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1.
J Cell Sci ; 134(10)2021 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-34037233

RESUMO

Zα domains recognize the left-handed helical Z conformation of double-stranded nucleic acids. They are found in proteins involved in the nucleic acid sensory pathway of the vertebrate innate immune system and host evasion by viral pathogens. Previously, it has been demonstrated that ADAR1 (encoded by ADAR in humans) and DAI (also known as ZBP1) localize to cytoplasmic stress granules (SGs), and this localization is mediated by their Zα domains. To investigate the mechanism, we determined the interactions and localization pattern for the N-terminal region of human DAI (ZαßDAI), which harbours two Zα domains, and for a ZαßDAI mutant deficient in nucleic acid binding. Electrophoretic mobility shift assays demonstrated the ability of ZαßDAI to bind to hyperedited nucleic acids, which are enriched in SGs. Furthermore, using immunofluorescence and immunoprecipitation coupled with mass spectrometry, we identified several interacting partners of the ZαßDAI-RNA complex in vivo under conditions of arsenite-induced stress. These interactions are lost upon loss of nucleic acid-binding ability or upon RNase treatment. Thus, we posit that the mechanism for the translocation of Zα domain-containing proteins to SGs is mainly mediated by the nucleic acid-binding ability of their Zα domains. This article has an associated First Person interview with Bharath Srinivasan, joint first author of the paper.


Assuntos
DNA Forma Z , Ácidos Nucleicos , Adenosina Desaminase/metabolismo , Grânulos Citoplasmáticos/metabolismo , Humanos , Conformação de Ácido Nucleico , RNA , Proteínas de Ligação a RNA
2.
Biochem J ; 479(16): 1727-1741, 2022 08 31.
Artigo em Inglês | MEDLINE | ID: mdl-35969150

RESUMO

DNA/RNA molecules adopting the left-handed conformation (Z-form) have been attributed with immunogenic properties. However, their biological role and importance have been a topic of debate for many years. The discovery of Z-DNA/RNA binding domains (Zα domains) in varied proteins that are involved in the innate immune response, such as the interferon inducible form of the RNA editing enzyme ADAR1 (p150), Z-DNA binding protein 1 (ZBP1), the fish kinase PKZ and the poxvirus inhibitor of interferon response E3L, indicates important roles of Z-DNA/RNA in immunity and self/non-self-discrimination. Such Zα domain-containing proteins recognize left-handed Z-DNA/RNA in a conformation-specific manner. Recent studies have implicated these domains in virus recognition. Given these important emerging roles for the Zα domains, it is pivotal to understand the mechanism of recognition of the Z-DNA/Z-RNA by these domains. To this end, we assessed the binding thermodynamics of Zα domain from ORF112 and ADAR1 on T(CG)3 and T(CG)6 oligonucleotides which have high propensity to adopt the Z-conformation. Our study highlights important differences in the mode of oligonucleotide binding by the two Zα domains originating from different proteins. Site-directed mutagenesis was employed together with isothermal titration calorimetry to tease apart finer details of the binding thermodynamics. Our work advances the understanding on binding thermodynamics of Zα domains to their cognate nucleic acid substrates and paves the ground for future efforts to gain a complete appreciation of this process.


Assuntos
DNA Forma Z , Ácidos Nucleicos , Adenosina Desaminase/metabolismo , Animais , DNA/metabolismo , DNA Forma Z/genética , Interferons/genética , Conformação de Ácido Nucleico , Oligonucleotídeos , RNA/metabolismo , Termodinâmica
3.
Med Res Rev ; 40(5): 1776-1793, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32285494

RESUMO

Understanding protein-small-molecule interactions is a critical component of rational drug-design. Structure-activity relationship (SAR)-guided medicinal chemistry is informed by the biological outcome, as assessed by biochemical activity or cellular effect, of chemical modifications on small molecules. The effectiveness of SAR is reliant on the sturdiness and durability of assay design and the quality of information garnered from assays. Lack of quality data at this step can lead to obstruction of the drug discovery pipeline with profound implications for the timelines of introducing a drug into the market. Hence, it would not be an overstatement to consider biochemical/biological assays as the backbone of drug-discovery. Enzyme assays can fail for many different reasons, with the enzyme and the substrate being the principal players. Lack of clarity can hamper progress and can lead to mounting costs and potentially losing competitive advantage. Although each assay is unique and requires a specific approach to troubleshoot the problem at hand, there are general guidelines that can be followed to maximize the chances of success. This review is a step-by-step attempt at reintroducing fundamental biochemical concepts within the context of an enzyme assay, delineating probable causes for failure and potential approaches to get an assay back up and running.


