This study investigates the potential effects of essential oils (EOs) in enhancing the efficacy of clindamycin against Methicillin-resistant Staphylococcus aureus (MRSA) using in vitro and computer simulations. The research seeks to identify essential oils that exhibit synergistic activity with clindamycin and determine their potential key active components.

Essential oils commonly used in traditional medicine were tested for their antimicrobial activity against MRSA. The minimum inhibitory concentration (MIC) was determined using in vitro microdilution assays. A synergistic test with clindamycin was performed, and molecular docking studies evaluated the interaction between a key compound (trans-cinnamaldehyde) and MRSA protein.

EOs from Cinnamomum verum, Rosmarinus officinalis, Salvia officinalis, and Thymus vulgaris demonstrated significant inhibitory and synergistic activities against MRSA, standard strain, and human clinical isolates. Gas Chromatography/Mass Spectroscopy identified trans-cinnamaldehyde, eucalyptol, and thymol as prominent antibacterial compounds. Molecular docking studies confirmed trans-cinnamaldehyde's strong binding to MRSA's AgrA protein, elucidating its enhanced efficacy.

The study underscores the potential of plant-based therapies to augment the effectiveness of conventional antibiotics like clindamycin in combating MRSA and addressing antibiotic resistance by integrating traditional plant remedies with modern medical approaches.

This study investigated the potential of the indirubin-3'-oxime (I3O) compound to mitigate temperature-induced male infertility in Drosophila melanogaster. Elevated temperatures significantly reduced egg-hatching rates, but I3O supplementation improved these rates, suggesting it can partially restore fertility under heat stress. Additionally, I3O was found to inhibit soluble epoxide hydrolase (sEH), an enzyme involved in the metabolism of epoxyeicosatrienoic acids, which are vital for reproductive health. I3O exhibited sEH inhibitions with an IC50 value of 59.74 ± 0.41 µM. Enzyme kinetics revealed that I3O acts as a non-competitive inhibitor of sEH with a Ki value of 78.88 µM. Molecular docking showed strong interactions between I3O and key residues in the allosteric regions within the sEH enzyme, with a binding affinity of -9.2 kcal/mol. These interactions were supported by 100 ns molecular dynamics simulations, which confirmed the stability of the sEH-I3O complex.

Diabetic nephropathy (DN) is a diabetes mellitus (DM)-induced complication that poses high morbidity and mortality risks. The Astragalus and Salvia miltiorrhiza couplet medicines (AS) are commonly employed in DN clinical treatment in China, but their clinical efficacy and potential pharmacological mechanisms are yet to be evaluated.

A meta-analysis of 15 studies involving 1,443 patients was conducted. Furthermore, network pharmacology predicted components and targets, which were verified by molecular docking and in vivo validation.

In our meta-analysis, AS notably elevated clinical outcomes and renal function among patients with DN. Meanwhile, when the treatment duration exceeds 12 weeks, AS demonstrated a significant reduction in fasting blood glucose levels, indicating a time-dependent effect. Moreover, based on network pharmacology results, AS likely enhanced clinical outcomes by interacting with vital signaling pathways, including PI3K/Akt, MAPK, and NF-kappa B. Molecular docking studies have confirmed that PTGS2, the key therapeutic target of AS, can be closely combined with bioactive components GLY, quercetin, apigenin, and daidzein. Additionally, in vivo experiments have corroborated that AS can ameliorate renal function, UACR, and biomarkers associated with iron metabolism, such as GPX4, PTGS2, FTH1, and FTL1.

Through rigorous experimental validation, our study demonstrates AS's significant clinical efficacy in managing DN. Specifically, AS has been shown to enhance renal function, ameliorate renal fibrosis, and positively influence iron metabolism. Despite these promising outcomes, future research with a larger sample size must be conducted to further substantiate these findings.

African swine fever is a highly lethal disease caused by the African swine fever virus (ASFV), posing a significant threat to the global pig industry, wherease no approved treatments are currently available. The ASFV DNA-binding protein, pA104R, plays a critical role in viral genome packaging and replication, making it a key target for drug discovery. Through structure-based virtual screening, we identified a polyphenolic compound, thonningianin A, which disrupts the pA104R-DNA binding and significantly inhibits ASFV replication. Mechanistic study revealed that thonningianin A binds to the DNA-binding region of pA104R, forming strong hydrogen bonds with H100 and occupying the vital DNA-binding residues K92, R94, and K97. In addition, we resolved the high-resolution (1.8 Å) structure of pA104R (PDB ID 9JS5), providing valuable insights for future drug screening. Together, these results demonstrate that thonningianin A holds great potential for the development of anti-ASFV drug, as a herb extract with favourable pharmacokinetic properties and safety.

Chronic obstructive pulmonary disease (COPD) is characterized by restricted airflow that leads to significant respiratory difficulties. This progressive disease often results in diminished pulmonary function and the onset of additional respiratory conditions. Autophagy, a critical cellular homeostasis mechanism, plays a significant role in the exacerbation of COPD. In this study, we utilized various bioinformatics tools to identify autophagy-related genes activated by smoking in individuals with COPD. Furthermore, we explored the immune landscape of COPD through these genes, analyzing cell communication patterns using scRNA-seq data. This analysis focused on key pathways between epithelial cells and other cellular subpopulations with different autophagy scores, essential for understanding the initiation and progression of COPD.

