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1.
Int J Mol Sci ; 24(11)2023 May 26.
Artigo em Inglês | MEDLINE | ID: mdl-37298285

RESUMO

Fluoro-substituted pyrazoles have a wide range of biological activities, such as antibacterial, antiviral, and antifungal activities. The aim of this study was to evaluate the antifungal activities of fluorinated 4,5-dihydro-1H-pyrazole derivatives on four phytopathogenic fungi: Sclerotinia sclerotiorum, Macrophomina phaseolina, Fusarium oxysporum f. sp. lycopersici, and F. culmorum. Moreover, they were tested on two soil beneficial bacteria-Bacillus mycoides and Bradyrhizobium japonicum-as well as two entomopathogenic nematodes (EPNs)-Heterorhabditis bacteriophora and Steinernema feltiae. The molecular docking was performed on the three enzymes responsible for fungal growth, the three plant cell wall-degrading enzymes, and acetylcholinesterase (AChE). The most active compounds against fungi S. sclerotiorum were 2-chlorophenyl derivative (H9) (43.07% of inhibition) and 2,5-dimethoxyphenyl derivative (H7) (42.23% of inhibition), as well as H9 against F. culmorum (46.75% of inhibition). Compounds were shown to be safe for beneficial soil bacteria and nematodes, except for compound H9 on EPN H. bacteriophora (18.75% mortality), which also showed the strongest inhibition against AChE (79.50% of inhibition). The molecular docking study revealed that antifungal activity is possible through the inhibition of proteinase K, and nematicidal activity is possible through the inhibition of AChE. The fluorinated pyrazole aldehydes are promising components of future plant protection products that could be environmentally and toxicologically acceptable.


Assuntos
Fusarium , Rabditídios , Animais , Antifúngicos/farmacologia , Solo , Acetilcolinesterase , Simulação de Acoplamento Molecular , Pirazóis/farmacologia , Bactérias , Fungos
2.
Antioxidants (Basel) ; 12(6)2023 May 23.
Artigo em Inglês | MEDLINE | ID: mdl-37371871

RESUMO

As the world's population grows, so does the need for more and more animal feed. In 2006, the EU banned the use of antibiotics and other chemicals in order to reduce chemical residues in food consumed by humans. It is well known that oxidative stress and inflammatory processes must be combated to achieve higher productivity. The adverse effects of the use of pharmaceuticals and other synthetic compounds on animal health and product quality and safety have increased interest in phytocompounds. With the use of plant polyphenols in animal nutrition, they are gaining more attention as a supplement to animal feed. Livestock feeding based on a sustainable, environmentally friendly approach (clean, safe, and green agriculture) would also be a win-win for farmers and society. There is an increasing interest in producing healthier products of animal origin with a higher ratio of polyunsaturated fatty acids (PUFAs) to saturated fatty acids by modulating animal nutrition. Secondary plant metabolites (polyphenols) are essential chemical compounds for plant physiology as they are involved in various functions such as growth, pigmentation, and resistance to pathogenic organisms. Polyphenols are exogenous antioxidants that act as one of the first lines of cell defense. Therefore, the discoveries on the intracellular antioxidant activity of polyphenols as a plant supplement have contributed significantly to the improvement of antioxidant activity, as polyphenols prevent oxidative stress damage and eliminate excessively produced free radicals. To achieve animal welfare, reduce stress and the need for medicines, and increase the quality of food of animal origin, the addition of polyphenols to research and breeding can be practised in part with a free-choice approach to animal nutrition.

