Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 20
Filtrar
1.
Nucleic Acids Res ; 47(5): 2190-2204, 2019 03 18.
Artigo em Inglês | MEDLINE | ID: mdl-30759259

RESUMO

Nucleic acid mimics of fluorescent proteins can be valuable tools to locate and image functional biomolecules in cells. Stacking between the internal G-quartet, formed in the mimics, and the exogenous fluorophore probes constitutes the basis for fluorescence emission. The precision of recognition depends upon probes selectively targeting the specific G-quadruplex in the mimics. However, the design of probes recognizing a G-quadruplex with high selectivity in vitro and in vivo remains a challenge. Through structure-based screening and optimization, we identified a light-up fluorescent probe, 9CI that selectively recognizes c-MYC Pu22 G-quadruplex both in vitro and ex vivo. Upon binding, the biocompatible probe emits both blue and green fluorescence with the excitation at 405 nm. With 9CI and c-MYC Pu22 G-quadruplex complex as the fluorescent response core, a DNA mimic of fluorescent proteins was constructed, which succeeded in locating a functional aptamer on the cellular periphery. The recognition mechanism analysis suggested the high selectivity and strong fluorescence response was attributed to the entire recognition process consisting of the kinetic match, dynamic interaction, and the final stacking. This study implies both the single stacking state and the dynamic recognition process are crucial for designing fluorescent probes or ligands with high selectivity for a specific G-quadruplex structure.


Assuntos
Corantes Fluorescentes/análise , Quadruplex G , Genes myc/genética , Sondas Moleculares/análise , Linhagem Celular Tumoral , Sobrevivência Celular , Avaliação Pré-Clínica de Medicamentos , Humanos , Ligantes , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Conformação de Ácido Nucleico
2.
Biochemistry ; 58(45): 4480-4493, 2019 11 12.
Artigo em Inglês | MEDLINE | ID: mdl-31633931

RESUMO

Histone deacetylase (HDAC) enzymes that catalyze removal of acetyl-lysine post-translational modifications are frequently post-translationally modified. HDAC8 is phosphorylated within the deacetylase domain at conserved residue serine 39, which leads to decreased catalytic activity. HDAC8 phosphorylation at S39 is unique in its location and function and may represent a novel mode of deacetylation regulation. To better understand the impact of phosphorylation of HDAC8 on enzyme structure and function, we performed crystallographic, kinetic, and molecular dynamics studies of the S39E HDAC8 phosphomimetic mutant. This mutation decreases the level of deacetylation of peptides derived from acetylated nuclear and cytoplasmic proteins. However, the magnitude of the effect depends on the peptide sequence and the identity of the active site metal ion [Zn(II) vs Fe(II)], with the value of kcat/KM for the mutant decreasing 9- to >200-fold compared to that of wild-type HDAC8. Furthermore, the dissociation rate constant of the active site metal ion increases by ∼10-fold. S39E HDAC8 was crystallized in complex with the inhibitor Droxinostat, revealing that phosphorylation of S39, as mimicked by the glutamate side chain, perturbs local structure through distortion of the L1 loop. Molecular dynamics simulations of both S39E and phosphorylated S39 HDAC8 demonstrate that the perturbation of the L1 loop likely occurs because of the lost hydrogen bond between D29 and S39. Furthermore, the S39 perturbation causes structural changes that propagate through the protein scaffolding to influence function in the active site. These data demonstrate that phosphorylation plays an important regulatory role for HDAC8 by affecting ligand binding, catalytic efficiency, and substrate selectivity.


