Docking Experiments Research Articles

Evaluation of phenolic and antioxidant profiles of pink Guava peel (Psidium guajava L. cv Arka kiran) during fruit ripening and its in silico Anti SARS-CoV-2 property

Guava (Psidium guajava L.) is a highly nutritious and economically important fruit. Although fruit peel is generally regarded as a waste, researchers believe that the peel of the guava is rich in bioactive constituents, even higher than the fruit's flesh. The present study aimed to estimate phenolic content (total phenolic and total flavonoid) and assess antioxidant properties of guava fruit peel (pink variety, cv Arka kiran) by 2,2-di (4-tert-octylphenyl)-1-picryl-hydrazyl (DPPH), 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid (ABTS) and Ferric Reducing Antioxidant Potential (FRAP) assays at five different ripening stages (stage 1 to 5). The TPC and TFC assays were performed by Folin-Ciocalteu and aluminium chloride (AlCl3) methods, respectively. The molecular docking experiment between the major phenolic of guava peel, Catechin and the spike protein of SARS-CoV-2 was performed by the Dockthor online server. Results showed that the peel had high phenolic (highest TPC and TFC, 7307.3 mg gallic acid equivalent/g dry weight [DW] and 433.9 mg quercetin equivalent/g DW, respectively) and antioxidant values (highest DPPH, ABTS and FRAP values 4784.8, 206.6 and 2451 mg ascorbic acid equivalent/g DW, respectively) throughout all stages, although there was a gradual decline in the activity at the later stages. Furthermore, it was found that catechin had a strong binding affinity (-7.591 kcal mol-1) with the spike protein, in silico when compared with the control drug ceftazidime (-7.250 kcal mol-1). The overall outcome of our experiemnts revealed that guava peel could be explored for future pharmacological applications through in vivo studies, and the ‘green mixed with the yellow’ stage of ripening is optimum for such studies.

In silico identifying MET/FN1/TGFBI as molecular targets in drug-resistant head and neck cancer and preclinical repurposing sulfasalazine for enhanced therapeutic efficacy

Head and neck squamous cell carcinoma (HNSCC) is a highly aggressive cancer affecting over half a million people worldwide each year. Although recent FDA-approved treatments, like cetuximab, have shown promise, the five-year survival rate remains below 50 %. This underscores the need to identify molecular signatures predicting clinical outcomes and potential therapeutic targets. Notably, the alteration of tyrosine-protein kinase Met (c-Met), a hepatocyte growth factor (HGF) receptor, stimulates tumor growth and metastasis across various cancers. However, its role and clinical implications in HNSCC remain unexplored. In HNSCC, MET's downstream signaling, mediated by phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt), is activated by fibronectin 1 (FN1), an extracellular matrix protein, fostering cancer progression. Additionally, FN1 and transforming growth factor-β (TGFB) are known to induce epithelial-mesenchymal transition in numerous cancers, leading to metastasis. Our computational analysis revealed significant upregulation of MET/FN1/TGFBI in HNSC at the mRNA level compared to normal samples. Given the immune system's pivotal role in HNSC progression, we analyzed the association of our target genes with immune infiltration. Our findings suggest a correlation between MET/FN1/TGFBI oncogenes and various stromal cells, highlighting their potential role in cancer recurrence and therapeutic resistance. We further explored the therapeutic potential of sulfasalazine, an anti-inflammatory drug. Molecular docking experiments revealed that sulfasalazine had a strong affinity for MET, FN1, and TGFBI, outperforming standard inhibitors in binding energy. These observations suggest sulfasalazine could be a promising MET/FN1/TGFBI gene signature inhibitor. Our study offers preclinical evidence supporting sulfasalazine as a standalone therapeutic agent and an adjunct to counteract cisplatin resistance in HNSC cells.

