Strong Binding Affinity Research Articles

Exploring molecular interactions and ADMET profiles of novel MAO-B inhibitors: toward effective therapeutic strategies for neurodegenerative disorders

BackgroundNeurodegenerative disorders (NDs), primarily affecting the elderly, are marked by complex pathophysiological processes and are projected to become the second leading cause of death. Parkinson’s disease (PD), one of the most common NDs, is characterized by motor impairments due to reduced dopamine levels in the substantia nigra (SN), a crucial midbrain region involved in motor control and reward mechanisms. PD also impacts cognitive functions, potentially leading to depression and sleep disturbances. Recent research highlights the importance of MAO-B inhibitors in PD management, as these enzymes play a critical role in regulating neurotransmitter levels by catalyzing the oxidative deamination of intracellular amines and monoamine neurotransmitters.ResultComputational virtual screening of several quinoline-based ligands against the target protein MAO-B (PDB ID: 1OJA) was performed using molecular docking simulation and ADMET studies to identify promising inhibitors for neurodegenerative disease treatment. The most active hit, Compound PA001, exhibited a MolDock score of − 207.76 kcal/mol. Subsequent investigation of 6-methoxy-2-(4-phenylpiperazin-1-yl)quinoline (Compound PA001) using molecular dynamics (MD) simulations with GROMACS revealed potent inhibition and significant interactions at key active site residues. MD simulations confirmed the stability of the Compound PA001-MAO-B complex under physiological conditions. Additionally, ADMET analysis demonstrated that Compound PA001 possesses favorable drug-like properties, including absorption, distribution, metabolism, excretion, and toxicity profiles. These findings underscore 6-methoxy-2-(4-phenylpiperazin-1-yl)quinoline (Compound PA001) as a promising candidate for developing new MAO-B inhibitors to treat neurodegenerative diseases.ConclusionThe research highlighted 6-methoxy-2-(4-phenylpiperazin-1-yl)quinoline (Compound PA001) as a promising MAO-B inhibitor, exhibiting strong binding affinity, stability, and desirable drug-like characteristics for the treatment of neurodegenerative diseases. Among the top ten molecules, Compound PA001 was selected for molecular dynamics (MD) simulation using GROMACS. The compound showed potent inhibition, significant interactions with key active site residues, and stable complex formation under physiological conditions. ADMET analysis further confirmed its favorable pharmacokinetic profile.

In Silico and Glioblastoma Cell Line Evaluation of Thioflavin-Derived Zinc Nanoparticles Targeting Beclin Protein.

This study explores the anticancer potential of Thioflavin-derived zinc nanoparticles (Th-ZnNPs) using both in vitro and in silico methods. Thioflavin, known for its specific binding properties, faces challenges such as bioavailability, rapid metabolism, and solubility. To overcome these limitations and enhance therapeutic efficacy, nanotechnology was utilized to synthesizeTh-ZnNPs. These nanoparticles (NPs) are designed to improve drug delivery and effectiveness. The Beclin protein, which plays a critical role in regulating autophagy in cancer cells, was identified as a potential target for these NPs. The study aims to evaluate the interaction between Th-ZnNPs and Beclin protein in glioblastoma cell lines and assess the potential of these NPs as novel anticancer agents. Th-ZnNPs were synthesized using advanced nanotechnology techniques to improve the bioavailability and solubility of Thioflavin. To explore their anticancer potential, in silico analyses were performed, including molecular docking studies to evaluate the binding affinity between the ZnNPs and Beclin protein, which is integral to autophagy regulation. This computational approach identified the Beclin protein as a promising target for the ZnNPs. Complementary in vitro assays were then conducted, where glioblastoma cell lines (procured from the National Centre for Cell Science, Pune, India) were treated with ZnNPs to assess their cytotoxic effects. The assays also included mechanistic studies to validate the interaction between ZnNPs and Beclin protein and to understand their influence on autophagy pathways. The synthesis ofTh-ZnNPs successfully enhanced their solubility and bioavailability compared to Thioflavin alone. In silico findings showed a strong binding affinity between the Th-ZnNPs and the Beclin protein, suggesting that these NPs may effectively target cancer cells through this interaction. Beclin protein was validated as a relevant target due to its critical role in autophagy regulation. In vitro assays further confirmed the anticancer potential of the Th-ZnNPs, as they exhibited significant cytotoxic effects on glioblastoma cells. Additionally, mechanistic studies revealed that Th-ZnNPs impact Beclin protein and modulate autophagy pathways, supporting their proposed role as effective anticancer agents. The study highlights the promising anticancer potential of Th-ZnNPs. By overcoming the limitations of Thioflavin through nanotechnology, these NPs show significant therapeutic promise in targeting glioblastoma cells. The strong binding affinity between Th-ZnNPs and the Beclin protein, coupled with confirmed cytotoxiceffects, underscores their potential as novel anticancer agents. This integrated approach not only enhances the delivery and efficacy of Thioflavin but also opens new avenues for targeted therapy in glioblastoma treatment.

