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1.
Molecules ; 26(9)2021 Apr 25.
Artículo en Inglés | MEDLINE | ID: mdl-33923034

RESUMEN

Present in all organisms, DNA ligases catalyse the formation of a phosphodiester bond between a 3' hydroxyl and a 5' phosphate, a reaction that is essential for maintaining genome integrity during replication and repair. Eubacterial DNA ligases use NAD+ as a cofactor and possess low sequence and structural homology relative to eukaryotic DNA ligases which use ATP as a cofactor. These key differences enable specific targeting of bacterial DNA ligases as an antibacterial strategy. In this study, four small molecule accessible sites within functionally important regions of Escherichia coli ligase (EC-LigA) were identified using in silico methods. Molecular docking was then used to screen for small molecules predicted to bind to these sites. Eight candidate inhibitors were then screened for inhibitory activity in an in vitro ligase assay. Five of these (geneticin, chlorhexidine, glutathione (reduced), imidazolidinyl urea and 2-(aminomethyl)imidazole) showed dose-dependent inhibition of EC-LigA with half maximal inhibitory concentrations (IC50) in the micromolar to millimolar range (11-2600 µM). Two (geneticin and chlorhexidine) were predicted to bind to a region of EC-LigA that has not been directly investigated previously, raising the possibility that there may be amino acids within this region that are important for EC-LigA activity or that the function of essential residues proximal to this region are impacted by inhibitor interactions with this region. We anticipate that the identified small molecule binding sites and inhibitors could be pursued as part of an antibacterial strategy targeting bacterial DNA ligases.


Asunto(s)
ADN Ligasas/antagonistas & inhibidores , Inhibidores Enzimáticos/aislamiento & purificación , Escherichia coli/enzimología , Sitios de Unión/efectos de los fármacos , ADN Ligasas/química , Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/farmacología , Escherichia coli/efectos de los fármacos , Simulación del Acoplamiento Molecular
2.
Curr Med Chem ; 26(10): 1761-1787, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-29110590

RESUMEN

BACKGROUND: Antimicrobial resistance is found in all microorganisms and has become one of the biggest threats to global health. New antimicrobials with different action mechanisms are effective weapons to fight against antibiotic-resistance. OBJECTIVE: This review aims to find potential drugs which can be further developed into clinic practice and provide clues for developing more effective antimicrobials. METHODS: DNA replication universally exists in all living organisms and is a complicated process in which multiple enzymes are involved in. Enzymes in bacterial DNA replication of initiation and elongation phases bring abundant targets for antimicrobial development as they are conserved and indispensable. In this review, enzyme inhibitors of DNA helicase, DNA primase, topoisomerases, DNA polymerase and DNA ligase were discussed. Special attentions were paid to structures, activities and action modes of these enzyme inhibitors. RESULTS: Among these enzymes, type II topoisomerase is the most validated target with abundant inhibitors. For type II topoisomerase inhibitors (excluding quinolones), NBTIs and benzimidazole urea derivatives are the most promising inhibitors because of their good antimicrobial activity and physicochemical properties. Simultaneously, DNA gyrase targeted drugs are particularly attractive in the treatment of tuberculosis as DNA gyrase is the sole type II topoisomerase in Mycobacterium tuberculosis. Relatively, exploitation of antimicrobial inhibitors of the other DNA replication enzymes are primeval, in which inhibitors of topo III are even blank so far. CONCLUSION: This review demonstrates that inhibitors of DNA replication enzymes are abundant, diverse and promising, many of which can be developed into antimicrobials to deal with antibioticresistance.


Asunto(s)
Antibacterianos/farmacología , Farmacorresistencia Microbiana/efectos de los fármacos , Inhibidores de la Síntesis del Ácido Nucleico/farmacología , Inhibidores de Topoisomerasa II/farmacología , Antibacterianos/química , Bacterias/efectos de los fármacos , ADN Helicasas/antagonistas & inhibidores , ADN Ligasas/antagonistas & inhibidores , ADN Primasa/antagonistas & inhibidores , Humanos , Inhibidores de la Síntesis del Ácido Nucleico/química , Inhibidores de Topoisomerasa II/química
3.
PLoS Pathog ; 13(12): e1006784, 2017 12.
Artículo en Inglés | MEDLINE | ID: mdl-29287110

RESUMEN

Hepadnavirus covalently closed circular (ccc) DNA is the bona fide viral transcription template, which plays a pivotal role in viral infection and persistence. Upon infection, the non-replicative cccDNA is converted from the incoming and de novo synthesized viral genomic relaxed circular (rc) DNA, presumably through employment of the host cell's DNA repair mechanisms in the nucleus. The conversion of rcDNA into cccDNA requires preparation of the extremities at the nick/gap regions of rcDNA for strand ligation. After screening 107 cellular DNA repair genes, we herein report that the cellular DNA ligase (LIG) 1 and 3 play a critical role in cccDNA formation. Ligase inhibitors or functional knock down/out of LIG1/3 significantly reduced cccDNA production in an in vitro cccDNA formation assay, and in cccDNA-producing cells without direct effect on viral core DNA replication. In addition, transcomplementation of LIG1/3 in the corresponding knock-out or knock-down cells was able to restore cccDNA formation. Furthermore, LIG4, a component in non-homologous end joining DNA repair apparatus, was found to be responsible for cccDNA formation from the viral double stranded linear (dsl) DNA, but not rcDNA. In conclusion, we demonstrate that hepadnaviruses utilize the whole spectrum of host DNA ligases for cccDNA formation, which sheds light on a coherent molecular pathway of cccDNA biosynthesis, as well as the development of novel antiviral strategies for treatment of hepatitis B.


