Docking Target Research Articles

AI-assisted models to predict chemotherapy drugs modified with C60 fullerene derivatives.

Employing quantitative structure-activity relationship (QSAR)/ quantitative structure-property relationship (QSPR) models, this study explores the application of fullerene derivatives as nanocarriers for breast cancer chemotherapy drugs. Isolated drugs and two drug-fullerene complexes (i.e., drug-pristine C60 fullerene and drug-carboxyfullerene C60-COOH) were investigated with the protein CXCR7 as the molecular docking target. The research involved over 30 drugs and employed Pearson's hard-soft acid-base theory and common QSAR/QSPR descriptors to build predictive models for the docking scores. Energetic descriptors were computed using quantum chemistry at the density functional-based tight binding DFTB3 level. The results indicate that drug-fullerene complexes interact more with CXCR7 than isolated drugs. Specific binding sites were identified, with varying locations for each drug complex. Predictive models, developed using multiple linear regression and IBM Watson artificial intelligence (AI), achieved mean absolute percentage errors below 12%, driven by AI-identified key variables. The predictive models included mainly quantitative descriptors collected from datasets as well as computed ones. In addition, a water-soluble fullerene was used to compare results obtained by DFTB3 with a conventional density functional theory approach. These findings promise to enhance breast cancer chemotherapy by leveraging fullerene-based drug nanocarriers.

Network pharmacology and phytochemical composition combined with validation in vivo and in vitro reveal the mechanism of platycodonis radix ameliorating PM2.5-induced acute lung injury

Ethnopharmacological relevancePlatycodonis radix (PR), the root of Platycodon grandiflorus (Jacq.) A. DC., is a traditional Chinese medicine recognized for its dual role as both a medicinal and dietary substance, exhibiting significant anti-inflammatory properties. It is frequently utilized in the treatment of lung diseases. However, the molecular mechanisms by which PR exerts its effects in the treatment of acute lung injury (ALI) remain unclear. Aim of the studyThis study presents a novel strategy that integrates network pharmacology, molecular docking, untargeted metabolomics analysis and experimental validation to investigate the molecular mechanisms through which PR treats ALI. Materials and methodInitially, the bioactive components of PR, along with its targets and pathways in the treatment of ALI, were identified using network pharmacology. Following this, preliminary validation was conducted through molecular docking. The active ingredients in the aqueous extract of PR were characterized using HPLC-MS. Finally, in vivo and in vitro experiments were performed to further validate the findings from the network pharmacology. ResultsA total of 14 bioactive components and 156 effective targets were identified using the TCMSP, DisGeNET, Genecard, OMIM databases and Venny 2.1.0. Protein-protein interaction (PPI) analysis revealed 22 core targets including TP53, AKT1, STAT3 and JUN. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that these targets primarily participate in the regulation of cellular apoptosis, lung cancer and inflammatory pathways. Molecular docking demonstrated that four bioactive components exhibited strong affinities with their respective docking targets. LC-MS analysis confirmed that the aqueous extract of PR contained 87 components, including two active ingredients identified through network pharmacology and molecular docking. Preliminary validation was conducted in mice with ALI induced by acute PM2.5 exposure, revealing that the aqueous extract of PR reduced inflammatory factor levels in bronchoalveolar lavage fluid, enhanced antioxidant capacity in lung tissue, and decreased lung cell apoptosis in PM2.5-exposed mice. Notably, PR alleviated PM2.5-induced ALI through the STAT3, JUN, and AKT1 signaling pathways. Similarly, the results of in vitro intervention experiments further confirmed that the aqueous extract of PR protected pulmonary epithelial cells against PM2.5 exposure through activating AKT1 sinalling pathway, and inhibiting STAT3 and JUN signalling pathways. ConclusionThis study identifies the active components of PR and elucidates the molecular mechanisms by which PR alleviates ALI, specifically by inhibiting the phosphorylation levels of STAT3 and c-JUN, or by activating the phosphorylation level of AKT1. These results provide a foundational basis for the application of PR in the treatment or prevention of lung injuries induced by particulate matter.

In Silico Screening of Phytocompounds from West African Traditional Medicine and Molecular Docking Targeting Dengue Virus Protein NS2B/NS3.

