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1.
J Biomol Struct Dyn ; : 1-18, 2023 Dec 26.
Artigo em Inglês | MEDLINE | ID: mdl-38147408

RESUMO

A series of S-adenosyl-L-homosysteine (SAH) analogs, with modification in the base and sugar moiety, have been designed, synthesized and screened as nsp14 and PLpro inhibitors of severe acute respiratory syndrome corona virus (SARS-CoV-2). The outcomes of ADMET (Adsorption, Distribution, Metabolism, Excretion, and Toxicity) studies demonstrated that the physicochemical properties of all analogs were permissible for development of these SAH analogs as antiviral agents. All molecules were screened against different SARS-CoV-2 targets using molecular docking. The docking results revealed that the SAH analogs interacted well in the active site of nsp14 protein having H-bond interactions with the amino acid residues Arg289, Val290, Asn388, Arg400, Phe401 and π-alkyl interactions with Arg289, Val290 and Phe426 of Nsp14-MTase site. These analogs also formed stable H-bonds with Leu163, Asp165, Arg167, Ser246, Gln270, Tyr274 and Asp303 residues of PLpro proteins and found to be quite stable complexes therefore behaved as probable nsp14 and PLpro inhibitors. Interestingly, analog 3 showed significant in silico activity against the nsp14 N7 methyltransferase of SARS-CoV-2. The molecular dynamics (MD) and post-MD results of analog 3 unambiguously established the higher stability of the nsp14 (N7 MTase):3 complex and also indicated its behavior as probable nsp14 inhibitor like the reference sinefungin. The docking and MD simulations studies also suggested that sinefungin did act as SARS-CoV-2 PLpro inhibitor as well. This study's findings not only underscore the efficacy of the designed SAH analogs as potent inhibitors against crucial SARS-CoV-2 proteins but also pinpoint analog 3 as a particularly promising candidate. All the study provides valuable insights, paving the way for potential advancements in antiviral drug development against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.


HighlightsSAH analogs bearing modified bases and sugar moiety have been synthesized as antivirals against SARS-CoV-2.Molecular dynamics simulation established the stability of ligand-protein complex of analog 3 with nsp14 (N7-MTase) protein of SARS-CoV-2.Molecular docking studies of SAH analogs indicated them as nsp14 N7 methyltranferase as well as the PLpro inhibitors of SARS-CoV-2.The in silico antiviral activity of SAH analogs has been found comparable to the reference drug Sinefungin.

2.
Comput Biol Chem ; 106: 107910, 2023 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-37422940

RESUMO

A novel series of pyrimidine derivatives, bearing modified benzimidazoles at N-1 position, has been designed, synthesized and screened as NNRTIs against HIV and as broad-spectrum antiviral agents. The molecules were screened against different HIV targets using molecular docking experiment. The docking results indicated that the molecules interacted well with the residues Lys101, Tyr181, Tyr188, Trp229, Phe227 and Tyr318 present in NNIBP of HIV-RT protein, formed quite stable complexes and, thus, behaved as probable NNRTIs. Among these compounds, 2b and 4b showed anti-HIV activity with IC50 values as 6.65 µg/mL (SI = 15.50) and 15.82 µg/mL (SI = 14.26), respectively. Similarly, compound 1a showed inhibitory property against coxsackie virus B4 and compound 3b against different viruses. Molecular dynamics simulation results unequivocally demonstrated the higher stability of the complex HIV-RT:2b than the HIV-RT:nevirapine complex. The MM/PBSA-based binding free energy (-) 114.92 kJ/mol of HIV-RT:2b complex in comparison to that of HIV-RT:nevirapine complex (-) 88.33 kJ/mol, further demonstrated the higher binding strength of 2b and thus, established the potential of compound 2b as a lead molecule as an HIV-RT inhibitor.