Assuntos
Histona Desacetilases/química , Proteínas Repressoras/química , Cristalografia por Raios X , Histona Desacetilases/genética , Histona Desacetilases/metabolismo , Humanos , Simulação de Dinâmica Molecular , Fosforilação , Mutação Puntual , Conformação Proteica , Proteínas Repressoras/genética , Proteínas Repressoras/metabolismo , Especificidade por Substrato
3.
Chem Sci ; 15(11): 3879-3892, 2024 Mar 13.
Artigo em Inglês | MEDLINE | ID: mdl-38487227

RESUMO

Accelerated SuFEx Click Chemistry (ASCC) is a powerful method for coupling aryl and alkyl alcohols with SuFEx-compatible functional groups. With its hallmark favorable kinetics and exceptional product yields, ASCC streamlines the synthetic workflow, simplifies the purification process, and is ideally suited for discovering functional molecules. We showcase the versatility and practicality of the ASCC reaction as a tool for the late-stage derivatization of bioactive molecules and in the array synthesis of sulfonate-linked, high-potency, microtubule targeting agents (MTAs) that exhibit nanomolar anticancer activity against multidrug-resistant cancer cell lines. These findings underscore ASCC's promise as a robust platform for drug discovery.

4.
J Chem Inf Model ; 52(5): 1179-92, 2012 May 25.
Artigo em Inglês | MEDLINE | ID: mdl-22500887

RESUMO

Signal Transducers and Activators of Transcription (STAT) proteins are a group of latent cytoplasmic transcription factors involved in cytokine signaling. STAT3 is a member of the STAT family and is expressed at elevated levels in a large number of diverse human cancers and is now a validated target for anticancer drug discovery.. Understanding the dynamics of the STAT3 dimer interface, accounting for both protein-DNA and protein-protein interactions, with respect to the dynamics of the latent unphosphorylated STAT3 monomer, is important for designing potential small-molecule inhibitors of the activated dimer. Molecular dynamics (MD) simulations have been used to study the activated STAT3 homodimer:DNA complex and the latent unphosphorylated STAT3 monomer in an explicit water environment. Analysis of the data obtained from MD simulations over a 50 ns time frame has suggested how the transcription factor interacts with DNA, the nature of the conformational changes, and ways in which function may be affected. Examination of the dimer interface, focusing on the protein-DNA interactions, including involvement of water molecules, has revealed the key residues contributing to the recognition events involved in STAT3 protein-DNA interactions. This has shown that the majority of mutations in the DNA-binding domain are found at the protein-DNA interface. These mutations have been mapped in detail and related to specific protein-DNA contacts. Their structural stability is described, together with an analysis of the model as a starting-point for the discovery of novel small-molecule STAT3 inhibitors.


Assuntos
Proteínas de Ligação a DNA/metabolismo , DNA/metabolismo , Simulação de Dinâmica Molecular , Fator de Transcrição STAT3/metabolismo , DNA/genética , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/genética , Dimerização , Humanos , Modelos Moleculares , Mutação , Fator de Transcrição STAT3/química , Fator de Transcrição STAT3/genética , Água/química
5.
Nucleic Acids Res ; 38(16): 5569-80, 2010 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-20413582

RESUMO

DNA telomeric repeats in mammalian cells are transcribed to guanine-rich RNA sequences, which adopt parallel-stranded G-quadruplexes with a propeller-like fold. The successful crystallization and structure analysis of a bimolecular human telomeric RNA G-quadruplex, folded into the same crystalline environment as an equivalent DNA oligonucleotide sequence, is reported here. The structural basis of the increased stability of RNA telomeric quadruplexes over DNA ones and their preference for parallel topologies is described here. Our findings suggest that the 2'-OH hydroxyl groups in the RNA quadruplex play a significant role in redefining hydration structure in the grooves and the hydrogen bonding networks. The preference for specific nucleotides to populate the C3'-endo sugar pucker domain is accommodated by alterations in the phosphate backbone, which leads to greater stability through enhanced hydrogen bonding networks. Molecular dynamics simulations on the DNA and RNA quadruplexes are consistent with these findings. The computations, based on the native crystal structure, provide an explanation for RNA G-quadruplex ligand binding selectivity for a group of naphthalene diimide ligands as compared to the DNA G-quadruplex.


