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1.
Acta Vet Scand ; 66(1): 20, 2024 May 20.
Article in English | MEDLINE | ID: mdl-38769566

ABSTRACT

Bacteriophage-encoded endolysins, peptidoglycan hydrolases breaking down the Gram-positive bacterial cell wall, represent a groundbreaking class of novel antimicrobials to revolutionize the veterinary medicine field. Wild-type endolysins exhibit a modular structure, consisting of enzymatically active and cell wall-binding domains, that enable genetic engineering strategies for the creation of chimeric fusion proteins or so-called 'engineered endolysins'. This biotechnological approach has yielded variants with modified lytic spectrums, introducing new possibilities in antimicrobial development. However, the discovery of highly similar endolysins by different groups has occasionally resulted in the assignment of different names that complicate a straightforward comparison. The aim of this review was to perform a homology-based comparison of the wild-type and engineered endolysins that have been characterized in the context of bovine mastitis-causing streptococci and staphylococci, grouping homologous endolysins with ≥ 95.0% protein sequence similarity. Literature is explored by homologous groups for the wild-type endolysins, followed by a chronological examination of engineered endolysins according to their year of publication. This review concludes that the wild-type endolysins encountered persistent challenges in raw milk and in vivo settings, causing a notable shift in the field towards the engineering of endolysins. Lead candidates that display robust lytic activity are nowadays selected from screening assays that are performed under these challenging conditions, often utilizing advanced high-throughput protein engineering methods. Overall, these recent advancements suggest that endolysins will integrate into the antibiotic arsenal over the next decade, thereby innovating antimicrobial treatment against bovine mastitis-causing streptococci and staphylococci.


Subject(s)
Bacteriophages , Endopeptidases , Mastitis, Bovine , Staphylococcus , Animals , Mastitis, Bovine/microbiology , Mastitis, Bovine/drug therapy , Cattle , Endopeptidases/pharmacology , Endopeptidases/metabolism , Endopeptidases/chemistry , Endopeptidases/genetics , Staphylococcus/drug effects , Staphylococcal Infections/veterinary , Staphylococcal Infections/drug therapy , Streptococcus/drug effects , Female , Streptococcal Infections/veterinary , Streptococcal Infections/drug therapy , Anti-Bacterial Agents/pharmacology
2.
Microbiology (Reading) ; 170(5)2024 May.
Article in English | MEDLINE | ID: mdl-38739436

ABSTRACT

Endolysins are bacteriophage (or phage)-encoded enzymes that catalyse the peptidoglycan breakdown in the bacterial cell wall. The exogenous action of recombinant phage endolysins against Gram-positive organisms has been extensively studied. However, the outer membrane acts as a physical barrier when considering the use of recombinant endolysins to combat Gram-negative bacteria. This study aimed to evaluate the antimicrobial activity of the SAR-endolysin LysKpV475 against Gram-negative bacteria as single or combined therapies, using an outer membrane permeabilizer (polymyxin B) and a phage, free or immobilized in a pullulan matrix. In the first step, the endolysin LysKpV475 in solution, alone and combined with polymyxin B, was tested in vitro and in vivo against ten Gram-negative bacteria, including highly virulent strains and multidrug-resistant isolates. In the second step, the lyophilized LysKpV475 endolysin was combined with the phage phSE-5 and investigated, free or immobilized in a pullulan matrix, against Salmonella enterica subsp. enterica serovar Typhimurium ATCC 13311. The bacteriostatic action of purified LysKpV475 varied between 8.125 µg ml-1 against Pseudomonas aeruginosa ATCC 27853, 16.25 µg ml-1 against S. enterica Typhimurium ATCC 13311, and 32.50 µg ml-1 against Klebsiella pneumoniae ATCC BAA-2146 and Enterobacter cloacae P2224. LysKpV475 showed bactericidal activity only for P. aeruginosa ATCC 27853 (32.50 µg ml-1) and P. aeruginosa P2307 (65.00 µg ml-1) at the tested concentrations. The effect of the LysKpV475 combined with polymyxin B increased against K. pneumoniae ATCC BAA-2146 [fractional inhibitory concentration index (FICI) 0.34; a value lower than 1.0 indicates an additive/combined effect] and S. enterica Typhimurium ATCC 13311 (FICI 0.93). A synergistic effect against S. enterica Typhimurium was also observed when the lyophilized LysKpV475 at ⅔ MIC was combined with the phage phSE-5 (m.o.i. of 100). The lyophilized LysKpV475 immobilized in a pullulan matrix maintained a significant Salmonella reduction of 2 logs after 6 h of treatment. These results demonstrate the potential of SAR-endolysins, alone or in combination with other treatments, in the free form or immobilized in solid matrices, which paves the way for their application in different areas, such as in biocontrol at the food processing stage, biosanitation of food contact surfaces and biopreservation of processed food in active food packing.


