Molecular Binding Research Articles

Celastrol induces ferroptosis by suppressing RRM2 in hepatocellular carcinoma

Introduction and ObjectivesFerroptosis is a novel form of cell death driven by iron dependence and lipid peroxidation, presenting a promising potential as an innovative strategy for cancer treatment. Celastrol (Cel) is particularly effective in inducing ferroptosis, but its molecular mechanism remains unclear. The study aims to elucidate the potential mechanism through both in vitro and in vivo experiments. Materials and methodsCCK-8 assay, Western blot analysis and measurements of reactive oxygen species (ROS), malondialdehyde (MDA), and glutathione (GSH) were performed to investigate how Cel inhibits the proliferation of hepatocellular carcinoma (HCC) cells via the ferroptosis mechanism. Bioinformatics analysis based on the TCGA-LIHC and FerrDb databases was performed to identify the target gene RRM2, and molecular docking-simulated binding between RRM2 and Cel. The role of RRM2 in the effects of Cel was determined through lentiviral transfection, Transwell assays, and in vivo experiments. ResultsCel inhibited HCC cell proliferation via the ferroptosis pathway. Inhibition RRM2 significantly reduces mTOR protein phosphorylation, while overexpressing RRM2 can attenuate theeffects of Cel on the proliferation, migration, invasion, and ferroptosis induction of HCC cells. The result of in vivo experiments in nude mice demonstrated that Cel inhibited tumor growth without adversely affecting liver and kidney function indicators. Immunohistochemistry and Western blot analyses revealed that Cel activated the key proteins in the ferroptosis pathway and affected crucial indicators such as malondialdehyde (MDA) and glutathione (GSH). ConclusionIn this study, we clarifiy the molecular mechanism of Cel, thus broadening its clinical applications for treating various cancer types, including liver cancer.

Anti-rheumatoid arthritis potential of Acorus calamus L. extract by interleukin-17 inhibition: Molecular insights through an in silico study

Context: Interleukin-17 (IL-17) is a pro-inflammatory cytokine that plays a crucial role in immunity and inflammation. Aims: To evaluate the potential therapeutic effects of two compounds, magnosalicine and neotatarine, derived from the ethanolic extract of Acorus calamus L. rhizome, against IL-17. Methods: Utilizing LC/MS analysis combining molecular docking simulations, drug likeness, ADME and toxicity analysis. This study explored the molecular interactions and binding affinities of identified compounds from A. calamus with crucial residues of IL-17, including Tyr62, Pro63, Ile66, Gln94, Ile96, Leu97, and Leu99. Results: The results revealed that magnosalicine and neotatarine exhibited remarkable binding affinities of -10.16 kcal/mol and -9.53 kcal/mol, respectively, indicating their strong interactions with IL-17. Moreover, both compounds displayed superior binding energies compared to other extract constituents. Interestingly, this study highlighted that all terpenoid compounds from the A. calamus rhizome extract were capable of interacting with these key residues of IL-17, resembling the interactions observed with the natural ligand (RMK) and methotrexate. Meanwhile, the analysis results revealed a safer ADME and toxicity profile for neotatarine compared to magnolalicine. Conclusions: This research unveils the promising potential of neotatarine as candidates for further exploration in therapeutic interventions targeting IL-17-related pathways. These findings shed light on the molecular insights of Acorus calamus L. compounds, providing valuable information for developing novel treatments for IL-17-associated disorders.

Evaluation of doxorubicin and β-lapachone analogs as anticancer agents, a biological and computational study.

We have conducted an experimental and computational evaluation of new doxorubicin (4a-c) and β-lapachone (5a-c) analogs. These novel anticancer analogs were previously synthesized, but had not been tested or characterized until now. We have evaluated their antiproliferative and DNA cleavage inhibition properties using breast (MCF-7 and MDA-MB-231) and prostate (PC3) cancer cell lines. Additionally, cell cycle analysis was performed using flow cytometry. Computational studies, including molecular docking, pharmacokinetic properties, and an analysis of DFT and QTAIM chemical descriptors, were performed to gain insights into the electronic structure and elucidate the molecular binding of the new β-lapachone and doxorubicin analogs with a DNA sequence and Topoisomerase II (Topo II)α. Our results show that 4a analog displays the highest antiproliferative activity in cancer cell lines by inducing cell death. We observed that stacking interactions and hydrogen bonding are essential to stabilize the molecule-DNA-Topo IIα complex. Moreover, 4a and 5a analogs inhibited Topo's DNA cleavage activity. Pharmacodynamic results indicated that studied molecules have favorable adsorption and permeability properties. The calculated chemical descriptors indicate that electron accumulation in quinone rings is relevant to the reactivity and biological activity. Based on our results, 4a is a strong candidate for becoming an anticancer drug.

