A comparative study on inclusion complex formation between formononetin and β-cyclodextrin derivatives through multiscale classical and umbrella sampling simulations

Identification of acetylcholinesterase inhibitors and stability analysis of THC@HP-β-CD inclusion complex: A comprehensive computational study

Complexing medications with cyclodextrins can enhance their solubility and stability. In this study, we investigated the host-guest complexation between Tetrahydrocurcumin (THC) and Hydroxypropyl-β-Cyclodextrin (HP-β-CD) using density functional theory (DFT) at the B3LYP-D3/TPZ level of theory in two possible orientations. To determine the reactive sites in both complexes for electrophilic and nucleophilic attacks, we calculated and interpreted the binding energy, HOMO and LUMO orbitals, global chemical reactivity descriptors, natural bond orbital (NBO) analysis, and Fukui indices. The results indicate that Orientation A is energetically more favorable than Orientation B. Non-covalent interactions (NCI) were analyzed using reduced density gradient (RDG) approaches, providing detailed insights into host-guest interactions, including hydrogen bonding and van der Waals forces. To further assess stability, we conducted 1000 ns molecular dynamics (MD) simulations and analyzed the root mean square deviations (RMSD) for systems containing 1, 2, and 10 complexes. The RMSD analysis confirmed the stability of the systems, with average RMSD values of 2.01, 3.21, and 4.29 Å, respectively. In the second part of this study, we examined the interaction between THC and the target protein Acetylcholinesterase (E.C. 3.1.1.7) with PDB ID 1QTI. Molecular docking was performed to identify the binding modes and interaction energies of the THC-protein complex. Subsequently, 1000 ns MD simulations were conducted to assess the stability and dynamic behavior of the THC-protein complex over an extended period. The analysis provided valuable insights into the binding interactions and stability of THC with the target protein, further confirming its potential as a therapeutic agent.

Identification of novel inhibitors for epidermal growth factor receptor tyrosine kinase using absolute binding free-energy simulations

Mutations in the kinase domain of the epidermal growth factor receptor (EGFR), a critical biological macromolecule involved in cell growth and division, can lead to drug resistance in patients undergoing chemotherapy with kinase inhibitors. Notably, the emergence of the C797S mutation poses new challenges for targeted EGFR therapy, highlighting the urgent need for agents effective against this triple mutation (L858R/T790M/C797S, EGFR™). Building on our previous finding that sulfonyl and piperidinyl groups significantly contribute to the EGFR™-inhibitor interactions, we have identified the best-in-class inhibitors containing these groups through functional-group-based screening and formally exact absolute binding free-energy calculations. Our new strategy offers greater flexibility than traditional workflows leaning on relative binding free-energy calculations and accommodates ligands with substantial structural variations. The result shows that the top candidate exhibits a binding affinity of -15.8 kcal/mol towards the EGFR™ mutant, surpassing BLU-945, a state-of-the-art fourth-generation inhibitor with a binding free energy of -12.6 kcal/mol. Subsequent free-energy decomposition indicates that the presented top candidate primarily enhances interactions with the K745, D800 and R841 residues, suggesting its potential to overcome resistance from the C797S mutation. Notably, K745 forms highly favorable hydrogen bonds and cation-π interactions with C6. Targeting lysine has emerged as a promising strategy, especially in cases where the C797S mutation renders traditional covalent inhibitors ineffective. We propose that these novel inhibitors represent promising drug candidates for non-small cell lung cancer treatment and offer new strategies to overcome drug resistance caused by EGFR mutation.

Interactions of flavonoid and coumarin derivative compounds with transforming growth factor-beta receptor 1 (TGF-βR1): integrating virtual screening, molecular dynamics, maximum common substructure, and ADMET approaches in the treatment of idiopathic pulmonary fibrosis

CONTEXT

Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive lung disease characterized by very limited treatment options and significant side effects from existing therapies, highlighting the urgent need for more effective drug-like molecules. Transforming growth factor-beta receptor 1 (TGF-βR1) is a key player in the pathogenesis of IPF and represents a critical target for therapeutic intervention. In this study, the potential of plant-derived flavonoid and coumarin compounds as novel TGF-βR1 inhibitors was explored. A total of 1206 flavonoid and coumarin derivatives were investigated through a series of computational approaches, including drug-like filtering, virtual screening, molecular docking, 200-ns molecular dynamics (MD) simulations in triplicate, maximum common substructure (MCS) analysis, and absorption-distribution-metabolism-excretion-toxicity (ADMET) profiling. 2',3',4'-trihydroxyflavone and dicoumarol emerged as promising plant-based hit candidates, exhibiting comparable docking scores, MD-based structural stability, and more negative MM/PBSA binding free energy relative to the co-crystallized inhibitor, while surpassing pirfenidone in these parameters and demonstrating superior pharmacological properties. In light of the findings from this study, 2',3',4'-trihydroxyflavone and dicoumarol could be considered novel TGF-βR1 inhibitors for IPF treatment, and it is recommended that their structural optimization be pursued through in vitro binding assays and in vivo animal studies.

METHODS

The initial dataset of 1206 flavonoid and coumarin derivatives was filtered for drug-likeness using Lipinski's Rule of Five in the ChemMaster-Pro 1.2 program, resulting in 161 potential candidates. These compounds were then subjected to virtual screening against the TGF-βR1 kinase domain (PDB ID: 6B8Y) using AutoDock Vina 1.2.5, identifying the top three hit compounds-dicoumarol, 2',3',4'-trihydroxyflavone, and 2',3'-dihydroxyflavone. These hits underwent further exhaustive molecular docking for refinement of docking poses, followed by 200-ns MD simulations in triplicate using the AMBER03 force field in GROMACS. Subsequently, the binding free energies were calculated using the Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) method. MCS analysis was conducted to determine shared structural features among the top three hits, while ADMET properties were predicted using Deep-PK, a deep learning-based platform. Finally, the ligand-protein interactions were further visualized, analyzed, and rendered using ChimeraX, Discovery Studio Visualizer, and Visual Molecular Dynamics (VMD) program.