Subject(s)
Anti-Bacterial Agents , Endopeptidases , Glucans , Polymyxin B , Salmonella Phages , Endopeptidases/pharmacology , Endopeptidases/chemistry , Endopeptidases/metabolism , Polymyxin B/pharmacology , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/chemistry , Salmonella Phages/genetics , Salmonella Phages/physiology , Salmonella Phages/chemistry , Glucans/chemistry , Glucans/pharmacology , Animals , Microbial Sensitivity Tests , Gram-Negative Bacteria/drug effects , Gram-Negative Bacteria/virology , Mice , Salmonella typhimurium/virology , Salmonella typhimurium/drug effects , Bacteriophages/physiology , Bacteriophages/genetics , Viral Proteins/genetics , Viral Proteins/metabolism , Viral Proteins/pharmacology , Viral Proteins/chemistry
3.
Protein Eng Des Sel ; 372024 Jan 29.
Article in English | MEDLINE | ID: mdl-38696722

ABSTRACT

The yeast endoplasmic reticulum sequestration and screening (YESS) system is a broadly applicable platform to perform high-throughput biochemical studies of post-translational modification enzymes (PTM-enzymes). This system enables researchers to profile and engineer the activity and substrate specificity of PTM-enzymes and to discover inhibitor-resistant enzyme mutants. In this study, we expand the capabilities of YESS by transferring its functional components to integrative plasmids. The YESS integrative system yields uniform protein expression and protease activities in various configurations, allows one to integrate activity reporters at two independent loci and to split the system between integrative and centromeric plasmids. We characterize these integrative reporters with two viral proteases, Tobacco etch virus (TEVp) and 3-chymotrypsin like protease (3CLpro), in terms of coefficient of variance, signal-to-noise ratio and fold-activation. Overall, we provide a framework for chromosomal-based studies that is modular, enabling rigorous high-throughput assays of PTM-enzymes in yeast.


Subject(s)
Endoplasmic Reticulum , Saccharomyces cerevisiae , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Endoplasmic Reticulum/metabolism , Endoplasmic Reticulum/genetics , Protein Processing, Post-Translational , Genes, Reporter , Endopeptidases/genetics , Endopeptidases/metabolism , Plasmids/genetics , Plasmids/metabolism
4.
Food Funct ; 15(10): 5539-5553, 2024 May 20.
Article in English | MEDLINE | ID: mdl-38712538

ABSTRACT

A novel processing method combining short-time ozone pretreatment with hydrolysis has been developed to reduce whey protein allergenicity. The results showed that ozone treatment altered the whey protein spatial structure, initially increasing the surface hydrophobicity index, and then decreasing due to polymer formation as the time increased. Under the optimized conditions of alkaline protease-mediated hydrolysis, a 10-second pre-exposure to ozone significantly promoted the reduction in the IgE binding capacity of whey protein without compromising the hydrolysis efficiency. Compared with whey protein, the degranulation of KU812 cells stimulated by this hydrolysate decreased by 20.54%, 17.99%, and 22.80% for IL-6, ß-hexosaminidase, and histamine, respectively. In vitro simulated gastrointestinal digestion confirmed increased digestibility and reduced allergenicity. Peptidomics identification revealed that short-time ozonation exposed allergen epitopes, allowing alkaline protease to target these epitopes more effectively, particularly those associated with α-lactalbumin. These findings suggest the promising application of this processing method in mitigating the allergenicity of whey protein.


Subject(s)
Allergens , Epitopes , Ozone , Whey Proteins , Whey Proteins/chemistry , Whey Proteins/pharmacology , Ozone/chemistry , Ozone/pharmacology , Allergens/chemistry , Allergens/immunology , Humans , Epitopes/chemistry , Epitopes/immunology , Immunoglobulin E/immunology , Hydrolysis , Endopeptidases/metabolism , B-Lymphocytes/drug effects , B-Lymphocytes/immunology
5.
J Med Chem ; 67(10): 8460-8472, 2024 May 23.
Article in English | MEDLINE | ID: mdl-38717104

ABSTRACT

Recognizing the significance of SPECT in nuclear medicine and the pivotal role of fibroblast activation protein (FAP) in cancer diagnosis and therapy, this study focuses on the development of 99mTc-labeled dimeric HF2 with high tumor uptake and image contrast. The dimeric HF2 was synthesized and radiolabeled with 99mTc in one pot using various coligands (tricine, TPPTS, EDDA, and TPPMS) to yield [99mTc]Tc-TPPTS-HF2, [99mTc]Tc-EDDA-HF2, and [99mTc]Tc-TPPMS-HF2 dimers. SPECT imaging results indicated that [99mTc]Tc-TPPTS-HF2 exhibited higher tumor uptake and tumor-to-normal tissue (T/NT) ratio than [99mTc]Tc-EDDA-HF2 and [99mTc]Tc-TPPMS-HF2. Notably, [99mTc]Tc-TPPTS-HF2 exhibited remarkable tumor accumulation and retention in HT-1080-FAP and U87-MG tumor-bearing mice, thereby surpassing the monomeric [99mTc]Tc-TPPTS-HF. Moreover, [99mTc]Tc-TPPTS-HF2 achieved acceptable T/NT ratios in the hepatocellular carcinoma patient-derived xenograft (HCC-PDX) model, which provided identifiable contrast and imaging quality. In conclusion, this study presents proof-of-concept research on 99mTc-labeled FAP inhibitor dimers for the visualization of multiple tumor types. Among these candidate compounds, [99mTc]Tc-TPPTS-HF2 showed excellent clinical potential, thereby enriching the SPECT tracer toolbox.