Traditional medicine offers a wide range of application for in silico study techniques. This drug research and development strategy is embryonic in the West African context, particularly in Burkina Faso, which is increasingly faced with emerging diseases such as dengue fever. Circulation of the 4 serotypes of this virus has been documented in the country. This study aims to evaluate the therapeutic potential of phytocompounds contained in the West African pharmacopoeia against dengue virus NS2B/NS3 protein, using computational methods integrating several software packages and databases. Based on a literature review, we identified 191 molecules from 30 plants known for their antiviral effects. Five met the inclusion criteria for molecular docking: patulin from calotropis procera, resiniferonol from Euphorbia poissonii, Securinol A from Flueggea virosa, Shikimic acid and Methyl gallate from Terminalia macroptera. The best binding scores were observed between resiniferonol and the serotypes 1, 2 and 4 NS2B/NS3 protease, with binding energies of -7.4 Kcal/mol, -6.8 Kcal/mol and -7.3 Kcal/mol respectively; while the NS2B/NS3 protease of serotype 3 had the best affinity for securinol A (-7 Kcal/mol). This study points the way to further research in computer aided drug design field and calls for multidisciplinary collaboration to promote West African medicinal plants against health challenges.

Harmine acts as a quorum sensing inhibitor decreasing the virulence and antibiotic resistance of Pseudomonas aeruginosa

BackgroundAs antimicrobial resistance (AMR) has become a global health crisis, new strategies against AMR infection are urgently needed. Quorum sensing (QS), responsible for bacterial communication and pathogenicity, is among the targets for anti-virulence drugs that thrive as one of the promising treatments against AMR infection.MethodsWe identified a natural compound, Harmine, through virtual screening based on three QS receptors of Pseudomonas aeruginosa (P. aeruginosa) and explored the effect of Harmine on QS-controlled and pathogenicity-related phenotypes including pyocyanin production, exocellular protease excretion, biofilm formation, and twitching motility of P. aeruginosa PA14. The protective effect of Harmine on Caenorhabditis elegans (C. elegans) and mice infection models was determined and the synergistic effect of Harmine combined with common antibiotics was explored. The underlaying mechanism of Harmine’s QS inhibitory effect was illustrated by molecular docking analysis, transcriptomic analysis, and target verification assay.ResultsIn vitro results suggested that Harmine possessed QS inhibitory effects on pyocyanin production, exocellular protease excretion, biofilm formation, and twitching motility of P. aeruginosa PA14, and in vivo results displayed Harmine’s protective effect on C. elegans and mice infection models. Intriguingly, Harmine increased susceptibility of both PA14 and clinical isolates of P. aeruginosa to polymyxin B and kanamycin when used in combination. Moreover, Harmine down-regulated a series of QS controlled genes associated with pathogenicity and the underlying mechanism may have involved competitively antagonizing autoinducers’ receptors LasR, RhlR, and PqsR.ConclusionsThis study shed light on the anti-virulence potential of Harmine against QS targets, suggesting the possible use of Harmine and its derivates as anti-virulence compounds.

Baicalin attenuates aflatoxin B1-induced hepatotoxicity via suppressing c-Jun-N-terminal kinase-mediated cell apoptosis.

Aflatoxin B1 (AFB1) is classified as a Class I carcinogen and common pollutant in human and animal food products. Prolonged exposure to AFB1 can induce hepatocyte apoptosis and lead to hepatotoxicity. Therefore, preventing AFB1-induced hepatotoxicity remains a critical issue and is of great significance. Baicalin, a polyphenolic compound derived from Scutellaria baicalensis Georgi, has a variety of pharmacodynamic activities, such as antiapoptotic and anticancer activities. This study systematically investigated the alleviating effect of baicalin on AFB1-induced hepatotoxicity from the perspective of apoptosis and explored the possible molecular mechanism. In the normal human liver cell line L02, baicalin treatment significantly inhibited AFB1-induced c-Jun-N-terminal Kinase (JNK) activation and cell apoptosis. In addition, the in vitro mechanism study demonstrated that baicalin alleviates AFB1-induced hepatocyte apoptosis through suppressing the translocation of phosphorylated JNK to the nucleus and decreasing the phosphorylated c-Jun/c-Jun ratio and the Bax/Bcl2 ratio. Molecular docking and drug affinity responsive target stability assays demonstrated that baicalin has the potential to target JNK. This study provides a basis for the therapeutic effect of baicalin on hepatocyte apoptosis caused by AFB1, indicating that the development of baicalin and JNK pathway inhibitors has broad application prospects in the prevention of hepatotoxicity, especially hepatocyte apoptosis.

