Docking Analysis Research Articles

Comparison of Combined Dissipation Behaviors and Dietary Risk Assessments of Thiamethoxam, Bifenthrin, Dinotefuran, and Their Mixtures in Tea.

In the tea-planting process, insecticides are commonly combined, potentially prolonging the pre-harvest interval and heightening the risk of dietary exposure. This study focused on three frequently used insecticides in tea cultivation: thiamethoxam, bifenthrin, and dinotefuran, aiming to investigate their dissipation behaviors and associated dietary risks upon individual and simultaneous application. The dissipation kinetics of thiamethoxam, bifenthrin, and dinotefuran were successfully characterized by first-order kinetics, yielding respective half-lives of 5.44, 9.81, and 10.16 days. Upon joint application, the dissipation half-lives of thiamethoxam and bifenthrin were notably prolonged compared with their individual applications, resulting in final concentrations after 28 days that were correspondingly elevated by 1.41 and 1.29 times. Assessment of the dietary intake risk revealed that the chronic and acute risk quotients associated with thiamethoxam and bifenthrin escalated by 1.44-1.59 times following their combined application. Although dietary risks associated with Tianmuhu white tea, as determined by the exposure assessment model, were deemed acceptable, the cumulative risks stemming from pesticide mixtures across various dietary sources warrant attention. Molecular docking analyses further unveiled that thiamethoxam and bifenthrin competitively bound to glutathione S-transferase (GST) at amino acid residues, notably at the 76th GLU and the 25th PHE, pivotal in the metabolism and absorption of exogenous substances. Moreover, the interactions between P-glycoprotein and pesticides during transport and absorption were likely to influence dissipation behaviors post-joint application. This research offers valuable insights and data support for optimizing joint pesticide application strategies and assessing risks associated with typical pesticides used in tea cultivation.

Expanded Gene Regulatory Network Reveals Potential Light-Responsive Transcription Factors and Target Genes in Cordyceps militaris.

Cordyceps militaris, a fungus widely used in traditional Chinese medicine and pharmacology, is recognized for its abundant bioactive compounds, including cordycepin and carotenoids. The growth, development, and metabolite production in various fungi are influenced by the complex interactions between regulatory cascades and light-signaling pathways. However, the mechanisms of gene regulation in response to light exposure in C. militaris remain largely unexplored. This study aimed to identify light-responsive genes and potential transcription factors (TFs) in C. militaris through an integrative transcriptome analysis. To achieve this, we reconstructed an expanded gene regulatory network (eGRN) comprising 507 TFs and 8662 regulated genes using both interolog-based and homolog-based methods to build the protein-protein interaction network. Aspergillus nidulans and Neurospora crassa were chosen as templates due to their relevance as fungal models and the extensive study of their light-responsive mechanisms. By utilizing the eGRN as a framework for comparing transcriptomic responses between light-exposure and dark conditions, we identified five key TFs-homeobox TF (CCM_07504), FlbC (CCM_04849), FlbB (CCM_01128), C6 zinc finger TF (CCM_05172), and mcrA (CCM_06477)-along with ten regulated genes within the light-responsive subnetwork. These TFs and regulated genes are likely crucial for the growth, development, and secondary metabolite production in C. militaris. Moreover, molecular docking analysis revealed that two novel TFs, CCM_05727 and CCM_06992, exhibit strong binding affinities and favorable docking scores with the primary light-responsive protein CmWC-1, suggesting their potential roles in light signaling pathways. This information provides an important functional interactive network for future studies on global transcriptional regulation in C. militaris and related fungi.

A Novel Approach for Apical Periodontitis Prevention Through RIPK3 Inhibition Using Organic Flavonoids

