Molecular Dynamics Simulation Analysis Research Articles

An effective strategy to enhance phosphoric acid retention and proton conductivity stability: Construction of proton transfer channels with starch rather than H3PO4

To enhance the phosphoric acid (PA) retention as well as maintain high proton conductivity of phosphoric acid doped proton exchange membranes at high temperature, we successfully design a series of phosphoric acid doped biobased composite membranes by incorporation of starch and graphene oxide (GO) into poly arylene ether ketones (PAEK). Proton transfer channels should be mainly built through dense hydrogen bonds formed from massive oxygen-containing groups of starch mainchain, which is confirmed by Molecular dynamics (MD) simulation, FT-IR and XRD analysis. The dense hydrogen-bond structure could construct fast proton transfer channels with extreme low doping level (0.00484 molH3PO4). The excellent PA retention properties with almost unchanged proton conductivity at high temperature (200 °C) for 600 min indicates that PA molecules are firmly fixed into membranes. Thus, in this study, we suggest a novel strategy for stablizing proton conductivity at high temperature and improving PA retention properties of PA doped membranes, which is building dense hydrogen-bond structure with low PA doping level.Based on the results in this study and the Grotthuss proton transfer mechanism, dense hydrogen-bonds from oxygen-containing groups in polymer backbones should be more stable than hydrogen-bonds from massive H3PO4 molecules with high acid doping levels to promote proton conduction.

Novel chiral phthalimides: Antimicrobial evaluation and docking study against Acinetobacter baumannii's OmpA protein

Antibiotics have been a vital component in the fight against microbial diseases for over 75 years, saving countless lives. However, the global rise of multi-drug-resistance (MDR) bacterial infections is pushing us closer to a post-antibiotic era where common infections may once again become lethal. To combat MDR Acinetobacter baumannii, we investigated chiral phthalimides and used molecular docking to identify potential targets. Outer membrane protein A (OmpA) is crucial for A. baumannii resistant to antibiotics, making it a pathogen of great concern due to its high mortality rate and limited treatment options. In this study, we evaluated three distinct compounds against the OmpA protein: FIA (2-(1,3-dioxoindolin-2yl)-3-phenylpropanoic acid), FIC (2-(1,3-dioxoindolin-2yl)-4-(methylthio) butanoic acid), and FII (3-(1,3-dioxoindolin-2yl)-3-phenylpropanoic acid). Molecular docking results showed that these three compounds exhibited strong interactions with the OmpA protein. Molecular dynamics (MD) simulation analysis further confirmed the stability and binding efficacy of these compounds with OmpA. Their antimicrobial activities were assessed using the agar well diffusion method, revealing that FIA had an optimal zone of inhibition of 24 mm. Additionally, the minimum inhibitory concentrations (MIC) of these compounds were determined, demonstrating their bactericidal properties against A. baumannii, with MICs of 11 μg/μL for FIA, 46 μg/μL for FIC, and 375 μg/μL for FII. In vitro cytotoxicity data indicated that none of the three compounds were hemolytic when exposed to human red blood cells. This finding is particularly significant as it highlights the superior efficacy of FIA against A. baumannii compared to the other compounds. With thorough pharmacokinetic validations, these chiral phthalimides are promising alternative therapeutic options for treating infections caused by A. baumannii, offering new hope in the face of rising antibiotic resistance.

In-silico screening of Staphylococcus aureus antibacterial agents based on Isatin scaffold: QSAR, molecular docking, molecular dynamics simulation and DFT analysis

The design of novel antimicrobial drugs is necessary due to the increasing resistance to many existing antibiotics. Considering that the drug discovery process requires a lot of time and resources, computational chemistry and molecular docking as the basic components in the drug discovery process, can help the acceleration of this prolonged process and minimise the research costs. In this study, 64 molecules containing the Isatin scaffold were subjected to quantitative structure–activity relationship analysis to identify the necessary features for designing effective antimicrobial agents. Three chemometrics methods were employed to establish a connection between structural parameters and antibacterial effects. MLR was identified as the best model, demonstrating high accuracy compared to the other models. Based on the obtained model, ten novel lead compounds were designed, and their antibacterial potency of these compounds was assessed. The outputs of the molecular docking study revealed that compound S4 fits well in the ATP-binding site and blocks ATPase activity. Additionally, it was observed that compound S4 exhibited adequate binding affinity against the DNA gyrase target. An appropriate relationship was observed between QSAR, DFT and molecular modelling approaches. Therefore, compound S4 can be considered as a promising candidate for further development as an antibacterial agent.

