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1.
Int J Mol Sci ; 24(10)2023 May 20.
Artigo em Inglês | MEDLINE | ID: mdl-37240378

RESUMO

The stimulator of interferon genes (STING) is an adaptor protein involved in the activation of IFN-ß and many other genes associated with the immune response activation in vertebrates. STING induction has gained attention from different angles such as the potential to trigger an early immune response against different signs of infection and cell damage, or to be used as an adjuvant in cancer immune treatments. Pharmacological control of aberrant STING activation can be used to mitigate the pathology of some autoimmune diseases. The STING structure has a well-defined ligand binding site that can harbor natural ligands such as specific purine cyclic di-nucleotides (CDN). In addition to a canonical stimulation by CDNs, other non-canonical stimuli have also been described, whose exact mechanism has not been well defined. Understanding the molecular insights underlying the activation of STING is important to realize the different angles that need to be considered when designing new STING-binding molecules as therapeutic drugs since STING acts as a versatile platform for immune modulators. This review analyzes the different determinants of STING regulation from the structural, molecular, and cell biology points of view.


Assuntos
Adjuvantes Imunológicos , Nucleotídeos Cíclicos , Animais , Sítios de Ligação
2.
Int J Mol Sci ; 22(18)2021 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-34576138

RESUMO

Osteoarthritis is a degenerative disease, often resulting in chronic joint pain and commonly affecting elderly people. Current treatments with anti-inflammatory drugs are palliative, making the discovery of new treatments necessary. The inhibition of matrix metalloproteinase MMP-13 is a validated strategy to prevent the progression of this common joint disorder. We recently described polybrominated benzotriazole derivatives with nanomolar inhibitory activity and a promising selectivity profile against this collagenase. In this work, we have extended the study in order to explore the influence of bromine atoms and the nature of the S1' heterocyclic interacting moiety on the solubility/selectivity balance of this type of compound. Drug target interactions have been assessed through a combination of molecular modeling studies and NMR experiments. Compound 9a has been identified as a water-soluble and highly potent inhibitor with activity in MG-63 human osteosarcoma cells.


Assuntos
Desenho de Fármacos , Inibidores de Metaloproteinases de Matriz/farmacologia , Osteossarcoma/patologia , Água/química , Linhagem Celular Tumoral , Química Click , Humanos , Concentração Inibidora 50 , Espectroscopia de Ressonância Magnética , Metaloproteinase 13 da Matriz/metabolismo , Inibidores de Metaloproteinases de Matriz/síntese química , Inibidores de Metaloproteinases de Matriz/química , Modelos Moleculares , Solubilidade
3.
Molecules ; 26(18)2021 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-34577077

RESUMO

Protein degradation by the Ubiquitin-Proteasome System is one of the main mechanisms of the regulation of cellular proteostasis, and the E3 ligases are the key effectors for the protein recognition and degradation. Many E3 ligases have key roles in cell cycle regulation, acting as checkpoints and checkpoint regulators. One of the many important proteins involved in the regulation of the cell cycle are the members of the Histone Deacetylase (HDAC) family. The importance of zinc dependent HDACs in the regulation of chromatin packing and, therefore, gene expression, has made them targets for the design and synthesis of HDAC inhibitors. However, achieving potency and selectivity has proven to be a challenge due to the homology between the zinc dependent HDACs. PROteolysis TArgeting Chimaera (PROTAC) design has been demonstrated to be a useful strategy to inhibit and selectively degrade protein targets. In this review, we attempt to summarize the E3 ligases that naturally ubiquitinate HDACs, analyze their structure, and list the known ligands that can bind to these E3 ligases and be used for PROTAC design, as well as the already described HDAC-targeted PROTACs.


