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1.
Chem Biol Interact ; 330: 109236, 2020 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-32866467

RESUMO

A series of novel pyrrolopyrimidine urea derivatives were synthesized and evaluated for their anticancer activity against colon cancer cell lines. Compounds showed the remarkable cytotoxic activity on HCT-116 wt cell line. The most potent compound 4c (IC50 = 0.14 µM) induced apoptosis in HCT-116 wt and HCT-116 p53-/- cell lines. Otherwise, treatment of HCT-116 BAX-/-BAK-/- cells with compound 4c didn't lead to activation of apoptosis, suggesting that compound 4c induces apoptotic cell death by activating BAX/BAK-dependent pathway. Moreover, while the compound 4c increase the activation of caspase-3 and caspase-9 levels in HCT-116 wt and HCT-116 p53-/- cells, caspase-3 or caspase-9 activation was not observed in HCT-116 BAX-/-BAK-/- cells. In addition, compound 4c induced mitochondrial apoptosis in cells grown as oncospheroids, which better mimic the in vivo milieu of tumors. 4c treatment also activated JNK along with inhibition of prosurvival kinases such as Akt and ERK 1/2 in HCT-116 wt and HCT-116 p53 -/- cells as well as in HCT-116 BAX-/-BAK-/- cells. Notably, our results indicated that compound 4c induced mitochondrial apoptosis through activation p53-independent apoptotic signaling pathways.


Assuntos
Apoptose/efeitos dos fármacos , Neoplasias do Colo/tratamento farmacológico , Pirimidinas/farmacologia , Pirróis/farmacologia , Proteína Supressora de Tumor p53/fisiologia , Caspase 3/genética , Caspase 9/genética , Linhagem Celular Tumoral , Neoplasias do Colo/patologia , Técnicas de Inativação de Genes , Células HCT116 , Humanos , Mitocôndrias/metabolismo , Pirimidinas/síntese química , Pirimidinas/química , Pirróis/síntese química , Pirróis/química , Proteína Supressora de Tumor p53/genética , Proteína Killer-Antagonista Homóloga a bcl-2/genética , Proteína X Associada a bcl-2/genética
2.
Gene ; 763: 144997, 2020 Dec 30.
Artigo em Inglês | MEDLINE | ID: mdl-32783992

RESUMO

The CRISPR-Cas system currently stands as one of the best multifaceted tools for site-specific genome engineering in mammals. An important aspect of research in this field focusses on improving the specificity and efficacy of precise genome editing in multiple model systems. The cornerstone of this mini-review is one of the extensively investigated small molecule inhibitor, SCR7, which abrogates NHEJ, a Ligase IV-dependent DSB repair pathway, thus guiding integration of the foreign DNA fragment via the more precise homology directed repair during genome editing. One of our recent studies sheds light on properties of different forms of SCR7. Here, we give a succinct account on the use of SCR7 and its different forms in CRISPR-Cas system, highlighting their chemical properties and biological relevance as potent efficiency-enhancing CRISPR tools.


Assuntos
Sistemas CRISPR-Cas , Inibidores Enzimáticos/farmacologia , Edição de Genes/métodos , Pirimidinas/farmacologia , Reparo de DNA por Recombinação/efeitos dos fármacos , Bases de Schiff/farmacologia , Animais , DNA Ligase Dependente de ATP/antagonistas & inibidores , Inibidores Enzimáticos/química , Humanos , Pirimidinas/química , Bases de Schiff/química
3.
Life Sci ; 256: 117912, 2020 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-32504755

RESUMO

Histone deacetylase enzymes were prominent chromatin remodeling drug that targets in the pathophysiology of Alzheimer's disease associated with transcriptional dysregulation. In vitro and in vivo models of AD have demonstrated overexpression of HDAC activity. Non-specificity and non-selectivity of HDAC are the major problems of existing HDAC inhibitors. Hence, we aim to set up a methodology describing the rational development of isoform-selective HDAC inhibitor targeting class, I and class IIb. A convenient multistage virtual screening followed by machine learning and IC50 screenings were used to classify the 5064 compounds into inhibitors and non-inhibitors classes retrieved from the ChEMBL database. ADMET analysis identified the pharmacokinetics and pharmacodynamics properties of selected compounds. Molecular docking, along with mutational analysis of eleven compounds, characterized the inhibiting potency. Herein, for the first time, we reported ChEMBL1834473 (2-[[5-(4-chlorophenyl)-1,3,4-thiadiazol-2-yl]amino]-N-hydroxypyrimidine-5-carboxamide) as the isoform-selective HDAC inhibitor, which interact central Zn2+ atom. The negative energy and interacting residue of the ChEMBL1834473 with six HDAC isoform has also been tabulated and mapped. Moreover, our findings concluded histidine, glycine, phenylalanine, and aspartic acid as key residues in protein-ligand interaction and classify 2347 compounds as HDAC inhibitors. Later, a protein-protein interaction network of six HDAC with the key proteins involved in the progression of an AD and signaling pathway, which describes the relationship between ChEMBL1834473 and AD, has been demonstrated using PPI network where the chosen inhibitor will work. Altogether, we conclude that the compound ChEMBL1834473 may be capable of inhibiting all isoforms of class I and class IIb HDAC based on computational analysis for AD therapeutics.


