Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 301
Filtrar
Mais filtros

Base de dados
Tipo de documento
Intervalo de ano de publicação
1.
Bioorg Med Chem Lett ; 40: 127966, 2021 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-33744441

RESUMO

Antibiotic resistance represents one of the biggest public health challenges in the last few years. Mur ligases (MurC-MurF) are involved in the synthesis of UDP-N-acetylmuramyl-pentapeptide, the main building block of bacterial peptidoglycan polymer. They are essential for the survival of bacteria and therefore important antibacterial targets. We report herein the synthesis and structure-activity relationships of Mur ligases inhibitors with an azastilbene scaffold. Several compounds showed promising inhibitory potencies against multiple ligases and one compound also possessed moderate antibacterial activity. These results represent a solid ground for further development and optimization of structurally novel antimicrobial agents to combat the rising bacterial resistance.


Assuntos
Antibacterianos/farmacologia , Proteínas de Bactérias/antagonistas & inibidores , Compostos de Benzilideno/farmacologia , Inibidores Enzimáticos/farmacologia , Peptídeo Sintases/antagonistas & inibidores , Piridinas/farmacologia , Antibacterianos/síntese química , Antibacterianos/metabolismo , Proteínas de Bactérias/metabolismo , Compostos de Benzilideno/síntese química , Compostos de Benzilideno/metabolismo , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/metabolismo , Simulação de Acoplamento Molecular , Estrutura Molecular , Peptídeo Sintases/metabolismo , Ligação Proteica , Piridinas/síntese química , Piridinas/metabolismo , Staphylococcus aureus/efeitos dos fármacos , Staphylococcus aureus/enzimologia , Relação Estrutura-Atividade
2.
Chem Pharm Bull (Tokyo) ; 69(2): 222-225, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33518604

RESUMO

The gatekeeping adenylation (A) domain of the non-ribosomal peptide synthetase (NRPS) selectively incorporates specific proteinogenic/non-proteinogenic amino acid into a growing peptide chain. The EntE of the enterobactin NRPS is a discrete aryl acid A-domain with 2,3-dihydroxybenzoic acid (DHB) substrate specificity. Reprogrammed EntE N235G variant possesses an enlarged substrate recognition site, and is capable of accepting non-native aryl acids. Biochemical characterization of this unique substrate recognition site should provide a better understanding of activi-site microenvironments. Here, we synthesized a non-hydrolysable adenylate analogue with 2-aminobenzoic acid (2-ABA), 3-aminobenzoic acid (3-ABA), and 4-aminobenzoic acid (4-ABA) and used them to calculate the apparent inhibition constants (Kiapp.). Dose-response experiments using 3-ABA-sulfamoyladenosine (AMS) provided Kiapp. values of 596 nM for wild-type EntE and 2.4 nM for the N235G variants. These results suggest that 3-amino group of benzoic acid plays an important role in substrate recognition by the N235G variant. These findings would help designing aryl acid substrates with substituents at the 2- and 3-positions.


Assuntos
Simulação de Dinâmica Molecular , Peptídeo Sintases/metabolismo , Ácido 4-Aminobenzoico/química , Ácido 4-Aminobenzoico/metabolismo , Sítios de Ligação , Enterobactina/química , Enterobactina/metabolismo , Cinética , Mutagênese Sítio-Dirigida , Peptídeo Sintases/antagonistas & inibidores , Peptídeo Sintases/genética , Ligação Proteica , Domínios Proteicos , Especificidade por Substrato
3.
Molecules ; 26(21)2021 Oct 25.
Artigo em Inglês | MEDLINE | ID: mdl-34770835

RESUMO

Staphylococcus aureus is an opportunistic pathogen that can cause fatal bacterial infections. MurD catalyzes the formation of peptide bond between UDP-N-acetylehyl-l-alanine and d-glutamic acid, which plays an important role in the synthesis of peptidoglycan and the formation of cell wall by S. aureus. Because S. aureus is resistant to most existing antibiotics, it is necessary to develop new inhibitors. In this study, Schrodinger 11.5 Prime homology modeling was selected to prepare the protein model of MurD enzyme, and its structure was optimized. We used a virtual screening program and similarity screening to screen 47163 compounds from three marine natural product libraries to explore new inhibitors of S. aureus. ADME provides analysis of the physicochemical properties of the best performing compounds during the screening process. To determine the stability of the docking effect, a 100 ns molecular dynamics was performed to verify how tightly the compound was bound to the protein. By docking analysis and molecular dynamics analysis, both 46604 and 46608 have strong interaction with the docking pocket, have good pharmacological properties, and maintain stable conformation with the target protein, so they have a chance to become drugs for S. aureus. Through virtual screening, similarity screening, ADME study and molecular dynamics simulation, 46604 and 46608 were selected as potential drug candidates for S. aureus.