In silico study to explore the mechanism of Toxoplasma-induced inflammation and target therapy based on sero and salivary Toxoplasma

We aimed to assess salivary and seroprevalence of Toxoplasma immunoglobulins in risky populations and evaluate drug docking targeting TgERP. A cross-sectional study was conducted in Alexandria University hospitals’ outpatient clinics. 192 participants were enrolled from September 2022 to November 2023. Anti-Toxoplasma IgG and IgM were determined in serum and saliva by ELISA. An in-Silico study examined TgERP’s protein–protein interactions (PPIs) with pro-inflammatory cytokine receptors, anti-inflammatory cytokine, cell cycle progression regulatory proteins, a proliferation marker, and nuclear envelope integrity-related protein Lamin B1. Our findings revealed that anti-T. gondii IgG were detected in serum (66.1%) and saliva (54.7%), with 2.1% of both samples were positive for IgM. Salivary IgG had 75.59% sensitivity, 86.15% specificity, 91.40% PPV, 64.40% NPP, 79.17% accuracy and fair agreement with serum IgG. On the other hand, the sensitivity, specificity, PPV, NPV, and accuracy in detecting salivary IgM were 75.0%, 99.47%, 75.0%, 99.47%, and 98.96%. AUC 0.859 indicates good discriminatory power. Examined synthetic drugs and natural products can target specific amino acids residues of TgERP that lie at the same binding interface with LB1 and Ki67, subsequently, hindering their interaction. Hence, salivary samples can be a promising diagnostic approach. The studied drugs can counteract the pro-inflammatory action of TgERP.

Discovery of components in honeysuckle for treating COVID-19 and diabetes based on molecular docking, network analysis and experimental validation.

Molecular docking screening identified ochnaflavone, madreselvin B and hydnocarpin as key components for treating COVID-19 with diabetes in honeysuckle using 3 C-like protease (Mpro), angiotensin-converting enzyme 2 (ACE2), and dipeptidyl peptidase 4 (DPP4) as molecular docking targets, ACE2, DPP4, IL2, NFKB1, PLG, TBK1, TLR4 and TNF were the core targets, and multiple antiviral and anti-inflammatory signalling pathways were involved. Further, the levels of IL-1β and DPP4 in cell supernatant that had been activated by LPS was decreased by hypnocarpin, and ACE2 protein and DPP4 mRNA in cells were down-regulated. Overall, we have identified three components from honeysuckle that have potency to treat COVID-19 combined with diabetes. SARS-CoV-2 transcription may be inhibited by these components in honeysuckle, reducing virus invasion, inhibiting inflammatory factors, and improving immune response. Our findings could provide a basis for the clinical application and further development of honeysuckle.

Hydrangea paniculata coumarins alleviate adriamycin-induced renal lipotoxicity through activating AMPK and inhibiting C/EBPβ

Ethnopharmacological relevanceThroughout Chinese history, Hydrangea paniculata Siebold has been utilized as a traditional medicinal herb to treat a variety of ailments associated to inflammation. In a number of immune-mediated kidney disorders, total coumarins extracted from Hydrangea paniculata (HP) have demonstrated a renal protective effect. Aim of the studyTo investigate renal beneficial effect of HP on experimental Adriamycin nephropathy (AN), and further clarify whether reversing lipid metabolism abnormalities by HP contributes to its renoprotective effect and find out the underlying critical pathways. Materials and methodsAfter establishment of rat AN model, HP was orally administrated for 6 weeks. Biochemical indicators related to kidney injury were determined. mRNAs sequencing using kidney tissues were performed to clarify the underlying mechanism. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis, western blot, molecular docking, and drug affinity responsive target stability (DARTS) assay was carried out to further explore and confirm pivotal molecular pathways and possible target by which HP and 7-hydroxylcoumarin (7-HC) played their renal protection effect via modulating lipid metabolism. ResultsHP could significantly improve renal function, and restore renal tubular abnormal lipid metabolism and interstitial fibrosis in AN. In vitro study demonstrated that HP and its main metabolite 7-HC could reduce ADR-induced intracellular lipid deposition and fibrosis characteristics in renal tubular cells. Mechanically, HP and 7-HC can activate AMP-activated protein kinase (AMPK) via direct interaction, which contributes to its lipid metabolism modulation effect. Moreover, HP and 7-HC can inhibit fibrosis by inhibiting CCAAT/enhancer binding protein beta (C/EBPβ) expression in renal tubular cells. Normalization of lipid metabolism by HP and 7-HC further provided protection of mitochondrial structure integrity and inhibited the nuclear factor kappa-B (NF-κB) pathway. Long-term toxicity using beagle dogs proved the safety of HP after one-month administration. ConclusionCoumarin derivates from HP alleviate adriamycin-induced lipotoxicity and fibrosis in kidney through activating AMPK and inhibiting C/EBPβ.

