Advancing Aptamers as Molecular Probes for Cancer Theranostic Applications—The Role of Molecular Dynamics Simulation

Theranostics cover emerging technologies for cell biomarking for disease diagnosis and targeted introduction of drug ingredients to specific malignant sites. Theranostics development has become a significant biomedical research endeavor for effective diagnosis and treatment of diseases, especially cancer. An efficient biomarking and targeted delivery strategy for theranostic applications requires effective molecular coupling of binding ligands with high affinities to specific receptors on the cancer cell surface. Bioaffinity offers a unique mechanism to bind specific target and receptor molecules from a range of non‐targets. The binding efficacy depends on the specificity of the affinity ligand toward the target molecule even at low concentrations. Aptamers are fragments of genetic materials, peptides, or oligonucleotides which possess enhanced specificity in targeting desired cell surface receptor molecules. Aptamer–target binding results from several inter‐molecular interactions including hydrogen bond formation, aromatic stacking of flat moieties, hydrophobic interaction, electrostatic, and van der Waals interactions. Advancements in Systematic Evolution of Ligands by Exponential Enrichment (SELEX) assay has created the opportunity to artificially generate aptamers that specifically bind to desired cancer and tumor surface receptors with high affinities. This article discusses the potential application of molecular dynamics (MD) simulation to advance aptamer‐mediated receptor targeting in targeted cancer therapy. MD simulation offers real‐time analysis of the molecular drivers of the aptamer‐receptor binding and generate optimal receptor binding conditions for theranostic applications. The article also provides an overview of different cancer types with focus on receptor biomarking and targeted treatment approaches, conventional molecular probes, and aptamers that have been explored for cancer cells targeting.     

定点突变提高解淀粉芽孢杆菌JP-21脲酶应用特性

氨基甲酸乙酯(Ethylcarbamate,EC)是一种存在于发酵食品和酒精饮料中的可致癌物,过量摄入可能会影响人体健康。酶法降解是减少发酵食品中氨基甲酸乙酯及其前体尿素含量的有效方法之一。脲酶具有氨基甲酸乙酯水解酶和尿素酶两种活性,因此在减少发酵食品中氨基甲酸乙酯及其前体尿素方面具有良好的应用前景。目前脲酶降解发酵酒精饮料中氨基甲酸乙酯面临的主要问题是脲酶对氨基甲酸乙酯的催化活性及亲和力较低,因而其降解效果不理想。文中成功在大肠杆菌Escherichia coli中表达了来源于解淀粉芽孢杆菌Bacillus amyloliquefaciens JP-21的脲酶,表达水平为尿素酶3 291.74 U/L,氨基甲酸乙酯水解酶227.26 U/L。通过模拟脲酶中催化亚基UreC与氨基甲酸乙酯对接的结构,确定了M326和M374这两个影响酶与底物结合的位点。采用点饱和突变获得了3株氨基甲酸乙酯水解酶活性提高的突变体M374A、M374T和M326V,以EC为底物时的Km分别为101.84mmol/L、129.49 mmol/L和121.67 mmol/L,比野生型分别降低了37.47%–50.82%。突变体可以降解黄酒中97%的尿素,M374T对黄酒中EC的降解效果最好,可将黄酒中EC从513.90μg/L降至393.57μg/L,降解率是野生脲酶的1.97倍。研究结果对今后改造脲酶催化特性和改善其应用特性具有重要意义,可为开发减控发酵食品中的微生物代谢氨(胺)类危害物策略提供参考。     

Thiophene bioisosteres of GluN2B selective NMDA receptor antagonists: Synthesis and pharmacological evaluation of [7]annuleno[b]thiophen-6-amines

Thiophene bioisosteres of potent GluN2B receptor negative allosteric modulators were prepared and evaluated pharmacologically. The five-step synthesis of 4,5,7,8-tetrahydro[7]annuleno[b]thiophen-6-one (10) was considerably improved by carboxylation of thiophene-3-carboxylic acid (8) in the first reaction step. Reductive amination and alkylation led to three homologous series of secondary and tertiary phenylalkylamines 5, 11 and 12. Metalation, reaction with 1-formylpiperidine and subsequent reduction provided hydroxymethyl derivatives 15 and 16, which had been designed as bioisosteres of phenols. 2-Bromo derivatives 18 were obtained by bromination of ketone 10 with NBS and subsequent reductive amination. High GluN2B affinity was achieved with [7]annuleno[b]thiophenes bearing a 3-phenylpropylamino or 4-phenylbutylamino moiety (e.g. 5c: K_i = 5.9 nM; 11d: K_i = 9.0 nM). Tertiary ethylamines 12 showed lower GluN2B affinity than tertiary methylamines 11 or secondary amines 5 (e.g. 5c: K_i = 5.9 nM; 11c: K_i = 6.0; 12c: K_i = 51 nM). A Br-atom or a hydroxymethyl moiety in 2-position were less tolerated by the GluN2B receptor. Very similar relationships between the structure and GluN2B affinity and structure and σ affinity, in particular σ₂ affinity, were detected. A slight preference for the ifenprodil binding site of GluN2B receptors over σ₁ and σ₂ receptors was found for methylamines 11c (≈2-fold) and 11d (≈1.5–2-fold) as well as for bromo derivative 18c (≈3-fold).     

黑芝麻多酚氧化酶的重组表达及其酶学特性

为明确黑芝麻多酚氧化酶的酶学性质,利用大肠杆菌Escherichia coli原核表达了黑芝麻多酚氧化酶 (Black sesame polyphenol oxidase,BsPPO)。将合成的基因构建至pMAL-c5x载体,并在大肠杆菌中进行表达,对重组蛋白进行分离纯化及融合标签切除,获得的BsPPO蛋白用于酶学性质探究。结果表明,合成的Bsppo基因1 752 bp,编码585个氨基酸,理论蛋白分子量为65.3 kDa;构建的pMAL-c5x-Bsppo重组质粒在大肠杆菌Escherichia coli BL21(DE3) 中可溶表达了MBP-BsPPO蛋白;酶切去除MBP融合标签后对BsPPO进行了酶学性质研究,结果表明BsPPO的最适温度和pH分别为25 ℃和4.0,在低温和弱酸性环境中有较好的稳定性。短时间低强度的光照和Cu2+可激活BsPPO的活性,Zn2+和Ca2+能抑制其活性。BsPPO可催化单酚、二酚以及三酚类化合物,对l-酪氨酸以及香草酸表现出较高的催化活性,此外BsPPO还对黑芝麻中含有的2-甲氧基肉桂酸、吲哚3-羧酸和根皮素表现出良好的催化活性。研究结果为黑芝麻多酚氧化酶酶学特性的明确奠定了理论基础。     

基于深度学习与多层次信息融合的药物靶标亲和力预测*

药物研发是非常重要但也十分耗费人力物力的过程。利用计算机辅助预测药物与蛋白质亲和力的方法可以极大地加快药物研发过程。药物靶标亲和力预测的关键在于对药物和蛋白质进行准确详细地信息表征。提出一种基于深度学习与多层次信息融合的药物靶标亲和力的预测模型,试图通过综合药物与蛋白质的多层次信息,来获得更好的预测表现。首先将药物表述成分子图和扩展连接指纹两种形式,分别利用图卷积神经网络模块和全连接层进行学习;其次将蛋白质序列和蛋白质K-mer特征分别输入卷积神经网络模块和全连接层来学习蛋白质潜在特征;随后将4个通道学习到的特征进行融合,再利用全连接层进行预测。在两个基准药物靶标亲和力数据集上验证了所提方法的有效性,并与其他已有模型作对比研究。结果说明提出的模型相比基准模型能得到更好的预测性能,表明提出的综合药物与蛋白质多层次信息的药物靶标亲和力预测策略是有效的。     

基于生物膜干涉技术检测PDL1抗体与PDL1抗原的亲和力

生物膜干涉（biolayer interferometry,BLI）技术可对抗体与抗原的相互作用进行亲和力、动力学的全面分析。在抗体克隆筛选、动力学常数测定中对链霉亲和素（streptavidin,SA）生物传感器的需求量较大,但目前鲜有关于SA传感器重复利用的报道。基于BLI技术、再生SA生物传感器建立一种使用再生后的传感器检测PDL1抗体与PDL1抗原亲和力的方法。通过将生物素化的PDL1抗原偶联至SA生物传感器上,再与单链抗体、双价单链抗体、完整抗体和双特异性抗体这4类PDL1抗体结合,计算抗原抗体的亲和力常数,利用甘氨酸（10 mmol·L^-1,pH 1.7）再生SA传感器,再次进行分子间相互作用力分析。结果显示,重复性相对标准偏差（relative standard deviation,RSD）均值为6.87%,批间重复性RSD为0.82%,稳定性RSD均值为6.13%,说明运用甘氨酸再生后的SA生物传感器测分子间的亲和力数据可靠、重现性好、稳定性高,再生后的传感器可继续用于本样品的实时、无标记的抗原抗体相互作用力分析。BLI技术可节省检测成本,为SA传感器的重复利用提供理论依据。     

Constitutive heat shock protein 70 interacts with α-enolase and protects cardiomyocytes against oxidative stress

Abstract

Constitutive heat shock protein 70 (Hsc70) is a molecular chaperone that has been shown to protect cardiomyocytes against oxidative stress. However, the molecular mechanism responsible for this protection remains uncertain. To understand the mechanism associated with the myocardial protective role of Hsc70, we have embarked upon a systematic search for Hsc70-interacting proteins. Using adenosine diphosphate (ADP) affinity chromatography and mass spectrometry, we have identified α-enolase, a rate-limiting enzyme in glycolysis, as a novel Hsc70-interacting protein in the myocardium of both sham and myocardial ischemia-reperfused Sprague–Dawley rat hearts. This interaction was confirmed by co-immunoprecipitation (IP) assays in the myocardial tissues and H9c2 cardiomyocytes and protein overlay assay (POA). It was further shown that Hsc70-overexpression alleviated the H₂O₂-induced decrease of α-enolase activity and cell damage, and Hsc70 deficiency aggravated the decrease of α-enolase activity and cell damage in H₂O₂ treated H9c2 cells. Our research suggests that the protective effect of Hsc70 on the cardiomyocytes against oxidative stress is partly associated with its interaction with α-enolase.     

Ratiometric Ca+2 measurement in human recombinant muscarinic receptor subtypes using the Flexstation scanning fluorometer

In modern drug discovery, numerous assay formats are available to screen and quantitate receptor-ligand interactions. Radioactive assays are “gold standard” because they are fast, easy, and reproducible; however, they are hazardous, produce radioactive waste, require special lab conditions, and are expensive on a large scale. Thus, it provides a lot of importance to the “mix & measure” assays that have an optical readout. Fluorescence techniques are likely to be among the most important detection approaches used for high throughput screening due to their high sensitivity and amenability to automation. The aim of the present study was to determine the functional antagonistic affinities of standard muscarinic antagonists in CHO cells over expressing m1, m3, and m5 receptors and to compare them with the respective binding affinities. This study was further extended to elucidate that Ca⁺² measurement assays can serve as a functional screening tool for GPCRs. For this purpose, standard muscarinic receptor antagonists, namely, tolterodine, oxybutynin, and atropine were used. We determined and compard the IC₅₀ values of these three standard inhibitors in fura 2 AM loaded m1, m3, and m5 overexpressing CHO cells and in radioligand binding assay. Both the assays exhibited comparable rank order potencies of the standard inhibitors. This study suggests that Ca⁺² mobilization assays can be an alternate to radioligand binding assays.     

OPTIMIZATION OF AFFINITY DIGESTION FOR THE ISOLATION OF CELLULOSOMES FROM Clostridium thermocellum

The affinity digestion process for cellulase purification consisting of binding to amorphous cellulose, and amorphous cellulose hydrolysis in the presence of dialysis (Morag et al., 1991), was optimized to obtain high activity recoveries and consistent protein recoveries in the isolation of Clostridium thermocellum cellulase. Experiments were conducted using crude supernatant prepared from C. thermocellum grown on either Avicel or cellobiose. While no difference was observed between Avicel-grown or cellobiose-grown cellulase in the adsorption step, differences were observed during the hydrolysis step. The optimal amorphous cellulose loading was found to be 3 mg amorphous cellulose per milligram supernatant protein. At this loading, 90–100% of activity in the crude supernatant was adsorbed. Twenty-four-hour incubation with the amorphous cellulose during the adsorption stage was found to result in maximal and stable adsorption of activity to the substrate. By fitting the adsorption data to the Langmuir model, an adsorption constant of 410 L/g and a binding capacity of 0.249 g cellulase/g cellulose were obtained. The optimal length of time for hydrolysis was found to be 3 hr for cellulase purified from Avicel cultures and 4 hr for cellulase purified from cellobiose cultures. These loadings and incubation times allowed for more than 85% activity recovery.     

Purification of carbonic anhydrase from dog erythrocytes and investigation of in vitro inhibition by various compounds

The enzyme carbonic anhydrase (E.C. 4.2.1.1) has a stimulatory effect on glaucoma, an eye disease that has a risk to dogs, which are models for the human eye disease, that is similar to that in humans.

In this study, some sulfonamide derivatives, 2-(3-cyclohexene-1-carbamido)-1,3,4-thiadiazole-5-sulfonamide (CCTS), 4-(3-cyclohexene-1-carbamido) methyl-benzenesulfonamide (CCBS), 2-(9-octadecenoylamido)-1,3,4-thiadiazole-5-sulfonamide (ODTS), 2-(4,7,10-trioxa-tetradecanoylamido)-1,3,4-thiadiazole-5-sulfonamide (TDTS), and 2-(8-methoxycoumarine-3-carbamido)-1,3,4-thiadiazole-5-sulfonamide (MCTS), as well as some anionic compounds (perchlorate and chloride) and existing medicines (dorzolamide-HCl, gentamicine sulphate, tropicamide, and procaine-HCl) were assayed for their inhibition of dog carbonic anhydrase (dCA), which was purified from erythrocytes on an affinity gel of L-tyrosine-sulfonamide-Sepharose 4B. ODTS showed the highest potency amongst the synthetic compounds with IC₅₀ value 1.18 × 10^{? 5} M. Amongst the medicines tested, only dorzolamide showed inhibition with IC₅₀ value 5.05 × 10^{? 4} M. Procaine and tropicamide actually showed an activatory effect, whereas gentamicine sulfate had no significant effect. The inhibitory effects of anionic compounds such as perchlorate and chloride were also investigated; whereas perchlorate showed inhibition, chloride did not.