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1.
Radiol Oncol ; 58(3): 406-415, 2024 Sep 01.
Article in English | MEDLINE | ID: mdl-39287162

ABSTRACT

BACKGROUND: Administering gadolinium-based contrast agent before electroporation allows the contrast agent to enter the cells and enables MRI assessment of reversibly electroporated regions. The aim of this study was evaluation of contrast agent entrapment in Chinese hamster ovary (CHO) cells and comparison of these results with those determined by standard in vitro methods for assessing cell membrane permeability, cell membrane integrity and cell survival following electroporation. MATERIALS AND METHODS: Cell membrane permeabilization and cell membrane integrity experiments were performed using YO-PRO-1 dye and propidium iodide, respectively. Cell survival experiments were performed by assessing metabolic activity of cells using MTS assay. The entrapment of gadolinium-based contrast agent gadobutrol inside the cells was evaluated using T1 relaxometry of cell suspensions 25 min and 24 h after electroporation and confirmed by inductively coupled plasma mass spectrometry. RESULTS: Contrast agent was detected 25 min and 24 h after the delivery of electric pulses in cells that were reversibly electroporated. In addition, contrast agent was present in irreversibly electroporated cells 25 min after the delivery of electric pulses but was no longer detected in irreversibly electroporated cells after 24 h. Inductively coupled plasma mass spectrometry showed a proportional decrease in gadolinium content per cell with shortening of T1 relaxation time (R 2 = 0.88 and p = 0.0191). CONCLUSIONS: Our results demonstrate that the contrast agent is entrapped in cells exposed to reversible electroporation but exits from cells exposed to irreversible electroporation within 24 h, thus confirming the hypothesis on which detection experiments in vivo were based.


Subject(s)
Cell Survival , Contrast Media , Cricetulus , Electroporation , Magnetic Resonance Imaging , Organometallic Compounds , Animals , Electroporation/methods , CHO Cells , Magnetic Resonance Imaging/methods , Organometallic Compounds/pharmacokinetics , Cricetinae , Cell Membrane Permeability
2.
J Gen Physiol ; 156(11)2024 Nov 04.
Article in English | MEDLINE | ID: mdl-39302317

ABSTRACT

Two closely related connexins, Cx26 and Cx30, share widespread expression in the cochlear cellular networks. Gap junction channels formed by these connexins have been shown to have different permeability profiles, with Cx30 showing a strongly reduced preference for anionic tracers. The pore-forming segment of the first extracellular loop, E1, identified by computational studies of the Cx26 crystal structure to form a parahelix and a narrowed region of the pore, differs at a single residue at position 49. Cx26 contains an Ala and Cx30, a charged Glu at this position, and cysteine scanning in hemichannels identified this position to be pore-lining. To assess whether the Ala/Glu difference affects permeability, we modeled and quantified Lucifer Yellow transfer between HeLa cell pairs expressing WT Cx26 and Cx30 and variants that reciprocally substituted Glu and Ala at position 49. Cx26(A49E) and Cx30(E49A) substitutions essentially reversed the Lucifer Yellow permeability profile when accounting for junctional conductance. Moreover, by using a calcein efflux assay in single cells, we observed a similar reduced anionic preference in undocked Cx30 hemichannels and a reversal with reciprocal Ala/Glu substitutions. Thus, our data indicate that Cx26 and Cx30 gap junction channels and undocked hemichannels retain similar permeability characteristics and that a single residue difference in their E1 domains can largely account for their differential permeabilities to anionic tracers. The higher anionic permeability of Cx26 compared with Cx30 suggests that these connexins may serve distinct signaling functions in the cochlea, perhaps reflected in the vastly higher prevalence of Cx26 mutations in human deafness.


Subject(s)
Connexin 26 , Connexin 30 , Gap Junctions , Humans , Connexin 26/metabolism , Connexin 26/genetics , HeLa Cells , Connexin 30/metabolism , Connexin 30/genetics , Gap Junctions/metabolism , Connexins/metabolism , Connexins/genetics , Anions/metabolism , Permeability , Glutamic Acid/metabolism , Alanine/metabolism , Alanine/genetics , Isoquinolines/metabolism , Cell Membrane Permeability/physiology
3.
Molecules ; 29(17)2024 Aug 28.
Article in English | MEDLINE | ID: mdl-39274926

