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1.
J Mol Recognit ; 34(9): e2894, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-33719110

RESUMO

Enterococcus faecalis (E. faecalis) is a Gram-positive coccoid, non-sporulating, facultative anaerobic, multidrug resistance bacterium responsible for almost 65% to 80% of all enterococcal nosocomial infections. It usually causes infective endocarditis, urinary tract and surgical wound infections. The increase in E. faecalis resistance to conventionally available antibiotic has rekindled intense interest in developing useful antibacterial drugs. In E. faecalis, diaminopimelate epimerase (DapF) is involved in the lysine biosynthetic pathway. The product of this pathway is precursors of peptidoglycan synthesis, which is a component of bacterial cell wall. Also, because mammals lack this enzyme, consequently E. faecalis diaminopimelate epimerase (EfDapF) represents a potential target for developing novel class of antibiotics. In this regard, we have successfully cloned, overexpressed the gene encoding DapF in BL-21(DE3) and purified with Ni-NTA Agarose resin. In addition to this, binding studies were performed using fluorescence spectroscopy in order to confirm the bindings of the identified lead compounds (acetaminophen and dexamethasone) with EfDapF. Docking studies revealed that acetaminophen found to make hydrogen bonds with Asn72 and Asn13 while dexamethasone interacted by forming hydrogen bonds with Asn205 and Glu223. Thus, biochemical studies indicated acetaminophen and dexamethasone, as potential inhibitors of EfDapF and eventually can reduce the catalytic activity of EfDapF.


Assuntos
Acetaminofen/farmacologia , Isomerases de Aminoácido/antagonistas & inibidores , Dexametasona/farmacologia , Enterococcus faecalis/enzimologia , Simulação de Acoplamento Molecular , Isomerases de Aminoácido/química , Isomerases de Aminoácido/metabolismo , Proteínas de Bactérias/antagonistas & inibidores , Sítios de Ligação , Reposicionamento de Medicamentos , Enterococcus faecalis/efeitos dos fármacos , Conformação Proteica
2.
Biochemistry (Mosc) ; 85(2): 248-256, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-32093601

RESUMO

Streptococcus iniae is a pathogenic and zoonotic bacterium responsible for human diseases and mortality of many fish species. Recently, this bacterium has demonstrated an increasing trend for antibiotics resistance, which has warranted a search for new approaches to tackle its infection. Glutamate racemase (MurI) is a ubiquitous enzyme of the peptidoglycan synthesis pathway that plays an important role in the cell wall integrity maintenance; however, the significance of this enzyme differs in different species. In this study, we knocked out the MurI gene in S. iniae in order to elucidate the role of glutamate racemase in maintaining cell wall integrity in this bacterial species. We also cloned, expressed, and purified MurI and determined its biochemical characteristics. Biochemical analysis revealed that the MurI gene in S. iniae encodes a functional enzyme with a molecular weight of 30 kDa, temperature optimum at 35°C, and pH optimum at 8.5. Metal ions, such as Cu2+, Mn2+, Co2+ and Zn2+, inhibited the enzyme activity. MurI was found to be essential for the viability and cell wall integrity of S. iniae. The optimal growth of the MurI-deficient S. iniae mutant can be achieved only by adding a high concentration of D-glutamate to the medium. Membrane permeability assay of the mutant showed an increasing extent of the cell wall damage with time upon D-glutamate starvation. Moreover, the mutant lost its virulence when incubated in fish blood. Our results demonstrated that the MurI knockout leads to the generation of S. iniae auxotroph with damaged cell walls.


Assuntos
Isomerases de Aminoácido/metabolismo , Parede Celular , Viabilidade Microbiana , Streptococcus iniae/enzimologia , Isomerases de Aminoácido/antagonistas & inibidores , Isomerases de Aminoácido/genética , Parede Celular/efeitos dos fármacos , Parede Celular/metabolismo , Concentração de Íons de Hidrogênio , Metais Pesados/farmacologia , Viabilidade Microbiana/efeitos dos fármacos , Mutação , Streptococcus iniae/efeitos dos fármacos , Streptococcus iniae/metabolismo
3.
Nat Prod Rep ; 36(12): 1687-1705, 2019 12 11.
Artigo em Inglês | MEDLINE | ID: mdl-30994146

RESUMO

Covering: up to March 2019 Amino acid racemases and epimerases are key enzymes that invert the configuration of common amino acids and supply many corresponding d-isomers in living organisms. Some d-amino acids are inherently bioactive, whereas others are building blocks for important biomolecules, for example lipid II, the bacterial cell wall precursor. Peptides containing them have enhanced proteolytic stability and can act as important recognition elements in mammalian systems. Selective inhibition of certain amino acid racemases (e.g. glutamate racemase) is believed to offer a promising target for new antibacterial drugs effective against pathogens resistant to current antibiotics. Many amino acid racemases employ imine formation with pyridoxal phosphate (PLP) as a cofactor to accelerate the abstraction of the alpha proton. However, the group reviewed herein achieves racemization of free amino acids without the use of cofactors or metals, and uses a thiol/thiolate pair for deprotonation and reprotonation. All bacteria and higher plants contain such enzymes, for example diaminopimelate epimerase, which is required for lysine biosynthesis in these organisms. This process cannot be accomplished without an enzyme catalyst as the acidities of a thiol and the substrate α-hydrogen are inherently mismatched by at least 10 orders of magnitude. This review describes the structural and mechanistic studies on PLP-independent racemases and the evolving view of key enzymatic machinery that accomplishes these remarkable transformations.