Assuntos
Histona Desacetilases/metabolismo , Complexo de Endopeptidases do Proteassoma/metabolismo , Proteólise , Ubiquitina-Proteína Ligases/metabolismo , Animais , Humanos , Complexo de Endopeptidases do Proteassoma/efeitos dos fármacos , Zinco/metabolismo
4.
ACS Med Chem Lett ; 11(5): 713-719, 2020 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-32435375

RESUMO

Four potent CK2 inhibitors derived from CX-4945 are described. They also provided nanomolar activity against HDAC1, therefore having promising utility as dual-target agents for cancer. The linker length between the hydroxamic acid and the CX-4945 scaffold plays an important role in dictating balanced activity against the targeted enzymes. The seven-carbon linker (compound 15c) was optimal for inhibition of both CK2 and HDAC1. Remarkably, 15c showed 3.0 and 3.5 times higher inhibitory activity than the reference compounds CX-4945 (against CK2) and SAHA (against HDAC1), respectively. Compound 15c exhibited micromolar activity in cell-based cytotoxic assays against multiple cell lines.

5.
Molecules ; 25(7)2020 Mar 25.
Artigo em Inglês | MEDLINE | ID: mdl-32218358

RESUMO

The design of multitarget drugs (MTDs) has become an innovative approach for the search of effective treatments in complex diseases such as cancer. In this work, we communicate our efforts in the design of multi-targeting histone deacetylase (HDAC) and protein kinase CK2 inhibitors as a novel therapeutic strategy against cancer. Using tetrabromobenzotriazole (TBB) and 2-dimethylamino-4,5,6,7-tetrabromo-benzimidazole (DMAT) as scaffolds for CK2 inhibition, and a hydroxamate to coordinate the zinc atom present in the active site of HDAC (zinc binding group, ZBG), new multitarget inhibitors have been designed and synthesized. According to the in vitro assays, N-Hydroxy-6-(4,5,6,7-tetrabromo-2-(dimethylamino)-1H-benzo[d]imidazol-1-yl)hexanamide (11b) is the most interesting compound, with IC50 values of 0.66; 1.46 and 3.67 µM. for HDAC6; HDAC1 and CK2; respectively. Cellular assays on different cancer cell lines rendered promising results for N-Hydroxy-8-(4,5,6,7-tetrabromo-2-(dimethylamino)-1H-benzo[d]imidazol-1-yl)octanamide (11d). This inhibitor presented the highest cytotoxic activity, proapoptotic capability, and the best mitochondria-targeting and multidrug-circumventing properties, thus being the most promising drug candidate for further in vivo studies.


Assuntos
Antineoplásicos/farmacologia , Caseína Quinase II/análise , Inibidores de Histona Desacetilases/farmacologia , Inibidores de Proteínas Quinases/farmacologia , Apoptose/efeitos dos fármacos , Caseína Quinase II/antagonistas & inibidores , Pontos de Checagem do Ciclo Celular/efeitos dos fármacos , Linhagem Celular Tumoral , Resistencia a Medicamentos Antineoplásicos/efeitos dos fármacos , Inibidores de Histona Desacetilases/síntese química , Inibidores de Histona Desacetilases/química , Humanos , Inibidores de Proteínas Quinases/síntese química , Inibidores de Proteínas Quinases/química , Espécies Reativas de Oxigênio/metabolismo
6.
Molecules ; 24(16)2019 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-31426440

RESUMO

Matrix metalloproteinases (MMPs) are a family of zinc- and calcium-dependent endopeptidases which are secreted or anchored in the cell membrane and are capable of degrading the multiple components of the extracellular matrix (ECM). MMPs are frequently overexpressed or highly activated in numerous human diseases. Owing to the important role of MMPs in human diseases, many MMP inhibitors (MMPIs) have been developed as novel therapeutics, and some of them have entered clinical trials. However, so far, only one MMPI (doxycycline) has been approved by the FDA. Therefore, the evaluation of the activity of a specific subset of MMPs in human diseases using clinically relevant imaging techniques would be a powerful tool for the early diagnosis and assessment of the efficacy of therapy. In recent years, numerous MMPIs labeled imaging agents have emerged. This article begins by providing an overview of the MMP subfamily and its structure and function. The latest advances in the design of subtype selective MMPIs and their biological evaluation are then summarized. Subsequently, the potential use of MMPI-labeled diagnostic agents in clinical imaging techniques are discussed, including positron emission tomography (PET), single-photon emission computed tomography (SPECT) and optical imaging (OI). Finally, this article concludes with future perspectives and clinical utility.