Assuntos
Descoberta de Drogas , Ensaios Enzimáticos , Bioensaio , Humanos , Cinética , Relação Estrutura-Atividade
4.
Genome ; 63(2): 61-90, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31557446

RESUMO

Nucleobindin-1 is an EF-hand calcium-binding protein with a distinctive profile, predominantly localized to the Golgi in insect and wide-ranging vertebrate cell types, alike. Its putative involvements in intracellular calcium (Ca2+) homeostasis have never been phenotypically characterized in any model organism. We have analyzed an adult-viable mutant that completely disrupts the G protein α-subunit binding and activating (GBA) motif of Drosophila Nucleobindin-1 (dmNUCB1). Such disruption does not manifest any obvious fitness-related, morphological/developmental, or behavioral abnormalities. A single copy of this mutation or the knockdown of dmnucb1 in restricted sets of cells variously rescues pleiotropic mutant phenotypes arising from impaired inositol 1,4,5-trisphosphate receptor (IP3R) activity (in turn depleting cytoplasmic Ca2+ levels across diverse tissue types). Additionally, altered dmNUCB1 expression or function considerably reverses lifespan and mobility improvements effected by IP3R mutants, in a Drosophila model of amyotrophic lateral sclerosis. Homology modeling-based analyses further predict a high degree of conformational conservation in Drosophila, of biochemically validated structural determinants in the GBA motif that specify in vertebrates, the unconventional Ca2+-regulated interaction of NUCB1 with Gαi subunits. The broad implications of our findings are hypothetically discussed, regarding potential roles for NUCB1 in GBA-mediated, Golgi-associated Ca2+ signaling, in health and disease.


Assuntos
Proteínas de Ligação ao Cálcio/fisiologia , Cálcio/metabolismo , Proteínas de Drosophila/fisiologia , Receptores de Inositol 1,4,5-Trifosfato/genética , Nucleobindinas/fisiologia , Alelos , Motivos de Aminoácidos , Animais , Proteínas de Ligação ao Cálcio/química , Proteínas de Ligação ao Cálcio/genética , Proteínas de Ligação ao Cálcio/metabolismo , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Proteínas de Drosophila/química , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Drosophila melanogaster/genética , Drosophila melanogaster/crescimento & desenvolvimento , Drosophila melanogaster/metabolismo , Subunidades alfa de Proteínas de Ligação ao GTP/metabolismo , Genes Letais , Pleiotropia Genética , Complexo de Golgi/metabolismo , Homeostase , Humanos , Inositol 1,4,5-Trifosfato/metabolismo , Mutação , Nucleobindinas/química , Nucleobindinas/genética , Nucleobindinas/metabolismo , Domínios Proteicos , Homologia Estrutural de Proteína
5.
Med Res Rev ; 39(2): 684-705, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30192413

RESUMO

Escherichia coli Dihydrofolate reductase is an important enzyme that is essential for the survival of the Gram-negative microorganism. Inhibitors designed against this enzyme have demonstrated application as antibiotics. However, either because of poor bioavailability of the small-molecules resulting from their inability to cross the double membrane in Gram-negative bacteria or because the microorganism develops resistance to the antibiotics by mutating the DHFR target, discovery of new antibiotics against the enzyme is mandatory to overcome drug-resistance. This review summarizes the field of DHFR inhibition with special focus on recent efforts to effectively interface computational and experimental efforts to discover novel classes of inhibitors that target allosteric and active-sites in drug-resistant variants of EcDHFR.


Assuntos
Antibacterianos/farmacologia , Infecções Bacterianas/tratamento farmacológico , Inibidores Enzimáticos/farmacologia , Escherichia coli/enzimologia , Antagonistas do Ácido Fólico/farmacologia , Tetra-Hidrofolato Desidrogenase/química , Algoritmos , Sítio Alostérico , Animais , Domínio Catalítico , Desenho de Fármacos , Descoberta de Drogas , Humanos , Ligantes , Permeabilidade/efeitos dos fármacos , Relação Estrutura-Atividade
6.
Drug Dev Ind Pharm ; 44(11): 1845-1856, 2018 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-30028215

