Integrated bioinformatics-cheminformatics approach toward locating pseudo-potential antiviral marine alkaloids against SARS-CoV-2-Mpro

Chemometric profiling and anti-arthritic activity of aerial parts of Glinus oppositifolius (L.) Aug. DC

ETHNOPHARMACOLOGICAL RELEVANCE

Glinus oppositifolius (L.) Aug. DC. belongs to the family Molluginaceae, an annual prostrate herb traditionally used to treat inflammations, arthritis, malarial, wounds, fevers, diarrhoea, cancer, stomach discomfort, jaundice, and intestinal parasites. However, the anti-arthritic activity of the aerial part has still not been reported.

AIM OF THE STUDY

To investigate the antioxidant and anti-arthritic activity of G. oppositifolius in Complete Freund's Adjuvant (CFA) induced rats.

MATERIALS AND METHODS

The dried aerial parts of this plant material were defatted with n-hexane and extracted by methanol using a soxhlet apparatus. The in vitro anti-arthritic activity of methanolic extract of G. oppositifolius (MEGO) was evaluated in protein denaturation, membrane stabilization, and inhibition of proteinase assay at 25, 50, 100, 200, and 400 μg/ml concentrations. Female Wistar rats were immunized sub-dermally into the right hind paw with 0.1 ml of CFA. Rats were administered with MEGO at doses of 200 and 400 mg/kg once daily for fourteen days after arthritis induction. Assessment of arthritis was performed by measuring paw diameter, arthritic index, arthritic score, body weight, organ weight, and hematological and biochemical parameters, followed by the analysis of pro-inflammatory cytokines such as tumor necrosis factor-alpha (TNF-α), interleukin 6 (IL-6), interleukin-1-beta (IL-1β), cyclooxygenase-2 (COX-2), interleukin 13 (IL-13) and interleukin 10 (IL-10) and histopathological study. In vivo antioxidant effect was investigated in enzymatic assays. The presence of phytoconstituents was analyzed by Gas Chromatography-Mass Spectrometry (GC-MS) and Liquid Chromatography-Mass Spectrometry (LC-MS), respectively. In silico molecular docking study of the compounds was carried out against COX-2, IL-1β, IL-6, and TNF-α using AutoDock 4.2 and BIOVIA-Discovery Studio Visualizer software.

RESULTS

MEGO's in vitro anti-arthritic activity showed dose-dependent inhibition of protein denaturation, membrane stabilization, and proteinase inhibition, followed by significant in vivo anti-arthritic activity. The rats treated with MEGO showed tremendous potential in managing arthritis-like symptoms by restoring hematological, biochemical, and histological changes in CFA-induced rats. MEGO (200 and 400 mg/kg) showed a significant alleviation in the levels of hyper expressed inflammatory mediators (TNF-α, IL-1β, and IL-6) and oxidative stress (SOD, CAT, GSH, and LPO) in CFA-induced rats. Spergulagenin-A as identified by LC-MS analysis, exhibited the highest binding affinity against COX-2 (-8.6), IL-1β (7.2 kcal/mol), IL-6 (-7.4 kcal/mol), and TNF-α (-6.5 kcal/mol).

CONCLUSIONS

Provided with the comprehensive investigation, methanolic extract of G. oppositifolius against arthritic-like condition is a proof of concept that revalidates its ethnic claim. The presence of Spergulagenin-A might be responsible for the anti-arthritic activity.

Antidiabetic potency and molecular insights of natural products bearing indole moiety: A systematic bioinformatics investigation targeting AKT1

Diabetic mellitus (DM) is a chronic disorder, and type 2 DM (T2DM) is the most prevalent among all categories (nearly 90%) across the globe every year. With the availability of potential drugs, the prevalence rate has remained uncontrollable, while natural resources showed a promising potency, and exploring such potential candidates at the preclinical stage is essential. An extensive literature search selected 89 marine and plant-derived indole derivatives with anti-inflammatory, antioxidant, lipid-lowering, etc., activities. However, as we know, drugs have not been able to convert from 'lead' to 'mainstream' due to inadequate drug-ability profiles, as our systematic investigation proved and selected herdmanine_A (HERD_A) and penerpene_D (PENE_D) as the most potential antidiabetic candidates from the library of indole derivatives. Based on our previous network pharmacology study, we selected three new target enzymes: Acetyl-CoA carboxylase 2 (ACACB; PDB ID: 3JRX), cyclin-dependent kinase 4 (CDK4; PDB ID: 3G33), and alpha serine/threonine-protein kinase 1 (AKT1; PDB ID: 3O96) to assess the antidiabetic potency of selected indole derivatives through binding energy or docking score. To conduct molecular docking studies with these enzymes, we used the PyRx-AutoDock platform. Furthermore, molecular dynamic simulation at 100 ns, physicochemical analysis, pharmacokinetics, toxicity assessment, and drug-likeness evaluation suggested that HERD_A and penerpene PENE_D were the most potent inhibitors against AKT1 compared to koenimbine (most potential based on the recorded IC50 value) and murrayakonine_A (most potential based on the docking score). In summary, HERD_A and/or PENE_D have the potential to be used as alternative therapeutic agent for the treatment of diabetes after some pharmacological investigation.

Potential pharmacological mechanisms of tanshinone IIA in the treatment of human neuroblastoma based on network pharmacological and molecular docking Technology

Tanshinone IIA (Tan-IIA) is the main bioactive component of Chinese herbal medicine salvia miltiorrhiza (Danshen). Sodium sulfonate of Tan-IIA is widely used in the treatment of cardiovascular and cerebrovascular diseases. Tan-IIA also has inhibitory effects on tumor cells such as gastric cancer, but its therapeutic effect and mechanism on human neuroblastoma have not been evaluated, so its pharmacological mechanism is systematically evaluated by the combined method of network pharmacology and molecular docking. PharmMapper and SwissTargetPrediction predicted 331 potential Tan-IIA-related targets, and 1,152 potential neuroblastoma-related targets were obtained from GeneCards, DisGeNET, DrugBank, OMIM and Therapeutic Target databases (TTD), 107 common targets for Tan-IIA and neuroblastoma. Through gene ontology (GO) functional annotation, Kyoto Encyclopedia of Genes and Genomesa (KEGG) pathway enrichment, protein-protein interaction (PPI) network and cytoHubba plug-in, 10 related signal pathways (Pathways in cancer, PI3K-Akt signaling pathway, Prostate cancer, etc.) and 10 hub genes were identified. The results of molecular docking showed that Tan-IIA could interact with 10 targets: GRB2, SRC, EGFR, PTPN1, ESR1, IGF1, MAPK1, PIK3R1, AKT1 and IGF1R. This study analyzed the related pathways and targets of Tan-IIA in the treatment of human neuroblastoma, as well as the potential anticancer and anti-tumor targets and related signaling pathways of Tan-IIA, which provides a reference for us to find and explore effective drugs for the treatment of human neuroblastoma.

Natural products as a source of Coronavirus entry inhibitors

The COVID-19 pandemic has had a significant and lasting impact on the world. Four years on, despite the existence of effective vaccines, the continuous emergence of new SARS-CoV-2 variants remains a challenge for long-term immunity. Additionally, there remain few purpose-built antivirals to protect individuals at risk of severe disease in the event of future coronavirus outbreaks. A promising mechanism of action for novel coronavirus antivirals is the inhibition of viral entry. To facilitate entry, the coronavirus spike glycoprotein interacts with angiotensin converting enzyme 2 (ACE2) on respiratory epithelial cells. Blocking this interaction and consequently viral replication may be an effective strategy for treating infection, however further research is needed to better characterize candidate molecules with antiviral activity before progressing to animal studies and clinical trials. In general, antiviral drugs are developed from purely synthetic compounds or synthetic derivatives of natural products such as plant secondary metabolites. While the former is often favored due to the higher specificity afforded by rational drug design, natural products offer several unique advantages that make them worthy of further study including diverse bioactivity and the ability to work synergistically with other drugs. Accordingly, there has recently been a renewed interest in natural product-derived antivirals in the wake of the COVID-19 pandemic. This review provides a summary of recent research into coronavirus entry inhibitors, with a focus on natural compounds derived from plants, honey, and marine sponges.

The potential of some functional group compounds substituted 8-Manzamine A as RSK1 inhibitors: molecular docking and molecular dynamics simulations

Cancer, an incurable global disease, demands urgent anti-cancer drug development. Marine alkaloids like Manzamine and its derivatives show promise as RSK inhibitors against cancer cell invasion. Replacing the hydrogen at the 8-position of Manzamine A with a hydroxyl group has been shown to significantly enhance its biological activity. In this article, we designed various functional group compounds (A1-A21) substituted 8-Manzamine A by docking, MM-GBSA, molecular dynamics (MD) simulation, and well-tempered metadynamics (WT-MetaD) simulations to evaluate their potential as RSK1 inhibitors. Ligands A1-A21 were docked in the RSK1 N-terminal kinase domain (PDB ID: 2Z7Q) using the Glide module. The calculation of binding energy was performed using Prime MM-GB/SA, while MD simulations were conducted with the Desmond module of Schrodinger suite 2023. Compound A5 exhibits the highest G-score (-7.01) compared to 8-Hydroxymanzamine A (-6.08). Additionally, compounds A6, A10, A12, A17, A11, A4, and A13 demonstrate increased activity against RSK1 when compared to both 8-Hydroxymanzamine A and Manzamine A. Residues LEU68, VAL76, LEU141, PHE143, LEU144, PHE150, ASP148, GLU191, and LEU194 of RSK1 protein play a key role in binding with ligands. An MD simulation of Compound A5 was carried out to explore the dynamic interactions within the protein-ligand complex. Furthermore, WT-MetaD simulations validated the docking study results and identified the most energetically favored conformations for the A5/RSK1 complex. Ligands A5, A6, A10, A12, A17, A11, A4, and A13, featuring diverse functional groups and good Glide scores, may have the potential for significant RSK1 activity and merit further development.Communicated by Ramaswamy H. Sarma.

Exploring imidazo[4,5-g]quinoline-4,9-dione derivatives as Acinetobacter baumannii efflux pump inhibitor: an in silico approach

Antimicrobial resistance (AMR) is fast becoming a medical crisis affecting the entire global population. World Health Organization (WHO) statistics show that globally 0.7 million people are dying yearly due to the emergence of AMR. By 2050, the expected number of lives lost will be 10 million per year. Acinetobacter baumannii is a dreadful nosocomial pathogen that has developed multidrug resistance (MDR) to several currently prescribed antibiotics worldwide. Overexpression of drug efflux transporters (DETs) is one of the mechanisms of multidrug resistance (MDR) in Acinetobacter baumannii. Therefore, blocking the DET can raise the efficacy of the existing antibiotics by increasing their residence time inside the bacteria. In silico screening of five synthetic compounds against three drug efflux pump from A. baumannii has identified KSA5, a novel imidazo[4,5-g]quinoline-4,9-dione derivative, to block the efflux of antibiotics. Molecular docking and simulation results showed that KSA5 could bind to adeB, adeG, and adeJ by consistently interacting with ligand-binding site residues. KSA5 has a higher binding free energy and a lower HOMO-LUMO energy gap than PAβN, suggesting a better ability to interact and inhibit DETs. Further analysis showed that KSA5 is a drug-like molecule with optimal physicochemical and ADME properties. Hence, KSA5 could be combined with antibiotics to overcome antimicrobial resistance.Communicated by Ramaswamy H. Sarma.

Alpha-glucosidase inhibitory activities of astilbin contained in Bauhinia strychnifolia Craib. stems: an investigation by in silico and in vitro studies

INTRODUCTION

Bioactive compounds from traditional medicines are good alternatives to standard diabetes therapies and may lead to new therapeutic discoveries. The stems of Bauhinia strychnifolia Craib. (BC) have a possible antihyperglycemic effect; However, the extraction of astilbin from BC has never been recorded in alpha-glucosidase inhibitory activities.

METHODS

Using liquid chromatography-mass spectrometry (LC-MS/MS), 32 compounds were detected in the BC extract. The screening was based on peak area. Seven compounds found. PASS recognized all seven compounds as potential alpha-glucosidase (AG) inhibitors. Astilbin and quercetin 3-rhamnoside were the most likely inhibitors of AG. Arguslab, AutoDock, and AutoDock Vina investigated the binding of the two compounds and AG. The binding stability was confirmed by molecular dynamics (MD). In addition, the optimum solvent extraction was studied via CosmoQuick, and extracts were examined with ¹H-NMR prior to testing with AG.

RESULTS

All three software programs demonstrated that both compounds inhibit AG more effectively than acarbose. According to the sigma profile, THF is recommended for astilbin extraction. The BC extract with THF showed outstanding AG inhibitory action with an IC₅₀ of 158 ± 1.30 µg mL-1, which was much lower than that of the positive control acarbose (IC₅₀ = 190 ± 6.97 µg mL-1). In addition, astilbin from BC was found to inhibit AG strongly, IC50 = 22.51 ± 0.70 µg mL-1 through the extraction method of large-scale astilbin with THF has the best extraction capacity compared to other solvents, hence the initial stage of extraction employs THF to extract and precipitate them with ethyl acetate and water.

CONCLUSION

In silico and in vitro studies reveal that astilbin inhibits AG and is superior to acarbose, validating its promise as an AG inhibitor. Overall, astilbin was the most bioactive component of BC for antidiabetic action.

Combined Bioinformatics and Combinatorial Chemistry Tools to Locate Drug-Able Anti-TB Phytochemicals: A Cost-Effective Platform for Natural Product-Based Drug Discovery

Based on extensive experimental studies, a huge number of phytochemicals showed potential activity against tuberculosis (TB) at a lower minimum inhibitory concentration (MIC) and fewer toxicity profiles. However, these promising drugs have not been able to convert from 'lead' to 'mainstream' due to inadequate drug-ability profiles. Thus, early drug-prospective analyses are required at the primary stage to accelerate natural-product-based drug discovery with limited resources and time. In the present study, we have selected seventy-three potential anti-TB phytochemicals (MIC value ≤10 μg/mL) and assessed the drug-ability profiles using bioinformatics and combinatorial chemistry tools, systematically. Primarily, the molecular docking study was done against two putative drug targets, catalase-peroxidase enzyme (katG) and RNA polymerase subunit-β (rpoB) of Mycobacterium tuberculosis (Mtb) using AutoDock 4.2 software. Further, assessed the drug-ability score from Molsoft, toxicity profiles from ProTox, pharmacokinetics from SwisADME, hierarchical cluster analysis (HCA) by ChemMine tools and frontier molecular orbitals (FMOs) with Avogadro and structural activity relationships (SAR) analysis with ChemDraw 18.0 software. Above analyses indicated that, lower MIC exhibited anti-TB phytochemicals, abietane, 12-demethylmulticaulin exhibited poor docking and drug-ability scores, while tiliacorinine, 2-nortiliacorinine showed higher binding energy and drug-ability profiles. Overall, tiliacorinine, 2-nortiliacorinine, 7α-acetoxy-6β-hydroxyroyleanone (AHR), (2S)-naringenin and isovachhalcone were found as the most active and drug-able anti-TB candidates from 73 candidates. Phytochemicals are always a vital source of mainstream drugs, but the MIC value of a phytochemical is not sufficient for it to be promoted. An ideal drug-ability profile is therefore essential for achieving clinical success, where advanced bioinformatics tools help to assess and analyse that profile. Additionally, several natural pharmacophores found in existing anti-TB drugs in SAR analyses also provide crucial information for developing potential anti-TB drug. As a conclusion, combined bioinformatics and combinatorial chemistry are the most effective strategies to locate potent-cum-drug-able candidates in the current drug-development module.

Network Pharmacology-Integrated Molecular Docking Reveals the Expected Anticancer Mechanism of Picrorhizae Rhizoma Extract

This study sought to explore the anticancer mechanism of Picrorhizae Rhizoma (PR) extract based on network pharmacology and molecular docking. The potential chemicals of PR were screened through the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database and relevant literatures. Corresponding targets of active ingredients were found with the help of the UniProtKB database, and therapeutic targets for cancer action were screened with the help of the GeneCards database. We used Cytoscape software to construct the compound-target-pathway network of PR extract. We utilized the STRING database to obtain the protein-protein interaction (PPI) network. We used DAVID database combining Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Finally, molecular docking was employed for initial efficacy checking. We have identified 16 potential active components of PR through screening, involving 112 disease action targets. Utilizing the GeneCards database, 112 intersecting targets between PR extract and cancer were found, which mainly exerts anticancer effects by regulating tumor necrosis factor (TNF), recombinant caspase 3 (CASP3), c-Jun NH2-terminal kinase (JNK)/JUN, epidermal growth factor receptor (EGFR), and estrogen receptor-1 (ESR1) with some other target genes and pathways associated with cancer. The major anticancer species are prostate cancer, colorectal cancer, small cell lung cancer, etc. In the molecular docking study, herbactin had a strong affinity for TNF. Based on network pharmacology and molecular docking studies, PR and their compounds have demonstrated potential anticancer activities against several key targets. Our preliminary findings provide a strong foundation for further experiments with PR constituents.