Background: Apical periodontitis (AP) entails inflammatory bone resorption facilitated by the induction of necroptosis through receptor-interacting protein kinase 3 (RIPK3). Consequently, the inhibition of RIPK3 holds the potential for favorable effects in addressing AP. A comprehensive investigation, encompassing 44 flavonoids, was undertaken to identify potential inhibitors of RIPK3. Methods: The crystal structure of the RIPK3 catalytic domain (PDB ID: 7MON) underwent meticulous preparation through the removal of ligands and energy optimization. Overall, 44 flavonoids were examined in this study. Utilizing AutoDock 4.0, molecular docking analyses were performed to evaluate the binding energies within the active site of RIPK3 concerning the examined herbal isolates, with subsequent comparison to the results obtained from a positive control inhibitor. Furthermore, the BIOVIA Discovery Studio Visualizer played a crucial role in elucidating the interactions between the top-ranked flavonoids and the residues of RIPK3. Results: Five distinct flavonoids—orientin, rutin, vicenin-2, amentoflavone, and nicotiflorin—manifested notable inhibitory effects on RIPK3, boasting inhibition constant values at either the femtomolar or picomolar scale. Notably, the first three members of this set showcased superior binding affinity to the active site of RIPK3 compared to the reference compound. Conclusion: The proposition arises that flavonoid, particularly orientin, rutin, vicenin-2, amentoflavone, and nicotiflorin, stand as promising herbal isolates for the therapeutic management of AP.

Development of low oil emulsion gels by solidification of oil droplets and determination of their rheological properties

This study aims to develop low-fat emulsion gels by physically solidifying oil droplets using a combination of pectin, soy protein, and bovine gelatin, and to investigate the rheological properties of these emulsion gels. The emulsion gels were formulated with different combinations of these biopolymers [PSG30 (pectin + soy protein + gelatin + 30% oil), PS30 (pectin + soy protein + 30% oil), P30 (pectin + 30% oil), G30 (gelatin + 30% oil)] and compared with commercially available low-fat mayonnaise (DYM40, 40% oil), mayonnaise (TM80, 80% oil), and spreadable fat (SY59, 59% oil) samples. The consistency index (K, Pa.sn) of the emulsion gels ranged from 1.903 to 150.739 Pa.sn, with PSG30 and PS30 formulations exhibiting higher K values than the commercial samples. The highest structural recovery percentage was observed in the SY59 sample at 114.91%. Thermal stability tests demonstrated that PSG30 and PS30 maintained their viscosity and storage modulus (G') values over a wide temperature range. Fourier Transform Infrared Spectroscopy (FTIR) analysis revealed significant hydrogen bonding and cross-linking interactions between pectin, soy protein, and gelatin. Microstructural imaging showed that PSG30 had the most homogeneous structure, consistent with its superior rheological performance. Molecular docking analysis determined the binding energy between gelatin and pectin to be -6.40 kcal/mol. Interaction between pectin (Arg-522 residue) and soy protein (11S globulin TGT) was facilitated by salt bridge formation. The developed formulations of pectin, soy protein, and gelatin demonstrate potential for producing low-fat emulsion gels with acceptable texture and stability properties for various food applications.

Molecular docking and dynamics simulation of farnesol as a potential anticancer agent targeting mTOR pathway.

Farnesol is a natural acyclic sesquiterpene alcohol, found in various essential oils such as, lemon grass, citronella, tuberose, neroli, and musk. It has a molecular mass of 222.372g/mol and chemical formula of C₁₅H₂₆O. The main objective of this study was to assess the effect of farnesol on mTOR and its two downstream effectors, p70S6K and eIF4E, which are implicated in the development of cancer, via molecular dynamic simulation, and docking analysis in an in silico study. A multilayer, primarily computer-based analysis was conducted to assess farnesol's anticancer potential, with a focus on primary cancer targets. From the calculations performed, farnesol showed a binding affinity of - 9.66kcal/mol, followed by binding affinity of - 7.4kcal/mol and - 7.8kcal/mol for mTOR, p70S6K and eIF4E respectively. Rapamycin showed the binding affinity of - 10.45kcal/mol for mTOR, for p70S6K and eIF4E the calculated binding affinity was - 10.65kcal/mol and 8.16kcal/mol respectively. The binding affinity of farnesol was comparable to the standard drug rapamycin indicating its potential as an mTOR inhibitor. Molecular dynamics simulations suggest that the ligands (farnesol and rapamycin) were well trapped within the active site of the protein over a time gap of 50 ns. It is clear that farnesol showed relatively stable MD simulation results, with minor fluctuations and maintains a consistent binding orientation, suggesting a strong and stable interaction with the target proteins when compared to simulation data of standard drug. This study explores the potential of farnesol as an anticancer agent through an in-silico approach, focusing on its interaction with mTOR and its downstream effectors. Inhibition of mTOR signaling pathway may be responsible for the anticancer effect of farnesol. As this pathway plays a crucial role in cell proliferation and survival, making it a significant target in cancer research.