Assuntos
Antibacterianos/farmacologia , Organismos Aquáticos/química , Produtos Biológicos/farmacologia , Inibidores Enzimáticos/farmacologia , Peptídeo Sintases/antagonistas & inibidores , Staphylococcus aureus/efeitos dos fármacos , Staphylococcus aureus/enzimologia , Sequência de Aminoácidos , Antibacterianos/química , Produtos Biológicos/química , Fenômenos Químicos , Descoberta de Drogas , Avaliação Pré-Clínica de Medicamentos , Inibidores Enzimáticos/química , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Peptídeo Sintases/química , Bibliotecas de Moléculas Pequenas , Relação Estrutura-Atividade
4.
Angew Chem Int Ed Engl ; 60(41): 22207-22211, 2021 10 04.
Artigo em Inglês | MEDLINE | ID: mdl-34396662

RESUMO

Peptidyl asparaginyl ligases (PALs) are powerful tools for peptide macrocyclization. Herein, we report that a derivative of Asn, namely Nγ -hydroxyasparagine or Asn(OH), is an unnatural P1 substrate of PALs. By Asn(OH)-mediated cyclization, we prepared cyclic peptides as new matrix metalloproteinase 2 (MMP2) inhibitors displaying the hydroxamic acid moiety of Asn(OH) as the key pharmacophore. The most potent cyclic peptide (Ki =2.8±0.5 nM) was built on the hyperstable tetracyclic scaffold of rhesus theta defensin-1. The Asn(OH) residue in the cyclized peptides can also be readily oxidized to Asp. By this approach, we synthesized several bioactive Asp-containing cyclic peptides (MCoTI-II, kB2, SFTI, and integrin-targeting RGD peptides) that are otherwise difficult targets for PAL-catalyzed cyclization owing to unfavorable kinetics of the P1-Asp substrates. This study demonstrates that substrate engineering is a useful strategy to expand the application of PAL ligation in the synthesis of therapeutic cyclic peptides.


Assuntos
Aminoácidos/farmacologia , Asparagina/farmacologia , Inibidores Enzimáticos/farmacologia , Peptídeo Sintases/antagonistas & inibidores , Peptídeos Cíclicos/farmacologia , Aminoácidos/química , Asparagina/química , Inibidores Enzimáticos/química , Peptídeo Sintases/metabolismo , Peptídeos Cíclicos/química , Especificidade por Substrato
5.
FASEB J ; 33(7): 8008-8021, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-30913399

RESUMO

Schwann cells are the main supportive cells of the peripheral nerves. Schwann cells suffer inhibition of autophagy under hyperglycemia treatment in diabetic peripheral neuropathy (DPN). However, the exact mechanism is still not fully elucidated. We first observed the decrease of autophagy markers (LC3-II/LC3-I, P62) in the sciatic nerves of diabetic mice vs. normal mice, accompanied with the loss of myelinated nerve fibers and abnormal myelin sheath. In line with this, LC3-II/LC3-I and P62 were also significantly reduced in high glucose-treated rat Schwann cell 96 (RSC96) cells compared with normal glucose-treated cells. Furthermore, we found that trichostatin A [an inhibitor of histone deacetylase (HDAC)] evidently improved LC3-II/LC3-I in high glucose-treated RSC96 cells, without an effect on P62 expression. Again, HDAC1 and HDAC5 were revealed to be increased in RSC96 cells stimulated with high glucose. Inhibition of HDAC1 but not HDAC5 by small hairpin RNA vector enhanced LC3-II/LC3-I in high glucose-cultured RSC96 cells. In addition, LC3-II conversion regulators [autophagy-related protein (Atg)3, Atg5, and Atg7] were detected in high glucose-treated and HDAC1-knockdown RSC96 cells, and Atg3 was proven to be the key target of HDAC1. The presuppression of Atg3 offset the improvement of LC3-II/LC3-I resulting from HDAC1 inhibition in high glucose-treated RSC96 cells. The Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling pathway was activated in RSC96 cells treated with high glucose, which was indicated by increased STAT3 phosphorylation. Blocking STAT3 phosphorylation by chemical inhibitor AG490 induced HDAC1 down-regulation followed by increases in Atg3 and LC3-II/LC3-I. Interestingly, we also found that AG490 treatment enhanced P62 expression in high glucose-stimulated RSC96 cells. Taken together, our findings demonstrate that hyperglycemia inhibits LC3-II/LC3-I in an HDAC1-Atg3-dependent manner and decreases P62 expression in an HDAC-independent manner via the JAK-STAT3 signaling pathway in the Schwann cells of DPN.-Du, W., Wang, N., Li, F. Jia, K., An, J., Liu, Y., Wang, Y., Zhu, L., Zhao, S. Hao, J. STAT3 phosphorylation mediates high glucose-impaired cell autophagy in an HDAC1-dependent and -independent manner in Schwann cells of diabetic peripheral neuropathy.


