Molecular modelling

分子建模
  • 文章类型: Journal Article
    这项研究的重点是煅烧层状双氢氧化物(CLDH)粘土在吸附两种抗逆转录病毒药物(ARVD)中的功效,即依非韦伦(EFV)和奈韦拉平(NVP),从废水。使用共沉淀法合成粘土,随后在马弗炉中在500°C下煅烧4小时。对纯净和煅烧的粘土样品进行各种表征技术以阐明其物理和化学性质。响应面模型(RSM)用于评估溶液的初始pH,吸附剂负载,反应温度,和初始污染物浓度。此外,吸附动力学,热力学,并对吸附剂的可重用性进行了评价。结果表明,NVP比EFV表现出更快的吸附速率,两者在20-24小时内达到平衡。伪二阶(PSO)模型为动力学数据提供了良好的拟合。热力学分析表明,吸附过程是自发放热的,主要由物理吸附相互作用控制。吸附等温线遵循Freundlich模型,EFV和NVP的最大吸附容量分别为2.73mg/g和2.93mg/g,分别。通过计算分析对吸附机理的评估表明,NVP和EFV均与CLDH形成稳定的配合物,NVP表现出更高的亲和力。NVP的相关吸附能为-731.78kcal/mol,EFV为-512.6kcal/mol。可视化的非共价相互作用(NCI)图表明,氢键在ARVD-CLDH相互作用中起着重要作用,进一步强调物理吸附是主要的吸附机制。
    This study focused on the efficacy of a calcined layered double hydroxide (CLDH) clay in adsorbing two antiretroviral drugs (ARVDs), namely efavirenz (EFV) and nevirapine (NVP), from wastewater. The clay was synthesized using the co-precipitation method, followed by subsequent calcination in a muffle furnace at 500 °C for 4 h. The neat and calcined clay samples were subjected to various characterization techniques to elucidate their physical and chemical properties. Response surface modelling (RSM) was used to evaluate the interactions between the solution\'s initial pH, adsorbent loading, reaction temperature, and initial pollutant concentration. Additionally, the adsorption kinetics, thermodynamics, and reusability of the adsorbent were evaluated. The results demonstrated that NVP exhibited a faster adsorption rate than EFV, with both reaching equilibrium within 20-24 h. The pseudo-second order (PSO) model provided a good fit for the kinetics data. Thermodynamics analysis revealed that the adsorption process was spontaneous and exothermic, predominantly governed by physisorption interactions. The adsorption isotherms followed the Freundlich model, and the maximum adsorption capacities for EFV and NVP were established to be 2.73 mg/g and 2.93 mg/g, respectively. Evaluation of the adsorption mechanism through computational analysis demonstrated that both NVP and EFV formed stable complexes with CLDH, with NVP exhibiting a higher affinity. The associated adsorption energies were established to be -731.78 kcal/mol for NVP and -512.6 kcal/mol for EFV. Visualized non-covalent interaction (NCI) graphs indicated that hydrogen bonding played a significant role in ARVDs-CLDH interactions, further emphasizing physisorption as the dominant adsorption mechanism.
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  • 文章类型: Journal Article
    霉菌毒素是已知的可能污染食品和饲料链的环境污染物。许多国家对一些霉菌毒素进行监管,以限制受污染和有害商品的交易。然而,所谓的新兴真菌毒素知之甚少,需要进一步研究。镰刀酸是一种新兴的霉菌毒素,对植物和动物有害,但已知羟基化时对植物的毒性较小。对动物有效的解毒途径尚未阐明。在这种情况下,这项研究整合了计算机和体外技术,以发现潜在的生物修复途径,将镰刀酸转化为毒性较小的代谢物。这些形式在人类中的毒理学也已得到解决。计算机筛选过程,其次是分子对接和动力学研究,从细菌沼泽红假单胞菌HaA2中鉴定出CYP199A4是一种潜在的镰刀酸生物转化酶。在体外证实了其活性。然而,羟基化的作用似乎对模拟的针对人类靶标的毒性动力学影响有限.这项研究代表了开发一种混合的硅/体外管道的起点,以寻找其他食品的生物修复剂,饲料和环境污染物。
    Mycotoxins are known environmental pollutants that may contaminate food and feed chains. Some mycotoxins are regulated in many countries to limit the trading of contaminated and harmful commodities. However, the so-called emerging mycotoxins are poorly understood and need to be investigated further. Fusaric acid is an emerging mycotoxin, noxious to plants and animals, but is known to be less toxic to plants when hydroxylated. The detoxification routes effective in animals have not been elucidated yet. In this context, this study integrated in silico and in vitro techniques to discover potential bioremediation routes to turn fusaric acid to its less toxic metabolites. The toxicodynamics of these forms in humans have also been addressed. An in silico screening process, followed by molecular docking and dynamics studies, identified CYP199A4 from the bacterium Rhodopseudomonas palustris HaA2 as a potential fusaric acid biotransforming enzyme. Its activity was confirmed in vitro. However, the effect of hydroxylation seemed to have a limited impact on the modelled toxicodynamics against human targets. This study represents a starting point to develop a hybrid in silico/in vitro pipeline to find bioremediation agents for other food, feed and environmental contaminants.