ABSTRACT

The growth of (multi)drug resistance in bacteria is among the most urgent global health issues. Monocationic amphiphilic α-hydrazido acid derivatives are structurally simple mimics of antimicrobial peptides (AMPs) with fewer drawbacks. Their mechanism of membrane permeabilization at subtoxic concentrations was found to begin with an initial electrostatic attraction of isolated amphiphile molecules to the phospholipid heads, followed by a rapid insertion of the apolar portions. As the accumulation into the bilayer proceeded, the membrane increased its fluidity and permeability without being subjected to major structural damage. After having ascertained that α-hydrazido acid amphiphiles do not interact with bacterial DNA, they were subjected to synergy evaluation for combinations with conventional antibiotics. Synergy was observed for combinations with tetracycline against sensitive S. aureus and E. coli, as well as with ciprofloxacin and colistin against resistant strains. Additivity with a remarkable recovery in activity of conventional antibiotics (from 2-fold to ≥32-fold) together with largely subtoxic concentrations of α-hydrazido acid derivatives was found for combinations with ciprofloxacin toward susceptible S. aureus and methicillin toward MRSa. However, no potentiation of conventional antibiotics was observed for combinations with linezolid and gentamicin against the corresponding resistant S. aureus and E. coli strains.


Subject(s)
Anti-Bacterial Agents , Cell Membrane Permeability , Drug Synergism , Escherichia coli , Microbial Sensitivity Tests , Staphylococcus aureus , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/chemistry , Cell Membrane Permeability/drug effects , Escherichia coli/drug effects , Staphylococcus aureus/drug effects , Ciprofloxacin/pharmacology , Ciprofloxacin/chemistry , Drug Resistance, Bacterial/drug effects , Drug Resistance, Multiple, Bacterial/drug effects , Colistin/pharmacology , Colistin/chemistry
4.
Nat Commun ; 15(1): 8008, 2024 Sep 13.
Article in English | MEDLINE | ID: mdl-39271671

ABSTRACT

Upon stimulation of membrane receptors, nicotinic acid adenine dinucleotide phosphate (NAADP) is formed as second messenger within seconds and evokes Ca2+ signaling in many different cell types. Here, to directly stimulate NAADP signaling, MASTER-NAADP, a Membrane permeAble, STabilized, bio-rEversibly pRotected precursor of NAADP is synthesized and release of its active NAADP mimetic, benzoic acid C-nucleoside, 2'-phospho-3'F-adenosine-diphosphate, by esterase digestion is confirmed. In the presence of NAADP receptor HN1L/JPT2 (hematological and neurological expressed 1-like protein, HN1L, also known as Jupiter microtubule-associated homolog 2, JPT2), this active NAADP mimetic releases Ca2+ and increases the open probability of type 1 ryanodine receptor. When added to intact cells, MASTER-NAADP initially evokes single local Ca2+ signals of low amplitude. Subsequently, also global Ca2+ signaling is observed in T cells, natural killer cells, and Neuro2A cells. In contrast, control compound MASTER-NADP does not stimulate Ca2+ signaling. Likewise, in cells devoid of HN1L/JPT2, MASTER-NAADP does not affect Ca2+ signaling, confirming that the product released from MASTER-NAADP is a bona fide NAADP mimetic.


Subject(s)
Calcium Signaling , Calcium , NADP , NADP/analogs & derivatives , NADP/metabolism , Animals , Humans , Calcium/metabolism , Mice , Second Messenger Systems , Cell Membrane Permeability , Ryanodine Receptor Calcium Release Channel/metabolism , Killer Cells, Natural/metabolism , T-Lymphocytes/metabolism
5.
Int J Mol Sci ; 25(16)2024 Aug 12.
Article in English | MEDLINE | ID: mdl-39201461

ABSTRACT

Electroporation-based procedures employing nanosecond bipolar pulses are commonly linked to an undesirable phenomenon known as the cancelation effect. The cancellation effect arises when the second pulse partially or completely neutralizes the effects of the first pulse, simultaneously diminishing cells' plasma membrane permeabilization and the overall efficiency of the procedure. Introducing a temporal gap between the positive and negative phases of the bipolar pulses during electroporation procedures may help to overcome the cancellation phenomenon; however, the exact thresholds are not yet known. Therefore, in this work, we have tested the influence of different interphase delay values (from 0 ms to 95 ms) using symmetric bipolar nanoseconds (300 and 500 ns) on cell permeabilization using 10 Hz, 100 Hz, and 1 kHz protocols. As a model mouse hepatoma, the MH-22a cell line was employed. Additionally, we conducted in vitro electrochemotherapy with cisplatin, employing reduced interphase delay values (0 ms and 0.1 ms) at 10 Hz. Cell plasma membrane permeabilization and viability dependence on a variety of bipolar pulsed electric field protocols were characterized. It was shown that it is possible to minimize bipolar cancellation, enabling treatment efficiency comparable to monophasic pulses with identical parameters. At the same time, it was highlighted that bipolar cancellation has a significant influence on permeabilization, while the effects on the outcome of electrochemotherapy are minimal.


