Chronic liver diseases, such as cirrhosis and carcinoma caused by the hepatitis B virus (HBV), remain an important global health issue. Despite availabilities of efficacious nucleoside analogs-based drugs, the emergence of HBV polymerase mutations associated with drug resistance restrict their clinical use. Therefore, phytochemicals have been reported for promising anti-HBV activities in vitro or in vivo. In this study, we have assessed the anti-HBV potential of myristicin and isoimperatorin, isolated from the n-hexane extract of Petroselinum crispum and characterized by NMR spectroscopy. Both compounds (6.25-50.0 mu g/mL) pre-tested for their nonhepatocytotoxicity in cultured HepG2.2.15 cells, were subjected to anti-HBV assays using HBsAg and HBeAg ELISA kits. At the selected optimal-active dose (12.5 mu g/mL), the compounds showed dose-and time-dependent activities in relation to the untreated control at day 5. Therein, while Myristicin moderately inhibited HBsAg (similar to 38.2%) and HBeAg (similar to 36.6%), isoimperatorin strongly suppressed HBsAg (similar to 60.2%) and HBeAg (58.9%) close to those of Quercetin (standard). Further molecular docking analysis of isoimperatorin with HBV polymerase revealed high docking score (-8.6 kcal/mol) comparable to lamivudine (standard), suggesting its anti-HBV effect through blocking the polymerase enzymatic activity. In conclusion, to our best knowledge, we demonstrate significantly strong anti-HBV efficacy of isoimperatorin, warranting its further pre-clinical studies.

Stomata play a critical role in plant physiology by balancing gas exchange and water conservation. Their development is driven by a precisely orchestrated sequence of cell divisions and differentiation events, regulated by basic helix-loop-helix (bHLH) transcription factors such as MUTE. Previous research reports stomidazolone, a doubly sulfonylated imidazolone derivative, as an effective inhibitor of stomatal development which has been shown to bind strongly to MUTE, interfering with its interaction with SCRM, effectively suppressing stomatal differentiation. The ACTL domain, a conserved structural feature in plant bHLH proteins, acts as a potential site for chemical inhibition, enabling selective disruption of stomatal formation. This suggests a promising approach for enhancing drought resilience in plants by reducing water loss through transpiration. While experimental data support stomidazolone's inhibitory role, the molecular details of its binding to MUTE remain inadequately characterized. To address this gap, a comprehensive in silico analysis combining molecular docking and density functional theory (DFT) was performed to elucidate the binding interactions, electronic properties, and reactive potential of stomidazolone, thereby uncovering the molecular features that underpin its affinity and specificity toward MUTE. An all-atom molecular dynamics (MD) simulations was then carried out to provide mechanistic insights beyond static binding models, followed by a number of post-simulation analyses assessing system stability and dynamics to gain deeper insight into the Stomidazolone-Mediated Inhibition of MUTE. Our results reveal the formation of a stable and compact stomidazolone-MUTE complex, characterized by a lower average RMSD (1.45 ± 0.12 nm) compared to the Apo state (1.65 ± 0.18 nm), while hydrogen bonding analysis further demonstrated persistent interactions involving Arg62 and Ser69, along with a stabilizing contribution from Glu163, collectively supporting the strong binding affinity of stomidazolone within the MUTE active site. Principal component analysis further highlighted the conformational coherence and coordinated atomic motion, while the free energy landscape showed well-defined energy minima, underscoring the stability of the interaction and energetic favorability of the complex. Together, these findings provide a molecular framework for understanding the inhibitory mechanism of stomidazolone on MUTE, offering a basis for the rational design of next-generation agrochemicals targeting stomatal development. The study also highlights the conceptual novelty of small-molecule modulation of lineage-specific transcription factors as a potential strategy for the synthetic control of plant developmental plasticity. While the results are computational, they outline clear directions for experimental validation and scaffold optimization, paving the way for future efforts to translate these insights into practical applications for improving crop resilience and water-use efficiency. Importantly, this study provides the first mechanistic, residue-level insight into how stomidazolone engages the ACT-Like (ACTL) domain of MUTE, revealing the specific molecular interactions and dynamic features that underpin its inhibitory effect.