Assuntos
Inibidores Enzimáticos/farmacologia , Fosfato de Piridoxal/metabolismo , Racemases e Epimerases/química , Racemases e Epimerases/metabolismo , Isomerases de Aminoácido/antagonistas & inibidores , Isomerases de Aminoácido/química , Isomerases de Aminoácido/metabolismo , Inibidores Enzimáticos/química , Conformação Proteica , Racemases e Epimerases/antagonistas & inibidores , Compostos de Sulfidrila/metabolismo
4.
Appl Microbiol Biotechnol ; 103(2): 843-851, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30456576

RESUMO

Increasing drug resistance in pathogens including Mycobacterium tuberculosis (MTB) has been ascribed to mutations in the known target genes. However, many of these drugs have multiple targets; some of which have not been identified so far. Understanding the mechanism of action of these drugs holds a great promise in better management of disease especially by drug-resistant strains. In this study, we report glutamate racemase (MurI), a crucial enzyme of phase I peptidoglycan (PG) biosynthesis pathway of MTB, as an additional target of ethambutol (EMB). The effect on EMB on the MurI protein at structural and functional level was studied using different spectroscopic, biochemical, and insilico approaches. Spectroscopic analysis revealed that EMB-modified protein undergoes conformational alterations. Furthermore, in vitro racemization studies of the MurI protein suggest that EMB decreases its functional activity. Docking studies revealed that EMB interacts with most of the active residues at the binding site and blocks the binding pocket. Overall, data suggests that EMB, a primary drug used for the treatment of tuberculosis (TB), acts as a competitive inhibitor of substrate for binding to mycobacterial MurI protein. The study also points out to our lacunae in understanding the site and mechanism of action of existing drugs. Furthermore, glutamate racemase is a conserved protein of the bacterial kingdom; therefore, ethambutol could be a promising candidate as a broad-spectrum antibiotic for many other bacterial diseases.


Assuntos
Isomerases de Aminoácido/antagonistas & inibidores , Antituberculosos/farmacologia , Inibidores Enzimáticos/farmacologia , Etambutol/farmacologia , Mycobacterium tuberculosis/efeitos dos fármacos , Peptidoglicano/biossíntese , Isomerases de Aminoácido/química , Isomerases de Aminoácido/metabolismo , Sítios de Ligação , Parede Celular/metabolismo , Simulação de Acoplamento Molecular , Mycobacterium tuberculosis/enzimologia , Ligação Proteica , Conformação Proteica , Análise Espectral
5.
Bioorg Med Chem ; 26(1): 177-190, 2018 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-29239770

RESUMO

Mycobacterium tuberculosis glutamate racemase is an essential enzyme involved in peptidoglycan synthesis and conserved in most bacteria. Small molecule inhibitors were reported on other bacterial species whereas in M. tuberculosis it wasn't explored much. In this study we have screened in house compound library using fluorescence thermal shift assay and enzyme inhibition assay, form this (1-(3-(benzo[d]thiazol-2-yl)phenyl)-3-(p-tolyl)thiourea) was identified as lead compound with IC50 19.47 ±â€¯0.81 µM. Further lead optimization by synthesis resulted in twenty-three compounds, of which Compound 25 has shown more efficacy compared to lead 1 showing non-competitive mode of inhibition with IC50 1.32 ±â€¯0.43 µM. It also showed significant activity (represented in log reduction) in nutrient starved dormant M. tuberculosis model (2.1), M. tuberculosis biofilm assay (2.0) and in vivo M. marinum infected zebrafish model (3.5).


Assuntos
Isomerases de Aminoácido/antagonistas & inibidores , Antituberculosos/farmacologia , Inibidores Enzimáticos/farmacologia , Mycobacterium tuberculosis/efeitos dos fármacos , Isomerases de Aminoácido/metabolismo , Animais , Antituberculosos/síntese química , Antituberculosos/química , Sobrevivência Celular/efeitos dos fármacos , Relação Dose-Resposta a Droga , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/química , Camundongos , Testes de Sensibilidade Microbiana , Estrutura Molecular , Mycobacterium tuberculosis/enzimologia , Mycobacterium tuberculosis/crescimento & desenvolvimento , Células RAW 264.7 , Relação Estrutura-Atividade
6.
Antimicrob Agents Chemother ; 60(10): 6091-9, 2016 10.
Artigo em Inglês | MEDLINE | ID: mdl-27480853