Subject(s)
Organotechnetium Compounds , Tomography, Emission-Computed, Single-Photon , Animals , Humans , Mice , Tomography, Emission-Computed, Single-Photon/methods , Organotechnetium Compounds/chemistry , Organotechnetium Compounds/pharmacokinetics , Organotechnetium Compounds/chemical synthesis , Cell Line, Tumor , Drug Design , Radiopharmaceuticals/chemistry , Radiopharmaceuticals/chemical synthesis , Radiopharmaceuticals/pharmacokinetics , Technetium/chemistry , Tissue Distribution , Dimerization , Mice, Nude , Membrane Proteins/antagonists & inhibitors , Membrane Proteins/metabolism , Membrane Proteins/chemistry , Endopeptidases/metabolism , Serine Endopeptidases/metabolism , Serine Endopeptidases/chemistry
6.
Nat Commun ; 15(1): 4479, 2024 May 27.
Article in English | MEDLINE | ID: mdl-38802343

ABSTRACT

Deposition of amyloid-ß (Aß) peptides in the brain is a hallmark of Alzheimer's disease. Aßs are generated through sequential proteolysis of the amyloid precursor protein by the γ-secretase complexes (GSECs). Aß peptide length, modulated by the Presenilin (PSEN) and APH-1 subunits of GSEC, is critical for Alzheimer's pathogenesis. Despite high relevance, mechanistic understanding of the proteolysis of Aß, and its modulation by APH-1, remain incomplete. Here, we report cryo-EM structures of human GSEC (PSEN1/APH-1B) reconstituted into lipid nanodiscs in apo form and in complex with the intermediate Aß46 substrate without cross-linking. We find that three non-conserved and structurally divergent APH-1 regions establish contacts with PSEN1, and that substrate-binding induces concerted rearrangements in one of the identified PSEN1/APH-1 interfaces, providing structural basis for APH-1 allosteric-like effects. In addition, the GSEC-Aß46 structure reveals an interaction between Aß46 and loop 1PSEN1, and identifies three other H-bonding interactions that, according to functional validation, are required for substrate recognition and efficient sequential catalysis.


Subject(s)
Amyloid Precursor Protein Secretases , Amyloid beta-Peptides , Cryoelectron Microscopy , Membrane Proteins , Presenilin-1 , Humans , Amyloid Precursor Protein Secretases/metabolism , Amyloid Precursor Protein Secretases/chemistry , Presenilin-1/metabolism , Presenilin-1/chemistry , Presenilin-1/genetics , Amyloid beta-Peptides/metabolism , Amyloid beta-Peptides/chemistry , Membrane Proteins/metabolism , Membrane Proteins/chemistry , Endopeptidases/metabolism , Endopeptidases/chemistry , Amyloid beta-Protein Precursor/metabolism , Amyloid beta-Protein Precursor/chemistry , Protein Binding , Protein Isoforms/metabolism , Protein Isoforms/chemistry , Alzheimer Disease/metabolism , Peptide Fragments/metabolism , Peptide Fragments/chemistry , Peptide Hydrolases/metabolism , Peptide Hydrolases/chemistry , Models, Molecular , Proteolysis
7.
Viruses ; 16(5)2024 05 11.
Article in English | MEDLINE | ID: mdl-38793641

ABSTRACT

Acinetobacter baumannii has developed multiple drug resistances, posing a significant threat to antibiotic efficacy. LysECD7, an endolysin derived from phages, could be a promising therapeutic agent against multi-drug resistance A. baumannii. In this study, in order to further enhance the antibacterial efficiency of the engineered LysECD7, a few lipopolysaccharide-interacting peptides (Li5, MSI594 and Li5-MSI) were genetically fused with LysECD7. Based on in vitro antibacterial activity, the fusion protein Lys-Li5-MSI was selected for further modifications aimed at extending its half-life. A cysteine residue was introduced into Lys-Li5-MSI through mutation (Lys-Li5-MSIV12C), followed by conjugation with a C16 fatty acid chain via a protonation substitution reaction(V12C-C16). The pharmacokinetic profile of V12C-C16 exhibited a more favorable characteristic in comparison to Lys-Li5-MSI, thereby resulting in enhanced therapeutic efficacy against lethal A. baumannii infection in mice. The study provides valuable insights for the development of novel endolysin therapeutics and proposes an alternative therapeutic strategy for combating A. baumannii infections.