Biochemical and molecular docking-based strategies of Acalypha indica and Boerhavia diffusa extract by targeting bacterial strains and cancer proteins

Antibiotic-resistant microbes have emerged around the world, presenting a risk to health. Plant-derived drugs have become a potential source for the production of antibiotic-resistant drugs and cancer therapies. In this study, we investigated the antibacterial, cytotoxic and antioxidant properties of Acalypha indica and Boerhavia diffusa, and conducted in silico molecular docking experiments against EGFR and VEGFR-2 proteins. The metabolic extract of A. indica inhibited Streptococcus iniae and Staphylococcus sciuri with inhibition zones of 21.66 ± 0.57 mm and 20.33 ± 0.57 mm, respectively. The B. diffusa leaf extract produced inhibition zones of 20.3333 ± 0.5773 mm and 20.33 ± 0.57 mm against Streptococcus iniae and Edwardsiella anguillarum, respectively. A. indica and B. diffusa extracts had toxicities of 162.01 μg/ml and 175.6 μg/ml, respectively. Moreover, B. diffusa (IC50 =154.42 µg/ml) leaf extract exhibited moderately higher antioxidant activity compared with the A. indica (IC50 = 218.97 µg/ml) leaf extract. Multiple interactions were observed at Leu694, Met769 and Leu820 sites for EGFR and at Asp1046 and Cys1045 sites for VEGFR during the molecular docking study. CID-235030, CID-70825 and CID-156619353 had binding energies of −7.6 kJ/mol, −7.5 kJ/mol and −7.6 kJ/mol, respectively, with EGFR protein. VEGFR-2 protein had docking energies of −7.5 kJ/mol, −7.6 kJ/mol and −7.3 kJ/mol, respectively, for CID-6420353, CID-156619353 and CID-70825 compounds. The MD simulation trajectories revealed the hit compound; CID-235030 and EGFR complex, CID-6420353 and VEGFR-2 exhibit stable profile in the root mean square deviation (RMSD), radius of gyration (Rg), solvent accessible surface area (SASA), hydrogen bond and root mean square fluctuation (RMSF) and the binding free energy by MM-PBSA method. This study indicates that methanol extracts of A. indica and B. diffusa may play a crucial role in developing antibiotic-resistant and cancer drugs. Communicated by Ramaswamy H. Sarma

Mechanisms of Actinidia chinensis Planch in treating colon cancer based on the integration of network pharmacology, molecular docking, and experimental verification

BackgroundAs an anticancer Chinese herbal medicine, the effective components and mechanism of Actinidia chinensis Planch (ACP, Tengligen) in the treatment of colon cancer are still unclear. In the present study, the integration of network pharmacology, molecular docking, and cell experiments was employed to study the effective mechanism of ACP against colon cancer.MethodsThe Venn diagram and STRING database were used to construct the protein–protein interaction network (PPI) of ACP-colon cancer, and further topological analysis was used to obtain the key target genes of ACP in colon cancer. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to visualize the related functions and pathways. Molecular docking between key targets and compounds was determined using software such as AutoDockTools. Finally, the effect of ACP on CT26 cells was observed in vitro.ResultsThe study identified 40 ACP-colon key targets, including CASP3, CDK2, GSK3B, and PIK3R1. GO and KEGG enrichment analyses found that these genes were involved in 211 biological processes and 92 pathways, among which pathways in cancer, PI3K-Akt, p53, and cell cycle might be the main pathways of ACP against colon cancer. Molecular docking verified that the key components of ACP could stably bind to the corresponding targets. The experimental results showed that ACP could inhibit proliferation, induce apoptosis, and downregulate the phosphorylation of PIK3R1, Akt, and GSK3B in CT26 cells.ConclusionACP is an anti-colon cancer herb with multiple components, and involvement of multiple target genes and signaling pathways. ACP can significantly inhibit proliferation and induce apoptosis of colon cancer cells, which may be closely related to the regulation of PI3K/AKT/GSK3B signal transduction.

Chemical Comparison and Identification of Xanthine Oxidase Inhibitors of Dioscoreae Hypoglaucae Rhizoma and Dioscoreae Spongiosae Rhizoma by Chemometric Analysis and Spectrum-Effect Relationship.