Eco-Technological Evaluation of Natural Phytochemicals Potential Drug Molecules Against Main Protease: A Machine Learning Algorithm.

Introduction: The global viral pandemic has rapidly spread, leading to many individuals experiencing the infection. Coronaviruses (CoVs) are among many viral families that infect different types of mammals. They can spread to humans and cause gastrointestinal, neurological, and respiratory problems. The present investigation has discovered flavonoid compounds as promising molecular agents with potential antiviral activity against virus proteins, specifically main protease (Mpro). Methodology: A comprehensive in silico screening of natural compounds derived from medicinal plants was performed in the present study. It included parameter assessments such as drug-likeness, pharmacokinetics, molecular docking, toxicity evaluations, bioavailability assessments, and molecular target exploration. In this systematic approach, the primary objective was to identify potential lead compounds. These phytochemicals were investigated as drug candidates to provide a detailed understanding of their molecular properties. Results: The Mpro binding energy values were -10.637, -12.752, -7.813, -15.732, -6.449, -5.578, -8.037, and -8.52 kcal/molfor isoquercetin, narirutin, myricetin, hesperidin, silibinin, baicalein, taxifolin, and petunidin. Molecular simulations were conducted on two flavonoid compounds - hesperidin and narirutin - stable over 100 nanoseconds in the Coronavirus protein. Conclusions: The computational study we conducted is promising, but to validate the action of these compounds, further experimental studies are needed, with a critical component of the research being the conduct of in vitro and in vivo experiments.

Exploring promising natural compounds for breast cancer treatment: in silico molecular docking targeting WDR5-MYC protein interaction

Cancer is an aberrant differentiation of normal cells, characterized by uncontrolled growth and the potential to acquire invasive and aggressive properties that ultimately lead to metastasis. In the realm of scientific exploration, a multitude of pathways has been investigated and targeted by researchers, among which one specific pathway is recognized as WDR5-MYC. Continuous investigations and research show that WDR5-MYC is a therapeutic target protein. Hence, the discovery of naturally occurring compounds with anticancer properties has been suggested as a rapid and efficient alternative for the development of anticancerous therapeutics. A virtual screening approach was used to identify the most potent compounds from the NP-lib database at the MTiOpenScreen webserver against WDR5-MYC. This process yielded a total of 304 identified compounds. Subsequently, after screening, four potent compounds, namely Estrone (ZINC000003869899), Ethyl-1,2-benzanthracene (ZINC000003157052), Strychnine (ZINC000000119434) and 7H-DIBENZO [C, G] CARBAZOLE (ZINC000001562130), along with a cocrystallized 5-[4-(trifluoromethyl) phenyl]-1H-tetrazole inhibitor (QBP) as a reference ligand, were considered for stringent molecular docking. Thus, each compound exhibited significant docking energy between −8.2 and −7.7 kcal/mol and molecular contacts with essential residue Asn225, Lys250, Ser267 and Lys272 in the active pocket of WDR5-MYC against the QBP inhibitor (the native ligand QBP serves as a reference in the comparative analysis of docked complexes). The results support the potent compounds for drug-likeness and strong binding affinity with WDR5-MYC protein. Further, the stability of the selected compounds was predicted by molecular dynamics simulation (100 ns) contributed by intermolecular hydrogen bonds and hydrophobic interactions. This demonstrates the potential of the selected compounds to be used against breast cancer treatment. Communicated by Ramaswamy H. Sarma

