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1.
Proc Natl Acad Sci U S A ; 119(26): e2122897119, 2022 06 28.
Artigo em Inglês | MEDLINE | ID: mdl-35700355

RESUMO

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolves rapidly under the pressure of host immunity, as evidenced by waves of emerging variants despite effective vaccinations, highlighting the need for complementing antivirals. We report that targeting a pyrimidine synthesis enzyme restores inflammatory response and depletes the nucleotide pool to impede SARS-CoV-2 infection. SARS-CoV-2 deploys Nsp9 to activate carbamoyl-phosphate synthetase, aspartate transcarbamoylase, and dihydroorotase (CAD) that catalyzes the rate-limiting steps of the de novo pyrimidine synthesis. Activated CAD not only fuels de novo nucleotide synthesis but also deamidates RelA. While RelA deamidation shuts down NF-κB activation and subsequent inflammatory response, it up-regulates key glycolytic enzymes to promote aerobic glycolysis that provides metabolites for de novo nucleotide synthesis. A newly synthesized small-molecule inhibitor of CAD restores antiviral inflammatory response and depletes the pyrimidine pool, thus effectively impeding SARS-CoV-2 replication. Targeting an essential cellular metabolic enzyme thus offers an antiviral strategy that would be more refractory to SARS-CoV-2 genetic changes.


Assuntos
Antivirais , Aspartato Carbamoiltransferase , Tratamento Farmacológico da COVID-19 , Carbamoil Fosfato Sintase (Glutamina-Hidrolizante) , Di-Hidro-Orotase , Inibidores Enzimáticos , Pirimidinas , SARS-CoV-2 , Replicação Viral , Animais , Antivirais/farmacologia , Antivirais/uso terapêutico , Aspartato Carbamoiltransferase/antagonistas & inibidores , Carbamoil Fosfato Sintase (Glutamina-Hidrolizante)/antagonistas & inibidores , Di-Hidro-Orotase/antagonistas & inibidores , Ativação Enzimática/efeitos dos fármacos , Inibidores Enzimáticos/farmacologia , Inibidores Enzimáticos/uso terapêutico , Humanos , Inflamação/tratamento farmacológico , Camundongos , Pirimidinas/antagonistas & inibidores , Pirimidinas/biossíntese , Proteínas de Ligação a RNA/metabolismo , SARS-CoV-2/efeitos dos fármacos , SARS-CoV-2/fisiologia , Fator de Transcrição RelA/metabolismo , Proteínas não Estruturais Virais/metabolismo , Replicação Viral/efeitos dos fármacos
2.
Front Cell Infect Microbiol ; 12: 841833, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35310840

RESUMO

Malaria remains one of the most prominent and dangerous tropical diseases. While artemisinin and analogs have been used as first-line drugs for the past decades, due to the high mutational rate and rapid adaptation to the environment of the parasite, it remains urgent to develop new antimalarials. The pyrimidine biosynthesis pathway plays an important role in cell growth and proliferation. Unlike human host cells, the malarial parasite lacks a functional pyrimidine salvage pathway, meaning that RNA and DNA synthesis is highly dependent on the de novo synthesis pathway. Thus, direct or indirect blockage of the pyrimidine biosynthesis pathway can be lethal to the parasite. Aspartate transcarbamoylase (ATCase), catalyzes the second step of the pyrimidine biosynthesis pathway, the condensation of L-aspartate and carbamoyl phosphate to form N-carbamoyl aspartate and inorganic phosphate, and has been demonstrated to be a promising target both for anti-malaria and anti-cancer drug development. This is highlighted by the discovery that at least one of the targets of Torin2 - a potent, yet unselective, antimalarial - is the activity of the parasite transcarbamoylase. Additionally, the recent discovery of an allosteric pocket of the human homology raises the intriguing possibility of species selective ATCase inhibitors. We recently exploited the available crystal structures of the malarial aspartate transcarbamoylase to perform a fragment-based screening to identify hits. In this review, we summarize studies on the structure of Plasmodium falciparum ATCase by focusing on an allosteric pocket that supports the catalytic mechanisms.


Assuntos
Antimaláricos , Aspartato Carbamoiltransferase , Antimaláricos/química , Aspartato Carbamoiltransferase/antagonistas & inibidores , Aspartato Carbamoiltransferase/química , Ácido Aspártico/química , Cristalografia por Raios X , Descoberta de Drogas , Plasmodium falciparum/enzimologia , Proteínas de Protozoários/antagonistas & inibidores , Proteínas de Protozoários/química
3.
FEBS J ; 287(16): 3579-3599, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-31967710

RESUMO

Aspartate transcarbamoylase (ATCase) is a key enzyme which regulates and catalyzes the second step of de novo pyrimidine synthesis in all organisms. Escherichia coli ATCase is a prototypic enzyme regulated by both product feedback and substrate cooperativity, whereas human ATCase is a potential anticancer target. Through structural and biochemical analyses, we revealed that R167/130's loop region in ATCase serves as a gatekeeper for the active site, playing a new and unappreciated regulatory role in the catalytic cycle of ATCase. Based on virtual compound screening simultaneously targeting the new regulatory region and active site of human ATCase, two compounds were identified to exhibit strong inhibition of ATCase activity, proliferation of multiple cancer cell lines, and growth of xenograft tumors. Our work has not only revealed a previously unknown regulatory region of ATCase that helps uncover the catalytic and regulatory mechanism of ATCase, but also successfully guided the identification of new ATCase inhibitors for anticancer drug development using a dual-targeting strategy. DATABASE: Structure data are available in Protein Data Bank under the accession numbers: 6KJ7 (G166P ecATCase), 6KJ8 (G166P ecATCase-holo), 6KJ9 (G128/130A ecATCase), and 6KJA (G128/130A ecATCase-holo).


