Dynamics Simulation Analysis Research Articles

Molecular dynamics mechanism of incorporating ZnO with varying particle sizes into ECTFE coatings and its impact on corrosion resistance

A composite coating of zinc oxide/chlorotrifluoroethylene copolymer (ZnO/ECTFE) was prepared on the surface of carbon steel via electrostatic spraying and heat treatment at 260 ℃. The influence of ZnO particle size variations on the anticorrosive properties of ECTFE coating was investigated by characterizing the microstructure, adhesion, hydrophilic/hydrophobic properties, electrochemical corrosion performance, as well as the dynamics simulation analysis on water molecule and chloride ions diffusion in the coating. The results show that the ECTFE coating incorporated with 100nm ZnO has the highest surface roughness (Roughness coefficient Ra = 30.6nm), the most robust adhesion (Bonding pull-out strength = 5.22MPa), and the lowest corrosion current density after a 90-day immersion (Icorr,90d = 4.05 × 10⁻⁸ A∙cm⁻²). These improvements represent an increase of 81.67% and 59.9% compared to the pure copolymer coating (Icorr,90d = 2.21 × 10⁻⁷ A∙cm⁻²) and the coating incorporated with 200nm ZnO (Icorr,90d = 1.01 × 10⁻⁷ A∙cm⁻²), respectively. This phenomenon can be attributed to the addition of small-sized ZnO, which enhances the density of the coating, induces a hydrophobic transition on its surface, strengthens the double electric layer effect, thereby improving its resistance against water molecule and chloride ions diffusion and ultimately enhances the corrosion resistance.

In-silico Docking and Dynamics Simulation Analysis of Peroxisome Proliferator-Activated Receptor-Gamma and β-Carotene

Background: Peroxisome proliferator-activated receptor-gamma (PPAR-γ) plays a crucial role in regulating lipid and glucose metabolism, cancer, and inflammation, making it an attractive target for drug development. Meanwhile, β-Carotene, known for its antioxidant, anticancer and antiinflammatory properties, holds promise for modulating PPAR-γ activity. Understanding their interaction is crucial. Objective: This study aims to explore the therapeutic potential of β-carotene in modulating PPAR-γ activity by investigating their binding interactions. Methods: Screening of bioactive compounds from PubChem was conducted using GlideXP to identify potential PPAR-γ (PDB: 2PRG) ligands. During this screening, both protein and bioactive compounds were prepared following established protocols. Subsequently, the compounds were docked into the ligand binding domain (LBD) of the protein using XP docking. Rosiglitazone was used as an internal control. β-Carotene emerged as a lead based on Lipinski’s rule, docking score, free energy, and LBD interactions. Molinspiration analysis assessed its drug likeness. Molecular dynamics (MD) simulations utilizing Desmond with OPLS 2005 force field were employed to examine the dynamics and stability of the PPAR-γ/β-carotene complex. Results: β-carotene had strong hydrophobic interactions with specific residues within the ligandbinding domain of PPAR-γ. The calculated binding affinity (-9.07 kcal/mol) indicated a strong interaction between β-carotene and PPAR-γ, suggesting that β-carotene may modulate the activity of PPAR-γ. On a time scale of 100 ns, the MD simulations provided insights into the conformational changes, flexibility, and intermolecular interactions within the complex. Conclusion: In silico docking and dynamics simulation analyses show that PPAR-γ and β-carotene can form a stable complex, suggesting potential implications for metabolic modulation.

Discovery and characterization of temperature adaptation modules by mining L-glutamate decarboxylase derived from psychrophilic microorganisms

Directed alterations of the enzyme's temperature adaptations, such as thermostability and optimal catalytic temperature (Topt), are usually the way to go in order to meet the applications, however they are limited by the understanding between protein structure and function. Glutamate decarboxylase (GADs) is a common enzyme in the food industry. In this study, we identified and characterized three novel L-glutamate decarboxylases from psychrophilic microorganisms. Interestingly, the two enzymes (Gad Psy.Y/Gad Psy.F) showed significant differences in temperature adaptation. Through multiple sequence alignment and structural analysis, two potential regions that may affect the Topt and thermostability of the GAD, termed temperature adaptation modules (TAMs), were targeted. To validate the role of TAMs, we constructed mutants with bi-directional transplants of TAMs, which ultimately significantly altered the temperature adaptation of Gad Psy.Y and Gad Psy.F. Molecular dynamics simulations analysis demonstrated that the introduction and disruption of salt bridges in the mutant TAMs are crucial for this alteration. These findings deepen the understanding of the mechanisms of protein temperature adaptation and provide implications for protein engineering, while also offering advantageous enzymes to support the biosynthesis of GABA.