RESUMO

OBJECTIVE: In this study, we investigated the potential of thiolated chitosan-based mucoadhesive film, loaded with risedronate sodium in the treatment of osteoporosis. SIGNIFICANCE: Risedronate sodium is a bisphosphonate derivative having very low bioavailability when administered through the oral route. Moreover, the adverse effects associated with the drug when administered through GIT necessitate an alternative and feasible route which can improve its bioavailability and therapeutic efficacy. METHODS: Thiolation of chitosan was interpreted by different analytical techniques. The mucoadhesive films were prepared by the solvent evaporation method and evaluated for drug content analysis, swelling degree, mucoadhesive parameters, and permeation characterization. For the screening of preclinical efficacy and pharmacodynamic parameters, a methylprednisolone induced osteoporotic rat model was used. The trabecular microarchitecture and biochemical markers were evaluated for determination of bone resorption. RESULTS: The different analytical characterization of synthesized thiolated chitosan revealed that chitosan was successfully incorporated with thiol groups. The formulation containing 2:1 ratio of thiolated chitosan and HPMC-4KM was found to have the maximum swelling degree, mucoadhesive strength with a good force of adhesion and better in vitro permeability compared to the marketed formulation. With respect to trabecular microarchitecture, the drug-loaded film formulation showed superior and promising results. Furthermore, the film formulation also improved the serum level of biomarkers better than the marketed formulation. CONCLUSIONS: The results significantly suggest that risedronate loaded novel mucoadhesive film formulation could be a logical approach in the therapeutic intervention of osteoporosis.


Assuntos
Osso e Ossos/efeitos dos fármacos , Quitosana/química , Metilprednisolona/toxicidade , Osteoporose/tratamento farmacológico , Ácido Risedrônico/química , Animais , Osso e Ossos/diagnóstico por imagem , Osso e Ossos/patologia , Modelos Animais de Doenças , Composição de Medicamentos , Feminino , Microscopia Eletrônica de Varredura , Osteoporose/induzido quimicamente , Osteoporose/patologia , Ratos , Espectroscopia de Infravermelho com Transformada de Fourier , Termogravimetria
7.
J Comput Chem ; 38(15): 1252-1259, 2017 06 05.
Artigo em Inglês | MEDLINE | ID: mdl-27864975

RESUMO

Conventional small molecule drug-discovery approaches target protein pockets. However, the limited number of geometrically distinct pockets leads to widespread promiscuity and deleterious side-effects. Here, the idea of COmposite protein LIGands (COLIG) that interact with each other as well as the protein within a single ligand binding pocket is examined. As a practical illustration, experimental evidence that E. coli Dihydrofolate reductase inhibitors are COLIGs is presented. Then, analysis of a non-redundant set of all holo PDB structures indicates that almost 47-76% of proteins (based on different sequence identity thresholds) can simultaneously bind multiple, interacting ligands in the same pocket. Moreover, most ligands that are either Singletons and COLIGs bind at the bottom of ligand binding pocket and occupy 30% and 43% of the volume of the bottom of the pocket. This suggests the use of COLIGs as a potential new class of small molecule drugs. © 2016 Wiley Periodicals, Inc.


Assuntos
Escherichia coli/enzimologia , Antagonistas do Ácido Fólico/farmacologia , Proteínas/metabolismo , Bibliotecas de Moléculas Pequenas/farmacologia , Tetra-Hidrofolato Desidrogenase/metabolismo , Sítios de Ligação , Descoberta de Drogas , Escherichia coli/efeitos dos fármacos , Infecções por Escherichia coli/tratamento farmacológico , Antagonistas do Ácido Fólico/química , Humanos , Ligantes , Simulação de Acoplamento Molecular , Ligação Proteica , Conformação Proteica , Proteínas/química , Bibliotecas de Moléculas Pequenas/química , Tetra-Hidrofolato Desidrogenase/química
8.
Bioorg Med Chem Lett ; 27(17): 4133-4139, 2017 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-28739043

RESUMO

Traditional structure and ligand based virtual screening approaches rely on the availability of structural and ligand binding information. To overcome this limitation, hybrid approaches were developed that relied on extraction of ligand binding information from proteins sharing similar folds and hence, evolutionarily relationship. However, they cannot target a chosen pocket in a protein. To address this, a pocket centric virtual ligand screening approach is required. Here, we employ a new, iterative implementation of a pocket and ligand-similarity based approach to virtual ligand screening to predict small molecule binders for the olfactomedin domain of human myocilin implicated in glaucoma. Small-molecule binders of the protein might prevent the aggregation of the protein, commonly seen during glaucoma. First round experimental assessment of the predictions using differential scanning fluorimetry with myoc-OLF yielded 7 hits with a success rate of 12.7%; the best hit had an apparent dissociation constant of 99nM. By matching to the key functional groups of the best ligand that were likely involved in binding, the affinity of the best hit was improved by almost 10,000 fold from the high nanomolar to the low picomolar range. Thus, this study provides preliminary validation of the methodology on a medically important glaucoma associated protein.


