence of exogenous pyridoxal 5'-phosphate suggested that the cofactor is bound to the enzyme. Additionally, the UV-visible absorption spectra indicated that the activity was pH independece, of VV-visible absorption spectra suggests that the bound PLP exists as a protonated Schiff's base. Furthermore, the loss of activity observed in the apoenzyme suggested that bound PLP is required for catalysis. Finally, the enzyme followed non-competitive and mixed inhibition kinetics for hydroxylamine and propionate with a K(i) of 160 microM and 30 mM, respectively. [BMB reports 2009; 42(1): 47-52].


Subject(s)
Alanine Racemase/metabolism , Bacillus anthracis/enzymology , Spores, Bacterial/enzymology , Alanine Racemase/antagonists & inhibitors , Alanine Racemase/isolation & purification , Bacillus anthracis/drug effects , Biocatalysis/drug effects , Enzyme Inhibitors/pharmacology , Kinetics , Molecular Weight , Mutant Proteins/isolation & purification , Mutant Proteins/metabolism , Pyridoxal Phosphate/metabolism , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Spores, Bacterial/drug effects , Substrate Specificity/drug effects
10.
Curr Med Chem ; 14(12): 1291-324, 2007.
Article in English | MEDLINE | ID: mdl-17504214

ABSTRACT

The vitamin B(6)-derived pyridoxal 5'-phosphate (PLP) is the cofactor of enzymes catalyzing a large variety of chemical reactions mainly involved in amino acid metabolism. These enzymes have been divided in five families and fold types on the basis of evolutionary relationships and protein structural organization. Almost 1.5% of all genes in prokaryotes code for PLP-dependent enzymes, whereas the percentage is substantially lower in eukaryotes. Although about 4% of enzyme-catalyzed reactions catalogued by the Enzyme Commission are PLP-dependent, only a few enzymes are targets of approved drugs and about twenty are recognised as potential targets for drugs or herbicides. PLP-dependent enzymes for which there are already commercially available drugs are DOPA decarboxylase (involved in the Parkinson disease), GABA aminotransferase (epilepsy), serine hydroxymethyltransferase (tumors and malaria), ornithine decarboxylase (African sleeping sickness and, potentially, tumors), alanine racemase (antibacterial agents), and human cytosolic branched-chain aminotransferase (pathological states associated to the GABA/glutamate equilibrium concentrations). Within each family or metabolic pathway, the enzymes for which drugs have been already approved for clinical use are discussed first, reporting the enzyme structure, the catalytic mechanism, the mechanism of enzyme inactivation or modulation by substrate-like or transition state-like drugs, and on-going research for increasing specificity and decreasing side-effects. Then, PLP-dependent enzymes that have been recently characterized and proposed as drug targets are reported. Finally, the relevance of recent genomic analysis of PLP-dependent enzymes for the selection of drug targets is discussed.


Subject(s)
Carboxy-Lyases/antagonists & inhibitors , Enzymes/drug effects , Pyridoxal Phosphate/physiology , Transaminases/antagonists & inhibitors , Alanine Racemase/antagonists & inhibitors , Biotin/biosynthesis , Carbon-Oxygen Lyases/antagonists & inhibitors , Carboxy-Lyases/genetics , Drug Design , Glycine Hydroxymethyltransferase/antagonists & inhibitors , Humans , Hydrolases/antagonists & inhibitors , Intramolecular Transferases/antagonists & inhibitors , Lyases/antagonists & inhibitors , Lyases/genetics , Transaminases/genetics
11.
Protein Expr Purif ; 51(1): 39-48, 2007 Jan.
Article in English | MEDLINE | ID: mdl-16843006

ABSTRACT

Acetobacter aceti converts ethanol to acetic acid, and survives acetic acid exposure by tolerating cytoplasmic acidification. Alanine racemase (Alr) is a pyridoxal 5' phosphate (PLP) -dependent enzyme that catalyzes the interconversion of the d- and l-isomers of alanine and has a basic pH optimum. Since d-alanine is essential for peptidoglycan biosynthesis, Alr must somehow function in the acidic cytoplasm of A. aceti. We report the partial purification of native A. aceti Alr (AaAlr) and evidence that it is a rather stable enzyme. The C-terminus of AaAlr has a strong resemblance to the ssrA-encoded protein degradation signal, which thwarted initial protein expression experiments. High-activity AaAlr forms lacking a protease recognition sequence were expressed in Escherichia coli and purified. Biophysical and enzymological experiments confirm that AaAlr is intrinsically acid-resistant, yet has the catalytic properties of an ordinary Alr.