A multi-epitope self-amplifying mRNA SARS-CoV-2 vaccine design using a reverse vaccinology approach

Background and purpose: Massive vaccine distribution is a crucial step to prevent the spread of SARS-CoV2 as the causative agent of COVID-19. This research aimed to design the multi-epitope self-amplifying mRNA (saRNA) vaccine from the spike and nucleocapsid proteins of SARS-CoV2. Experimental approach: Commonly distributed constructions class I and II alleles of the Indonesian population were used to determine peptide sequences that trigger this population’s high specificity T-cell response. The best vaccine candidate was selected through the analysis of tertiary structure validation and molecular docking of each candidate with TLR-4, TLR-8, HLA-A*24:02, and HLA-DRB1*04:05. The selected multi-epitope vaccine combined with the gene encoding the replication machinery that allows the RNA amplification in the host cell. Findings/Results: Seven B-cell and four T-cell epitopes from the protein target were highly antigenic and conserved, non-allergen, non-toxic, and hydrophilic. Tertiary structure validation then determined the best multi-epitope construction with 269 AA in length containing hBD-2 adjuvant and PADRE. Most residues are predicted to be accessible by solvent and show high population coverage (99,26%). Molecular docking analysis demonstrated a stable and strong binding affinity with immune receptors. A recombinant plasmid as the template for mRNA production was constructed by inserting the multi-epitope DNA and non-structural polyprotein 1-4 gene of VEEV, which encodes the RNA replication complex to the cloning site of pcDNA3.1(+). Conclusion and implication: In silico, design of self-amplifying mRNA could be a potential COVID-19 vaccine candidate since its ability to be amplified in the host cell can efficiently reduce the intake doses.

Interactions of memantine and rivastigmine with graphene oxide nanocarrier and beta-amyloid protein using molecular docking and in-silico methods

Alzheimer's disease is characterized by the accumulation of beta-amyloid plaques and neurofibrillary tangles. Effective therapeutic strategies involve inhibiting the formation of beta-amyloid aggregates and destabilizing existing ones. A significant challenge in current treatments is the inability of therapeutic agents to cross the blood-brain barrier, a limitation addressed by employing drug nanocarriers. This study investigates the interactions between memantine, rivastigmine, beta-amyloid structures, and graphene oxide nanocarriers using molecular docking and in silico methods. The goal is to enhance drug development through cost-effective and efficient computational techniques. Results indicate that the binding energies for memantine-beta-amyloid and rivastigmine-beta-amyloid complexes are −9.03 kcal/mol and −7.81 kcal/mol, respectively, suggesting superior stability for the memantine-beta-amyloid complex. The electrostatic energies are −1.91 kcal/mol for memantine and −0.81 kcal/mol for rivastigmine, further supporting the greater stability of the memantine complex. Additionally, memantine's interaction with graphene oxide results in more negative adsorption energy (−92.47 kJ/mol) compared to rivastigmine (−86.36 kJ/mol), indicating a stronger binding affinity. The charge transfer (Q) values are −0.41 kJ/mol for memantine and −0.33 kJ/mol for rivastigmine. The negative enthalpy (ΔH) of −85.71 kJ/mol and Gibbs free energy (ΔG) of −41.52 kJ/mol for the memantine-graphene oxide interaction suggest a spontaneous process. Both memantine and rivastigmine display similar electronic properties, but memantine shows a more effective interaction with graphene oxide, likely due to its amine functional group and spatial configuration. The adsorption energy analysis confirms that memantine forms a more stable complex with graphene oxide than rivastigmine.

Antimicrobial and Molecular Docking Studies of Anthrones from the Leaf Latex of Aloe pirottae A. Berger against Some Plant Pathogenic Microbes