BioProtIS: Streamlining protein-ligand interaction pipeline for analysis in genomic and transcriptomic exploration

The identification of protein-ligand interactions plays a pivotal role in elucidating biological processes and discovering potential bioproducts. Harnessing the capabilities of computational methods in drug discovery, we introduce an innovative Inverted Virtual Screening (IVS) pipeline. This pipeline Integrated molecular dynamics and docking analyses to ensure that protein structures are not only energetically favorable but also representative of stable conformations. The primary objective of this pipeline is to automate and streamline the analysis of protein-ligand interactions at both genomic and transcriptomic scales. In the contemporary post-genomic era, high-throughput computational screening for bioproducts, biological systems, and therapeutic drugs has become a cornerstone practice. This approach offers the promise of cost-effectiveness, time efficiency, and optimization of laboratory work. Nevertheless, a notable deficiency persists in the availability of efficient pipelines capable of automating the virtual screening process, seamlessly integrating input and output, and leveraging the full potential of open-source tools. To bridge this critical gap, we have developed a versatile pipeline known as BioProtIS. This tool seamlessly integrates a suite of state-of-the-art tools, including Modeller, AlphaFold, Gromacs, FPOCKET, and AutoDock Vina, thus facilitating the streamlined docking of ligands with an expansive repertoire of proteins sourced from genomes and transcriptomes, and substrates. To assess the pipeline's performance, we employed the transcriptomes of Cereus jamacaru (a cactus species) and Aspisoma lineatum (firefly), along with the genome of Homo sapiens. This integration not only improves the accuracy of ligand-protein interactions by minimizing replicability deviations but also optimizes the discovery process by enabling the simultaneous evaluation of multiple substrates. Furthermore, our pipeline accommodates distinct testing scenarios, such as blind docking or site-specific targeting, which are invaluable in applications ranging from drug repositioning to the exploration of new allosteric binding sites and toxicity assessments. BioProtIS has been designed with modularity at its core. This inherent flexibility empowers users to make custom modifications directly within the source code, tailoring the pipeline to their specific research needs. Moreover, it lays the foundation for seamless integration of diverse docking algorithms in future iterations, promising ongoing advancements in the field of computational biology. This pipeline is available for free distribution and can be download at: https://github.com/BBMDO/BioProtIS.

Efficacy of fumigant compounds from essential oil of feverfew (Chrysanthemum parthenium L.) against maize weevil (Sitophilus zeamais Mots.): Fumigant toxicity test and in-silico study

Post-harvest insects are among the significant problems in the agricultural sector. The most accessible tools available for managing post-harvest arthropod-pests are fumigants because of the convenience of their applications and fast action in disinfecting. This study aimed to examine the fumigant toxicity of essential oil (EO) against maize weevil and identify the specific fumigants among the major components. The EO was extracted from aerial part of Chrysanthemum parthenium L. using Clevenger apparatus and was tested for fumigant toxicity. GC-MS was used to determine the chemical composition of EO. The major components were identified and screened virtually using Auto dock vina 1.2. in PyRx 0.8 platform. Dm AChE PDB ID: 6XYY was used as a target for molecular docking and malathion and pirimiphusmethyl were used as a reference for comparison. From the results of binding affinities, most of the major EO components showed better fumigant activity than the reference fumigants. More specifically 1,6-dioxaspiro[4,4]non-ene, b-farensen, bornyl-tiglate, g-terpinene, p-cymene, bornyl-acetate, bornyl-isovalerate, terpinen-4-ol, trans-chrysanthenyl-acetate and a-phellandrene were found to be effective fumigants against maize weevil. The above findings suggest that the EO of the aerial part of C. parthenium can be a potential candidate for the development of novel natural fumigants for stored products.
 KEY WORDS: Essential oil, Fumigants, Insecticides, Binding affinity, Maize weevil
 Bull. Chem. Soc. Ethiop. 2024, 38(2), 457-472. 
 DOI: https://dx.doi.org/10.4314/bcse.v38i2.13

Development of Orally Active Anti-Inflammatory Agents: In Vivo and In Silico Analysis of Naphthalene-Chalcone Derivatives Based on 2-Acetyl-6-Methoxy Naphthalene