Dioscoreae hypoglaucae Rhizoma (DH) and Dioscoreae spongiosae Rhizoma (DS) are two similar Chinese herbal medicines derived from the Dioscorea family. DH and DS have been used as medicines in China and other Asian countries for a long time, but study on their phytochemicals and bioactive composition is limited. This present study aimed to compare the chemical compositions of DH and DS, and explore the anti-xanthine oxidase components based on chemometric analysis and spectrum-effect relationship. Firstly, an HPLC method was used to establish the chemical fingerprints of DH and DS samples, and nine common peaks were selected. Then, hierarchical clustering analysis, principal component analysis and orthogonal partial least squares discriminant analysis were employed to compare and discriminate DH and DS samples based on the fingerprints data, and four steroidal saponins compounds (protodioscin, protogracillin, dioscin, gracillin) could be chemical markers responsible for the differences between DH and DS. Meanwhile, the anti-xanthine oxidase activities of these two herbal medicines were evaluated by xanthine oxidase inhibitory assay in vitro. Pearson correlation analysis and partial least squares regression analysis were subsequently used to investigate the spectrum-effect relationship between chemical fingerprints and xanthine oxidase inhibitory activities. The results showed that four steroidal saponins, including protodioscin, protogracillin, methyl protodioscin and pseudoprogracillin could be potential anti-xanthine oxidase compounds in DH and DS. Furthermore, the xanthine oxidase inhibitory activities of the four selected inhibitors were validated by anti-xanthine oxidase inhibitory assessment and molecular docking experiments. The present work provided evidence for understanding of the chemical differences and the discovery of the anti-xanthine oxidase constituent of DH and DS, which could be useful for quality evaluation and bioactive components screening of these two herbal medicines.

Anticancerous Properties of Tetragonula travancorica (stingless bee) Honey on Reproductive Cancer Cells

Honey from stingless bee is highly regarded as a medicine in many global communities due to its nutritional and therapeutic value. There is a comparatively restricted amount of research on the biological characteristics of stingless bee honey (SBH) in contrast to Indian bee honey (IBH). Therefore, the objective of this research is to explore the anti-cancer properties of Tetragonula travancorica honey. In the present investigation, antioxidant activity of honey was evaluated using ABTS, DPPH and SOD radical scavenging assays. Anti-proliferative effects was examined on various cell lines using the MTT assay. Liquid chromatography-mass spectrometry (LCMS) analysis was employed to characterize the honey. Binding capabilities of compounds identified in SBH on estrogen receptors (ER) α and ER β were explored through Schrödinger Maestro software. Results indicated that SBH effectively scavenged ABTS, DPPH and SOD free radicals with IC50 values of 22, 36.15, and 79.85 v/v, respectively. SBH exhibited anti-proliferative activity against MCF-7 and HeLa cell lines, with IC50 values of 58.11 and 66.68 v/v, respectively. LCMS analysis, shows the presence of methyl syringate, 2-hydroxycinnamic acid, and fumaric acid in SBH which were not present in IBH. Docking experiments determined that these compounds, with the exception of fumaric acid, interacted stronger with the binding sites of ER β than ER α. The comprehensive findings from antioxidant, anti-proliferative, and docking studies underscore the potential anti-cancer properties of Tetragonula travancorica honey, particularly its heightened cytotoxicity against reproductive system cancer cell lines, such as those in the breast and cervix. Keywords : Anti-proliferative, estrogen receptor, stingless bee, cytotoxicity.

Moist Heat Synthesis of Magnetic EGCG-Cappedα-Fe2O3 Nanoparticles and Their In Vitro and In Silico Interactions with Pristine HSA- and NDM-1-Producing Bacteria.

A simple, facile, moist-heating (e.g., autoclave), one-step procedure for EGCG-mediated biosynthesis of narrow-size magnetic iron oxide (α-Fe2O3) nanoparticles (EGCG-MINPs) was developed. The influence of pH of the reaction mixture over the size distribution of as-synthesized EGCG-MINPs was investigated systematically by employing UV-visible (UV-vis) spectroscopy and dynamic light scattering (DLS)-based hydrodynamic size, surface charge (zeta-potential), and polydispersity index (PDI). The FE-SEM, TEM, and XRD characterizations revealed that the EGCG-MINPs synthesized at pH 5.0 were in the size range of 6.20-16.7 nm and possess well-crystalline hexagonal shaped nanostructures of hematite (α-Fe2O3) crystal phase. The role of EGCG in Fe3+ ion reduction and EGCG-MINP formation was confirmed by FTIR analysis. The VSM analysis has revealed that EGCG-MINPs were highly magnetic nanostructures with the hysteretic feature of saturation magnetization (Ms), remanent magnetization (Mr), and coercivity (Hc) as 33.64 emu/g, 12.18 emu/g, and 0.33 Oe, respectively. Besides, significant (p < 0.001) dose-dependent (250-1000 μg/mL) antibacterial and antibiofilm activities against the NDM-1-producing Gram-negative Escherichia coli (AK-33), Klebsiella pneumoniae (AK-65), Pseudomonas aeruginosa (AK-66), and Shigella boydii (AK-67) bacterial isolates warranted the as-synthesized EGCG-MINPs as a promising alternative for clinical management of chronic bacterial infections in biomedical settings. In addition, molecular docking experiments revealed that compared to free Fe3+ and EGCG alone, the EGCG-MINPs or Fe-EGCG complex possess significantly high binding affinity toward HSA and hence can be considered as promising biocompatible nanodrug carriers in in vivo drug delivery systems.