Assuntos
Aterosclerose/diagnóstico por imagem , Doenças Cardiovasculares/diagnóstico por imagem , Pneumopatias/diagnóstico por imagem , Inibidores de Metaloproteinases de Matriz/farmacocinética , Metaloproteinases da Matriz/química , Sondas Moleculares/farmacocinética , Neoplasias/diagnóstico por imagem , Osteoartrite/diagnóstico por imagem , Animais , Aterosclerose/metabolismo , Aterosclerose/patologia , Doenças Cardiovasculares/metabolismo , Doenças Cardiovasculares/patologia , Domínio Catalítico/genética , Modelos Animais de Doenças , Encefalomielite Autoimune Experimental/diagnóstico por imagem , Encefalomielite Autoimune Experimental/metabolismo , Encefalomielite Autoimune Experimental/patologia , Matriz Extracelular/metabolismo , Matriz Extracelular/patologia , Humanos , Pneumopatias/metabolismo , Pneumopatias/patologia , Inibidores de Metaloproteinases de Matriz/síntese química , Metaloproteinases da Matriz/genética , Metaloproteinases da Matriz/metabolismo , Imagem Molecular/métodos , Sondas Moleculares/síntese química , Esclerose Múltipla/diagnóstico por imagem , Esclerose Múltipla/metabolismo , Esclerose Múltipla/patologia , Neoplasias/metabolismo , Neoplasias/patologia , Osteoartrite/metabolismo , Osteoartrite/patologia , Tomografia por Emissão de Pósitrons/métodos , Tomografia Computadorizada de Emissão de Fóton Único/métodos
7.
Org Biomol Chem ; 17(4): 916-929, 2019 01 23.
Artigo em Inglês | MEDLINE | ID: mdl-30629065

RESUMO

In this article, we describe our efforts in the search of MMP2/CK2 dual targeting inhibitors. We have followed a rational drug design approach based on our experience in the selective inhibition of these two enzymes. We have successfully obtained highly active MMP2 (10, IC50 = 70 nM; 11, IC50 = 100 nM) and CK2 (16a, IC50 = 500 nM) inhibitors. However, structural fine tuning of these small molecules to simultaneously target both enzymes turned out to be an unattainable goal. Unexpectedly, we were lucky to identify new and selective MMP13 inhibitors (10, IC50 = 3.7 nM and 11, IC50 = 5.6 nM) with a novel TBB-derived scaffold. These compounds constitute an interesting starting point for further optimization.


Assuntos
Caseína Quinase II/antagonistas & inibidores , Metaloproteinase 13 da Matriz/metabolismo , Metaloproteinase 2 da Matriz/metabolismo , Inibidores de Proteínas Quinases/farmacologia , Caseína Quinase II/metabolismo , Linhagem Celular Tumoral , Relação Dose-Resposta a Droga , Humanos , Modelos Moleculares , Estrutura Molecular , Inibidores de Proteínas Quinases/química , Relação Estrutura-Atividade
8.
Eur J Med Chem ; 157: 946-959, 2018 Sep 05.
Artigo em Inglês | MEDLINE | ID: mdl-30165342

RESUMO

A series of new azolopyrimidine-peptide hybrids and indolomethylideneimidazolones were obtained and evaluated as calpain inhibitors. The hybrid compounds were inactive, whereas some members of the initial azolomethylideneimidazolone series showed interesting calpain inhibitory activity. By using 4b as a hit compound, a new series of analogs were synthesized by an efficient synthetic procedure based on a multicomponent reaction followed by an unprecedented reaction at the methylene position of the molecule. The best inhibitor found for calpain I (IC50 = 20 nM) was about 20 times more potent than the hit compound. Studies on 4b showed that its inhibition is consistent with an uncompetitive inhibition mode. This compound did not exhibit cellular toxicity at any of the doses tested (0.1-10 µM) and further studies indicated that it was capable of blockading chemical ischemia induction of apoptosis by preventing sodium azide-dependent calpain activation in intact human kidney tubular epithelial cells. The results of molecular modeling studies rationalized the inhibitory activity found for this series and account, from a structural point of view, for the most active compound identified (4j).