In silico analysis reveals α-amylase inhibitory potential of Taraxerol (Coccinia indica) and Epoxywithanolide-1 (Withania coagulans): a possible way to control postprandial hyperglycemia-induced endothelial dysfunction and cardiovascular events.

Postprandial hyperglycemia (PPG) exacerbates endothelial dysfunction and impairs vascular function in diabetes as well in healthy people. Though synthetic drugs are available to regulate PPG, the severe gastrointestinal side effects of those medications have prompted the search for alternative treatments. Recently, some phytochemicals captured the attention because of their inhibitory effects on α-amylase to control diabetes. The aim of this study was to investigate and identify potential alpha-amylase inhibitors in C. indica and W. coagulans. This study also aims to understand one of the possible mechanisms of action of plants for their anti-diabetic activity. A total of 36 phytochemical ligands were subjected for protein-ligand docking analysis. Among the phytochemicals, Taraxerol and Epoxywithanolide-I demonstrated significant binding free energy of -10.2kcal/mol and -11.9kcal/mol respectively, which was higher than the reference acarbose with -8.6kcal/mol. These molecules were subjected for molecular dynamics simulation (MDS) analysis with alpha-amylase protein for a duration of 150ns. Among the three complexes, Taraxerol and Epoxywithanolide-I complexes demonstrates strong potential as inhibitors of the target protein. MDS results were analyzed via root mean square deviation (RMSD), fluctuation of residues, potential energy, radii of gyration and solvent access surface area analysis. Taraxerol demonstrated a significantly low potential energy of -1,924,605.25kJ/mol, and Epoxywithanolide-I demonstrated -1,964,113.3kJ/mol of potential energy. RMSD plot shows that Epoxywithanolide-I has much higher stability than the other MDS complexes. Drugability and toxicity studies show that the test ligands are demonstrating strong potential as drug like molecules. The results of the study conclude that, Taraxerol of C. indica and Epoxywithanolide-I of W. coagulans are strong inhibitors of alpha-amylase enzyme and that, this is one of the possible mechanisms of action of the plants for their reported anti-diabetic activities. Further in-vitro analysis is in demand to prove the observed results.

Pyridazine Derivatives as New Antidiabetic Agents: Synthesis, In‐Vitro α‐Amylase Inhibitory Activity, Molecular Docking and Molecular Dynamics Simulations Studies

AbstractThis study involved the synthesis, characterization, and assessment of fourteen pyridazine analogs (designated as 1–14) to investigate their efficacy in inhibiting the α‐amylase enzyme for potential diabetes treatment using an in vitro approach. Additionally, in silico molecular docking and molecular dynamic (MD) simulations were conducted to assess the inhibitory properties of these analogs. Physicochemical and pharmacokinetic properties of the fourteen pyridazine analogs were predicted using the DataWarrior tool. Results indicated that all tested compounds demonstrated significant α‐amylase inhibitory activity, with IC50 values ranging from 81.28±0.00 to 1623.54±2.67 μM compared to the standard drug acarbose (IC50=220.42±36.40 μM). Notably, compounds 8 and 12 exhibited the most potent α‐amylase inhibitory activity, with IC50 values of 81.28±0.00 μM and 200.60±34.65 μM, respectively. Molecular docking analysis revealed binding energies ranging from −7.53 to −5.77 kcal/mol and inhibition constants ranging from 3.00 to 58.96 μM, with compounds 9, 7, 8, 5, and 3 demonstrating the best binding energies. Subsequent MD simulation analyses indicated that all five compound formed stable complexes after 100 ns MD simulation. Consequently, these compounds hold promise as potential α‐amylase inhibitors pending successful clinical validation.

Integrating bioinformatics and ferroptosis to reveal the protective mechanism of Astragaloside IV on chronic heart failure rats

Ferroptosis is an important pathological mechanism of chronic heart failure (CHF). This study aimed to investigate the protective mechanism of Astragaloside IV (AS-IV) on CHF rats by integrating bioinformatics and ferroptosis. CHF-related targets and ferroptosis-related targets were collected. After the intersection, the common targets were obtained. The PPI network of the common targets was constructed, and topological analysis of the network was carried out. The target with the highest topological parameter values was selected as the key target. The key target p53 was obtained through bioinformatics analysis, and its molecular docking model with AS-IV was obtained, as well as molecular dynamics simulation analysis. The rat models of CHF after myocardial infarction were established by ligation of left coronary artery and treated with AS-IV for 4 weeks. AS-IV treatment significantly improved cardiac function in CHF rats, improved cardiomyocyte morphology and myocardial fibrosis, reduced mitochondrial damage, decreased myocardial MDA and Fe2+ content, increased GSH content, inhibited the expression of p53 and p-p53, and up-regulated the expression of SLC7A11 and GPX4. In conclusion, AS-IV improved cardiac function in CHF rats, presumably by regulating p53/SLC7A11/GPX4 signaling pathway and inhibiting myocardial ferroptosis.

Design, synthesis, and antifungal activity of novel cyanoacrylate derivatives containing a naphthalene moiety as potential myosin-5 inhibitor

In search of innovative antifungal solutions for the control of plant diseases, a series of cyanoacrylate derivatives containing naphthalene groups were designed and synthesized, and their inhibition activity against four plant pathogenic fungi was evaluated. The results of in vitro bioassay revealed that some target compounds possessed obvious antifungal effect against Fusarium graminearum. As the most prominent one, compound A2 showed a inhibition rate of 98.46 % at 10 µg/mL and an EC50 value of 0.26 µg/mL, which was close to that of the positive control phenamacril (with a inhibition rate of 100 % at 10 µg/mL and EC50 value of 0.14 µg/mL). The compound A2 also markedly inhibited the growth of F. graminearum inoculated on rice leaves at 200 μg/mL with the protective and curative efficiencies of 89.03 % and 90.91 %, respectively, which were close to that of the positive control phenamacril (with the protective and curative efficiencies of 94.54 % and 96.36 %, respectively). The observation under scanning electron microscopy and measurement of relative conductivity revealed that compound A2 caused the hyphal surface become shrunken and rough, and made the cell membrane permeability increased. Molecular docking and molecular dynamics simulation analyses showed that compound A2 interacted with the key residues in the active site of myosin-5 in a similar mode as phenamacril. These results suggested that target compounds were potential myosin-5 inhibitors, they could serve as the lead compounds for further structural optimization to develop new fungicides against F. graminearum.

Network pharmacology and bioinformatics approach to unravel the mechanism of Xiao-chai-hu-tang herbal formula in tinnitus treatment

BackgroundTinnitus treatment remains a global challenge, and current therapeutic approaches are still controversial. This study aims to elucidate the potential mechanisms of Xiao-Chai-Hu-Tang (XCHT) in treating tinnitus through the analysis of network pharmacology, mendelian randomization and molecular docking, and molecular dynamics simulation analysis. We hope to contribute to the research on the target of action of traditional Chinese medicine and exploration of the mechanism of tinnitus. MethodsWe utilized network pharmacology to screen potential targets of action of XCHT on tinnitus. Mendelian randomization was employed to determine the causal relationship between potential targets of action and tinnitus. Finally, molecular docking and molecular dynamics simulation with clear targets and the combination of the active ingredient in effectiveness. ResultsThrough network pharmacology, we identified 38 potential targets of action. Mendelian randomization analysis revealed that HIF1A (OR [95 % CI] = 0.78 [0.65, 0.94], P = 0.008) and CCND1 (OR [95 % CI] = 1.22 [1.00, 1.49], P = 0.04) exhibited significant results with tinnitus. Molecular docking and molecular dynamics simulation of HIF1A and active ingredients demonstrated good binding efficacy. ConclusionHIF1A may play a key role in the treatment of tinnitus by XCHT, which may play a certain protective role in tinnitus patients and may inhibit the occurrence and development of tinnitus. However, the specific mechanism and effect need to be further studied and verified.

Design, Molecular Docking and Molecular Dynamic Simulation of New Heterocyclic Derivatives as Potential Anticancer Agents

Background: Despite significant progress in the development of anticancer medications, obstacles such as drug resistance, poor efficacy, and excessive toxicity have significantly impacted the daily lives of cancer patients. Consequently, the search for highly selective, effective, and non-toxic molecules remains a major challenge for cancer researchers. Objective: To utilize a computer program for evaluating new benzothiophene derivatives to investigate how they influence the estrogen-related receptor-gamma (ERRγ) active sites as anticancer agents. Methods: The molecular docking method used the Cambridge Crystallographic Data Centre's (CCDC) Genetic Optimization for Ligand Docking (GOLD) tool. We used the Desmond modules of the Schrodinger 2023 to perform MDS on the derivative with the highest docking score. The Swiss ADME server then assessed our drugs' pharmacokinetic profile, which included how well they crossed the blood-brain barrier (BBB), bound to P-gp, and were bioavailable. Results: The compounds were docked with the ERRγ crystal structure (2GPV) to assess their binding affinity to active sites. One of them earned a high score (102.62), and six compounds had a higher binding energy than the gold standard medication, tamoxifen. The molecular dynamic simulation analysis found that compound 1 closely matched the ERRγ based on RMSD and RMSF data. After examining the ADME study of practically active substances, they follow Lipinski's laws and other pharmacokinetic features. Conclusions: These chemicals have the potential to act as precursors in the development of new anticancer medicines.

TgVax452, an epitope-based candidate vaccine targeting Toxoplasma gondii tachyzoite-specific SAG1-related sequence (SRS) proteins: immunoinformatics, structural simulations and experimental evidence-based approaches

BackgroundThe highly expressed surface antigen 1 (SAG1)-related sequence (SRS) proteins of T. gondii tachyzoites, as a widespread zoonotic parasite, are critical for host cell invasion and represent promising vaccine targets. In this study, we employed a computer-aided multi-method approach for in silico design and evaluation of TgVax452, an epitope-based candidate vaccine against T. gondii tachyzoite-specific SRS proteins.MethodsUsing immunoinformatics web-based tools, structural modeling, and static/dynamic molecular simulations, we identified and screened B- and T-cell immunodominant epitopes and predicted TgVax452’s antigenicity, stability, safety, adjuvanticity, and physico-chemical properties.ResultsThe designed protein possessed 452 residues, a MW of 44.07 kDa, an alkaline pI (6.7), good stability (33.20), solubility (0.498), and antigenicity (0.9639) with no allergenicity. Comprehensive molecular dynamic (MD) simulation analyses confirmed the stable interaction (average potential energy: 3.3799 × 106 KJ/mol) between the TLR4 agonist residues (RS09 peptide) of the TgVax452 in interaction with human TLR4, potentially activating innate immune responses. Also, a dramatic increase was observed in specific antibodies (IgM and IgG), cytokines (IFN-γ), and lymphocyte responses, based on C-ImmSim outputs. Finally, we optimized TgVax452’s codon adaptation and mRNA secondary structure for efficient expression in E. coli BL21 expression machinery.ConclusionOur findings suggest that TgVax452 is a promising candidate vaccine against T. gondii tachyzoite-specific SRS proteins and requires further experimental studies for its potential use in preclinical trials.

Molecular docking studies and molecular dynamic simulation analysis: To identify novel ATP-competitive inhibition of Glycogen synthase kinase-3β for Alzheimer’s disease

Background The discovery of an ideal and effective therapy is urgently required for the treatment of Alzheimer’s disease. The main pathological hallmarks of Alzheimer’s disease that appear before the clinical symptoms are neurofibrillary tangles, amyloid plaques, brain inflammation, and neuronal atrophy throughout the cerebral cortex and hippocampus. GSK-3β (Glycogen Synthase Kinase-3β) is regarded as the most important and promising target for therapeutic use because GSK-3β expression levels increase with age and are the most abundant and hyperactive in the brains of patients with Alzheimer’s disease. Methods We used Maestro, which is Schrodinger, for our computational simulation studies. In the present work, we have used different modules that were used in previous studies with a little modification, the modules such as Protein Preparation with the help of Protein Preparation Wizard, Ligand Preparation with the help of LigPrep, for ADME (Absorption, Distribution, Metabolism and Excretion) prediction we used Qikprop, Docking studies we used Glide module, Binding energy prediction we used Prime and Molecular dynamic simulation studies by Desmond Results Our focus is mainly on an in-silico approach, focusing on library generation; we first drew an imidazo [1,5-a]pyridine-3-carboxamide (IMID 2) scaffold structure at Enamine and subjected it to a substructure search to target the receptor grid region (ATP-competitive site) of 6Y9R. They were then subjected to various screening processes. Finally, we selected nine compounds and subjected them to molecular dynamic simulation studies. Conclusions Nine compounds showed good results with the most stable interactions. Further experiments and studies are required to confirm these results.

Heat shock protein (Hsp27)-ceramide synthase (Cers1) protein-protein interactions provide a new avenue for unexplored anti-cancer mechanism and therapy

Hsp27 is a member of the small heat-shock proteins (sHSPs) – the known cellular line of defence against abnormal protein folding behaviors. Nevertheless, its upregulation is linked to a variety of pathological disorders, including several types of cancers. The ceramide synthases (CerS) mediate the synthesis of ceramide, a critical structural and signaling lipid. Functionally, downstream ceramide metabolites are implicated in the apoptosis process and their abnormal functionality has been linked to anticancer resistance. Studies showed that CerS1 are possibly inhibited by Hsp27 leading to biochemical anticancer effects in vitro. Nevertheless, the nature of such protein-protein interaction (PPI) has not been considerably investigated in molecular terms, hence, we present the first description of the dynamics CerS1-Hsp27 interaction landscapes using molecular dynamics simulations. Time-scale molecular dynamics simulation analysis indicated a system-wide conformational events of decreased stability, increased flexibility, reduced compactness, and decreased folding of CerS1. Analysis of binding energy showed a favorable interaction entailing 56 residues at the interface and a total stabilizing energy of −158 KJ/mol. The CerS1 catalytic domain experienced an opposite trend compared to the protein backbone. Yet, these residues adopted a highly compact conformation as per DCCM and DSSP analysis. Furthermore, conserved residues (SER 212, ASP 213, ALA 240, GLY 243, ASP 319) comprising the substrate shuttling machinery showed notable rigidity implying a restrained ceramide precursor access and assembly; hence, a possible inhibitory mechanism. Findings from this report would streamline a better molecular understanding of CerS1-Hsp27 interactions and decipher its potential avenue toward unexplored anti-cancer mechanisms and therapy.

Computational Analysis of Boerhavia diffusa Plant Extracts Targeting Alpha actinin4 against Focal Segmental Glomerulosclerosis

The most common protein lost in urine (proteinuria) is albumin, which is a symptom of the kidney illness focal segmental glomerulosclerosis (FSGS). It causes damage to podocyte foot processes, resulting in effacement of foot processes, and injury to foot processes leads to the leaking of plasma proteins into the urine, resulting in nephrotic syndrome. Alpha actinin (ACTN4) is extensively produced in glomerular podocytes, has a function in non-muscle cytoskeletal activity, and is enhanced early in the course of nephrotic illness in various types. Mutations in ACTN4 induce autosomal and sporadic steroid-resistance nephritic syndrome, which causes disturbance in podocyte foot process and function. All of the FSGS-causing mutations are situated on actin actin-binding domain of the ACTN4 protein. FSGS is typically treated by decreasing dietary salt and using immune-suppressing medications such as glucocorticoids. There is a risk associated with these drugs for cancer patients. Several studies have found that up to 80% of individuals with primary FSGS are resistant to steroid therapy, even though all other therapeutic options have been exhausted. Patients with steroid-resistant FSGS have a higher incidence of end-stage renal failure. Therefore, several new treatment strategies were put forward to cure the disease form of which use of phytochemicals is one such sustainable modality. In addition to this, our study intended to predict the stability of mutant protein’s structure as compared to wild type structure through molecular dynamic simulation analysis. With this, we extend our study to predict the potency of phytochemicals of Boerhaviadiffusa against FSGS by using molecular docking analysis. From our study, we conclude that the actin-binding domain of ACTN4 protein becomes more unstable or loses its stability after the mutation at position W59R among all the studied mutation positions. The boeravinone F phytochemical of the Boerhaviadiffusa plant shows the best inhibitory effect on the mutant actin-binding domain of ACTN4 protein and it confirms a stable binding confirmation at minimum energy of -7.5 kcal/mol. Hence it may be taken into consideration for future research work.

Free Energy Evaluation of Cavity Formation in Metastable Liquid Based on Stochastic Thermodynamics.

Nucleation is a fundamental and general process at the initial stage of first-order phase transition. Although various models based on the classical nucleation theory (CNT) have been proposed to explain the energetics and kinetics of nucleation, detailed understanding at nanoscale is still required. Here, in view of the homogeneous bubble nucleation, we focus on cavity formation, in which evaluation of the size dependence of free energy change is the key issue. We propose the application of a formula in stochastic thermodynamics, the Jarzynski equality, for data analysis of molecular dynamics (MD) simulation to evaluate the free energy of cavity formation. As a test case, we performed a series of MD simulations with a Lennard-Jones (LJ) fluid system. By applying an external spherical force field to equilibrated LJ liquid, we evaluated the free energy change during cavity growth as the Jarzynski's ensemble average of required works. A fairly smooth free energy curve was obtained as a function of bubble radius in metastable liquid of mildly negative pressure conditions.

Identification of Peregrin inhibitors-modulators by harnessing the computational prowess of molecular simulation and machine learning algorithms

Peregrin is marked as a potential drug target due to its pivotal role in the epigenetic maintenance of cellular metabolism. It is counted among those of the bromodomain-containing protein family. The protein binds to the acetylated lysine of N-terminus histone proteins of the nucleosomes. This bound form neutralizes the otherwise positively charged histone and, thus, crucially impacts the DNA replication mechanism. In several diseases like cancer, bone loss, and leukemia, this peregrin binding impacts the genes’ overexpression. Hence, the present study, computational screening of the bromodomain-specific inhibitors from a library of 5430 compounds retrieved from the ChemDiv database. Two different scoring functions based molecular docking studies have been employed for molecular interaction analysis. Followed by an artificial intelligence-based absolute binding affinity prediction has been confirmed through KDeep, which follows a machine learning step to obtain a precise binding energy score for the set of best compounds in the screening process. The resultant compounds were then screened for pharmacokinetics and drug-likeliness properties. Using molecular dynamics (MD) simulation analysis, the dynamic behavior of the four suggested compounds and Peregrin has been investigated for a 100 ns period. Identified compounds are found to be sufficiently effective in holding their strong interaction affinity toward Peregrin for an adequate time span, and structural integrity is also found to be comparable with the standard compound considered in the study. Mostly, all four potent compounds (K788-9421, S357-0084, S357-0893, S357-0915) are hydrophobic and evaluated for thermodynamics property analysis using MM-GBSA and free energy landscape (FEL) calculations. However, among all, K788-9421 shows comparatively better and energetically most favorable interactions with peregrin. Overall, study findings can lead to further research in developing next-generation broad-spectrum Peregrin inhibitors-modulators; they need extensive experimental validation for considering the compounds for clinical-trial application for being an excellent drug-candidate entity against Peregrin protein.

Insights into fatigue crack propagation behaviour of WAAM produced SS316 stainless steel: Molecular dynamics simulation and experimental analysis

The current work focuses on the crack growth mechanism / behavior of wire arc additively manufactured SS316L. Beside the experimental investigation, a molecular dynamics based polycrystalline model is developed to simulate the crack propagation under cyclic loading. The purpose of this work is to understand the crack growth behavior of wire arc additively manufactured SS316L, particularly the directional dependence of crack propagation. The experiments and molecular dynamics analysis are performed for the crack propagation along the build and traverse direction for the SS316L deposit. The experimental procedure involves fatigue crack growth rate tests, while the molecular dynamics simulations model the crack propagation in polycrystalline structures of different grain sizes. The ultimate tensile strength in build and traverse direction were 535±2 MPa and 495 ± 2 MPa, respectively. The experimental results reveal faster crack propagation along build direction in comparison to traverse direction. The values for Paris law material constants i.e. C and m are 7x10-15 and 6.78 along build direction while 8x10-14 and 6.02 along traverse direction, respectively. The crack growth along the build direction is primarily intergranular, which leads to high crack growth rate. The molecular dynamics simulations reveal the initiation and closure of secondary cracks for the traverse direction, which leads to slower crack growth rate along the traverse direction. The fractography of the fractured surfaces from fatigue crack growth rate test also indicate the formation of secondary cracks for the case of traverse direction. The molecular dynamics simulations performed with three grain sizes and thickness variation indicate the insensitivity of predicted crack growth mechanisms with respect to grain sizes used for simulations.

Role of Solvents in Oriented Attachment of Ag Nanoparticles: Insights from Molecular Dynamics Simulations and Topological Analysis.

Although the solvation force is considered one of the key forces behind the oriented attachment (OA), the precise roles of solvents in this process remain incompletely elucidated. In this study, we examined the effect of solvent polarities (water, acetone, and chloroform) on the attachment of silver nanoparticles by calculating the free energy curves for the OA process. The observed magnitudes of the binding energies and approaching and dissociation energy barriers are commensurate with the respective solvent polarities. Consequently, OA is more likely to occur in acetone with an intermediate permittivity relative to that of water and chloroform. Additionally, we identified a topological descriptor, namely, the Euler characteristic, of the solvent network, especially the water network, between two approaching surfaces, which manifests a linear correlation with the observed free energy profiles. This descriptor holds promise as a quantitative tool for predicting interactions between nanoparticles in solvent environments featuring hydrogen bond networks.

A novel multi-epitope peptide vaccine targeting immunogenic antigens of Ebola and monkeypox viruses with potential of immune responses provocation in silico.

The emergence or reemergence of monkeypox (Mpox) and Ebola virus (EBOV) agents causing zoonotic diseases remains a huge threat to human health. Our study aimed at designing a multi-epitope vaccine (MEV) candidate to target both the Mpox and EBOV agents using immunoinformatics tools. Viral protein sequences were retrieved, and potential nonallergenic, nontoxic, and antigenic epitopes were obtained. Next, cytotoxic and helper T-cell (CTL and HTL, respectively) and B-cell (BCL) epitopes were predicted, and those potential epitopes were fused utilizing proper linkers. The in silico cloning and expression processes were implemented using Escherichia coli K12. The immune responses were prognosticated using the C-ImmSim server. The MEV construct (29.53kDa) included four BCL, two CTL, and four HTL epitopes and adjuvant. The MEV traits were pertinent in terms of antigenicity, non-allergenicity, nontoxicity, physicochemical characters, and stability. The MEV candidate was also highly expressed in E. coli K12. The strong affinity of MEV-TLR3 was confirmed using molecular docking and molecular dynamics simulation analyses. Immune simulation analyses unraveled durable activation and responses of cellular and humoral arms alongside innate immune responses. The designed MEV candidate demonstrated appropriate traits and was promising in the prediction of immune responses against both Mpox and EBOV agents. Further experimental assessments of the MEV are required to verify its efficacy.

Spectroscopic and computational methods in the characterization of deep eutectic solvent, Gallic acid, and Glycerol

Several researchers have shown experimentally that Gallic acid has antioxidant, anti-inflammatory, and anti-aging properties, signifying its value in skin care. Glycerol has properties, such as increasing skin hydration, softening skin, and reducing skin dryness. The present work aims to understand the vibrational and spectroscopic study of the interacting mechanism of Deep Eutectic solvent mixture of Gallic acid and Glycerol. The theoretical analysis is performed using the Density Functional Theory with B3LYP/6-311 + g(d,p) level of theory. The optimized structure and frequency of the monomers and their biomolecular complex are obtained using Gauss view 6.0 and Gaussian16. The vibrational analysis is carried out using Vibrational Energy Distribution Analysis. The Natural Bond Orbital, molecular docking of the Glycerol-Gallic acid complex, and the molecular dynamics simulation of the docked protein-ligand system are carried out to understand the mechanism better. The theoretical and experimental frequencies are found to agree with each other. The Molecular Dynamic simulation analysis predicts that the protein-ligand complexation is relatively stable.

Pinpointing prime structural attributes of potential MMP-2 inhibitors comprising alkyl/arylsulfonyl pyrrolidine scaffold: a ligand-based molecular modelling approach validated by molecular dynamics simulation analysis

ABSTRACT MMP-2 overexpression is strongly related to several diseases including cancer. However, none of the MMP-2 inhibitors have been marketed as drug candidates due to various adverse effects. Here, a set of sulphonyl pyrrolidines was subjected to validation of molecular modelling followed by binding mode analysis to explore the crucial structural features required for the discovery of promising MMP-2 inhibitors. This study revealed the importance of hydroxamate as a potential zinc-binding group compared to the esters. Importantly, hydrophobic and sterical substituents were found favourable at the terminal aryl moiety attached to the sulphonyl group. The binding interaction study revealed that the S1′ pocket of MMP-2 similar to ‘a basketball passing through a hoop’ allows the aryl moiety for proper fitting and interaction at the active site to execute potential MMP-2 inhibition. Again, the sulphonyl pyrrolidine moiety can be a good fragment necessary for MMP-2 inhibition. Moreover, some novel MMP-2 inhibitors were also reported. They showed the significance of the 3rd position substitution of the pyrrolidine ring to produce interaction inside S2′ pocket. The current study can assist in the design and development of potential MMP-2 inhibitors as effective drug candidates for the management of several diseases including cancers in the future.