RESUMO

The increasing global prevalence of drug resistance among many leading human pathogens necessitates both the development of antibiotics with novel mechanisms of action and a better understanding of the physiological activities of preexisting clinically effective drugs. Inhibition of peptidoglycan (PG) biosynthesis and cross-linking has traditionally enjoyed immense success as an antibiotic target in multiple bacterial pathogens, except in Mycobacterium tuberculosis, where it has so far been underexploited. d-Cycloserine, a clinically approved antituberculosis therapeutic, inhibits enzymes within the d-alanine subbranch of the PG-biosynthetic pathway and has been a focus in our laboratory for understanding peptidoglycan biosynthesis inhibition and for drug development in studies of M. tuberculosis During our studies on alternative inhibitors of the d-alanine pathway, we discovered that the canonical alanine racemase (Alr) inhibitor ß-chloro-d-alanine (BCDA) is a very poor inhibitor of recombinant M. tuberculosis Alr, despite having potent antituberculosis activity. Through a combination of enzymology, microbiology, metabolomics, and proteomics, we show here that BCDA does not inhibit the d-alanine pathway in intact cells, consistent with its poor in vitro activity, and that it is instead a mechanism-based inactivator of glutamate racemase (MurI), an upstream enzyme in the same early stage of PG biosynthesis. This is the first report to our knowledge of inhibition of MurI in M. tuberculosis and thus provides a valuable tool for studying this essential and enigmatic enzyme and a starting point for future MurI-targeted antibacterial development.


Assuntos
Isomerases de Aminoácido/química , Antituberculosos/farmacologia , Proteínas de Bactérias/química , Inibidores Enzimáticos/farmacologia , Mycobacterium tuberculosis/efeitos dos fármacos , beta-Alanina/análogos & derivados , Isomerases de Aminoácido/antagonistas & inibidores , Isomerases de Aminoácido/genética , Isomerases de Aminoácido/metabolismo , Sequência de Aminoácidos , Antituberculosos/química , Proteínas de Bactérias/antagonistas & inibidores , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Domínio Catalítico , Clonagem Molecular , Inibidores Enzimáticos/química , Escherichia coli/genética , Escherichia coli/metabolismo , Expressão Gênica , Cinética , Testes de Sensibilidade Microbiana , Mycobacterium tuberculosis/enzimologia , Mycobacterium tuberculosis/genética , Mycobacterium tuberculosis/crescimento & desenvolvimento , Peptidoglicano/biossíntese , Ligação Proteica , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Alinhamento de Sequência , Especificidade por Substrato , beta-Alanina/química , beta-Alanina/farmacologia
7.
Antimicrob Agents Chemother ; 59(4): 2337-42, 2015 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-25645840

RESUMO

A pyridodiazepine amine inhibitor of Helicobacter pylori glutamate racemase (MurI) was characterized. The compound was selectively active against H. pylori, and growth suppression was shown to be mediated through the inhibition of MurI by several methods. In killing kinetics experiments, the compound showed concentration-independent activity, with about a 2-log loss of viability in 24 h. A demonstration of efficacy in a mouse infection model was attempted but not achieved, and this was attributed to the failure to attain extended exposure levels above the MIC for >95% of the time. This index and magnitude were derived from pharmacokinetic-pharmacodynamic (PK-PD) studies with amoxicillin, another inhibitor of peptidoglycan biosynthesis that showed slow killing kinetics similar to those of the pyridodiazepine amines. These studies indicate that MurI and other enzymes involved in peptidoglycan biosynthesis may be less desirable targets for monotherapy directed against H. pylori if once-a-day dosing is required.


Assuntos
Isomerases de Aminoácido/antagonistas & inibidores , Antibacterianos/uso terapêutico , Azepinas/uso terapêutico , Infecções por Helicobacter/tratamento farmacológico , Helicobacter pylori/efeitos dos fármacos , Helicobacter pylori/enzimologia , Piridinas/uso terapêutico , Amoxicilina/farmacocinética , Amoxicilina/farmacologia , Animais , Antibacterianos/farmacocinética , Azepinas/farmacocinética , Feminino , Mucosa Gástrica/metabolismo , Infecções por Helicobacter/sangue , Infecções por Helicobacter/microbiologia , Cinética , Camundongos , Testes de Sensibilidade Microbiana , Peptidoglicano/metabolismo , Piridinas/farmacocinética , Ratos , Ratos Sprague-Dawley
8.
Amino Acids ; 47(5): 975-85, 2015 May.
Artigo em Inglês | MEDLINE | ID: mdl-25646960

RESUMO

D-Aspartate (D-Asp) has important physiological functions, and recent studies have shown that substantial amounts of free D-Asp are present in a wide variety of mammalian tissues and cells. Biosynthesis of D-Asp has been observed in several cultured rat cell lines, and a murine gene (glutamate-oxaloacetate transaminase 1-like 1, Got1l1) that encodes Asp racemase, a synthetic enzyme that produces D-Asp from L-Asp, was proposed recently. The product of this gene is homologous to mammalian glutamate-oxaloacetate transaminase (GOT). Here, we tested the hypothesis that rat and human homologs of mouse GOT1L1 are involved in Asp synthesis. The following two approaches were applied, since the numbers of attempts were unsuccessful to prepare soluble GOT1L1 recombinant proteins. First, the relationship between the D-Asp content and the expression levels of the mRNAs encoding GOT1L1 and D-Asp oxidase, a primary degradative enzyme of D-Asp, was examined in several rat and human cell lines. Second, the effect of knockdown of the Got1l1 gene on D-Asp biosynthesis during culture of the cells was determined. The results presented here suggest that the rat and human homologs of mouse GOT1L1 are not involved in D-Asp biosynthesis. Therefore, D-Asp biosynthetic pathway in mammals is still an urgent issue to be resolved.