Prominent Neuroprotective Potential of Indole-2-N-methylpropargylamine: High Affinity and Irreversible Inhibition Efficiency towards Monoamine Oxidase B Revealed by Computational Scaffold Analysis

Background: Monoamine oxidases (MAO) are flavoenzymes that metabolize a range of brain neurotransmitters, whose dysregulation is closely associated with the development of various neurological disorders. This is why MAOs have been the central target in pharmacological interventions for neurodegeneration for more than 60 years. Still, existing drugs only address symptoms and not the cause of the disease, which underlines the need to develop more efficient inhibitors without adverse effects. Methods: Our drug design strategy relied on docking 25 organic scaffolds to MAO-B, which were extracted from the ChEMBL20 database with the highest cumulative counts of unique member compounds and bioactivity assays. The most promising candidates were substituted with the inactivating propargylamine group, while further affinity adjustment was made by its N-methylation. A total of 46 propargylamines were submitted to the docking and molecular dynamics simulations, while the best binders underwent mechanistic DFT analysis that confirmed the hydride abstraction mechanism of the covalent inhibition reaction. Results: We identified indole-2-propargylamine 4fH and indole-2-N-methylpropargylamine 4fMe as superior MAO-B binders over the clinical drugs rasagiline and selegiline. DFT calculations highlighted 4fMe as more potent over selegiline, evident in a reduced kinetic requirement (ΔΔG‡ = −2.5 kcal mol−1) and an improved reaction exergonicity (ΔΔGR = −4.3 kcal mol−1), together with its higher binding affinity, consistently determined by docking (ΔΔGBIND = −0.1 kcal mol−1) and MM-PBSA analysis (ΔΔGBIND = −1.5 kcal mol−1). Conclusions: Our findings strongly advocate 4fMe as an excellent drug candidate, whose synthesis and biological evaluation are highly recommended. Also, our results reveal the structural determinants that influenced the affinity and inhibition rates that should cooperate when designing further MAO inhibitors, which are of utmost significance and urgency with the increasing prevalence of brain diseases.

Expression analysis, molecular docking and molecular dynamics simulations to identify potential BTK inhibitors: strategy for targeting pan-cancer

ABSTRACT Bruton's Tyrosine Kinase (BTK), a soluble tyrosine kinase plays an essential role in the growth, development, and signalling of B cells. It is a non-receptor kinase that is crucial for leukemic cell survival, proliferation, and oncogenic signalling in many B cell malignancies. The enhanced metastasis caused by BTK expression may be reduced by BTK inhibitors, which also have powerful therapeutic effects. The goal of the study is to identify potential inhibitors which have good binding affinity with BTK. The current study also aims to investigate the expression pattern and the prognostic significance of BTK across all cancer types. Interestingly, it was found that BTK was highly overexpressed in numerous cancer types including; clear cell renal carcinoma, glioblastoma, head and neck, liver and breast cancer. BTK was found to reduce the relapse-free and overall survival rate. Furthermore, using in silico approach two structural analogues of Pirtobrutinib namely; 163207918 and 129269825 that bind to BTK with higher affinity were identified. Using drug-likeness analysis the therapeutic possibility of screened Pirtobrutinib analogues were evaluated. The Molecular docking and dynamic analysis revealed that the new Pirtobrutinib analogues could be potent inhibitors with higher binding affinity and stability in comparison with the parent compound. In conclusion, after preclinical and clinical research, the identified analogues may open the door for their prospective use in cancer therapy.

Integrating network pharmacology, molecular docking and experimental verification to explore the therapeutic effect and potential mechanism of nomilin against triple-negative breast cancer