Assuntos
Autofagia/efeitos dos fármacos , Neuropatias Diabéticas/metabolismo , Glucose/farmacologia , Histona Desacetilase 1/fisiologia , Processamento de Proteína Pós-Traducional , Fator de Transcrição STAT3/metabolismo , Células de Schwann/efeitos dos fármacos , Animais , Proteínas Relacionadas à Autofagia/antagonistas & inibidores , Proteínas Relacionadas à Autofagia/biossíntese , Proteínas Relacionadas à Autofagia/genética , Biomarcadores , Linhagem Celular , Diabetes Mellitus Experimental/metabolismo , Diabetes Mellitus Experimental/patologia , Neuropatias Diabéticas/patologia , Técnicas de Silenciamento de Genes , Histona Desacetilase 1/antagonistas & inibidores , Histona Desacetilase 1/genética , Histona Desacetilases/genética , Histona Desacetilases/fisiologia , Ácidos Hidroxâmicos/farmacologia , Camundongos , Proteínas Associadas aos Microtúbulos/biossíntese , Proteínas Associadas aos Microtúbulos/genética , Bainha de Mielina/patologia , Fibras Nervosas Mielinizadas/patologia , Peptídeo Sintases/antagonistas & inibidores , Peptídeo Sintases/biossíntese , Peptídeo Sintases/genética , Fosforilação , Interferência de RNA , RNA Interferente Pequeno/genética , RNA Interferente Pequeno/farmacologia , Ratos , Células de Schwann/metabolismo , Nervo Isquiático/metabolismo , Nervo Isquiático/patologia , Tirfostinas/farmacologia , Regulação para Cima
6.
Biochem J ; 476(21): 3125-3139, 2019 11 15.
Artigo em Inglês | MEDLINE | ID: mdl-31488574

RESUMO

CoaBC, part of the vital coenzyme A biosynthetic pathway in bacteria, has recently been validated as a promising antimicrobial target. In this work, we employed native ion mobility-mass spectrometry to gain structural insights into the phosphopantothenoylcysteine synthetase domain of E. coli CoaBC. Moreover, native mass spectrometry was validated as a screening tool to identify novel inhibitors of this enzyme, highlighting the utility and versatility of this technique both for structural biology and for drug discovery.


Assuntos
Carboxiliases/química , Avaliação Pré-Clínica de Medicamentos/métodos , Proteínas de Escherichia coli/química , Escherichia coli/enzimologia , Espectrometria de Massas/métodos , Complexos Multienzimáticos/química , Peptídeo Sintases/química , Carboxiliases/antagonistas & inibidores , Carboxiliases/metabolismo , Dimerização , Inibidores Enzimáticos/química , Escherichia coli/química , Escherichia coli/efeitos dos fármacos , Escherichia coli/genética , Proteínas de Escherichia coli/antagonistas & inibidores , Proteínas de Escherichia coli/metabolismo , Cinética , Complexos Multienzimáticos/antagonistas & inibidores , Complexos Multienzimáticos/metabolismo , Peptídeo Sintases/antagonistas & inibidores , Peptídeo Sintases/metabolismo , Domínios Proteicos
7.
Molecules ; 25(21)2020 Oct 26.
Artigo em Inglês | MEDLINE | ID: mdl-33114668

RESUMO

The synthesis of hitherto unknown 5'-deoxy-5'-(4-substituted-1,2,3-triazol-1-yl)-uridine and its evaluation, through an one-pot screening assay, against MurA-F enzymes involved in Mycobacterium tuberculosis (Mtb), are described. Starting from UDP-N-acetylmuramic acid (UDP-MurNAc), the natural substrate involved in the peptidoglycan biosynthesis, our strategy was to substitute the diphosphate group of UDP-MurNAc by a 1,2,3-triazolo spacer under copper-catalyzed azide-alkyne cycloaddition conditions. The structure-activity relationship was discussed and among the 23 novel compounds developed, N-acetylglucosamine analogues 11c and 11e emerged as the best inhibitors against the Mtb MurA-F enzymes reconstruction pathway with an inhibitory effect of 56% and 50%, respectively, at 100 µM. Both compounds are selective inhibitors of Mtb MurE, the molecular docking and molecular dynamic simulation suggesting that 11c and 11e are occupying the active site of Mtb MurE ligase.


Assuntos
Desenho de Fármacos , Mycobacterium tuberculosis/enzimologia , Peptídeo Sintases/antagonistas & inibidores , Triazóis/química , Uridina/síntese química , Uridina/farmacologia , Domínio Catalítico , Técnicas de Química Sintética , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/química , Inibidores Enzimáticos/farmacologia , Simulação de Acoplamento Molecular , Peptídeo Sintases/química , Peptídeo Sintases/metabolismo , Uridina/química
8.
J Recept Signal Transduct Res ; 39(1): 45-54, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31162992

