Search Results (25)

Background: The Fc region of immunoglobulin G (IgG) is a key target in therapeutic and analytical applications, such as antibody purification and site-specific bioconjugation. Although Protein A exhibits strong Fc-binding affinity, its large molecular weight and limited chemical flexibility pose challenges for use in compact or chemically defined systems. To address these limitations, we designed two α-helical peptides, SpA h1 and SpA h2, based on the Fc-binding helices of the Z34C domain from Staphylococcus aureus Protein A. Method: To enhance the structural stability and Fc-binding capability of these peptides, a lactam-based stapling strategy was employed by introducing lysine and glutamic acid residues at positions i and i + 4. Result: The resulting stapled peptides, (s)SpA h1 and (s)SpA h2, exhibited significantly improved α-helical content and IgG-binding performance, as demonstrated by circular dichroism (CD) spectroscopy and fluorescence-based IgG capture assays. Surface plasmon resonance (SPR) analysis confirmed specific, concentration-dependent interactions with the Fc region of human IgG, with (s)SpA h1 consistently showing the binding affinity and stability. Proteolytic resistance assays using α-chymotrypsin revealed that (s)SpA h1 maintained its structural integrity over time, exhibiting markedly enhanced resistance to enzymatic degradation compared to its linear counterpart. Furthermore, (s)SpA h1 exhibited strong Fc selectivity with minimal Fab affinity, confirming its suitability as a compact and Fc-specific binding ligand. Conclusions: These results confirm the successful design and development of structurally reinforced Fc-binding peptides that overcome the inherent limitations of short linear sequences through both high-affinity sequence optimization and lactam-based stapling. Among them, (s)SpA h1 demonstrates the most promising characteristics as a compact yet stable Fc-binding ligand, suitable for applications such as antibody purification and site-specific bioconjugation. Full article

The growing emergence of multidrug-resistant bacterial pathogens drives the need for new antibacterial agents. Punicalagin exhibits efficacy against methicillin-resistant Staphylococcus aureus (MRSA), but its specific antibacterial mechanisms remain unclear. This study unveiled the specific antibacterial mechanism of punicalagin against MRSA via phenotypic and transcriptomic analyses. Punicalagin was found to induce severe cell wall damage and membrane disruption. Competitive binding assays identified lipoteichoic acid (LTA) as a potential target, and transcriptomic analysis further revealed that punicalagin downregulated key genes involved in cell wall synthesis (murA, murE) and LTA biosynthesis (dltA-D), consistent with the disruption of the cell wall. Additionally, punicalagin disrupted membrane homeostasis by inhibiting fatty acid synthesis (fabD, fabZ) and amino acid metabolism (dapA, dapB), leading to increased membrane permeability, which aligned with the phenotypic manifestations of membrane damage. Collectively, this work links phenotypic changes to specific gene expression patterns, unveiling that punicalagin inactivates MRSA via the multi-pathway regulation of the cell wall (LTA) and membrane function—providing insights for combating antibiotic-resistant pathogens in food safety and clinical settings. Full article

Background/Objectives: Severe malaria, mainly caused by Plasmodium falciparum, remains a significant therapeutic challenge due to increasing drug resistance and adverse effects. Flavonoids, known for their wide range of bioactivities, offer a promising route for antimalarial drug discovery. The aim of this study was to elucidate key structural features associated with antimalarial activity in flavonoids and to develop accurate, interpretable predictive models. Methods: Curated databases of flavonoid structures and their activity against P. falciparum strains and enzymes were constructed. Molecular fingerprinting and decision tree analyses were used to identify key pharmacophoric groups. Subsequently, molecular descriptors were generated and reduced to build multiple classification and regression models. Results: These models demonstrated high predictive accuracy, with test set accuracies ranging from 92.85% to 100%, and R² values from 0.64 to 0.97. Virtual screening identified novel flavonoid candidates with potential inhibitory activity. These were further evaluated using molecular docking and molecular dynamics simulations to assess binding affinity and stability with Plasmodium proteins (FabG, FabZ, and FabI). The predicted active ligands exhibited stable pharmacophore interactions with key protein residues, providing insights into binding mechanisms. Conclusions: This study provides highly predictive models for antimalarial flavonoids and enhances the understanding of structure–activity relationships, offering a strong foundation for further experimental validation. Full article

