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1.
Sci Rep ; 14(1): 12876, 2024 06 05.
Article in English | MEDLINE | ID: mdl-38834612

ABSTRACT

This study investigates quercetin complexes as potential synergistic agents against the important respiratory pathogen Streptococcus pneumoniae. Six quercetin complexes (QCX1-6) were synthesized by reacting quercetin with various metal salts and boronic acids and characterized using FTIR spectroscopy. Their antibacterial activity alone and in synergism with antibiotics was evaluated against S. pneumoniae ATCC 49619 using disc diffusion screening, broth microdilution MIC determination, and checkerboard assays. Complexes QCX-3 and QCX-4 demonstrated synergy when combined with levofloxacin via fractional inhibitory concentration indices ≤ 0.5 as confirmed by time-kill kinetics. Molecular docking elucidated interactions of these combinations with virulence enzymes sortase A and sialidase. A biofilm inhibition assay found the synergistic combinations more potently reduced biofilm formation versus monotherapy. Additionally, gene-gene interaction networks, biological activity predictions and in-silico toxicity profiling provided insights into potential mechanisms of action and safety.


Subject(s)
Anti-Bacterial Agents , Biofilms , Microbial Sensitivity Tests , Molecular Docking Simulation , Quercetin , Streptococcus pneumoniae , Streptococcus pneumoniae/drug effects , Quercetin/pharmacology , Quercetin/chemistry , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/chemistry , Biofilms/drug effects , Drug Synergism , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/antagonists & inhibitors , Cysteine Endopeptidases/metabolism , Cysteine Endopeptidases/chemistry , Aminoacyltransferases/antagonists & inhibitors , Aminoacyltransferases/metabolism , Neuraminidase/antagonists & inhibitors , Neuraminidase/metabolism
2.
Appl Microbiol Biotechnol ; 108(1): 360, 2024 Jun 05.
Article in English | MEDLINE | ID: mdl-38836914

ABSTRACT

In the fight against hospital-acquired infections, the challenge posed by methicillin-resistant Staphylococcus aureus (MRSA) necessitates the development of novel treatment methods. This study focused on undermining the virulence of S. aureus, especially by targeting surface proteins crucial for bacterial adherence and evasion of the immune system. A primary aspect of our approach involves inhibiting sortase A (SrtA), a vital enzyme for attaching microbial surface components recognizing adhesive matrix molecules (MSCRAMMs) to the bacterial cell wall, thereby reducing the pathogenicity of S. aureus. Verbascoside, a phenylethanoid glycoside, was found to be an effective SrtA inhibitor in our research. Advanced fluorescence quenching and molecular docking studies revealed a specific interaction between verbascoside and SrtA, pinpointing the critical active sites involved in this interaction. This molecular interaction significantly impedes the SrtA-mediated attachment of MSCRAMMs, resulting in a substantial reduction in bacterial adhesion, invasion, and biofilm formation. The effectiveness of verbascoside has also been demonstrated in vivo, as shown by its considerable protective effects on pneumonia and Galleria mellonella (wax moth) infection models. These findings underscore the potential of verbascoside as a promising component in new antivirulence therapies for S. aureus infections. By targeting crucial virulence factors such as SrtA, agents such as verbascoside constitute a strategic and potent approach for tackling antibiotic resistance worldwide. KEY POINTS: • Verbascoside inhibits SrtA, reducing S. aureus adhesion and biofilm formation. • In vivo studies demonstrated the efficacy of verbascoside against S. aureus infections. • Targeting virulence factors such as SrtA offers new avenues against antibiotic resistance.


Subject(s)
Aminoacyltransferases , Anti-Bacterial Agents , Bacterial Adhesion , Bacterial Proteins , Biofilms , Cysteine Endopeptidases , Glucosides , Methicillin-Resistant Staphylococcus aureus , Molecular Docking Simulation , Phenols , Staphylococcal Infections , Bacterial Proteins/metabolism , Bacterial Proteins/antagonists & inhibitors , Aminoacyltransferases/antagonists & inhibitors , Aminoacyltransferases/metabolism , Cysteine Endopeptidases/metabolism , Methicillin-Resistant Staphylococcus aureus/drug effects , Methicillin-Resistant Staphylococcus aureus/pathogenicity , Glucosides/pharmacology , Animals , Staphylococcal Infections/drug therapy , Staphylococcal Infections/microbiology , Phenols/pharmacology , Bacterial Adhesion/drug effects , Biofilms/drug effects , Anti-Bacterial Agents/pharmacology , Moths/microbiology , Virulence/drug effects , Disease Models, Animal , Virulence Factors/metabolism , Enzyme Inhibitors/pharmacology , Polyphenols
3.
Biomacromolecules ; 25(5): 2762-2769, 2024 May 13.
Article in English | MEDLINE | ID: mdl-38689446

