Computational Insights Research Articles

Bridging in silico and in vitro perspectives to unravel molecular mechanisms underlying the inhibition of β-glucuronidase by coumarins from Hibiscus trionum

Unraveling the intricacies of β-glucuronidase inhibition is pivotal for developing effective strategies in applications specific to gastrointestinal health and drug metabolism. Our study investigated the efficacy of some Hibiscus trionum phytochemicals as β-glucuronidase inhibitors. The results showed that cleomiscosin A and mansonone H emerged as the most potent inhibitors, with IC50 values of 3.97 ± 0.35 μM and 10.32 ± 1.85 μM, respectively. Mechanistic analysis of β-glucuronidase inhibition indicated that cleomiscosin A and the reference drug EGCG displayed a mixed inhibition mode against β-glucuronidase, while mansonone H exhibited noncompetitive inhibition against β-glucuronidase. Docking studies revealed that cleomiscosin A and mansonone H exhibited the lowest binding affinities, occupying the same site as EGCG, and engaged significant key residues in their binding mechanisms. Using a 30 ns molecular dynamics (MD) simulation, we explored the interaction dynamics of isolated compounds with β-glucuronidase. Analysis of various MD parameters showed that cleomiscosin A and mansonone H exhibited consistent trajectories and significant energy stabilization with β-glucuronidase. These computational insights complemented experimental findings, underscoring the potential of cleomiscosin A and mansonone H as β-glucuronidase inhibitors.

Computational insights into CRISP3 downregulation in cervical cancer and its cervical lineages pattern.

Cysteine-rich secretory protein 3 (CRISP3) emerges as a potential biomarker in the study of many cancers, including cervical cancer (CC). This study aimed to analyze the expression pattern of CRISP3 in CC patients and CC cell lineages, following treatment with the epigenetic drugs: trichostatin A (TSA) and 5-aza-2'-deoxycytidine (5-aza). The differentially expressed genes identified in GSE63514 were used to construct a protein-protein interaction network. CRISP3 was selected for subsequent analyses. We utilized data from the TCGA and GENT2 projects to evaluate the expression profile and clinical behavior of CRISP3. Additionally, we conducted cell culture experiments to analyze the expression profile of CRISP3 in cells. Low levels of CRISP3 were observed in squamous cell carcinoma (SCC) and human papillomavirus (HPV)16+, along with being associated with worse overall survival (OS). MIR-1229-3p was analyzed, and its high expression was associated with worse prognostic outcomes. In CC-derived cell lines, we observed low levels of CRISP3 in SiHa, followed by SW756, C33A, HeLa, and higher levels in CaSki. All cells were treated with TSA, 5-aza, or both. In all cell lines, treatment with TSA resulted in increased transcription of CRISP3. We identified a significant downregulation of CRISP3 in CC, particularly in cases with HPV16 infection and SCC, which was associated with poorer OS. Preliminary findings suggest that epigenetic treatments with TSA and 5-aza may modulate CRISP3 expression, warranting further research to elucidate its regulatory mechanisms and potential as a prognostic biomarker.

Computational Insights into the Influence of Surface Functionalization Groups on Zirconium Carbide MXenes as Anode Materials for Lithium-Ion Batteries

Computational Insights into the Influence of Surface Functionalization Groups on Zirconium Carbide MXenes as Anode Materials for Lithium-Ion Batteries

Computational Insights into Reproductive Toxicity: Clustering, Mechanism Analysis, and Predictive Models.

Reproductive toxicity poses significant risks to fertility and progeny health, making its identification in pharmaceutical compounds crucial. In this study, we conducted a comprehensive in silico investigation of reproductive toxic molecules, identifying three distinct categories represented by Dimethylhydantoin, Phenol, and Dicyclohexyl phthalate. Our analysis included physicochemical properties, target prediction, and KEGG and GO pathway analyses, revealing diverse and complex mechanisms of toxicity. Given the complexity of these mechanisms, traditional molecule-target research approaches proved insufficient. Support Vector Machines (SVMs) combined with molecular descriptors achieved an accuracy of 0.85 in the test dataset, while our custom deep learning model, integrating molecular SMILES and graphs, achieved an accuracy of 0.88 in the test dataset. These models effectively predicted reproductive toxicity, highlighting the potential of computational methods in pharmaceutical safety evaluation. Our study provides a robust framework for utilizing computational methods to enhance the safety evaluation of potential pharmaceutical compounds.

Computational insights into the underlying mechanism of zinc ion-specificity of the fluorescent probe, BDA-1

Ion specificity is crucial for developing fluorescence probes. Using a recently reported optical sensor (BDA-1) of Zn2+ as a representative, we carried out extensive quantum chemical calculations on its photophysical properties using density function theory. According to the calculated optimized geometries, excitation energies and transition oscillator strengths, the weak fluorescence of BDA-1 observed in experiments is attributed to the suppression of fluorescence emission by efficient internal conversion, rather than the previously proposed photoinduced electron transfer (PET) mechanism. With the addition of Zn2+ or Cd2+ ions, the tetradentate chelates [M:BDA-1-H+]+ (M=Zn, Cd) are produced. According to frontier molecular orbital and interfragment charge transfer analyses of these complexes, PET is preferentially confirmed to occur upon photo-excitation. Notably, as one coordination bond in the excited [Cd:BDA-1-H+]+ complex is significantly weakened in comparison to that of [Zn:BDA-1-H+]+, their molecular orbital compositions in the S1 state are completely different. As a result, absorption and radiation transitions of [Zn:BDA-1-H+]+ both have considerable oscillator strength, while fluorescence radiation from the excited [Cd:BDA-1-H+]+ is doubly suppressed. This difference causes that the fluorescence intensity of BDA-1 is sensitive to the addition of metal ions, and exhibits the zinc ion-specificity.

Computational insights into intrinsically disordered regions in protein-nucleic acid complexes

We study transitions in intrinsically disordered regions (IDRs) upon complex formation, utilizing X-ray-solved structural dataset of protein-DNA and protein-RNA complexes, along with their available unbound protein forms. The identified IDRs are categorized into three classes: Disordered-to-Ordered (D-O), Disordered-to-Partial Ordered (D-PO) and Disordered-to-Disordered (D-D) after comparing them in unbound and complex forms. In the D-O class, IDRs form secondary structures like coils, helices, and strands upon binding to nucleic acids. Though a majority of these IDRs are present at the surface of the complexes, a significant number of IDRs are also observed at the interfaces and are involved in polar interactions. The hydrogen bonds made by the interface IDRs (B_IDRs) with phosphates and bases of nucleic acids are comparatively more than those formed with sugars. B_IDRs form more H-bonds with the ribose in protein-RNA than with the deoxyribose in protein-DNA. Among the B_IDRs, Arg and Lys prefer to interact with the major and minor grooves of DNA and RNA, respectively. Ser, however, prefers the minor groove in both the nucleic acids. Interestingly, we report 61 and 48 IDRs in 31 protein-DNA and 22 protein-RNA complexes, respectively, suggesting nucleic acid binding to proteins may also result in ordered-to-disordered transitions.

Influence of Material Properties on Surface Chemistry Induced Circular Dichroism in Halide Perovskite: Computational Insights.

The chirality transfer phenomenon is attractive for enhancing the optical functionality of nanomaterials by inducing sensitivity to the circular polarization states of photons. An underexplored aspect is how material properties of the achiral semiconductor impact the induced chiroptical signatures. Here we apply atomistic time-dependent density functional theory simulations to investigate the material properties that influence the chiroptical signatures of a lead halide perovskite nanocrystal with a chiral molecule bound to the surface. First, we find that both lattice disorder created by surface strain and halide substitution can increase the chiroptical response of the perovskite quantum dots by an order of magnitude. Both phenomena are attributed to a broadening of the density of the electronically excited states. Second, the intensity of the anisotropy spectra decreases with increasing dot size with a power law decay. Overall, these insights can be used to help guide experimental realization of highly resolvable polarized optical features in semiconducting nanomaterials.

Computational Insights into Papaveroline as an In Silico Drug Candidate for Alzheimer's Disease via Fyn Tyrosine Kinase Inhibition.