Assuntos
Azóis/farmacologia , Calpaína/antagonistas & inibidores , Descoberta de Drogas , Glicoproteínas/química , Glicoproteínas/farmacologia , Imidazolidinas/farmacologia , Peptídeos/farmacologia , Apoptose/efeitos dos fármacos , Azóis/química , Calpaína/metabolismo , Células Cultivadas , Relação Dose-Resposta a Droga , Células Epiteliais/efeitos dos fármacos , Células Epiteliais/metabolismo , Glicoproteínas/síntese química , Humanos , Imidazolidinas/química , Túbulos Renais/efeitos dos fármacos , Túbulos Renais/metabolismo , Modelos Moleculares , Estrutura Molecular , Peptídeos/química , Relação Estrutura-Atividade
9.
Neuropharmacology ; 137: 86-95, 2018 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-29753117

RESUMO

Pleiotrophin (PTN) and Midkine (MK) are neurotrophic factors that are upregulated in the prefrontal cortex after alcohol administration and have been shown to reduce ethanol drinking and reward. PTN and MK are the endogenous inhibitors of Receptor Protein Tyrosine Phosphatase (RPTP) ß/ζ (a.k.a. PTPRZ1, RPTPß, PTPζ), suggesting a potential role for this phosphatase in the regulation of alcohol effects. To determine if RPTPß/ζ regulates ethanol consumption, we treated mice with recently developed small-molecule inhibitors of RPTPß/ζ (MY10, MY33-3) before testing them for binge-like drinking using the drinking in the dark protocol. Mice treated with RPTPß/ζ inhibitors, particularly with MY10, drank less ethanol than controls. MY10 treatment blocked ethanol conditioned place preference, showed limited effects on ethanol-induced ataxia, and potentiated the sedative effects of ethanol. We also tested whether RPTPß/ζ is involved in ethanol signaling pathways. We found that ethanol treatment of neuroblastoma cells increased phosphorylation of anaplastic lymphoma kinase (ALK) and TrkA, known substrates of RPTPß/ζ. Treatment of neuroblastoma cells with MY10 or MY33-3 also increased levels of phosphorylated ALK and TrkA. However, concomitant treatment of neuroblastoma cells with ethanol and MY10 or MY33-3 prevented the increase in pTrkA and pALK. These results demonstrate for the first time that ethanol engages TrkA signaling and that RPTPß/ζ modulates signaling pathways activated by alcohol and behavioral responses to this drug. The data support the hypothesis that RPTPß/ζ might be a novel target of pharmacotherapy for reducing excessive alcohol consumption.


Assuntos
Consumo Excessivo de Bebidas Alcoólicas/enzimologia , Depressores do Sistema Nervoso Central/farmacologia , Etanol/farmacologia , Proteínas Tirosina Fosfatases Classe 5 Semelhantes a Receptores/antagonistas & inibidores , Dissuasores de Álcool/síntese química , Dissuasores de Álcool/química , Dissuasores de Álcool/farmacologia , Quinase do Linfoma Anaplásico/metabolismo , Animais , Consumo Excessivo de Bebidas Alcoólicas/tratamento farmacológico , Linhagem Celular Tumoral , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/química , Inibidores Enzimáticos/farmacologia , Humanos , Masculino , Camundongos Endogâmicos C57BL , Receptor trkA/metabolismo , Proteínas Tirosina Fosfatases Classe 5 Semelhantes a Receptores/metabolismo
10.
Eur J Med Chem ; 144: 318-329, 2018 Jan 20.
Artigo em Inglês | MEDLINE | ID: mdl-29275231

RESUMO

A new series of blood-brain barrier permeable molecules designed to mimic the activity of Pleiotrophin in the CNS has been designed and synthesized. These compounds exert their action by interacting with the intracellular domain PD1 of the Protein Tyrosine-Phosphatase Receptor Z1 (PTPRZ1), and inhibiting its tyrosine phosphatase activity. The most potent compounds 10a and 12b (IC50 = 0,1 µM) significantly increase the phosphorylation of key tyrosine residues of PTPRZ1 substrates involved in neuronal survival and differentiation, and display protective effects against amphetamine-induced toxicity. Docking and molecular dynamics experiments have been used to analyze the binding mode and to explain the observed selectivity against PTP1B. An In vivo experiment has demonstrated that 10a can cross the BBB, thus promoting the possibility of moving forward these candidates for the development of drugs for the treatment of CNS disorders, such as drug addiction and neurodegenerative diseases.