Assuntos
Antivirais , HIV-1 , Antivirais/farmacologia , Pirimidinas/química , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Inibidores da Transcriptase Reversa/farmacologia , HIV-1/genética , Nevirapina , Relação Estrutura-Atividade , Desenho de Fármacos
3.
J Biomol Struct Dyn ; 41(16): 8068-8080, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36229234

RESUMO

To improve rationally the efficacy of the non-nucleoside human immunodeficiency virus (HIV-1) inhibitors, it is important to have a precise and detailed understanding of the HIV-1 reverse transcriptase (RT) and inhibitor interactions. For the 1-[(2-hydroxyethoxy) methyl]-6-(phenylthio) thymine (HEPT) type of nucleoside reverse transcriptase inhibitors (NNRTIs), the H-bond between the N-3H of the inhibitor and the backbone carbonyl group of K101 represents the major hydrophilic interaction. This H-bond contributes to the NNRTI binding affinity. The descriptor analyses of different uracil derivatives proved their good cell internalization. The bioactivity score reflected higher drug likeness score and the ligands showed interesting docking results. All molecules were deeply buried and stabilized into the allosteric site of HIV-1 RT. For majority of molecules, residues Lys101, Lys103, Tyr181 and Tyr188 were identified as key protein residues responsible for generation of H-bond and major interactions were similar to all known NNRTIs while very few molecules interacted with residues Phe227 and Tyr318. The TOPKAT protocol available in Discovery Studio 3.0 was used to predict the pharmacokinetics of the designed uracil derivatives in the human body. The molecular dynamics (MD) and post-MD analyses results reflected that the complex HIVRT:5 appeared to be more stable than the complex HIVRT:HEPT, where HEPT was used as reference. Different uracil derivatives have been synthesized by using uracil as starting material and commercially available propargyl bromide. The N-1 derivative of uracil was further reacted with sodamide and different aldehydes/ketones bearing alkyl and phenyl ring to obtain hydroxyalkynyl uracil derivatives as NNRTIs.Communicated by Ramaswamy H. Sarma.

4.
Curr Pharm Des ; 28(27): 2211-2233, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35909276

RESUMO

COVID-19, a dreaded and highly contagious pandemic, is flagrantly known for its rapid prevalence across the world. Till date, none of the treatments are distinctly accessible for this life-threatening disease. Under the prevailing conditions of a medical emergency, one creative strategy for the identification of novel and potential antiviral agents gaining momentum in research institutions and progressively being leveraged by pharmaceutical companies is target-based drug repositioning/repurposing. Continuous monitoring and recording of results offer anticipation that this strategy may help to reveal new medications for viral infections. This review recapitulates the neoteric illation of COVID-19, its genomic dispensation, molecular evolution via phylogenetic assessment, drug targets, the most frequently worldwide used repurposed drugs and their therapeutic applications, and a recent update on vaccine management strategies. The available data from solidarity trials exposed that the treatment with several known drugs, viz. lopinavir-ritonavir, chloroquine, hydroxychloroquine, etc. had displayed various antagonistic effects along with no impactful result in the diminution of mortality rate. The drugs, like remdesivir, favipiravir, and ribavirin, have proved to be quite safer therapeutic options for treatment against COVID-19. Similarly, dexamethasone, convalescent plasma therapy and oral administration of 2DG are expected to reduce the mortality rate of COVID-19 patients.


Assuntos
Tratamento Farmacológico da COVID-19 , COVID-19 , Antivirais/farmacologia , Antivirais/uso terapêutico , COVID-19/terapia , Reposicionamento de Medicamentos , Humanos , Imunização Passiva , Filogenia , SARS-CoV-2 , Vacinação , Soroterapia para COVID-19
5.
J Biomol Struct Dyn ; 40(21): 10519-10542, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34253149

RESUMO

A new series of quinoline derivatives has been designed and synthesized as probable protease inhibitors (PIs) against severe acute respiratory syndrome coronavirus 2. In silico studies using DS v20.1.0.19295 software have shown that these compounds behaved as PIs while interacting at the allosteric site of target Mpro enzyme (6LU7). The designed compounds have shown promising docking results, which revealed that all compounds formed hydrogen bonds with His41, His164, Glu166, Tyr54, Asp187, and showed π-interaction with His41, the highly conserved amino acids in the target protein. Toxicity Prediction by Komputer Assisted Technology results confirmed that the compounds were found to be less toxic than the reference drug. Further, molecular dynamics simulations were performed on compound 5 and remdesivir with protease enzyme. Analysis of conformational stability, residue flexibility, compactness, hydrogen bonding, solvent accessible surface area (SASA), and binding free energy revealed comparable stability of protease:5 complex to the protease: remdesivir complex. The result of hydrogen bonding showed a large number of intermolecular hydrogen bonds formed between protein residues (Glu166 and Gln189) and ligand 5, indicating strong interaction, which validated the docking result. Further, compactness analysis, SASA and interactions like hydrogen-bonding demonstrated inhibitory properties of compound 5 similar to the existing reference drug. Thus, the designed compound 5 might act as a potential inhibitor against the protease enzyme.Communicated by Ramaswamy H. SarmaHighlightsQuinoline derivatives have been designed as protease inhibitors against SARS-CoV-2.The compounds were docked at the allosteric site of SARS-CoV-2-Mpro enzyme (PDB ID: 6LU7) to study the stability of protein-ligand complex.Docking studies indicated the stable ligand-protein complexes for all designed compounds.The Toxicity Prediction by Komputer Assisted Technology protocol in DS v20.1.0.19295 software was used to evaluate the toxicity of the designed quinoline derivatives.Molecular dynamics studies indicated the formation of stable ligand-Mpro complexes.