Background/Objectives: Rhamnolipids (RLs) are biosurfactants with significant industrial and environmental potential, which physicochemical properties depend greatly on their fatty acyl chain composition. This study investigated the impact of genetically modulating the fatty acid synthesis genes fabA and fabZ on RL composition and functionality in Pseudomonas aeruginosa PAO1. Methods and Results: Using temperature-sensitive mutants and suppressor strains for these essential genes, we successfully engineered RLs with altered fatty acyl chain lengths and saturation levels. LC–MS/MS analyses showed that deletion and overexpression of fabA and fabZ significantly shifted RL fatty acid profiles. Functional analyses indicated that these structural changes markedly influenced RL emulsification activity and critical micelle concentration (CMC). Conclusions: These findings demonstrate the feasibility of optimizing RL properties through targeted genetic manipulation, offering valuable insights for designing customized biosurfactants for diverse industrial and environmental applications. Full article

We used molecular docking to determine the binding energy and interactions of apigenin and 16 related flavonoids, with 24 distinct proteins having diverse biological functions. We aimed to identify potential inhibitors of these proteins and understand the structural configurations of flavonoids impacting their binding energy. Our results demonstrate that apigenin exhibits high binding energies (a surrogate for binding affinity or inhibitory potential) to all tested proteins. The strongest binding energy was −8.21 kcal/mol for p38 mitogen-activated protein kinases, while the weakest was −5.34 kcal/mol for cyclin-dependent kinase 4. Apigenin and many other flavonoids showed high binding energies on xanthine oxidase (1.1–1.5 fold of febuxostat) and DNA methyltransferases (1.1–1.2 fold of azacytidine). We uncovered high binding energies of apigenin and certain flavonoids with mutated Kirsten rat sarcoma viral oncogene homolog at G12D (KRAS G12D), G12V, and G12C. Consequently, apigenin and certain flavonoids have the potential to effectively inhibit pan-KRAS oncogenic activity, not just on specific KRAS mutations. Apigenin and certain flavonoids also have high binding energies with aromatase (involved in estrogen production) and bacterial infections, i.e., DNA gyrase B and 3R-hydroxy acyl-ACP dehydratase (FABZ). Our findings are pivotal in identifying specific flavonoids that can effectively inhibit targeted proteins, paving the way for the development of innovative flavonoid-based drugs. Full article

The arid mountainous region of Hail in Saudi Arabia has a variety of desert vegetation, some of which are conventionally used in Bedouin traditional medicine. These plants need scientific examination. This research seeks to examine Blepharis ciliaris using a thorough multi-analytical methodology that includes antibacterial and antioxidant assessments as well as computational modeling. GC–MS analysis of the methanolic extract revealed 17 organic compounds, including pentadecanoic acid, ethyl methyl ester (2.63%); hexadecanoic acid, methyl ester (1.00%); 9,12-octadecadienoic acid (Z,Z)-, methyl ester (2.74%); 9-octadecenoic acid, methyl ester (E) (2.78%); octadecanoic acid (5.88%); 9-tetradecenoic acid (Z) (3.22%); and undec-10-enoic acid, undec-2-n-1-yl ester (5.67%). The DPPH test evaluated antioxidant activity, revealing a notable increase with higher concentrations of the methanolic extract, achieving maximum inhibition of 81.54% at 1000 µg/mL. The methanolic extract exhibited moderate antibacterial activity, with average inhibition zones of 10.33 ± 1.53 mm, 13.33 ± 1.53 mm, 10.67 ± 1.53 mm, and 10.00 ± 2.00 mm against Staphylococcus aureus, Bacillus subtilis, Escherichia coli, and Serratia marcescens, respectively, as determined by the disk diffusion method. The minimum inhibitory concentration (MIC) values were 500 µg/mL for S. aureus and B. subtilis, whereas E. coli and S. marcescens showed susceptibility at 1000 µg/mL. Computational simulations were employed to assess the toxicity, drug-likeness, and ADMET profiles of compounds derived from Blepharis ciliaris. Thirteen bioactive compounds were assessed in silico against Staphylococcus aureus sortase A (PDB: 1T2O), Bacillus subtilis BsFabHb (PDB: 8VDB), Escherichia coli LPS assembly protein (LptD) (PDB: 4RHB), and a modeled Serratia marcescens outer-membrane protein TolC, focusing on cell wall and membrane structures. Compound 3, (+)-Ascorbic acid 2,6-dihexadecanoate, shown significant binding affinities to B. subtilis BsFabHb, E. coli LPS assembly protein, and S. marcescens TolC. Full article