RESUMO

Staphylococcus aureus MurE enzyme catalyzes the addition of l-lysine as third residue of the peptidoglycan peptide moiety. Due to the high substrate specificity and its ubiquitous nature among bacteria, MurE enzyme is considered as one of the potential target for the development of new therapeutic agents. In the present work, induced fit docking (IFD), binding free energy calculation, and molecular dynamics (MD) simulation were carried out to elucidate the inhibition potential of 2-thioxothiazolidin-4-one based inhibitor 1 against S. aureus MurE enzyme. The inhibitor 1 formed majority of hydrogen bonds with the central domain residues Asn151, Thr152, Ser180, Arg187, and Lys219. Binding free-energy calculation by MM-GBSA approach showed that van der Waals (ΔGvdW, -57.30 kcal/mol) and electrostatic solvation (ΔGsolv, -36.86 kcal/mol) energy terms are major contributors for the inhibitor binding. Further, 30-ns MD simulation was performed to validate the stability of ligand-protein complex and also to get structural insight into mode of binding. Based on the IFD and MD simulation results, we designed four new compounds D1-D4 with promising binding affinity for the S. aureus MurE enzyme. The designed compounds were subjected to the extra-precision docking and binding free energy was calculated for complexes. Further, a 30-ns MD simulation was performed for D1/4C13 complex.


Assuntos
Proteínas de Bactérias/antagonistas & inibidores , Inibidores Enzimáticos/metabolismo , Simulação de Dinâmica Molecular , Peptídeo Sintases/antagonistas & inibidores , Peptídeo Sintases/metabolismo , Staphylococcus aureus/efeitos dos fármacos , Domínio Catalítico , Desenho de Fármacos , Inibidores Enzimáticos/química , Ligação Proteica , Relação Estrutura-Atividade , Especificidade por Substrato
9.
J Recept Signal Transduct Res ; 39(3): 283-293, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31538846

RESUMO

A new series of benzothiazol-2-ylcarbamodithioate functional compounds 5a-f has been designed, synthesized and characterized by spectral data. These compounds were screened for their in vitro antibacterial activity against strains of Staphylococcus aureus (NCIM 5021, NCIM 5022 and methicillin-resistant isolate 43300), Bacillus subtilis (NCIM 2545), Escherichia coli (NCIM 2567), Klebsiella pneumoniae (NCIM 2706) and Psudomonas aeruginosa (NCIM 2036). Compounds 5a and 5d exhibited significant activity against all the tested bacterial strains. Specifically, compounds 5a and 5d showed potent activity against K. pneumoniae (NCIM 2706), while compound 5a also displayed potent activity against S. aureus (NCIM 5021). Compound 5d showed minimum IC50 value of 13.37 µM against S. aureus MurD enzyme. Further, the binding interactions of compounds 5a-f in the catalytic pocket have been investigated using the extra-precision molecular docking and binding free energy calculation by MM-GBSA approach. A 30 ns molecular dynamics simulation of 5d/modeled S. aureus MurD enzyme was performed to determine the stability of the predicted binding conformation.


Assuntos
Benzotiazóis/síntese química , Benzotiazóis/farmacologia , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/farmacologia , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Peptídeo Sintases/antagonistas & inibidores , Staphylococcus aureus/enzimologia , Antibacterianos/síntese química , Antibacterianos/química , Antibacterianos/farmacocinética , Antibacterianos/farmacologia , Benzotiazóis/química , Benzotiazóis/farmacocinética , Inibidores Enzimáticos/química , Inibidores Enzimáticos/farmacocinética , Concentração Inibidora 50 , Testes de Sensibilidade Microbiana , Peptídeo Sintases/metabolismo , Staphylococcus aureus/efeitos dos fármacos , Termodinâmica
10.
Bioorg Med Chem Lett ; 29(9): 1031-1042, 2019 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-30846252

RESUMO

Synthetic pseudopeptides that fit well with the active site architecture allow the most effective binding to enzymes, similar to native substrates in high-energy transition states. Phosphinic acid peptide analogs that comprise the tetrahedral phosphorus moiety introduced to replace an internal amide bond exert such an isosteric or isoelectronic resemblance, combined with providing other advantageous features, for example, metal complexing properties. Accordingly, they are capable of inhibiting metal-dependent enzymes involved in biological functions in eukaryotic and prokaryotic cells. These enzymes are associated with notorious human diseases, such as cancer, e.g., matrix metalloproteinases, or are etiological factors of protozoal and bacterial infections, e.g., metalloaminopeptidases. The affinity and selectivity of these compounds can be conveniently adjusted, either by structural modification of dedicated side chains or by backbone elongation to enhance specific interactions with the corresponding binding pockets. Recent approaches to the synthesis of these compounds are illustrated by examples of the preparation of rationally designed structures of inhibitors of particular enzymes. Activity against appealing enzymatic targets is presented, along with the molecular mechanisms of action and therapeutic implications. Innovative aspects of phosphinic peptide application, e.g., as activity-based probes, and ligands of complexes of radioisotopes for nuclear medicine are also outlined.