Assuntos
Aspartato Carbamoiltransferase/antagonistas & inibidores , Domínio Catalítico , Inibidores Enzimáticos/farmacologia , Simulação de Dinâmica Molecular , Regulação Alostérica , Sequência de Aminoácidos , Animais , Antineoplásicos/química , Antineoplásicos/farmacologia , Aspartato Carbamoiltransferase/química , Aspartato Carbamoiltransferase/metabolismo , Biocatálise/efeitos dos fármacos , Linhagem Celular Tumoral , Sobrevivência Celular/efeitos dos fármacos , Cristalografia por Raios X , Inibidores Enzimáticos/química , Feminino , Células HeLa , Humanos , Camundongos Endogâmicos BALB C , Camundongos Nus , Estrutura Molecular , Homologia de Sequência de Aminoácidos , Ensaios Antitumorais Modelo de Xenoenxerto/métodos
4.
Gut ; 69(1): 158-167, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-30833451

RESUMO

OBJECTIVE: Hepatitis D virus (HDV) is a circular RNA virus coinfecting hepatocytes with hepatitis B virus. Chronic hepatitis D results in severe liver disease and an increased risk of liver cancer. Efficient therapeutic approaches against HDV are absent. DESIGN: Here, we combined an RNAi loss-of-function and small molecule screen to uncover host-dependency factors for HDV infection. RESULTS: Functional screening unravelled the hypoxia-inducible factor (HIF)-signalling and insulin-resistance pathways, RNA polymerase II, glycosaminoglycan biosynthesis and the pyrimidine metabolism as virus-hepatocyte dependency networks. Validation studies in primary human hepatocytes identified the carbamoyl-phosphatesynthetase 2, aspartate transcarbamylase and dihydroorotase (CAD) enzyme and estrogen receptor alpha (encoded by ESR1) as key host factors for HDV life cycle. Mechanistic studies revealed that the two host factors are required for viral replication. Inhibition studies using N-(phosphonoacetyl)-L-aspartic acid and fulvestrant, specific CAD and ESR1 inhibitors, respectively, uncovered their impact as antiviral targets. CONCLUSION: The discovery of HDV host-dependency factors elucidates the pathogenesis of viral disease biology and opens therapeutic strategies for HDV cure.


Assuntos
Aspartato Carbamoiltransferase/genética , Ácido Aspártico/análogos & derivados , Carbamoil Fosfato Sintase (Glutamina-Hidrolizante)/genética , Di-Hidro-Orotase/genética , Receptor alfa de Estrogênio/metabolismo , Fulvestranto/farmacologia , Hepatite D Crônica/tratamento farmacológico , Ácido Fosfonoacéticos/análogos & derivados , Pirimidinas/biossíntese , Antivirais/farmacologia , Aspartato Carbamoiltransferase/antagonistas & inibidores , Aspartato Carbamoiltransferase/metabolismo , Ácido Aspártico/farmacologia , Carbamoil Fosfato Sintase (Glutamina-Hidrolizante)/antagonistas & inibidores , Carbamoil Fosfato Sintase (Glutamina-Hidrolizante)/metabolismo , Linhagem Celular , Di-Hidro-Orotase/antagonistas & inibidores , Di-Hidro-Orotase/metabolismo , Antagonistas do Receptor de Estrogênio/farmacologia , Receptor alfa de Estrogênio/antagonistas & inibidores , Inativação Gênica , Hepatite D Crônica/genética , Hepatite D Crônica/metabolismo , Vírus Delta da Hepatite/fisiologia , Hepatócitos , Humanos , Subunidade alfa do Fator 1 Induzível por Hipóxia/metabolismo , Resistência à Insulina , Estágios do Ciclo de Vida , Mutação com Perda de Função , Ácido Fosfonoacéticos/farmacologia , Interferência de RNA , RNA Interferente Pequeno/genética , RNA Viral/metabolismo , Transdução de Sinais , Replicação Viral
5.
Artigo em Inglês | MEDLINE | ID: mdl-29723133