Assuntos
Doença de Alzheimer/tratamento farmacológico , Inibidores de Histona Desacetilases/química , Inibidores de Histona Desacetilases/uso terapêutico , Pirimidinas/química , Pirimidinas/uso terapêutico , Ácido Aspártico/metabolismo , Bases de Dados de Compostos Químicos , Avaliação Pré-Clínica de Medicamentos , Glicina/metabolismo , Histona Desacetilases/metabolismo , Humanos , Aprendizado de Máquina , Simulação de Acoplamento Molecular , Estrutura Molecular , Terapia de Alvo Molecular , Fenilalanina/metabolismo , Isoformas de Proteínas/química , Termodinâmica , Zinco/metabolismo
4.
Adv Pharmacol ; 88: 173-191, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32416867

RESUMO

The glucagon-like peptide-1 receptor (GLP-1R) is a significant therapeutic target for small molecule drug discovery given the therapeutic impact of peptide agonists in the diabetes sphere. We review the discovery and subsequent characterization of the small molecule GLP-1R allosteric modulator 4-(3-(Benzyloxy)phenyl)-2-(ethylsulfinyl)-6-(trifluoromethyl)pyrimidine (BETP). BETP is a covalent modulator of the GLP-1R, and we discuss the pharmacological implications and possible structural basis of this novel mode of action. We highlight the insights into class B G-protein coupled receptor pharmacology and biology provided by studies conducted with BETP. These include the descriptions of exquisite allosteric modulator probe dependence and biased signaling in vitro and in vivo. We conclude with an analysis of the utility of BETP as a chemical probe for the GLP-1R.


Assuntos
Descoberta de Drogas , Receptor do Peptídeo Semelhante ao Glucagon 1/agonistas , Pirimidinas/farmacologia , Regulação Alostérica/efeitos dos fármacos , Sequência de Aminoácidos , Animais , AMP Cíclico/metabolismo , Receptor do Peptídeo Semelhante ao Glucagon 1/química , Humanos , Pirimidinas/química , Bibliotecas de Moléculas Pequenas/farmacologia
5.
J Chromatogr A ; 1622: 461104, 2020 Jul 05.
Artigo em Inglês | MEDLINE | ID: mdl-32376023

RESUMO

The coexistence of the anilinopyrimidine fungicides pyrimethanil (PYR) and cyprodinil (CYP), and suspected metabolites in wine samples was investigated by liquid chromatography (LC) with tandem mass spectrometry (MS/MS), based on triple quadrupole (QqQ) and quadrupole time-of-flight (QTOF) MS instruments. For the first time, quantitative data obtained after solid-phase extraction (SPE) of wine samples have demonstrated the systematic presence of 4-hydroxyanilino derivatives of PYR and CYP in wines containing residues of parent fungicides, at concentrations from 0.2 to 58 ng mL-1. Higher concentration ratios (hydroxylated derivative/active fungicide) were measured in red than in white wines, particularly in case of PYR. On average, the concentrations of PYR-4OH were twice those measured for PYR in red wines. A targeted search of hydroxyl derivatives in wine extracts by LC-QTOF-MS showed the existence of additional hydroxylation positions in the pyrimidine ring and/or in the alkyl substituents bond to this cycle in the structure of both anti-botrytis fungicides. Moreover, free and glycosylated forms of the hydroxylated metabolites for both fungicides coexist in wine samples. In case of CYP, it is proved that hydroxylated and glycosylated metabolites are already present in grapes before vinification.


Assuntos
Fungicidas Industriais/análise , Resíduos de Praguicidas/análise , Pirimidinas/análise , Vinho/análise , Cromatografia Líquida , Fungicidas Industriais/química , Fungicidas Industriais/metabolismo , Resíduos de Praguicidas/química , Resíduos de Praguicidas/isolamento & purificação , Resíduos de Praguicidas/metabolismo , Pirimidinas/química , Pirimidinas/metabolismo , Extração em Fase Sólida , Espectrometria de Massas em Tandem
6.
PLoS One ; 15(5): e0233089, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32459810