Subject(s)
Cell Membrane Permeability , Electrochemotherapy , Electrochemotherapy/methods , Animals , Mice , Cell Membrane Permeability/drug effects , Cell Line, Tumor , Electroporation/methods , Cisplatin/pharmacology , Cell Membrane/metabolism , Cell Membrane/drug effects , Cell Survival/drug effects , Carcinoma, Hepatocellular/drug therapy , Antineoplastic Agents/pharmacology
6.
Anal Methods ; 16(36): 6193-6200, 2024 Sep 19.
Article in English | MEDLINE | ID: mdl-39189983

ABSTRACT

Mitochondrial sulfur dioxide (SO2) plays a double-edged role in cells, and the real-time and in situ tracing of its dynamic behaviors to elucidate its complicated functions in detail is of great significance. Here, we developed a simple mitochondria-targeted fluorescent probe ZW for tracing SO2 with good membrane permeability. In probe ZW, the 1-phenylpyrrolidine-decorated benzopyrylium unit is employed as the selective response site for SO2. Besides, it also acts as the main fluorophore for signal conversion. The spectral results displayed that ZW could emit near-infrared (NIR) fluorescence (670 nm) and has a highly sensitive and selective response to SO2 (LOD = 0.19 µM). For biological imaging, compared with the control probe ZE, concentration- and time-dependent results verified that probe ZW has remarkable cell delivery with low concentration (200 nM) and fast response time (3 min). Furthermore, the NIR emission of ZW rendered high-fidelity imaging in living cells. Owing to its positive charge, ZW showed favorable mitochondria-targeting properties by colocalization experiments. Probe ZW could detect SO2 in real-time and in situ with high photostability in cells. Significantly, it has the ability to monitor the changes of endogenous SO2 during ferroptosis.


Subject(s)
Ferroptosis , Fluorescent Dyes , Mitochondria , Sulfur Dioxide , Fluorescent Dyes/chemistry , Mitochondria/metabolism , Sulfur Dioxide/chemistry , Sulfur Dioxide/analysis , Sulfur Dioxide/metabolism , Humans , Ferroptosis/drug effects , Optical Imaging/methods , HeLa Cells , Cell Membrane Permeability
7.
Am J Physiol Cell Physiol ; 327(4): C913-C928, 2024 Oct 01.
Article in English | MEDLINE | ID: mdl-39159387

ABSTRACT

Confluent populations of the epithelial cell line, MDCK II, develop circumferential tight junctions joining adjacent cells to create a barrier to the paracellular movement of solutes and water. Treatment of MDCK II cell populations from the apical surface with 1 mM Na-caprate increased permeability to macromolecules (Leak Pathway) without increasing monolayer disruption or cell death. Graphical analysis of the apparent permeability versus solute Stokes radius for a size range of fluorescein-dextran species indicates apical 1 mM Na-caprate enhances Leak Pathway permeability by increasing the number of Leak Pathway openings without significantly affecting opening size. Na-caprate treatment did not alter the content of any tight junction protein examined. Treatment of MDCK II cell populations with apical 1 mM Na-caprate disrupted basal F-actin stress fibers and decreased the tortuosity of the tight junctions. Treatment of MDCK II cell populations with blebbistatin, a myosin ATPase inhibitor, alone had little effect on Leak Pathway permeability but synergistically increased Leak Pathway permeability when added with 1 mM Na-caprate. Na-caprate exhibited a similar ability to increase Leak Pathway permeability in wild-type MDCK II cell monolayers and ZO-1 knockdown MDCK II cell monolayers but an enhanced ability to increase Leak Pathway permeability in monolayers of TOCA-1 knockout MDCK II cells. These results demonstrate that Na-caprate increases MDCK II cell population Leak Pathway permeability by increasing the number of Leak Pathway openings. This action is likely mediated by alterations in F-actin organization, primarily involving disruption of basal F-actin stress fibers.NEW & NOTEWORTHY This study determines the underlying change in the openings in the epithelial tight junction permeability barrier structure that leads to a change in the paracellular permeability to macromolecules (the Leak Pathway) and connects this to disruption of specific F-actin structures within the cells. It provides important and novel insights into how tight junction permeability to macromolecules is modulated by specific changes to cellular and tight junction composition/organization.


