Molecular Docking Research Articles

Demonstration of Interaction between Carbapenem Group Antibiotics and Different Immunosuppressant Drugs by Molecular Docking

Background: It has been shown that drugs used parenterally cause errors in immunosuppressant concentrations measured by LC-MS / MS method. It is yet unknown whether this measurement error is due to drug-drug interaction or analytical interference. Objective: The aim of this study is to investigate the possible interaction and inhibition concentrations of broad-spectrum antibiotics (ertapenem, meropenem, imipenem) with 4 different immunosuppressants (tacrolimus, sirolimus, everolimus, cyclosporine A) by molecular docking. Method: The docking results of ertapenem, meropenem, and imipenem-cilastatin drugs, which are frequently used in intensive care units and wards, were analyzed with the Autodock 4.2 program. Binding energy levels and inhibition concentrations were recorded. Results: The highest binding energies of the most stable conformations, providing the best compatibility among the active ingredients, belong to cilastatin. The interaction energy of cilastatin with sirolimus in 320 conformations was calculated as -4.08 kcal/mol. Sirolimus interacted with ertapenem at -3.43, imipenem at -2.53, and meropenem at -3.84 kcal/mol. According to these values, the receptor, which is the most compatible host with all ligand molecules, is sirolimus. The least interaction energy value was calculated between cyclosporine and imipenem (-1.12 kcal / mol). Conclusion: Concerning the most stable conformations of models docked with Autodock tools, it has been determined that carbapenems interact with immunosuppressants. Since the detected inhibition concentration levels can be seen in blood samples taken immediately after carbapenem injection, immunosuppressant measurement is recommended before the use of carbapenem in immunosuppressant monitoring of transplant patients.

Exploring Mechanisms of Houshiheisan in Treating Ischemic Stroke with Network Pharmacology and Independent Cascade Model.

Houshiheisan (HSHS) has been effective in the treatment of ischemic stroke (IS) for centuries. However, its mechanisms are still underexplored. The objective of this study is to identify the active ingredients and mechanisms of HSHS in treating IS. We searched the main active compounds in HSHS and their potential targets, and key targets related to IS. Based on the common targets of HSHS and IS, we further expanded genes by KEGG database to obtain target genes and related genes, as well as gene interactions in the form of A→B, and then constructed a directed network including traditional Chinese medicines (TCMs), active compounds and genes. Finally, based on enrichment analysis, independent cascade (IC) model, and molecular docking, we explored the mechanisms of HSHS in treating IS. A directed network with 6,348 nodes and 64,996 edges was constructed. The enrichment analysis suggested that the AGE pathway, glucose metabolic pathway, lipid metabolic pathway, and inflammation pathway played critical roles in the treatment of IS by HSHS. Furthermore, the gene ontologies (GOs) of three monarch drugs in HSHS mainly involved cellular response to chemical stress, blood coagulation, hemostasis, positive regulation of MAPK cascade, and regulation of inflammatory response. Several candidate drug molecules were identified by molecular docking. This study advocated potential drug development with targets in the AGE signaling pathway, with emphasis on neuroprotective, anti-inflammatory, and anti-apoptotic functions. The molecular docking simulation indicated that the ligand-target combination selection method based on the IC model was effective and reliable.

Synthesis and computational study of metal complex of α-mangostin as an anticancer candidate

Context: The number of breast cancer patients from year to year is increasing, accompanied by an increase in global mortality; the position in Indonesia has reached 60-70% with end-stage conditions. ERα antiproliferative activity exists in α-mangostin compounds, but this compound still has several physicochemical problems, including its solubility. Therefore, efforts are needed to increase the activity of α-mangostin and its affinity as an alpha estrogen receptor antagonist through a structure-based design method. Aims: To obtain new compounds derived from α-mangostin in the form of a metal complex with cobalt (AM-Co), platinum (AM-Pt), and iron (AM-Fe) as medicinal ingredients that can be used as breast cancer therapeutic agents. Methods: The research methods include in silico studies (pharmacokinetic and toxicity prediction, molecular docking, and molecular dynamics), semi-synthesis to form a complex compound, and testing cytotoxic activity against MCF-7 and T-47D human breast cancer cells. Results: From the in vitro test results, it can be seen that the AM-Pt compound showed the best anticancer activity on MCF-7 cells compared to others from IC50 and SI values; this was supported by the results of in silico studies either through molecular docking or molecular dynamics, where this compound was more effective. Conclusions: Furthermore, it can be used as an anticancer candidate; particularly, its activity is predicted to be more potent as an ER antagonist than -mangostin and cisplatin.