RESUMO

Many drugs are promiscuous and bind to multiple targets. On the one hand, these targets may be linked to unwanted side effects, but on the other, they may achieve a combined desired effect (polypharmacology) or represent multiple diseases (drug repositioning). With the growth of 3D structures of drug-target complexes, it is today possible to study drug promiscuity at the structural level and to screen vast amounts of drug-target interactions to predict side effects, polypharmacological potential, and repositioning opportunities. Here, we pursue such an approach to identify drugs inactivating B-cells, whose dysregulation can function as a driver of autoimmune diseases. Screening over 500 kinases, we identified 22 candidate targets, whose knock out impeded the activation of B-cells. Among these 22 is the gene KDR, whose gene product VEGFR2 is a prominent cancer target with anti-VEGFR2 drugs on the market for over a decade. The main result of this paper is that structure-based drug repositioning for the identified kinase targets identified the cancer drug ibrutinib as micromolar VEGFR2 inhibitor with a very high therapeutic index in B-cell inactivation. These findings prove that ibrutinib is not only acting on the Bruton's tyrosine kinase BTK, against which it was designed. Instead, it may be a polypharmacological drug, which additionally targets angiogenesis via inhibition of VEGFR2. Therefore ibrutinib carries potential to treat other VEGFR2 associated disease. Structure-based drug repositioning explains ibrutinib's anti VEGFR2 action through the conservation of a specific pattern of interactions of the drug with BTK and VEGFR2. Overall, structure-based drug repositioning was able to predict these findings at a fraction of the time and cost of a conventional screen.


Assuntos
Reposicionamento de Medicamentos/métodos , Pirazóis/química , Pirazóis/farmacologia , Pirimidinas/química , Pirimidinas/farmacologia , Receptor 2 de Fatores de Crescimento do Endotélio Vascular/antagonistas & inibidores , Tirosina Quinase da Agamaglobulinemia/antagonistas & inibidores , Tirosina Quinase da Agamaglobulinemia/metabolismo , Linfócitos B/metabolismo , Humanos , Células Jurkat , Interferência de RNA , Transdução de Sinais/efeitos dos fármacos , Suramina/química , Suramina/farmacologia , Receptor 2 de Fatores de Crescimento do Endotélio Vascular/metabolismo
7.
Arch Biochem Biophys ; 688: 108389, 2020 07 30.
Artigo em Inglês | MEDLINE | ID: mdl-32387178

RESUMO

The hydroxymethylpyrimidine phosphate kinases (HMPPK) encoded by the thiD gene are involved in the thiamine biosynthesis pathway, can perform two consecutive phosphorylations of 4-amino-5-hydroxymethyl-2-methyl pyrimidine (HMP) and are found in thermophilic and mesophilic bacteria, but only a few characterizations of mesophilic enzymes are available. The presence of another homolog enzyme (pyridoxal kinase) that can only catalyze the first phosphorylation of HMP and encoded by pdxK gene, has hampered a precise annotation in this enzyme family. Here we report the kinetic characterization of two HMPPK with structure available, the mesophilic and thermophilic enzyme from Salmonella typhimurium (StHMPPK) and Thermus thermophilus (TtHMPPK), respectively. Also, given their high structural similarity, we have analyzed the structural determinants of protein thermal stability in these enzymes by molecular dynamics simulation. The results show that pyridoxal kinases (PLK) from gram-positive bacteria (PLK/HMPPK-like enzymes) constitute a phylogenetically separate group from the canonical PLK, but closely related to the HMPPK, so the PLK/HMPPK-like and canonical PLK, both encoded by pdxK genes, are different and must be annotated distinctly. The kinetic characterization of StHMPPK and TtHMPPK, shows that they perform double phosphorylation on HMP, both enzymes are specific for HMP, not using pyridoxal-like molecules as substrates and their kinetic mechanism involves the formation of a ternary complex. Molecular dynamics simulation shows that StHMPPK and TtHMPPK have striking differences in their conformational flexibility, which can be correlated with the hydrophobic packing and electrostatic interaction network given mainly by salt bridge bonds, but interestingly not by the number of hydrogen bond interactions as reported for other thermophilic enzymes. ENZYMES: EC 2.7.1.49, EC 2.7.4.7, EC 2.7.1.35, EC 2.7.1.50.


Assuntos
Proteínas de Bactérias/química , Fosfotransferases (Aceptor do Grupo Fosfato)/química , Proteínas de Bactérias/isolamento & purificação , Ensaios Enzimáticos , Ligação de Hidrogênio , Interações Hidrofóbicas e Hidrofílicas , Cinética , Simulação de Dinâmica Molecular , Fosfotransferases (Aceptor do Grupo Fosfato)/isolamento & purificação , Conformação Proteica , Estabilidade Proteica , Pirimidinas/química , Salmonella typhimurium/enzimologia , Eletricidade Estática , Especificidade por Substrato , Thermus thermophilus/enzimologia
8.
J Environ Sci Health B ; 55(7): 599-603, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32253976

RESUMO

A method was developed for the simultaneous qualitative and quantitative determination of azoxystrobin and its relevant impurity (Z)-azoxystrobin using high performance liquid chromatography with diode array detector (HPLC-DAD) in suspension concentrate (SC) pesticide formulations, with the aim of the product quality control. Method validation was realized according to SANCO/3030/99 rev. 5. The proposed method was characterized by acceptable accuracy and precision. The repeatability expressed as ratio standard deviation (%RSD) to relative standard deviation (%RSDr) was lower than 1, whereas individual recoveries were in the range of 97-103% and 90-110% for azoxystrobin and (Z)-azoxystrobin, respectively. The limit of quantification (LOQ) for the impurity ((Z)-azoxystrobin) amounted to 0.3 µg mL-1 and was acceptable because it was lower than the maximum permitted level according to Commission Implementing Regulation (EU) No 703/2011 of 20 July 2011 for the active substance (azoxystrobin) being 25 g kg-1 of the azoxystrobin content found. The method described in this paper is simple, precise, accurate and selective as well as represents a new and reliable way of simultaneous determination of azoxystrobin and its relevant impurity in formulated products.