3.
J Biomol Struct Dyn ; 41(16): 7567-7581, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36106968

RESUMO

Dipeptidyl peptidase III (DPP III) is a zinc-dependent enzyme that sequentially hydrolyzes biologically active peptides by cleaving dipeptides from their N-termini. Although its fundamental role is not been fully elucidated, human DPP III (hDPP III) has been recognized in several pathophysiological processes of interest for drug development. In this article 27 quinazolinone-Schiff's bases were studied for their inhibitory activity against hDPP III combining an in vitro experiment with a computational approach. The biochemical assay showed that most compounds exhibited inhibitory activity at the 100 µM concentration. The best QSAR model included descriptors from the following 2D descriptor groups: information content indices, 2D autocorrelations, and edge adjacency indices. Five compounds were found to be the most potent inhibitors with IC50 values below 10 µM, while molecular docking predicted that these compounds bind to the central enzyme cleft and interact with residues of the substrate binding subsites. Molecular dynamics simulations of the most potent inhibitor (IC50=0.96 µM) provided valuable information explaining the role of PHE109, ARG319, GLU327, GLU329, and ILE386 in the mechanism of the inhibitor binding and stabilization. This is the first study that gives insight into quinazolinone-Schiff's bases binding to this metalloenzyme.Communicated by Ramaswamy H. Sarma.

4.
Antioxidants (Basel) ; 11(5)2022 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-35624834

RESUMO

The feeding of domestic animals with diets in which polyphenols are present is increasingly attracting the attention of nutritionists and scientists. This review summarizes the knowledge regarding polyphenols' possible positive and negative effects and their bioavailability. The bioavailability of substances is a prerequisite for any postabsorption effect in vivo. Positive and negative properties have been confirmed in previous studies on the diets of domestic animals rich in polyphenols, such as secondary metabolites of plants. Free radicals are formed in every organism, leading to oxidative stress. Free radicals are highly reactive molecules and can react in cells with macromolecules and can cause damage, including in reproductive cells. Some polyphenols at specific concentrations have antioxidant properties that positively affect animal reproduction by improving the quality of male and female gametes. The intake of phytoestrogens that mimic estrogen function can induce various pathological conditions in the female reproductive tract, including ovarian, fallopian, and uterine dysfunction. The metabolism of genistein and daidzein yields the metabolites equol and p-phenyl-phenol, leading to a decline in cow fertilization. The findings so far confirm that numerous questions still need to be answered. This review points out the importance of using polyphenols that have both benificial and some unfavorable properties in specific diets.

5.
Molecules ; 27(9)2022 May 07.
Artigo em Inglês | MEDLINE | ID: mdl-35566358

RESUMO

Dipeptidyl peptidase III (DPP III) was originally thought to be a housekeeping enzyme that contributes to intracellular peptide catabolism. More specific roles for this cytosolic metallopeptidase, in the renin-angiotensin system and oxidative stress regulation, were confirmed, or recognized, only recently. To prove indicated (patho)physiological functions of DPP III in cancer progression, cataract formation and endogenous pain modulation, or to reveal new ones, selective and potent inhibitors are needed. This review encompasses natural and synthetic compounds with experimentally proven inhibitory activity toward mammalian DPP III. Except for the polypeptide aprotinin, all others are small molecules and include flavonoids, coumarin and benzimidazole derivatives. Presented are current strategies for the discovery or development of DPP III inhibitors, and mechanisms of inhibitory actions. The most potent inhibitors yet reported (propioxatin A and B, Tyr-Phe- and Phe-Phe-NHOH, and JMV-390) are active in low nanomolar range and contain hydroxamic acid moiety. High inhibitory potential possesses oligopeptides from the hemorphin group, valorphin and tynorphin, which are poor substrates of DPP III. The crystal structure of human DPP III-tynorphin complex enabled the design of the transition-state peptidomimetics inhibitors, effective in low micromolar concentrations. A new direction in the field is the development of fluorescent inhibitor for monitoring DPP III activity.


Assuntos
Inibidores da Dipeptidil Peptidase IV , Peptidomiméticos , Inibidores da Enzima Conversora de Angiotensina , Animais , Aprotinina , Dipeptidil Peptidase 4/química , Inibidores da Dipeptidil Peptidase IV/química , Inibidores da Dipeptidil Peptidase IV/farmacologia , Dipeptidil Peptidases e Tripeptidil Peptidases , Humanos , Mamíferos/metabolismo
6.
Molecules ; 27(7)2022 Mar 28.
Artigo em Inglês | MEDLINE | ID: mdl-35408596