Assuntos
Proteínas do Citoesqueleto/antagonistas & inibidores , Proteínas do Olho/antagonistas & inibidores , Glaucoma/tratamento farmacológico , Glicoproteínas/antagonistas & inibidores , Proteínas de Transferência de Fosfolipídeos/antagonistas & inibidores , Bibliotecas de Moléculas Pequenas/farmacologia , Sítios de Ligação/efeitos dos fármacos , Proteínas do Citoesqueleto/química , Relação Dose-Resposta a Droga , Avaliação Pré-Clínica de Medicamentos , Proteínas do Olho/química , Glicoproteínas/química , Humanos , Ligantes , Estrutura Molecular , Proteínas de Transferência de Fosfolipídeos/química , Bibliotecas de Moléculas Pequenas/química , Relação Estrutura-Atividade
9.
Bioorg Med Chem Lett ; 27(14): 3048-3054, 2017 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-28554871

RESUMO

A series of new of furan derivatised [1,4] benzothiazepine analogues were synthesized starting from 1-(furan-2-yl)ethanone. 1-(Furan-2-yl)ethanone was converted into chalcones by its reaction with various aromatic aldehydes, then were reacted with 2-aminobenzenethiol in acidic conditions to obtain the title compounds in good yields. The synthesized new compounds were characterized by 1H NMR, 13C NMR, Mass spectral studies and elemental analyses. All the new compounds were evaluated for their in vitro VRV-PL-8a and H+/K+ ATPase inhibitor properties. Preliminary studies revealed that, some molecules amongst the designed series showed promising VRV-PL-8a and H+/K+ ATPase inhibitor properties. Further, rigid body docking studies were performed to understand possible docking sites of the molecules on the target proteins and the mode of binding. This finding presents a promising series of lead molecules that can serve as prototypes for the treatment of inflammatory related disorder that can mitigate the ulcer inducing side effect shown by other NSAIDs.


Assuntos
Desenho de Fármacos , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/farmacologia , Fosfolipases A2 do Grupo II/antagonistas & inibidores , ATPase Trocadora de Hidrogênio-Potássio/química , Tiazepinas/síntese química , Tiazepinas/farmacologia , Anti-Inflamatórios não Esteroides/síntese química , Anti-Inflamatórios não Esteroides/química , Anti-Inflamatórios não Esteroides/metabolismo , Anti-Inflamatórios não Esteroides/farmacologia , Sítios de Ligação , Chalconas/química , Ativação Enzimática/efeitos dos fármacos , Inibidores Enzimáticos/química , Inibidores Enzimáticos/metabolismo , Furanos/química , Fosfolipases A2 do Grupo II/metabolismo , ATPase Trocadora de Hidrogênio-Potássio/metabolismo , Concentração Inibidora 50 , Espectroscopia de Ressonância Magnética , Conformação Molecular , Simulação de Acoplamento Molecular , Estrutura Terciária de Proteína , Inibidores da Bomba de Prótons/síntese química , Inibidores da Bomba de Prótons/química , Inibidores da Bomba de Prótons/metabolismo , Inibidores da Bomba de Prótons/farmacologia , Tiazepinas/química , Tiazepinas/metabolismo
10.
Bioorg Med Chem Lett ; 27(16): 3806-3811, 2017 08 15.
Artigo em Inglês | MEDLINE | ID: mdl-28676270

RESUMO

Oxidative-stress induces inflammatory diseases. Further, infections caused by drug-resistant microbial strains are on the rise. This necessitates the discovery of novel small-molecules for intervention therapy. A series of 3-(2,3-dichlorophenyl)-1-(aryl)prop-2-en-1-ones are synthesized as intermediates via Claisen-Schmidt reaction approach. Subsequently, these intermediates were transformed into 2-pyrazolines by their reaction with phenylhydrazine hydrochlorides in methanol and few drops of acetic acid under reflux conditions. Synthesized compounds were characterized by spectroscopic, crystallographic and elemental analyses studies and then, were evaluated for their in vitro antimicrobial and anti-inflammatory activities. Amongst the series, 3-(4-chlorophenyl)-5-(2,3-dichlorophenyl)-1-phenyl-4,5-dihydro-1H-pyrazole (5e), 5-(2,3-dichlorophenyl)-3-(4-fluorophenyl)-1-phenyl-4,5-dihydro-1H-pyrazole (5c) and 5-(2,3-dichlorophenyl)-3-(4-methoxyphenyl)-1-phenyl-4,5-dihydro-1H-pyrazole (5h) showed significant inhibition of phospholipase A2 with IC50 values of 10.2, 11.1 and 11.9µM, respectively. Protein structure modelling and docking studies indicated that the compounds showed binding to a highly conserved calcium-binding pocket on the enzyme. Further, compounds (5e), 1-(3-chlorophenyl)-5-(2,3-dichlorophenyl)-3-phenyl-4,5-dihydro-1H-pyrazole (5b), and 1-(3-chlorophenyl)-3-(4-chlorophenyl)-5-(2,3-dichlorophenyl)-4,5-dihydro-1H-pyrazole (5f) showed excellent antimicrobial activities against various bacterial and fungal strains. In conclusion, this study is a successful attempt at the synthesis and characterization of chalcone derivatives that can target phospholipase A2, an enzyme that is a prominent player in the physiological inflammatory cascade. Thus, these compounds show promise for development as next-generation nonsteroidal anti-inflammatory drugs.