Subject(s)
Acinetobacter Infections , Acinetobacter baumannii , Anti-Bacterial Agents , Endopeptidases , Lipopolysaccharides , Acinetobacter baumannii/drug effects , Animals , Endopeptidases/pharmacology , Endopeptidases/metabolism , Endopeptidases/chemistry , Endopeptidases/genetics , Mice , Acinetobacter Infections/drug therapy , Acinetobacter Infections/microbiology , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/chemistry , Lipopolysaccharides/metabolism , Fatty Acids/metabolism , Fatty Acids/chemistry , Fatty Acids/pharmacology , Microbial Sensitivity Tests , Peptides/pharmacology , Peptides/chemistry , Recombinant Fusion Proteins/pharmacology , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/chemistry , Female , Mice, Inbred BALB C , Disease Models, Animal
8.
Int J Biol Macromol ; 269(Pt 2): 132166, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38723822

ABSTRACT

Improving the ability of bacteria to secrete protein is essential for large-scale production of food enzymes. However, due to the lack of effective tracking technology for target proteins, the optimization of the secretory system is facing many problems. In this study, we utilized the split-GFP system to achieve self-assembly into mature GFP in Bacillus amyloliquefaciens and successfully tracked the alkaline protease AprE. The split-GFP system was employed to assess the signal peptidases, a crucial component in the secretory system, and signal peptidase sipA was identified as playing a role in the secretion of AprE. Deletion of sipA resulted in a higher accumulation of the precursor protein of AprE compared to other signal peptidase deletion strains. To explore the mechanism of signal peptidase on signal peptide, molecular docking and calculation of free energy were performed. The action strength of the signal peptidase is determined by its binding affinity with the tripeptides at the C-terminal of the signal peptide. The functions of signal peptides YdbK and NucB rely on sipA, and overexpression of sipA by integrating it into genome of B. amyloliquefaciens increased the activity of extracellular AprE by 19.9 %. These findings provide insights into enhancing the secretion efficiency of chassis strains.


Subject(s)
Bacillus amyloliquefaciens , Bacterial Proteins , Endopeptidases , Green Fluorescent Proteins , Bacillus amyloliquefaciens/enzymology , Bacillus amyloliquefaciens/genetics , Bacillus amyloliquefaciens/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Bacterial Proteins/chemistry , Endopeptidases/metabolism , Endopeptidases/genetics , Endopeptidases/chemistry , Green Fluorescent Proteins/metabolism , Green Fluorescent Proteins/genetics , Molecular Docking Simulation , Protein Sorting Signals , Membrane Proteins , Serine Endopeptidases , Membrane Transport Proteins
9.
Life Sci ; 348: 122674, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38692507

ABSTRACT

AIMS: Ubiquitin specific peptidase 5 (USP5), a member of deubiquitinating enzymes, has garnered significant attention for its crucial role in cancer progression. This study aims to explore the role of USP5 and its potential molecular mechanisms in cholangiocarcinoma (CCA). MAIN METHODS: To explore the effect of USP5 on CCA, gain-of-function and loss-of-function assays were conducted in human CCA cell lines RBE and HCCC9810. The CCK8, colony-forming assay, EDU, flow cytometry, transwell assay and xenografts were used to assess cell proliferation, migration and tumorigenesis. Western blot and immunohistochemistry were performed to measure the expression of related proteins. Immunoprecipitation and immunofluorescence were applied to identify the interaction between USP5 and Y box-binding protein 1 (YBX1). Ubiquitination assays and cycloheximide chase assays were carried out to confirm the effect of USP5 on YBX1. KEY FINDINGS: We found USP5 is highly expressed in CCA tissues, and upregulated USP5 is required for the cancer progression. Knockdown of USP5 inhibited cell proliferation, migration and epithelial-mesenchymal transition (EMT) in vitro, along with suppressed xenograft tumor growth and metastasis in vivo. Mechanistically, USP5 could interact with YBX1 and stabilize YBX1 by deubiquitination in CCA cells. Additionally, silencing of USP5 hindered the phosphorylation of YBX1 at serine 102 and its subsequent translocation to the nucleus. Notably, the effect induced by USP5 overexpression in CCA cells was reversed by YBX1 silencing. SIGNIFICANCE: Our findings reveal that USP5 is required for cell proliferation, migration and EMT in CCA by stabilizing YBX1, suggesting USP5-YBX1 axis as a promising therapeutic target for CCA.