Assuntos
Quadruplex G , Modelos Moleculares , RNA/química , Telômero/química , Cristalografia por Raios X , DNA/química , Desoxirribose/química , Humanos , Ligantes , Simulação de Dinâmica Molecular
6.
J Am Chem Soc ; 132(35): 12263-72, 2010 Sep 08.
Artigo em Inglês | MEDLINE | ID: mdl-20718414

RESUMO

Structure-based modeling methods have been used to design a series of disubstituted triazole-linked acridine compounds with selectivity for human telomeric quadruplex DNAs. A focused library of these compounds was prepared using click chemistry and the selectivity concept was validated against two promoter quadruplexes from the c-kit gene with known molecular structures, as well as with duplex DNA using a FRET-based melting method. Lead compounds were found to have reduced effects on the thermal stability of the c-kit quadruplexes and duplex DNA structures. These effects were further explored with a series of competition experiments, which confirmed that binding to duplex DNA is very low even at high duplex:telomeric quadruplex ratios. Selectivity to the c-kit quadruplexes is more complex, with some evidence of their stabilization at increasing excess over human telomeric quadruplex DNA. Selectivity is a result of the dimensions of the triazole-acridine compounds, and in particular the separation of the two alkyl-amino terminal groups. Both lead compounds also have selective inhibitory effects on the proliferation of cancer cell lines compared to a normal cell line, and one has been shown to inhibit the activity of the telomerase enzyme, which is selectively expressed in tumor cells, where it plays a role in maintaining telomere integrity and cellular immortalization.


Assuntos
Acridinas/farmacologia , Antineoplásicos/farmacologia , Inibidores Enzimáticos/farmacologia , Quadruplex G/efeitos dos fármacos , Proteínas Proto-Oncogênicas c-kit/química , Acridinas/síntese química , Acridinas/química , Antineoplásicos/síntese química , Antineoplásicos/química , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , DNA/efeitos dos fármacos , Ensaios de Seleção de Medicamentos Antitumorais , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/química , Fibroblastos/efeitos dos fármacos , Humanos , Ligantes , Modelos Moleculares , Estrutura Molecular , Proteínas Proto-Oncogênicas c-kit/genética , Estereoisomerismo , Relação Estrutura-Atividade , Telomerase/antagonistas & inibidores , Telômero/química , Telômero/efeitos dos fármacos , Triazóis/química
7.
Biochem Soc Trans ; 37(Pt 3): 583-8, 2009 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-19442254

RESUMO

The extreme 3'-ends of human telomeres consist of 150-250 nucleotides of single-stranded DNA sequence together with associated proteins. Small-molecule ligands can compete with these proteins and induce a conformational change in the DNA to a four-stranded quadruplex arrangement, which is also no longer a substrate for the telomerase enzyme. The modified telomere ends provide signals to the DNA-damage-response system and trigger senescence and apoptosis. Experimental structural data are available on such quadruplex complexes comprising up to four telomeric DNA repeats, but not on longer systems that are more directly relevant to the single-stranded overhang in human cells. The present paper reports on a molecular modelling study that uses Molecular Dynamics simulation methods to build dimer and tetramer quadruplex repeats. These incorporate ligand-binding sites and are models for overhang-ligand complexes.


Assuntos
Acridinas/química , Quadruplex G , Modelos Moleculares , Telômero/química , Acridinas/metabolismo , Sequência de Bases , Sítios de Ligação/genética , Simulação por Computador , DNA de Cadeia Simples/química , DNA de Cadeia Simples/genética , DNA de Cadeia Simples/metabolismo , Humanos , Conformação de Ácido Nucleico , Sequências de Repetição em Tandem , Telômero/genética , Telômero/metabolismo
8.
Chem Commun (Camb) ; (27): 4097-9, 2009 Jul 21.
Artigo em Inglês | MEDLINE | ID: mdl-19568645

RESUMO

We report a novel class of biaryl polyamides highly selective for G-quadruplex DNA, and with significant cytotoxicity in several cancer cell lines; they form planar U-shaped structures that match the surface area dimensions of a terminal G-quartet in quadruplex structures rather than the grooves of duplex DNA.


