Density functional theory (DFT), molecular docking, and xanthine oxidase inhibitory studies of dinaphthodiospyrol S from Diospyros kaki L

Targeting quorum sensing in Pseudomonas aeruginosa with high-affinity inhibitors: A high-throughput screening and in-silico analysis

Pseudomonas aeruginosa is a major pathogen in clinical settings, notorious for its intrinsic resistance to multiple antibiotics and ability to form biofilms, therefore, complicating treatment. This study reporting the results of a high-throughput screen of an antibacterial library targeting LasR, a key QS regulator in P. aeruginosa MB638, isolated from an infected surgical implant. The species identity was confirmed as P. aeruginosa via 16S rDNA analysis (accession number MT643188). The strain demonstrated strong biofilm formation and multidrug resistance, along with significant production of the quorum sensing signalling molecule N-(3-oxododecanoyl)-L-homoserine lactone (OdDHL). We screened a ∼1400-compound library and identified inhibitors compounds that surpass the binding affinity of LasR's native ligand. The ADMET analysis revealed that among these, compounds Inh-1, Inh-2 and Inh-3 demonstrated favourable absorption, permeability and broader bioactivity profiles. Inh-1 exhibited a suitable profile, being non-toxic, non-hepatotoxic, and non-mutagenic, with low carcinogenic and immunotoxin potential. Molecular docking studies using GLIDE identified key binding interactions and residues within the LasR ligand-binding domain (LBD), with Inh-1, Inh-2 and Inh-3 showing the highest binding affinities and favourable docking scores of -14.587, -13.645 and -12.967, respectively. Structural Interaction Molecular dynamics simulation at 100 ns showed Inh-1 maintained stable hydrophobic and hydrophilic contacts within the active site. RMSD analysis confirmed the stability of the Inh-1 complex, while RMSF indicated conformational adaptability. Inh-1 stands out as promising lead for LasR inhibition, warranting further experimental study. These inhibitors hold promise for disrupting quorum sensing in P. aeruginosa and may serve as potential therapeutic agent against resistant infections.

Chromene flavanones from Dalea boliviana as xanthine oxidase inhibitors: in vitro biological evaluation and molecular docking studies

Background

Prenylated flavanones represent a structurally diverse class of natural compounds with significant biological potential. Among them, chromene flavanones (CFs) constitute a rare and specialized subgroup with promising therapeutic applications. These molecules have gained attention due to their potential to inhibit xanthine oxidase (XO), a key enzyme involved in oxidative stress-related disorders such as gout and hyperuricemia. Their distinctive structural features, combined with notable bioactivity, make them compelling candidates for further pharmacological exploration. Given their potential relevance, this study focuses on the in vitro and in silico evaluation of three CFs isolated from Dalea boliviana Britton [Fabacea], assessing their capacity to inhibit XO and elucidating key structure-activity relationships (SARs) that contribute to their biological effectiveness.

Purpose

This study aims to investigate the in vitro and in silico interactions of the chromene flavanones, namely, (2S) 5,2'-dihydroxy-6″,6″-dimethylchromeno-(7,8:2″,3″)-flavanone (1), (2S) 5,2'-dihydroxy-6″,6″-dimethylchromeno-(7,8:2″,3″)-3'-prenylflavanone (2), and obovatin (3), obtained from D. boliviana, with XO, in order to explore their potential as XO inhibitors and their potential therapeutic applications for hyperuricemic diseases.

Material and Methods

XO inhibition by the three chromene flavanones was measured spectroscopically. The relationships between their structures and inhibitory activities were evaluated. Moreover, molecular docking studies were performed to propose the binding modes of the most active natural compounds.

Results and discussion

Compounds 1 and 2 exhibited potent inhibition, with IC50 values in the nanomolar range (0.5 ± 0.01 nM and 1.7 ± 0.46 nM, respectively), demonstrating significantly higher activity than allopurinol (AL), the reference inhibitor (IC50 = 247 ± 4 nM). In contrast, compound 3 displayed only weak inhibition. SAR analysis revealed that the presence of a chromene moiety in the A-ring, combined with hydroxyl and prenyl groups in the B-ring, played a crucial role in enhancing inhibitory activity. Molecular docking studies confirmed the strong binding affinities of compounds 1 and 2 within the active site of XO (PDB ID: 3NVY), with binding energies of -6.1687 kcal/mol and -6.7820 kcal/mol, respectively. Key stabilizing interactions involved π-π interactions with Phe914 and hydrogen bonding with residues such as Leu873 and Leu1014. These findings highlight the structural features essential for potent XO inhibition and suggest that chromene flavanones represent a valuable scaffold for the development of novel inhibitors. Further molecular dynamics simulations could provide deeper insights into their stability and interaction dynamics, aiding in the rational design of more effective XO inhibitors.

Conclusion

Our findings lead us to propose these chromene flavanones as lead compounds for the design and development of novel XO inhibitors for treating diseases in which exacerbated activity of this enzyme is involved.

Chiral recognition of amino acids through homochiral metallacycle [ZnCl2L]2

Chiral recognition holds tremendous significance in both life science and chemistry. The ability to differentiate between enantiomers is crucial because one enantiomer typically holds greater biological relevance while its counterpart is often not only unnecessary but also potentially harmful. In this regard, homochiral metallacycle [ZnCl2L]2 is used in this study to understand and differentiate between the R and S enantiomers of amino acids (alanine, proline, serine, and valine). The electronic, geometric, and thermodynamic stabilities of the amino acid enantiomers inside the metallacycle are determined through various analyses. The greater interaction energy (Eint) is obtained for the ser@metallacycle complexes i.e., -33.03 and -30.75 kcal mol-1, respectively for the S and R enantiomers. The highest chiral discrimination energy of 3.11 kcal mol-1 is achieved for ala@metallacycle complexes. Regarding the electronic properties, the frontier molecular orbital (FMO) analysis indicates that the energy gap decreases after complexation, which is confirmed through density of states (DOS) analysis. Moreover, natural bond orbital (NBO) analysis determines the amount and direction of charge transfer i.e., from metallacycle towards amino acids. The maximum NBO charge transfer is observed for S-pro@metallacycle complex i.e., -0.291 |e|. Electron density difference (EDD) analysis further proves the direction of charge transfer. Noncovalent interaction index (NCI) and quantum theory of atoms in molecules (QTAIM) analyses demonstrate that the noncovalent interactions present between the host and guest are the weak van der Waals forces and hydrogen bonding. The results of NCI and QTAIM analyses for all the complexes are in alignment with those of the interaction energy (Eint) and chiral discrimination energy (Echir) analyses, i.e., significantly greater non-bonding interactions are observed for the complexes with greater Echir, i.e., for ala@metallacycle. Overall, our analyses demonstrate the excellent chiral discrimination ability of metallacycle towards chiral molecules, i.e., for enantiomers of amino acids through host-guest supramolecular chemistry.

Controlled tuning of HOMO and LUMO levels in supramolecular nano-Saturn complexes