This study investigates the mycochemical profile and biological activities of hydroethanolic (EtOH), chloroform (CHCl3), and hot water (H2O) extracts of Sanghuangporus lonicerinus from Uzbekistan. Antioxidant capacity was assessed using 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS), NO, and FRAP assays, and in vitro hypoglycaemic effects were evaluated through α-amylase and α-glucosidase inhibition. Antiproliferative potential was explored by analysing the binding affinities of EtOH and H2O extracts to estrogen receptor α (ERα), ERβ, androgen receptor (AR), and glucocorticoid receptor (GR), with molecular docking providing structural insights. LC-MS/MS analysis revealed solvent-dependent phenolic profiles, with the EtOH extract containing the highest total phenolic content (143.15 ± 6.70 mg GAE/g d.w.) and the best antioxidant capacity. The EtOH extract showed significant hypoglycaemic effects, with 85.29 ± 5.58% inhibition of α-glucosidase and 41.21 ± 0.79% inhibition of α-amylase. Moderate ERβ binding suggests potential for estrogen-mediated cancer therapy, while strong AKR1C3 inhibition by the EtOH extract supports its therapeutic potential.

Lespedeza bicolour Turcz. is a traditional medicinal plant with a wide range of ethnomedicinal values. The main components of L. bicolour essential oil (EO) were β-pinene (15.41%), β-phellandrene (12.43%), and caryophyllene (7.79%). The EO of L. bicolour showed antioxidant activity against ABTS radical and DPPH radical with an IC50 value of 0.69 ± 0.03 mg/mL and 10.44 ± 2.09 mg/mL, respectively. The FRAP antioxidant value was 81.96 ± 6.17 μmol/g. The EO had activities against acetylcholinesterase, α-glucosidase, and β-lactamase with IC50 values of 309.30 ± 11.16 μg/mL, 360.47 ± 35.67 μg/mL, and 27.54 ± 1.21 μg/mL, respectively. Molecular docking showed methyl dehydroabietate docked well with all tested enzymes. Sclareol and (+)-borneol acetate showed the strongest binding affinity to α-glucosidase and β-lactamase, respectively. The present study provides a direction for searching enzyme inhibitors for three tested enzymes and shows L. bicolour EO possesses the potential to treat a series of diseases.

In light of searching for new breast cancer therapies, DNA-targeted small molecules were rationally designed to simultaneously bind DNA and inhibit human dihydrofolate reductase (hDHFR). Fourteen new arylidene-hydrazinyl-1,3-thiazoles (5-18) were synthesised and their dual DNA groove binding potential and in vitro hDHFR inhibition were performed. Two compounds, 5 and 11, proved their dual efficacy. Molecular docking and molecular dynamics simulations were performed for those active derivatives to explore their mode of binding and stability of interactions inside DHFR active site. Anti-breast cancer activity was assessed for 5 and 11 on MCF-7 cells using MTX as reference. IC50 measurements revealed that both compounds were more potent and selective than MTX. Cytotoxicity was examined against normal skin fibroblasts to examine safety and selectivity Moreover, mechanistic studies including apoptosis induction and wound healing were performed. Further in silico ADMET assessment was conducted to determine their eligibility as drug leads suitable for future optimisation and development.

This study explores the therapeutic potential of Abrus precatorius leaves in arthritis treatment using computational methods and LC-MS analysis.

The plant material was taxonomically authenticated, and phytochemical analysis identified bioactive compounds such as alkaloids, flavonoids, and triterpenoids.

Swiss ADME analysis confirmed that multiple compounds complied with Lipinski's Rule of Five, while OSIRIS software indicated minimal toxicity. PASS analysis predicted anti-inflammatory and antioxidant activities. Molecular docking simulations of Abrine with key rheumatoid arthritis (RA) targets revealed strong binding affinities, suggesting potential mechanisms for RA treatment.

This research highlights the medicinal potential of Abrus precatorius leaves and emphasizes the importance of computational tools in understanding their pharmacological properties for arthritis management.

This study investigates the impact of tryptophan substitution on the properties of the Medisin family peptide MS-PT. By substituting hydrophobic amino acids in MS-PT1 with tryptophan, a series of derivative peptides were synthesized. Among them, the 7W peptide stood out with its unique N-terminal random curl and α-helix structure. In vitro, 7W effectively inhibited the secretion of pro-inflammatory cytokines like IL-6 and TNF-α in LPS-induced Membrane-Proximal Macrophages (MPMs) by blocking the MAPK/NF-κB signaling pathway. It also exhibited stronger antimicrobial activity against Gram-positive bacteria compared to the parent peptide MS-PT1, with good safety as indicated by a low hemolysis rate. In vivo, in the CLP-induced sepsis mouse model, 7W alleviated lung and liver injury, suppressed the expression of inflammatory factors in serum and tissues, and had a relatively long plasma half-life of 46.8 h. Mechanistically, 7W interacted preferentially with bacterial mimic membranes and LPS, and its anti-inflammatory effect might be mediated by binding to TLR4. These findings not only clarify the role of tryptophan substitution in modulating peptide properties but also offer a new strategy for the development of multifunctional antimicrobial peptides, suggesting that 7W has great potential as a therapeutic agent for sepsis and other inflammatory diseases.

Neurodegenerative diseases such as Parkinson's and Alzheimer's lead to the gradual decline of the nervous system, resulting in cognitive and motor impairments. With an aging population, the prevalence and associated healthcare costs are anticipated to rise. Misfolded protein aggregates are central to these diseases, disrupting cellular function and causing neuronal death. Preventing these toxic aggregates could preserve neurons and slow disease progression. Understanding how to inhibit protein aggregation is crucial for developing effective treatments. We explored the effect of nalidixic acid (NA) on protein aggregation using human serum albumin (HSA) as model protein. In vitro assays demonstrated that NA significantly reduced ThT fluorescence by 47.10 % and decreased turbidity by 63.07 %. NA also protected the protein's hydrophobic surfaces. The α-helical content of HSA dropped from 56.23 % to 11.43 % but was restored to 38.53 % with NA. We then utilized advanced molecular simulations to understand the kinetics and mechanism of aggregation inhibition by NA. Binding studies showed that NA attaches to HSA's subdomain IIA with a binding energy of -7.8 kcal/mol through hydrogen bonds, Van der Waals forces, and hydrophobic interactions. Molecular simulations confirmed the stability of HSA-NA complex. Additionally, NA increased solvent accessibility of HSA282-292 oligomers, reduced hydrogen bonding, and prevented β-sheet formation. Compared to existing anti-aggregation strategies, NA offers a promising alternative with its potential therapeutic applications in neurodegenerative diseases by stabilizing protein structures and preventing misfolding. These findings highlight NA's potential as a candidate for inhibiting protein aggregation and offer insights for therapeutic approaches. Further experimental studies utilizing in vivo models are needed to validate the anti-aggregation potential of NA.