Molecular structure, characterization, in vitro and in-silico studies of N,N-dimethyl aminophenyl schiff's base-chalcone hybrid

This study reports the synthesis and characterization of a novel compound, a chalcone-based Schiff base (SBC), with potential applications in anti-inflammatory and anti-diabetic treatments. Chalcones, known for their diverse biological activities, are combined with Schiff bases, versatile compounds, to create the SBC. The synthesis process involves aldol condensation and Schiff base formation. The compound's structure is confirmed through NMR, FT-IR, and mass spectroscopic analyses. The UV–visible spectroscopy reveals the compound's electronic properties, and molecular docking experiments indicate its potential to interact with enzymes related to inflammation and diabetes. Anti-inflammatory activity is evaluated through a protein denaturation assay using bovine serum albumin. SBC demonstrates significant anti-inflammatory activity, outperforming standard drug molecules, and exhibits concentration-dependent effects. In an α-amylase inhibitory assay, a vital enzyme in the digestive process related to diabetes, SBC shows remarkable inhibition, surpassing standard drug performance, especially at higher concentrations. Molecular docking studies suggest the compound's potential interactions with enzymes responsible for inflammation and diabetes. SBC displays strong binding energies and inhibition constants with α-amylase, indicating its suitability for diabetes-related studies. The synthesis and characterization of SBC, combined with its excellent anti-inflammatory and anti-diabetic activities, underscore its potential as a promising candidate for further biomedical research and therapeutic development.

Transplacental transport of per- and polyfluoroalkyl substances (PFAS): Mechanism exploration via BeWo cell monolayer model

Per- and polyfluoroalkyl substances (PFAS) have received global concern on adverse effects on pregnancy outcomes. Although human studies have reported fetal exposure to PFAS, the underlying mechanisms driving transplacental transfer of PFAS have not been sufficiently understood. The present study aimed to investigate chemical-specific transplacental transfer of PFAS and potential mechanisms based on a BeWo cell monolayer model. The findings of concentration- and time-dependent transport, asymmetry in bidirectional transport, molecular docking and transporter inhibition experiments indicate that passive diffusion and membrane transporter-involved active transport could collectively determine transplacental transport of PFAS. Membrane transporters could play important roles in chemical-specific transport. The inhibition of OAT transporter resulted in promotion of trans-monolayer transport for most PFAS, while an opposite trend was observed when P-gp, BCRP and MRP transporters were prohibited. By contrast, inhibition of OCT resulted in inhibitory effects on the transport of some PFAS (i.e., PFHxA, PFHpA, PFOA, and PFNA), and promotive effects on the other substances (i.e., PFUdA, PFHpS, PFOS, 6:2 Cl-PFESA and PFOSA). Therefore, simultaneous involvement of diverse membrane transporters in utero could result in complicated influence on transplacental transport. Our work constitutes a solid ground for further exploration of the effects of gestational PFAS exposure on birth outcomes.

Targeting antimalarial metabolites from the actinomycetes associated with the Red Sea sponge Callyspongia siphonella using a metabolomic method