Subject(s)
Bile Duct Neoplasms , Cell Movement , Cell Proliferation , Cholangiocarcinoma , Disease Progression , Epithelial-Mesenchymal Transition , Mice, Nude , Y-Box-Binding Protein 1 , Humans , Cholangiocarcinoma/pathology , Cholangiocarcinoma/genetics , Cholangiocarcinoma/metabolism , Bile Duct Neoplasms/pathology , Bile Duct Neoplasms/metabolism , Bile Duct Neoplasms/genetics , Animals , Mice , Cell Line, Tumor , Y-Box-Binding Protein 1/metabolism , Y-Box-Binding Protein 1/genetics , Ubiquitination , Mice, Inbred BALB C , Male , Endopeptidases/metabolism , Endopeptidases/genetics , Gene Expression Regulation, Neoplastic , Female
10.
J Med Chem ; 67(9): 7068-7087, 2024 May 09.
Article in English | MEDLINE | ID: mdl-38656144

ABSTRACT

Fibroblast activation protein (FAP) is a very reliable biomarker for tissue remodeling. FAP has so far mainly been studied in oncology, but there is growing interest in the enzyme in other diseases like fibrosis. Recently, FAP-targeting diagnostics and therapeutics have emerged, of which the so-called FAPIs are among the most promising representatives. FAPIs typically have a relatively high molecular weight and contain very polar, multicharged chelator moieties. While this is not limiting the application of FAPIs in oncology, more druglike FAPIs could be required to optimally study diseases characterized by denser, less permeable tissue. In response, we designed the first druglike 18F-labeled FAPIs. We report target potencies, biodistribution, and pharmacokinetics and demonstrate FAP-dependent uptake in murine tumor xenografts. Finally, this paper puts forward compound 10 as a highly promising, druglike FAPI for 18F-PET imaging. This molecule is fit for additional studies in fibrosis and its preclinical profile warrants clinical investigation.


Subject(s)
Endopeptidases , Fluorine Radioisotopes , Gelatinases , Membrane Proteins , Positron-Emission Tomography , Serine Endopeptidases , Animals , Positron-Emission Tomography/methods , Endopeptidases/metabolism , Fluorine Radioisotopes/chemistry , Gelatinases/metabolism , Gelatinases/antagonists & inhibitors , Membrane Proteins/metabolism , Membrane Proteins/antagonists & inhibitors , Humans , Mice , Tissue Distribution , Serine Endopeptidases/metabolism , Radiopharmaceuticals/chemistry , Radiopharmaceuticals/pharmacokinetics , Radiopharmaceuticals/chemical synthesis , Radiopharmaceuticals/pharmacology , Cell Line, Tumor , Female
11.
Emerg Microbes Infect ; 13(1): 2348526, 2024 Dec.
Article in English | MEDLINE | ID: mdl-38683015

ABSTRACT

The foot-and-mouth disease virus (FMDV) Leader proteinase Lpro inhibits host mRNA translation and blocks the interferon response which promotes viral survival. Lpro is not required for viral replication in vitro but serotype A FMDV lacking Lpro has been shown to be attenuated in cattle and pigs. However, it is not known, whether leaderless viruses can cause persistent infection in vivo after simulated natural infection and whether the attenuated phenotype is the same in other serotypes. We have generated an FMDV O/FRA/1/2001 variant lacking most of the Lpro coding region (ΔLb). Cattle were inoculated intranasopharyngeally and observed for 35 days to determine if O FRA/1/2001 ΔLb is attenuated during the acute phase of infection and whether it can maintain a persistent infection in the upper respiratory tract. We found that although this leaderless virus can replicate in vitro in different cell lines, it is unable to establish an acute infection with vesicular lesions and viral shedding nor is it able to persistently infect bovine pharyngeal tissues.


Subject(s)
Cattle Diseases , Foot-and-Mouth Disease Virus , Foot-and-Mouth Disease , Persistent Infection , Serogroup , Virus Replication , Animals , Cattle , Foot-and-Mouth Disease Virus/genetics , Foot-and-Mouth Disease Virus/physiology , Foot-and-Mouth Disease Virus/classification , Foot-and-Mouth Disease Virus/pathogenicity , Foot-and-Mouth Disease Virus/isolation & purification , Foot-and-Mouth Disease/virology , Cattle Diseases/virology , Persistent Infection/virology , Cell Line , Endopeptidases/genetics , Endopeptidases/metabolism , Virus Shedding
12.
World J Microbiol Biotechnol ; 40(6): 186, 2024 Apr 29.
Article in English | MEDLINE | ID: mdl-38683213

ABSTRACT

The ability of most opportunistic bacteria to form biofilms, coupled with antimicrobial resistance, hinder the efforts to control widespread infections, resulting in high risks of negative outcomes and economic costs. Endolysins are promising compounds that efficiently combat bacteria, including multidrug-resistant strains and biofilms, without a low probability of subsequent emergence of stable endolysin-resistant phenotypes. However, the details of antibiofilm effects of these enzymes are poorly understood. To elucidate the interactions of bacteriophage endolysins LysAm24, LysAp22, LysECD7, and LysSi3 with bacterial films formed by Gram-negative species, we estimated their composition and assessed the endolysins' effects on the most abundant exopolymers in vitro. The obtained data suggests a pronounced efficiency of these lysins against biofilms with high (Klebsiella pneumoniae) and low (Acinetobacter baumannii) matrix contents, or dual-species biofilms, resulting in at least a twofold loss of the biomass. These peptidoglycan hydrolases interacted diversely with protective compounds of biofilms such as extracellular DNA and polyanionic carbohydrates, indicating a spectrum of biofilm-disrupting effects for bacteriolytic phage enzymes. Specifically, we detected disruption of acid exopolysaccharides by LysAp22, strong DNA-binding capacity of LysAm24, both of these interactions for LysECD7, and neither of them for LysSi3.