Assuntos
Antivirais , Inibidores de Proteases , Quinolinas , SARS-CoV-2 , Ligantes , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Peptídeo Hidrolases , Inibidores de Proteases/farmacologia , SARS-CoV-2/efeitos dos fármacos , Quinolinas/farmacologia , Antivirais/farmacologia
6.
Curr Pharm Des ; 28(3): 232-247, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34727852

RESUMO

BACKGROUND: Traditionally, various plant extracts having interesting biological properties were the main source of new drugs. In the last 30 years, the role of chemistry in combination with new technologies, like various computational techniques in chemistry, has witnessed a major upsurge in drug discovery and targeted drug delivery. OBJECTIVE: This article provides a succinct overview of recent techniques of chemistry that have a great impact on the drug development process in general and also against HIV/AIDS. It focuses on new methods employed for drug development with an emphasis on in silico studies, including identifying drug targets, especially the proteins associated with specific diseases. METHODS: The rational drug development process starts with the identification of a drug target as the first phase, which helps in the computer-assisted design of new drug molecules. Synthetic chemistry has a major impact on the drug development process because it provides new molecules for future study. Natural products based semisynthesis or microwave assisted synthesis is also involved in developing newly designed drug molecules. Further, the role of analytical chemistry involves extraction, fractionation, isolation and characterization of newly synthesized molecules. RESULTS: Chemistry plays a key role in drug discovery and delivery by natural process or with the help of synthetic nanoparticles or nanomedicines. So, nanochemistry is also deeply involved in the development of new drugs and their applications. CONCLUSION: The previous era of drug discovery was dominated only by chemistry, but the modern approaches involve a comprehensive knowledge of synthetic chemistry, medicinal chemistry, computational chemistry and the concerned biological phenomenon.


Assuntos
Fármacos Anti-HIV , Fármacos Anti-HIV/farmacologia , Química Farmacêutica/métodos , Desenho de Fármacos , Descoberta de Drogas/métodos , Humanos , Preparações Farmacêuticas/química
7.
Int J Clin Pract ; 75(11): e14515, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34118111

RESUMO

COVID-19 infection, affecting every one of us from the last year. Emerging reports have indicated thromboembolism in serious cases of COVID-19. The aspirin is useful to reduce mortality of serious patients with acute respiratory distress syndrome without COVID-19. Thus, we have conducted a metanalysis to find out the role of aspirin in the mortality of COVID-19 patients using RevMan 5. A total of 10 studies containing 56 696 COVID-19 patients were found appropriate for quantitative analysis. The quality of articles was assessed using Newcastle-Ottawa scale. The fixed-effect model was used to calculate the odds ratio with 95% confidence interval (CI). The odd ratio was found to be 0.70 [0.63, 0.77] which indicates a lesser likelihood of having death in COVID-19 patients in aspirin group as compared with non-aspirin group. However, no effect 0.00 [-0.04, 0.04] was observed after the exclusion of outliers. Thus, further clinical evidence is required to make valid conclusion.