RESUMO

The pyrimidine de novo nucleotide synthesis consists of 6 sequential steps. Various inhibitors against these enzymes have been developed and evaluated in the clinic for their potential anticancer activity: acivicin inhibits carbamoyl-phosphate-synthase-II, N-(phosphonacetyl)-L- aspartate (PALA) inhibits aspartate-transcarbamylase, Brequinar sodium and dichloroallyl-lawsone (DCL) inhibit dihydroorotate-dehydrogenase, and pyrazofurin (PF) inhibits orotate-phosphoribosyltransferase. We compared their growth inhibition against 3 cell lines from head-and-neck-cancer (HEP-2, UMSCC-14B and UMSCC-14C) and related the sensitivity to their effects on nucleotide pools. In all cell lines Brequinar and PF were the most active compounds with IC50 (50% growth inhibition) values between 0.06-0.37 µM, Acivicin was as potent (IC50s 0.26-1 µM), but DCL was 20-31-fold less active. PALA was most inactive (24-128 µM). At equitoxic concentrations, all pure antipyrimidine de novo inhibitors depleted UTP and CTP after 24 hr exposure, which was most pronounced for Brequinar (between 6-10% of UTP left, and 12-36% CTP), followed by DCL and PF, which were almost similar (6-16% UTP and 12-27% CTP), while PALA was the least active compound (10-70% UTP and 13-68% CTP). Acivicin is a multi-target inhibitor of more glutamine requiring enzymes (including GMP synthetase) and no decrease of UTP was found, but a pronounced decrease in GTP (31-72% left). In conclusion, these 5 inhibitors of the pyrimidine de novo nucleotide synthesis varied considerably in their efficacy and effect on pyrimidine nucleotide pools. Inhibitors of DHO-DH were most effective suggesting a primary role of this enzyme in controlling pyrimidine nucleotide pools.


Assuntos
Antineoplásicos/farmacologia , Compostos de Bifenilo/farmacologia , Carcinoma de Células Escamosas/metabolismo , Neoplasias de Cabeça e Pescoço/metabolismo , Nucleotídeos de Purina/antagonistas & inibidores , Nucleotídeos de Pirimidina/antagonistas & inibidores , Ribonucleosídeos/farmacologia , Amidas , Aspartato Carbamoiltransferase/antagonistas & inibidores , Ácido Aspártico/análogos & derivados , Ácido Aspártico/farmacologia , Carbamoil Fosfato Sintase (Glutamina-Hidrolizante)/antagonistas & inibidores , Linhagem Celular Tumoral , Di-Hidro-Orotato Desidrogenase , Humanos , Isoxazóis/farmacologia , Naftoquinonas/farmacologia , Orotato Fosforribosiltransferase/antagonistas & inibidores , Oxirredutases atuantes sobre Doadores de Grupo CH-CH/antagonistas & inibidores , Ácido Fosfonoacéticos/análogos & derivados , Ácido Fosfonoacéticos/farmacologia , Nucleotídeos de Purina/biossíntese , Pirazóis , Nucleotídeos de Pirimidina/biossíntese , Ribose
6.
Biochem Biophys Res Commun ; 497(3): 835-842, 2018 03 11.
Artigo em Inglês | MEDLINE | ID: mdl-29476738

RESUMO

Aspartate transcarbamoylase catalyzes the second step of de-novo pyrimidine biosynthesis. As malarial parasites lack pyrimidine salvage machinery and rely on de-novo production for growth and proliferation, this pathway is a target for drug discovery. Previously, an apo crystal structure of aspartate transcarbamoylase from Plasmodium falciparum (PfATC) in its T-state has been reported. Here we present crystal structures of PfATC in the liganded R-state as well as in complex with the novel inhibitor, 2,3-napthalenediol, identified by high-throughput screening. Our data shows that 2,3-napthalediol binds in close proximity to the active site, implying an allosteric mechanism of inhibition. Furthermore, we report biophysical characterization of 2,3-napthalenediol. These data provide a promising starting point for structure based drug design targeting PfATC and malarial de-novo pyrimidine biosynthesis.


Assuntos
Antiparasitários/química , Antiparasitários/farmacologia , Aspartato Carbamoiltransferase/antagonistas & inibidores , Plasmodium falciparum/enzimologia , Aspartato Carbamoiltransferase/química , Aspartato Carbamoiltransferase/metabolismo , Domínio Catalítico/efeitos dos fármacos , Cristalografia por Raios X , Descoberta de Drogas , Inibidores Enzimáticos/química , Inibidores Enzimáticos/farmacologia , Humanos , Malária Falciparum/tratamento farmacológico , Malária Falciparum/parasitologia , Simulação de Acoplamento Molecular , Plasmodium falciparum/química , Plasmodium falciparum/efeitos dos fármacos
7.
Structure ; 24(7): 1081-94, 2016 07 06.
Artigo em Inglês | MEDLINE | ID: mdl-27265852

RESUMO

CAD, the multienzymatic protein that initiates and controls de novo synthesis of pyrimidines in animals, associates through its aspartate transcarbamoylase (ATCase) domain into particles of 1.5 MDa. Despite numerous structures of prokaryotic ATCases, we lack structural information on the ATCase domain of CAD. Here, we report the structure and functional characterization of human ATCase, confirming the overall similarity with bacterial homologs. Unexpectedly, human ATCase exhibits cooperativity effects that reduce the affinity for the anti-tumoral drug PALA. Combining structural, mutagenic, and biochemical analysis, we identified key elements for the necessary regulation and transmission of conformational changes leading to cooperativity between subunits. Mutation of one of these elements, R2024, was recently found to cause the first non-lethal CAD deficit. We reproduced this mutation in human ATCase and measured its effect, demonstrating that this arginine is part of a molecular switch that regulates the equilibrium between low- and high-affinity states for the ligands.


