Molecular modelling

分子建模
  • 文章类型: Journal Article
    非甾体抗炎药(NSAIDs)过量对人体的毒性是其水溶性低的结果,高剂量,和人口容易进入。新的药物递送系统(DDS)对于克服与NSAID相关的生物利用度和毒性是必要的。在这种情况下,UiO-66(Zr)金属有机骨架(MOF)显示出高孔隙率,稳定性,和负载能力,因此是一个有前途的DDS。然而,几乎没有描述不同NSAIDs的吸附和释放能力。在这项工作中,生物相容性UiO-66(Zr)MOF用于研究布洛芬的吸附和释放条件,萘普生,和双氯芬酸使用理论和实验近似。DFT结果表明,MOF-药物相互作用是由于缺陷位点基团的质子之间的分子间氢键,(μ3-OH,和-OH2)和NSAID的一对孤对氧羧基官能团。此外,实验结果表明,溶解药物的溶剂会影响吸附过程。药物之间的吸附动力学相似,但每种药物的最大负载能力不同。释放动力学分析显示出溶剂依赖性动力学,其最大释放能力受药物与材料之间相互作用的影响。最后,生物试验表明,所研究的系统中没有一个对HMVEC具有细胞毒性。此外,伤口愈合试验表明UiO-66(Zr)材料在伤口愈合过程中具有潜在的应用。然而,应该做进一步的研究。
    The toxicity for the human body of non-steroidal anti-inflammatory drugs (NSAIDs) overdoses is a consequence of their low water solubility, high doses, and facile accessibility to the population. New drug delivery systems (DDS) are necessary to overcome the bioavailability and toxicity related to NSAIDs. In this context, UiO-66(Zr) metal-organic framework (MOF) shows high porosity, stability, and load capacity, thus being a promising DDS. However, the adsorption and release capability for different NSAIDs is scarcely described. In this work, the biocompatible UiO-66(Zr) MOF was used to study the adsorption and release conditions of ibuprofen, naproxen, and diclofenac using a theoretical and experimental approximation. DFT results showed that the MOF-drug interaction was due to an intermolecular hydrogen bond between protons of the groups in the defect sites, (μ3 - OH, and - OH2) and a lone pair of oxygen carboxyl functional group of the NSAIDs. Also, the experimental results suggest that the solvent where the drug is dissolved affects the adsorption process. The adsorption kinetics are similar between the drugs, but the maximum load capacity differs for each drug. The release kinetics assay showed a solvent dependence kinetics whose maximum liberation capacity is affected by the interaction between the drug and the material. Finally, the biological assays show that none of the systems studied are cytotoxic for HMVEC. Additionally, the wound healing assay suggests that the UiO-66(Zr) material has potential application on the wound healing process. However, further studies should be done.
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  • 文章类型: Journal Article
    结核分枝杆菌(MTB)的吡嗪酰胺(PZA)抗性菌株的兴起对常规结核病(TB)治疗提出了重大挑战。PZA,结核病治疗的基石,必须被分枝杆菌酶吡嗪酰胺酶(PZase)激活以转化其活性形式,吡嗪酸,靶向核糖体蛋白S1。阻力,通常与RpsA蛋白的突变有关,使治疗复杂化,并突出了在理解结构动力学和耐药机制方面的关键差距,特别是在G97D突变的背景下。这项研究利用了一种新颖的计算技术集成,包括多尺度生物分子和分子动力学模拟,物理化学和药物化学预测,来自ZINC和Chembridge数据库的量子计算和虚拟筛选,阐明耐药机制并确定有可能改善PZA耐药MTB治疗结果的先导化合物,即ZINC15113786、ZINC20735155、Chem10269711、Chem10279789和Chem10295790。这些计算方法提供了一种具有成本效益的,通过绕过对有机受试者的需求,同时提供对新候选药物的结合位点和功效的高度准确的见解,快速替代传统药物试验。需要快速和适当的药物开发强调需要强大的计算分析,以证明通过体外和体内实验进一步验证。
    The rise of pyrazinamide (PZA)-resistant strains of Mycobacterium tuberculosis (MTB) poses a major challenge to conventional tuberculosis (TB) treatments. PZA, a cornerstone of TB therapy, must be activated by the mycobacterial enzyme pyrazinamidase (PZase) to convert its active form, pyrazinoic acid, which targets the ribosomal protein S1. Resistance, often associated with mutations in the RpsA protein, complicates treatment and highlights a critical gap in the understanding of structural dynamics and mechanisms of resistance, particularly in the context of the G97D mutation. This study utilizes a novel integration of computational techniques, including multiscale biomolecular and molecular dynamics simulations, physicochemical and medicinal chemistry predictions, quantum computations and virtual screening from the ZINC and Chembridge databases, to elucidate the resistance mechanism and identify lead compounds that have the potential to improve treatment outcomes for PZA-resistant MTB, namely ZINC15913786, ZINC20735155, Chem10269711, Chem10279789 and Chem10295790. These computational methods offer a cost-effective, rapid alternative to traditional drug trials by bypassing the need for organic subjects while providing highly accurate insight into the binding sites and efficacy of new drug candidates. The need for rapid and appropriate drug development emphasizes the need for robust computational analysis to justify further validation through in vitro and in vivo experiments.
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  • 文章类型: Journal Article
    基于环糊精的金属有机骨架(CD-MOF)由于其优异的可食性和高的载药量而被广泛用于各种递送系统。然而,其通常庞大的尺寸和在水溶液中的高脆性对实际应用提出了重大挑战。这里,我们提出了一种超声辅助快速合成均匀尺寸纳米级CD-MOF的方法,然后通过酯键交联(Nano-CMOF)进行疏水改性。适当的超声处理有效地将颗粒尺寸减小到纳米级(393.14nm)。值得注意的是,碳酸酯交联法显著提高了水稳定性,而不改变其立方体形状和高孔隙率(1.3cm3/g),导致在各种介质中的保留率超过90%。此外,槲皮素的负载没有破坏立方结构,并显示出显着的储存稳定性。Nano-CMOF在水环境和消化中均可实现槲皮素的控制释放。此外,Nano-CMOF表现出优异的抗氧化剂(自由基清除82.27%)和生物相容性,表明其作为食品和生物医学领域新型营养输送系统的巨大潜力。
    Cyclodextrin-based metal-organic framework (CD-MOF) has been widely used in various delivery systems due to its excellent edibility and high drug loading capacity. However, its typically bulky size and high brittleness in aqueous solutions pose significant challenges for practical applications. Here, we proposed an ultrasonic-assisted method for rapid synthesis of uniformly-sized nanoscale CD-MOF, followed by its hydrophobic modification through ester bond cross-linking (Nano-CMOF). Proper ultrasound treatment effectively reduced particle size to nanoscale (393.14 nm). Notably, carbonate ester cross-linking method significantly improved water stability without altering its cubic shape and high porosity (1.3 cm3/g), resulting in a retention rate exceeding 90% in various media. Furthermore, the loading of quercetin did not disrupt cubic structure and showcased remarkable storage stability. Nano-CMOF achieved controlled release of quercetin in both aqueous environments and digestion. Additionally, Nano-CMOF demonstrated exceptional antioxidant (free radical scavenging 82.27%) and biocompatibility, indicating its significant potential as novel nutritional delivery systems in food and biomedical fields.
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  • 文章类型: Journal Article
    基于手性碳量子点(cCQDs)荧光探针的谷氨酰胺对映体手性鉴定新方法.以L-色氨酸为碳源,手性源,采用一步水热法制备cCQDs,产生呈现蓝色发光的球形纳米颗粒。添加手性对映体谷氨酰胺(L/D-Gln)后,cCQDs的荧光强度(F)增强或猝灭,因此,cCQDs,作为荧光探针,可用于L/D-Gln的对映选择性传感。荧光增强值(ΔFE)与L-Gln浓度在0.23-10.00mM范围内表现出良好的线性,检测限为0.14mM。荧光猝灭值(ΔFQ)在0.29-10.00mM范围内与D-Gln浓度呈良好的线性关系,检出限为0.18mM。通过分子模型和猝灭类型探索了荧光增强/猝灭的机理。该方法用于实际样品中L-Gln含量的测定。回收率令人满意。本研究为cCQDs的合成和氨基酸对映体的识别提供了新的途径。
    A novel method for chiral identification of glutamine enantiomers based on chiral carbon quantum dots (cCQDs) fluorescent probes. cCQDs were prepared using a one-step hydrothermal method with L-tryptophan as the carbon source and chiral source, producing spherical nanoparticles exhibiting a blue colour luminescence. The fluorescence intensity (F) of cCQDs was enhanced or quenched following the addition of chiral enantiomeric glutamine (L/D-Gln), and therefore cCQDs, as a fluorescence probe, could be used for enantioselective sensing of the L/D-Gln. The fluorescence enhancement value (∆FE ) exhibited good linearity with L-Gln concentration in the range 0.23-10.00 mM, and the limit of detection was 0.14 mM. The fluorescence quenching value (∆FQ ) showed a good linear relationship with D-Gln concentration in the range 0.29-10.00 mM, and the detection limit was 0.18 mM. The mechanism of fluorescence enhancement/quenching was explored by molecular modelling and the type of quenching. The method was applied to the determination of L-Gln content in real samples, and the recovery rate was satisfactory. This study provided a novel approach for the synthesis of cCQDs and the recognition of amino acid enantiomers.
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  • 文章类型: Journal Article
    描述了一种创新的通用印迹传感器设计,用于夹心式检测人血清样品中吉西他滨(GMT)。GMT广泛应用于不同肿瘤的治疗,比如肺,卵巢,胰腺,和乳腺癌。血清白蛋白-药物相互作用被转化为设计一种多功能的,基于比率和双模银纳米粒子的探针(BSA-Ag纳米探针),作为一个读出系统。随后,设计了聚吡咯印迹药物受体位点以选择性捕获换能器表面的GMT。将GMT夹在印迹受体表面和BSA-Ag纳米探针之间以产生光谱电化学信号。通过各种表征技术证实了纳米探针的形成,包括X射线衍射(XRD),傅里叶变换红外(FTIR)光谱,显微拉曼光谱,动态光散射(DLS),和紫外可见(UV-Vis)分析,而传感器制造的每个步骤都是通过场发射扫描电子显微镜(FE-SEM)表征的,静态水接触角测量,循环伏安法(CV),和电化学阻抗谱(EIS)。优化了不同的可变参数,以提高传感器设计的分析性能。在最优条件下,光谱电化学传感器允许线性范围在1至200μmolL-1和0.5-200μmolL-1之间,检测限(LOD)分别为0.4μmolL-1和0.15μmolL-1。此外,设计的传感器成功地区分了肺癌患者和健康志愿者的血清样本。所获得的结果通过对患者和健康志愿者血清样品的标准液相色谱-质谱(LC/MS)分析进行验证。最后,密度泛函理论(DFT)和分子对接计算揭示了分子印迹聚吡咯的GMT结合能力增强,来验证三明治传感器的设计。
    An innovative and universal imprinted sensor design for sandwich type detection of gemcitabine (GMT) in human serum samples is described. GMT is widely used in the treatment of different tumors, such as lung, ovarian, pancreatic, and breast cancer. The serum albumin-drug interaction was translated to design a multifunctional, ratiometric and dual mode silver nanoparticle based probe (BSA-Ag nanoprobe), as a read out system. Subsequently, polypyrrol imprinted drug receptor sites was engineered to selectively capture the GMT on the transducer surface. The GMT was sandwiched between imprinted receptor surface and BSA-Ag nanoprobe to generate the spectro-electrochemical signals. The formation of nanoprobe was confirmed through various characterization techniques, including X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, micro-Raman spectroscopy, Dynamic light scattering (DLS), and UV-Visible (UV-Vis) analysis, while each step of sensor fabrication was characterized via field emission scanning electron microscope (FE-SEM), Static water Contact angle measurements, cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS). Different variable parameters were optimized to improve the analytical performance of the sensor design. Under optimal conditions, spectro-electrochemical sensor permitted linear ranges between 1 and 200 μmol L-1 and 0.5-200 μmol L-1, with limits of detection (LOD) of 0.4 μmol L-1 and 0.15 μmol L-1 respectively. Furthermore, the designed sensor successfully differentiated the serum samples of lung cancer patients and healthy volunteers. The obtained results were validated with standard Liquid chromatography-mass spectrometry (LC/MS) analysis of the patients and healthy volunteer\'s serum samples. Lastly, density functional theory (DFT) and molecular docking calculations revealed the enhanced GMT binding capability of molecularly imprinted polypyrrole and molecular level interaction between the GMT and BSA, to validate the sandwich sensor design.
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  • 文章类型: Journal Article
    具有非对称通道几何结构和/或电荷布局的离子二极管在离子传输操纵和反向电渗析(RED)能量收集方面表现出出色的性能,但是工作机制仍然模糊。在这里,通过耦合Poisson-Nernst-Planck和Navier-Strokes方程,我们系统地研究了基于直型纳米通道的双极离子二极管的RED能量转换。纳米通道结构的影响,充电极性,研究了工作流体对输出电压和输出功率的对称性以及特性。结果表明,当采用高浓度补料液时,与单极通道RED系统相比,基于双极离子二极管的RED系统具有更高的输出电压和输出功率。在最优条件下,双极通道的电压输出增加了100%,功率输出增加了260%。这项工作为高性能盐度能量采集器的设计和优化以及海水淡化开辟了一条新途径。
    Ionic diodes constructed with asymmetric channel geometry and/or charge layout have shown outstanding performance in ion transport manipulation and reverse electrodialysis (RED) energy collection, but the working mechanism is still indistinct. Herein, we systematically investigated RED energy conversion of straight nanochannel-based bipolar ionic diode by coupling the Poisson-Nernst-Planck and Navier-Strokes equations. The effects of nanochannel structure, charging polarity, and symmetricity as well as properties of working fluids on the output voltage and output power were investigated. The results show that as high-concentration feeding solution is applied, the bipolar ionic diode-based RED system gives higher output voltage and output power compared to the unipolar channel RED system. Under optimal conditions, the voltage output of the bipolar channel is increased by ∼100% and the power output is increased by ∼260%. This work opens a new route for the design and optimization of high-performance salinity energy harvester as well as for water desalination.
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  • 文章类型: Journal Article
    患者来源的肿瘤类器官(PDTOs)有可能用于预测患者对化疗的反应。然而,PDTO药物敏感性的半数最大抑制浓度(IC50)的截断值尚未在临床队列数据中得到验证.我们建立了PDTOs,并对242例接受FOLFOX或XELOX化疗的CRC患者的277个样本进行了药物测试。在随访和比较PDTO药物测试和最终临床结果后,PDTO药物敏感性的最佳IC50截断值为43.26μmol/L。这个PDTO药物测试定义的截止值可以以75.36%的灵敏度预测患者的反应,74.68%的特异性,75%的准确度。此外,这个值区分了在生存获益方面存在显著差异的患者组.我们的研究首次定义了PDTO药物测试的IC50截止值,以有效区分具有化学敏感性或非敏感性的CRC患者并预测生存益处。
    Patient-derived tumor organoids (PDTOs) have the potential to be used to predict the patient response to chemotherapy. However, the cutoff value of the half-maximal inhibition concentration (IC50) for PDTO drug sensitivity has not been validated with clinical cohort data. We established PDTOs and performed a drug test in 277 samples from 242 CRC patients who received FOLFOX or XELOX chemotherapy. After follow-up and comparison of the PDTO drug test and final clinical outcome results, the optimal IC50 cutoff value for PDTO drug sensitivity was 43.26 μmol/L. This PDTO drug test-defined cutoff value could predict patient response with 75.36% sensitivity, 74.68% specificity, and 75% accuracy. Moreover, this value distinguished groups of patients with significant differences in survival benefit. Our study is the first to define the IC50 cutoff value for the PDTO drug test to effectively distinguish CRC patients with chemosensitivity or nonsensitivity and predict survival benefits.
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  • 文章类型: Journal Article
    设计,合成,描述了一系列新型的HIV-1蛋白酶抑制剂的生物学评估,这些抑制剂包含吡咯烷,具有多种接头作为P2配体和各种芳香族衍生物作为P2配体。许多抑制剂在酶和细胞测定中均显示出有效的功效,以及相对较低的细胞毒性。特别是,具有(R)-吡咯烷-3-甲酰胺P2配体和4-羟苯基P2配体的抑制剂34b表现出优异的酶抑制活性,IC50值为0.32nM。此外,图34b还表现出对野生型HIV-1和具有低微摩尔EC50值的耐药变体两者的强大抗病毒活性。此外,分子模型研究揭示了抑制剂34b与野生型和耐药性HIV-1蛋白酶的主链残基之间的广泛相互作用。这些结果表明利用吡咯烷衍生物作为P2配体的可行性,并为进一步设计和优化高效HIV-1蛋白酶抑制剂提供了有价值的信息。
    The design, synthesis, and biological evaluation of a novel series of HIV-1 protease inhibitors containing pyrrolidines with diverse linkers as the P2 ligands and various aromatic derivatives as the P2\' ligands were described. A number of inhibitors demonstrated potent efficacy in both enzyme and cellular assays, as well as relatively low cytotoxicity. In particular, inhibitor 34b with a (R)-pyrrolidine-3-carboxamide P2 ligand and a 4-hydroxyphenyl P2\' ligand displayed exceptional enzyme inhibitory activity with an IC50 value of 0.32 nM. Furthermore, 34b also exhibited robust antiviral activity against both wild-type HIV-1 and drug-resistant variant with low micromolar EC50 values. In addition, the molecular modelling studies revealed the extensive interactions between inhibitor 34b and the backbone residues of both wild-type and drug-resistant HIV-1 protease. These results suggested the feasibility of utilizing pyrrolidine derivatives as the P2 ligands and provided valuable information for further design and optimization of highly potent HIV-1 protease inhibitors.
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  • 文章类型: Journal Article
    这里,引入乙醇介导的方法来制造γ-环糊精基金属有机骨架(γ-CD-MOFs)作为表没食子儿茶素-3-没食子酸酯(EGCG)的微载体。通过调节乙醇气体扩散温度和乙醇液体进料速度,我们实现了结晶效率和晶体尺寸的控制没有额外的表面活性剂。在乙醇分两个阶段的顺序监管下,所获得的具有立方形状的γ-CD-MOFs表现出优异的结晶度,高表面积,和均匀的尺寸分布。通过氢键的相互作用,疏水相互作用和π堆叠,EGCG分子可以有效地存储在γ-CD-MOF的空腔和隧道内,具有334mgg-1的高负载能力。更重要的是,EGCG在框架内的结合不会瓦解γ-CD-MOFs独特的体心立方结构,反过来,可以提高EGCG的热稳定性和抗氧化活性。重要的是,所有食品级材料确保了γ-CD-MOFs在食品和生物医学应用中的高接受度和适用性。
    Here, an ethanol-mediated method was introduced to fabricate γ-cyclodextrin-based metal-organic frameworks (γ-CD-MOFs) as microcarriers for epigallocatechin-3-gallate (EGCG). Through adjusting ethanol gas diffusion temperature and ethanol liquid feed speed, we achieved control of crystallization efficiency and crystals size without extra surfactants. Under the sequential regulatory by ethanol in two phases, the obtained γ-CD-MOFs with cubic shape exhibited excellent crystallinity, high surface area, and uniform size distribution. Through the interplay of hydrogen bonding, hydrophobic interactions and π stacking, EGCG molecules could be stored efficiently within cavities and tunnels of the γ-CD-MOFs with high load capability of 334 mg g-1. More importantly, the incorporation of EGCG within frameworks wouldn\'t disintegrate the unique body-centered cubic structure of γ-CD-MOFs, in turn, would improve the thermostability and antioxidative activity of EGCG. Significantly, all food-grade materials ensured the γ-CD-MOFs high acceptance and applicability for food and biomedical applications.
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  • 文章类型: Journal Article
    持续的抗生素耐药性危机正在成为影响公共卫生的全球性问题。迫切需要设计针对病原细菌物种的新疗法。布鲁氏菌是布鲁氏菌病的病原体,主要影响绵羊和山羊,但也报道了一些牛的病例,水牛,牦牛和狗.受感染的动物也是人类感染的主要来源。开发更安全有效的布鲁氏菌病疫苗仍然是支持动物疾病控制和根除以及预防人类感染的优先事项。在这项研究中,我们使用计算方法设计了一种芯片多表位疫苗。使用减法蛋白质组学筛选病原体核心蛋白质组的良好疫苗候选物,反向疫苗学和免疫信息学工具。总的来说,10种蛋白质:过氧化氢酶;铁载体ABC转运蛋白底物结合蛋白;吡哆胺5-磷酸氧化酶;超氧化物歧化酶;肽基氨酰异构酶;超氧化物歧化酶家族蛋白;分离蛋白A;假设蛋白;结合蛋白依赖性转运系统内膜成分;和4-羟基-2-氧代庚二酸醛缩酶被选择用于表位预测。诱导细胞和抗体基础免疫反应,疫苗必须同时包含B和T细胞表位。接下来筛选表位的抗原性,过敏性和水溶性和可能的抗原性,不过敏,水溶性无毒9个表位入围多表位疫苗构建。设计的疫苗构建体包含274个氨基酸长的序列,具有28.14kDa的分子量和27.62的不稳定性指数。进一步评估疫苗构建体与免疫细胞受体的结合功效。对接结果表明,设计的疫苗与选定的免疫细胞受体具有良好的结合能力。此外,疫苗-MHC-I,基于-5.48kcal/mol的最小结合能评分选择疫苗-MHC-II和疫苗-TLR-4复合物,0.64kcal/mol和-2.69kcal/mol。然后对选定的对象进行能量精炼,并进行模拟研究,以了解对接复合体的动态运动。通过MMPBSA和MMGBSA分析进一步验证对接结果。MMPBSA计算的-235.18kcal/mol,-206.79千卡/摩尔,和-215.73kcal/mol净结合自由能,而MMGBSA估计为-259.48千卡/摩尔,-206.79kcal/mol和-215.73kcal/mol对于TLR-4,MHC-I和MHC-II复合物,分别。这些发现通过水交换和熵计算得到了验证。总的来说,设计的疫苗构建体可以引起适当的免疫反应,该构建体可能有助于实验研究人员配制针对动物和人类使用的目标病原体的保护性疫苗。
    The ongoing antibiotic-resistance crisis is becoming a global problem affecting public health. Urgent efforts are required to design novel therapeutics against pathogenic bacterial species. Brucella melitensis is an etiological agent of brucellosis, which mostly affects sheep and goats but several cases have also been reported in cattle, water buffalo, yaks and dogs. Infected animals also represent the major source of infection for humans. Development of safer and effective vaccines for brucellosis remains a priority to support disease control and eradication in animals and to prevent infection to humans. In this research study, we designed an in-silico multi-epitopes vaccine for B. melitensis using computational approaches. The pathogen core proteome was screened for good vaccine candidates using subtractive proteomics, reverse vaccinology and immunoinformatic tools. In total, 10 proteins: catalase; siderophore ABC transporter substrate-binding protein; pyridoxamine 5\'-phosphate oxidase; superoxide dismutase; peptidylprolyl isomerase; superoxide dismutase family protein; septation protein A; hypothetical protein; binding-protein-dependent transport systems inner membrane component; and 4-hydroxy-2-oxoheptanedioate aldolase were selected for epitopes prediction. To induce cellular and antibody base immune responses, the vaccine must comprise both B and T-cells epitopes. The epitopes were next screened for antigenicity, allergic nature and water solubility and the probable antigenic, non-allergic, water-soluble and non-toxic nine epitopes were shortlisted for multi-epitopes vaccine construction. The designed vaccine construct comprises 274 amino acid long sequences having a molecular weight of 28.14 kDa and instability index of 27.62. The vaccine construct was further assessed for binding efficacy with immune cell receptors. Docking results revealed that the designed vaccine had good binding potency with selected immune cell receptors. Furthermore, vaccine-MHC-I, vaccine-MHC-II and vaccine-TLR-4 complexes were opted based on a least-binding energy score of -5.48 kcal/mol, 0.64 kcal/mol and -2.69 kcal/mol. Those selected were then energy refined and subjected to simulation studies to understand dynamic movements of the docked complexes. The docking results were further validated through MMPBSA and MMGBSA analyses. The MMPBSA calculated -235.18 kcal/mol, -206.79 kcal/mol, and -215.73 kcal/mol net binding free energy, while MMGBSA estimated -259.48 kcal/mol, -206.79 kcal/mol and -215.73 kcal/mol for TLR-4, MHC-I and MHC-II complexes, respectively. These findings were validated by water-swap and entropy calculations. Overall, the designed vaccine construct can evoke proper immune responses and the construct could be helpful for experimental researchers in formulation of a protective vaccine against the targeted pathogen for both animal and human use.
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