Assuntos
Cromatografia Líquida de Alta Pressão/métodos , Pirimidinas/análise , Estrobilurinas/análise , Fungicidas Industriais/análise , Pirimidinas/química , Controle de Qualidade , Reprodutibilidade dos Testes , Estrobilurinas/química
9.
J Environ Sci Health B ; 55(7): 630-645, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32338140

RESUMO

Effect of the wheat straw ash (WSA) on pretilachlor and the rice straw ash (RSA) on sulfosulfuron kinetics and adsorption behavior was studied. Kinetics study suggested that adsorption of herbicides in soil/soil + 0.2% ash mixture was best explained by the pseudo second order model. Ashes at 0.1%-0.5% levels increased adsorption of respective herbicide; but, effect varied with ash content and soil type. Effect of ash (0.2%) on herbicide's adsorption was more in the sandy loam soil (144%-188%) than in the clay loam soil (112%-122%) suggesting masking of ash particles. The Freundlich adsorption isotherm explained the adsorption of herbicides in the soils/soil + ash mixtures and sorption was highly nonlinear as 1/n (slope) values varied between 0.57 and 1.25 for pretilachlor and 0.32 and 0.77 for sulfosulfuron. Adsorption increased with increase in temperature. High surface area unburnt carbon in ashes was responsible for increase in adsorption and decrease in desorption of herbicides in ash mixed soils. The pH of soil/soil + ash mixtures affected herbicide adsorption, but effect was significant for pretilachlor. The negative free energy change (ΔG) values suggested that the sorption process was exothermic and spontaneous in nature. This study has implications in identifying the role of crop residue burning on fate of herbicides applied in succeeding crop.


Assuntos
Produtos Agrícolas/química , Herbicidas/química , Poluentes do Solo/química , Acetanilidas/química , Adsorção , Carbono , Argila , Índia , Cinética , Oryza/química , Pirimidinas/química , Solo/química , Sulfonamidas/química , Triticum/química
10.
Chemistry ; 26(24): 5441-5448, 2020 Apr 24.
Artigo em Inglês | MEDLINE | ID: mdl-32271495

RESUMO

N6 -(2-Deoxy-α,ß-d-erythropentofuranosyl)-2,6-diamino-4-hydroxy-5-formamidopyrimidine (Fapy⋅dG) is a major DNA lesion produced from 2'-deoxyguanosine under oxidizing conditions. Fapy⋅dG is produced from a common intermediate that leads to 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-OxodGuo), and in greater quantities in cells. The impact of Fapy⋅dG on DNA structure and function is much less well understood than that of 8-OxodGuo. This is largely due to the significantly greater difficulty in synthesizing oligonucleotides containing Fapy⋅dG than 8-OxodGuo. We describe a synthetic approach for preparing oligonucleotides containing Fapy⋅dG that will facilitate intensive studies of this lesion in DNA. A variety of oligonucleotides as long as 30 nucleotides are synthesized. We anticipate that the chemistry described herein will provide an impetus for a wide range of studies involving Fapy⋅dG.


Assuntos
8-Hidroxi-2'-Desoxiguanosina/síntese química , DNA/química , Desoxiguanosina/química , Formamidas/síntese química , Furanos/síntese química , Oligonucleotídeos/síntese química , Pirimidinas/síntese química , 8-Hidroxi-2'-Desoxiguanosina/química , Formamidas/química , Furanos/química , Oligonucleotídeos/química , Oxirredução , Estresse Oxidativo , Pirimidinas/química
11.
PLoS One ; 15(4): e0231877, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32315352