Assuntos
Anti-Inflamatórios não Esteroides/farmacologia , Proteínas de Transporte/farmacologia , Doenças do Sistema Nervoso Central/tratamento farmacológico , Citocinas/farmacologia , Inibidores Enzimáticos/farmacologia , Proteínas Tirosina Fosfatases Classe 5 Semelhantes a Receptores/antagonistas & inibidores , Animais , Anti-Inflamatórios não Esteroides/síntese química , Anti-Inflamatórios não Esteroides/química , Barreira Hematoencefálica/efeitos dos fármacos , Barreira Hematoencefálica/metabolismo , Proteínas de Transporte/síntese química , Proteínas de Transporte/química , Linhagem Celular , Sobrevivência Celular/efeitos dos fármacos , Doenças do Sistema Nervoso Central/metabolismo , Citocinas/síntese química , Citocinas/química , Relação Dose-Resposta a Droga , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/química , Humanos , Camundongos , Modelos Moleculares , Estrutura Molecular , Ratos , Proteínas Tirosina Fosfatases Classe 5 Semelhantes a Receptores/metabolismo , Relação Estrutura-Atividade
11.
Bioorg Med Chem ; 25(24): 6597-6604, 2017 12 15.
Artigo em Inglês | MEDLINE | ID: mdl-29137939

RESUMO

Hypothermia has been proved to have a beneficial effect on several pathologies. CIRBP is one of the so termed cold-shock proteins involved in this process. In this work, we have detected small molecules capable of modulating the activity of CIRBP in the absence of a cold stimulus, by High Throughput Virtual Screening (HTVS) of the Diversity Set IV of the NCI and 15 compounds of our in-house data base. Fifteen compounds were selected from the HTVS to carry out a second screening through a cell-based Western blot assay. This assay, together with molecular modeling studies allowed us to select compound zr17-2 for an in vivo experiment, which showed an interesting increase of CIRBP expression in several organs of experimental animals. Therefore, we have demonstrated that the effect of hypothermia can be mimicked by small molecules, which can be developed as first-in-class new drugs for the treatment of several diseases.


Assuntos
Hipotermia/tratamento farmacológico , Bibliotecas de Moléculas Pequenas/uso terapêutico , Animais , Linhagem Celular , Proteínas e Peptídeos de Choque Frio/biossíntese , Relação Dose-Resposta a Droga , Ensaios de Triagem em Larga Escala , Hipotermia/metabolismo , Masculino , Modelos Moleculares , Estrutura Molecular , Proteínas de Ligação a RNA/biossíntese , Ratos , Bibliotecas de Moléculas Pequenas/síntese química , Bibliotecas de Moléculas Pequenas/química , Relação Estrutura-Atividade
12.
Org Biomol Chem ; 13(1): 142-56, 2015 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-25348733

RESUMO

MMP-2 is a validated target for the development of anticancer agents. Herein we describe the synthesis of a new series of potent phenylalanine derived hydroxamates, with increased MMP-2/MMP-9 selectivity compared to analogous hydroxamates described previously. Docking and molecular dynamics experiments have been used to account for this selectivity, and to clarify the role of the triazole ring in the binding process.


Assuntos
Desenho de Fármacos , Gelatinases/antagonistas & inibidores , Ácidos Hidroxâmicos/síntese química , Ácidos Hidroxâmicos/farmacologia , Inibidores de Metaloproteinases de Matriz/síntese química , Inibidores de Metaloproteinases de Matriz/farmacologia , Técnicas de Química Sintética , Gelatinases/química , Gelatinases/metabolismo , Ácidos Hidroxâmicos/química , Ácidos Hidroxâmicos/metabolismo , Inibidores de Metaloproteinases de Matriz/química , Inibidores de Metaloproteinases de Matriz/metabolismo , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Fenilalanina/química , Especificidade por Substrato , Triazóis/química
13.
J Med Chem ; 57(12): 5470-6, 2014 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-24871162

RESUMO

Hybrids of vinca alkaloids and phomopsin A have been elaborated with the aim of interfering with the "vinca site" and the "peptide site" of the vinca domain in tubulin. They were synthesized by an efficient one-pot procedure that directly links the octahydrophomopsin lateral chain to the velbenamine moiety of 7'-homo-anhydrovinblastine. In their modeled complexes with tubulin, these hybrids were found to superimpose nicely on the tubulin-bound structures of vinblastine and phomopsin A. This good matching can account for the fact that two of them are very potent inhibitors of microtubules assembly and are cytotoxic against four cancer cell lines.


