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1.
Gut Microbes ; 16(1): 2379566, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-39013030

RESUMO

Necrotizing enterocolitis (NEC) is a leading cause of morbidity and mortality in premature infants with no specific treatments available. We aimed to identify the molecular mechanisms underlying NEC and investigate the therapeutic effects of Bacteroides fragilis on NEC. Clinical samples of infant feces, bile acid-targeted metabolomics, pathological staining, bioinformatics analysis, NEC rat model, and co-immunoprecipitation were used to explore the pathogenesis of NEC. Taxonomic characterization of the bile salt hydrolase (bsh) gene, enzyme activity assays, 16S rRNA sequencing, and organoids were used to explore the therapeutic effects of B. fragilis on NEC-related intestinal damage. Clinical samples, NEC rat models, and in vitro experiments revealed that total bile acid increased in the blood but decreased in feces. Moreover, the levels of FXR and other bile acid metabolism-related genes were abnormal, resulting in disordered bile acid metabolism in NEC. Taurochenodeoxycholic acid accelerated NEC pathogenesis and taurodeoxycholate alleviated NEC. B. fragilis displayed bsh genes and enzyme activity and alleviated intestinal damage by restoring gut microbiota dysbiosis and bile acid metabolism abnormalities by inhibiting the FXR-NLRP3 signaling pathway. Our results provide valuable insights into the therapeutic role of B. fragilis in NEC. Administering B. fragilis may substantially alleviate intestinal damage in NEC.


Assuntos
Amidoidrolases , Bacteroides fragilis , Ácidos e Sais Biliares , Enterocolite Necrosante , Microbioma Gastrointestinal , Proteína 3 que Contém Domínio de Pirina da Família NLR , Receptores Citoplasmáticos e Nucleares , Transdução de Sinais , Enterocolite Necrosante/metabolismo , Enterocolite Necrosante/microbiologia , Enterocolite Necrosante/tratamento farmacológico , Animais , Proteína 3 que Contém Domínio de Pirina da Família NLR/metabolismo , Proteína 3 que Contém Domínio de Pirina da Família NLR/genética , Bacteroides fragilis/metabolismo , Bacteroides fragilis/genética , Transdução de Sinais/efeitos dos fármacos , Ácidos e Sais Biliares/metabolismo , Ratos , Receptores Citoplasmáticos e Nucleares/metabolismo , Receptores Citoplasmáticos e Nucleares/genética , Microbioma Gastrointestinal/efeitos dos fármacos , Amidoidrolases/metabolismo , Amidoidrolases/genética , Humanos , Ratos Sprague-Dawley , Recém-Nascido , Modelos Animais de Doenças , Masculino , Feminino , Probióticos/administração & dosagem , Probióticos/farmacologia , Recém-Nascido Prematuro , Disbiose/microbiologia
2.
J Agric Food Chem ; 72(29): 16403-16411, 2024 Jul 24.
Artigo em Inglês | MEDLINE | ID: mdl-39004912

RESUMO

As a highly toxic mycotoxin, ochratoxin A (OTA) is widely contaminating agricultural products and has various toxicological effects. Bioenzymes for OTA degradation have shown promising potential for detoxification. Other than the efficient amidohydrolase ADH3 previously, two novel amidohydrolases ADH1 and AMD3 were obtained in this study. During Escherichia coli expression, the expressed protein solubility was very low and will limit future industrial application. Here, high copy number integrations were screened, and the amidohydrolases were efficiently secretory expressed by Pichia pastoris GS115. The protein yields from 1.0 L of fermentation supernatant were 53.5 mg for ADH1, 89.15 mg for ADH3, and 79.5 mg for AMD3. The catalytic efficiency (Kcat/Km) of secretory proteins was 124.95 s-1 mM-1 for ADH3, 123.21 s-1 mM-1 for ADH1, and 371.99 s-1 mM-1 for AMD3. In comparison to E. coli expression, the active protein yields substantially increased 15.78-51.53 times. Meanwhile, two novel amidohydrolases (ADH1 and AMD3) showed much higher activity than ADH3 that produced by secretory expression.


Assuntos
Amidoidrolases , Expressão Gênica , Ocratoxinas , Ocratoxinas/metabolismo , Ocratoxinas/química , Hidrólise , Amidoidrolases/genética , Amidoidrolases/metabolismo , Amidoidrolases/química , Proteínas Recombinantes/metabolismo , Proteínas Recombinantes/genética , Proteínas Recombinantes/química , Escherichia coli/genética , Escherichia coli/metabolismo , Saccharomycetales/genética , Saccharomycetales/enzimologia , Saccharomycetales/metabolismo , Cinética , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Proteínas Fúngicas/química , Fermentação , Pichia/genética , Pichia/metabolismo
3.
Int J Mol Sci ; 25(13)2024 Jun 21.
Artigo em Inglês | MEDLINE | ID: mdl-38999960