ABSTRACT

Protein-based encapsulin nanocompartments, known for their well-defined structures and versatile functionalities, present promising opportunities in the fields of biotechnology and nanomedicine. In this investigation, we effectively developed a sortase A-mediated protein ligation system in Escherichia coli to site-specifically attach target proteins to encapsulin, both internally and on its surfaces without any further in vitro steps. We explored the potential applications of fusing sortase enzyme and a protease for post-translational ligation of encapsulin to a green fluorescent protein and anti-CD3 scFv. Our results demonstrated that this system could attach other proteins to the nanoparticles' exterior surfaces without adversely affecting their folding and assembly processes. Additionally, this system enabled the attachment of proteins inside encapsulins which varied shapes and sizes of the nanoparticles due to cargo overload. This research developed an alternative enzymatic ligation method for engineering encapsulin nanoparticles to facilitate the conjugation process.


Subject(s)
Aminoacyltransferases , Bacterial Proteins , Cysteine Endopeptidases , Escherichia coli , Protein Processing, Post-Translational , Aminoacyltransferases/metabolism , Aminoacyltransferases/chemistry , Cysteine Endopeptidases/metabolism , Cysteine Endopeptidases/chemistry , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Escherichia coli/metabolism , Green Fluorescent Proteins/metabolism , Green Fluorescent Proteins/chemistry , Nanoparticles/chemistry , Single-Chain Antibodies/chemistry , Single-Chain Antibodies/metabolism
4.
ACS Sens ; 9(5): 2605-2613, 2024 May 24.
Article in English | MEDLINE | ID: mdl-38718161

ABSTRACT

Several new lines of research have demonstrated that a significant number of amyloid-ß peptides found in Alzheimer's disease (AD) are truncated and undergo post-translational modification by glutaminyl cyclase (QC) at the N-terminal. Notably, QC's products of Abeta-pE3 and Abeta-pE11 have been active targets for investigational drug development. This work describes the design, synthesis, characterization, and in vivo validation of a novel PET radioligand, [18F]PB0822, for targeted imaging of QC. We report herein a simplified and robust chemistry for the synthesis of the standard compound, [19F]PB0822, and the corresponding [18F]PB0822 radioligand. The PET probe was developed with 99.9% radiochemical purity, a molar activity of 965 Ci.mmol-1, and an IC50 of 56.3 nM, comparable to those of the parent PQ912 inhibitor (62.5 nM). Noninvasive PET imaging showed that the probe is distributed in the brain 5 min after intravenous injection. Further, in vivo PET imaging with [18F]PB0822 revealed that AD 5XFAD mice harbor significantly higher QC activity than WT counterparts. The data also suggested that QC activity is found across different brain regions of the tested animals.


Subject(s)
Alzheimer Disease , Aminoacyltransferases , Positron-Emission Tomography , Alzheimer Disease/diagnostic imaging , Alzheimer Disease/metabolism , Positron-Emission Tomography/methods , Aminoacyltransferases/metabolism , Aminoacyltransferases/antagonists & inhibitors , Animals , Mice , Fluorine Radioisotopes/chemistry , Brain/diagnostic imaging , Brain/metabolism , Brain/enzymology , Radiopharmaceuticals/chemistry , Radiopharmaceuticals/chemical synthesis , Biomarkers/metabolism , Humans , Amyloid beta-Peptides/metabolism , Amyloid beta-Peptides/analysis , Ligands
5.
Adv Sci (Weinh) ; 11(21): e2305605, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38581131

ABSTRACT

Wild-type sortase A is an important virulence factor displaying a diverse array of proteins on the surface of bacteria. This protein display relies on the transpeptidase activity of sortase A, which is widely engineered to allow protein ligation and protein engineering based on the interaction between sortase A and peptides. Here an unknown interaction is found between sortase A from Staphylococcus aureus and nucleic acids, in which exogenously expressed engineered sortase A binds oligonucleotides in vitro and is independent of its canonical transpeptidase activity. When incubated with mammalian cells, engineered sortase A further mediates oligonucleotide labeling to the cell surface, where sortase A attaches itself and is part of the labeled moiety. The labeling reaction can also be mediated by many classes of wild-type sortases as well. Cell surface GAG appears involved in sortase-mediated oligonucleotide cell labeling, as demonstrated by CRISPR screening. This interaction property is utilized to develop a technique called CellID to facilitate sample multiplexing for scRNA-seq and shows the potential of using sortases to label cells with diverse oligonucleotides. Together, the binding between sortase A and nucleic acids opens a new avenue to understanding the virulence of wild-type sortases and exploring the application of sortases in biotechnology.


