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Evaluation of Terpenoids as Dipeptidyl Peptidase 4 Lead Molecules: Molecular Docking and Dynamics Simulation Study 萜类化合物作为二肽基肽酶4先导分子的评价:分子对接与动力学模拟研究
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-10-31 DOI: 10.33263/briac134.376
About 966 billion US dollars have been spent globally treating and managing diabetic patients. Notwithstanding individuals' substantial access to the required primary medical services and essential medicines, it is tempting to get momentum in identifying new chemical entities, biologics, or small molecules as drug candidates that are prophylactically and therapeutically effective against lifestyle-based maladies, thereby backing the overall health mission of Sustainable Development Goals. Towards this context, the study aims to screen natural inhibitor(s) targeting dipeptidyl peptidase 4 using hybrid approaches of bioinformatics and medicinal chemistry. Data set of 513 ligands of terpenoids in nature was retrieved from the naturally occurring plant-based anticancerous compound-activity-target database (NPACT) and performed docking studies. Sitagliptin depicted substantial binding affinity among reference drugs with dipeptidyl peptidase 4 (DPP IV) (binding energy: -8.63 kcal/mol, Inhibition constant: 163.65 μM). Among all terpenoids, Asiatic acid (ΔG: -9.95 kcal/mol, 85.23 μM), Aucubin (-9.86 kcal/mol, 98.98 μM), Ailanquassin A (-9.25 kcal/mol, 156.23 μM), and 6-α-hydroxyneopulchellin (-9.18 kcal/mol, 189.76 μM) depicted strong binding affinities with DPP IV compared to Sitagliptin. Based on the MD simulation findings, Asiatic acid and Aucubin were better lead molecules than Sitagliptin. However, holistic wet-lab validations are required before manifesting their therapeutic implications against diabetes.
全球用于治疗和管理糖尿病患者的费用约为9660亿美元。尽管个人可以大量获得所需的初级医疗服务和基本药物,但人们很容易在确定新的化学实体、生物制剂或小分子作为候选药物方面取得势头,这些候选药物对与生活方式有关的疾病具有预防和治疗效果,从而支持可持续发展目标的总体卫生使命。在此背景下,本研究旨在利用生物信息学和药物化学的混合方法筛选靶向二肽基肽酶4的天然抑制剂。从天然植物抗癌化合物活性靶点数据库(NPACT)中检索到513种天然萜类化合物配体数据集,并进行对接研究。西格列汀与二肽基肽酶4 (DPP IV)具有较强的结合亲和力(结合能为-8.63 kcal/mol,抑制常数为163.65 μM)。与西格列汀相比,亚洲酸(ΔG: -9.95 kcal/mol, 85.23 μM)、桃叶苷(-9.86 kcal/mol, 98.98 μM)、丁香素A (-9.25 kcal/mol, 156.23 μM)和6-α-羟基新紫皮素(-9.18 kcal/mol, 189.76 μM)与DPP IV具有较强的结合亲和力。MD模拟结果表明,亚洲酸和桃叶苷是比西格列汀更好的先导分子。然而,在显示其对糖尿病的治疗意义之前,需要全面的湿实验室验证。
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引用次数: 1
A Systematic Review on the Impact of Micro-Nanoplastics Exposure on Human Health and Diseases 微纳米塑料暴露对人类健康和疾病影响的系统评价
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-10-31 DOI: 10.33263/briac134.381
Plastic production is continuously increasing worldwide for daily use. Micro-plastics and nano-plastics remain major emerging pollutants and threaten the environment, ecosystem, human health, and well-being. Micro-nanoplastics (MNPs) are also exposed to humans through cosmetics, inhalation, ingestion, drinking water, dietary sources, and drug formulations. Oral uptake is the major among the different exposure routes of MNPs to humans. After entry, it gets absorbed due to its nano size (˂100 nm) and easily distributed to all parts of the body through blood, affecting multiple organs, especially vital organs of the human body leading to severe diseases. It causes cancer, heart, liver, and kidney diseases, crosses the blood-brain barrier, and affects the brain. Its adsorption with protein leads to multi-layered corona formation in human blood plasma. MNPs interact with immune cells and induce pro-inflammatory mediators, inflammatory reactions, reactive oxygen species (ROS) production, and associated cytotoxicity. MNPs suppress T lymphocyte activity which results in a lack of immune regulation leading to autoimmune diseases. Hence, it is necessary to understand the impact of MNPs exposure on humans. Strict control measures for the production and use of plastics and developing appropriate strategies for safe disposal would prevent MNPs-mediated toxicity in humans.
全世界日常使用的塑料产量不断增加。微塑料和纳米塑料仍然是主要的新兴污染物,威胁着环境、生态系统、人类健康和福祉。微纳米塑料(MNPs)也通过化妆品、吸入、摄入、饮用水、饮食来源和药物配方暴露于人类。在MNPs对人类的不同暴露途径中,口服摄取是主要的。进入后,由于其纳米尺寸(100 nm),它被吸收,并容易通过血液分布到身体的各个部位,影响多个器官,尤其是人体的重要器官,从而导致严重疾病。它会导致癌症、心脏、肝脏和肾脏疾病,穿过血脑屏障,影响大脑。它与蛋白质的吸附导致人类血浆中形成多层电晕。MNPs与免疫细胞相互作用,诱导促炎介质、炎症反应、活性氧(ROS)产生和相关的细胞毒性。MNPs抑制T淋巴细胞活性,导致缺乏免疫调节,从而导致自身免疫性疾病。因此,有必要了解MNPs暴露对人类的影响。对塑料的生产和使用采取严格的控制措施,并制定适当的安全处置战略,将防止MNPs介导的人类毒性。
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引用次数: 1
Reduced Graphene Oxide/Silica Nanocomposite as Anticancer Drug Delivery Nanocarrier 还原氧化石墨烯/二氧化硅纳米复合材料作为抗癌药物递送纳米载体
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-10-31 DOI: 10.33263/briac134.383
This study synthesized a reduced graphene oxide-silica-based (rGO/SiO2) nanocomposite for quercetin delivery as an anticancer model drug delivery. The synthesized rGO/SiO2 nanocomposite was investigated by several characterization methods such as Fourier-transform infrared (FT-IR) spectroscopy, X-ray diffraction (XRD) analysis, and Transmission electron microscopy (TEM), and Energy-dispersive X-ray spectroscopy (EDX). The experiments result show that the rGO/SiO2 nanocomposite has been synthesized successfully and has an average particle size of 50-120 nm.
本研究合成了一种用于槲皮素递送的还原氧化石墨烯-二氧化硅基(rGO/SiO2)纳米复合材料,作为抗癌模型药物递送。通过傅立叶变换红外光谱(FT-IR)、X射线衍射(XRD)分析、透射电子显微镜(TEM)和能量色散X射线光谱(EDX)等表征方法对合成的rGO/SiO2纳米复合材料进行了研究。实验结果表明,成功合成了rGO/SiO2纳米复合材料,其平均粒径为50~120nm。
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引用次数: 0
Synthesis and Characterization of Heat-Tempered Cu2Zn0.6Ca0.4SnS4 Alloy Thin Film 热处理Cu2Zn0.6Ca0.4SnS4合金薄膜的合成与表征
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-10-31 DOI: 10.33263/briac134.390
Six samples of Cu2Zn0.6Ca0.4SnS4 labeled Y1 – Y6 were spin-coated on a pre-cleaned glass from 20 ml each of 0.067 moll Calcium sulfate (CaSO4, 98.5% KermerR) and 0.1 mol each of zinc nitrate (Zn(NO3)2, 99% Aldrich), Copper(II)sulfate hexahydrate (Cu2SO4.6H2O, 98.5% KermerR), stannous sulfate (SnSO4, 99% KermerR), and sodium thiosulfate (Na2S2O3, 98.5% Aldrich) with ammonium hydroxide (NH4OH, 99% DHR) and triethanolamine (C6H15NO3, 99% KermerR) used as complexing agents. They were left to dry at room temperature. Y2 – Y6 were subjected to heat tempering in a carbolite furnace between 150 - 750 ℃ with a step height of 150 ℃. The alloy thin films were structurally, morphologically, and optically characterized. The grain sizes for Y1, Y2, Y3, Y4, Y5, and Y6 are 15 nm, 40nm,43 nm, 45 nm, 44 nm, and 42 nm, respectively. The interruption of the normal stacking sequence of atomic planes initially decreases as the temperature increases and the microstrain. The microstrain and stacking fault energy both climaxed at 600 ℃. Microstrain and stacking fault energy exhibit a sine and allometric relationship with the temperature (T). As the temperature increases, the band gap reduces from 3.60 eV to 3.26 eV. The residue effect of heat on the band gap variation gives a relative exponential decay of the crystallite. The difference between a shift in energy and a change in optical band gap (∆Estrain) as a function of temperature is given as -0.031 ±3.66667×10^(-4) T.
用0.067 mol硫酸钙(CaSO4, 98.5% KermerR)和0.1 mol硝酸锌(Zn(NO3)2, 99% Aldrich)、六水硫酸铜(Cu2SO4.6H2O, 98.5% KermerR)、硫酸亚锡(SnSO4, 99% KermerR)和硫代硫酸钠(Na2S2O3, 98.5% Aldrich)各20 ml,以氢氧化铵(NH4OH, 99% DHR)和三乙乙醇胺(C6H15NO3, 99% KermerR)为络合剂,在预清洗玻璃上自旋涂覆6个标记为Y1 - Y6的样品。它们在室温下晾干。Y2 - Y6在150 ~ 750℃的碳石炉中进行步高150℃的回火。对合金薄膜进行了结构、形貌和光学表征。Y1、Y2、Y3、Y4、Y5和Y6的晶粒尺寸分别为15 nm、40nm、43 nm、45 nm、44 nm和42 nm。随着温度的升高和微应变的增大,原子平面正常堆积顺序的中断度开始减小。微应变和层错能均在600℃达到峰值。微应变和层错能随温度(T)呈正弦和异速生长关系,随着温度的升高,带隙从3.60 eV减小到3.26 eV。热对带隙变化的残余效应导致晶体的相对指数衰减。能量位移和光带隙变化(∆Estrain)随温度的变化之差为-0.031±3.66667×10^(-4) T。
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引用次数: 0
A New Approach to the Synthesis of 4H-1,3,5-Oxadiazine Derivatives 合成4h -1,3,5-恶二嗪衍生物的新方法
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-10-31 DOI: 10.33263/briac134.379
Derivatives of 1,3,5-oxadiazine are of great interest as potential biologically active compounds. In this work, we report on a new method for synthesizing 1,3,5-oxadiazine derivatives. The method is based on the elimination of hydrogen sulfide from N-((1-carboxamido-2,2,2-trichloroethyl)carbamothioyl)benzamides by the action of dicyclohexylcarbodiimide (DCC). Presumably, at the first stage of the transformation, an intermediate carbodiimide is formed, which then enters into the [4+2] cycloaddition reaction with another DCC molecule to form the final products - N-(2,2,2-trichloro-1-(((2Z,4E)-3-cyclohexyl-2-(cyclohexylimino)-6-phenyl-2,3-dihydro-4H-1,3,5-oxadiazin-4-ylidene)amino)ethyl)carboxamides. Target products were obtained in 68-89% yields. The structure of the obtained compounds was confirmed by IR, 1H NMR, 13C NMR spectroscopy, and mass spectrometry.
1,3,5-恶二嗪衍生物作为一种潜在的生物活性化合物而备受关注。本文报道了一种合成1,3,5-恶二嗪衍生物的新方法。该方法基于通过二环己基碳二亚胺(DCC)的作用从N-((1-甲酰胺-2,2,2-三氯乙基)氨基甲硫基)苯甲酰胺中消除硫化氢。据推测,在转化的第一阶段,形成中间体碳二亚胺,然后与另一个DCC分子进行[4+2]环加成反应,形成最终产物-N-(2,2,2-三氯-1-(((2Z,4E)-3-环己基-2-(环己基氨基)-6-苯基-2,3-二氢-4H-1,3,5-恶二嗪-4-亚基)氨基)乙基)羧酰胺。以68-89%的产率获得目标产物。通过IR、1H NMR、13C NMR光谱和质谱来确认所获得的化合物的结构。
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引用次数: 1
Selected Polyphenols from Date (Phoenix dactylifera) as Anti-Virulence of Candida albicans Through Multiple Enzyme Targets 枣多酚通过多种酶靶点抗白色念珠菌的作用
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-10-31 DOI: 10.33263/briac134.386
Candida albicans (C. albicans) have long been attributed to various diseases like candidiasis and systemic diseases and exacerbate the symptoms of immunocompromised patients. C. albicans has enzymes that could function as drug targets to decrease its pathogenicity and eradicate the fungi. This research aimed to investigate the potency of selected polyphenols contained in dates (Phoenix dactylifera) in inhibiting important enzymes of C. albicans through molecular docking simulation. The structures of four target enzymes (Sap 1, Sap 2, Sap 3, Sap 5) of C. albicans and six selected polyphenol compounds from dates were downloaded from PDB and prepared using YASARA Structure. A molecular docking simulation was conducted using YASARA Structure. Docking results showed that procyanidin has a high binding affinity with target protein Sap 1 and Sap 5, while beta carotene has a high binding affinity with Sap 2 and Sap 3. The binding affinity range of all ligand-receptor complexes was as follows: Sap 1 (5.782 – 9.907 kcal/mol), Sap 2 (5.943 – 9.343 kcal/mol), Sap 3 (5.732 – 8.905 kcal/mol), and Sap 5 (5.873 – 9.430 kcal/mol). The interactions formed included hydrogen bonding, electrostatic and hydrophobic interactions, and unfavorable bindings. The data generated from molecular docking analysis warrant further experiments are necessary.
白色念珠菌(C. albicans)长期以来被认为是念珠菌病和全身性疾病等各种疾病的病因,并加剧免疫功能低下患者的症状。白色念珠菌具有可作为药物靶点的酶,以降低其致病性并根除真菌。本研究旨在通过分子对接模拟研究红枣(Phoenix dactylifera)中所含的部分多酚对白色念珠菌重要酶的抑制作用。从PDB上下载了白念珠菌的4个目标酶(sap1、sap2、sap3、sap5)和6个从枣中提取的多酚化合物的结构,并利用YASARA Structure进行了结构分析。利用YASARA结构进行了分子对接模拟。对接结果表明,原花青素与靶蛋白Sap 1和Sap 5具有较高的结合亲和力,β -胡萝卜素与靶蛋白Sap 2和Sap 3具有较高的结合亲和力。所有配体-受体复合物的结合亲和力范围分别为:sap1 (5.782 ~ 9.907 kcal/mol)、sap2 (5.943 ~ 9.343 kcal/mol)、sap3 (5.732 ~ 8.905 kcal/mol)和sap5 (5.873 ~ 9.430 kcal/mol)。形成的相互作用包括氢键、静电和疏水相互作用以及不利结合。分子对接分析得到的数据证明有必要进行进一步的实验。
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引用次数: 1
Quality by Design approach for Optimization and Development of Cyclodextrin-Surfactant Complex Based Formulations for Bioavailability Enhancement of Valsartan 环糊精-表面活性剂复合制剂提高缬沙坦生物利用度的质量设计优化与研制
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-10-31 DOI: 10.33263/briac134.388
The main objective of the present research is to increase the oral bioavailability of Valsartan by inclusion complexes (ICVs) with a cyclodextrin-surfactant combination followed by the formulation of fast-dissolving tablets (FDTs). The solvent evaporation method was used for the preparation of ICVs. Methyl-ß-cyclodextrin and Hydroxypropyl-ß- cyclodextrin were evaluated with the combination of poloxamer 188 to get the formulations with the desired solubility. Central composite design (CCD) was used as the experimental design as a part of the quality by design (QbD) approach. The optimized ICVs were further developed into FDTs by direct compression technique. Taking concentration of povidone, type and concentration of disintegrant as the formulation factors, the FDTs were optimized using CCD. In-vivo bioavailability study in rats was performed for the optimized FDTs against the marketed tablets. The optimized ICVs were found to have a 3.12 mg/mL solubility. The optimized FDTs were found to be disintegrated in 18.7 sec and dissolved 90% of the dose in 6.3 min. The In-vivo results indicated that the FDTs exhibited rapid absorption and an increase in bioavailability by 24.1% against the marketed tablets. The results indicated that the QbD approach successfully improved Valsartan's oral bioavailability through cyclodextrin-surfactant complexation.
本研究的主要目的是通过包合物(ICVs)与环糊精-表面活性剂的组合,然后配制快溶片(FDTs),提高缬沙坦的口服生物利用度。溶剂蒸发法用于制备ICVs。用泊洛沙姆188组合评价甲基-ß-环糊精和羟丙基-坙-环状糊精,得到具有所需溶解度的制剂。中心复合设计(CCD)被用作实验设计,作为设计质量(QbD)方法的一部分。通过直接压缩技术将优化后的ICV进一步发展为FDT。以聚维酮的浓度、崩解剂的种类和浓度为处方因素,利用CCD对FDTs进行了优化。针对市售片剂,对优化的FDTs进行了大鼠体内生物利用度研究。发现优化的ICVs具有3.12mg/mL的溶解度。发现优化的FDTs在18.7秒内崩解,并在6.3分钟内溶解90%的剂量。体内结果表明,与市售片剂相比,FDTs表现出快速吸收和24.1%的生物利用度增加。结果表明,QbD方法通过环糊精-表面活性剂的络合作用,成功地提高了缬沙坦的口服生物利用度。
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引用次数: 0
In Silico Interactions of Some of the Triazole Derivatives with the Main Protease of Coronavirus 某些三唑衍生物与冠状病毒主要蛋白酶的硅内相互作用
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-10-31 DOI: 10.33263/briac134.382
E. Salarrezaei, K. Harismah, M. Mirzaei
This work was done to assess in silico interactions of some of the 1,2,4-triazole derivatives with the main protease (MPro) of coronavirus to approach insights into enzymatic activity inhibition. Fifteen models of triazole derivatives (T2-T16) were investigated in this work to examine such benefits of structural modifications of T1 for approaching better ligand structures. The density functional theory (DFT) calculations indicated that the derivative ligand models were in their new characteristic specifications compared with the original T1 ligand and other T ligands. One important point was that the derivatives ligands were in higher levels of activity in comparison with the original T1 affirming the benefits of employing such structural modifications. Next, the results of molecular docking simulations indicated the potential of derivative ligands for participating in efficient interactions with the MPro target of coronavirus. As a result, the ligand models were stabilized. Their interactions with the MPro of coronavirus revealed that the investigated triazole derivatives could be considered possible inhibitors of MPro of coronavirus.
这项工作是为了评估一些1,2,4-三唑衍生物与冠状病毒主要蛋白酶(MPro)的硅相互作用,以深入了解酶活性抑制。本研究研究了15种三唑衍生物(T2-T16)模型,以检验T1的结构修饰对获得更好的配体结构的好处。密度泛函理论(DFT)计算表明,与原T1配体和其他T配体相比,衍生配体模型符合新的特征规范。重要的一点是,与原始T1相比,衍生物配体的活性水平更高,这肯定了采用这种结构修饰的好处。下一步,分子对接模拟结果表明,衍生物配体可能参与与冠状病毒MPro靶点的有效相互作用。因此,配体模型是稳定的。它们与冠状病毒MPro的相互作用表明,所研究的三唑类衍生物可能是冠状病毒MPro的抑制剂。
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引用次数: 0
Review of Pistachio (Pistacia) Shell Use to Remove Pollutants from Aqua Media 开心果壳去除水中污染物的研究进展
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-10-31 DOI: 10.33263/briac134.389
The paper summarizes literature data on using crushed pistachio shells (Pistacia vera L.) as sorption materials to remove ions of various metals, dyes, and antibiotics from aqueous media. It provides brief information on the amount of pistachio processing waste, its chemical composition, and its recycling methods. It gives the adsorption process parameters and the values of pistachio shell sorption parameters for the studied pollutants. It was shown that pistachio shells' sorption characteristics for various pollutants could be increased by chemical modification with various chemical reagents. The isotherms of pollutant adsorption with pistachio shells were found to be, in most cases, more accurately described by the Langmuir model, and the process kinetics to follow in most cases, the pseudo-second-order model. It is shown that the pistachio shell is a good precursor for activated carbons production, which can also be used for the adsorption of various pollutants from aqueous media.
本文总结了使用破碎的开心果壳(Pistacia vera L.)作为吸附材料从水介质中去除各种金属、染料和抗生素离子的文献数据。它提供了开心果加工废物的数量、化学成分和回收方法的简要信息。给出了所研究污染物的吸附过程参数和开心果壳吸附参数值。结果表明,用各种化学试剂对开心果壳进行化学改性,可以提高其对各种污染物的吸附特性。发现在大多数情况下,开心果壳对污染物的吸附等温线由Langmuir模型更准确地描述,在大多数情况中,过程动力学遵循伪二阶模型。研究表明,开心果壳是生产活性炭的良好前驱体,也可用于吸附水介质中的各种污染物。
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引用次数: 1
Different Dimensions of the Effects of SARS-CoV-2 in Causing Fluctuations in the Blood Pressure of Patients SARS-CoV-2对患者血压波动影响的不同维度
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-10-31 DOI: 10.33263/briac134.377
M. A. Ozma, E. Nabizadeh, M. R. Valiollahzadeh, J. Rashedi, B. M. Poor, V. Asgharzadeh, H. Kafil, E. Khodadadi, Z. Taghinejad, A. Abbasi, A. Esmaeili, M. Asgharzadeh
In late 2019, SARS-CoV-2 was transmitted from animal to human in China. Subsequently, the virus spread rapidly throughout the world by human-to-human transmission and caused high mortality the people with underlying diseases, especially hypertension. This virus binds to its receptor, angiotensin-converting enzyme-2 (ACE2), via the S protein. ACE2 has a negative regulatory function in the renin-angiotensin system (RAS) and degrades angiotensin 2 (Ang II) as a vasoconstrictor which causes blood pressure regulation. It also converts Ang II to Ang1-7, which has anti-inflammatory and anti-oxidative effects. SARS-CoV-2 infection in patients with hypertension reduces ACE2 levels due to virus binding, which decreases Ang II degradation. Consequently, the complications associated with hypertension are raised, and blood pumping from the lungs into the left atrium lowers. On the other hand, the final product, Ang1-7, is reduced, and its related anti-inflammatory activity is also eliminated. The virus multiplies and damages lung cells, causing inflammation and edema of the lung tissue through the function of immune cells and cytokines, which eventually leads to lung damage, reduced oxygen delivery, and death. Careful care of patients with hypertension can prevent their infection and reduce their death with appropriate oxygen therapy and possibly using exogenous ACE2 supplements.
2019年末,严重急性呼吸系统综合征冠状病毒2型在中国通过动物传播给人类。随后,该病毒通过人与人之间的传播在世界各地迅速传播,并导致患有潜在疾病,特别是高血压的人的高死亡率。这种病毒通过S蛋白与其受体血管紧张素转换酶-2(ACE2)结合。ACE2在肾素-血管紧张素系统(RAS)中具有负调节功能,并降解血管紧张素2(Ang II)作为引起血压调节的血管收缩剂。它还将Ang II转化为Ang1-7,具有抗炎和抗氧化作用。高血压患者感染严重急性呼吸系统综合征冠状病毒2型由于病毒结合降低了ACE2水平,从而降低了Ang II的降解。因此,与高血压相关的并发症增加,从肺部泵入左心房的血液减少。另一方面,最终产物Ang1-7减少,其相关的抗炎活性也被消除。病毒繁殖并损害肺细胞,通过免疫细胞和细胞因子的功能引起肺组织的炎症和水肿,最终导致肺损伤、氧气输送减少和死亡。仔细护理高血压患者可以通过适当的氧气治疗和可能使用外源性ACE2补充剂来预防他们的感染并减少他们的死亡。
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引用次数: 0
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Biointerface Research in Applied Chemistry
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