Subject(s)
Actins , Epithelial Cells , Tight Junctions , Dogs , Animals , Actins/metabolism , Madin Darby Canine Kidney Cells , Epithelial Cells/metabolism , Epithelial Cells/drug effects , Tight Junctions/metabolism , Tight Junctions/drug effects , Cell Membrane Permeability/drug effects , Zonula Occludens-1 Protein/metabolism , Zonula Occludens-1 Protein/genetics , Heterocyclic Compounds, 4 or More Rings/pharmacology , Actin Cytoskeleton/metabolism
8.
Int J Biol Macromol ; 278(Pt 3): 134634, 2024 Oct.
Article in English | MEDLINE | ID: mdl-39128760

ABSTRACT

Bacterial resistance to antibiotics is a significant challenge that is associated with increased morbidity and mortality. Gram-negative bacteria are particularly problematic due to an outer membrane (OM). Current alternatives to antibiotics include antimicrobial peptides or proteins and multifunctional systems such as dendrimers. Antimicrobial proteins such as lysins can degrade the bacterial cell wall, whereas dendrimers can permeabilize the OM, enhancing the activity of endolysins against gram-negative bacteria. In this study, we present a three-stage action of endolysin combined with two different carbosilane (CBS) silver metallodendrimers, in which the periphery is modified with N-heterocyclic carbene (NHC) ligands coordinating a silver atom. The different NHC ligands contained hydrophobic methyl or N-donor pyridyl moieties. The effects of these endolysin/dendrimer combinations are based on OM permeabilization, peptidoglycan degradation, and reactive oxygen species production. The results showed that CBS possess a permeabilization effect (first action), significantly reduced bacterial growth at higher concentrations alone and in the presence of endolysin, increased ROS production (second action), and led to bacterial cell damage (third action). The complex formed between the CHAP domain of endolysin and a CBS silver metallodendrimer, with a triple mechanism of action, may represent an excellent alternative to other antimicrobials with only one resistance mechanism.


Subject(s)
Anti-Bacterial Agents , Dendrimers , Endopeptidases , Gram-Negative Bacteria , Peptidoglycan , Reactive Oxygen Species , Silanes , Peptidoglycan/metabolism , Peptidoglycan/chemistry , Reactive Oxygen Species/metabolism , Silanes/chemistry , Silanes/pharmacology , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/chemistry , Dendrimers/chemistry , Dendrimers/pharmacology , Endopeptidases/metabolism , Endopeptidases/chemistry , Gram-Negative Bacteria/drug effects , Microbial Sensitivity Tests , Silver/chemistry , Silver/pharmacology , Protein Domains , Cell Membrane Permeability/drug effects
9.
Chem Commun (Camb) ; 60(69): 9242-9245, 2024 Aug 22.
Article in English | MEDLINE | ID: mdl-39115107

ABSTRACT

We designed and synthesized an N-ortho-nitrobenzylated benzanilide-based amino acid having a cis-amide structure that facilitates cyclization of peptides containing it. Photo-induced removal of the nitrobenzyl group from this residue in the resulting cyclized peptides dramatically alters their conformation and passive membrane permeability via complete cis-amide to trans-amide conversion.


Subject(s)
Amino Acids , Cell Membrane Permeability , Peptides, Cyclic , Peptides, Cyclic/chemistry , Peptides, Cyclic/metabolism , Amino Acids/chemistry , Anilides/chemistry , Nitrobenzenes/chemistry , Cyclization , Protein Conformation
10.
Int J Pharm ; 662: 124544, 2024 Sep 05.
Article in English | MEDLINE | ID: mdl-39094920

ABSTRACT

Periodontitis is a chronic inflammatory disease that causes destruction of the periodontium and eventual tooth loss. The priority in the periodontal treatment is to remove the subgingival biofilm. Chemical removal of biofilms using antimicrobial agents has been applied in clinical practice. However, their clinical effect is still limited because the agents must overcome biofilm's significant drug tolerance, which is primarily caused by the extracellular matrix, a physical barrier that attenuates drug diffusion. This study aimed to study the use of ionic liquids (ILs), a new class of biocompatible materials, for controlling subgingival biofilms because of their excellent permeability. Choline and geranate (CAGE) IL was tested for its highly potent antiseptic behavior and permeability. Antibacterial tests revealed that the significant efficacy of CAGE against periodontopathic microorganisms was derived from their ability to destroy cell membrane, as demonstrated by membrane permeability assay and transmission electron microscopy imaging. Antibiofilm tests using two pathogenic biofilm models revealed that CAGE exerted efficacy against the biofilm-embedded bacteria, conspicuously neutralized the biofilms, and eventually destroyed the biofilm structure. Furthermore, the penetration of CAGE into the biofilm was visually confirmed using confocal laser scanning microscopy. This study highlighted the potential of CAGE as a powerful antibiofilm therapeutic.