Assuntos
COVID-19 , Síndrome do Desconforto Respiratório , Aspirina/uso terapêutico , Humanos , SARS-CoV-2
8.
Protein Expr Purif ; 182: 105843, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-33631310

RESUMO

Commercial applications of ß-glucosidase (BGL) demands its purity and availability on a large scale. In the present study, we aim to optimize the expression and secretion of a thermostable BGL from Pyrococcus furiosus (PfuBGL) in B. subtilis strain RIK1285. Initial studies with base strain BV002 harboring aprE signal peptide (aprESP) showed PfuBGL yield of 0.743 ± 0.19 pNP U/ml only. A library of 173 different homologous SPs from B. subtilis 168 genome was fused with target PfuBGL gene (PF0073) in pBE-S vector and extracellularly expressed in RIK1285 strain to identify optimal SP for PfuBGL secretion. High-throughput screening of the resulting SP library for BGL activity with a synthetic substrate followed by systematic scaling of the clones yielded a gene construct with CitHSP reporting a sixteen fold enhancement of PfuBGL secretion in comparison to base strain. Batch fermentation (7.5 L scale) PfuBGL yield of the BV003 strain with CitHSP-PF0073 fusion was observed to be 12.08 ± 0.21 pNP U/ml with specific activity of 35.52 ± 0.53 U/mg. Thus, the study represents report on the secretory expression of thermostable PfuBGL using B. subtilis as a host organism and demonstrating its high potential for industrial production of any protein/enzyme.


Assuntos
Proteínas Arqueais , Bacillus subtilis , Sinais Direcionadores de Proteínas/genética , Pyrococcus furiosus , beta-Glucosidase , Proteínas Arqueais/biossíntese , Proteínas Arqueais/química , Proteínas Arqueais/genética , Proteínas Arqueais/isolamento & purificação , Bacillus subtilis/genética , Bacillus subtilis/metabolismo , Pyrococcus furiosus/enzimologia , Pyrococcus furiosus/genética , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , beta-Glucosidase/biossíntese , beta-Glucosidase/química , beta-Glucosidase/genética , beta-Glucosidase/isolamento & purificação
9.
J Biomol Struct Dyn ; 39(7): 2430-2446, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32216610

RESUMO

In view of the low toxicity of NNRTIs in comparison to NRTIs, a new series of diarylpyrimidine derivatives has been designed as NNRTIs against HIV-1. In silico studies using DS 3.0 software have shown that these compounds behaved as NNRTIs while interacting at the allosteric site of HIV-RT. The designed compounds have shown promising docking results, which revealed that all compounds formed hydrogen bonds with Lys101, Lys103, Tyr181, Tyr318 and π- interactions with Tyr181, Tyr188, Phe227 and Trp229 amino acid residues located in the non-nucleoside inhibitor binding pocket (NNIBP) of HIV-RT protein. The intended molecules have shown high binding affinity with HIV-1 RT, analogous to standard drug molecule-etravirine. TOPKAT results confirmed that the designed compounds were found to be less toxic than the reference drug. Further, employing molecular dynamics simulations, the complexes of the best screened compound 6 and etravirine with the HIV-1 RT protein were analyzed by calculating the RMSD, RMSF, Rg, number of hydrogen bonds, principal components of the coordinates, molecular mechanics-Poisson-Boltzmann surface area-based binding free energy and their decomposition for different interactions. The analysis demonstrated the higher stability of compound 6 than the standard drug etravirine with HIV-1 RT. The interactions like hydrogen-bonding, van-der-Waals, electrostatic and the solvent accessible surface energy have favorable contributions to the complex stability. Thus, the shortlisted designed compound has great promise as a potential inhibitor against HIV-1 RT.


Assuntos
Fármacos Anti-HIV , Inibidores da Transcriptase Reversa , Fármacos Anti-HIV/farmacologia , Sítios de Ligação , Desenho de Fármacos , Transcriptase Reversa do HIV , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Inibidores da Transcriptase Reversa/farmacologia
10.
Comput Biol Chem ; 89: 107400, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33068917

RESUMO

A series of alkylated benzimidazole derivatives was synthesized and screened for their anti-HIV, anti-YFV, and broad-spectrum antiviral properties. The physicochemical parameters and drug-like properties of the compounds were assessed first, and then docking studies and MD simulations on HIV-RT allosteric sites were conducted to find the possible mode of their action. DFT analysis was also performed to confirm the nature of the hydrogen bonding interaction of active compounds. The in silico studies indicated that the molecules behaved like possible NNRTIs. The nature - polar or non-polar and position of the substituent present at fifth, sixth, and N-1 positions of the benzimidazole moiety played an important role in determining the antiviral properties of the compounds. Among the various compounds, 2-(5,6-dibromo-2-chloro-1H-benzimidazol-1-yl)ethan-1-ol (3a) showed anti-HIV activity with an appreciably low IC50 value as 0.386 × 10-5µM. Similarly, compound 2b, 3-(2-chloro-5-nitro-1H-benzimidazol-1-yl) propan-1-ol, showed excellent inhibitory property against the yellow fever virus (YFV) with EC50 value as 0.7824 × 10-2µM.