RESUMO

The initial adoption of penicillin as an antibiotic marked the start of exploring other compounds essential for pharmaceuticals, yet resistance to penicillins and their side effects has compromised their efficacy. The N-terminal nucleophile (Ntn) amide-hydrolases S45 family plays a key role in catalyzing amide bond hydrolysis in various compounds, including antibiotics like penicillin and cephalosporin. This study comprehensively analyzes the structural and functional traits of the bacterial N-terminal nucleophile (Ntn) amide-hydrolases S45 family, covering penicillin G acylases, cephalosporin acylases, and D-succinylase. Utilizing structural bioinformatics tools and sequence analysis, the investigation delineates structurally conserved regions (SCRs) and substrate binding site variations among these enzymes. Notably, sixteen SCRs crucial for substrate interaction are identified solely through sequence analysis, emphasizing the significance of sequence data in characterizing functionally relevant regions. These findings introduce a novel approach for identifying targets to enhance the biocatalytic properties of N-terminal nucleophile (Ntn) amide-hydrolases, while facilitating the development of more accurate three-dimensional models, particularly for enzymes lacking structural data. Overall, this research advances our understanding of structure-function relationships in bacterial N-terminal nucleophile (Ntn) amide-hydrolases, providing insights into strategies for optimizing their enzymatic capabilities.


Assuntos
Amidoidrolases , Amidoidrolases/química , Amidoidrolases/metabolismo , Amidoidrolases/genética , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/genética , Sítios de Ligação , Relação Estrutura-Atividade , Sequência Conservada , Bactérias/enzimologia , Sequência de Aminoácidos , Modelos Moleculares , Especificidade por Substrato
4.
Arch Biochem Biophys ; 758: 110079, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38969195

RESUMO

Streptococcus oralis an opportunistic bacterium has been reported to be involved in various blood borne infections like subacute bacterial endocarditis, septicemia, bacterial meningitis and in some cases dental caries too. Among various targets the peptide deformylase, of S.oralis appears to be most potent druggable target as it is involved in protein synthesis is opted for the current study. Due to unavailability of PDB structure of peptide deformylase from S. oralis the study initiates with homology modelling of the protein and 6OW2 of S pneumoniae is considered as the template. Thereafter, Molecular docking, Molecular dynamic simulation, ADME analysis, and MMPBSA analysis was carried out to explore the inhibitory potential of phyto-constituents as potential inhibitors for Peptide deformylase from S.oralis. Actinonin was considered as reference drug. Among 2370 phyto compounds the best observations were recorded for A1-Barrigenol (IMPHY010984) with binding affinity of -8.5 kcal/mol. Calculated RMSD, RMSF, Binding Free Energy for IMPHY010984 averaged at about 0.10 ± 0.03 nm, 0.08 ± 0.05 nm, 131 ± 21 kJ/mol respectively whereas the RMSD, RMSF, Binding Free Energy recorded for reference drug averaged at about 0.19 ± 0.04 nm, 0.11 ± 0.08 nm, -94 ± 18 kJ/mol respectively. Based on in silico observations IMPHY010984 is proved out as superior candidate over reference drug. The study reflects the potential of IMPHY010984 as prophylactic therapeutics for S.oralis.


Assuntos
Amidoidrolases , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Streptococcus oralis , Amidoidrolases/antagonistas & inibidores , Amidoidrolases/metabolismo , Amidoidrolases/química , Streptococcus oralis/enzimologia , Streptococcus oralis/efeitos dos fármacos , Inibidores Enzimáticos/farmacologia , Inibidores Enzimáticos/química , Compostos Fitoquímicos/química , Compostos Fitoquímicos/farmacologia , Proteínas de Bactérias/antagonistas & inibidores , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/química , Ácidos Hidroxâmicos
5.
Sci Rep ; 14(1): 14900, 2024 06 28.
Artigo em Inglês | MEDLINE | ID: mdl-38942903

RESUMO

Eukaryotic cells can synthesize formyl-methionine (fMet)-containing proteins not only in mitochondria but also in the cytosol to some extent. Our previous study revealed substantial upregulation of N-terminal (Nt)-fMet-containing proteins in the cytosol of SW480 colorectal cancer cells. However, the functional and pathophysiological implications remain unclear. Here, we demonstrated that removal of the Nt-formyl moiety of Nt-fMet-containing proteins (via expressing Escherichia coli PDF peptide deformylase) resulted in a dramatic increase in the proliferation of SW480 colorectal cancer cells. This proliferation coincided with the acquisition of cancer stem cell features, including reduced cell size, enhanced self-renewal capacity, and elevated levels of the cancer stem cell surface marker CD24 and pluripotent transcription factor SOX2. Furthermore, deformylation of Nt-fMet-containing proteins promoted the tumorigenicity of SW480 colorectal cancer cells in an in vivo xenograft mouse model. Taken together, these findings suggest that cytosolic deformylation has a tumor-enhancing effect, highlighting its therapeutic potential for cancer treatment.