Asunto(s)
ADN Ligasas/metabolismo , ADN Circular/biosíntesis , ADN Viral/biosíntesis , Hepadnaviridae/metabolismo , Línea Celular , ADN Ligasa (ATP)/antagonistas & inhibidores , ADN Ligasa (ATP)/genética , ADN Ligasa (ATP)/metabolismo , ADN Ligasas/antagonistas & inhibidores , ADN Ligasas/genética , Reparación del ADN/genética , Técnicas de Silenciamiento del Gen , Técnicas de Inactivación de Genes , Células HEK293 , Células Hep G2 , Hepadnaviridae/genética , Hepadnaviridae/patogenicidad , Virus de la Hepatitis B/genética , Virus de la Hepatitis B/metabolismo , Virus de la Hepatitis B/patogenicidad , Hepatocitos/metabolismo , Hepatocitos/virología , Interacciones Huésped-Patógeno/genética , Interacciones Huésped-Patógeno/fisiología , Humanos , Redes y Vías Metabólicas , Proteínas de Unión a Poli-ADP-Ribosa/antagonistas & inhibidores , Proteínas de Unión a Poli-ADP-Ribosa/genética , Proteínas de Unión a Poli-ADP-Ribosa/metabolismo
4.
Molecules ; 22(1)2017 Jan 17.
Artículo en Inglés | MEDLINE | ID: mdl-28106753

RESUMEN

The DNA ligases, enzymes that seal breaks in the backbones of DNA, are essential for all organisms, however bacterial ligases essential for DNA replication use ß-nicotinamide adenine dinucleotide as their co-factor, whereas those that are essential in eukaryotes and viruses use adenosine-5'-triphosphate. This fact leads to the conclusion that NAD⁺-dependent DNA ligases in bacteria could be targeted by their co-factor specific inhibitors. The development of novel alternative medical strategies, including new drugs, are a top priority focus areas for tuberculosis research due to an increase in the number of multi-drug resistant as well as totally drug resistant tubercle bacilli strains. Here, through the use of a virtual high-throughput screen and manual inspection of the top 200 records, 23 compounds were selected for in vitro studies. The selected compounds were evaluated in respect to their Mycobacterium tuberculosis NAD⁺ DNA ligase inhibitory effect by a newly developed assay based on Genetic Analyzer 3500 Sequencer. The most effective agents (e.g., pinafide, mitonafide) inhibited the activity of M. tuberculosis NAD⁺-dependent DNA ligase A at concentrations of 50 µM. At the same time, the ATP-dependent (phage) DNA LigT4 was unaffected by the agents at concentrations up to 2 mM. The selected compounds appeared to also be active against actively growing tubercle bacilli in concentrations as low as 15 µM.


Asunto(s)
Antituberculosos/farmacología , ADN Ligasas/antagonistas & inhibidores , Mycobacterium tuberculosis/efectos de los fármacos , Naftalimidas/farmacología , Proteínas Bacterianas/antagonistas & inhibidores , Inhibidores Enzimáticos/farmacología , Ensayos Analíticos de Alto Rendimiento , Isoquinolinas/farmacología , Simulación del Acoplamiento Molecular , NAD
5.
Curr Pharm Des ; 23(14): 2117-2130, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-27784238

RESUMEN

With the serious problem of multiple drug resistance to antibiotics among pathogenic bacteria spreading across the world over the past 30 years, it is crucial to search for novel inhibitors with distinct modes of action from diverse chemical classes. NAD+-dependent DNA ligases (LigAs) are essential enzymes in bacteria, vital for DNA replication and repair. Additionally, LigAs exclusively exist in eubacteria and some viruses and are not found in humans. Those enzymes have therefore been identified as attractive antibacterial drug targets. In this review we explore the discovered inhibitors of LigA through high-throughput screening or virtual screening respectively and their further structure optimization.