Subject(s)
Aminoacyltransferases , Bacterial Proteins , Cysteine Endopeptidases , Nucleic Acids , Staphylococcus aureus , Aminoacyltransferases/metabolism , Aminoacyltransferases/genetics , Cysteine Endopeptidases/metabolism , Cysteine Endopeptidases/genetics , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Staphylococcus aureus/genetics , Staphylococcus aureus/enzymology , Staphylococcus aureus/metabolism , Nucleic Acids/metabolism , Humans , Animals , Staining and Labeling/methods
6.
Toxins (Basel) ; 16(4)2024 Apr 16.
Article in English | MEDLINE | ID: mdl-38668619

ABSTRACT

Cholera toxoid is an established tool for use in cellular tracing in neuroscience and cell biology. We use a sortase labeling approach to generate site-specific N-terminally modified variants of both the A2-B5 heterohexamer and B5 pentamer forms of the toxoid. Both forms of the toxoid are endocytosed by GM1-positive mammalian cells, and while the heterohexameric toxoid was principally localized in the ER, the B5 pentamer showed an unexpectedly specific localization in the medial/trans-Golgi. This study suggests a future role for specifically labeled cholera toxoids in live-cell imaging beyond their current applications in neuronal tracing and labeling of lipid rafts in fixed cells.


Subject(s)
Cholera Toxin , Cysteine Endopeptidases , Golgi Apparatus , Humans , Cholera Toxin/metabolism , Cysteine Endopeptidases/metabolism , Golgi Apparatus/metabolism , Animals , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Aminoacyltransferases/metabolism , Aminoacyltransferases/genetics , Endocytosis
7.
ACS Infect Dis ; 10(5): 1767-1779, 2024 May 10.
Article in English | MEDLINE | ID: mdl-38619138

ABSTRACT

Peptidoglycan synthesis is an underutilized drug target in Mycobacterium tuberculosis (Mtb). Diazabicyclooctanes (DBOs) are a class of broad-spectrum ß-lactamase inhibitors that also inhibit certain peptidoglycan transpeptidases that are important in mycobacterial cell wall synthesis. We evaluated the DBO durlobactam as an inhibitor of BlaC, the Mtb ß-lactamase, and multiple Mtb peptidoglycan transpeptidases (PonA1, LdtMt1, LdtMt2, LdtMt3, and LdtMt5). Timed electrospray ionization mass spectrometry (ESI-MS) captured acyl-enzyme complexes with BlaC and all transpeptidases except LdtMt5. Inhibition kinetics demonstrated durlobactam was a potent and efficient DBO inhibitor of BlaC (KI app 9.2 ± 0.9 µM, k2/K 5600 ± 560 M-1 s-1) and similar to clavulanate (KI app 3.3 ± 0.6 µM, k2/K 8400 ± 840 M-1 s-1); however, durlobactam had a lower turnover number (tn = kcat/kinact) than clavulanate (1 and 8, respectively). KI app values with durlobactam and clavulanate were similar for peptidoglycan transpeptidases, but ESI-MS captured durlobactam complexes at more time points. Molecular docking and simulation demonstrated several productive interactions of durlobactam in the active sites of BlaC, PonA1, and LdtMt2. Antibiotic susceptibility testing was conducted on 11 Mtb isolates with amoxicillin, ceftriaxone, meropenem, imipenem, clavulanate, and durlobactam. Durlobactam had a minimum inhibitory concentration (MIC) range of 0.5-16 µg/mL, similar to the ranges for meropenem (1-32 µg/mL) and imipenem (0.5-64 µg/mL). In ß-lactam + durlobactam combinations (1:1 mass/volume), MICs were lowered 4- to 64-fold for all isolates except one with meropenem-durlobactam. This work supports further exploration of novel ß-lactamase inhibitors that target BlaC and Mtb peptidoglycan transpeptidases.


Subject(s)
Mycobacterium tuberculosis , beta-Lactamase Inhibitors , beta-Lactamases , Mycobacterium tuberculosis/drug effects , Mycobacterium tuberculosis/enzymology , beta-Lactamase Inhibitors/pharmacology , beta-Lactamase Inhibitors/chemistry , beta-Lactamases/metabolism , beta-Lactamases/chemistry , Peptidyl Transferases/antagonists & inhibitors , Peptidyl Transferases/metabolism , Azabicyclo Compounds/pharmacology , Azabicyclo Compounds/chemistry , Microbial Sensitivity Tests , Antitubercular Agents/pharmacology , Antitubercular Agents/chemistry , Molecular Docking Simulation , Peptidoglycan/metabolism , Peptidoglycan/chemistry , Bacterial Proteins/metabolism , Bacterial Proteins/antagonists & inhibitors , Bacterial Proteins/chemistry , Kinetics , Aminoacyltransferases
8.
J Proteome Res ; 23(5): 1859-1870, 2024 May 03.
Article in English | MEDLINE | ID: mdl-38655723