RESUMO

Coumarin derivatives have been reported as strong antifungal agents against various phytopathogenic fungi. In this study, inhibitory effects of nine coumarinyl Schiff bases were evaluated against the plant pathogenic fungi (Fusarium oxysporum f. sp. lycopersici, Fusarium culmorum, Macrophomina phaseolina and Sclerotinia sclerotiourum). The compounds were demonstrated to be efficient antifungal agents against Macrophomina phaseolina. The results of molecular docking on the six enzymes related to the antifungal activity suggested that the tested compounds act against plant pathogenic fungi, inhibiting plant cell-wall-degrading enzymes such as endoglucanase I and pectinase. Neither compound exhibited inhibitory effects against two beneficial bacteria (Bacillus mycoides and Bradyrhizobium japonicum) and two entomopathogenic nematodes. However, compound 9 was lethal (46.25%) for nematode Heterorhabditis bacteriophora and showed an inhibitory effect against acetylcholinesterase (AChE) (31.45%), confirming the relationship between these two activities. Calculated toxicity and the pesticide-likeness study showed that compound 9 was the least lipophilic compound with the highest aquatic toxicity. A molecular docking study showed that compounds 9 and 8 bind directly to the active site of AChE. Coumarinyl Schiff bases are promising active components of plant protection products, safe for the environment, human health, and nontarget organisms.


Assuntos
Ascomicetos , Fusarium , Nematoides , Acetilcolinesterase/farmacologia , Animais , Antifúngicos/química , Antifúngicos/farmacologia , Bactérias , Fungos , Simulação de Acoplamento Molecular , Doenças das Plantas/microbiologia , Plantas , Bases de Schiff/farmacologia , Solo
7.
Pharmaceuticals (Basel) ; 14(6)2021 Jun 05.
Artigo em Inglês | MEDLINE | ID: mdl-34198854

RESUMO

Dipeptidyl peptidase III (DPP III), a zinc-dependent exopeptidase, is a member of the metalloproteinase family M49 with distribution detected in almost all forms of life. Although the physiological role of human DPP III (hDPP III) is not yet fully elucidated, its involvement in pathophysiological processes such as mammalian pain modulation, blood pressure regulation, and cancer processes, underscores the need to find new hDPP III inhibitors. In this research, five series of structurally different coumarin derivatives were studied to provide a relationship between their inhibitory profile toward hDPP III combining an in vitro assay with an in silico molecular modeling study. The experimental results showed that 26 of the 40 tested compounds exhibited hDPP III inhibitory activity at a concentration of 10 µM. Compound 12 (3-benzoyl-7-hydroxy-2H-chromen-2-one) proved to be the most potent inhibitor with IC50 value of 1.10 µM. QSAR modeling indicates that the presence of larger substituents with double and triple bonds and aromatic hydroxyl groups on coumarin derivatives increases their inhibitory activity. Docking predicts that 12 binds to the region of inter-domain cleft of hDPP III while binding mode analysis obtained by MD simulations revealed the importance of 7-OH group on the coumarin core as well as enzyme residues Ile315, Ser317, Glu329, Phe381, Pro387, and Ile390 for the mechanism of the binding pattern and compound 12 stabilization. The present investigation, for the first time, provides an insight into the inhibitory effect of coumarin derivatives on this human metalloproteinase.