Antiviral potential of selenium complexes from Brassicaceae by inhibiting protein bond between MAP4 and the spike of SARS-CoV-2

Context: Coronavirus disease 2019 (COVID-19), a highly contagious viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a worldwide pandemic. Selenium derived from the plants of the Brassicaceae family plays an important role in several biological functions, often as an antioxidant or antiviral. In particular, selenium can be used as an adjuvant in the treatment of various viral infections. Aims: To determine the potential drug, as well as the affinity and the bond energy associated with chemical interaction bonds between the complex selenium compounds from Brassicaceae as inhibitors of the SARS-CoV-2 spike protein and MAP4 through the use of in silico studies. Methods: The methods used in this study consisted of receptor and ligand data collection, ADMET analysis, molecular docking, and molecular dynamics. Results: The results of this study indicate that the selenium complex compounds have the potential to be used as a spike inhibitor drug for SARS-CoV-2, as they have passed the Lipinski test and showed promise in the pharmacokinetic analysis. The results of the bond docking show that several complex selenium compounds, such as ethaselen, selenomethionine, and selenocystine, have stronger binding affinity values than the controls. This is compared to the control MAP4, which yielded binding affinities of -6.1 kcal/mol and spike protein -7 kcal/mol, respectively. Controlled bisoxatin and estramustine are drugs with mechanisms targeted to MAP4 and spike protein, which are the usual standards used. Conclusions: The similarity of sites, the binding of several amino acid residues dominated by hydrogen bonds, and the result of molecular dynamic results for the selenium compound derived from Brassicaceae showed a stable bond to the spike protein and MAP4 with low fluctuation levels.

Predicting Potential Therapeutic Targets and Small Molecule Drugs for Early-Stage Lung Adenocarcinoma

Lung cancer is a leading cause of cancer-related mortality worldwide, with non-small cell lung cancer (NSCLC) constituting the majority, and its main subtype being lung adenocarcinoma (LUAD). Despite substantial advances in LUAD diagnosis and treatment, early diagnostic biomarkers inadequately fulfill clinical requirements. Thus, we conducted bioinformatics analysis to identify potential biomarkers and corresponding therapeutic drugs for early-stage LUAD patients. Here we identified a total of 10 differentially expressed genes (DEGs) with survival significance through the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA). Subsequently, we identified a promising small molecule drug, Aminopurvalanol A, based on the 10 key genes using the L1000FWD application, which was validated by molecular docking followed by in vivo and in vitro experiments. The results highlighted TOP2A, CDH3, ASPM, CENPF, SLC2A1, and PRC1 as potential detection biomarkers for early LUAD. We confirmed the efficacy and safety of Aminopurvalanol A, providing valuable insights for the clinical management of LUAD.

Reniformin A suppresses non-small cell lung cancer progression by inducing TLR4/NLRP3/caspase-1/GSDMD-dependent pyroptosis

