Docking Energy Research Articles

Structural analysis and theoretical studies of 2-(2-chlorobenzylidene) malononitrile (CS) “a riot controlling agent”

In solvent methanol, malononitrile and 2-chlorobenzaldehyde were stirred in the presence of base piperidine to synthesise the target chemical 2-(2-chlorobenzylidene) malononitrile (CS). The crystal structure of the target compound C10H5ClN2 has been elucidated through X-ray crystallographic analysis. It crystallises in the monoclinic crystal system within the P21 space group, containing four molecules per asymmetric unit. The unit cell dimensions are a = 3.8825(3) Å, b = 21.0202(18) Å, c = 21.3481(18) Å, and β = 95.096(4)°. The phenyl and malononitrile groups, which make up the molecular components, are each planar but slanted towards one another at a dihedral angle of 12.7° (4). Besides this, target molecule is also stabilized by hydrogen bonding, halogen bonding and π stacking interactions. Solid-state structure has been analysed through Hirshfeld surface analysis, including the evaluation of the different energy frameworks, indicating that the molecular sheets are primarily formed by hydrogen bonds and halogen bonds and the stabilization is dominated via the electrostatic energy contribution. Fingerprint plots were carried out to study the relative contribution of noncovalent interactions in the target compound CS. Further, the density functional theory calculations were employed using B3LYP hybrid functional with 6-311++G level basic set to optimize the structural coordinates in gas phase and in different solvents (chloroform, water, and methanol). The chemically active regions of the target compound were identified by the analysis of molecular electrostatic potential surface. Further, from PASS analysis and literature reports, molecular docking of title compounds was carried out with human transient receptor potential ankyrin 1 ion channel (hTRPA1) (PDB-ID 6PQO). ΔGb (docking energy) and inhibition constant was calculated to be −7.53 kcal/mol and 3.33 μM respectively, with the target ion channel.

Integrating network pharmacology and experimental verification to explore the pharmacological mechanisms of Guanxin Shutong capsule in treating heart failure.

The Guanxin Shutong capsule (GXST), a traditional Chinese medicine, is commonly used for treating cardiovascular disease, it has shown efficacy in improving symptoms and enhancing the quality of life for patients with heart failure (HF). However, the specific mechanism of action of GXST in HF remains unclear. In this study, we employed a comprehensive approach combining network pharmacology, molecular dynamics (MD) simulations, and in vitro validations to investigate the potential targets and molecular mechanisms of GXST against HF. We collected active ingredients and target genes of GXST, as well as related genes of HF, from multiple public databases. Using bioinformatics analysis, we constructed networks of ingredients-disease-targets and performed functional annotations of the core targets. MD simulations were conducted to verify the binding between the core protein-ligand complexes. In vitro evaluations, including cell proliferation, apoptosis, and protein expression in human umbilical vein endothelial cells (HUVECs) and H9C2 cells were treated with GXST, were performed for pharmacodynamics evaluation. Network analysis revealed 320 intersection genes and 74 active ingredients in the Herbs-ingredients-target genes-disease network. We identified key active ingredients and target genes that overlapped. The KEGG pathways of the intersection genes were primarily enriched in the PI3K-Akt signaling pathway and apoptosis. The protein-protein interaction network highlighted proteins such as AKT1, VEGFR2, and eNOS. MD simulations confirmed stable docking and lower binding energy between 4 identified ingredients (kaempferol, quercetin, (2R)-5,7-dihydroxy-2-(4-hydroxyphenyl) chroman-4-one, and ellagic acid) and their respective core proteins (VEGFR2, eNOS, and AKT). In vitro experiments demonstrated the protective effects of GXST against H2O2-induced apoptosis in both HUVECs and H9C2 cells. Notably, consistent with the in silico predictions, GXST effectively activates the VEGFR2/AKT/eNOS signaling pathways in HUVECs. This study provides insights into the underlying mechanism of GXST's therapeutic effects in heart failure. The involvement of the VEGFR2/AKT/eNOS signaling pathways suggests their importance in further elucidating and applying GXST in the clinical treatment of heart failure.

Investigating the Inhibitory Potential of Flavonoids against Aldose Reductase: Insights from Molecular Docking, Dynamics Simulations, and gmx_MMPBSA Analysis.