Asunto(s)
Antibacterianos/farmacología , ADN Ligasas/antagonistas & inhibidores , Descubrimiento de Drogas , Inhibidores Enzimáticos/farmacología , NAD/metabolismo , Animales , Antibacterianos/química , ADN Ligasas/metabolismo , Relación Dosis-Respuesta a Droga , Evaluación Preclínica de Medicamentos , Inhibidores Enzimáticos/química , Ensayos Analíticos de Alto Rendimiento , Humanos , Estructura Molecular , Relación Estructura-Actividad
6.
Artículo en Inglés | MEDLINE | ID: mdl-26520366

RESUMEN

Ionizing radiation (IR) induces double strand breaks (DSBs) in cellular DNA, which if not repaired correctly can cause chromosome translocations leading to cell death or cancer. Incorrect joining of DNA ends generating chromosome translocations can be catalyzed either by the dominant DNA-PKcs-dependent, classical non-homologous end-joining (c-NHEJ), or by an alternative end-joining (alt-EJ) process, functioning as backup to abrogated c-NHEJ, or homologous recombination repair. Alt-EJ operates with slower kinetics as compared to c-NHEJ and generates larger alterations at the junctions; it is also considered crucial to chromosome translocation-formation. A recent report posits that this view only holds for rodent cells and that in human cells c-NHEJ is the main mechanism of chromosome translocation formation. Since this report uses designer nucleases that induce DSBs with unique characteristics in specific genomic locations and PCR to detect translocations, we revisit the issue using stochastically distributed DSBs induced in the human genome by IR during the G2-phase of the cell cycle. For visualization and analysis of chromosome translocations, which manifest as chromatid translocations in cells irradiated in G2, we employ classical cytogenetics. In wild-type cells, we observe a significant contribution of alt-EJ to translocation formation, as demonstrated by a yield-reduction after treatment with inhibitors of Parp, or of DNA ligases 1 and 3 (Lig1, Lig3). Notably, a nearly fourfold increase in translocation formation is seen in c-NHEJ mutants with defects in DNA ligase 4 (Lig4) that remain largely sensitive to inhibitors of Parp, and of Lig1/Lig3. We conclude that similar to rodent cells, chromosome translocation formation from randomly induced DSBs in human cells largely relies on alt-EJ. We discuss DSB localization in the genome, characteristics of the DSB and the cell cycle as potential causes of the divergent results generated with IR and designer nucleases.


Asunto(s)
Cromosomas Humanos/efectos de la radiación , Reparación del ADN por Unión de Extremidades , Fase G2/efectos de la radiación , Translocación Genética , Línea Celular , Análisis Citogenético , Roturas del ADN de Doble Cadena , Reparación del ADN por Unión de Extremidades/efectos de los fármacos , ADN Ligasa (ATP) , ADN Ligasas/antagonistas & inhibidores , ADN Ligasas/genética , ADN Ligasas/metabolismo , Fase G2/efectos de los fármacos , Células HCT116 , Humanos , Poli(ADP-Ribosa) Polimerasa-1 , Inhibidores de Poli(ADP-Ribosa) Polimerasas/farmacología , Poli(ADP-Ribosa) Polimerasas/genética , Poli(ADP-Ribosa) Polimerasas/metabolismo , Pirimidinas/farmacología , Bases de Schiff/farmacología , Translocación Genética/efectos de los fármacos
7.
Bioorg Med Chem Lett ; 25(22): 5172-7, 2015 Nov 15.
Artículo en Inglés | MEDLINE | ID: mdl-26463129

RESUMEN

Two novel compounds, pyridopyrimidines (1) and naphthyridines (2) were identified as potent inhibitors of bacterial NAD(+)-dependent DNA ligase (Lig) A in a fragment screening. SAR was guided by molecular modeling and X-ray crystallography. It was observed that the diaminonitrile pharmacophore made a key interaction with the ligase enzyme, specifically residues Glu114, Lys291, and Leu117. Synthetic challenges limited opportunities for diversification of the naphthyridine core, therefore most of the SAR was focused on a pyridopyrimidine scaffold. The initial diversification at R(1) improved both enzyme and cell potency. Further SAR developed at the R(2) position using the Negishi cross-coupling reaction provided several compounds, among these compounds 22g showed good enzyme potency and cellular potency.


Asunto(s)
Antibacterianos/farmacología , Proteínas Bacterianas/antagonistas & inhibidores , ADN Ligasas/antagonistas & inhibidores , NAD/metabolismo , Naftiridinas/farmacología , Pirimidinas/farmacología , Antibacterianos/síntesis química , Proteínas Bacterianas/química , ADN Ligasas/química , Haemophilus influenzae/efectos de los fármacos , Pruebas de Sensibilidad Microbiana , Naftiridinas/síntesis química , Pirimidinas/síntesis química , Staphylococcus aureus/efectos de los fármacos , Streptococcus pneumoniae/efectos de los fármacos , Relación Estructura-Actividad
8.
FEMS Microbiol Lett ; 362(21)2015 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-26420852

RESUMEN

DNA ligases play an essential role in many aspects of DNA metabolism in all three domains of life. The haloarchaeal organism Haloferax volcanii encodes both ATP- and NAD(+)-dependent DNA ligase enzymes designated LigA and LigN, respectively. Neither LigA nor LigN alone is required for cell viability but they share an essential function, most likely the ligation of Okazaki fragments during chromosome replication. Here we show that 2-(cyclopentyloxy)-5'-deoxyadenosine (referred to as CPOdA), originally developed as a inhibitor of bacterial NAD(+)-dependent DNA ligases, is a potent inhibitor of the growth of Hfx. volcanii cells expressing LigN alone, causing chromosome fragmentation and cell death, while cells expressing LigA are unaffected. Growth inhibition occurs at significantly lower CPOdA concentrations (MIC ≤ 50 ng ml(-1)) than those required for inhibition of bacterial growth (≥2 µg ml(-1)). CPOdA has the potential to become a vital tool in DNA replication and repair studies in this important model organism.