ABSTRACT

To understand how upregulated isoglutaminyl cyclase (isoQC) is involved in the initiation of diseases such as cancer, we developed a human KYSE30 carcinoma cell model in which isoQC was stably overexpressed. GO and KEGG analysis of the DEGs (228) and DEPs (254) respectively implicated isoQC on the proliferation invasion and metastasis of cells and suggested that isoQC might participate in the regulation of MAPK, RAS, circadian rhythm, and related pathways. At the functional level, isoQC-overexpressing KYSE30 cells showed enhanced proliferation, migration, and invasion capacity. Next, we decided to study the precise effect of isoQC overexpression on JNK, p-JNK, AKT, p-AKT, ERK, p-ERK, and PER2, as RNA levels of these proteins are significantly correlated with signal levels indicated in RNA-Seq analysis, and these candidates are the top correlated DEPs enriched in RT-qPCR analysis. We saw that only p-ERK expression was inhibited, while PER2 was increased. These phenotypes were inhibited upon exposure to PER2 inhibitor KL044, which allowed for the restoration of p-ERK levels. These data support upregulated isoQC being able to promote cancer cell proliferation and migration in vitro, likely by helping to regulate the MAPK and RAS signaling pathways, and the circadian protein PER2 might be a potential mediator.


Subject(s)
Aminoacyltransferases , Cell Movement , Cell Proliferation , MAP Kinase Signaling System , Humans , Cell Proliferation/genetics , Cell Movement/genetics , MAP Kinase Signaling System/genetics , Cell Line, Tumor , Gene Expression Regulation, Neoplastic , Period Circadian Proteins/genetics , Period Circadian Proteins/metabolism , Neoplasm Invasiveness , Up-Regulation , Neoplasms/genetics , Neoplasms/pathology , Neoplasms/metabolism
9.
Int J Antimicrob Agents ; 63(5): 107144, 2024 May.
Article in English | MEDLINE | ID: mdl-38494147

ABSTRACT

OBJECTIVES: Daptomycin is one of the few last-line antimicrobials available for the treatment of multidrug-resistant Staphylococcus aureus infections. An increasing number of daptomycin non-susceptible S. aureus infections has been reported worldwide, including Australia. Resistance to daptomycin is multifactorial and involves chromosomal mutations in genes encoding proteins involved in cell membrane and cell wall synthesis. METHODS: In this study, we performed broth microdilution (BMD) to determine the daptomycin minimum inhibitory concentration (MIC) of 66 clinical isolates of S. aureus previously reported as daptomycin non-susceptible by the VITEKⓇ 2. We used whole-genome sequencing to characterise the isolates and screened the genomes for mutations associated with daptomycin non-susceptibility. RESULTS: Only 56 of the 66 isolates had a daptomycin MIC >1 mg/L by BMD. Although the 66 isolates were polyclonal, ST22 was the predominant sequence type and one-third of the isolates were multidrug resistant. Daptomycin non-susceptibility was primarily associated with MprF mutations-at least one MprF mutation was identified in the 66 isolates. Twelve previously reported MprF mutations associated with daptomycin non-susceptibility were identified in 83% of the isolates. Novel MprF mutations identified included P314A, P314F, P314T, S337T, L341V, F349del, and T423R. CONCLUSIONS: Daptomycin non-susceptible S. aureus causing infections in Australia are polyclonal and harbour MprF mutation(s). The identification of multidrug-resistant daptomycin non-susceptible S. aureus is a public health concern.


Subject(s)
Aminoacyltransferases , Anti-Bacterial Agents , Bacterial Proteins , Daptomycin , Microbial Sensitivity Tests , Mutation , Staphylococcal Infections , Staphylococcus aureus , Whole Genome Sequencing , Daptomycin/pharmacology , Humans , Anti-Bacterial Agents/pharmacology , Australia , Staphylococcus aureus/drug effects , Staphylococcus aureus/genetics , Staphylococcal Infections/microbiology , Staphylococcal Infections/drug therapy , Bacterial Proteins/genetics , Aminoacyltransferases/genetics , Male , Drug Resistance, Multiple, Bacterial/genetics , Female , Genome, Bacterial/genetics , Middle Aged , Aged , Adult
10.
Nucleic Acids Res ; 52(5): 2130-2141, 2024 Mar 21.
Article in English | MEDLINE | ID: mdl-38407292