RESUMO

Alterations in fibroblast growth factor receptor (FGFR) genes have been identified as potential driver oncogenes. Pharmacological targeting of FGFRs may therefore provide therapeutic benefit to selected cancer patients, and proof-of-concept has been established in early clinical trials of FGFR inhibitors. Here, we present the molecular structure and preclinical characterization of INCB054828 (pemigatinib), a novel, selective inhibitor of FGFR 1, 2, and 3, currently in phase 2 clinical trials. INCB054828 pharmacokinetics and pharmacodynamics were investigated using cell lines and tumor models, and the antitumor effect of oral INCB054828 was investigated using xenograft tumor models with genetic alterations in FGFR1, 2, or 3. Enzymatic assays with recombinant human FGFR kinases showed potent inhibition of FGFR1, 2, and 3 by INCB054828 (half maximal inhibitory concentration [IC50] 0.4, 0.5, and 1.0 nM, respectively) with weaker activity against FGFR4 (IC50 30 nM). INCB054828 selectively inhibited growth of tumor cell lines with activation of FGFR signaling compared with cell lines lacking FGFR aberrations. The preclinical pharmacokinetic profile suggests target inhibition is achievable by INCB054828 in vivo with low oral doses. INCB054828 suppressed the growth of xenografted tumor models with FGFR1, 2, or 3 alterations as monotherapy, and the combination of INCB054828 with cisplatin provided significant benefit over either single agent, with an acceptable tolerability. The preclinical data presented for INCB054828, together with preliminary clinical observations, support continued investigation in patients with FGFR alterations, such as fusions and activating mutations.


Assuntos
Morfolinas/uso terapêutico , Neoplasias/tratamento farmacológico , Inibidores de Proteínas Quinases/uso terapêutico , Pirimidinas/uso terapêutico , Pirróis/uso terapêutico , Receptor Tipo 1 de Fator de Crescimento de Fibroblastos/antagonistas & inibidores , Receptor Tipo 2 de Fator de Crescimento de Fibroblastos/antagonistas & inibidores , Receptor Tipo 3 de Fator de Crescimento de Fibroblastos/antagonistas & inibidores , Administração Oral , Animais , Linhagem Celular Tumoral , Feminino , Meia-Vida , Humanos , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Nus , Camundongos SCID , Morfolinas/química , Morfolinas/farmacocinética , Neoplasias/patologia , Inibidores de Proteínas Quinases/química , Inibidores de Proteínas Quinases/farmacocinética , Pirimidinas/química , Pirimidinas/farmacocinética , Pirróis/química , Pirróis/farmacocinética , Ratos , Ratos Nus , Receptor Tipo 1 de Fator de Crescimento de Fibroblastos/metabolismo , Receptor Tipo 2 de Fator de Crescimento de Fibroblastos/metabolismo , Receptor Tipo 3 de Fator de Crescimento de Fibroblastos/metabolismo , Ensaios Antitumorais Modelo de Xenoenxerto
12.
Mol Pharmacol ; 97(6): 392-401, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32234810

RESUMO

G protein-coupled receptor (GPCR) kinases (GRKs) play a key role in terminating signals initiated by agonist-bound GPCRs. However, chronic stimulation of GPCRs, such as that which occurs during heart failure, leads to the overexpression of GRKs and maladaptive downregulation of GPCRs on the cell surface. We previously reported the discovery of potent and selective families of GRK inhibitors based on either the paroxetine or GSK180736A scaffold. A new inhibitor, CCG258747, which is based on paroxetine, demonstrates increased potency against the GRK2 subfamily and favorable pharmacokinetic parameters in mice. CCG258747 and the closely related compound CCG258208 also showed high selectivity for the GRK2 subfamily in a kinome panel of 104 kinases. We developed a cell-based assay to screen the ability of CCG258747 and 10 other inhibitors with different GRK subfamily selectivities and with either the paroxetine or GSK180736A scaffold to block internalization of the µ-opioid receptor (MOR). CCG258747 showed the best efficacy in blocking MOR internalization among the compounds tested. Furthermore, we show that compounds based on paroxetine had much better cell permeability than those based on GSK180736A, which explains why GSK180736A-based inhibitors, although being potent in vitro, do not always show efficacy in cell-based assays. This study validates the paroxetine scaffold as the most effective for GRK inhibition in living cells, confirming that GRK2 predominantly drives internalization of MOR in the cell lines we tested and underscores the utility of high-resolution cell-based assays for assessment of compound efficacy. SIGNIFICANCE STATEMENT: G protein-coupled receptor kinases (GRKs) are attractive targets for developing therapeutics for heart failure. We have synthesized a new GRK2 subfamily-selective inhibitor, CCG258747, which has nanomolar potency against GRK2 and excellent selectivity over other kinases. A live-cell receptor internalization assay was used to test the ability of GRK2 inhibitors to impart efficacy on a GRK-dependent process in cells. Our data indicate that CCG258747 blocked the internalization of the µ-opioid receptor most efficaciously because it has the ability to cross cell membranes.