Assuntos
Antineoplásicos/síntese química , Micotoxinas/síntese química , Vimblastina/análogos & derivados , Vimblastina/síntese química , Antineoplásicos/química , Antineoplásicos/farmacologia , Linhagem Celular Tumoral , Ensaios de Seleção de Medicamentos Antitumorais , Humanos , Modelos Moleculares , Micotoxinas/química , Micotoxinas/farmacologia , Tubulina (Proteína)/química , Moduladores de Tubulina/síntese química , Moduladores de Tubulina/química , Moduladores de Tubulina/farmacologia , Vimblastina/química , Vimblastina/farmacologia
14.
ACS Chem Biol ; 9(4): 1033-43, 2014 Apr 18.
Artigo em Inglês | MEDLINE | ID: mdl-24524625

RESUMO

The binding of epothilones to dimeric tubulin and to microtubules has been studied by means of biochemical and NMR techniques. We have determined the binding constants of epothilone A (EpoA) and B (EpoB) to dimeric tubulin, which are 4 orders of magnitude lower than those for microtubules, and we have elucidated the conformation and binding epitopes of EpoA and EpoB when bound to tubulin dimers and microtubules in solution. The determined conformation of epothilones when bound to dimeric tubulin is similar to that found by X-ray crystallographic techniques for the binding of EpoA to the Tubulin/RB3/TTL complex; it is markedly different from that reported for EpoA bound to zinc-induced sheets obtained by electron crystallography. Likewise, only the X-ray structure of EpoA bound to the Tubulin/RB3/TTL complex at the luminal site, but not the electron crystallography structure, is compatible with the results obtained by STD on the binding epitope of EpoA bound to dimeric tubulin, thus confirming that the allosteric change (structuring of the M-loop) is the biochemical mechanism of induction of tubulin assembly by epothilones. TR-NOESY signals of EpoA bound to microtubules have been obtained, supporting the interaction with a transient binding site with a fast exchange rate (pore site), consistent with the notion that epothilones access the luminal site through the pore site, as has also been observed for taxanes. Finally, the differences in the tubulin binding affinities of a series of epothilone analogues has been quantitatively explained using the newly determined binding pose and the COMBINE methodology.


Assuntos
Epotilonas/metabolismo , Microtúbulos/metabolismo , Tubulina (Proteína)/metabolismo , Dimerização , Estabilidade de Medicamentos , Epotilonas/química , Ligantes , Imageamento por Ressonância Magnética , Microtúbulos/química , Modelos Moleculares , Ligação Proteica , Termodinâmica , Tubulina (Proteína)/química
15.
Biochem J ; 458(3): 547-57, 2014 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-24392963

RESUMO

DHQ2 (type II dehydroquinase), which is an essential enzyme in Helicobacter pylori and Mycobacterium tuberculosis and does not have any counterpart in humans, is recognized to be an attractive target for the development of new antibacterial agents. Computational and biochemical studies that help understand in atomic detail the catalytic mechanism of these bacterial enzymes are reported in the present paper. A previously unknown key role of certain conserved residues of these enzymes, as well as the structural changes responsible for triggering the release of the product from the active site, were identified. Asp89*/Asp88* from a neighbouring enzyme subunit proved to be the residue responsible for the deprotonation of the essential tyrosine to afford the catalytic tyrosinate, which triggers the enzymatic process. The essentiality of this residue is supported by results from site-directed mutagenesis. For H. pylori DHQ2, this reaction takes place through the assistance of a water molecule, whereas for M. tuberculosis DHQ2, the tyrosine is directly deprotonated by the aspartate residue. The participation of a water molecule in this deprotonation reaction is supported by solvent isotope effects and proton inventory studies. MD simulation studies provide details of the required motions for the catalytic turnover, which provides a complete overview of the catalytic cycle. The product is expelled from the active site by the essential arginine residue and after a large conformational change of a loop containing two conserved arginine residues (Arg109/Arg108 and Arg113/Arg112), which reveals a previously unknown key role for these residues. The present study highlights the key role of the aspartate residue whose blockage could be useful in the rational design of inhibitors and the mechanistic differences between both enzymes.