ABSTRACT

Outliers in scientific observations are often ignored and mostly remain unreported. However, presenting them is always beneficial since they could reflect the actual anomalies that might open new avenues. Here, we describe two examples of the above that came out of the laboratories of two of the pioneers of nucleic acid research in the area of protein biosynthesis, Paul Berg and Donald Crothers. Their work on the identification of D-aminoacyl-tRNA deacylase (DTD) and 'Discriminator hypothesis', respectively, were hugely ahead of their time and were partly against the general paradigm at that time. In both of the above works, the smallest and the only achiral amino acid turned out to be an outlier as DTD can act weakly on glycine charged tRNAs with a unique discriminator base of 'Uracil'. This peculiar nature of glycine remained an enigma for nearly half a century. With a load of available information on the subject by the turn of the century, our work on 'chiral proofreading' mechanisms during protein biosynthesis serendipitously led us to revisit these findings. Here, we describe how we uncovered an unexpected connection between them that has implications for evolution of different eukaryotic life forms.


Subject(s)
Aminoacyltransferases , Eukaryota , Glycine , Protein Biosynthesis , Amino Acids/genetics , Aminoacyltransferases/genetics , Glycine/genetics , RNA, Transfer, Amino Acyl/metabolism , Research , Biochemistry , Eukaryota/chemistry , Eukaryota/genetics
11.
Chem Biodivers ; 21(5): e202301659, 2024 May.
Article in English | MEDLINE | ID: mdl-38407541

ABSTRACT

Sortase A (SrtA) is an attractive target for developing new anti-infective drugs that aim to interfere with essential virulence mechanisms, such as adhesion to host cells and biofilm formation. Herein, twenty hydroxy, nitro, bromo, fluoro, and methoxy substituted chalcone compounds were synthesized, antimicrobial activities and molecular modeling strategies against the SrtA enzyme were investigated. The most active compounds were found to be T2, T4, and T19 against Streptococcus mutans (S. mutans) with MIC values of 1.93, 3.8, 3.94 µg/mL, and docking scores of -6.46, -6.63, -6.73 kcal/mol, respectively. Also, these three active compounds showed better activity than the chlorohexidine (CHX) (MIC value: 4.88 µg/mL, docking score: -6.29 kcal/mol) in both in vitro and in silico. Structural stability and binding free energy analysis of S.mutans SrtA with active compounds were measured by molecular dynamic (MD) simulations throughout 100 nanoseconds (ns) time. It was observed that the stability of the critical interactions between these compounds and the target enzyme was preserved. To prove further, in vivo biological evaluation studies could be conducted for the most promising precursor compounds T2, T4, and T19, and it might open new avenues to the discovery of more potent SrtA inhibitors.


Subject(s)
Aminoacyltransferases , Bacterial Proteins , Cysteine Endopeptidases , Microbial Sensitivity Tests , Streptococcus mutans , Aminoacyltransferases/antagonists & inhibitors , Aminoacyltransferases/metabolism , Cysteine Endopeptidases/metabolism , Cysteine Endopeptidases/chemistry , Bacterial Proteins/antagonists & inhibitors , Bacterial Proteins/metabolism , Bacterial Proteins/chemistry , Streptococcus mutans/drug effects , Streptococcus mutans/enzymology , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/chemical synthesis , Anti-Bacterial Agents/chemistry , Structure-Activity Relationship , Molecular Dynamics Simulation , Molecular Docking Simulation , Molecular Structure , Models, Molecular , Chalcone/chemistry , Chalcone/pharmacology , Chalcone/chemical synthesis , Dose-Response Relationship, Drug
12.
Angew Chem Int Ed Engl ; 63(14): e202316777, 2024 Apr 02.
Article in English | MEDLINE | ID: mdl-38366985

ABSTRACT

Topological transformations and permutations of proteins have attracted significant interest as strategies to generate new protein functionalities or stability. These efforts have mainly been inspired by naturally occurring post-translational modifications, such as head-to-tail cyclization, circular permutation, or lasso-like entanglement. Such approaches can be realized experimentally via genetic encoding, in the case of circular permutation, or via enzymatic processing, in the case of cyclization. Notably, these previously described strategies leave the polypeptide backbone orientation unaltered. Here we describe an unnatural protein permutation, the protein domain inversion, whereby a C-terminal portion of a protein is enzymatically inverted from the canonical N-to-C to a C-to-C configuration with respect to the N-terminal part of the protein. The closest conceptually analogous biological process is perhaps the inversion of DNA segments as catalyzed by recombinases. We achieve these inversions using an engineered sortase A, a widely used transpeptidase. Our reactions proceed efficiently under mild conditions at 4-25 °C and are compatible with entirely heterologously-produced protein substrates.