Subject(s)
Anti-Bacterial Agents , Biofilms , Choline , Ionic Liquids , Biofilms/drug effects , Choline/chemistry , Ionic Liquids/chemistry , Ionic Liquids/pharmacology , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/administration & dosage , Anti-Bacterial Agents/chemistry , Periodontitis/drug therapy , Periodontitis/microbiology , Cell Membrane Permeability/drug effects
11.
Biomolecules ; 14(8)2024 Aug 13.
Article in English | MEDLINE | ID: mdl-39199383

ABSTRACT

Herein, we investigated the toxicity and membrane-permeabilizing capabilities of Lpt and Lpt-like peptides, belonging to type I toxin-antitoxin systems carried by plasmid DNA of Lacticaseibacillus strains. These 29 amino acid peptides are predicted to form α-helical structures with a conserved central hydrophobic sequence and differently charged hydrophilic termini. Like Lpt, the expression of Lpt-like in E. coli induced growth arrest, nucleoid condensation, and cell membrane damage, suggesting membrane interaction as the mode of action. The membrane permeabilization activity of both peptides was evaluated by using liposome leakage assays, dynamic light scattering, and CD spectroscopy. Lpt and Lpt-like showed liposome leakage activity, which did not lead to liposome disruption but depended on peptide concentration. Lpt was generally more effective than Lpt-like, probably due to different physical chemical properties. Leakage was significantly reduced in larger liposomes and increased with negatively charged PCPS liposomes, indicating that electrostatic interactions and membrane curvature influence peptide activity. Contrary to most membrane-active peptides, Lpt an Lpt-like progressively lost their α-helical structure upon interaction with liposomes. Our data are inconsistent with the formation of membrane-spanning peptide pores but support a mechanism relying on the transient failure of the membrane permeability barrier possibly through the formation of "lipid pores".


Subject(s)
Cell Membrane Permeability , Escherichia coli , Liposomes , Liposomes/chemistry , Liposomes/metabolism , Escherichia coli/metabolism , Escherichia coli/genetics , Peptides/chemistry , Peptides/metabolism , Cell Membrane/metabolism , Cell Membrane/chemistry , Amino Acid Sequence
12.
Brief Bioinform ; 25(5)2024 Jul 25.
Article in English | MEDLINE | ID: mdl-39210505

ABSTRACT

Cyclic peptides are versatile therapeutic agents that boast high binding affinity, minimal toxicity, and the potential to engage challenging protein targets. However, the pharmaceutical utility of cyclic peptides is limited by their low membrane permeability-an essential indicator of oral bioavailability and intracellular targeting. Current machine learning-based models of cyclic peptide permeability show variable performance owing to the limitations of experimental data. Furthermore, these methods use features derived from the whole molecule that have traditionally been used to predict small molecules and ignore the unique structural properties of cyclic peptides. This study presents CycPeptMP: an accurate and efficient method to predict cyclic peptide membrane permeability. We designed features for cyclic peptides at the atom-, monomer-, and peptide-levels and seamlessly integrated these into a fusion model using deep learning technology. Additionally, we applied various data augmentation techniques to enhance model training efficiency using the latest data. The fusion model exhibited excellent prediction performance for the logarithm of permeability, with a mean absolute error of $0.355$ and correlation coefficient of $0.883$. Ablation studies demonstrated that all feature levels contributed and were relatively essential to predicting membrane permeability, confirming the effectiveness of augmentation to improve prediction accuracy. A comparison with a molecular dynamics-based method showed that CycPeptMP accurately predicted peptide permeability, which is otherwise difficult to predict using simulations.