Asunto(s)
ADN Ligasas/antagonistas & inhibidores , Replicación del ADN/efectos de los fármacos , Inhibidores Enzimáticos/farmacología , Haloferax volcanii/enzimología , Haloferax volcanii/genética , ADN Ligasa (ATP) , Reparación del ADN/efectos de los fármacos , Desoxiadenosinas/farmacología , Haloferax volcanii/efectos de los fármacos , Haloferax volcanii/crecimiento & desarrollo , NAD/metabolismo
9.
Curr Med Chem ; 22(34): 3991-4028, 2015.
Artículo en Inglés | MEDLINE | ID: mdl-26295463

RESUMEN

About 500 NAD (P)-dependent enzymes in the cell use NAD (P) as a cofactor or a substrate. This family of broadly diversified enzymes is crucial for maintaining homeostasis of all living organisms. The NAD binding domain of these enzymes is conserved and it was believed that NAD mimics would not be of therapeutic value due to lack of selectivity. Consequently, only mycophenolic acid which selectively binds at the cofactor pocket of NAD-dependent IMP-dehydrogenase (IMPDH) has been approved as an immunosuppressant. Recently, it became clear that the NAD (P)-binding domain was structurally much more diversified than anticipated and numerous highly potent and selective inhibitors of NAD (P) dependent enzymes have been reported. It is likely, that as in the case of protein kinases inhibitors, inhibitors of NAD (P)-dependent enzymes would find soon their way to the clinic. In this review, recent developments of selective inhibitors of NAD-dependent human IMPDH, as well as inhibitors of IMPDHs from parasites, and from bacterial sources are reported. Therapies against Cryptosporidium parvum and the development of new antibiotics that are on the horizon will be discussed. New inhibitors of bacterial NAD-ligases, NAD-kinases, NMN-adenylyl transferases, as well as phosphoribosyl transferases are also described. Although none of these compounds has yet to be approved, the progress in revealing and understanding crucial factors that might allow for designing more potent and efficient drug candidates is enormous and highly encouraging.


Asunto(s)
Antineoplásicos/química , Inhibidores Enzimáticos/química , NAD/química , Antineoplásicos/farmacología , Antineoplásicos/uso terapéutico , Bacterias/efectos de los fármacos , Sitios de Unión , Supervivencia Celular/efectos de los fármacos , ADN Ligasas/antagonistas & inhibidores , ADN Ligasas/metabolismo , Inhibidores Enzimáticos/farmacología , Inhibidores Enzimáticos/uso terapéutico , Humanos , IMP Deshidrogenasa/antagonistas & inhibidores , IMP Deshidrogenasa/metabolismo , Simulación de Dinámica Molecular , NAD/farmacología , NAD/uso terapéutico , Neoplasias/tratamiento farmacológico , Fosfotransferasas (Aceptor de Grupo Alcohol)/antagonistas & inhibidores , Fosfotransferasas (Aceptor de Grupo Alcohol)/metabolismo
10.
Org Biomol Chem ; 13(22): 6380-98, 2015 Jun 14.
Artículo en Inglés | MEDLINE | ID: mdl-25974621

RESUMEN

We report the chemical synthesis and conformational analysis of a collection of 2-, 6- and 8-substituted derivatives of ß-NAD(+) and AMP, and their biochemical evaluation against NAD(+)-dependent DNA ligases from Escherichia coli and Mycobacterium tuberculosis. Bacterial DNA ligases are validated anti-microbial targets, and new strategies for their inhibition are therefore of considerable scientific and practical interest. Our study includes several pairs of ß-NAD(+) and AMP derivatives with the same substitution pattern at the adenine base. This has enabled the first direct comparison of co-substrate and inhibitor behaviour against bacterial DNA ligases. Our results suggest that an additional substituent in position 6 or 8 of the adenine base in ß-NAD(+) is detrimental for activity as either co-substrate or inhibitor. In contrast, substituents in position 2 are not only tolerated, but appear to give rise to a new mode of inhibition, which targets the conformational changes these DNA ligases undergo during catalysis. Using a molecular modelling approach, we highlight that these findings have important implications for our understanding of ligase mechanism and inhibition, and may provide a promising starting point for the rational design of a new class of inhibitors against NAD(+)-dependent DNA ligases.