Focal Adhesion Kinase (FAK) is a non-receptor tyrosine kinase that plays a crucial role in cell proliferation, migration, and signal transduction. FAK is overexpressed in metastatic and advanced-stage cancers, where it is considered a key kinase in cancer growth and metastasis. However, recent research has revealed that FAK activity decreases in various diseases. we aimed to identify compounds that could enhance FAK activity using structure-based virtual screening and artificial intelligence models from a vast chemical database. We began with an extensive chemical database containing over 10 million compounds and used our newly developed pipeline to screen candidate molecules. To select compounds structurally similar to ZINC40099027 (ZN27), a known FAK activator, we calculated Tanimoto Similarity scores and chose compounds with a score of at least 0.8. Clustering was performed using K-means based on the molecular properties. Subsequently, we utilized docking simulation, deep learning and SAScorer to evaluate and predict the protein-ligand docking affinity and physicochemical properties of the candidate compounds. The deep learning models were selected as state-of-the-art models: GLAM predicts the blood-brain barrier permeability of FAK, and elEmBERT predicts the potential toxicity of compound. The combined results were used to create an evaluation matrix. We selected 10 promising candidate compounds from the initial dataset of 10 million. To evaluate the stability of these top 10 candidate compounds in interaction with the FAK protein, we conducted Molecular Dynamics (MD) simulations. We performed a molecular dynamics simulation for a total of 50 ns and identified the top three promising candidate compounds.

Cancer is a significant health and economic concern worldwide. Prostate cancer (PC) ranks as the fourth leading cause of global death and is the second most prevalent malignancy in males. Androgens are essential for the progress and growth of the prostate gland. PC is caused by androgens binding to receptors, which activates genes that promotes the development of PC. Nilutamide (NLM) is an antiandrogen medicine used in the treatment of PC. However, throughout treatment, it induces various toxicities and leads to resistance in patients. The objective of the work was to designed and evaluated safer NLM analogues using computational approaches with optimized pharmacokinetic profiles and less toxicity. Newer bioisosteres of the designed NLM analogues and their ADMET scores were calculated using the MolOpt and ADMETlab 3.0 tools, respectively. We conducted docking investigations of the designed ligands using AutoDock Vina software. The MolOpt web server produces 1575 bioisosteres of NLM using the scaffold transformation method. The 47 bioisosteres were selected based on pharmacokinetic profiles, drug likeness (DL) and drug score (DS) prediction scores and were determined to be optimum to excellent in comparison to NLM. The analogues NLM28, NLM31, NLM34, NLM38, NLM40, NLM44, NLM45, and NLM47 exhibited favorable interactions and docking scores with the protein (PDB ID: 2AM9). The molecular dynamics (MD) simulation results revealed that the NLM34 and NLM40 complexes were found stable during the 100 ns run. The findings indicate that the NLM analogues, particularly NLM34 and NLM40 have the potential to be used as promising antiandrogen agents for PC therapy.

Adverse Outcome Pathways (AOPs) in toxicology describe the sequence of key events from chemical exposure to adverse outcomes, facilitating the development of predictive models. The EU ONTOX project uses this framework to predict liver, developmental brain, and kidney toxicity without animal testing. Focusing on Molecular Initiating Events (MIEs), more concretely on the interaction of chemicals with key proteins, we have developed an automated workflow for docking small molecules onto over 20 pre-processed protein structures, implemented in the online tool DockTox. This tool generates conformers of small molecules, performs docking on MIE-associated proteins, and provides binding energy, interacting residues, and interaction maps. Additionally, it compares the interactions to a reference list of known ligands, producing an interaction fraction as an additional similarity measure. Evaluation of the docking workflow's predictive performance on Peroxisome Proliferator-Activated Receptor α (PPARα) showed that interaction fraction values are more informative than binding energy alone for distinguishing binders from non-binders. This unique feature enhances the understanding of target protein interactions. DockTox supports the virtual screening of small molecules targeting MIE-associated proteins, offering insights into binding energies and interaction profiles. It is a valuable tool for anticipating adverse outcomes from chemical exposure in a tiered risk assessment approach.