Subject(s)
Aminoacyltransferases , Peptidyl Transferases , Protein Domains , Peptides/chemistry , Bacterial Proteins/metabolism , Aminoacyltransferases/chemistry , Peptidyl Transferases/metabolism , DNA , Catalysis
13.
Cancer Biol Ther ; 25(1): 2321767, 2024 12 31.
Article in English | MEDLINE | ID: mdl-38417050

ABSTRACT

Doxorubicin (DOX) is one of the most effective and widely used chemotherapeutic drugs. However, DOX resistance is a critical risk problem for breast cancer treatment. Previous studies have demonstrated that metadherin (MTDH) involves in DOX resistance in breast cancer, but the exact mechanism remains unclear. In this study, we found that glutaminyl-peptide cyclotransferase (QPCT) was a MTDH DOX resistance-related downstream gene in breast cancer. Elevated expression of QPCT was found in the GEPIA database, breast cancer tissue, and breast cancer cells. Clinical data showed that QPCT expression was positively associated with poor prognosis in DOX-treated patients. Overexpression of QPCT could promote the proliferation, invasion and migration, and reduce DOX sensitivity in MCF-7 and MDA-MB-231 cells. Mechanistically, MTDH positively regulates the expressions of NF-κB (p65) and QPCT, and NF-κB (p65) directly regulates the expression of QPCT. Therefore, MTDH/NF-κB (p65)/QPCT signal axis was proposed. Collectively, our findings delineate the mechanism by which the MTDH/NF-κB (p65) axis regulate QPCT signaling and suggest that this complex may play an essential role in breast cancer progression and affect DOX sensitivity.


Subject(s)
Aminoacyltransferases , Breast Neoplasms , Humans , Female , Breast Neoplasms/drug therapy , Breast Neoplasms/genetics , Breast Neoplasms/metabolism , NF-kappa B/metabolism , Cell Line, Tumor , Doxorubicin/pharmacology , Doxorubicin/therapeutic use , Membrane Proteins/genetics , Membrane Proteins/metabolism , RNA-Binding Proteins/genetics
14.
Cell Commun Signal ; 22(1): 87, 2024 01 31.
Article in English | MEDLINE | ID: mdl-38297346

ABSTRACT

BACKGROUND: Arginyltransferase (Ate1) orchestrates posttranslational protein arginylation, a pivotal regulator of cellular proteolytic processes. In eukaryotic cells, two interconnected systems-the ubiquitin proteasome system (UPS) and macroautophagy-mediate proteolysis and cooperate to maintain quality protein control and cellular homeostasis. Previous studies have shown that N-terminal arginylation facilitates protein degradation through the UPS. Dysregulation of this machinery triggers p62-mediated autophagy to ensure proper substrate processing. Nevertheless, how Ate1 operates through this intricate mechanism remains elusive. METHODS: We investigated Ate1 subcellular distribution through confocal microscopy and biochemical assays using cells transiently or stably expressing either endogenous Ate1 or a GFP-tagged Ate1 isoform transfected in CHO-K1 or MEFs, respectively. To assess Ate1 and p62-cargo clustering, we analyzed their colocalization and multimerization status by immunofluorescence and nonreducing immunoblotting, respectively. Additionally, we employed Ate1 KO cells to examine the role of Ate1 in autophagy. Ate1 KO MEFs cells stably expressing GFP-tagged Ate1-1 isoform were used as a model for phenotype rescue. Autophagy dynamics were evaluated by analyzing LC3B turnover and p62/SQSTM1 levels under both steady-state and serum-starvation conditions, through immunoblotting and immunofluorescence. We determined mTORC1/AMPk activation by assessing mTOR and AMPk phosphorylation through immunoblotting, while mTORC1 lysosomal localization was monitored by confocal microscopy. RESULTS: Here, we report a multifaceted role for Ate1 in the autophagic process, wherein it clusters with p62, facilitates autophagic clearance, and modulates its signaling. Mechanistically, we found that cell-specific inactivation of Ate1 elicits overactivation of the mTORC1/AMPk signaling hub that underlies a failure in autophagic flux and subsequent substrate accumulation, which is partially rescued by ectopic expression of Ate1. Statistical significance was assessed using a two-sided unpaired t test with a significance threshold set at P<0.05. CONCLUSIONS: Our findings uncover a critical housekeeping role of Ate1 in mTORC1/AMPk-regulated autophagy, as a potential therapeutic target related to this pathway, that is dysregulated in many neurodegenerative and cancer diseases.