Objective/Background: Aloe pirottae A. Berger has traditionally been used in Ethiopia to treat various ailments. While previous studies have examined the antimicrobial activity of different parts of A. pirottae against human pathogens, this study aimed to investigate whether its antimicrobial activity extends to plant pathogenic bacteria and fungi. Methods: Compounds were isolated from the leaf latex of A. pirottae using silica gel column chromatography, and their structures were determined using 1H-NMR, 13C-NMR, and ESI-MS spectral data. Both the leaf latex and the isolated compounds were evaluated for their antimicrobial activity against three bacterial ( Pseudomonas syringae pv. gaarcae, Ralstonia solanacearum and Xanthomonas vasicola pv. musacearum) and three fungal ( Fusarium graminarum, Fusaium oxysporum, and Fusarium solani) plant pathogens. Results: A mixture of two diastereoisomeric anthrones was isolated from the leaf latex of A. pirottae and characterized as aloin A/B using 1H-NMR, 13C-NMR, and ESI-MS. Aloin A/B showed the most potent activity against X. vasicola among the bacteria and F. oxysporum among the fungi strains tested, with minimum inhibitory concentrations (MIC) of 3.12 mg/mL and 6.25 mg/mL, respectively. Further exploration uncovered strong binding affinity of aloin A/B towards key proteins in these pathogens, specifically with topoisomerase II (−10.060 kcal/mol) and UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2, 6-diaminopimelate ligase (murE) (−8.861 kcal/mol) in F. oxysporum and X. vasicola, respectively, through molecular docking studies. Conclusion: The present findings highlight aloin A/B as promising natural antimicrobial agents and lead compounds for new plant pathogen treatments. Further research is recommended to explore their activity against a wider range of plant pathogens.

Airways Relaxant and Antiasthmatic Activity of Aconitum heterophyllum Wall ex Royle. Roots: A Mechanistic Insight.

Aconitum heterophyllum Wall ex Royle. (Ranunculaceae) is a traditional medicinal herb that has shown extensive pharmacological potential to treat cough, diarrhea, and infectious diseases but no scientific evidence is available to validate its antiasthmatic potential. In this study, we have investigated the tracheal relaxation and antiasthmatic activity of the selected bioactive fraction of A. heterophyllum. Chemical profiling of the most effective fraction obtained via bioassay-guided fractionation was done using LC-MS (Liquid chromatography-mass spectrometry, a technique utilized in the identification, separation, and quantification of known and unknown compounds). Molecular docking analysis of characterized constituents was performed to recognize the binding receptors, followed by an evaluation of the tracheal relaxation ability of active fraction. An acute oral toxicity study of the most effective fraction was done using OECD guidelines 423. Further, the therapeutic efficacy of the fraction was validated in asthma using a guinea pig model of ovalbumin (OVA) induced allergic asthma. The bio-guided activity revealed that hydro-methanolic extract of A. heterophyllum roots (F-1) was the most active fraction. LC-MS analysis of F-1 showed the presence of six major bioactive compounds in F-1. Molecular docking studies revealed strong binding affinities of identified constituents with histaminic receptor (H1) and muscarinic receptor (M3). The ex vivo study demonstrated smooth muscle relaxant activity of F-1 via dysregulating diverse signal transduction pathways viz. histaminic and muscarinic receptors antagonism (non-competitive), stimulation of β2-adrenergic receptor pathway, and soluble guanylyl cyclase activation. The findings of acute oral toxicity studies revealed that F-1 had no toxicity up to the dose of 2000 mg/Kg. The anti-asthmatic therapeutic efficacy of F-1 was further confirmed by the amelioration of respiratory hyperresponsiveness in asthmatic guinea pigs. This is the first evidence-based study showing the antiasthmatic therapeutic potential of the traditionally used herb A. heterophyllum through, computational and animal studies.

Molecular docking and antimicrobial activities of photoexcited inhibitors in antimicrobial photodynamic therapy against Enterococcus faecalis biofilms in endodontic infections

Antimicrobial photodynamic therapy (aPDT) is a promising approach to combat antibiotic resistance in endodontic infections. It eliminates residual bacteria from the root canal space and reduces the need for antibiotics. To enhance its effectiveness, an in silico and in vitro study was performed to investigate the potential of targeted aPDT using natural photosensitizers, Kojic acid and Parietin. This approach aims to inhibit the biofilm formation of Enterococcus faecalis, a frequent cause of endodontic infections, by targeting the Ace and Esp proteins. After determining the physicochemical characteristics of Ace and Esp proteins and model quality assessment, the molecular dynamic simulation was performed to recognize the structural variations. The stability and physical movement of the protein-ligand complexes were evaluated. In silico molecular docking was conducted, followed by ADME/Tox profiling, pharmacokinetics characteristics, and assessment of drug-likeness properties of the natural photosensitizers. The study also investigated the changes in the expression of genes (esp and ace) involved in E. faecalis biofilm formation. The results showed that both Kojic acid and Parietin complied with Lipinski’s rule of five and exhibited drug-like properties. In silico analysis indicated stable complexes between Ace and Esp proteins and the natural photosensitizers. The molecular docking studies demonstrated good binding affinity. Additionally, the expression of the ace and esp genes was significantly downregulated in aPDT using Kojic acid and Parietin with blue light compared to the control group. This investigation concluded that Kojic acid and Parietin with drug-likeness could efficiently interact with Ace and Esp proteins with a strong binding affinity. Hence, natural photosensitizers-mediated aPDT can be considered a promising adjunctive treatment against endodontic infections.

Unraveling the potential effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on the Protein structure and function of the human SLC30A8 gene on type 2 diabetes and colorectal cancer: An In silico approach

Background and aimsThe single nucleotide polymorphisms (SNPs) in SLC30A8 gene have been recognized as contributing to type 2 diabetes (T2D) susceptibility and colorectal cancer. This study aims to predict the structural stability, and functional impacts on variations in non-synonymous SNPs (nsSNPs) in the human SLC30A8 gene using various computational techniques. Materials and methodsSeveral in silico tools, including SIFT, Predict-SNP, SNPs&GO, MAPP, SNAP2, PhD-SNP, PANTHER, PolyPhen-1,PolyPhen-2, I-Mutant 2.0, and MUpro, have been used in our study. ResultsAfter data analysis, out of 336 missenses, the eight nsSNPs, namely R138Q, I141N, W136G, I349N, L303R, E140A, W306C, and L308Q, were discovered by ConSurf to be in highly conserved regions, which could affect the stability of their proteins. Project HOPE determines any significant molecular effects on the structure and function of eight mutated proteins and the three-dimensional (3D) structures of these proteins. The two pharmacologically significant compounds, Luzonoid B and Roseoside demonstrate strong binding affinity to the mutant proteins, and they are more efficient in inhibiting them than the typical SLC30A8 protein using Autodock Vina and Chimera. Increased binding affinity to mutant SLC30A8 proteins has been determined not to influence drug resistance. Ultimately, the Kaplan-Meier plotter study revealed that alterations in SLC30A8 gene expression notably affect the survival rates of patients with various cancer types. ConclusionFinally, the study found eight highly deleterious missense nsSNPs in the SLC30A8 gene that can be helpful for further proteomic and genomic studies for T2D and colorectal cancer diagnosis. These findings also pave the way for personalized treatments using biomarkers and more effective healthcare strategies.

Disease-Inspired Design of Biomimetic Tannic Acid-Based Hybrid Nanocarriers for Enhancing the Treatment of Bacterial-Induced Sepsis.

This study explored the development of novel biomimetic tannic acid-based hybrid nanocarriers (HNs) for targeted delivery of ciprofloxacin (CIP-loaded TAH-NPs) against bacterial-induced sepsis. The prepared CIP-loaded TAH-NPs exhibited appropriate physicochemical characteristics and demonstrated biocompatibility and nonhemolytic properties. Computational simulations and microscale thermophoresis studies validated the strong binding affinity of tannic acid (TA) and its nanoformulation to human Toll-like receptor 4, surpassing that of the natural substrate lipopolysaccharide (LPS), suggesting a potential competitive inhibition against LPS-induced inflammatory responses. CIP released from TAH-NPs displayed a sustained release profile over 72 h. The in vitro antibacterial activity studies revealed that CIP-loaded TAH-NPs exhibited enhanced antibacterial efficacy and efflux pump inhibitory activity. Specifically, they showed a 3-fold increase in biofilm eradication activity against MRSA and a 2-fold increase against P. aeruginosa compared to bare CIP. Time-killing assays demonstrated complete bacterial clearance within 8 h of treatment with CIP-loaded TAH-NPs. In vitro DPPH scavenging and anti-inflammatory investigations confirmed the ability of the prepared hybrid nanosystem to neutralize reactive oxygen species (ROS) and modulate LPS-induced inflammatory responses. Collectively, these results suggest that CIP-loaded TAH-NPs may serve as an innovative nanocarrier for the effective and targeted delivery of antibiotics against bacterial-induced sepsis.

Network pharmacology-based mechanism analysis of dauricine on the alleviating Aβ-induced neurotoxicity in Caenorhabditis elegans

BackgroundDauricine (DAU), a benzyl tetrahydroisoquinoline alkaloid isolated from the root of Menispermum dauricum DC, exhibits promising anti-Alzheimer’s disease (AD) effects, but its underlying mechanisms remain inadequately investigated. This paper aims to identify potential targets and molecular mechanisms of DAU in AD treatment.MethodsNetwork pharmacology and molecular docking simulation method were used to screen and focus core targets. Various transgenic Caenorhabditis elegans models were chosen to validate the anti-AD efficacy and mechanism of DAU.ResultsThere are 66 potential DAU-AD target intersections identified from 100 DAU and 3036 AD-related targets. Subsequent protein-protein interaction (PPI) network analysis identified 16 core targets of DAU for anti-AD. PIK3CA, AKT1 and mTOR were predicted to be the central targets with the best connectivity through the analysis of “compound-target-biological process-pathway network”. Molecular docking revealed strong binding affinities between DAU and PIK3CA, AKT1, and mTOR. In vivo experiments demonstrated that DAU effectively reduced paralysis in AD nematodes caused by Aβ aggregation toxicity, downregulated expression of PIK3CA, AKT1, and mTOR homologues (age-1, akt-1, let-363), and upregulated expression of autophagy genes and the marker protein LGG-1. Simultaneously, DAU increased lysosomal content and enhanced degradation of the autophagy-related substrate protein P62. Thioflavin T（Th-T）staining experiment revealed that DAU decreased Aβ accumulation in AD nematodes. Further experiments also confirmed DAU’s protein scavenging activity in polyglutamine (polyQ) aggregation nematodes.ConclusionCollectively, the mechanism of DAU against AD may be related to the activation of the autophagy-lysosomal protein clearance pathway, which contributes to the decrease of Aβ aggregation and the restoration of protein homeostasis.

Thiourea Derivatives as Estrogen Receptor Alpha Inhibitors for Breast Cancer Therapy: An In Silico Evaluation with ADMET Prediction and Molecular Docking

Breast cancer remains a significant public health concern, necessitating the discovery of novel therapeutic agents. This study investigates the potential of thiourea derivatives, specifically HU, HTMX, and BMPTU compounds, as estrogen receptor alpha (ERα) inhibitors using computational approaches. Drug-likeness assessments using Lipinski's Ro5 confirmed the oral bioavailability of all compounds. Additionally, ADMET analysis indicated favorable pharmacokinetic properties, with minimal metabolic interactions and acceptable safety profiles, except for BMPTU2, which showed potential hepatotoxicity. Molecular docking simulations revealed strong binding affinities between BMPTU derivatives, particularly BMPTU2, BMPTU3, and BMPTU4, and key ERα residues. These interactions suggest their potential as ERα modulators, warranting further in silico and experimental validation. In conclusion, the findings highlight the potential of BMPTU derivatives, especially BMPTU2, BMPTU3, and BMPTU4, as promising lead compounds for developing novel ERα-targeted breast cancer therapies. Further optimization and validation are crucial to fully elucidate their therapeutic potential.

Exploration of date palm (Phoenix dactylifera) bioactivity as anti-SARS-CoV-2: in silico study

The COVID-19 pandemic has highlighted the need for innovation and the development of antiviral agents. One plant with potential antiviral properties is the date palm (Phoenix dactylifera). However, research on the antiviral activity of dates against SARS-CoV-2 is limited. This study aims to assess the antiviral potential of compounds found in date palm fruit using a molecular docking method. Specifically, we compare these compounds to the antiviral drugs ritonavir and nirmatrelvir in their ability to inhibit SARS-CoV-2 proteins. The molecular docking analysis was conducted using various tools and software, including Autodock Vina, DS Visualizer, Autodock Tools, Python, and Marvin Sketch. The results of the study indicate that compounds such as apigenin, diosmetin, and luteolin have strong potential as antiviral agents. The binding affinity of apigenin in date fruit with various SARS-CoV-2 proteins is as follows: -7.6 kcal/mol for 3CL-Pro, -8.7 kcal/mol for Nsp3, -5.7 kcal/mol for PD-ACE-2, and -7.0 kcal/mol for RBD-S. Diosmetin exhibits similar binding affinities with these proteins: -6.7 kcal/mol, -8.5 kcal/mol, -5.6 kcal/mol, and -7.2 kcal/mol, respectively. Luteolin also shows strong binding affinities: -7.9 kcal/mol, -8.6 kcal/mol, -5.7 kcal/mol, and -7.3 kcal/mol. In comparison, nirmatrelvir achieved docking scores of -7.2 kcal/mol, -7.5 kcal/mol, -5.1 kcal/mol, and -6.3 kcal/mol with the same proteins, while ritonavir scored -7.0 kcal/mol, -8.2 kcal/mol, -5.6 kcal/mol, and -6.7 kcal/mol, respectively. Apigenin, diosmetin, and luteolin demonstrate stronger potential than nirmatrelvir and ritonavir, as evidenced by their lower docking scores when compared to these drugs.

Affinity of Nintedanib Towards New Candidate Target for Idiopathic Pulmonary Fibrosis

Idiopathic pulmonary fibrosis (IPF) is a progressive disease due to aggregation of fibroblasts on lung parenchyma. Nintedanib, an indolinone-derived tyrosine kinase inhibitor (TKi) has been approved for the treatment of IPF and it is a well-known inhibitor of platelet-derived growth factor (PDGF) receptor-α and -β, fibroblast growth factor (FGF) receptor-1–3 and vascular endothelial growth factor (VEGF) receptor-1–3. This study aims to evaluate the binding interaction between new therapeutic protein candidates for IPF such as autotaxin, galectin-3, interleukin-13, chitotriosidase-1, JNK, RhoE-ROCK-1, ROCK-2 against nintedanib. In this investigation we predicted, computed, and analyzed the binding interactions of the drug nintedanib using an in silico approach called molecular docking. Our docking studies demonstrated that RhoE-ROCK1 and autotaxin showed strong binding affinities towards nintedanib compared to known targets such as VEGFR2 and FGFR1. We can therefore hypothesize a further contribution of nintedanib to the improvement of pathology due to its affinity towards new targets in the pathogenesis of IPF. The next step will be to evaluate the effects of this affinity in vitro on specific cellular models.

Antimigraine activity of Asarinin by OPRM1 pathway with multifaceted impacts through network analysis

Migraine is a debilitating neurological disorder impacting millions worldwide. Calcitonin Gene-Related Peptide (CGRP) has emerged as a key player in migraine pathophysiology, leading to the development of targeted therapies. This study reviews novel CGRP-targeted treatments, including monoclonal antibodies small molecule inhibitors/nutraceuticals and introduces Asarinin as a potential modulator of the pathway. Asarinin, a natural compound found in various plants, is examined for its pharmacological potential in migraine management. Pharmacokinetic assessments, toxicological modelling, molecular property analysis, and network pharmacology were conducted. Molecular docking and dynamics studies with CGRP reveal potential interactions, providing a foundation for understanding Asarinin's therapeutic effects. Asarinin's favourable pharmacokinetics, safety profile, and bioactivity, supporting its candidacy as a therapeutic agent. In-depth molecular docking studies with the CGRP receptor (PDB: 6ZHO) demonstrate strong binding affinity (− 10.3kcal/mol), while molecular dynamics simulations unveil the dynamic behavior of the Asarinin-CGRP complex, (− 10.53 kcal/mol) for Atogepant-CGRP complex. Network analysis highlights key proteins in migraine pathology, indicating Asarinin's potential efficacy. The groundwork for future investigations, suggests Asarinin as a promising candidate for migraine management by targeting OPRM1 pathway. The integration of diverse assessments provides a comprehensive understanding of Asarinin's potential and paves the way for further preclinical and clinical research.

Mechanistic insights into antidiabetic potential of Ficus viren against multi organ specific diabetic targets: molecular docking, MDS, MM-GBSA analysis

Ficus viren has been traditionally used to treat diabetes, and its extract inhibits carbohydrate/lipid metabolism and possesses anti-hyperglycemic potential. However, there is conflicting investigation related to F. viren extract effect on carbohydrate metabolism. Thus, bioactive and mechanism behind its antidiabetic potential is still scanty. This study explored F. viren’s anti-diabetic property by identifying potential phytoconstituents and mechanism. A sequential in-silico approach was used i.e., druglikeness, molecular docking, post-docking MM-GBSA, ADMET studies, molecular dynamic simulation (MDS), and post-MDS MM-GBSA. We screened ∼32 phytoconstituents and twelve potential organ-specific diabetic targets (O.S.D.Ts i.e., IR, DPP-4, ppar-γ, ppar-α, ppar-δ, GLP-1R, SIRT-1, AMPK, GSK-3β, RAGE, and AR). Drug likeness study identified 18 druggable candidates among 32 phytoconstituents. K3A, quercetin, scutellarein, sorbifolin, and vogeline J identified as potential ligands from druggable ligands, using IR as the standard target. Subsequently, potential ligands docked with remaining O.S.D.Ts. and data showed that K3A binds strongly with AMPK, ppar-δ, DPP-4, and GSK-3β, while scutellarein binds with AR and ppar-α. Sorbifolin, quercetin, and vogeline J binds with ppar-α, ppar-γ, and RAGE, respectively. Post-docking MM-GBSA data (∆GBind) also depicted potential ligand’s strong binding affinities with their corresponding targets. Thereafter, simulation data revealed that only scutellarein and sorbifolin showed dynamic stability with their respective targets, i.e., AR/ppar-α and ppar-α, respectively. Interestingly, post-MDS MM-GBSA revealed that only scutellarein exhibited strong ∆GBind of −55.08 kcal/mol and −75.48 kcal/mol with AR and ppar-α, respectively. Though, collective computational analysis supports antidiabetic potential of F. viren through AR and ppar-α modulation by scutellarein.

Discovery of Novel (5-Mercapto-4-phenyl-4H-1,2,4-triazol-3-yl)methyl Phenyl Carbamate as a Potent Phytoene Desaturase Inhibitor through Scaffold Hopping and Linker Modification.

Phytoene desaturase (PDS) is a key rate-limiting enzyme in the carotenoid biosynthesis pathway. Although commercial PDS inhibitors have been developed for decades, it remains necessary to develop novel PDS inhibitors with higher bioactivity. In this work, we used the scaffold hopping and linker modification approaches to design and synthesize a series of compounds (7a-7o, 8a-8l, and 14a-14d). The postemergence application assay demonstrated that 8e and 7e separately showed the best herbicidal activity at 750 g a.i./ha and lower doses (187.5 g, 375g a.i./ha) without no significant toxicity to maize and wheat. The surface plasmon resonance revealed strong binding affinity between 7e and Synechococcus PDS (SynPDS). The HPLC analysis confirmed that 8e at 750 g a.i./ha caused significant phytoene accumulation in Arabidopsis seedlings. This work demonstrates the efficacy of structure-guided optimization through scaffold hopping and linker modification to design potent PDS inhibitors with enhanced bioactivity and crop safety.

Investigating the Therapeutic Property of Galium verum L. (GV) for MSG induced Audiogenic Epilepsy (AEs) and Neuroprotection through In-Silico and In-Vitro Analysis.

Audiogenic Epilepsy (AEs) is a subtype of epileptic seizure that is generally caused by high-intensity sounds. A large number of traditional medicines has been explored in this lieu where our study chased Galium verum L. (Rubiaceae), an herbal plant which is commonly known as Lady's Bedstraw, that contains a highly rich chemical composition including flavonoids (Hispidulin, Quercetin, and Kaempferol), and phenolic acids (chlorogenic acid, caftaric acid, and gallic acid). G verum is well known for its antioxidant, neuroprotective, and anti-inflammatory properties. Recently, the unique role of Adhesion G Protein- Coupled Receptor V1 (ADGRV1) protein in the progression of audiogenic epilepsy has been explored. This study aimed to examine the potent phytoconstituents of the hydroalcoholic extract of G. verum L. (HEGV) using analytical techniques. Additionally, our study sought to evaluate the antioxidant, neuroprotective, anti-inflammatory properties, and antiepileptic potency of HEGV by targeting ADGRV1 via in silico and in vitro analyses using SHSY5Y cells. HPLC and LC-MS techniques were employed to identify the flavonoids, iridoids, and phenolic acid derivatives present in HEGV. DPPH (2,2-diphenyl-1-picrylhydrazyl), nitric oxide (NO), and hydroxyl (OH) radical scavenging assays were performed to confirm the antioxidant potential of the extract. Additionally, in silico molecular docking and molecular dynamic studies were performed using AutoDock Vina software to analyze the possible interactions between crucial phytoconstituents of HEGV and ADGRV1, followed by cell line analysis. In the in vitro analysis, antioxidant, neuroprotective, and anti-inflammatory properties were assessed via cell viability assay, IL, GABA, and glutamate estimation. LC-MS and HPLC analyses revealed high concentrations of hispidulin, a major flavonoid found in HEGV. HEGV exhibited moderate-to-high free radical-scavenging activities comparable to those of ascorbic acid. Docking analysis demonstrated that hispidulin has a stronger binding affinity with ADGRV1 (Vina score = -8.6 kcal/mol) than other compounds. Furthermore, cell line analysis revealed that the MSG exacerbates the neurodegeneration and neuroinflammation, whereas, HEGV and Hispidulin both possess neuroprotective, antioxidant, and antiepileptic activities. HEGV and Hispidulin proved to be promising candidates for treating audiogenic epilepsy by modulating ADGRV1.

Callus of Mundulea sericea as potential anti-diabetic agents; an in silico approach

Mundulea sericea, a rare plant of the fabaceae family, has high medicinal value but a low regeneration rate in its natural habitat. The present study aims to conduct in vitro propagation and screen the potential bioactive compounds in the callus through in silico analysis. The explants were collected, sterilized, and inoculated in a standardized MS media with growth regulators in vitro to obtain sterile plants. The experiment resulted in the formation of a greenish-brown callus at a rate of 82.41 % on MS medium supplemented with BAP (6.66 µM L−1). The callus was powdered and subjected to GC–MS analysis. A total of 31 compounds were identified in the methanolic extract, along with their corresponding peak values. The compounds underwent ADME analysis for toxicity predictions. Eight compounds were chosen further based on pharmacokinetic and pharmacodynamic properties. The selected ligands were docked with anti-diabetic targets α-amylase and α-glucosidase. As a result, the compound CID 5283663 exhibited a strong binding affinity of −9.3 with the α-amylase receptor. The ligand CID 33010 exhibits a strong interaction of −7.5 with the α-glucosidase receptor. Glibenclamide and acarbose were used as standards. This study is the first attempt to identify compounds in the callus extract that could inhibit α-amylase and α-glucosidase enzymes. The findings from molecular docking analysis suggest these compounds could become potent treatments for diabetics, showcasing the promise of natural sources in drug discovery.