Assuntos
Antineoplásicos/farmacologia , Quadruplex G/efeitos dos fármacos , Nylons/farmacologia , Antineoplásicos/síntese química , Antineoplásicos/química , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Dicroísmo Circular , Fibroblastos/efeitos dos fármacos , Fibroblastos/metabolismo , Humanos , Concentração Inibidora 50 , Ligantes , Nylons/síntese química , Nylons/química
9.
Nucleic Acids Res ; 35(17): 5799-808, 2007.
Artigo em Inglês | MEDLINE | ID: mdl-17720713

RESUMO

The 22-nt c-kit87 promoter sequence is unique within the human genome. Its fold and tertiary structure have recently been determined by NMR methods [Phan,A.T., Kuryavyi,V., Burge,S., Neidle,S. and Patel,D.J. (2007) Structure of an unprecedented G-quadruplex scaffold in the c-kit promoter. J. Am. Chem. Soc., 129, 4386-4392], and does not have precedent among known DNA quadruplexes. We show here using bioinformatics and molecular dynamics simulations methods that (i) none of the closely related sequences (encompassing all nucleotides not involved in the maintenance of structural integrity) occur immediately upstream (<100 nt) of a transcription start site, and (ii) that all of these sequences correspond to the same stable tertiary structure. It is concluded that the c-kit87 tertiary structure may also be formed in a very small number of other loci in the human genome, but the likelihood of these playing a significant role in the expression of particular genes is very low. The c-kit87 quadruplex thus fulfils a fundamental criterion of a 'good' drug target, in that it possesses distinctive three-dimensional structural features that are only present in at most a handful of other genes.


Assuntos
DNA/química , Regiões Promotoras Genéticas , Proteínas Proto-Oncogênicas c-kit/genética , Sequência de Bases , Dicroísmo Circular , Biologia Computacional , Simulação por Computador , Quadruplex G , Genômica , Humanos , Modelos Moleculares
10.
J Med Chem ; 61(6): 2500-2517, 2018 03 22.
Artigo em Inglês | MEDLINE | ID: mdl-29356532

RESUMO

Human pancreatic ductal adenocarcinoma (PDAC) involves the dysregulation of multiple signaling pathways. A novel approach to the treatment of PDAC is described, involving the targeting of cancer genes in PDAC pathways having over-representation of G-quadruplexes, using the trisubstituted naphthalene diimide quadruplex-binding compound 2,7-bis(3-morpholinopropyl)-4-((2-(pyrrolidin-1-yl)ethyl)amino)benzo[ lmn][3,8]phenanthroline-1,3,6,8(2 H,7 H)-tetraone (CM03). This compound has been designed by computer modeling, is a potent inhibitor of cell growth in PDAC cell lines, and has anticancer activity in PDAC models, with a superior profile compared to gemcitabine, a commonly used therapy. Whole-transcriptome RNA-seq methodology has been used to analyze the effects of this quadruplex-binding small molecule on global gene expression. This has revealed the down-regulation of a large number of genes, rich in putative quadruplex elements and involved in essential pathways of PDAC survival, metastasis, and drug resistance. The changes produced by CM03 represent a global response to the complexity of human PDAC and may be applicable to other currently hard-to-treat cancers.


Assuntos
Antineoplásicos/síntese química , Antineoplásicos/farmacologia , Carcinoma Ductal Pancreático/tratamento farmacológico , Quadruplex G , Neoplasias Pancreáticas/tratamento farmacológico , Animais , Antimetabólitos Antineoplásicos/farmacologia , Carcinoma Ductal Pancreático/genética , Linhagem Celular Tumoral , Biologia Computacional , Simulação por Computador , Dano ao DNA , Desoxicitidina/análogos & derivados , Desoxicitidina/farmacologia , Regulação para Baixo/efeitos dos fármacos , Desenho de Fármacos , Resistencia a Medicamentos Antineoplásicos , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Humanos , Camundongos , Camundongos Nus , Neoplasias Pancreáticas/genética , Ensaios Antitumorais Modelo de Xenoenxerto , Gencitabina
11.
J Mol Biol ; 326(1): 117-25, 2003 Feb 07.
Artigo em Inglês | MEDLINE | ID: mdl-12547195