The synthesis of tetra- and pentanorlabdane compounds with rearranged cycle B based on commercially available (+)-sclareolide is reported. Desired compounds were prepared from intermediate ketones via Baeyer–Villiger oxidation. The structures of synthesized compounds were confirmed by spectral IR, 1D (¹H, ¹³C, and DEPT), and 2D (H-COSY, H,C-HSQC, H,C-HMBC, H,N-HMBC, NOESY) NMR analyses, mass-spectrometry and single crystal X-rays diffraction. Two out of the four synthesized compounds showed high antifungal and antibacterial activities comparable to and exceeding standard antifungal (caspofungin) and antibacterial (kanamycin) agents. DFT calculations show that in gas and DCM, compound 4 is more stable than 3 with a difference in the Gibbs free energy of 23.3 kJ/mol and 20.7 kJ/mol, respectively. In water and methanol, compound 3 is slightly more stable, by 2.4 kJ/mol and 2.78 kJ/mol, respectively. Molecular docking to four targets DNA gyrase from E. coli (1KZN), Fabz from P. aeruginosa (1U1Z), dihydrofolate reductase from C. albicans (3QLS) and MurB from E. coli (2Q85) showed good agreement with the results of in vitro evaluation and confirmed the biological activity of compounds 3 and 4, with binding affinities comparable and for some targets exceeding that of Caspofungin and Kanamycin. Full article

Background: Functionalized nanoparticles (NPs) represent a cutting edge in innovative clinical approaches, allowing for the delivery of selected compounds with higher specificity in a wider time frame. They also hold promise for novel theranostic applications that integrate both diagnostic and therapeutic functions. Pathogens are continuously evolving to try to escape the strategies designed to treat them. Objectives: In this work, we describe the development of a biotechnological device, Nano-Immuno-Probes (NIPs), for early detection and infections treatment. Human Herpes Simplex Virus 2 was chosen as model pathogen. Methods: NIPs consist of PLGA-PEG-Sulfone polymeric NPs conjugated to recombinant Fab antibody fragments targeting the viral glycoprotein G2. NIPs synthesis involved multiple steps and was validated through several techniques. Results: DLS analysis indicated an expected size increase with a good polydispersity index. Z-average and z-potential values were measured for PLGA-PEG-Bis-Sulfone NPs (86.6 ± 10.9 nm; –0.7 ± 0.3 mV) and NIPs (151 ± 10.4 nm; −5.1 ± 1.9 mV). SPR assays confirmed NIPs’ specificity for the glycoprotein G2, with an apparent K_D of 1.03 ± 0.61 µM. NIPs exhibited no cytotoxic effects on VERO cells at 24 and 48 h. Conclusions: This in vitro study showed that NIPs effectively target HSV-2, suggesting the potential use of these nanodevices to deliver both contrast agents as well as therapeutic compounds. Full article

Multidrug-resistant Pseudomonas aeruginosa poses a global challenge due to its virulence and biofilm-forming ability, leading to persistent infections. This study had a dual focus: first, it aimed to investigate the biofilm activity and antibiotic resistance profiles of Pseudomonas aeruginosa isolates obtained from a fish-rearing farm. Second, it explored the potential of algal extracts as effective antibacterial and antibiofilm agents. The study analyzed 23 isolates of P. aeruginosa from the farm, assessing antibiotic resistance and biofilm formation. The antimicrobial and antibiofilm activities of two algal extracts, Arthrospira platensis (cyanobacteria) acetone extract (AAE) and Polysiphonia scopulorum (Rhodophyta) methanol extract (PME), were tested individually and combined (COE). The effects on biofilm-related gene expression were examined. AAE, PME, and COE were evaluated for antimicrobial and antibiofilm properties. Biofilm-related gene expression was measured and the extracts were analyzed for physicochemical properties and toxicity. Most P. aeruginosa isolates (86.9%) were antibiotic-resistant and formed biofilms. AAE, PME, and COE displayed promising antibacterial and antibiofilm effects, with COE being particularly effective. COE reduced a key biofilm-related gene expression. The fatty acid content (56% in AAE and 34% in PME) correlated with the effects. Specific compounds, such as phytol, bromophenol, and dihydroxy benzaldehyde, contributed to the activities. The extracts showed favorable characteristics and interactions with FabZ protein amino acids. This study suggests the potential of algal extracts as antibacterial and antibiofilm agents against drug-resistant infections. Further exploration in clinical applications is warranted. Full article