8.
Int J Mol Sci ; 22(14)2021 Jul 06.
Artigo em Inglês | MEDLINE | ID: mdl-34298898

RESUMO

The aim was to study the inhibitory effects of coumarin derivatives on the plant pathogenic fungi, as well as beneficial bacteria and nematodes. The antifungal assay was performed on four cultures of phytopathogenic fungi by measuring the radial growth of the fungal colonies. Antibacterial activity was determined by the broth microdilution method performed on two beneficial soil organisms. Nematicidal activity was tested on two entomopathogenic nematodes. The quantitative structure-activity relationship (QSAR) model was generated by genetic algorithm, and toxicity was estimated by T.E.S.T. software. The mode of inhibition of enzymes related to the antifungal activity is elucidated by molecular docking. Coumarin derivatives were most effective against Macrophomina phaseolina and Sclerotinia sclerotiorum, but were not harmful against beneficial nematodes and bacteria. A predictive QSAR model was obtained for the activity against M. phaseolina (R2tr = 0.78; R2ext = 0.67; Q2loo = 0.67). A QSAR study showed that multiple electron-withdrawal groups, especially at position C-3, enhanced activities against M. phaseolina, while the hydrophobic benzoyl group at the pyrone ring, and -Br, -OH, -OCH3, at the benzene ring, may increase inhibition of S. sclerotiourum. Tested compounds possibly act inhibitory against plant wall-degrading enzymes, proteinase K. Coumarin derivatives are the potentially active ingredient of environmentally friendly plant-protection products.


Assuntos
Antibacterianos/farmacologia , Antifúngicos/farmacologia , Cumarínicos/farmacologia , Plantas/microbiologia , Ascomicetos/efeitos dos fármacos , Testes de Sensibilidade Microbiana/métodos , Simulação de Acoplamento Molecular/métodos , Relação Quantitativa Estrutura-Atividade
9.
Food Chem ; 358: 129812, 2021 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-33940289

RESUMO

Prunus fruits are recognized to be rich sources of polyphenols with health promoting effect. In this work we evaluated the phenolic profile and bioactivity, namely antioxidant capacity, antiproliferative effect in HT29, and inhibition capacity of α-glucosidase (α-Gls), α-amylase (α-Amy) and human dipeptidyl peptidase III (hDPP III) activities, of traditional Prunus fruits grown in Serbia. Fifteen Prunus samples were investigated and compared: common European plum and three old plum subspecies ('vlaskaca', damson plum and white damson), purple-leaf cherry plum, red and white cherry plum, sweet cherry, sweet cherry-wild type, sour cherry, steppe cherry, mahaleb cherry, blackthorn, peach, and apricot. Principal Component Analysis highlighted steppe cherry and blackthorn as Prunus species with the highest bioactive potential. In silico analysis pointed out rutinoside derivatives of cyanidin and quercetin as the most potent inhibitors of α-Gls, α-Amy and hDPP III enzymes. Quercetin 3-O-rutinoside showed the highest binding energy to α-Gls (-10.6 kcal/mol).


Assuntos
Antioxidantes/análise , Frutas/química , Inibidores de Glicosídeo Hidrolases/farmacologia , Polifenóis/análise , Prunus/química , Antocianinas/análise , Antocianinas/farmacologia , Antioxidantes/farmacologia , Proliferação de Células/efeitos dos fármacos , Simulação por Computador , Avaliação Pré-Clínica de Medicamentos/métodos , Glucosídeos/metabolismo , Glucosídeos/farmacologia , Inibidores de Glicosídeo Hidrolases/química , Células HT29 , Humanos , Simulação de Acoplamento Molecular , Fenóis/análise , Polifenóis/farmacologia , Quercetina/análogos & derivados , Quercetina/metabolismo , Quercetina/farmacologia , alfa-Amilases/antagonistas & inibidores
10.
Food Chem ; 335: 127619, 2021 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-32739809

RESUMO

In the present research, seven different cornelian cherry (Cornus mas L.) cultivars and selections were examined. In vitro and in silico methods were applied for determining and correlating phytochemical constituents and biological potential. Loganic acid, cornuside, cyanidin3-galactoside, and pelargonidin 3-galactoside were determined as the most dominant compounds, presenting ≥90% of the all detected iridoid and phenolic constituents in the extracts. Cornelian cherry fruits were characterized by high antioxidant capacity and antiproliferative activity on human colon cancer cells (HT29). It was observed the strong inhibitory potential of α-amylase, α-glucosidase, and dipeptidyl peptidase III (DPP III) enzyme activities. Principal component analysis (PCA) was used as a very helpful tool to discriminate the constituents with the highest contribution to tested bioactivities and to highlight the most potent genotypes. PCA, together with binding energies measurements and docking analysis, pointed out pelargonidin 3-robinobioside as the strongest inhibitor of α-glucosidase.