RESUMO

Stabilisation of G-quadruplex structures formed from telomeric DNA, by means of quadruplex-selective ligands, is a means of inhibiting the telomerase enzyme from catalysing the synthesis of telomeric DNA repeats. In order to understand the molecular basis of ligand-quadruplex recognition, the crystal structure has been determined of such a complex, at 1.75A resolution. This complex is between a dimeric antiparallel G-quadruplex formed from the Oxytricha nova telomeric DNA sequence d(GGGGTTTTGGGG), and a di-substituted aminoalkylamido acridine compound. The structure shows that the acridine moiety is bound at one end of the stack of G-quartets, within one of the thymine loops. It is held in place by a combination of stacking interactions and specific hydrogen bonds with thymine bases. The stability of the ligand in this binding site has been confirmed by a 2ns molecular dynamics simulation.


Assuntos
Acridinas/química , Acridinas/metabolismo , DNA/química , DNA/metabolismo , Conformação de Ácido Nucleico , Pirrolidinas/química , Pirrolidinas/metabolismo , Telômero/química , Telômero/metabolismo , Animais , Sequência de Bases , Sítios de Ligação , Cristalografia por Raios X , DNA/genética , Quadruplex G , Ligação de Hidrogênio , Ligantes , Modelos Moleculares , Oxytricha/genética , Telômero/genética
12.
Sci Rep ; 5: 11385, 2015 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-26077929

RESUMO

We report here that a tetra-substituted naphthalene-diimide derivative (MM41) has significant in vivo anti-tumour activity against the MIA PaCa-2 pancreatic cancer xenograft model. IV administration with a twice-weekly 15 mg/kg dose produces ca 80% tumour growth decrease in a group of tumour-bearing animals. Two animals survived tumour-free after 279 days. High levels of MM41 are rapidly transported into cell nuclei and were found to accumulate in the tumour. MM41 is a quadruplex-interactive compound which binds strongly to the quadruplexes encoded in the promoter sequences of the BCL-2 and k-RAS genes, both of which are dis-regulated in many human pancreatic cancers. Levels of BCL-2 were reduced by ca 40% in tumours from MM41-treated animals relative to controls, consistent with BCL-2 being a target for MM41. Molecular modelling suggests that MM41 binds to a BCL-2 quadruplex in a manner resembling that previously observed in co-crystal structures with human telomeric quadruplexes. This supports the concept that MM41 (and by implication other quadruplex-targeting small molecules) can bind to quadruplex-forming promoter regions in a number of genes and down-regulate their transcription. We suggest that quadruplexes within those master genes that are up-regulated drivers for particular cancers, may be selective targets for compounds such as MM41.


Assuntos
Antineoplásicos/farmacologia , Imidas/farmacologia , Naftalenos/farmacologia , Neoplasias Pancreáticas/tratamento farmacológico , Regiões Promotoras Genéticas , Proteínas Proto-Oncogênicas c-bcl-2/metabolismo , Animais , Antineoplásicos/química , Linhagem Celular Tumoral , Esquema de Medicação , Feminino , Quadruplex G , Expressão Gênica , Humanos , Imidas/química , Injeções Intravenosas , Camundongos , Camundongos Nus , Simulação de Dinâmica Molecular , Naftalenos/química , Neoplasias Pancreáticas/genética , Neoplasias Pancreáticas/metabolismo , Neoplasias Pancreáticas/patologia , Proteínas Proto-Oncogênicas c-bcl-2/antagonistas & inibidores , Proteínas Proto-Oncogênicas c-bcl-2/química , Proteínas Proto-Oncogênicas c-bcl-2/genética , Proteínas Proto-Oncogênicas p21(ras)/genética , Proteínas Proto-Oncogênicas p21(ras)/metabolismo , Transcrição Gênica , Carga Tumoral/efeitos dos fármacos , Ensaios Antitumorais Modelo de Xenoenxerto
13.
Chem Biol Drug Des ; 82(5): 620-9, 2013 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-23906044