Subject(s)
Aminoacyltransferases , Aminoacyltransferases/genetics , Aminoacyltransferases/metabolism , Ubiquitin/metabolism , Autophagy , Proteasome Endopeptidase Complex/metabolism , Mechanistic Target of Rapamycin Complex 1 , Protein Isoforms
15.
J Med Chem ; 67(2): 1127-1146, 2024 Jan 25.
Article in English | MEDLINE | ID: mdl-38170998

ABSTRACT

Sortase A (SrtA) is a membrane-associated cysteine transpeptidase required for bacterial virulence regulation and anchors surface proteins to cell wall, thereby assisting biofilm formation. SrtA is targeted in antivirulence treatments against Gram-positive bacterial infections. However, the development of potent small-molecule SrtA inhibitors is constrained owing to the limited understanding of the mode of action of inhibitors in the SrtA binding pocket. Herein, we designed and synthesized a novel class of covalent SrtA inhibitors based on the binding mode detailed in the X-ray crystal structure of the ML346/Streptococcus pyogenes SrtA complex. ML346 analog Y40 exhibited 2-fold increased inhibitory activity on Staphylococcus aureus SrtA and showed superior inhibitory effects on biofilm formation in vitro. Y40 protected Galleria mellonella larvae fromS. aureusinfections in vivo while minimally attenuating staphylococcal growth in vitro. Our study indicates that the covalent SrtA inhibitor Y40 is an antivirulence agent that is effective againstS. aureusinfections.


Subject(s)
Aminoacyltransferases , Staphylococcus aureus , Bacterial Proteins , Cysteine Endopeptidases/metabolism
16.
J Biomol Struct Dyn ; 42(3): 1157-1169, 2024.
Article in English | MEDLINE | ID: mdl-37184111

ABSTRACT

Staphylococcus aureus is a prevalent Gram-positive bacteria leading cause of a wide range of human pathologies. Moreover, antibiotic résistance of pathogenesis bacteria is one of the worldwide health problems. In Gram-positive bacteria, the enzyme of SrtA, is responsible for the anchoring of surface-exposed proteins to the cell wall peptidoglycan. Because of its critical role in Gram-positive bacterial pathogenesis, SrtA is an attractive target for anti-virulence during drug development. To date, some SrtA inhibitors have been discovered most of them being derived from flavonoid compounds, like Myricetin. In order to provide potential hit molecules against SrtA for clinical use, we obtained a total of 293 compounds by performing in silico shape-based screening of compound libraries against Myristin as a reference structure. Employing molecular docking and scoring functions, the top 3 compounds Apigenin, Efloxate, and Compound 8261032 were screened by comparing their docking scores with Myricetin. Furthermore, MD simulations and MM-PBSA binding energy calculation studies revealed that only Compound 8261032 strongly binds to the catalytic core of the SrtA enzyme than Myricetin, and stable behavior was consistently observed in the docking complex. Compound 8261032 showed a good number of hydrogen bonds with SrtA and higher MM-PBSA binding energy when compared to all three molecules. Also, it makes strength interactions with Arg139 and His62, which are critical for SrtA biological activity. This study showed that the development of this inhibitor could be a fundamental strategy against resistant bacteria, but further studies in vitro are needed to confirm this claim.Communicated by Ramaswamy H. Sarma.


Subject(s)
Aminoacyltransferases , Cysteine Endopeptidases , Staphylococcus aureus , Humans , Molecular Dynamics Simulation , Molecular Docking Simulation , Bacterial Proteins/chemistry , Aminoacyltransferases/chemistry
17.
Angew Chem Int Ed Engl ; 63(12): e202310910, 2024 Mar 18.
Article in English | MEDLINE | ID: mdl-38081121

ABSTRACT

Sortase-mediated ligation (SML) has emerged as a powerful and versatile methodology for site-specific protein conjugation, functionalization/labeling, immobilization, and design of biohybrid molecules and systems. However, the broader application of SML faces several challenges, such as limited activity and stability, dependence on calcium ions, and reversible reactions caused by nucleophilic side-products. Over the past decade, protein engineering campaigns and particularly directed evolution, have been extensively employed to overcome sortase limitations, thereby expanding the potential application of SML in multiple directions, including therapeutics, biorthogonal chemistry, biomaterials, and biosensors. This review provides an overview of achieved advancements in sortase engineering and highlights recent progress in utilizing SML in combination with other state-of-the-art chemical and biological methodologies. The aim is to encourage scientists to employ sortases in their conjugation experiments.