Subject(s)
Cell Membrane Permeability , Peptides, Cyclic , Peptides, Cyclic/chemistry , Peptides, Cyclic/metabolism , Machine Learning , Deep Learning , Computational Biology/methods
13.
Nat Commun ; 15(1): 7281, 2024 Aug 23.
Article in English | MEDLINE | ID: mdl-39179607

ABSTRACT

Membrane active peptides are known to porate lipid bilayers, but their exact permeabilization mechanism and the structure of the nanoaggregates they form in membranes have often been difficult to determine experimentally. For many sequences at lower peptide concentrations, transient leakage is observed in experiments, suggesting the existence of transient pores. For two well-know peptides, alamethicin and melittin, we show here that molecular mechanics simulations i) can directly distinguish equilibrium poration and non-equilibrium transient leakage processes, and ii) can be used to observe the detailed pore structures and mechanism of permeabilization in both cases. Our results are in very high agreement with numerous experimental evidence for these two peptides. This suggests that molecular simulations can capture key membrane poration phenomena directly and in the future may develop to be a useful tool that can assist experimental peptide design.


Subject(s)
Lipid Bilayers , Melitten , Molecular Dynamics Simulation , Melitten/chemistry , Melitten/metabolism , Lipid Bilayers/metabolism , Lipid Bilayers/chemistry , Alamethicin/chemistry , Alamethicin/metabolism , Cell Membrane Permeability , Permeability
14.
Mar Drugs ; 22(8)2024 Jul 25.
Article in English | MEDLINE | ID: mdl-39195451

ABSTRACT

Aquaporins (AQPs) are a family of integral membrane proteins that selectively transport water and glycerol across the cell membrane. Because AQPs are involved in a wide range of physiological functions and pathophysiological conditions, AQP-based therapeutics may have the broad potential for clinical utility, including for disorders of water and energy balance. However, AQP modulators have not yet been developed as suitable candidates for clinical applications. In this study, to identify potential modulators of AQPs, we screened 31 natural products by measuring the water and glycerol permeability of mouse erythrocyte membranes using a stopped-flow light scattering method. None of the tested natural compounds substantially affected the osmotic water permeability. However, several compounds considerably affected the glycerol permeability. Stichoposide C increased the glycerol permeability of mouse erythrocyte membranes, whereas rhizochalin decreased it at nanomolar concentrations. Immunohistochemistry revealed that AQP7 was the main aquaglyceroporin in mouse erythrocyte membranes. We further verified the effects of stichoposide C and rhizochalin on aquaglyceroporins using human AQP3-expressing keratinocyte cells. Stichoposide C, but not stichoposide D, increased AQP3-mediated transepithelial glycerol transport, whereas the peracetyl aglycon of rhizochalin was the most potent inhibitor of glycerol transport among the tested rhizochalin derivatives. Collectively, stichoposide C and the peracetyl aglycon of rhizochalin might function as modulators of AQP3 and AQP7, and suggests the possibility of these natural products as potential drug candidates for aquaglyceroporin modulators.


Subject(s)
Aquaglyceroporins , Glycerol , Animals , Mice , Aquaglyceroporins/metabolism , Humans , Glycerol/metabolism , Water/chemistry , Water/metabolism , Erythrocyte Membrane/drug effects , Erythrocyte Membrane/metabolism , Aquaporin 3/metabolism , Keratinocytes/drug effects , Keratinocytes/metabolism , Biological Transport/drug effects , Aquaporins/metabolism , Cell Membrane Permeability/drug effects
15.
ACS Infect Dis ; 10(9): 3332-3345, 2024 Sep 13.
Article in English | MEDLINE | ID: mdl-39116454

ABSTRACT

Primary amoebic meningoencephalitis is caused by the free-living amoeba Naegleria fowleri. The lack of standardized treatment has significantly contributed to the high fatality rates observed in reported cases. Therefore, this study aims to explore the anti-Naegleria activity of eight synthesized cyanoacrylamides and 5-iminopyrrol-2-ones. Notably, QOET-109, QOET-111, QOET-112, and QOET-114 exhibited a higher selectivity index against Naegleria compared to those of the rest of the compounds. Subsequently, these chemicals were assessed against the resistant stage of N. fowleri, demonstrating activity similar to that observed in the vegetative stage. Moreover, characteristic events of programmed cell death were evidenced, including chromatin condensation, increased plasma membrane permeability, mitochondrial damage, and heightened oxidative stress, among others. Finally, this research demonstrated the in vitro activity of the cyanoacrylamide and 5-iminopyrrol-2-one molecules, as well as the induction of metabolic event characteristics of regulated cell death in Naegleria fowleri.