Assuntos
Aspartato Carbamoiltransferase/química , Antineoplásicos/farmacologia , Aspartato Carbamoiltransferase/antagonistas & inibidores , Aspartato Carbamoiltransferase/metabolismo , Ácido Aspártico/análogos & derivados , Ácido Aspártico/farmacologia , Domínio Catalítico , Inibidores Enzimáticos/farmacologia , Humanos , Ácido Fosfonoacéticos/análogos & derivados , Ácido Fosfonoacéticos/farmacologia
8.
J Biomol Struct Dyn ; 32(4): 591-601, 2014 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-23663010

RESUMO

Enzymes involved in the pyrimidine biosynthesis pathway have become an important target for the pharmacological intervention. One among those enzymes, Aspartate Trans Carbamoylase (ATCase), catalyses the condensation of aspartate and carbamoyl phosphate to form N-carbamoyl-l-aspartate and inorganic phosphate. The present study provides the molecular insights into the enzyme ATCase. The three-dimensional structure of ATCase from Thermus thermophilus HB8 was modeled based on the crystal structure of ATCase in Pyrococcus abyssi (PDB ID:1ML4). Molecular dynamics simulation was performed to identify the conformational stability of TtATCase with and without its ligand complexes. Based on the pharmacokinetic properties and the glide-docking scores of ligands from four databases (Maybridge, Binding, Asinex and Technology for Organic Synthesis (TOS laboratory) for the screening of ligands, we identified four potential ligand molecules for TtATCase. From the molecular docking results, we proposed that the residues Thr53, Arg104, and Gln219 are consistently involved in strong hydrogen-bonding interactions and play a vital role in the TtATCase activity. From the results of molecular dynamics simulation, the ligand molecules are found to bind appropriately to the target enzyme. However, the structure of TtATCase needs to be determined experimentally to confirm this.


Assuntos
Aspartato Carbamoiltransferase/química , Modelos Moleculares , Thermus thermophilus/enzimologia , Sequência de Aminoácidos , Aspartato Carbamoiltransferase/antagonistas & inibidores , Aspartato Carbamoiltransferase/metabolismo , Sítios de Ligação , Domínio Catalítico , Inibidores Enzimáticos/química , Inibidores Enzimáticos/farmacologia , Ensaios de Triagem em Larga Escala , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Dados de Sequência Molecular , Ligação Proteica , Conformação Proteica , Pirimidinas/metabolismo , Alinhamento de Sequência , Interface Usuário-Computador
9.
Biochemistry ; 51(36): 7128-37, 2012 Sep 11.
Artigo em Inglês | MEDLINE | ID: mdl-22906065

RESUMO

Escherichia coli aspartate transcarbamoylase (ATCase) allosterically regulates pyrimidine nucleotide biosynthesis. The enzyme is inhibited by CTP and can be further inhibited by UTP, although UTP alone has little or no influence on activity; however, the mechanism for the synergistic inhibition is still unknown. To determine how UTP is able to synergistically inhibit ATCase in the presence of CTP, we determined a series of X-ray structures of ATCase·nucleotide complexes. Analysis of the X-ray structures revealed that (1) CTP and dCTP bind in a very similar fashion, (2) UTP, in the presence of dCTP or CTP, binds at a site that does not overlap the CTP/dCTP site, and (3) the triphosphates of the two nucleotides are parallel to each other with a metal ion, in this case Mg(2+), coordinated between the ß- and γ-phosphates of the two nucleotides. Kinetic experiments showed that the presence of a metal ion such as Mg(2+) is required for synergistic inhibition. Together, these results explain how the binding of UTP can enhance the binding of CTP and why UTP binds more tightly in the presence of CTP. A mechanism for the synergistic inhibition of ATCase is proposed in which the presence of UTP stabilizes the T state even more than CTP alone. These results also call into question many of the past kinetic and binding experiments with ATCase with nucleotides as the presence of metal contamination was not considered important.


Assuntos
Aspartato Carbamoiltransferase/química , Aspartato Carbamoiltransferase/metabolismo , Escherichia coli/enzimologia , Magnésio/metabolismo , Regulação Alostérica/efeitos dos fármacos , Aspartato Carbamoiltransferase/antagonistas & inibidores , Domínio Catalítico/efeitos dos fármacos , Nucleotídeos de Desoxicitosina/metabolismo , Nucleotídeos de Desoxicitosina/farmacologia , Sinergismo Farmacológico , Inibidores Enzimáticos/metabolismo , Inibidores Enzimáticos/farmacologia , Modelos Moleculares , Especificidade por Substrato , Uridina Trifosfato/metabolismo
10.
Gastroenterology ; 142(7): 1483-92.e6, 2012 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-22387394

RESUMO

BACKGROUND & AIMS: Polymorphisms that reduce the function of nucleotide-binding oligomerization domain (NOD)2, a bacterial sensor, have been associated with Crohn's disease (CD). No proteins that regulate NOD2 activity have been identified as selective pharmacologic targets. We sought to discover regulators of NOD2 that might be pharmacologic targets for CD therapies. METHODS: Carbamoyl phosphate synthetase/aspartate transcarbamylase/dihydroorotase (CAD) is an enzyme required for de novo pyrimidine nucleotide synthesis; it was identified as a NOD2-interacting protein by immunoprecipitation-coupled mass spectrometry. CAD expression was assessed in colon tissues from individuals with and without inflammatory bowel disease by immunohistochemistry. The interaction between CAD and NOD2 was assessed in human HCT116 intestinal epithelial cells by immunoprecipitation, immunoblot, reporter gene, and gentamicin protection assays. We also analyzed human cell lines that express variants of NOD2 and the effects of RNA interference, overexpression and CAD inhibitors. RESULTS: CAD was identified as a NOD2-interacting protein expressed at increased levels in the intestinal epithelium of patients with CD compared with controls. Overexpression of CAD inhibited NOD2-dependent activation of nuclear factor κB and p38 mitogen-activated protein kinase, as well as intracellular killing of Salmonella. Reduction of CAD expression or administration of CAD inhibitors increased NOD2-dependent signaling and antibacterial functions of NOD2 variants that are and are not associated with CD. CONCLUSIONS: The nucleotide synthesis enzyme CAD is a negative regulator of NOD2. The antibacterial function of NOD2 variants that have been associated with CD increased in response to pharmacologic inhibition of CAD. CAD is a potential therapeutic target for CD.