Assuntos
Benzimidazóis/farmacologia , HIV/efeitos dos fármacos , Inibidores da Transcriptase Reversa/farmacologia , Vírus da Febre Amarela/efeitos dos fármacos , Animais , Benzimidazóis/síntese química , Benzimidazóis/farmacocinética , Domínio Catalítico , Chlorocebus aethiops , Teoria da Densidade Funcional , HIV/enzimologia , Transcriptase Reversa do HIV/química , Transcriptase Reversa do HIV/metabolismo , Testes de Sensibilidade Microbiana , Modelos Químicos , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Estrutura Molecular , Inibidores da Transcriptase Reversa/síntese química , Inibidores da Transcriptase Reversa/farmacocinética , Relação Estrutura-Atividade , Células Vero , Vírus da Febre Amarela/enzimologia
11.
Comput Biol Chem ; 77: 226-239, 2018 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-30366286

RESUMO

A series of molecules bearing oxathiadiazole, a five membered heterocyclic ring has been designed, synthesized and screened for antimicrobial activity. Molecules, 1a, 1b, 1d, 3a-b and 4a-b were found to be highly active (MIC value upto 1.5 µg/mL) against different human pathogens, namely S. aureus, B. cerus, P. aeruginosa and E. coli. Some of the compounds, 1a, 1b and 1d have also shown the antifungal activity (MIC value upto 6.2 µg/mL) against Candida albicans, Candida glubrate and Candida crusei. During in vitro cytotoxicity study, the oxathiadiazole derivatives showed less toxicity than the reference used against PBM, CEM and Vero (African green monkey kidney) cell lines. Docking studies suggested that all designed ligands interacted well within active site of PDF enzyme (PDB ID: 1G2A). Oxathiadiazole ring of all ligands formed H-bond with amino acid Leu91 at a distance ranging between 2.5-2.8 Å and also exhibited π - + and π - π interactions with amino acid residues Arg97 and His132, respectively. In silico ADMET evaluations of compounds showed more than 90% intestinal absorption for all compounds except 4b (87.45%), which too was greater than the reference drugs sulfamethoxazole (76.46%) and chloramphenicol (69.94%). TOPKAT results also supported the lower cytotoxicity of all compounds.


Assuntos
Anti-Infecciosos/química , Anti-Infecciosos/farmacologia , Bactérias/efeitos dos fármacos , Candida/efeitos dos fármacos , Tiadiazóis/química , Tiadiazóis/farmacologia , Amidoidrolases/metabolismo , Animais , Anti-Infecciosos/síntese química , Bactérias/enzimologia , Infecções Bacterianas/tratamento farmacológico , Candida/enzimologia , Candidíase/tratamento farmacológico , Domínio Catalítico/efeitos dos fármacos , Linhagem Celular , Chlorocebus aethiops , Descoberta de Drogas , Humanos , Simulação de Acoplamento Molecular , Tiadiazóis/síntese química , Células Vero
12.
Comput Biol Chem ; 76: 1-16, 2018 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-29857255