Assuntos
Amidoidrolases , Proliferação de Células , Citosol , Células-Tronco Neoplásicas , Humanos , Células-Tronco Neoplásicas/metabolismo , Células-Tronco Neoplásicas/patologia , Animais , Citosol/metabolismo , Camundongos , Linhagem Celular Tumoral , Amidoidrolases/metabolismo , Neoplasias Colorretais/metabolismo , Neoplasias Colorretais/patologia , Antígeno CD24/metabolismo , Fatores de Transcrição SOXB1/metabolismo , Progressão da Doença , Metionina/metabolismo , Metionina/análogos & derivados
6.
Drug Des Devel Ther ; 18: 2143-2167, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38882045

RESUMO

Over the past decade, the idea of targeting the endocannabinoid system to treat anxiety disorders has received increasing attention. Previous studies focused more on developing cannabinoid receptor agonists or supplementing exogenous cannabinoids, which are prone to various adverse effects due to their strong pharmacological activity and poor receptor selectivity, limiting their application in clinical research. Endocannabinoid hydrolase inhibitors are considered to be the most promising development strategies for the treatment of anxiety disorders. More recent efforts have emphasized that inhibition of two major endogenous cannabinoid hydrolases, monoacylglycerol lipase (MAGL) and fatty acid amide hydrolase (FAAH), indirectly activates cannabinoid receptors by increasing endogenous cannabinoid levels in the synaptic gap, circumventing receptor desensitization resulting from direct enhancement of endogenous cannabinoid signaling. In this review, we comprehensively summarize the anxiolytic effects of MAGL and FAAH inhibitors and their potential pharmacological mechanisms, highlight reported novel inhibitors or natural products, and provide an outlook on future directions in this field.


Assuntos
Amidoidrolases , Ansiolíticos , Endocanabinoides , Inibidores Enzimáticos , Monoacilglicerol Lipases , Humanos , Ansiolíticos/farmacologia , Ansiolíticos/química , Amidoidrolases/antagonistas & inibidores , Amidoidrolases/metabolismo , Monoacilglicerol Lipases/antagonistas & inibidores , Monoacilglicerol Lipases/metabolismo , Animais , Endocanabinoides/metabolismo , Inibidores Enzimáticos/farmacologia , Inibidores Enzimáticos/química , Transtornos de Ansiedade/tratamento farmacológico , Transtornos de Ansiedade/metabolismo
7.
ACS Sens ; 9(6): 3387-3393, 2024 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-38850514

RESUMO

Fatty acid amide hydrolase (FAAH) plays a crucial role in the metabolism of the endocannabinoid system by hydrolyzing a series of bioactive amides, whose abnormal levels are associated with neuronal disorders including Alzheimer's disease (AD). However, due to the lack of suitable quantitative sensing tools, real-time and accurate monitoring of the activity of FAAH in living systems remains unresolved. Herein, a novel enzyme-activated near-infrared two-photon ratiometric fluorescent probe (CANP) based on a naphthylvinylpyridine monofluorophore is successfully developed, in which the electron-withdrawing amide moiety is prone to be hydrolyzed to an electron-donating amine group under the catalysis of FAAH, leading to the activation of the intramolecular charge transfer process and the emergence of a new 80 nm red-shifted emission, thereby achieving a ratiometric luminescence response. Benefiting from the high selectivity, high sensitivity, and ratiometric response to FAAH, the probe CANP is successfully used to quantitatively monitor and image the FAAH levels in living neurons, by which an amyloid ß (Aß)-induced upregulation of endogenous FAAH activity is observed. Similar increases in FAAH activity are found in various brain regions of AD model mice, indicating a potential fatty acid amide metabolite-involved pathway for the pathological deterioration of AD. Moreover, our quantitative FAAH inhibition experiments further demonstrate the great value of CANP as an efficient visual probe for in situ and precise assessment of FAAH inhibitors in complex living systems, assisting the discovery of FAAH-related therapeutic agents.


Assuntos
Amidoidrolases , Encéfalo , Corantes Fluorescentes , Neurônios , Amidoidrolases/metabolismo , Animais , Corantes Fluorescentes/química , Corantes Fluorescentes/síntese química , Encéfalo/diagnóstico por imagem , Encéfalo/metabolismo , Neurônios/metabolismo , Camundongos , Peptídeos beta-Amiloides/metabolismo , Peptídeos beta-Amiloides/análise , Humanos , Piridinas/química , Doença de Alzheimer/metabolismo , Doença de Alzheimer/diagnóstico por imagem , Fótons
8.
Proc Natl Acad Sci U S A ; 121(25): e2321890121, 2024 Jun 18.
Artigo em Inglês | MEDLINE | ID: mdl-38857388