Structural insights into molecular and cellular level FXR binding potentials of GW4064 and LY2562175 hybrids by multi in silico modelling analyses

CONTEXT

Non-alcoholic fatty liver disease (NAFLD) has become a significant health concern. Existing farnesoid X receptor (FXR) agonists like GW4064 and LYS2562175 show poor pharmacokinetics, prompting researchers to develop alternative molecules. This study aims to pinpoint the structural features responsible for exhibiting FXR agonism of a series of hybrid structures of GW4064 and LYS2562175 with improved pharmacokinetic properties which supersede the existing parent ligands. Electronegative components were found to critically influence biological activity on the molecular level, supported by 2D- and 3D-Quantitative Structure Activity Relationship (2D- and 3D-QSAR) analyses. Quantitative Activity-Activity Relationship (QAAR) highlighted key descriptors impacting cellular level FXR binding potential. Molecular dynamics (MD) simulations identified pivotal interactions, such as π-π and H-bond interactions with key residues. Furthermore, binding free energy calculated with Molecular Mechanics with Generalised Born and Surface Area solvation (MM-GBSA) analyses with selected compounds reflected the variations in their binding potential towards FXR protein.

METHODS

The study began by curating ligand SMILES and preparing a dataset with molecular and cellular activity as dependent variables. AlvaDesc descriptors and interpretable descriptors were calculated using the OCHEM webserver. QSAR analyses were performed using Sequential Forward Selection (SFS) and Genetic Algorithm (GA) methods, while QAAR analysis used 50% effective concentration at the molecular level as an independent variable with the same algorithms. 3D QSAR analysis was performed with the Open3DQSAR tool. Docking studies in AutoDock 4.2 with FXR protein identified optimal ligand poses, and 500 ns MD simulations were performed with Amber 20. The use of open-access tools ensures reproducibility and accessibility for future research.

Computational analysis of antimicrobial peptides targeting key receptors in infection-related cardiovascular diseases: molecular docking and dynamics insights

Infection-related cardiovascular diseases (CVDs) pose a significant health challenge, driving the need for novel therapeutic strategies to target key receptors involved in inflammation and infection. Antimicrobial peptides (AMPs) show the potential to disrupt pathogenic processes and offer a promising approach to CVD treatment. This study investigates the binding potential of selected AMPs with critical receptors implicated in CVDs, aiming to explore their therapeutic potential. A comprehensive computational approach was employed to assess AMP interactions with CVD-related receptors, including ACE2, CRP, MMP9, NLRP3, and TLR4. Molecular docking studies identified AMPs with high binding affinities to these targets, notably Tachystatin, Pleurocidin, and Subtilisin A, which showed strong interactions with ACE2, CRP, and MMP9. Following docking, 100 ns molecular dynamics (MD) simulations confirmed the stability of AMP-receptor complexes, and MM/PBSA calculations provided quantitative insights into binding energies, underscoring the potential of these AMPs to modulate receptor activity in infection and inflammation contexts. The study highlights the therapeutic potential of Tachystatin, Pleurocidin, and Subtilisin A in targeting infection-related pathways in CVDs. These AMPs demonstrate promising receptor binding properties and stability in computational models. Future research should focus on in vitro and in vivo studies to confirm their efficacy and safety, paving the way for potential clinical applications in managing infection-related cardiovascular conditions.

Identification biomarkers and therapeutic targets of disulfidptosis-related in rheumatoid arthritis via bioinformatics, molecular dynamics simulation, and experimental validation

The relationship between disulfidptosis and rheumatoid arthritis (RA) remains unclear. We aimed to identified biomarkers disulfidptosis-related in RA and revealed potential targeted drugs. Two microarray datasets (GSE93272, GSE45291) related to RA were downloaded from the Gene Expression Omnibus (GEO) database. Disulfidptosis-related genes(DRGs) were extracted from FerrDb database. GSE93272 was used to identify DRGs, and GSE45291 was used to verify results. Multivariate Cox regression analysis was used to identify candidate disulfidptosis-associated hub genes. The differentiated values of DRGs were determined by receiver operator characteristic (ROC) monofactor analysis to judge their potential quality as biomarkers. RT-qPCR were used to validate the expression of hub genes. Additionally, we analyzed the connection between the hub genes and the filtration of immune cells in RA. We made predictions about the miRNAs, TFs and possible drugs that regulate the hub genes. Subsequently, molecular docking was carried out to predict the combination of drugs with hub targets. Finally, molecular dynamics simulation was conducted to further verify the findings. Oxoacyl-ACP Synthase Mitochondrial(OXSM) was identified as a biomarker with high diagnostic value, and an RA diagnostic model based on OXSM for a single gene was constructed. The model showed high accuracy in distinguishing RA and healthy controls (AUC = 0.802) and was validated by external datasets, showing excellent diagnostic power (AUC = 0.982). Twelve potential drugs against RA were recognized by comparative toxicogenomics database (CTD). Molecular docking results showed that ICG 001 had the highest binding affinity to OXSM, and molecular dynamics simulations confirmed the stability of this complexes. Furthermore, CIBERSORT analysis showed a significant correlation between immune cell infiltration and OXSM, and a regulatory network of TFs-gene-miRNAs comprising 8 miRNAs and 34 TFs was identified. Finally, the RT-qPCR results showed that OXSM was significantly increased in the peripheral blood of RA patients compared with healthy controls, consistent with the bioinformatics analysis. These studies suggest that OXSM may be a potential biomarker and therapeutic target for diagnosing RA, and ICG 001 may be a potential drug for RA. These findings may provide new avenues for the effective diagnosis and treatment of RA.

Computational study on the mechanism of small molecules inhibiting NLRP3 with ensemble docking and molecular dynamic simulations

NLRP3 (Nucleotide-binding oligomerization domain, LRR and pyrin domain-containing protein 3) is a pivotal regulator of inflammation, with strong implications in gout, neurodegenerative diseases, and various inflammatory conditions. Consequently, the exploration of NLRP3 inhibitors is of great significance for the treatment of diseases. MCC950, NP3-146, compound (3), and YQ128 are four highly bioactive NLRP3 inhibitors that show great potential; however, their mechanism of action is currently limited to targeting the ATP binding region (NACHT site) of the NLRP3 protein. To gain deeper insights into the defining features of NLRP3 inhibitors and to develop more potent inhibitors, it is imperative to elucidate the interaction mechanism between NLRP3 and these inhibitors. In this study, we employ a comprehensive computational approach to investigate the binding mechanism between NLRP3 and representative inhibitors. Utilizing the molecular mechanics/generalized Born surface area (MM/GBSA) method, we calculate the binding free energy and pinpoint the key residues involved in the binding of the four inhibitors to NLRP3. The decomposition of binding free energy by the MM/GBSA method reveals that the residues Val71, Arg195, Ile255, Phe419, Arg422, and Met505, situated around the binding pocket, play a crucial role in conferring the high bioactivity of NLRP3 inhibitors. Furthermore, pharmacophore analysis of the four NLRP3 complexes indicates that the primary interaction between the inhibitors and NLRP3 was mainly hydrophobic interaction. Our study provides a profound understanding of the interaction mechanism between NLRP3 and its inhibitors, identifies the key residues involved, and provides theoretical guidance for the design of more efficient NLRP3 inhibitors.

Taste-masking mechanism of brivaracetam oral solution using cyclodextrin and sodium carboxymethyl cellulose

Brivaracetam is a novel antiepileptic medication that can be indicated for the management of epilepsy in pediatric patients over one month old. To facilitate its administration to children, an oral solution is the most suitable option. However, the inherently bitter taste of brivaracetam poses a challenge in terms of palatability, necessitating the development of a taste masking strategy for the solution. In this study, a palatable brivaracetam oral solution was prepared by meticulously screening various taste masking techniques. Then the interaction relationship between brivaracetam and pivotal excipients (sodium carboxymethyl cellulose (CMC-Na) and 2-Hydroxypropyl-β-cyclodextrin (HP-β-CD)) within the optimized formulation was investigated by molecular dynamics simulations. It turned out that brivaracetam did not encapsulate within HP-β-CD, but instead forms a robust association through hydrogen bonding and π-stacking interactions, facilitated by the presence of CMC-Na. Further exploration through molecular docking elucidated that the optimized formulation effectively masks the bitter taste by diminishing the binding affinity of brivaracetam to bitter taste receptors. In summary, this study achieved taste masking of brivaracetam under solution conditions by investigated the interactions of brivaracetam and key excipient interactions as well as the mechanisms of taste masking of optimized formulations, providing valuable insights for similar pharmaceutical applications.

Encapsulation of menthol by cyclodextrins-comparison between experiments and molecular simulations

Cyclodextrins (CDs) are a traditional wall material for encapsulating flavor ingredients. Given the substantial structural differences among flavor ingredients, experimentally deriving the selection criteria for CDs suitable for these flavor substances is a time-consuming process. However, most existing literature relies on the embedding efficiency from practical experiments to evaluate the binding effect between flavor ingredients and CDs. This article used menthol as the research subject and investigated the binding effects of three different CDs through experiments and computer simulations. The experimental results revealed that β-CD exhibited the optimal encapsulation efficiency (EE, 36.54%) on menthol, subsequently, γ-CD showed a 33.35% EE value, whereas α-CD was unable to form an inclusion complex (IC) with menthol. Conformation changes, root mean square deviation (RMSD), radius of gyration (Rg), Radial distribution function (RDF), solvent accessible surface area (SASA), and hydrogen bonds, and binding free energy were analyzed through molecular dynamics simulation and compared with the experimental results. The results indicated that the IC formed between β-CD and menthol (menthol/β-CD-IC) is the most stable, with a binding free energy (ΔGbind) of -7.27 kcal/mol. The IC formed between α-CD and menthol (menthol/α-CD-IC) is the least stable one (ΔGbind = 2.59 kcal/mol). The results revealed a high degree of consistency between the experimental outcomes and those of molecular simulation, so molecular simulation can serve as a more efficient screening method, an alternative to practical experiments, to obtain the combination ability between host-guest molecules.

Formononetin: a review of its source, pharmacology, drug combination, toxicity, derivatives, and drug delivery systems

Formononetin (FMN) is a common natural metabolite that can be extracted and isolated from some common botanical drugs. In recent years, FMN has garnered increasing attention due to its beneficial biological activities. In this paper, we systematically summarize the sources of FMN and provide a comprehensive review of its pharmacological activities and molecular mechanisms, co-administration, toxicity, derivatives, and drug delivery systems in the last 5 years. The study results found that FMN has a wide range of pharmacological activities in neurological disorders, organ damage and cancer, showing great potential for clinical application and broad prospects. Researchers are exploring various types of delivery systems, including nanoparticle carriers, ligand modifications and polymer microspheres. These advanced delivery systems can enhance the stability of FMN, prolong its release time in vivo, and improve targeting, thereby optimizing its therapeutic efficacy and reducing side effects, and greatly improving its bioavailability. In conclusion, FMN is a natural metabolite with considerable research value, and its diverse biological activities make it a promising candidate for drug development and medical research.

Computer-aided drug repurposing & discovery for Hepatitis B capsid protein

The primary objective of this study is to harness computer-aided drug repurposing (CADR) techniques to identify existing FDA-approved drugs that can potentially disrupt the assembly of the Hepatitis B Virus (HBV) core protein (HBcAg), an essential process in the virus's life cycle. By targeting this critical step, our study aims to expand the repertoire of therapeutic options for managing chronic Hepatitis B infection, a major global health challenge. Utilizing a combination of computational methods, including the CavityPlus server for ability to analyze druggable protein cavities and extract pharmacophore features and LigandScout for pharmacophore-based virtual screening of a vast library of FDA-approved drugs was conducted. Molecular dynamic simulation (MDS) was employed to evaluate the stability of HBcAg, complexed with Heteroaryldihydropyrimidine (HAP) and statins exhibiting particularly strong binding energies and conformational compatibility. Our approach focused on identifying pharmacophore features that align with known HBcAg inhibitors. The study identified several promising candidates, including Ciclopirox olamine, Voriconazole, Enasidenib, and statins, demonstrating potential interactions with HBc protein residues. Molecular docking further validated these interactions. The significance of these findings lies in their potential to offer new, effective therapeutic strategies for HBV treatment, particularly as alternatives to current therapies that often suffer from issues of viral resistance and adverse side effects. MDS analysis verified the robustness of HAP and statins by showing a high level of binding energies and compatibility with HBcAg. Our results provide a foundation for further experimental validation and underscore the utility of computer-aided drug repurposing as a rapid, cost-effective approach to drug discovery in antiviral research. This study contributes to our understanding of HBV biology and opens avenues for developing novel anti-HBV therapies based on repurposed drugs. The highlighted compound may also enhance the challenges of drug resistance when used as a combination therapy.

Discovery of novel inhibitors of dengue viral RNA-dependent RNA polymerase by molecular docking, in vitro assay, DFT, and MD simulations

Dengue virus (DENV) is a significant significant mosquito-borne pathogen. Its RNA-dependent RNA polymerase (RdRp) plays a crucial role in viral replication, making it a critical target for antiviral drug development. The goal of this study was to identify potential inhibitors of the DENV RdRp through virtual screening and experimental assays. In this study, based on Topscience and TargetMol database. 47 compounds were stand out from 1.1 million compounds with high binding energies between -77.24 kcal/mol and-44.08 kcal/mol by initial virtual screening. Their inhibition activity against dengue virus was evaluated by cell-based antiviral and RdRp enzyme assays, and 4 compounds (R2, R29, R37, and R39) identified in our study demonstrated promising in vitro activity, with IC₅₀ values of less than 10 μM, indicating their strong potential as antiviral agents against DENV. The RdRp enzyme inhibition assay revealed that R37 demonstrated significant activity against the DENV RdRp enzyme, with an IC₅₀ of 10.86 ± 2.06 μM, which was lower than that of 3'-dATP (IC₅₀ = 30.09 ± 8.26 μM). These 4 compounds were further subjected to DFT calculations and MD simulation, which not only provided valuable structural insights but also enhanced the reliability of our findings by offering a detailed understanding of the stability and binding interactions of the top compounds with the DENV RdRp enzyme. These results suggest that the identified compounds are promising candidates for novel DENV RdRp inhibitors and provide both theoretical and experimental groundwork for further optimization and validation.

In silico pentapeptide design for the inhibition between S100 calcium-binding A9 (S100A9) proteins

CONTEXT

S100 calcium-binding protein A9 (S100A9) is easily assembled into amyloid aggregates in solution. These amyloid aggregates cause retinal toxicity and act as an attachment core for Aβ fibrillar plaques that contribute to Alzheimer's disease progression. The overexpression of S100A9 is also noticed in various malignancies. Therefore, the S100A9 amyloid formation inhibition is of significant interest. In comparison with small-molecule drugs, short peptides demonstrate higher specificity, potency, and biosafety. Hence, it could be beneficial to identify potential peptides to inhibit or disrupt S100A9 amyloid aggregation. Typical peptide design and identification via experimental means requires extensive preparation procedures and is limited to random selection of peptides. Virtual screening therefore offers an unbiased, higher throughput, and economically efficient approach in peptide drug development. Here, we reported in silico pentapeptide design against S100A9 and studied the interaction of pentapeptide with S100A9 that leads to the binding of the peptide with S100A9.

METHOD

Docking simulation resulted in three top binding free energy tripeptides (WWF, WPW, and YWF) with comparable affinity towards a known S100A9 inhibitor (polyphenol oleuropein aglycone; OleA). Subsequently, pentapeptides that consist of the three core tripeptides were selected from a pre-constructed pentapeptide library for further evaluation with docking simulation. Based on best docked binding free energy, two pentapeptides (WWPWH and WPWYW) were selected and subjected to 500 ns molecular dynamics (MD) simulation to study the important features that lead to the binding with S100A9. MMGBSA binding free energy calculation estimated - 30.38, - 24.58, and - 30.31 kcal/mol for WWPWH, WPWYW, and OleA, respectively. The main driving force for pentapeptide-S100A9 recognition was contributed by the electrostatic interaction. The results demonstrate that at in silico level, this workflow is able to design potential pentapeptides that are comparable with OleA and might be the lead molecule for future use to disaggregate S100A9 fibrils.

Curcumin as a potential inhibitor of TGFβ3 computational insights for breast cancer therapy

Previous research indicates that Transforming growth factor beta-3 (TGFβ3) expression levels correlate with breast cancer metastasis, and elevated TGFβ3 levels have been linked with poor overall survival in breast cancer patients. The study used computational methods to examine curcumin's effects on TGFβ3, a chemical with antiviral and anticancer characteristics. The curcumin has low Molecular Weight 368.130 (MW) and follows Lipinski Rule, Pfizer Rule, GSK Rule, Golden Triangle, BMS Rule, zero PAINS alert and Acute Toxicity Rule with zero alert. Any drug-like contender must follow these qualities. Through molecular docking analyses, curcumin displayed favourable binding affinities at the TGFβ3 binding pocket, forming key interactions such as hydrogen bonds with residues like ASP323, ARG325, VAL333, HIS334, PRO336, LYS337, GLY393, and ARG394. 500 ns molecular dynamic simulations examined docking interactions. Molecular dynamics (MD) simulations trajectories analysis, by calculating lower structural deviation, minimal residual fluctuations, structural compactness assessment by calculating radius of gyration, surface area calculation which interact with solvent, role of hydrogen bonding, and secondary structural analyses. Furthermore, principal component, Gibbs free energy landscape and MMPBSA analysis, signifying system stability. These data suggest curcumin may inhibit TGFβ3, providing a framework for developing new compounds targeting this protein.

Assessment of the usefulness of β-cyclodextrin in the removal of progesterone from the environment

The paper presents the results and interpretation of theoretical calculations for the progesterone-β-cyclodextrin (P@β-CD; G4MP2) and progesterone-β-cyclodextrin-β-cyclodextrin (P@β-CD-β-CD; G2) systems. The geometry of the progesterone molecule was optimized on basis of the DFT theory using the B3LYP, PBE1PBE and M06-2X functionals, for selected Pople basis sets [6-31G, 6-31++G, 6-31++G(d,p), 6-311G, 6-311++G, 6-311++G(d,p)] and the Dunning basis set (aug-cc-pVDZ). Presented results of theoretical calculations provide insight into the mechanism of formation of supramolecular systems of progesterone and β-cyclodextrin, allowing us to understand the impact of differences in the polarizability of specific fragments of the "guest" molecule, through the analysis of the Mulliken population distribution, on the tendency for equilibrium inclusion by "host" molecules characterized by selective affinity towards hydrophilic and hydrophobic molecular systems. The comparison of model structures of "guest-host" systems with 1:1 and 1:2 stoichiometry allows us to assess the contribution of a given type of non-covalent interactions (hydrogen bonds, van der Waals interactions, London dispersion forces) in the formation of supramolecular complexes. Due to the complexity of the real research object, including interactions between large molecules in solution, in this work it was decided to choose an approximation that reflects only the key effects. The results presented in this paper constitute a starting point for both theoretical research on analogous supramolecular systems based on β-cyclodextrin derivatives, as well as instrumental studies (NMR, FT-IR, HPLC) of preparations of real inclusion complexes. The approach adopted now can contribute to a better understanding of the phenomenon used in the development of water purification technologies.

Efficient glycosylation of polyphenols via dynamic complexation of cyclodextrin and synchronous coupling reaction with cyclodextrin glycosyltransferase in water

Glycosylation is an effective way to promote the total intake of polyphenols in humans by increasing the solubility of polyphenols. In this study, an efficient glycosylation system was built via the dynamic complexation of CD with polyphenols and synchronous coupling reaction with cyclodextrin glycosyltransferase (CGTase) in water. The glycosylation efficiencies of quercetin, naringenin, rutin, resveratrol and caffeic acid were 20.9, 3.6, 2.7, 3.4 and 1.5 times higher than the non-complexed system. To quantify conversion rate and determine the rate-limiting step, the mixed product was treated with amyloglucosidase to obtain α-glucosyl rutin, which was identified as rutin 4"-O-α-D-glucopyranoside with purity of 93.6 % and yield of 34.8 % from NMR, MS and HPLC analysis. The results of half-reaction kinetics showed that the catalytic efficiencies of ring-opening of γ-CD (k1) and glycosylation reaction of rutin (k2) were 621.92 and 9.43 mM-1·s-1. The rate-limiting step was clarified for the first time, showing that the ring-opening ability of CGTase to CD was much higher than its glycosylation ability to polyphenols. It is speculated that the rapid ring-opening reaction of CD affected its dynamic complexation, releasing many polyphenols which were not utilized by CGTase in time. Therefore, adjusting the ratio and concentration of CD resulted in an optimal glycosylation molar yield of 84.1 % for rutin, which was the highest yield reported so far in water. This study established a universal system and clarified the rate-limiting step in the enzymatic glycosylation, providing theoretical guidance for efficient production of polyphenol glycosylation.

Formononetin-Loaded Self-Microemulsion Drug Delivery Systems for Improved Solubility and Oral Bioavailability: Fabrication, Characterization, In Vitro and In Vivo Evaluation

This study aimed to construct a self-microemulsion drug delivery system (SMEDDS) for Formononetin (FMN) to improve its solubility and bioavailability while combining the nanocrystals (NCs) technology. The SMEDDS prescription composition was optimized with a pseudo-three-phase diagram, followed by a series of in vitro and in vivo evaluations of the selected optimal prescriptions. FMN-NCs loaded SMEDDS showed a homogeneous spherical shape in the Transmission electron microscope and the particle size was measured as (20.65 ± 1.42) nm. The in vitro cumulative release rate in each dissolution medium within 30 min was higher than 80%, much higher than that of FMN (6%) and FMN-NCs (40%); Cellular experiments confirm that the formulation has a high safety profile and significantly promotes cellular uptake. The results of pharmacokinetics and intestinal absorption in rats showed that the relative bioavailability of FMN-NCs and FMN-NCs loaded SMEDDS were (154.80 ± 3.76)% and (557.73 ± 32.88)%, respectively, and both of them significantly increased the rate and extent of absorption of the drug in intestinal segments. FMN-NCs loaded SMEDDS significantly enhanced the solubility and bioavailability of FMN.

Preparation, structural analysis of alcohol aroma compounds/β-cyclodextrin inclusion complexes and the application in strawberry preservation

The dynamic combination of aromas and cyclodextrins is an important means to achieve their stability and controllability, and accurately revealing their interaction rules is the key to designing and constructing high-quality aroma nanocarriers. In this study, the inclusion mechanism between alcohol aroma compounds with different structures and β-cyclodextrin (β-CD) was studied by combining molecular dynamics simulation and experimental methods. Results showed that the selected alcohol aroma compounds formed inclusion complexes (ICs) with β-CD in a 1:1 ratio, while alcohol aroma compounds containing cyclic structures were more tightly bound to β-CD. Van der Waals forces were the primary forces driving the formation and stabilization of the ICs. Cinnamyl alcohol/β-CD ICs showed the most significant antimicrobial effect and notably prolonged the shelf life of strawberries. This study aimed to provide theoretical support for precisely designing and preparing highly stable flavours and fragrances, as well as expanding their application range.

Computational and experimental analysis of Luteolin-β-cyclodextrin supramolecular complexes: Insights into conformational dynamics and phase solubility

Investigating the structural stability of poorly-soluble luteolin (LuT) after encapsulation within cyclodextrins (CDs) is crucial for unlocking the therapeutic potential of LuT bioactive molecule. Herein, native and modified β-CD were employed to investigate LuT inclusion complex formation. Molecular mechanics (MM) and quantum mechanics (QM) were utilized for structural dynamics analysis. Microsecond timescale MD simulations yielded insights into LuT-CD interactions. The binding affinity between LuT and selected β-CDs was assessed by calculating the binding free energy using MM-PBSA and umbrella sampling simulations. The MM-PBSA results indicated that Heptakis-O-(2-hydroxypropyl)-β-CD (HP-β-CD) (-82.59+/-11.67 kJ/mol) and Di-O-methyl-β-CD (DM-β-CD) (-54.01+/-11.07 kJ/mol) exhibited good binding affinity for LuT. Subsequently, derivative screening of HP-β-CD revealed that only 2-HP-β-CD (HP-β-CD-1)/LuT (-21.38 kJ/mol) displayed a superior binding free energy (obtained from umbrella sampling) than HP-β-CD/LuT (-19.15 kJ/mol) inclusion complex. We conducted QM calculations on the top three complexes namelly HP-β-CD, DM-β-CD, and HP-β-CD-1 employing wB97X-D/6-311 + G(d,p) model chemistry to strengthen the MM results. The computational analysis aligns with experimental findings (phase solubility analysis), validating HP-β-CD-1 as most effective cavitand molecule for improving the solubility of LuT. This study offers critical structural insights for developing novel HP-β-CD derivatives with enhanced host capacity to encapsulate guest molecules efficiently.

Driving forces and large scale affinity calculations for piperine/γ-cyclodxetrin complexes: Mechanistic insights from umbrella sampling simulation and DFT calculations

Piperine (PiP), a bioactive molecule, exhibits numerous health benefits and is frequently employed as a co-delivery agent with various phytomedicines (e.g., curcumin) to enhance their bioavailability. This is attributed to PiP's inhibitory activity against drug-metabolizing proteins, notably CYP3A4. Nevertheless, PiP encounters solubility challenges addressed in this study using cyclodextrins (CDs). Specifically, γ-CD and its derivatives, Hydroxypropyl-γ-CD (HP-γ-CD), and Octakis (6-O-sulfo)-γ-CD (Octakis-S-γ-CD), were employed to form supramolecular complexes with PiP. The conformational space of the complexes was assessed through 1 μs molecular dynamics simulations and umbrella sampling. Additionally, quantum mechanical calculations using wB97X-D dispersion-corrected DFT functional and 6-311 + G(d,p) basis set were conducted on the complexes to examine the thermodynamics and kinetic stability. Results indicated that Octakis-S-γ-CD exhibits superior host capabilities for PiP, with the most favorable complexation energy (-457.05 kJ/mol), followed by HP-γ-CD (-249.16 kJ/mol). Furthermore, two conformations of the Octakis-S-γ-CD/PiP complex were explored to elucidate the optimal binding orientation of PiP within the binding pocket of Octakis-S-γ-CD. Supramolecular chemistry relies significantly on non-covalent interactions. Therefore, our investigation extensively explores the critical atoms involved in these interactions, elucidating the influence of substituted groups on the stability of inclusion complexes. This comprehensive analysis contributes to emphasizing the γ-CD derivatives with improved host capacity.

High-throughput virtual screening of potential inhibitors of GPR52 using docking and biased sampling method for Huntington's disease therapy

Huntington's disease (HD) is a rare and progressive neurodegenerative disorder caused by polyglutamine (poly-Q) mutations of the huntingtin (HTT) gene resulting in chorea, cognitive, and psychiatric dysfunctions. Being a monogenic condition, reducing the levels of the mutated huntingtin protein (mHTT) holds promise as an effective therapeutic approach. GPR52, an orphan G-protein coupled receptor (GPCR), enriched in the striatum, is a novel target for slowing down the progression of HD by lowering the mHTT levels. Therefore, the study focuses on identifying potent small-molecule inhibitors for GPR52 using a combination of robust high-throughput virtual screening (HTVS) and pharmacokinetics profiling followed by fast pulling of ligand (FPL) and umbrella sampling (US) simulations. Initially, screening a library of 2,36,545 compounds was done against the binding pocket of GPR52. Based on binding affinity, stereochemical and non-bonded interactions, and pharmacokinetic profiling, 50 compounds were shortlisted. Selected hit compounds 1, 2, and 3 were subjected to FPL simulations with applied external bias potential to investigate their unique dissociation pathways and intermolecular interactions over time. Subsequently, the US simulations were performed on the selected hit compounds to estimate their binding free energy (ΔG). The analysis of the trajectories obtained from simulations revealed that the residues TYR34, TYR185, GLY187, ASP188, ILE189, SER299, PHE300, and THR303 within the active site of GPR52 were significant for efficient ligand binding through the formation of various hydrogen bond interactions and hydrophobic contacts. Out of the three hit compounds, compound 3 had the lowest ΔG of - 20.82 ± 0.44 kcal/mol. The study identified compounds 1, 2, and 3 as potential molecules that can be developed as GPR52 inhibitors holding promise for lowering mHTT levels.

β-Cyclodextrin-based nanoassemblies for the treatment of atherosclerosis

Atherosclerosis, a chronic and progressive condition characterized by the accumulation of inflammatory cells and lipids within artery walls, remains a leading cause of cardiovascular diseases globally. Despite considerable advancements in drug therapeutic strategies aimed at managing atherosclerosis, more effective treatment options for atherosclerosis are still warranted. In this pursuit, the emergence of β-cyclodextrin (β-CD) as a promising therapeutic agent offers a novel therapeutic approach to drug delivery targeting atherosclerosis. The hydrophobic cavity of β-CD facilitates its role as a carrier, enabling the encapsulation and delivery of various therapeutic compounds to affected sites within the vasculature. Notably, β-CD-based nanoassemblies possess the ability to reduce cholesterol levels, mitigate inflammation, solubilize hydrophobic drugs and deliver drugs to affected tissues, making these nanocomponents promising candidates for atherosclerosis management. This review focuses on three major classes of β-CD-based nanoassemblies, including β-CD derivatives-based, β-CD/polymer conjugates-based and polymer β-CD-based nanoassemblies, highlighting a variety of formulations and assembly methods to improve drug delivery and therapeutic efficacy. These β-CD-based nanoassemblies exhibit a variety of therapeutic mechanisms for atherosclerosis and offer systematic strategies for overcoming barriers to drug delivery. Finally, we discuss the present obstacles and potential opportunities in the development and application of β-CD-based nanoassemblies as novel therapeutics for managing atherosclerosis and addressing cardiovascular diseases.

Hyaluronic acid-based multifunctional bio-active coating integrated with cinnamaldehyde/hydroxypropyl-β-cyclodextrin inclusion complex for fruit preservation

Natural preservatives such as cinnamaldehyde (CIN) are garnering increasing interest to replace their synthetic counterparts in maintaining fruit freshness and safety. However, their long-term effectiveness and widespread application have been greatly limited due to high volatility and potent aroma. To address these challenges, we developed a viable and simple strategy to prepare a multifunctional active coating for fruit preservation by incorporating host-guest inclusion complex of CIN and 2-hydroxypropyl-β-cyclodextrin (HP-β-CD) CIN@HP-β-CD into hyaluronic acid (HA), a natural polysaccharide with exceptional film-forming properties. The as-prepared HA/CIN@HP-β-CD coatings exhibited universal surface affinity, excellent antimicrobial performance, and satisfactory antioxidant properties with no potential toxicity. Release kinetic studies have demonstrated that CIN in the coating is continuously and slowly released. Furthermore, freshness preservation experiments on bananas and fresh-cut apples demonstrated that the developed coating is effective in preserving the color of fruit, decreasing the weight loss rate, preventing the microorganism's growth, and significantly extending the period of freshness, exhibiting the potential for application in fruit preservation.