Assuntos
Aspartato Carbamoiltransferase/fisiologia , Carbamoil Fosfato Sintase (Glutamina-Hidrolizante)/fisiologia , Doença de Crohn/imunologia , Desoxirribonucleases/fisiologia , Di-Hidro-Orotase/fisiologia , Mucosa Intestinal/microbiologia , Proteína Adaptadora de Sinalização NOD2/imunologia , Aspartato Carbamoiltransferase/antagonistas & inibidores , Aspartato Carbamoiltransferase/uso terapêutico , Carbamoil Fosfato Sintase (Glutamina-Hidrolizante)/antagonistas & inibidores , Carbamoil Fosfato Sintase (Glutamina-Hidrolizante)/uso terapêutico , Linhagem Celular , Células Cultivadas , Doença de Crohn/tratamento farmacológico , Doença de Crohn/microbiologia , Di-Hidro-Orotase/antagonistas & inibidores , Di-Hidro-Orotase/uso terapêutico , Inibidores Enzimáticos/farmacologia , Humanos , Imuno-Histoquímica , Imunoprecipitação , Mucosa Intestinal/imunologia , Espectrometria de Massas , NF-kappa B/fisiologia , Proteína Adaptadora de Sinalização NOD2/fisiologia , Salmonella/crescimento & desenvolvimento , Salmonella/imunologia , Transdução de Sinais
11.
Bioorg Med Chem ; 17(22): 7680-9, 2009 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-19828320

RESUMO

The design, synthesis, and evaluation of a series of novel inhibitors of aspartate transcarbamoylase (ATCase) are reported. Several submicromolar phosphorus-containing inhibitors are described, but all-carboxylate compounds are inactive. Compounds were synthesized to probe the postulated cyclic transition-state of the enzyme-catalyzed reaction. In addition, the associated role of the protonation state at the phosphorus acid moiety was evaluated using phosphinic and carboxylic acids. Although none of the synthesized inhibitors is more potent than N-phosphonacetyl-l-aspartate (PALA), the compounds provide useful mechanistic information, as well as the basis for the design of future inhibitors and/or prodrugs.


Assuntos
Aspartato Carbamoiltransferase/antagonistas & inibidores , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/farmacologia , Aspartato Carbamoiltransferase/metabolismo , Ácido Aspártico/análogos & derivados , Ácido Aspártico/química , Sítios de Ligação/efeitos dos fármacos , Biocatálise/efeitos dos fármacos , Avaliação Pré-Clínica de Medicamentos , Inibidores Enzimáticos/metabolismo , Estabilidade Enzimática/efeitos dos fármacos , Escherichia coli/enzimologia , Modelos Químicos , Ácido Fosfonoacéticos/análogos & derivados , Ácido Fosfonoacéticos/química , Relação Estrutura-Atividade
12.
J Mol Biol ; 384(1): 206-18, 2008 Dec 05.
Artigo em Inglês | MEDLINE | ID: mdl-18823998

RESUMO

Here, we present a study of the conformational changes of the quaternary structure of Escherichia coli aspartate transcarbamoylase, as monitored by time-resolved small-angle X-ray scattering, upon combining with substrates, substrate analogs, and nucleotide effectors at temperatures between 5 and 22 degrees C, obviating the need for ethylene glycol. Time-resolved small-angle X-ray scattering time courses tracking the T-->R structural change after mixing with substrates or substrate analogs appeared to be a single phase under some conditions and biphasic under other conditions, which we ascribe to multiple ligation states producing a time course composed of multiple rates. Increasing the concentration of substrates up to a certain point increased the T-->R transition rate, with no further increase in rate beyond that point. Most strikingly, after addition of N-phosphonacetyl-l-aspartate to the enzyme, the transition rate was more than 1 order of magnitude slower than with the natural substrates. These results on the homotropic mechanism are consistent with a concerted transition between structural and functional states of either low affinity, low activity or high affinity, high activity for aspartate. Addition of ATP along with the substrates increased the rate of the transition from the T to the R state and also decreased the duration of the R-state steady-state phase. Addition of CTP or the combination of CTP/UTP to the substrates significantly decreased the rate of the T-->R transition and caused a shift in the enzyme population towards the T state even at saturating substrate concentrations. These results on the heterotropic mechanism suggest a destabilization of the T state by ATP and a destabilization of the R state by CTP and CTP/UTP, consistent with the T and R state crystallographic structures of aspartate transcarbamoylase in the presence of the heterotropic effectors.