[Background] Bacillus LFB112 is a strain of Bacillus amyloliquefaciens screened in our laboratory. Previous studies found that it has a strong ability for fatty acid metabolism and can improve the lipid metabolism of broilers when used as feed additives. [Methods] This study aimed to confirm the fatty acid metabolism of Bacillus LFB112. Sterilized soybean oil (SSO) was added to the Beef Peptone Yeast (BPY) medium, and its effect on fatty acid content in the supernatant and bacteria, as well as expression levels of genes related to fatty acid metabolism, were studied. The control group was the original culture medium without oil. [Results] Acetic acid produced by the SSO group of Bacillus LFB112 decreased, but the content of unsaturated fatty acids increased. The 1.6% SSO group significantly increased the contents of pyruvate and acetyl-CoA in the pellets. Furthermore, the mRNA levels of enzymes involved in the type II fatty acid synthesis pathway of FabD, FabH, FabG, FabZ, FabI, and FabF were up-regulated. [Conclusions] Soybean oil increased the content of acetyl-CoA in Bacillus LFB112, activated its type II fatty acid synthesis pathway, and improved the fatty acid metabolism level of Bacillus LFB112. These intriguing results pave the way for further investigations into the intricate interplay between Bacillus LFB112 and fatty acid metabolism, with potential applications in animal nutrition and feed additive development. Full article

Among oral diseases, dental caries is one of the most frequent to affect human health. The current research work aimed to ascertain the antibacterial, anti-biofilm, and antioxidative potential of Piper betle leaf extract against bacteria isolated from dental caries. Analysis for the presence of phytochemical compounds revealed compounds, such as tannins, steroids, phenolic compounds, and alkaloids, which were also confirmed by TLC and FTIR. GC-MS analysis elucidated the presence of 20 phytocompounds, among which were some well-reported bioactive compounds. The chloroform extract of P. betle demonstrated good antibacterial activity (7 mm) and minimum inhibitory concentration (MIC) (100 mg mL⁻¹) against Bacillus gaemokensis MW067143, which was the frequent biofilm producer among isolated bacterial strains. Fractions of the extract were isolated through column chromatography, after which the antibacterial activity was again evaluated. Spirost-8-en-11-one,3-hydroxy(3β,5α,14β,20β,22β,25R), an oxosteroid in nature, was observed to exhibit remarkable antibacterial potential (12 mm) against B. gaemokensis. Bacterial cells treated with P. betle extract had elevated SOD, APOX, POX, and GR activity, while its proteolytic activity against whole bacterial proteins was pronounced with the suppression of several proteins (50, 40, 15, and 10 kDa) in SDS-PAGE. Bacterial cells treated with P. betle extract demonstrated decreased growth, while the extract was also observed to exhibit inhibition of biofilm formation (70.11%) and demolition of established B. gaemokensis biofilms (57.98%). SEM analysis revealed significant changes to bacterial morphology post treatment with P. betle, with cellular disintegration being prominent. In silico network pharmacology analysis elucidated proteins like ESR1 and IL6 to be majorly involved in biological pathways of dental caries, which also interact with the protective ability of P. betle. Gene Ontology (GO) terms and KEGG pathways were also screened using enrichment analysis. Molecular docking demonstrated the highest binding affinity of Spirost-8-en-11-one,3-hydroxy-,(3β,5α,14β,20β,22β,25R) with bacterial proteins FabI (−12 kcal/mol), MurB (−17.1 kcal/mol), and FtsZ (−14.9 kcal/mol). Therefore, it is suggested that P. betle can serve a potentially therapeutic role and could be used in the preparation of herbal formulations for managing bacterial flora. Full article