Assuntos
Proteínas de Bactérias/química , Helicobacter pylori/enzimologia , Hidroliases/química , Mycobacterium tuberculosis/enzimologia , Arginina/química , Ácido Aspártico/química , Proteínas de Bactérias/genética , Catálise , Hidroliases/genética , Cinética , Simulação de Dinâmica Molecular , Mutagênese Sítio-Dirigida , Teoria Quântica , Solventes
16.
J Med Chem ; 56(15): 6088-100, 2013 Aug 08.
Artigo em Inglês | MEDLINE | ID: mdl-23822556

RESUMO

Sixteen new 7'-homo-anhydrovinblastine derivatives were prepared in one or two steps from vinorelbine by means of an original and regiospecific rearrangement and subsequent diastereoselective reduction. This strategy has allowed fast access to a family of vinca alkaloid derivatives with an enlarged and functionalized ring C'. Their synthesis and biological evaluation are reported. One compound (compound 35) is 1.7 times more active than vinorelbine as a tubulin assembly inhibitor. Moreover, some of these compounds are highly cytotoxic, and two of them are more potent than vinorelbine on HCT116 and K562 cell lines. Molecular modeling studies, carried out with two of the new vinca derivatives, provide useful hints about how a given functionalization introduced at positions 7' and 8' of the C' ring results in improved binding interactions between one of the new derivatives and the interdimer interface when compared to the parent compound vinblastine.


Assuntos
Antineoplásicos/síntese química , Moduladores de Tubulina/síntese química , Vimblastina/análogos & derivados , Vimblastina/síntese química , Antineoplásicos/farmacologia , Ciclo Celular/efeitos dos fármacos , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Ensaios de Seleção de Medicamentos Antitumorais , Humanos , Microtúbulos/química , Modelos Moleculares , Estereoisomerismo , Relação Estrutura-Atividade , Moduladores de Tubulina/farmacologia , Vimblastina/farmacologia
17.
Org Biomol Chem ; 11(18): 3046-56, 2013 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-23532250

RESUMO

Ten novel taxanes bearing modifications at the C2 and C13 positions of the baccatin core have been synthesized and their binding affinities for mammalian tubulin have been experimentally measured. The design strategy was guided by (i) calculation of interaction energy maps with carbon, nitrogen and oxygen probes within the taxane-binding site of ß-tubulin, and (ii) the prospective use of a structure-based QSAR (COMBINE) model derived from an earlier series comprising 47 congeneric taxanes. The tubulin-binding affinity displayed by one of the new compounds (CTX63) proved to be higher than that of docetaxel, and an updated COMBINE model provided a good correlation between the experimental binding free energies and a set of weighted residue-based ligand-receptor interaction energies for 54 out of the 57 compounds studied. The remaining three outliers from the original training series have in common a large unfavourable entropic contribution to the binding free energy that we attribute to taxane preorganization in aqueous solution in a conformation different from that compatible with tubulin binding. Support for this proposal was obtained from solution NMR experiments and molecular dynamics simulations in explicit water. Our results shed additional light on the determinants of tubulin-binding affinity for this important class of antitumour agents and pave the way for further rational structural modifications.


Assuntos
Simulação por Computador , Taxoides/metabolismo , Tubulina (Proteína)/metabolismo , Animais , Sítios de Ligação , Humanos , Espectroscopia de Ressonância Magnética , Modelos Biológicos , Estrutura Molecular , Relação Quantitativa Estrutura-Atividade , Taxoides/síntese química , Taxoides/farmacologia , Termodinâmica , Tubulina (Proteína)/química , Tubulina (Proteína)/efeitos dos fármacos
18.
ChemMedChem ; 8(5): 740-7, 2013 May.
Artigo em Inglês | MEDLINE | ID: mdl-23450741

RESUMO

Herein we report comparative binding energy (COMBINE) analyses to derive quantitative structure-activity relationship (QSAR) models that help rationalize the determinants of binding affinity for inhibitors of type II dehydroquinase (DHQ2), the third enzyme of the shikimic acid pathway. Independent COMBINE models were derived for Helicobacter pylori and Mycobacterium tuberculosis DHQ2, which is an essential enzyme in both these pathogenic bacteria that has no counterpart in human cells. These studies quantify the importance of the hydrogen bonding interactions between the ligands and the water molecule involved in the DHQ2 reaction mechanism. They also highlight important differences in the ligand interactions with the interface pocket close to the active site that could provide guides for future inhibitor design.