Subject(s)
Acrylamides , Naegleria fowleri , Naegleria fowleri/drug effects , Acrylamides/pharmacology , Acrylamides/chemistry , Antiprotozoal Agents/pharmacology , Antiprotozoal Agents/chemical synthesis , Antiprotozoal Agents/chemistry , Oxidative Stress/drug effects , Apoptosis/drug effects , Cell Membrane Permeability/drug effects
16.
J Med Chem ; 67(16): 13765-13777, 2024 Aug 22.
Article in English | MEDLINE | ID: mdl-38976596

ABSTRACT

Permeability is a key factor driving the absorption of orally administered drugs. In early discovery, the efficient evaluation of permeability, particularly for compounds violating Lipinski's Rule of 5, remains challenging. Addressing this, we established a high-throughput method to measure the experimental polar surface area (HT-EPSA) as an in vitro surrogate to measure permeability. Compared to earlier methods, HT-EPSA significantly reduces data acquisition time with enhanced sensitivity, selectivity, and data quality. In the effort of translating EPSA to human in vitro and in vivo passive permeability, we demonstrated the application of EPSA for predicting Caco-2 cell and human intestinal permeability, showing improvements over topological polar surface area and the parallel artificial membrane permeability assay for rank-ordering permeability in a proteolysis targeting chimera case study. The HT-EPSA method is expected to be highly beneficial in guiding early stage compound rank-ordering, faster decision-making, and in predicting in vitro and/or in vivo human intestinal permeability.


Subject(s)
High-Throughput Screening Assays , Permeability , Tandem Mass Spectrometry , Humans , Caco-2 Cells , High-Throughput Screening Assays/methods , Tandem Mass Spectrometry/methods , Intestinal Absorption , Cell Membrane Permeability , Animals
17.
Bioinformatics ; 40(8)2024 08 02.
Article in English | MEDLINE | ID: mdl-39067027

ABSTRACT

MOTIVATION: There has been a burgeoning interest in cyclic peptide therapeutics due to their various outstanding advantages and strong potential for drug formation. However, it is undoubtedly costly and inefficient to use traditional wet lab methods to clarify their biological activities. Using artificial intelligence instead is a more energy-efficient and faster approach. MuCoCP aims to build a complete pre-trained model for extracting potential features of cyclic peptides, which can be fine-tuned to accurately predict cyclic peptide bioactivity on various downstream tasks. To maximize its effectiveness, we use a novel data augmentation method based on a priori chemical knowledge and multiple unsupervised training objective functions to greatly improve the information-grabbing ability of the model. RESULTS: To assay the efficacy of the model, we conducted validation on the membrane-permeability of cyclic peptides which achieved an accuracy of 0.87 and R-squared of 0.503 on CycPeptMPDB using semi-supervised training and obtained an accuracy of 0.84 and R-squared of 0.384 using a model with frozen parameters on an external dataset. This result has achieved state-of-the-art, which substantiates the stability and generalization capability of MuCoCP. It means that MuCoCP can fully explore the high-dimensional information of cyclic peptides and make accurate predictions on downstream bioactivity tasks, which will serve as a guide for the future de novo design of cyclic peptide drugs and promote the development of cyclic peptide drugs. AVAILABILITY AND IMPLEMENTATION: All code used in our proposed method can be found at https://github.com/lennonyu11234/MuCoCP.


Subject(s)
Neural Networks, Computer , Peptides, Cyclic , Peptides, Cyclic/chemistry , Machine Learning , Cell Membrane Permeability
18.
Biosci Rep ; 44(7)2024 Jul 31.
Article in English | MEDLINE | ID: mdl-39011584

ABSTRACT

Botulinum neurotoxins (BoNTs) are valuable tools to unveil molecular mechanisms of exocytosis in neuronal and non-neuronal cells due to their peptidase activity on exocytic isoforms of SNARE proteins. They are produced by Clostridia as single-chain polypeptides that are proteolytically cleaved into light, catalytic domains covalently linked via disulfide bonds to heavy, targeting domains. This format of two subunits linked by disulfide bonds is required for the full neurotoxicity of BoNTs. We have generated a recombinant version of BoNT/B that consists of the light chain of the toxin fused to the protein transduction domain of the human immunodeficiency virus-1 (TAT peptide) and a hexahistidine tag. His6-TAT-BoNT/B-LC, expressed in Escherichia coli and purified by affinity chromatography, penetrated membranes and exhibited strong enzymatic activity, as evidenced by cleavage of the SNARE synaptobrevin from rat brain synaptosomes and human sperm cells. Proteolytic attack of synaptobrevin hindered exocytosis triggered by a calcium ionophore in the latter. The novel tool reported herein disrupts the function of a SNARE protein within minutes in cells that may or may not express the receptors for the BoNT/B heavy chain, and without the need for transient transfection or permeabilization.