Peripheral nerve injury enhances mitochondrial translocator protein (TSPO) expression in the spinal cord and dorsal root ganglia (DRG), which is associated with neuroinflammation and mitochondrial dysfunction contributing to chronic pain development. Here, we investigate the effect of TSPO ligand Etifoxine, on the development of chronic pain and motor dysfunction following sciatic nerve injury. Mechanical and thermal sensitivity, as well as motor function, were measured in rats before and after sciatic nerve crush (SNC). Rats were treated with the Etifoxine (50 mg/kg, twice daily) for one week. At the end of the experiment, RT-PCR and immunohistochemistry (IHC) were performed to assess mitochondrial stress and neuroinflammation. Additionally, high-resolution respirometry (O2k) was used to evaluate mitochondrial function in the spinal cord following mitochondrial permeability transition pore (mPTP) induction by Ca2+. Etifoxine treatment post-SNC alleviated mechanical and thermal hypersensitivity, as well as motor dysfunction in rats. In addition, Etifoxine treatment modulates neuroinflammation and mitochondrial stress. Specifically, we found a significant reduction in microglia presence and the transcription of pro-inflammatory cytokines (TNFα, IL-6, IL-1β) in the DRG and spinal cord of the SNC/etifoxine-treated group. Furthermore, Etifoxine treatment prevent the decline in mitochondrial respiration, including non-phosphorylation, ATP-linked respiration, and maximal respiration, after mPTP induction by Ca2+. Our findings suggest that TSPO-ligand Etifoxine protects against motor dysfunction and the development of chronic pain by reducing neuroinflammation and apoptosis in the DRG and spinal cord. Importantly, the beneficial effects of TSPO-ligands are reflected in the restoration of the mitochondrial function under challenging conditions.

Drug-target affinity prediction is a fundamental task in the field of drug discovery. Extracting and integrating structural information from proteins effectively is crucial to enhance the accuracy and generalization of prediction, which remains a substantial challenge. This paper proposes a pocket-based multimodal deep learning model named PocketDTA for drug-target affinity prediction, based on the principle of "structure determines function". PocketDTA introduces the pocket graph structure that encodes protein residue features pretrained using a biological language model as nodes, while edges represent different protein sequences and spatial distances. This approach overcomes the limitations of lack of spatial information in traditional prediction models with only protein sequence input. Furthermore, PocketDTA employs relational graph convolutional networks at both atomic and residue levels to extract structural features from drugs and proteins. By integrating multimodal information through deep neural networks, PocketDTA combines sequence and structural data to improve affinity prediction accuracy. Experimental results demonstrate that PocketDTA outperforms state-of-the-art prediction models across multiple benchmark datasets by showing strong generalization under more realistic data splits and confirming the effectiveness of pocket-based methods for affinity prediction.

Ubiquitous per- and poly-fluoroalkyl substances (PFAS) threaten human's health and attract worldwide attention. PFAS-mediated toxicity involves adverse effects of PFAS on proteins, and assessment of PFAS-protein binding interactions helps to explain PFAS' adverse effects on human health. In-silico modeling can generate information and decrease experimental costs. Accordingly, in this study, molecular docking was used to determine the binding affinities of 430 PFAS with human serum albumin (HSA), peroxisome proliferator-activated receptor gamma (PPARγ), and transthyretin (TTR). Specifically, analytic hierarchy process, fuzzy comprehensive evaluation, and quantitative structure-activity relationship model were used to assess and predict the binding affinities between PFAS and HSA, PPARγ, and TTR. The binding patterns were determined by defining "PEOE_RPC-, E_vdw, MNDO_LUMO, and vsurf features" as key factors related to charge, energy and shape characteristic of PFAS. Finally, Kronecker-regularized least squares (Kron-RLS) model was applied to predict the binding affinities between PFAS- and G protein-coupled receptor 40 (GPR40), as a new target for prediction. Results showed that the Kron-RLS model exhibited good performance and generated precise predictions (R2 = 0.94). In conclusion, this study demonstrated that computational simulations could be used to aid the scientific management of the growing number of PFAS, and could be broadened to include a wide range of environmental contaminations.

The mangosteen pericarp contains unstable non-acylated ACNs, rendering it prone to degradation. Therefore, intermolecular copigmentation of semi-purified ACNs (SPA) with tartaric acid (SPA-TA), sinapic acid (SPA-SA), catechin (SPA-CE), and sucrose (SPA-SU) in 1:5 and 1:10 M ratios were used to increase their stability during storage for 77 days at 25 ± 1 °C in pH 3 buffer solution. The SPA-TA1:5 complex showed the significant highest stability of total monomeric ACN content (TMAC) with a half-life (t1/2) = 56.9 days, cyanidin-3-O-sophoroside (C3S) with t1/2 = 48.1 days and color retention (69.80 %) compare to SPA with TMAC (t1/2 = 37.4), C3S (t1/2 = 13.3) and color retention (57.2 %) after 49 days (p < 0.05). The thermal stability of SPA-TA1:5 at 60 °C improved after high-pressure processing (HPP) at 300 and 500 MPa for 10 min. Fourier-transform infrared spectroscopy (FT-IR) and molecular docking indicate copigmentation interactions, including hydrogen bonding and π-π interactions. This study demonstrates a sustainable method to stabilize non-acylated ACNs, offering a natural alternative to synthetic dyes for food and beverage applications.

β-N-acetylglucosaminidase (NagZ) plays an important role in the bacterial cell wall biosynthetic pathway. Inhibiting its activity could potentially impede bacterial growth. We report a study on the design and synthesis of cinnamoyl amides derived from rosmarinic acid (RA), and their enzymatic, antibacterial activity against NagZ and Pseudomonas aeruginosa respectively. In vitro enzyme activity determination showed that the best synthetic RA analogues displayed higher inhibitory activity than that of parent RA, in the same range than the most potent NagZ inhibitors reported so far. Remarkably, compounds 11h and Br-6 displayed interesting binding affinity values with Ki=3.3 ± 0.5 and 3.5 ± 1.0 μM, respectively. Docking simulations evidenced significant binding interactions of cinnamoyl amide derivatives with the active site of NagZ. Moreover, kinetic evaluations indicated these compounds displayed competitive behavior. Additionally, MICs of 11h and Br-6 combined with two β-Lactam antibiotics (imipenem and ceftazidime) were evaluated against P. aeruginosa by microdilution checkerboard assay, establishing that antibacterial agents show synergistic effects. In vivo antibacterial efficacy assay using a full-thickness skin defect model with P. aeruginosa infection confirmed these observations.