Assuntos
Inibidores Enzimáticos/metabolismo , Inibidores Enzimáticos/farmacologia , Hidroliases/antagonistas & inibidores , Hidroliases/metabolismo , Sítios de Ligação , Inibidores Enzimáticos/química , Helicobacter pylori/enzimologia , Hidroliases/química , Ligação de Hidrogênio , Modelos Moleculares , Estrutura Molecular , Mycobacterium tuberculosis/enzimologia , Relação Quantitativa Estrutura-Atividade , Termodinâmica
19.
ChemMedChem ; 7(5): 836-43, 2012 May.
Artigo em Inglês | MEDLINE | ID: mdl-22431398

RESUMO

The conformational preferences of epothilone A (EPA) and a 12,13-cyclopropyl C12-epimerized analogue were explored in aqueous solution using molecular dynamics simulations. The simulated conformers that provided an optimal fit in the paclitaxel binding site of mammalian ß-tubulin were then selected. The resulting modeled complexes were simulated before and after refinement of the M-loop to improve the fitting and assess ligand stability within the binding pocket. The tubulin-bound conformation of EPA was found to be unlike a previously reported solution obtained through mixed crystallographic/NMR/modeling studies. However, our conformation was in agreement with an NMR-based proposal although the exact binding pose within the site was different. Molecular models were built for the complexes of 14 epothilone derivatives with ß-tubulin. A projection to latent structures regression method succeeded in providing a good prediction of the experimentally measured binding enthalpies for the whole set of ligands by assigning weights to a selection of interaction energy terms. These receptor-based, quantitative structure-activity relationships support the proposed binding mode, help confirm and interpret previously acquired experimental data, shed additional light on the effect of several ß-tubulin mutations on ligand binding, and can potentially direct further experimental studies.


Assuntos
Epotilonas/metabolismo , Tubulina (Proteína)/metabolismo , Sítios de Ligação , Epotilonas/química , Modelos Moleculares , Paclitaxel/química , Paclitaxel/metabolismo , Relação Quantitativa Estrutura-Atividade , Termodinâmica , Tubulina (Proteína)/química
20.
Anticancer Agents Med Chem ; 12(3): 219-25, 2012 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-22044006

RESUMO

The Vinca alkaloids are a group of widely used anticancer drugs, originally extracted from the Madagascar periwinkle, that disrupt microtubule dynamics in mammalian cells by interfering with proper assembly of α,ß-tubulin heterodimers. They favor curved tubulin assemblies that destabilize microtubules and induce formation of spiral aggregates. Their binding energy profiles have been characterized by means of sedimentation velocity assays and the binding site of vinblastine at the interface between two tubulin dimers (α1ß1 � α2ß2) has been ascertained by X-ray crystallographic studies on a complex of tubulin with the stathmin-like domain of protein RB3, albeit at relatively low resolution. Here we use molecular modeling and simulation techniques to build, refine and perform a comparative analysis of the three-dimensional complexes of vinblastine, vincristine, vinorelbine and vinflunine with a ß1α2-tubulin interface in explicit water to rationalize the binding affinity differences in structural and energetic terms. Our results shed some more light into the binding determinants and the structure-activity relationships of these clinically useful agents.


Assuntos
Antimitóticos/química , Antimitóticos/farmacologia , Antineoplásicos Fitogênicos/química , Antineoplásicos Fitogênicos/farmacologia , Tubulina (Proteína)/química , Alcaloides de Vinca/química , Alcaloides de Vinca/farmacologia , Sequência de Aminoácidos , Sítios de Ligação , Simulação de Dinâmica Molecular , Dados de Sequência Molecular , Estrutura Terciária de Proteína , Homologia de Sequência de Aminoácidos , Relação Estrutura-Atividade
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