Assuntos
Antioxidantes/análise , Cornus/química , Iridoides/análise , Polifenóis/análise , Simulação por Computador , Humanos
11.
J Chem Inf Model ; 59(8): 3437-3453, 2019 08 26.
Artigo em Inglês | MEDLINE | ID: mdl-31274304

RESUMO

The main aim of this work was to find parameters for the zinc ion in human dipeptidyl peptidase III (DPP III) active site that would enable its reliable modeling. Since the parameters publicly available failed to reproduce the zinc ion coordination in the enzyme, we developed a new set of the hybrid bonded/nonbonded parameters for the zinc ion suitable for molecular modeling of the human DPP III, dynamics, and ligand binding. The parameters allowed exchange of the water molecules coordinating the zinc ion and proved to be robust enough to enable reliable modeling not only of human DPP III and its orthologues but also of the other zinc-dependent peptidases with the zinc ion coordination similar to that in dipeptidyl peptidases III, i.e., peptidases with the zinc ion coordinated with two histidines and one glutamate. The new parameters were tested on a set of 21 different systems comprising 8 different peptidases, 5 DPP III orthologues, thermolysin, neprilysin, and aminopeptidase N, and the results are summarized in the second part of the article.


Assuntos
Dipeptidil Peptidases e Tripeptidil Peptidases/química , Dipeptidil Peptidases e Tripeptidil Peptidases/metabolismo , Zinco/metabolismo , Humanos , Imidazóis/química , Conformação Proteica , Prótons
12.
J Biomol Struct Dyn ; 37(14): 3596-3606, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-30198396

RESUMO

Human dipeptidyl peptidase III (hDPP III) is a zinc-exopeptidase of the family M49 involved in final steps of intracellular protein degradation and in cytoprotective pathway Keap1-Nrf2. Biochemical and structural properties of this enzyme have been extensively investigated, but the knowledge on its contacts with other proteins is scarce. Previously, polypeptide aprotinin was shown to be a competitive inhibitor of hDPP III hydrolytic activity. In this study, aprotinin was first investigated as a potential substrate of hDPP III, but no degradation products were demonstrated by MALDI-TOF mass spectrometry. Subsequently, molecular details of the protein-protein interaction between aprotinin and hDPP III were studied by molecular modeling. Docking and long molecular dynamics (MD) simulations have shown that aprotinin interacts by its canonical binding epitope with the substrate binding cleft of hDPP III. Thereby, free N-terminus of aprotinin is distant from the active-site zinc. Enzyme-inhibitor complex is stabilized by intermolecular hydrogen bonding network, electrostatic and hydrophobic interactions which mostly involve constituent amino acid residues of the hDPP III substrate binding subsites S1, S1', S2, S2' and S3'. This is the first study that gives insight into aprotinin binding to a metallopeptidase. Communicated by Ramaswamy H. Sarma.


Assuntos
Aprotinina/metabolismo , Dipeptidil Peptidases e Tripeptidil Peptidases/metabolismo , Aminoácidos/química , Sítios de Ligação , Dipeptidil Peptidases e Tripeptidil Peptidases/química , Humanos , Ligação de Hidrogênio , Simulação de Dinâmica Molecular , Ligação Proteica , Mapeamento de Interação de Proteínas , Proteólise , Solventes , Eletricidade Estática , Especificidade por Substrato , Zinco/metabolismo
13.
RSC Adv ; 8(24): 13310-13322, 2018 Apr 09.
Artigo em Inglês | MEDLINE | ID: mdl-35542530

RESUMO

The hydrogen deuterium exchange (HDX) mass spectrometry combined with molecular dynamics (MD) simulations was employed to investigate conformational dynamics and ligand binding within the M49 family (dipeptidyl peptidase III family). Six dipeptidyl peptidase III (DPP III) orthologues, human, yeast, three bacterial and one plant (moss) were studied. According to the results, all orthologues seem to be quite compact wherein DPP III from the thermophile Caldithrix abyssi seems to be the most compact. The protected regions are located within the two domains core and the overall flexibility profile consistent with semi-closed conformation as the dominant protein form in solution. Besides conservation of conformational dynamics within the M49 family, we also investigated the ligand, pentapeptide tynorphin, binding. By comparing HDX data obtained for unliganded protein with those obtained for its complex with tynorphin it was found that the ligand binding mode is conserved within the family. Tynorphin binds within inter-domain cleft, close to the lower domain ß-core and induces its stabilization in all orthologues. Docking combined with MD simulations revealed details of the protein flexibility as well as of the enzyme-ligand interactions.