RESUMO

A series of 2-Cl-benzimidazole derivatives was synthesized and assessed for antibacterial activity. Antibacterial results indicated that compounds 2d, 2e, 3a, 3b, 3c, 4d and 4e showed promising activity against B. cerus, S. aureus and P. aeruginosa (MIC: 6.2 µg/mL) and excellent efficacy against E. coli (MIC: 3.1 µg/mL). Furthermore, compounds 3d and 3e displayed better activity (MIC: 3.1 µg/mL) than the reference drugs chloramphenicol and cycloheximide against gram positive and gram negative bacterial strains. The compounds 3d-e also showed better activity than the reference drug paromomycin against B. cerus and P. aeruginosa and showed similar inhibition pattern against S. aureus and E. coli. (MIC: 3.1 µg/mL). Studies on fractional inhibitory concentration (FIC) determination of compounds 1a-e, 2a-c, 4a-c and the reference antibiotic via combination approach revealed a synergistic effect as the MIC values were lowered up to 1/8th to 1/33rd of the original MIC. In-vitro cytotoxicity study indicated that 2-Cl-benzimidazole derivatives showed less toxicity than the reference used against PBM, CEM and Vero cell lines. Docking studies and MD simulations of compounds on bacterial protein (eubacterial ribosomal decoding A site, PDB: 1j7t) have been conducted to find the possible mode of action of the molecules. In silico ADMET evaluations of compounds 3d and 3e showed promising results comparable to the reference drugs used in this study.


Assuntos
Antibacterianos/farmacologia , Benzimidazóis/farmacologia , Animais , Antibacterianos/síntese química , Antibacterianos/metabolismo , Antibacterianos/toxicidade , Bacillus cereus/efeitos dos fármacos , Benzimidazóis/síntese química , Benzimidazóis/metabolismo , Benzimidazóis/toxicidade , Linhagem Celular , Cloranfenicol/farmacologia , Chlorocebus aethiops , Cicloeximida/farmacologia , Sinergismo Farmacológico , Escherichia coli/efeitos dos fármacos , Humanos , Ligantes , Testes de Sensibilidade Microbiana , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Paromomicina/farmacologia , Ligação Proteica , Pseudomonas aeruginosa/efeitos dos fármacos , RNA Ribossômico 16S/metabolismo , Staphylococcus aureus/efeitos dos fármacos , Relação Estrutura-Atividade
13.
Bioorg Med Chem ; 26(12): 3414-3428, 2018 07 23.
Artigo em Inglês | MEDLINE | ID: mdl-29778528

RESUMO

A new series of heterocyclic molecules bearing sulfonamide linkage has been synthesized and screened for antibacterial activity. During antibacterial screening using broath dilution method, molecules were found to be highly active (MIC value 50-3.1 µg/mL) against different human pathogens, namely B. cerus, S. aureus, E. coli and P. aeruginosa, and most effective against E. coli. A great synergistic effect was observed during determination of FIC where molecules were used in combination with reference drugs chloramphenicol and sulfamethoxazole. The MIC value of the combination - varying concentration of test compounds and ½ MIC of reference drugs or varying concentration of reference drugs and ½ MIC of test compounds, was reduced up to 1/4 or 1/32 of the original value, indicating thereby the combination was 4-32 times more potent than the test molecule. The molecules also showed low degree of cytotoxicity against PBM, CEM and VERO cell lines. The results positively indicated towards the development of lead antibacterials using the combination approach.


Assuntos
Antibacterianos/síntese química , Simulação de Acoplamento Molecular , Sulfonamidas/química , Animais , Antibacterianos/química , Antibacterianos/farmacologia , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Benzimidazóis/química , Benzotiazóis/química , Sítios de Ligação , Domínio Catalítico , Sobrevivência Celular/efeitos dos fármacos , Chlorocebus aethiops , Desenho de Fármacos , Bactérias Gram-Negativas/efeitos dos fármacos , Bactérias Gram-Positivas/efeitos dos fármacos , Indazóis/química , Testes de Sensibilidade Microbiana , Relação Estrutura-Atividade , Sulfametoxazol/farmacologia , Sulfonamidas/síntese química , Tiazóis/química , Células Vero
14.
J Struct Biol ; 202(1): 70-81, 2018 04.
Artigo em Inglês | MEDLINE | ID: mdl-29241954