Assuntos
Anti-Inflamatórios não Esteroides/farmacologia , Inibidores de Fosfolipase A2/farmacologia , Fosfolipases A2/metabolismo , Pirazóis/farmacologia , Relação Quantitativa Estrutura-Atividade , Anti-Inflamatórios não Esteroides/síntese química , Anti-Inflamatórios não Esteroides/química , Cristalografia por Raios X , Relação Dose-Resposta a Droga , Humanos , Modelos Moleculares , Estrutura Molecular , Inibidores de Fosfolipase A2/síntese química , Inibidores de Fosfolipase A2/química , Pirazóis/síntese química , Pirazóis/química
11.
Biochem J ; 473(14): 2165-77, 2016 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-27208174

RESUMO

The presence of latent activities in enzymes is posited to underlie the natural evolution of new catalytic functions. However, the prevalence and extent of such substrate and catalytic ambiguity in evolved enzymes is difficult to address experimentally given the order-of-magnitude difference in the activities for native and, sometimes, promiscuous substrate/s. Further, such latent functions are of special interest when the activities concerned do not fall into the domain of substrate promiscuity. In the present study, we show a special case of such latent enzyme activity by demonstrating the presence of two mechanistically distinct reactions catalysed by the catalytic domain of receptor protein tyrosine phosphatase isoform δ (PTPRδ). The primary catalytic activity involves the hydrolysis of a phosphomonoester bond (C─O─P) with high catalytic efficiency, whereas the secondary activity is the hydrolysis of a glycosidic bond (C─O─C) with poorer catalytic efficiency. This enzyme also displays substrate promiscuity by hydrolysing diester bonds while being highly discriminative for its monoester substrates. To confirm these activities, we also demonstrated their presence on the catalytic domain of protein tyrosine phosphatase Ω (PTPRΩ), a homologue of PTPRδ. Studies on the rate, metal-ion dependence, pH dependence and inhibition of the respective activities showed that they are markedly different. This is the first study that demonstrates a novel sugar hydrolase and diesterase activity for the phosphatase domain (PD) of PTPRδ and PTPRΩ. This work has significant implications for both understanding the evolution of enzymatic activity and the possible physiological role of this new chemistry. Our findings suggest that the genome might harbour a wealth of such alternative latent enzyme activities in the same protein domain that renders our knowledge of metabolic networks incomplete.


Assuntos
Proteínas Tirosina Fosfatases Semelhantes a Receptores/química , Proteínas Tirosina Fosfatases Semelhantes a Receptores/metabolismo , Catálise , Domínio Catalítico , Biologia Computacional , Proteínas Tirosina Fosfatases Semelhantes a Receptores/genética , Eletricidade Estática , Especificidade por Substrato
12.
Biogerontology ; 17(5-6): 907-920, 2016 11.
Artigo em Inglês | MEDLINE | ID: mdl-27484416

RESUMO

There is great interest in drugs that are capable of modulating multiple aging pathways, thereby delaying the onset and progression of aging. Effective strategies for drug development include the repurposing of existing drugs already approved by the FDA for human therapy. FDA approved drugs have known mechanisms of action and have been thoroughly screened for safety. Although there has been extensive scientific activity in repurposing drugs for disease therapy, there has been little testing of these drugs for their effects on aging. The pool of FDA approved drugs therefore represents a large reservoir of drug candidates with substantial potential for anti-aging therapy. In this paper we employ FINDSITEcomb, a powerful ligand homology modeling program, to identify binding partners for proteins produced by temperature sensing genes that have been implicated in aging. This list of drugs with potential to modulate aging rates was then tested experimentally for lifespan and healthspan extension using a small invertebrate model. Three protein targets of the rotifer Brachionus manjavacas corresponding to products of the transient receptor potential gene 7, ribosomal protein S6 polypeptide 2 gene, or forkhead box C gene, were screened against a compound library consisting of DrugBank drugs including 1347 FDA approved, non-nutraceutical molecules. Twenty nine drugs ranked in the top 1 % for binding to each target were subsequently included in our experimental analysis. Continuous exposure of rotifers to 1 µM naproxen significantly extended rotifer mean lifespan by 14 %. We used three endpoints to estimate rotifer health: swimming speed (mobility proxy), reproduction (overall vitality), and mitochondria activity (cellular senescence proxy). The natural decline in swimming speed with aging was more gradual when rotifers were exposed to three drugs, so that on day 6, mean swimming speed of females was 1.19 mm/s for naproxen (P = 0.038), 1.20 for fludarabine (P = 0.040), 1.35 for hydralazine (P = 0.038), as compared to 0.88 mm/s in the control. The average reproduction of control females in the second half of their reproductive lifespan was 1.08 per day. In contrast, females treated with 1 µM naproxen produced 1.4 offspring per day (P = 0.027) and females treated with 10 µM fludarabine or 1 µM hydralazine produced 1.72 (P = <0.001) and 1.66 (P = 0.001) offspring per day, respectively. Mitochondrial activity naturally declines with rotifer aging, but B. manjavacas treated with 1 µM hydralazine or 10 µM fludarabine retained 49 % (P = 0.038) and 89 % (P = 0.002) greater mitochondria activity, respectively, than untreated controls. Our results demonstrate that coupling computation to experimentation can quickly identify new drug candidates with anti-aging potential. Screening drugs for anti-aging effects using a rotifer bioassay is a powerful first step in identifying compounds worthy of follow-up in vertebrate models. Even if lifespan extension is not observed, certain drugs could improve healthspan, slowing age-dependent losses in mobility and vitality.