RESUMO

Nine new 17-(piperazin-1-yl)pyridin-5-yl)steroids as abiraterone analogues were synthesized. Compounds 5d and 5g showed selective activities against 17α-hydroxylase/C17,20-lyase (CYP17A1) and aromatase (CYP19), respectively. IC50 values of 5d were 5.09 and >50 µm, whereas these values for 5g were >50 µm and 7.40 µm, respectively, for CYP17A1 and CYP19. Molecular modelling highlighted that the inhibitor designed to bind cytochrome P450 haem iron is a necessary condition but not the only rationale to explain inhibitory activity. These abiraterone analogues were then evaluated on hormone-independent prostate cancer cell lines DU-145 and PC-3 and on hormone-dependent breast and prostate cancer cell lines MCF-7 and LNCaP, respectively. Compounds 5e, 5g and 5i have showed potent activities only on hormone-independent prostate cancer cell lines DU-145 and PC-3 with 60-85% inhibition of both cell viability and growth at 10 nm with pro-apoptotic mechanism as illustrated in PC-3 cells by DNA ladder assay and Western blotting of Bax, Casp-3 and its substrate, the poly (ADP-ribose) polymerase. We conclude that hybrid heterocycle steroids could be good lead compounds in the drug design especially against hormone-independent prostate cancer.


Assuntos
Androstenóis/química , Antineoplásicos/química , Antineoplásicos/farmacologia , Apoptose/efeitos dos fármacos , Esteroides/química , Esteroides/farmacologia , Androstenos , Androstenóis/síntese química , Androstenóis/farmacologia , Antineoplásicos/síntese química , Aromatase/química , Aromatase/metabolismo , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Clivagem do DNA/efeitos dos fármacos , Humanos , Células MCF-7 , Masculino , Piperazinas/química , Neoplasias da Próstata/metabolismo , Neoplasias da Próstata/patologia , Piridinas/química , Esteroide 17-alfa-Hidroxilase/antagonistas & inibidores , Esteroide 17-alfa-Hidroxilase/metabolismo , Esteroides/síntese química
14.
Biochimie ; 93(8): 1239-51, 2011 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-21635933

RESUMO

This focused review article discusses in detail, all available high-resolution small molecule ligand/G-quadruplex structural data derived from crystallographic and NMR based techniques, in an attempt to understand key factors in ligand binding and to highlight the biological importance of these complexes. In contrast to duplex DNA, G-quadruplexes are four-stranded nucleic acid structures folded from guanine rich repeat sequences stabilized by the stacking of guanine G-quartets and extensive Watson-Crick/Hoogsteen hydrogen bonding. Thermally stable, these topologies can play a role in telomere regulation and gene expression. The core structures of G-quadruplexes form stable scaffolds while the loops have been shown, by the addition of small molecule ligands, to be sufficiently adaptable to generate new and extended binding platforms for ligands to associate, either by extending G-quartet surfaces or by forming additional planar dinucleotide pairings. Many of these structurally characterised loop rearrangements were totally unexpected opening up new opportunities for the design of selective ligands. However these rearrangements do significantly complicate attempts to rationally design ligands against well defined but unbound topologies, as seen for the series of napthalene diimides complexes. Drawing together previous findings and with the introduction of two new crystallographic quadruplex/ligand structures we aim to expand the understanding of possible structural adaptations available to quadruplexes in the presence of ligands, thereby aiding in the design of new selective entities.