BackgroundNomilin is a limonoid compound known for its multiple biological activities, but its role in triple negative breast cancer (TNBC) remains unclear. This study aims to uncover the potential therapeutic effect of nomilin on TNBC and elucidate the specific mechanism of its action.MethodsWe employed weighted gene co-expression network analysis (WGCNA), differential expression analysis, and the GeneCards database to identify potential targets for TNBC. Simultaneously, we utilized the Swiss Target Prediction, ChEMBL, and STITCH databases to identify potential targets of nomilin. The core targets and mechanisms of nomilin against TNBC were predicted through protein-protein interaction (PPI) network analysis, molecular docking, and enrichment analysis. The results of the network pharmacology were corroborated by conducting experiments.ResultsA total of 17,204 TNBC targets were screened, and 301 potential targets of nomilin were identified. Through the PPI network, eight core targets of nomilin against TNBC were pinpointed, namely BCL2, Caspase3, CyclinD1, EGFR, HSP90AA1, KRAS, PARP1, and TNF. Molecular docking, molecular dynamics simulation and proteome microarray revealed that nomilin exhibits strong binding activity to these core proteins. Enrichment analysis results indicated that the anti-TNBC effect of nomilin is associated with PI3K/Akt pathway. In vitro and in vivo experiments have demonstrated that nomilin inhibits TNBC cell proliferation and migration while promoting cell apoptosis through the PI3K/Akt pathway.ConclusionFor the first time, the research effectively discovered the objectives and mechanisms of nomilin in combating TNBC using network pharmacology, molecular docking, molecular dynamics simulation, proteome microarray and experimental confirmation, presenting a hopeful approach for treating TNBC.Graphical

Integrative bioinformatic and experimental analysis of benzoylbenzodioxol derivatives: hypoglycemic potential in diabetic mice.

We investigated the hypoglycemic activity and pharmacokinetic study of two synthesized benzoyl benzodioxol derivatives, compound I (methyl 2-(6-(2-bromobenzoyl)benzo[d][1,3]dioxol-5-yl)acetate), and compound II, 2-(6-benzoylbenzo[d][1,3]dioxol-5-yl)acetic acid, which showed very strong α-amylase inhibiting activity in our previous study. Then, diabetes was induced by the injection of streptozotocin to mice. The molecular docking simulations and analyses of density functional theory analyses were conducted to study the binding interactions with human pancreatic alpha-amylase, and their pharmacokinetic properties were further evaluated by ADMET profiling. Compound I showed the most important hypoglycemic effect, decreasing the blood glucose by 32.4%, higher than that of compound II by 14.8% and even the positive control acarbose by 22.9%. Histopathological examination revealed that diabetic livers showed portal inflammation with some apoptotic hepatocytes due to streptozotocin treatment, whereas controls without any treatment maintained normal liver architecture. Molecular docking studies gave results for the best binding affinity of the compound I, through its strong water bridges and π-π interactions, and also through analysis with density functional theory, was more stable and reactive when compared to compound II. Further ADMET analysis showed that both compounds shared a promising pharmacokinetic profile, and compound I had the potential for CNS penetration. Thus, compound I was selected as the best candidate for developing new hypoglycemic agents with potent efficacy, good binding interactions, and excellent pharmacokinetic properties.

Exploring the anti-cancer and antimetastatic effect of Silymarin against lung cancer

Lung cancer metastasis remains a significant challenge in cancer therapy, necessitating the exploration of novel treatment modalities. Silymarin, a natural compound derived from milk thistle, has demonstrated promising anticancer properties. This work explored the inhibitory effects of silymarin on lung cancer metastasis and revealed the underlying processes, focusing on matrix metalloproteinase (MMP) 2 and MMP-9 activities. Using a combination of in vitro and molecular docking analyses, we found that silymarin effectively reducing the lung cancer cells' motility and invasion by modulation of expression of MMP-2 and MMP-9. Furthermore, MTT assays revealed a dose-dependent inhibition of cell proliferation upon silymarin treatment and found the IC50 value at 58 μM. We observe that apoptotic morphology characteristic in silymarin treated groups. Cell cycle analysis exhibit the cell cycle arrest at G1 phase, 25.8 % increased apoptosis in silymarin treated groups, as evidenced by Annexin V staining. Moreover, silymarin treatment shows the lipid peroxidation in elevated level and reduced in enzymatic antioxidant level, indicating its potential role in mitigating oxidative stress induce cell death. Gelatin zymography assay indicates the silymarin has ability to inhibit the MMP-2 and MMP-9 expression in lung cancer. Additionally, cell migration assays and colony formation assays demonstrated impaired migratory and colony-forming abilities of lung cancer cells when treated with silymarin. Molecular docking studies further supported the binding affinity of silymarin with MMP-2 and MMP-9, demonstrate the −10.26 and −6.69 kcal/mol of binding energy. Collectively, our findings highlight the multifaceted anticancer properties of silymarin against lung cancer metastasis, providing insights into its therapeutic potential as an adjuvant treatment strategy.