Asunto(s)
Adenosina Monofosfato/farmacología , ADN Ligasas/antagonistas & inhibidores , Inhibidores Enzimáticos/farmacología , Escherichia coli/enzimología , Mycobacterium tuberculosis/enzimología , NAD/farmacología , Adenosina Monofosfato/síntesis química , Adenosina Monofosfato/química , Antibacterianos/síntesis química , Antibacterianos/química , Antibacterianos/farmacología , ADN Ligasas/aislamiento & purificación , ADN Ligasas/metabolismo , Relación Dosis-Respuesta a Droga , Inhibidores Enzimáticos/síntesis química , Inhibidores Enzimáticos/química , Escherichia coli/efectos de los fármacos , Modelos Moleculares , Conformación Molecular , Mycobacterium tuberculosis/efectos de los fármacos , NAD/síntesis química , NAD/química , Relación Estructura-Actividad
11.
Antimicrob Agents Chemother ; 59(7): 3736-47, 2015 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-25845868

RESUMEN

Lymphatic filarial nematodes maintain a mutualistic relationship with the endosymbiont Wolbachia. Depletion of Wolbachia produces profound defects in nematode development, fertility, and viability and thus has great promise as a novel approach for treating filarial diseases. NAD(+)-dependent DNA ligase is an essential enzyme of DNA replication, repair, and recombination. Therefore, in the present study, the antifilarial drug target potential of the NAD(+)-dependent DNA ligase of the Wolbachia symbiont of Brugia malayi (wBm-LigA) was investigated using dispiro-cycloalkanone compounds. Dispiro-cycloalkanone specifically inhibited the nick-closing and cohesive-end ligation activities of the enzyme without inhibiting human or T4 DNA ligase. The mode of inhibition was competitive with the NAD(+) cofactor. Docking studies also revealed the interaction of these compounds with the active site of the target enzyme. The adverse effects of these inhibitors were observed on adult and microfilarial stages of B. malayi in vitro, and the most active compounds were further monitored in vivo in jirds and mastomys rodent models. Compounds 1, 2, and 5 had severe adverse effects in vitro on the motility of both adult worms and microfilariae at low concentrations. Compound 2 was the best inhibitor, with the lowest 50% inhibitory concentration (IC50) (1.02 µM), followed by compound 5 (IC50, 2.3 µM) and compound 1 (IC50, 2.9 µM). These compounds also exhibited the same adverse effect on adult worms and microfilariae in vivo (P < 0.05). These compounds also tremendously reduced the wolbachial load, as evident by quantitative real-time PCR (P < 0.05). wBm-LigA thus shows great promise as an antifilarial drug target, and dispiro-cycloalkanone compounds show great promise as antifilarial lead candidates.


Asunto(s)
Brugia Malayi/microbiología , ADN Ligasas/antagonistas & inhibidores , Filaricidas/farmacología , Cetonas/farmacología , Compuestos de Espiro/farmacología , Wolbachia/efectos de los fármacos , Animales , Antibacterianos/farmacología , ADN Ligasa (ATP) , ADN Ligasas/efectos de los fármacos , Escherichia coli/genética , Escherichia coli/metabolismo , Gerbillinae , Cetonas/síntesis química , Masculino , Pruebas de Sensibilidad Microbiana , Modelos Moleculares , Simulación del Acoplamiento Molecular , Murinae/parasitología , Compuestos de Espiro/síntesis química , Simbiosis , Wolbachia/enzimología
12.
Org Biomol Chem ; 13(19): 5475-87, 2015 May 21.
Artículo en Inglés | MEDLINE | ID: mdl-25875403

RESUMEN

DNA ligases are critical components for DNA metabolism in all organisms. NAD(+)-dependent DNA ligases (LigA) found exclusively in bacteria and certain entomopoxviruses are drawing increasing attention as therapeutic targets as they differ in their cofactor requirement from ATP-dependent eukaryotic homologs. Due to the similarities in the cofactor binding sites of the two classes of DNA ligases, it is necessary to find determinants that can distinguish between them for the exploitation of LigA as an anti-bacterial target. In the present endeavour, we have synthesized and evaluated a series of tricyclic dihydrobenzoxazepine and tetracyclic indole derivatives for their ability to distinguish between bacterial and human DNA ligases. The in vivo inhibition assays that employed LigA deficient E. coli GR501 and S. typhimurium LT2 bacterial strains, rescued by ATP-dependent T4 DNA ligase or Mycobacterium tuberculosis NAD(+)-dependent DNA ligase (Mtb LigA), respectively, showed that the compounds can specifically inhibit bacterial LigA. The in vitro enzyme inhibition assays using purified MtbLigA, human DNA ligase I & T4 DNA ligase showed specific inhibition of MtbLigA at low micromolar range. Our results demonstrate that tricyclic dihydrobenzoxazepine and tetracyclic indole derivatives can distinguish between bacterial and human DNA ligases by ∼5-folds. In silico docking and enzyme inhibition assays identified that the compounds bind to the cofactor binding site and compete with the cofactor. Ethidium bromide displacement and gel-shift assays showed that the inhibitors do not exhibit any unwanted general interactions with the substrate DNA. These results set the stage for the detailed exploration of this compound class for development as antibacterials.