Assuntos
Aspartato Carbamoiltransferase/antagonistas & inibidores , Aspartato Carbamoiltransferase/química , Escherichia coli/enzimologia , Regulação Alostérica/efeitos dos fármacos , Ácido Aspártico/metabolismo , Escherichia coli/efeitos dos fármacos , Etilenoglicol/farmacologia , Cinética , Ligantes , Nucleotídeos/farmacologia , Estrutura Quaternária de Proteína , Espalhamento a Baixo Ângulo , Especificidade por Substrato/efeitos dos fármacos , Temperatura , Termodinâmica , Fatores de Tempo , Difração de Raios X
13.
J Enzyme Inhib Med Chem ; 23(4): 483-92, 2008 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-18665995

RESUMO

Quinazolinone derivatives have been studied as both in vitro and in vivo inhibitors of aspartate transcarbamylase (ATCase). In vitro treatment of mammalian ATCase with four compounds revealed that they inhibited enzyme activity and that 2-phenyl-1,3-4(H)benzothiazin-4-thione was the most potent one. This compound acts as a noncompetitive inhibitor towards both aspartate and carbamoyl phosphate. The values of the inhibition constant (K(i)) indicate that this compound exerts a potent inhibitory effect upon ATCase activity. Moreover, in vivo treatment with different doses of these derivatives showed also an inhibitory effect upon ATCase, the relative activity being decreased by 40%-58% with a 1 mg dose. These data support the inhibition of ATCase by quinazolinone derivatives as a new type of inhibitor for the enzyme.


Assuntos
Antifúngicos/farmacologia , Aspartato Carbamoiltransferase/antagonistas & inibidores , Quinazolinonas/farmacologia , Animais , Antifúngicos/síntese química , Aspartato Carbamoiltransferase/metabolismo , Células Cultivadas , Cinética , Quinazolinonas/síntese química
14.
Biochem Biophys Res Commun ; 372(1): 40-4, 2008 Jul 18.
Artigo em Inglês | MEDLINE | ID: mdl-18477471

RESUMO

Aspartate carbamoyltransferase (ATCase) is a paradigm for allosteric regulation of enzyme activity. B-class ATCases display very similar homotropic allosteric behaviour, but differ extensively in their heterotropic patterns. The ATCase from the thermoacidophilic archaeon Sulfolobus acidocaldarius, for example, is strongly activated by its metabolic pathway's end product CTP, in contrast with Escherichia coli ATCase which is inhibited by CTP. To investigate the structural basis of this property, we have solved the crystal structure of the S. acidocaldarius enzyme in complex with CTP. Structure comparison reveals that effector binding does not induce similar large-scale conformational changes as observed for the E. coli ATCase. However, shifts in sedimentation coefficients upon binding of the bi-substrate analogue PALA show the existence of structurally distinct allosteric states. This suggests that the so-called "Nucleotide-Perturbation model" for explaining heterotropic allosteric behaviour, which is based on global conformational strain, is not a general mechanism of B-class ATCases.


Assuntos
Regulação Alostérica , Proteínas Arqueais/química , Aspartato Carbamoiltransferase/química , Citidina Trifosfato/química , Sulfolobus acidocaldarius/enzimologia , Aspartato Carbamoiltransferase/antagonistas & inibidores , Sítios de Ligação , Cristalografia por Raios X , Escherichia coli/enzimologia , Conformação Proteica
15.
Proteins ; 71(3): 1088-96, 2008 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-18004787

RESUMO

The mechanism of domain closure and the allosteric transition of Escherichia coli aspartate transcarbamoylase (ATCase) are investigated using L-Asn, in the presence of carbamoyl phosphate (CP), and N-phosphonacetyl-L-asparagine (PASN). ATCase was found to catalyze the carbamoylation of L-Asn with a K(m) of 122 mM and a maximal velocity 10-fold lower than observed with the natural substrate, L-Asp. As opposed to L-Asp, no cooperativity was observed with respect to L-Asn. Time-resolved small-angle X-ray scattering (SAXS) and fluorescence experiments revealed that the combination of CP and L-Asn did not convert the enzyme from the T to the R state. PASN was found to be a potent inhibitor of ATCase exhibiting a K(D) of 8.8 microM. SAXS experiments showed that PASN was able to convert the entire population of molecules to the R state. Analysis of the crystal structure of the enzyme in the presence of PASN revealed that the binding of PASN was similar to that of the R-state complex of ATCase with N-phosphonaceyl-L-aspartate, another potent inhibitor of the enzyme. The linking of CP and L-Asn into one molecule, PASN, correctly orients the asparagine moiety in the active site to induce domain closure and the allosteric transition. This entropic effect allows for the high affinity binding of PASN. However, the binding of L-Asn, in the presence of a saturating concentration of CP, does not induce the closure of the two domains of the catalytic chain, nor does the enzyme undergo the transition to the high-activity high- affinity R structure. These results imply that Arg229, which interacts with the beta-carboxylate of L-Asp, plays a critical role in the orientation of L-Asp in the active site and demonstrates the requirement of the beta-carboxylate of L-Asp in the mechanism of domain closure and the allosteric transition in E. coli ATCase.