Chiral discrimination plays a pivotal role in the development of enantiomerically pure pharmaceuticals, as stereochemistry directly influences both the pharmacological efficacy and safety profiles. In this study, a twisted nitrogen-substituted cyclacene comprising 15 fused benzene rings was employed as a host framework for the enantiomeric recognition of chiral bicyclo[1.1.1]pentane (BCP) analogues. Unlike conventional diastereomer-based chiral resolution methods, the cyclacene host enables direct enantiomeric discrimination of BCP analogues. The interaction behavior of four R/S enantiomeric pairs of BCP derivatives with the cyclacene host was systematically explored by using density functional theory (DFT) simulations. Key interaction parameters, including binding energies, hydrogen bonding, noncovalent interaction (NCI), and electron density difference (EDD) maps, were examined in detail. The results indicate that the R enantiomers exhibit stronger binding affinities and enhanced chiral selectivity relative to their S counterparts, as evidenced by a greater number of hydrogen bonds and more favorable host-guest interaction distances. Remarkably, BCP3 and BCP4 demonstrated the highest degrees of chiral discrimination, highlighting the nitrogen-substituted twisted cyclacene as a promising candidate for enantioselective separation. Collectively, these findings provide valuable theoretical insights into the rational design and development of advanced nanostructured host systems for selective chiral recognition and separation technologies. Furthermore, this study may contribute to the advancement of next-generation supramolecular materials for pharmaceutical purification, asymmetric sensing, and molecular-scale recognition systems, thereby supporting broader efforts toward safer drug development and more efficient enantiomeric separation methodologies.

Chronic pain is a maladaptive state where pain signals persist beyond the expected resolution of injury or illness. Morphine and related compounds, acting as µ-opioid receptor (µOR) agonists, are effective analgesics for managing this condition. However, chronic morphine administration can disrupt µOR trafficking and activate β-arrestin-mediated pathways, leading to opioid tolerance. The role of µOR in mood disorders is less well-defined. The organoselenium compound m-trifluoromethyl diphenyl diselenide (TFDD) has shown promising antinociceptive and antidepressant-like effects in experimental models and attenuated morphine withdrawal symptoms in mice.1 However, the molecular mechanisms governing TFDD's interaction with the µOR at the atomic level remain unexplored through theoretical methodologies. To bridge this knowledge gap, the current research sought to characterize the pharmacological profile of TFDD using an integrated computational approach that included quantum chemical calculations, molecular dynamics simulations, and thermodynamic analysis. The simulations revealed the formation of persistent halogen bonds between TFDD's trichlorobenzene moiety and specific residues within the µOR binding pocket, namely Gln1242.60 and Glu2995.58 with bond distances of 2.83 and 3.73 Å respectively. These interactions, spanning transmembrane helices 2 through 5 (TM2-TM5), contribute to the stabilization of TFDD within the receptor's binding site. Notably, key microswitch residues, such as Asp1473.32, Met1513.36, and Trp2936.48, which are critical for maintaining the µOR active conformation and modulating β-arrestin signaling, were observed to interact with TFDD. These conformational dynamics subsequently influence the G protein-biased activation of the µOR. To examine the conformational space of the µOR bound to TFDD and the morphinan agonist BU72, principal component analysis was used to determine the leading modes of motion. Subsequently, free energy landscapes were constructed to identify energetically favorable conformational states and the transitions between them, providing insights into the thermodynamic behavior of the µOR-ligand bound complexes. Furthermore, dynamic cross-correlation matrix analysis was performed to evaluate differences in the correlated motions of µOR residues upon binding of BU72 and TFDD. Alchemical free energy calculations, utilizing thermodynamic integration across various λ states, were employed to quantitatively estimate the binding affinities of both ligands TFDD and BU72. The calculated total binding free energy values were -42.54 ± 1.92 kJ/mol for TFDD and -39.76 ± 0.74 kJ/mol for BU72. This computational study elucidates the molecular basis of TFDD's interaction with µOR, integrating experimental data with atomic-level modeling. This enhances our understanding of TFDD's potential to reduce morphine tolerance, improve pain relief, and minimize side effects, ultimately informing the development of better opioid-based pain management strategies.

The androgen receptor (AR) is a nuclear receptor involved in regulating gene expression, maintaining the sexual phenotype, and contributing to the development of prostate cancer (PCa). The binding of agonists, such as dihydrotestosterone (DHT), triggers conformational changes in the AR, affecting coactivator interactions, and regulates downstream signaling pathways. Although AR activation depends on interactions between its ligand-binding domain (LBD) and coactivators, the precise impact of ligand binding on these interactions remains unclear. Antagonists such as apalutamide, bicalutamide, and enzalutamide inhibit AR activation and are used to treat PCa. However, their long-term effectiveness is often reduced due to mutations in AR-LBD, which can shift the AR from an antagonistic to an agonistic state, diminishing treatment efficacy. The mechanisms driving this conversion have not been fully elucidated. This study employed atomic-level investigations through molecular dynamics simulation with multiple replicas covering a total time frame of 10.5 μs, to investigate ligand induced perturbations in mutants AR_LBD, particularly focusing on conformational changes and the effect on AR-coactivator interaction. The results demonstrated that DHT, an agonist, stabilizes the activation function-2 region (AF-2), thereby promoting AR-coactivator interactions, while antagonists induce distinct changes in helix 12 that disrupt these interactions. In addition, F876L and T877A mutations in AR-LBD alter the ligand-to-coactivator allosteric pathway involving the coactivator, helix 3 (H3), helix 4 (H4), the loop between H3-H4, and helix 12 (H12), potentially converting the AR-apalutamide complex from an antagonistic to an agonistic state. The free energy decomposition calculations exhibited that AR mutant systems possess higher binding affinities than antagonistic ARs, with electrostatic interactions and conformational entropies associated with the determination of the binding free energies. The study suggests that point mutations in AR-LBD induce a shift from an antagonistic to an agonistic state by altering the AR and AF-2 structure, resulting in continuous coactivator recruitment and sustained AR activity. Through the application of a dynamic cross-correlation matrix, principal component analysis, free energy landscape computation, and structural community analysis, this research offers valuable insights into AR-coactivator interactions, paving the way for more effective treatments against castration-resistant prostate cancer.

Flame retardants (FR) encompass a wide range of chemicals designed to inhibit and reduce the spread of fire by forming protective layers on materials. While originally considered relatively safe due to their rapid metabolism, growing evidence indicates that organophosphate flame retardants (OPFRs) can be extensively released into the environment, leading to toxic effects in humans, particularly endocrine disruption. Although the endocrine-disrupting potential of OPFRs is well-documented, the mechanisms through which their metabolites exert toxic effects remain largely unexplored. In this study, a comprehensive computational framework incorporating molecular docking, density functional theory, and all-atom molecular dynamic simulations were employed to investigate the binding and interactions of three key OPFR metabolites, BCIPP, BDCIPP, and DPHP, with human estrogen receptors (ER) and mineralocorticoid receptors (MR). The results revealed that these metabolites formed stable and compact complexes with both MR and ER, although high per residue atomic fluctuations were observed in ER complexes, likely due to the reactive nature of the metabolites. Binding free energy analysis further indicated favorable interactions between the OPFR metabolites and target receptors. Principal component analysis, leveraging machine learning algorithms, showed consistent motion, while free energy profiles demonstrated stable energy basins with minimal variations. These findings suggest that OPFR metabolites have strong binding affinities with MR and ER, hinting at their potential endocrine-disrupting effects at the molecular level. This study lays the groundwork for future research into the hazards posed by OPFR metabolites.

Cyclin-dependent kinase 2 (CDK2) dysregulation is a significant contributor to the onset of several cancer types. Recently, N-(pyridin-3-yl)pyrimidin-4-amine (NPPA) analogues have been identified as potent candidates for the inhibition of overexpressed CDK2 in cancers. This study examines how the NPPA analogues are endowed with remarkable inhibitory potencies against CDK2. An integrated computational approach is employed by examining the structural properties and reactivities of the NPPA analogues at an electronic level and their molecular interactions with the binding site residues. The effects of inhibitor binding onto the protein structure are dynamically explored and the binding affinities are calculated through a MM/PBSA approach. Our findings reveal that the NPPA analogues hold better chemical reactivity than the reference inhibitor (AZD5438) and are relatively electrophilic in nature. The NPPA analogues establish strong inhibitory interactions within the CDK2 active site and stabilize the protein structure in a well-folded compact state by lowering the fluctuations in the protein structure at the residue level. The binding free energy calculations reveal strong affinities of these inhibitors towards CDK2 inhibition, and the conformational dynamics of the protein structure have unveiled stable protein conformations attained by the inhibitor binding. Out of all the NPPA analogues, NPPA3 has shown remarkable effectiveness as a CDK2 inhibitor. It has favorable chemical properties, forms strong intermolecular interactions with CDK2 active site residues (with a binding affinity of -68.23 kJ mol-1), and achieves improved protein stability through interactions with crucial active site residues. Additionally, it stabilizes the protein in dynamically stable conformations. These findings support the future development of novel CDK2 inhibitors by highlighting some crucial parameters underlying the activity of potent inhibitors.

The adsorption of ciprofloxacin (CIP) and levofloxacin (LEVO) on pristine boron carbide (BC3) and Zn-decorated boron carbide (Zn-BC3) monolayer is explored using the density functional theory (DFT) study. Investigations were conducted using the quantum theory of atoms in molecules (QTAIM) analysis, natural bond orbital (NBO) charge analysis, electrostatic potential maps (ESP), non-covalent interaction (NCI) analysis, and density of states (DOS) plots. The adsorption of antibiotics on the pristine BC3 monolayer was weak physisorption. However, the adsorption of CIP and LEVO on Zn-BC3 was chemisorption with adsorption energies of-1.37 and-1.36 eV, respectively. QTAIM analysis depicted the presence of strong interactions between the drug molecules and the Zn-BC3 monolayer. From the NBO analysis, it was observed that the charge transfer in the LEVO@Zn-BC3 complex was the highest (0.588 e-) compared to the CIP@Zn-BC3 (0.240 e-). LEVO@Zn-BC3 complex exhibited the smallest HOMO-LUMO gap (Eg = 2.33 eV) among the two, suggesting that the adsorption of LEVO on the Zn-BC3 was more favorable. The decrease in Eg significantly enhances the electrical conductivity, which can be converted to an electrical signal; thus, it can be used as an electronic sensor for detecting these drug molecules. This study demonstrated the promising application of BC3 monolayer as an effective adsorbing/sensing material for the removal of ciprofloxacin and levofloxacin.

Streptococcus mutans, a primary cariogenic bacterium, plays a central role in dental caries, one of the most widespread chronic diseases globally. Glucosyltransferases (GTFs) are key virulence factors in this process, as they synthesize extracellular polysaccharides that contribute to biofilm formation and pathogenicity. Targeting GTFs has emerged as a promising strategy for preventing dental caries, with previous studies demonstrating its potential efficacy. This study builds on our prior work by providing detailed molecular insights into the binding modes of previously identified GTF inhibitors. Using computational tools, including density functional theory, molecular docking, and molecular dynamics simulations, we examined the binding interactions and structural stability of selected inhibitors. All investigated candidates demonstrated superior binding behavior compared to the reference ligand, acarbose, as indicated by multiple structural parameters. Structural dynamics analysis revealed significant stability in the binding interactions of Complex III and V, with average deviations of 2.06 ± 0.38 and 2.07 ± 0.30 Å, respectively. Similarly, a trend in structural compactness was observed, with gyration values of 32.98 ± 0.23 and 33.01 ± 0.24 Å, respectively. Principal component analysis indicated that the constructed pattern approaches zero with the achievement of a global energy minimum, particularly for Complex III and V. Furthermore, MM/PBSA free energy calculations identified Compound V as the most favorable binder, with a binding free energy of -24.20 kcal/mol. Our findings provide valuable molecular-level insights into the inhibitory mechanisms of GTF-targeting compounds, strengthening their potential as anti-cariogenic agents. By elucidating key binding interactions, this study contributes to the ongoing search for improved scaffolds that may hinder biofilm-mediated infections and advance therapeutic strategies against dental caries.

The present study reports the chemical investigation on the aerial parts of Cleome droserifolia yielding the related eudesmane sesquiterpene solyraterpenoid A (1) and the novel cledrone A (2) from the acetonitrile fraction of the dichloromethane extract. These compounds were separated by column chromatography, centrifugal thin layer chromatography (CTLC) followed by semipreparative reversed-phase high performance liquid chromatography (RP-HPLC). The chemical structure of these compounds was determined by mono and bidimensional NMR techniques, IR spectroscopy, and HRESIMS, while the absolute configuration was established by computational analysis of ECD spectra. Furthermore, the structure and absolute configuration of both 1 and 2 were unambiguously confirmed via single crystal X-ray diffraction (scXRD). Both compounds showed antibacterial activity against Escherichia coli and Pseudomonas aeruginosa strains, with compound 2 being more active.

Dental caries is a multifactorial, biofilm-mediated disease primarily caused by Streptococcus mutans, a key etiological agent. This bacterium secretes extracellular enzymes known as glucosyltransferases (Gtfs), also termed glucansucrases, which play a pivotal role in the synthesis of exopolysaccharides through the metabolism of dietary sucrose. These exopolysaccharides provide binding sites for the attachment and colonization of other microorganisms, contributing to the initiation and progression of dental caries. This study investigates the catalytic mechanisms of glucosyltransferases from S. mutans using molecular dynamics simulations, with a focus on the conformational dynamics and interactions of amino acid residues that modulate enzymatic activity. Wild-type and mutant models of glucosyltransferase, bound to maltose, sucrose (substrates), and acarbose (an inhibitor), were generated to analyze the binding patterns of these molecules. The systems' stability was assessed using root-mean-square deviation, fluctuation, radius of gyration, principal component analysis, free energy landscape, and dynamic cross-correlation matrix analysis. The MMGBSA method was employed to evaluate the relative binding free energies of the systems. Our findings revealed that mutations increased stability in the sucrose-bound system while decreasing stability in the acarbose-bound system, with consistent fluctuation patterns observed across different ligands. These dynamic changes in glucosyltransferase behavior could influence its catalytic efficiency.

Introduction: Histamine Type I Receptor Antagonists (H1 blockers) are widely used to mitigate histamine-induced inflammation, particularly in allergic reactions. Histamine, a biogenic amine found in endothelial cells, vascular smooth muscle, bronchial smooth muscle, and the hypothalamus, is a key player in these responses. H1 blockers are essential in cough syrups and flu medications and are divided into two generations: first-generation H1 blockers, which are sedating and have numerous side effects, and second-generation blockers, which are non-sedating and generally less toxic but may still exhibit cross-reactivity with other receptors. Method: In this study, a comprehensive database of compounds was utilized alongside fexofenadine as a benchmark to discover compounds with potentially superior efficacy and reduced side effect profiles. In particular, multidimensional K-means clustering, a machine-learning technique, was applied to identify compounds with chemical structures similar to fexofenadine. Result: Utilizing computational prediction of pharmacokinetic profile and molecular docking experiments, the action of these drugs on the H1 receptor was assessed. Furthermore, the crossreactivity of antihistamines was investigated by conducting a structure-based pharmacophore feature analysis of the docked poses of highly toxic antihistamines with various receptors. Conclusion: By identifying and proposing the removal of common toxic features, we aim to facilitate the development of antihistamines with fewer adverse effects.

IL-17A is a pivotal pro-inflammatory cytokine implicated in a wide spectrum of immunological responses. However, its dysregulation is linked to the progression of various pathological conditions, from mild inflammation to malignant cancers. When IL-17A binds to its cognate receptor, IL-17RA, it forms a complex that initiates a series of molecular signaling cascades within the cell, contributing to various inflammatory processes. Currently, there are no specific oral drugs targeting this pathway, underscoring the urgent need for novel non-inflammatory drugs to address autoimmune and inflammatory diseases. Targeting IL-17A presents a unique opportunity to develop innovative therapies for autoimmune conditions. This research employs ligand-based pharmacophore modeling, followed by screening and docking simulations found six potential drugs that effectively disrupt the IL-17A-IL-17RA combination. Molecular dynamics simulations further demonstrated the stability and inhibitory potential of these compounds, highlighting their interactions within the IL-17A binding site. These interactions involve key residues such as Arg39, Trp51, Trp67, Gln94, Glu95, Leu97, Leu99, Lys114, and Ser118, which are crucial for locking the associated signaling cascade. Mechanistic studies, including dynamic simulations and calculation of free energy, support the efficacy of the identified compounds. Notably, Compounds 1 and 4 exhibit higher binding affinities compared to the native reference inhibitor of target. Our results revealed that both the peptide (Compound 1) and macrocyclic compounds (Compound 3) significantly disrupt the IL-17A/IL-17RA complex, confirming the validity of our approach and reinforcing its potential therapeutic relevance, as highlighted in prior studies. These IL-17A inhibitors show enormous promise as prospective therapeutic candidates for the treatment of inflammatory disorders.

Apigenin, a naturally occurring bioflavonoid, has shown promise as an anti-diabetic agent due to its abilities to inhibit α-glucosidase, stimulate insulin action and secretion, regulate reactive oxygen species (ROS), and mitigate complications associated with diabetes. Recognized as a potential insulin secretagogues, Apigenin enhances glucose-stimulated insulin secretion, positioning it as a strong candidate for diabetes treatment. Nevertheless, the exact atomic-level activation mechanism is still elusive. In order to improve the dynamic research, and rigorously characterize, as well as explore the mechanistic insights of apigenin's action as agonist for PKA, principal component analysis (PCA) and Free energy profile were linked with molecular dynamics (MD) simulations and binding free energy calculations, alongside in vitro assessments in isolated pancreatic islets from mice, and in vivo evaluations in diabetic rat models were correlated. Our results focus on the dynamic behavior of the different structural motifs of PKA, specifically the N3A motif, CNB-A, and CNB-B of the PKA regulatory subunit, during single ligand-bound states (B-bound) and double ligand-bound states (AB-bound), to uncover the intrinsic dynamics in particular functional areas. The stability matrices revealed average deviation values ranging from 0.12 to 0.72 nm for the B-bound state and 0.19-0.52 nm for the AB-bound state. The residue-level fluctuations indicated that the binding of apigenin conferred enhanced stability relative to cAMP, both in the B-bound and AB-bound states. Furthermore, the gyration values extracted from the simulated trajectories were found in the range of 2.21-2.26 nm for B-bound state and 2.11-2.23 for AB-bound state. Apigenin demonstrated remarkable results, mimicking cAMP and exhibiting a good correlation with biological activity. The PCA results of Apigenin featured flipback confirmation with relatively less variance and constricted conformational landscape than cAMP. The stable ensembles and reduced variation in turns might be the possible reasons for its outstanding performance. The binding insight with crucial residues, MD matrices, PCA, Free energy profile, and Binding energy calculation indicate stable binding of Apigenin at the cyclic nucleotide binding domains of the regulatory subunit of PKA. The study reveals that Apigenin could be a promising lead for the treatment of T2D. Future studies on PKA activation may benefit from the knowledge gathered from this investigation.

Bromo-DragonFLY (BDF), a potent designer psychedelic drug with hallucinogenic properties, has recently emerged as a significant recreational substance. Named for its dragonfly-like molecular structure, BDF induces prolonged psychedelic effects, with hallucinations lasting several days. Clinical reports highlight severe toxicity, including confusion, tachycardia, hypertension, seizures, renal failure, and, in extreme cases, death. BDF acts as a potent agonist of the 5-HT2A serotonin receptor subtype, which mediates the behavioral and psychedelic effects of hallucinogens. Despite its increasing prevalence and associated clinical implications, the precise molecular mechanisms underlying BDF's interaction with 5-HT2A remain inadequately characterized, particularly from an in silico perspective. This study addresses this gap by employing a comprehensive in silico framework to investigate the molecular interactions of BDF with the 5-HT2A receptor. Molecular docking was used to identify binding sites, while all-atom molecular dynamics (MD) simulations provided insights into the stability of the protein-ligand complex, assessing deviations, local flexibility, and time-dependent gyration patterns. The results revealed stable and compact complex formation between BDF and 5-HT2A, characterized by minimal per-residue fluctuations and high hydrogen bond occupancy, suggesting a highly stable interaction as shown experimentally. Additionally, principal component analysis, leveraging machine learning algorithms, demonstrated consistent motion, while free energy profiles highlighted stable energy basins with minimal variations for the BDF-5-HT2A complex. These findings suggest strong binding affinities of BDF with the serotonin receptor, leading to highly stable complex formation. This study provides a foundational understanding of BDF's molecular interactions, offering critical insights into its role as a potent psychedelic agent and laying the groundwork for future investigations into the risks posed by novel designer drugs.

Ecdysterone, often dubbed a “natural steroid,” has garnered significant attention among athletes for its reputed growth-promoting and anabolic properties. Unlike synthetic anabolic steroids, which are classified as controlled substances, ecdysteroids remain largely unregulated in many countries and are widely marketed as dietary supplements. Notably, ecdysterone has been included in the World Anti-Doping Agency (WADA) monitoring program, highlighting its potential impact on athletic performance and raising questions about its regulation. Emerging evidence indicates that, unlike traditional anabolic steroids that act primarily via the Androgen Receptor (AR), ecdysterone’s anabolic effects may be mediated through Estrogen Receptors (ERs), particularly Estrogen Receptor beta (ERβ). Despite these insights, the precise molecular mechanisms underlying ecdysterone’s biological activity remain poorly characterized, particularly from an in-silico perspective. This paper aims to address these gaps by exploring ecdysterone’s mechanism of action through computational and molecular modeling approaches. This study employs an advanced computational framework to unravel the binding dynamics and interaction mechanisms of ecdysterone with Androgen Receptor (AR), Estrogen Receptor alpha (ERα), and Estrogen Receptor beta (ERβ). Using chemical descriptor analysis, inter-molecular interaction mapping, and all-atom molecular dynamics simulations spanning 250 ns for each system, the study reveals that ecdysterone preferentially binds to ERβ, forming stable and compact complexes characterized by minimal per-residue fluctuations as evident in the average RMSD, RMSF, and Rg values observed for ERβ - Ecdysterone as 1.98 ± 0.31 Å, 1.07 ± 0.52 Å, and 18.44 ± 0.08 Å respectively which are significantly comparable with the ERβ - native complex, while high hydrogen bond occupancy was also observed for ERβ - Ecdysterone complex. Although binding free energy calculations suggest stronger interactions with ERα, the associated high fluctuations diminish its binding efficacy. In contrast, interactions with ERβ remain consistent and robust. Machine learning-based principal component analysis highlights coordinated motion patterns, while free energy profiles demonstrate stable energy basins with minimal variation. These findings underscore the pivotal role of ERβ in mediating ecdysterone’s anabolic effects, distinguishing it from traditional androgenic steroids, and provide critical insights into its unique mechanism of action. This work lays the foundation for further exploration of ecdysterone as a potential anabolic agent.

Obesity-induced insulin resistance impairs glucose tolerance and β-cell function, significantly contributing to the pathogenesis of type 2 diabetes (T2D). Protein kinase A (PKA), being one of the key effector molecules of the cyclic AMP (cAMP) pathway, increases insulin secretion via membrane activity, gene expression, and exocytosis of insulin granules. The previous studies were limited to either target cAMP analogs as PKA agonist or mostly flavonoids using In vivo and In vitro studies (Hameed in Int J Biol Macromol 119:149–156, 2018;Shahab in Biomed Pharmacother 177, 2024;Hameed in Eur J Pharmacol 820:245–255, 2018;Hameed in Eur J Pharmacol 858, 2019;Hafizur in Med Chem Res 27:1408–1418, 2018;). To speed up the process, this study aimed to identify potential PKA activators as therapeutic agents for restoring β-cell function in Type 2 Diabetes (T2D) using a multistage virtual screening approach. In the initial phase, a ligand-based pharmacophore model was constructed to screen an in-house small molecule database for potential PKA agonists. By targeting the essential pharmacophoric features necessary for interaction with the cyclic nucleotide-binding (CNB) domain of PKA, the goal was to identify compounds with strong binding affinities and therapeutic promise. To gain deeper insights into the molecular mechanisms of PKA activation and evaluate key interactions and dynamic stability, a subset of promising hits was subjected to all-atom molecular dynamics simulations. Simulations showed significant conformational changes in PKA complexes, with average backbone root mean square deviations (RMSD) of 0.37 ± 0.15 nm for Comp-03, 0.53 ± 0.18 nm for Comp-11, 0.31 ± 0.06 nm for Comp-17, 0.28 ± 0.03 nm for Comp-38, and 0.48 ± 0.13 nm for Comp-41. The N3A motif showed consistent fluctuations, suggesting increased flexibility. Binding free energy calculations showed binding free energies (ΔGbind) for cAMP, Comp-03, Comp-17, Comp-38, and Comp-41, with ΔGbind values of − 62.87 ± 10.04, − 68.57 ± 12.77, − 78.13 ± 16.36, − 62.67 ± 13.06, and − 80.87 ± 10.45 kcal/mol, respectively. To further probe the conformational stability of these complexes, multidimensional scaling and free energy profiling were carried out. This exhaustive research study, involving examination of stability dynamics, deviation patterns, interaction networks, conformational changes, and energy profiles, provides profound understanding about mechanisms that activate PKA. The findings highlight several promising lead compounds, notably Comp-03, Comp-17, Comp-38, and Comp-41, which exhibit superior potential to activate PKA compared to cAMP. These findings lay a strong foundation for the development of novel PKA activators as potential therapeutic agents for managing T2D.

In this study, Zeolitic Imidazolate Framework-8 (ZIF-8) nanomaterials were synthesized using a co-precipitation one-pot method that uses ethanol, methanol, and water as solvents for the precursors (2-methylimidazole and Zinc nitrate hexahydrate), resulting in yields of 66.77%, 73.14%, and 68.12%, respectively. The as-synthesized ZIF-8 nanomaterials were thoroughly characterized by X-ray diffraction analysis, transmission electron microscopy, ultraviolet-visible spectroscopy, and Fourier-transform infrared spectroscopy. The X-ray diffraction analysis showed that the crystallite size of ethanol-based ZIF-8 (24.76 +/- 1.67 nm) was smaller than those synthesized in water (26.92 +/- 1.89 nm) and methanol (31.39 +/- 1.03 nm). However, methanol-based ZIF-8 exhibited lower crystallinity (85.93%) than water-based ZIF-8 (91.48%) and ethanol-based ZIF-8 (92.71%). Zeta potential studies revealed that ethanol-based ZIF-8 had a larger surface charge (+37 mV) than water-based ZIF-8 (+35 mV) or methanol-based ZIF-8 (+24 mV). Transmission electron microscopy analysis confirmed particle sizes of 54.35 +/- 2.11 nm for ethanol-based ZIF-8, 57.91 +/- 2.26 nm for water-based ZIF-8, and 63.25 +/- 4.12 nm for methanol-based ZIF-8. Thermogravimetric analysis indicated thermal stability up to 800 degrees C, with mass losses of 55.98% for ethanol-ZIF-8, 50.12% for water-based ZIF-8, and 65.36% for methanol-based ZIF-8 by 600 degrees C. In antibacterial studies, water-based ZIF-8 exhibited the largest zone of growth inhibition (17.30 +/- 0.26 mm) against Escherichia coli compared to ethanol-based ZIF-8 (15.57 +/- 0.32 mm) and methanol-based ZIF-8 (14.70 +/- 0.20 mm). Pearson's correlation study revealed that zeta potential, crystallinity, and antibacterial activity are positively related. Furthermore, water-based ZIF-8, with a minimum inhibitory concentration of 50 mu g/100 mu L, confirmed evident cell membrane disruption. Molecular docking experiments revealed ZIF-8's significant binding affinity for the E. coli protein 5AZC, supporting its robust antibacterial activity.

The multifaceted impact of IL-1β has been proposed to have a central role in a spectrum of immunological responses spanning physiological reactions to aggressive inflammatory reactions and autoimmune disorders. Once IL-1β binds to its cognate receptor it initiates IL-1R1/TLR4 signaling cascade, leading to transcriptional modifications that sustain the inflammatory response. Extensive structural and functional investigations on IL-1β have yielded various inhibitors aimed at disrupting the formation of ligand receptor complex. Unfortunately, most have proven unsuccessful in clinical trials. Therefore, directing efforts towards IL-1β/IL-1R1 presents a unique opportunity to formulate an alternative therapy for the treatment of inflammatory disorders. In view of this, the present study aimed to identify small molecules obstructing protein-protein interactions (PPIs) to impede heterocomplex formation. In this context, a search query was formulated by integrating a ligand-based pharmacophore mapping alongside a multi-stage molecular docking to assess the potential of the predicted hits in terms of binding modes within the targeted cavity of the IL-1β and the associated binding affinities. Thus, via a stepwise screening process starting from an initial pool of 40,000 compounds, 8 potential hits were identified for detailed atomic studies employing molecular dynamic simulation encompassing a total time frame of 0.9 μs. The investigation in dynamic behavior was followed by the estimation of free energies using molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) calculations. The stability matrices revealed that the chosen virtual hits possess a notable potential to hinder the complex formation between IL-1β/IL-1RI. The average backbone deviations recorded for the conformational ensembles of the ligand free IL-1β/IL-1RI exhibited significant dynamics, featuring the average value of 0.35 nm. Conversely, the identified hits particularly, inhouse-2603 and inhouse-1325 demonstrated a high degree of stability with mean values of 0.32 ± 0.05, 0.31 ± 0.03, respectively. The residue-wise fluctuations were maximum for Compound-1303, with the mean value of 0.31 nm and minimal for Compound-2691 with the mean value 0.21 nm. The MMPBSA revealed the highest binding energy of -89.50 ± 10.63, and -81.32 ± 14.9 kcal/mol, for the IL-1β/IL-1RI complex with compound-2603, and Compound-1325 respectively. The principal component analysis (PCA) in conjunction with free energy landscape (FEL) further shed light on the conformational space in terms of energetic stability. Considering the essential role of IL-1β in mediating several inflammatory cascades, it is proposed that the identified PPI inhibitors since demonstrated stable behavior and promising attributes in regard to inhibitory potential as outlined by mechanistic exploration, may serve as new chemotypes for the future exploration aimed at mitigation inflammatory disorders.

Background: Stachys schimperi Vatke has been previously reported for its analgesic, antipyretic, antioxidant, antimicrobial and cardioprotective properties. Objectives: Phytochemical analysis and assessment of anti-hepatitis B virus (anti-HBV) activity of S. schimperi. Materials and Methods: Surface extraction was performed to isolate the phytoconstituents using chromatographic techniques, including HPLC. The isolates were identified by a 1D and 2D NMR spectroscopic data. Further, the isolates were tested for cytotoxicity using an MTT assay. Non-cytotoxic doses of the isolates were assessed for their antiviral potential on cultured HepG2.2.15 cells. To rationalize the plausible mechanisms of the tested anti-HBV active compounds, molecular docking studies were carried out using HBV polymerase (Pol) enzyme. Results:The NMR data proved the structure of isolates as artemetin [5-hydroxy, 3 & sbquo; 3 ',4 '& sbquo;6,7-penta methoxy flavone] (1), chrysosplenetin [5,4 '-dihydroxy, 3 & sbquo;3 '& sbquo; 6,7-tetra methoxy flavone] (2) and calycopterin [5,4 '-dihydroxy, 3 & sbquo; 6,7 & sbquo;8-tetra methoxy flavone] (3). Notably, this is the first report on the isolation of these three compounds from S. schimperi as well as artemetin and calycopterin from the genus Stachys. Further antiviral assessment of the non-cytotoxic dose showed marked inhibitions of HBV antigens (HBsAg/HBeAg) by artemetin (52.28%/46.52%) and calycopterin (61.24%/57.26%) in HepG2.2.15 cells. Chrysosplenetin, however, did not show any anti-HBV activity. Artemetin and calycopterin exhibited anti-HBV activity, possibly through inhibition of HBV-Pol as revealed by molecular docking. Conclusion: We report the identification of anti-HBV active flavones artemetin and Calycopterin from S. shimperi. Our data strongly warrant further molecular and pharmacological studies on artemetin and calycopterin toward developing potential anti-HBV therapeutics.