Results Of Molecular Dynamics Simulations Research Articles

Synthesis of All-Peptide-Based Rotaxane from a Proline-Containing Cyclic Peptide.

Rotaxane cross-linkers enhance the toughness of the resulting rotaxane cross-linked polymers through a stress dispersion effect, which is attributed to the mobility of the interlocked structure. To date, the compositional diversity of rotaxane cross-linkers has been limited, and the poor compatibility of these cross-linkers with peptides and proteins has made their use in such materials challenging. The synthesis of a rotaxane composed of peptides may result in a biodegradable cross-linker that is compatible with peptides and proteins, allowing the fortification of polypeptides and proteins and ultimately leading to the development of innovative materials that possess excellent mechanical properties and biodegradability. However, the chemical synthesis of all-peptide-based rotaxanes has remained elusive because of the absence of strong binding motifs in peptides, which prevents an axial peptide from penetrating a cyclic peptide. Here, we synthesized all-peptide-based rotaxanes using an active template method for proline-containing cyclic peptides. The results of molecular dynamics simulations suggested that cyclic peptides with an expansive inner cavity and carbonyl oxygens oriented toward the center are favorable for rotaxane synthesis. This rotaxane synthesis method is expected to accelerate the synthesis of peptides and proteins with mechanically interlocked structures, potentially leading to the development of peptide- and protein-based materials with unprecedented functionalities.

Pervaporation recovery of aniline using the degradable material poly(butylene adipate‐terephthalate): Experiment and molecular simulation

AbstractPervaporation has been considered a promising technique in the recovery of organic matter in low concentrations. Developing new and efficient pervaporation membrane materials remains the main challenge. In this study, the biodegradable poly (butylene adipate‐terephthalate) (PBAT) membrane was used to recover aniline by pervaporation for the first time. The PBAT membrane showed a good pervaporation performance due to its unique affinity with aniline by the surface adsorption energy calculations. When the aniline concentration in the feed solution was 0.4 wt%, the separation factor of the PBAT membrane exceeded 80. Besides, the results showed that the flux rose with the aniline concentration increasing, which was because of the incremental free volume of PBAT membrane. Moreover, the H‐bond length between aniline and PBAT (1.947 Å) was shorter than that between water and PBAT (2.091 Å) according to the density functional theory (DFT) calculations, which could account for the low diffusion coefficient of aniline from the result of molecular dynamics (MD) simulations. In addition, PBAT membranes displayed excellent stability in pervaporation experiments of more than 80 h. It is anticipated that the PBAT membrane may have great potential in pervaporation recovery of valuable chemicals from dilute aqueous solutions.Highlights Biodegradable PBAT membrane was first used to recover aniline by pervaporation. Low diffusion coefficient of aniline was further explained combining MD and DFT. The PBAT membranes exhibited excellent performance for aniline recovery.

Molecular mechanism of Danxiong Tongmai Granules in treatment of coronary heart disease.

Danxiong Tongmai Granules (DXTMG) are widely utilized in treating coronary heart disease (CHD) in China. This study aims to explore the molecular mechanisms underlying the therapeutic effects of DXTMG on CHD by employing a network pharmacology approach, complemented with experimental validation. Traditional Chinese Medicine (TCM) compounds and targets were identified via searches in the BATMAN-TCM database, and the GeneCards database was used to obtain the main target genes involved in CHD. We combined disease targets with the drug targets to identify common targets. The "TCM-compound-target" network was plotted using Cytoscape 3.7.2 software and a protein-protein interaction (PPI) network was constructed using the STRING database from which core targets were obtained. Gene ontology (GO) function analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed for common drug-disease targets using R Version 4.0.4 (64 bit) software. Molecular docking of core protein-small molecule ligand interaction was modeled using AutoDock software. A molecular dynamics simulation was conducted on the optimal protein-small molecule complex identified through molecular docking, using Amber18 software. The rat model for myocardial ischemia was established through pre-gavage administration of DXTMG, followed by dorsal hypodermic injection of isoprenaline. Myocardial tissues from the rats were analyzed using hematoxylin and eosin (HE) staining and Masson's trichrome staining. Relevant targets were validated by enzyme-linked immunosorbent assay (ELISA) and immunohistochemistry. 162 potential targets of DXTMG involved in CHD were identified. These included INS, ALB, IL-6 and TNF according to PPI network studies. GO enrichment analysis identified a total of 3365 GO pathways, including 3049 biological process pathways (BP) concerned with the heart and circulatory system; 109 cellular component (CC) pathways, including cation channels and membrane rafts and 207 molecular function (MF) pathways related to receptor ligands and activators. KEGG analysis revealed a total of 137 pathways (P < 0.05), including those related to AGE-RAGE signaling associated with diabetic complications, fluid shear stress and atherosclerosis. The results of molecular docking and molecular dynamics simulations demonstrated the robust binding affinity between the compounds and target proteins. Animal experiment findings indicated that, compared with the model group, the DXTMG group effectively ameliorated inflammation and fibrosis in rat myocardial tissues, reduced LDH, cTn-I, and MDA levels (P < 0.05, P < 0.01), elevated SOD and GSH-PX levels (P < 0.05), and reduced the percentage of positive area for IL-6 and TNF-α (P < 0.05). This study preliminarily suggests that DXTMG can modulate oxidative stress, inflammation response, and cardiomyocyte regulation, thereby mitigating the onset and progression of CHD.

Experimental and theoretical studies on the compatibility of DNTF and typical hydrocarbon polymer binders.

3,4-bis(3-nitrofurazan-4-yl) furoxan (DNTF) is one of the third-generation energetic compounds with excellent comprehensive properties, which can be added to polymer bonded explosive (PBX) to improve energy levels and regulate sensitivity, so the compatibility of DNTF with other components in PBX, especially the binder, is the first question. Herein, two typical hydrocarbon polymers commonly used in PBX, which are hydroxyl-terminated polybutadiene (HTPB) and polyisobutylene (PIB), were selected as the binder, and the compatibility of HTPB and PIB with DNTF was investigated by differential scanning calorimetry (DSC), the vacuum stability test (VST), and in situ infrared spectroscopy (in situ IR). The results of compatibility experiments were verified by using the binding energy and solubility parameter criteria in molecular dynamics (MD). Experimental and MD simulation results showed that DNTF could be compatible with PIB but incompatible with HTPB. The frontier molecular orbital theory in quantum chemistry (QC) was adopted to explore the frontier orbital electron distribution and energy levels of DNTF/HTPB and DNTF/PIB composite systems to better understand the microscopic compatibility mechanism. The compatibility results of the two composite systems were explained from the perspective of electron transfer. All these can deduce that a hydrocarbon polymer binder with a saturated carbon-hydrogen bond at the end of the molecular chain has good compatibility with DNTF, compared with a hydroxyl group, which has bad compatibility with DNTF.

Novel Pyrido[4,3-d]pyrimidine Derivatives as Potential Sterol 14α-Demethylase Inhibitors: Design, Synthesis, Inhibitory Activity, and Molecular Modeling.

Thirty-four new pyrido[4,3-d]pyrimidine analogs were designed, synthesized, and characterized. The crystal structures for compounds 2c and 4f were measured by means of X-ray diffraction of single crystals. The bioassay results showed that most target compounds exhibited good fungicidal activities against Pyricularia oryzae, Rhizoctonia cerealis, Sclerotinia sclerotiorum, Botrytis cinerea, and Penicillium italicum at 16 μg/mL. Compounds 2l, 2m, 4f, and 4g possessed better fungicidal activities than the commercial fungicide epoxiconazole against B. cinerea. Their half maximal effective concentration (EC50) values were 0.191, 0.487, 0.369, 0.586, and 0.670 μg/mL, respectively. Furthermore, the inhibitory activities of the bioactive compounds were determined against sterol 14α-demethylase (CYP51). The results displayed that they had prominent activities. Compounds 2l, 2m, 4f, and 4g also showed better inhibitory activities than epoxiconazole against CYP51. Their half maximal inhibitory concentration (IC50) values were 0.219, 0.602, 0.422, 0.726, and 0.802 μg/mL, respectively. The results of molecular dynamics (MD) simulations exhibited that compounds 2l and 4f possessed a stronger affinity to CYP51 than epoxiconazole.

Thermodynamic and transport properties of triangular-well fluids from molecular dynamics

Thermodynamic and transport properties of particles interacting via the triangular-well potential in the range of 1.4 ≤ λ ≤ 2.6 have been studied using perturbation theory and Molecular Dynamics simulations. We present thermodynamic properties such as vapour-liquid coexistence, vapour pressures, and density for different values of the attractive range potential. Good agreement is observed between the theoretical approach and computer simulations in a wide range of densities, temperatures, and pressures. Additionally, we show Molecular Dynamic simulation results of transport properties such as the self-diffusion coefficient as a function of both density and temperature. Finally, thermodynamic and transport properties of real fluids like oxygen, methane, hydrogen sulfide, and fluoromethane have been predicted using both approaches. Results of vapour-liquid coexistence, vapour pressures, and critical points were in excellent agreement with experimental data. The coupling of perturbation theory, Molecular Dynamics simulations, and the triangular-well pair potential offers a versatile and efficient method to explore various real fluid systems, which would include associating fluids, complex molecular liquids, and colloidal systems. This approach can advance our understanding of these systems using a simple approach and to contribute the development of more accurate and predictive models.

New analytical thermodynamic models developed for pure H2, CH4, CO2 and H2 containing mixtures based on molecular simulations

Pressure-volume-temperature-composition (PVTX) properties of gas mixtures are important to model and predict flow and compression performance in a range of industrial processes. It is time consuming and sometimes impractical to obtain these properties from experiments. Here, molecular dynamics (MD) simulations were conducted to compute the thermodynamic volumetric properties of pure H2, CH4, CO2, and binary mixtures of H2/CH4 and H2/CO2 at temperatures of 310.9–470 K, pressures up to 172 MPa. MD simulation results were used to develop five analytical equations explicit in pressure as a function of density or volume, temperature, and composition, for the pure gases and mixtures. Our simulated results matched very well with the predictions from the established GERG-2008 equation and data published by NIST. The simplified equations of state (EOS) developed in this work will be more computationally efficient than other EOS for mixed systems. This can be significant in reservoir simulations.

A systematic mutation analysis of 13 major SARS-CoV-2 variants

SARS-CoV-2 evolves constantly with various novel mutations. Due to their enhanced infectivity, transmissibility and immune evasion, a comprehensive understanding of the association between these mutations and the respective functional changes is crucial. However, previous mutation studies of major SARS-CoV-2 variants remain limited. Here, we performed systematic analyses of full-length amino acids mutation, phylogenetic features, protein physicochemical properties, molecular dynamics and immune escape as well as pseudotype virus infection assays among thirteen major SARS-CoV-2 variants. We found that Omicron exhibited the most abundant and complex mutation sites, higher indices of hydrophobicity and flexibility than other variants. The results of molecular dynamics simulation suggest that Omicron has the highest number of hydrogen bonds and strongest binding free energy between the S protein and ACE2 receptor. Furthermore, we revealed 10 immune escape sites in 13 major variants, some of them were reported previously, but four of which (i.e. 339/373/477/496) are first reported to be specific to Omicron, whereas 462 is specific to Epslion. The infectivity of these variants was confirmed by the pseudotype virus infection assays. Our findings may help us understand the functional consequences of the mutations within various variants and the underlying mechanisms of the immune escapes conferred by the S proteins.

Effect of voltage gradients on EK-PRB remediation: Experimental and molecular dynamics simulations

Electrokinetic-Permeable Reaction Barrier (EK-PRB) coupled remediation technology can effectively treat heavy metal-contaminated soil near coal mines. This study was conducted on cadmium (Cd), a widely present element in the soil of the mining area. To investigate the impact of the voltage gradient on the remediation effect of EK-PRB, the changes in current, power consumption, pH, and Cd concentration content during the macroscopic experiment were analyzed. A three-dimensional visualized kaolinite-heavy metal-water simulation system was constructed and combined with the Molecular Dynamics (MD) simulations to elucidate the migration mechanism and binding active sites of Cd on the kaolinite (001) crystalline surface at the microscopic scale. The results showed that the voltage gradient positively correlates with the current, power consumption, and Cd concentration during EK-PRB remediation, and the average removal efficiency increases non-linearly with increasing voltage gradient. Considering power consumption, average removal efficiency, and cost-effectiveness, the voltage range is between 1.5 and 3.0 V/cm, with 2.5 V/cm being the optimal value. The results of MD simulations and experiments correspond to each other. Cd2+ formed a highly stable adsorption structure in contrast to the Al–O sheet on the kaolinite (001) crystalline surface. The mean square displacement (MSD) curve of Cd2+ under the electric field exhibits anisotropy, the total diffusion coefficient DTotal increases and the Cd2+ migration rate accelerates. The electric field influences the microstructure of Cd2+ complexes. With the enhancement of the voltage gradient, the complexation between Cd2+ and water molecules is enhanced, and the interaction between Cd2+ and Cl− in solution is weakened.

The synergistic effect of body modification and surface coating for the moisture barrier of hydrophilic PU film

Polyurethane (PU) films have established a distinctive position among various protective materials due to their outstanding chemical and physical properties. However, their limited moisture barrier performance hinders their broader applications. To solve this difficult problem, PU film is first modified by adding reactive fillers (MgO) and physical barrier fillers (Modified graphene oxide, M-GO), and then Si-DLC coating is deposited on the surface of the film by hollow cathode plasma immersion ion implantation (HCPIII) method at near room temperature. MgO can react with the water molecules diffused into the film, while the addition of M-GO extends the diffusion path of water molecules. It is revealed that the addition of 5% MgO and 0.5% M-GO, along with the deposition of a 2.56 μm Si-doped DLC coating, leads to a remarkable 14.67-fold reduction in the water vapor transmittance rate (WVTR). The result of molecular dynamics simulations shows that the reactive sheet filler captures the water molecules and reduces the WVTR. In addition, the combination method of PU body modification and surface coating is suitable for polyurethane foam (PUF) to reduce the WVTR as a double coating. It’s amazing that the WVTR of PUF significantly reduces by 15.29 times after double-coating. The combination of body modification and surface coating provides an effective route for significantly improving the moisture barrier property of hydrophilic polymer film and polymer foam.

Topological isomerism design of Demulsifiers: A fusion of molecular dynamics simulation and experiment

Demulsifiers are crucial for enhancing crude oil extraction and transportation efficiency by facilitating the separation of oil–water emulsions. However, research conducted on the design and synthesis of demulsifiers based on the results of molecular dynamics simulation remains scarce. Herein, we designed eight block polyethers, and explored their interfacial behaviors at the oil–water interface via molecular dynamics simulation. Correspondingly, eight block polyether demulsifiers were synthesized, and their interface properties were tested. The simulation results were consistent with the experimental results, indicating that the energy of simulation systems could be efficiently reduced by designed molecules, and that the prepared demulsifiers with the same structure could achieve effective demulsification correspondingly. Based on the simulation and experimental results, a “hand-shaped” demulsification mechanism model was proposed. The demulsifiers with hydrophobic “palm” and hydrophilic “fingers” demonstrated a more efficient performance in demulsification. The hydrophobic “palm” was stable in the continuous oil phase, and the hydrophilic “fingers” could attract dispersed water droplets to aggregate, facilitating demulsification. The study also finds that longer hydrophilic “fingers” exert stronger molecular force. Combining molecular dynamics simulation and experiment significantly accelerates the development of new demulsifiers, highlighting the utility of this approach in the research on demulsifiers.

Correlation of rare earth coordination and spectral properties in Er3+ doped Na2O–Al2O3–SiO2 glasses with different Al2O3 concentrations by molecular dynamics simulations

The molecular structure of Er2O3 doped Na2O–Al2O3–SiO2 glasses with varying Na2O/Al2O3 ratios is explored via molecular dynamics (MD) simulations using the so-called inherent structure sampling method, which allows the calculation of a large number of local structures of low concentration, as needed to determine the surrounding of low concentration dopants. General structural parameters, including radial distribution functions, coordination numbers and interatomic distances of all network forming and network modifying ions are reported. However, in this work, special attention is devoted to the effect of Al2O3 concentration on the local surrounding of the doped Er3+ ions. It is shown that the Er atoms coordinate 5-6 oxygen ions in their first coordination sphere in the investigated glasses. The Er-O coordination number increases monotonically with increasing Al2O3 concentration and decreasing Na2O/Al2O3 ratio. It is found that the Er atoms are preferably connected to non-bridging oxygen atoms (NBO) in all glasses, even in the peraluminous composition. Additionally, the MD simulation results are compared to the glasses spectral properties that were already investigated in detail by Tanabe and Hanada. The increasing Er-NBO coordination number derived by MD simulations could be correlated with the increased peak splitting of the Er3+ absorption peaks reported by Tanabe and Hanada. Furthermore, a correlation between the Judd-Ofelt parameters published by Tanabe and Hanada and the Er3+ coordination in the glass structure is discussed. It is shown that the Er-O coordination increases with increasing Ω2 parameter as the Al2O3 concentration increases in the glass composition. A correlation of the average overall Er-O coordination number with the symmetry of the local Er site is proposed.

Influence of hydrogen volume/specimen surface area ratio on hydrogen embrittlement sensitivity of X52 pipeline steel

In the transition towards green energy, long distance transportation of gaseous hydrogen by pipeline is considered to be an economically attractive solution. For safe transportation of hydrogen, it is important to conduct relevant mechanical tests in representative hydrogen environments and working conditions of pipelines to demonstrate acceptable hydrogen embrittlement resistance of the steel. One important issue is the testing condition for the ratio of gaseous hydrogen volume over specimen surface area required in mechanical testing since this has not been specified in any testing standards and codes or investigated. This study investigated this issue by performing slow strain rate tensile (SSRT) testing of an X52 pipeline steel in gaseous hydrogen with different ratios of hydrogen volume/specimen surface area, Rv/s, ml/mm2. It was found that, with increasing Rv/s ratio, the area reduction of the steel decreased and hydrogen embrittlement sensitivity increased in the range of the Rv/s ratios investigated. The saturating Rv/s ratio appeared to be ∼2.0 beyond which the effect of Rv/s ratio on hydrogen embrittlement sensitivity was relatively small. The macroscopic and microscopic observations on both the fracture and side surfaces of the SSRT tested specimens also found that the tendency to cleavage fracture increased with increasing Rv/s ratio. The results of the ab initio molecular dynamics (AIMD) simulations performed also predicted a dependence of hydrogen embrittlement on hydrogen volume when Rv/s ratio is relatively small.

Biomimetic management of bone healing stages: MOFs induce tunable degradability and enhanced angiogenesis-osteogenesis coupling

Currently, biodegradable biomaterials are extensively used in bone regeneration. Nevertheless, a significant challenge remains in accurately adjusting their degradation rates to match bone healing stages to achieve bone regeneration. Herein, we present a novel biodegradable bone grafts integrated with zeolite imidazole framework-8 (ZIF-8) nanocrystals, fabricated via microinjection molding. Apart from the reinforcing effect derived from the in-situ fibrillation of PCL in PLGA, nanoscale ZIF-8 is inspiringly demonstrated to control the PLGA degradation. Both molecular dynamic simulation and experimental results indicate that Zn2+ derived from ZIF-8 nanocrystals acts as a Lewis acid to participate the degradation of PLGA matrix, thus successfully reconciles the contradiction between degradation of matrix and maintenance of reinforcing phase. Moreover, nanometric ZIF-8 modified bone grafts improve the angiogenesis-osteogenesis coupling. In vitro, it directly boosts HIF-1α and capillary-like network formation of endothelial cells (ECs), and RUNX2 and OCN expression in bone marrow mesenchymal stem cells (BMSCs). In vivo, bone grafts with a moderate concentration (0.5 %) of ZIF-8 nanoparticles aid vascularized bone regeneration by tunable biodegradation matching bone healing stages. Further, RNA sequencing shows PLGA/PCL@nZ bone grafts promote angiogenesis-osteogenesis by cooperatively regulating calcium signaling pathway in both ECs and BMSCs. Collectively, this study delineates a groundbreaking bone repair strategy with profound clinical application potential.

Modeling steady state rate- and temperature-dependent strain hardening behavior of glassy polymers

In this paper, we use molecular dynamics (MD) simulations to investigate the origin of strain hardening in glassy polymers, with a particular focus on the influences of strain rate and temperature. We demonstrate that strain hardening in uniaxial tension arises from bond stretching and is relaxed by bond rotation, characterized by the evolution of dihedral angles. Based on this rotational relaxation, strain rate plays a role analogous to temperature, resulting in a steady state behavior in the hardening region identifiable by strain rate and temperature. Following these observations, we propose a constitutive model to describe the rate- and temperature-dependent strain hardening behavior of glassy polymers using a viscous potential as a function of strain rate. To capture the elastic and yield behavior at small strains, we integrate this viscous potential with a conventional elasto-viscoplastic (EVP) model, giving rise to our V-EVP model. The V-EVP model is shown to be thermodynamically consistent and is validated by comparison to MD simulation results of glassy polymers undergoing uniaxial tension tests across a broad range of temperatures and strain rates.

Mechanism of Cordyceps militaris in gouty nephropathy explored using network pharmacology and molecular docking technology

Cordyceps militaris Link. (C. militaris) with strong anti-hyperuricemia effects could be detected in mice urine and serum after oral administration as we previously proved. In this study, the mechanism and molecular effects of anti-hyperuricemia by C. militaris in gouty nephropathy (GN) mice were firstly investigated, and its key active structure was further explored. The results showed C. militaris could significantly reduce the uric acid (UA) level and related inflammatory factors. Meanwhile, C. militaris maintain the normal dynamic balance of UA by inhibiting hepatic xanthine oxidase (XO) and regulating the expression of renal transport proteins ABCG2, GLUT9 and URAT1. Then we employed network pharmacology to theoretically determine two active components in C. militaris, cordycepin and ergosterol, that act on GN. Moreover, the molecular docking and molecular dynamic simulation results showed cordycepin and ergosterol could stably bind to XO and cyclooxygenase-2 (COX-2) due to hydrogen bonding and hydrophobic interactions. This study could provide theoretical evidence for utilization of C. militaris in hyperuricemia-management functional foods.

Structural Pharmacology of TRPV4 Antagonists.

The nonselective calcium-permeable Transient Receptor Potential Cation Channel Subfamily V Member4 (TRPV4)channel regulates various physiological activities. Dysfunction of TRPV4 is linked to many severe diseases, including edema, pain, gastrointestinal disorders, lung diseases, and inherited neurodegeneration. Emerging TRPV4 antagonists show potential clinical benefits. However, the molecular mechanisms of TRPV4 antagonism remain poorly understood. Here, cryo-electron microscopy (cryo-EM) structures of human TRPV4 are presented in-complex with two potent antagonists, revealing the detailed binding pockets and regulatory mechanisms of TRPV4 gating. Both antagonists bind to the voltage-sensing-like domain (VSLD) and stabilize the channel in closed states. These two antagonists induce TRPV4 to undergo an apparent fourfold to twofold symmetry transition. Moreover, it is demonstrated that one of the antagonists binds to the VSLD extended pocket, which differs from the canonical VSLD pocket. Complemented with functional and molecular dynamics simulation results, this study provides crucial mechanistic insights into TRPV4 regulation by small-molecule antagonists, which may facilitate future drug discovery targeting TRPV4.

High‐Strength Wear‐Resistant Cu/Tungsten Carbide/Diamond Composites Fabricated by Powder Metallurgy

Copper‐based diamond composites are widely used for thermal management and wear‐resistant materials. In this work, Cu/diamond, Cu/tungsten carbide (WC)/diamond, and Cu–0.92Cr/WC/diamond composites are fabricated by high‐energy ball milling and rapid hot‐pressing sintering. Physical characteristics, compressive strength, and tribological properties of the studied composites are investigated. The compressive strength of Cu/7wt%WC/diamond composites is 102% higher than the Cu/diamond composites, reaching 415 MPa. Compression fractures extend from the interface due to compression cracks, consistent with the compression curves from molecular dynamics (MD) simulations. The crack propagates from the interface during the compression experiment, which is consistent with the result of MD simulation. The Cu/7wt%WC/diamond composites exhibit a wear rate of 0.6 × 10−6 mm3 (N m)−1 and a friction coefficient of 0.37 at 50 N. The addition of WC and diamond improves the compressive strength and wear resistance. These findings are helpful in the development of copper composites with high compression strength and wear resistance.

The crosslinking sites and molecular conformation of gelatin hydrogel modified by transglutaminase

This work aimed to investigate the covalent crosslinking sites induced by transglutaminase (TGase, EC 2.3.2.13) in gelatin hydrogel and their impact on the gelatin molecular conformation. LC-MS/MS results demonstrated that Lys644 and Gln1351 of α1 chain and Gln19 of α2 chain were the main sites. The results of molecular dynamic (MD) simulation indicated that at the moderate degree of covalent crosslinking (13.55%), Radius of gyration (Rg) values decreased from 11.5 to 10.0 nm at 4 °C and led to a more compact structure, therefore enhancing structural tightness and gel strength. As the degree of crosslinking rose, the number of crosslinking sites gradually increased, with a predominant distribution in the C-terminal pro-peptide of gelatin chain. At the high crosslinking degree (37.48%), Rg value decreased at 100 °C and gelatin chains were connected through a “head to tail” linkage configuration, resulting in a significant reduction in the triple helix-like structure. The structure maintained the gel-forming ability at high temperature while lowering the aggregation energy of water molecules from −2.359 × 105 to −2.455 × 105 kJ/mol, leading to thermal irreversibility of gelatin hydrogel.

Benchmarking docking, density functional theory and molecular dynamics studies to assess the aldose reductase inhibitory potential of Trigonella foenum-graecum compounds for managing diabetes-associated complications

Inhibition of aldose reductase (AR) could be a beneficial strategy for managing diabetes-associated complications. Trigonella foenum-graecum (TFG) is used around the globe as a traditional medicine for the management of diabetes. Our study aimed to assess the potential of TFG phytocompounds as inhibitors of AR in the context of diabetes-related complications. Our research work employed molecular docking, density functional theory (DFT) and molecular dynamics (MD) to evaluate the efficacy of TFG compounds. The study compared the predictive power of AutoDock and AutoDock Vina docking software and found that AutoDock Vina performs better in ranking and discriminating actives and decoys. The research identified five compounds as potential AR inhibitors from fifty-eight reported TFG phytoconstituents. Tigogenin and Gitogenin stood out as the most promising AR inhibitors. The electronic properties of the compounds were analysed through DFT studies and provided insights into their binding potential. Finally, the results of MD simulations indicated that Tigogenin and Gitogenin bound robustly with AR throughout the simulation period. This study predicted the AR inhibitory potential of TFG compounds for managing diabetes-associated complications and supports further drug development from TFG. The benchmarking approach used in this study improves the accuracy and dependability of bioactivity prediction.