Asunto(s)
Bacterias/enzimología , ADN Ligasas/antagonistas & inhibidores , Dibenzoxazepinas/farmacología , Indoles/farmacología , Antibacterianos/farmacología , ADN/metabolismo , ADN Ligasa (ATP) , ADN Ligasas/metabolismo , Dibenzoxazepinas/síntesis química , Dibenzoxazepinas/química , Pruebas de Enzimas , Inhibidores Enzimáticos/síntesis química , Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/farmacología , Escherichia coli/enzimología , Humanos , Indoles/síntesis química , Indoles/química , Pruebas de Sensibilidad Microbiana , Simulación del Acoplamiento Molecular , Mycobacterium tuberculosis/enzimología , Salmonella typhimurium/enzimología
13.
J Recept Signal Transduct Res ; 35(1): 15-25, 2015 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-25055026

RESUMEN

Staphylococcus aureus has been recognized as an important human pathogen for more than 100 years. It is among the most important causative agent of human infections in the twenty-first century. DNA ligase is the main protein responsible for the replication of S. aureus. In order to control the replication mechanism, DNA ligase is a successive drug target, hence we have chosen this protein for this study. We performed virtual screening using ZINC database for identification of potent inhibitor against DNA ligase. Based on the scoring methods, we have selected best five compounds from the ZINC database. In order to improve the accuracy, selected compounds were subjected into Quantum Polarized Ligand Docking (QPLD) docking, for which the results showed high docking score, compared to glide docking score. QPLD is more accurate as it includes charges in the scoring function, which was not available in the glide docking. Binding energy calculation results also indicated that selected compounds have good binding capacity with the target protein. In addition, these compounds on screening have good absorption, distribution, metabolism, excretion and toxicity property. In this study, we identified few compounds that particularly work against DNA ligase protein, having better interaction phenomenon and it would help further the experimental analysis.


Asunto(s)
ADN Ligasas/antagonistas & inhibidores , Replicación del ADN/efectos de los fármacos , Infecciones Estafilocócicas/tratamiento farmacológico , Staphylococcus aureus/efectos de los fármacos , Secuencia de Aminoácidos , ADN Ligasas/genética , Humanos , Ligandos , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Conformación Proteica/efectos de los fármacos , Infecciones Estafilocócicas/microbiología , Staphylococcus aureus/enzimología , Staphylococcus aureus/patogenicidad
14.
BMC Res Notes ; 7: 287, 2014 May 09.
Artículo en Inglés | MEDLINE | ID: mdl-24885075

RESUMEN

BACKGROUND: DNA ligase seals the nicks in the phosphodiester backbone between Okazaki fragments during DNA replication. DNA ligase has an unusual Bi Ter Ping Pong kinetic mechanism. Its substrates in eubacteria are NAD+ and nicked DNA (nDNA). Its products are nicotinamide mononucleotide (NMN), adenosine 5'-monophosphate (AMP), and sealed DNA. Investigation of the kinetic mechanism and measurement of the kinetic constants of DNA ligase using steady-state kinetics would benefit from the availability of the complete steady-state rate equation, including terms for product concentrations and product-related kinetic constants, which has not previously been published. RESULTS: The rate equations for two possible Bi Ter kinetic mechanisms for DNA ligase, including products, are reported. The mechanisms differ according to whether the last two products, AMP and sealed DNA, are released in an ordered or rapid-equilibrium random (RER) manner. Steady-state kinetic studies of product inhibition by NMN and AMP were performed with Haemophilus influenzae NAD+-dependent DNA ligase. The complete rate equation enabled measurement of dissociation constants for NAD+, NMN, and AMP and eliminated one of 3 possible product release mechanisms. CONCLUSIONS: Steady-state kinetic product inhibition experiments and complete steady-state kinetic rate equations were used to measure dissociation constants of NAD+, NMN, and AMP and eliminate the possibility that AMP is the second product released in an ordered mechanism. Determining by steady-state kinetics whether the release of sealed DNA and AMP products goes by an ordered (AMP last off) or RER mechanism was shown to require a product inhibition study using sealed DNA.