In vitro and in silico characterization of the transport of selected perfluoroalkyl carboxylic acids and perfluoroalkyl sulfonic acids by human organic anion transporter 1 (OAT1), OAT2 and OAT3

Perfluoroalkyl carboxylic acids (PFCAs) and perfluoroalkyl sulfonic acids (PFSAs) belong to the group of poly- and perfluoroalkyl substances (PFASs), which may accumulate in humans due to their limited excretion. To provide more insight into the active renal excretion potential of PFASs in humans, this work investigated in vitro the transport of three PFCAs (PFHpA, PFOA, PFNA) and three PFSAs (PFBS, PFHxS and PFOS) using OAT1-, OAT2- or OAT3-transduced human embryonic kidney (HEK) cells. Only PFHpA and PFOA showed clear uptake in OAT1-transduced HEK cells, while no transport was observed for PFASs in OAT2-transduced HEK cells. In OAT3-transduced HEK cells only PFHpA, PFOA, PFNA, and PFHxS showed clear uptake. To study the interaction with the transporters, molecular docking and dynamics simulation were performed for PFHpA and PFHxS, for which a relatively short and long half-life in humans has been reported, respectively. Docking analyses could not always distinguish the in vitro transported from the non-transported PFASs (PFHpA vs. PFHxS), whereas molecular dynamic simulations could, as only a stable interaction of the PFAS with the inner part of transporter mouth was detected for those that were transported in vitro (PFHpA with OAT1, none with OAT2, and PFHpA and PFHxS with OAT3). Altogether, this study presents in vitro and in silico insight with respect to the selected PFASs transport by the human renal secretory transporters OAT1, OAT2, and OAT3, which provides further understanding about the differences between the capability of PFAS congeners to accumulate in humans.

Molecular interaction mechanisms on (−)-epigallocatechin-3-gallate improving activities of inhibited acetylcholinesterase by selected organophosphorus pesticides in vitro & vivo

(−)-Epigallocatechin-3-gallate (EGCG) is reported to have benefits for the treatment of Alzheimer’s disease by binding with acetylcholinesterase (AChE) to enhance the cholinergic neurotransmission. Organophosphorus pesticides (OPs) inhibited AChE and damaged the nervous system. This study investigated the combined effects of EGCG and OPs on AChE activities in vitro & vivo. The results indicated that EGCG significantly reversed the inhibition of AChE caused by OPs. In vitro, EGCG reactived AChE in three group tubes incubated for 110 min, and in vivo, it increased the relative activities of AChE from less than 20% to over 70% in brain and vertebral of zebrafish during the exposure of 34 h. The study also proposed the molecular interaction mechanisms through the reactive kinetics and computational analyses of density functional theory, molecular docking, and dynamic modeling. These analyses suggested that EGCG occupied the key residues, preventing OPs from binding to the catalytic center of AChE, and interfering with the initial affinity of OPs to the central active site. Hydrogen bonding, conjugation, and steric interactions were identified as playing important roles in the molecular interactions. The work suggests that EGCG antagonized the inhibitions of OPs on AChE activities and potentially offered the neuroprotection against the induced damage.

Ethanol extract of Nymphaea lotus Linn. inhibited hepatic fibrogenesis in carbon tetrachloride-intoxicated Wistar rats

BackgroundNymphaea lotus is a plant used as food and to manage various ailments including liver diseases. Liver fibrosis is a pathological state which progresses to more chronic and fatal liver diseases but without any approved drug yet. This study thus aimed to investigate the anti-liver fibrosis mechanism of N. lotus.MethodologyLiver fibrosis was induced by carbon tetrachloride (CCl4:Olive oil, 1:1 ip). Fibrotic animals were treated with 50, 100 and 200 mg/kg b.wt. N. lotus extract. The activities of alanine aminotransaminase (ALT), aspartate aminotransferase (AST), in the serum, and levels of Malondialdehyde (MDA), superoxide dismutase (SOD), catalase, and reduced glutathione (GSH) in the liver, and histopathology of the liver were determined. The expression of fibrosis-related proteins namely alpha-smooth muscle actin (α-SMA), Collagen-4 (COL4A), Transforming growth factor-β1 (TGFβ1), Mothers against decapentaplegic homolog 2 (SMAD2), SMAD3 and matrix metalloproteinase 2 (MMP2) in the liver was also evaluated. Molecular docking and simulation analysis of N. lotus-derived phytochemicals to TGFβ1 and SMAD3 was also performed.ResultsThe extract significantly reduced the levels of ALT, AST, and MDA, increased the expression of antioxidant enzymes namely; SOD and GSH, and downregulated the expression of fibrosis-related proteins namely α-SMA, COL4A, TGFβ1, SMAD3 and MMP2. It also ameliorated CCl4-induced hepatic lesions. N. lotus-derived phytochemicals also showed a good binding affinity and interaction with the active sites of TGFβ1 and SMAD3.ConclusionN. lotus inhibited liver fibrosis by inhibiting oxidative stress and the TGFβ/SMAD signalling pathway. This demonstrates its beneficial and protective effect against CCl4-induced hepatoxicity and thus supports its use for the traditional management of liver diseases.