Integrated bioinformatics-cheminformatics approach toward locating pseudo-potential antiviral marine alkaloids against SARS-CoV-2-Mpro

The emergence of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) with the most contagious variants, alpha (B.1.1.7), beta (B.1.351), delta (B.1.617.2), and Omicron (B.1.1.529) has continuously added a higher number of morbidity and mortality, globally. The present integrated bioinformatics-cheminformatics approach was employed to locate potent antiviral marine alkaloids that could be used against SARS-CoV-2. Initially, 57 antiviral marine alkaloids and two repurposing drugs were selected from an extensive literature review. Then, the putative target enzyme SARS-CoV-2 main protease (SARS-CoV-2-Mpro) was retrieved from the protein data bank and carried out a virtual screening-cum-molecular docking study with all candidates using PyRx 0.8 and AutoDock 4.2 software. Further, the molecular dynamics (MD) simulation of the two most potential alkaloids and a drug docking complex at 100 ns (with two ligand topology files from PRODRG and ATB server, separately), the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) free energy, and contributions of entropy were investigated. Then, the physicochemical-toxicity-pharmacokinetics-drug-likeness profiles, the frontier molecular orbitals energies (highest occupied molecular orbital, lowest unoccupied molecular orbital, and ΔE), and structural-activity relationship were assessed and analyzed. Based on binding energy, 8-hydroxymanzamine (-10.5 kcal/mol) and manzamine A (-10.1 kcal/mol) from all alkaloids with darunavir (-7.9 kcal/mol) and lopinavir (-7.4 kcal/mol) against SARS-CoV-2-Mpro were recorded. The MD simulation (RMSD, RMSF, Rg, H-bond, MM/PBSA binding energy) illustrated that the 8-hydroxymanzamine exhibits a static thermodynamic feature than the other two complexes. The predicted physicochemical, toxicity, pharmacokinetics, and drug-likeness profiles also revealed that the 8-hydroxymanzamine could be used as a potential lead candidate individually and/or synergistically with darunavir or lopinavir to combat SARS-CoV-2 infection after some pharmacological validation.

In Silico Molecular Docking Analysis of Karanjin against Alzheimer's and Parkinson's Diseases as a Potential Natural Lead Molecule for New Drug Design, Development and Therapy

Parkinson's disease (PD) and Alzheimer's disease (AD) are neurodegenerative disorders that have emerged as among the serious health problems of the 21st century. The medications currently available to treat AD and PD have limited efficacy and are associated with side effects. Natural products are one of the most vital and conservative sources of medicines for treating neurological problems. Karanjin is a furanoflavonoid, isolated mainly from Pongamia pinnata with several medicinal plants, and has been reported for numerous health benefits. However, the effect of karanjin on AD and PD has not yet been systematically investigated. To evaluate the neuroprotective effect of karanjin, extensive in silico studies starting with molecular docking against five putative targets for AD and four targets for PD were conducted. The findings were compared with three standard drugs using Auto Dock 4.1 and Molegro Virtual Docker software. Additionally, the physiochemical properties (Lipinski rule of five), drug-likeness and parameters including absorption, distribution, metabolism, elimination and toxicity (ADMET) profiles of karanjin were also studied. The molecular dynamics (MD) simulations were performed with two selective karanjin docking complexes to analyze the dynamic behaviors and binding free energy at 100 ns time scale. In addition, frontier molecular orbitals (FMOs) and density-functional theory (DFT) were also investigated from computational quantum mechanism perspectives using the Avogadro-ORCA 1.2.0 platform. Karanjin complies with all five of Lipinski's drug-likeness rules with suitable ADMET profiles for therapeutic use. The docking scores (kcal/mol) showed comparatively higher potency against AD and PD associated targets than currently used standard drugs. Overall, the potential binding affinity from molecular docking, static thermodynamics feature from MD-simulation and other multiparametric drug-ability profiles suggest that karanjin could be considered as a suitable therapeutic lead for AD and PD treatment. Furthermore, the present results were strongly correlated with the earlier study on karanjin in an Alzheimer's animal model. However, necessary in vivo studies, clinical trials, bioavailability, permeability and safe dose administration, etc. must be required to use karanjin as a potential drug against AD and PD treatment, where the in silico results are more helpful to accelerate the drug development.