Diabetes mellitus (DM) is a complex metabolic disorder characterized by chronic hyperglycemia, with aldose reductase playing a critical role in the pathophysiology of diabetic complications. This study aimed to investigate the efficacy of flavonoid compounds as potential aldose reductase inhibitors using a combination of molecular docking and molecular dynamics (MD) simulations. The three-dimensional structures of representative flavonoid compounds were obtained from PubChem, minimized, and docked against aldose reductase using Discovery Studio's CDocker module. The top 10 compounds Daidzein, Quercetin, Kaempferol, Butin, Genistein, Sterubin, Baicalein, Pulchellidin, Wogonin, and Biochanin_A were selected based on their lowest docking energy values for further analysis. Subsequent MD simulations over 100 ns revealed that Daidzein and Quercetin maintained the highest stability, forming multiple conventional hydrogen bonds and strong hydrophobic interactions, consistent with their favorable interaction energies and stable RMSD values. Comparative analysis of hydrogen bond interactions and RMSD profiles underscored the ligand stability. MMPBSA analysis further confirmed the significant binding affinities of Daidzein and Quercetin, highlighting their potential as aldose reductase inhibitors. This study highlights the potential of flavonoids as aldose reductase inhibitors, offering insights into their binding interactions and stability, which could contribute to developing novel therapeutics for DM complications.

In Silico Analysis of Vitamin D Interactions with Aging Proteins: Docking, Molecular Dynamics, and Solvation Free Energy Studies

Aging is a natural process that is also influenced by some factors like the food someone eats, lifestyle decisions, and impacts on general health. Despite the recognized role of nutrition in modulating the molecular and cellular mechanisms underlying aging, there is a lack of comprehensive exploration into potential interventions that can effectively mitigate these effects. In this study, we investigated the potential anti-aging properties of vitamin D by examining its interactions with key molecular targets involved in aging-related pathways. By using molecular docking and dynamics techniques, we evaluate the interactions and stability of vitamins D2 and D3 with key proteins involved in aging pathways, such as SIRT1, mTOR, AMPK, Klotho, AhR, and MAPK. Our results reveal promising binding affinities between vitamin D and SIRT1 forms, with energy values of −48.33 kJ/mol and −45.94 kJ/mol for vitamins D2 and D3, respectively, in aqueous environments. Moreover, molecular dynamics simulations revealed that the vitamin D3–SIRT1 complex exhibited greater stability compared with the vitamin D2–SIRT1 complex. The study calculated the solvation free energy to compare the solubility of vitamins D2 and D3 in water and various organic solvents. Despite their strong interactions with water, both vitamins exhibited low solubility, primarily due to the high energy cost associated with cavity formation in the aqueous environment. Compared with other solvents, water demonstrated particularly low solubility for both vitamins. This suggested that vitamins D2 and D3 preferred binding to aging receptors over dissolving in bulk aqueous environments, supporting their strong therapeutic interactions with these receptors. These findings shed light on the molecular mechanisms underlying vitamin D’s potential anti-aging effects and lay the groundwork for developing nutraceuticals targeting aging and associated diseases. Understanding these mechanisms holds promise for future interventions aimed at promoting healthy aging and enhancing overall well-being.

Effect of N-substituted aliphatic glycine presence on bioactivity, cytotoxicity, and selectivity of Pt(II) and Pd(II) complexes in cancer treatment

In this study, four new platinum (II) and palladium(II) complexes were synthesized to develop metallo-drugs that can attach to DNA and prevent the division of cancer cells. The complexes, 1: [Pt(bipy)(LP)]NO3, 2: [Pt(bipy)(LA)]NO3, 3: [Pd(bipy)(LP)]NO3, and 4: [Pd(phen)(LP)]NO3 (where LP is propylglycine, LA is 2-heptyl glycine, bipy is 2,2-bipyridine, and phen is 1,10-phenanthroline), were structurally characterized using computational and experimental analysis. Their stability, solubility, and lipophilicity were evaluated. Single-crystal X-ray and powder X-ray crystallographic analyses were performed for [Pt(bipy)(LA)]NO3. Density functional theory calculations were performed to investigate the reactivity, stability descriptors, and natural bond orbital analysis of these complexes. The in vitro cytotoxicity of these substances was examined against the human colorectal carcinoma (HCT116), A549 (Human Caucasian lung carcinoma), MCF7 (breast cancer), and HFF (Human Freskin Fibroblast) cell lines. According to the findings, complexes 4 and 3 had near oxaliplatin concentrations and more than carboplatin due to lipophilic ligands in their structure. Also, regarding IC50 values on normal HFF cell line, 4 is selectively toxic against the A549 cancer cell line with SI=5.6. Fluorescence, electronic absorption spectroscopy, and CD spectroscopy were used to investigate the binding affinities of compounds to CT-DNA and HSA. The results revealed that they could interact with CT-DNA through groove mode and with HSA via hydrogen bond and van der Waals forces. Electronic absorption and CD spectra indicated that compounds changed the way the HSA folded by increasing the proportion of a-helix. The binding posture of the metal complex to both biomolecules was predicted using docking simulation, which also verified the groove binding for DNA-complex. The findings indicated that complex 4 had a greater negative docking energy and a higher propensity for CT-DNA and HSA interaction.

2-isopropyl-4-methoxy-5-methylphenol-hydrazone derivatives : Synthesis, characterization, and in-silico assessment of EGFR and Bcl2 inhibitory activity

The exploration of hydrazones, characterized by the -N(H)N=CH group, in combination with thymol, has garnered significant attention in pharmacology due to their versatility and ease of synthesis. The synthesized hydrazone compounds 10a-e underwent thorough scrutiny utilizing HRMS, 1H NMR and 13C NMR spectroscopy, affirming the presence of azomethine linkages. Moreover, computational investigations through molecular docking and dynamic simulations were carried out to unveil the binding mechanisms between the synthesized hydrazones and EGFR and BCl2. The docking energies of compounds 10a-e for Bcl-2 were determined to be -6.6, -6.9, -6.5, and -7.3 kcal mol-1, respectively. Similarly, the docking energies of compounds 10a-e for EGFR were observed to be -9.2, -9.4, -9.2, -9.0 and -9.6 kcal mol-1, respectively.

In-silico analysis of ethanol peel extract of Citrus sinensis on mercury chloride-induced prefrontal cortex damage in Wistar rat

This study evaluated the effect of ethanolic extract of Citrus sinensis peel on mercury chloride-induced changes in the prefrontal cortex of adult Wistar rats. Twenty-five Wistar rats were purchased and divided into five groups containing five animals in each group. Group 1 was administered with distilled water, Group 2, Group 3, Group 4, and Group 5 were administered with 5 mg/kg of mercury chloride only, 5 mg/kg of mercury chloride and 140 mg/kg Silymarin, 5 mg/kg mercury chloride and 1000 mg/kg of ethanoic extract of orange peel, and 5 mg/kg mercury chloride and 1500 mg/kg of ethanoic extract of orange peel. All administration was done orally and the administration lasted for 14 days. The animals were sacrificed humanely using 75 mg/kg ketamine intraperitoneally and prefrontal was dissected out. Part was homogenized in 0.1M phosphate buffered saline for the estimation of superoxide dismutase (SOD), and catalase (CAT) activities, and Malondialdehyde (MDA) level and the other part was fixed by immersion in 10 neutral buffered formal-saline for histological evaluation. The chemical structure of sixteen compounds from Citrus sinensis peel obtained from GC-MS analysis reported in the literature were retrieved from the PubChem compound database and the crystal structure of human peroxisome proliferator- activated receptor gamma (PPARγ; PDB:ID: 2P4Y) reported to increase the expression of catalase gene, human extracellular copper-zinc superoxide dismutase enzyme (PDB ID: 2JLP) and mammalian 15-lipoxygenase - 1 enzyme (PDB ID: 2P0M) responsible for the production of lipid peroxidation were retrieved from the PDB database. Ligands and protein preparation, docking and MM-GBSA relative binding free energy calculation were done in Maestro 2023.1. Data obtained was analyzed using the IBM SPSS (version 25) using one-way ANOVA and p-value < 0.05 was considered statistically significant. The results indicate that the MDA level in control Group(13.29±1.183 μmol) is statistically significantly lower compared to the Group 2 (21.88±1.96 μmol), group 3 (27.44±3.52 μmol), Group 4 (22.20±1.16 μmol) and Group 5 (25.40±3.13 μmol). No statistically significant difference was observed in SOD activity. The CAT activities in control group (53.51±6.83 nmol/ml) was statistically significantly lower compared to the group 2 (26.21±3.70 nmol/ml), Group 3 (27.17±5.32 nmol/ml), Group 4 (25.30±4.24 nmol/ml) and Group5 (26.59±4.22 nmol/ml).The present study suggests, ethanolic extract of Citrus sinensis peel have protective effects on mercury-induced changes in prelimbic part of the prefrontal cortex of adult Wistar rats.

Design, Synthesis, Characterization, Molecular Docking Studies, In vitro and In vivo Cervical Cancer Activity of Novel N-Substituted Pyrazole Derivatives

The aim of this study is to design, synthesize, characterize few novel N-substituted pyrazole derivatives and evaluated for their anticancer capabilities; these compounds were selected based on their ability to inhibit the HPV E6 protein. The IR, 1H & 13C NMR, mass spectral and elemental analysis were used to determine the structural details of the newly synthesized substances. The molecular docking was performed using Auto Dock Vina, and the protein-ligand interaction was analyzed using Discovery Studio. The sulforhodamine B (SRB) assay was used to determine the in vitro anticancer activity against the HeLa cell line. Body weight analysis, mean survival time and % increase in life span approaches were used to assess in vivo anticancer effectiveness in Swiss albino mice bearing Dalton’s Lymphoma Ascites (DAL) tumor model. Synthesized compounds have excellent docking energies, according to docking experiments. Compounds I, II and III were selected for anticancer activity in vivo DAL-bearing mice based on the findings of their in vitro and SRB assays exhibiting the antiproliferative activity. Pyrazole derivatives, compounds I and III, demonstrated significant potential as anticancer agents.

Abstract B010: Design of personalized neoantigen mRNA vaccines against breast cancer patients in Pakistan based on next-generation sequencing data

Abstract Breast cancer is the most common malignancy among women in Pakistan, with an outrageous increase in the incidence and mortality rate. Because of decreased effectiveness and lower survival rates, there is an urgent need for developing novel, personalized vaccines with enhanced activity. The development of a personalized mRNA vaccine illustrates a promising approach to combating the prevalence of breast cancer. We used the whole exome sequencing (WES) data of Pakistani tumor samples to predict immunogenic neoantigens. The WES data was aligned to the GRCM39 reference genome using BWA. The genome analysis toolkit (GATK) was employed for variant calling to identify somatic mutations. Using immune-bioinformatics tools, we predicted cytotoxic CD8+ T cell epitopes and helper CD4+ T cell epitopes within the identified neoantigens and designed vaccines by assembling the fusion of CTL neoepitopes, helper sequences, and adjuvants together with linkers. The Insilco ImmSim algorithm was used to examine the immune responses of the vaccine. The vaccine design was further explored by checking its simulation effect on the immune system, its physiochemical characteristics, its binding to specific immune system molecules, and cloning into an appropriate vector. In addition, molecular docking, MD simulation, and binding free energies were performed to investigate the interaction mechanism between the construct vaccine and Toll-like receptors (TLR2, TLR4, TLR7, and TLR9).By examining these factors, we aimed to ensure the vaccine's safety, stability, and ability to bind tightly to specific immune cells (class I MHC molecules), ultimately triggering a comprehensive immune response against breast cancer cells. Citation Format: Kayode Yomi Raheem, Muhammad Muddassar. Design of personalized neoantigen mRNA vaccines against breast cancer patients in Pakistan based on next-generation sequencing data [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr B010.

Novel umami-enhancing peptides of beef M. Semimembranosus hydrolysates and interactions with the T1R1/T1R3 taste receptor

The taste mechanisms of beef umami and umami-enhancing peptides are not well understood. Therefore, novel umami and umami-enhancing peptides from beef M. semimembranosus hydrolysates were explored. Beef hydrolysates treated with Flavourzyme® showed an overall strong umami intensity compared to those treated with Alcalase®, papain, or Protamex®. The peptides were isolated via consecutive separation processes, and 31 potential umami peptides were identified. Molecular docking results showed that WGSEPIRIQ and TERGYSF had considerably low docking energies with the T1R1/T1R3 taste receptor through potential key binding sites for hydrogen bonding, including Ser48, Gly49, and Gln278 in T1R1, and Ser67, Asn68, and Arg247 in the T1R3 subunit. The taste of the identified peptides dissolved in ultrapure water was dominated by sourness. Instead, they demonstrated an umami-enhancing effect in the presence of monosodium glutamate. These results broaden our understanding of the taste mechanisms of beef umami-enhancing peptides and their potential applications as flavoring agents.