Investigating the Role of Inflammatory Response in Polycystic Ovary Syndrome Using Integrated RNA-Seq Analysis.

An important factor in the pathogenesis of polycystic ovary syndrome (PCOS) is chronic low-grade inflammation. However, the exact pathophysiology of PCOS is currently unknown, which makes clinical diagnosis and the development of effective treatments more difficult. We aimed to investigate the role of the inflammatory response in initiating and progressing PCOS. 13 control granulosa cell samples and 15 granulosa cell samples from patients with PCOS were obtained from the GSE102293, GSE34526, and GSE5850 datasets. The gene set variation analysis (GSVA) method was used to calculate the inflammatory response score. Subsequently, the genes associated with inflammation in the hub were identified using differential expression analysis and weighted gene co-expression network analysis (WGCNA). The findings were confirmed by analysis of independent datasets and examination of clinical samples by qRT-PCR analysis. A consensus cluster analysis was conducted to categorize the PCOS samples into subtypes related to inflammation. Functional enrichment and analysis of immune cell infiltration were conducted to explore the potential mechanisms involved. Additionally, the CMap database was utilized to predict potential drugs, and the results were confirmed through molecular docking. During the training cohort analysis, we identified five distinct genes (TGFBR2, ICAM3, WIPF1, SLC11A1, and NCF2) that could serve as potential diagnostic markers for PCOS. The expression levels of these genes were confirmed through validation in both the test set and clinical samples. In training cohort, two distinct inflammatory patterns (C1 and C2) were identified, and the C2 subtype exhibited activated immune- and inflammation-related pathways. Esmolol was shown to have potential as a drug to treat PCOS and it showed good results for molecular binding at TGFBR2, ICAM3, WIPF1, SLC11A1, and NCF2 proteins. Five diagnostic biomarkers and two inflammation-related molecular types associated with PCOS were identified, and esmolol was a potential drug for PCOS treatment. Our findings provided new diagnostic markers and potential small-molecule drugs for PCOS diagnosis and prevention.

Molecular Dynamics Simulations and Binding Free Energy Calculations to Discover New Insights into NLRP3 Inhibitors

Background: Inflammation is an immunological reaction against an aggressor agent. NLRP3 inflammasome is a component of the immune system, which, when excessively activated, results in several inflammatory diseases, making it an attractive target for discovering antiinflammatory drugs. Computer-Aided Drug Design (CADD) techniques are powerful tools used to search for new drugs in less time and financial cost. Recently, studies demonstrated the CADD methods to discover information about NLRP3 inhibitors MCC950 and NP3-146. In addition, the discovery of GDC-2394 and its evaluation in clinical trials instigate new studies to find binding modes and structural attributes that can used in drug design works against this target. Objectives: Here, molecular modeling methods were used to discover the significant interactions of GDC-2394, MCC950, and NP3-146 with NLRP3 to obtain helpful information in drug design compared to other inhibitors. Methods: Molecular docking was performed using GOLD software. The best complexes were submitted into molecular dynamics simulations using GROMACS software, and the MM-PBSA was used to provide the free binding energy, which was performed using the tool g_mmpbsa compiled in GROMACS. Results: The RMSD, RMSF, Rg, SASA, and H-bond plots showed that the compound was stable during MD simulation time (100 ns) for GDC-2394. The PCA analysis for all compounds verified similar variance of the complex with the inhibitors to the apo-NLRP3, indicative of stability. DCCM analysis showed the best correlation in residues 134 - 371 region, which contains critical amino acids from the binding site (Ala227, Ala228, and Arg578), besides the newly identified residues. Using MMPBSA to provide the binding free energy, it was observed that the high affinity of the drugs against NLRP3 is related to the lower rigidity of the structure. Furthermore, we identified the critical residues Phe575, Pro352, Tyr632, and Met661 related to the coupling process. result: Then, RMSD, RMSF, Rg, SASA, and H-bond plots showed that the compound was stable during MD simulation time (100 ns) for GDC-2394. The PCA analysis for all compounds verified similar variance of the complex with the inhibitors to the apo-NLRP3, indicative of stability. Through DCCM analysis, the best correlation was observed in residues 134 - 371 region, which contains critical amino acids from the binding site (Ala227, Ala228, and Arg578), besides the newly identified residues. Using MM-PBSA to provide the binding free energy, it was observed that the high affinity of the drugs against NLRP3 is related to the lower rigidity of the structure. Furthermore, we identified the critical residues Phe575, Pro352, Tyr632, and Met661 related to the coupling process. Conclusion: Thus, these discoveries may contribute to the development of new anti-inflammatory drugs, such as NLRP3 inhibitors.