Alpha-linolenic acid and stearidonic acid are precursors of omega-3 polyunsaturated fatty acids, essential nutrients in the human diet. The ability of cyanobacteria to directly convert atmospheric carbon dioxide into bio-based compounds makes them promising microbial chassis to sustainably produce omega-3 fatty acids. However, their potential in this area remains unexploited, mainly due to important gaps in our knowledge of fatty acid synthesis pathways. To gain insight into the cyanobacterial fatty acid biosynthesis pathways, we analyzed two enzymes involved in the elongation cycle, FabG and FabZ, in Synechococcus elongatus PCC 7942. Overexpression of these two enzymes led to an increase in C18 fatty acids, key intermediates in omega-3 fatty acid production. Nevertheless, coexpression of these enzymes with desaturases DesA and DesB from Synechococcus sp. PCC 7002 did not improve alpha-linolenic acid production, possibly due to their limited role in fatty acid synthesis. In any case, efficient production of stearidonic acid was not achieved by cloning DesD from Synechocystis sp. PCC 6803 in combination with the aforementioned DesA and DesB, reaching maximum production at 48 h post induction. According to current knowledge, this is the first report demonstrating that S. elongatus PCC 7942 can be used as an autotrophic chassis to produce stearidonic acid. Full article

Sodium and sulfate ions are among the suggested abundant ions on Europa, a moon of Jupiter. In order to investigate the potential habitability of Europa, we study the effects of sodium sulfate (Na₂SO₄) on a non-halophilic bacterium by subjecting Escherichia coli (E. coli) to a wide range of Na₂SO₄ concentrations (0–1.0 m). We discover that, as the concentration of sodium sulfate increases, the biomass doubling time increases and the cell growth is completely inhibited at $1.0$ m Na₂SO₄. Furthermore, we find that E. coli exhibits three distinct morphological phenotypes—(i) shortened, (ii) normal, and (iii) elongated/filamented cells at $0.6$ m and $0.8$ m Na₂SO₄. We have examined the expression of different genes involved in sodium and sulfate transport (nhaA, nhaB, cysZ, sbp), osmotically driven transport of water (aqpZ), sulfate metabolism (cysN), fatty acid production (fabA), and a global transcriptional regulator (osmZ). Our results suggest that the expression of these genes is not affected significantly at high concentrations of sodium sulfate in the exponential growth phase. Using our experimental data and the existing data in the literature, we show that the osmotic pressure difference may play a major role in determining the growth inhibition of E. coli and B. subtilis at high concentrations of salt. Full article

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) triggers disease with nonspecific symptoms that overlap those of infections caused by other seasonal respiratory viruses (RVs), such as the influenza virus (Flu) or respiratory syncytial virus (RSV). A molecular assay for accurate and rapid detection of RV and SARS-CoV-2 is crucial to manage these infections. Here, we compared the analytical performance and clinical reliability of Allplex™ SARS-CoV-2/FluA/FluB/RSV (SC2FabR; Seegene Inc., Seoul, South Korea) kit with those of four commercially available RV detection kits. Upon testing five target viral strains (SARS-CoV-2, FluA, FluB, RSV A, and RSV B), the analytical performance of SC2FabR was similar to that of the other kits, with no significant difference (p ≥ 0.78) in z-scores. The efficiency of SC2FabR (E-value, 81–104%) enabled reliable SARS-CoV-2 and seasonal RV detection in 888 nasopharyngeal swab specimens processed using a fully automated nucleic acid extraction platform. Bland–Altman analyses revealed an agreement value of 95.4% (SD ± 1.96) for the kits, indicating statistically similar results for all five. In conclusion, SC2FabR is a rapid and accurate diagnostic tool for both SARS-CoV-2 and seasonal RV detection, allowing for high-throughput RV analysis with efficiency comparable to that of commercially available kits. This can be used to help manage respiratory infections in patients during and after the coronavirus disease 2019 pandemic. Full article