Chalcone compounds are reported to have diverse biological activities such as antiviral, antimicrobial, antimalarial, antitumor, antifungal, anticancer, and so forth. Herewith, we wish to report the in-vivo anti-inflammatory activities of previously synthesized naphthalene-chalcone hybrids from 2-Acetyl-6-Methoxy Naphthalene derivatives (C1-C25). All synthesized chalcones (C1-C25) were thoroughly characterized with standard spectroscopic techniques and tested for their in-vivo anti-inflammatory activities. The currently employed in-silico docking methodology uses the ‘Molegro Virtual Docker’ as a docking tool and target proteins as COX-1 (PDB ID: 1EQH) and COX-2 (PDB ID: 1PXX). Molecular docking analysis of chalcones (C1-C25) suggested that compound C-24 exhibited best docking score of -117.495 kcal/mol than the standard flurbiprofen -115.259 kcal/mol on COX-1 target. To understand more about pharmacokinetics aspects, we predicted theoretical ADME properties using ‘QikProp, 2022’ and found that all compounds were exhibited acceptable pharmacokinetic properties.

Network pharmacology and experiment validation investigate the potential mechanism of triptolide in oral squamous cell carcinoma.

Objective: This study aimed to investigate the molecular mechanism of triptolide in the treatment of oral squamous cell carcinoma (OSCC) via network pharmacology and experimental validation. Methods: The network pharmacological method was used to predict the key targets, detect the signal pathways for the treatment of OSCC, and screen the critical components and targets for molecular docking. Predicted targets were validated in cellular and xenograft mouse model. Results: In this study, we predicted action on 17 relevant targets of OSCC by network pharmacology. PPI network demonstrated that Jun, MAPK8, TP53, STAT3, VEGFA, IL2, CXCR4, PTGS2, IL4 might be the critical targets of triptolide in the treatment of OSCC. These potential targets are mainly closely related to JAK-STAT and MAPK signaling pathways. The analysis of molecular docking showed that triptolide has high affinity with Jun, MAPK8 and TP53. Triptolide can suppress the growth of OSCC cells and xenograft mice tumor, and downregulate the expression of Jun, MAPK8, TP53, STAT3, VEGFA, IL2, CXCR4, PTGS2 to achieve the therapeutic effect of OSCC. Conclusion: Through network pharmacological methods and experimental studies, we predicted and validated the potential targets and related pathways of triptolide for OSCC treatment. The results suggest that triptolide can inhibit the growth of OSCC via several key targets.

Model study of the protein-ligand binding in the development of hypersensitivity to folic acid and its analogs

Folic acid (FA) plays a vital role in various metabolic processes, including synthesis and repair of DNA, cell division, the production of red blood cells, and fetal development. However, hypersensitivity to FA and its analogs can occur, leading to various symptomatic manifestations, including shortness of breath, skin rashes, itching, hives, swelling, gastrointestinal disturbances, tachycardia, and anaphylaxis. The mechanism of hypersensitivity to FA and its analogs is not well understood. However, it is known that human serum albumin (HSA) serves as a major pharmacokinetic effector for many substances and drugs, including FA and its analogs such as 5-methyltetrahydrofolic acid (5-MTHF), tetrahydrofolic acid (THFA), and methotrexate (MTX). HSA can interact with these compounds, affecting their distribution and metabolism. The study aimed to study the energetic and topological characteristics of the non-covalent complexes formed between HSA and FA and its analogs in order to obtain more complete information about the potential mechanisms involved in hypersensitivity reactions. Molecular docking was applied to search for the most energetically favorable conformations of the protein-ligand complexes and score the geometries based on their lowest binding energy. The 3D structure of HSA (PDB ID: 1AO6) was used as the docking target, which was obtained from the protein database. The structures of the ligands (FA, 5-MTHF, THFA, and MTX) were downloaded from PubChem, an open chemistry database at the National Institutes of Health. The surface area, volume, and depth of the binding pocket were determined using Proteins Plus. The identification of non-covalent interactions between HSA and the ligands was carried out using the PoseView and DoGSiteScorer web tools. It has been demonstrated that hydrophobic interactions and hydrogen bonds predominantly stabilize all the studied HSA-ligand complexes. Molecular docking analysis revealed that HSA binds the ligands within subdomains IB, IIA, and IIIA, with a binding energy of less than –10.0 kcal/mol. Identifying specific binding sites within the new antigen structures (the complex of HSA with the ligands) can be valuable in determining the energetically favorable binding of epitopes from these antigens to the active sites of IgE antibodies or immune cell receptors.