Assuntos
Envelhecimento/efeitos dos fármacos , Descoberta de Drogas/métodos , Avaliação Pré-Clínica de Medicamentos/métodos , Ensaios de Triagem em Larga Escala/métodos , Medicamentos sob Prescrição/química , Animais , Aprovação de Drogas , Reposicionamento de Medicamentos , Rotíferos , Estados Unidos , United States Food and Drug Administration
13.
Bioorg Med Chem Lett ; 26(2): 690-694, 2016 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-26631319

RESUMO

A series of novel coumarin pyrazole hybrids of biological interest were synthesized from the hydrazones, carbazones and thiocarbazones via Vilsmeier Haack formylation reaction. These intermediates and formyl pyrazoles were evaluated for antimicrobial and antioxidant activities. Among the series, compounds 6g and 6h showed excellent antimicrobial activity against different bacterial and fungal strains and compounds 7g, 7h were found to be potent antioxidant agents in both DPPH and hydroxyl radical scavenging assays. Further, detailed quantitative structure-activity relationship (QSAR) analysis indicated the molecular parameters that contribute to increased potency of inhibition. The above findings would further encourage our understanding in employing coumarin pyrazole hybrids as potential antibiotic agents for treating infections caused by pathogenic microbes and fungi. Further, it also paves the way for exploration of these compounds as potential therapeutic agents to treat conditions arising because of excessive oxidative damage.


Assuntos
Anti-Infecciosos/química , Anti-Infecciosos/farmacologia , Antioxidantes/química , Antioxidantes/farmacologia , Cumarínicos/química , Cumarínicos/farmacologia , Anti-Infecciosos/síntese química , Antioxidantes/síntese química , Bactérias/efeitos dos fármacos , Infecções Bacterianas/tratamento farmacológico , Cumarínicos/síntese química , Fungos/efeitos dos fármacos , Humanos , Testes de Sensibilidade Microbiana , Micoses/tratamento farmacológico , Pirazóis/síntese química , Pirazóis/química , Pirazóis/farmacologia , Relação Quantitativa Estrutura-Atividade
14.
Bioorg Med Chem Lett ; 26(15): 3621-5, 2016 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-27318538

RESUMO

Ethyl 2-(4-methoxyphenyl)-3-(thiophene-2-carbonyl)cyclopropanecarboxylates 2(a-f) and ethyl 4-aryl-7-oxo-4,5,6,7-tetrahydrobenzo[b]thiophene-5-carboxylates 4(a-f) were synthesized by simple procedure. The synthesized new compounds were screened in vitro for their antimicrobial and antioxidant activities. The compounds 2b and 4f showed excellent antibacterial activity; while 2b and 4f showed remarkable antifungal properties. The results of antioxidant activity studies revealed that compounds 4b and 4f manifested profound antioxidant potential. The docking studies were done for the final compounds. The ADME result indicates that all these molecules possess pharmaceutical properties in the range of 95% of drugs.