Structure-activity relationship of pharmacophores and toxicophores: the need for clinical strategy.

Sometimes clinical efficacy and potential risk of therapeutic and toxic agents are difficult to predict over a long period of time. Hence there is need for literature search with a view to assessing cause of toxicity and less efficacy of drugs used in clinical practice. Hence literatures were searched for physicochemical properties, chemical formulas, molecular masses, pH values, ionization, receptor type, agonist and antagonist, therapeutic, toxic and structure-activity relationship of chemical compounds with pharmacophore and toxicophore, with a view to identifying high efficacious and relative low toxic agents. Inclusion criteria were manuscripts published on PubMed, Scopus, Web of Science, PubMed Central, Google Scholar among others, between 1960 and 2023. Keywords such as pharmacophore, toxicophore, structure-activity-relationship and disease where also searched. The exclusion criteria were the chemicals that lack pharmacophore, toxicophore and manuscripts published before 1960. Findings have shown that pharmacophore and toxicophore functional groups determine clinical efficacy and safety of therapeutics, but if they overlap therapeutic and toxicity effects go concurrently. Hence the functional groups, dose, co-administration and concentration of drugs at receptor, drug-receptor binding and duration of receptor binding are the determining factors of pharmacophore and toxicophore activity. Molecular mass, chemical configuration, pH value, receptor affinity and binding capacity, multiple pharmacophores, hydrophilic/lipophilic nature of the chemical contribute greatly to functionality of pharmacophore and toxicophore. Daily single therapy, avoidance of reversible pharmacology, drugs with covalent adduct, maintenance of therapeutic dose, and the use of multiple pharmacophores for terminal diseases will minimize toxicity and improve efficacy.

Integration of molecular docking and molecular dynamics simulations with subtractive proteomics approach to identify the novel drug targets and their inhibitors in Streptococcus gallolyticus

Streptococcus gallolyticus (Sg) is a non-motile, gram-positive bacterium that causes infective endocarditis (inflammation of the heart lining). Because Sg has gained resistance to existing antibiotics and there is currently no drug available, developing effective anti-Sg drugs is critical. This study combined core proteomics with a subtractive proteomics technique to identify potential therapeutic targets for Sg. Several bioinformatics approaches were used to eliminate non-essential and human-specific homologous sequences from the bacterial proteome. Then, virulence, druggability, subcellular localization, and functional analyses were carried out to specify the participation of significant bacterial proteins in various cellular processes. The pathogen’s genome contained three druggable proteins, glucosamine-1phosphate N-acetyltransferase (GlmU), RNA polymerase sigma factor (RpoD), and pantetheine-phosphate adenylyltransferase (PPAT) which could serve as effective targets for developing novel drugs. 3D structures of target protein were modeled through Swiss Model. A natural product library containing 10,000 molecules from the LOTUS database was docked against therapeutic target proteins. Following an evaluation of the docking results using the glide gscore, the top 10 compounds docked against each protein receptor were chosen. LTS001632, LTS0243441, and LTS0236112 were the compounds that exhibited the highest binding affinities against GlmU, PPAT, and RpoD, respectively, among the compounds that were chosen. To augment the docking data, molecular dynamics simulations and MM-GBSA binding free energy were also utilized. More in-vitro research is necessary to transform these possible inhibitors into therapeutic drugs, though computer validations were employed in this study. This combination of computational techniques paves the way for targeted antibiotic development, which addresses the critical need for new therapeutic strategies against S. gallolyticus infections.

Trace metals in the teleost fish gill: biological roles, uptake regulation, and detoxification mechanisms.