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  • 文章类型: Journal Article
    合成了两个三核氧氧为中心的单烯酸和盐霉素(HL)的铁(III)配位化合物,并使用物理化学/热方法研究了其光谱性质(FT-IR,TG-DTA,TG-MS,EPR,穆斯堡尔谱学,粉末XRD)和元素分析。数据表明[Fe3(µ3-O)L3(OH)4]的形成,并且使用DFT方法对可能的复杂结构进行了建模。将优化的构建体的计算光谱参数与实验测量的光谱参数进行比较。在每个复合体中,三个金属中心在轴向位置通过μ3-O单元连接在一起以形成{Fe3O}7+芯。抗生素单阴离子通过位于末端的羧酸根和羟基充当二齿配体。羧酸盐部分起到桥接每两个金属中心的双重作用。氢氧阴离子确保了配位物种的整体中性特性。Mössbauer光谱显示出不对称的四极双峰,这与具有不同环境的两种类型的高自旋铁(III)位点的存在一致-两个Fe[O5]和一个Fe[O6]中心。固态EPR研究证实了铁的3氧化态,每个三核簇的总自旋St=5/2。所研究的络合物是迄今为止报道的莫能菌素和盐霉素的第一个铁(III)配位化合物。
    Two trinuclear oxo-centred iron(III) coordination compounds of monensic and salinomycinic acids (HL) were synthesized and their spectral properties were studied using physicochemical/thermal methods (FT-IR, TG-DTA, TG-MS, EPR, Mössbauer spectroscopy, powder XRD) and elemental analysis. The data suggested the formation of [Fe3(µ3-O)L3(OH)4] and the probable complex structures were modelled using the DFT method. The computed spectral parameters of the optimized constructs were compared to the experimentally measured ones. In each complex, three metal centres were joined together at the axial position by a μ3-O unit to form a {Fe3O}7+ core. The antibiotics monoanions served as bidentate ligands through the carboxylate and hydroxyl groups located at the termini. The carboxylate moieties played a dual role bridging each two metal centres. Hydroxide anions secured the overall neutral character of the coordination species. Mössbauer spectra displayed asymmetric quadrupole doublets that were consistent with the existence of two types of high-spin iron(III) sites with different environments-two Fe[O5] and one Fe[O6] centres. The solid-state EPR studies confirmed the +3 oxidation state of iron with a total spin St = 5/2 per trinuclear cluster. The studied complexes are the first iron(III) coordination compounds of monensin and salinomycin reported so far.
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  • 文章类型: Journal Article
    玉米赤霉烯酮是由镰刀菌真菌污染谷物和谷物产品产生的一种雌激素,由于其内分泌干扰作用而威胁人类和动物的健康。德国的行动机制,玉米赤霉烯酮可以激活雌激素受体并抑制雌激素产生酶芳香化酶(CYP19A1)。两者均显示人类中的单核苷酸变体(SNV)与被激活或抑制的不同易感性相关。这些变化可能会改变玉米赤霉烯酮的内分泌干扰作用,需要专门的研究,以提高其毒理学的理解。这项工作集中在通过3D分子建模研究人类芳香化酶,迄今为止报道的某些变体(n=434)是否会影响玉米赤霉烯酮的抑制潜力。还计算了α-玉米赤霉烯醇的抑制能力,玉米赤霉烯酮的最突出和雌激素有效的I相代谢产物,针对那些预期被ZEN抑制的不同敏感性的芳香化酶变体。该研究:i)描述了SNV可能与玉米赤霉烯酮和α-玉米赤霉烯醇抑制的不同易感性相关-像T310S一样,可能更容易受到抑制,或D309G和S478F可能是无活性的变体;ii)证明可能存在个体间对玉米赤霉烯酮的易感性;iii)优先考虑芳香化酶变体,以便将来在个体水平上更好地理解ZEN异种雌激素性。
    Zearalenone (ZEN) is a mycoestrogen produced by Fusarium fungi contaminating cereals and in grain-based products threatening human and animal health due to its endocrine disrupting effects. Germane to the mechanisms of action, ZEN may activate the estrogen receptors and inhibit the estrogens-producing enzyme aromatase (CYP19A1). Both show single nucleotide variants (SNVs) among humans associated with a diverse susceptibility of being activated or inhibited. These variations might modify the endocrine disrupting action of ZEN, requiring dedicated studies to improve its toxicological understanding. This work focused on human aromatase investigating via 3D molecular modelling whether some of the SNVs reported so far (n = 434) may affect the inhibitory potential of ZEN. It has been also calculated the inhibition capability of α-zearalenol, the most prominent and estrogenically potent phase I metabolite of ZEN, toward those aromatase variants with an expected diverse sensitivity of being inhibited by ZEN. The study: i) described SNVs likely associated with a different susceptibility to ZEN and α-zearalenol inhibition - like T310S that is likely more susceptible to inhibition, or D309G and S478F that are possibly inactive variants; ii) proofed the possible existence of inter-individual susceptibility to ZEN; iii) prioritized aromatase variants for future investigations toward a better comprehension of ZEN xenoestrogenicity at an individual level.
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  • 文章类型: Journal Article
    背景:药物发现的常规过程过于昂贵,耗时且成功率有限。寻找具有明显安全性和潜在功效的替代品可以节省资金,时间和改善目前的治疗方案结果。
    方法:临床植物疗法意味着使用天然来源的提取物进行预防,治疗,或人类疾病的管理。在这项工作中,已经探讨了常见无花果(无花果)在COVID-19感染管理中的潜在作用。在常见图中丰富的花青素-3-鼠李糖苷的抗病毒作用已经在COVID-19靶标上得到了说明。免疫调节作用和改善与冠状病毒感染相关的细胞因子风暴的能力也已被强调。这项工作涉及各种计算研究,以调查普通无花果在COVID-19病毒感染管理中的潜在作用。
    结果:从MOE开始,对普通无花果中的所有活性成分进行了两项分子对接研究,以提供初步见解,其次是AutodockVina,以进一步确认具有最佳对接得分的前五名化合物的结果。
    结论:最后,使用GROMACS进行分子动力学模拟和MMPBSA计算以认可和验证整个工作。
    BACKGROUND: The conventional processes of drug discovery are too expensive, timeconsuming and the success rate is limited. Searching for alternatives that have evident safety and potential efficacy could save money, time and improve the current therapeutic regimen outcomes.
    METHODS: Clinical phytotherapy implies the use of extracts of natural origin for prophylaxis, treatment, or management of human disorders. In this work, the potential role of common Fig (Ficus carica) in the management of COVID-19 infections has been explored. The antiviral effects of Cyanidin 3-rhamnoglucoside which is abundant in common Figs have been illustrated on COVID-19 targets. The immunomodulatory effect and the ability to ameliorate the cytokine storm associated with coronavirus infections have also been highlighted. This work involves various computational studies to investigate the potential roles of common figs in the management of COVID-19 viral infections.
    RESULTS: Two molecular docking studies of all active ingredients in common Figs were conducted starting with MOE to provide initial insights, followed by Autodock Vina for further confirmation of the results of the top five compounds with the best docking score.
    CONCLUSIONS: Finally, Molecular dynamic simulation alongside MMPBSA calculations were conducted using GROMACS to endorse and validate the entire work.
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  • 文章类型: Journal Article
    金丝雀乙酸乙酯和甲醇提取物的植物化学分析。叶子导致八种(1-8)已知分子的分离,其中七(2-8)首次从该物种中分离出来,其中包括(+)-氧化淋胺(2),goniodiol-7-单乙酸酯(3),goniodiol-8-单乙酸酯(4),goniodiol(5),(+)-8-epi-9-脱氧吡喃酮(6)等..通过3和4的乙酰化进行的植物化学修饰得到了具有绝对构型(6R,7R,8R)经单晶X射线衍射证实。化合物3-9对乳腺有细胞毒性,卵巢,前列腺癌和结肠癌细胞系,IC50<10μM。使用gonioidol-7-单乙酸盐(3)对MDA-MB-231细胞的细胞周期分析和膜联蛋白-V测定表现出凋亡反应以及坏死反应,并显示在G2/M期的细胞增殖停滞。通过共价对接用α-微管蛋白靶标进行这些分子的计算机靶标鉴定。为了深入了解并确定这些蛋白质-配体复合物在热力学能级上的稳定性,基于通过DFT研究的反应能量分析,对与α-微管蛋白的Cys-316结合的分离分子进行进一步评估,该研究提示分离分子可能是类似于Pironetin的α-微管蛋白抑制剂。分子动力学重申了这些观察结果。
    The phytochemical analysis of ethyl acetate and methanol extract of Goniothalamus wynaadensis Bedd. leaves led to an isolation of eight (1-8) known molecules, among them seven (2-8) isolated for the first time from this species, which includes (+)-goniothalamin oxide (2), goniodiol-7-monoacetate (3), goniodiol-8-monoacetate (4), goniodiol (5), (+)-8-epi-9-deoxygoniopypyrone (6) etc. The phytochemical modification by acetylation of 3 and 4 gave goniodiol diacetate (9) with absolute configuration (6R, 7R, 8R) confirmed by single crystal X-ray diffraction. Compounds 3-9 were cytotoxic against breast, ovarian, prostate and colon cancer cell lines with IC50 <10 μM. Cell cycle analysis and Annexin-V assay on MDA-MB-231 cell using goniodiol-7-monoacetate (3) exhibited apoptotic response as well as necrotic response and showed cell proliferation arrest at G2/M phase. An in silico target identification for these molecules was carried out with an α-tubulin protein target by covalent docking. To gain an in-depth understanding and identify the stability of these protein-ligand complexes on thermodynamic energy levels, further assessment of the isolated molecules binding to the Cys-316 of α-tubulin was performed based on reaction energetic analysis via DFT studies which hinted the isolated molecules may be α-tubulin inhibitors similar to Pironetin. Molecular dynamics reiterated the observations.
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  • 文章类型: Journal Article
    抗病毒剂的直接结合;达拉他韦和伐昔洛韦和绿色合成的纳米颗粒鲑鱼精子DNA已在比较研究中进行了评估。纳米颗粒是通过水热高压釜方法合成的,并且已经过充分的表征。除了热力学性质外,还通过紫外可见光谱法深入研究了分析物与DNA的相互作用行为和竞争结合。在生理pH条件下监测daclatasvir的结合常数为1.65×106、4.92×105和3.12×105,伐昔洛韦和量子点,分别。所有分析物的光谱特征的显著变化已经证明了嵌入结合。竞争性研究证实,daclatasvir,伐昔洛韦,并且量子点表现出沟槽结合。所有分析物均显示出良好的熵值和焓值,表明稳定的相互作用。通过研究不同浓度KCl溶液中的结合相互作用,确定了静电和非静电动力学参数。已应用分子建模研究来证明结合相互作用及其机制。获得的结果是互补的,并为治疗应用提供了新的时代。
    The direct binding of antiviral agents; Daclatasvir and valacyclovir and green synthesized nanoparticles to salmon sperm DNA have been assessed in a comparative study. The nanoparticles were synthesized by the hydrothermal autoclave method and have been fully characterized. The interactive behavior and competitive binding of the analytes to DNA in addition to the thermodynamic properties were deeply investigated by the UV-visible spectroscopy. The binding constants were monitored in the physiological pH conditions to be 1.65 × 106, 4.92 × 105 and 3.12 × 105 for daclatasvir,valacyclovir and quantum dots, respectively. The significant changes in the spectral features of all analytes have proven intercalative binding. The competitive study has confirmed that, daclatasvir, valacyclovir, and the quantum dots have exhibited groove binding. All analytes have shown good entropy and enthalpy values indicating stable interactions. The electrostatic and non-electrostatic kinetic parameters have been determined through studying the binding interactions at different concentrations of KCl solutions. A molecular modelling study has been applied to demonstrate the binding interactions and their mechanisms. The obtained results were complementary and afforded new eras for the therapeutic applications.
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  • 文章类型: Journal Article
    乳腺癌是主要的癌症类型,在2020年超过220万例,是女性死亡的主要原因;2020年全球有68.5万人死亡。雌激素受体至少参与70%的乳腺癌诊断,这种受体中药物的激动剂和拮抗剂特性在控制这种疾病中起着关键作用。这项工作通过采用分子对接和动态模拟评估了30大麻素的激动剂和拮抗剂机制。对接分数<-8kcal/mol的化合物在300ns时通过分子动力学模拟进行分析,并给出了有关蛋白质结构变化的相关见解,以α-螺旋H3、H8、H11和H12的螺旋度为中心。大麻是呈现最佳相对无结合能(-34.96kcal/mol)的大麻素,基于合理的修改,我们发现了一种新的基于天然物质的化合物,其相对无结合能(-44.83kcal/mol)优于对照羟基他莫昔芬和安康芬。提出了可以增加生物活性的结构修饰。
    Breast cancer is the main cancer type with more than 2.2 million cases in 2020, and is the principal cause of death in women; with 685000 deaths in 2020 worldwide. The estrogen receptor is involved at least in 70% of breast cancer diagnoses, and the agonist and antagonist properties of the drug in this receptor play a pivotal role in the control of this illness. This work evaluated the agonist and antagonist mechanisms of 30 cannabinoids by employing molecular docking and dynamic simulations. Compounds with docking scores < -8 kcal/mol were analyzed by molecular dynamic simulation at 300 ns, and relevant insights are given about the protein\'s structural changes, centered on the helicity in alpha-helices H3, H8, H11, and H12. Cannabicitran was the cannabinoid that presented the best relative binding-free energy (-34.96 kcal/mol), and based on rational modification, we found a new natural-based compound with relative binding-free energy (-44.83 kcal/mol) better than the controls hydroxytamoxifen and acolbifen. Structure modifications that could increase biological activity are suggested.
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  • 文章类型: Journal Article
    Kokumi是一种重要的味觉感知,其化学基础仍需要澄清,因此需要开发高通量分析工具。钙敏感受体(CaSR)的激活被描述为kokumi感知的基础,从而可以使用分子建模来加深其化学原理和相关机制。本研究集中于γ-谷氨酰三肽,通过计算提供有关其CaSR激活特性的机械见解,并扩展了对其结构-活动关系的理解。还筛选了400个γ-谷氨酰三肽的文库。基于它们有前途的CaSR激活潜力,确定了γ-Glu-Pro-Ala和γ-Glu-Pro-Ser进行进一步的专门研究,应在食品基质中相应检查它们的存在,以更好地描述kokumi指纹。这项工作为自顶向下分析kokumi活性分子提供了有意义的工具,该工具可以支持隐藏在食品中的kokumi分子的鉴定或从头合理设计kokumi活性分子。
    Kokumi is an important taste perception whose chemical basis still needs clarifications and for which the development of high-throughput tools of analysis is desirable. The activation of Calcium-sensing receptor (CaSR) was described as the basis of kokumi perception allowing the use of molecular modelling to deepen its chemical rationale and related mechanisms. This study focused on γ-Glutamyl tripeptides, computationally providing mechanistic insights on their CaSR-activating properties and extended the comprehension of their structure-activity relationship. A library of 400 γ-Glutamyl tripeptides was also screened. γ-Glu-Pro-Ala and γ-Glu-Pro-Ser were identified for further dedicated investigations based on their promising CaSR-activating potential and their presence should be checked accordingly in food matrices to better profile the kokumi fingerprint. This work provided a meaningful tool for the top-down analysis of kokumi-active molecules that may support either the identification of kokumi molecules concealed in food or the rational design of kokumi-active molecules de novo.
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  • 文章类型: Journal Article
    急性心力衰竭(AHF)是老年最常见的疾病之一,可导致死亡。全身性低灌注与肝脏缺血再灌注损伤有关,这可能是不可逆转的。由AHF引起的缺血性肝炎与肝损伤的发病机理有关。在本研究中,我们广泛研究了线粒体动力学相关蛋白及其表观遗传调控在急性心力衰竭后缺血性肝损伤中的作用,并探讨了卡维地洛可能的保肝作用.生化分析表明,AHF后的缺血性肝损伤显着升高丙氨酸转氨酶(ALT)的活性,天冬氨酸转氨酶(AST),和碱性磷酸酶(ALP)酶,总胆红素和直接胆红素的水平,和肝有丝分裂原活化蛋白激酶(MAPK)的表达,dynamin-1-likeprotein(DNM1L),和肝脏miRNA-17。同时,它显著降低了血清白蛋白水平,肝超氧化物歧化酶(SOD)的活性,线粒体过氧化物酶体增殖物激活受体-1α(PGC-1α)的表达,和mitofusin2(Mtf2)。肝组织的组织学检查显示退化的肝细胞。有趣的是,在异丙肾上腺素诱导的AHF之前或之后施用卡维地洛显著改善了肝功能并逆转了AHF诱导的缺血性肝炎的恶化效应,正如生物化学所证明的那样,免疫组织化学,和组织学分析。我们的结果表明,卡维地洛在改善肝缺血损伤中的肝保护作用可归因于其靶向线粒体动力学相关蛋白(Mtf2,DNM1L和PGC-1α)的能力,以及它们的表观遗传调节子miRNA-17。为了进一步探索卡维地洛的作用模式,我们已经调查过了,在硅,卡维地洛靶向dynamin-1-like蛋白和线粒体动力学蛋白(MID51)的能力。我们的结果表明,卡维地洛对DNM1L蛋白的结合袋具有很高的结合亲和力(-14.83kcal/mol)。总之,我们的研究强调了卡维地洛在减轻与AHF相关的缺血性肝炎中的保肝药理应用。
    Acute heart failure (AHF) is one of the most common diseases in old age that can lead to mortality. Systemic hypoperfusion is associated with hepatic ischemia-reperfusion injury, which may be irreversible. Ischemic hepatitis due to AHF has been linked to the pathogenesis of liver damage. In the present study, we extensively investigated the role of mitochondrial dynamics-related proteins and their epigenetic regulation in ischemic liver injury following AHF and explored the possible hepatoprotective role of carvedilol. The biochemical analysis revealed that the ischemic liver injury following AHF significantly elevated the activity of alanine aminotransferase (ALT), aspartate aminotransferase (AST), and alkaline phosphatase (ALP) enzymes, the level of total and direct bilirubin, and the expression of hepatic mitogen-activated protein kinase (MAPK), dynamin-1-like protein (DNM1L), and hepatic miRNA-17. At the same time, it significantly reduced the serum albumin level, the activity of hepatic superoxide dismutase (SOD), and the expression of mitochondrial peroxisome proliferator-activated receptor-1α (PGC-1α), and mitofusin 2 (Mtf2). The histological examination of the liver tissue revealed degenerated hepatocytes. Interestingly, administration of carvedilol either prior to or after isoprenaline-induced AHF significantly improved the liver function and reversed the deterioration effect of AHF-induced ischemic hepatitis, as demonstrated by biochemical, immunohistochemical, and histological analysis. Our results indicated that the hepatoprotective effect of carvedilol in ameliorating hepatic ischemic damage could be attributed to its ability to target the mitochondrial dynamics-related proteins (Mtf2, DNM1L and PGC-1α), but also their epigenetic regulator miRNA-17. To further explore the mode of action of carvedilol, we have investigated, in silico, the ability of carvedilol to target dynamin-1-like protein and mitochondrial dynamics protein (MID51). Our results revealed that carvedilol has a high binding affinity (-14.83 kcal/mol) toward the binding pocket of DNM1L protein. In conclusion, our study highlights the hepatoprotective pharmacological application of carvedilol to attenuate ischemic hepatitis associated with AHF.
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