Designing and preparing supramolecular encapsulation systems based on fraxetin and cyclodextrins for highly selective detection of nicotine

Herein, a series of water-soluble supramolecular inclusion complexes (ICs) probes were prepared using cyclodextrins (CDs) and fraxetin (FRA) to detect nicotine (NT) with high selectivity in vitro and in vivo. The FRA/CD ICs prepared through the saturated solution method exhibited excellent water solubility, stability, and biocompatibility. A clear host-guest inclusion model was provided by the theoretical calculations. The investigation revealed that NT was able to enter into the cavities of FRA/β-CD IC and FRA/γ-CD IC, and further formed charge transfer complexes with FRA in the CD cavities, resulting in a rapid and highly selective fluorescence-enhanced response with the lowest detection limits of 1.9 × 10-6 M and 9.7 × 10-7 M, and the linear response ranged from 0.02 to 0.3 mM and 0.01-0.05 mM, respectively. The IC probes showed good anti-interference performance to common interferents or different pH environments, with satisfactory reproducibility and repeatability of response to NT. Furthermore, the potentiality of the probes was confirmed through fluorescence imaging experiments using human lung cancer cells and the lung tissue of mice. This study offers a fresh perspective for detecting NT in environmental and biomedical analysis.

New insights into the influence of encapsulation materials on the feasibility of ultrasonic-assisted encapsulation of Mosla chinensis essential oil

The study aimed to estimate the feasibility of α-cyclodextrin (α-CD), β-cyclodextrin (β-CD), and γ-cyclodextrin (γ-CD) to encapsulate Mosla chinensis essential oil (EO) by ultrasonic-assisted method. The physical properties variations, stabilization mechanisms, and formation processes of the inclusion complexes (ICs) were investigated using experimental methods, molecular docking, and molecular dynamics (MD) simulation. Scanning electron microscopy, fourier transform infrared spectroscopy, thermogravimetric analysis, and gas chromatography-mass spectrometry showed that the ICs were successfully prepared, which differentially improved the thermal stability and retained the chemical composition of EO. The dissolution profile showed that the Peppas model can be used to describe the diffuse release mechanism of EO. Finally, molecular docking and MD simulation theoretically confirmed the interaction and conformational changes of carvacrol (the main active component of Mosla chinensis EO) inside the cavity of CDs. The results indicate that hydrogen bonding was the primary driving force for the carvacrol spontaneous access to the cavity. Further, a binding dynamic balance occurs between carvacrol and β-CD, whereas a bind and away dynamic balance occurs in the IC between carvacrol and α-CD, γ-CD. The comprehensive results show that the medium cavity size of β-CD is a suitable host molecule for Mosla chinensis EO of encapsulation, release, and stabilization. A combination of experimental and theoretical calculations is useful for the pinpoint targeted design and optimization of CD molecular encapsulation of small entity molecules. β-CD was rationally screened as a better candidate for stabilizing EO, which provides an option for a meaningful path to realistic EO applications.

Highly robust quantum mechanics and umbrella sampling studies on inclusion complexes of curcumin and β-cyclodextrin

The poor aqueous solubility of curcumin (CUR) obstructs its wide utilization in nutraceuticals, cosmetics, and pharmaceutical companies. This study is dedicated to investigate the stability of CUR inside the hydrophobic pocket of β-cyclodextrin (β-CD), hydroxypropyl-β-CD (HP-β-CD), and 2,6-Di-O-methyl-β-CD (DM-β-CD). Initially, molecular mechanics (MM) calculations and subsequently quantum mechanical (QM) calculations were performed on inclusion complexes to strengthen the MM results. We performed microsecond timescale MD simulations to observe the structural dynamics of CUR inside the cavity of CDs. We elucidated the most stable binding orientations of CUR inside the cavity of CDs based on binding free energy obtained from the Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) and umbrella sampling simulations. Furthermore, the two-layered ONIOM (B3LYP/6-311+G(2d,p):PM7) method with CPCM implicit water model was used to derive the complete energetics and thermodynamics of inclusion complexes at 1:1 stoichiometry. Each inclusion reaction was exothermic and spontaneous. The chemical reactivity and kinetic stability of inclusion complexes were described by HOMO-LUMO molecular orbital energies. In conclusion, our studies revealed that HP-β-CD had the highest binding affinity for CUR with the most negative complexation energy (-6520.69 kJ/mol) and Gibb's free energy change (-6448.20 kJ/mol). The atomic-level investigation of noncovalent interactions between CUR and the hydroxypropyl groups in HP-β-CD/CUR complex may be helpful to drive new derivatives of HP-β-CD with better host capacity. The computational strategy adopted here might serve as a benchmark for increasing the solubility of numerous clinically significant molecules.

Synthesis of Formononetin Derivatives and Cardioprotective Effects

This study aims to design and synthesize a series of novel formononetin (FMN) derivatives and explore their protective effects on oxygen glucose deprivation/relapse (OGD/R) damage to H9C2 cells, along with their molecular regulatory mechanisms. The OGD/R model was established to simulate myocardial ischemia-reperfusion injury. The protective effects of these novel compounds on H9C2 cells were evaluated using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method, while the apoptosis rate, myocardial enzyme activity, and autophagy reaction post-compound treatment were assessed using kit-based methods. The formation of autophagosomes in H9C2 cells was observed via transmission electron microscopy, and the expression levels of autophagy-related proteins phosphatidylinositol 3-kinase (PI3K), Akt, Beclin-1, and P62 were determined using Western blotting. The experimental findings demonstrated that compounds 1-6 (C1-6) exhibited varying degrees of protective effects on damaged H9C2 cells, generally outperforming the parent compound FMN. Among these compounds, C4 demonstrated the most significant activity, even surpassing the positive control drug diltiazem. Further mechanistic investigations revealed that C4 could mitigate apoptosis rates, reduce the activity of myocardial enzyme (such as aspartate aminotransferase (AST), lactate dehydrogenase (LDH), and CK), diminish the number of autophagic vesicles, and restore excessive autophagy. Additionally, C4 exerted its protective effects by downregulating the expression of autophagic proteins PI3K, Akt, Beclin-1, P62, LC3 and ATG12. These results indicated that C4 regulates autophagy through the PI3K/Akt/Beclin-1 signaling pathway, thereby exerting a protective effect on cardiomyocytes. Therefore, C4 emerges as a potential myocardial protective drug, offering a new research direction and strategy for the treatment of myocardial ischemia-reperfusion injury.

Nearly complete structure of bacteriophage DT57C reveals architecture of head-to-tail interface and lateral tail fibers

The T5 family of viruses are tailed bacteriophages characterized by a long non-contractile tail. The bacteriophage DT57C is closely related to the paradigmal T5 phage, though it recognizes a different receptor (BtuB) and features highly divergent lateral tail fibers (LTF). Considerable portions of T5-like phages remain structurally uncharacterized. Here, we present the structure of DT57C determined by cryo-EM, and an atomic model of the virus, which was further explored using all-atom molecular dynamics simulations. The structure revealed a unique way of LTF attachment assisted by a dodecameric collar protein LtfC, and an unusual composition of the phage neck constructed of three protein rings. The tape measure protein (TMP) is organized within the tail tube in a three-stranded parallel α-helical coiled coil which makes direct contact with the genomic DNA. The presence of the C-terminal fragment of the TMP that remains within the tail tip suggests that the tail tip complex returns to its original state after DNA ejection. Our results provide a complete atomic structure of a T5-like phage, provide insights into the process of DNA ejection as well as a structural basis for the design of engineered phages and future mechanistic studies.

Enhancing Anticancer Efficacy of Formononetin Microspheres via Microfluidic Fabrication

Formononetin is a flavonoid compound with anti-tumor and anti-inflammatory properties. However, its low solubility limits its clinical use. We employed microfluidic technology to prepare formononetin-loaded PLGA-PEGDA microspheres (Degradable polymer PLGA, Crosslinking agent PEGDA), which can encapsulate and release drugs in a controlled manner. We optimized and characterized the microspheres, and evaluated their antitumor effects. The microspheres had uniform size, high drug loading efficiency, high encapsulation efficiency, and stable release for 35 days. They also inhibited the proliferation, migration, and apoptosis. The antitumor mechanism involved the induction of reactive oxygen species and modulation of Bcl-2 family proteins. These findings suggested that formononetin-loaded PLGA-PEGDA microspheres, created using microfluidic technology, could be a novel drug delivery system that can overcome the limitations of formononetin and enhance its antitumor activity.

Dispersion-corrected DFT calculations and umbrella sampling simulations to investigate stability of Chrysin-cyclodextrin inclusion complexes

The study of inclusion complexes of Chrysin (ChR) with three forms of cyclodextrins (CDs) α-, β-, and γ-CD was accomplished to examine the stability of ChR inside the central cavities of CDs. The aim of study was to identify the most suitable form of CD to improve the hydro-solubility of poorly soluble ChR bioactive molecule. Microsecond timescale molecular dynamics (MD) simulations were performed on four inclusion complexes (α-CD/ChR, β-CD/ChR, and two conformations of γ-CD/ChR) to examine the dynamics of ChR inside the cavity of CDs. The first conformation of γ-CD/ChR inclusion complex (γ-CD1/ChR) was identified to possess the highest affinity between host and guest molecule on the basis of binding energy calculated by employing Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) and umbrella sampling simulations. To further strengthen the claims of classical and biased MD studies, Our own N-layered Integrated molecular Orbital and Molecular mechanics (ONIOM) (wB97XD/6-311+g(d,p):pm7) calculations were performed on the selected inclusion complexes. The ONIOM based complexation energy reaffirmed that ChR had highest affinity for the γ-CD1 host molecule. Further, the non-covalent interaction analysis was conducted using Multiwfn software on QM-optimized inclusion complexes with wB97XD/6-311+G(d,p) model chemistry, revealing non-covalent interactions between ChR and CDs. This atomic level information helped us to gain better insights into critical atoms of ChR and CD that participated in intermolecular interactions and identify γ-CD as a suitable host molecule for improving the hydro-solubulity of ChR. The structural insights would help to derive new derivatives of γ-CD with better host capacity.

Bidirectional crosstalk of the cAMP/ROS-dependent signaling pathways in inflammatory macrophage: An activation of formononetin

Bacterial lipopolysaccharide (LPS) is a toxic stimulant to macrophage inflammation. Inflammation intersects cell metabolism and often directs host immunopathogenesis stress. We aim here at pharmacological discovering of formononetin (FMN) action, to which anti-inflammatory signaling spans across immune membrane receptors and second messenger metabolites. In ANA-1 macrophage stimulated by LPS, and simultaneous treatment with FMN, results show the Toll-like receptor 4 (TLR4) and estrogen receptor (ER) signals, in concert with reactive oxygen species (ROS) and cyclic adenosine monophosphate (cAMP), respectively. LPS stimulates inactivation of the ROS-dependent nuclear factor erythroid 2-related factor 2 (Nrf2) by upregulating TLR4, but it does not affect cAMP. However, FMN treatment not only activates Nrf2 signaling by TLR4 inhibition, but also it activates cAMP-dependent protein kinase activities by upregulating ER. The cAMP activity gives rise to phosphorylation (p-) of protein kinase A, liver kinase B1 and 5'-AMP activated protein kinase (AMPK). Moreover, bidirectional signal crosstalk is amplified between p-AMPK and ROS, as FMN combinational validation with AMPK activator/inhibitor/target small-interfering RNA or ROS scavenger. The signal crosstalk is well positioned serving as the 'plug-in' knot for rather long signaling axis, and the immune-to-metabolic circuit via ER/TLR4 signal transduction. Collectively, convergence of the FMN-activated signals drives significant reduction of cyclooxygenase-2, interleukin-6 and NLR family pyrin domain-containing protein 3, in LPS-stimulated cell. Although anti-inflammatory signaling is specifically related to the immune-type macrophage, the p-AMPK antagonizing effect arises from FMN combination with ROS scavenger H-bond donors. Information of our work assists in predictive traits against macrophage inflammatory challenges, using phytoestrogen discoveries.