In fish, the gill plays a vital role in regulating the absorption of trace metals and is also highly susceptible to metal toxicity. Trace metals such as iron (Fe), copper (Cu), zinc (Zn), and manganese (Mn) are involved in various catalytic activities and molecular binding within the gill, thereby supporting a range of physiological processes in this organ. While beneficial at normal levels, these metals can become toxic when present in excess. Conversely, nonessential metals like cadmium (Cd) and lead (Pb) can gain entry into gill cells through similar metal transport pathways, potentially interfering with various cellular processes. The transepithelial transport of these metals across the gill epithelium is governed by a variety of metal transport and metal binding proteins. These include the Cu transporter 1 (CTR1), divalent metal transporter 1 (DMT1), and members of the Zrt-/Irt-like protein (ZIP) and zinc transport (ZnT) families. Additionally, some of these metals can compete with major ions (e.g., calcium, sodium) for absorption sites in the gill. This complex crosstalk suggests an interdependent mechanism that balances metal uptake to meet physiological needs while preventing excessive accumulation. In this article, I review the roles of trace metals in proteins/enzymes that support the different functions in the gill of teleost fish. I also discuss current understanding of the pathways involved in regulating the branchial uptake of metals and their influence on ionic regulation, and the potential detoxification mechanisms in the gill. Finally, I summarize knowledge gaps and potential areas for further investigation.

Network pharmacology and molecular docking analysis of cold‐pressed rapeseed oil active components for anti‐inflammatory effects

AbstractInvestigating the anti‐inflammatory effects of bioactive components present in cold‐pressed rapeseed oil through the use of network pharmacology and molecular docking methods. The components of cold‐pressed rapeseed oil were identified by liquid chromatography‐mass spectrometry. We then conducted Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis using bioinformatics databases on overlapping targets affected by active components and inflammation. Finally, molecular docking was used to predict the interactions between core components and key targets. Analysis identified 13 phenols, four steroids, and one retinoid in cold‐pressed rapeseed oil, with 143 overlapping targets related to inflammation. Bioinformatics analysis revealed that 25‐Hydroxycholesterol, Rosmarinic acid, 9‐cis‐Retinoic acid, Soyasapogenol B and α‐Tocopherol in cold‐pressed rapeseed oil could play a positive role in treating inflammation. They achieved this by regulating key targets (MMP9, EGFR, AKT1, ESR1, and PTGS2) involved in the peroxisome proliferator‐activated receptor signaling pathway and other related pathways. The molecular docking binding energy of the core components and the key targets were less than −5.0 kcal/mol, indicating that the components and the targets can be stably bound. This result indicated that the active components found in cold‐pressed rapeseed oil may exert an anti‐inflammatory effect through a synergistic mechanism involving multicomponent, multitarget and multipathway interactions.

Molecular determinants of olfactory receptor activation: Comparative analysis of Olfr205 and Olfr740 family member responses to indole

Indole is widely present in nature and contributes significantly to the smell of flowers and animal excretion. However, the odor perception mechanism for indole is unclear, despite previous reports suggesting that it activates the Olfr740 family of receptors. In this study, we successfully identified another receptor, Olfr205, that is responsive to indole. Molecular model construction and binding pocket analysis predicted that the A202 residue in transmembrane helix 5 of Olfr205 forms a crucial hydrogen bond with indole, facilitating receptor activation. Additionally, G112 in transmembrane helix 3 of the Olfr740 family is involved in indole activation of receptors. Finally, our mutant function assay showed that substitution of A202 in Olfr205 and G112 in Olfr740 with other amino acids significantly decreased the receptor response to indole, which provides robust evidence to confirm the docking results. In summary, our study is the first to reveal that Olfr205 is an olfactory receptor distinct from those in the Olfr740 family that is activated by indole. Moreover, these receptors display different indole-binding mechanisms. This study sheds light on molecular binding mechanisms and contributes to a deeper understanding of indole perception.