RESUMO

In bacteria, attenuation of protein-tyrosine phosphorylation occurs during oxidative stress. The main described mechanism behind this effect is the H2O2-triggered conversion of bacterial phospho-tyrosines to protein-bound 3,4-dihydroxyphenylalanine. This disrupts the bacterial tyrosine phosphorylation-based signaling network, which alters the bacterial polysaccharide biosynthesis. Herein, we report an alternative mechanism, in which oxidative stress leads to a direct inhibition of bacterial protein-tyrosine kinases (BY-kinases). We show that DefA, a minor peptide deformylase, inhibits the activity of BY-kinase PtkA when Bacillus subtilis is exposed to oxidative stress. High levels of PtkA activity are known to destabilize B. subtilis pellicle formation, which leads to higher sensitivity to oxidative stress. Interaction with DefA inhibits both PtkA autophosphorylation and phosphorylation of its substrate Ugd, which is involved in exopolysaccharide formation. Inactivation of defA drastically reduces the capacity of B. subtilis to cope with oxidative stress, but it does not affect the major oxidative stress regulons PerR, OhrR, and Spx, indicating that PtkA inhibition is the main pathway for DefA involvement in this stress response. Structural analysis identified DefA residues Asn95, Tyr150, and Glu152 as essential for interaction with PtkA. Inhibition of PtkA depends also on the presence of a C-terminal α-helix of DefA, which resembles PtkA-interacting motifs from known PtkA activators, TkmA, SalA, and MinD. Loss of either the key interacting residues or the inhibitory helix of DefA abolishes inhibition of PtkA in vitro and impairs postoxidative stress recovery in vivo, confirming the involvement of these structural features in the proposed mechanism.


Assuntos
Bacillus subtilis , Proteínas de Bactérias , Estresse Oxidativo , Bacillus subtilis/metabolismo , Bacillus subtilis/genética , Fosforilação , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/genética , Proteínas Tirosina Quinases/metabolismo , Peróxido de Hidrogênio/metabolismo , Amidoidrolases/metabolismo
9.
Appl Microbiol Biotechnol ; 108(1): 392, 2024 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-38910173

RESUMO

In the last decades, biocatalysis has offered new perspectives for the synthesis of (chiral) amines, which are essential building blocks for pharmaceuticals, fine and bulk chemicals. In this regard, amidases have been employed due to their broad substrate scope and their independence from expensive cofactors. To expand the repertoire of amidases, tools for their rapid identification and characterization are greatly demanded. In this work an ultra-high throughput growth selection assay based on the production of the folate precursor p-aminobenzoic acid (PABA) is introduced to identify amidase activity. PABA-derived amides structurally mimic the broad class of commonly used chromogenic substrates derived from p-nitroaniline. This suggests that the assay should be broadly applicable for the identification of amidases. Unlike conventional growth selection assays that rely on substrates as nitrogen or carbon source, our approach requires PABA in sub-nanomolar concentrations, making it exceptionally sensitive and ideal for engineering campaigns that aim at enhancing amidase activities from minimally active starting points, for example. The presented assay offers flexibility in the adjustment of sensitivity to suit project-specific needs using different expression systems and fine-tuning with the antimetabolite sulfathiazole. Application of this PABA-based assay facilitates the screening of millions of enzyme variants on a single agar plate within two days, without the need for laborious sample preparation or expensive instruments, with transformation efficiency being the only limiting factor. KEY POINTS: • Ultra-high throughput assay (tens of millions on one agar plate) for amidase screening • High sensitivity by coupling selection to folate instead of carbon or nitrogen source • Highly adjustable in terms of sensitivity and expression of the engineering target.


Assuntos
Ácido 4-Aminobenzoico , Amidoidrolases , Ensaios de Triagem em Larga Escala , Amidoidrolases/metabolismo , Amidoidrolases/genética , Ensaios de Triagem em Larga Escala/métodos , Ácido 4-Aminobenzoico/metabolismo , Ácido 4-Aminobenzoico/química , Especificidade por Substrato , Escherichia coli/genética , Escherichia coli/enzimologia , Escherichia coli/metabolismo
10.
Cell Death Dis ; 15(6): 399, 2024 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-38849335

RESUMO

The loss of dopaminergic neurons in the substantia nigra is a hallmark of pathology in Parkinson's disease (PD). Dimethylarginine dimethylaminohydrolase-1 (DDAH-1) is the critical enzyme responsible for the degradation of asymmetric dimethylarginine (ADMA) which inhibits nitric oxide (NO) synthase and has been implicated in neurodegeneration. Mitochondrial dysfunction, particularly in the mitochondria-associated endoplasmic reticulum membrane (MAM), plays a critical role in this process, although the specific molecular target has not yet been determined. This study aims to examine the involvement of DDAH-1 in the nigrostriatal dopaminergic pathway and PD pathogenesis. The distribution of DDAH-1 in the brain and its colocalization with dopaminergic neurons were observed. The loss of dopaminergic neurons and aggravated locomotor disability after rotenone (ROT) injection were showed in the DDAH-1 knockout rat. L-arginine (ARG) and NO donors were employed to elucidate the role of NO respectively. In vitro, we investigated the effects of DDAH-1 knockdown or overexpression on cell viability and mitochondrial functions, as well as modulation of ADMA/NO levels using ADMA or ARG. MAM formation was assessed by the Mitofusin2 oligomerization and the mitochondrial ubiquitin ligase (MITOL) phosphorylation. We found that DDAH-1 downregulation resulted in enhanced cell death and mitochondrial dysfunctions, accompanied by elevated ADMA and reduced NO levels. However, the recovered NO level after the ARG supplement failed to exhibit a protective effect on mitochondrial functions and partially restored cell viability. DDAH-1 overexpression prevented ROT toxicity, while ADMA treatment attenuated these protective effects. The declines of MAM formation in ROT-treated cells were exacerbated by DDAH-1 downregulation via reduced MITOL phosphorylation, which was reversed by DDAH-1 overexpression. Together, the abundant expression of DDAH-1 in nigral dopaminergic neurons may exert neuroprotective effects by maintaining MAM formation and mitochondrial function probably via ADMA, indicating the therapeutic potential of targeting DDAH-1 for PD.