Pyroptosis is an inflammatory form of programmed cell death that plays an important role in regulating tumor progression. Reniformin A (RA) is a natural compound isolated from the medicinal herb Isodon excisoides that has been applied as folk medicine in the treatment of esophageal cancer. However, whether RA has an individual function in cancer and the molecular mechanisms remain unclear. Here, we show that in non-small-cell lung cancer (NSCLC), RA inhibits tumor growth by functioning as a pyroptosis inducer to promote TLR4/NLRP3/caspase-1/GSDMD axis. Specially, RA treatment increased Toll-like receptor 4 (TLR4) protein expression level by enhancing the TLR4 stability. Based on the molecular docking, we identified that RA directly bound to TLR4 to activate the NLRP3 inflammasome and promote pyroptosis in A549 cells. Moreover, TLR4 is essential for RA-induced pyroptosis, and loss of TLR4 abolished RA-induced pyroptosis and further reduced the inhibitory effect of RA on NSCLC. In vivo experiments confirmed that RA inhibited the growth of lung tumors in mice by affecting pyroptosis in a dose-dependent manner. Furthermore, TLR4 knockdown abolished RA-induced pyroptosis and inhibited the effect of RA chemotherapy in vivo. In conclusion, we propose that RA has a significant anticancer effect in NSCLC by inducing TLR4/NLRP3/caspase-1/GSDMD-mediated pyroptosis, which may provide a potential strategy for the treatment of NSCLC.

The antimicrobial effectiveness of Rosmarinus officinalis, Lavandula angustifolia, and Salvia officinalis essential oils against Klebsiella pneumoniae and Pseudomonas aeruginosa in vitro and in silico

This study aimed to explore the phytochemical analyses and antibacterial potential of three essential oils (EOs) using both in-vitro and in-silico experiments for drug discovery. The Eos of Rosmarinus officinalis, Lavandula angustifolia, and Salvia officinalis were extracted by hydrodistillation, and GC–MS determined the chemical composition. The antibacterial activities of each EO were studied by the disc diffusion method. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of these EOs were determined by micro-dilution. In addition, the EOs were combined with ineffective antibiotics (Aztreonam et al.) against clinical bacteria (P. aeruginosa and K. pneumoniae) to determine this association's effect. The in-vitro toxicological study was based on the MTT cytotoxicity assay. Finally, in-silico methods were employed to estimate their possible antibacterial mechanisms. Molecular docking was performed to calculate the predictive binding affinities of five major volatile components to three proteins key in the bacterial cycle using the AutoDock Vina program; prediction of drug-likeness properties and Toxicity prediction were carried out respectively by SwissADME and ProToxII online server. The results showed that the three EOs possessed antibacterial activity against ATCC and clinical K. pneumoniae. We note that P. aeruginosa was resistant to lavender and sage EOs. Surprisingly, adding EOs to antibiotics ineffective against resistant bacteria showed a significant synergistic antibacterial effect. Cytotoxicity assay of essential oils showed different values ranging from 0.22 to 0.43 µL/mL. Finally, the molecular docking study revealed that both compounds (1,8-Cineol, 1-Dodecene, Linalool, cis-Thujone, and Camphor) from the three EOs have a significant potential to inhibit the protein target involved in bacteria resistance. Furthermore, the SwissADME prediction results showed that all five components satisfy the rule of five and exhibit acceptable drug-like characteristics. findings suggest that the three EOs have interesting antibacterial activity. The in-vitro and in-silico studies gave a great potentiation and may constitute a promising option to control the emergence of MDR P. aeruginosa and K. pneumoniae.

Discovery of Novel Inhibitors of Cruzain Cysteine Protease of Trypanosoma cruz.

Chagas disease (CD) is a parasitic disease endemic in several developing countries. According to the World Health Organization, approximately 6-8 million people worldwide are inflicted by CD. The scarcity of new drugs, mainly for the chronic phase, is the main reason for treatment limitation in CD. Therefore, there is an urgent need to discover new targets for which new therapeutical agents could be developed. Cruzain cysteine protease (CCP) is a promising alternative because this enzyme exhibits pleiotropic effects by acting as a virulence factor, modulating host immune cells, and interacting with host cells. This systematic review was conducted to discover new compounds that act as cruzain inhibitors, and their effects in vitro were studied through enzymatic assays and molecular docking. Additionally, the advances and perspectives of these inhibitors are discussed. These findings are expected to contribute to medicinal chemistry in view of the design of new, safe, and efficacious inhibitors against Trypanosoma cruzi CCP detected in the last decade (2013-2022) to provide scaffolds for further optimization, aiming toward the discovery of new drugs.