Alzheimer's disease (AD) poses a significant global health challenge, necessitating the exploration of novel therapeutic strategies. Fyn Tyrosine Kinase has emerged as a key player in AD pathogenesis, making it an attractive target for drug development. This study focuses on investigating the potential of Papaveroline as a drug candidate for AD by targeting Fyn Tyrosine Kinase. The research employed high-throughput virtual screening and QSAR analysis were conducted to identify compounds with optimal drug-like properties, emphasizing adherence to ADMET parameters for further evaluation. Molecular dynamics simulations to analyze the binding interactions between Papaveroline and Staurosporine with Fyn Tyrosine Kinase over a 200-ns period. The study revealed detailed insights into the binding mechanisms and stability of the Papaveroline-Fyn complex, showcasing the compound's potential as an inhibitor of Fyn Tyrosine Kinase. Comparative analysis with natural compounds and a reference compound highlighted Papaveroline's unique characteristics and promising therapeutic implications for AD treatment. Overall, the findings underscore Papaveroline's potential as a valuable drug candidate for targeting Fyn Tyrosine Kinase in AD therapy, offering new avenues for drug discovery in neurodegenerative diseases. This study contributes to advancing our understanding of molecular interactions in AD pathogenesis and paves the way for further research and development in this critical area.

Discovery of a novel homocysteine thiolactone hydrolase and the catalytic activity of its natural variants.

Homocysteine thiolactone (HTL), a toxic metabolite of homocysteine (Hcy) in hyperhomocysteinemia (HHcy), is known to modify protein structure and function, leading to protein damage through formation of N-Hcy-protein. HTL has been highly linked to HHcy-associated cardiovascular and neurodegenerative diseases. The protective role of HTL hydrolases against HTL-associated vascular toxicity and neurotoxicity have been reported. Although several endogeneous enzymes capable of hydrolyzing HTL have been identified, the primary enzyme responsible for its metabolism remains unclear. In this study, three human carboxylesterases were screened to explore new HTL hydrolase and human carboxylesterase 1 (hCES1) demonstrates the highest catalytic activity against HTL. Given the abundance of hCES1 in the liver and the clinical significance of its single-nucleotide polymorphisms (SNPs), six common hCES1 nonsynonymous coding SNP (nsSNPs) variants were examined and characterized for their kinetic parameters. Variants E220G and G143E displayed 7.3-fold and 13.2-fold lower catalytic activities than its wild-type counterpart. In addition, the detailed catalytic mechanism of hCES1 for HTL hydrolysis was computational investigated and elucidated by Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) method. The function of residues E220 and G143 in sustaining its hydrolytic activity of hCES1 was analyzed, and the calculated energy difference aligns well with experimental-derived results, supporting the validity of our computational insights. These findings provide insights into the potential protective role of hCES1 against HTL-associated toxicity, and warrant future studies on the possible association between specific genetic variants of hCES1 with impaired catalytic function and clinical susceptibility of HTL-associated cardiovascular and neurodegenerative diseases.

Computational Insights into Chromene/pyran Derivatives: Molecular Docking, ADMET Studies, DFT Calculations, and MD Simulations as Promising Candidates for Parkinson's Disease.

Parkinson's disease (PD) is a neurodegenerative condition characterized by both motor and non-motor symptoms. Although PD is commonly associated with a decline of dopaminergic neurons in the substantia nigra, other diagnostic criteria and biomarkers also exist. In the search for novel therapeutic agents, chromene and pyran derivatives have shown potential due to their diverse pharmacological activities. This study utilizes a comprehensive computational approach to investigate the viability of chromene/pyran compounds as potential treatments for PD. The drug-likeness characteristics of these molecules were analyzed using ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) studies. Molecular docking was performed against PDB ID: 2V5Z. The best three molecules chosen were compound 7, compound 24, and compound 67 have a binding energy of -6.7, -8.6, and -10.9 kcal/mol. Molecules demonstrating positive blood-brain barrier permeability, good solubility, and favorable binding affinity were further evaluated using Density Functional Theory (DFT) calculations and Molecular Dynamics (MD) simulations to assess their electronic structure and stability. DFT calculations indicated that molecule 82 has a dipole moment of 15.70 D. RMSD and RMSF results confirmed the stability of the complexes over a 100 ns simulation, with a maximum of 3 hydrogen bonds formed.

Structural and computational insights into two completely unanticipated Cu(II) and Ni(II) complexes derived from a bifunctional salamo-type bis(pyridine)-arm ligand

A bifunctional Salamo-type bis(pyridine)-arm ligand H2L (4,4′-Methyl-6,6′-pyridinenitrilomethylidyne-2,2′-[ethylenedioxybis(nitrilomethylidyne)]diphenol) was designed and synthesized, which can react with Cu(II) and Ni(II) nitrates to hydrolyze & break the C = N double bonds of new ligand H2L′ (4,4′-Methyl-6,6′-formal-2,2′-[ethylenedioxybis(nitrilomethylidyne)]diphenol). The ligand reacted with Cu(II) and Ni(II) salts to form respectively complexes [Cu(L′)] (1) and [Ni2(L′)(H2O)2](NO3)2 (2). They were elucidated by single crystal X-ray method. Many important noncovalent interactions, such as intramolecular hydrogen bonding, intermolecular hydrogen bonding and π···π stacking interactions, can be observed in the crystal structures of the two complexes. IR & UV–Vis absorbent spectroscopic analysis showed that the ligand unit is involved in the coordination with copper(II) and nickel(II) atoms, and ultraviolet titration and fluorescence titration spectra verified that the coordinating radios of the two complexes formed in liquid phase are in accordance with those of single-crystal X-ray diffraction. Through DFT theoretical calculations and electrostatic potential analyses (MESP) of the ligand and its complexes, the configuration of the ligand at the lowest energy were deeply understood, and it was demonstrated that the coordination reaction at salamo sites requires a great torsional force, and the weak intermolecular interaction force and the energy gaps of HOMO-LUMO orbitals were profoundly discussed, and the Cu(II) and Ni(II) complexes exhibit anomalous fluorescence enhancement behaviors.

Court, Judges and the Pandemic: Computational Legal Insights from the Ontario Court of Appeal Corpus 2008-2021

Court, Judges and the Pandemic: Computational Legal Insights from the Ontario Court of Appeal Corpus 2008-2021

Multi-step nucleation of C-S-H: DFT simulation on silicate oligomerization and Si(Qn) evolution dynamics

Understanding the nucleation processes of calcium-silicate-hydrate (C-S-H) is fundamental to advancing the performance of cement. This study employs Density Functional Theory (DFT) to reveal the initial stages of C-S-H formation by focusing on silicate oligomerization. It examines the progression from monomer silicate species to the precursor formation, containing a range of silicate tetrahedra. Through DFT simulations, free energy changes and barriers of oligomerization reactions up to pentamers are obtained, unveiling an anionic condensation mechanism that establishes the kinetic and thermodynamic profile of this transformation. Observations reveal a dynamic evolution of Si species, with Si(Q3) indicating a transient presence, suggesting an intricate pathway towards the well-established silicate chain structure of C-S-H. This study provides detailed computational insight into the energy barriers, reaction pathways, and the thermodynamics of C-S-H formation, contributing substantial knowledge to the field of cement chemistry and its multi-step nucleation theory.

Computational insights of double perovskite X2CaCdH6 (X = Rb and Cs) hydride materials for hydrogen storage applications: A DFT analysis

Perovskite materials play a backbone role in materials science to investigate various applications including photocatalytic, photovoltaic, and hydrogen storage. Hydrogen storage is a modern technique to fulfill energy consumption and demands. We inspect the structural, hydrogen, electronic, optical, and thermodynamic properties of X2CaCdH6 (X = Rb and Cs) perovskite substances for hydrogen (H2) storage applications. The research shows substances have 225 Fm3m cubic natures and 40 atoms. The formation and cohesive energies of the examined structures show that X2CaCdH6 (X = Rb and Cs) substances may be produced and are thermodynamically stable. Electronic characteristics indicate that substances are semi-metallic, with correspondingly indirect bandgap Eg energies of 2.13 eV and 2.30 eV. The mechanical stability (Born stability), brittle (B/G = 1.22, 1.15 and α = 0.17, 0.18), hard (6.255, 5.481), and anisotropic (0.278, 0.171) of the X2CaCdH6 (X = Rb and Cs) perovskite substances are demonstrated by the examined elastic values. The Debye temperature ΘD (289.395, 320.837)K, melting temperature Tm (646.961, 650.714)K, acoustic velocities (vm, vl, vt) m/s, minimum thermal conductivity Kmin (0.63, 0.75) (W/mK), and Grüneisen parameter (18.121, 19.521) of substances are also computed by investigating their thermodynamic characteristics. Cs2CaCdH6 and Rb2CaCdH6 have gravimetric ratios of 1.39 wt% and 1.69 wt%, correspondingly. Our findings shed light on using double perovskites X2CaCdH6 (X = Rb and Cs) as a hydrogen (H2) storage substance.

Exploring the antidiabetic and anti-inflammatory potential of Lavandula officinalis essential oil: In vitro and in silico insights

Medicinal plants have been utilized for centuries in traditional medicine systems worldwide, providing a rich source of bioactive compounds with diverse biological activities. Lavandula officinalis, a member of the Lamiaceae family, has been recognized for its multifaceted pharmacological activities. In this current investigation, our primary objective was to scrutinize the in vitro inhibitory potential of L. officinalis essential oil (LOEO) against alpha-amylase and alpha-glucosidase, with the aim of understanding its antidiabetic effects. Additionally, the assay encompassed tyrosinase and lipoxygenase (LOX) to assess its anti-inflammatory attributes. Unraveling the underlying molecular mechanisms of these activities prompted an in-silico study. The purpose was to establish correlations between in-vitro observations and computational insights derived from molecular docking, which forecasts the interaction of LOEO molecules with their respective targets, alongside ADMET prediction. The Gas Chromatography-Mass Spectrometry (GC-MS) analysis allow to identify eighteen compounds, with the dominance of L−camphor (43.12 %), 1,8−cineole (34.27 %) and borneol (8.60 %) in LOEO. The antidiabetic evaluation revealed that LOEO exhibited noteworthy inhibitory activity against both α-amylase and α-glucosidase, displaying IC50 values of 3.14 ± 0.05 mg/mL and 2.07 ± 0.03 mg/mL, respectively. The subsequent in-silico study highlighted the particularly strong binding affinity of (E)-Farnesene, with a binding score of −7.4 kcal/mol for alpha-glucosidase, while Germacrene D displayed the highest affinity among the ligands (−7.9 kcal/mol) for the alpha-amylase target. Furthermore, the investigation into in vitro anti-inflammatory activity unveiled LOEO efficacy against tyrosinase (IC50 = 42.74 μg/mL) and LOX (IC50 = 11.58 ± 0.07 μg/mL). The in-silico analysis echoed these findings, indicating α-Cadinene's notable binding affinity of 6 kcal/mol with tyrosinase and α-Cedrene's binding score of −6.5 kcal/mol for LOX. Impressively, for both COX-1 and COX-2, α-Cedrene exhibited significant binding affinities of −7.6 and −7.3 kcal/mol, respectively. The convergence between the in vitro and in silico outcomes underscores the potential of LOEO and its constituent compounds as potent inhibitors targeting both diabetes and the inflammatory processes.

Structural and Computational Insights into the Noncanonical Aromatization in Fungal Polyketide Biosynthesis

Structural and Computational Insights into the Noncanonical Aromatization in Fungal Polyketide Biosynthesis

Unveiling the Mechanism of Phenamacril Resistance in F. graminearum: Computational and Experimental Insights into the C423A Mutation in FgMyoI.