Subject(s)
Acetobacter/enzymology , Alanine Racemase/isolation & purification , Alanine Racemase/antagonists & inhibitors , Alanine Racemase/genetics , Alanine Racemase/metabolism , Circular Dichroism , Electrophoresis, Polyacrylamide Gel , Enzyme Stability , Hydrogen-Ion Concentration , Kinetics , Molecular Sequence Data , Recombinant Fusion Proteins/antagonists & inhibitors , Recombinant Fusion Proteins/isolation & purification
12.
FEMS Microbiol Lett ; 256(1): 16-21, 2006 Mar.
Article in English | MEDLINE | ID: mdl-16487314

ABSTRACT

Free D-amino acids are implicated in several biological functions. This study examined the presence of D-alanine in Leishmania amazonensis. Measuring chiral amino acid content by high-performance liquid chromatography we detected a significant amount of free D-alanine in promastigotes of these parasites. D-alanine accounts for 8.9% of total free alanine and is found primarily in the soluble fraction. Specific racemization of L-alanine to D-alanine was detected in cell lysates and this enzyme activity was inhibited by D-cycloserine, an alanine racemase inhibitor. Furthermore, we were able to decrease this pool of D-amino acid by treating our cultures with D-cycloserine. We demonstrate for the first time the existence of a significant amount of free D-alanine in L. amazonensis and an alanine racemase activity present in cell lysates. The restriction of D-alanine to bacteria, some fungi and now in L. amazonensis opens a new perspective on treatment of diseases caused by these microorganisms.


Subject(s)
Alanine Racemase/metabolism , Alanine/analysis , Alanine/metabolism , Leishmania mexicana/chemistry , Leishmania mexicana/enzymology , Alanine/chemistry , Alanine Racemase/antagonists & inhibitors , Animals , Cells, Cultured , Chromatography, High Pressure Liquid/methods , Cycloserine/pharmacology , Life Cycle Stages , Time Factors
13.
Biochemistry ; 44(14): 5317-27, 2005 Apr 12.
Article in English | MEDLINE | ID: mdl-15807525

ABSTRACT

The requirement for d-alanine in the peptidoglycan layer of bacterial cell walls is fulfilled in part by alanine racemase (EC 5.1.1.1), a pyridoxal 5'-phosphate (PLP)-assisted enzyme. The enzyme utilizes two antiparallel bases focused at the C(alpha) position and oriented perpendicular to the PLP ring to facilitate the equilibration of alanine enantiomers. Understanding how this two-base system is utilized and controlled to yield reaction specificity is therefore a potential means for designing antibiotics. Cycloserine is a known alanine racemase suicide substrate, although its mechanism of inactivation is based on transaminase chemistry. Here we characterize the effects of a Y265F mutant (Tyr265 acts as the catalytic base in the l-isomer case) of Bacillus stearothermophilus alanine racemase on cycloserine inactivation. The Y265F mutant reduces racemization activity 1600-fold [Watanabe, A., Yoshimura, T., Mikami, B., and Esaki, N. (1999) J. Biochem. 126, 781-786] and only leads to formation of the isoxazole end product (the result of the transaminase pathway) in the case of d-cycloserine, in contrast to results obtained using the wild-type enzyme. l-Cycloserine, on the other hand, utilizes a number of alternative pathways in the absence of Y265, emphasizing the importance of Y265 in both the inactivation and racemization pathway. In combination with the kinetics of inactivation, these results suggest roles for each of the two catalytic bases in racemization and inactivation, as well as the importance of Y265 in "steering" the chemistry to favor one pathway over another.


Subject(s)
Alanine Racemase/chemistry , Cycloserine/pharmacology , Mutation , Alanine Racemase/antagonists & inhibitors , Alanine Racemase/genetics , Amination , Geobacillus stearothermophilus/enzymology , Models, Molecular , Spectrophotometry, Ultraviolet
14.
Appl Environ Microbiol ; 70(1): 310-7, 2004 Jan.
Article in English | MEDLINE | ID: mdl-14711657

ABSTRACT

This paper describes the use of the alr gene, encoding alanine racemase, as a promoter-screening tool for the identification of conditional promoters in Lactobacillus plantarum. Random fragments of the L. plantarum WCFS1 genome were cloned upstream of the promoterless alr gene of Lactococcus lactis in a low-copy-number plasmid vector. The resulting plasmid library was introduced into an L. plantarum Deltaalr strain (MD007), and 40,000 clones were selected. The genome coverage of the library was estimated to be 98%, based on nucleotide insert sequence and restriction analyses of the inserts of randomly selected clones. The library was screened for clones that were capable of complementing the D-alanine auxotroph phenotype of MD007 in media containing up to 10, 100, or 300 micro g of the competitive Alr inhibitor D-cycloserine per ml. Western blot analysis with polyclonal antibodies raised against lactococcal Alr revealed that the Alr production level required for growth increased in the presence of increasing concentrations of D-cycloserine, adding a quantitative factor to the primarily qualitative nature of the alr complementation screen. Screening of the alr complementation library for clones that could grow only in the presence of 0.8 M NaCl resulted in the identification of eight clones that upon Western blot analysis showed significantly higher Alr production under high-salt conditions than under low-salt conditions. These results established the effectiveness of the alanine racemase complementation screening method for the identification of promoters on their conditional or constitutive activity.


Subject(s)
Alanine Racemase/genetics , DNA Probes , Genetic Vectors , Lactobacillus/growth & development , Promoter Regions, Genetic , Alanine Racemase/antagonists & inhibitors , Alanine Racemase/metabolism , Base Sequence , Culture Media , Cycloserine/metabolism , Cycloserine/pharmacology , Gene Expression Regulation, Bacterial , Genetic Complementation Test , Genomic Library , Lactobacillus/genetics , Molecular Sequence Data , Sodium Chloride/pharmacology
16.
Biochemistry ; 42(19): 5775-83, 2003 May 20.
Article in English | MEDLINE | ID: mdl-12741835

ABSTRACT

Alanine racemase (EC 5.1.1.1) catalyzes the interconversion of alanine enantiomers, and thus represents the first committed step involved in bacterial cell wall biosynthesis. Cycloserine acts as a suicide inhibitor of alanine racemase and as such, serves as an antimicrobial agent. The chemical means by which cycloserine inhibits alanine racemase is unknown. Through spectroscopic assays, we show here evidence of a pyridoxal derivative (arising from either isomer of cycloserine) saturated at the C4' carbon position. We additionally report the L- and D-cycloserine inactivated crystal structures of Bacillus stearothermophilus alanine racemase, which corroborates the spectroscopy via evidence of a 3-hydroxyisoxazole pyridoxamine derivative. Upon the basis of the kinetic and structural properties of both the L- and D-isomers of the inhibitor, we propose a mechanism of alanine racemase inactivation by cycloserine. This pathway involves an initial transamination step followed by tautomerization to form a stable aromatic adduct, a scheme similar to that seen in cycloserine inactivation of aminotransferases.


Subject(s)
Alanine Racemase/chemistry , Alanine Racemase/metabolism , Cycloserine/chemistry , Cycloserine/metabolism , Alanine Racemase/antagonists & inhibitors , Catalytic Domain , Crystallography, X-Ray , Cycloserine/pharmacology , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/metabolism , Enzyme Inhibitors/pharmacology , Geobacillus stearothermophilus/enzymology , Kinetics , Models, Molecular , Protein Conformation , Spectrophotometry , Static Electricity , Stereoisomerism
17.
J Antibiot (Tokyo) ; 56(2): 160-8, 2003 Feb.
Article in English | MEDLINE | ID: mdl-12715876

ABSTRACT

A select series of N(2)-substituted D,L-cycloserine derivatives were prepared a ndevaluated for inhibitory activity against purified alanine racemases (alr gene product) from Escherichia coli, Staphylococcus aureus, and Mycobacterium tuberculosis, as well as in a growth inhibition assay. N(2)-Modification led to loss of enzymatic inhibitory activity in most cases consistent with a recent proposal for cycloserine function.


Subject(s)
Alanine Racemase/antagonists & inhibitors , Antibiotics, Antitubercular/chemical synthesis , Cycloserine/analogs & derivatives , Enzyme Inhibitors/chemical synthesis , Enzyme Inhibitors/pharmacology , Alanine Racemase/metabolism , Antibiotics, Antitubercular/chemistry , Antibiotics, Antitubercular/pharmacology , Chromatography, Thin Layer , Cycloserine/pharmacology , Enzyme Inhibitors/chemistry , Escherichia coli/drug effects , Escherichia coli/enzymology , Mass Spectrometry , Microbial Sensitivity Tests , Mycobacterium tuberculosis/drug effects , Mycobacterium tuberculosis/enzymology , Nuclear Magnetic Resonance, Biomolecular , Spectroscopy, Fourier Transform Infrared , Staphylococcus aureus/drug effects , Staphylococcus aureus/enzymology , Structure-Activity Relationship
18.
J Comput Aided Mol Des ; 16(12): 935-53, 2002 Dec.
Article in English | MEDLINE | ID: mdl-12825624