Targeting LRRC41 as a potential therapeutic approach for hepatocellular carcinoma.

Introduction: Hepatocellular carcinoma (HCC) is the most common primary liver cancer, characterized by high mortality rate. In clinical practice, several makers of liver cancer, such as VEGFR1, FGFR1 and PDGFRα, were identified and their potentials as a therapeutic target were explored. However, the unsatisfied treatment results emphasized the needs of new therapeutic targets. Methods: 112 HCC patients samples were obtained to evaluate the expression of LRRC41, SOX9, CD44, and EPCAM in HCC, combined with prognosis analysis. A DEN-induced HCC rat model was constructed to verify the expression of LRRC41 and SOX9 in HCC and lung metastasis tissues. Immune score evaluation was analysized by bioinformatics methods. Network pharmacology was performed to explored the potential FDA-approved drugs targeting LRRC41. Results: Through analysis of the Timer database and tissue micro-array, we confirmed that LRRC41 was over-expressed in HCC and exhibited a significant positive correlation with recurrence and metastasis. Immunohistochemistry staining of human HCC tissue samples revealed significant upregulation of LRRC41, SOX9, CD44, and EPCAM, with LRRC41 showing a positive correlation with SOX9, CD44, and EPCAM expression. UALCAN database analysis indicated that LRRC41 and SOX9 contribute to poor prognosis whereas CD44 and EPCAM did not demonstrate the same significance. Furthermore, analysis of a DEN-induced HCC rat model confirmed the significantly elevated expression of LRRC41 and SOX9 in HCC and lung metastasis tissues. Drug sensitivity analysis and molecular docking targeting LRRC41 identified several FDA-approved drugs, which may have potential antitumor effects on HCC by targeting LRRC41. Conclusion: Our findings highlight the role of LRRC41 overexpression in promoting HCC progression and its association with a poor prognosis. Drug sensitivity analysis and molecular docking shows several FDA-approved drugs may be potential therapeutic targets for HCC. Targeting LRRC41 may hold promise as a potential therapeutic strategy for HCC.

Prediction of Novel Natural Small Molecules From Schinus molle as an Inhibitor of PI3K Protein Target in Cancer Cells Using In Silico Screening.

Introduction Cancer continues to pose a significant challenge in medical research. Phytochemicals derived from plants have emerged as a promising avenue for pioneering drug discovery due to their potential for reduced toxicity. The phosphatidylinositol 3-kinase (PI3K) pathway has gained recognition as a pivotal signaling pathway with implications across multiple facets of cancer initiation and progression. This study focuses on the virtual screening of phytochemicals from Schinus molle, evaluating their potential as inhibitors of PI3K, a crucial target in cancer therapy. Methods and materials The present study involved a comprehensive in silico screening of phytochemicals derived from S. molle. The screening process encompassed various parameters, such as drug-likeness, pharmacokinetics, molecular docking, toxicity analysis, bioavailability assessment, and molecular target exploration. The primary objective of this systematic approach was to identify potential lead compounds. The study aimed to provide a detailed understanding of the molecular properties of the phytochemicals and their potential as drug candidates. Results Upon analyzing 18 compounds, two compounds were noteworthy. Beta-spathulene and kaempferol demonstrated significant affinity for PI3K and favorable attributes concerning drug-likeness, pharmacokinetics, and bioavailability. Conclusion While our computational investigation lays a promising foundation, it is essential to emphasize that further experimental studies, including in vitro and in vivo experiments, are imperative to validate the action of these lead compounds.

Network pharmacology integrated with molecular docking technology to reveal the potential mechanism of Shuganfang against drug-induced liver injury.