Malaria is a persistent illness that is still a public health issue. On the other hand, marine organisms are considered a rich source of anti‑infective drugs and other medically significant compounds. Herein, we reported the isolation of the actinomycete associated with the Red Sea sponge Callyspongia siphonella. Using "one strain many compounds" (OSMAC) approach, a suitable strain was identified and then sub-cultured in three different media (M1, ISP2 and OLIGO). The extracts were evaluated for their in-vitro antimalarial activity against Plasmodium falciparum strain and subsequently analyzed by Liquid chromatography coupled with high-resolution mass spectrometry (LC-HR-MS). In addition, MetaboAnalyst 5.0 was used to statistically analyze the LC-MS data. Finally, Molecular docking was carried out for the dereplicated metabolites against lysyl-tRNA synthetase (PfKRS1). The phylogenetic study of the 16S rRNA sequence of the actinomycete isolate revealed its affiliation to Streptomyces genus. Antimalarial screening revealed that ISP2 media is the most active against Plasmodium falciparum strain. Based on LC-HR-MS based metabolomics and multivariate analyses, the static cultures of the media, ISP2 (ISP2-S) and M1 (M1-S), are the optimal media for metabolites production. OPLS-DA suggested that quinone derivatives are abundant in the extracts with the highest antimalarial activity. Fifteen compounds were identified where eight of these metabolites were correlated to the observed antimalarial activity of the active extracts. According to molecular docking experiments, saframycin Y3 and juglomycin E showed the greatest binding energy scores (-6.2 and -5.13) to lysyl-tRNA synthetase (PfKRS1), respectively. Using metabolomics and molecular docking investigation, the quinones, saframycin Y3 (5) and juglomycin E (1) were identified as promising antimalarial therapeutic candidates. Our approach can be used as a first evaluation stage in natural product drug development, facilitating the separation of chosen metabolites, particularly biologically active ones.

Isolation and in silico investigation of cannflavins from Cannabis sativa leaves as potential anti-SARS-CoV-2 agents targeting the Papain-Like Protease

This study aimed to isolate and identify three prenylflavonoids (cannflavin A, B, and C) from Cannabis sativa leaves using different chromatographic techniques. The potential of the isolated compounds against SARS-CoV-2 was suggested through several in silico analysis. Structural similarity studies against nine co-crystallized ligands of SARS-CoV-2’s proteins indicated the similarities of the isolated cannflavins with the SARS-CoV-2 Papain-Like Protease (PLP) ligand, Y95. Then, flexible allignment study confirmed this similarity. Docking experiments showed successful binding of all cannflavins within the active pocket of PLP, with energies comparable to Y95. Among them, cannflavin A demonstrated the most similar binding mode, while cannflavin C exhibited the best energy. Molecular dynamics (MD) simulations and MM-GPSA confirmed the accurate binding of cannflavin A to the PLP. In silico ADMET studies indicated favourable drug-like properties for all three compounds, suggesting their potential as anti-SARS-CoV-2 agents. Further In vitro and In vivo investigations are necessary to validate these findings and establish their efficacy and safety profiles.

An investigation of the mechanism of ZiyinDianji decoction in treating follicular dysplasia based on network pharmacology and molecular docking.

Follicular development disorder is a common gynaecological endocrine disease that can cause infertility, menstrual disorders, abortion, and other complications. ZiyinDianji decoction (ZYDJD) is a commonly used traditional Chinese medicine in clinical practice to promote follicular growth and development, but its pharmacological activity and mechanism of action are not clear. We combined network pharmacology with molecular docking and in vivo animal experiments to investigate the mechanism of ZYDJD in follicular development disorder. Cytoscape software was used for constructing ZYDJD-active component-target and PPI networks. GO biological process and KEGG pathway enrichment analyses were performed. The main components and key targets were selected for molecular docking. Finally, animal experiments were conducted for validation. The network pharmacology results showed that ZYDJD contained 83 active components and 159 core targets. The six most important active components were quercetin, luteolin, kaempferol, baicalein, isorhamnetin, and β-sitosterol, and the most important disease targets were AKT1, TNF, IL-6, and P53. GO analysis mainly involved 470 cell biological processes, including effect on hormones, vascular morphogenesis, development, and cell proliferation. KEGG analysis involved cancer pathways, lipid metabolism pathways, and PI3K/AKT signalling pathways. Molecular docking showed good results, and animal experiments further verified that ZYDJD prevented cyclophosphamide from causing excessive activation of primordial follicles. ZYDJD maintained ovarian reserve and reproductive function by inhibiting the hyperphosphorylation of key molecules of the PI3K/Akt pathway, reducing FOXO3a, thereby ensuring the development of normal follicles. In conclusion, based on network pharmacology, molecular docking, and animal experiments, ZYDJD may act through the PI3K/Akt/FOXO3a pathway.

