Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 55
Filter
1.
Arch Biochem Biophys ; 761: 110151, 2024 Sep 10.
Article in English | MEDLINE | ID: mdl-39265694

ABSTRACT

Important biological structures known for their exceptional mechanical qualities, lipid bilayers are essential to many cellular functions. Fluidity, elasticity, permeability, stiffness, tensile strength, compressibility, shear viscosity, line tension, and curvature elasticity are some of the fundamental characteristics affecting their behavior. The purpose of this review is to examine these characteristics in more detail by molecular dynamics simulation, elucidating their importance and the elements that lead to their appearance in lipid bilayers. Comprehending the mechanical characteristics of lipid bilayers is critical for creating medications, drug delivery systems, and biomaterials that interact with biological membranes because it allows one to understand how these materials respond to different stresses and deformations. The influence of mechanical characteristics on important lipid bilayer properties is examined in this review. The mechanical properties of lipid bilayers were clarified through the use of molecular dynamics simulation analysis techniques, including bilayer thickness, stress-strain analysis, lipid bilayer area compressibility, membrane bending rigidity, and time- or ensemble-averaged the area per lipid evaluation. We explain the significance of molecular dynamics simulation analysis methods, providing important new information about the stability and dynamic behavior of the bilayer. In the end, we hope to use molecular dynamics simulation to provide a comprehensive understanding of the mechanical properties and behavior of lipid bilayers, laying the groundwork for further studies and applications. Taken together, careful investigation of these mechanical aspects deepens our understanding of the adaptive capacities and functional roles of lipid bilayers in biological environments.

2.
Cell Mol Biol (Noisy-le-grand) ; 70(8): 235-243, 2024 Sep 08.
Article in English | MEDLINE | ID: mdl-39262266

ABSTRACT

Recent research has emphasized the development of efficient drug delivery systems to facilitate the delivery of biological compounds such as polyphenols via skin absorption. Phytozomes have been employed as carriers of plant compounds in this context Hydrogen bonding between plant polyphenols and the phospholipid phosphate group enables efficient encapsulation of potent compounds for enhanced drug delivery systems. Additionally, the strong affinity of phytosomes for the skin's phospholipids enhances skin absorption. In this study, phytosomes were initially formulated using the thin-layer hydration method After optimizing the synthetic parameters, phytosomes were loaded with Resveratrol and Quercetin for enhanced delivery and skin absorption potential to assess the characteristics of the synthesized phytosomes, tests were conducted to determine particle distribution and size, zeta potential, and examine the microstructure morphology using a scanning electron microscope (SEM). Furthermore, a siloxane gel base was formulated in this study, and the stability of the physicochemical and biological properties of the final prepared nanoformulation was investigated. The results of this study indicated that the formulated phytosomes exhibit optimal characteristics for facilitating high skin penetration of resveratrol and quercetin. A high skin absorption was observed after 60 days of synthesis. Additionally, the base of the siloxane gel can play a significant role in preventing the formation of scars by reducing the passage of water vapor.


Subject(s)
Cicatrix , Gels , Quercetin , Resveratrol , Siloxanes , Resveratrol/chemistry , Resveratrol/administration & dosage , Resveratrol/pharmacokinetics , Gels/chemistry , Siloxanes/chemistry , Quercetin/chemistry , Quercetin/administration & dosage , Quercetin/pharmacokinetics , Skin Absorption/drug effects , Particle Size , Animals , Drug Carriers/chemistry , Drug Delivery Systems/methods , Skin/metabolism , Skin/drug effects , Phytochemicals/chemistry , Phytosomes
3.
BMC Bioinformatics ; 24(1): 65, 2023 Feb 24.
Article in English | MEDLINE | ID: mdl-36829112