This study aimed to investigate the active composition and mechanism of the Shuganfang (SGF) in treating drug-induced liver injury (DILI) using network pharmacology and molecular docking. The potential active ingredients and targets of SGF were obtained from the Traditional Chinese Medicine Systems Pharmacology Database (TCMSP) database. DILI-related targets were queried from various databases including GEO, GeneCards, OMIM, NCBI, and DisGeNET. The STRING database was used to establish a protein-protein interaction (PPI) network. DAVID was utilized for conducting gene ontology (GO) function enrichment and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analyses. The data visualization and analysis of herb-ingredient-target and disease-pathway-target-ingredient networks were conducted using Cytoscape software (version 3.7.2). PyMoL and AutoDock software was used to select the best binding target for molecular docking. A total of 177 active ingredients,126 targets and 10112 disease targets were obtained, including 122 intersection targets. The identified potential active ingredients consisted of quercetin, kaempferol, luteolin, tanshinone IIa, nobiletin, isorhamnetin, beta-sitosterol and naringenin. The core targets implicated in the study were IL6, estrogen receptor 1 (ESR1), hypoxia-inducible factor alpha subunit 1 (HIF1A), MYC and vascular endothelial growth factor A (VEGFA). KEGG analysis revealed that the treatment of DILI with SGF mainly acted through apoptosis, the PI3K-Akt signaling pathway, and the tumor necrosis factor (TNF) signaling pathway. Furthermore, the binding affinities between the potential ingredients and the core targets were subsequently confirmed through molecular docking experiments. The findings indicated that the docking outcomes remained consistent and demonstrated a favorable capacity for binding. SGF exerts a therapeutic effect on DILI through multiple active ingredients, multiple targets and multiple pathways. Our findings contribute to a positive investigation and establish a theoretical basis for further extensive exploration of SGF as a potential treatment for DILI in future research.

Nutritional composition, antioxidant properties, and molecular docking strategy of muricidae operculum (Chicoreus ramosus)

The murrcidae gastropod operculum has many therapeutic uses in ayurveda, including treating cancer, gastric, hepatic, cardiovascular, and immunological disorders. Antibacterial, cell reinforcement, FTIR, and mass spectrum datas were used to identify important functional groups and chemical constituents in Chicoreus ramosus operculum concentrate. At 100 ​mg/L, the operculum extract showed stronger inhibitory movement (125 ​mm) against Bacillus subtilis and less (08 ​mm) against Staphylococcus aureus. Operculum extract's biochemical composition, total antioxidant properties, protein denaturation, metal chelation movement, all-out cell reinforcement action, and anti-diabetic action were 85.71%, 80.98%, 32.03%, and 76.47% at 1000 ​μg/mL concentration. The operculum remove FTIR showed nine significant groups, including amines, esters, and fragrant mixtures. 11 dynamic mixtures from GC–MS analysis of operculum rough concentrate. These bioactive fractions interacted with IL 23 in molecular docking experiments. Androst-1-en-3-one, Bis (2-ethylhexyl) phthalate, and 3-Methoxy-2,4,5-trifluorobenzoic acid had the highest docking scores and target protein receptor interactions. −11.9 ​kcal/mol, −08.6 ​kcal/mol and −7.7 ​kcal/mol are the maximum scores. These compounds are therapeutic and antimicrobial. These bioactive compounds in operculum extracts allow C. ramosus to be used in conventional medicine and may lead to the development of new drugs.

Structural modeling of hERG channel-drug interactions using Rosetta.

The human ether-a-go-go-related gene (hERG) not only encodes a potassium-selective voltage-gated ion channel essential for normal electrical activity in the heart but is also a major drug anti-target. Genetic hERG mutations and blockage of the channel pore by drugs can cause long QT syndrome, which predisposes individuals to potentially deadly arrhythmias. However, not all hERG-blocking drugs are proarrhythmic, and their differential affinities to discrete channel conformational states have been suggested to contribute to arrhythmogenicity. We used Rosetta electron density refinement and homology modeling to build structural models of open-state hERG channel wild-type and mutant variants (Y652A, F656A, and Y652A/F656A) and a closed-state wild-type channel based on cryo-electron microscopy structures of hERG and EAG1 channels. These models were used as protein targets for molecular docking of charged and neutral forms of amiodarone, nifekalant, dofetilide, d/l-sotalol, flecainide, and moxifloxacin. We selected these drugs based on their different arrhythmogenic potentials and abilities to facilitate hERG current. Our docking studies and clustering provided atomistic structural insights into state-dependent drug-channel interactions that play a key role in differentiating safe and harmful hERG blockers and can explain hERG channel facilitation through drug interactions with its open-state hydrophobic pockets.