Cytotoxicity of dioncophylline A and related naphthylisoquinolines in leukemia cells, mediated by NF-κB inhibition, angiogenesis suppression, G2/M cell cycle arrest, and autophagy induction

BackgroundInhibition of NF-κB activity represents a strategy to treat acute myeloid leukemia, one of the most lethal leukemia types. Naphthylisoquinolines (NIQs) are cytotoxic alkaloids from lianas of the families Ancistrocladaceae and Dioncophyllaceae, which are indigenous to tropical rainforests. PurposeUncovering therapeutic possibilities and underlying molecular mechanisms of dioncophylline A and its derivatives towards NF-κB related cellular processes. MethodsResazurin-based cell viability assay was performed for dioncophylline A and three derivatives on wild-type CCRF-CEM and multidrug-resistant CEM/ADR5000 cells. Transcriptome analysis was executed to discover cellular functions and molecular networks associated with dioncophylline A treatment. Expression changes obtained by mRNA microarray hybridization were confirmed using qRT-PCR. Molecular docking was applied to predict the affinity of the NIQs with NF-κB. To validate the in silico approach, NF-κB reporter assays were conducted on HEK-Blue™ Null1 cells. Cell death mechanisms and cell cycle arrest were studied using flow cytometry. The potential activity on angiogenesis was evaluated with the endothelial cell tube formation assay on HUVECs using fluorescence microscopy. Intracellular NF-κB location in HEK-Blue™ Null1 cells was visualized with immunofluorescence. Finally, the anti-tumor activity of dioncophylline A was studied by a xenograft zebrafish model in vivo. ResultsOur study demonstrated that dioncophylline A and its derivatives exerted potent cytotoxicity on leukemia cells. Using Ingenuity Pathway Analysis, we identified the NF-κB network as the top network, and docking experiments predicted dioncophylline A and two of its derivatives sharing the same binding pocket with the positive control compound, triptolide. Dioncophylline A showed the best inhibitory activity in NF-κB reporter assays compared to its derivatives, caused autophagy rather than apoptosis, and induced G2/M arrest. It also prevented NF-κB translocation from the cytoplasm to the nucleus. Tube formation as an angiogenesis marker was significantly suppressed by dioncophylline A treatment. Finally, the remarkable anti-tumor activity of dioncophylline A was proven in zebrafish in vivo. ConclusionTaken together, we report for the first time the molecular mechanism behind the cytotoxic effect of dioncophylline A on leukemia cells. Dioncophylline A showed strong cytotoxic activity, inhibited NF-κB translocation, significantly affected the NF-κB in silico and in vitro, subdued tube formation, induced autophagy, and exerted antitumor activity in vivo. Our findings enlighten both the cellular functions including the NF-κB signaling pathway and the cytotoxic mechanism affected by dioncophylline A.

Effects of exopolysaccharide by Pediococcus acidilactici S1 on the gelation properties and microstructure of porcine myofibrillar protein

The utilization of extracellular polysaccharides (EPS) derived from lactobacilli is widely observed in the dairy and cereal sectors, whereas their implementation in meat products has received limited research attention. This study was to enhance the utilization of EPS from Pediococcus acidilactici S1 (S1-EPS) in the meat industry and optimize the gel properties of myofibrillar protein (MP)-based food systems. In the study, the impact of incorporating S1-EPS on the properties of MP gels was investigated, revealing significant improvements in water retention, strength, textural characteristics, and rheological behavior. Furthermore, it was observed that S1-EPS facilitated myosin aggregation through hydrophobic interactions and induced a transition in the secondary structure and microstructure of MP from disorder to order. In molecular docking experiments, S1-EPS demonstrated stable binding to myosin through hydrogen bonding and robust electrostatic interactions, indicating its potential as a valuable gelling agent for meat products and contribution to the development of MP gel structure following heat treatment.

Analysis of RNA Recognition and Binding Characteristics of OsCPPR1 Protein in Rice

Pentatricopeptide repeat (PPR) proteins represent one of the largest protein families in plants and typically localize to organelles like mitochondria and chloroplasts. By contrast, CYTOPLASM- LOCALIZED PPR1 (OsCPPR1) is a cytoplasm-localized PPR protein that can degrade OsGOLDEN- LIKE1 (OsGLK1) mRNA in the tapetum of rice anther. However, the mechanism, by which OsCPPR1 recognizes and binds to OsGLK1 transcripts, remains unknown. Through protein structure prediction and macromolecular docking experiments, we observed that distinct PPR motif structures of OsCPPR1 exhibited varying binding efficiencies to OsGLK1 RNA. Moreover, RNA-electrophoretic mobility shift assay experiment demonstrated that the recombinant OsCPPR1 can directly recognize and bind to OsGLK1 mRNA in vitro. This further confirmed that the mutations in the conserved amino acids in each PPR motif resulted in loss of activity, while truncation of OsCPPR1 decreased its binding efficiency. These findings collectively suggest that it may require some co-factors to assist in cleavage, a facet that warrants further exploration in subsequent studies.

Exploring of multi-functional umami peptides from Stropharia rugosoannulata: Saltiness-enhancing effect and mechanism, antioxidant activity and potential target sites

Umami peptides enhance flavor and offer potential health benefits. We analyzed the taste-value profiles of five novel umami peptides from Stropharia rugosoannulata using E-tongue, exhibiting significant saltiness characteristics. While the peptides PHEMQ and SEPSHF exhibited higher saltiness, their mixture with salt did not enhance saltiness compared to individual peptides. Surprisingly, SGCVNEL, which was initially weak in saltiness, showed remarkably enhanced saltiness when mixed with salt, possibly due to have strong binding with receptors. Molecular docking elucidated the salt-forming mechanism of TMC4, highlighting the P2-domain and hydrogen bonds’ role in the composite structure stability. Evaluation of the antioxidant activity evaluation demonstrated dose-dependent effects primarily through free radical scavenging via the single-electron transfer potential mechanism for SGCVNEL, EPLCNQ, and ESCAPQL. Docking experiments with antioxidant targets revealed varied binding stabilities, indicating diverse antioxidant effects of the peptides. These findings provide valuable insights into the exploration and application of versatile bioactive flavor peptides.

The previously uncharacterized RnpM (YlxR) protein modulates the activity of ribonuclease P in Bacillus subtilis in vitro.

Even though Bacillus subtilis is one of the most studied organisms, no function has been identified for about 20% of its proteins. Among these unknown proteins are several RNA- and ribosome-binding proteins suggesting that they exert functions in cellular information processing. In this work, we have investigated the RNA-binding protein YlxR. This protein is widely conserved in bacteria and strongly constitutively expressed in B. subtilis suggesting an important function. We have identified the RNA subunit of the essential RNase P as the binding partner of YlxR. The main activity of RNase P is the processing of 5' ends of pre-tRNAs. In vitro processing assays demonstrated that the presence of YlxR results in reduced RNase P activity. Chemical cross-linking studies followed by in silico docking analysis and experiments with site-directed mutant proteins suggest that YlxR binds to the region of the RNase P RNA that is important for binding and cleavage of the pre-tRNA substrate. We conclude that the YlxR protein is a novel interaction partner of the RNA subunit of RNase P that serves to finetune RNase P activity to ensure appropriate amounts of mature tRNAs for translation. We rename the YlxR protein RnpM for RNase P modulator.

Determination of the pharmacodynamic substances and mechanism of Shiwuwei Saierdou Pills against cholestatic hepatitis through chemical profile identification and network pharmacology analysis

Cholestatic hepatitis (CH) is a liver lesion caused by abnormal bile production, secretion and excretion and has a complex pathogenesis. The Tibetan medicine Shiwuwei Saierdou Pills (SSP) is an empirical Tibetan medicine formula for the treatment of CH, but its chemical composition is complex and the material basis of its efficacy is not yet clear. So, in this study, the main chemical constituents and its blood-incorporated constituents in SSP were analyzed by ultra-high-performance liquid chromatography-quadruple-electrostatic field orbitrap high resolution mass spectrometry (UHPLC-Q-Exactive Orbitrap/MS), Then, the blood-incorporated constituents were subjected to network pharmacology analysis to preliminarily clarify its potential pharmacological substances and mechanism. and further, it was verified through molecular docking and in vivo animal experiments. As a result, a total of 80 chemical components were identified in the SSP, of which 11 were confirmed by reference standards and 20 blood-incorporated constituents (including 10 prototypes and 10 metabolites) were characterized in the serum containing the medicine. The core targets of SSP for the treatment of CH were identified as AKT1, VEGFA, CASP3, SRC and MAPK3 through the screening of the relationship between the blood-incorporated constituents and the targets. Combined with the results of molecular docking, swertiamarin, ellagic acid, taurocholic acid and bellidifolin in the ten prototypes may be the key pharmacodynamic substances for SSP to treat CH. The results of animal experiments showed that SSP could significantly inhibit the pathological changes of the CH rat model, and inhibit the protein expression of AKT1, VEGFA, CASP3, SRC and MAPK3. In summary, we used network pharmacology, molecular docking and animal experiments to preliminarily determine the main medicinal components, targets and pathways of SSP in the treatment of CH, which provides a scientific basis for further revealing the material basis and mechanism of SSP in treating CH.

