Docking Complex Research Articles

Usenamine A: a potential therapeutic agent for rheumatoid arthritis and ankylosing spondylitis through its anti-inflammatory activity

BackgroundUsenamine A (UA) is a natural compound isolated from the lichen Usnea diffracta, and its therapeutic effects on rheumatic diseases are not well understood. This study aimed to evaluate the potential anti-inflammatory effects of UA and its therapeutic effects on rheumatoid arthritis (RA) and ankylosing spondylitis (AS).Materials and methodsMolecular docking was performed between the 3D structure of UA and the TNF-TNFR2 complex. Peripheral blood mononuclear cells (PBMCs) from RA and AS patients were treated with UA, and cell viability was measured using the MTS assay and flow cytometry. The in vitro effects of co-culture with UA were determined by measuring inflammatory cytokines, including IFN-γ, IL-17A, and GM-CSF, using flow cytometry and enzyme-linked immunosorbent assay (ELISA). The in vivo effects of UA were evaluated using an arthritis mouse model.ResultsThe docking complex of UA bound to the TNF-TNFR2 complex exhibited docking scores of −5.251 kcal/mol and −6.274 kcal/mol, confirming their active sites. UA did not affect cell viability and suppressed the production of inflammatory cytokines in the PBMCs of RA (IFN-γ, IL-17A, and GM-CSF) and AS (GM-CSF) patients. The ELISA also confirmed reduced cytokine levels in the co-culture of UA and PBMCs from RA or AS patients. In the arthritis mouse model, significantly reduced clinical and histological scores were observed in the UA treatment group.ConclusionOur findings suggest that UA has potential as a binding target for TNF, suppresses inflammatory cytokines in PBMCs, and exhibits anti-inflammatory effects on arthritis in a mouse model.

Design, synthesis, structural characterization, cytotoxicity and computational studies of Usnic acid derivative as potential anti-breast cancer agent against MCF7 and T47D cell lines

Development of novel inhibitors is necessary to counteract the rising prevalence of breast cancer (BC) in women in recent years, as evidenced by the side-effect profiles of a few clinically approved inhibitors. In this study, the usnic acid derivative (UA1) was synthesized due to the effectiveness of usnic acid (UA) against BC cell line. Furthermore, the structure of synthesized compound was determined using FT-IR, 1H-NMR, 13C-NMR, HSQC, and HMBC spectroscopic techniques. The anticancer potential of UA1 was assessed using the MTT assay on two different cell lines of BC including MCF7 and T47D. To ascertain the binding affinity and stability of the docking complex, further procedures included the in silico molecular docking, molecular dynamic simulation, principal component analysis, and binding free energy experiments. The cytotoxicity results show that the UA1 exhibits strong antitumor activities and comparable effects against BC cell lines with the IC50 values of 9.21µM for MCF7 cell and 14.8µM for T47D cell, respectively, where the positive control cisplatin showed the IC50 values of 8.95µM for MCF7 cell and 10.9µM for T47D cell. Additionally, the molecular docking results of UA1 showed that it interacts strongly into the active site of target protein. Molecular dynamics simulation results also revealed that the docking complex was formed stability with the RMSD and RMSF values of 0.50nm and 0.19nm, respectively. According to the PCA analysis, the target protein displays good conformational space behaviour when bound with UA1. Furthermore, the UA1 showed the free binding energy value of -18.52kcal/mol with the target protein, which indicating that UA1 may prevent BC.

Structural Bioinformatics Study Revealed Inhibition of Acute Myeloid Leukemia through Targeting Inhibition BTG2 Gene by Using Herbal Medicine

Acute myeloid leukemia (AML) is responsible for more than 40% of adult patients suffering from adverse effects leading to death around the world. The B-cell translocation gene 2 (BTG2) gene work as a tumor suppressor. In this study, a list of medicinal herb compounds and drugs was investigated for their pharmacokinetic properties and cytotoxicity by applying the SwissADME, pkCSM, and Molsoft LLC websites. The molecular docking between the medicinal herbs and AML-standard drugs against the human BTG2 gene was carried out by Auto-dock Vina. Furthermore, protein-protein interactions, gene ontology, and gene enrichment analysis were investigated to display the biological pathways related to BTG2. Also, molecular dynamics simulation was examined to study the behavior of the BTG2 protein and the protein-ligand complex. The present work exhibited that hesperidin displayed the highest binding affinity of −7.0 kcal/mol when interacting and docked against the BTG2 protein, while Cytarabinee and daunorubicin had binding affinity of 5.0 and 5.8 kcal/mol, respectively. The PPI highlighted 101 interactions with P-values less than 10 e-16., and the highest similarity score of 0.13 was found in P53 transcriptional gene network pathways. Interestingly, gene enrichment analysis illustrated that RNA degradation was the most significant enrichment pathway. Also, BTG2 contributes to the P53 signaling pathway in chronic myeloid leukemia. Via GADD45A gene. Molecular dynamics simulations were carried out for the highest binding docking (BTG2-hesperidin) complex, and the results revealed conformational alterations with more pronounced surface residue fluctuations in BTG2. The direct interaction of hesperidin with various crucial amino-acid residues like HIS 49, CYS 67, ARG 69, ASN 71, ASP 75, ARG 112, and THR 101 causes modifications in these residues, which ultimately attenuate the activity of the BTG-2 protein. The molecular dynamics determine the four numbers of H-bonds for executing the interaction between BTG2 and hesperidin. The best residue with high energy around all poses is Arg69. Finally, the present work highlighted that hesperidin was the highest phytochemical compound binding to BTG2 protein.

New targets and biomarkers for doxorubicin-induced cardiotoxicity in humans: implications drawn from toxicogenomic data and molecular modelling

The doxorubicin-induced cardiotoxicity continues to be a life-threatening adverse effect in the clinic. Doxorubicin-induced acute cardiotoxicity is reversible, whereas chronic cardiotoxicity is irreversible, leading to dilated cardiomyopathy and heart failure. The aim of this study was to identify the molecular mechanisms associated with doxorubicin metabolites in doxorubicin-induced chronic cardiotoxicity. For this purpose, literature searches and in silico toxicogenomic analyses were conducted using various tools, including the Comparative Toxicogenomic Database, GeneMANIA, Metascape, MIENTURNET, ChEA3, and AutoDock. Additionally, molecular dynamics simulations were performed for 500 ns using Schrödinger software to assess the stability and dynamics of the representative docked complexes. We observed that doxorubicin biotransformed into five metabolites in the human heart and identified 11 common genes related to doxorubicin, its metabolites, dilated cardiomyopathy, and heart failure. Our findings revealed that doxorubicin and its metabolites primarily exhibited binding affinity to the beta-1 adrenergic receptor and fatty acid synthase. Furthermore, we identified several key transcription factors, especially the Homeobox protein Nkx-2.6, and hsa-miR-183-3p associated with this cardiotoxicity. Finally, we observed that, in addition to doxorubicinol, 7-deoxidoxorubicinone, another metabolite of doxorubicin, may also contribute to this cardiotoxicity. These findings contribute to our understanding of the processes underlying doxorubicin-induced chronic cardiotoxicity.

Assessment of the binding mechanism of ergothioneine to human serum albumin: Multi-spectroscopy, molecular docking and molecular dynamic simulation

Ergothioneine (EGT) has attracted great attention due to its extremely potent antioxidant properties, universally acknowledged as ‘longevity vitamin’. In order to comprehensive understanding of its pharmacodynamics and pharmacokinetics, the binding mechanism of EGT with human serum albumin (HSA) was clarified by cutting-edged multi-spectroscopic approaches and in silico molecular docking coupled with molecular dynamic simulation. Our fluorescence quenching results revealed that the binding of EGT to HSA was in a static quenching mode validated by the descending Stern–Volmer constant (Ksv) values (2.82, 2.36, 1.48 × 104 L mol−1) and biomolecular quenching rate constant (Kq) values (2.82, 2.36, 1.48 × 1012 L mol−1) at 298 K, 305 K, and 310 K, respectively. van’t Hoff criterion revealed the combination of EGT with HSA was a spontaneous exothermic process (ΔG = −24.16 kJ mol−1) via hydrogen bonding and van der Waals force interactions (ΔH = −60.25 kJ mol−1, ΔS = −129.44 J mol−1 K−1) at 310 K. The analysis of UV–vis absorption spectrum, synchronous fluorescence spectrum, three-dimensional fluorescence spectrum and circular dichroism indicated the addition of EGT affected the microenvironment of Trp214 and rearranged the structure of HSA. The binding replacement assay interpreted their binding site was near the subdomain IIA of HSA (Sudlow’s site I), which was intuitively exhibited by molecular docking. In addition of obvious van der Wall forces, attractive charge and Pi-alkyl interactions, the chiral betaine group (N+(CH3+)3) in the side chain of EGT was inclined to form hydrogen bonds with Lys199, Ser287 and Arg257 in the hydrophobic cavity of albumin. Moreover, the dynamic simulation reinforced the equilibrium and stability of formed docking complex by four indicators (RMSD, RMSF, Rg, SASA) within 100 ns.

Multi-Epitopic Peptide Vaccine Against Newcastle Disease Virus: Molecular Dynamics Simulation and Experimental Validation.

Newcastle disease virus (NDV) is a highly contagious and economically devastating pathogen affecting poultry worldwide, leading to significant losses in the poultry industry. Despite existing vaccines, outbreaks continue to occur, highlighting the need for more effective vaccination strategies. Developing a multi-epitopic peptide vaccine offers a promising approach to enhance protection against NDV. Here, we aimed to design and evaluate a multi-epitopic vaccine against NDV using molecular dynamics (MD) simulation. We retrieved NDV sequences for the fusion (F) protein and hemagglutinin-neuraminidase (HN) protein. Subsequently, B-cell and T-cell epitopes were predicted. The top potential epitopes were utilized to design the vaccine construct, which was subsequently docked against chicken TLR4 and MHC1 receptors to assess the immunological response. The resulting docked complex underwent a 1 microsecond (1000 ns) MD simulation. For experimental evaluation, the vaccine's efficacy was assessed in mice and chickens using a controlled study design, where animals were randomly divided into groups receiving either a local ND vaccine or the peptide vaccine or a control treatment. The 40 amino acid peptide vaccine demonstrated strong binding affinity and stability within the TLR4 and MHC1 receptor-peptide complexes. The root mean square deviation of peptide vaccine and TLR4 receptor showed rapid stabilization after an initial repositioning. The root mean square fluctuation revealed relatively low fluctuations (below 3 Å) for the TLR4 receptor, while the peptide exhibited higher fluctuations. The overall binding energy of the peptide vaccine with TLR4 and MHC1 receptors amounted to -15.7 kcal·mol-1 and -36.8 kcal·mol-1, respectively. For experimental evaluations in mice and chicken, the peptide vaccine was synthesized using services of GeneScript Biotech® (Singapore) PTE Limited. Experimental evaluations showed a significant immune response in both mice and chickens, with the vaccine eliciting robust antibody production, as evidenced by increasing HI titers over time. Statistical analysis was performed using an independent t-test with Type-II error to compare the groups, calculating the p-values to determine the significance of the immune response between different groups. Multi-epitopic peptide vaccine has demonstrated a good immunological response in natural hosts.

Development of novel CDK9 and CYP3A4 inhibitors for cancer therapy through field and computational approaches.

Cyclin-dependent kinase 9 (CDK9) and cytochrome P450 3A4 (CYP3A4) have emerged as promising targets in the development of anticancer drugs, presenting a consistent challenge in the quest for potent inhibitors. CDK9 inhibitors can selectively target fast-growing cancer cells by disrupting transcription elongation, which in turn hinders the production of proteins essential for cell cycle progression and survivaŚ. Understanding how CYP3A4 metabolizes specific chemotherapy drugs allows for personalized treatment plans, optimizing drug dosages according to a patient's metabolic profile. Since many cancer patients undergo combination therapies, and CYP3A4 is vital in drug metabolism, its inhibition or induction by one drug can alter the plasma levels of others, potentially leading to treatment failure or increased toxicity. Therefore, managing CYP3A4 activity is critical for effective cancer treatment. Employing a range of computational methodologies, this study systematically investigated the binding mechanisms of pyrimidine derivatives against CDK9 and CYP3A4. The field-based model demonstrated high R 2 values (0.99), with Q2 (0.66), demonstrating its ability to predict in silico inhibitory activity against the target of this study. The screening process followed in this work led to the discovery of powerful new inhibitor compounds. Of the 15 new compounds designed, three have a high affinity with the target (ranging from -8 to -9kcal/molkcal/mol) and were singled out through docking filtration for more detailed investigation. As well as, a reference compound with a substantial pIC50 value of 8.4, serving as the foundation for the development of the new compounds, was included for comparative analysis. To elucidate the essential features of CDK9 and CYP3A4 inhibitor design, a comparative analysis was conducted between 3D-QSAR-generated contours and molecular docking conformations of ligands. Molecular dynamics simulations were carried out for a duration of 100 ns on selected docked complexes, specifically those involving novel compounds with CDK9 and CYP3A4 enzymes. Additionally, the binding free energy for these complexes was assessed using the MM/PBSA method, which evaluates the free energy landscape of protein-ligand interactions. The results of MM/PBSA highlighted the strength of the new compounds in enhancing interactions with the target protein, which favors the results of molecular docking and MD simulation. These insights contribute to a deeper understanding of the mechanisms underlying CDK9 and CYP3A4 inhibition, offering potential avenues for the development of innovative and effective CDK9 inhibitors.

Antifungal Efficacy of Ultrashort β-Peptides against Candida Species: Mechanistic Understanding and Therapeutic Implications.

Candidiasis, a condition spurred by the unchecked proliferation of Candida species, poses a formidable global health threat, particularly in immunocompromised individuals. The emergence of drug-resistant strains complicates management strategies, necessitating novel therapeutic avenues. Antimicrobial peptides (AMPs) have garnered attention for their potent antifungal properties and broad-spectrum activity against Candida species. This study assessed the antifungal effectiveness of ultrashort β-peptides against Candida strains, with a specific focus on peptide P3 (LAU-β3,3-Pip-β2,2-Ac6c-PEA). Our findings showed P3's remarkable fungistatic and fungicidal activities against Candida albicans, exhibiting an MIC of 4 μg/mL, comparable to those of standard antifungal drugs. The MIC value remained unchanged in the presence of ADC and BSA, indicating that serum albumin does not diminish the activity of P3. P3 demonstrates synergistic effects when combined with Fluconazole (FLU), Itraconazole (ITR), and Nystatin (NYS) to the extent that it becomes effective at 0.125, 0.125, and 0.03125 μg/mL, respectively. Concentration versus time-kill kinetics showed its time-dependent activity up to the first 12 h against C. albicans, and later concentration also played a role; indeed, at 24 h the whole culture was sterilized at 8× MIC. Post-antifungal effect assays confirmed prolonged suppression of pathogen growth after the removal of P3 from the media for significant durations. More importantly, P3 inhibits hyphae formation and biofilm development of Candida, outperforming Fluconazole with respect to these properties. Mechanistic insights display P3's potential to disrupt fungal cell membrane integrity and dose-dependent inhibition of ergosterol biosynthesis, essential for fungal cell wall integrity. Using the Bradford assay, it was observed that extracellular protein concentrations increased with higher doses of the compound, thereby validating the effect of P3 on membrane integrity. A comparative gene analysis using RT-PCR showed that P3 downregulates ERG3, ERG11, and HWP1, which are crucial for the survival and pathogenicity of C. albicans. The impact of P3 on ERG11 and ERG3 is more effective than that of Fluconazole. Molecular docking studies revealed strong binding of P3 to various isoforms of lanosterol 14-α-demethylase, a key enzyme in ergosterol synthesis. Furthermore, molecular dynamic simulations validated the stability of the most promising docking complex. Overall, our findings underscore P3's potential as a leading candidate for the development of innovative antifungal therapies, warranting further investigation and optimization.

Exploring the Potential Molecular Mechanism of the Shugan Jieyu Capsule in the Treatment of Depression through Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation.

Shugan Jieyu Capsule (SJC) is a pure Chinese medicine compound prepared with Hypericum perforatum and Acanthopanacis senticosi. SJC has been approved for the clinical treatment of depression, but the mechanism of action is still unclear. Network pharmacology, molecular docking, and molecular dynamics simulation (MDS) were applied in the present study to explore the potential mechanism of SJC in the treatment of depression. TCMSP, BATMAN-TCM, and HERB databases were used, and related literature was reviewed to screen the effective active ingredients of Hypericum perforatum and Acanthopanacis senticosi. TCMSP, BATMAN-TCM, HERB, and STITCH databases were used to predict the potential targets of effective active ingredients. GeneCards database, DisGeNET database, and GEO data set were used to obtain depression targets and clarify the intersection targets of SJC and depression. STRING database and Cytoscape software were used to build a protein-protein interaction (PPI) network of intersection targets and screen the core targets. The enrichment analysis on the intersection targets was conducted. Then the receiver operator characteristic (ROC) curve was constructed to verify the core targets. The pharmacokinetic characteristics of core active ingredients were predicted by SwissADME and pkCSM. Molecular docking was performed to verify the docking activity of the core active ingredients and core targets, and molecular dynamics simulations were performed to evaluate the accuracy of the docking complex. We obtained 15 active ingredients and 308 potential drug targets with quercetin, kaempferol, luteolin, and hyperforin as the core active ingredients. We obtained 3598 targets of depression and 193 intersection targets of SJC and depression. A total of 9 core targets (AKT1, TNF, IL6, IL1B, VEGFA, JUN, CASP3, MAPK3, PTGS2) were screened with Cytoscape 3.8.2 software. A total of 442 GO entries and 165 KEGG pathways (p <0.01) were obtained from the enrichment analysis of the intersection targets, mainly enriched in IL-17, TNF, and MAPK signaling pathways. The pharmacokinetic characteristics of the 4 core active ingredients indicated that they could play a role in SJC antidepressants with fewer side effects. Molecular docking showed that the 4 core active components could effectively bind to the 8 core targets (AKT1, TNF, IL6, IL1B, VEGFA, JUN, CASP3, MAPK3, PTGS2), which were related to depression by the ROC curve. MDS showed that the docking complex was stable. SJC may treat depression by using active ingredients such as quercetin, kaempferol, luteolin, and hyperforin to regulate targets such as PTGS2 and CASP3 and signaling pathways such as IL-17, TNF, and MAPK, and participate in immune inflammation, oxidative stress, apoptosis, neurogenesis, etc.

Insilico Insights into Resveratrol as a Potential Inhibitor of Mycobacterium Tuberculosis Enoyl-ACP Reductase (InhA) Protein

Mycobacterium tuberculosis, the causative agent of tuberculosis, is a global cause of death. Thus, the development of innovative treatment strategies is required. Objective: To develop in-silico drugs by phytochemicals to inhibit the Enoyl-ACP reductase (InhA) protein, which is essential for synthesizing mycobacterial cell walls. Methods: The 3D structure of InhA was taken from the Protein Data Bank. The Ramachandran plot validated the model with a score of 98.7% from the favoured Ramachandran plot. Computed Atlas of Surface Topography of Proteins was used to detect the active sites for ligand interaction. Resveratrol were selected based on existing studies and further listed for drug-likeness. Absorption, Distribution, Metabolism, Excretion, and Toxicity analysis showed the possibility of resveratrol as a drug candidate, with no violation of Lipinski rules and excellent absorption in the Gastrointestinal Tract. Results: The boiled egg model confirmed the ability of ligands to go through the blood-brain barrier. Toxicity predictions of resveratrol indicated low risks with several other systems of organs. Molecular docking with CB-Dock2 showed the strong binding of Resveratrol to InhA, with a Vina score equal to -8.8 kcal/mol. Further exploration of the docking complex by molecular docking simulation using the Integrated Management of the Public Distribution System was carried out, and the trajectory confirmed stable interaction and protein flexibility. Conclusions: It was concluded that resveratrol acts as a potent, non-toxic candidate for tuberculosis treatment and highlights its inhibition capacity of InhA. Results need future vitro and in vivo validation to develop this highly reliable therapeutic alternative for combating tuberculosis.

The 3D-QSAR Study, Molecular Docking, and ADMET Analysis of Darunavir Derivatives of HIV-1 Protease Inhibitors

Background: Acquired Immunodeficiency Syndrome (AIDS) is one of most prevalent infectious diseases in the world , and HIV-1 protease (PR) is a vital target of drug design. Nowadays, three-dimensional quantitative structure-activity relationships (3D-QSAR) are applied to help design new protease inhibitions (PIs). Objective: The primary objective of this study is to apply the 3D-QSAR study to a series of 42 derivatives of Darunavir (DRV) and to design new molecules possessing high antivirus activity. Methods: Partial Least Squares (PLS) were used to cross-validate the dataset of compounds, and the optimal number of principal components (ONC), cross-validate coefficient (q²), standard error of estimate (SEE), non-cross-validated correlation coefficient (R²) and fisher test value (F) were calculated to assess model robustness. In this study, the CoMSIA-DAH model (q²=0.754, r²= 0.988, rpred2=0.57) possessed the highest predicted activity. Newly designed molecules were analyzed by docking studies with compound 25 taken as a template. Results: Within eight newly designed drugs, compound N02 possessed the highest antivirus activity (IC50=0.00461 nM) predicted by the CoMSIA-DAH model. The Surflex-Dock module of SYBYL-X 2.0 was used to affirm the predicted anti-PR activity of the newly designed compounds and the results of docking complex structure could be visualized. All newly designed molecules were in agreement with CSore above four and the docking study revealed that Asp29, Asp30, Ile50, Asp124, Asp128, Asp129 and Ile149 were critical residues in the process of inhibiting PR. Conclusion: One of the main aspects of this study is the successful design of a series of molecules with excellent investigatory values, which elucidates explicit quantitative structure-activity relationships of DRV derivatives and will provide significant suggestions for future pharmaceutical research.

Cheminformatics approaches to predict the bioactivity and to discover the pharmacophoric traits crucial to block NF-κB

Many human disorders include NF-kB signaling pathways, making IKK a therapeutic target in cancer treatment. Inflammatory illnesses and cancer are examples. COVID-19 is one of several triggers that stimulate NF-kB signaling. The activation of the NF-kB pathway is necessary for COVID-19 to cease its development. To learn more about the mechanism and structural features essential to IKK inhibition (IC50), molecular modeling studies have been undertaken on experimentally reported 503. QSAR analysis explores certain reported and hidden structural features critical for IKKβ inhibition. The OECD guidelines guided the construction of the QSAR model, which achieved all the endorsed threshold values for all validation parameters (R2tr:0.81, R2LMO:0.80, and R2ext:0.78). The present QSAR study shows that IKK inhibitory activity is linked to the following structural features: lipophilic hydrogen atoms within 2 A units of the molecule's center of mass; ring nitrogen atoms within one bond of planar nitrogen atoms; ring carbon atoms exactly four bonds from the non-ring nitrogen atoms; planar nitrogen atoms exactly four bonds from sp2 hybridized carbon atoms; and so on. Pharmacophore modeling highlighted QSAR-identified structural characteristics. To investigate binding, we docked all 503 molecules. The observation indicates that the QSAR and molecular docking/pharmacophore modeling findings are in agreement. Following this, we conducted 200 ns of molecular dynamics simulation to validate the molecular docking protocol. MMGBSA analysis determined the binding energy of the dock complex. Thus, the current study found unique pharmacophoric properties that may assist in optimizing lead/hit compounds for anti-IKKβ activity.

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.

Characterization of urease active calcite-producing strain YX-3 combined with the whole genome

Urease found in a wide range of microorganisms plays a vital role in ureolytic induced calcite precipitation (UICP). However, the genomic information on urease-producing strains is limited, and there is a need for further in-depth studies on aspects such as the regulation of urease activity by nickel ligand residues. The present study delved into the elucidation of urease activity in a newly isolated strain YX-3 coupled with nickel-ligand residues by employing the genetic architecture of biomineralization-controlled growth, molecular docking, molecular dynamics simulation (MDS), and site-directed mutagenesis. Genome-wide sequencing showed the presence of urease gene clusters, comprising structural genes ureA, ureB, and ureC, alongside auxiliary genes ureD, ureE, ureF, and ureG. RT-qPCR analysis showed that the addition of NiCl2 resulted in a significant up-regulation of ureC expression. His267, His294, and Gly325 in the domain of UreC were further proved to coordinate with nickel ions and urea simultaneously through homology modeling and molecular docking, and molecular dynamics simulations (MDS) showed the urease-urea docking complexes exhibited degressive binding stability by four metrics including root mean square deviations (RMSD) when those residues were mutated into alanine respectively. Western blotting exhibited that mutations of H267A, H294A, and G325A led to a reduction in the relative expression of urease, wherein urease activity was about 62%, 45%, and 20% times that of the wild type (WT), respectively. The overexpression results further confirmed the importance of these residues for urease activity and CaCO3 precipitation. These results would help to deepen the understanding of urease-producing strains at a molecular level and expand the theoretical basis for modulating urease activity.

Synthesis, structure, supramolecular assembly inspection by Hirshfeld surface analysis, DFT study and molecular docking inspection of 4,5-bis(2-chlorophenyl)-8a-phenylhexahydropyrimido[4,5-d]pyrimidine-2,7(1H,3H)-dithione

We studied the three-component condensation of 2-chloraldehyde, acetophenone, and thiourea in conjunction with HCl, resulting in the formation of a new compound: 4,5-bis(2-chlorophenyl)-8a-phenylhexahydropyrimido[4,5-d]pyrimidine-2,7(1H,3H)-dithione (CPPD). The compound's structure was affirmed via X-ray diffraction study. The asymmetric unit contained two molecules that were independent relative to crystallography and an ethanol solvent. The difference between independent molecules was explored by dihedral angles between similar rings in both molecular. The difference between molecules was further explored by molecular overlay plot. The supramolecular assembly was supported via diverse intermolecular interactions which were studied through the use of Hirshfeld surface analysis. Electronic structure computations were carried out at the ωb97xd/tzvp level. Natural bonding orbital (NBO), and FMO study reveal reactivity and charge transfer mechanisms within the compound. Furthermore, the nature of bonding in the present molecule is characterized through quantum theory of atoms in molecules (QTAIM), ELF, and LOL studies. Ab-initio molecular dynamic (AIMD) revealed the kinetic and thermodynamic stability at 300 K. The DFT results have excellent correlation with experimental data. The molecular docking and molecular dynamics simulation further revealed the compound to get deep access in the active pocket of type 2 anti-diabetes GLUT4 protein. This was validated by the stable dynamics as demonstrated by the uniform behavior of the root mean square deviation (RMSD) plot. The root mean square fluctuation (RMSF) also showed stable interactions with amino acids in the presence of the compound. Further, simulation trajectories on the basis of binding free energies indicate the significant role of van der Waals force in the formation of the intermolecular docked complex. This concluded the compound might be a potent structure for the development of anti-diabetic compounds.

Computational modeling study of IL-15-NGR peptide fusion protein: a targeted therapeutics for hepatocellular carcinoma

The primary challenge to improving existing cancer treatment is to develop drugs that specifically target tumor cell. NGR peptide is tumor homing peptide that selectively target cancer cells while interleukin 15 is a pleiotropic cytokine with anticancer properties. This study computationally engineered a IL15-NGR fusion peptide by linking the homing peptide NGR with the targeting peptide IL-15. After evaluating and validating the chimeric peptide, we docked it to the IL-15Rα/IL-15Rβ/γc heterodimer receptor, examining the interactions and binding energy and lastly, molecular dynamics simulations were performed. The secondary and tertiary structures, along with physicochemical properties of the designed IL-15-NGR chimeric protein, were predicted using GOR IV, trRosetta and ProtParam online servers respectively. The quality and 3D structure validation were confirmed via ProSA-web and SAVES 6.0 analysis which predicted an ERRAT score of 96.72%, with 97.6% of residues in the Ramachandran plot, validating its structure. Finally, Docking, MD simulations and interaction analysis were performed using ClusPro 2.0 and GROMACS and PDBsum, which exhibited significant hydrogen bonding and salt bridges, confirming the formation of a stable docked complex. These results were further corroborated by simulation analysis, which demonstrated a stable and dynamic behavior of the docked complex in a biological environment. The predicted high expression value of fusion protein was 0.844 in E.coli using SOLUPROT tool. These findings suggest efficient expression of the IL15-NGR fusion protein if its gene is inserted into E. coli and indicates its potential as a safe and effective anticancer treatment, paving the way for targeted therapeutic interventions.Graphical abstract

Bioinformatic elucidation of conserved epitopes to design a potential vaccine candidate against existing and emerging SARS-CoV-2 variants of concern

The COVID-19 pandemic caused by SARS-CoV-2 poses a significant adverse effects on health and economy globally. Due to mutations in genome, COVID-19 vaccine efficacy decreases. We used immuno-informatics to design a Multi epitope vaccine (MEV) candidate for SARS-CoV-2 variants of concern (VOCs). Hence, we predicted binders/epitopes MHC-I, CD8+, MHC-II, CD4+, and CTLs from spike, membrane and envelope proteins of VOCs. In addition, we assessed the conservation of these binders and epitopes across different VOCs. Subsequently, we designed MEV by combining the predicted CTL and CD4+ epitopes from spike protein, peptide linkers, and an adjuvant. Further, we evaluated the binding of MEV candidate against immune receptors namely HLA class I histocompatibility antigen, HLA class II histocompatibility antigen, and TLR4, achieving binding scores of −1265.3, −1330.7, and −1337.9. Molecular dynamics and normal mode analysis revealed stable docking complexes. Moreover, immune simulation suggested MEV candidate elicits both innate and adaptive immune response. We anticipate that this conserved MEV candidate will provide protection from VOCs and emerging strains.

Localisation and function of key axonemal microtubule inner proteins and dynein docking complex members reveal extensive diversity among vertebrate motile cilia.

Vertebrate motile cilia are classified as (9+2) or (9+0), based on the presence or absence of the central pair apparatus, respectively. Cryogenic electron microscopy analyses of (9+2) cilia have uncovered an elaborate axonemal protein composition. The extent to which these features are conserved in (9+0) cilia remains unclear. CFAP53, a key axonemal filamentous microtubule inner protein (fMIP) and a centriolar satellites component, is essential for motility of (9+0), but not (9+2) cilia. Here, we show that in (9+2) cilia, CFAP53 functions redundantly with a paralogous fMIP, MNS1. MNS1 localises to ciliary axonemes, and combined loss of both proteins in zebrafish and mice caused severe outer dynein arm loss from (9+2) cilia, significantly affecting their motility. Using immunoprecipitation, we demonstrate that, whereas MNS1 can associate with itself and CFAP53, CFAP53 is unable to self-associate. We also show that additional axonemal dynein-interacting proteins, two outer dynein arm docking (ODAD) complex members, show differential localisation between types of motile cilia. Together, our findings clarify how paralogous fMIPs, CFAP53 and MNS1, function in regulating (9+2) versus (9+0) cilia motility, and further emphasise extensive structural diversity among these organelles.

Evolution of heritage and development in Liverpool's waterfront over 40 years

The recent delisting of Liverpool’s World Heritage Site has highlighted the adverse impacts of ongoing urban developments on the city’s heritage. This study aims to address the critical question of how Liverpool can safeguard its heritage following the loss of its World Heritage status. As this status withdrawal implies a lack of international policy consideration, it raises important questions: What additional measures should be implemented? How could we reassess Liverpool's heritage in this new context? To tackle these issues, we investigate the changing relationship between safeguarding heritage and urban development on Liverpool Waterfront’s Historic Urban Landscape over the past 40 years. This study analyses the impact of developments on Liverpool’s heritage values, specifically focusing on Integrity, Authenticity, and Outstanding Universal Value. By employing a novel, top-down heritage impact assessment methodology, we evaluate the influence of urban and architectural developments on these values. This methodology is distinguished by its comprehensive comparative analysis of diverse elements drawn from heritage policy documents, spanning both tangible and intangible domains. In addition, we conducted interviews with experts familiar with Liverpool's heritage context to deepen our understanding of developmental impacts. The analysis framework comprises three case study areas and their associated developments: the adaptive reuse of the Albert Dock Complex (1981–1988), the Pier Head Developments (2007–2013), and the Stanley Dock Conservation Area (2021 onwards). The findings indicate that adaptive reuse schemes have been reasonably successful in preserving heritage values, whereas certain urban interventions have had detrimental effects. This study underscores the need for stricter regulations and broader stakeholder involvement to protect Liverpool's heritage. Further research is recommended, incorporating more development case studies and examining successful urban interventions in other heritage cities, to strengthen Liverpool’s heritage safeguarding strategies amidst evolving urban development pressures.

Immuno-informatics study identifies conserved T cell epitopes in non-structural proteins of Bluetongue virus serotypes: formulation of a computationally optimized next-generation broad-spectrum multi-epitope vaccine.

Bluetongue (BT) poses a significant threat to the livestock industry, affecting various animal species and resulting in substantial economic losses. The existence of numerous BT virus (BTV) serotypes has hindered control efforts, highlighting the need for broad-spectrum vaccines. In this study, we evaluated the conserved amino acid sequences within key non-structural (NS) proteins of BTV and identified numerous highly conserved murine- and bovine-specific MHC class I-restricted (MHC-I) CD8+ and MHC-II-restricted CD4+ epitopes. We then screened these conserved epitopes for antigenicity, allergenicity, toxicity, and solubility. Using these epitopes, we developed in silico-based broad-spectrum multiepitope vaccines with Toll-like receptor (TLR-4) agonists. The predicted proinflammatory cytokine response was assessed in silico using the C-IMMSIM server. Structural modeling and refinement were achieved using Robetta and GalaxyWEB servers. Finally, we assessed the stability of the docking complexes through extensive 100-nanosecond molecular dynamics simulations before considering the vaccines for codon optimization and in silico cloning. We found many epitopes that meet these criteria within NS1 and NS2 proteins and developed in silico broad-spectrum vaccines. The immune simulation studies revealed that these vaccines induce high levels of IFN-γ and IL-2 in the vaccinated groups. Protein-protein docking analysis demonstrated promising epitopes with strong binding affinities to TLR-4. The docked complexes were stable, with minimal Root Mean Square Deviation and Root Mean Square Fluctuation values. Finally, the in silico-cloned plasmids have high % of GC content with > 0.8 codon adaptation index, suggesting they are suitable for expressing the protein vaccines in prokaryotic system. These next-generation vaccine designs are promising and warrant further investigation in wet lab experiments to assess their immunogenicity, safety, and efficacy for practical application in livestock. Our findings offer a robust framework for developing a comprehensive, broad-spectrum vaccine, potentially revolutionizing BT control and prevention strategies in the livestock industry.