Assuntos
Peptídeos/química , Ácidos Fosfínicos/química , Bactérias/enzimologia , Inibidores Enzimáticos/química , Inibidores Enzimáticos/metabolismo , Humanos , Metaloproteinases da Matriz/química , Metaloproteinases da Matriz/metabolismo , Metais/química , Peptídeo Sintases/antagonistas & inibidores , Peptídeo Sintases/metabolismo , Peptídeos/síntese química , Peptídeos/metabolismo , Antígeno Prostático Específico/química , Antígeno Prostático Específico/metabolismo
11.
Chemotherapy ; 64(1): 22-27, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31167192

RESUMO

BACKGROUND: Pantothenate, the fundamental precursor to coenzyme A, is required for optimal growth and virulence of microbial pathogens. It is synthesized by the enzyme-catalyzed condensation of ß-alanine and pantoate, which has shown susceptibility to inhibition by analogs of its molecular constituents. Accordingly, analogs of ß-alanine are gaining inquiry as potential antimicrobial chemotherapeutics. METHODS: We synthesized and evaluated 35 derivatives of ß-alanine, substituted at the α, ß, amine, and carboxyl sites, derived from in silico, dynamic molecular modeling to be potential competitive inhibitors of pantothenate synthetase. Employing the Clinical Laboratory Standards M7-A6 broth microdilution method, we tested these for inhibition of growth in Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa. RESULTS: All compounds proved entirely ineffective in all species tested, with no inhibition of growth being observed up to 200 µM/mL. CONCLUSIONS: Upon revision of the literature, we conclude that high enzyme selectivity or external salvage mechanisms may render this strategy futile against most bacteria.


Assuntos
Proteínas de Bactérias/metabolismo , Peptídeo Sintases/metabolismo , beta-Alanina/metabolismo , Proteínas de Bactérias/antagonistas & inibidores , Sítios de Ligação , Escherichia coli/efeitos dos fármacos , Escherichia coli/enzimologia , Escherichia coli/crescimento & desenvolvimento , Simulação de Acoplamento Molecular , Peptídeo Sintases/antagonistas & inibidores , Estrutura Terciária de Proteína , Pseudomonas aeruginosa/efeitos dos fármacos , Pseudomonas aeruginosa/crescimento & desenvolvimento , Staphylococcus aureus/efeitos dos fármacos , Staphylococcus aureus/crescimento & desenvolvimento , beta-Alanina/análogos & derivados , beta-Alanina/farmacologia
12.
Parasitology ; 145(2): 184-195, 2018 02.
Artigo em Inglês | MEDLINE | ID: mdl-27804891

RESUMO

Tuberculosis is an infectious disease associated with significant mortality and morbidity worldwide, particularly in developing countries. The rise of antibiotic resistance in Mycobacterium tuberculosis (Mtb) urgently demands the development of new drug leads to tackle resistant strains. Fragment-based methods have recently emerged at the forefront of pharmaceutical development as a means to generate more effective lead structures, via the identification of fragment molecules that form weak but high quality interactions with the target biomolecule and subsequent fragment optimization. This review highlights a number of novel inhibitors of Mtb targets that have been developed through fragment-based approaches in recent years.


Assuntos
Proteínas de Bactérias/efeitos dos fármacos , Descoberta de Drogas/métodos , Mycobacterium tuberculosis/efeitos dos fármacos , Tuberculose/tratamento farmacológico , Sistema Enzimático do Citocromo P-450/efeitos dos fármacos , Humanos , Peptídeo Sintases/antagonistas & inibidores , Peptídeo Sintases/efeitos dos fármacos , Proteínas Repressoras/efeitos dos fármacos , Transaminases/efeitos dos fármacos , Tuberculose/microbiologia
13.
Molecules ; 23(2)2018 Feb 03.
Artigo em Inglês | MEDLINE | ID: mdl-29401644

RESUMO

(1) Background: d-alanine-d-alanine ligase (DdlA), an effective target for drug development to combat against Mycobacterium tuberculosis (Mtb), which threatens human health globally, supplies a substrate of d-alanyl-d-alanine for peptidoglycan crosslinking by catalyzing the dimerization of two d-alanines. To obtain a better understanding of DdlA profiles and develop a colorimetric assay for high-throughput inhibitor screening, we focused on explicating and characterizing Tb-DdlA. (2) Methods and Results: Rv2981c (ddlA) was expressed in Escherichia coli, and the purified Tb-DdlA was identified using (anti)-polyhistidine antibody followed by DdlA activity confirmation by measuring the released orthophosphate via colorimetric assay and the yielded d-alanyl-d-alanine through high performance thin layer chromatography (HP-TLC). The kinetic assays on Tb-DdlA indicated that Tb-DdlA exhibited a higher affinity to ATP (KmATP: 50.327 ± 4.652 µmol/L) than alanine (KmAla: 1.011 ± 0.094 mmol/L). A colorimetric assay for Tb-DdlA activity was developed for high-throughput screening of DdlA inhibitors in this study. In addition, we presented an analysis on Tb-DdlA interaction partners by pull-down assay and MS/MS. Eight putative interaction partners of Tb-DdlA were identified. (3) Conclusions: Our dataset provided a valuable resource for exploring Tb-DdlA biology, and developed an easy colorimetric assay for screening of Tb-DdlA inhibitors.