In silico Identification of HDAC Inhibitors for Multiple Myeloma: A Structure-based Virtual Screening, Drug Likeness, ADMET Profiling, Molecular Docking, and Molecular Dynamics Simulation Study

Background: Multiple myeloma (MM) is a hematological malignancy of plasma cells that produce a monoclonal immunoglobulin protein. Despite significant advances in the treatment of MM, currently available therapies are associated with toxicity and resistance. As a result, there is an increasing demand for novel, effective therapeutics. Inhibition of histone deacetylases (HDACs) is emerging as a potential method for treating cancer. HDAC6 is one of 18 different HDAC isoforms that regulate tubulin lysine 40 and function in the microtubule network. HDAC6 participates in tumorigenesis and metastasis through protein ubiquitination, tubulin, and Hsp90. Several studies have found that inhibiting HDAC6 causes AKT and ERK dephosphorylation, which leads to decreased cell proliferation and promotes cancer cell death via the PI3K/AKT and MAPK/ERK signaling pathways. Objective: The objective of this study is to target HDAC6 and identify potent inhibitors for the treatment of multiple myeloma by employing computer-aided drug design. Materials and Methods: A total of 199,611,439 molecules from five different chemical databases, such as CHEMBL25, ChemSpace, Mcule, MolPort, and ZINC, have been screened against HDAC6 by structure- based virtual screening, followed by filtering for various drug-likeness, ADME, toxicity, consensus molecular docking, and 100 ns MD simulation. Results: Our research work resulted in three molecules that have shown strong binding affinity (CHEMBL2425964 -9.99 kcal/mol, CHEMBL2425966 -9.89 kcal/mol, and CSC067477144 -9.86 kcal/mol) at the active site HDAC6, along with effective ADME properties, low toxicity, and high stability. Inhibiting HDAC6 with these identified molecules will induce AKT and ERK dephosphorylation linked to reduced cell proliferation and promote cancer cell death. Conclusion: CHEMBL2425964, CHEMBL2425966, and CSC067477144 could be effective against multiple myeloma.

Characterization and Mechanism Analysis of Sugar Transporter Protein Obtained from Monascus pilosus

Sugar transporter protein family is very common among different organisms in nature and plays a key role in the transportation, absorption, and synthesis of secondary metabolites. To investigate the functional characteristics of sugar transporter proteins in Monascus pilosus, cDNA sequence of sugar transporter protein gene MpST collected from M. pilosus CICC 5045 was cloned in this research. Furthermore, bioinformatics methods and molecular docking techniques were applied to analyze MpST protein. The obtained results revealed that the coding region of MpST was 1677 bp in length, which coded 558 amino acids, and it was a stable protein. Phylogenetic tree analysis found a close relationship between MpST and two other proteins from M. purpureus (BDD61243.1 and TQB74099.1). Bioinformatics analyses indicated that this protein is a hydrophilic protein with 11 transmembrane domains and its functional domains were mainly consisted of the conserved domains of major facilitator superfamily (MFS) and sugar transporter proteins, suggesting that this protein belonged to MFS transporter protein family. Molecular docking results suggested that the receptor protein could spontaneously bind with high affinity to small molecular ligands such as galactose, raffinose, glucose, xylose, and maltose. From the above analyses, it was predicted that this protein might have good transport function for the above five sugars. This study lays the foundation for further in-depth research on the functions and applications of this protein.

Network toxicology, molecular docking technology, and experimental verification revealed the mechanism of cantharidin-induced testicular injury in mice

As a protein kinase inhibitor, cantharidin (CTD) exhibits antitumor activities. However, CTD is highly toxic, thereby limiting clinical applications. Moreover, relatively few studies have investigated CTD-induced reproductive toxicity, thus the underlying mechanism remains unclear. In this study, the toxic effects of CTD on mouse testis were confirmed in vivo and the potential mechanism was predicted by network toxicology (NT) and molecular docking technology. Proteins involved in the signaling pathways and core targets were verified. The results showed that different concentrations of CTD induced weight loss increased the testicular coefficient, and caused obvious pathological damage to testicular cells. The NT results showed that the main targets of CTD-induced testicular injury (TI) included AKT1, Caspase 3, Bcl-2, and Bax. The results of pathway enrichment analysis showed that CTD-induced TI was closely related to apoptosis and the PI3K/AKT and HIF-1 signaling pathways. Molecular docking methods confirmed high affinity between CTD and key targets. Western blot analysis showed that CTD inhibited expression of PI3K, AKT, and the anti-apoptotic protein Bcl-2, while promoting expression of the pro-apoptotic proteins Bax and Caspase 3. These results suggest that CTD-induced TI involves multiple targets and pathways, and the underlying mechanism was associated with inhibition of the apoptosis-related PI3K/AKT signaling pathway.

Honokiol suppress the PD-L1 expression to improve anti-tumor immunity in lung cancer

Lung cancer is a serious health issue globally, and current treatments have proven to be inadequate. Therefore, immune checkpoint inhibitors (ICIs) that target the PD-1/PD-L1 pathway have become a viable treatment option in lun cancer. Honokiol, a lignan derived from Magnolia officinalis, has been found to possess anti-inflammatory, antioxidant, and antitumor properties. Our research found that honokiol can effectively regulate PD-L1 through network pharmacology and transcriptome analysis. Cell experiments showed that honokiol can significantly reduce PD-L1 expression in cells with high PD-L1 expression. Molecular docking, cellular thermal shift assay (CETSA) and Bio-Layer Interferometry (BLI)indicated that Honokiol can bind to PD-L1. Co-culture experiments on lung cancer cells and T cells demonstrated that honokiol mediates PD-L1 degradation, stimulates T cell activation, and facilitates T cell killing of tumor cells. Moreover, honokiol activates CD4 + and CD8 + T cell infiltration in vivo, thus suppressing tumor growth in C57BL/6 mice. In conclusion, this study has demonstrated that honokiol can inhibit the growth of lung cancer by targeting tumor cell PD-L1, suppressing PD-L1 expression, blocking the PD-1/PD-L1 pathway, and enhancing anti-tumor immunity.

Single and multiple inhibitors of the biosynthesis of 5-, 12-, 15-lipoxygenase products derived from cinnamyl-3,4-dihydroxy-α-cyanocinnamate: Synthesis and structure-activity relationship.

The involvement of lipoxygenases in various pathologies, combined with the unavailability of safe and effective inhibitors of the biosynthesis of their products, is a source of inspiration for the development of new inhibitors. Based on a structural analysis of known inhibitors of lipoxygenase products biosynthesis, a comprehensive structure-activity study was carried out, which led to the discovery of several novel compounds (16a-c, 17a) demonstrating promising potency to inhibit the biosynthesis of products of 5-, 12- and 15-LO. Compounds 16b and 16c outperformed zileuton (1), the only FDA-approved 5-LO inhibitor, as well as known inhibitors such as caffeic acid phenethyl ester (CAPE (2)) and cinnamyl-3,4-dihydroxy-α-cyanocinnamate (CDC (4)). However, the introduction of a cyano group at the α-position of the carbonyl abolished the activity. Compounds 16a and 17a also inhibited the biosynthesis of 12- and 15-LO products. Compounds 16a, 17a far surpassed baicalein, a known 12-LO inhibitor, as inhibitors of 12-LO products biosynthesis. Compound 17a and CDC (4) showed equivalent inhibition of LO products, proposing that the double bond in the ester moiety is not necessary for the inhibitory activity. The introduction of the cyano group, as in compound 17a, at the α-position of the carbonyl in compound 16a significantly reduced the inhibitory activity against the biosynthesis of 15-LO products. In addition to the interactions with residues His372 and Phe421 also found with zileuton and CAPE, compounds 16a and 16c each interact with residue His367 as shown by molecular docking. This new interaction may explain their high affinity with the 5-LO active site.