RESUMO

In bacteria, biosynthesis of riboflavin occurs through a series of enzymatic steps starting with one molecule of GTP and two molecules of ribulose-5-phosphate. In Bacillus subtilis (B. subtilis) the genes (ribD/G, ribE, ribA, ribH and ribT) which are involved in riboflavin biosynthesis are organized in an operon referred as rib operon. All the genes of rib operon are characterized functionally except for ribT. The ribT gene with unknown function is found at the distal terminal of rib operon and annotated as a putative N-acetyltransferase. Here, we report the crystal structure of ribT from B. subtilis (bribT) complexed with coenzyme A (CoA) at 2.1 Šresolution determined by single wavelength anomalous dispersion method. Our structural study reveals that bribT is a member of GCN5-related N-acetyltransferase (GNAT) superfamily and contains all the four conserved structural motifs that have been in other members of GNAT superfamily. The members of GNAT family transfers the acetyl group from acetyl coenzyme A (AcCoA) to a variety of substrates. Moreover, the structural analysis reveals that the residues Glu-67 and Ser-107 are suitably positioned to act as a catalytic base and catalytic acid respectively suggesting that the catalysis by bribT may follow a direct transfer mechanism. Surprisingly, the mutation of a non-conserved amino acid residue Cys-112 to alanine or serine affected the binding of AcCoA to bribT, indicating a possible role of Cys-112 in the catalysis.


Assuntos
Acetiltransferases/genética , Bacillus subtilis/genética , Proteínas de Bactérias/genética , Óperon , Acetilcoenzima A/química , Acetilcoenzima A/genética , Acetilcoenzima A/metabolismo , Acetiltransferases/química , Acetiltransferases/metabolismo , Bacillus subtilis/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Sítios de Ligação/genética , Domínio Catalítico/genética , Cristalografia por Raios X , Modelos Moleculares , Mutação , Ligação Proteica , Riboflavina/biossíntese
15.
Interdiscip Sci ; 10(4): 748-761, 2018 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-28194576

RESUMO

Design, synthesis, and antibacterial activities of a series of arylsulphonamide derivatives as probable peptide deformylase (PDF) inhibitors have been discussed. Compounds have been designed following Lipinski's rule and after docking into the active site of PDF protein (PDB code: 1G2A) synthesized later on. Furthermore, to assess their antibacterial activity, screening of the compound was done in vitro conditions against Gram-positive and Gram-negative bacterial strains. In silico, studies revealed these compounds as potential antibacterial agents and this fact was also supported by their prominent scoring functions. Antibacterial results indicated that these molecules possessed a significant activity against Staphylococcus aureus, Bacillus cereus, Pseudomonas aeruginosa, and Escherichia coli with MIC values ranging from 0.06 to 0.29 µM. TOPKAT results showed that high LD50 values and the compounds were assumed non-carcinogenic when various animal models were studied computationally.


Assuntos
Antibacterianos/síntese química , Antibacterianos/farmacologia , Desenho de Fármacos , Compostos Heterocíclicos/síntese química , Compostos Heterocíclicos/farmacologia , Sulfonamidas/síntese química , Sulfonamidas/farmacologia , Antibacterianos/toxicidade , Bactérias/efeitos dos fármacos , Compostos Heterocíclicos/toxicidade , Ligantes , Testes de Sensibilidade Microbiana , Simulação de Acoplamento Molecular , Medição de Risco , Relação Estrutura-Atividade , Sulfonamidas/toxicidade
16.
J Biol Chem ; 292(2): 638-651, 2017 Jan 13.
Artigo em Inglês | MEDLINE | ID: mdl-27913623

RESUMO

Glutathione degradation plays an important role in glutathione and redox homeostasis, and thus it is imperative to understand the enzymes and the mechanisms involved in glutathione degradation in detail. We describe here ChaC2, a member of the ChaC family of γ-glutamylcyclotransferases, as an enzyme that degrades glutathione in the cytosol of mammalian cells. ChaC2 is distinct from the previously described ChaC1, to which ChaC2 shows ∼50% sequence identity. Human and mouse ChaC2 proteins purified in vitro show 10-20-fold lower catalytic efficiency than ChaC1, although they showed comparable Km values (Km of 3.7 ± 0.4 mm and kcat of 15.9 ± 1.0 min-1 toward glutathione for human ChaC2; Km of 2.2 ± 0.4 mm and kcat of 225.2 ± 15 min-1 toward glutathione for human ChaC1). The ChaC1 and ChaC2 proteins also shared the same specificity for reduced glutathione, with no activity against either γ-glutamyl amino acids or oxidized glutathione. The ChaC2 proteins were found to be expressed constitutively in cells, unlike the tightly regulated ChaC1. Moreover, lower eukaryotes have a single member of the ChaC family that appears to be orthologous to ChaC2. In addition, we determined the crystal structure of yeast ChaC2 homologue, GCG1, at 1.34 Å resolution, which represents the first structure of the ChaC family of proteins. The catalytic site is defined by a fortuitous benzoic acid molecule bound to the crystal structure. The mechanism for binding and catalytic activity of this new enzyme of glutathione degradation, which is involved in continuous but basal turnover of cytosolic glutathione, is proposed.