Assuntos
Quadruplex G , Ligantes , Acridinas/química , Acridinas/metabolismo , Sítios de Ligação , Cristalografia , Daunorrubicina/química , Distamicinas/química , Regulação da Expressão Gênica , Naftalenos/química , Porfirinas/química , Porfirinas/metabolismo , Telômero
15.
Biochimie ; 93(8): 1275-9, 2011 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-21641959

RESUMO

Solvent-accessible surface area calculations have been performed on two human telomeric quadruplex structures, the parallel crystal structure and an (3 + 1) anti-parallel structure determined by NMR methods. The differences in net ligand solvent-accessible surface area (Δ(SASA)) for four structurally distinct categories of small-molecule ligand have been computed, using docked structures of complexes with both types of quadruplex, as well as the relative contributions of polar and non-polar surface areas. It has been hypothesized that the surface area occupied by the ligand is a determinant of selectivity between different quadruplex topologies, where the ligand maximizes the accessible surface area by contacting all accessible atoms at one end of a quadruplex structure. This has enabled selectivity for a particular ligand to be assessed, for parallel compared an anti-parallel topology. The predictions for the ligands chosen, all of which have their quadruplex topological preferences experimentally determined and reported in the literature, are fully in accord with observation. It is suggested that this approach, which does not depend on energy functions, can be useful in the rational design of topology-specific ligands, especially in the case of polymorphic quadruplexes.


Assuntos
Quadruplex G , Telômero/metabolismo , Humanos , Ligantes , Modelos Moleculares , Ressonância Magnética Nuclear Biomolecular , Solventes , Telômero/química
16.
J Mol Biol ; 400(5): 1078-98, 2010 Jul 30.
Artigo em Inglês | MEDLINE | ID: mdl-20595043

RESUMO

A molecular model for the P450 enzyme cytochrome P450 C17 (CYP17) is presented based on sequence alignments of multiple template structures and homology modeling. This enzyme plays a central role in the biosynthesis of testosterone and is emerging as a major target in prostate cancer, with the recently developed inhibitor abiraterone currently in advanced clinical trials. The model is described in detail, together with its validation, by providing structural explanations to available site-directed mutagenesis data. The CYP17 molecule in this model is in the form of a triangular prism, with an edge of approximately 55 A and a thickness of approximately 37 A. It is predominantly helical, comprising 13 alpha helices interspersed by six 3(10) helices and 11 beta-sheets. Multinanosecond molecular dynamics simulations in explicit solvent have been carried out, and principal components analysis has been used to reveal the details of dynamics around the active site. Coarse-grained methods have also been used to verify low-frequency motions, which have been correlated with active-site gating. The work also describes the results of docking synthetic inhibitors, including the drug abiraterone and the natural substrate pregnenolone, in the CYP17 active site together with molecular dynamics simulations on the complexes.


Assuntos
Inibidores Enzimáticos/uso terapêutico , Neoplasias da Próstata/tratamento farmacológico , Esteroide 17-alfa-Hidroxilase/química , Sequência de Aminoácidos , Domínio Catalítico , Inibidores Enzimáticos/farmacologia , Humanos , Ligantes , Masculino , Modelos Moleculares , Dados de Sequência Molecular , Neoplasias da Próstata/enzimologia , Homologia de Sequência de Aminoácidos , Esteroide 17-alfa-Hidroxilase/antagonistas & inibidores
17.
Chem Commun (Camb) ; 46(31): 5680-2, 2010 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-20582382

RESUMO

A bis-guanylhydrazone derivative of diimidazo[1,2-a:1,2-c]pyrimidine has unexpectedly been found to be a potent stabiliser of several quadruplex DNAs, whereas there is no significant interaction with duplex DNA. Molecular modeling suggests that the guanylhydrazone groups play an active role in quadruplex binding.


Assuntos
Quadruplex G , Mitoguazona/análogos & derivados , Pirimidinas/química , Simulação por Computador , DNA/química , Transferência Ressonante de Energia de Fluorescência , Mitoguazona/química , Modelos Moleculares
18.
Chem Commun (Camb) ; (48): 7482-4, 2009 Dec 28.
Artigo em Inglês | MEDLINE | ID: mdl-20024253

RESUMO

Quadruplex RNAs are less well understood than their DNA counterparts, yet of potentially high biological relevance. The interactions of several quadruplex-binding ligands with telomeric RNA quadruplexes are reported and compared with their binding to the analogous DNA quadruplexes.


