Affinity Chromatography-Based Assays for the Screening of Potential Ligands Selective for G-Quadruplex Structures

DNA G-quadruplexes (G4s) are key structures for the development of targeted anticancer therapies. In this context, ligands selectively interacting with G4s can represent valuable anticancer drugs. Aiming at speeding up the identification of G4-targeting synthetic or natural compounds, we developed an affinity chromatography-based assay, named G-quadruplex on Oligo Affinity Support (G4-OAS), by synthesizing G4-forming sequences on commercially available polystyrene OAS. Then, due to unspecific binding of several hydrophobic ligands on nude OAS, we moved to Controlled Pore Glass (CPG). We thus conceived an ad hoc functionalized, universal support on which both the on-support elongation and deprotection of the G4-forming oligonucleotides can be performed, along with the successive affinity chromatography-based assay, renamed as G-quadruplex on Controlled Pore Glass (G4-CPG) assay. Here we describe these assays and their applications to the screening of several libraries of chemically different putative G4 ligands. Finally, ongoing studies and outlook of our G4-CPG assay are reported.     

Multiphase Flow Regime Characterization and Liquid Flow Measurement Using Low-Field Magnetic Resonance Imaging

Multiphase flow metering with operationally robust, low-cost real-time systems that provide accuracy across a broad range of produced volumes and fluid properties, is a requirement across a range of process industries, particularly those concerning petroleum. Especially the wide variety of multiphase flow profiles that can be encountered in the field provides challenges in terms of metering accuracy. Recently, low-field magnetic resonance (MR) measurement technology has been introduced as a feasible solution for the petroleum industry. In this work, we study two phase air-water horizontal flows using MR technology. We show that low-field MR technology applied to multiphase flow has the capability to measure the instantaneous liquid holdup and liquid flow velocity using a constant gradient low flip angle CPMG (LFA-CPMG) pulse sequence. LFA-CPMG allows representative sampling of the correlations between liquid holdup and liquid flow velocity, which allows multiphase flow profiles to be characterized. Flow measurements based on this method allow liquid flow rate determination with an accuracy that is independent of the multiphase flow profile observed in horizontal pipe flow for a wide dynamic range in terms of the average gas and liquid flow rates.     

Stages of melting of graphene model in two-dimensional space

Spontaneous melting of a perfect crystalline graphene model in 2D space is studied via molecular dynamics simulation. Model containing 10⁴ atoms interacted via long-range bond-order potential (LCBOP) is heated up from 50 to 8,450 K in order to see evolution of various thermodynamic quantities, structural characteristics and occurrence of various structural defects. We find that spontaneous melting of our graphene model in 2D space exhibits a first-order behaviour of the transition from solid 2D graphene sheet into a ring-like structure 2D liquid. Occurrence and clustering of Stone–Wales defects are the first step of melting process followed by breaking of C–C bonds, occurrence/growth of various types of vacancies and multi-membered rings. Unlike that found for melting of a 2D crystal with an isotropic bonding, these defects do not occur homogeneously throughout the system, they have a tendency to aggregate into a region and liquid phase initiates/grows from this region via tearing-like or crack-propagation-like mechanism. Spontaneous melting point of our graphene model occurs at T_m = 7,750 K. The validity of classical nucleation theory and Berezinsky–Kosterlitz–Thouless–Nelson–Halperin–Young (BKTNHY) one for the spontaneous melting of our graphene model in strictly 2D space is discussed.     

Cucurbit[7]uril⋅Guest Pair with an Attomolar Dissociation Constant

Host?guest complexes between cucurbit[7] (CB[7]) or CB[8] and diamantane diammonium ion guests 3 or 6 were studied by ¹H NMR spectroscopy and X‐ray crystallography. ¹H NMR competition experiments revealed that CB[7]? 6 is among the tightest monovalent non‐covalent complexes ever reported in water with K_a=7.2×10¹⁷ M ^?1 in pure D₂O and 1.9×10¹⁵ M ^?1 in D₂O buffered with NaO₂CCD₃ (50 mM ). The crystal structure of CB[7]? 6 allowed us to identify some of the structural features responsible for the ultratight binding, including the distance between the NMe₃⁺ groups of 6 (7.78 Å), which allows it to establish 14 optimal ion‐dipole interactions with CB[7], the complementarity of the convex van der Waals surface contours of 6 with the corresponding concave surfaces of CB[7], desolvation of the C?O portals within the CB[7]? 6 complex, and the co‐linearity of the C₇ axis of CB[7] with the N⁺???N⁺ line in 6 . This work further blurs the lines of distinction between natural and synthetic receptors.     

Aromatic Superhalogens

No organic molecules with electron affinities near or above those of halogens are known. We show for the first time that aromaticity rules can be used to design molecules with electron affinities far exceeding those of halogen atoms either by tailoring the ligands of cyclopentadienyl or by multiple benzoannulations of cyclopentadienyl in conjunction with the substitution of CH groups with isoelectronic N atoms. Results based on density functional theory revealed that the electron affinities of some of these organic molecules can reach as high as 5.59 eV, thus opening the door to new class of superhalogens that contain neither a metal nor a halogen atom.     

蛋白质对测定水产品中氯苯类化合物的影响及消除

提出了气相色谱-质谱法测定水产品中1,3-二氯苯,1,2-二氯苯,1,2,4-三氯苯等3种氯苯类化合物含量的方法。采用荧光猝灭法研究了氯苯类化合物与蛋白质之间的结合作用,结果表明氯苯类化合物与鱼血清白蛋白之间存在较强的结合作用。水产品样品以丙酮-磷酸氢二钾-水双水相体系进行前处理。在气相色谱分离中用DB-WAX毛细管色谱柱为固定相,在质谱分析中采用选择离子监测模式。3种氯苯类化合物的质量浓度均在0.5~5.0mg·L-1范围内与其峰面积呈线性关系。以空白样品为基体进行加标回收试验,所得回收率在77.0%~116%之间,相对标准偏差(n=6)在2.6%~7.1%之间。     

Work function and negative electron affinity of ultrathin barium fluoride films

Thin films of barium fluorides with different thicknesses were deposited on GaAs substrate by electron beam evaporation. The aim of the work was to identify the best growth conditions for the production of coatings with a low work function suitable for the anode of hybrid thermionic-photovoltaic (TIPV) devices. The chemical composition and work function φ of the films with different thicknesses were investigated by X-ray photoelectron spectroscopy (XPS) and ultraviolet photoelectron spectroscopy (UPS). The lowest value of φ = 2.1 eV was obtained for the film with a thickness of ~2 nm. In the valence band spectra of the films at low kinetic energy, near the cutoff, a characteristic peak of negative electron affinity was present. This effect contributed to a further reduction of the film's work function.     

Taba: A Tool to Analyze the Binding Affinity

Evaluation of ligand-binding affinity using the atomic coordinates of a protein-ligand complex is a challenge from the computational point of view. The availability of crystallographic structures of complexes with binding affinity data opens the possibility to create machine-learning models targeted to a specific protein system. Here, we describe a new methodology that combines a mass-spring system approach with supervised machine-learning techniques to predict the binding affinity of protein-ligand complexes. The combination of these techniques allows exploring the scoring function space, generating a model targeted to a protein system of interest. The new model shows superior predictive performance when compared with classical scoring functions implemented in the programs Molegro Virtual Docker, AutoDock4, and AutoDock Vina. We implemented this methodology in a new program named Taba. Taba is implemented in Python and available to download under the GNU license at https://github.com/azevedolab/taba . © 2019 Wiley Periodicals, Inc.     

Accurate prediction of relative binding affinities of a series of HIV-1 protease inhibitors using semi-empirical quantum mechanical charge

A major challenge in computer-aided drug design is the accurate estimation of ligand binding affinity. Here, a new approach that combines the adaptive steered molecular dynamics (ASMD) and partial atomic charges calculated by semi-empirical quantum mechanics (SQMPC), namely ASMD-SQMPC, is suggested to predict the ligand binding affinities, with 24 HIV-1 protease inhibitors as testing examples. In the ASMD-SQMPC, the relative binding free energy (ΔG) is reflected by the average maximum potential of mean force (<PMF>_max) between bound and unbound states. The correlation coefficient (R²) between the <PMF>_max and experimentally determined ΔG is 0.86, showing a significant improvement compared with the conventional ASMD (R² = 0.52). Therefore, this study provides an efficient approach to predict the relative ΔG and reveals the significance of precise partial atomic charges in the theoretical simulations.     

两种表征核酸适配体-靶蛋白亲和作用的毛细管电泳方法比较

适配体-靶分子间的亲和作用表征是理解和应用核酸适配体发挥特异亲和作用的基本前提,CE技术则为上述表征提供了多模式的简捷途径,但多种模式体系间的结果往往存在差异,导致CE亲和评价可靠性和进一步应用受到限制,亟须建立多CE方法测定适配体-靶分子间亲和作用的系统比较研究。该研究以凝血酶及其特异性作用于肝素结合位点的适配体29mer为模型体系,基于CE-激光诱导荧光检测,引入CE-迎头分析（FA）评价方法,并比较其与预平衡-毛细管区带电泳（PE-CZE）的异同。首先进行了CE-FA方法分离条件的优化,37 ℃、0.5 h孵育完全后进样,进样时间为30 s,在较低工作温度（15 ℃）、较短毛细管长度（30 cm）及生物相容性好的缓冲体系2×TG（Tris-甘氨酸缓冲液,pH 8.5）条件下,经15 kV分离时,得到了稳定的荧光标记29mer（F29mer）-凝血酶复合物及游离F29mer平台峰。加入1 g/L牛血清白蛋白（BSA）,有效提高了CE-FA平台峰高及迁移时间的重复性。详细讨论了两种方法下6种拟合方式的结果及特点。针对CE-FA和PE-CZE法,以结合适配体/游离适配体的浓度比对游离适配体浓度非线性拟合、平台峰高变化对浓度间的非线性拟合、平衡混合物的非平衡CE（NECEEM）计算等进行拟合。结果表明,6种拟合结果中5种不存在显著性差异,得到的解离常数（K_d）值均介于24~64 nmol/L范围。CE-FA法中的3种拟合结果符合度较好,说明CE-FA法易于在非平衡的CE分离体系下保持适配体-复合物间的结合-解离平衡,所测得K_d准确度较高。PE-CZE法中,借由降低的游离F29mer峰高对凝血酶浓度间的非线性拟合所得K_d值偏差过大;选择凝血酶浓度为F29mer浓度的0.5~2倍,且观察到明显的两峰间"指数桥"为前提,可经NECEEM法进行数据计算求解得到较为准确的K_d值。CE-FA法可与PE-CZE法互为印证,提高了亲和作用评价的可靠性。首选推荐使用多浓度平台峰高变化进行非线性拟合的CE-FA法,可相对有效克服高压电场对复合物稳定性的影响,具有适用范围广、方法稳定、结果拟合简便准确等特点。