Phenamacril (PHA) is a highly selective fungicide for controlling fusarium head blight (FHB) mainly caused by F. graminearum and F. asiaticum. However, the C423A mutation in myosin I of F. graminearum (FgMyoI) leads to natural resistance to PHA. Here, based on the computational approaches and biochemical validation, we elucidate the atomic-level mechanism behind the natural resistance of F. graminearum to the fungicide PHA due to the C423A mutation in FgMyoI. The mutation leads to a rearrangement of pocket residues, resulting in increased size and flexibility of the binding pocket, which impairs the stable binding of PHA. MST experiments confirm that the mutant protein FgMyoIC423A exhibits significantly reduced affinity for PHA compared to wild-type FgMyoI and the nonresistant C423K mutant. This decreased binding affinity likely underlies the development of PHA resistance in F. graminearum. Conversely, the nonresistant C423K mutant retains sensitivity to PHA due to the introduction of a strong hydrogen bond donor, which facilitates stable binding of PHA in the pocket. These findings shed light on the molecular basis of PHA resistance and provide new directions for the creation of new myosin inhibitors.

Recent Advances in Ligand-Controlled Regio- or Stereodivergent Transition-Metal-Catalyzed Hydroelementation (H[E]) (E = H, B, Si, Ge) of C–C Unsaturated Systems

AbstractReductive functionalization of C–C unsaturated systems, including alkenes and alkynes, with a range of hydroelements (H[E]) is one of the most fundamental and highly practical methods for the synthesis of functionalized hydrocarbons. Since the resultant hydrocarbon products have strong applicability as synthetic intermediates, numerous homogeneous organo(metallic) catalysts have been intensively utilized to date for reductive functionalization reactions. In particular, well-defined transition-metal-based catalysts capable of controlling the regio- or stereoselectivity of a product by harnessing the addition of H[E] (E = H, B, Si, Ge) into Cα–Cβ unsaturated bonds have drawn special attention. In this review, we describe recent examples of transition-metal catalytic systems (M = Fe, Co, Rh, Pd, Ni) for regio- or stereodivergent hydroelementation reactions of (conjugated) alkenes, alkynes, and allenes to give a pair of isomeric products in high selectivities from the same starting compounds simply by variation of the ligand. Mechanistic aspects of the ligand-controlled selectivity divergence are discussed in detail on the basis of experimental observations and/or computational insights.1 Introduction2 Hydroelementation of Alkenes and Alkynes3 Hydroelementation of Conjugated Dienes and Diynes4 Hydroelementation of Allenes5 Summary and Outlook

Computational insights into three-centre four-electron bridging hydride bond in boryl type PBP-M dihydride complexes

Computational insights into three-centre four-electron bridging hydride bond in boryl type PBP-M dihydride complexes

Computational Insights into Enzyme‐Substrate Binding Interplay Exhibit Variable Binding Attributes: A Framework for Implementing Oxidoreductase‐Based Applications

AbstractLaccase (LAC) is a potent multicopper oxidase that relies on O2 for its catalytic activity. LAC has been affirmed as an environmentally friendly biocatalyst that often catalyzes a wide array of phenolic substrates. Bacterial‐derived LACs have been less investigated for non‐phenolic substrates in contrast to fungi‐derived LAC. To comprehend the substrates (3,4‐Dimethoxybenzyl alcohol, and Dimer (Guaiacyl 4‐O‐5 guaiacyl) binding interactions of LAC (Thermus thermophilus HB27) was carried out and contrasted with fungal‐derived Lignin peroxidase (LiP) (Trametes cervina) exploiting computational methods, including physicochemical properties, Sequence Annotated by Structure (SAS), Extra precision docking (Glide), and DESMOND‐directed MD‐ simulation. Protein structures exhibited by LAC, and LiP have diverse dissimilar component architects. The XP docking suggested LiP‐Dimer seems to have a comparatively lowest binding affinity (−8.413 kcal/mol), with an MMGBSA score of −33.249 kcal/mol. Further, docked complexes were validated leveraging 50 ns NPT system‐based MD‐simulation for structural and functional stability. The system achieved equilibrium and stability at the end of the simulation, with only the LiP‐3,4‐Dimethoxybenzyl alcohol complex maintained stability. The results of this study offer a framework for improving the binding ability of substrates by way of the use of in‐silico protein engineering, which might eventually result in more effective catalytic applications.