Assuntos
DNA/química , Quadruplex G , RNA/química , Telômero/química , Sítios de Ligação , Dicroísmo Circular , Humanos , Ligantes
19.
J Med Chem ; 52(12): 3774-83, 2009 Jun 25.
Artigo em Inglês | MEDLINE | ID: mdl-19469547

RESUMO

Most of human gastrointestinal stromal tumors (GIST) are driven by activating mutations in the proto-oncogene KIT, a tyrosine kinase receptor. Clinical treatment with imatinib targets the kinase domain of KIT, but tumor regrowth occurs as a result of the development of resistant mutations in the kinase active site. An alternative small-molecule approach to GIST therapy is described, in which the KIT gene is directly targeted, and thus, kinase resistance may be circumvented. A naphthalene diimide derivative has been used to demonstrate the concept of dual quadruplex targeting. This compound strongly stabilizes both telomeric quadruplex DNA and quadruplex sites in the KIT promoter in vitro. It is shown here that the compound is a potent inducer of growth arrest in a patient-derived GIST cell line at a concentration (approximately 1 microM) that also results in effective inhibition of telomerase activity and almost complete suppression of KIT mRNA and KIT protein expression. Molecular modeling studies with a telomeric quadruplex have been used to rationalize aspects of the experimental quadruplex melting data.


Assuntos
Tumores do Estroma Gastrointestinal/tratamento farmacológico , Fenantrolinas/farmacologia , Proteínas Proto-Oncogênicas c-kit/efeitos dos fármacos , Sequência de Bases , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Simulação por Computador , Relação Dose-Resposta a Droga , Ensaios de Seleção de Medicamentos Antitumorais , Tumores do Estroma Gastrointestinal/genética , Humanos , Imidas , Modelos Químicos , Modelos Moleculares , Dados de Sequência Molecular , Estrutura Molecular , Peso Molecular , Naftalenos , Fenantrolinas/química , Proto-Oncogene Mas , Proteínas Proto-Oncogênicas c-kit/genética , RNA Mensageiro/efeitos dos fármacos , RNA Mensageiro/genética
20.
Bioorg Med Chem Lett ; 14(23): 5845-9, 2004 Dec 06.
Artigo em Inglês | MEDLINE | ID: mdl-15501053

RESUMO

The synthesis and evaluation of a group of 2,6-, 2,7- and 3,6-bis-aminoalkylamido acridones are reported, which show a similar level of activity against telomerase in vitro compared to their acridine counterparts. Computer modelling and calculations of relative binding energies suggest an equivalent binding mode to human intramolecular G-quadruplex DNA, but with significantly reduced affinity, as a result of the limited delocalisation of the acridone chromophore compared to the acridine system. Thermal melting studies on acridone and acridine quadruplex complexes using a FRET approach support these predictions. Long-term cell proliferation studies at sub-cytotoxic doses with two representative acridones using the SKOV3 cell line, show that neither compound produces growth arrest, in contrast with the effects produced by the tri-substituted acridine compound BRACO-19. It is concluded that telomerase inhibitory activity is a necessary though by itself insufficient property in order for cellular growth arrest to occur at sub-toxic concentrations, and that tight quadruplex binding is also required.


Assuntos
Acridinas/química , Acridinas/metabolismo , DNA/metabolismo , Telomerase/antagonistas & inibidores , Telomerase/metabolismo , Acridinas/farmacologia , Acridonas , Linhagem Celular Tumoral , Avaliação Pré-Clínica de Medicamentos/métodos , Inibidores Enzimáticos , Quadruplex G , Humanos , Modelos Moleculares , Ligação Proteica/fisiologia
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA