Evaluation Of Binding Affinity Research Articles

Discovery of Small Molecule Inhibitors Targeting CTNNB1 (β-catenin) for Endometrial cancer: Employing 3D QSAR, Drug-Likeness Assessment, ADMET Predictions, Molecular Docking and Simulation.

Endometrial carcinoma (EC) is a type of cancer that originates in the lining of the uterus, known as the endometrium. It is associated with various treatment options such as surgery, radiation therapy, chemotherapy, and hormone therapy, each presenting unique challenges and limitations. Beta-catenin, a protein involved in the development and progression of several cancers, including EC, plays a crucial role. Abnormal beta-catenin signaling is often linked to the emergence of specific EC subtypes, affecting tumor growth and invasion. The study's objective is to identify compounds targeting the beta-catenin protein for treating endometrial cancer (EC) using in silico drug design. Our approach includes molecular docking to evaluate binding affinities, ADME profiling for pharmacokinetic properties, toxicity assessments, and molecular dynamics simulations to assess compound stability and interactions. Approximately one thousand anti-cancer phytochemicals were sourced from PubChem and subjected to molecular docking simulations against the beta-catenin protein. The compounds were evaluated based on their binding affinities, with the top five selected for further analysis. These five molecules underwent toxicity and ADME profiling. The Prediction of Activity Spectra for Substances (PASS) tool was used to identify compounds targeting CTNNB1. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were employed to establish quantitative structure-activity relationship (QSAR) models for the five CTNNB1 antagonist molecules. The selected five compounds, namely Pazopanib, Binimetinib, Telatinib, 4-(2,3-Dihydrobenzo[ b][1,4]dioxin-6-yl)-3-((5-nitrothiazol-2-yl)thio)-1H-1,2,4-triazol-5(4H)-one, and Ribavirin, demonstrated efficacy against CTNN1. MD simulations of the docked complexes confirmed the stability of these drugs in binding to the target protein. All five molecules showed promising safety and effectiveness profiles according to their ADME and toxicity evaluations. Through a comprehensive screening process employing in silico drug design methods, this study successfully identified five potential human anticancer drug candidates targeting the beta-catenin protein. These findings offer a foundation for further experimental validation and development towards the treatment of EC.

Elucidating Chiral Resolution of Aromatic Amino Acids Using Glycopeptide Selectors: A Combined Molecular Docking and Chromatographic Study.

An asymmetric synthesis is a favorable approach for obtaining enantiomerically pure substances, but racemic resolution remains an efficient strategy. This study aims to elucidate the chiral resolution of aromatic amino acids and their elution order using glycopeptides as chiral selectors through molecular docking analysis. Chiral separation experiments were conducted using Vancomycin as a chiral additive in the mobile phase (CMPA) at various concentrations, coupled with an achiral amino column as the stationary phase. The Autodock Vina 1.1.2 software was employed to perform molecular docking simulations between each enantiomer (ligand) and Vancomycin (receptor) to evaluate binding affinities, demonstrate enantiomeric resolution feasibility, and elucidate chiral recognition mechanisms. Utilizing Vancomycin as CMPA at a concentration of 1.5 mM enabled the separation of tryptophan enantiomers with a resolution of 3.98 and tyrosine enantiomers with a resolution of 2.97. However, a poor chiral resolution was observed for phenylalanine and phenylglycine. Molecular docking analysis was employed to elucidate the lack of separation and elution order for tryptophan and tyrosine enantiomers. By calculating the binding energy, docking results were found to be in good agreement with experimental findings, providing insights into the underlying mechanisms governing chiral recognition in this system and the interaction sites. This comprehensive approach clarifies the complex relationship between chiral discrimination and molecular architecture, offering valuable information for creating and improving chiral separation protocols.

Multifaceted targets of cannabidiol in epilepsy: Modulating glutamate signaling and beyond

Cannabidiol has been reported to interact with broad-spectrum biological targets with pleiotropic pharmacology including epilepsy although a cohesive mechanism is yet to be determined. Even though some studies propose that cannabidiol may manipulate glutamatergic signals, there is insufficient evidence to support cannabidiol direct effect on glutamate signaling, which is important in intervening epilepsy. Therefore, the present study aimed to analyze the epilepsy-related targets for cannabidiol, assess the differentially expressed genes with its treatment, and identify the possible glutamatergic signaling target. In this study, the epileptic protein targets of cannabidiol were identified using the Tanimoto coefficient and similarity index-based targets fishing which were later overlapped with the altered expression, epileptic biomarkers, and genetically altered proteins in epilepsy. The common proteins were then screened for possible glutamatergic signaling targets with differentially expressed genes. Later, molecular docking and simulation were performed using AutoDock Vina and GROMACS to evaluate binding affinity, ligand-protein stability, hydrophilic interaction, protein compactness, etc. Cannabidiol identified 30 different epilepsy-related targets of multiple protein classes including G-protein coupled receptors, enzymes, ion channels, etc. Glutamate receptor 2 was identified to be genetically varied in epilepsy which was targeted by cannabidiol and its expression was increased with its treatment. More importantly, cannabidiol showed a direct binding affinity with Glutamate receptor 2 forming a stable hydrophilic interaction and comparatively lower root mean squared deviation and residual fluctuations, increasing protein compactness with broad conformational changes. Based on the cheminformatic target fishing, evaluation of differentially expressed genes, molecular docking, and simulations, it can be hypothesized that cannabidiol may possess glutamate receptor 2-mediated anti-epileptic activities.

Application of a Fluorescence Recovery-Based Polo-Like Kinase 1 Binding Assay to Polo-Like Kinase 2 and Polo-Like Kinase 3.

Assay systems for evaluating compound protein-binding affinities are essential for developing agonists and/or antagonists. Targeting individual members of a protein family can be extremely important and for this reason it is critical to have methods for evaluating selectivity. We have previously reported a fluorescence recovery assay that employs a fluorescein-labelled probe to determine IC50 values of ATP-competitive type 1 inhibitors of polo-like kinase 1 (Plk1). This probe is based on the potent Plk1 inhibitor BI2536 [fluorescein isothiocyanate (FITC)-polyethylene glycol (PEG)-lysine (Lys) (BI2536) 1]. Herein, we extend this approach to the highly homologous Plk2 and Plk3 members of this kinase family. Our results suggest that this assay system is suitable for evaluating binding affinities against Plk2 and Plk3 as well as Plk1. The new methodology represents the first example of evaluating N-terminal catalytic kinase domain (KD) affinities of Plk2 and Plk3. It represents a simple and cost-effective alternative to traditional kinase assays to explore the KD-binding compounds against Plk2 and Plk3 as well as Plk1.

The mechanism of polyphyllin in the treatment of gastric cancer was verified based on network pharmacology and experimental validation

BackgroundPolyphyllin is a class of saponins extracted from Paris polyphylla rhizomes and has been used in clinical application in China for more than 2000 years. However, the mechanism for treating gastric cancer (GC) is still unclear. This study was designed to predict the targets and mechanisms of total Polyphyllin from Paris polyphylla rhizomes for the treatment of GC. MethodFirstly, PubChem and Swiss Target Prediction databases were utilized to collect the 12 ingredients of total Polyphyllin from Paris polyphylla rhizomes and their targets. GC-related genes were obtained from the GEO database. Then the intersecting targets to all these molecules that identified using Venny. Secondly, the intersecting targets were imported into STRING platform for protein-protein interaction (PPI) network. Moreover, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted in DAVID website. In addition, the GEPIA was applied to perform the expression levels, transcript levels, staging, and overall survival of hub genes. In addition, we used AutoDock Vina to evaluate binding affinity of molecular docking between key ingredients and anti-GC targets. In vitro cell experiments, we detected the cell viability of gastric cancer cells at 24, 36, and 48 h using CCK-8 assay. The G0/G1 of cell cycle and apoptosis were detected by flow cytometry. Finally, quantitative real time polymerase chain reaction (qRT-PCR) was used to detect the level of hub genes, and Western blot was used to detect the changes of PI3K/Akt signal pathway. ResultsFirstly, we identified 12 ingredients and 286 targets of total Polyphyllin. A total of 2653 GC-related differentially expressed genes (DEGs) were collected, including 1366 up-regulated genes and 1287 down-regulated genes. Moreover, 45 targets were obtained after intersection. Secondly, results of the GO enrichment suggested that these genes were closely related to cell proliferation, migration and aging. KEGG analysis suggested that Polyphyllin in GC therapy were mostly regulated by multiple pathways, including the pathways in cancer, calcium signaling pathway, Rap1 signaling pathway, phospholipase D signaling pathway, etc. In addition, GEPIA results exhibited that PDGFRB, KIT, FGF1, GLI1, F2R, and HIF1A were associated with GC progression, stage, and survival. Besides, the molecular docking results further confirmed that the binding energy of Polyphyllin Ⅲ with HIF1A was minimal. In vitro cell experiments, Polyphyllin Ⅲ inhibited the cell viability of gastric cancer cells, blocked the cell cycle G0/G1 phase, and induced cell apoptosis. In addition, Polyphyllin Ⅲ down-regulated the mRNA levels of PDGFRB, KIT, FGF1, GLI1, F2R, and HIF1A, and regulated the PI3K/Akt signal pathway. ConclusionsThe results revealed that total Polyphyllin treated GC through multiple targets, multiple channels, and multiple pathways. In addition, Polyphyllin Ⅲ played an anti-gastric cancer role by inhibiting the proliferation of gastric cancer.

Analysing the Anticancer Properties of Pterostilbene Through Absorption, Distribution, Metabolism, and Excretion (ADME) and Molecular Docking Studies.

Aim The aim of this study is to examine the possible therapeutic effect of pterostilbene (PTS), a chemical present in grapes and blueberries, in the treatment of liver cancer by analysing its interactions with important proteins linked to the wingless/integrated (Wnt) signaling system. Objective Using computational techniques like molecular docking and absorption, distribution, metabolism, and excretion (ADME) studies, this research focuses on examining the pharmacokinetics and molecular interactions of PTS with proteins such as vimentin (Vim), glycogen synthase kinase 3 beta (GSK3-β), epithelial cadherin (E-cadherin), interleukin-6 (IL-6), interleukin-1 beta (IL-1β), c-Jun N-terminal kinase (JNK), and Wnt, all of which are connected to the Wnt signaling pathway in liver cancer. Methods The study includes the synthesis of proteins and ligands, ADME investigations for PTS, and AutoDock Vina molecular docking simulations to evaluate binding affinities and interactions. PTS is obtained from PubChem, while protein structures are obtained from the Protein Data Bank. Results Strong binding affinities between PTS and essential proteins in the Wnt signaling cascade are shown by molecular docking, which also highlights noteworthy hydrogen bonds, hydrophobic interactions, and electrostatic contacts. According to an ADME study, PTS has advantageous pharmacokinetic properties, such as moderate solubility, membrane permeability, and a minimal chance of drug interactions. Conclusion The extensive study highlights PTS's potential as a viable treatment option for liver cancer. The study promotes its investigation in cutting-edge liver cancer therapy approaches and urges more investigation into the molecular mechanisms, underpinning its anticancer properties. This paper sheds important light on the role of natural chemicals in cancer therapy and emphasizes the need for computational methods in drug discovery.

Herbal Metabolites as Potential Carbonic Anhydrase Inhibitors: Promising Compounds for Cancer and Metabolic Disorders.

Human carbonic anhydrases (CAs) play a role in various pathological mechanisms by controlling intracellular and extracellular pH balance. Irregular expression and function of CAs have been associated with multiple human diseases, such as obesity, cancer, glaucoma, and epilepsy. In this work, we identify herbal compounds that are potential inhibitors of CA VI. We used the AutoDock tool to evaluate binding affinity between the CA VI active site and 79 metabolites derived from flavonoids, anthraquinones, or cinnamic acids. Compounds ranked at the top were chosen for molecular dynamics (MD) simulations. Interactions between the best CA VI inhibitors and residues within the CA VI active site were examined before and after MD analysis. Additionally, the effects of the most potent CA VI inhibitor on cell viability were ascertained in vitro through the 2,5-diphenyl-2H-tetrazolium bromide (MTT) assay. Kaempferol 3-rutinoside-4-glucoside, orientin, kaempferol 3-rutinoside-7-sophoroside, cynarin, and chlorogenic acid were estimated to establish binding with the CA VI catalytic domain at the picomolar scale. The range of root mean square deviations for CA VI complexes with kaempferol 3-rutinoside-4-glucoside, aloe-emodin 8-glucoside, and cynarin was 1.37 to 2.05, 1.25 to 1.85, and 1.07 to 1.54 Å, respectively. The MTT assay results demonstrated that cynarin had a substantial effect on HCT-116 cell viability. This study identified several herbal compounds that could be potential drug candidates for inhibiting CA VI.

Characterization of Bismuth Trioxide Nanoparticles and Evaluating Binding Affinity with Proteins

AbstractProtein‐nanoparticle conjugation, or protein‐corona, is important for nanomedicine, nano diagnostic, and nano therapy applications. α‐Bismuth oxide nanoparticles (α‐Bi2O3 NPs) were prepared from bismuth nitrate powder using the sol‐gel method and characterized using various techniques, including Energy Dispersive X‐Ray Spectroscopy (EDS), X‐ray Diffraction (XRD), Raman spectroscopy, Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), UV‐VIS‐NIR Spectroscopy, and Brunauer‐Emmett‐Teller (BET). X‐ray diffraction studies revealed that NPs are in the alpha phase with a monoclinic structure. The energy band gap, average surface area and crystallite size are 2.81 eV, 2.42 m2, and 15–106 nm, respectively. Transmission electron microscopy revealed particle size is 32.21 nm, with a d‐spacing of 2.529 Å. The surface‐to‐volume ratio is calculated and found to be 2.553×106 m−1. For the first time, a direct protein interaction with NPs was examined with standard proteins such as bovine serum albumin (BSA), carbonic anhydrase, phosphorylase b, and total human serum proteins and analyzed using mass spectroscopy. Proteomic analysis showed that proteins such as BSA, phosphorylase b, and carbonic anhydrase exhibited a strong affinity with Bi2O3 NPs. However, it was found that there was less or no association between Annexin A6, human serum albumin, Zinc finger protein, and Bestrophin‐2 with Bi2O3 NPs.

Phytochemical Investigation, In silico/In vivo Analgesic, and Anti-inflammatory Assessment of the Egyptian Cassia occidentalis L.

Cassia occidentalis L., from Fabaceae family phytochemical screening, revealed several biologically active principles mainly flavonoids and anthraquinones. GLC analysis of the lipoidal matter afforded 12 hydrocarbons: 9-dodecyl-tetradecahydro-anthracene (48.97 %), 9-dodecyl-tetradecahydro-phenanthrene (14.43 %), and 6 sterols/triterpenes: isojaspisterol (11.99%) and fatty acids were palmitic acid (50 %), and Linoleic acid (16.06%). Column chromatography led to the isolation of fifteen compounds (1–15), elucidated using spectroscopic evidence. First report of undecanoic acid (4) from the family Fabaceae, while p-dimethyl amino-benzaldehyde (15) was first time isolated from a natural origin. Eight compounds isolated for the first time from C. occidentalis L.; β-amyrin (1), β-sitosterol (2), stigmasterol (3), camphor (5), lupeol (6), chrysin (7), pectolinargenin (8), and 1, 2, 5-trihydroxy anthraquinone (14) besides five known compounds previously isolated; apigenin (9), kaempferol (10), chrysophanol (11), physcion (12), and aloe-emodin (13). In-vivo evaluation of anti-inflammatory and analgesic effects of C. occidentalis L. extracts where the n-butanol and total extracts showed the highest activities. The percentage of the inhibitory effect of the n-butanol extract was 29.7 at a dose of 400 mg/Kg. Furthermore, identified phytoconstituents were docked into the active sites of enzymes nAChRs, COX-1, and COX-2 to evaluate binding affinity. Phyto-compounds Physcion, aloe-emodin, and chrysophanol were found to have a good affinity for targeted receptors compared to co-crystalized inhibitors, validating the analgesic and anti-inflammatory effects of the phytochemicals.

Design and synthesis of novel 1,2,3-triazole linked hybrids: Molecular docking, MD simulation, and their antidiabetic efficacy as α-Amylase inhibitors

Novel 1,2,3-triazole linked coumarin and cinnamic acid analogs were designed, synthesized, characterized, and evaluated for their ability to inhibit the α-amylase enzyme in order to treat diabetes. Porcine pancreatic α-amylase isoenzyme II was used in the investigation and analysis of in silico molecular docking and molecular dynamic simulations. The server PreADME/toxicity was used to predict pharmacokinetics and pharmacodynamics properties. In vitro and in silico results revealed that compounds 7d, 7e and 7f showed excellent antidiabetic activity with IC50 in the range of 0.133–0.192 μM and percentage inhibitions in the range of 88.22±1.43 to 98.87±2.63%, respectively, indicating their better potency than the standard acarbose. Furthermore, synthesized compounds were docked into the active sites of the porcine pancreatic alpha-amylase isoenzyme II to evaluate binding affinity and hybrid most potent 7f was lodged in the active site via many strong hydrogen and hydrophobic interactions. Through a 100-ns dynamic simulation research, stability and binding interactions between the promising hybrid 7f and the active residues of the investigated α-amylase isoenzyme II were confirmed. The biological assessments, ADMET, molecular docking, and MD simulations of synthesized analogs allude to the possibility of using hybrids 7d, 7e, and 7f in the development of new antidiabetic therapeutics.

Large-scale transcriptomic analysis of coding and non-coding pathological biomarkers, associated with the tumor immune microenvironment of thyroid cancer and potential target therapy exploration.

Papillary thyroid carcinoma (PTC) is the most prevalent endocrine malignancy with a steadily increasing global incidence in recent decades. The pathogenesis of PTC is poorly understood, and the present diagnostic protocols are deficient. Thus, identifying novel prognostic biomarkers to improve our understanding of the mechanisms of pathogenesis, diagnosis, and designing therapeutic strategies for PTC is crucial. In this study, we integrated 27 PTC transcriptomic datasets and identified overlapping differentially expressed genes (DEGs) and differentially expressed microRNAs, collectively known as thyroid tumor-enriched proteins (TTEPs), and TTEmiRs, respectively. Our integrated bioinformatics analysis revealed that TTEPs were associated with tumor stages, poor surgical outcomes, distant metastasis, and worse prognoses in PTC cohorts. In addition, TTEPs were found to be associated with tumor immune infiltrating cells and immunosuppressive phenotypes of PTC. Enrichment analysis suggested the association of TTEPs with epithelial-to-mesenchymal transition (EMT), cell-matrix remodeling, and transcriptional dysregulation, while the TTEmiRs (miR-146b-5p and miR-21-5p) were associated with the modulation of the immune response, EMT, migration, cellular proliferation, and stemness. Molecular docking simulations were performed to evaluate binding affinities between TTEPs and antrocinnamomin, antcin, and antrocin, the bioactive compounds from one of the most reputable Taiwan indigenous medicinal plants (Antrodia camphorata). Our results revealed that antcin exhibited higher binding efficacies toward FN1, ETV5, and NRCAM, whereas antrocin demonstrated the least. Among the targets, fibronectin (FN1) demonstrated high ligandability potential for the compounds whereas NRCAM demonstrated the least. Collectively, our results hinted at the potential of antcin for targeting TTEPs. In conclusion, this comprehensive bioinformatics analysis strongly suggested that TTEPs and TTEmiRs could be used as potential diagnostic biomarker signatures and be exploited as potential targets for therapeutics development.

Sfcnn: a novel scoring function based on 3D convolutional neural network for accurate and stable protein-ligand affinity prediction.

BackgroundComputer-aided drug design provides an effective method of identifying lead compounds. However, success rates are significantly bottlenecked by the lack of accurate and reliable scoring functions needed to evaluate binding affinities of protein–ligand complexes. Therefore, many scoring functions based on machine learning or deep learning have been developed to improve prediction accuracies in recent years. In this work, we proposed a novel featurization method, generating a new scoring function model based on 3D convolutional neural network.ResultsThis work showed the results from testing four architectures and three featurization methods, and outlined the development of a novel deep 3D convolutional neural network scoring function model. This model simplified feature engineering, and in combination with Grad-CAM made the intermediate layers of the neural network more interpretable. This model was evaluated and compared with other scoring functions on multiple independent datasets. The Pearson correlation coefficients between the predicted binding affinities by our model and the experimental data achieved 0.7928, 0.7946, 0.6758, and 0.6474 on CASF-2016 dataset, CASF-2013 dataset, CSAR_HiQ_NRC_set, and Astex_diverse_set, respectively. Overall, our model performed accurately and stably enough in the scoring power to predict the binding affinity of a protein–ligand complex.ConclusionsThese results indicate our model is an excellent scoring function, and performs well in scoring power for accurately and stably predicting the protein–ligand affinity. Our model will contribute towards improving the success rate of virtual screening, thus will accelerate the development of potential drugs or novel biologically active lead compounds.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12859-022-04762-3.

Genotoxic and cytotoxic effects of pethoxamid herbicide on Allium cepa cells and its molecular docking studies to unravel genotoxicity mechanism.

Pethoxamid is chloroacetamide herbicide. Pethoxamid is commonly used to kill different weeds in various crops. Pethoxamid can leach in the water and soil and can cause toxic effects to other non-target species. Current study is therefore aimed to perform the investigation of the cytotoxic and genotoxic effects of pethoxamid on Allium cepa cells.The root growth, mitotic index (MI), chromosomal aberrations (CAs), and DNA damage were assessed through root growth inhibition, A. cepa ana-telophase, and alkaline comet assays, respectively. Furthermore, molecular docking was performed to evaluate binding affinity of pethoxamid on DNA and very-long-chain fatty acid (VLCFA) synthases. In root growth inhibition test, onion root length was statistically significantly decreased in a concentration dependent manner.Concentration- and time-dependent decreases in MI were observed, whereas increase in CAs such as disturbed ana-telophase, chromosome laggards, stickiness, anaphase bridges, and DNA damage was caused by the pethoxamid on A. cepa root cells. Molecular docking revealed that pethoxamid binds selectively to GC-rich regions in the minor groove of the DNA structure and showed remarkable binding affinity against all synthases taking part in the sequential biosynthesis of VLCFAs. It was concluded that the pethoxamid-induced genotoxicity and cytotoxicity may be through multiple binding ability of this herbicide with DNA and VLCFA synthases.

Synthesis, antimicrobial, anticancer activities, PASS prediction, molecular docking, molecular dynamics and pharmacokinetic studies of designed methyl α-D-glucopyranoside esters

Carbohydrates are abundant naturally occurring biomolecules that play essential roles in a wide variety of biological processes. In this paper, we describe the synthesis of a series of methyl α-D-glucopyranoside (α-MGP) esters through regioselective acylation, by modification of the hydroxyl (-OH) group. Synthesized 6-O-acyl derivatives were further converted to 2,3,4-tri-O-acyl esters, in good yield. Structures of the newly designed α-MGP esters (termed compounds 1–8) were elucidated by spectroscopic, physicochemical, and elemental analyses. PASS (prediction of activity spectra for substances) and in vitro screening of compounds 1–8 against human and plant pathogenic microorganisms revealed substantial antibacterial and antifungal activities. Most of them showed >70% inhibition of fungal mycelial growth. In vitro effect of compound 7 against Ehrlich ascites carcinoma (EAC) cells, by MTT colorimetric assay, showed 23.97% of cell growth inhibition with an IC50 value of 1101.34 µg/ml. Molecular docking and nonbonding interaction studies were performed for three pathogen proteins Escherichia coli lectin FimH, Bacillus subtilis Obg GTP-binding protein, and Aspergillus flavus urate oxidase to evaluate binding affinities and interactions of compounds 1–8 with receptor proteins. A 100-ns molecular dynamics (MD) simulation study revealed the stable conformation and binding patterns/energy in a stimulating environment. In silico pharmacokinetics prediction and drug-likeness analysis of the compounds revealed improved kinetic parameters and satisfaction of all drug-likeness rules in regard to biological activity. Structure-activity relationship (SAR) studies, in combination with in vitro and in silico findings, indicated that among various acyl chains, lauroyl (C-12) and myristoyl (C-14), combined with α-MGP, were most effective against the tested bacterial and fungal pathogens. In conclusion, the designed α-MGP esters displayed enhanced pharmaceutical activities, and strong potential for development as antimicrobial agents.

Metformin-Derived Water-Soluble Cobalt Complexes: Thermal, Spectroscopic, DNA Interaction, and Molecular Docking Studies.

Novel three water-soluble cobalt (II) complexes of type [Co(metf)(o-phen)2]Cl2 (1), [Co(metf)(opda)2]Cl2 (2), and [Co(metf)(2-2'bipy)2]Cl2 (3) (Metf, metformin; o-phen, ortho-phenanthroline; opda, ortho-phenylenediamine; 2,2'-bipy, 2,2'-bipyridine) were synthesized and characterized by various analytical and spectral techniques. Based on these studies, octahedral geometry is assigned to these complexes. The stability of the complexes has been calculated from quantum chemical parameters using HOMO-LUMO energies. Thermal degradation pattern of the compounds was studied and Coats-Redfern method is used to determine kinetic parameters for complexes 1, 2, and 3 from thermal studies. The DNA interaction of these complexes was investigated by absorption, emission, and viscosity studies. From the spectral data, it was concluded that the complexes bind to DNA through groove mode of binding. The intrinsic binding constants (Kb) from absorption spectroscopy were 2.49 × 104, 2.48 × 104, and 2.64 × 104M-1 for 1, 2, and 3, respectively, and Stern-Volmer quenching constants (Ksv) from emission spectroscopy were 0.21, 0.20, and 0.13, respectively. These complexes were screened for nuclease activity of pUC19 DNA, in the presence of H2O2. Discovery studio 2.1 software was used to evaluate binding affinity and interaction pattern of complexes with B-DNA receptor protein and the maximum dock score is seen for complex 2.

Multi-scale mechanism of antiviral drug-alike phytoligands from Ayurveda in managing COVID-19 and associated metabolic comorbidities: insights from network pharmacology.

The novel coronavirus disease (COVID-19), which emerged in Wuhan, China, is continuously spreading worldwide, creating a huge burden on public health and economy. Ayurveda, the oldest healing schema of Traditional Indian Medicinal (TIM) system, is considered as a promising CAM therapy to combat various diseases/ disorders. To explore the regulatory mechanisms of 3038 Ayurvedic herbs (AHs) against SARS-CoV-2, in this study, multi-targeting and synergistic actions of constituent 34,472 phytochemicals (APCs) are investigated using a comprehensive approach comprising of network pharmacology and molecular docking. Immunomodulatory prospects of antiviral drug-alike potentially effective phytochemicals (PEPs) are presented as a special case study, highlighting the importance of 6 AHs in eliciting the antiviral immunity. By evaluating binding affinity of 292 PEPs against 24 SARS-CoV-2 proteins, we develop and analyze a high-confidence “bi-regulatory network” of 115 PEPs having ability to regulate protein targets in both virus and its host human system. Furthermore, mechanistic actions of PEPs against cardiovascular complications, diabetes mellitus and hypertension are also investigated to address the regulatory potential of AHs in dealing with COVID-19-associated metabolic comorbidities. The study further reports 12 PEPs as promising source of COVID-19 comorbidity regulators.Graphical abstract Supplementary InformationThe online version contains supplementary material available at 10.1007/s11030-021-10352-x.

FoldAffinity: binding affinities from nDSF experiments

Differential scanning fluorimetry (DSF) using the inherent fluorescence of proteins (nDSF) is a popular technique to evaluate thermal protein stability in different conditions (e.g. buffer, pH). In many cases, ligand binding increases thermal stability of a protein and often this can be detected as a clear shift in nDSF experiments. Here, we evaluate binding affinity quantification based on thermal shifts. We present four protein systems with different binding affinity ligands, ranging from nM to high μM. Our study suggests that binding affinities determined by isothermal analysis are in better agreement with those from established biophysical techniques (ITC and MST) compared to apparent Kds obtained from melting temperatures. In addition, we describe a method to optionally fit the heat capacity change upon unfolding (Delta {C}_{p}) during the isothermal analysis. This publication includes the release of a web server for easy and accessible application of isothermal analysis to nDSF data.

Cytotoxic and genotoxic evaluation of copper oxychloride through Allium test and molecular docking studies.

Copper oxychloride gained great importance due to its broad-spectrum antifungal action to combat various fungal diseases of plants. However, excess quantity of cupric fungicides on plants causes enzymatic changes and toxic effects. Thus, the current study was aimed to investigate the cytotoxicity and genotoxicity of copper oxychloride on Allium cepa root cells. The root growth, mitotic index (MI), chromosomal aberrations (CAs), and DNA damage were assessed through root growth inhibition, A. cepa ana-telophase, and alkaline comet assays. Furthermore, molecular docking was performed to evaluate binding affinities of two copper oxychloride polymorphs (atacamite and paratacamite) on DNA. In root growth inhibition test, onion root length was statistically significantly decreased by changing the copper oxychloride concentration from lower (2.64±0.11 cm) to higher (0.92±0.12 cm). Concentration- and time-dependent decrease in MI was observed whereas increase in CAs such as disturbed ana-telophase, chromosome laggards, stickiness, anaphase bridges, and DNA damage were caused by the copper oxychloride on A. cepa root cells. Molecular docking results revealed that the two main polymorphs of copper oxychloride (atacamite and paratacamite) bind selectively to G and C nucleotides on the B-DNA structure. It is concluded that the atacamite- and paratacamite-induced DNA damage may be through minor groove recognition and intercalation. Findings of the current study revealed the cytotoxic and genotoxic effects of copper oxychloride on A. cepa root cells. However, further studies should be carried out at the molecular level to reveal the cyto-genotoxic mechanism of action of copper oxychloride in detail.

Investigation of lipase-ligand interactions in porcine pancreatic extracts by microscale thermophoresis.

The evaluation of binding affinities between large biomolecules and small ligands is challenging and requires highly sensitive techniques. Microscale thermophoresis (MST) is an emerging biophysical technique used to overcome this limitation. This work describes the first MST binding method to evaluate binding affinities of small ligands to lipases from crude porcine pancreatic extracts. The conditions of the MST assay were thoroughly optimized to successfully evaluate the dissociation constant (Kd) between pancreatic lipases (PL) and triterpenoid compounds purified from oakwood. More precisely, the fluorescent labeling of PL (PL*) using RED-NHS dye was achieved via a buffer exchange procedure. The MST buffer was composed of 20mM NaH2PO4 + 77mM NaCl (pH6.6) with 0.05% Triton-X added to efficiently prevent protein aggregation and adsorption, even when using only standard, uncoated MST capillaries. Storage at -20°C ensured stability of PL* and its fluorescent signal. MST results showed that crude pancreatic extracts were suitable as a source of PL for the evaluation of binding affinities of small ligands. Quercotriterpenoside-I (QTT-I) demonstrated high PL* binding affinity (31nM) followed by 3-O-galloylbarrinic acid (3-GBA) (500nM) and bartogenic acid (BA) (1327nM). To enrich the 50 kDa lipase responsible for the majority of hydrolysis activity in the crude pancreatic extracts, ammonium sulfate precipitation was attempted and its efficiency confirmed using capillary electrophoresis (CE)-based activity assays and HRMS. Moreover, to accurately explain enzyme modulation mechanism, it is imperative to complement binding assays with catalytic activity ones.

Xinyang Tablet inhibits MLK3-mediated pyroptosis to attenuate inflammation and cardiac dysfunction in pressure overload

Ethnopharmacological relevanceXinyang tablet (XYT) has been traditionally used in the treatment of cardiovascular diseases (CVDs). Our previous study indicated that XYT exhibited protective effects in heart failure (HF). Aim of the studyThe aim of the present study was to determine the protective effects of XYT in pressure overload induced HF and to elucidate its underlying mechanisms of action. Materials and methodsWe analyzed XYT content using high-performance liquid chromatography (HPLC.). Mice were subjected to transverse aortic constriction (TAC) to generate pressure overload–induced cardiac remodeling and were then orally administered XYT or URMC-099 for 1 week after the operation. HL1 mouse cardiomyoblasts were induced by lipopolysaccharides (LPS) to trigger pyroptosis and were then treated with XYT or URMC-099. We used echocardiography (ECG), hematoxylin and eosin (H&E) staining, Masson's trichrome staining and a terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labeling (TUNEL) assay to evaluate the effects of XYT. Messenger ribonucleic acid (mRNA) levels of collagen metabolism biomarkers and inflammation-related factors were detected. We determined protein levels of inflammation- and pyroptosis-related signaling pathway members via Western blot (WB). Caspase-1 activity was measured in cell lysate using a Caspase-1 Activity Assay Kit. Subsequently, to define the candidate ingredients in XYT that regulate mixed-lineage kinase-3 (MLK3), we used molecular docking (MD) to predict and evaluate binding affinity with MLK3. Finally, we screened 24 active potential compounds that regulate MLK3 via MD. ResultsECG, H&E staining, Masson's trichrome staining and TUNEL assay results showed that XYT remarkably improved heart function, amelorated myocardial fibrosis and inhibited apoptosis in vivo. Moreover, it reduced expression of proteins or mRNAs related to collagen metabolism, including collagen type 1 (COL1), fibronectin (FN), alpha smooth-muscle actin (α-SMA), and matrix metalloproteinases-2 and -9 (MMP-2, MMP-9). XYT also inhibited inflammation and the induction of pyroptosis at an early stage, as well as attenuated inflammation and pyroptosis levels in vitro. ConclusionOur data indicated that XYT exerted protective effects against pressure overload induced myocardial fibrosis (MF), which might be associated with the induction of pyroptosis-mediated MLK3 signaling.