ABSTRACT

We report a new structure-based strategy for the identification of novel inhibitors. This approach has been applied to Bacillus stearothermophilus alanine racemase (AlaR), an enzyme implicated in the biosynthesis of the bacterial cell wall. The enzyme catalyzes the racemization of L- and D-alanine using pyridoxal 5'-phosphate (PLP) as a cofactor. The restriction of AlaR to bacteria and some fungi and the absolute requirement for D-alanine in peptidoglycan biosynthesis make alanine racemase a suitable target for drug design. Unfortunately, known inhibitors of alanine racemase are not specific and inhibit the activity of other PLP-dependent enzymes, leading to neurological and other side effects. This article describes the development of a receptor-based pharmacophore model for AllaR, taking into account receptor flexibility (i.e. a 'dynamic' pharmacophore model). In order to accomplish this, molecular dynamics (MD) simulations were performed on the full AlaR dimer from Bacillus stearothermophilus (PDB entry, 1 sft) with a D-alanine molecule in one active site and the non-covalent inhibitor, propionate, in the second active site of this homodimer. The basic strategy followed in this study was to utilize conformations of the protein obtained during MD simulations to generate a dynamic pharmacophore model using the property mapping capability of the LigBuilder program. Compounds from the Available Chemicals Directory that fit the pharmacophore model were identified and have been submitted for experimental testing. The approach described here can be used as a valuable tool for the design of novel inhibitors of other biomolecular targets.


Subject(s)
Alanine Racemase/antagonists & inhibitors , Alanine Racemase/chemistry , Computer-Aided Design , Drug Design , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Computer Simulation , Crystallography, X-Ray , Databases, Factual , Drug Evaluation, Preclinical , Geobacillus stearothermophilus/enzymology , Models, Molecular , Molecular Structure , Protein Conformation , Thermodynamics
19.
Comp Biochem Physiol B Biochem Mol Biol ; 126(4): 599-608, 2000 Aug.
Article in English | MEDLINE | ID: mdl-11026672

ABSTRACT

Fresh water crayfish Procambarus clarkii is known to accumulate D-alanine remarkably in muscle after seawater acclimation, accompanied by an increase in alanine racemase activity. We have purified alanine racemase from crayfish muscle to homogeneity. The enzyme is a monomeric protein with a molecular mass of 58 kDa. It is highly specific to alanine and does not racemize L-serine, L-aspartate, L-glutamate, L-valine and L-arginine. The enzyme shows the highest activity at pH 9.0 in the conversion of L- to D-alanine and at pH 8.5 in the reverse conversion. Properties such as amino acid sequence, quaternary structure, pyridoxal 5'-phosphate (PLP)-dependency, pH-dependency and kinetic parameters seem to be distinct from those of the microbial alanine racemases. Various salts including NaCl at concentrations around seawater level were potently inhibitory for the activity in both of L- to -D and D- to -L direction.


Subject(s)
Alanine Racemase/chemistry , Alanine Racemase/metabolism , Amino Acids/metabolism , Astacoidea/enzymology , Alanine Racemase/antagonists & inhibitors , Alanine Racemase/isolation & purification , Amino Acids/chemistry , Animals , Electrophoresis, Polyacrylamide Gel , Hydrogen-Ion Concentration , Kinetics , Pyridoxal Phosphate/metabolism , Salts/metabolism
20.
Amino Acids ; 18(4): 375-87, 2000.
Article in English | MEDLINE | ID: mdl-10949920

ABSTRACT

Spore coat-associated alanine racemase of Bacillus subtilis, which converts L-alanine to D-alanine, that is, the germinant to the competitive inhibitor, to regulate spore germination for survival of the organism under unfavorable growth conditions, was examined. The dormant spores, L-alanine-initiated germination of which is inhibited by diphenylamine, were used to characterize the enzyme in the native form because of its unextractablility from dormant spores. The presence of isozymes, Enz-I and Enz-II with Km for L-alanine of about 20mM and 50mM and optimum activity at around 40 degrees C and 65 degrees C, respectively, was proposed. The enzymes were selectively used depending on the L-alanine concentration and the temperature. The pH profiles of the activity (optimun at pH 9.0) and the stability (stable between pH 6-11 at 60 degrees C) were similar, but Enz-II was more heat-stable than Enz-I and the denaturation curve demonstrated a two-domain structure for Enz-II. Sensitivity to D-penicillamine, hydroxylamine and HgCl2 was similar between Enz-I and Enz-II, while that to D-cycloserine, L- and D-aminoethylphosphonic acid, monoiodoacetate and N-ethylmaleimide was different; HgCl2 was the most effective inhibitor among these compounds.


Subject(s)
Alanine Racemase/chemistry , Alanine Racemase/metabolism , Alanine/chemistry , Alanine/metabolism , Bacillus subtilis/enzymology , Alanine Racemase/antagonists & inhibitors , Enzyme Inhibitors/pharmacology , Enzyme Stability , Hydrogen-Ion Concentration , Hydroxylamine/pharmacology , Isoenzymes , Kinetics , Spores, Bacterial/chemistry , Spores, Bacterial/enzymology , Temperature
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