Assuntos
Antibacterianos/farmacologia , Antifúngicos/farmacologia , Antioxidantes/farmacologia , Ciclopropanos/farmacologia , Lignanas/farmacologia , Antibacterianos/síntese química , Antibacterianos/química , Antifúngicos/síntese química , Antifúngicos/química , Antioxidantes/síntese química , Antioxidantes/química , Bactérias/efeitos dos fármacos , Ciclopropanos/química , Relação Dose-Resposta a Droga , Fungos/efeitos dos fármacos , Lignanas/química , Testes de Sensibilidade Microbiana , Simulação de Acoplamento Molecular , Estrutura Molecular , Relação Estrutura-Atividade
15.
Bioorg Med Chem ; 24(19): 4750-4758, 2016 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-27567076

RESUMO

Peptide:N-glycanase (NGLY1) is an enzyme responsible for cleaving oligosaccharide moieties from misfolded glycoproteins to enable their proper degradation. Deletion and truncation mutations in this gene are responsible for an inherited disorder of the endoplasmic reticulum-associated degradation pathway. However, the literature is unclear whether the disorder is a result of mutations leading to loss-of-function, loss of substrate specificity, loss of protein stability or a combination of these factors. In this communication, without burdening ourselves with the mechanistic underpinning of disease causation because of mutations on the NGLY1 protein, we demonstrate the successful application of virtual ligand screening (VLS) combined with experimental high-throughput validation to the discovery of novel small-molecules that show binding to the transglutaminase domain of NGLY1. Attempts at recombinant expression and purification of six different constructs led to successful expression of five, with three constructs purified to homogeneity. Most mutant variants failed to purify possibly because of misfolding and the resultant exposure of surface hydrophobicity that led to protein aggregation. For the purified constructs, our threading/structure-based VLS algorithm, FINDSITE(comb), was employed to predict ligands that may bind to the protein. Then, the predictions were assessed by high-throughput differential scanning fluorimetry. This led to the identification of nine different ligands that bind to the protein of interest and provide clues to the nature of pharmacophore that facilitates binding. This is the first study that has identified novel ligands that bind to the NGLY1 protein as a possible starting point in the discovery of ligands with potential therapeutic applications in the treatment of the disorder caused by NGLY1 mutants.


Assuntos
Degradação Associada com o Retículo Endoplasmático/efeitos dos fármacos , Peptídeo-N4-(N-acetil-beta-glucosaminil) Asparagina Amidase/metabolismo , Bibliotecas de Moléculas Pequenas/química , Bibliotecas de Moléculas Pequenas/farmacologia , Humanos , Ligantes , Simulação de Acoplamento Molecular
16.
Bioorg Med Chem Lett ; 25(6): 1163-70, 2015 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-25690787

RESUMO

Coincidence of the properties of ligand binding pockets in native proteins with those in proteins generated by computer simulations without selection for function shows that pockets are a generic protein feature and the number of distinct pockets is small. Similar pockets occur in unrelated protein structures, an observation successfully employed in pocket-based virtual ligand screening. The small number of pockets suggests that off-target interactions among diverse proteins are inherent; kinases, proteases and phosphatases show this prototypical behavior. The ability to repurpose FDA approved drugs is general, and minor side effects cannot be avoided. Finally, the implications to drug discovery are explored.


Assuntos
Evolução Molecular , Ligantes , Proteínas/química , Sítios de Ligação , Avaliação Pré-Clínica de Medicamentos , Simulação de Dinâmica Molecular , Ligação Proteica , Proteínas Quinases/química , Proteínas Quinases/metabolismo , Estrutura Terciária de Proteína , Proteínas/metabolismo
17.
J Chem Inf Model ; 55(8): 1757-70, 2015 Aug 24.
Artigo em Inglês | MEDLINE | ID: mdl-26225536

RESUMO

Often in pharmaceutical research the goal is to identify small molecules that can interact with and appropriately modify the biological behavior of a new protein target. Unfortunately, most proteins lack both known structures and small molecule binders, prerequisites of many virtual screening, VS, approaches. For such proteins, ligand homology modeling, LHM, that copies ligands from homologous and perhaps evolutionarily distant template proteins, has been shown to be a powerful VS approach to identify possible binding ligands. However, if we want to target a specific pocket for which there is no homologous holo template protein structure, then LHM will not work. To address this issue, in a new pocket-based approach, PoLi, we generalize LHM by exploiting the fact that the number of distinct small molecule ligand-binding pockets in proteins is small. PoLi identifies similar ligand-binding pockets in a holo template protein library, selectively copies relevant parts of template ligands, and uses them for VS. In practice, PoLi is a hybrid structure and ligand-based VS algorithm that integrates 2D fingerprint-based and 3D shape-based similarity metrics for improved virtual screening performance. On standard DUD and DUD-E benchmark databases, using modeled receptor structures, PoLi achieves an average enrichment factor of 13.4 and 9.6, respectively, in the top 1% of the screened library. In contrast, traditional docking-based VS using AutoDock Vina and homology-based VS using FINDSITE(filt) have an average enrichment of 1.6 (3.0) and 9.0 (7.9) on the DUD (DUD-E) sets, respectively. Experimental validation of PoLi predictions on dihydrofolate reductase, DHFR, using differential scanning fluorimetry, DSF, identifies multiple ligands with diverse molecular scaffolds, thus demonstrating the advantage of PoLi over current state-of-the-art VS methods.