Assuntos
Indazóis/química , Paroxetina/química , Pirimidinas/química , Receptores Opioides mu/antagonistas & inibidores , Receptores Opioides mu/metabolismo , Animais , Western Blotting , Permeabilidade da Membrana Celular , Cristalografia por Raios X , Feminino , Células HEK293 , Humanos , Indazóis/farmacologia , Camundongos , Microssomos Hepáticos/efeitos dos fármacos , Microssomos Hepáticos/metabolismo , Estrutura Molecular , Pirimidinas/farmacologia
13.
Acta Crystallogr C Struct Chem ; 76(Pt 4): 359-366, 2020 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-32229717

RESUMO

Derivatives of pyrimidine-2(1H)-selenone are a group of compounds with very strong antimicrobial activity. In order to study the effect of the position of the methoxy substituent on biological activity, molecular geometry and intermolecular interactions in the crystal, three derivatives were prepared and evaluated with respect to their antimicrobial activities, and their crystal structures were determined by X-ray diffraction. The investigated compounds, namely, 1-(X-methoxyphenyl)-4-methyl-6-phenylpyrimidine-2(1H)-selenones (X = 2, 3 and 4 for 1, 2 and 3, respectively), C18H16N2OSe, showed very strong activity against selected strains of Gram-positive bacteria and fungi. Two compounds, 1 and 2, crystallize in the monoclinic space group P21/c, while 3 crystallizes in the space group P21/n; 1 has two molecules in the asymmetric unit and the other two (2 and 3) have one molecule. The geometries of the investigated compounds differ slightly in the mutual orientations of the aromatic and pyrimidineselenone rings. The O atom in 1 stabilizes the conformation of the molecules via intramolecular C-H...O hydrogen bonding. The packing of molecules is determined by weak C-H...N and C-H...Se intermolecular interactions and additionally in 1 and 2 by C-H...O intermolecular interactions. The introduction of the methoxy substituent results in greater selectivity of the investigated compounds.


Assuntos
Anti-Infecciosos/química , Pirimidinas/química , Anti-Infecciosos/farmacologia , Cristalografia por Raios X , Fungos , Ligação de Hidrogênio , Estrutura Molecular
14.
J Med Chem ; 63(8): 3908-3914, 2020 04 23.
Artigo em Inglês | MEDLINE | ID: mdl-32208684

RESUMO

Aminoacyl-tRNA synthetase interacting multifunctional proteins (AIMPs) have recently been considered novel therapeutic targets in several cancers. In this publication we report the development of novel 2-aminophenylpyrimidines as new AIMP2-DX2 inhibitors. In particular, aminophenylpyrimidine 3 not only exhibited promising in vitro and in vivo potency but also exerted selective inhibition of H460 and A549 cells and AIMP2-DX2 rather than WI-26 cells and AIMP2. Aminophenylpyrimidine 3 offers possible therapeutic potential in the treatment of lung cancer.


Assuntos
Aminoacil-tRNA Sintetases/antagonistas & inibidores , Neoplasias Pulmonares/tratamento farmacológico , Neoplasias Pulmonares/metabolismo , Proteínas Nucleares/antagonistas & inibidores , Pirimidinas/farmacologia , Pirimidinas/uso terapêutico , Células A549 , Aminoacil-tRNA Sintetases/metabolismo , Animais , Linhagem Celular Tumoral , Feminino , Humanos , Neoplasias Pulmonares/patologia , Camundongos , Camundongos Endogâmicos BALB C , Proteínas Nucleares/metabolismo , Pirimidinas/química , Resultado do Tratamento , Ensaios Antitumorais Modelo de Xenoenxerto/métodos
15.
J Mol Model ; 26(4): 68, 2020 Mar 04.
Artigo em Inglês | MEDLINE | ID: mdl-32130533

RESUMO

Pro-inflammatory activation of caspase-1 in the neurodegenerative pathway has been associated with age-dependent cognitive impairment and Alzheimer's disease (AD) in humans. A recent report highlighted 2,4-diaminopyrimidine ring as an essential fragment in the inhibition of human caspase-1. However, the role of the ring and its enzyme inhibitory mechanism is not thoroughly investigated at the molecular level. The purpose of this study is therefore in twofold: (1) to understand the enzyme binding mechanism of the 2,4-diaminopyrimidine ring and (2) to search for more potent caspase-1 inhibitors that contain the ring, using integrative per-residue energy decomposition (PRED) pharmacophore modeling. Ligand interaction profile of a reference compound revealed a peculiar hydrogen formation of the amino group of 2,4-diaminopyrimidine with active site residue Arg341, possibly forming the bases for its inhibitory prowess against caspase-1. A generated pharmacophore model for structure-based virtual screening identified compounds, ZINC724667, ZINC09908119, and ZINC09933770, as potential caspase-1 inhibitors that possessed desirable pharmacokinetic and physiochemical properties. Further analyses revealed active site residues, Arg179, Ser236, Cys285, Gln283, Ser339, and Arg341, as crucial to inhibitor binding by stabilizing and forming hydrogen bonds, hydrophobic, and pi-pi interactions with the 2,4-diaminopyrimidine rings. Common interaction patterns of the hits could have accounted for their selective and high-affinity ligand binding, which was characterized by notable disruptions in caspase-1 structural architecture. These compounds could further be explored as potential leads in the development of novel caspase-1 inhibitors.


Assuntos
Doença de Alzheimer , Caspase 1/química , Inibidores de Caspase/química , Pirimidinas/química , Doença de Alzheimer/tratamento farmacológico , Doença de Alzheimer/enzimologia , Inibidores de Caspase/uso terapêutico , Humanos , Pirimidinas/uso terapêutico
16.
Proc Natl Acad Sci U S A ; 117(10): 5319-5328, 2020 03 10.
Artigo em Inglês | MEDLINE | ID: mdl-32094190

RESUMO

Terminal oligopyrimidine (TOP) motifs are sequences at the 5' ends of mRNAs that link their translation to the mTOR Complex 1 (mTORC1) nutrient-sensing signaling pathway. They are commonly regarded as discrete elements that reside on ∼100 mRNAs that mostly encode translation factors. However, the full spectrum of TOP sequences and their prevalence throughout the transcriptome remain unclear, primarily because of uncertainty over the mechanism that detects them. Here, we globally analyzed translation targets of La-related protein 1 (LARP1), an RNA-binding protein and mTORC1 effector that has been shown to repress TOP mRNA translation in a few specific cases. We establish that LARP1 is the primary translation regulator of mRNAs with classical TOP motifs genome-wide, and also that these motifs are extreme instances of a broader continuum of regulatory sequences. We identify the features of TOP sequences that determine their potency and quantify these as a metric that accurately predicts mTORC1/LARP1 regulation called a TOPscore. Analysis of TOPscores across the transcriptomes of 16 mammalian tissues defines a constitutive "core" set of TOP mRNAs, but also identifies tissue-specific TOP mRNAs produced via alternative transcription initiation sites. These results establish the central role of LARP1 in TOP mRNA regulation on a transcriptome scale and show how it connects mTORC1 to a tunable and dynamic program of gene expression that is tailored to specific biological contexts.


Assuntos
Autoantígenos/metabolismo , Motivos de Nucleotídeos , Proteína de Ligação a Regiões Ricas em Polipirimidinas/química , Biossíntese de Proteínas , Pirimidinas/química , RNA Mensageiro/química , Ribonucleoproteínas/metabolismo , Células HEK293 , Humanos , Alvo Mecanístico do Complexo 1 de Rapamicina/química , Proteína de Ligação a Regiões Ricas em Polipirimidinas/genética , RNA Mensageiro/genética , Transcriptoma
17.
Org Biomol Chem ; 18(8): 1602-1606, 2020 02 26.
Artigo em Inglês | MEDLINE | ID: mdl-32065206

RESUMO

The self-assembly of triaminopyrimidines with barbiturates and with cyanates was investigated in chloroform solution. Equimolar mixtures of two complementary components form stable macrocyclic 3 : 3 complexes (rosettes). The thermodynamics of self-assembly were quantified by using 1H NMR titrations to measure the strength of pairwise H-bonding interactions between two rosette components (K), allosteric cooperativity associated with formation of a second H-bonding interaction with each component, and the effective molarity for cyclisation of the rosette motif (EM). Pyrimidine-cyanurate interactions are an order of magnitude more favourable than pyrimidine-barbiturate interactions, so the cyanurate rosettes are significantly more stable than barbiturate rosettes. There is no allosteric cooperativity associated with rosette formation, but the chelate cooperativity quantified by the product K EM is exceptionally high (102-104), indicating that there are no other species present that compete with rosette assembly. The values of EM for rosette formation are approximately 2 M for all four rosettes studied and are not affected by differences in peripheral substituents or intrinsic H-bond strength.


Assuntos
Compostos Macrocíclicos/síntese química , Termodinâmica , Barbitúricos/química , Clorofórmio , Cianatos/química , Ciclização , Ligação de Hidrogênio , Compostos Macrocíclicos/química , Espectroscopia de Ressonância Magnética , Pirimidinas/química
18.
Int J Mol Sci ; 21(1)2020 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-31948054

RESUMO

Background: Codon directional asymmetry (CDA) classifies the 64 codons into palindromes (XYX, CDA = 0), and 5'- and 3'-dominant (YXX and XXY, CDA < 0 and CDA > 0, respectively). Previously, CDA was defined by the purine/pyrimidine divide (A,G/C,T), where X is either a purine or a pyrimidine. For the remaining codons with undefined CDA, CDA was defined by the 5' or 3' nucleotide complementary to Y. This CDA correlates with cognate amino acid tRNA synthetase classes, antiparallel beta sheet conformation index and the evolutionary order defined by the self-referential genetic code evolution model (CDA < 0: class I, high beta sheet index, late genetic code inclusion). Methods: We explore associations of CDAs defined by nucleotide classifications according to complementarity strengths (A:T, weak; C:G, strong) and keto-enol/amino-imino groupings (G,T/A,C), also after swapping 1st and 2nd codon positions with amino acid physicochemical and structural properties. Results: Here, analyses show that for the eight codons whose purine/pyrimidine-based CDA requires using the rule of complementarity with the midposition, using weak interactions to define CDA instead of complementarity increases associations with tRNA synthetase classes, antiparallel beta sheet index and genetic code evolutionary order. CDA defined by keto-enol/amino-imino groups, 1st and 2nd codon positions swapped, correlates with amino acid parallel beta sheet formation indices and Doolittle's hydropathicities. Conclusions: Results suggest (a) prebiotic swaps from N2N1N3 to N1N2N3 codon structures, (b) that tRNA-mediated translation replaced direct codon-amino acid interactions, and (c) links between codon structures and cognate amino acid properties.