Subject(s)
Bacteriophages , Biofilms , Endopeptidases , Biofilms/drug effects , Biofilms/growth & development , Endopeptidases/metabolism , Endopeptidases/pharmacology , Endopeptidases/chemistry , Bacteriophages/enzymology , Acinetobacter baumannii/drug effects , Klebsiella pneumoniae/drug effects , Viral Proteins/metabolism , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/chemistry , N-Acetylmuramoyl-L-alanine Amidase/metabolism , N-Acetylmuramoyl-L-alanine Amidase/chemistry
13.
Int J Cardiol ; 406: 132044, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38614364

ABSTRACT

INTRODUCTION: Tissue Fibroblast Activation Protein alpha (FAP) is overexpressed in various types of acute and chronic cardiovascular disease. A soluble form of FAP has been detected in human plasma, and low circulating FAP concentrations are associated with increased risk of death in patients with acute coronary syndrome. However, little is known about the regulation and release of FAP from fibroblasts, and whether circulating FAP concentration is associated with tissue FAP expression. This study characterizes the release of FAP in human cardiac fibroblasts (CF) and analyzes the association of circulating FAP concentrations with in vivo tissue FAP expression in patients with acute (ST-segment elevation myocardial infarction, STEMI) and chronic (severe aortic stenosis, AS) myocardial FAP expression. METHODS AND RESULTS: FAP was released from CF in a time- and concentration-dependent manner. FAP concentration was higher in supernatant of TGFß-stimulated CF, and correlated with cellular FAP concentration. Inhibition of metallo- and serine-proteases diminished FAP release in vitro. Median FAP concentrations of patients with acute (77 ng/mL) and chronic (75 ng/mL, p = 0.50 vs. STEMI) myocardial FAP expression did not correlate with myocardial nor extra-myocardial nor total FAP volume (P ≥ 0.61 in all cases) measured by whole-body FAP-targeted positron emission tomography. CONCLUSION: We describe a time- and concentration dependent, protease-mediated release of FAP from cardiac fibroblasts. Circulating FAP concentrations were not associated with increased in vivo tissue FAP expression determined by molecular imaging in patients with both chronic and acute myocardial FAP expression. These data suggest that circulating FAP and tissue FAP expression provide complementary, non-interchangeable information.


Subject(s)
Endopeptidases , Gelatinases , Membrane Proteins , Molecular Imaging , Myocardium , Serine Endopeptidases , Humans , Serine Endopeptidases/metabolism , Serine Endopeptidases/blood , Serine Endopeptidases/biosynthesis , Endopeptidases/metabolism , Membrane Proteins/metabolism , Membrane Proteins/biosynthesis , Membrane Proteins/blood , Male , Gelatinases/metabolism , Gelatinases/biosynthesis , Gelatinases/blood , Female , Aged , Middle Aged , Myocardium/metabolism , Myocardium/pathology , Molecular Imaging/methods , Fibroblasts/metabolism , Cells, Cultured , ST Elevation Myocardial Infarction/blood , ST Elevation Myocardial Infarction/metabolism , ST Elevation Myocardial Infarction/diagnostic imaging , Biomarkers/blood , Biomarkers/metabolism
14.
Aging (Albany NY) ; 16(7): 6613-6626, 2024 Apr 08.
Article in English | MEDLINE | ID: mdl-38613804

ABSTRACT

Ubiquitination of the proteins is crucial for governing protein degradation and regulating fundamental cellular processes. Deubiquitinases (DUBs) have emerged as significant regulators of multiple pathways associated with cancer and other diseases, owing to their capacity to remove ubiquitin from target substrates and modulate signaling. Consequently, they represent potential therapeutic targets for cancer and other life-threatening conditions. USP43 belongs to the DUBs family involved in cancer development and progression. This review aims to provide a comprehensive overview of the existing scientific evidence implicating USP43 in cancer development. Additionally, it will investigate potential small-molecule inhibitors that target DUBs that may have the capability to function as anti-cancer medicines.


Subject(s)
Neoplasms , Humans , Neoplasms/metabolism , Neoplasms/drug therapy , Animals , Ubiquitination , Endopeptidases/metabolism , Deubiquitinating Enzymes/metabolism , Signal Transduction , Antineoplastic Agents/therapeutic use , Antineoplastic Agents/pharmacology
15.
Comput Biol Med ; 174: 108397, 2024 May.
Article in English | MEDLINE | ID: mdl-38603896