Stabilization effect and interaction mechanism of mannoprotein on anthocyanins in mulberry juice

This study aimed to investigate the problem of color instability in mulberry juice, examine the effect of mannoprotein (MP) dosage on improving the stability of anthocyanins in mulberry juice, and explore the molecular binding mechanism between them. As the mass ratio of anthocyanins to MP of 1.07 × 10−3: 1–1.65 × 10−3: 1, the retention rates of anthocyanins in mulberry juice and simulated system were significantly improved in the photostability experiment, with the highest increase of 128.89 % and 24.11 %, respectively. In the thermal stability experiment, it increased by 7.96 % and 18.49 %, respectively. The synergistic effect of combining MP with anthocyanins has been demonstrated to greatly enhance their antioxidant capacity, as measured by ABTS, FRAP, and potassium ferricyanide reduction method. Furthermore, MP stabilized more anthocyanins to reach the intestine in simulated in vitro digestion. MP and cyanidin-3-glucoside (C3G) interacted with each other through hydrogen bonding and hydrophobic interactions. Specific amino acid residues involved of MP in binding process were identified as threonine (THR), isoleucine (ILE) and arginine (ARG). The identification of the effective mass concentration ratio range and binding sites of MP and anthocyanins provided valuable insights for the application of MP in mulberry juice.

N6-methyladenosine dynamics in placental development and trophoblast functions, and its potential role in placental diseases

N6-methyladenosine (m6A) is the most abundant modification controlling RNA metabolism and cellular functions, but its roles in placental development are still poorly understood. Here, we characterized the synchronization of m6A modifications and placental functions by mapping the m6A methylome in human placentas (n = 3, each trimester), revealing that the dynamic patterns of m6A were associated with gene expression homeostasis and different biological pathways in placental development. Then, we generated trophoblast-specific knockout mice of Wtap, a critical component of methyltransferase complex, and demonstrated that Wtap was essential for trophoblast proliferation, placentation and perinatal growth. Further in vitro experiments which includes cell viability assays and series molecular binding assays demonstrated that WTAP-m6A-IGF2BP3 axis regulated the RNA stability and translation of Anillin (ANLN) and VEGFA, promoting trophoblast proliferation and secretion. Dysregulation of this regulatory axis was observed in placentas from pregnancies with fetal growth restriction (FGR) or preeclampsia, revealing the pathogenic effects of imbalanced m6A modifications. Therefore, our findings provide novel insights into the functions and regulatory mechanisms of m6A modifications in placental development and placental-related gestational diseases.

Design, Synthesis, and Biological Evaluation of Chroman Derivatives as PD-1/PD-L1 Antagonists.

Programmed death-ligand 1 (PD-L1) has emerged as a promising therapeutic target for various cancers due to its crucial role in promoting tumor immune evasion. Here, we report a novel class of chroman-like small-molecule PD-L1 inhibitors exhibiting significant activity in inhibiting the PD-1/PD-L1 interaction. Employing a "ring-close" strategy for conformational restriction, we have achieved compound C27, which demonstrates superior PD-1/PD-L1 inhibitory activity compared to the positive control. Molecular dynamics simulation and binding free energy calculation predict that (R)-C27 with inhibitory activity surpassed (S)-C27. The experimental results from bioassay and X-ray structural analysis corroborate these findings. All these results collectively indicate that (R)-C27 is a promising lead compound deserving further exploration.

Isolation, purification, characterization, and analysis of the antioxidant activity of antioxidant peptides from walnut milk fermented with Lactobacillus paracasei SMN-LBK

Microbial fermentation is an important method to obtain antioxidant peptides. In this study, Lactobacillus paracasei SMN-LBK was used to ferment biprotein (walnut milk) to enhance the antioxidant capacity of the active peptide. The optimal fermentation process of 5% inoculum, 1:7 plant protein ratio, 37 °C and 12 h resulted in 77.63% ± 0.36% DPPH scavenging, 93.31% ± 0.25% ABTS scavenging and 79.37% ± 0.02% metal ion chelating capacity. The hydrolysis products were classified into three molecular weight classes using an ultrafiltration membrane system. DPAP-3 with a molecular weight of less than 3 kDa had the highest antioxidant activity. DPAP-3 was further separated into three subclasses using gel filtration chromatography. These subclasses were characterized using nano-liquid chromatography-tandem mass spectrometry (NanoLC-MS/MS) and screened by searching https://biochemia.uwm.edu. Four antioxidant peptides were identified using a combination of hydrophobic amino acids, positive ion-charge interactions, and numerical values. Two of these peptides were from animals and one from plants. Their amino acid sequences are as follows PCRGVLLR, IHIPLPRWV, QSKVLPVPQK, and KVLPVPQKA, with molecular docking binding energies of −7.8, −8.3, −7.4, and −7.7 kcal/mol, respectively. The results suggest that fermentation of plant-animal proteins with Lactobacillus paracasei can produce antioxidant peptides that can be used as functional ingredients in food products. This has the potential to conserve animal protein resources.