Evaluation of Cytotoxicity of 1H-1,2,4-Triazole-3-carboxamide Derivatives in Various Cancer Cell Lines using MTT Assay: Synthesis, Characterization and Molecular Docking Studies

The pursuit of discovering efficacious novel anticancer agents is an ongoing and perpetual endeavour. The ongoing research endeavour involves the discovery of a new set of various substituted 1,2,4-triazole carboxamide derivatives. The synthetic process involves multiple steps: converting thiooxamic acid ethyl ester to ethyl b-N-boc-oxalamidrazone (2), preparing ethyl esters of 5-substituted 1,2,4-triazole-3-carboxylic acid (3) and synthesizing 5-substituted 1,2,4-triazole-3-carboxylic acid amides (4a-n) using potassium tert.-butoxide. The resulting compounds are characterized using 1H and 13C NMR spectroscopy and HRMS. Molecula docking experiments were performed using the synthesized compounds against two cancer targets, viz. EGFR (6LUD) and CDK-4 (7SJ3). The compounds were assessed for their anticancer potential against four different cancer cell lines, namely non-small cell lung cancer (A-549), pancreatic cancer (PANC-1), colorectal cancer (HCT-116) and cervical cancer (HaLa) cell lines. Additionally, a normal human embryonic kidney cell line (HEK-293) was used for comparison. The results obtained from molecular docking analysis demonstrated that the 1,2,4-triazole carboxamides (4c, 4e, 4h, 4m and 4n) exhibited more favourable binding interactions compared to the ligands that were co-crystallized. All the compounds exhibited a satisfactory cytotoxicity profile in comparison to the reference drug doxorubicin. Among the compounds that tested, it was observed that compounds 4e and 4m displayed the most pronounced inhibitory activity across all the cell lines that were tested.

Combining Network Pharmacology, Molecular Docking and Preliminary Experiments to Explore the Mechanism of Action of FZKA Formula on Non-small Cell Lung Cancer.

Clinically, Fuzhengkangai formulation (FZKA) has been proven to have significant therapeutic effects on non-small lung cancer (NSCLC), although the mechanism is unknown. We aimed to explore the potential mechanism of FZKA in the treatment of NSCLC in this study. We obtained the active components and targets of FZKA by TCMSP. The target genes of NSCLC were searched from OMIM, GEO (GSE18842), and GeneCards database. Cytoscape (3.7.2) software was used to construct a "drug-compound-cross-target interaction" interaction network, and the STING database was used to analyze previous cross-target interactions. Meanwhile, the results were visualized and processed by performing GO enrichment analysis and KEGG signaling pathway enrichment analysis at the target site. The core targets were docked with active components through AutoDockTools-1.5.6 software. Finally, we used cellular experiments to validate the bioinformatics predictions. There were 40 active and 465 potential genes from the TCMSP database. Key active chemicals, namely Quercetin, Kaempferol, Luteolin, and Tanshinone IIA, and 176 targets were deemed as targets of FZKA against NSCLC by PPI network analysis. GO and KEGG enrichment analyses suggest that FZKA acts primarily through the PI3K-AKT and MAPK signaling pathways in the treatment of NSCLC. Moreover, cellular assays showed that Quercetin, Kaempferol, Luteolin, and Tanshinone IIA not only reduced the viability of A549 cells and promoted apoptosis but also significantly decreased the p-AKT/AKT and p-ERK1/2/ERK1/2 ratios. Our data suggested that FZKA can be involved in the treatment of NSCLC through multiple components, targets and pathways.