High Polygenic Risk Scores Positively Associated with Gastric Cancer Risk Interact with Coffee and Polyphenol Intake and Smoking Status in Korean Adults.

This study investigated the relationship between single nucleotide polymorphisms (SNPs) and gastric cancer (GC) risk, while also examining the interaction of genetic factors with lifestyle variables including the nutrient and bioactive compound intake in Korean adults of a large hospital-based cohort. We conducted a genome-wide association study (GWAS) comparing GC patients (n = 312) with healthy controls without cancers (n = 47,994) to identify relevant genetic variants. Generalized multifactor dimensionality reduction (GMDR) was employed to detect SNP interactions between diets and lifestyles. We utilized polygenic risk scores (PRSs) to assess individuals' GC risk based on multiple SNP loci. Among the selected SNPs, since SEMA3C_rs1527482 was a missense mutation, bioactive compounds which decrease the binding energy were found with its wild and mutated proteins by molecular docking analysis. Individuals with high PRSs exhibited a 4.12-fold increased risk of GC compared to those with low PRSs. Additional factors associated with elevated GC risk included a low white blood cell count (OR = 5.13), smoking (OR = 3.83), and low coffee consumption (OR = 6.30). The SEMA3C_rs1527482 variant showed a positive correlation with GC risk. Molecular docking analyses suggested that certain polyphenols, including theaflavate, rugosin E, vitisifuran B, and plantacyanin, reduced the binding free energy in both wild-type and mutated SEMA3C_rs1527482. However, some polyphenols exhibited differential binding energies between its wild and mutated forms, suggesting they might modulate wild and mutated proteins differently. High PRSs and SEMA3C_rs1527482 interact with immune function, coffee intake, polyphenol consumption, and smoking status to influence GC risk. These findings could contribute to developing personalized nutrition and lifestyle interventions to reduce GC risk.

Evodiamine inhibits proliferation and induces apoptosis of nasopharyngeal carcinoma cells via the SRC/ERBB2-mediated MAPK/ERK signaling pathway

This study aimed to investigate the effect and potential mechanism of evodiamine (EVO) on proliferation and apoptosis of nasopharyngeal carcinoma (NPC) cells. EVO inhibited proliferation, blocked cell cycle progression, and induced apoptosis of NPC cells. There are 27 known anti-NPC targets of EVO, of which eight are core targets, namely SRC, ERBB2, STAT3, MAPK8, NOS3, CXCL8, APP, and HDAC1. Molecular docking analysis showed that the binding of EVO with its key targets (SRC, ERBB2) was good. EVO also reduced the expression of SRC and ERBB2, the key proteins p-MEK and p-ERK1/2 of the MAPK/ERK signaling pathway, and the downstream proteins PCNA and XIAP. EVO inhibited the growth of NPC xenografts in nude mice and reduced the expression levels of SRC, ERBB2, ERK1/2, p-ERK1/2, PCNA and XIAP in NPC tissue. When the MAPK/ERK signaling pathway was activated by epidermal growth factor (EGF), the expression levels of PCNA and XIAP increased, the cell proliferation index increased, and the apoptosis rate decreased in the EGF + EVO treatment group compared to treatment with EVO alone. These changes indicated that the inhibitory effect of EVO on proliferation and apoptosis of NPC cells was related to the down-regulation of SRC and ERBB2 expression, and further inhibition of the MAPK/ERK signaling pathway.