Optoelectronics usually deals with the fabrication of devices that can interconvert light and electrical energy using semiconductors. The modification of electronic properties is crucial in the field of optoelectronics. The tuning of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and their energy gaps is of paramount interest in this domain. Herein, three nano-Saturn supramolecular complex systems are designed, i.e., Al12N12@S-belt, Mg12O12@S-belt, and B12P12@S-belt, using S-belt as the host and Al12N12, Mg12O12, and B12P12 nanocages as guests. The high interaction energies ranging from -22.03 to -63.64 kcal mol-1 for the complexes demonstrate the stability of these host-guest complexes. Frontier molecular orbital (FMO) analysis shows that the HOMO of the complexes originates from the HOMO of the host, and the LUMO of the complexes originate entirely from the LUMO of the guests. The partial density of states (PDOS) analysis is in corroboration with FMO, which provides graphical illustration of the origin of HOMO and LUMO levels and the energy gaps. The shift in the electron density upon complexation is demonstrated by the natural bond orbital (NBO) charge analysis. For the Al12N12@S-belt and B12P12@S-belt complexes, the direction of electron density shift is towards the guest species, as indicated by the overall negative charge on encapsulated Al12N12 and B12P12. For the Mg12O12@S-belt complex, the overall NBO charge is positive, elaborating the direction of overall shift of electronic density towards the S-belt. Electron density difference (EDD) analysis verifies and corroborates with these findings. Noncovalent interaction index (NCI) and quantum theory of atoms in molecules (QTAIM) analyses signify that the complexes are stabilized via van der Waals interactions. Absorption analysis explains that all the complexes absorb in the ultraviolet (UV) region. Overall, this study explains the formation of stable host-guest supramolecular nano-Saturn complexes along with the controlled tuning of HOMO and LUMO levels over the host and guests, respectively.

Investigate the binding of pesticides with the TLR4 receptor protein found in mammals and zebrafish using molecular docking and molecular dynamics simulations

The widespread use of pesticides poses significant threats to both environmental and human health, primarily due to their potential toxic effects. The study investigated the cardiovascular toxicity of selected pesticides, focusing on their interactions with Toll-like receptor 4 (TLR4), an important part of the innate immune system. Using computational tools such as molecular docking, molecular dynamics (MD) simulations, principal component analysis (PCA), density functional theory (DFT) calculations, and ADME analysis, this study identified C160 as having the lowest binding affinity (-8.2 kcal/mol), followed by C107 and C165 (-8.0 kcal/mol). RMSD, RMSF, Rg, and hydrogen bond metrics indicated the formation of stable complexes between specific pesticides and TLR4. PCA revealed significant structural changes upon ligand binding, affecting stability and flexibility, while DFT calculations provided information about the stability, reactivity, and polarity of the compounds. ADME studies highlighted the solubility, permeability, and metabolic stability of C107, C160, and C165, suggesting their potential for bioavailability and impact on cardiovascular toxicity. C107 and C165 exhibit higher bioactivity scores, indicating favourable absorption, metabolism, and distribution properties. C165 also violated rule where molecular weight is greater than 500 g/mol. Further, DFT and NCI analysis of post MD conformations confirmed the binding of ligands at the binding pocket. The analysis shed light on the molecular mechanisms of pesticide-induced cardiovascular toxicity, aiding in the development of strategies to mitigate their harmful effects on human health.

Unveiling potent Schiff base derivatives with selective xanthine oxidase inhibition: In silico and in vitro approach

This research describes the synthesis by an environmentally-friendly method, microwave irradiation, development and analysis of three novel and one previously identified Schiff base derivative as a potential inhibitor of bovine xanthine oxidase (BXO), a key enzyme implicated in the progression of gout. Meticulous experimentation revealed that these compounds (10, 9, 4, and 7) have noteworthy inhibitory effects on BXO, with IC50 values ranging from 149.56 µM to 263.60 µM, indicating their good efficacy compared to that of the standard control. The validation of these results was further enhanced through comprehensive in silico studies, which revealed the pivotal interactions between the inhibitors and the catalytic sites of BXO, with a particular emphasis on the imine group (-C = N-) functionalities. Intriguingly, the compounds exhibiting the highest inhibition rates also showcase advantageous ADMET profiles, alongside encouraging initial assessments via PASS, hinting at their broad-spectrum potential. The implications of these findings are profound, suggesting that these Schiff base derivatives not only offer a new vantage point for the inhibition of BXO but also hold considerable promise as innovative therapeutic agents in the management and treatment of gout, marking a significant leap forward in the quest for more effective gout interventions.