ABSTRACT

BACKGROUND: It seems that several members of intestinal gut microbiota like Streptococcus bovis, Bacteroides fragilis, Helicobacter pylori, Fusobacterium nucleatum, Enterococcus faecalis, Escherichia coli, Peptostreptococcus anaerobius may be considered as the causative agents of Colorectal Cancer (CRC). The present study used bioinformatics and immunoinformatics approaches to design a potential epitope-based multi-epitope vaccine to prevent CRC with optimal population coverage. METHODS: In this study, ten amino acid sequences of CRC-related pathogens were retrieved from the NCBI database. Three ABCpred, BCPREDS and LBtope online servers were considered for B cells prediction and the IEDB server for T cells (CD4+ and CD8+) prediction. Then, validation, allergenicity, toxicity and physicochemical analysis of all sequences were performed using web servers. A total of three linkers, AAY, GPGPG, and KK were used to bind CTL, HTL and BCL epitopes, respectively. In addition, the final construct was subjected to disulfide engineering, molecular docking, immune simulation and codon adaptation to design an effective vaccine production strategy. RESULTS: A total of 19 sequences of different lengths for linear B-cell epitopes, 19 and 18 sequences were considered as epitopes of CD4+ T and CD8+ cells, respectively. The predicted epitopes were joined by appropriate linkers because they play an important role in producing an extended conformation and protein folding. The final multi-epitope construct and Toll-like receptor 4 (TLR4) were evaluated by molecular docking, which revealed stable and strong binding interactions. Immunity simulation of the vaccine showed significantly high levels of immunoglobulins, helper T cells, cytotoxic T cells and INF-γ. CONCLUSION: Finally, the results showed that the designed multi-epitope vaccine could serve as an excellent prophylactic candidate against CRC-associated pathogens, but in vitro and animal studies are needed to justify our findings for its use as a possible preventive measure.


Subject(s)
Colorectal Neoplasms , Epitopes, T-Lymphocyte , Animals , Molecular Docking Simulation , Epitopes, T-Lymphocyte/chemistry , Vaccines, Subunit/chemistry , Epitopes, B-Lymphocyte , Computational Biology/methods
4.
Environ Res ; 214(Pt 3): 113966, 2022 11.
Article in English | MEDLINE | ID: mdl-35952738

ABSTRACT

Alginate-grafted polyaniline (Alg-g-PANI) microparticles were synthesized through the grafting of aniline onto functionalized Alg followed by double crosslinking by glutaraldehyde and calcium chloride. The performance of the developed microparticles as adsorbent in simultaneous removal of malachite green (MG) and congo red (CR) dyes were examined by the batch method. Experimental parameters, including adsorbent amount, pH, initial dyes concentrations, and contact time were optimized. Langmuir and Freundlich adsorption models were employed to explore the equilibrium isotherm. As the Langmuir model results, the maximum adsorption capacities (Qm) of microparticles for the MG and CR dyes were obtained as 578.3 and 409.6 mgg-1, respectively. Adsorption kinetics for both dyes were well-fitted with the pseudo-second-order model that confirm the rate-limiting step might be the chemical adsorption. The adsorbent was regenerated via desorption process and was reusable five times without a substantial decrease in its adsorption efficacy in first three cycles. Adsorbent-dyes interactions were computationally evaluated using Gromacs package, and it was found that both MG and CR are able to interact strongly with the adsorbent. In accordance with experimental results, simulation data revealed that MG can be removed more efficiently than those of the CR. As the experimental results, we could conclude that the synthesized Alg-g-PANI microparticles can be used as a nature-inspired adsorbent for simultaneous removals of CR and MG dyes.


Subject(s)
Coloring Agents , Water Pollutants, Chemical , Adsorption , Anions , Cations , Congo Red , Hydrogen-Ion Concentration , Kinetics , Water Pollutants, Chemical/analysis
5.
Bioorg Chem ; 106: 104355, 2021 01.
Article in English | MEDLINE | ID: mdl-33223200

ABSTRACT

In this study, we prepared a novel amino cellulose derivative (benzyl cellulose-g-poly [2-(N,N-Dimethylamino)ethyl methacrylate]) via a homogeneous ATRP method. The successful synthesis of the novel amino cellulose was confirmed by FT-IR and 1H NMR. This study addressed the different characteristics of the prepared polymer including the thermal stability, solubility, and X-ray diffraction pattern. The antibacterial activity of the synthesized cellulose derivative was investigated using the diffusion disk method against both gram-negative (Escherichia coli, Salmonella enterica) and gram-positive (Staphylococcus aureus, Bacillus subtilis) bacteria. Based on the inhibition zone, it was confirmed that the prepared benzyl cellulose-g-PDMAEMA possesses acceptable antibacterial activity against Escherichia coli, Salmonella enterica, and Staphylococcus aureus while Bacillus subtilis is resistant to the prepared polymer. Also according to the inhibition zone, it was shown that benzyl cellulose-g-PDMAEMA has more impact on E. coli and Salmonella enterica than Staphylococcus aureus. Molecular dynamics simulation was also used to study the interaction of the synthesized cellulose derivative with a model membrane which presented atomistic details of the polymer-lipid interactions. According to the results obtained from the molecular dynamics simulation, the polymer was able to destabilize the structure of the membrane and clearly express its signs of degradation.


Subject(s)
Anti-Bacterial Agents/pharmacology , Cellulose/analogs & derivatives , Cellulose/pharmacology , Methacrylates/pharmacology , Nylons/pharmacology , Anti-Bacterial Agents/chemical synthesis , Anti-Bacterial Agents/metabolism , Bacteria/drug effects , Cellulose/metabolism , Lipid Bilayers/chemistry , Lipid Bilayers/metabolism , Methacrylates/chemical synthesis , Methacrylates/metabolism , Microbial Sensitivity Tests , Molecular Dynamics Simulation , Nylons/chemical synthesis , Nylons/metabolism , Solubility
6.
Microvasc Res ; 128: 103952, 2020 03.
Article in English | MEDLINE | ID: mdl-31704243

ABSTRACT

Testis-specific gene antigen 10 (TSGA10) is a protein overexpressed in most cancers; except for some certain types where its expression is reduced. TSGA10 overexpression in HeLa cells has been shown to disrupt hypoxia inducible factor-1α (HIF-1α) axis and exert potent inhibitory effects. Since HIF-1α is structurally and biochemically similar to HIF-2α, TSGA10 is expected to bind HIF-2α and inhibit its function as well. This study elucidated that increased expression of TSGA10 in manipulated human umbilical vein endothelial cells (HUVECs) decreased the proliferation and migration of these cells as affirmed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and wound healing tests, respectively. It also inhibited in vitro angiogenesis of these cells in 3D collagen-cytodex model. Expression levels of genes controlled by HIF-2α including autocrine vascular endothelial growth factor (VEGF) were also assessed using real-time PCR. Our bioinformatic analysis also showed that TSGA10 could bind HIF-2α. Moreover, flow cytometry results indicated a cell cycle arrest in G2/M. Therefore, this study showed that overexpression of TSGA10, as a tumor suppressor gene, in endothelial cells resulted in decreased proliferation, migration and therefore, angiogenic activity of HUVECs. Since angiogenesis is vital for tumor development and metastasis, our findings could be of clinical significance in cancer therapy.


Subject(s)
Basic Helix-Loop-Helix Transcription Factors/metabolism , Cytoskeletal Proteins/metabolism , Human Umbilical Vein Endothelial Cells/metabolism , Neovascularization, Physiologic , Autocrine Communication , Basic Helix-Loop-Helix Transcription Factors/genetics , Cell Movement , Cell Proliferation , Cells, Cultured , Cytoskeletal Proteins/genetics , G2 Phase Cell Cycle Checkpoints , Humans , Protein Interaction Domains and Motifs , Signal Transduction , Up-Regulation , Vascular Endothelial Growth Factor A/genetics , Vascular Endothelial Growth Factor A/metabolism
7.
Neurochem Res ; 44(11): 2482-2498, 2019 Nov.
Article in English | MEDLINE | ID: mdl-31489534

ABSTRACT

Cuprizone (cup) model targets oligodendrocytes (OLGs) degeneration and is frequently used for the mechanistic understanding of de- and remyelination. Improperly, this classic model is time-consuming and the extent of brain lesions and behavioral deficits are changeable (both temporally and spatially) within a mouse strain. We aimed to offer an alternative, less time-consuming, and more reproducible cup model. Mice (C57BL/6) were treated with cup (400 mg kg-1 day-1/gavage) for three consecutive weeks to induce OLGs degeneration with or without YM155 (1 mg kg-1 day-1) to examine the effects of this molecule in cup neurotoxicity. Co-administration of cup and YM155 (cuYM) accelerated the intrinsic apoptosis of mature OLGs (MOG positive cells) through the upregulation of caspase-9 and caspase-3. In addition to the stimulation of oxidative stress via reduction of glutathione peroxidase and induction of malondialdehyde, behavioral deficits in both Open-field and Rota-rod tests were worsened by cuYM. In the cuYM group, the expression of BIRC5, BIRC4 and NAIP was reduced, but no significant changes were observed in the abundance of the other inhibitor of apoptosis proteins (cIAP1 and cIAP2) in comparison with the cup group. Moreover, in silico analysis validated that YM155 directly interrupts the binding sites of certain transcription factors, such as krüppel-like family (Klf), specificity proteins (SPs), myeloid zinc fingers (MZFs), zinc finger proteins (ZNFPs), and transcription factor activating enhancer-binding proteins (TFAPs), on the promoters of target genes. In conclusion, this modified model promotes cup-induced redox and apoptosis signaling, elevates behavioral deficits, saves time, minimizes variations, and can be employed for early evaluation of novel neuroprotective agents in oligodendropathies.


Subject(s)
Apoptosis/drug effects , Demyelinating Diseases/metabolism , Disease Models, Animal , Imidazoles/pharmacology , Naphthoquinones/pharmacology , Oligodendroglia/drug effects , Oxidative Stress/drug effects , Animals , Base Sequence , Caspase 3/metabolism , Caspase 9/metabolism , Corpus Callosum/metabolism , Cuprizone/pharmacology , Imidazoles/chemistry , Inhibitor of Apoptosis Proteins/genetics , Inhibitor of Apoptosis Proteins/metabolism , Male , Mice, Inbred C57BL , Molecular Docking Simulation , Naphthoquinones/chemistry , Oligodendroglia/metabolism , Promoter Regions, Genetic
8.
Pharm Res ; 36(4): 62, 2019 Mar 08.
Article in English | MEDLINE | ID: mdl-30850895

ABSTRACT

PURPOSE: The aim of this study is to show a new mesomicroscopic insight into Letrozole (LTZ) loaded nanocomplexes and their ex vivo characteristics as a drug delivery system. METHODS: The LTZ loaded hybrid chitosan-based carrier was fabricated using a modified ionic crosslinking technique and characterized in more detail. To understand the mechanism of LTZ action encapsulated in the hybrid polymer-lipid carrier, all-atom molecular dynamics simulations were also used. RESULTS: The physicochemical properties of the carrier demonstrated the uniform morphology, but different drug loading ratios. In vitro cytotoxic activity of the optimized carrier demonstrated IC50 of 67.85 ± 0.55 nM against breast cancer cell line. The ex vivo study showed the positive effect of nanocomplex on LTZ permeability 7-10 fold greater than the free drug. The molecular dynamic study also confirmed the prsence of hydrophobic peak of lipids at a distance of 5 Å from the center of mass of LTZ which proved drug entrapment in the core of nanocomplex. CONCLUSIONS: The hybrid nanoparticle increased the cytotoxicity and tissue permeability of LTZ for oral delivery. This study also confirmed the atomic mesostructures and interaction of LTZ in the core of hybrid polymer-lipid nanoparticles.


Subject(s)
Chitosan/chemistry , Letrozole/chemistry , Lipids/chemistry , Nanoparticles/chemistry , Animals , Cell Line, Tumor , Drug Carriers/chemistry , Drug Delivery Systems/methods , Humans , Hydrophobic and Hydrophilic Interactions , MCF-7 Cells , Male , Molecular Dynamics Simulation , PC12 Cells , Particle Size , Polymers/chemistry , Rats
9.
Bioorg Chem ; 88: 102972, 2019 07.
Article in English | MEDLINE | ID: mdl-31078769

ABSTRACT

Dipyridamole (DP) elevates cyclic Adenosine Monophosphate (cAMP) levels in platelets, erythrocytes, and endothelial cells and also blocks adenosine reuptake. It is used to dilate blood vessels in people with peripheral arterial disease and coronary artery disease (CAD). The flexible backbone, hydrophobic nature, and several available hydrogen bond (H-bond) donors and acceptors are well suited structural features of DP for inhibition/activation of enzymes. Substrates of α-amylase (α-Amy) and α-Glucosidase (α-Glu), known as key absorbing enzymes, have functional groups (OH groups) similar to DP. Since hypoglycemia can occur in diabetes disease and there is a significant link between diabetes and cardiovascular diseases (CVD), thus this study aimed to evaluate the inhibitory properties of DP against α-Amy and α-Glu, as enzyme targets of interest under hypoglycemia condition. DP inhibited the α-Glu and α-Amy activity in a dose dependent manner with IC50 values 19.4 ±â€¯0.3 and 30.1 ±â€¯0.4 µM, respectively. Further, the Ki values of DP for α-Glu and α-Amy were determined as 2.9 ±â€¯0.2 and 3.1 ±â€¯0.4 µM in a competitive-mode and mixed-mode inhibition, respectively. Also, DP had binding energies of -7.3 and -6.5 kcal/mol, to communicate with the active site of α-Glu and α-Amy, respectively. In addition, in-vivo studies revealed that the blood glucose concentration diminished after taking of DP compared to positive control group (p < 0.01). Accordingly, the results of the current work may prompt the scientific community to investigate the possible interconnection between DP clinical (side) effects and its α-Glu and α-Amy inhibitory properties.


Subject(s)
Dipyridamole/pharmacology , Enzyme Inhibitors/pharmacology , alpha-Amylases/antagonists & inhibitors , alpha-Glucosidases/metabolism , Animals , Dipyridamole/chemistry , Dose-Response Relationship, Drug , Enzyme Inhibitors/chemistry , Male , Models, Molecular , Molecular Structure , Rats , Rats, Wistar , Structure-Activity Relationship , alpha-Amylases/metabolism
10.
J Environ Manage ; 246: 776-784, 2019 Sep 15.
Article in English | MEDLINE | ID: mdl-31228691

ABSTRACT

This study evaluates the ability of heterogeneous Fenton-like reaction (nano zero-valent iron (NZVI)/H2O2) in combination with weak magnetic field (WMF) under continuous oxygen supply by air bubbling for pollutant abatement (using ciprofloxacin as a model pollutant). The considered operating variables were initial pH, catalyst dosage, reaction time and different intensities of magnetic field. Results indicated that NZVI/H2O2/aeration/weak magnetic field could effectively decompose ciprofloxacin at neutral condition and higher removal rates are observed at higher pH and NZVI concentrations. Superimposing a weak magnetic field leads to 20% enhancement in ciprofloxacin removal by catalytic Fenton under aeration condition. Employing simultaneously magnetic field induction and aeration exhibit excellent capability to the NZVI oxidation and significantly increased the dissolution rate of iron. Based on Fourier transform infrared spectroscopy, transformation products of NZVI are Fe3O4 and FeO(OH). The faster mass transport due to Lorentz and field gradient force, more oxygen diffusion to the iron surface and promoted electrochemical reactions results in more OH° production. Generation of weak magnetic field by permanent magnets and using aeration for both mixing and in situ oxygen supply significantly enhanced the Fenton reaction performance. This combination technology doesn't need any energy input and costly chemicals hence can be used easily for wastewater treatment applications.


Subject(s)
Ciprofloxacin , Water Pollutants, Chemical , Hydrogen Peroxide , Iron , Magnetic Fields
11.
Cell Mol Biol (Noisy-le-grand) ; 64(5): 85-90, 2018 Apr 30.
Article in English | MEDLINE | ID: mdl-29729711

ABSTRACT

Detection and quantification of various biological and non-biological species today is one of the most important pillars of all experimental sciences, especially sciences related to human health. This may apply to a chemical in the factory wastewater or to identify a cancer cell in a person's body, it may be apply to trace a useful industrial microorganism or human or plant pathogenic microorganisms. In this regard, scientists from various sciences have always striven to design and provide tools and techniques for identifying and quantifying as accurately as possible to trace various analyte types with greater precision and specificity. Nano science, which has flourished in recent years and is nowadays widely used in all fields of science, also has a unique place in the design and manufacture of sensors and this, in addition to the new and special characteristics of nanoparticles, is due to the ability of nano-devices to penetrate into very tiny places to track the species. On the other hand, due to the high specificity of biological molecules in identifying and connecting to their receptors that have evolved over millions of years, Scientists are now trying to design hybrid devices using nano science and biology, called Nano-biosensors So that they can trace and quantify target molecules in very small amounts and in inaccessible places, such as within the organs and even the cells.


Subject(s)
Biosensing Techniques , Electrochemical Techniques , Molecular Biology/methods , Nanoparticles/chemistry , Nanotechnology/methods , Neoplasms/diagnosis , Aptamers, Nucleotide/chemistry , Humans , MicroRNAs/analysis , MicroRNAs/genetics , MicroRNAs/metabolism , Molecular Biology/instrumentation , Molecular Imaging/methods , Nanotechnology/instrumentation , Neoplasms/genetics , Neoplasms/metabolism , RNA, Neoplasm/analysis , RNA, Neoplasm/genetics , RNA, Neoplasm/metabolism , Surface Plasmon Resonance
12.
Cell Mol Biol (Noisy-le-grand) ; 64(7): 1-7, 2018 May 30.
Article in English | MEDLINE | ID: mdl-29974838

ABSTRACT

Reviewing the mode of interaction between this kind of active pharmaceutical ingredients and DNA has received much more attention in current years. Anthracycline drugs such as Epirubicin are frequently used in cancer treatment for breast cancer treatment. In the present study, the Epirubicin -calf thymus DNA interaction was investigated by using spectroscopic, fluorimetric and molecular docking methods. Water-soluble quantum dots (QDs) with nanometric particle size fabricated and characterized by transmission electron microscope and photon correlation spectroscopy. The binding constant value and the free energy change for this interaction were obtained to be 3.00×106 M-1 and -42.26 kJ mol-1, using the spectroscopic method and docking investigations, respectively. Additionally, fluorescent thioglycolic acid-capped CdTe QDs were used for investigation of EPI and DNA interaction. Epirubicin as a quencher quenched the fluorescence of CdTe QDs after electrostatic adsorption on the surface of QDs. With the addition of DNA, EPI will be desorbed from the surface of CdTe QDs, inserted into the DNA. Subsequently, fluorescence changes of QDs were used for calculation of binding constant value, which was in good agreement with that obtained by the spectroscopic method. By the comparison of the achieved results, the intercalation mode of interaction between Epirubicin and DNA proved.


Subject(s)
Antibiotics, Antineoplastic/chemistry , DNA/chemistry , Epirubicin/chemistry , Molecular Docking Simulation , Quantum Dots/chemistry , Spectrophotometry, Ultraviolet , Cadmium Chloride/chemistry , Fluorescence , Hydrophobic and Hydrophilic Interactions , Molecular Conformation , Nanoparticles/chemistry , Particle Size , Tellurium/chemistry , Thioglycolates/chemistry
13.
Nanomedicine (Lond) ; 19(23): 1931-1951, 2024.
Article in English | MEDLINE | ID: mdl-39143926

ABSTRACT

Despite the development of new generations of antibiotics, vancomycin remained as a high-efficacy antibiotic for treating the infections caused by MRSA. Researchers have explored various nanoformulations, aiming to enhance the therapeutic efficacy of vancomycin. Such novel formulations improve the effectiveness of drug cargoes in treating bacterial infections and minimizing the risk of adverse effects. The vast of researches have focuses on enhancing the permeation ability of vancomycin through different biological barriers especially those of gastrointestinal tract. Increasing the drug loading and tuning the drug release from nanocarrier are other important goal for many conducted studies. This study reviews the newest nano-based formulations for vancomycin as a key antibiotic in treating hospitalized bacterial infections.


[Box: see text].


Subject(s)
Anti-Bacterial Agents , Drug Delivery Systems , Nanostructures , Vancomycin , Vancomycin/administration & dosage , Vancomycin/chemistry , Humans , Anti-Bacterial Agents/administration & dosage , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/pharmacology , Drug Delivery Systems/methods , Nanostructures/chemistry , Animals , Drug Carriers/chemistry , Methicillin-Resistant Staphylococcus aureus/drug effects , Drug Liberation , Staphylococcal Infections/drug therapy
14.
Heliyon ; 10(7): e28666, 2024 Apr 15.
Article in English | MEDLINE | ID: mdl-38590881

ABSTRACT

Fungal pathogen "Neoscytalidium novaehollandiae" is the causal agent of trunk canker in mulberry trees. Mulberry is considered as most valuable tree for landscaping in Tehran. Here in, for the first time, chitosan nanoparticles (CSNPs) were used to inhibit canker disease causal agent of mulberry. For this purpose, CSNPs were synthesized with a yield of 86%, and after characterization of the synthesized nanoparticles, the growth inhibition rate of fungus (GI%) was evaluated. The results of in vitro assays showed that the concentration of 1500 ppm significantly (P ≤ 0.05) decreased the radial growth of the fungus in comparison with control. For in vivo experiments, 2-year-old branches from healthy randomly selected mulberry trees in the landscape, were inoculated artificially in the laboratory with mycelial plugs from a 7-day-old culture of fungus. The infected branches were then treated with 500, 1000, and 1500 ppm of CSNPs. The results indicated that the disease severity (DS%) in all the treatments and the control plants increased over time. However, the slope of the changes in DS was less in CSNPs treated compared to control. This effect was concentration dependent so that no disease progress was observed at 1500 ppm of CSNPs. The findings indicate the effectiveness of CSNPs in control of canker disease of mulberry caused by N. novaehollandiae.

15.
Nanoscale Adv ; 2024 Sep 24.
Article in English | MEDLINE | ID: mdl-39386119

ABSTRACT

Nanobiocatalysis is a novel area integrating various advantages of nanotechnology and enzymatic catalysis. However, great efforts are still needed to fully understand the interactions between nanostructures and enzymes. The biological properties of nano-hybrid enzymes greatly depend on the size and chemical properties of their nano element. However, the impact of nanostructure chirality on the structure/function of the enzymes has not yet been fully investigated. In this study, using experimental and computational approaches, the interaction of Photinus pyralis firefly luciferase with chiral carbon quantum dots containing l and d-tryptophan constituent (l/d-Trp-CQDs) was investigated. Both the CQDs increased K m of the enzyme for luciferin and resulted in the loss of luciferase activity dose-dependently with more profound effects for d-Trp-CQDs. d-Trp-CQD treatment had significantly increased K m of the enzyme for ATP (3.5 fold) compared to the untreated enzyme. The changes in the secondary structure of luciferase upon interaction with d-Trp-CQDs were more drastic compared to l-Trp-CQDs, as determined by circular dichroism spectroscopy. Molecular dynamic simulation further confirmed higher conformational changes of luciferase induced by d-Trp-CQDs compared to l-Trp-CQDs. d-Trp-CQD has led to conformational changes of several amino acids involved in the active site, substrate binding site and the flexible loop of luciferase (352-359 residues) that governs the activity of luciferase.

16.
Comput Biol Med ; 183: 109245, 2024 Oct 09.
Article in English | MEDLINE | ID: mdl-39388840

ABSTRACT

Understanding how proteins behave dynamically and undergo conformational changes is essential to comprehending their biological roles. This review article examines the potent tool of using Molecular Dynamics simulations in conjunction with Principal Component Analysis (PCA) to explore protein dynamics. Molecular dynamics data can be made easier to read by removing prominent patterns through the use of PCA, a sophisticated dimensionality reduction approach. Researchers can obtain critical insights into the fundamental principles governing protein function by using PCA on MD simulation data. We provide a systematic approach to PCA that includes data collection, input coordinate selection, and result interpretation. Protein collective movements and fundamental dynamics are made visible by PCA, which makes it possible to identify conformational substates that are crucial to function. By means of principal component analysis, scientists are able to observe and measure large-scale movements, like hinge bending and domain motions, as well as pinpoint areas of protein structural stiffness and flexibility. Moreover, PCA allows temporal separation, distinguishing slower global motions from faster local changes. A strong foundation for researching protein dynamics is provided by the combination of PCA and Molecular Dynamics simulations, which have applications in drug development and enhance our comprehension of intricate biological systems.

17.
J Biomol Struct Dyn ; : 1-13, 2024 Jan 29.
Article in English | MEDLINE | ID: mdl-38285617

ABSTRACT

In this study, the inhibitory potential of 99 fungal derived secondary metabolites was predicted against SARS-CoV-2 main protease by using of computational approaches. This protein plays an important role in replication and is one of the important targets to inhibit viral reproduction. Among the 99 reported compounds, the 9 of them with the highest binding energy to Mpro obtained from the molecular docking method were selected for the molecular dynamic simulations. The compounds were then investigated by using the SwissADME serve to evaluate the compounds in terms of pharmacokinetic and druglikness properties. The overall results of different analysis show that the compound RKS-1778 is potentially more effective than others and form strong complexes with viral protease. It also had better pharmacokinetic properties than other metabolites, so predicted to be a suitable candidate as anti SARS-CoV-2 bioactive.Communicated by Ramaswamy H. Sarma.

18.
Int J Biol Macromol ; 260(Pt 2): 129503, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38244744

ABSTRACT

Despite of growing interest in use of carbon-based nanomaterials as carriers of functional proteins, less attention has been paid to the effects of these nanomaterials on the structure and function of the proteins. In this study, with the aim of shedding light on the mechanisms of interaction between carbon-based nanomaterials and proteins, the interactions of carbon quantum dots (CQDs) containing amine (CQD-NH2) or carboxyl groups (CQD-COOH) with Photinus pyralis firefly luciferase enzyme were investigated by experimental and computational approaches. The structural changes and reduction in activity of the luciferase upon treatment with CQDs were experimentally proved. CQD-NH2 induced more reduction in enzyme activity (15 %) compared to CQD-COOH (7.4 %). The interactions CQD-NH2 with luciferase led to higher affinity of the enzyme for its substrate. It was found by molecular dynamic simulations that CQD-NH2 binds to multiple regions on the surface of luciferase. Secondary structure analysis showed that CQD-NH2 had more profound effects on the active site amino acids, the adjacent amino acids to the active site and the residues involved in ATP binding site. In addition, CQD-NH2 interactions with luciferase were suggested to be stronger than CQD-COOH based on the number of hydrogen bonds and the binding energies.


Subject(s)
Quantum Dots , Quantum Dots/chemistry , Luciferases, Firefly , Amines , Carbon/chemistry , Luciferases/metabolism , Amino Acids
19.
Int J Pharm ; : 124142, 2024 Apr 20.
Article in English | MEDLINE | ID: mdl-38648941

ABSTRACT

Microfluidics has emerged as a transformative force in the field of drug delivery, offering innovative avenues to produce a diverse range of nano drug delivery systems. Thanks to its precise manipulation of small fluid volumes and its exceptional command over the physicochemical characteristics of nanoparticles, this technology is notably able to enhance the pharmacokinetics of drugs. It has initiated a revolutionary phase in the domain of drug delivery, presenting a multitude of compelling advantages when it comes to developing nanocarriers tailored for the delivery of poorly soluble medications. These advantages represent a substantial departure from conventional drug delivery methodologies, marking a paradigm shift in pharmaceutical research and development. Furthermore, microfluidic platformsmay be strategically devised to facilitate targeted drug delivery with the objective of enhancing the localized bioavailability of pharmaceutical substances. In this paper, we have comprehensively investigated a range of significant microfluidic techniques used in the production of nanoscale drug delivery systems. This comprehensive review can serve as a valuable reference and offer insightful guidance for the development and optimization of numerous microfluidics-fabricated nanocarriers.

20.
J Biomol Struct Dyn ; : 1-11, 2023 Aug 22.
Article in English | MEDLINE | ID: mdl-37608542

ABSTRACT

In this study the efficacy of different edible lipids for drug permeation enhancement of vancomycin through biological membrane was investigated using molecular dynamic simulation. In this regard, at first the ability of the lipids for complex formation with the drug was evaluated for number of most common edible lipids including tripalmitin (TPA), trimyristin (TMY), labrafil (LAB), glycerol monostearate (GMS), glycerol monooleate (GMO), Distearoylphosphorylethanolamine (DSPE), dipalmitoylphosphatidylethanolamine (DPPE), Dipalmitoylphosphatidylcholine (DPPC), cholesterol (CL), stearic acid (SA), palmitic acid (PA) and oleic acid (OA). Then the complexes were pulled thorough a bilayer membrane while the changes in force were probed. The results showed that besides the SA, PA and OA the other examined lipids were able to perform a perfect molecular complex with the drug. Also the results of pulling simulation revealed that the least of force was needed for drug transmittance through the membrane when it was covered by LAB, TMY and DSPE. These results indicated that these lipids can be the excellent materials of choice as permeation enhancer for preparing a proper oral formulation of vancomycin.Communicated by Ramaswamy H. Sarma.

SELECTION OF CITATIONS
SEARCH DETAIL