Allocryptopine Attenuates Inflammatory Responses in Microglial Cells Via TLR4-Dependent NF-κB and p38 MAPK Pathways.

Studies in the existing literature propose that allocryptopine possesses both antioxidant and anti-inflammatory properties, showcasing its neuroprotective effects by potentially mitigating oxidative stress and inflammation. This study aims to investigate the antioxidant and anti-inflammatory effects of allocryptopine on various targets and potential mechanisms that have not been previously explored in the literature. Initially, we used MTT and LDH methods to evaluate the effects of allocryptopine on cell viability in BV-2 cells exposed to LPS-induced damage. Subsequently, we evaluated the impact of allocryptopine on pro-inflammatory cytokines (IL-1β, IL-6, and TNF-α), other inflammatory mediators (Cox-2 and iNOS), and p38 MAPK genes and proteins through qRT-PCR and Western blot analyses. Also, we evaluated the impact of allocryptopine on NF-κB proteins (TLR4, MyD88, IκBα, p-p50, and p-p65) through ELISA assay. Molecular docking analyses were performed to investigate the potential binding of allocryptopine to target proteins (TLR4, MyD88, IκBα, p50, p65, MKK3, MKK4, MKK6, p38, AP-1 (c-Jun and ATF2), IL-1β, IL-6, TNF-α, Cox-2, and iNOS) associated with the TLR4, NF-κB, and p38 MAPK pathways. Our results indicate that allocryptopine exerts a comprehensive influence on pro-inflammatory cytokines and other inflammatory mediators by inhibiting TLR4 signaling and modulating the NF-κB and p38 MAPK pathways. The outcomes of our study suggest that the antioxidant and anti-inflammatory efficacy of allocryptopine is intricately linked to the modulation of key molecular pathways associated with oxidative stress and inflammation. These findings highlight the potential of allocryptopine as a therapeutic agent for addressing neurodegenerative diseases by safeguarding neuronal health.

The cytotoxic activities of the major diterpene extracted from Salvia multicaulis (Bardakosh) are mediated by the regulation of heat-shock response and fatty acid metabolism pathways in human leukemia cells

BackgroundLeukemia is one of the most lethal cancers worldwide and represents the sixth-leading cause of cancer deaths. The results of leukemia treatment have not been as positive as desired, and recurrence is common. PurposeThus, there is an urgent requirement for the development of new therapeutic drugs. Salvia multicaulis (Bardakosh) is a widespread species that contains multiple phytochemical components with anti-cancer activities. MethodsWe isolated and characterized the major diterpene candesalvone B methyl ester from S. multicaulis and investigated its action as a cytotoxic agent towards sensitive and drug-resistant leukemia cells by the resazurin reduction assay. Additionally, the targeted genes and the affected molecular mechanisms attributed to the potent cytotoxic activities were discovered by transcriptome-wide mRNA expression profiling. The targets predicted to be regulated by candesalvone B methyl ester in each cell line were confirmed by qRT-PCR, molecular docking, microscale thermophoresis, and western blotting. Moreover, cell cycle distribution and apoptosis were analyzed by flow cytometry. ResultsCandesalvone B methyl ester was cytotoxic with IC50 values of 20.95 ± 0.15 µM against CCRF-CEM cells and 4.13 ± 0.10 µM against multidrug-resistant CEM/ADR5000 leukemia cells. The pathway enrichment analysis disclosed that candesalvone B methyl ester could regulate the heat-shock response signaling pathway via targeting heat shock factor 1 (HSF1) in CCRF-CEM cells and ELOVL fatty acid elongase 5 (ELOVL5) controls the fatty acid metabolism pathway in CEM/ADR5000 cells. Microscale thermophoresis showed the binding of candesalvone B methyl ester with HSF1 and ELOVL5, confirming the results of molecular docking analysis. Down-regulation of both HSF1 and ELOVL5 by candesalvone B methyl ester as detected by both western blotting and RT-qPCR was related to the reversal of drug resistance in the leukemia cells. Furthermore, candesalvone B methyl ester increased the arrest in the sub-G1 phase of the cell cycle in a dose-dependent manner from 1.3 % to 32.3 % with concomitant induction of apoptosis up to 29.0 % in CCRF-CEM leukemic cells upon inhibition of HSF1. ConclusionCandesalvone B methyl ester isolated from S. multicaulis exerted cytotoxicity by affecting apoptosis, cell division, and modulation of expression levels of genes contributing to the heat stress signaling and fatty acid metabolism pathways that could relieve drug resistance of leukemia cells.