Identification of Potential Therapeutic Drugs for Diabetic Cardiomyopathy

This study focused on identifying potential therapeutic drugs and mechanisms of action for diabetic cardiomyopathy (DCM). Using gene expression profiles from the GSE197850 dataset, we applied Weighted Correlation Network Analysis, Limma, and Gene Set Variation Analysis (GSVA) to uncover DCM-related gene sets and pathways. Subsequently, we conducted protein interaction network analysis with String and identified 10 hub genes through Cytoscape: ACTN2, ITGA1, CASP3, PXN, PCNA, CAV1, GAPDH, FEN1, PTPN11, and ESR1. In vitro validation using Rat H9C2 cardiomyocytes showed upregulation of FEN1, PCNA, PTPN11, CAV1, GAPDH, CASP3, PXN, and ACTN2, and downregulation of ESR1 and ITGA11 in high-glucose conditions. We further performed immune infiltration analysis with CIBERSORT and explored potential therapeutic agents through molecular docking with Autodock Vina. Our findings identified estradiol, valproic acid, acetaminophen, and resveratrol as potential drugs for DCM. Among these, resveratrol showed promise by promoting autophagy. This study leveraged comprehensive bioinformatic and experimental methods to pinpoint DCM-related genes, elucidate key hub genes, and propose resveratrol as a latent drug for DCM.

Exploring Novel PLK1 Inhibitors based on Computational Studies of 2,4-Diarylaminopyrimidine Derivatives

Background: Polo-like kinase 1 (PLK1) is an important target for anti-cancer drugs. A series of novel 2,4-diarylaminopyrimidine derivatives (DAPDs) as PLK1 inhibitors (PLKIs) with remarkable activities have been reported recently. Methods: A systemically computational study was performed on these DAPDs, including threedimensional quantitative structure-activity relationship (3D-QSAR) modeling, molecular docking, and molecular dynamics (MD) simulation. Results: The constructed 3D-QSAR models exhibited reliable predictability with satisfactory validation parameters. The dockings revealed the binding modes of DAPDs in PLK1 protein, and two key residue, Cys133 and Phe183, could interact with DAPDs by hydrogen bonds and π-π stacking, which might be significant for the activity of these PLKIs. Eight compounds with higher predicted activity than the most active DAPD-compound (16) were designed based on the 3D-QSAR models. These newly designed compounds also exhibited higher docking scores than compound 16 in the binding pocket of PLK1. The ADME predictions and MD simulations further indicated that two hit compounds with reasonable pharmacokinetics properties could stably bind with PLK1 and have the potential to become novel PLKIs. Conclusion: Two newly designed compounds might have the potential to be novel PLKIs. These results might provide important information for the design and development of novel PLKIs.

Identifying the Anti-inflammatory Effects of Astragalus Polysaccharides in Anti-N-Methyl-D-Aspartate Receptor Encephalitis: Network Pharmacology and Experimental Validation.

Astragalus polysaccharides (APS), a group of bioactive compounds obtained from the natural source Astragalus membranaceus(AM), exhibits numerous pharmacological actions in the central nervous system, such as anti-inflammatory, antioxidant, and immunomodulatory properties. Despite the remarkable benefits, the effectiveness of APS in treating anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis and the corresponding mechanism have yet to be fully understood. As such, this study aims to investigate the impact of APS on anti-NMDAR encephalitis and explore the potential molecular network mechanism. The impact of APS intervention on mice with anti-NMDAR encephalitis was assessed, and the possible molecular network mechanism was investigated utilizing network pharmacology and bioinformatics techniques such as Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG),protein-protein interaction (PPI) network, and molecular docking. Enzyme-linked immunosorbent assay (ELISA) was applied to detect the expression of core target proteins. APS significantly ameliorated cognitive impairment and reduced susceptibility to PTZ-induced seizures in mice with anti-NMDAR encephalitis, confirming the beneficial effect of APS on anti-NMDAR encephalitis. Seventeen intersecting genes were identified between APS and anti-NMDAR encephalitis. GO and KEGG analyses revealed the characteristics of the intersecting gene networks. STRING interaction in the PPI network was applied to find crucial molecules. The results of molecular docking suggested that APS may regulate interleukin-1β (IL-1β), tumor necrosis factor-α (TNF-α), and interleukin-6 (IL-6) as potential targets in anti-NMDAR encephalitis. Furthermore, the levels of IL-1β, IL-6, and TNF-α detected by ELISA in anti-NMDAR encephalitis mice were significantly downregulated in response to the administration of APS. The findings of this study demonstrate the significant role of APS in the treatment of anti-NMDAR encephalitis, as it effectively suppresses inflammatory cytokines. These results suggest that APS has the potential to be considered as a viable herbal medication for the treatment of anti-NMDAR encephalitis.