Asunto(s)
ADN Ligasas/metabolismo , Haemophilus influenzae/enzimología , NAD/metabolismo , Adenosina Monofosfato , ADN Ligasa (ATP) , ADN Ligasas/antagonistas & inhibidores , Cinética , Análisis de los Mínimos Cuadrados , Mononucleótido de Nicotinamida/metabolismo , Dinámicas no Lineales
16.
J Chem Inf Model ; 54(3): 781-92, 2014 Mar 24.
Artículo en Inglés | MEDLINE | ID: mdl-24593844

RESUMEN

Human DNA ligases are enzymes that are indispensable for DNA replication and repair processes. Among the three human ligases, ligase I is attributed to the ligation of thousands of Okazaki fragments that are formed during lagging strand synthesis during DNA replication. Blocking ligation therefore can lead to the accumulation of thousands of single strands and subsequently double strand breaks in the DNA, which is lethal for the cells. The reports of the high expression level of ligase I protein in several cancer cells (versus the low ligase expression level and the low rate of division of most normal cells in the adult body) support the belief that ligase I inhibitors can target cancer cells specifically with minimum side effects to normal cells. Recent publications showing exciting data for a ligase IV inhibitor exhibiting antitumor activity in mouse models also strengthens the argument for ligases as valid antitumor targets. Keeping this in view, we performed a pharmacophore-based screening for potential ligase inhibitors in the Maybridge small molecule library and procured some of the top-ranking compounds for enzyme-based and cell-based in vitro screening. We report here the identification of novel ligase I inhibitors with potential anticancer activity against a colon cancer cell line.


Asunto(s)
Antineoplásicos/química , Antineoplásicos/farmacología , ADN Ligasas/antagonistas & inhibidores , Descubrimiento de Drogas , Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/farmacología , Línea Celular Tumoral , Proliferación Celular/efectos de los fármacos , ADN/metabolismo , ADN Ligasa (ATP) , ADN Ligasas/metabolismo , Humanos , Simulación del Acoplamiento Molecular , Neoplasias/tratamiento farmacológico , Neoplasias/enzimología
17.
Med Res Rev ; 34(3): 567-95, 2014 May.
Artículo en Inglés | MEDLINE | ID: mdl-23959747

RESUMEN

Living organisms belonging to all three domains of life, viz., eubacteria, archaeabacteria, and eukaryotes encode one or more DNA ligases. DNA ligases are indispensable in various DNA repair and replication processes and a deficiency or an inhibition of their activity can lead to accumulation of DNA damage and strand breaks. DNA damage, specially strand breaks at unsustainable levels can lead to replication block and/or cell death. DNA ligases as potential anticancer targets have been realized only recently. There is enough rationale to suggest that ligases have a tremendous potential for novel therapeutics including anticancer and antibacterial therapy, specially when the world is facing acute problems of drug resistance and chemotherapy failure, with an immediate need for new therapeutic targets. Here, we review the current state of the art in the development of human ligase inhibitors, their structures, molecular mechanisms, physiological effects, and their potential in future cancer therapy. Citing examples, we focus on strategies for improving the activity and specificity of existing and novel inhibitors by using structure-based rational approaches. In the end, we describe potential new sites on the ligase I protein that can be targeted for the development of novel inhibitors. This is the first comprehensive review to compile all known human ligase inhibitors and to provide a rationale for the further development of ligase inhibitors for cancer therapy.


Asunto(s)
ADN Ligasas/metabolismo , Neoplasias/enzimología , Neoplasias/terapia , Secuencia de Aminoácidos , ADN Ligasas/antagonistas & inhibidores , ADN Ligasas/química , Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/clasificación , Inhibidores Enzimáticos/farmacología , Humanos , Datos de Secuencia Molecular , Terapia Molecular Dirigida
18.
Bioorg Med Chem Lett ; 24(1): 360-6, 2014 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-24287382

RESUMEN

In an attempt to identify novel inhibitors of NAD(+)-dependent DNA ligase (LigA) that are not affected by a known resistance mutation in the adenosine binding pocket, a detailed analysis of the binding sites of a variety of bacterial ligases was performed. This analysis revealed several similarities to the adenine binding region of kinases, which enabled a virtual screen of known kinase inhibitors. From this screen, a thienopyridine scaffold was identified that was shown to inhibit bacterial ligase. Further characterization through structure and enzymology revealed the compound was not affected by a previously disclosed resistance mutation in Streptococcus pneumoniae LigA, Leu75Phe. A subsequent medicinal chemistry program identified substitutions that resulted in an inhibitor with moderate activity across various Gram-positive bacterial LigA enzymes.


Asunto(s)
ADN Ligasas/antagonistas & inhibidores , Inhibidores Enzimáticos/farmacología , Streptococcus pneumoniae/enzimología , ADN Ligasas/metabolismo , Relación Dosis-Respuesta a Droga , Inhibidores Enzimáticos/síntesis química , Inhibidores Enzimáticos/química , Modelos Moleculares , Estructura Molecular , Relación Estructura-Actividad
19.
Oncogene ; 32(14): 1784-93, 2013 Apr 04.
Artículo en Inglés | MEDLINE | ID: mdl-22641215