Brevianamide F Exerts Antithrombotic Effects by Modulating the MAPK Signaling Pathway and Coagulation Cascade.

Existing antithrombotic drugs have side effects such as bleeding, and there is an urgent need to discover antithrombotic drugs with better efficacy and fewer side effects. In this study, a zebrafish thrombosis model was used to evaluate the antithrombotic activity and mechanism of Brevianamide F, a deep-sea natural product, with transcriptome sequencing analysis, RT-qPCR analysis, and molecular docking. The results revealed that Brevianamide F significantly attenuated the degree of platelet aggregation in the thrombus model zebrafish, leading to an increase in the number of circulating platelets, an augmentation in the return of blood to the heart, an elevated heart rate, and a significant restoration of caudal blood flow velocity. Transcriptome sequencing and RT-qPCR validation revealed that Brevianamide F may exert antithrombotic effects through the modulation of the MAPK signaling pathway and the coagulation cascade reaction. Molecular docking analysis further confirmed this result. This study provides a reference for the development of therapeutic drugs for thrombosis.

Lanostane triterpenoids from Ganoderma calidophilum exhibit potent anti-tumor activity by inhibiting PTP1B

The species Ganoderma calidophilum represents a distinct variety within the genus Ganoderma and used by the indigenous Li ethnic group as a medicinal agent for the prevention and treatment of cancer. However, the precise biological activity and role of G. calidophilum in antitumor treatment remain largely unresolved. Several lanostane triterpenoids have been isolated from G. calidophilum. The enzyme activity analysis revealed that four lanostane triterpenoids exhibited PTP1B inhibition activity, with minimal inhibition towards SHP2, SHP1, PTPN5, PTPRA, STEP and TCPTP. Molecular docking analysis demonstrated that these compounds primarily bind to the substrate recognition and entry regions of PTP1B. Further analysis indicated that among them, ganoderic aldehyde A (GAA) is a selective and non-competitive PTP1B inhibitor. GAA inhibited the proliferation, colony formation and migration of C33A and MDA-MB-231 cells in a dose-dependent manner. GAA has the capacity to induce apoptosis in a cell-type-specific manner, both in a caspase-dependent and -independent manner. PTP1B siRNA significantly reduced the cytotoxic effect of GAA, while overexpression of PTP1B significantly increased cell growth after GAA treatment. These findings confirm that PTP1B is a functional target of GAA. Research into the mechanisms of action of GAA has revealed that it could inhibit the activation of AKT by inhibiting PTP1B, while simultaneously activating p38, which promotes cell death. It is possible to develop specific PTP1B inhibitors based on the lanosterol triterpene skeleton. G. calidophilum has the potential to be developed into functional foods or drugs with the aim of preventing and treating cancer.

Structure-guided mutations in CDRs for enhancing the affinity of neutralizing SARS-CoV-2 nanobody

The optimization of antibodies to attain the desired levels of affinity and specificity holds great promise for the development of next generation therapeutics. This study delves into the refinement and engineering of complementarity-determining regions (CDRs) through in silico affinity maturation followed by binding validation using isothermal titration calorimetry (ITC) and pseudovirus-based neutralization assays. Specifically, it focuses on engineering CDRs targeting the epitopes of receptor-binding domain (RBD) of the spike protein of SARS-CoV-2. A structure-guided virtual library of 112 single mutations in CDRs was generated and screened against RBD to select the potential affinity-enhancing mutations. Protein-protein docking analysis identified 32 single mutants of which nine mutants were selected for molecular dynamics (MD) simulations. Subsequently, biophysical ITC studies provided insights into binding affinity, and consistent with in silico findings, six mutations that demonstrated better binding affinity than native nanobody were further tested in vitro for neutralization activity against SARS-CoV-2 pseudovirus. Leu106Thr mutant was found to be most effective in virus-neutralization with IC50 values of ∼0.03 μM, as compared to the native nanobody (IC50 ∼0.77 μM). Thus, in this study, the developed computational pipeline guided by structure-aided interface profiles and thermodynamic analysis holds promise for the streamlined development of antibody-based therapeutic interventions against emerging variants of SARS-CoV-2 and other infectious pathogens.