Science & Technology Development Journal: Natural Sciences

Structure modeling and molecular dynamics simulation in protein-protein interaction study

Nguyen Van Minh Thuong — 2024-12-31

Protein is a vital macromolecule that contributes to the living system. Functionally, proteins not only work independently, but also form a close network via protein-protein interactions (PPIs), the decisive factor in most biological processes in living organisms. Nevertheless, the study of PPIs has encountered many obstacles due to the lack of experimental structures of the complexes or proteins involved in the interactions. Thanks to the support of bioinformatics tools, methods, and algorithms, the prediction of protein interaction structure has emerged as a potential solution to solve the above difficulties. Molecular docking and molecular dynamics simulation (MDs) are two commonly used methods for predicting PPIs because of their ability to model structure and approximate biological processes, which are consistent with the natural state of the realistic system. Applying these bioinformatics advances has shortened the time, effort, and research costs for scientists. This review provides information on the protein-protein complex structure prediction method and some tools to assist in previous studies. In addition, the force field component of the molecular kinetics simulation method is highlighted, and simulation programs are extensively used.

Protein display on lactic acid bacteria cell surface

Phuong-Thao Thi Nguyen — 2025-02-17

The strong development of novel protein expression systems, especially in lactic acid bacteria, has attracted a lot of attention and presented many challenges for scientists, not only in terms of safety but also in the ability to preserve food. With the advantage of possessing a rigid cell wall structure and typical acid resistance, lactic acid bacteria have become a potential target not only as a cell factory for producing recombinant proteins used in the food industry but also as a means of delivering antigens for mucosal vaccine development. To achieve this goal, a series of target protein expression systems have been developed in many lactic acid bacteria. This review summarizes recent developments in foreign protein expression systems in both secretion and surface display forms in lactic acid bacteria, including prominent examples such as Lactococcus lactis and Lactobacillus plantarum, as well as current research on developing promising promoter systems to not only improve their ability but also increase their expression efficiency on the surface of lactic acid bacteria.

Fabrication of a ternary biocomposite membrane based on chitosan, cellulose nanocrystals and Ag nanoparticles for water treatment

An Nang Vu — 2024-12-31

The paper presented the preparation of a ternary biocomposite membranes based on chitosan (CS) with cellulose nanocrystals (CNC) and silver nanoparticles (Ag) with the aim for water treatment. The mCS/CNC/Ag membranes were fabricated using a two-stage process. Initially, mCS/CNC membranes were synthesized by the cryogenic gelation method. The mCS/CNC membrane morphology was studied by scanning electron microscopy (SEM). SEM results indicated that the mCS/CNC semi-permeable membrane had a porous structure with pore size of 50–200 µm. The morphology of the pores on the two sides of the membrane's surface showed significantly different in which one surface of the membrane had less pores and a smaller pore size than the other. This proved that the obtained mCS/CNC membrane had an asymmetrical structure. Then, Ag nanoparticles (Ag NPs) were attached to the mCS/CNC membrane by UVC irradiation. The presence of Ag in the mCS/CNC membrane structure was confirmed through the results of X-ray diffraction (XRD), Fourier-transform infrared (FT-IR) spectroscopy and energy-dispersive X-ray (EDX) spectroscopy. The SEM image results showed that after the Ag NPs were formed, they were then inserted into the mCS/CNC membrane, breaking the pore structure to form the mCS/CNC/Ag membrane. The mCS/CNC/Ag biocomposite membrane had a high methylene blue removal efficiency (more than 90%) in 1 minute in the presence of NaBH4. The presence of CNC improved the mechanical properties of the membrane and could help to reuse the membrane after processing.

Preparation of CoFe2O4/α-Fe2O3 magnetic composite as a fenton photocatalyst for methylene blue degradation under visible radiation

An Nang Vu — 2024-12-31

CoFe2O4 (CFO) material was prepared by solvothermal method and then used to synthesize the magnetic CFO/α-Fe2O3 composite. CFO/α-Fe2O3 material was fabricated using the sol-gel technique and sintering at 500oC. The chemical structure, surface morphology and properties of materials were analyzed by X-ray diffraction, Fourier-transform infrared spectroscopy, thermal analysis, energy dispersive X-ray spectroscopy, field emission scanning electron microscopy and vibrating sample magnetometer. The prepared CFO/α-Fe2O3 material possessed a spherical form with an average size of 98 ± 23 nm. The formation and binding of α‒Fe2O3 on the CFO surface caused decreasing the saturation magnetization value of CFO/α-Fe2O3 and increasing the coercivity value compared to the CFO matrix phase. CFO/α-Fe2O3 was then used as a Fenton photocatalyst in the decomposition reaction of methylene blue (MB) under visible radiation with the presence of the electron donor oxalic acid. The resulted apparent rate constant value was 0.696 h-1. The photocatalytic Fenton process followed the pseudo-first-order kinetic equation with the result of after 180 minutes of reaction, the MB content was decomposed by 90%. The binding of α-Fe2O3 changed the material structure's phase composition and caused a redistribution of metal cations on the surface of CFO/α-Fe2O3. The increase of Fe on the surface of CFO/α-Fe2O3 promoted the formation of surface ferrioxalate complexes via the reaction between the Fe3+ ion on the surface and oxalic acid. Then, under visible radiation, these ferrioxalate complexes could be stimulated and produced free radicals such as C2O4•-, •OH, and O2•- which could effectively decompose the MB molecule in solution. In addition, the CFO/α-Fe2O3 catalyst showed high stability and good performance after five consecutive reuses. The results would be promising for the practical application of this material in treating toxic organic dyes in water.

The phytochemical constituents of the ethyl acetate extract of the Schefflera elliptica leaves

Trọng Nghĩa Ngô — 2024-12-31

Schefflera elliptica belonging to the Araliaceae family, is a shrub or small tree widely grown in many places in Vietnam. This plant is used in traditional Vietnamese medicine for the treatment of pain in tendons and bones, rheumatism, cancer, and to stimulate digestion. To the best of our knowledge, the phytochemical compositions and biological activities of this species have not been investigated. This is the first time a chemical investigation of S. elliptica has been conducted. This study contributes to the acknowledgment of the phytochemical profile and provides a foundation for further biological investigations. The leaves of S. elliptica were dried, powdered, and extracted in ethanol 96o at room temperature to provide the crude extract. The crude extract was then subjected to liquid-liquid separation with n-hexane and EtOAc, to obtain the n-hexane, ethyl acetate extracts. From the ethyl acetate extract of the leaves of S. elliptica, two phytosphingolipids, 1-O-β-D-glucopyranosyl-(2S,3S,4R,9Z)-2-[(2R)-2-hydroxytetracosanoylamino]-octadec-9-en-1,3,4-triol (1), and 1-O-β-D-glucopyranosyl-(2S,3S,4R,9E)-2-[(2R)-2-hydroxyhexadecanoylamino]-octadec-9-en-1,3,4-triol (2), along with three flavonoids, kaempferol (3), quercetin (4), and astragalin (5) were isolated by various chromatographic column techniques over normal-phase and/or reverse-phase silica gel, and confirmed by thin layer chromatography. The chemical structures of all separated substances were clearly elucidated using High Resolution Mass spectrometry with the ElectroSpray Ionization source, such as HR-ESI-MS, and HR-ESI-MS/MS techniques, Nuclear Magnetic Resonance spectroscopy 1D & 2D NMR data, and further comparison to those database of the published literatures. For the first time, all purified compounds were identified from this species, and compounds (1, 2) were determined to be from the Schefflera genus.

Some terpenoid compounds from the ethyl acetate extract of Annona muricata L. leaves and their α-glucosidase inhibitory activity

Trường Nhật Văn Đỗ — 2024-12-31

Annona muricata L., a species from the Annonaceae family, known as “Mãng cầu xiêm” in Vietnam. It is an edible plant that contains a plethora of nutrition such as vitamins, fiber and mineral. Multiple researches about the chemical constituents of Annona muricata L. had been carried out across the world, from different parts such as the stems, leaves, fruits, and seeds and several compounds such as acetogenin, megastigmane, polyphenol, alkaloid, … had been isolated. Other researches about its biological activity also showed that Annona muricata L. had plenty of crucial biological activities including anti-inflammatory, anticancer, hypoglycemia, antioxidant and antibacterial. From the ethyl acetate extract of leaves’ s Annona muricata L., five compounds were isolated, including three megastigmanes (1−3) and two acyclic diterpenoids (4−5). Using one-dimension and two-dimension NMR, high resolution mass spectrometric analysis and comparing to the corresponding data in the literature, the chemical structure of the isolated compounds were elucidated as dehydrovomifoliol (1), vomifoliol (2), vomifoliol acetate (3), trans-phytol (4) and 1-O-acetylphytol (5). Except 2, the four remaining compounds have not been reported in the plant. All the five compounds were tested for their inhibitory activity against enzyme α-glucosidase, compounds 1, 3 and 4 showed moderate α-glucosidase inhibitory effect with the IC50 values of 45−210 µM, compared to the positive control acarbose (IC50 214.5 µM).

Preparation of magnetic Ag/CoFe2O4 composite as an antibacterial material and efficient catalyst for 4-nitrophenol reduction

Hoa Thi Ngoc Le — 2025-02-17

In this study, CoFe2O4 (CFO) material was prepared by hydrothermal method and then used to synthesize nanometer-sized magnetic Ag/CoFe2O4 (Ag/CFO) composite. Ag/CFO materials were also prepared by the hydrothermal technique of AgNO3 solution containing CFO and investigated as a catalyst to reduce 4-nitrophenol (4-NP). The structure, surface morphology and properties of the materials were analyzed by physicochemical methods, including X-ray diffraction (PXRD), Fourier - transform infrared spectroscopy (FT-IR), energy-dispersive X-ray spectroscopy (EDX), field-emission scanning electron microscopy (FE-SEM), EDX mapping, and vibrating sample magnetometer (VSM). Ag/CFO composite materials are granular with an average diameter of about 18 - 20 nm. Although the Ag content in Ag/CFO is small (0.34% atom), the material has a high catalytic activity in 4-NP reduction in the presence of NaBH4, with a reaction efficiency greater than 99% only in one minute reaction time. In this reaction, the Ag component in Ag/CFO acts as a direct electron transfer from the BH4- ion to 4-NP, to form 4-aminophenol (4-AP). In addition, Ag/CFO also showed good antibacterial effect against both the Gram-positive bacterium Staphylococcus aureus and the Gram-negative bacterium Pseudomonas aeruginosa.

The novel and green synthesis of 6-amino-4-phenyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carbonitrile via the solvent-free biginelli multi-component reaction catalysed by Choline chloride/2ZnCl2

Trang Minh Tran — 2025-02-17

The pyrimidine scaffold is one of the common frameworks presenting in many biologically active compounds, especially in commercial drugs such as anti-cancer (5-fluorouracil, gemcitabine, ...), antibiotics (iclaprim, ...), anti-HIV (stavudine, ...), etc. Therefore, pyrimidines have been studied with several synthetic pathways, however, the well-known route via the multi-component Bignelli reaction has been paid more attention. The Biginelli reaction has been recognized for over 100 years and has been developed using a variety of substrates and catalysts to improve the efficiency, selectivity, and diversity of pyrimidines produced. With the trend towards green chemistry in organic synthesis, catalysts with high recovery and reusability have been explored and developed. For these above reasons, a solvent−free multicomponent reaction between benzaldehyde, malononitrile, and thiourea was investigated with several traditional and green catalysts to afford the main product, 6-amino-4-phenyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carbonitrile. Among the wide range of catalysts studied, the deep eutectic solvent ChCl:2ZnCl2 showed the best efficiency, with a reaction yield of 62%. Some factors of the reaction such as molar ratio, amount of catalyst, the temperature and reaction time were all investigated. The best conditions including the molar ratio of benzaldehyde (2 mmol): malononitrile (2 mmol): thiourea (2 mmol) and the amount of catalyst 0.3 mmol were chosen and performed at 80oC for 2 hours to afford the highest yield of 62%. Furthermore, DES ChCl:2ZnCl2 was able to be recovered and reused two times.

Green synthesis of magnetic CoFe2O4 nanoparticles as recyclable photo-Fenton catalysts by sol-gel method with the assistance of tamarind fruit extract

Tuyet Suong Dinh Thi — 2025-02-17

Nowadays, there is a growing imperative to develop environmentally friendly methods for the synthesis of catalytic materials. This paper presented a synthesis of magnetic photo−Fenton catalysts based on CoFe2O4 nanoparticles using sol−gel method with tamarind fruit extract as an inexpensive and naturally available gel−forming agent. After the gelation process, the samples were calcined at various temperatures (700, 800, 900°C) and characterized by XRD, FE-SEM, EDS, FTIR, VSM, and N2 absorption experiments. Their photo−Fenton catalytic activities were evaluated through the degradation of methylene blue and methyl orange under UVA light or visible light. The results showed that the combination of using tamarind fruit extract during the gelation and the subsequent calcination process effectively facilitated the production of CoFe2O4 nanoparticles with a cubic spinel single-phase structure. These samples not only demonstrated a high photo−Fenton activity for the degradation of both cationic and anionic dyes, but also exhibited impressive magnetic properties, allowing for easy recovery after use. In particular, the calcination temperature emerged as a pivotal factor in governing the distribution of metal ions on the surface as well as the particle size and the specific surface area of catalysts, thereby significantly affecting their activity.

Synthesis, Characterization of Activated Carbon from Rice Husk Ash and Influence of NaOH Ratio on its Properties

Thanh Luu Huynh — 2025-02-17

This study presents the synthesis and characterization of activated carbon (AC) derived from rice husk ash (RHA) using a chemical activation method that does not require high-temperature heating. RHA, obtained from burning rice husks as a fuel for industrial boilers, was subjected to silica extraction to form biochar (BC). BC is then activated with NaOH using an ultrasound machine and vacuum-dried to form activated carbon (AC). The influence of the mass ratio of NaOH to BC (mNaOH:mBC) on the specific properties of the activated carbon was systematically analyzed such as structure, porous morphology, and thermal behavior. The results show that the activated carbon exhibits an amorphous structure with a surface consisting of randomly distributed particles of several micrometers in size. Furthermore, the activated carbon possessed a porous and hollow structure with varying pore sizes. Notably, the maximum surface area of the activated carbon was achieved at a NaOH to BC activation ratio of 7:1, reaching 823,913 m2/g. These findings underscore the suitability of the synthesized activated carbon for applications as adsorbent materials in water or gas, suggesting its potential for environmental remediation purposes.

Knockdown duch (Drosophila ubiquitin carboxy−terminal hydrolase) play a role on the regulation of the oxidative stress in fruit fly eye

Tuan Anh Nguyen — 2025-02-18

UCH−L1 is a ubiquitous protein in human neurons. The abnormal expression of UCH−L1 has been reported in several neurodegenerative diseases and cancers, suggesting a cellular function of UCH−L1. However, the role of UCH−L1 in tissue development remains poorly understood. Using Drosophila melanogaster, this paper presented the demonstration of the loss function of dUCH, a protein that is homologous to UCH−L1. This protein could exert an abnormal eye phenotype, increase reactive oxygen species in the eye imaginal disc and decrease the expression of the sod2, gstd1 and gstd2 antioxidant genes. Except for the induced abnormal eye phenotype, the effects of the decreased dUCH expression were ameliorated by feeding flies with 2.5 mM vitamin C. The results suggested that dUCH could affect the fly eye development by regulating the oxidative stress.

Synthesis and evaluation of composite δ-MnO2/C65 material properties for hybrid capacitive deionization application

Minh Dai To — 2025-02-18

Capacitive deionization (CDI) has emerged as a revolutionary method for removing salt from solutions, gaining immense attraction due to its manifold benefits compared to the traditional desalination methods. This electrochemical technique offers a distinctive amalgamation of cost-effectiveness, energy efficiency, environmental sustainability, and operational simplicity. Moreover, the evolution of Hybrid Capacitive Deionization (HCDI) has furthered the possibilities within water desalination. By integrating carbon electrodes with those capable of redox reactions, HCDI displays significantly heightened ion adsorption efficiency in contrast to its precursor, conventional CDI which relies solely on carbon electrodes. The pivotal aspect revolving around materials not only facilitated redox reactions but also intricately entwined ions within their structural framework. This paper presented the synthesis of a layered δ-MnO2/C65 composite material using the sol-gel method. Characterization techniques of XRD, SEM and BET analyses showed critical insights into crystal phases, morphology, and structural attributes. Further assessment of its electrochemical properties via cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) unequivocally underscores its potential in capacitive deionization applications. Notably, employing an asymmetric salt adsorption configuration with an activated carbon anode electrode derived from coconut shell (AC) in an AC||δ-MnO2/C65 model yielded exceptional results. The δ-MnO2/C65-1 composite emerged as the top performer showcasing the highest recorded salt adsorption capacity (SAC) of 38.4 mg/g, accompanied by an unparalleled salt adsorption rate (ASAR) of 2.1 mg/g.s-1. Detailed structural, morphological, and electrochemical analyses unequivocally identified the δ-MnO2/C65-1 composite as the optimal ratio, heralding superior efficacy and performance in salt removal and ion adsorption, a significant leap forward in capacitive deionization technology.