RESUMEN

Resistance to imatinib (IM) and other tyrosine kinase inhibitors (TKI)s is an increasing problem in leukemias caused by expression of BCR-ABL1. As chronic myeloid leukemia (CML) cell lines expressing BCR-ABL1 utilize an alternative non-homologous end-joining pathway (ALT NHEJ) to repair DNA double-strand breaks (DSB)s, we asked whether this repair pathway is a novel therapeutic target in TKI-resistant disease. Notably, the steady state levels of two ALT NHEJ proteins, poly-(ADP-ribose) polymerase 1 (PARP1) and DNA ligase IIIα, were increased in the BCR-ABL1-positive CML cell line K562 and, to a greater extent, in its imatinib-resistant (IMR) derivative. Incubation of these cell lines with a combination of DNA ligase and PARP inhibitors inhibited ALT NHEJ and selectively decreased survival with the effect being greater in the IMR derivative. Similar results were obtained with TKI-resistant derivatives of two hematopoietic cell lines that had been engineered to stably express BCR-ABL1. Together our results show that the sensitivity of cell lines expressing BCR-ABL1 to the combination of DNA ligase and PARP inhibitors correlates with the steady state levels of PARP1 and DNA ligase IIIα, and ALT NHEJ activity. Importantly, analysis of clinical samples from CML patients confirmed that the expression levels of PARP1 and DNA ligase IIIα correlated with the sensitivity to the DNA repair inhibitor combination. Thus, the expression levels of PARP1 and DNA ligase IIIα serve as biomarkers to identify a subgroup of CML patients who may be candidates for therapies that target the ALT NHEJ pathway when treatment with TKIs has failed.


Asunto(s)
Benzamidas/farmacología , Roturas del ADN de Doble Cadena/efectos de los fármacos , Reparación del ADN por Unión de Extremidades/efectos de los fármacos , ADN Ligasas/antagonistas & inhibidores , Resistencia a Antineoplásicos/efectos de los fármacos , Leucemia Mielógena Crónica BCR-ABL Positiva/tratamiento farmacológico , Piperazinas/farmacología , Inhibidores de Poli(ADP-Ribosa) Polimerasas , Pirimidinas/farmacología , Protocolos de Quimioterapia Combinada Antineoplásica , Apoptosis/efectos de los fármacos , Western Blotting , Proliferación Celular/efectos de los fármacos , Hibridación Genómica Comparativa , ADN Ligasa (ATP) , ADN Ligasas/genética , ADN Ligasas/metabolismo , Inhibidores Enzimáticos/farmacología , Técnica del Anticuerpo Fluorescente , Proteínas de Fusión bcr-abl/metabolismo , Humanos , Mesilato de Imatinib , Técnicas para Inmunoenzimas , Leucemia Mielógena Crónica BCR-ABL Positiva/genética , Leucemia Mielógena Crónica BCR-ABL Positiva/patología , Poli(ADP-Ribosa) Polimerasa-1 , Poli(ADP-Ribosa) Polimerasas/genética , Poli(ADP-Ribosa) Polimerasas/metabolismo , Proteínas de Unión a Poli-ADP-Ribosa , Inhibidores de Proteínas Quinasas/farmacología , ARN Mensajero/genética , ARN Interferente Pequeño/genética , Reacción en Cadena en Tiempo Real de la Polimerasa , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Células Tumorales Cultivadas , Proteínas de Xenopus
20.
Cell ; 151(7): 1474-87, 2012 Dec 21.
Artículo en Inglés | MEDLINE | ID: mdl-23260137

RESUMEN

DNA Ligase IV is responsible for sealing of double-strand breaks (DSBs) during nonhomologous end-joining (NHEJ). Inhibiting Ligase IV could result in amassing of DSBs, thereby serving as a strategy toward treatment of cancer. Here, we identify a molecule, SCR7 that inhibits joining of DSBs in cell-free repair system. SCR7 blocks Ligase IV-mediated joining by interfering with its DNA binding but not that of T4 DNA Ligase or Ligase I. SCR7 inhibits NHEJ in a Ligase IV-dependent manner within cells, and activates the intrinsic apoptotic pathway. More importantly, SCR7 impedes tumor progression in mouse models and when coadministered with DSB-inducing therapeutic modalities enhances their sensitivity significantly. This inhibitor to target NHEJ offers a strategy toward the treatment of cancer and improvement of existing regimens.


Asunto(s)
Roturas del ADN de Doble Cadena , Reparación del ADN por Unión de Extremidades/efectos de los fármacos , ADN Ligasas/antagonistas & inhibidores , Neoplasias/tratamiento farmacológico , Neoplasias/patología , Pirimidinas/uso terapéutico , Bases de Schiff/uso terapéutico , Secuencia de Aminoácidos , Animales , Línea Celular Tumoral , ADN Ligasa (ATP) , ADN Ligasas/química , ADN Ligasas/genética , Modelos Animales de Enfermedad , Diseño de Fármacos , Resistencia a Antineoplásicos , Humanos , Linfocitos/efectos de los fármacos , Linfoma/tratamiento farmacológico , Linfoma/patología , Masculino , Ratones , Ratones Endogámicos BALB C , Ratones Desnudos , Modelos Moleculares , Datos de Secuencia Molecular , Estructura Terciaria de Proteína , Pirimidinas/síntesis química , Pirimidinas/química , Tolerancia a Radiación , Ratas , Bases de Schiff/síntesis química , Bases de Schiff/química , Alineación de Secuencia
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