Subject(s)
Aminoacyltransferases , Bacterial Proteins , Bacterial Proteins/metabolism , Aminoacyltransferases/chemistry , Protein Engineering/methods , Power, Psychological
18.
Angew Chem Int Ed Engl ; 63(8): e202310862, 2024 Feb 19.
Article in English | MEDLINE | ID: mdl-38072831

ABSTRACT

Quantitative and selective labelling of proteins is widely used in both academic and industrial laboratories, and catalytic labelling of proteins using transpeptidases, such as sortases, has proved to be a popular strategy for such selective modification. A major challenge for this class of enzymes is that the majority of procedures require an excess of the labelling reagent or, alternatively, activated substrates rather than simple commercially sourced peptides. We report the use of a coupled enzyme strategy which enables quantitative N- and C-terminal labelling of proteins using unactivated labelling peptides. The use of an aminopeptidase in conjunction with a transpeptidase allows sequence-specific degradation of the peptide by-product, shifting the equilibrium to favor product formation, which greatly enhances the reaction efficiency. Subsequent optimisation of the reaction allows N-terminal labelling of proteins using essentially equimolar ratios of peptide label to protein and C-terminal labelling with only a small excess. Minimizing the amount of substrate required for quantitative labelling has the potential to improve industrial processes and facilitate the use of transpeptidation as a method for protein labelling.


Subject(s)
Aminoacyltransferases , Peptidyl Transferases , Aminopeptidases , Bacterial Proteins/metabolism , Aminoacyltransferases/metabolism , Peptides/metabolism
19.
Biopolymers ; 115(1): e23539, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37227047

ABSTRACT

Many species of pathogenic gram-positive bacteria display covalently crosslinked protein polymers (called pili or fimbriae) that mediate microbial adhesion to host tissues. These structures are assembled by pilus-specific sortase enzymes that join the pilin components together via lysine-isopeptide bonds. The archetypal SpaA pilus from Corynebacterium diphtheriae is built by the Cd SrtA pilus-specific sortase, which crosslinks lysine residues within the SpaA and SpaB pilins to build the shaft and base of the pilus, respectively. Here, we show that Cd SrtA crosslinks SpaB to SpaA via a K139(SpaB)-T494(SpaA) lysine-isopeptide bond. Despite sharing only limited sequence homology, an NMR structure of SpaB reveals striking similarities with the N-terminal domain of SpaA (N SpaA) that is also crosslinked by Cd SrtA. In particular, both pilins contain similarly positioned reactive lysine residues and adjacent disordered AB loops that are predicted to be involved in the recently proposed "latch" mechanism of isopeptide bond formation. Competition experiments using an inactive SpaB variant and additional NMR studies suggest that SpaB terminates SpaA polymerization by outcompeting N SpaA for access to a shared thioester enzyme-substrate reaction intermediate.


Subject(s)
Aminoacyltransferases , Corynebacterium diphtheriae , Fimbriae Proteins/chemistry , Fimbriae Proteins/metabolism , Corynebacterium diphtheriae/metabolism , Bacterial Proteins/metabolism , Lysine , Cadmium/metabolism , Aminoacyltransferases/metabolism
20.
J Antimicrob Chemother ; 79(2): 403-411, 2024 Feb 01.
Article in English | MEDLINE | ID: mdl-38153239

ABSTRACT

BACKGROUND: Streptococcus suis is an important pig pathogen and an emerging zoonotic agent. In a previous study, we described a high proportion of penicillin-resistant serotype 9 S. suis (SS9) isolates on pig farms in Italy. OBJECTIVES: We hypothesized that resistance to penicillin emerged in some SS9 lineages characterized by substitutions at the PBPs, contributing to the successful spread of these lineages in the last 20 years. METHODS: Sixty-six SS9 isolates from cases of streptococcosis in pigs were investigated for susceptibility to penicillin, ceftiofur and ampicillin. The isolates were characterized for ST, virulence profile, and antimicrobial resistance genes through WGS. Multiple linear regression models were employed to investigate the associations between STs, year of isolation, substitutions at the PBPs and an increase in MIC values to ß-lactams. RESULTS: MIC values to penicillin increased by 4% each year in the study period. Higher MIC values for penicillin were also positively associated with ST123, ST1540 and ST1953 compared with ST16. The PBP sequences presented a mosaic organization of blocks. Within the same ST, substitutions at the PBPs were generally more frequent in recent isolates. Resistance to penicillin was driven by substitutions at PBP2b, including K479T, D512E and K513E, and PBP2x, including T551S, while reduced susceptibility to ceftiofur and ampicillin were largely dependent on substitutions at PBP2x. CONCLUSIONS: Here, we identify the STs and substitutions at the PBPs responsible for increased resistance of SS9 to penicillin on Italian pig farms. Our data highlight the need for monitoring the evolution of S. suis in the coming years.


Subject(s)
Aminoacyltransferases , Cephalosporins , Streptococcus suis , Animals , Swine , Penicillins/pharmacology , Penicillin-Binding Proteins/genetics , Streptococcus suis/genetics , Bacterial Proteins/genetics , Streptococcus pneumoniae/genetics , Serogroup , Aminoacyltransferases/genetics , Microbial Sensitivity Tests , Penicillin Resistance/genetics , Genomics , Ampicillin , Clone Cells , Anti-Bacterial Agents/pharmacology
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