The C-C chemokine receptor type 5 is a G protein-coupled receptor expressed on various immune cells, playing a crucial role in inflammation and chemotaxis. Beyond its physiological functions, C-C chemokine receptor type 5 is implicated in numerous diseases, including cardiovascular, central nervous system, immune system, and infectious diseases, as well as in the progression of cancer. The therapeutic potential of C-C chemokine receptor type 5 inhibition has been demonstrated by antagonists targeting the extracellular domain, notably maraviroc, a Food and Drug Administration-approved Human Immunodeficiency Virus entry inhibitor. However, challenges such as suboptimal pharmacokinetics and efficacy necessitate new antagonists with unique modes of action. Recent advancements in G protein-coupled receptor structural characterization have identified a novel intracellular allosteric binding site in chemokine receptors. This study introduces a series of disubstituted [1,2,5]oxadiazolo-[3,4-b]pyrazines targeting the intracellular allosteric binding pocket of C-C chemokine receptor type 5. Among these, compound 3ad emerged as a promising C-C chemokine receptor type 5-selective allosteric antagonist with a half-maximal inhibitory concentration of 1.09 μM and an almost 30-fold selectivity over C-C chemokine receptor type 2. Molecular dynamics simulations and a competition assay with a Gαq11 mimetic were used to confirm the intracellular binding mode of these compounds. This novel class of C-C chemokine receptor type 5-selective intracellular antagonists offers a foundation for developing molecular tools and therapeutic agents, potentially overcoming the limitations of current extracellular C-C chemokine receptor type 5 antagonists.

Herein, a highly efficient and recyclable biocatalyst was developed using stabilized enzyme aggregates on amino-functionalized magnetic biochar for removing persistent organic pollutants from water. The biochar derived from biomass featured abundant hydroxyl functional groups, after functionalization with amino functional groups and magnetic nanoparticles, it was employed for laccase immobilization via enzyme electrostatic adsorption, precipitation and cross-linking in a favorable orientation. This immobilized enzyme aggregates exhibited enhanced pH tolerance, thermal and storage stability than free enzyme. Complete removal of 20 mg/L bisphenol A was achieved within 60 min via C-C bond cleavage and hydroxylation. Notably, the removal efficiency remained at approximately 90 % even after six cycles. Furthermore, this biocatalyst was also successfully applied to efficiently remove other various persistent organic pollutants and demonstrated applicability in real environmental water samples. This study highlights the substantial potential of enzyme-based biocatalysts, presenting a sustainable and efficient approach for water purification and biomass resource recovery.

The chemical structures of the parental compounds of flavonoids from Boesenbergia rotunda were modified by conjugation with cinnamic acid to form cinnamoyl-flavonoid hybrid derivatives with enhanced anti-inflammatory and SARS-CoV-2 Mpro-inhibitory properties. Cinnamoyl-flavonoid hybrid derivatives 6 and 10 showed the potential to inhibit SARS-CoV-2 Mpro with IC50 values of 52.49 and 22.62 μM. Compounds 6 and 10 showed lower cytotoxicity in the human lung cell lines MRC-5 and A549 at concentrations greater than 50 μM. The effects of compounds 6 and 10 on cell viability were studied in a 3D co-culture model of A549 and MRC-5 treated with lipopolysaccharide (LPS) and observed through confocal microscopy. Compounds 6 and 10 downregulated p65 mRNA expression, resulting in a reduction of pro-inflammatory cytokines, including Interleukin 8 (IL-8) and Monocyte Chemoattractant Protein-1 (MCP-1/CCL2), leading to an anti-inflammatory response through Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signalling pathways. Compound 6 showed potential anti-inflammatory activity, downregulating Bcl-2 Associated X gene (BAX), which resulted in inhibition of apoptotic cell death when compared to compound 10. In silico molecular dynamic simulation shed light on how these cinnamoyl-flavonoid hybrid derivatives interact with myeloid differentiation factor 2 (MD-2), which is involved in the inflammatory response. Our findings suggest that cinnamoyl-flavonoid hybrid derivatives show potential as anti-inflammatory drugs and anti-SARS-CoV-2 drugs.

In the present work, we designed and successfully synthesized novel steroid sulfatase (STS) inhibitors based on coumarin, tyramine, triazole, and flavone cores with an additional glutamic acid residue in the structure. The molecular modeling studies revealed that designed derivatives have potential to bind to the molecular target active site, at least theoretically. The biological activity of synthesized compounds was evaluated under a two-step procedure including enzymatic assay and cellular studies using human choriocarcinoma JEG-3 cells. Among the synthesized compounds, the derivative 54E was the most active in both enzymatic and cellular experiments. This result agreed with the molecular modeling data, which indicated that derivative 54E demonstrates the highest affinity to the STS active site. In the enzymatic assay, the remaining STS activity values of 12.97, 17.58, and 20.52 % were observed at 10, 1, and 0.1 μM concentrations of compound 54E, respectively. The IC50 value of 22 nM determined in an experiment with JEG-3 cells for compound 54E was close to the IC50 value determined for the reference STS inhibitor Irosustat (2.7 nM). During the evaluation of the uptake mechanism of the compound 54E, we found that organic anion transporting polypeptides (OATPs) may be responsible for its internalization into the cells. Furthermore, the incubation of zebrafish larvae with the compound 54E revealed no detectable toxic effects in vivo indicating that the compound 54E is a very promising candidate for further preclinical investigations.