Assuntos
Asparagina/análogos & derivados , Asparagina/química , Aspartato Carbamoiltransferase/química , Proteínas de Escherichia coli/química , Escherichia coli/enzimologia , Organofosfonatos/química , Asparagina/metabolismo , Aspartato Carbamoiltransferase/antagonistas & inibidores , Aspartato Carbamoiltransferase/metabolismo , Sítios de Ligação , Catálise , Cristalização , Cristalografia por Raios X , Proteínas de Escherichia coli/metabolismo , Holoenzimas/química , Holoenzimas/metabolismo , Organofosfonatos/metabolismo , Conformação Proteica , Espalhamento de Radiação , Raios X
16.
Bioorg Med Chem Lett ; 17(7): 2086-90, 2007 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-17336518

RESUMO

A series of inhibitors of the aspartate transcarbamoylase, an enzyme involved in pyrimidine nucleotide biosynthesis, has been synthesized. These inhibitors are analogues of a highly potent inhibitor of this enzyme, N-phosphonacetyl-L-aspartate (PALA). Analogues have been synthesized with modifications at the alpha- and beta-carboxylates as well as at the aspartate moiety. The ability of these compounds to inhibit the enzyme was evaluated. These studies, with functional group modified PALA derivatives, showed that amide groups can be a useful substitute of the carboxylate in order to reduce the charge on the molecule, and indicate that the relative position of the functional group in the beta-position is more critical than the nature of the functional group. Some of the molecules synthesized here are potent inhibitors of the enzyme.


Assuntos
Aspartato Carbamoiltransferase/antagonistas & inibidores , Ácido Aspártico/análogos & derivados , Ácido Aspártico/química , Química Farmacêutica/métodos , Escherichia coli/enzimologia , Ácido Fosfonoacéticos/análogos & derivados , Amidas/química , Ácido Aspártico/síntese química , Ácido Aspártico/farmacologia , Domínio Catalítico , Desenho de Fármacos , Cinética , Modelos Químicos , Conformação Molecular , Estrutura Molecular , Ácido Fosfonoacéticos/síntese química , Ácido Fosfonoacéticos/farmacologia , Relação Estrutura-Atividade , Especificidade por Substrato
17.
J Med Chem ; 49(20): 5932-8, 2006 Oct 05.
Artigo em Inglês | MEDLINE | ID: mdl-17004708

RESUMO

The synthesis of a new inhibitor, N-phosphonacetyl-L-isoasparagine (PALI), of Escherichia coli aspartate transcarbamoylase (ATCase) is reported, as well as structural studies of the enzyme.PALI complex. PALI was synthesized in 7 steps from beta-benzyl L-aspartate. The KD of PALI was 2 microM. Kinetics and small-angle X-ray scattering experiments showed that PALI can induce the cooperative transition of ATCase from the T to the R state. The X-ray structure of the enzyme.PALI complex showed 22 hydrogen-bonding interactions between the enzyme and PALI. The kinetic characterization and crystal structure of the ATCase.PALI complex also provides detailed information regarding the importance of the alpha-carboxylate for the binding of the substrate aspartate.


Assuntos
Asparagina/análogos & derivados , Aspartato Carbamoiltransferase/antagonistas & inibidores , Aspartato Carbamoiltransferase/química , Escherichia coli/enzimologia , Organofosfonatos/síntese química , Asparagina/síntese química , Asparagina/química , Ácido Aspártico/análogos & derivados , Ácido Aspártico/química , Sítios de Ligação , Cristalografia por Raios X , Ligação de Hidrogênio , Cinética , Modelos Moleculares , Estrutura Molecular , Organofosfonatos/química , Ácido Fosfonoacéticos/análogos & derivados , Ácido Fosfonoacéticos/química
18.
Biochemistry ; 45(33): 10062-71, 2006 Aug 22.
Artigo em Inglês | MEDLINE | ID: mdl-16906764

RESUMO

Escherichia coli aspartate transcarbamoylase (ATCase) catalyzes the committed step in pyrimidine nucleotide biosynthesis, the reaction between carbamoyl phosphate (CP) and l-aspartate to form N-carbamoyl-l-aspartate and inorganic phosphate. The enzyme exhibits homotropic cooperativity and is allosterically regulated. Upon binding l-aspartate in the presence of a saturating concentration of CP, the enzyme is converted from the low-activity low-affinity T state to the high-activity high-affinity R state. The potent inhibitor N-phosphonacetyl-l-aspartate (PALA), which combines the binding features of Asp and CP into one molecule, has been shown to induce the allosteric transition to the R state. In the presence of only CP, the enzyme is the T structure with the active site primed for the binding of aspartate. In a structure of the enzyme-CP complex (T(CP)), two CP molecules were observed in the active site approximately 7A apart, one with high occupancy and one with low occupancy. The high occupancy site corresponds to the position for CP observed in the structure of the enzyme with CP and the aspartate analogue succinate bound. The position of the second CP is in a unique site and does not overlap with the aspartate binding site. As a means to generate a new class of inhibitors for ATCase, the domain-open T state of the enzyme was targeted. We designed, synthesized, and characterized three inhibitors that were composed of two phosphonacetamide groups linked together. These two phosphonacetamide groups mimic the positions of the two CP molecules in the T(CP) structure. X-ray crystal structures of ATCase-inhibitor complexes revealed that each of these inhibitors bind to the T state of the enzyme and occupy the active site area. As opposed to the binding of Asp in the presence of CP or PALA, these inhibitors are unable to initiate the global T to R conformational change. Although the best of these T-state inhibitors only has a K(i) value in the micromolar range, the structural information with respect to their mode of binding provides important information for the design of second generation inhibitors that will have even higher affinity for the active site of the T state of the enzyme.