Assuntos
Aminoácidos/genética , Aminoacil-tRNA Sintetases/metabolismo , Códon , Purinas/química , Pirimidinas/química , Aminoácidos/química , Evolução Molecular , Código Genético , Ligação de Hidrogênio , Interações Hidrofóbicas e Hidrofílicas , Modelos Genéticos , Nucleotídeos/química , Biossíntese de Proteínas
19.
Biochim Biophys Acta Gen Subj ; 1864(4): 129531, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-31953125

RESUMO

BACKGROUND: Bruton's tyrosine kinase (BTK) is a key component of the B-cell receptor (BCR) pathway and a clinically validated target for small molecule inhibitors such as ibrutinib in the treatment of B-cell malignancies. Tirabrutinib (GS-4059/ONO-4059) is a selective, once daily, oral BTK inhibitor with clinical activity against many relapsed/refractory B-cell malignancies. METHODS: Covalent binding of tirabrutinib to BTK Cys-481 was assessed by LC-MSMS analysis of BTK using compound as a variable modification search parameter. Inhibition potency of tirabrutinib, ibrutinib, acalabrutinib, and spebrutinib against BTK and related kinases was studied in a dose-dependent manner either after a fixed incubation time (as used in conventional IC50 studies) or following a time course where inactivation kinetics were measured. RESULTS: Tirabrutinib irreversibly and covalently binds to BTK Cys-481. The inactivation efficiency kinact/Ki was measured and used to calculate selectivity among different kinases for each of the four inhibitors studied. Tirabrutinib showed a kinact/Ki value of 2.4 ± 0.6 × 104 M-1 s-1 for BTK with selectivity against important off-targets. CONCLUSIONS: For the BTK inhibitors tested in this study, analysis of the inactivation kinetics yielded a more accurate measurement of potency and selectivity than conventional single-time point inhibition measurements. Subtle but clear differences were identified between clinically tested BTK inhibitors which may translate into differentiated clinical efficacy and safety. GENERAL SIGNIFICANCE: This is the first study that offers a detailed side-by-side comparison of four clinically-relevant BTK inhibitors with respect to their inactivation of BTK and related kinases.


Assuntos
Tirosina Quinase da Agamaglobulinemia/antagonistas & inibidores , Imidazóis/farmacologia , Inibidores de Proteínas Quinases/farmacologia , Pirimidinas/farmacologia , Tirosina Quinase da Agamaglobulinemia/metabolismo , Relação Dose-Resposta a Droga , Humanos , Imidazóis/química , Cinética , Espectrometria de Massas , Estrutura Molecular , Inibidores de Proteínas Quinases/química , Pirimidinas/química , Relação Estrutura-Atividade
20.
J Med Chem ; 63(5): 2557-2576, 2020 03 12.
Artigo em Inglês | MEDLINE | ID: mdl-31922409

RESUMO

Decaprenylphosphoryl-ß-d-ribose 2'-epimerase (DprE1) is an essential enzyme in Mycobacterium tuberculosis and has recently been studied as a potential drug target, with inhibitors progressing to clinical studies. Here we describe the identification of a novel series of morpholino-pyrimidine DprE1 inhibitors. These were derived from a phenotypic high-throughput screening (HTS) hit with suboptimal physicochemical properties. Optimization strategies included scaffold-hopping, synthesis, and evaluation of fragments of the lead compounds and property-focused optimization. The resulting optimized compounds had much improved physicochemical properties and maintained enzyme and cellular potency. These molecules demonstrated potent efficacy in an in vivo tuberculosis murine infection model.


Assuntos
Oxirredutases do Álcool/antagonistas & inibidores , Antituberculosos/farmacologia , Proteínas de Bactérias/antagonistas & inibidores , Inibidores Enzimáticos/farmacologia , Mycobacterium tuberculosis/efeitos dos fármacos , Pirimidinas/farmacologia , Tuberculose/tratamento farmacológico , Oxirredutases do Álcool/metabolismo , Animais , Antituberculosos/química , Antituberculosos/uso terapêutico , Proteínas de Bactérias/metabolismo , Inibidores Enzimáticos/química , Inibidores Enzimáticos/uso terapêutico , Humanos , Masculino , Camundongos , Morfolinas/química , Morfolinas/farmacologia , Morfolinas/uso terapêutico , Mycobacterium tuberculosis/enzimologia , Pirimidinas/química , Pirimidinas/uso terapêutico , Tuberculose/microbiologia
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