Assuntos
Trifosfato de Adenosina/metabolismo , Alanina/metabolismo , Proteínas de Bactérias/metabolismo , Dipeptídeos/metabolismo , Mycobacterium tuberculosis/enzimologia , Peptídeo Sintases/metabolismo , Proteínas de Bactérias/antagonistas & inibidores , Proteínas de Bactérias/genética , Bioensaio , Clonagem Molecular , Inibidores Enzimáticos/química , Escherichia coli/genética , Escherichia coli/metabolismo , Expressão Gênica , Cinética , Mycobacterium tuberculosis/genética , Peptídeo Sintases/antagonistas & inibidores , Peptídeo Sintases/genética , Plasmídeos/química , Plasmídeos/metabolismo , Ligação Proteica , Mapeamento de Interação de Proteínas , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Especificidade por Substrato
14.
J Recept Signal Transduct Res ; 37(5): 522-534, 2017 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-28768454

RESUMO

The discovery of clinically relevant inhibitors against MurF enzyme has proven to be a challenging task. In order to get further insight into the structural features required for the MurF inhibitory activity, we performed pharmacophore and atom-based three-dimensional quantitative structure-activity relationship studies for novel thiophene-3-carbonitriles based MurF inhibitors. The five-feature pharmacophore model was generated using 48 inhibitors having IC50 values ranging from 0.18 to 663 µm. The best-fitted model showed a higher coefficient of determination (R2 = 0.978), cross-validation coefficient (Q2 = 0.8835) and Pearson coefficient (0.9406) at four component partial least-squares factor. The model was validated with external data set and enrichment study. The effectiveness of the docking protocol was validated by docking the co-crystallized ligand into the catalytic pocket of MurF enzyme. Further, binding free energy calculated by the molecular mechanics generalized Born surface area approach showed that van der Waals and non-polar solvation energy terms are the main contributors to ligand binding in the active site of MurF enzyme. A 10-ns molecular dynamic simulation was performed to confirm the stability of the 3ZM6-ligand complex. Four new molecules are also designed as potent MurF inhibitors. These results provide insights regarding the development of novel MurF inhibitors with better binding affinity.


Assuntos
Peptídeo Sintases/química , Infecções Pneumocócicas/tratamento farmacológico , Streptococcus pneumoniae/enzimologia , Tiofenos/química , Sítios de Ligação/efeitos dos fármacos , Domínio Catalítico/efeitos dos fármacos , Inibidores Enzimáticos/química , Inibidores Enzimáticos/farmacologia , Humanos , Ligação de Hidrogênio/efeitos dos fármacos , Ligantes , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Peptídeo Sintases/antagonistas & inibidores , Peptídeo Sintases/genética , Infecções Pneumocócicas/enzimologia , Infecções Pneumocócicas/microbiologia , Ligação Proteica , Relação Quantitativa Estrutura-Atividade , Streptococcus pneumoniae/efeitos dos fármacos , Streptococcus pneumoniae/patogenicidade , Tiofenos/metabolismo , Tiofenos/farmacologia
15.
Drug Resist Updat ; 28: 43-64, 2016 09.
Artigo em Inglês | MEDLINE | ID: mdl-27620954

RESUMO

Mammalians are devoid of autonomous biosynthesis of folates and hence must obtain them from the diet. Reduced folate cofactors are B9-vitamins which play a key role as donors of one-carbon units in the biosynthesis of purine nucleotides, thymidylate and amino acids as well as in a multitude of methylation reactions including DNA, RNA, histone and non-histone proteins, phospholipids, as well as intermediate metabolites. The products of these S-adenosylmethionine (SAM)-dependent methylations are involved in the regulation of key biological processes including transcription, translation and intracellular signaling. Folate-dependent one-carbon metabolism occurs in several subcellular compartments including the cytoplasm, mitochondria, and nucleus. Since folates are essential for DNA replication, intracellular folate cofactors play a central role in cancer biology and inflammatory autoimmune disorders. In this respect, various folate-dependent enzymes catalyzing nucleotide biosynthesis have been targeted by specific folate antagonists known as antifolates. Currently, antifolates are used in drug treatment of multiple human cancers, non-malignant chronic inflammatory disorders as well as bacterial and parasitic infections. An obligatory key component of intracellular folate retention and intracellular homeostasis is (anti)folate polyglutamylation, mediated by the unique enzyme folylpoly-γ-glutamate synthetase (FPGS), which resides in both the cytoplasm and mitochondria. Consistently, knockout of the FPGS gene in mice results in embryonic lethality. FPGS catalyzes the addition of a long polyglutamate chain to folates and antifolates, hence rendering them polyanions which are efficiently retained in the cell and are now bound with enhanced affinity by various folate-dependent enzymes. The current review highlights the crucial role that FPGS plays in maintenance of folate homeostasis under physiological conditions and delineates the plethora of the molecular mechanisms underlying loss of FPGS function and consequent antifolate resistance in cancer.