Assuntos
Amidoidrolases , Arginina , Neurônios Dopaminérgicos , Retículo Endoplasmático , Mitocôndrias , Óxido Nítrico , Doença de Parkinson , Neurônios Dopaminérgicos/metabolismo , Neurônios Dopaminérgicos/efeitos dos fármacos , Neurônios Dopaminérgicos/patologia , Animais , Amidoidrolases/metabolismo , Amidoidrolases/genética , Mitocôndrias/metabolismo , Mitocôndrias/efeitos dos fármacos , Doença de Parkinson/metabolismo , Doença de Parkinson/patologia , Doença de Parkinson/genética , Arginina/metabolismo , Arginina/análogos & derivados , Retículo Endoplasmático/metabolismo , Retículo Endoplasmático/efeitos dos fármacos , Ratos , Óxido Nítrico/metabolismo , Masculino , Ratos Sprague-Dawley , Humanos , GTP Fosfo-Hidrolases/metabolismo , GTP Fosfo-Hidrolases/genética , Rotenona/farmacologia , Proteínas Mitocondriais/metabolismo , Membranas Associadas à Mitocôndria
11.
Int J Mol Sci ; 25(11)2024 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-38891799

RESUMO

Emerging research links the endocannabinoid system to gut microbiota, influencing nociception, mood, and immunity, yet the molecular interactions remain unclear. This study focused on the effects of probiotics on ECS markers-cannabinoid receptor type 2 (CB2) and fatty acid amide hydrolase (FAAH)-in dancers, a group selected due to their high exposure to physical and psychological stress. In a double-blind, placebo-controlled trial (ClinicalTrials.gov NCT05567653), 15 dancers were assigned to receive either a 12-week regimen of Lactobacillus helveticus Rosell-52 and Bifidobacterium longum Rosell-17 or a placebo (PLA: n = 10, PRO: n = 5). There were no significant changes in CB2 (probiotic: 0.55 to 0.29 ng/mL; placebo: 0.86 to 0.72 ng/mL) or FAAH levels (probiotic: 5.93 to 6.02 ng/mL; placebo: 6.46 to 6.94 ng/mL; p > 0.05). A trend toward improved sleep quality was observed in the probiotic group, while the placebo group showed a decline (PRO: from 1.4 to 1.0; PLA: from 0.8 to 1.2; p = 0.07841). No other differences were noted in assessed outcomes (pain and fatigue). Probiotic supplementation showed no significant impact on CB2 or FAAH levels, pain, or fatigue but suggested potential benefits for sleep quality, suggesting an area for further research.


Assuntos
Amidoidrolases , Endocanabinoides , Fadiga , Dor , Probióticos , Sono , Humanos , Probióticos/uso terapêutico , Endocanabinoides/metabolismo , Feminino , Método Duplo-Cego , Fadiga/metabolismo , Adulto , Masculino , Dor/tratamento farmacológico , Sono/efeitos dos fármacos , Sono/fisiologia , Amidoidrolases/metabolismo , Adulto Jovem , Receptor CB2 de Canabinoide/metabolismo , Microbioma Gastrointestinal/efeitos dos fármacos , Adolescente
12.
Protein Sci ; 33(7): e5067, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38864716

RESUMO

The N-degron pathway determines the half-life of proteins by selectively destabilizing the proteins bearing N-degrons. N-terminal glutamine amidohydrolase 1 (NTAQ1) plays an essential role in the arginine N-degron (Arg/N-degron) pathway as an initializing enzyme via the deamidation of the N-terminal (Nt) glutamine (Gln). However, the Nt-serine-bound conformation of hNTAQ1 according to the previously identified crystal structure suggests the possibility of other factors influencing the recognition of Nt residues by hNTAQ1. Hence, in the current study, we aimed to further elucidate the substrate recognition of hNTAQ1; specifically, we explored 12 different substrate-binding conformations of hNTAQ1 depending on the subsequent residue of Nt-Gln. Results revealed that hNTAQ1 primarily interacts with the protein Nt backbone, instead of the side chain, for substrate recognition. Here, we report that the Nt backbone of proteins appears to be a key component of hNTAQ1 function and is the main determinant of substrate recognition. Moreover, not all second residues from Nt-Gln, but rather distinctive and charged residues, appeared to aid in detecting substrate recognition. These new findings define the substrate-recognition process of hNTAQ1 and emphasize the importance of the subsequent Gln residue in the Nt-Gln degradation system. Our extensive structural and biochemical analyses provide insights into the substrate specificity of the N-degron pathway and shed light on the mechanism underlying hNTAQ1 substrate recognition. An improved understanding of the protein degradation machinery could aid in developing therapies to promote overall health through enhanced protein regulation, such as targeted protein therapies.