ABSTRACT

The equilibrium of cellular protein levels is pivotal for maintaining normal physiological functions. USP5 belongs to the deubiquitination enzyme (DUBs) family, controlling protein degradation and preserving cellular protein homeostasis. Aberrant expression of USP5 is implicated in a variety of diseases, including cancer, neurodegenerative diseases, and inflammatory diseases. In this paper, a multi-level virtual screening (VS) approach was employed to target the zinc finger ubiquitin-binding domain (ZnF-UBD) of USP5, leading to the identification of a highly promising candidate compound 0456-0049. Molecular dynamics (MD) simulations were then employed to assess the stability of complex binding and predict hotspot residues in interactions. The results indicated that the candidate stably binds to the ZnF-UBD of USP5 through crucial interactions with residues ARG221, TRP209, GLY220, ASN207, TYR261, TYR259, and MET266. Binding free energy calculations, along with umbrella sampling (US) simulations, underscored a superior binding affinity of the candidate relative to known inhibitors. Moreover, US simulations revealed conformational changes of USP5 during ligand dissociation. These insights provide a valuable foundation for the development of novel inhibitors targeting USP5.


Subject(s)
Endopeptidases , Zinc Fingers , Humans , Endopeptidases/chemistry , Endopeptidases/metabolism , Molecular Dynamics Simulation , Protein Binding , Protein Domains
16.
Biochem J ; 481(7): 515-545, 2024 Apr 10.
Article in English | MEDLINE | ID: mdl-38572758

ABSTRACT

Maintaining stability of the genome requires dedicated DNA repair and signalling processes that are essential for the faithful duplication and propagation of chromosomes. These DNA damage response (DDR) mechanisms counteract the potentially mutagenic impact of daily genotoxic stresses from both exogenous and endogenous sources. Inherent to these DNA repair pathways is the activity of protein factors that instigate repair processes in response to DNA lesions. The regulation, coordination, and orchestration of these DDR factors is carried out, in a large part, by post-translational modifications, such as phosphorylation, ubiquitylation, and modification with ubiquitin-like proteins (UBLs). The importance of ubiquitylation and UBLylation with SUMO in DNA repair is well established, with the modified targets and downstream signalling consequences relatively well characterised. However, the role of dedicated erasers for ubiquitin and UBLs, known as deubiquitylases (DUBs) and ubiquitin-like proteases (ULPs) respectively, in genome stability is less well established, particularly for emerging UBLs such as ISG15 and UFM1. In this review, we provide an overview of the known regulatory roles and mechanisms of DUBs and ULPs involved in genome stability pathways. Expanding our understanding of the molecular agents and mechanisms underlying the removal of ubiquitin and UBL modifications will be fundamental for progressing our knowledge of the DDR and likely provide new therapeutic avenues for relevant human diseases, such as cancer.


Subject(s)
Peptide Hydrolases , Ubiquitin , Humans , Ubiquitin/genetics , Ubiquitin/metabolism , Peptide Hydrolases/metabolism , Ubiquitination , Protein Processing, Post-Translational , Ubiquitins/genetics , Ubiquitins/metabolism , DNA Damage , Endopeptidases/metabolism , Genomic Instability
17.
J Exp Med ; 221(6)2024 Jun 03.
Article in English | MEDLINE | ID: mdl-38652464

ABSTRACT

OTULIN-related autoinflammatory syndrome (ORAS), a severe autoinflammatory disease, is caused by biallelic pathogenic variants of OTULIN, a linear ubiquitin-specific deubiquitinating enzyme. Loss of OTULIN attenuates linear ubiquitination by inhibiting the linear ubiquitin chain assembly complex (LUBAC). Here, we report a patient who harbors two rare heterozygous variants of OTULIN (p.P152L and p.R306Q). We demonstrated accumulation of linear ubiquitin chains upon TNF stimulation and augmented TNF-induced cell death in mesenchymal stem cells differentiated from patient-derived iPS cells, which confirms that the patient has ORAS. However, although the de novo p.R306Q variant exhibits attenuated deubiquitination activity without reducing the amount of OTULIN, the deubiquitination activity of the p.P152L variant inherited from the mother was equivalent to that of the wild-type. Patient-derived MSCs in which the p.P152L variant was replaced with wild-type also exhibited augmented TNF-induced cell death and accumulation of linear chains. The finding that ORAS can be caused by a dominant-negative p.R306Q variant of OTULIN furthers our understanding of disease pathogenesis.


Subject(s)
Ubiquitination , Female , Humans , Endopeptidases/genetics , Endopeptidases/metabolism , Hereditary Autoinflammatory Diseases/genetics , Hereditary Autoinflammatory Diseases/pathology , Hereditary Autoinflammatory Diseases/metabolism , Induced Pluripotent Stem Cells/metabolism , Mesenchymal Stem Cells/metabolism , Mutation , Pedigree , Tumor Necrosis Factor-alpha/metabolism , Tumor Necrosis Factor-alpha/genetics , Ubiquitin/metabolism , Infant, Newborn
18.
Biochem Biophys Res Commun ; 715: 149957, 2024 Jun 30.
Article in English | MEDLINE | ID: mdl-38688057