Assuntos
Proteínas/química , Proteínas/metabolismo , Algoritmos , Sítios de Ligação , Bases de Dados de Proteínas , Descoberta de Drogas , Ligantes , Simulação de Acoplamento Molecular , Conformação Proteica
18.
Exp Parasitol ; 151-152: 56-63, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-25655405

RESUMO

Members of the haloacid dehalogenase (HAD) superfamily are emerging as an important group of enzymes by virtue of their role in diverse chemical reactions. In different Plasmodium species their number varies from 16 to 21. One of the HAD superfamily members, PVX_123945, a hypothetical protein from Plasmodium vivax, was selected for examining its substrate specificity. Based on distant homology searches and structure comparisons, it was predicted to be a phosphatase. Thirty-eight metabolites were screened to identify potential substrates. Further, to validate the prediction, biochemical and kinetic studies were carried out that showed that the protein was a monomer with high catalytic efficiency for ß-glycerophosphate followed by pyridoxal 5'-phosphate. The enzyme also exhibited moderate catalytic efficiencies for α-glycerophosphate, xanthosine 5'-monophosphate and adenosine 5'-monophosphate. It also hydrolyzed the artificial substrate p-nitrophenyl phosphate (pNPP). Mg(2+) was the most preferred divalent cation and phosphate inhibited the enzyme activity. The study is the first attempt at understanding the substrate specificity of a hypothetical protein belonging to HAD superfamily from the malarial parasite P. vivax.


Assuntos
Glicerofosfatos/metabolismo , Hidrolases/metabolismo , Monoéster Fosfórico Hidrolases/metabolismo , Plasmodium vivax/enzimologia , Fosfato de Piridoxal/metabolismo , Monofosfato de Adenosina/metabolismo , Biologia Computacional , Hidrolases/antagonistas & inibidores , Hidrolases/química , Cinética , Magnésio/metabolismo , Estrutura Molecular , Peso Molecular , Nitrofenóis/metabolismo , Compostos Organofosforados/metabolismo , Fosfatos/farmacologia , Monoéster Fosfórico Hidrolases/antagonistas & inibidores , Monoéster Fosfórico Hidrolases/química , Dobramento de Proteína , Ribonucleotídeos/metabolismo , Especificidade por Substrato , Xantina
19.
J Food Sci Technol ; 51(4): 743-9, 2014 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-24741169

RESUMO

Halubai, a traditional Indian sweet is conventionally prepared by soaking and grinding whole cereals/millets to a fine paste, straining it through a cloth and cooking the resultant dispersion until it starts gelatinizing. Cooking is continued further with the addition of jaggery water, stirring constantly with intermittent addition of ghee. This process involves many unit operations, which are energy and time consuming. Hence a modified method was developed which is energy efficient and time saving without compromising the quality of the product. One fine fraction (200 mesh, BS) of cereal/millet flours were used in modified method instead of whole cereals. Sensory and instrumental analysis of the samples showed that quality of Halubai prepared using modified method was comparable to that of samples from conventional method. Correlation studies on sensory data of Halubai showed positive relation for the set (r = 0.94) and smoothness (r = 0.84); and negative relation for stickiness (r = -0.94) with the overall quality. Modified method of Halubai preparation which was simple and energy efficient, resulted in products with good sensory quality.

20.
Environ Sci Pollut Res Int ; 31(26): 38061-38082, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38806984

RESUMO

Sunscreens are essential in protecting the skin from harmful effects of ultraviolet radiation (UVR). These formulations, designed to absorb, block, or scatter UVR, offer vital protection against skin aging, sunburns, and the development of skin cancers like melanomas. However, some sunscreens, especially those containing organic/chemical compounds, can cause allergic reactions. To address this, researchers are extensively investigating formulations that incorporate plant extracts rich in polyphenols, such as flavonoids and carotenoids, which can be considered safer alternatives. Products derived from plants are commonly used in cosmetics to counteract skin aging due to their antioxidant activity that combat harmful free radicals. This review focuses on evaluating the advancements in chemical and natural sunscreens, exploring the integration of polyphenolic nanocarriers within sunscreen formulas, their interaction with UVR, and utilizing nanotechnology to enhance their effectiveness. An attempt has been made to highlight the concerns related to toxicity associated with their use and notable advancements in the regulatory aspects governing their utilization.


Assuntos
Nanotecnologia , Polifenóis , Protetores Solares , Raios Ultravioleta , Protetores Solares/química , Polifenóis/química , Humanos , Nanopartículas
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