The present research investigates the double-chain deoxyribonucleic acid model, which is important for the transfer and retention of genetic material in biological domains. This model is composed of two lengthy uniformly elastic filaments, that stand in for a pair of polynucleotide chains of the deoxyribonucleic acid molecule joined by hydrogen bonds among the bottom combination, demonstrating the hydrogen bonds formed within the chain's base pairs. The modified extended Fan sub equation method effectively used to explain the exact travelling wave solutions for the double-chain deoxyribonucleic acid model. Compared to the earlier, now in use methods, the previously described modified extended Fan sub equation method provide more innovative, comprehensive solutions and are relatively straightforward to implement. This method transforms a non-linear partial differential equation into an ODE by using a travelling wave transformation. Additionally, the study yields both single and mixed non-degenerate Jacobi elliptic function type solutions. The complexiton, kink wave, dark or anti-bell, V, anti-Z and singular wave shapes soliton solutions are a few of the creative solutions that have been constructed utilizing modified extended Fan sub equation method that can offer details on the transversal and longitudinal moves inside the DNA helix by freely chosen parameters. Solitons propagate at a consistent rate and retain their original shape. They are widely used in nonlinear models and can be found everywhere in nature. To help in understanding the physical significance of the double-chain deoxyribonucleic acid model, several solutions are shown with graphics in the form of contour, 2D and 3D graphs using computer software Mathematica 13.2. All of the requisite constraint factors that are required for the completed solutions to exist appear to be met. Therefore, our method of strengthening symbolic computations offers a powerful and effective mathematical tool for resolving various moderate nonlinear wave problems. The findings demonstrate the system's potentially very rich precise wave forms with biological significance. The fundamentals of double-chain deoxyribonucleic acid model diffusion and processing are demonstrated by this work, which marks a substantial development in our knowledge of double-chain deoxyribonucleic acid model movements.
A practical and facile synthesis of various coumarin derivatives was conducted using a liquid phase of 4,4'-trimethylenedipiperidine as a safe and greener dual-task reagent under catalyst-free and solvent-free conditions. This reagent is a commercially available solid and can be handled easily, having a liquid phase over a vast temperature range, high thermal stability, low toxicity, and good solubility in green solvents such as water and ethanol. It is worth mentioning that 4,4'-trimethylenedipiperidine could be completely recovered and regenerated after a simple process. The current method has other merits, including (a) minimizing the use of high-risk and toxic reagents and solvents; (b) the use of a secure and recoverable medium-organocatalyst instead of metal-based catalysts, (c) avoid tedious processes, harsh conditions, and a multi-step process for the preparation of catalysts, (d) transform phenol and salicyladehyde derivatives into the corresponding coumarin derivatives in good to high yields, (e) minimize hazardous waste generation. TMDP could be easily recovered and reused several times with no change in its activity. Furthermore, the current work demonstrated that the liquid phase of 4,4'-trimethylenedipiperidine can be a promising medium in organic reaction at higher temperatures due to its broad liquid range temperature, thermal stability, acceptor/donor hydrogen bond property, and other unique merits. New methodology for the synthesis of coumarines using liquid phase of TMDP under mild conditions.
The synthesis of Janus nanosheets using κ-carrageenan (κ-Ca) as a green template endows a greener and more straightforward method compared to traditional approaches of using wax template. We hypothesize that the hydrogen bonding interaction between κ-Ca and graphene oxide (GO) allows partial masking of GO's single facet, paving the way for the asymmetric modification of the exposed surface. GO is first encapsulated within the porous hydrogel matrix formed by κ-Ca to isolate one of the facets. The exposed surface was then selectively hydrophobized to produce an amphiphilic asymmetrically modified graphene oxide (AMGO). The properties of AMGO synthesized under different κ-Ca/GO ratios were studied. The κ-Ca/GO interactions and the properties of GO and AMGO were investigated and characterized. AMGO was successfully produced with a yield of 90.37 % under optimized synthesis conditions. The separation of κ-Ca and AMGO was conducted without organic solvents, and the κ-Ca could be subsequently recovered. Furthermore, the porous hydrogel matrix formed by κ-Ca and GO exhibited excellent shape-retaining properties with high thermal tolerance of up to 50 °C. Given these benefits, this newly developed method endows sustainability and open the possibility of formulating more flexible material synthesis protocols.
In this study, we have investigated a series of indole-based compounds for their inhibitory study against pancreatic α-amylase and intestinal α-glucosidase activity. Inhibitors of carbohydrate degrading enzymes appear to have an essential role as antidiabetic drugs. All analogous exhibited good to moderate α-amylase (IC50 = 3.80 to 47.50 μM), and α-glucosidase inhibitory interactions (IC50 = 3.10-52.20 μM) in comparison with standard acarbose (IC50 = 12.28 μM and 11.29 μM). The analogues 4, 11, 12, 15, 14 and 17 had good activity potential both for enzymes inhibitory interactions. Structure activity relationships were deliberated to propose the influence of substituents on the inhibitory potential of analogues. Docking studies revealed the interaction of more potential analogues and enzyme active site. Further, we studied their kinetic study of most active compounds showed that compounds 15, 14, 12, 17 and 11 are competitive for α-amylase and non- competitive for α-glucosidase.
Transiently associating amines with therapeutic agents through the formation of ion-pairs has been established both in vitro and in vivo as an effective means to systemically direct drug delivery to the lung via the polyamine transport system (PTS). However, there remains a need to better understand the structural traits required for effective PTS uptake of drug ion-pairs. This study aimed to use a structurally related series of amine counterions to investigate how they influenced the stability of theophylline ion-pairs and their active uptake in A549 cells. Using ethylamine (mono-amine), ethylenediamine (di-amine), spermidine (tri-amine) and spermine (tetra-amine) as counterions the ion-pair affinity was shown to increase as the number of protonated amine groups in the counterion structure increased. The mono and diamines generated a single hydrogen bond and the weakest ion-pair affinities (pKFTIR: 1.32 ± 0.04 and 1.43 ± 0.02) whereas the polyamines produced two hydrogen bonds and thus the strongest ion-pair affinities (pKFTIR: 1.93 ± 0.05 and 1.96 ± 0.04). In A549 cells depleted of endogenous polyamines using α-difluoromethylornithine (DFMO), the spermine-theophylline uptake was significantly increased (p
Protein-protein interaction plays an essential role in almost all cellular processes and biological functions. Coupling molecular dynamics (MD) simulations and nanoparticle tracking analysis (NTA) assay offered a simple, rapid, and direct approach in monitoring the protein-protein binding process and predicting the binding affinity. Our case study of designed ankyrin repeats proteins (DARPins)-AnkGAG1D4 and the single point mutated AnkGAG1D4-Y56A for HIV-1 capsid protein (CA) were investigated. As reported, AnkGAG1D4 bound with CA for inhibitory activity; however, it lost its inhibitory strength when tyrosine at residue 56 AnkGAG1D4, the most key residue was replaced by alanine (AnkGAG1D4-Y56A). Through NTA, the binding of DARPins and CA was measured by monitoring the increment of the hydrodynamic radius of the AnkGAG1D4-gold conjugated nanoparticles (AnkGAG1D4-GNP) and AnkGAG1D4-Y56A-GNP upon interaction with CA in buffer solution. The size of the AnkGAG1D4-GNP increased when it interacted with CA but not AnkGAG1D4-Y56A-GNP. In addition, a much higher binding free energy (∆GB) of AnkGAG1D4-Y56A (-31 kcal/mol) obtained from MD further suggested affinity for CA completely reduced compared to AnkGAG1D4 (-60 kcal/mol). The possible mechanism of the protein-protein binding was explored in detail by decomposing the binding free energy for crucial residues identification and hydrogen bond analysis.
Conformational search for the most stable geometry connection of 16 sets of polydopamine (PDA) tetramer subunits has been systematically investigated using density functional theory (DFT) calculations. Our results indicated that the more planar subunits are, the more stable they are. This finding is in good agreement with recent experimental observations, which have suggested that PDA are composed of the nearly planar subunits that appear to be stacked together via the π-π interactions to form graphite-like layered aggregates associated with the balance of the intramolecular hydrogen bonds and steric effects from the indole and catechol moieties. Molecular dynamics (MD) simulations of 16 spherical clusters of the tetramer subunits of PDA in the gas and aqueous phase were performed at 298 K and confirmed the stability of supramolecular tetramer aggregates. The complex formation and binding energy of all 16 clusters are very strong although the shapes of the clusters in aqueous solution are not spherical and are very much different from those in the gas phase. The aggregations of all 16 clusters in aqueous solution were also confirmed from the profiles of the Kratky plot and the radius of gyration of all clusters. Our MD results in both gas phase and aqueous solution pointed out that there are high possibilities of aggregations of the 16 kinds of tetramer subunits although the conformations of each tetramer subunit are not flat. In summary, this work brings an insight into the controversial structure of PDA tetramer units and explains some of the important structural features found in the aqueous phase in comparison to the gas phase.
Extracellular signal-regulated kinases 1 and 2 (ERK1/2) play key roles in promoting cell survival and proliferation through the phosphorylation of various substrates. Remarkable antitumour activity is found in many inhibitors that act upstream of the ERK pathway. However, drug-resistant tumour cells invariably emerge after their use due to the reactivation of ERK1/2 signalling. ERK1/2 inhibitors have shown clinical efficacy as a therapeutic strategy for the treatment of tumours with mitogen-activated protein kinase (MAPK) upstream target mutations. These inhibitors may be used as a possible strategy to overcome acquired resistance to MAPK inhibitors. Here, we report a class of repeat proteins-designed ankyrin repeat protein (DARPin) macromolecules targeting ERK2 as inhibitors. The structural basis of ERK2-DARPin interactions based on molecular dynamics (MD) simulations was studied. The information was then used to predict stabilizing mutations employing a web-based algorithm, MAESTRO. To evaluate whether these design strategies were successfully deployed, we performed all-atom, explicit-solvent molecular dynamics (MD) simulations. Two mutations, Ala → Asp and Ser → Leu, were found to perform better than the original sequence (DARPin E40) based on the associated energy and key residues involved in protein-protein interaction. MD simulations and analysis of the data obtained on these mutations supported our predictions.
Rhinoviruses (RV), especially Human rhinovirus (HRVs) have been accepted as the most common cause for upper respiratory tract infections (URTIs). Pleconaril, a broad spectrum anti-rhinoviral compound, has been used as a drug of choice for URTIs for over a decade. Unfortunately, for various complications associated with this drug, it was rejected, and a replacement is highly desirable. In silico screening and prediction methods such as sub-structure search and molecular docking have been widely used to identify alternative compounds. In our study, we have utilised sub-structure search to narrow down our quest in finding relevant chemical compounds. Molecular docking studies were then used to study their binding interaction at the molecular level. Interestingly, we have identified 3 residues that is worth further investigation in upcoming molecular dynamics simulation systems of their contribution in stable interaction.
The NS2B/NS3 protease is crucial for the pathogenesis of the DENV. Therefore, the inhibition of this protease is considered to be the key strategy for the development of new antiviral drugs. In the present study, malabaricones C (3) and E (4), acylphenols from the fruits of Myristica cinnamomea King, have been respectively identified as moderate (27.33 ± 5.45 μM) and potent (7.55 ± 1.64 μM) DENV-2 NS2B/NS3 protease inhibitors, thus making this the first report on the DENV-2 NS2B/NS3 protease inhibitory activity of acylphenols. Based on the molecular docking studies, compounds 3 and 4 both have π-π interactions with Tyr161. While compound 3 has hydrogen bonding interactions with Gly151, Gly153 and Tyr161, compound 4 however, forms hydrogen bonds with Ser135, Asp129, Phe130 and Ile86 instead. The results from the present study suggests that malabaricones C (3) and E (4) could be employed as lead compounds for the development of new dengue antivirals from natural origin.
The binding characteristics of DNA in deep eutectic solvents (DESs), particularly the binding energy and interaction mechanism, are not widely known. In this study, the binding of tetrabutylammonium bromide (TBABr) based DES of different hydrogen bond donors (HBD), including ethylene glycol (EG), glycerol (Gly), 1,3-propanediol (1,3-PD) and 1,5-pentanediol (1,5-PD), to calf thymus DNA was investigated using fluorescence spectroscopy. It was found that the shorter the alkyl chain length (2 carbons) and higher EG ratios of TBABr:EG (1:5) increased the binding constant (Kb) between DES and DNA up to 5.75 × 105 kJ mol-1 and decreased the binding of Gibbs energy (ΔGo) to 32.86 kJ mol-1. Through displacement studies, all synthesised DESs have been shown to displace DAPI (4',6-diamidino-2-phenylindole) and were able to bind on the minor groove of Adenine-Thymine (AT)-rich DNA. A higher number of hydroxyl (OH) groups caused the TBABr:Gly to form more hydrogen bonds with DNA bases and had the highest ability to quench DAPI from DNA, with Stern-Volmer constants (Ksv) of 115.16 M-1. This study demonstrated that the synthesised DESs were strongly bound to DNA through a combination of electrostatic, hydrophobic, and groove binding. Hence, DES has the potential to solvate and stabilise nucleic acid structures.
The lyotropic phase behavior of four common and easily accessible glycosides, n-octyl α-d-glycosides, namely, α-Glc-OC8, α-Man-OC8, α-Gal-OC8, and α-Xyl-OC8, was investigated. The presence of normal hexagonal (HI), bicontinuous cubic (VI), and lamellar (Lα) phases in α-Glc-OC8 and α-Man-OC8 including their phase diagrams in water reported previously was verified by deuterium nuclear magnetic resonance (2H NMR), via monitoring the D2O spectra. Additionally, the partial binary phase diagrams and the liquid crystal structures formed by α-Gal-OC8 and α-Xyl-OC8 in D2O were constructed and confirmed using small- and wide-angle X-ray scattering and 2H NMR. The average number of bound water molecules (nb) per headgroup in the Lα phase was determined by the systematic measurement of the quadrupolar splitting of D2O over a wide range of molar ratio values (glycoside/D2O), especially at high glucoside composition. The number of bound water molecules bound to the headgroup was found to be around 1.5-2.0 for glucoside, mannoside, and galactoside, all of which possesses four OH groups. In the case of xyloside, which has only three OH groups, the bound water content is ∼2.0. Our findings confirmed that the bound water content of all n-octyl α-d-glycosides studied is lower compared to the number of possible hydrogen bonding sites possibly due to the fact that most of the OH groups are involved in intralayer interaction that holds the lipid assembly together.
Increasing environmental concerns have led to greater attention to the development of biodegradable materials. The aim of this paper is to investigate the effect of banana leaf fibre (BLF) on the thermal and mechanical properties of thermoplastic cassava starch (TPCS). The biocomposites were prepared by incorporating 10 to 50 wt.% BLF into the TPCS matrix. The samples were characterised for their thermal and mechanical properties. The results showed that there were significant increments in the tensile and flexural properties of the materials, with the highest strength and modulus values obtained at 40 wt.% BLF content. Thermogravimetric analysis showed that the addition of BLF had increased the thermal stability of the material, indicated by higher-onset decomposition temperature and ash content. Morphological studies through scanning electron microscopy (SEM) exhibited a homogenous distribution of fibres and matrix with good adhesion, which is crucial in improving the mechanical properties of biocomposites. This was also attributed to the strong interaction of intermolecular hydrogen bonds between TPCS and fibre, proven by the FT-IR test that observed the presence of O-H bonding in the biocomposite.
In this study, caffeine (CA) was encapsulated into food-grade starch matrices, including swelled starch (SS), porous starch (PS), and V-type starch (VS). The bitterness of the microcapsules and suppression mechanisms were investigated using an electronic tongue, molecular dynamics (MD) simulation and the in vitro release kinetics of CA. All the CA-loaded microcapsules showed a lower bitterness intensity than the control. The MD results proved that the weak interactions between starch and CA resulted in a moderate CA release rate for SS-CA microcapsules. The PS-CA microcapsule presented the longest CA release, up to 40 min, whereas the VS-CA microcapsule completely released CA in 9 min. The CA release rate was found to be related to the microcapsule structure and rehydration properties. A low CA bitterness intensity could be attributed to a delay in the CA release rate and resistance to erosion of the microcapsules. The results of this work are valuable for improving starch-based microcapsules (oral-targeted drug-delivery systems) by suppressing the bitterness of alkaloid compounds.
Folate receptor alpha (FRα) is known as a biological marker for many cancers due to its overexpression in cancerous epithelial tissue. The folic acid (FA) binding affinity to the FRα active site provides a basis for designing more specific targets for FRα. Heterocyclic rings have been shown to interact with many receptors and are important to the metabolism and biological processes within the body. Nineteen FA analogs with substitution with various heterocyclic rings were designed to have higher affinity toward FRα. Molecular docking was used to study the binding affinity of designed analogs compared to FA, methotrexate (MTX), and pemetrexed (PTX). Out of 19 FA analogs, analogs with a tetrazole ring (FOL03) and benzothiophene ring (FOL08) showed the most negative binding energy and were able to interact with ASP81 and SER174 through hydrogen bonds and hydrophobic interactions with amino acids of the active site. Hence, 100 ns molecular dynamics (MD) simulations were carried out for FOL03, FOL08 compared to FA, MTX, and PTX. The root mean square deviation (RMSD) and root mean square fluctuation (RMSF) of FOL03 and FOL08 showed an apparent convergence similar to that of FA, and both of them entered the binding pocket (active site) from the pteridine part, while the glutamic part was stuck at the FRα pocket entrance during the MD simulations. Molecular mechanics Poisson-Boltzmann surface accessible (MM-PBSA) and H-bond analysis revealed that FOL03 and FOL08 created more negative free binding and electrostatic energy compared to FA and PTX, and both formed stronger H-bond interactions with ASP81 than FA with excellent H-bond profiles that led them to become bound tightly in the pocket. In addition, pocket volume calculations showed that the volumes of active site for FOL03 and FOL08 inside the FRα pocket were smaller than the FA-FRα system, indicating strong interactions between the protein active site residues with these new FA analogs compared to FA during the MD simulations.
The use of antidiabetic agents which control glycemic levels in the blood and simultaneously inhibit oxidative stress is an important strategy in the prevention of Diabetes Mellitus and its complications. In our previous study, malabaricone C (3) and its dimer, giganteone A (5) exhibited significant DPPH free radical scavenging activities which were lower than the activity of the positive control, ascorbic acid. These compounds were evaluated for their α-glucosidase inhibitory activities at different concentrations (0.02-2.5 mM) in the present study. Compounds 3 (IC50 59.61 µM) and 5 (IC50 39.52 µM) were identified as active alpha-glucosidase inhibitors, each respectively being 24 and 37 folds more potent than the standard inhibitor, acarbose. Based on the molecular docking studies, compounds 3 and 5 docked into the active site of the α-glucosidase enzyme, forming mainly hydrogen bonds in the active site.
The current strategy for rapid wound healing treatment involves combining a biomaterial and cell-secreted proteins or biomolecules. This study was aimed at characterizing 3-dimensional (3D) collagen hydrogels fortified with dermal fibroblast-conditioned medium (DFCM) as a readily available acellular skin substitute. Confluent fibroblasts were cultured with serum-free keratinocyte-specific medium (KM1 and KM2) and fibroblast-specific medium (FM) to obtain DFCM. Subsequently, the DFCM was mixed with collagen (Col) hydrogel and chondroitin-4-sulphate (C4S) to fabricate 3D constructs termed Col/C4S/DFCM-KM1, Col/C4S/DFCM-KM2, and Col/C4S/DFCM-FM. The constructs successfully formed soft, semi-solid and translucent hydrogels within 1 h of incubation at 37 °C with strength of <2.5 Newton (N). The Col/C4S/DFCM demonstrated significantly lower turbidity compared to the control groups. The Col/C4S/DFCM also showed a lower percentage of porosity (KM1: 35.15 ± 9.76%; KM2: 6.85 ± 1.60%; FM: 14.14 ± 7.65%) compared to the Col (105.14 ± 11.87%) and Col/C4S (143.44 ± 27.72%) constructs. There were no changes in both swelling and degradation among all constructs. Fourier transform infrared spectrometry showed that all groups consisted of oxygen-hydrogen bonds (O-H) and amide I, II, and III. In conclusion, the Col/C4S/DFCM constructs maintain the characteristics of native collagen and can synergistically deliver essential biomolecules for future use in skin therapeutic applications.
Recent trend to recover value-added products from wastewater calls for more effective pre-treatment technology. Conventional landfill leachate treatment is often complex and thus causes negative environmental impacts and financial burden. In order to facilitate downstream processing of leachate wastewater for production of energy or value-added products, it is pertinent to maximize leachate treatment performance by using simple yet effective technology that removes pollutants with minimum chemical added into the wastewater that could potentially affect downstream processing. Hence, the optimization of coagulation-flocculation leachate treatment using multivariate approach is crucial. Central composite design was applied to optimize operating parameters viz. Alum dosage, pH and mixing speed. Quadratic model indicated that the optimum COD removal of 54% is achieved with low alum dosage, pH and mixing speed of 750 mgL-1, 8.5 and 100 rpm, respectively. Optimization result showed that natural pH of the mature landfill leachate sample is optimum for alum coagulation process. Hence, the cost of pH adjustment could be reduced for industrial application by adopting optimized parameters. The inherent mechanism of pollutant removal was elucidated by FTIR peaks at 3853 cm-1 which indicated that hydrogen bonds play a major role in leachate removal by forming well aggregated flocs. This is concordance with SEM image that the floc was well aggregated with the porous linkages and amorphous surface structure. The optimization of leachate treatment has been achieved by minimizing the usage of alum under optimized condition.
The disease Tuberculosis (TB) is caused by a bacterium called Mycobacterium tuberculosis (Mtb). The bacterial cell-wall consists of peptidoglycan layer maintains the cellular integrity and cell viability. The main problem resides in the cell cycle of Mycobacterium tuberculosis in its quiescent form which is not targeted by any drugs hence there is an immediate need for new antibiotics to target the cell wall. The current study deals with the dTDP-4-dehydrorahmnose reductase (RmlD) which is the final enzyme in the series of cell-wall proteins of Mtb. The RmlD is a part of Carbohydrate biosynthesis has been considered as a good drug target for the novel class of antibiotics. Our study begins with the protein structure prediction, Homology studies were conducted using the Phyre2 web server. The structure is then refined and subjected to molecular dynamics simulations for 50 ns using GROMACS. The clustering analysis has been carried out and generated 41 clusters with 2 Å as the cut-off. Blind docking virtual screening was performed against RmlD protein using the Super Natural-II database with AutoDock4.0. its results helped to screen top ligands based on best binding energies. In both dockings, there are some common residues in which the ligands are interacting and forming the Hydrogen bonds such as Asp-105, Val-158, Thr-160, Gly-161, Arg-224, Arg-256. The ligand-567 giving the best results by being in the top-3 of all the clusters in both blind docking as well as the active-site docking. Hence ligand-567 can be a potential inhibitor of RmlD which can further inhibit the cell-wall synthesis of Mycobacterium tuberculosis.Communicated by Ramaswamy H. Sarma.
Activated carbons have been reported to be useful for adsorptive removal of the volatile anaesthetic sevoflurane from a vapour stream. The surface functionalities on activated carbons could be modified through aqueous oxidation using oxidising solutions to enhance the sevoflurane adsorption. In this study, an attempt to oxidise the surface of a commercial activated carbon to improve its adsorption capacity for sevoflurane was conducted using 6 mol/L nitric acid, 2 mol/L ammonium persulfate, and 30 wt per cent (wt%) of hydrogen peroxide (H2O2). The adsorption tests at fixed conditions (bed depth: 10 cm, inlet concentration: 528 mg/L, and flow rate: 3 L/min) revealed that H2O2 oxidation gave desirable sevoflurane adsorption (0.510 ± 0.005 mg/m2). A parametric study was conducted with H2O2 to investigate the effect of oxidation conditions to the changes in surface oxygen functionalities by varying the concentration, oxidation duration, and temperature, and the Conductor-like Screening Model for Real Solvents (COSMO-RS) was applied to predict the interactions between oxygen functionalities and sevoflurane. The H2O2 oxidation incorporated varying degrees of both surface oxygen functionalities with hydrogen bond (HB) acceptor and HB donor characters under the studied conditions. Oxidised samples with enriched oxygen functionalities with HB acceptor character and fewer HB donor character exhibited better adsorption capacity for sevoflurane. The presence of a high amount of oxygen functional groups with HB donor character adversely affected the sevoflurane adsorption despite the enrichment of oxygen functional groups with HB acceptor character that have a higher tendency to adsorb sevoflurane.