Assuntos
Isomerases de Aminoácido/metabolismo , D-Aspartato Oxidase/metabolismo , Ácido D-Aspártico/biossíntese , RNA Mensageiro/metabolismo , Isomerases de Aminoácido/antagonistas & inibidores , Isomerases de Aminoácido/genética , Animais , Linhagem Celular Tumoral , D-Aspartato Oxidase/genética , Expressão Gênica , Técnicas de Silenciamento de Genes , Células HeLa , Células Hep G2 , Humanos , Rim/enzimologia , Rim/patologia , Camundongos , Células PC12 , Hipófise/enzimologia , Hipófise/patologia , RNA Mensageiro/genética , RNA Interferente Pequeno/genética , RNA Interferente Pequeno/metabolismo , Ratos , Homologia de Sequência de Aminoácidos , Especificidade da Espécie
9.
Bioorg Med Chem Lett ; 24(1): 390-3, 2014 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-24314397

RESUMO

d-Amino acids can play important roles as specific biosynthetic building blocks required by organisms or act as regulatory molecules. Consequently, amino acid racemases that catalyze the formation of d-amino acids are potential therapeutic targets. Serine racemase catalyzes the reversible formation of d-serine (a modulator of neurotransmission) from l-serine, while proline racemase (an essential enzymatic and mitogenic protein in trypanosomes) catalyzes the reversible conversion of l-proline to d-proline. We show the substrate-product analogue α-(hydroxymethyl)serine is a modest, linear mixed-type inhibitor of serine racemase from Schizosaccharomyces pombe (Ki=167±21mM, Ki'=661±81mM, cf. Km=19±2mM). The bicyclic substrate-product analogue of proline, 7-azabicyclo[2.2.1]heptan-7-ium-1-carboxylate is a weak inhibitor of proline racemase from Clostridium sticklandii, giving only 29% inhibition at 142.5mM. However, the more flexible bicyclic substrate-product analogue tetrahydro-1H-pyrrolizine-7a(5H)-carboxylate is a noncompetitive inhibitor of proline racemase from C. sticklandii (Ki=111±15mM, cf. Km=5.7±0.5mM). These results suggest that substrate-product analogue inhibitors of racemases may only be effective when the active site is capacious and/or plastic, or when the inhibitor is sufficiently flexible.


Assuntos
Isomerases de Aminoácido/antagonistas & inibidores , Inibidores Enzimáticos/farmacologia , Prolina/farmacologia , Racemases e Epimerases/antagonistas & inibidores , Serina/análogos & derivados , Isomerases de Aminoácido/metabolismo , Clostridium sticklandii/enzimologia , Relação Dose-Resposta a Droga , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/química , Modelos Moleculares , Estrutura Molecular , Prolina/análogos & derivados , Prolina/química , Racemases e Epimerases/metabolismo , Schizosaccharomyces/enzimologia , Serina/síntese química , Serina/química , Serina/farmacologia , Relação Estrutura-Atividade
10.
Bioorg Med Chem Lett ; 24(5): 1432-6, 2014 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-24507924

RESUMO

D-Glutamate is an essential biosynthetic building block of the peptidoglycans that encapsulate the bacterial cell wall. Glutamate racemase catalyzes the reversible formation of D-glutamate from L-glutamate and, hence, the enzyme is a potential therapeutic target. We show that the novel cyclic substrate-product analogue (R,S)-1-hydroxy-1-oxo-4-amino-4-carboxyphosphorinane is a modest, partial noncompetitive inhibitor of glutamate racemase from Fusobacterium nucleatum (FnGR), a pathogen responsible, in part, for periodontal disease and colorectal cancer (Ki=3.1±0.6 mM, cf. Km=1.41±0.06 mM). The cyclic substrate-product analogue (R,S)-4-amino-4-carboxy-1,1-dioxotetrahydro-thiopyran was a weak inhibitor, giving only ∼30% inhibition at a concentration of 40 mM. The related cyclic substrate-product analogue 1,1-dioxo-tetrahydrothiopyran-4-one was a cooperative mixed-type inhibitor of FnGR (Ki=18.4±1.2 mM), while linear analogues were only weak inhibitors of the enzyme. For glutamate racemase, mimicking the structure of both enantiomeric substrates (substrate-product analogues) serves as a useful design strategy for developing inhibitors. The new cyclic compounds developed in the present study may serve as potential lead compounds for further development.


Assuntos
Isomerases de Aminoácido/metabolismo , Proteínas de Transporte/química , Inibidores Enzimáticos/química , Ácido Glutâmico/química , Proteolipídeos/química , Isomerases de Aminoácido/antagonistas & inibidores , Bacillus subtilis/enzimologia , Proteínas de Transporte/metabolismo , Domínio Catalítico , Inibidores Enzimáticos/metabolismo , Fusobacterium/enzimologia , Ácido Glutâmico/metabolismo , Ligação Proteica , Proteolipídeos/metabolismo , Especificidade por Substrato
11.
J Chem Inf Model ; 53(9): 2349-59, 2013 Sep 23.
Artigo em Inglês | MEDLINE | ID: mdl-24111836

RESUMO

Glutamate racemase (GR) is a cofactor independent amino acid racemase that has recently garnered increasing attention as an antimicrobial drug target. There are numerous high resolution crystal structures of GR, yet these are invariably bound to either D-glutamate or very weakly bound oxygen-based salts. Recent in silico screens have identified a number of new competitive inhibitor scaffolds, which are not based on D-Glu, but exploit many of the same hydrogen bond donor positions. In silico studies on 1-H-benzimidazole-2-sulfonic acid (BISA) show that the sulfonic acid points to the back of the GR active site, in the most buried region, analogous to the C2-carboxylate binding position in the GR-d-glutamate complex. Furthermore, BISA has been shown to be the strongest nonamino acid competitive inhibitor. Previously published computational studies have suggested that a portion of this binding strength is derived from complexation with a more closed active site, relative to weaker ligands, and in which the internal water network is more isolated from the bulk solvent. In order to validate key contacts between the buried sulfonate moiety of BISA and moieties in the back of the enzyme active site, as well as to probe the energetic importance of the potentially large number of interstitial waters contacted by the BISA scaffold, we have designed several mutants of Asn75. GR-N75A removes a key hydrogen bond donor to the sulfonate of BISA, but also serves to introduce an additional interstitial water, due to the newly created space of the mutation. GR- N75L should also show the loss of a hydrogen bond donor to the sulfonate of BISA, but does not (a priori) seem to permit an additional interstitial water contact. In order to investigate the dynamics, structure, and energies of this water-mediated complexation, we have employed the extended linear response (ELR) approach for the calculation of binding free energies to GR, using the YASARA2 knowledge based force field on a set of ten GR complexes, and yielding an R-squared value of 0.85 and a RMSE of 2.0 kJ/mol. Surprisingly, the inhibitor set produces a uniformly large interstitial water contribution to the electrostatic interaction energy (), ranging from 30 to >50%, except for the natural substrate (D-glutamate), which has only a 7% contribution of from water. The broader implications for predicting and exploiting significant interstitial water contacts in ligand-enzyme complexation are discussed.


Assuntos
Isomerases de Aminoácido/química , Isomerases de Aminoácido/metabolismo , Simulação de Dinâmica Molecular , Água/metabolismo , Isomerases de Aminoácido/antagonistas & inibidores , Isomerases de Aminoácido/genética , Bacillus subtilis/enzimologia , Domínio Catalítico , Inibidores Enzimáticos/farmacologia , Cinética , Ligantes , Mutação , Ligação Proteica , Termodinâmica
12.
Nature ; 447(7146): 817-22, 2007 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-17568739

RESUMO

Glutamate racemase is an enzyme essential to the bacterial cell wall biosynthesis pathway, and has therefore been considered as a target for antibacterial drug discovery. We characterized the glutamate racemases of several pathogenic bacteria using structural and biochemical approaches. Here we describe three distinct mechanisms of regulation for the family of glutamate racemases: allosteric activation by metabolic precursors, kinetic regulation through substrate inhibition, and D-glutamate recycling using a d-amino acid transaminase. In a search for selective inhibitors, we identified a series of uncompetitive inhibitors specifically targeting Helicobacter pylori glutamate racemase that bind to a cryptic allosteric site, and used these inhibitors to probe the mechanistic and dynamic features of the enzyme. These structural, kinetic and mutational studies provide insight into the physiological regulation of these essential enzymes and provide a basis for designing narrow-spectrum antimicrobial agents.


Assuntos
Isomerases de Aminoácido/química , Isomerases de Aminoácido/metabolismo , Bactérias/enzimologia , Regulação Alostérica/efeitos dos fármacos , Sítio Alostérico/efeitos dos fármacos , Isomerases de Aminoácido/antagonistas & inibidores , Isomerases de Aminoácido/genética , Antibacterianos/metabolismo , Antibacterianos/farmacologia , Bactérias/patogenicidade , Cristalografia por Raios X , Inibidores Enzimáticos/metabolismo , Inibidores Enzimáticos/farmacologia , Escherichia coli/enzimologia , Helicobacter pylori/enzimologia , Cinética , Modelos Moleculares , Conformação Proteica , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Relação Estrutura-Atividade
13.
J Enzyme Inhib Med Chem ; 28(5): 1026-33, 2013 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-22871135

RESUMO

Three glutamic acid derivatives, two boron-containing and one imide-containing compound, were synthesized and tested for antimicrobial activity targeting glutamate-racemase. Antimicrobial effect was evaluated over Bacillus spp. Docking analysis shown that the test compounds bind near the active site of racemase isoforms, suggesting an allosteric effect. The boron derivatives had greater affinity than the imide derivative. In vitro assays shown good antimicrobial activity for the boron-containing compounds, and no effectiveness for the imide-containing compounds. The minimum inhibitory concentration of tetracycline, used as standard, was lower than that of the boron-containing derivatives. However, it seems that the boron-containing derivatives are more selective for bacteria. Experimental evidence suggests that the boron-containing derivatives act by inhibiting the racemase enzyme. Therefore, these test compounds probably impede the formation of the bacterial cell wall. Thus, the boron-containing glutamic acid derivatives should certainly be of interest for future studies as antimicrobial agents for Bacillus spp.


Assuntos
Isomerases de Aminoácido/antagonistas & inibidores , Antibacterianos/farmacologia , Bacillus/efeitos dos fármacos , Inibidores Enzimáticos/farmacologia , Isomerases de Aminoácido/metabolismo , Antibacterianos/síntese química , Antibacterianos/química , Bacillus/citologia , Bacillus/enzimologia , Relação Dose-Resposta a Droga , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/química , Testes de Sensibilidade Microbiana , Modelos Moleculares , Estrutura Molecular , Relação Estrutura-Atividade
14.
Bioorg Med Chem Lett ; 22(17): 5600-7, 2012 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-22877632

RESUMO

Structure-activity relationships are presented around a series of pyrazolopyrimidinediones that inhibit the growth of Helicobacter pylori by targeting glutamate racemase, an enzyme that provides d-glutamate for the construction of N-acetylglucosamine-N-acetylmuramic acid peptidoglycan subunits assimilated into the bacterial cell wall. Substituents on the inhibitor scaffold were varied to optimize target potency, antibacterial activity and in vivo pharmacokinetic stability. By incorporating an imidazole ring at the 7-position of scaffold, high target potency was achieved due to a hydrogen bonding network that occurs between the 3-position nitrogen atom, a bridging water molecule and the side chains Ser152 and Trp244 of the enzyme. The lipophilicity of the scaffold series proved important for expression of antibacterial activity. Clearances in vitro and in vivo were monitored to identify compounds with improved plasma stability. The basicity of the imidazole may contribute to increased aqueous solubility at lower pH allowing for improved oral bioavailability.


Assuntos
Isomerases de Aminoácido/antagonistas & inibidores , Antibacterianos/química , Antibacterianos/farmacologia , Helicobacter pylori/efeitos dos fármacos , Pirimidinonas/química , Pirimidinonas/farmacologia , Administração Oral , Isomerases de Aminoácido/metabolismo , Animais , Antibacterianos/administração & dosagem , Antibacterianos/farmacocinética , Disponibilidade Biológica , Infecções por Helicobacter/tratamento farmacológico , Infecções por Helicobacter/microbiologia , Helicobacter pylori/enzimologia , Humanos , Imidazóis/química , Imidazóis/farmacologia , Camundongos , Modelos Moleculares , Pirazóis/administração & dosagem , Pirazóis/química , Pirazóis/farmacocinética , Pirazóis/farmacologia , Pirimidinonas/administração & dosagem , Pirimidinonas/farmacocinética , Relação Estrutura-Atividade
15.
Chem Biol Drug Des ; 99(4): 513-526, 2022 04.
Artigo em Inglês | MEDLINE | ID: mdl-34918458

RESUMO

Proline racemases (PRAC), catalyzing the l-proline and d-proline interconversion, are essential factors in eukaryotic pathogens such as Trypanosoma cruzi, Trypanosoma vivax, and Clostridioides difficile. If the discovery of irreversible inhibitors of T. cruzi PRAC (TcPRAC) led to innovative therapy of the Chagas disease, no inhibitors of CdPRAC have been discovered to date. However, C. difficile, due to an increased incidence in recent years, is considered as a major cause of health threat. In this work, we have taken into account the similarity between TcPRAC and CdPRAC enzymes to design new inhibitors of CdPRAC. Starting from (E) 4-oxopent-2-enoic acid TcPRAC irreversible inhibitors, we synthesized 4-aryl substituted analogs and evaluated their CdPRAC enzymatic inhibition against eleven strains of C. difficile. This study resulted in promising candidates and allowed for identification of (E)-4-(3-bromothiophen-2-yl)-4-oxobut-2-enoic acid 20 that was chosen for complementary in vivo studies and did not reveal in vivo toxicity.