Assuntos
Glutationa/química , gama-Glutamilciclotransferase/química , Animais , Catálise , Domínio Catalítico , Linhagem Celular , Cristalografia por Raios X , Regulação Enzimológica da Expressão Gênica/fisiologia , Glutationa/genética , Glutationa/metabolismo , Humanos , Camundongos , Saccharomyces cerevisiae/enzimologia , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , gama-Glutamilciclotransferase/genética , gama-Glutamilciclotransferase/isolamento & purificação , gama-Glutamilciclotransferase/metabolismo
17.
Sci Rep ; 6: 39634, 2016 12 23.
Artigo em Inglês | MEDLINE | ID: mdl-28008971

RESUMO

Cellulase catalyzes the hydrolysis of ß-1,4-linkages of cellulose to produce industrially relevant monomeric subunits. Cellulases find their applications in pulp and paper, laundry, food and feed, textile, brewing industry and in biofuel production. These industries always have great demand for cellulases that can work efficiently even in harsh conditions such as high salt, heat, and acidic environments. While, cellulases with high thermal and acidic stability are already in use, existence of a high halotolerant cellulase is still elusive. Here, we report a novel cellulase Cel5R, obtained from soil metagenome that shows high halotolerance and thermal stability. The biochemical and functional characterization of Cel5R revealed its endoglucanase activity and high halostability. In addition, the crystal structure of Cel5R determined at 2.2 Å resolution reveals a large number of acidic residues on the surface of the protein that contribute to the halophilic nature of this enzyme. Moreover, we demonstrate that the four free and non-conserved cysteine residues (C65, C90, C231 and C273) contributes to the thermal stability of Cel5R by alanine scanning experiments. Thus, the newly identified endoglucanase Cel5R is a promising candidate for various industrial applications.


Assuntos
Proteínas de Bactérias/química , Celulase/química , Metagenoma , Microbiologia do Solo , Alanina/química , Catálise , Celulose/metabolismo , Dicroísmo Circular , Cristalografia por Raios X , Cisteína/química , Temperatura Alta , Concentração de Íons de Hidrogênio , Microbiologia Industrial , Modelos Moleculares , Conformação Molecular , Mutação , Fases de Leitura Aberta , Plasmídeos/metabolismo , Proteínas Recombinantes/química , Sais/química , Solo , Solubilidade , Especificidade por Substrato , Temperatura
18.
J Fluoresc ; 26(4): 1431-8, 2016 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-27231013

RESUMO

Derivatives of 4-amino-1,8-naphthalimide containing a free alkyl chain bearing carboxyl group as linker and different substituents at 4-amino function have been synthesized, characterized and studied for their photophysical properties. Steady state fluorescence studies showed quantum yield varied from 0.45 to 0.65 with Stokes shift in the range of 5824-8558 cm(-1). Spectroscopic and physicochemical parameters, like electronic absorption, emission, and extinction coefficient were investigated in order to explore the analytical potential of compounds. Solvatochromic studies demonstrated that all compounds were sensitive towards the polarity of different solvents showing the highest degree of fluorescence in acetonitrile. In addition, the compounds in the presence of ions, viz. Na(+), K(+) and Mg(2+) at concentration of 0.1-2 equivalents, showed a decreasing trend in fluorescence with increasing ionic concentration. TCSPC set - up was used to measure the fluorescence lifetime of compounds, which was found to be bi-exponential with longer and shorter component at their respective amplitudes. The average lifetime of compounds was observed to be 5.76-9.96 ns indicating the possibility of their greater utilization in research and diagnosis.


Assuntos
1-Naftilamina/análogos & derivados , Sistemas de Liberação de Medicamentos , Corantes Fluorescentes/química , Corantes Fluorescentes/síntese química , Naftalimidas/química , Naftalimidas/síntese química , Quinolonas/química , Quinolonas/síntese química , 1-Naftilamina/síntese química , 1-Naftilamina/química , Técnicas de Química Sintética , Espectrometria de Fluorescência
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