AIMS Biophysics最新文献_第3页

Identification of potential SARS-CoV-2 papain-like protease inhibitors with the ability to interact with the catalytic triad 具有与催化三联体相互作用能力的潜在SARS-CoV-2木瓜蛋白酶抑制剂的鉴定

IF 1.5

AIMS Biophysics Pub Date : 2023-01-01 DOI: 10.3934/biophy.2023005

M. Muhammad, I. Habib, A. Yunusa, Tasiu A. Mikail, A. Alhassan, Ahed J. Alkhatib, H. Sule, S. Ismai̇l, Dong Liu

{"title":"Identification of potential SARS-CoV-2 papain-like protease inhibitors with the ability to interact with the catalytic triad","authors":"M. Muhammad, I. Habib, A. Yunusa, Tasiu A. Mikail, A. Alhassan, Ahed J. Alkhatib, H. Sule, S. Ismai̇l, Dong Liu","doi":"10.3934/biophy.2023005","DOIUrl":"https://doi.org/10.3934/biophy.2023005","url":null,"abstract":"Severe acute respiratory syndrome corona virus2 (SARS-CoV-2) is responsible for the current pandemic that led to so many deaths across the globe and still has no effective medication. One attractive target is Papain-like protease (PLpro), which plays a critical role in viral replication. Several important structural features dictate access to the PLpro narrow active site, which includes a series of loops surrounding the area. As such, it is difficult for chemical compounds to fit the SARS-CoV-2 PLpro active site. This work employed a computational study to discover inhibitors that could bind to the SARS-COV-2 PLpro active site, mainly by virtual screening, molecular dynamic simulation, MMPBSA and ADMET analysis. Eight potential inhibitors were identified: carbonoperoxoic acid, Chrysophanol-9-anthrone, Adrenolutin, 1-Dehydroprogesterone, Cholest-22-ene-21-ol, Cis-13-Octadecenoic acid, Hydroxycarbonate and 1-(4-(4-Methylphenyl)-5-phenyl-1,3-oxazol-2-yl) isoquinoline, with binding scores of −4.4, −6.7, −5.9, −6.7, −7.0, −4.6, −4.5 and −5.6 kcal/mol, respectively. All these compounds interacted with critical PLpro catalytic residues and showed stable conformation in molecular dynamics simulations with significant binding energies of −12.73 kcal/mol, −10.89 kcal/mol, −7.20 kcal/mol, −16.25 kcal/mol, −19.00 kcal/mol, −5.00 kcal/mol, −13.21 kcal/mol and −12.45 kcal/mol, respectively, as revealed by MMPBSA analysis. ADMET analysis also indicated that they are safe for drug development. In this study, we identified novel compounds that interacted with the key catalytic residues of SARS-CoV-2 PLpro with the potential to be utilized for anti-Covid-19 drug development.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"1 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70185294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Importance of modelling and simulation in biophysical applications 建模和仿真在生物物理应用中的重要性

IF 1.5

AIMS Biophysics Pub Date : 2023-01-01 DOI: 10.3934/biophy.2023017

Mehmet Yavuz, F. Usta

引用次数: 0

High-resolution phantom of a nephron for radiation nephrotoxicity evaluation in biophysical simulations 生物物理模拟中用于辐射肾毒性评估的高分辨率肾元模型

IF 1.5

AIMS Biophysics Pub Date : 2022-01-01 DOI: 10.3934/biophy.2022013

Masoud Jabbary, H. Rajabi

{"title":"High-resolution phantom of a nephron for radiation nephrotoxicity evaluation in biophysical simulations","authors":"Masoud Jabbary, H. Rajabi","doi":"10.3934/biophy.2022013","DOIUrl":"https://doi.org/10.3934/biophy.2022013","url":null,"abstract":"Computer simulation plays an important role in medical physics. The aim of this study was to generate an accurate model to calculate the absorbed dose at the cell level in a voxelized phantom of nephrons. In order to implement a model of kidney microdosimetry, a 3D mesh phantom of a human kidney nephron, representing a cortical nephron, was digitized to create a 3D voxelized phantom of a nephron for use in Monte Carlo simulations. The phantom was fed to GATE Monte Carlo toolkits, and simulations were performed to calculate the absorbed dose/energy from alpha and electron sources over a range of energy levels. The results were compared to the results published in literature that were derived by using a stylized phantom. The dose estimated in subunits of the voxelized and stylized phantoms showed a considerable bias (average of relative differences). The maximum difference for self-absorption was 12.5%, and up to 20% for cross-absorption. The digital phantom showed very significant differences in dose distribution among the cells in different subunits of the nephron. The results demonstrated that a small dissimilarity in the size and shape of subunits can lead to a considerable difference in the microdosimetry results. The model presented in this study offers a phantom that not only presents the realistic geometry of a nephron, which has been neglected in previous stylized models, but also one that has the capability of plotting the spatial distribution of the absorbed dose for any distribution of radiopharmaceuticals in nephron cells.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"1 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70185038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Effect of Rs5746136 genotypes on SOD activity and biomarkers levels in breast cancer patients Rs5746136基因型对乳腺癌患者SOD活性及生物标志物水平的影响

IF 1.5

AIMS Biophysics Pub Date : 2022-01-01 DOI: 10.3934/biophy.2023001

H. Abdulabbas, Y. H. Al-Mawlah

{"title":"Effect of Rs5746136 genotypes on SOD activity and biomarkers levels in breast cancer patients","authors":"H. Abdulabbas, Y. H. Al-Mawlah","doi":"10.3934/biophy.2023001","DOIUrl":"https://doi.org/10.3934/biophy.2023001","url":null,"abstract":"Oxidative stress factors are among the most common carcinogens, Superoxide dismutase enzyme-2 (SOD2) is an endogenous antioxidant involved in the scavenging of superoxide anions. This study aimed to investigate the effect of the SOD2 gene polymorphism (rs5746136) on SOD activity and biomarker levels in breast cancer patients. This study aimed to investigate the effect of SOD2 gene (rs5746136) polymorphisms on SOD activity and biomarkers levels in breast cancer patients. The spectrophotometry methods were used to detect malondialdehyde (MDA) and Catalase (CAT), Superoxide dismutase (SOD), and Glutathione (GSH) levels, which reflect antioxidant capacity, and the genotypes of rs5746136 were detected utilize PCR and RFLP. According to the current findings, the GA genotype of the control group was the most common (70%), followed by GG and AA genotypes (26.7% and 3.3%) respectively. In the patient group, the most common genotype was GG (45.6%), followed by the GA genotype (42.8%) and then the AA genotype (11.4%) The frequency of heterozygous genotype G/A compared to the homozygous genotype (G/G) [OR = 0.3571, 95% CI = 0.1375–0.9277, P = 0.0345]. The AA genotype is significantly associated with an increased risk of developing BC [OR = 2.00, p = 0.5403, CI: 0.2175–18.3883]. No significant differences were found in frequencies of the A allele between patients and control groups [OR = 0.7872, 95% CI = 0.4198–1.4762, P = 0.4558]. In addition, there are modest (P 0.05) relationships between serum biochemical parameters levels and rs5746136 genotype in breast cancer patients, but a substantial association between serum SOD activity and GSH concentration and GA and GG rs5746136 genotype in the control group. In conclusion, the current investigation suggests that the AA genotype of (rs5746136) in the MnSOD gene may be associated with an increased risk of breast cancer. The chosen SOD2 variants (rs5746136) play a crucial role in controlling the activity of the SOD enzyme.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"1 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70185205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Improvement in growth of plants under the effect of magnetized water 磁化水对植物生长的改善作用

IF 1.5

AIMS Biophysics Pub Date : 2022-01-01 DOI: 10.3934/biophy.2022029

Etimad M. Alattar, Eqbal Radwan, K. Elwasife

{"title":"Improvement in growth of plants under the effect of magnetized water","authors":"Etimad M. Alattar, Eqbal Radwan, K. Elwasife","doi":"10.3934/biophy.2022029","DOIUrl":"https://doi.org/10.3934/biophy.2022029","url":null,"abstract":"The magnetic field can change the polarity characteristics and hydrogen-bond structure of water; therefore, magnetized water can affect plant growth and development. Magnetized water is hexagonal water created by passing water through a specific magnet that can activate and ionize water molecules to change its structure. This review highlights the use of magnetized water in the agricultural sector to enhance plant growth and food productivity. We discussed the impact of magnetized water on seed germination, vegetative growth, fruit production, soil and pigments of treated plants. Plant growth and development can be improved both qualitatively and quantitatively via irrigation with magnetized water. It can promote seed germination, seedling early vegetative development, improvement of the mineral content of fruits and seeds, the enzyme activity of the soil, improved water use efficiency, higher nutrient content, and better transformation and consumption efficiency of nutrients; it can also mitigate soil salinity. Furthermore, magnetized water had a substantial good influence on the mobility and uptake of micronutrient concentrations, as well as promoted better growth criteria, all of which increased biomass and total yield. Also, irrigating plants with magnetized water resulted in a considerable increase in chloroplast pigments (carotenoids, chlorophyll a, and b) and photosynthetic activity. Magnetizing low-quality water (brackish water, saline water or water contaminated with metals) can be considered as an alternative tool to overcome the problem of scarcity and shortage of water resources. As a result, magnetic treatment of irrigation water could be a promising technique to boost agricultural production while also being environmentally beneficial in the future. The major challenge in using magnetized water in agriculture is creating pumps that are compatible with the technical and practical needs of magnetic systems while also effectively integrating irrigation components.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"1 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70185653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Interplay and multiscale modeling of complex biological systems 复杂生物系统的相互作用和多尺度建模

IF 1.5

AIMS Biophysics Pub Date : 2022-01-01 DOI: 10.3934/biophy.2022005

C. Bianca

引用次数: 0

Screening revealed the strong cytotoxic activity of Alchemilla smirnovii and Hypericum alpestre ethanol extracts on different cancer cell lines 筛选结果表明，金丝桃和金丝桃乙醇提取物对不同的癌细胞具有较强的细胞毒活性

IF 1.5

AIMS Biophysics Pub Date : 2022-01-01 DOI: 10.3934/biophy.2023002

M. Ginovyan, S. Hovhannisyan, Hayarpi Javrushyan, Gohar Sevoyan, Z. Karabekian, N. Zakaryan, N. Sahakyan, N. Avtandilyan

{"title":"Screening revealed the strong cytotoxic activity of Alchemilla smirnovii and Hypericum alpestre ethanol extracts on different cancer cell lines","authors":"M. Ginovyan, S. Hovhannisyan, Hayarpi Javrushyan, Gohar Sevoyan, Z. Karabekian, N. Zakaryan, N. Sahakyan, N. Avtandilyan","doi":"10.3934/biophy.2023002","DOIUrl":"https://doi.org/10.3934/biophy.2023002","url":null,"abstract":"Compounds of plant origin are considered promising alternative approaches in the development of medicines for the prevention and treatment of cancer. The large diversity of herbal species still requires careful exploration as a source for new anticancer compounds. The goal of the study was to screen different herbal extracts traditionally used in Armenian folk medicine for their cytotoxic effect against some cancer cell lines, and to find the prospective plant species among them. The cytotoxicity of the plant ethanol extracts was evaluated with MTT test against HeLa (human cervical carcinoma) and A549 (human lung adenocarcinoma) cells. Antioxidant properties were assessed with DPPH free radical scavenging assay. Five of the tested ten herbal extracts exhibited significant growth-inhibiting activity on HeLa cells. Moreover, Alchemilla smirnovii and Hypericum alpestre extracts also showed potent cytotoxicity on human lung adenocarcinoma cells. These two plants possessed high antiradical activity as well. Their DPPH stoichiometric values were 0.4234 and 0.14437 respectively, meaning that 1 µg of plant extract brought the reduction of DPPH equal to the respective stoichiometric values in µg. Thus, A. smirnovii and H. alpestre extracts expressed themselves as potent cytotoxic and antioxidant agents and could have promising anticancer potential. Further evaluation of their in vivo anticancer properties has much interest.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"1 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70185245","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Efficiency of GrowDex® nanofibrillar cellulosic hydrogel when generating homotypic and heterotypic 3D tumor spheroids GrowDex®纳米纤维纤维素水凝胶在生成同型和异型三维肿瘤球体时的效率

IF 1.5

AIMS Biophysics Pub Date : 2022-01-01 DOI: 10.3934/biophy.2022019

P. Balaji, Anbazhagan Murugadas, Lauri Paasonen, S. Shanmugaapriya, M. A. Akbarsha

{"title":"Efficiency of GrowDex® nanofibrillar cellulosic hydrogel when generating homotypic and heterotypic 3D tumor spheroids","authors":"P. Balaji, Anbazhagan Murugadas, Lauri Paasonen, S. Shanmugaapriya, M. A. Akbarsha","doi":"10.3934/biophy.2022019","DOIUrl":"https://doi.org/10.3934/biophy.2022019","url":null,"abstract":"In recent times, homotypic and heterotypic 3D tumor spheroid (HTS) models have been receiving increasing attention and come to be widely employed in preclinical studies. The present study is focused on the generation of homotypic (A549 and MDA-MB-231, separately) and heterotypic (A549 + NIH/3T3; MDA-MB-231 + NIH/3T3) 3D tumor spheroids by using GrowDex® nanofibrillar cellulosic (NFC) hydrogel as the scaffold. Light microscopic observations and F-actin staining confirmed the formation of spheroids. The proliferation efficiency indicated an expansion of cell population and an increase in spheroid size over time. The distribution, interaction pattern and influence of fibroblasts on the epithelial cell types were observed in terms of the size and shape of the HTS against homo-spheroids. An interesting observation was that, with an increase in the size of HTSs, many more fibroblast cells were found to occupy the core region, which, perhaps, was due to the faster growth of tumor cells over normal cells. Thus, normal and tumor cells, especially with origins from two different species, can be cultured together in 3D format, and this can potentially enhance our knowledge of tumor microenvironments and cell-cell interaction. These spheroids could be used to improve microphysiological systems for drug discovery and to better understand the tumor microenvironment.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"1 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70185484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

VV-hemorphin-5 association to lipid bilayers and alterations of membrane bending rigidity VV-hemorphin-5与脂质双分子层的关联及膜弯曲刚度的改变

IF 1.5

AIMS Biophysics Pub Date : 2022-01-01 DOI: 10.3934/biophy.2022025

I. Valkova, P. Todorov, V. Vitkova

{"title":"VV-hemorphin-5 association to lipid bilayers and alterations of membrane bending rigidity","authors":"I. Valkova, P. Todorov, V. Vitkova","doi":"10.3934/biophy.2022025","DOIUrl":"https://doi.org/10.3934/biophy.2022025","url":null,"abstract":"The morphinomimetic properties of hemorphins are intensively studied with regard to new peptide drug developments. In this respect, the investigation of mechanical properties and stability of lipid membranes provides a useful background for advancement in pharmacological applications of liposomes. Here we probed the effect of the endogenous heptapeptide VV-hemorphin-5 (valorphin) on the bending elasticity of biomimetic lipid membranes of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) by analysis of thermal shape fluctuations of nearly spherical giant unilamellar vesicles. In a wide concentration range covering valorphin concentrations applied in nociceptive screening in vivo, we report alterations of the bilayer bending rigidity in a concentration-dependent non-monotonic manner. We performed quantitative characterization of VV-hemorphin-5 association to POPC membranes by isothermal titration calorimetry in order to shed light on the partitioning of the amphiphilic hemorphin between the aqueous solution and membranes. The calorimetric results correlate with flicker spectroscopy findings and support the hypothesis about the strength of valorphin-membrane interaction related to the peptide bulk concentration. A higher strength of valorphin interaction with the bilayer corresponds to a more pronounced effect of the peptide on the membrane's mechanical properties. The presented study features the comprehensive analysis of membrane bending elasticity as a biomarker for physicochemical effects of peptides on lipid bilayers. The reported data on thermodynamic parameters of valorphin interactions with phosphatidylcholine bilayers and alterations of their mechanical properties is expected to be useful for applications of lipid membrane systems in pharmacology and biomedicine.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"1 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70185598","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Impact of viscosity on creeping viscous fluid flow through a permeable slit: a study for the artificial kidneys 粘度对通过可渗透狭缝蠕动的粘性流体流动的影响:人工肾脏的研究

IF 1.5

AIMS Biophysics Pub Date : 2022-01-01 DOI: 10.3934/biophy.2022026

K. Maqbool, H. Mehboob, A. Siddiqui

{"title":"Impact of viscosity on creeping viscous fluid flow through a permeable slit: a study for the artificial kidneys","authors":"K. Maqbool, H. Mehboob, A. Siddiqui","doi":"10.3934/biophy.2022026","DOIUrl":"https://doi.org/10.3934/biophy.2022026","url":null,"abstract":"The idea of this study is to present the mathematical model of two-dimensional biofluid flow having variable viscosity along the height of the channel (proximal renal tube of artificial kidney). This research describes that flow resistance is dependent on the height of the channel (proximal renal tube of artificial kidney) which makes the high flow near the centre and slow near the wall. The goal of this research is to provide the formulas to find the flow speed, average pressure, outflow flux and filtration rate of the viscous fluid having variable viscosity. The complex mathematical problem is solved by the Inverse method and results for axial velocity are plotted at the opening, central and departure region of the conduit. The numerical values for constant reabsorption and mean pressure are calculated against the filtration rate for the constant and variable viscosity. The numerical results of pressure rise show that when the viscosity of biofluid varies from centre to the boundary, then high change in pressure is required as compared with the biofluid having constant viscosity along the height of the slit. These mathematical formulas are very useful for the bioengineers to design the portable artificial kidney which works as a mechanical tool to filter the biofluid.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"37 3 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70185605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0