Molecular Dynamics Simulation Technique Research Articles

Exploration of the structural mechanism of hydrogen (H2)-promoted horseradish peroxidase (HRP) activity via multiple spectroscopic and molecular dynamics simulation techniques

Horseradish peroxidase (HRP) is an enzyme that is widely used in various fields. In this study, the effects of molecular hydrogen (H2) on the activity and structural characteristics of HRP were investigated by employing multiple spectroscopic techniques, atomic force microscopy (AFM) and molecular dynamics (MD) simulations. The results demonstrated that H2 could enhance HRP activity, especially in 1.5 mg/L hydrogen-rich water (HRW). The structural analysis results showed that H2 might alter HRP activity by affecting the active sites, secondary structure, hydrogen bonding network, CS groups, and morphological characteristics. The MD results also confirmed that H2 could increase the FeN bond distance in the active site, affect the secondary structure, and increase the number of hydrogen bonds. The MD results further suggested that H2 could increase the number of salt bridges, and lengthen the SS bonds in HRP. This study primarily revealed the mechanism by which H2 enhances the HRP activity, providing insight into the interactions between gas and macromolecular proteins. However, some of the results obtained via MD simulations still need to be verified experimentally. In addition, our study also provided a new convenient strategy to enhance enzyme activity.

Formononetin, a bioactive isoflavonoid constituent from Astragalus membranaceus (Fisch.) Bunge, ameliorates type 1 diabetes mellitus via activation of Keap1/Nrf2 signaling pathway: An integrated study supported by network pharmacology and experimental validation

Ethnopharmacological relevanceType 1 diabetes mellitus (T1DM) results from insulin deficiency due to the destruction of pancreatic β-cells. Previously, our studies showed that inhibition of Keap1/Nrf2 signaling pathway promoted the onset of T1DM, which suggests that finding drugs that can activate the Keap1/Nrf2 signaling may be a promising therapeutic strategy for the T1DM treatment. Astragalus membranaceus (Fisch.) Bunge is a common traditional Chinese medicine that has been frequently applied in Chinese clinics for the treatment of diabetes and other diseases. Formononetin (FMNT), one of the major isoflavonoid constituents isolated from this herbal medicine, possesses diverse pharmacological benefits and T1DM therapeutic potential. However, the exact molecular mechanisms underlying the action of FMNT in ameliorating T1DM have yet to be fully elucidated. Aims of the studyThis study is to investigate the regulation of FMNT on the Keap1/Nrf2 signaling pathway to ameliorate T1DM based on network pharmacology approach combined with experimental validation. Materials and methodsA mouse-derived pancreatic islet β-cell line (MIN6) was used for the in vitro studies. An alloxan (ALX)-induced T1DM model in wild-type and Nrf2 knockout (Nrf2−/−) C57BL/6J mice were established for the in vivo experiments. The protective effects of FMNT against ALX-stimulated MIN6 cell injury were evaluated using MTT, EdU, apoptosis and comet assays. The levels of blood glucose in mice were measured by using a blood monitor and test strips. The protein expression was detected by Western blot analysis. Furthermore, the binding affinity of FMNT to Keap1 was evaluated using cellular thermal shift assay (CETSA), drug affinity responsive target stability (DARTS) assay, and solvent-induced protein precipitation (SIP) assay. The interaction pattern between FMNT and Keap1 was assessed by molecular docking and molecular dynamics simulation techniques. ResultsNetwork pharmacology analysis revealed that FMNT exerted its therapeutic effect against T1DM by mainly regulating oxidative stress response-associated signaling molecules and pathways, such as Nrf2 regulating anti-oxidant/detoxification enzymes and Keap1-Nrf2 signaling pathway. The in vivo results showed that FMNT significantly deceased the ALX-induced high blood glucose levels and conversely increased the ALX-induced low insulin contents. In vitro, FMNT markedly protected MIN6 cells from ALX-induced cytotoxicity, proliferation inhibition and DNA damage and reduced the ALX-stimulated cell apoptosis. FMNT also inhibited ALX-induced overproduction of intracellular ROS to alleviate oxidative stress. In addition, FMNT could bind to Keap1 to notably activate the Keap1/Nrf2 signaling to upregulate Nrf2 expression and promote the Nrf2 translocation from the cytoplasm to the nucleus, resulting in enhancing the expression of antioxidant proteins HO-1 and NQO1. Inhibition of Keap1/Nrf2 signaling by ALX was also markedly abolished in the cells and mice exposed to FMNT. Moreover, these effects of FMNT in ameliorating T1DM were not observed in Nrf2−/− mice. ConclusionsThis study demonstrates that FMNT could bind to Keap1 to activate the Keap1/Nrf2 signaling to prevent intracellular ROS overproduction, thereby attenuating ALX-induced MIN6 cell injury and ameliorating ALX-stimulated T1DM. Results from this study might provide evidence and new insight into the therapeutic effect of FMNT and indicate that FMNT is a promising candidate agent for the treatment of T1DM in clinics.

Study of the Mechanism of Astragali Radix in Treating Type 2 Diabetes Mellitus and Its Renal Protection Based on Enzyme Activity, Network Pharmacology, and Experimental Verification.

Astragali Radix (AR) is a common Chinese medicine and food. This article aims to reveal the active role of AR in treating Type 2 diabetes mellitus (T2DM) and its renal protective mechanism. The hypoglycemic active fraction was screened by α-glucosidase and identified by UPLC-QE-Orbitrap-MS spectrometry. The targets and KEGG pathway were determined through the application of network pharmacology methodology. Molecular docking and molecular dynamics simulation technology were used for virtual verification. Subsequently, a mouse model of T2DM was established, and the blood glucose and renal function indexes of the mice after administration were analyzed to further prove the pharmacodynamic effect and mechanism of AR in the treatment of T2DM. HA was determined as the best hypoglycemic active fraction by the α-glucosidase method, with a total of 23 compounds identified. The main active components, such as calycoside-7-O-β-D-glucoside, methylnisoline, and formononetin, were revealed by network pharmacology. In addition, the core targets and the pathway have also been determined. Molecular docking and molecular dynamics simulation techniques have verified that components and targets can be well combined. In vivo studies have shown that AR can reduce blood sugar levels in model mice, enhance the anti-inflammatory and antioxidant activities of kidney tissue, and alleviate kidney damage in mice. And it also has regulatory effects on proteins such as RAGE, PI3K, and AKT. AR has a good therapeutic effect on T2DM and can repair disease-induced renal injury by regulating the RAGE/PI3K/Akt signaling pathway. This study provides ideas for the development of new drugs or dietary interventions for the treatment of T2DM.

Naturally Occurring Isorhamnetin Glycosides as Potential Agents Against Influenza Viruses: Antiviral and Molecular Docking Studies.

Influenza remains one of the most widespread infections, causing an annual illness in adults and children. Therefore, the search for new antiviral drugs is one of the priorities of practical health care. Eight isorhamnetin glycosides were purified from Persicaria species, characterized by nuclear magnetic resonance spectroscopy and mass spectrometry and then evaluated as potential agents against influenza virus. A comprehensive in vitro and in vivo assessment of the compounds revealed that compound 5 displayed the most potent inhibitory activity with an EC50 value of 1.2-1.3 μM, better than standard drugs (isorhamnetin 28.0-56.0 μM and oseltamivir 1.3-9.1 μM). Molecular docking results also revealed that compound 5 has the lowest binding energy (-10.7 kcal/mol) among the tested compounds and isorhamnetin (-8.1 kcal/mol). The ability of the isorhamnetin glycosides to suppress the reproduction of the influenza virus was studied on a model of a cell culture and chicken embryos. The ability of active compounds to influence the structure of the virion, as well as the activity of hemagglutinin and neuraminidase, has been demonstrated. Compound 1, 5, and 6 demonstrated the most effective inhibition of virus replication for all tested viruses. Molecular dynamics simulation techniques were run for 100 ns for compound 5 with two protein receptors Hem (1RUY) and Neu (3BEQ). These results revealed that the Hem-complex system acquired a relatively more stable conformation and even better descriptors than the other Neu-complex studied systems, suggesting that it can be an effective inhibiting drug toward hemagglutinin than neuraminidase inhibition. Based on the reported results, compound 5 can be a good candidate to be evaluated for effectiveness in preclinical testing.

Exploring the interaction of tepotinib with calf thymus DNA using molecular dynamics simulation and multispectroscopic techniques

In recent times, there has been a surge in the discovery of drugs that directly interact with DNA, influencing gene expression. As a result, understanding how biomolecules interact with DNA has become a major area of research. One such drug is Tepotinib (TPT), an FDA-approved anti-cancer medication known as a MET tyrosine kinase inhibitor, used in chemotherapy for metastatic non-small cell lung cancer (NSCLC) with MET exon 14 skipping alterations. In our study, we adopted both biophysical and in-silico methods to investigate the binding relationship of TPT and ctDNA. The absorption spectra of ctDNA exhibited a hypochromic effect when titrated with TPT and the binding constant of TPT–ctDNA complex was calculated, Ka = 9.91 × 104 M−1. By computing bimolecular enhancement constant (KB) and thermodynamic enhancement constant (KD) in fluorometric investigations, it was found that the fluorescence enhancement is a result of a static process involving the ctDNA-TPT complex formation in the ground state, as opposed to a dynamic process. The displacement assay results further supported this finding, showing that TPT exhibits a binding preference for minor groove of ct-DNA and was also demonstrated by KI quenching and CD spectroscopy. The molecular docking and molecular dynamic simulations validated TPT's groove binding nature and binding pattern with ctDNA, respectively. Thus, the results of our present investigation offer valuable insights into the interaction between TPT and ctDNA. It is evident that TPT, as an anti-cancer medication, binds to the minor groove of ctDNA.

Study on the sweetening mechanism of aroma compounds in yangshan peach using sensory analysis, molecular docking, and molecular dynamics simulation techniques

The demand for sugar reduction in food continues to rise, necessitating innovative approaches to reducing the sugar content without compromising consumer acceptance. The enhancement of odor-induced sweetness represents a promising method for achieving this objective. This study aims to investigate the volatile compounds in peach sourced from Yangshan, using headspace solid-phase microextraction, (HS-SPME), solvent-assisted flavor evaporation, (SAFE), gas chromatography-mass spectrometry (GC-MS), and gas chromatography-olfaction-taste (GC/O-AT) techniques. A total of 75 volatiles were identified by GC-MS, among which 30 volatiles had an aroma activity value ≥ 1. Subsequently, GC/O-AT was employed to screen 15 sweetness-related odors for sensory experiments. The results showed that 13 sweetness-related odorants could significantly enhance sweetness in a 40 g/L sucrose solution. Molecular docking results indicated that in the presence of sucrose, aroma substances can interact with amino acid residues on sweet receptors through hydrogen bonds and hydrophobic interactions. Molecular dynamics (MD) results implied that dihydro-beta-ionone formed hydrophobic interactions with amino acid residues of T1R2; sucrose formed hydrogen bonding interactions and hydrophobic interactions with amino acid residues of T1R2. Overall, the interactions between aroma substances and sweet taste receptors in the presence of sucrose primarily rely on hydrogen bonding and hydrophobic interactions.

Temperature Dependence Study of Water Dynamics in Fluorohectorite Clays Using Molecular Dynamics Simulations

We have carried out molecular dynamics (MD) simulation techniques to study the diffusion coefficient of interlayer molecules at different temperature. We have focused on the translation dynamics of water in bihydrated states within the context of water dynamics in clays. We concentrated on temperatures between 293 and 350 K, i.e., the range important to daily life wastewater handling. A natural clay has been modified as a synthetic clay called fluorohectorite clay, and the properties are studied using MD simulations, the result of which allows us to understand the determining parameters through a comparison with experiment values. The activation energyEais determined by our simulation to be between [0.09−0.17] eV per particle. The calculated diffusion constants are in the order of 10−5 cm2s−1. The simulation results are in a good agreement with experiments for the relevant set of conditions, and give insight into the origin of the observed dynamics.

Synergistic inhibition of glioblastoma multiforme through an in-silico analysis of luteolin and ferulic acid derived from Angelica sinensis and Cannabis sativa: Advancements in computational therapeutics.

The primary objective of this study is to uncover novel therapeutic agents for the treatment of Glioblastoma Multiforme (GBM), a highly aggressive form of brain cancer, and Alzheimer's Disease (AD). Given the complexity and resistance associated with both conditions, the study underscores the imperative need for therapeutic alternatives that can traverse the biological intricacies inherent in both neuro-oncological and neurodegenerative disorders. To achieve this, a meticulous, target-based virtual screening was employed on an ensemble of 50 flavonoids and polyphenol derivatives primarily derived from plant sources. The screening focused predominantly on molecular targets pertinent to GBM but also evaluated the potential overlap with neural pathways involved in AD. The study utilized molecular docking and Molecular Dynamic (MD) simulation techniques to analyze the interaction of these compounds with a key biological target, protein tyrosine phosphatase receptor-type Z (PTPRZ). Out of the 50 compounds examined, 10 met our stringent criteria for binding affinity and specificity. Subsequently, the highest value of binding energy was observed for the synergistic binding of luteolin and ferulic acid with the value of -10.5 kcal/mol. Both compounds exhibited inherent neuroprotective properties and demonstrated significant potential as pathway inhibitors in GBM as well as molecular modulators in AD. Drawing upon advanced in-silico cytotoxicity predictions and sophisticated molecular modeling techniques, this study casts a spotlight on the therapeutic capabilities of polyphenols against GBM. Furthermore, our findings suggest that leveraging these compounds could catalyze a much-needed paradigm shift towards more integrative therapeutic approaches that span the breadth of both neuro-oncology and neurodegenerative diseases. The identification of cross-therapeutic potential in flavonoids and polyphenols could drastically broaden the scope of treatment modalities against both fatal diseases.

Identification of a Staphylococcus aureus amidase catalytic domain inhibitor to prevent biofilm formation by sequential virtual screening, molecular dynamics simulation and biological evaluation

Staphylococcus aureus (S. aureus) is one of the common causes of implant associated biofilm infections and their biofilms are resistant to antibiotics. S. aureus amidase (AM) protein, a cell wall hydrolase that cleaves the amide bond between N-acetylmuramic acid and L-alanine residue of the stem peptide, is several fold over-expressed under biofilm conditions. Previous studies demonstrated an autolysin mutant in S. aureus that lacks the AM protein, is highly impaired in biofilm development. We carried out a structure-based small molecule design using the crystal structure of AM protein catalytic domain to identify inhibitors that can block amidase activity and therefore inhibits S. aureus biofilm formation. Sequential virtual screening followed by pharmacokinetic analysis and bioassay studies filtered 25 small molecules from different databases. Two compounds from the SPECS database, SPECS-1 and SPECS-2, were selected based on the best docking score and minimum biofilm inhibitory concentration towards S. aureus biofilms. SPECS-1 and SPECS-2 were further tested for their structural/energetic stability in complex with the AM protein using molecular dynamics simulation and MM-GBSA techniques. In vitro, biofilm inhibition studies on different surfaces confirmed that treatment with SPECS-1 and SPECS-2 at a concentration of 250 μg/ml exhibited significant prevention and disruption of S. aureus biofilms. Finally, the in vitro anti-biofilm activities of these two compounds were validated against Methicillin-resistant S. aureus clinical isolates. We concluded that the discovered compounds SPECS-1 and SPECS-2 are safe and exhibit biofilm preventive and disruption activity for inhibiting the S. aureus biofilms and hence can be used to treat implant-associated biofilm infections.

Nodakenin alleviates ovariectomy-induced osteoporosis by modulating osteoblastogenesis and osteoclastogenesis

Osteoporosis, a systemic bone disease defined by decreased bone mass and deterioration of bone microarchitecture, is becoming a global concern. Nodakenin (NK) is a furanocoumarin-like compound isolated from the traditional Chinese medicine Radix Angelicae biseratae (RAB). NK has been reported to have various pharmacological activities, but osteoporosis has not been reported to be affected by NK. In this study, we used network pharmacology, molecular docking and molecular dynamics simulation techniques to identify potential targets and pathways of NK in osteoporosis. We found that NK treatment significantly promoted osteogenic differentiation of BMSCs while activating the PI3K/AKT/mTOR signalling pathway by measuring alkaline phosphatase activity and the expression of various osteogenic markers. In contrast, LY294002, an inhibitor of PI3K, reversed these changes and inhibited the osteogenic differentiation-enabling effect of NK. Meanwhile, prevent the Akt and NFκB signalling pathways by down-regulating c-Src and TRAF6 thereby effectively inhibiting RANKL-induced osteoclastogenesis. In addition, oral administration of NK to mice significantly elevated bone mass and ameliorated ovariectomized (OVX)-mediated bone microarchitectural disorders. In conclusion, these data suggest that NK attenuates OVX-induced bone loss by enhancing osteogenesis and inhibiting osteoclastogenesis.

Investigation of the effects of chemical modification and oxidative aging on the properties and compatibility of rubber asphalt based on thermodynamic principles

This study is based on the principles of thermodynamics and utilizes the Hansen solubility parameter theory and molecular dynamics simulation techniques. By introducing solubility parameters and interaction parameters, modified molecular models for rubber and aged asphalt are constructed. The study systematically investigates the mechanisms underlying the effects of polyphenolic chemical modification and oxidative aging on the performance and compatibility changes of rubber asphalt. The results show that the solubility parameter (δT) of the asphalt system decreases gradually with increasing temperature. At a temperature of 160 °C, the solubility parameter difference (ΔδT) between the asphalt and rubber power (RP) is minimized, indicating the highest degree of compatibility between the two materials. After chemical modification, the solubility parameter of the RP increases, the difference in solubility parameter between the RP and asphalt decreases, and the chemical modification improves the compatibility of the two phases. Oxidative aging causes a shift in the composition ratio of asphalt towards asphaltene, leading to an increase in the solubility parameter of asphalt and a larger difference in solubility parameter between the system. As a result, the compatibility of modified asphalt decreases.

In-silico studies of Brassica oleracea active compounds and their role in thyroid peroxidase activity

Cabbage, a leafy vegetable that is widely consumed across the globe, holds a significant place within the Brassica family. For almost a century, its potential anti-thyroid effects have captured attention. The presence of compounds such as thiocyanate and goitrin in cabbage has been extensively investigated for their ability to impede sodium-iodide symporter and thyroid peroxidase (TPO) activities. The present study is focused on uncovering the active constituents in cabbage that could interact with TPO, while also examining their stability under cooking temperatures. Employing molecular docking and molecular dynamic simulation techniques, we quantified the binding strength of phytochemicals present in cabbage with the target. Out of the 60 compounds identified in cabbage leaves, only 18 exhibited docking scores surpassing those of the commercially available anti-thyroid drug, methimazole. These chosen compounds were studied for binding free energy and pharmacokinetic properties. A specific compound, gamma-Terpinene, classified as a monoterpene, emerged as noteworthy due to its alignment with all criteria and the highest observed binding free energy compared to others. Furthermore, we explored the stability of gamma-Terpinene at 373.15K (cooking temperature) and observed its susceptibility to degradation. This might contribute to the relatively diminished anti-thyroid effects of cabbage when consumed in cooked form. Consequently, our findings suggest that the consumption of cooked cabbage could be more conducive to maintaining normal thyroid function, as opposed to its raw counterpart. Communicated by Ramaswamy H. Sarma

Unraveling the potential mechanisms of the anti-osteoporotic effects of the Achyranthes bidentata-Dipsacus asper herb pair: a network pharmacology and experimental study.

Background: Osteoporosis is a prevalent bone metabolism disease characterized by a reduction in bone density, leading to several complications that significantly affect patients' quality of life. The Achyranthes bidentata-Dipsacus asper (AB-DA) herb pair is commonly used in Traditional Chinese Medicine (TCM) to treat osteoporosis. This study aimed to investigate the therapeutic compounds and potential mechanisms of AB-DA using network pharmacology, molecular docking, molecular dynamics simulation, and experimental verification. Methods: Identified compounds of AB-DA were collected from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), Traditional Chinese Medicine Information Database (TCM-ID), TCM@Taiwan Database, BATMAN-TCM, and relevant literature. The main bioactive ingredients were screened based on the criteria of "OB (oral bioavailability) ≥ 30, DL (drug-likeness) ≥ 0.18." Potential targets were predicted using the PharmMapper and SwissTargetPrediction websites, while disease (osteoporosis)-related targets were obtained from the GeneCards, DisGeNET, and OMIM databases. The PPI network and KEGG/GO enrichment analysis were utilized for core targets and pathway screening in the STRING and Metascape databases, respectively. A drug-compound-target-pathway-disease network was constructed using Cytoscape software to display core regulatory mechanisms. Molecular docking and dynamics simulation techniques explored the binding reliability and stability between core compounds and targets. In vitro and in vivo validation experiments were utilized to explore the anti-osteoporosis efficiency and mechanism of sitogluside. Results: A total of 31 compounds with 83 potential targets for AB-DA against osteoporosis were obtained. The PPI analysis revealed several hub targets, including AKT1, CASP3, EGFR, IGF1, MAPK1, MAPK8, and MAPK14. GO/KEGG analysis indicated that the MAPK cascade (ERK/JNK/p38) is the main pathway involved in treating osteoporosis. The D-C-T-P-T network demonstrated therapeutic compounds that mainly consisted of iridoids, steroids, and flavonoids, such as sitogluside, loganic acid, and β-ecdysterone. Molecular docking and dynamics simulation analyses confirmed strong binding affinity and stability between core compounds and targets. Additionally, the validation experiments showed preliminary evidence of antiosteoporosis effects. Conclusion: This study identified iridoids, steroids, and flavonoids as the main therapeutic compounds of AB-DA in treating osteoporosis. The underlying mechanisms may involve targeting core MAPK cascade (ERK/JNK/p38) targets, such as MAPK1, MAPK8, and MAPK14. In vivo experiments preliminarily validated the anti-osteoporosis effect of sitogluside. Further in-depth experimental studies are required to validate the therapeutic value of AB-DA for treating osteoporosis in clinical practice.

A Study on the Microscopic Properties of the Oil–Stone Interfacial Phase of a Reclaimed Asphalt Mixture Based on Molecular Dynamics Simulation

In recent years, there has been a growing body of research focused on aged asphalt and recycled asphalt. Nevertheless, despite diligent endeavors, the precise micro-interaction mechanism occurring at the interface of weathered asphalt, reclaimed asphalt, and aggregates still eludes our understanding. This study leveraged molecular dynamics simulation technology to scrutinize the inherent behavior of aged asphalt and recycled asphalt at the micro-scale, elucidating the intricate interaction mechanism occurring at the interface of recycled asphalt, aged asphalt, and aggregates. The diffusion and adhesion properties of three distinct asphalt–aggregate interfaces were meticulously compared and comprehensively analyzed using advanced molecular dynamics simulation techniques. The findings revealed a substantial decline in the performance of aged asphalt, while the diffusion and adhesion properties of recycled asphalt were observed to be largely restored, reaching a remarkable level of approximately 85% in comparison to aged asphalt. The high-temperature performance, low-temperature performance, and water stability characteristics of both aged the asphalt mixture and recycled asphalt mixture were thoroughly investigated through rigorous laboratory testing of the asphalt mixtures. Based on the experimental findings, it was observed that the overall performance of the aged asphalt mixture exhibited a reduction of approximately 40%. However, through the process of regeneration, the overall performance of the asphalt mixture could be restored to approximately 90% of its non-aged counterpart.

Grain refinement induced by grain boundary segregation in FeNiCrCoCu high-entropy alloys using molecular dynamics simulation of nanoindentation

Atomistic simulation of nanoindentation is performed to investigate the effect of Cu segregation at grain boundaries (GBs) on the mechanical properties of FeNiCrCoCu high-entropy alloys. Initially, a combined Monte Carlo and Molecular dynamics simulation technique is adopted to generate the models with Cu segregation, and further the cases of random Cu distribution are considered for the purpose of comparision. The dislocation density, shear strain and GB behavior in the process of nanoindentation are analyzed in detail. The results reveal that the Cu segregation at GBs leads to superiority in hardness, strength, and stiffness. Dislocation analysis shows that the sessile dislocation density is higher at the initial state for the segregation sample, while dislocation nucleation and movements are suppressed so that dislocation-mediated plasticity is weakened. Furthermore, microrotation analysis during the nanoindentation process indicates that segregation of Cu pins the GBs, thereby inhibiting GB rotation and consequently weakening GB-mediated plastic deformation. In this case, grain refinement is observed, and in good agreement with experiment results. Overall, this study provides insights into the influence of GB segregation of Cu on the mechanical properties and deformation response of FeNiCrCoCu HEAs, and highlights the importance of GB composition for tailoring high-strength materials.

Multiplex Cas9-based excision of CLCuV betasatellite and DNA-A revealed reduction of viral load with asymptomatic cotton plants.

Multiplexed Cas9-based genome editing of cotton resulted in reduction of viral load with asymptomatic cotton plants. In depth imaging of proteomic dynamics of resulting CLCuV betasatellite and DNA-A protein was also performed. The notorious cotton leaf curl virus (CLCuV), which is transmitted by the sap-sucking insect whitefly, continuously damages cotton crops. Although the application of various toxins and RNAi has shown some promise, sustained control has not been achieved. Consequently, CRISPR_Cas9 was applied by designing multiplex targets against DNA-A (AC2 and AC3) and betasatellite (βC1) of CLCuV using CRISPR direct and ligating into the destination vector of the plant using gateway ligation method. The successful ligation of targets into the destination vector was confirmed by the amplification of 1049 bp using a primer created from the promoter and target, while restriction digestion using the AflII and Asc1 enzymes determined how compact the plasmid developed and the nucleotide specificity of the plasmid was achieved through Sanger sequencing. PCR confirmed the successful introduction of plasmid into CKC-1 cotton variety. Through Sanger sequencing and correlation with the mRNA expression of DNA-A and betasatellite in genome-edited cotton plants subjected to agroinfiltration of CLCuV infectious clone, the effectiveness of knockout was established. The genome-edited cotton plants demonstrated edited efficacy of 72% for AC2 and AC3 and 90% for the (βC1) through amplicon sequencing, Molecular dynamics (MD) simulations were used to further validate the results. Higher RMSD values for the edited βC1 and AC3 proteins indicated functional loss caused by denaturation. Thus, CRISPR_Cas9 constructs can be rationally designed using high-throughput MD simulation technique. The confidence in using this technology to control plant virus and its vector was determined by the knockout efficiency and the virus inoculation assay.

In-silico modeling of the interplay between APOE4, NLRP3, and ACE2-SPIKE complex in neurodegeneration between Alzheimer and SARS-CoV: implications for understanding pathogenesis and developing therapeutic strategies

The multifaceted interplay between neurodegenerative pathologies, including Alzheimer’s disease (AD), and the highly virulent severe acute respiratory syndrome coronavirus (SARS-CoV), is implicated in various conditions. AD and SARS-CoV pathogenesis involve the APOE4 allele, NLRP3 inflammasome, and ACE2-SPIKE complex. APOE4, a genetic polymorphism of the APOE gene, is associated with an increased susceptibility to AD. NLRP3, an inflammatory protein of the innate immune system, plays a pivotal role in immune response cascades. In SARS-CoV, the ACE2 receptor serves as the principal portal for cellular entry, while APOE4 intricately interacts with the ACE2-spike protein complex, enhancing viral internalization process. The interaction of NLRP3 with the ACE2-spike protein complex leads to increased inflammatory signaling. The convergence of APOE4/NLRP3 and ACE2-spike protein complex interactions suggests a possible link between SARS and AD. Therefore, the current research centralizes the association between by utilizing SARS-CoV datasets to explore possible mechanisms that account for the pathogenesis of SARS-CoV and AD. The work is further extended to unveil the molecular interactions of APOE4 and NLRP3 with the ACE2-Spike protein complex at the molecular level by employing molecular dynamics simulation techniques. The therapeutic efficacy of Chyawanprash nutraceuticals is evaluated as their inhibitory potential towards APOE4-ACE2-Spike protein and NLRP3-ACE2-Spike protein complexes. Notably, our simulations unequivocally demonstrate the robust and enduring binding capability of the compound Phyllantidine with the target complexes throughout the simulation period. The findings of the studies further corroborate the primary hypothesis of APOE4 and NLRP3 as driver factors in the pathogenesis of both SARS-CoV and AD. Therefore, this research establishes a paradigm for comprehending the complex interaction between AD and SARS-CoV and lays the groundwork for further study in this domain. Communicated by Ramaswamy H. Sarma

Solubility, thermodynamic investigation and molecular dynamics simulation of guanidine hydrochloride in four binary solvents

Solubilities of guanidine hydrochloride (GuHCl) in organic solvents are of great importance for its development and optimization of industrial process. The study of the dissolution characteristics of GuHCl in DMF/2-meoxyethanol/methanol/NMP + n-propanol at different temperatures were experimentally investigated by using laser monitoring method. Results showed that GuHCl solubilities were observed to be increasing with the increment in experimental temperature and rising with higher mass fraction of DMF/2-meoxyethanol/methanol/NMP. Molecular dynamics (MD) simulation technique was utilized to reveal the microscopic behaviors of GuHCl and solvent mixtures and its effect on the dissolving capability of GuHCl in involved solvent systems. Also, five thermodynamic models were selected to regress the observed GuHCl equilibrium solubility. A comparison of the experimental values with corresponding estimated data indicated that the modified Apelblat equation provided the most excellent correlation in modelling GuHCl solubility. Finally, through the analyses of enthalpy change, entropy change and Gibbs free energy change, the dissolution thermodynamic features were evaluated.

Advantages of Using Hard X-ray Photons for Ultrafast Diffraction Measurements

We present a comparative theoretical study of silicon crystals irradiated with X-ray free-electron laser pulses, using hard X-ray photons of various energies. Simulations are performed with our in-house hybrid code XTANT based on Monte Carlo, Tight Binding and Molecular Dynamics simulation techniques. By comparing the strength of the coherently scattered signal and the corresponding electronic radiation damage for three X-ray photon energies available at the SACLA free-electron laser facility, we conclude that it would be beneficial to use higher photon energies for “diffraction-before-destruction” experiments.

A therapeutic epitopes-based vaccine engineering against Salmonella enterica XDR strains for typhoid fever: a Pan-vaccinomics approach

A prevalent food-borne pathogen, Salmonella enterica serotypes Typhi, is responsible for gastrointestinal and systemic infections globally. Salmonella vaccines are the most effective, however, producing a broad-spectrum vaccine remains challenging due to Salmonella’s many serotypes. Efforts are urgently required to develop a novel vaccine candidate that can tackle all S. Typhi strains because of their high resistance to multiple kinds of antibiotics (particularly the XDR H58 strain). In this work, we used a computational pangenome-based vaccine design technique on all available (n = 119) S. Typhi reference genomes and identified one TonB-dependent siderophore receptor (WP_001034967.1) as highly conserved and prospective vaccine candidates from the predicted core genome (n = 3,351). The applied pan-proteomics and Immunoinformatic approaches help in the identification of four epitopes that may trigger adequate host body immune responses. Furthermore, the proposed vaccine ensemble demonstrates a stable binding conformation with the examined immunological receptor (HLAs and TRL2/4) and has large interaction energy determined via molecular docking and molecular dynamics simulation techniques. Eventually, an expression vector for the Escherichia. coli K12 strain was constructed from the vaccine sequence. Additional analysis revealed that the vaccine may help to elicit strong immune responses for typhoid infections, however, experimental analysis is required to verify the vaccine’s effectiveness based on these results. Moreover, the applied computer-assisted vaccine design may considerably decrease vaccine development costs and speed up the process. The study’s findings are intriguing, but they must be evaluated in the experimental labs to confirm the developed vaccine’s biological efficiency against XDR S. Typhi. Communicated by Ramaswamy H. Sarma