Assuntos
Isomerases de Aminoácido , Antibacterianos , Clostridioides difficile , Isomerases de Aminoácido/antagonistas & inibidores , Antibacterianos/farmacologia , Clostridioides difficile/efeitos dos fármacos , Prolina
16.
J Exp Med ; 176(3): 751-60, 1992 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-1380976

RESUMO

FK-506 inhibits Ca(2+)-dependent transcription of lymphokine genes in T cells, and thereby acts as a powerful immunosuppressant. However, its potential therapeutic applications may be seriously limited by several side effects, including nephrotoxicity and neurotoxicity. At present, it is unclear whether these immunosuppressive and toxic effects result from interference with related biochemical processes. FK-506 is known to interact with FK-binding protein-12 (FKBP-12), an abundant cytosolic protein with cis-trans peptidyl-prolyl isomerase activity (PPIase) activity. Because rapamycin (RAP) similarly binds to FKBP-12, although it acts in a manner different from FK-506, by inhibiting T cell responses to lymphokines, such an interaction with FKBP-12 is not sufficient to mediate immunosuppression. Recently, it was found that the complex of FKBP-12 with FK-506, but not with RAP, inhibits the phosphatase activity of calcineurin. Here, we used L-685,818, the C18-hydroxy, C21-ethyl derivative of FK-506, to explore further the role of FKBP-12 in the immunosuppressive and toxic actions of FK-506. Although L-685,818 bound with high affinity to FKBP-12 and inhibited its PPIase activity, it did not suppress T cell activation, and, when complexed with FKBP-12, did not affect calcineurin phosphatase activity. However, L-685,818 was a potent antagonist of the immunosuppressive activity of both FK-506 and RAP. Moreover, L-685,818 did not induce any toxicity in dogs and rats or in a mouse model of acute FK-506 nephrotoxicity, but it blocked the effect of FK-506 in this model. Therefore, FK-506 toxicity involves the disruption of biochemical mechanisms related to those implicated in T cell activation. Like immunosuppression, this toxicity is not due to the inhibition of the PPIase activity of FKBP-12, but may be linked to the inhibition of the phosphatase activity of calcineurin by the drug FKBP-12 complex.


Assuntos
Imunossupressores/farmacologia , Polienos/antagonistas & inibidores , Tacrolimo/análogos & derivados , Tacrolimo/toxicidade , Isomerases de Aminoácido/antagonistas & inibidores , Animais , Calcineurina , Proteínas de Ligação a Calmodulina/antagonistas & inibidores , Proteínas de Ligação a Calmodulina/metabolismo , Proteínas de Transporte/antagonistas & inibidores , Proteínas de Transporte/metabolismo , Feminino , Ativação Linfocitária , Camundongos , Camundongos Endogâmicos BALB C , Camundongos Endogâmicos C57BL , Peptidilprolil Isomerase , Fosfoproteínas Fosfatases/antagonistas & inibidores , Fosfoproteínas Fosfatases/metabolismo , Sirolimo , Linfócitos T/imunologia , Tacrolimo/antagonistas & inibidores , Tacrolimo/farmacologia , Proteínas de Ligação a Tacrolimo
17.
Electrophoresis ; 31(16): 2831-7, 2010 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-20665524

RESUMO

Isomerases involved in the metabolism of D/L-amino acids represent promising therapeutic targets for treatment of disease. Herein, we report a tunable platform for the assessment of enzymatic kinetics involving amino acid isomerization by CE that offers improved selectivity and sensitivity over traditional methods. Enzyme activity and competition assays were evaluated for various hydroxyproline diastereoisomers, proline enantiomers and their structural analogs using 4-hydroxyproline-2-epimerase as a model system. In this work, pyrrole 2-carboxylic acid was found to be a selective inhibitor of 4-hydroxyproline-2-epimerase with a half-maximal inhibition concentration of (2.3 + or - 0.1) mM. Reliable methods for unambiguous characterization of amino acid isomerases are required for the screening of novel inhibitors with epimerase and/or racemase activity.


Assuntos
Isomerases de Aminoácido/metabolismo , Pseudomonas aeruginosa/enzimologia , Isomerases de Aminoácido/antagonistas & inibidores , Isomerases de Aminoácido/isolamento & purificação , Proteínas de Bactérias/antagonistas & inibidores , Proteínas de Bactérias/isolamento & purificação , Proteínas de Bactérias/metabolismo , Fibrose Cística/patologia , Eletroforese Capilar/métodos , Inibidores Enzimáticos/farmacologia , Humanos , Hidroxiprolina/metabolismo , Cinética , Prolina/metabolismo , Pseudomonas aeruginosa/patogenicidade , Sensibilidade e Especificidade
18.
ChemMedChem ; 15(4): 376-384, 2020 02 17.
Artigo em Inglês | MEDLINE | ID: mdl-31876113

RESUMO

Glutamate racemases (GR) are members of the family of bacterial enzymes known as cofactor-independent racemases and epimerases and catalyze the stereoinversion of glutamate. D-amino acids are universally important for the proper construction of viable bacterial cell walls, and thus have been repeatedly validated as attractive targets for novel antimicrobial drug design. Significant aspects of the mechanism of this challenging stereoinversion remain unknown. The current study employs a combination of MD and QM/MM computational approaches to show that the GR from H. pylori must proceed via a pre-activation step, which is dependent on the enzyme's flexibility. This mechanism is starkly different from previously proposed mechanisms. These findings have immediate pharmaceutical relevance, as the H. pylori GR enzyme is a very attractive allosteric drug target. The results presented in this study offer a distinctly novel understanding of how AstraZeneca's lead series of inhibitors cripple the H. pylori GR's native motions, via prevention of this critical chemical pre-activation step. Our experimental studies, using SPR, fluorescence and NMR WaterLOGSY, show that H. pylori GR is not inhibited by the uncompetitive mechanism originally put forward by Lundqvist et al.. The current study supports a deep connection between native enzyme motions and chemical reactivity, which has strong relevance to the field of allosteric drug discovery.