AI-Assisted Generation and In-depth In-silico Evaluation of Potential Inhibitor Targeting Aurora Kinase A (AURKA): An Anticancer Discovery Exploiting Synthetic Lethality Approach

Genetic alterations are lead causative agents behind the complex pathologies of cancers which render all treatments unarmed. Such alterations in oncogenes can be treated by direct inhibition by specific drugs while alteration in tumor suppressor genes mediating loss of function is challenging to treat. Identification of synthetic lethal partners to specific tumor suppressor genes and mediating their inhibition can be a potential approach to deal with loss of function mutations. Aurora kinase A (AURKA) has been established as an effective synthetic lethal partner of several tumor suppressor genes and is overexpressed in cancerous conditions, mediating adverse pathologies. The present AI-assisted study deals with the generation of novel inhibitor compounds against AURKA and the exhaustive evaluation of the best compound using molecular docking, molecular dynamic simulation, MM/PBSA, and QM/MMGBSA-based analysis. Out of the 200 novel compounds generated using features of ATP binding pocket of AURKA and previously reported inhibitor, compound 1 (4-{5-fluoro-6-[(1Z)-3-hydrazinyl-3-oxo-2-phenylprop-1-en-1-yl]pyridin-2-yl}benzoic acid) was identified as the most potent candidate with high negative binding energy of -10.4 kcal/mol in molecular docking analysis. The molecular dynamic simulation analysis of the AURKA-compound 1 complex and the apo-AURKA protein resulted in major conformational changes in the conserved DFG motif and loop 277-291 of AURKA in the AURKA-compound 1 complex thus inhibiting the entry of ATP to its binding site. The free energy landscape displayed a persistence of folded states of the enzyme in complex form. The MM/PBSA revealed effective Gibb’s free energy of binding of -11 kcal/mol for compound 1 inhibiting AURKA. The QM/MMGBSA analysis resulted in a significantly high negative binding energy of -13.98 kcal/mol proving significant inhibition potential of compound 1 against AURKA. Therefore, further in-vitro investigation can provide a novel effective, and safe treatment against a wide range of cancers by targeting a well-established cancer target AURKA.

A two-step dynamic FEM-FELA approach for seismic slope stability assessment

AbstractThe determination of the factor of safety (FoS) of slopes during seismic excitation can be complex if the relevant effects of pore water pressure accumulation, nonlinear material response and variable shear strength are duly accounted for. A rational two-step approach to tackle this task based on a hydro-mechanically coupled dynamic simulation and finite element limit analyses is henceforth introduced. To ensure accurate transfer of the hydro-mechanical soil state, a mapping concept is presented, accounting for spatial distributions of stresses, excess pore water pressures, inertial forces and shear strength. The proposed approach is compared to limit equilibrium method (LEM) for the case of a large-scale water-saturated open cast mine slope subjected to seismic loading. In comparison with LEM, the new approach to assess seismic slope stability proves to be simpler in its implementation and straightforward, which could be an important asset for practitioners.

DNA binding, and apoptosis-inducing activities of a β-ionone-derived ester in human myeloid leukemia cells: multispectral and molecular dynamic simulation analyses.

β-Ionone is the end-ring counterpart of β-carotenoids, which are widely found in fruits and vegetables. Recent studies have illustrated the antimetastatic, anti-proliferative, and apoptosis-inducing activities of β-ionone both in vitro and in vivo. We aimed to explore the anti-cancer potency of β-Ionone-derived ester, (E)-4-(2,6,6-trimethylcyclohex-1-enyl) but-3-en-2-ylpyrazine-2-carboxylate (4-TM.P). The cytotoxic effects of the compound on K562 cells were evaluated by MTT assay. The mechanisms of apoptosis induction were investigated by acridine orange/ethidium bromide (AO/EtBr) double staining, cell cycle analysis, and Annexin V/PI staining. Furthermore, the 4-TM.P-DNA interactions have been thoroughly elucidated by various methods, such as ultraviolet-visible spectroscopy, fluorescence assays, viscosity measurements, molecular docking, and dynamic simulation. The MTT cytotoxicity assay revealed that the growth of K562 cells was inhibited by treatment with β-ionone-derived ester, with an IC50 of 25 ± 5.0µM at 72h. Morphological studies revealed the occurrence of apoptosis in treated cells, and G0/G1 cell cycle arrest was observed after treatment of the cells with the IC50 value of the compound. Analyses of multi-spectroscopy and viscosity assays revealed that 4-TM.P binds to DNA in the minor groove mode, which was supported by molecular docking studies. The dynamic stability of the complex was also confirmed using molecular dynamic simulation analyses.

Revealing the potential therapeutic mechanism of Lonicerae Japonicae Flos in Alzheimer’s disease: a computational biology approach

BackgroundAlzheimer’s disease (AD) is a degenerative brain disease without a cure. Lonicerae Japonicae Flos (LJF), a traditional Chinese herbal medicine, possesses a neuroprotective effect, but its mechanisms for AD are not well understood. This study aimed to investigate potential targets and constituents of LJF against AD.MethodsNetwork pharmacology and bioinformatics analyses were performed to screen potential compounds and targets. Gene Expression Omnibus (GEO) datasets related to AD patients were used to screen core targets of differential expression. Gene expression profiling interactive analysis (GEPIA) was used to validate the correlation between core target genes and major causative genes of AD. The receiver operating characteristic (ROC) analysis was used to evaluate the predictive efficacy of core targets based on GEO datasets. Molecular docking and dynamics simulation were conducted to analyze the binding affinities of effective compounds with core targets.ResultsNetwork pharmacology analysis showed that 112 intersection targets were identified. Bioinformatics analysis displayed that 32 putative core targets were identified from 112 intersection targets. Only eight core targets were differentially expressed based on GEO datasets. Finally, six core targets of MAPK8, CTNNB1, NFKB1, EGFR, BCL2, and NFE2L2 were related to AD progression and had good predictive ability based on correlation and ROC analyses. Molecular docking and dynamics simulation analyses elucidated that the component of lignan interacted with EGFR, the component of β-carotene interacted with CTNNB1 and BCL2, the component of β-sitosterol interacted with BCL2, the component of hederagenin interacted with NFKB1, the component of berberine interacted with EGFR and BCL2, and the component of baicalein interacted with NFKB1, EGFR and BCL2.ConclusionThrough a comprehensive analysis, this study revealed that six core targets (MAPK8, CTNNB1, NFKB1, EGFR, BCL2, and NFE2L2) and six practical components (lignan, β-carotene, β-sitosterol, hederagenin, berberine, and baicalein) were involved in the mechanism of action of LJF against AD. Our work demonstrated that LJF effectively treats AD through its multi-component and multi-target properties. The findings of this study will establish a theoretical basis for the expanded application of LJF in AD treatment and, hopefully, can guide more advanced experimental research in the future.

Advances in machine learning methods in copper alloys: a review.

Advanced copper and copper alloys, as significant engineering structural materials, have recently been extensively used in energy, electron, transportation, and aviation domains. Higher requirements urge the emergence of high-performance copper alloys. However, the traditional trial-and-error experimental observations and computational simulation research used to design and develop novel materials are time-consuming and costly. With the accumulation of material research and rapid development of computational ability, the thorough application of material genome engineering has sped up the development of novel materials and facilitates the process of systematic engineering application. This review summarizes the benefits of data-driven machine learning techniques and the state of the art of machine learning research in the area of copper alloys. It also displays the widely used computational simulation approaches (e.g., the first-principles calculation, molecular dynamics simulation, phase-field simulations, and finite element analysis) and their combined applications in material design and property prediction. Finally, the limitations of machine learning research methods are outlined, and future development directions are proposed.

Design, Synthesis, and Evaluation of EA-Sulfonamides and Indazole-Sulfonamides as Promising Anticancer Agents: Molecular Docking, ADME Prediction, and Molecular Dynamics Simulations

New EA-sulfonamides and indazole-sulfonamides were synthesized, characterized, and evaluated for their anticancer activities. The target compound structures were elucidated using various spectroscopic techniques such as NMR-{1H and 13C}, infrared spectroscopy, and high-resolution mass spectrometry. The anticancer activities of the novel compounds were evaluated against four human cancer cell lines, namely A-549, MCF-7, Hs-683, and SK-MEL-28 as well as the normal cell line HaCaT, using 5-fluorouracil and etoposide as reference drugs. Among the tested compounds, 9, 10, and 13 exhibited potent anticancer activities which are better than or similar to the reference compounds 5-fluorouracil and etoposide, against the A-549, MCF-7, and Hs-683 cancer cell lines, with IC50 values ranging from 0.1 to 1 μM. Molecular docking studies of compounds 9, 10, and 13 showed a strong binding with selected protein kinase targets, which are linked to the tested cancer types. Furthermore, the analysis of the molecular dynamics simulation results demonstrated that compound 9 exhibits significant stability when bound to both JAK3 and ROCK1 kinases. This new compound has the potential to be developed as a novel therapeutic agent against various cancers.

Network Pharmacology and Molecular Dynamics Simulations Reveal the Mechanism of Total Alkaloid Components in Anisodus Tanguticus (Maxim.) Pascher in Treating Inflammation and Pain.

This study aimed to elucidate the mechanism that total alkaloids in Anisodus tanguticus (AT)(Maxim.) Pascher played anti-inflammatory and analgesic effects. In this paper, the anti-inflammatory effect in the total alkaloids of AT was confirmed via lipopolysaccharide (LPS)-induced inflammation model in RAW 264.7 cells and the main components of AT were immediately analyzed by UPLC/MS. Disease targets were obtained in GeneCards and DisGeNET. Targets of major compounds were searched in ETCM, TCMSP and other databases. The protein-protein interaction (PPI) network was constructed using STRING database, and Cytoscape was used for core targets screening. GO and KEGG enrichment analysis were performed using Daivid database. Sailvina was used for molecular docking. Molecular dynamics simulation analysis was performed using the Amber 20 program. The results showed that the main components in AT were anisodamine, atropine, fabiatrin, scopolamine, scopoletin and scopolin, possibly exerting anti-inflammatory and analgesic effects through pathways such as EGFR tyrosine kinase inhibitor resistance and IL-17 signaling pathway. Fabiatrin and scopolin could be potential drugs with good anti-inflammatory and analgesic effects.

Hybrid Molecules Containing Methotrexate, Vitamin D, and Platinum Derivatives: Synthesis, Characterization, In Vitro Cytotoxicity, In Silico ADME Docking, Molecular Docking and Dynamics.

Designing hybrid-based drugs is one promising strategy for developing effective anticancer drugs that explore combination therapy to enhance treatment efficacy, overcome the development of drug resistance, and lower treatment duration. Bisphosphonates and Vitamin D are commonly administered drugs for the treatment of bone diseases and the prevention of bone metastases. Platinum-based and methotrexate are widely used anticancer drugs in clinics. However, their use is hampered by adverse side effects. Hybrid-based compounds containing either bisphosphonate, vitamin D, platinum-based, or methotrexate were synthesized and characterized using FTIR, 1H-,31P, 13C-NMR, and UHPLC-HRMS which confirmed their successful synthesis. The hydroxyapatite bone binding assay revealed a promising percentage binding affinity of the bisphosphonate hybrid compounds. In vitro cytotoxicity assays on MCF-7 and HT-29 cell lines revealed a promising cytotoxic effect of hybrid 19 at 50 and 100 μg/mL on HT-29 and hybrid 15 on MCF-7 at 100 μg/mL. Molecular docking and dynamics simulation analysis revealed a binding affinity of -9.70 kcal/mol for hybrid 15 against Human 3 alpha-hydroxysteroid dehydrogenase type 3, showing its capability to inhibit Human 3 alpha-hydroxysteroid dehydrogenase type 3. The Swiss ADME, ProTox-II, GUSAR (General Unrestricted Structure-Activity Relationships), and molecular docking and dynamics studies revealed that these compounds are promising anticancer compounds.

Luteolin ameliorates chronic stress-induced depressive-like behaviors in mice by promoting the Arginase-1+ microglial phenotype via a PPARγ-dependent mechanism.

Accumulating evidence shows that neuroinflammation substantially contributes to the pathology of depression, a severe psychiatric disease with an increasing prevalence worldwide. Although modulating microglial phenotypes is recognized as a promising therapeutic strategy, effective treatments are still lacking. Previous studies have shown that luteolin (LUT) has anti-inflammatory effects and confers benefits on chronic stress-induced depression. In this study, we investigated the molecular mechanisms by which LUT regulates the functional phenotypes of microglia in mice with depressive-like behaviors. Mice were exposed to chronic restraint stress (CRS) for 7 weeks, and were administered LUT (10, 30, 40 mg· kg-1 ·day-1, i.g.) in the last 4 weeks. We showed that LUT administration significantly ameliorated depressive-like behaviors and decreased hippocampal inflammation. LUT administration induced pro-inflammatory microglia to undergo anti-inflammatory arginase (Arg)-1+ phenotypic polarization, which was associated with its antidepressant effects. Furthermore, we showed that LUT concentration-dependently increased the expression of PPARγ in LPS + ATP-treated microglia and the hippocampus of CRS-exposed mice, promoting the subsequent inhibition of the NLRP3 inflammasome. Molecular dynamics (MD) simulation and microscale thermophoresis (MST) analysis confirmed a direct interaction between LUT and peroxisome proliferator-activated receptor gamma (PPARγ). By using the PPARγ antagonist GW9662, we demonstrated that LUT-driven protection, both in vivo and in vitro, resulted from targeting PPARγ. First, LUT-induced Arg-1+ microglia were no longer detected when PPARγ was blocked. Next, LUT-mediated inhibition of the NLRP3 inflammasome and downregulation of pro-inflammatory cytokine production were reversed by the inhibition of PPARγ. Finally, the protective effects of LUT, which attenuated the microglial engulfment of synapses and prevented apparent synapse loss in the hippocampus of CRS-exposed mice, were eliminated by blocking PPARγ. In conclusion, this study showed that LUT ameliorates CRS-induced depressive-like behaviors by promoting the Arg-1+ microglial phenotype through a PPARγ-dependent mechanism, thereby alleviating microglial pro-inflammatory responses and reversing microglial phagocytosis-mediated synapse loss.

Molecular Docking Simulations of Protoporphyrin IX, Chlorin e6, and Methylene Blue for Target Proteins of Viruses Causing Skin Lesions: Monkeypox and HSV

Background: The replication of monkeypox in the skin is critical to understanding its pathogenesis and spread. p37, a highly conserved 37 kDa peripheral membrane protein encoded by the F13L gene in Orthopoxvitidae is a validated target for anti-poxviral medication like tecovirimat, the first FDA-approved anti-poxviral drug that was approved in 2018. The detailed recognition mechanism of tecovirimat on p37 of monkeypox has not been fully clarified. As p37, HSV-1 gD and HSV-2 gD proteins of HSV are viral envelope glycoproteins identified as ligands for the human nectin-1 as a functional receptor of permissive cells. The use of non-damaging light for microbial inactivation (MI) has been documented for different virus like HSV, where photosensitizers (PSs) are used as lightresponsive agents which could generate antiviral responses primarily by oxidation. In addition, some PSs could elicit antiviral responses in a light-independent way by interacting within the viral-cell recognition sites. Objective: This paper aims to evaluate the formation of complexes between the latest structural data available on the range of monkeypox and HSV-1/2 envelope proteins with the approved PSs protoporphyrin IX, chlorin e6, and methylene blue. Methods: Ligands and receptors preparation, and molecular docking analyses were performed with Chimera and the Autodock Vina Software. Molecular docking and molecular dynamics simulation (MD) analyses for a 100 ns trajectory were also performed for the p37 – Methylene blue complex. Results: PSs studies were found to form complexes into the patch regions of recognition between HSV-1/2 gD and human receptors, while MB was found to form a complex with the p37 protein into de pocket region where tecovirimat acts. MD simulation showed stability in the interaction of MB with the pocket region of the p37 protein. Conclusion: The molecular mechanisms of potential dual antiviral activity for these complexes were clarified showing that MI with the use of these PSs could be further evaluated for viral skin lesions produced by monkeypox and HSV.

Deciphering the conformational changes induced by high-risk nsSNPs in β-lactoglobulin

Whey protein from bovine milk is highly valued in the food and pharmaceutical industries because of its high protein content and abundance of essential amino acids. The relationship between whey protein and the β-lactoglobulin (BLG) gene has been extensively discussed because BLG is the most abundant whey protein, making up approximately 50 % of the total whey protein in bovine milk. In recent years, researchers have been interested in this gene because of its critical role in healthy milk production, and any genetic polymorphism in this gene may deteriorate the milk quality. In the current study, we identified several deleterious and damaging non-synonymous single nucleotide polymorphisms (nsSNPs) in BLG and analyzed their destabilizing effects using different computational algorithms. Cumulative results from all tools and evolutionary conservation profiles of BLG suggested that four nsSNPs, G17A, W19C, F136S, and C119R, were the most deleterious and could affect the structural integrity of the protein. Detailed molecular dynamics simulation analysis revealed that all variants induced major structural alterations, that affected the ability of the protein to interact with natural and synthetic ligands. Particularly, the G17A, F136S, and C119R variants induced large conformational changes in the EF loop and main α-helix of BLG, which may affect the access of natural and synthetic ligands to the central calyx of BLG. We hope that the suggested nsSNPs will guide future studies and assist researchers in improving the quality of bovine milk.

Nonlinear dynamic of flexible rotor supported by turbulent bearings with quadratic damping and temperature dependent viscosity

A nonlinear dynamic model of a rotor supported by the turbulent journal bearing with quadratic damping under nonlinear suspension is presented in this study, and the lubricating oil is assumed to be temperature-dependent. The bifurcation diagrams, dynamic trajectories, power spectra, Poincaré map, Lyapunov exponent, and fractal dimension are used to verify the dynamic characteristics of the rotor-bearing system, and abundant subharmonic, and even chaotic motions are found. Temperature is one of the key parameters affecting the dynamic responses of the system, and the dynamic responses will perform non-periodic or even chaotic motions with higher working temperatures of lubricant fluid, as proved in this study. Nonlinear dynamic simulation analysis results will help engineers avoid unnecessary trial and error when designing and applying rotating machinery systems.

Stability analysis of micro-probe landings in complex terrain

Abstract Addressing the problem of landing stability of the micro-probes on the surface of extraterrestrial objects, combined with the geometric properties of the orthotetrahedron, this paper proposes a structural design method of the four-spine microprobe landing bracket that can adapt to the complex terrain and carries out the analysis of the landing stability of the four-spine bracket under the state of three-legged landing and the optimization of the structure for combined terrain of stones and slopes. Referring to the ZMP theory, the harsh working conditions of the four-spine bracket when landing are sorted out and determined. Based on the kinematics theory, the collision mechanism between the four-spine bracket and the ground is analyzed, and a landing model suitable for the micro-probes is established, which provides the basis for determining the landing stability of the micro-probe. Around the collision mechanism and landing model, the dimension optimization of the four-spine bracket is carried out, and the results of Adams dynamics simulation analysis and prototype test show that the landing stability of the four-spine bracket is improved, which verifies the validity of the optimization idea.

Investigating the role of PmrB mutation on Colistin antibiotics drug resistance in Klebsiella Pneumoniae

Klebsiella pneumoniae, a member of the Enterobacteriaceae family, naturally resides in the digestive tracts of both healthy animals and humans. Carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a significant health risk for hospitalized patients worldwide, greatly reducing the effectiveness of commonly used antibiotics. This leaves healthcare providers with limited treatment options, often relying on colistin. PmrB is important for the survival of Klebsiella pneumonia and, a mutation in the PmrB protein is accountable for the development of colistin antibiotic resistance in Klebsiella pneumonia. This is especially important because colistin is a fundamental component in the treatment of pneumonia. Three mutated residues—T157P, G207D, and T246A—are responsible for colistin resistance. The structural alterations and underlying mechanisms in the PmrB protein that cause resistance owing to mutation remain unclear. As a result, this study is focused to the exploration of the putative mechanism of resistance resulting from these mutations, as well as the structure modification of normal and mutant PmrB proteins, using molecular docking and molecular dynamics simulations analysis. Our results demonstrated that the interaction paradigm for the mutants has been altered and thus showing a significant effect upon the hydrogen bonding network. Interestingly, the binding of Colistin with the three mutant demonstrate unstable behavior as compared with WT+Colistin. The proposed drug-resistance mechanism will help to guide the development of PmrB drugs. These finding may give a new framework for developing novel drugs against the mutant version of PmrB.

Rational Design for Enhancing Cellobiose Dehydrogenase Activity and Its Synergistic Role in Straw Degradation.

Addressing the demand for efficient biological degradation of straw, this study employed rational design coupled with structural biology and enzyme engineering techniques to enhance the catalytic activity of cellobiose dehydrogenase (PsCDH, CDH form Pycnoporus sanguineus). By predicting and modifying the active site and key amino acids of PsCDH, several CDH immobilized enzyme preparations with higher catalytic activities were successfully obtained. The excellent mutant T1 (C286Y/A461H/F464R) exhibited a 2.7-fold increase in enzyme activity compared to the wild type. Simulated calculations indicated that the enhancement of catalytic activity was primarily due to the formation of additional intermolecular interactions between CDH and the substrate, as well as the enlargement of the substrate pocket to reduce steric hindrance effects. Additionally, molecular dynamics simulation analysis revealed a potential correlation between structural stability and enzyme activity. When PsCDH was added to a multienzyme synergistic straw degradation system, the cellulose degradation rate increased by 1.84-fold. Moreover, mutant T1 further increased the degradation of lignocellulose in the mixed system. This study provides efficient enzyme sources and modification strategies for the high-efficiency biological conversion of straw and unconventional feedstock degradation, thereby possessing significant academic value and application prospects.

Insights into the Therapeutic Potential of Active Ingredients of Citri Reticulatae Pericarpium in Combatting Sarcopenia: An In Silico Approach.

Sarcopenia is a systemic medical disorder characterized by a gradual decline in muscular strength, function, and skeletal muscle mass. Currently, there is no medication specifically approved for the treatment of this condition. Therefore, the identification of new pharmacological targets may offer opportunities for the development of novel therapeutic strategies. The current in silico study investigated the active ingredients and the mode of action of Citri Reticulatae Pericarpium (CRP) in addressing sarcopenia. The active ingredients of CRP and the potential targets of CRP and sarcopenia were determined using various databases. The STRING platform was utilized to construct a protein-protein interaction network, and the key intersecting targets were enriched through the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses. Molecular docking was used to determine the binding interactions of the active ingredients with the hub targets. The binding affinities obtained from molecular docking were subsequently validated through molecular dynamics simulation analyses. Five active ingredients and 45 key intersecting targets between CRP and sarcopenia were identified. AKT1, IL6, TP53, MMP9, ESR1, NFKB1, MTOR, IGF1R, ALB, and NFE2L2 were identified as the hub targets with the highest degree node in the protein-protein interaction network. The results indicated that the targets were mainly enriched in PIK3-AKT, HIF-1, and longevity-regulating pathways. The active ingredients showed a greater interaction affinity with the hub targets, as indicated by the results of molecular docking and molecular dynamics simulations. Our findings suggest that the active ingredients of Citri Reticulatae Pericarpium, particularly Sitosterol and Hesperetin, have the potential to improve sarcopenia by interacting with AKT1 and MTOR proteins through the PI3K-AKT signaling pathway.

Phytoconstituents of Withania somnifera (L.) Dunal (Ashwagandha) unveiled potential cerebroside sulfotransferase inhibitors: insight through virtual screening, molecular dynamics, toxicity, and reverse pharmacophore analysis

Cerebroside sulfotransferase (CST) is considered as therapeutic target for substrate reduction therapy (SRT) for metachromatic leukodystrophy (MLD). The present study evaluates the therapeutic potential of 57 phytoconstituents of Withania somnifera against CST. Using binding score cutoff ≤-7.0 kcal/mol, top 10 compounds were screened and after ADME and toxicity-based screening, Withasomidienone, 2,4-methylene-cholesterol, and 2,3-Didehydrosomnifericin were identified as safe and potent drug candidates for CST inhibition. Key substrate binding site residues involved in interaction were LYS82, LYS85, SER89, TYR176, PHE170, PHE177. Four steroidal Lactone-based withanolide backbone of these compounds played a critical role in stabilizing their position in the active site pocket. 100 ns molecular dynamics simulation and subsequent trajectory analysis through structural deviation and compactness, principal components, free energy landscape and correlation matrix confirmed the stability of CST-2,3-Didehydrosomnifericin complex throughout the simulation and therefore is considered as the most potent drug candidate for CST inhibition and Withasomidienone as the second most potent drug candidate. The reverse pharmacophore analysis further confirmed the specificity of these two compounds towards CST as no major cross targets were identified. Thus, identified compounds in this study strongly present their candidature for oral drug and provide route for further development of more specific CST inhibitors.