Assuntos
Arginina , Humanos , Especificidade por Substrato , Arginina/química , Arginina/metabolismo , Modelos Moleculares , Glutamina/metabolismo , Glutamina/química , Amidoidrolases/química , Amidoidrolases/metabolismo , Amidoidrolases/genética , Conformação Proteica , Proteólise , Degrons
13.
Nat Commun ; 15(1): 4026, 2024 May 13.
Artigo em Inglês | MEDLINE | ID: mdl-38740822

RESUMO

Unstable proteins are prone to form non-native interactions with other proteins and thereby may become toxic. To mitigate this, destabilized proteins are targeted by the protein quality control network. Here we present systematic studies of the cytosolic aspartoacylase, ASPA, where variants are linked to Canavan disease, a lethal neurological disorder. We determine the abundance of 6152 of the 6260 ( ~ 98%) possible single amino acid substitutions and nonsense ASPA variants in human cells. Most low abundance variants are degraded through the ubiquitin-proteasome pathway and become toxic upon prolonged expression. The data correlates with predicted changes in thermodynamic stability, evolutionary conservation, and separate disease-linked variants from benign variants. Mapping of degradation signals (degrons) shows that these are often buried and the C-terminal region functions as a degron. The data can be used to interpret Canavan disease variants and provide insight into the relationship between protein stability, degradation and cell fitness.


Assuntos
Amidoidrolases , Doença de Canavan , Proteólise , Humanos , Amidoidrolases/genética , Amidoidrolases/metabolismo , Doença de Canavan/genética , Doença de Canavan/metabolismo , Células HEK293 , Substituição de Aminoácidos , Mutação , Complexo de Endopeptidases do Proteassoma/metabolismo , Complexo de Endopeptidases do Proteassoma/genética , Estabilidade Proteica , Ubiquitina/metabolismo , Termodinâmica
14.
Acta Biochim Pol ; 71: 12299, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38721302

RESUMO

This report describes a comprehensive approach to local random mutagenesis of the E. coli Ntn-amidohydrolase EcAIII, and supplements the results published earlier for the randomization series RDM1. Here, random mutagenesis was applied in the center of the EcAIII molecule, i.e., in the region important for substrate binding and its immediate neighborhood (series RDM2, RDM3, RDM7), in the vicinity of the catalytic threonine triplet (series RDM4, RDM5, RDM6), in the linker region (series RDM8), and in the sodium-binding (stabilization) loop (series RDM9). The results revealed that the majority of the new EcAIII variants have abolished or significantly reduced rate of autoprocessing, even if the mutation was not in a highly conserved sequence and structure regions. AlphaFold-predicted structures of the mutants suggest the role of selected residues in the positioning of the linker and stabilization of the scissile bond in precisely correct orientation, enabling the nucleophilic attack during the maturation process. The presented data highlight the details of EcAIII geometry that are important for the autoproteolytic maturation and for the catalytic mechanism in general, and can be treated as a guide for protein engineering experiments with other Ntn-hydrolases.


Assuntos
Amidoidrolases , Escherichia coli , Mutagênese , Amidoidrolases/genética , Amidoidrolases/metabolismo , Amidoidrolases/química , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Proteínas de Escherichia coli/química , Modelos Moleculares , Sequência de Aminoácidos , Mutação
15.
Biomacromolecules ; 25(6): 3607-3619, 2024 Jun 10.
Artigo em Inglês | MEDLINE | ID: mdl-38776179

RESUMO

Studying how synthetic polymer assemblies respond to sequential enzymatic stimuli can uncover intricate interactions in biological systems. Using amidase- and esterase-responsive PEG-based diblock (DBA) and triblock amphiphiles (TBAs), we created two distinct formulations: amidase-responsive DBA with esterase-responsive TBA and vice versa. We studied their cascade responses to the two enzymes and the sequence of their introduction. These formulations underwent cascade mesophase transitions upon the addition of the DBA-degrading enzyme, transitioning from (i) coassembled micelles to (ii) triblock-based hydrogel, and ultimately to (iii) dissolved polymers when exposed to the TBA hydrolyzing enzyme. The specific pathway of the two mesophase transitions depended on the compositions of the formulations and the enzyme introduction sequence. The results highlight the potential for designing polymeric formulations with programmable multistep enzymatic responses, mimicking the complex behavior of biological macromolecules.


Assuntos
Polietilenoglicóis , Polietilenoglicóis/química , Micelas , Esterases/química , Esterases/metabolismo , Amidoidrolases/química , Amidoidrolases/metabolismo , Transição de Fase , Polímeros/química , Hidrogéis/química
16.
Sci Rep ; 14(1): 10952, 2024 05 13.
Artigo em Inglês | MEDLINE | ID: mdl-38740850

RESUMO

It is recognized as a promising therapeutic strategy for cocaine use disorder to develop an efficient enzyme which can rapidly convert cocaine to physiologically inactive metabolites. We have designed and discovered a series of highly efficient cocaine hydrolases, including CocH5-Fc(M6) which is the currently known as the most efficient cocaine hydrolase with both the highest catalytic activity against (-)-cocaine and the longest biological half-life in rats. In the present study, we characterized the time courses of protein appearance, pH, structural integrity, and catalytic activity against cocaine in vitro and in vivo of a CocH5-Fc(M6) bulk drug substance produced in a bioreactor for its in vitro and in vivo stability after long-time storage under various temperatures (- 80, - 20, 4, 25, or 37 °C). Specifically, all the tested properties of the CocH5-Fc(M6) protein did not significantly change after the protein was stored at any of four temperatures including - 80, - 20, 4, and 25 °C for ~ 18 months. In comparison, at 37 °C, the protein was less stable, with a half-life of ~ 82 days for cocaine hydrolysis activity. Additionally, the in vivo studies further confirmed the linear elimination PK profile of CocH5-Fc(M6) with an elimination half-life of ~ 9 days. All the in vitro and in vivo data on the efficacy and stability of CocH5-Fc(M6) have consistently demonstrated that CocH5-Fc(M6) has the desired in vitro and in vivo stability as a promising therapeutic candidate for treatment of cocaine use disorder.


Assuntos
Cocaína , Estabilidade Enzimática , Animais , Cocaína/metabolismo , Ratos , Hidrólise , Concentração de Íons de Hidrogênio , Masculino , Meia-Vida , Temperatura , Amidoidrolases/metabolismo , Hidrolases de Éster Carboxílico , Proteínas Recombinantes
17.
mBio ; 15(6): e0094324, 2024 Jun 12.
Artigo em Inglês | MEDLINE | ID: mdl-38727244

RESUMO

Bile acids play a critical role in the emulsification of dietary lipids, a critical step in the primary function of the small intestine, which is the digestion and absorption of food. Primary bile acids delivered into the small intestine are conjugated to enhance functionality, in part, by increasing aqueous solubility and preventing passive diffusion of bile acids out of the gut lumen. Bile acid function can be disrupted by the gut microbiota via the deconjugation of primary bile acids by bile salt hydrolases (BSHs), leading to their conversion into secondary bile acids through the expression of bacterial bile acid-inducible genes, a process often observed in malabsorption due to small intestinal bacterial overgrowth. By modeling the small intestinal microbiota in vitro using human small intestinal ileostomy effluent as the inocula, we show here that the infusion of physiologically relevant levels of oxygen, normally found in the proximal small intestine, reduced deconjugation of primary bile acids, in part, through the expansion of bacterial taxa known to have a low abundance of BSHs. Further recapitulating the small intestinal bile acid composition of the small intestine, limited conversion of primary into secondary bile acids was observed. Remarkably, these effects were preserved among four separate communities, each inoculated with a different small intestinal microbiota, despite a high degree of taxonomic variability under both anoxic and aerobic conditions. In total, these results provide evidence for a previously unrecognized role that the oxygenated environment of the small intestine plays in the maintenance of normal digestive physiology. IMPORTANCE: Conjugated primary bile acids are produced by the liver and exist at high concentrations in the proximal small intestine, where they are critical for proper digestion. Deconjugation of these bile acids with subsequent transformation via dehydroxylation into secondary bile acids is regulated by the colonic gut microbiota and reduces their digestive function. Using an in vitro platform modeling the small intestinal microbiota, we analyzed the ability of this community to transform primary bile acids and studied the effect of physiological levels of oxygen normally found in the proximal small intestine (5%) on this metabolic process. We found that oxygenation of the small intestinal microbiota inhibited the deconjugation of primary bile acids in vitro. These findings suggest that luminal oxygen levels normally found in the small intestine may maintain the optimal role of bile acids in the digestive process by regulating bile acid conversion by the gut microbiota.


Assuntos
Ácidos e Sais Biliares , Microbioma Gastrointestinal , Intestino Delgado , Oxigênio , Ácidos e Sais Biliares/metabolismo , Humanos , Intestino Delgado/microbiologia , Intestino Delgado/metabolismo , Oxigênio/metabolismo , Bactérias/metabolismo , Bactérias/genética , Bactérias/classificação , Amidoidrolases
18.
Artigo em Inglês | MEDLINE | ID: mdl-38765527

RESUMO

Objective: To examine whether the DDAH2 promoter polymorphisms -1415G/A (rs2272592), -1151A/C (rs805304) and -449G/C (rs805305), and their haplotypes, are associated with PE compared with normotensive pregnant women, and whether they affect ADMA levels in these groups. Methods: A total of 208 pregnant women were included in the study and classified as early-onset (N=57) or late-onset PE (N =49), and as normotensive pregnant women (N = 102). Results: Pregnant with early-onset PE carrying the GC and GG genotypes for the DDAH2 -449G/C polymorphism had increased ADMA levels (P=0.01). No association of DDAH2 polymorphisms with PE in single-locus analysis was found. However, the G-C-G haplotype was associated with the risk for late-onset PE. Conclusion: It is suggested that DDAH2 polymorphisms could affect ADMA levels in PE, and that DDAH2 haplotypes may affect the risk for PE.