14.
Chem Biol Drug Des ; 89(4): 619-627, 2017 04.
Artigo em Inglês | MEDLINE | ID: mdl-27754592

RESUMO

Fifteen flavonoids were studied for their inhibitory activity against human dipeptidyl peptidase III (hDPP III) combining an in vitro assay with an in silico molecular modeling study. All analyzed flavonoids showed inhibitory effects against hDPP III with the IC50 values ranging from 22.0 to 437.2 µm. Our 3D QSAR studies indicate that the presence of hydrophilic regions at a flavonoid molecule increases its inhibitory activity, while the higher percentage of hydrophobic surfaces has negative impact on enzyme inhibition. Furthermore, molecular dynamics (MD) simulations of the complex of hDPP III with one of the most potent inhibitors, luteolin, were performed, and binding mode analysis revealed that the 3' and 4' hydroxyl group on B-ring as well as 5 and 7 hydroxyl group on A-ring helps luteolin to interact with the Asn391, Asn406, Tyr417, His450, Glu451, Val447, Glu512, Asn545, Gln566, and Arg572 residues. The MD results clearly provide valuable information explaining the importance of flavonoid hydroxyl groups in the mechanism for the binding pattern at the active site of hDPP III.


Assuntos
Dipeptidil Peptidases e Tripeptidil Peptidases/antagonistas & inibidores , Flavonoides/farmacologia , Inibidores de Proteases/farmacologia , Humanos , Interações Hidrofóbicas e Hidrofílicas , Simulação de Dinâmica Molecular , Análise de Componente Principal , Relação Quantitativa Estrutura-Atividade
15.
Acta Chim Slov ; 62(4): 867-78, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26680714

RESUMO

A molecular modeling study is performed on series of benzimidazol-based inhibitors of human dipeptidyl peptidase III (DPP III). An eight novel compounds were synthesized in excellent yields using green chemistry approach. This study is aimed to elucidate the structural features of benzimidazole derivatives required for antagonism of human DPP III activity using Quantitative Structure-Activity Relationship (QSAR) analysis, and to understand the mechanism of one of the most potent inhibitor binding into the active site of this enzyme, by molecular dynamics (MD) simulations. The best model obtained includes S3K and RDF045m descriptors which have explained 89.4 % of inhibitory activity. Depicted moiety for strong inhibition activity matches to the structure of most potent compound. MD simulation has revealed importance of imidazolinyl and phenyl groups in the mechanism of binding into the active site of human DPP III.


Assuntos
Benzimidazóis/síntese química , Dipeptidil Peptidases e Tripeptidil Peptidases/antagonistas & inibidores , Simulação de Dinâmica Molecular , Benzimidazóis/química , Benzimidazóis/farmacologia , Humanos , Relação Quantitativa Estrutura-Atividade
16.
Biol Chem ; 393(1-2): 37-46, 2012 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-22628297

RESUMO

Dipeptidyl peptidase III (DPP III), a member of the metallopeptidase family M49, was considered as an exclusively eukaryotic enzyme involved in intracellular peptide catabolism and pain modulation. In 2003, new data on genome sequences revealed the first prokaryotic orthologs, which showed low sequence similarity to eukaryotic ones and a cysteine (Cys) residue in the zinc-binding motif HEXXGH. Here we report the cloning and heterologous expression of DPP III from the human gut symbiont Bacteroides thetaiotaomicron. The catalytic efficiency of bacterial DPP III for preferred synthetic substrate hydrolysis was very similar to that of the human host enzyme. Substitution of Cys450 from the active-site motif by serine did not substantially change the enzymatic activity. However, this residue was wholly responsible for the inactivation effect of sulfhydryl reagents. Molecular modeling indicated seven basic amino acid residues in the local environment of Cys450 as a possible cause for its high reactivity. Sequence analysis of 81 bacterial M49 peptidases showed conservation of the HECLGH motif in 68 primary structures with the majority of proteins lacking an active-site Cys originated from aerobic bacteria. Data obtained suggest that Cys450 of B. thetaiotaomicron DPP III is a regulatory residue for the enzyme activity.