Screening and preparation of highly active antioxidant peptides of apricot and their inhibitory effect on ultraviolet radiation

In today's social environment, the objective reality of people's increasing life pressure, environmental deterioration, and enhanced ultraviolet rays caused by the destruction of the ozone layer has led to the aggravation of people's oxidative stress. Therefore, exogenous antioxidant peptides have become a hot topic in research. In the context of insufficient protein supply and resource recycling, almond meal was used as raw material in this study. As a by-product of oil processing, it has a protein content of 68 % and antioxidant-related amino acids accounted for 84.62 %, which can be used as a high-quality natural source of antioxidant peptides. Taking antioxidant activity as the only indicator, papain was screened as a hydrolase, and 7 antioxidant peptides such as YLSF, LPSYVN and SPHWNVN were separated and purified. The affinity energy of docking with Keap1-Nrf2-ARE protein molecules was −7.5—-8.9 kal/mol, and hydrophobic stacking, hydrogen bonding and intermolecular forces were maintained. Seven antioxidant peptides were synthesized in solid phase, and the IC50 values of in vitro ABTS+ scavenging rates were 3.59 μg/mL-6.73 μg/mL, and the antioxidant capacity was stronger than that of glutathione and ascorbic acid. In the in vitro cellular ROS scavenging capacity, all seven peptides had the effect of scavenging intracellular ROS, among which YLSF and ESWNPRDPQF had stronger scavenging capacity than glutathione. Finally, the mouse skin staining method determined that apricot antioxidant peptides had a significant inhibitory effect on UV damage to mouse skin, and targeted proteomics was used to clarify that apricot antioxidant peptides inhibited UV damage by mainly affecting three pathways, including the base excision repair pathway. This study not only improved the economic value of processing by-products, but also obtained 7 highly active almond antioxidant peptides, tapping the potential ability of apricot antioxidant peptides to be incorporated into functional food or cosmetic formulations.

Unveiling therapeutic biomarkers and druggable targets in ALS: An integrative microarray analysis, molecular docking, and structural dynamic studies

Amyotrophic lateral sclerosis (ALS), commonly known as Lou Gehrig's disease, is a debilitating neurodegenerative disorder characterized by the progressive degeneration of nerve cells in the brain and spinal cord. Despite extensive research, its precise etiology remains elusive, and early diagnosis is challenging due to the absence of specific tests. This study aimed to identify potential blood-based biomarkers for early ALS detection and monitoring using datasets from whole blood samples (GSE112680) and oligodendrocytes, astrocytes, and fibroblasts (GSE87385) obtained from the NCBI-GEO repository. Through bioinformatics analysis, including protein-protein interactions and molecular pathway analyses, we identified differentially expressed genes (DEGs) associated with ALS. Notably, ALS2, ADH7, ALDH8A1, ALDH3B1, ABHD2, ABHD17B, ABHD12, ABHD13, PGAM2, AURKB, ANAPC11, VAPA, UNC45B, and TNNT2 emerged as top-ranked DEGs, implicated in drug metabolism, protein depalmytilation, and the AKT/mTOR signaling pathways. Among these, AurKB established as a potential therapeutic biomarker with relevance to various neurological conditions. Consequently, AurKB was selected for identifying potential therapeutic molecules and utilized for in silico structural characterization studies. Exploration of the IMPATT database led to the discovery of a lead compound similar to Fostamatinib, currently used for AurKB. Initial molecular docking and MMGBSA-based binding energy analysis were followed by molecular dynamics simulation (MDS) and free energy landscape (FEL) analysis to validate the ligand's binding efficacy and understand dynamic processes within the biological system. The identified potential biomarkers and lead molecule provide novel insights into the correlation between blood cell transcripts and ALS pathology, paving the way for blood-based diagnostic tools for early ALS detection and ongoing disease monitoring.

Marine Compound-Carpatamide D as a Potential Inhibitor Against TOP2A and Its Mutant D1021Y in Colorectal Cancer: Insights from DFT, MEP and Molecular Dynamics Simulation.

Colorectal cancer (CRC) ranks as the third most prevalent cancer globally, hence there is an urgent need for new and effective therapeutic options. DNA topoisomerase 2A (TOP2A) plays a crucial role in the cell cycle and is involved in CRC progression, making it essential to identify structural and functional relevant alterations. Among the 24 mutations, our findings indicated that mutation D1021Y has the most deleterious effect on the TOP2A protein. Based on virtual screening of 31,561 compounds, we identified three lead candidates: 17683 (nigrospoxydon C), 28461 (carpatamide D), and 28853 (6'-O-acetyl-isohomaarbutin), which showed promising inhibitory effect against TOP2A and its mutant form. These compounds were assessed for their stability using density functional theory (DFT) analysis, where carpatamide D possessed the least energy gap of 4.398eV showing its high reactivity among all. Further, molecular docking also shows the carpatamide D as the top candidate, which exhibited favourable docking energy against the TOP2A wild type (- 7.47kcal/mol) and with D1021Y mutant (- 7.62kcal/mol) as compared to reference compound PK1, which showed - 6.11kcal/mol TOP2A wild type and - 6.24kcal/mol against mutant type. The molecular dynamics simulation was performed to analyse the dynamics and stability of complex, which revealed TOP2A_28641 and D1021Y_28641 complexes to be stable with least root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF). Molecular mechanics/Poisson-Boltzmann surface area calculations indicated that TOP2A_28641 and D1021Y_28641 complexes exhibited the lowest binding energy of - 23.55kcal/mol and - 25.03kcal/mol, respectively. Our findings suggest carpatamide D as a promising lead compound for the TOP2A_D1021Y targeted cancer therapies, which needs further experimental validation.

Effect and mechanism of green and aldehyde aroma compounds from sweet orange on sucrose sweetness perception

At present, there are relatively few studies on the influence of green aroma and aldehyde aroma compounds on the sweetness perception of sucrose. This study examined the effects of 11 aroma compounds from sweet orange, characterized by green and aldehyde flavors, on the sweetness of a 5 % sucrose solution. Using artificial sensory analysis and electronic tongue technology, it was found that most aromatic compounds can inhibit sweetness perception, and the inhibitory effect of trans-2-decenoaldehyde is the most significant. The mechanism of inhibition was explored through molecular simulation, revealing that the binding free energy of molecular docking was greater than −5.9 kcal/mol. Further molecular dynamics analysis showed that compared with the T1R2/T1R3 sucrose binary system, the addition of aroma substances reduced the number of hotspot residues involved in protein ligand binding, and did not enhance the binding ability of ligand proteins, indicating an inhibitory effect.

Exploring the Potential of Isoindole‐1,3‐Dione Derivatives as Novel Inhibitors of Aldose Reductase: An In Silico and In Vitro Insight into Therapeutic Strategies for Diabetic Complications

AbstractThis study explores the potential of isoindole‐1,3‐dione derivatives as novel inhibitors of aldose reductase (AR), focusing on their in silico and in vitro effects for therapeutic strategies against diabetic complications. Aldose reductase, a critical enzyme in the polyol pathway, plays a significant role in glucose metabolism and has been linked to diabetic complications. In this comprehensive study, isoindole‐1,3‐dione derivatives were synthesized and evaluated for their inhibitory effects on the recombinant human AR enzyme. The compounds’ inhibitory activities were measured both in vitro and through in silico techniques, employing molecular docking and free binding energy calculations and ADME studies. The newly synthesized compounds demonstrated varied inhibitory effects, with ethyl and phenyl substituents at specific positions enhancing inhibitory activity. Notably, compounds with carboxylic acid derivatives exhibited potent inhibitory effects, especially compound 6 with an IC50 value of 1.649 μM. In conclusion, this study provides valuable insights into the inhibitory potential of isoindole‐1,3‐dione derivatives against AR, suggesting their potential therapeutic application in mitigating diabetic complications. The combination of experimental and computational approaches offers a comprehensive understanding of the compounds’ interaction mechanisms and pharmacokinetic profiles, supporting their further exploration as antidiabetic agents.

Analyzing the FMN-heme interdomain docking interactions in neuronal and inducible NOS isoforms by pulsed EPR experiments and conformational distribution modeling.

Nitric oxide synthases (NOSs), a family offlavo-hemoproteins with relatively rigid domains linked by flexible regions, require optimal FMN domain docking to the heme domain for efficient interdomain electron transfer (IET). To probe the FMN-heme interdomain docking, the magnetic dipole interactions between the FMN semiquinone radical (FMNH•) and the low-spin ferric heme centers in oxygenase/FMN (oxyFMN) constructs of neuronal and inducible NOS (nNOS and iNOS, respectively) were measured using the relaxation-induced dipolar modulation enhancement (RIDME) technique. The FMNH•RIDME data were analyzed using the mesoscale Monte Carlo calculations of conformational distributions of NOS, which were improved to account for the native degrees of freedom of the amino acid residues constituting the flexible interdomain tethers. This combined computational and experimentalanalysis allowed for the estimation of the stabilization energies and populations of the docking complexes of calmodulin (CaM) and the FMN domain with the heme domain. Moreover, combining the five-pulse and scaled four-pulse RIDME data into a single trace has significantly reduced the uncertainty in the estimated docking probabilities. The obtained FMN-heme domain docking energies for nNOS and iNOS were similar (-3.8kcal/mol), in agreement with the high degree of conservation of the FMN-heme domain docking interface between the NOS isoforms. In spite of the similar energetics, the FMN-heme domain docking probabilities in nNOS and iNOS oxyFMN were noticeably different (~ 0.19 and 0.23, respectively), likely due to differences in the lengths of the FMN-heme interdomain tethers and the docking interface topographies. The analysis based on the IET theory and RIDME experiments indicates that the variations in conformational dynamics may account for half of the difference in the FMN-heme IET rates between the two NOS isoforms.

Phytochemical profiling and antibacterial activities of Ziziphora tenuior root extracts: a molecular docking against VanA of vancomycin-resistant enterococci.

Medicinal plants, renowned for their antibacterial phytocompounds and secondary metabolites, hold significant promise in addressing antibiotic-resistant bacterial strains. This study aimed to conduct phytochemical profiling of the methanolic and dichloromethane extracts of Ziziphora tenuior root using the GC-MS technique. These extracts' antioxidant potential was assessed via DPPH assay and their antibacterial activity was evaluated against S. aureus, E. coli, and VRE bacterial strains. Furthermore, the drug-ligand interactions between the extracts' biocompounds and d-alanyl-d-lactate ligase (VanA) protein of vancomycin-resistant enterococci strains (VRE) were analyzed using molecular docking. Based on the results, 74% of methanolic extract consisted of (3methyl, 24S)-stigmast-5-en-3-ol (which is a β-sitosterol), followed by Tetrasiloxane, decamethyl (15.5%), and 1-methyl-4-phenyl-5-thioxo-1,2,4-triazolidin-3-one (10.5%). Also, the only predominant compound identified in the dichloromethane extract was Benzo[h]quinoline, 2,4-dimethyl-. Both extracts showed antioxidant activity, while the antioxidant activity of the methanolic extract (IC50 = 95.33μg/ml) was significantly higher than that of the dichloromethane extract (IC50 = 934.23μg/ml). Also, both extracts displayed substantial antibacterial efficacy against the tested pathogens, particularly against VRE. Moreover, the in silico analysis revealed that (3methyl, 24S)-stigmast-5-en-3-ol and Benzo[h]quinoline,2,4-dimethyl- exhibited notable interactions with VanA through docking energy values of -9.0 and -9.1kcal/mol, respectively. Furthermore, these compounds formed 2 and 1 hydrogen bonds with VanA, respectively, highlighting their potential as effective interactants. These findings provide valuable visions into the therapeutic potentials of these plant-derived biocompounds in combating antibiotic-resistant bacterial infections.

Computational exploration of bioactive compounds from Albizia procera: Molecular docking, dynamics, and pharmacokinetics for AchE and BchE inhibition in Alzheimer's disease treatment

Current treatments for Alzheimer's disease (AD) are inadequate and primarily target inhibition of butyrylcholinesterase (BchE) and acetylcholinesterase (AChE) enzymes. This study focused on identifying potential anti-AD compounds from the leaf extract of Albizia procera using gas chromatography-tandem mass spectrometry (GC-MS) analysis and computational approaches. Ethanol seed extract analysis revealed 10 phytoconstituents, which were evaluated for their binding affinities using Autodock Vina and Desmond software against AD-related targets (PDB IDs: 4PQE, 2WJO, and 2POA). Five compounds, along with the control drug, showed significant docking energies. Subsequent in silico ADMET analysis assessed parameters such as intestinal absorption, blood-brain barrier permeability, gastrointestinal absorption, carcinogenicity, and acute oral toxicity. The results extract showed notable affinity for BchE and acetylcholinesterase targets. Molecular dynamics (MD) simulations supported the involvement of hydrogen bonding with ASP207 and GLY75 residues in binding these ligands, demonstrating that disrupting these forces causes destabilization. A ligand plot study also presented a two-dimensional plot of these interactions. The docking results indicate that 7-Oxabicyclo [4.1.0] heptan-2-one could be a promising agent for the treatment of AD because of its higher stability with respect to the two best ligands among all compounds tested. Therefore, from this study, it can be concluded that the compounds present in the leaf extract of A. procera have potential as targets linked to AD and may be helpful for the development of new drugs. Therefore, these data draw a focus on non-synthetic compounds during drug discovery and could possibly provide approaches for exploring existing therapies for AD.

Gene network analysis combined with preclinical studies to identify and elucidate the mechanism of action of novel irreversible Keap1 inhibitor for Parkinson's disease.

The cysteine residues of Keap1 such as C151, C273, and C288 are critical for its repressor activity on Nrf2. However, to date, no molecules have been identified to covalently modify all three cysteine residues for Nrf2 activation. Hence, in this study, our goal is to discover new Keap1 covalent inhibitors that can undergo a Michael addition with all three cysteine residues. The Keap1's intervening region was modeled using Modeller v10.4. Covalent docking and binding free energy were calculated using CovDock. Molecular dynamics (MD) was performed using Desmond. Various in-vitro assays were carried out to confirm the neuroprotective effects of the hit molecule in 6-OHDA-treated SH-SY5Y cells. Further, the best hit was evaluated in vivo for its ability to improve rotenone-induced postural instability and cognitive impairment in male rats. Finally, network pharmacology was used to summarize the complete molecular mechanism of the hit molecule. Chalcone and plumbagin were found to form the necessary covalent bonds with all three cysteine residues. However, MD analysis indicated that the binding of plumbagin is more stable than chalcone. Plumbagin displayed neuroprotective effects in 6-OHDA-treated SH-SY5Y cells at concentrations 0.01 and 0.1 μM. Plumbagin at 0.1 µM had positive effects on reactive oxygen species formation and glutathione levels. Plumbagin also improved postural instability and cognitive impairment in rotenone-treated male rats. Our network analysis indicated that plumbagin could also improve dopamine signaling. Additionally, plumbagin could exhibit anti-oxidant and anti-inflammatory activity through the activation of Nrf2. Cumulatively, our study suggests that plumbagin is a novel Keap1 covalent inhibitor for Nrf2-mediated neuroprotection in PD.

Multicomponent reaction for synthesis, molecular docking, and anti-inflammatory evaluation of novel indole-thiazole hybrid derivatives.

In this article, novel thiazol-indolin-2-one derivatives 4a-f have been synthesized via treatment of thiosemicarbazide (1) with some isatin derivative 2a-f and N-(4-(2-bromoacetyl)phenyl)-4-tolyl-sulfonamide (3) under reflux in ethanol in the presence of triethyl amine (TEA). The structures of new products were elucidated by elemental and spectral analyses. Moreover, all compounds were investigated for their in vivo anti-inflammatory activity using celecoxib as a reference drug. The target compound 4b was the most active anti-inflammatory candidate and exhibited higher edema inhibition (EI = 38.50%) than that recorded by celecoxib (EI = 34.58%) after 3h. Furthermore, the most active compounds 4b and 4f were subjected to a molecular docking study inside COX-2 enzyme to show their binding interactions. Both compounds 4b and 4f showed good fitting into COX-2 binding site with docking energy scores -11.45kcal/mol and -10.48kcal/mol, respectively which indicated that compound 4b revealed the most promising and effective anti-inflammatory potential.