Alcoholic liver disease (ALD) is becoming a major health threat in the world today. Alcohol dehydrogenase (ADH) plays an important role in alcohol metabolism. Pacific oyster (Crassostrea gigas) has been identified as a food-borne hepatoprotective agent. For the first time, we integrated in silico strategy, including simulated hydrolysis, bioinformatic prediction and molecular docking to screen ADH activating peptides from C. gigas. In vitro ADH activation activity and surface plasmon resonance (SPR) results showed that this strategy could stably screen ADH activating peptides. We selected six of them to further verify their protective effect on EtOH-induced HepG2 cells. Among them, peptide LQPPR (Leu-Gln-Pro-Pro-Arg) pretreatment increased cell viability, can effectively resist EtOH-induced cytotoxicity. And the transaminase (ALT, AST) in the cell supernatant decreased, indicating the cell damage was improved. The results also showed that the antioxidant capacity (SOD, GSH) of LQPPR pretreated cells increased, and the oxidative stress (MDA) decreased.

Through phytochemical analysis of the large roots of Paris polyphylla var. yunnanensis, three previously undescribed steroidal saponins (Polypharsis A-C, 1-3) and four known steroidal saponins (4-7) were isolated. The structures of 1-3 were elucidated by 1D/2D NMR, HR-ESI-MS, acid hydrolysis and ECD calculations. The cytotoxic activity tests of seven compounds against three tumor cell lines (HepG2, MCF-7, and A549) were conducted. Among them, compounds 6 and 7 belong to the protodioscin class of compounds. Compound 6 exhibits significant inhibition of HepG2 cell growth with an IC50 value of 7.53 ± 2.07 μM, comparable to that of Doxorubicin (6.82 ± 1.59 μM). Compound 7 shows a strong inhibitory effect on the growth of the MCF-7 cell line with an IC50 value of 0.69 ± 0.26 μM, which is more potent than Doxorubicin (5.56 ± 0.08 μM). Subsequently, the antitumor efficacy of compound 6 against HepG2 cells and compound 7 against MCF-7 cells was investigated through in vitro experiments, and their respective mechanisms of action were further predicted using network pharmacology and molecular docking.

The degradation of polyethylene terephthalate (PET) has garnered notable attention owing to its widespread accumulation and the challenges associated with its breakdown. Herein, the enzyme mimics with PET-hydrolytic activity were developed by combining peptide nanofibers with graphene oxide (GO). Inspired by native enzymes, we designed self-assembled peptides that included active amino acids (serine, histidine, aspartate and tryptophan) and different hydrophobic amino acids, with a 9-fluorenylmethoxycarbonyl group at the N-terminus. Our comparison of hydrophobic amino acids revealed that their content not only influenced the higher-order assembly of peptide but also affected molecular conformation and PET degradation ability. By co-assembling two peptides with catalytic and binding sites in a 1:1 ratio, a more effective active enzyme mimic was constructed which was owning to the cooperative interactions among the active amino acids; in addition, hydrogen bonds and π-π stacking interactions were the main forces in enhancing catalytic effects. To further improve PET-hydrolytic ability, the co-assembled enzyme mimic was functionalised with GO through π-π stacking. This GO-peptide nanofiber hybrid exhibited increased PET-hydrolytic, as GO provided a hydrophobic microenvironment for substrate attraction and abundant carbon for facilitating proton transfer. The GO-peptide nanofiber hybrid as enzyme mimics will be a promising material for PET degradation.

This study focused on the synthesis of secosteroids with good antiproliferative properties against hormone-dependent breast cancer. A straightforward and efficient method for synthesizing secosteroid - 1,3,4-oxadiazole hybrids was developed starting from 13α-hydroxy-3-methoxy-13,17-secoestra-1,3,5(10)-trien-17-oic acid hydrazide. The cyclization of hydrazide moiety with CS2 into 1,3,4-oxadiazole-2(3H)-thione fragment followed by sulfur alkylation resulted in the formation of various secosteroid - 2-mercapto-1,3,4-oxadiazole hybrids. These novel compounds were evaluated for their antiproliferative activity against the hormone-dependent human breast cancer cell line MCF-7. Among the synthesized hybrids, compounds 3i, 3o, and 3q displayed notable antiproliferative effects, with IC50 values ranging from 6.5 to 8.9 µM, comparable to the reference drug cisplatin. Furthermore, compound 3i showed minimal toxicity toward non-cancerous hFB-hTERT fibroblasts, indicating high selectivity. Compounds 3o and 3q exhibited antiestrogenic activity. Additionally, their effects on PARP and Bcl-2 suggest a pro-apoptotic mechanism of action. These findings highlight the potential of secosteroidal hybrids as promising candidates for the development of new anti-breast cancer agents targeting ERα and apoptosis pathways.

The rise of drug-resistant Candida albicans (C. albicans) has led to an urgent need for new therapeutic strategies. Histone deacetylases (HDACs) inhibition has been shown to limit fungal virulence while enhancing the efficacy of antifungal drugs against Candida. However, HDACs are highly conserved from yeast to humans, which has hindered the application of these inhibitors in the antifungal therapy. The aim of this study is to identify a suitable antifungal target and develop specific inhibitors targeting C. albicans HDACs. Based on sequence alignments, the HDAC Hos1 in C. albicans was proposed as a target for further investigation. We evaluated the impact of Hos1 on C. albicans pathogenicity using a murine model of disseminated candidiasis. Results showed that Hos1 null mutant caused less damage to mouse tissues. Additionally, we demonstrated that the reduced virulence was due to inhibition of cell wall O-mannan biosynthesis and altered metabolic flexibility, leading to decreased adaptability of C. albicans. Increased sensitivity of C. albicans to antifungal drugs was attributed to abnormal accumulation of ergosterol in the cell membrane. Furthermore, we identified Hos1 inhibitors from the ZINC database using molecular docking. These inhibitors exhibited highly specific inhibition of the deacetylation activity of C. albicans Hos1. Importantly, the inhibitors not only reduced colonization and invasion by C. albicans in vivo but also synergized with polyene drugs to combat C. albicans by causing abnormal accumulation of ergosterol. Our findings provide detailed insights into antifungal targets and a useful foundation for the discovery of antifungal drugs specifically targeting Candida.