Assuntos
Bacteroides/enzimologia , Cisteína/metabolismo , Dipeptidil Peptidases e Tripeptidil Peptidases/química , Dipeptidil Peptidases e Tripeptidil Peptidases/metabolismo , Motivos de Aminoácidos , Domínio Catalítico , Cisteína/química , Dipeptidil Peptidases e Tripeptidil Peptidases/isolamento & purificação , Ativação Enzimática , Estrutura Secundária de Proteína , Desdobramento de Proteína , Temperatura
17.
J Mol Recognit ; 24(5): 804-14, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-21812054

RESUMO

Human dipeptidyl peptidase III (DPP III) is a zinc-exopeptidase with implied roles in protein catabolism, pain modulation, and defense against oxidative stress. To understand the mode of ligand binding into its active site, we performed molecular modeling, site-directed mutagenesis, and biochemical analyses. Using the recently determined crystal structure of the human DPP III we built complexes between both, the wild-type (WT) protein and its mutant H568N with the preferred substrate Arg-Arg-2-naphthylamide (RRNA) and a competitive inhibitor Tyr-Phe-hydroxamate (Tyr-Phe-NHOH). The mutation of the conserved His568, structurally equivalent to catalytically important His231 in thermolysin, to Asn, resulted in a 1300-fold decrease of k(cat) for RRNA hydrolysis and in significantly lowered affinity for the inhibitor. Molecular dynamics simulations revealed the key protein-ligand interactions as well as the ligand-induced reorganization of the binding site and its partial closure. Simultaneously, the non-catalytic domain was observed to stretch and the opening at the wide side of the inter-domain cleft became enhanced. The driving force for these changes was the formation of the hydrogen bond between Asp372 and the bound ligand. The structural and dynamical differences, found for the ligand binding to the WT enzyme and the H568N mutant, and the calculated binding free energies, agree well with the measured affinities. On the basis of the obtained results we suggest a possible reaction mechanism. In addition, this work provides a foundation for further site-directed mutagenesis experiments, as well as for modeling the reaction itself.


Assuntos
Dipeptidil Peptidases e Tripeptidil Peptidases/química , Dipeptidil Peptidases e Tripeptidil Peptidases/metabolismo , Domínio Catalítico/genética , Domínio Catalítico/fisiologia , Dipeptídeos/química , Dipeptídeos/metabolismo , Dipeptidil Peptidases e Tripeptidil Peptidases/genética , Humanos , Simulação de Dinâmica Molecular , Mutagênese Sítio-Dirigida , Ligação Proteica/genética , Ligação Proteica/fisiologia , Estrutura Secundária de Proteína
18.
Plant Signal Behav ; 6(2): 251-7, 2011 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-21415600

RESUMO

The free proline content in maize ear-leaves, silk and pollen were analyzed in field grown plants which had matured to the pollination stage. Using maize hybrids PR34F02, PR35P12 and PR36B08 field trials were set up at two locations in eastern Croatia in two different years. Two enzymes of proline metabolism were analyzed in the same leaf samples and specific activities of synthetase (P5CS) and proline dehydrogenase (PDH). Plant productivity was evaluated at harvest by the estimation of total and fully developed grain number per ear and per plant, the mean single grain mass, and the mass of grain per plant. The year in which the plants were grown had a very significant effect on the free proline content in the leaf and pollen, as well as on the enzyme activities assayed. The differences between the plants from the two localities were very significant in all tested parameters of plant grain productivity. There was a significant genotype effect on proline content and P5CS total activity in leaf and on all the productivity parameters. Some of the correlations established suggest that the rate of proline synthesis and degradation in maize ear-leaf at pollination might contribute to the final grain production of the maize plant. Multiple regression analyses was used to further analyze the relationship between proline and grain productivity, but it is clear that future work should include other environmental conditions, plant species and organs such as roots.