Synthesis and Selective Anticancer Activity Evaluation of 2-phenylacrylonitrile Derivatives as Tubulin Inhibitors.

This study aimed at synthesizing 13 series of novel derivatives with 2-phenylacrylonitrile, evaluating antitumor activity both in vivo and in vitro, and obtaining novel tubulin inhibitors. The 13 series of 2-phenylacrylonitrile derivatives were synthesized by Knoevenagel condensation and the anti-proliferative activities were determined by MTT assay. The cell cycle and apoptosis were analyzed by flow cytometer. Quantitative cell migration was performed using 24-well Boyden chambers. The proteins were detected by western blotting. in vitro kinetics of microtubule assembly was measured using ELISA kit for Human β-tubulin (TUBB). Molecular docking was done by Discovery Studio (DS) 2017 Client online tool. Among the derivatives, compound 1g2a possessed strong inhibitory activity against HCT116 (IC50 = 5.9 nM) and BEL-7402 (IC50 = 7.8 nM) cells. Compound 1g2a exhibited better selective antiproliferative activities and specificities than all the positive control drugs, including taxol. Compound 1g2a inhibited proliferation of HCT116 and BEL-7402 cells by arresting them in the G2/M phase of the cell cycle, inhibited the migration of HCT116 and BEL-7402 cells and the formation of cell colonies. Compound 1g2a showed excellent tubulin polymerization inhibitory activity on HCT116 and BEL-7402 cells. The results of molecular docking analyses showed that 1g2a may inhibit tubulin to exert anticancer effects. Compound 1g2a shows outstanding antitumor activity both in vivo and in vitro and has the potential to be further developed into a highly effective antitumor agent with little toxicity to normal tissues.

Metabolomics combined with chemometric analysis to identify α-glucosidase inhibitors in Phaleria macrocarpa fruit extracts and its molecular docking simulation

Phaleria macrocarpa is a medicinal plant widely available in Malaysia. The plant parts have been traditionally used as an antidiabetic remedy. This study aimed to identify the putative inhibitors of the α-glucosidase enzyme from P. macrocarpa using a gas chromatography-mass spectrometry (GC–MS)-based metabolomics approach and further subjected them to in silico molecular docking analysis to elucidate the possible mechanism of action. This study assessed the inhibitory potential of P. macrocarpa fruit extracts (aqueous, 20 %, 40 %, 60 %, 80 %, and 100 % ethanol) against the α-glucosidase enzyme using GC–MS and chemometric analysis. Orthogonal partial least squares (OPLS) combined with GC–MS analysis were applied to correlate the inhibition of enzyme activity to the metabolites profile of P. macrocarpa. All the potential inhibitors identified were further docked to the yeast (Saccharomyces cerevisiae) protein crystal structure (PDB3A4A). The generated score scatter plot of OPLS showed a recognizable separation of all the extracts into six different clusters. GC–MS, incorporated with multivariate data analysis techniques, was used to identify significant chemical markers. Methyl α-d-glucopyranoside, squalene, palmitic acid, myo-inositol and isoquinoline metabolites were identified as putative inhibitors against α-glucosidase activity from P. macrocarpa. In conclusion, the GC–MS-based metabolomics approach identified potential chemical markers of P. macrocarpa that could be utilized in the development of herbal based medicine.