Assuntos
Antimetabólitos Antineoplásicos/farmacologia , Resistencia a Medicamentos Antineoplásicos/genética , Antagonistas do Ácido Fólico/farmacologia , Ácido Fólico/metabolismo , Regulação Neoplásica da Expressão Gênica , Neoplasias/tratamento farmacológico , Peptídeo Sintases/genética , Animais , Antimetabólitos Antineoplásicos/química , Antagonistas do Ácido Fólico/química , Homeostase/efeitos dos fármacos , Homeostase/genética , Humanos , Metilação/efeitos dos fármacos , Camundongos , Neoplasias/enzimologia , Neoplasias/genética , Neoplasias/patologia , Peptídeo Sintases/antagonistas & inibidores , Peptídeo Sintases/metabolismo , Ácido Poliglutâmico/metabolismo , S-Adenosilmetionina/metabolismo , Transdução de Sinais
16.
Bioorg Med Chem Lett ; 26(21): 5340-5345, 2016 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-27692545

RESUMO

Biosynthesis of bacterial natural-product virulence factors is emerging as a promising antibiotic target. Many such natural products are produced by nonribosomal peptide synthetases (NRPS) from amino acid precursors. To develop selective inhibitors of these pathways, we have previously described aminoacyl-AMS (sulfamoyladenosine) macrocycles that inhibit NRPS amino acid adenylation domains but not mechanistically-related aminoacyl-tRNA synthetases. To improve the cell permeability of these inhibitors, we explore herein replacement of the α-amino group with an α-hydroxy group. In both macrocycles and corresponding linear congeners, this leads to decreased biochemical inhibition of the cysteine adenylation domain of the Yersina pestis siderophore synthetase HMWP2, which we attribute to loss of an electrostatic interaction with a conserved active-site aspartate. However, inhibitory activity can be regained by installing a cognate ß-thiol moiety in the linear series. This provides a path forward to develop selective, cell-penetrant inhibitors of the biosynthesis of virulence factors to probe their biological functions and potential as therapeutic targets.


Assuntos
Adenosina/análogos & derivados , Adenosina/farmacologia , Aminoácidos/metabolismo , Inibidores Enzimáticos/química , Inibidores Enzimáticos/farmacologia , Peptídeo Sintases/antagonistas & inibidores , Adenosina/síntese química , Inibidores Enzimáticos/síntese química , Relação Estrutura-Atividade
17.
Bioorg Med Chem ; 24(6): 1298-307, 2016 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-26867485

RESUMO

In the present study, we have designed imidazo[2,1-b]thiazole and benzo[d]imidazo[2,1-b]thiazole derivatives from earlier reported imidazo[1,2-a]pyridine based Mycobacterium tuberculosis (MTB) pantothenate synthetase (PS) inhibitors. We synthesized thirty compounds and they were evaluated for MTB PS inhibition study, in vitro anti-TB activities against replicative and non-replicative MTB, in vivo activity using Mycobacterium marinum infected Zebra fish and cytotoxicity against RAW 264.7 cell line. Among them compound 2-methyl-N'-(4-phenoxybenzoyl)benzo[d]imidazo[2,1-b]thiazole-3-carbohydrazide (5bc) emerged as potent compound active against MTB PS with IC50 of 0.53±0.13 µM, MIC of 3.53 µM, 2.1 log reduction against nutrient starved MTB, with 33% cytotoxicity at 50 µM. It also showed 1.5 log reduction of M. marinum load in Zebra fish at 10mg/kg.


Assuntos
Antibacterianos/farmacologia , Desenho de Fármacos , Inibidores Enzimáticos/farmacologia , Imidazóis/farmacologia , Mycobacterium tuberculosis/efeitos dos fármacos , Mycobacterium tuberculosis/enzimologia , Peptídeo Sintases/antagonistas & inibidores , Tiazóis/farmacologia , Animais , Antibacterianos/síntese química , Antibacterianos/química , Relação Dose-Resposta a Droga , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/química , Imidazóis/síntese química , Imidazóis/química , Testes de Sensibilidade Microbiana , Estrutura Molecular , Peptídeo Sintases/metabolismo , Relação Estrutura-Atividade , Tiazóis/síntese química , Tiazóis/química , Peixe-Zebra/microbiologia
18.
Proc Natl Acad Sci U S A ; 110(32): 12984-9, 2013 Aug 06.
Artigo em Inglês | MEDLINE | ID: mdl-23872845

RESUMO

In fragment-based drug discovery, the weak affinities exhibited by fragments pose significant challenges for screening. Biophysical techniques are used to address this challenge, but there is no clear consensus on which cascade of methods is best suited to identify fragment hits that ultimately translate into bound X-ray structures and provide bona fide starting points for synthesis. We have benchmarked an integrated biophysical approach for fragment screening and validation against Mycobacterium tuberculosis pantothenate synthetase. A primary screen of 1,250 fragments library was performed by thermal shift, followed by secondary screen using one-dimensional NMR spectroscopy (water ligand observed gradient spectroscopy and saturation transfer difference binding experiments) and ultimate hit validation by isothermal titration calorimetry and X-ray crystallography. Our multibiophysical approach identified three distinct binding sites for fragments and laid a solid foundation for successful structure-based elaboration into potent inhibitors.