ABSTRACT

Clostridioides difficile endolysin (Ecd09610) consists of an unknown domain at its N terminus, followed by two catalytic domains, a glucosaminidase domain and endopeptidase domain. X-ray structure and mutagenesis analyses of the Ecd09610 catalytic domain with glucosaminidase activity (Ecd09610CD53) were performed. Ecd09610CD53 was found to possess an α-bundle-like structure with nine helices, which is well conserved among GH73 family enzymes. The mutagenesis analysis based on X-ray structures showed that Glu405 and Asn470 were essential for enzymatic activity. Ecd09610CD53 may adopt a neighboring-group mechanism for a catalytic reaction in which Glu405 acted as an acid/base catalyst and Asn470 helped to stabilize the oxazolinium ion intermediate. Structural comparisons with the newly identified Clostridium perfringens autolysin catalytic domain (AcpCD) in the P1 form and a zymography analysis demonstrated that AcpCD was 15-fold more active than Ecd09610CD53. The strength of the glucosaminidase activity of the GH73 family appears to be dependent on the depth of the substrate-binding groove.


Subject(s)
Catalytic Domain , Clostridioides difficile , Endopeptidases , Clostridioides difficile/enzymology , Clostridioides difficile/genetics , Crystallography, X-Ray , Endopeptidases/chemistry , Endopeptidases/metabolism , Endopeptidases/genetics , Models, Molecular , Hexosaminidases/chemistry , Hexosaminidases/genetics , Hexosaminidases/metabolism , Mutagenesis , Amino Acid Sequence , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Mutagenesis, Site-Directed , Protein Domains
19.
Protein Expr Purif ; 220: 106488, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38679188

ABSTRACT

The tobacco etch virus (TEV) protease is a commonly used reagent for removal of solubility and purification tags from recombinant proteins and is cited as being highly specific for its canonical cleavage site. Flexibility in some amino acids within this recognition sequence has been described in the literature but researchers generally assume few native human proteins will carry off-target sequences for TEV cleavage. We report here the aberrant cleavage of three human proteins with non-canonical TEV protease cleavage sites and identify broader sequence specificity rules that can be used to predict unwanted cleavage of recombinant proteins. Using these rules, 456 human proteins were identified that could be substrates for unwanted TEV protease cleavage.


Subject(s)
Endopeptidases , Humans , Endopeptidases/chemistry , Endopeptidases/metabolism , Endopeptidases/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Recombinant Proteins/isolation & purification , Proteolysis , Substrate Specificity
20.
CNS Neurosci Ther ; 30(4): e14711, 2024 04.
Article in English | MEDLINE | ID: mdl-38644551

ABSTRACT

OBJECTIVE: To elucidate the relationship between USP19 and O(6)-methylguanine-DNA methyltransferase (MGMT) after temozolomide treatment in glioblastoma (GBM) patients with chemotherapy resistance. METHODS: Screening the deubiquitinase pannel and identifying the deubiquitinase directly interacts with and deubiquitination MGMT. Deubiquitination assay to confirm USP19 deubiquitinates MGMT. The colony formation and tumor growth study in xenograft assess USP19 affects the GBM sensitive to TMZ was performed by T98G, LN18, U251, and U87 cell lines. Immunohistochemistry staining and survival analysis were performed to explore how USP19 is correlated to MGMT in GBM clinical management. RESULTS: USP19 removes the ubiquitination of MGMT to facilitate the DNA methylation damage repair. Depletion of USP19 results in the glioblastoma cell sensitivity to temozolomide, which can be rescued by overexpressing MGMT. USP19 is overexpressed in glioblastoma patient samples, which positively correlates with the level of MGMT protein and poor prognosis in these patients. CONCLUSION: The regulation of MGMT ubiquitination by USP19 plays a critical role in DNA methylation damage repair and GBM patients' temozolomide chemotherapy response.


Subject(s)
Antineoplastic Agents, Alkylating , DNA Methylation , DNA Modification Methylases , DNA Repair Enzymes , Drug Resistance, Neoplasm , Temozolomide , Tumor Suppressor Proteins , Humans , Temozolomide/pharmacology , Temozolomide/therapeutic use , DNA Repair Enzymes/metabolism , DNA Repair Enzymes/genetics , DNA Modification Methylases/metabolism , Antineoplastic Agents, Alkylating/pharmacology , Antineoplastic Agents, Alkylating/therapeutic use , Animals , Cell Line, Tumor , Drug Resistance, Neoplasm/drug effects , Drug Resistance, Neoplasm/genetics , Tumor Suppressor Proteins/metabolism , Tumor Suppressor Proteins/genetics , DNA Methylation/drug effects , Mice, Nude , Brain Neoplasms/drug therapy , Brain Neoplasms/genetics , Brain Neoplasms/metabolism , Glioblastoma/drug therapy , Glioblastoma/genetics , Glioblastoma/metabolism , Mice , Male , Female , Dacarbazine/analogs & derivatives , Dacarbazine/pharmacology , Dacarbazine/therapeutic use , DNA Repair/drug effects , Endopeptidases/metabolism , Endopeptidases/genetics , Xenograft Model Antitumor Assays , Ubiquitination/drug effects
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