Navigating the landscape of PD-1/PD-L1 imaging tracers: from challenges to opportunities.

Immunotherapy targeted to immune checkpoint inhibitors, such as the program cell death receptor (PD-1) and its ligand (PD-L1), has revolutionized cancer treatment. However, it is now well-known that PD-1/PD-L1 immunotherapy response is inconsistent among patients. The current challenge is to customize treatment regimens per patient, which could be possible if the PD-1/PD-L1 expression and dynamic landscape are known. With positron emission tomography (PET) imaging, it is possible to image these immune targets non-invasively and system-wide during therapy. A successful PET imaging tracer should meet specific criteria concerning target affinity, specificity, clearance rate and target-specific uptake, to name a few. The structural profile of such a tracer will define its properties and can be used to optimize tracers in development and design new ones. Currently, a range of PD-1/PD-L1-targeting PET tracers are available from different molecular categories that have shown impressive preclinical and clinical results, each with its own advantages and disadvantages. This review will provide an overview of current PET tracers targeting the PD-1/PD-L1 axis. Antibody, peptide, and antibody fragment tracers will be discussed with respect to their molecular characteristics and binding properties and ways to optimize them.

Qiju Dihuang Pill protects the lens epithelial cells via alleviating cuproptosis in diabetic cataract

Ethnopharmacological relevanceQiju Dihuang Pill (QDP) is a traditional Chinese medicine prescription for the treatment of eye diseases. Novel literature reports that copper-induced cell death, called as cuproptosis, is a copper-dependent and differs distinctly from other types of cell death. Aim of the studyThe present study aims to investigate whether QDP could protect lens epithelial cells via alleviating copper-induced death in diabetic cataract. Materials and methodsThe different concentration of QDP medicated serum was administrated on high glucose (HG)-induced human lens epithelial cells (HLECs). The copper concentration was tested using Elabscience Copper Assay kit. The proliferation was detected using CCK-8 and EdU assays. The molecular binding was identified using RIP-PCR and luciferase reporter assay. ResultsResults indicated that HG culture condition triggered the copper concentration and repressed the proliferation of HLECs. Then, the elesclomol-Cu (Es–Cu) administration up-regulated the copper concentration and inhibited the proliferation, and cuproptosis inhibitor tetrathiomolybdate (TTM) could specifically reverse the consequence. QDP treatment reduced the copper concentration and cuproptosis-related genes (SLC31A1, FDX1). MeRIP-Seq and RIP-PCR confirmed that QDP reduced the stability of SLC31A1 mRNA through m6A modified site, and copper actually synergized the molecular binding efficiency. Rescue assay verified the role of QDP and SLC31A1 on HLECs’ cuproptosis characteristic. ConclusionThis research identified the protective role of QDP on HG-induced HLECs in DC through decreasing m6A/SLC31A1-mediated cuproptosis in DC. This finding provides novel insights into mechanisms for QDP and sheds light on the multifaceted role of traditional prescription on DC.

Shedding Light on Dark Chemical Matter: The Discovery of a SARS-CoV-2 Mpro Main Protease Inhibitor through Intensive Virtual Screening and In Vitro Evaluation.

The development of specific antiviral therapies targeting SARS-CoV-2 remains fundamental because of the continued high incidence of COVID-19 and limited accessibility to antivirals in some countries. In this context, dark chemical matter (DCM), a set of drug-like compounds with outstanding selectivity profiles that have never shown bioactivity despite being extensively assayed, appears to be an excellent starting point for drug development. Accordingly, in this study, we performed a high-throughput screening to identify inhibitors of the SARS-CoV-2 main protease (Mpro) using DCM compounds as ligands. Multiple receptors and two different docking scoring functions were employed to identify the best molecular docking poses. The selected structures were subjected to extensive conventional and Gaussian accelerated molecular dynamics. From the results, four compounds with the best molecular behavior and binding energy were selected for experimental testing, one of which presented inhibitory activity with a Ki value of 48 ± 5 μM. Through virtual screening, we identified a significant starting point for drug development, shedding new light on DCM compounds.