Assuntos
Regulação Alostérica/efeitos dos fármacos , Aspartato Carbamoiltransferase/antagonistas & inibidores , Inibidores Enzimáticos/farmacologia , Escherichia coli/enzimologia , Regulação Alostérica/fisiologia , Aspartato Carbamoiltransferase/genética , Aspartato Carbamoiltransferase/metabolismo , Ácido Aspártico/análogos & derivados , Ácido Aspártico/metabolismo , Sítios de Ligação , Catálise , Cristalografia por Raios X , Escherichia coli/genética , Cinética , Modelos Moleculares , Compostos Organofosforados/química , Compostos Organofosforados/metabolismo , Fosfatos/química , Fosfatos/metabolismo , Espectrometria de Fluorescência
19.
Bioorg Med Chem ; 13(16): 4921-8, 2005 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-15975800

RESUMO

In this paper, we describe a short synthesis of N-(phosphonoacetyl)-L-aspartate (PALA) analogues. The mono- and difluorinated thioacetamide precursors were prepared in one step from methyl (diethoxyphosphono)di- and monofluoromethyldithioacetates 8 and 11 as starting materials. Antiproliferating properties on a L1210 strain and ATCase inhibition of these new compounds are disclosed. ThioPALA(FF) 5c showed a remarkable cytotoxic activity towards murine leukemia L1210, when used as tetraester.


Assuntos
Antineoplásicos/síntese química , Ácido Aspártico/análogos & derivados , Ácido Fosfonoacéticos/análogos & derivados , Animais , Antineoplásicos/farmacologia , Aspartato Carbamoiltransferase/antagonistas & inibidores , Ácido Aspártico/síntese química , Ácido Aspártico/farmacologia , Ensaios de Seleção de Medicamentos Antitumorais , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/farmacologia , Leucemia L1210/tratamento farmacológico , Ácido Fosfonoacéticos/síntese química , Ácido Fosfonoacéticos/farmacologia , Tioacetamida/síntese química , Tioacetamida/química
20.
Farmaco ; 60(6-7): 479-83, 2005.
Artigo em Inglês | MEDLINE | ID: mdl-15913614

RESUMO

Novel N-1-sulfonylpyrimidine derivatives have a strong antiproliferative activity and an ability to induce apoptosis in treated tumor cells. The purpose of this study was to elucidate the effects of two N-1-sulfonylpyrimidine nucleobases on catalytic activity of tumor cells' enzymes involved in DNA and RNA synthesis, and in de novo and salvage pyrimidine and purine syntheses. Investigations were performed in vitro on colon carcinoma cells (Caco2). The biosynthetic activity of the tumor cells' enzymes was determined using sensitive radio-assays. Enzyme activity in treated cells was calculated relative to untreated control cells. Both of the investigated compounds, 1-(p-toluenesulfonyl) cytosine (TsC) and 5-bromo-1-(methanesulfonyl) uracil (BMsU) inhibited activities of specific enzymes involved in nucleic acid synthesis. BMsU strongly inhibited activities of DNA polymerase alpha (53%), thymidine kinase (68%), thymidilate synthase (43%), and ribonucleotide reductase (46%). De novo biosynthesis of pyrimidine and purine was reduced by 20%. TsC was able to inhibit RNA polymerase (37%), orotate phosphoribosyltransferase (39%), uridine kinase (44%), ribonucleotid reductase (47%), and de novo purine synthesis (61%). Antitumor activity of 1-(p-toluenesulfonyl) cytosine (TsC) and 5-bromo-1-(methanesulfonyl) uracil (BMsU) is closely associated with their inhibitory activity on enzymes that play an important role in the metabolism of tumor cells.


Assuntos
Neoplasias do Colo/metabolismo , Pirimidinas/farmacologia , Sulfonas/farmacologia , Compostos de Tosil/farmacologia , Aspartato Carbamoiltransferase/antagonistas & inibidores , Aspartato Carbamoiltransferase/metabolismo , Células CACO-2 , Neoplasias do Colo/enzimologia , Neoplasias do Colo/patologia , DNA/biossíntese , DNA Polimerase I/antagonistas & inibidores , DNA Polimerase I/metabolismo , RNA Polimerases Dirigidas por DNA/antagonistas & inibidores , RNA Polimerases Dirigidas por DNA/metabolismo , Ensaios de Seleção de Medicamentos Antitumorais/métodos , Inibidores Enzimáticos/química , Inibidores Enzimáticos/farmacologia , Humanos , Mesilatos/química , Mesilatos/farmacologia , Orotato Fosforribosiltransferase/antagonistas & inibidores , Orotato Fosforribosiltransferase/metabolismo , Biossíntese de Proteínas/efeitos dos fármacos , Pirimidinas/química , Pirimidinas/metabolismo , Pirimidinas/uso terapêutico , RNA/biossíntese , Ribonucleotídeo Redutases/antagonistas & inibidores , Ribonucleotídeo Redutases/metabolismo , Sulfonas/metabolismo , Sulfonas/uso terapêutico , Timidina Quinase/antagonistas & inibidores , Timidina Quinase/metabolismo , Timidilato Sintase/antagonistas & inibidores , Timidilato Sintase/metabolismo , Compostos de Tosil/química , Uridina Quinase/antagonistas & inibidores , Uridina Quinase/metabolismo
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