The molecular and genetic mechanisms underlying vascular calcification remain unclear. This study aimed to determine the differences in calcification marker-related gene expression in macrophages.

The expression profiling datasets GSE104140 and GSE235995 were analysed to identify differentially expressed genes (DEGs) between fibroatheroma with calcification and diffuse intimal thickening. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, Weighted Gene Co-expression Network Analysis (WGCNA), and Gene Set Enrichment Analysis (GSEA) were performed to assess functional characteristics. Hub genes were identified through a protein-protein interaction (PPI) network and machine learning approaches. Single-cell RNA sequencing data (GSE159677) validated the expression of calcification-related genes in macrophages, while Mendelian randomization analysis explored their potential causal relationship with coronary calcification. Further validation was conducted using enzyme-linked immunosorbent assay (ELISA) on coronary calcification samples and immunohistochemistry in ApoE-/- mice. Intravascular ultrasound was performed to assess coronary calcification severity.

Two key biomarkers, ITGAX and MYD88, were identified as diagnostic indicators of cardiovascular calcification. Both biomarkers were significantly upregulated in calcified samples and were strongly associated with immune processes. Single-cell RNA sequencing confirmed their high expression in multiple immune cell types. Additionally, molecular docking analysis revealed that retinoic acid interacted with both biomarkers, suggesting potential therapeutic relevance. Immunohistochemical and ELISA analyses further validated their elevated expression in calcified samples. These findings provide novel insights into the molecular mechanisms of vascular calcification and highlight potential diagnostic and therapeutic targets.

The mechanism of molecular interaction between β-lactoglobulin (β-lg) and sorghum bran phenolic compounds from 4 genotypes was studied. Catechin (CA) and ferulic acid (FA) were used as model systems. Higher affinity for β-lg:FA interaction (Ksv ≈ 105 M-1) compared with β-lg:CA interaction (Ksv ≈ 104 M-1) was revealed, with different preferable binding sites identified through molecular docking. Nevertheless, regarding the molecular interaction between the proteins and the complex extracts of phenolic compounds, Ksv in the magnitude order of 104 M-1 were observed. Antioxidant capacity progressively increased after protein-phenolic interaction, indicating a potential synergistic effect. Concerning the thermal stability of the phenolic compounds, epimerization as the primary response of CA to thermal treatment (90 °C / 10 min) was identified, but the addition of β-lg exerted a protective effect against CA degradation (-7 % in β-lg:CA complexes); however, proteins were not able to protect complex phenolic matrices (e.g. sorghum extracts).

Olfaction biosensors are playing crucial roles in detecting volatile organic compounds (VOCs) in various domains, while the response pattern of biosensors to different alcohols and the underlying reasons for the differences in response remain unclear. Herein, this study presents a sensitive electrochemical olfactory biosensor utilizing Drosophila odorant-binding protein (LUSH) as a sensing material for the detection of 11 alcohols with different molecular structures (alkyl chain lengths, hydroxyl group numbers, and cyclic alcohols) and phenol. The electrodes covalently immobilized with the LUSH proteins were characterized by atomic force microscopy (AFM), electrochemical impedance spectroscopy (EIS), and cyclic voltammetry (CV), and their ability to detect alcohols was investigated through EIS. Results showed that the LUSH modified biosensor exhibited ultrasensitive detection of multiple alcohols (detection limits: 10-100 fM), with linear ranges from 10-14 to 10-7 M and coefficients of determination (R2) of 0.948-0.992. In addition, the biosensor demonstrated high selectivity toward interfering compounds (selectivity coefficients <0.22), excellent reproducibility (relative standard deviation, RSD: 1.2%, n = 4 for parallel sensors), and good stability (response decreased by 10.2% on the 10th day). Notably, the sensitivity of the biosensor to alcohols showed alkyl chain-length dependence of n-alcohols and was influenced by the number of hydroxyl groups and the cyclic structure. More importantly, molecular docking revealed the binding modes, binding energies, and key amino acids involved in the LUSH-alcohol interaction and explained the response discrepancies.

The design of new antimicrobial agents is an important challenge due to the growing resistance of microorganisms to existing antibiotics. In recent years, the trend towards the development of compounds and materials with (bio)degradable properties has emerged. In this work, we propose and develop a method for the synthesis of new peptidomimetics, i.e., water-soluble macrocyclic quaternary ammonium salts containing L-tyrosine fragments based on p-tert-butylthiacalix[4]arene in various stereoisomeric forms (cone, partial cone, and 1,3-alternate). These compounds have low cytotoxicity (IC50 = 80-267 μM) and high antibacterial activity (MIC = 0.5-15.6 μM) against Gram-positive bacterial strains including methicillin-resistant Staphylococcus aureus (MRSA). The obtained peptidomimetics can bind α-chymotrypsin with the formation of supramolecular systems and their subsequent degradation. Our results demonstrate the first example of multi-action thiacalixarene derivatives with antibacterial activity, protein binding ability and degradation induced by binding to α-chymotrypsin. The obtained results open the possibility of creating multi-action peptidomimetic systems with antimicrobial and biodegradable effect.