Assuntos
Biomassa , Prolina/metabolismo , Estresse Fisiológico , Zea mays/metabolismo , Genótipo , Glutamato-5-Semialdeído Desidrogenase/metabolismo , Folhas de Planta/química , Pólen/química , Prolina Oxidase/metabolismo , Sementes/química , Zea mays/genética
19.
Bioorg Chem ; 37(3): 70-6, 2009 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-19375145

RESUMO

The role of the unique fully conserved tryptophan in metallopeptidase family M49 (dipeptidyl peptidase III family) was investigated by site-directed mutagenesis on human dipeptidyl peptidase III (DPP III) where Trp300 was subjected to two substitutions (W300F and W300L). The mutant enzymes showed thermal stability equal to the wild-type DPP III. Conservative substitution of the Trp300 with phenylalanine decreased enzyme activity 2-4 fold, but did not significantly change the K(m) values for two dipeptidyl 2-naphthylamide substrates. However, the K(m) for the W300L mutant was elevated 5-fold and the k(cat) value was reduced 16-fold with Arg-Arg-2-naphthylamide. Both substitutions had a negative effect on the binding of two competitive inhibitors designed to interact with S1 and S2 subsites. These results indicate the importance of the aromatic nature of W300 in DPP III ligand binding and catalysis, and contribution of this residue in maintaining the functional integrity of this enzyme's S2 subsite.


Assuntos
Dipeptidil Peptidases e Tripeptidil Peptidases/metabolismo , Triptofano/química , Sequência de Aminoácidos , Ligação Competitiva , Biocatálise , Dipeptidil Peptidases e Tripeptidil Peptidases/antagonistas & inibidores , Dipeptidil Peptidases e Tripeptidil Peptidases/isolamento & purificação , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/química , Humanos , Ácidos Hidroxâmicos/síntese química , Ácidos Hidroxâmicos/química , Cinética , Dados de Sequência Molecular , Mutagênese Sítio-Dirigida , Proteínas Mutantes/antagonistas & inibidores , Proteínas Mutantes/isolamento & purificação , Proteínas Mutantes/metabolismo , Estabilidade Proteica , Homologia de Sequência de Aminoácidos , Especificidade por Substrato
20.
Bioorg Chem ; 35(2): 153-69, 2007 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-17174378

RESUMO

Dipeptidyl peptidase III (DPP III), also known as enkephalinase B, is a zinc-hydrolase with an indicated role in the mammalian pain modulatory system. In order to find a potent antagonist of this enzyme, we synthesized and screened the effect of a small set of benzimidazole derivatives on its activity. To improve the inhibitory potential, a cyclobutane ring was introduced as rigid conformation support to the diamidino substituted dibenzimidazoles. Two such compounds (1' and 4') from the group of cyclobutane derivatives containing amidino-substituted benzimidazole moieties, obtained by photochemical cyclization in water and by respecting rules of the "green chemistry" approach, were found to be strong DPP III inhibitors, with IC(50) value below 5 microM. Compound 1' displayed time-dependent inhibition towards human DPP III, characterized by the second-order rate constant of 6924+/-549 M(-1)min(-1) (K(i)=0.20 microM). The peptide substrate valorphin protected the enzyme from inactivation by 1'.


Assuntos
Benzimidazóis/síntese química , Benzimidazóis/farmacologia , Dipeptidil Peptidases e Tripeptidil Peptidases/antagonistas & inibidores , Inibidores de Proteases/síntese química , Inibidores de Proteases/farmacologia , Adamantano/análogos & derivados , Adamantano/farmacologia , Algoritmos , Amidas/química , Fenômenos Químicos , Físico-Química , Eritrócitos/efeitos dos fármacos , Eritrócitos/enzimologia , Cinética , Modelos Moleculares , Conformação Molecular , Relação Estrutura-Atividade
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