In silico approaches of gandarusa (Justicia gendarussa Burm. f.) potential for osteoporosis prevention via EGF pathway

Context: On a cellular level, osteoporosis is a metabolic bone disease caused by osteoclastic bone resorption that is not offset by osteoblastic bone synthesis. This increases the risk of fractures by making bones weak and brittle. The selective inactivation of the epidermal growth factor receptor (EGFR) in osteoblast lineage cells demonstrated that EGFR promotes bone formation by increasing the number of mesenchymal progenitors. Active compounds of gandarusa (Justicia gendarussa Burm. f.) are potentially playing crucial roles in EGFR activation. Aims: To evaluate the potential of J. gendarussa for osteoporosis prevention via EGF pathway in silico. Methods: A GC-MS approach was used to screen the active compounds from 70 and 95% methanol extraction, which was continued with molecular docking analysis by PyRx v0.8. The visualization and amino acid interactions were also revealed using Discovery Studio software R17. ADME analysis was performed using the SwissADME webserver to consider whether the best compound could be classified as a drug following Lipinsky rule’s of five. Results: The top five compounds with high binding affinity were selected from a total of 33 active compounds detected. One compound, namely eslicarbazepine, has a -6.7 kcal/mol affinity score and passes the threshold for drugs bioavailability, supported by the data of MW compounds 254.28 kDa, low rotatable bonds 1 bond, hydrogen bond acceptors and donors (2), high GI absorption, and ability to permeant to blood-brain barrier system. Conclusions: This finding added new insight into J. gendarussa extract potential as anti-osteoporosis in humans. Nevertheless, in vitro and in vivo experiments are necessary to confirm the potential.

Xanthohumol, a Prenylated Chalcone, Regulates Lipid Metabolism by Modulating the LXRα/RXR-ANGPTL3-LPL Axis in Hepatic Cell Lines and High-Fat Diet-Fed Zebrafish Models

Angiopoietin-like 3 (ANGPTL3) acts as an inhibitor of lipoprotein lipase (LPL), impeding the breakdown of triglyceride-rich lipoproteins (TGRLs) in circulation. Targeting ANGPTL3 is considered a novel strategy for improving dyslipidemia and atherosclerotic cardiovascular diseases (ASCVD). Hops (Humulus lupulus L.) contain several bioactive prenylflavonoids, including xanthohumol (Xan), isoxanthohumol (Isoxan), 6-prenylnaringenin (6-PN), and 8-prenylnaringenin (8-PN), with the potential to manage lipid metabolism. The aim of this study was to investigate the lipid-lowering effects of Xan, the effective prenylated chalcone in attenuating ANGPTL3 transcriptional activity, both in vitro using hepatic cells and in vivo using zebrafish models, along with exploring the underlying mechanisms. Xan (10 and 20μM) significantly reduced ANGPTL3 mRNA and protein expression in HepG2 and Huh7 cells, leading to a marked decrease in secreted ANGPTL3 proteins via hepatic cells. In animal studies, orally administered Xan significantly alleviated plasma triglyceride (TG) and cholesterol levels in zebrafish fed a high-fat diet. Furthermore, it reduced hepatic ANGPTL3 protein levels and increased LPL activity in zebrafish models, indicating its potential to modulate lipid profiles in circulation. Furthermore, molecular docking results predicted that Xan exhibits a higher binding affinity to interact with liver X receptor α (LXRα) and retinoic acid X receptor (RXR) than their respective agonists, T0901317 and 9-Cis-retinoic acid (9-Cis-RA). We observed that Xan suppressed hepatic ANGPTL3 expression by antagonizing the LXRα/RXR-mediated transcription. These findings suggest that Xan ameliorates dyslipidemia by modulating the LXRα/RXR-ANGPTL3-LPL axis. Xan represents a novel potential inhibitor of ANGPTL3 for the prevention or treatment of ASCVD.