Enhancing the efficacy of chemotherapy in treating triple-negative breast cancer (TNBC) remains crucial. Understanding the genes involved in cancer progression and targeted therapies may be beneficial for TNBC chemotherapy. Here, bioinformatics analysis revealed that AKT1 and the key gene of homologous recombination (HR), RAD51, were significantly upregulated in breast cancer. Meanwhile, we discovered that epirubicin (Epi) could activate AKT and HR pathways in MDA-MB-231 cells. Pharmacological inhibition of AKT or siAKT could reverse the activation of AKT and HR pathways and sensitize Epi. Hence, we sought natural products that could inhibit both AKT and HR pathways to enhance the sensitivity of Epi and expanded its therapeutic effects in TNBC. 2β-methoxy-2-deethoxyphantomolin (EM2) is a natural sesquiterpene lactone extracted from Elephantopus mollis with strong anticancer activity. We found that EM2 induced apoptosis of MDA-MB-231 cells by inhibiting AKT and HR pathways. Mechanistically, EM2 impaired transcription of AKT, directly bound to RAD51 protein, and facilitated the degradation of AKT and RAD51 in a caspase-dependent manner. Importantly, we determined that EM2 in combination with Epi treatment exhibited a synergistic anti-tumor effect in MDA-MB-231 cells. Moreover, overexpression of AKT could prevent EM2 from sensitizing Epi. The results of MDA-MB-231 xenograft tumor model confirmed that EM2 could reduce the dose of Epi and achieve anti-TNBC effect in vivo without toxicity to mice tissues. Overall, our work indicates EM2 in combination with Epi can greatly expand the therapeutic effect of Epi in TNBC, underscoring targeting AKT and RAD51 as a promising approach for TNBC chemotherapy sensitization.

Growing cancer resistance is a global threat that calls for development of newer chemotherapeutic analogues especially targeted based therapy to enhance efficacy and selectivity. In this contribution, herein, we report synthesis of selenium incorporated N-heterocyclic carbene (NHC) compounds to explore their potential cytotoxicity against HeLa cells. Test compounds were assured for suitability as drug candidates through physiochemical properties that showed lipophilicity logP 0.85-1.45 for C1-C3 and found stable in biological media (DMEM), whereas, least reactive with N-acetyl cysteine (NAC) and L-glutathione. All the studied compounds showed good cytotoxicity against various cancer strains while compound C1 [3,3-(hexane-1,6-diyl)bis(1-phenethyl-1H-imidazole-2(3H)-selenone)] and C2 [3,3-(hexane-1,6-diyl)bis(1-decyl-1H-imidazole-2(3H)-selenone)] showed promising results with IC50 values of 14.65 ± 0.66 and 8.05 ± 0.35 μg/mL respectively as compared to positive control 21.5 ± 0.05 μg/mL against HeLa cell lines. These compounds showed six-fold higher apoptosis than control with higher accumulation of Ca+ ions intracellularly that alters the expression level of autophagy proteins and increased capase-9 activity. Cell cycle analysis indicated an arrest of cycle in G1 phase of HeLa cells when treated with C1 & C2. Test compounds showed prominent affinity for binding with DNA and inhibiting thioredoxin reductase enzymes in time dependent manners. These findings indicate that Selenium NHC compounds are promising drug candidates to induce cytotoxicity via apoptosis, autophagy and mitochondrial membrane disruptions to manage tumor growth.

Group III hybrid histidine kinase (HHK3) is one of the most interesting signalling molecules and a novel drug target in fungi. HHK3 is converted into a cytotoxic phosphatase form in vivo by the action of a widely used agricultural fungicide indicating that HHK3 also exhibits dual functionality by acting as kinases and phosphatases towards their substrates like many bacterial sensor histidine kinases. However, this cytotoxic form of HHK3 remained elusive for further scientific exploitation. In this study, we have isolated a cytotoxic phosphatase LOCK-IN mutant of DhNik1, a prototype HHK3, and provided structural and functional insight into this form for the first time. The mutant DhNik1CT had an in-frame deletion in the poly-HAMP domain. The fusion of the poly-HAMP domain of DhNik1CT with the histidine kinase and receiver domain of another fungal hybrid histidine kinase also created a hybrid that was cytotoxic to the fungal cell. We generated the structural model of wild-type DhNik1 and DhNik1CT using AlphaFold multimer which highlighted the differences in HAMP domain arrangement and conformation between DhNik1 and DhNik1CT. MD simulation of the modelled structure revealed crucial role of ATP lid opening and closing in regulating the activity of DhNik1 and DhNik1CT. The structure of DhNik1CT was used for virtual screening to identify a small molecule which modulates the activity of DhNik1 towards cytotoxicity. Taken together, present study shows that the conversion of HHK3 to a toxic conformation by a small molecule is a feasible approach for discovering novel antifungal drug.

Poly (ADP-ribose) polymerase (PARP) inhibitors have been authorized for the treatment of breast cancer (BC) and prostate cancer (PC). Recent studies suggest that inhibiting angiogenesis through the vascular endothelial growth factor receptor (VEGFR) enhances cellular sensitivity to PARP inhibitors. This study presents the design, synthesis and full characterization of dual VEGFR-2 and PARP-1 inhibitors obtained by conjugating a PARP-1 inhibitor with VEGFR-2 inhibitor fragments (indole, benzofuran, and piperazine). Four compounds exhibited significant inhibitory activities against human prostate cancer cell lines (PC3) and breast cancer cell lines (MCF7) at 48 h. These compounds were identified as dual VEGFR-2 and PARP-1 inhibitors with low or sub-micromolar ranges, especially 12f, with IC50 values of 0.43 μM and 1.10 μM, respectively. Moreover, the potent compound 12f markedly decreased scratch wound closure and colony formation. Moreover, compound 12f significantly induced apoptosis in PC3 cells and arrested cells at the S phase. The dual inhibition of VEGFR-2 and PARP-1 protein kinase was further validated using western blotting. Applying molecular docking and dynamics determined the target compound's binding mechanism.