Assuntos
Isomerases de Aminoácido/antagonistas & inibidores , Inibidores Enzimáticos/farmacologia , Helicobacter pylori/efeitos dos fármacos , Simulação de Dinâmica Molecular , Regulação Alostérica/efeitos dos fármacos , Isomerases de Aminoácido/metabolismo , Antibacterianos/química , Antibacterianos/farmacologia , Relação Dose-Resposta a Droga , Inibidores Enzimáticos/química , Helicobacter pylori/enzimologia , Testes de Sensibilidade Microbiana , Estrutura Molecular , Relação Estrutura-Atividade
19.
Science ; 248(4957): 863-6, 1990 May 18.
Artigo em Inglês | MEDLINE | ID: mdl-1693013

RESUMO

The immunosuppressive agents cyclosporin A and FK506 inhibit the transcription of early T cell activation genes. The binding proteins for cyclosporin A and FK506, cyclophilin and FKBP, respectively, are peptidyl-prolyl-cis-trans isomerases, or rotamases. One proposed mechanism for rotamase catalysis by cyclophilin involves a tetrahedral adduct of an amide carbonyl and an enzyme-bound nucleophile. The potent FKBP rotamase inhibitor FK506 has a highly electrophilic carbonyl that is adjacent to an acyl-pipicolinyl (homoprolyl) amide bond. Such a functional group would be expected to form a stabilized, enzyme-bound tetrahedral adduct. Spectroscopic and chemical evidence reveals that the drug interacts noncovalently with its receptor, suggesting that the alpha-keto amid of FK506 serves as a surrogate for the twisted amide of a bound peptide substrate.


Assuntos
Isomerases de Aminoácido/antagonistas & inibidores , Antibacterianos/farmacologia , Imunossupressores , Antibacterianos/metabolismo , Sítios de Ligação , Proteínas de Transporte/antagonistas & inibidores , Proteínas de Transporte/metabolismo , Fenômenos Químicos , Química , Clonagem Molecular , Ciclosporinas/metabolismo , Ciclosporinas/farmacologia , Escherichia coli/genética , Expressão Gênica , Ativação Linfocitária , Espectroscopia de Ressonância Magnética , Estrutura Molecular , Peptidilprolil Isomerase , Proteínas Recombinantes , Linfócitos T/imunologia , Tacrolimo
20.
Science ; 274(5293): 1715-7, 1996 Dec 06.
Artigo em Inglês | MEDLINE | ID: mdl-8939863

RESUMO

The Hsp90 heat shock protein of eukaryotic cells regulates the activity of proteins involved in signal transduction pathways and may direct intracellular protein folding in general. Hsp90 performs at least part of its function in a complex with a specific set of partner proteins that include members of the prolyl isomerase family. The properties of the major components of the Hsp90 complex were examined through the use of in vitro protein folding assays. Two of the components, FKBP52 and p23, functioned as mechanistically distinct molecular chaperones. These results suggest the existence of a super-chaperone complex in the cytosol of eukaryotic cells.


Assuntos
Proteínas de Transporte/fisiologia , Citrato (si)-Sintase/química , Proteínas de Ligação a DNA/fisiologia , Proteínas de Choque Térmico HSP90/fisiologia , Proteínas de Choque Térmico/fisiologia , Chaperonas Moleculares/fisiologia , Fosfoproteínas/fisiologia , Dobramento de Proteína , Isomerases de Aminoácido/antagonistas & inibidores , Isomerases de Aminoácido/metabolismo , Proteínas de Transporte/antagonistas & inibidores , Proteínas de Transporte/metabolismo , Proteínas de Transporte/farmacologia , Proteínas de Ligação a DNA/metabolismo , Proteínas de Ligação a DNA/farmacologia , Proteínas de Drosophila , Inibidores Enzimáticos/farmacologia , Proteínas de Choque Térmico HSP90/metabolismo , Proteínas de Choque Térmico/metabolismo , Proteínas de Choque Térmico/farmacologia , Oxirredutases Intramoleculares , Janus Quinases , Chaperonas Moleculares/metabolismo , Chaperonas Moleculares/farmacologia , Peptidilprolil Isomerase , Fosfoproteínas/metabolismo , Fosfoproteínas/farmacologia , Polienos/farmacologia , Prostaglandina-E Sintases , Desnaturação Proteica , Proteínas Tirosina Quinases/metabolismo , Proteínas Tirosina Quinases/farmacologia , Proteínas Recombinantes/metabolismo , Sirolimo , Proteínas de Ligação a Tacrolimo , Temperatura , Fatores de Transcrição
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