Assuntos
Amidoidrolases , Arginina , Haplótipos , Polimorfismo Genético , Pré-Eclâmpsia , Humanos , Feminino , Amidoidrolases/genética , Pré-Eclâmpsia/genética , Pré-Eclâmpsia/sangue , Gravidez , Adulto , Arginina/análogos & derivados , Arginina/sangue , Arginina/genética , Adulto Jovem
19.
Drug Metab Pharmacokinet ; 56: 101007, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38797091

RESUMO

Arylacetamide deacetylase (AADAC) is involved in drug hydrolysis and lipid metabolism. In 23 human liver samples, no significant correlation was observed between AADAC mRNA (19.7-fold variation) and protein levels (137.6-fold variation), suggesting a significant contribution of post-transcriptional regulation to AADAC expression. The present study investigated whether AADAC is regulated by microRNA in the human liver and elucidate its biological significance. Computational analysis predicted two potential miR-222-3p recognition elements in the 3'-untranslated region (UTR) of AADAC. Luciferase assay revealed that the miR-222-3p recognition element was functional in downregulating AADAC expression. In HEK293 cells transfected with an AADAC expression plasmid containing 3'-UTR, miR-222-3p overexpression decreased AADAC protein level and activity, whereas miR-222-3p inhibition increased them. Similar results were observed in human hepatoma-derived Huh-1 cells endogenously expressing AADAC and HepaSH cells that are hepatocytes from chimeric mice with humanized livers. In individual human liver samples, AADAC protein levels inversely correlated with miR-222-3p levels. Overexpression of miR-222-3p resulted in increased lipid accumulation in Huh-1 cells, which was reversed by AADAC overexpression. In contrast, miR-222-3p inhibition decreased lipid accumulation, which was reversed by AADAC knockdown. In conclusion, we found that hepatic AADAC was downregulated by miR-222-3p, resulting in decreased drug hydrolysis and increased lipid accumulation.


Assuntos
Regulação para Baixo , Metabolismo dos Lipídeos , MicroRNAs , Animais , Humanos , Camundongos , Amidoidrolases/metabolismo , Amidoidrolases/genética , Hidrolases de Éster Carboxílico , Células HEK293 , Hidrólise , Metabolismo dos Lipídeos/genética , Fígado/metabolismo , MicroRNAs/genética , MicroRNAs/metabolismo
20.
Biomed Pharmacother ; 175: 116677, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38701570

RESUMO

The current pharmacological approaches to multiple sclerosis (MS) target its inflammatory and autoimmune components, but effective treatments to foster remyelination and axonal repair are still lacking. We therefore selected two targets known to be involved in MS pathogenesis: N-acylethanolamine-hydrolyzing acid amidase (NAAA) and glycogen synthase kinase-3ß (GSK-3ß). We tested whether inhibiting these targets exerted a therapeutic effect against experimental autoimmune encephalomyelitis (EAE), an animal model of MS. The combined inhibition of NAAA and GSK-3ß by two selected small-molecule compounds, ARN16186 (an NAAA inhibitor) and AF3581 (a GSK-3ß inhibitor), effectively mitigated disease progression, rescuing the animals from paralysis and preventing a worsening of the pathology. The complementary activity of the two inhibitors reduced the infiltration of immune cells into the spinal cord and led to the formation of thin myelin sheaths around the axons post-demyelination. Specifically, the inhibition of NAAA and GSK-3ß modulated the over-activation of NF-kB and STAT3 transcription factors in the EAE-affected mice and induced the nuclear translocation of ß-catenin, reducing the inflammatory insult and promoting the remyelination process. Overall, this work demonstrates that the dual-targeting of key aspects responsible for MS progression could be an innovative pharmacological approach to tackle the pathology.


Assuntos
Amidoidrolases , Encefalomielite Autoimune Experimental , Glicogênio Sintase Quinase 3 beta , Camundongos Endogâmicos C57BL , Esclerose Múltipla , Animais , Glicogênio Sintase Quinase 3 beta/metabolismo , Glicogênio Sintase Quinase 3 beta/antagonistas & inibidores , Encefalomielite Autoimune Experimental/tratamento farmacológico , Esclerose Múltipla/tratamento farmacológico , Esclerose Múltipla/metabolismo , Camundongos , Amidoidrolases/antagonistas & inibidores , Amidoidrolases/metabolismo , Feminino , Medula Espinal/efeitos dos fármacos , Medula Espinal/metabolismo , Medula Espinal/patologia , NF-kappa B/metabolismo , Inibidores Enzimáticos/farmacologia , Bainha de Mielina/metabolismo , Bainha de Mielina/efeitos dos fármacos
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