Machine learning-based QSAR modeling, molecular docking, dynamics simulation studies for cytotoxicity prediction in MDA-MB231 triple-negative breast cancer cell line

Triple-negative breast cancer (TNBC) is the most aggressive cancer type that tests negative for progesterone, estrogen, and HER2 protein receptors. Therefore, TNBC is unlikely to respond either to drugs that target HER2 receptors or to hormonal therapy drugs. In the present study, 2D-QSAR model was developed to predict the inhibitory concentration (IC50) of terpene derivatives against human breast cancer metastatic cell line MDA-MB231, using V-Life MDS v4.5, module. The model was developed using the forward stepwise multiple linear regression method, with a regression coefficient (r2) of 0.86, and a cross-validated r2 (q2) of 0.8448. Molecular descriptors namely electronegativity (Epsilon-3), carbon atoms separated through five bond distances (T_C_C_5), Sum of Electrotopological state indices of –CH2 group (SssCH2count), Dipole moment of coordinate-z (Zcomp Dipole), and Distance between highest positive and negative electrostatic potential on van-der Waals surface area (Most +ve & -ve Potential Distance) were found to be the most potent contributing chemical descriptors for cytotoxicity against TNBC MDA-MB231 cell line. Additionally, binding affinities and interaction patterns revealed that the proposed compounds exhibit good binding affinities and substantial stability with c-Met-and β-tubulin receptors, as assessed by docking studies. Molecular dynamics simulations (100 ns) and binding free energy calculations were also performed using the MMGBSA method. The pharmacokinetic and eADME/T analysis of predicted compounds were assessed through Discovery Studio software. These findings may be of immense importance in the optimization and development of dual inhibitory potent anti-cancer inhibitors against the MDA-MB231 TNBC cell line. Moreover, this novel QSAR based prediction model/method is implemented in R-package and software tool developed for virtual screening purposes and available online for download through the public repository GitHub.

Homologous Design and Three-Dimensional Quantitative Structure-Activity Relationship Study of Acaricidal 2,4-Diphenyloxazolines Containing Different Heteroatoms and Alkyl Chains.

In order to speculate the three-dimensional structure of the potential binding pocket of the chitin synthase inhibitor, a series of 2,4-diphenyloxazoline derivatives with different lengths of alkyl chains and heteroatoms were designed and synthesized by a homologous strategy. The bioassay results indicate that both the length of the alkyl chains and the type of substituents can affect the acaricidal activity against mite eggs. Compounds containing chloropropyl, alkoxyalkyl, and para-substituted phenoxyalkyl or phenylthioalkyl groups exhibit good activity, while those containing steric hindrance substituents or carbonyl substituents on the benzene ring exhibit reduced activity. Three-dimensional quantitative structure-activity relationship (3D-QSAR) study showed that there may be a narrow hydrophobic region deep in the pocket, and the steric effect plays a more important role than the electrostatic effect. The current work will provide assistance for future molecular design and target binding research.

An integrated investigation combining network pharmacology and computer simulation dissects the potential mechanism of anti-obesity of Monascus pigments (MPs)

Monascus pigments (MPs), the secondary metabolites of Monascus-fermented foods, have been widely studied for their anti-obesity effects. However, the specific targets and potential mechanism of MPs for anti-obesity remain unclear. In this study, we applied network pharmacology and computer simulation to investigate the anti-obesity potential and action mechanism of MPs. Based on public databases, 117 potential therapeutic obesity targets of MPs were predicted. Five key targets (STAT3, ESR1, BCL2, PPARG, and MMP9) were obtained by protein-protein interaction (PPI) analysis and microarray data validation. The enrichment results showed that MPs exerted anti-obesity effects through multiple targets and multiple pathways, especially insulin resistance. Molecular docking demonstrated the binding of five key targets to MPs ligands through hydrophobic interactions and hydrogen bonding. Molecular dynamics simulation and binding free energy analysis revealed a higher stability in the binding of ESR1, BCL2, and PPARG targets with MPs ligands. In addition, free energy landscape (FEL) and independent gradient model (IGM) analysis showed that van der Waals forces were also the main driving force in stabilizing the binding of key targets and MPs ligands. This study systematically illustrated the potential anti-obesity mechanism of MPs and established the foundation for the development and application of MPs as anti-obesity functional additives.