Subject(s)
Botulinum Toxins, Type A , Exocytosis , Animals , Humans , Rats , Botulinum Toxins, Type A/metabolism , Botulinum Toxins, Type A/genetics , Botulinum Toxins, Type A/isolation & purification , SNARE Proteins/metabolism , SNARE Proteins/genetics , Male , Synaptosomes/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Recombinant Fusion Proteins/metabolism , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/isolation & purification , Recombinant Proteins/metabolism , Recombinant Proteins/isolation & purification , Recombinant Proteins/genetics , Cell Membrane Permeability/drug effects , Botulinum Toxins/metabolism , Botulinum Toxins/genetics , Botulinum Toxins/chemistry , Botulinum Toxins/isolation & purification
19.
Bioorg Med Chem ; 111: 117849, 2024 Sep 01.
Article in English | MEDLINE | ID: mdl-39068873

ABSTRACT

The search for new agents targeting different forms of cell death is an important research focus for developing new and potent antitumor therapies. As a contribution to this endeavor, we have designed and synthesized a series of new substituted 3,4-dihydro-2H-1,4-benzoxazine derivatives. These compounds have been evaluated for their efficacy against MCF-7 breast cancer and HCT-116 colon cancer cell lines. Overall, substituting this heterocycle led to improved antiproliferative activity compared to the unsubstituted derivative 1. The most active compounds, 2b and 4b, showed IC50 values of 2.27 and 3.26 µM against MCF-7 cells and 4.44 and 7.63 µM against HCT-116 cells, respectively. To investigate the mechanism of action of the target compounds, the inhibition profile of 8 kinases involved in cell signaling was studied highlighting residual activity on HER2 and JNK1 kinases. 2b and 4b showed a consistent binding mode to both receptor kinases, establishing significant interactions with known and catalytically important domains and residues. Compounds 2b and 4b exhibit potent cytotoxic activity by disrupting cell membrane permeability, likely triggering both inflammatory and non-inflammatory cell death mechanisms. This dual capability increases their versatility in the treatment of different stages or types of tumors, providing greater flexibility in clinical applications.


Subject(s)
Antineoplastic Agents , Benzoxazines , Cell Membrane Permeability , Cell Proliferation , Drug Screening Assays, Antitumor , Humans , Antineoplastic Agents/pharmacology , Antineoplastic Agents/chemistry , Antineoplastic Agents/chemical synthesis , Benzoxazines/chemistry , Benzoxazines/pharmacology , Benzoxazines/chemical synthesis , Structure-Activity Relationship , Cell Membrane Permeability/drug effects , Cell Proliferation/drug effects , Cell Death/drug effects , Molecular Structure , Protein Kinase Inhibitors/pharmacology , Protein Kinase Inhibitors/chemistry , Protein Kinase Inhibitors/chemical synthesis , Dose-Response Relationship, Drug , HCT116 Cells , MCF-7 Cells
20.
Int J Mol Sci ; 25(13)2024 Jun 27.
Article in English | MEDLINE | ID: mdl-39000152

ABSTRACT

Global public health is facing a major issue with emerging resistance to antimicrobial agents. Antimicrobial agents that are currently on the market are strong and efficient, but it has not been ruled out that these medications will eventually cause resistance to bacteria. Exploring novel bioactive compounds derived from natural sources is therefore, crucial to meet future demands. The present study evaluated the mode of action of the antimicrobial potential protease enzyme SH21. Protease SH21 exhibited antimicrobial activity, strong heat stability (up to 100 °C), and pH stability (pH 3.0 to 9.0). In terms of mode of action, we found that protease SH21 was able to disrupt the bacterial cell membrane as the results of the nucleotide leakage and cell membrane permeability assay. In addition, we also checked inner membrane permeability by PI uptake assay which suggested that protease SH21 has the ability to enter the bacterial cell membrane. Our results revealed that the antimicrobial protease SH21 might be a promising candidate for treating microbial infections.


Subject(s)
Bacillus , Microbial Sensitivity Tests , Cell Membrane/drug effects , Cell Membrane/metabolism , Cell Membrane Permeability/drug effects , Peptide Hydrolases/metabolism , Hydrogen-Ion Concentration , Anti-Infective Agents/pharmacology , Anti-Infective Agents/chemistry , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/chemistry , Bacterial Proteins/metabolism , Enzyme Stability
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