Retention of methicillin susceptibility in Staphylococcus aureus using natural adjuvant as an allosteric modifier of penicillin-binding protein 2a

The emergence of methicillin-resistant Staphylococcus aureus (MRSA) poses a significant global public health challenge due to its resistance to conventional antibiotics, primarily mediated by the mutated penicillin-binding protein, PBP2a. This study aims to investigate the potential of phytochemicals derived from medicinal plants in the Indian subcontinent to serve as adjuvants, enhancing the efficacy of methicillin against MRSA through allosteric modification of PBP2a using molecular docking and molecular dynamics (MD) simulation. After comprehensive Absorption, Distribution, Metabolism, and Excretion (ADME) profiling, along with AMES and hepatotoxicity tests, 9 compounds were shortlisted as suitable adjuvant candidates. Among them, nimbolide, quercetin, emodin, daidzein, eriodictyol, luteolin, and apigenin exhibited strong binding affinity to the allosteric site of PBP2a, with docking scores ranging from −8.7 to −7.3 kcal/mol. These phytochemicals facilitated enhanced methicillin binding, as evidenced by improved docking scores ranging from −6.1 to −6.8 kcal/mol, compared to −5.6 kcal/mol for methicillin alone. Molecular dynamics simulations confirmed the stability and favorable conformations of phytochemical-PBP2a complexes. Quercetin and daidzein were identified as the most promising adjuvant candidates, forming stable and energetically favorable complexes with PBP2a. Experimental validation showed that quercetin, at 30 mg/mL, effectively retained methicillin's antibacterial efficacy against MRSA. This study underscores the potential of natural compounds in overcoming antibiotic resistance and suggests that phytochemical-antibiotic synergism could be a viable strategy to combat multidrug-resistant bacterial infections.

New Approach as Inhibitor Against Head-Neck Cancer by In silico, DFT, FMOs, Docking, Molecular Dynamic, and ADMET of Euphorbia tirucalli (Pencil Cactus)

Background: Head and neck cancer (HNC) is on the rise worldwide, endangering lives and straining healthcare systems in both developing and developed nations. Despite the availability of a number of therapy options, the success rate for treating and controlling head and neck cancer remains dismal. To combat the aggressiveness and drug resistance of Epstein-Barr virus (EBV)-positive Head-Neck cancer cells, this study looks into the potential of Euphorbia tirucalli (pencil cactus) leaf extract. Objectives: The goal of this study is to identify prospective therapeutic candidates from the extract of Euphorbia tirucalli (pencil cactus) leaves, which have the ability to inhibit Epstein-Barr virus (EBV)-positive Head-Neck cancer cells. Materials and Methods: The thirteen most important chemical components found in Euphorbia tirucalli (pencil cactus) leaves were analyzed by means of molecular modeling techniques such as Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET), Quantum Mechanics (QM) calculation, Molecular Dynamics (MD) profiling, molecular docking, and molecular dynamics (MD) simulations. Using the Prediction of Activity Spectra for Substances (PASS) model, we assess the potency of these compounds in vitro against an Epstein- Barr virus (EBV)-positive head-neck cancer cell line. Important molecular properties such as chemical potential, electronegativity, hardness, and softness can be determined with the use of quantum chemical calculations employing HOMO-LUMO analysis. These drugs' safety and toxicological characteristics are better understood thanks to assessments of their pharmacokinetics and ADMET. These tests show that there is no risk of hepatotoxicity or cancer in humans and that they are safe to use. In order to verify binding interactions and complex stability, molecular dynamics simulations are used to reveal stable docked complexes. Results: The molecular docking analysis identifies ligands (01), (02), and (10) as strong competitors, with strong binding affinity for the Epstein-Barr virus (EBV)-positive Head-Neck cancer cell line. Not only do the ligands (01), (02), and (10) match the criteria for a potential new inhibitor of head-neck cancer, but they also outperform the present FDA-approved treatment. Conclusion: Taraxerol, euphol, and ephorginol, three phytochemicals isolated from the leaves of the Euphorbia tirucalli (pencil cactus), have been identified as effective anti-cancer agents with the potential to serve as a foundation for novel head-neck cancer therapies, particularly those targeting the Epstein-Barr virus (EBV)-overexpressing subtype of this disease. An effective, individualized treatment plan for head-neck cancer is a long way off, but this study is a major step forward that could change the lives of patients and lessen the global burden of this disease.