Molecular Dynamics Study Research Articles

Molecular dynamics study on the microstructure evolution of Ti2AlNb-based alloy subjected to tensile pre-strain and electric current treatment

Molecular dynamics study on the microstructure evolution of Ti2AlNb-based alloy subjected to tensile pre-strain and electric current treatment

Molecular docking and dynamics studies to identify novel active compounds targeting potential breast cancer receptor proteins from an indigenous herb Euphorbia thymifolia Linn

Background Breast cancer has become the most prevalent disease and its incidence has almost doubled in the Indian population. This increased burden demands new targeted therapies with novel compounds either synthetically produced or derived from indigenous plants, which could be a promising approach for the development of drugs. Euphorbia thymifolia L is a widely growing tropical herb that has been reported to have various ethnopharmacological properties. Although Euphorbia genus is reported to have anticancer properties, E. thymifolia is not reported to have anticancer properties to date. Therefore, the aim of the present study was to screen the phytoconstituents and identify the active compounds present in the methanolic extract of E. thymifolia (ME.ET) as ligands to inhibit human cancer cell lines with special reference to potential protein targets implicated in breast cancer using an In-silico approach. Methods ME.ET was subjected to GC-MS analysis to screen the phytoconstituents, and the identified compounds were docked with protein targets such as extracellular signal-regulated kinases (ERK1), a serine/threonine kinase-1(AKT1), human epidermal growth factor 2 (HER2), estrogen receptor (ER), maternal embryonic leucine zipper kinase (MELK), polo-like kinase-1(PLK1), and protein tyrosine kinase (PTK6). Compounds with good docking scores were further subjected to dynamic studies to understand the protein ligand binding stability, ligand pathway calculation, and molecular mechanics energies combined with Poisson-Boltzmann (MM/PBSA) calculations using the Schrodinger suite. Results GC-MS analysis revealed the presence of 245 phytoconstituents, 219 of which were unique. When subjected to docking, these phytocompounds, namely 3,6,9,12-tetraoxatetradecane-1,14-diyl dibenzoate (TTDB) and succinic acid, 2-(dimethylamino) ethyl 4-isopropylphenyl ester (SADPE), showed good docking scores. Molecular dynamics studies showed a high affinity and low binding energy for TTDB with HER2, ERK1, and SADPE with ER. Conclusions Hence, in this study, we identified two lead compounds in E.thymifolia linn. Further invitro and invivo anticancer studies can be performed to confirm these results and to understand the molecular mechanism by which they exhibit anticancer activity against breast cancer.

Enhancing Mass Transfer of Reactive Oxygen and Nitrogen Species in Plasma‐Activated Water: A Molecular Dynamics Study on the Impact of Plasma Electric Fields

ABSTRACTThis study investigates the impact of plasma electric fields on the mass transfer characteristics of reactive oxygen and nitrogen species (RONS), specifically NO2 and O3, in water using molecular dynamics simulations. The results demonstrate that the plasma electric field significantly increases the thickness of the Gibbs Dividing Surface, reduces surface tension at the gas–liquid interface, and disrupts the hydrogen bond network. These changes lead to an enhanced solubility and self‐diffusion coefficient for both NO2 and O3. Due to stronger dipole–dipole interactions, NO2 exhibits superior mass transfer performance compared to O₃. This research provides theoretical support for the application of plasma‐activated water technology.

Molecular dynamics study on the effect of ferrite structure on the mechanical characteristics of pearlite

Molecular dynamics study on the effect of ferrite structure on the mechanical characteristics of pearlite

Targeting Nudix Hydrolase 5 with Bioactive Flavonoids: Molecular Dynamics and Docking Studies for Breast Cancer Therapy.

Breast cancer (BC) is the most prevalent malignancy among women globally and the leading cause of cancer-related mortality. Consequently, there is an urgent need for new, effective treatment strategies for breast cancer. Research has shown that the enzyme nudix hydrolase 5 (NUDT5) plays a critical role in promoting breast cancer aggressiveness and serves as a key regulator of oncogenic pathways. The development of NUDT5 inhibitors presents a viable strategy for enhancing treatment results in managing BC. The ability of the flavonoids to modulate key biochemical pathways and improve therapeutic outcomes highlights their promise in developing novel breast cancer treatments. Hence, the main objective of the present investigation is to identify the potential interaction of structurally diverse bioactive flavonoids with the active site of the target NUDT5. Our docking analysis revealed that the flavonoids such as naringin and genistein have shown a significant binding association with residues Arg51, Asp60, Gln82, Arg84, Ala96, Leu98, Glu112, Glu116, Met132, Cys139, Ile141, and Glu166 of NUDT5, suggesting its potential as a potent inhibitor. The stabilizing effects of these leads (naringin and genistein) were further validated using molecular dynamics investigations, including RMSD, RMRF, Rg, SASA, PCA, and FEL. The results of the MD simulation studies evidenced a more significant interaction between genistein and NUDT5, indicating a steady and robust affinity, making genistein a more promising inhibitor. In conclusion, the flavonoid genistein has a strong potential as a therapeutic agent for targeting NUDT5 in breast cancer treatment making it viable candidates for further preclinical and clinical investigations.

Integrative analysis of a novel immunogenic PANoptosis‑related gene signature in diffuse large B-cell lymphoma for prognostication and therapeutic decision-making

This study aimed to develop a PANoptosis-related gene prognostic index (PANGPI) to explore its potential value in predicting the prognosis and immunotherapy response of diffuse large B-cell lymphoma (DLBCL). Differentially expressed genes of DLBCL from GEO databases were analyzed and mapped to the PANoptosis gene set. The independent prognostic value of the PANGPI signature was evaluated using LASSO Cox regression and multivariate Cox regression. Additionally, the tumor infiltrating lymphocyte (TIL) characteristics and mutation landscape of both subgroups were evaluated, and drug sensitivity was predicted using the GDSC database. Furthermore, in silico docking and molecular dynamic simulation studies were presented to elucidate the mode of interaction of these predicted drugs. The PANGPI risk score was an independent risk factor for the prognosis of patients with DLBCL and exhibited good prognostic predictive performance. Furthermore, the cytolytic activity of the TILs was positively correlated with the PANGPI scores. Additionally, the PANGPI enabled the identification of 3 chemotherapeutic agents, including BMS-536924, Gefitinib, Navitoclax for DLBCL patients in the high-risk group. We established a novel PANoptosis-related gene subtyping system in DLBCL, which could shed a novel light on the development of new biomarkers for DLBCL.

Giardia duodenalis Flavohemoglobin is a Target of 5-Nitroheterocycle and Benzimidazole Compounds Acting as Enzymatic Inhibitors or Subversive Substrates.

Giardia duodenalis causes giardiasis in humans, companion, livestock and wild animals. Control of infection involves drugs as benzimidazoles (e.g., albendazole, ABZ) and 5-nitroheterocyclics [5-NHs: metronidazole (MTZ), furazolidone (FZD), nitazoxanide (NTZ)] as first-line agents. During infection, Giardia is exposed to immune and pro-oxidant host responses involving nitric oxide (NO). In Giardia, NO is detoxified by a flavohemoglobin (gFlHb), a heme-containing enzyme which is absent in mammals. gFlHb has NO dioxygenase and NADH oxidase activities converting NO into nitrate and producing a superoxide anion (O2•-) that causes oxidative stress and parasite death. The modulation of gFlHb activities may provide novel approaches for treatment of giardiasis. We investigated the capacity of selected benzimidazole-2-carbamates (BZCs: ABZ, oxibendazole, nocodazole), non-BZCs (thiabendazole), an ehtylphenylcarbamate (LQM-996) and 5-NHs (MTZ, NTZ, FZD and some derivatives) to bind to recombinant gFlHb at the heme group, modifying NADH consumption activity and/or inducing ROS production. Of these, BZCs and NTZ bind to heme and increased O2•- production (i.e. caused enzyme subversion), whereas MTZ binds to heme but inhibited NADH consumption. LQM-996 decreased NADH consumption and two out of four NTZ derivatives altered NADH oxidase activity. In silico docking and molecular dynamics studies suggested the interaction of distinct drug moieties in ABZ and NTZ with gFlHb sites involved in NADH and NO catalysis. These findings provide new insights on gFlHb as a novel target of BZCs, MTZ and NTZ, and provides a useful platform to assess the compounds binding capacity to gFlHb prior to experimental and clinical trials in giardiasis.

Computational dissection through network pharmacology and structure-based analysis unravels mechanistic actions of bioactive compounds in a hepatoprotective herb, Picrorhiza kurroa for the treatment of NAFLD and NASH

Non-Alcoholic fatty liver disease has become a silent pandemic worldwide with no authorized medicine available. Picrorhiza kurroa is a traditional hepatoprotective herb wherein extracts provide therapeutic efficacy but not the individual compounds. Hence, the aim of the study is exploration of active molecules in P. kurroa extracts and identification of mechanistic actions to pinpoint potential leads towards drug development. We employed network pharmacology to identify the significance of combinatorial effect of compounds on multiple targets. The NAFLD/NASH associated genes encoding protein targets overlapped with the predicted protein targets of P. kurroa compounds. Then, overlapping targets were considered further to capture the interactive targets from Protein-Protein-Interaction network of NAFLD and NASH. The networks were generated to capture the role of proteins in different signaling pathways, diseases, and effective compounds as therapeutics. Furthermore, structural, and biophysical analysis was performed for significant complexes. We observed that the compounds like astragalin, Picroside-I, Vernicoside, Rutin, Quercetin, Kaempferol, Gallic acid, Ellagic acid in P. kurroa acted synergistically by enhancing the bioavailability of active compounds and affecting various morbidities of NAFLD through involvement in different signaling and disease pathways such as oxidative phosphorylation, FoxO signaling, inflammation, several cancerous and diabetic pathways. The network pharmacology revealed the interactive behavior of proteins involved in NAFLD treated by P. kurroa compounds. Furthermore, molecular docking and molecular dynamic simulation study showed potential candidates in therapeutics. Overall, the study suggested multi-target drug discovery for treating complex diseases by providing leads in herbal extracts as potential therapeutic botanicals.

Mechanism analysis of oil-in-water-in-oil droplet deformation and breaking under pulsed alternating current field: A molecular dynamics study

Mechanism analysis of oil-in-water-in-oil droplet deformation and breaking under pulsed alternating current field: A molecular dynamics study

Molecular dynamics study on effects of the synergistic effect of anions and cations on the dissolution of cellulose in ionic liquids

This work systematically explores the interaction between cellulose and various ionic liquids (ILs) formed by the pairing of glycine cations with diverse anions. Results show that the interaction of anions with cellulose decreases in the order of [CH3COO]− > [Im]− > [SCN]− > Cl− > [PF6]−, differing from imidazole-based ionic liquids. The synergistic effect of anions and cations is crucial for cellulose dissolution. Moreover, the electronegativity of anions can enhance their interaction with cellulose. Short alkyl chains (n = 1, 3, 5) reduce hydrogen bonding due to steric hindrance, while longer chains (n = 9) promote diffusion and hydrogen bond formation. The introduction of electron-withdrawing groups to anions weakens their interaction with cellulose, while marginally strengthening the association between cations and cellulose. Overall, a delicate balance among anion-cation-cellulose interactions is essential for effective cellulose dissolution. The obtained results are anticipated to be of significant importance in the rational design of innovative amino acid-based ionic liquids, aiming to achieve efficient cellulose dissolution.

Investigation of the Penetration of Water and Chloride into Unsaturated Concrete: An Experimental and Molecular Dynamics Study

Investigation of the Penetration of Water and Chloride into Unsaturated Concrete: An Experimental and Molecular Dynamics Study

Molecular dynamics study on the impact of surface nanostructures and interfacial coupling strength on thermal transport at the Cu-water interface

Molecular dynamics study on the impact of surface nanostructures and interfacial coupling strength on thermal transport at the Cu-water interface

Effect of Graphene Network Reinforcement and Interface Orientation on the Mechanical Behavior of Nickel Composites: A Molecular Dynamics Study

Effect of Graphene Network Reinforcement and Interface Orientation on the Mechanical Behavior of Nickel Composites: A Molecular Dynamics Study

Metformin's modulation of gut microbiota and its implications for non-alcoholic fatty liver disease: A network pharmacology and molecular dynamics study

Metformin's modulation of gut microbiota and its implications for non-alcoholic fatty liver disease: A network pharmacology and molecular dynamics study

A molecular dynamics study on microscopic mechanism of nano-polished single crystal copper

Molecular dynamics simulations are performed to investigate the microscopic mechanism of diamond abrasive grain (DAG) polishing on the surface of single crystal copper (SCC). In this paper, the polishing parameters including the incident angle and the polishing force applied to the DAG are varied to analyze the surface morphology, friction and subsurface damage state of the workpiece. The polishing process on scratched SCC surface was also investigated. It is found that variations in the incident angle and the polishing force have significant effects on the swarf formation and internal structure of the workpiece. At small incident angle, unstable DAG motion and obvious friction fluctuations is observed. As the incident angle becomes larger, the sliding of the DAG on the workpiece surface becomes stable, and the friction force undergoes transition from the rapid growth to the stabilization phase. However, the fluctuation of dislocation density increases with the incident angle. As the polishing force increases, the sliding distance required to reach the peak of dislocation density becomes longer. In addition, the friction as well as the dislocation density show different characteristics on the scratched surface compared to the smooth surface.

Evaluations of FDA-approved Drugs Targeting 3CLP of SARS-CoV-2 Employing a Repurposing Strategy.

The SARS-CoV-2 coronavirus (COVID-19) has raised innumerable global concerns, and few effective treatment strategies have yet been permitted by the FDA to lighten the disease burden. SARS-CoV-2 3C-like proteinase (3CLP) is a crucial protease and plays a key role in the viral life cycle, as it controls replication, and thus, it is viewed as a target for drug design. In this study, we performed structure-based virtual screening of FDA drugs approved during 2015-2019 (a total of 220 drugs) for interaction with the active site of 3CLP (PDB ID 6LU7) using AutoDock 4.2. We report the top ten drugs that outperform the reported drugs against 3CLP (Elbasvir and Nelfinavir), particularly Cefiderocol, having the highest affinity among the compounds tested, with a binding energy of -9.97 kcal/mol. H-bond (LYS102:HZ2-ligand: O49), hydrophobic (ligand-VAL104), and electrostatic (LYS102:NZ-ligand: O50) interactions were observed in the cefiderocol-3CLP complex. The docked complex was subjected to a 50 ns molecular dynamics study to check its stability, and stable RMSD and RMSF graphs were observed. Accordingly, we suggest cefiderocol might be effective against SARS-CoV-2 and urge that experimental validation be performed to determine the antiviral efficacy of cefiderocol against SARS-CoV-2. Along with these, cefiderocol is effective for treating respiratory tract pathogens and a wide range of gram-negative bacteria for whom there are limited therapeutic alternatives. This article aimed to explore the FDA-approved drugs as a repurposing study against 3CLP for COVID-19 management.

Microscopic swelling behaviors and structural responses of aggregate system: A coarse-grained molecular dynamics study

Microscopic swelling behaviors and structural responses of aggregate system: A coarse-grained molecular dynamics study

DFT and Molecular Dynamics Study of the Optical and Electronic Properties of Nitrobenzofurazan-Based Molecules for Photovoltaic and Nonlinear Optical Applications

DFT and Molecular Dynamics Study of the Optical and Electronic Properties of Nitrobenzofurazan-Based Molecules for Photovoltaic and Nonlinear Optical Applications

Molecular dynamics study of the interaction between LeIBP ICE-binding protein and alcohol dehydrogenase enzyme

Molecular dynamics study of the interaction between LeIBP ICE-binding protein and alcohol dehydrogenase enzyme

Molecular dynamics studies reveal the structural impacts of LRRK2 R1441C and LRRK2 D1994A mutations in Parkinson's disease

Parkinson's Disease (PD) is a continuingly deteriorating neurological ailment affecting over 8.5 million patients globally as of 2019, and the numbers are expected to keep rising. To aid in identifying therapeutic targets, molecular dynamics simulations are convenient and cost-effective methods for enriching our knowledge of the molecular pathophysiology of diseases. Many proteins and their corresponding mutations have been identified to contribute to this disease, of which Leucine-rich repeat kinase 2 (LRRK2) is accountable for a significant percentage. Several mutations involving the domains in LRRK2 have been studied, which are known to interfere with various enzymatic processes, ultimately leading to trademark features of PD like aggregation of protein inclusions called Lewy Bodies (LBs), mitochondrial dysfunctions, etc. The precise molecular mechanism of the mutations' pathophysiology is still unclear. This research article looks at the structural effects of mutations, namely the R1441C and D1994A mutations, on the surrounding residues in the protein, offering novel insights into pathophysiological changes at an atomistic level. Our results indicate a gain of electrostatic interactions with a stable αβ motif within the LRR-Roc linker, amongst other changes. This article also highlights the potential involvement and importance of the αβ motif in LRRK2 associated PD.