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Molecular dynamics-driven exploration of peptides targeting SARS-CoV-2,with special attention on ACE2,S protein,M^(pro),and PL^(pro):A review

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BIOCELL 2023年第8期47卷 1727-1742页

作者： MOHAMAD ZULKEFLEE SABRI JOANNA BOJARSKA FAI-CHU WONG TSUN-THAI CHAI Green Chemistry and Sustainable Technology Cluster Bioengineering SectionUniversiti Kuala LumpurMalaysian Institute of Chemical and Bioengineering Technology(UniKL MICET)Alor Gajah78000Malaysia Institute of General and Ecological Chemistry Faculty of ChemistryLodz University of TechnologyLodz90-924Poland Department of Chemical Science Faculty of ScienceUniversiti Tunku Abdul RahmanKampar31900Malaysia Center for Agriculture and Food Research Universiti Tunku Abdul RahmanKampar31900Malaysia

Molecular dynamics(MD)simulation is a computational technique that analyzes the movement of a system of particles over a given *** can provide detailed information about the fluctuations and conformational changes of biomolecules at the atomic level over *** recent years,MD has been widely applied to the discovery of peptides and peptide-like molecules that may serve as severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)*** review summarizes recent advances in such explorations,focusing on four protein targets:angiotensin-converting enzyme 2(ACE2),spike protein(S protein),main protease(M^(pro)),and papain-like protease(PL^(pro)).These four proteins are important druggable targets of SARS-CoV-2 because of their roles in viral entry,maturation,and infectivity of the virus.A review of the literature revealed that ACE2,S protein,and M^(pro) have received more attention in MD research than PL^(pro).Inhibitors of the four targets identified by MD simulations included peptides derived from food and other bioresources,peptides designed using the targets as templates,and peptide-like molecules retrieved from *** of the inhibitors have yet to be validated in experimental assays for ***,the role of MD simulation as an efficient tool in the early stages of anti-SARS-CoV-2 drug discovery agents has been demonstrated.

关键词： COVID-19 Anti-SARS-CoV-2 agent Receptor binding domain Computational screening Drug discovery

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Preliminary study on polyisoprene-modified natural rubber via in-situ polymerization of isoprene in deproteinized natural rubber latex

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Materials Today: Proceedings 2022年 66卷 2962-2966页

作者： Safuan, M.A. Ong, S.K. Solehah, M.N. Ibrahim, D.A. Hashim, A.S. Section of Polymer Engineering Technology Malaysian Institute of Chemical & Bioengineering Technology Universiti Kuala Lumpur Lot 1988 Kawasan Perindustrian Bandar Vendor Taboh Naning Melaka Alor Gajah 78000 Malaysia

Modification of natural rubber (NR) using vinyl monomers, particularly styrene, has been widely studied. Compared to unmodified NR, the resulting graft copolymer is stronger and stiffer but sacrificed on NR elasticity. This is because of the higher glass transition temperature (Tg) of styrene as compared to NR. Therefore, the modification of NR via isoprene monomer was investigated as isoprene will have the same Tg as NR. The focus of this research is to study the effect of in-situ polymerization of isoprene in deproteinized natural rubber (DPNR) latex with unmodified DPNR latex. The success of the modification was evidenced by the degree of conversion and Fourier Transform Infrared (FTIR). The average degree conversion of polyisoprene modified natural rubber (I-DPNR) obtained was 81.42%. Comparing the FTIR of I-DPNR and DPNR, the presence of trans-1,4 polyisoprene peaks and lower transmission of cis-1,4 polyisoprene was observed. The dynamic mechanical analysis (DMA) showed that I-DPNR and DPNR has a similar Tg. Stress–strain curves obtained from the tensile test of both the unvulcanized and vulcanized rubbers revealed that I-DPNR is more elastic as compared to the DPNR. These results obtained are consistent with the hypothesis that modification of NR with the isoprene monomer can result in similar properties as the DPNR. Higher elasticity reported for I-DPNR is a result of its higher entanglement as compared to unmodified NR. © 2022

关键词： Emulsion polymerization

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Magnetic chitosan hydrogel beads as adsorbent for copper removal from aqueous solution

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Materials Today: Proceedings 2023年 74卷 499-503页

作者： Afifah Khalil, Nor Syafiqah Abdul Rahman, Aida Mubin Abu Huraira, Alnazirul Nur Dalillah Fattin Janurin, Siti Noor Syimir Fizal, Ahmad Ahmad, Norkhairi Zulkifli, Muzafar Sohrab Hossain, Md. Naim Ahmad Yahaya, Ahmad Universiti Kuala Lumpur Branch Campus Malaysian Institute of Chemical and BioEngineering Technology 78000 Alor Gajah Melaka Malaysia Student Development Section Branch Campus Malaysian France Institute Universiti Kuala Lumpur Selangor Bandar Baru Bangi 43650 Malaysia Aero Composite Cluster Universiti Kuala Lumpur Branch Campus Malaysian Institute of Aviation Technology Selangor Dengkil 43400 Malaysia HICoE-Centre for Biofuel and Biochemical Research Institute of Self-Sustainable Building Fundamental and Applied Sciences Department Universiti Teknologi PETRONAS 32610 Seri Iskandar Perak Malaysia Green Chemistry and Sustainability Cluster Universiti Kuala Lumpur Branch Campus Malaysian Institute of Chemical and BioEngineering Technology 78000 Alor Gajah Melaka Malaysia

Magnetic chitosan hydrogel beads (MCHB) were synthesized by blending chitosan and magnetite (Fe3O4) in sodium alginate solution. The MCHB was used to remove Cu (II) metal ions in an aqueous solution. The performance of MCHB to remove Cu (II) ions was evaluated experimentally at different parameters (the initial pH of the solution, contact time, and various magnetite ratios of the hydrogel beads) in the batch adsorption set-up. This study indicated that MCHB managed to remove Cu (II) ions by adsorption at pH 5 at 24 h of contact time. The hydrogel beads of MCHB-0.5 (C:M:A ratio by weight of 1:0.5:2) show the highest Cu (II) ions removal efficiency of 56.51%. The addition of magnetite at the minimal ratio does not hinder the adsorption of Cu (II) ions onto MCHB. The magnetite in the beads also eases the separation of the hydrogel beads from the solution by an external magnet after treatment. © 2022

关键词： Magnetite

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Graphene oxide-chitosan composite material as adsorbent in removing methylene blue dye from synthetic wastewater

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Materials Today: Proceedings 2022年 64卷 1587-1596页

作者： Bryan, M.Y.K. Chai, P.V. Law, J.Y. Mahmoudi, E. Department of Chemical & Petroleum Engineering Faculty of Engineering Technology & Built Environment UCSI University Cheras Kuala Lumpur 56000 Malaysia Process Engineering Technology Section Universiti Kuala Lumpur Malaysian Institute of Chemical and Bioengineering Technology Alor Gajah Melaka 78000 Malaysia Department of Chemical and Process Engineering Faculty of Engineering and Built Environment Universiti Kebangsaan Malaysia Bangi Selangor Darul Ehsan 43600 Malaysia Faculty of Engineering and Built Environment Universiti Kebangsaan Malaysia Bangi Selangor Darul Ehsan 43600 Malaysia

Graphene oxide (GO) and graphene oxide-chitosan (GO-C) were synthesized and its performance in removing methylene blue (MB) dye synthetic wastewater were evaluated. Characterization technique such as measurement of zeta potential and FITR were employed to examine the surface potential of the adsorbent and presence of functional group respectively. The adsorption of MB by GO and GO-C was favored at the alkaline condition and lower temperature. The optimum conditions for the adsorption of MB using GO and GO-C were pH 10, a contact time of 50 min, a temperature of 30 °C and a dosage of 1250 mg/L. GO-C demonstrated higher adsorption capacity and dye removal efficacy due to the presence of the secondary adsorption sites that were attributed to the cross-linking of chitosan with GO. GO-C achieved 99.36 % of dye sequestration in MB synthetic dye wastewater after optimization of all parameters had been performed. Spent GO and GO-C were regenerated efficiently using absolute ethanol. GO and GO-C retained 91.79% and 91.90% of MB dye sequestration, respectively, after three cycles of adsorption–desorption and therefore, proving that GO-based adsorbents have an excellent ability to regenerate and reuse in synthetic dye wastewater. © 2022

关键词： Chitosan

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Protein-Water Interactions and Textural Characteristics of Dried Beancurds Affected by Sodium Chloride and Star Anise Extract

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SSRN 2025年

作者： Wang, Ying Huang, Yiqun Wang, Yifen School of Food Science and Bioengineering Changsha University of Science and Technology 960 2nd Section Wanjiali South Rd Hunan Changsha410114 China Department of Biosystems Engineering Auburn University AuburnAL36849 United States

To simplify the process of traditional flavored dried beancurds and meet the growing consumer demand for high-quality plant-based foods, this research aimed to investigate the effects of table salt (0.75% w/v) and star anise (SA) extract (SA1: 4.44%;SA2: 6.67%;v/v) on the textural characteristics of high-calcium dried beancurds. Adding salt to soymilk with or without SA resulted in an average of 22.6 – 23.9% increase in the water binding capacity of soy protein (WBCpro) in dried beancurds. This change was attributed to the significant (p © 2025, The Authors. All rights reserved.

关键词： Sodium chloride

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Impacts of the Extent of Pasteurization Treatments on Advanced Glycation End-Products in Fish Steaks: Initial Heating, Storage, and Reheating

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SSRN 2025年

作者： Tan, Linzhi Li, Lin Chu, Fuyu Lai, Keqiang Huang, Yiqun School of Food Science and Bioengineering Changsha University of Science & Technology 960 2nd Section Wanjiali South Road Hunan Changsha410004 China College of Food Science and Technology Shanghai Ocean University No. 999 Hucheng Huan Road LinGang New City Shanghai201306 China

The impacts of the extent of pasteurization treatments (90 °C;8 min, mimicked home cooking;15 min;25 min, mimicked commercial pasteurization) on NΕ-carboxymethyllysine (CML) and NΕ-carboxyethyllysine (CEL) formation in fish steaks were investigated from the initial pasteurization throughout the later storage (0 °C, 0 – 7 d) and reheating (75 °C, 10 min). A more intensive pasteurization treatment led to more CML and CEL produced in fish steaks during pasteurization and later storage. The rate constant (0-order reaction) for the change of CML (0.214 – 0.523 mg kg-1 d-1) or CEL (0.503 – 0.980 mg kg-1 d-1) in pasteurized fish steaks during storage increased as the pasteurization time increased. The reheated fish steaks previously subjected to commercial pasteurization followed by 7 d of storage contained 4.3-fold of CML and 2.2-fold of CEL as the home-cooked fish steaks, implying the urgent need to reduce these compounds in commercial precooked meat. © 2025, The Authors. All rights reserved.

关键词： Food storage

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Development and evaluation of ciprofloxacin-bacterial cellulose composites produced through in situ incorporation method

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Biotechnology Reports 2022年 34卷 e00726页

作者： Syed Abdullah, Sharifah Soplah Faisul Aris, Fathin Amila Said Azmi, Siti Nur Nadhirah Anak John, Jessica Harriette Supang Khairul Anuar, Nurul Nabilah Mohd Asnawi, Ahmad Syafiq Fauzan Section of Bioengineering Technology Universiti Kuala Lumpur Branch Campus Malaysian Institute of Chemical and Bioengineering Technology Lot 1988 Vendor City Taboh Naning Melaka Alor Gajah 78000 Malaysia Section of Food Engineering Technology Universiti Kuala Lumpur Branch Campus Malaysian Institute of Chemical and Bioengineering Technology Lot 1988 Vendor City Taboh Naning Melaka Alor Gajah 78000 Malaysia Section of Chemical Engineering Universiti Kuala Lumpur Branch Campus Malaysian Institute of Chemical and Bioengineering Technology Lot 1988 Vendor City Taboh Naning Melaka Alor Gajah 78000 Malaysia

This paper describes the interaction and properties of bacterial cellulose (BC)–ciprofloxacin composites synthesized by in situ incorporation method. Ciprofloxacin's susceptibility to BC's producer, Acetobacter xylinum 0416, was first tested to determine its inhibitory activity against the bacteria. In situ incorporation method was performed by introducing 0.2% (w/v) ciprofloxacin into Hestrin–Schramm medium at the onset of exponential phase of A. xylinum 0416 growth. Following a 10-day incubation at 28 °C, BC–ciprofloxacin composites were harvested and further characterised, while another BC–ciprofloxacin composite was harvested and purified prior to characterisation. The interaction between ciprofloxacin and BC was proven by the presence of quinolines and fluorine groups of ciprofloxacin on unpurified BC–ciprofloxacin composite and the reduction of crystallinity index as compared to the native BC. Moreover, deposited ciprofloxacin crystals on BC film and its composition were exhibited via SEM-Energy-dispersive X-ray analysis. Unpurified BC–ciprofloxacin film was determined to have strongly inhibited the following selected diabetic foot ulcer bacteria: E. coli, K. pneumoniae and P. aeruginosa. BC has the potential to be used as a wound dressing and a carrier for ciprofloxacin. © 2022

关键词： Acetobacter xylinum Bacterial cellulose Ciprofloxacin In situ incorporation

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Prevalence of Salmonella Spp. In Meat, Seafood, and Leafy Green Vegetables from Local Markets and Vegetable Farms in Phnom Penh, Cambodia

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SSRN 2024年

作者： Huoy, Laingshun Vuth, Sireyvathanak Hoeng, Sophanith Chhean, Chilean Yi, Phalla San, Chenda Chhim, Panha Thorn, Sopacphear Ouch, Bunsopheana Put, Dengrachda Aong, Lyna Phan, Kongkea Nasirzadeh, Leila Tieng, Siteng Bongcam-Rudloff, Erik Lewerin, Susanna Sternberg Boqvist, Sofia Department of Bioengineering Faculty of Engineering Royal University of Phnom Penh Phnom Penh Cambodia Department of Animal Biosciences Bioinformatics section Swedish University of Agricultural Sciences Uppsala75007 Sweden Department of Food Chemistry Faculty of Science and Technology International University Phnom Penh Cambodia

Salmonella is a major bacterial concern for public health globally. Although there are limited published studies on the prevalence of Salmonella species in Cambodia’s food chain, reports indicate that salmonellosis is a severe gastrointestinal infection in its population and especially in children. To investigate the presence of Salmonella spp., 285 food samples (75 meat, 50 seafood, and 160 leafy green vegetable samples) were randomly collected from various local markets in Phnom Penh and nearby farms in Cambodia. Simultaneously, observational data were collected on food hygiene and related practices. All samples were analyzed using bacterial culture and plate counts, and the findings were confirmed with biochemical, serological, and PCR tests. The observational data on food hygiene and practices from farm to market revealed several factors that could pose risks of spreading Salmonella in the food-value chain from farmer to consumer. The overall prevalence of Salmonella spp. was 48.4% (138/285), while the prevalence in meat, seafood, and vegetables was 71% (53/75), 64% (32/50), and 33% (53/160), respectively. Mean plate count ranged from 1.2 to 7.40 log10 CFU/g and there was no significant difference in bacterial counts between meat, seafood, and vegetable samples (P> 0.05). The most common serogroups among the isolated Salmonella spp. were B and C. These results suggest that a large proportion of meat, seafood, and vegetable products sold at local markets in Phnom Penh are contaminated with Salmonella spp. This is likely linked to inadequate hygiene and sanitation practices, including handling, storage, and preservation conditions. Observations on farms suggested that the prevalence of Salmonella in vegetables sold at market could be linked to contamination relating to agricultural practices. Thus, controlling the spread of foodborne salmonellosis through the Cambodian food-value chain from farms, and retailers to consumers is essential to enhance the food safety.

关键词： Salmonella

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Fresh oil palm frond juice as a novel and alternative fermentation medium for bacterial cellulose production

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Materials Today: Proceedings 2021年 42卷 101-106页

作者： Siti Nur Nadhirah Said Azmi Siti Nur Najwa Farhah Mohd Fabli Fathin Amila Faisul Aris Zainatul 'Asyiqin Samsu Ahmad Syafiq Fauzan Mohd Asnawi Yuhanees Mohamed Yusof Hidayah Ariffin Sharifah Soplah Syed Abdullah Section of BioEngineering Technology Universiti Kuala Lumpur Branch Campus Malaysian Institute of Chemical and BioEngineering Technology Vendor City Taboh Naning 78000 Alor Gajah Melaka Malaysia Section of Chemical Engineering Universiti Kuala Lumpur Branch Campus Malaysian Institute of Chemical and BioEngineering Technology Vendor City Taboh Naning 78000 Alor Gajah Melaka Malaysia Department of Bioprocess Universiti Putra Malaysia Serdang 43400 Selangor Malaysia

In this study, fresh oil palm frond (OPF) juice was explored as an alternative fermentation medium for the production of bacterial cellulose (BC) by Acetobacter xylinum 0416. The effect of surface area to volume of fermentation medium (S/V) ratio and nitrogen sources supplementation to OPF juice were investigated to improve the BC production. The S/V ratio of 0.25, 0.50 and 0.75 were initially prepared using Hestrin and Schramm (HS) medium. The medium was inoculated with A. xylinum 0416 and incubated statically at 28 ± 1 °C for 10 days. The yield and properties of BC produced were measured where the highest yield and best properties obtained reflects the optimum S/V ratio. The production of BC from supplemented OPF juice with yeast extract and peptone were carried out at the same fermentation condition and optimum S/V ratio. The thickness and yield of BC obtained were measured while its characteristics were analysed using scanning electron microscopy (SEM), X-ray diffraction (XRD) and tensile strength. Results showed that the lowest S/V ratio at 0.25 gave the highest yield of BC, superior crystallinity and tensile strength as compared to the higher S/V ratio. SEM images of BC samples exhibited a slight difference on the surface morphology of BC network between the three S/V ratios, whilst denser BC network was obtained from OPF juice. The production of BC from OPF juice showed outstanding performance by increasing the yield up to six times higher to that produced in HS medium. Moreover, the BC exhibited superior tensile strength and crystallinity compared to the BC produced from HS medium. Therefore, the findings from this study offer a promising alternative fermentation feedstock from OPF juice for BC production.

关键词： Bacterial cellulose Oil palm frond juice Acetobacter xylinum 0416 Fermentation feedstock

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Inhibition of Advanced Glycation End-Products in Frozen-Thawed and Reheated Pork by Pigskin Gelatin Hydrolysates

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SSRN 2024年

作者： Lin, Yi Chu, Fuyu Huang, Yiqun Miao, Junjian Lai, Keqiang College of Food Science and Technology Shanghai Ocean University No. 999 Hucheng Huan RoadShanghai LinGang New City201306 China School of Food Science and Bioengineering Changsha University of Science & Technology 960 2nd Section Wanjiali South Road Hunan Changsha410004 China Engineering Research Center of Food Thermal-Processing Technology Shanghai Ocean University Shanghai201306 China

This study investigated the effect of pigskin gelatin hydrolysates (PGH, 4%) as a cryoprotectant on the advanced glycation end-products (AGEs) of pre-heated pork after freeze-thaw cycles and subsequent reheating. During the freeze-thaw process, pre- heated pork exhibited an increase in AGEs and their α-dicarbonyl precursors (α-DPs;glyoxal and methylglyoxal), 2-thiobarbituric acid-reactive substances (TBARs), and carbonyl content, while sulfhydryl groups content decreased. After reheating (100 °C, 10 min), AGEs levels increased by 1.94% to 123.21%, while the average contents of glyoxal and methylglyoxal decreased by 17.00% and 15.24%, respectively. The content of AGEs in pork was significantly reduced by the addition of hydrolysates compared to that in the control group. (P © 2024, The Authors. All rights reserved.

关键词： Meats

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