Assuntos
Proteínas de Bactérias/antagonistas & inibidores , Descoberta de Drogas/métodos , Inibidores Enzimáticos/farmacologia , Peptídeo Sintases/antagonistas & inibidores , Bibliotecas de Moléculas Pequenas/farmacologia , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Biofísica/métodos , Calorimetria , Cristalografia por Raios X , Inibidores Enzimáticos/química , Inibidores Enzimáticos/metabolismo , Cinética , Ligantes , Espectroscopia de Ressonância Magnética , Modelos Moleculares , Estrutura Molecular , Mycobacterium tuberculosis/efeitos dos fármacos , Mycobacterium tuberculosis/enzimologia , Peptídeo Sintases/química , Peptídeo Sintases/metabolismo , Ligação Proteica , Estrutura Terciária de Proteína , Desdobramento de Proteína , Bibliotecas de Moléculas Pequenas/química , Bibliotecas de Moléculas Pequenas/metabolismo , Temperatura
19.
J Am Chem Soc ; 137(20): 6500-5, 2015 May 27.
Artigo em Inglês | MEDLINE | ID: mdl-25964995

RESUMO

The transpeptidases involved in the synthesis of the bacterial cell wall (also known as penicillin-binding proteins, PBPs) have evolved to bind the acyl-D-Ala-D-Ala segment of the stem peptide of the nascent peptidoglycan for the physiologically important cross-linking of the cell wall. The Tipper-Strominger hypothesis stipulates that ß-lactam antibiotics mimic the acyl-D-Ala-D-Ala moiety of the stem and, thus, are recognized by the PBPs with bactericidal consequences. We document that this mimicry exists also at the allosteric site of PBP2a of methicillin-resistant Staphylococcus aureus (MRSA). Interactions of different classes of ß-lactam antibiotics, as mimics of the acyl-D-Ala-D-Ala moiety at the allosteric site, lead to a conformational change, across a distance of 60 Å to the active site. We directly visualize this change using an environmentally sensitive fluorescent probe affixed to the protein loops that frame the active site. This conformational mobility, documented in real time, allows antibiotic access to the active site of PBP2a. Furthermore, we document that this allosteric trigger enables synergy between two different ß-lactam antibiotics, wherein occupancy at the allosteric site by one facilitates occupancy by a second at the transpeptidase catalytic site, thus lowering the minimal-inhibitory concentration. This synergy has important implications for the mitigation of facile emergence of resistance to these antibiotics by MRSA.


Assuntos
Staphylococcus aureus Resistente à Meticilina/química , Proteínas de Ligação às Penicilinas/química , Proteínas de Ligação às Penicilinas/metabolismo , Peptídeo Sintases/química , Peptídeo Sintases/metabolismo , Sítio Alostérico/efeitos dos fármacos , Antibacterianos/química , Antibacterianos/farmacologia , Staphylococcus aureus Resistente à Meticilina/efeitos dos fármacos , Staphylococcus aureus Resistente à Meticilina/metabolismo , Modelos Moleculares , Estrutura Molecular , Proteínas de Ligação às Penicilinas/antagonistas & inibidores , Peptídeo Sintases/antagonistas & inibidores , beta-Lactamas/química , beta-Lactamas/farmacologia
20.
J Bacteriol ; 196(4): 772-9, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-24296672

RESUMO

Aminoimidazole carboxamide ribotide (AICAR) is a purine biosynthetic intermediate and a by-product of histidine biosynthesis. In bacteria, yeast, and humans, accumulation of AICAR has been shown to affect an array of cellular processes by both direct and indirect mechanisms. In purine biosynthesis, AICAR is the substrate of the bifunctional protein phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase (PurH, EC 2.1.2.3/3.5.4.10). Strains lacking PurH accumulate AICAR and have a defect in the synthesis of the 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) moiety of thiamine. The formation of HMP is also compromised in vivo when coenzyme A (CoA) levels are reduced. Our results show that the in vivo accumulation of AICAR decreased total CoA pools and, further, that AICAR inhibited the activity of pantoate ß-alanine ligase in vitro (PanC, EC 6.3.2.1). These results demonstrated a mechanism of AICAR action and provide new insights into the metabolic consequences of disrupting purine metabolism.


Assuntos
Aminoimidazol Carboxamida/análogos & derivados , Coenzima A/antagonistas & inibidores , Coenzima A/biossíntese , Inibidores Enzimáticos/metabolismo , Ribonucleotídeos/metabolismo , Salmonella enterica/efeitos dos fármacos , Salmonella enterica/metabolismo , Aminoimidazol Carboxamida/metabolismo , Peptídeo Sintases/antagonistas & inibidores
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA