基于糖和苯硼酸动态共价键的高效蛋白质表面修饰方法

糖和蛋白质的相互作用参与了很多重要的生命过程.研究糖和蛋白质的相互作用有多种手段,石英晶体微天平(QCM)是其中重要的一种.研究中常需要将蛋白质通过共价键连接在天平芯片的表面.但是,用于检测糖分子的蛋白质多为植物凝集素,它们的分子量大,表面可修饰位点少,通过共价键修饰在芯片表面的效率偏低.本文提出一种基于糖和苯硼酸之间动态共价键的新修饰方法,能够大幅度提高蛋白质在芯片表面的修饰效率.     

软骨细胞体外增殖去分化的拉曼光谱分析

基于显微拉曼光谱技术,对组织工程的软骨种子细胞在传代增殖过程中的去分化进行单细胞分析。首先,对体外单层培养的第1-4代(P1-P4)大鼠软骨细胞样本进行了单细胞拉曼光谱检测,由此识别出软骨细胞中各种碱基、糖基、氨基酸等主要物质分子结构的特征峰集合。随后,分析拉曼光谱中若干重点特征峰强度随细胞传代次数的变化,发现软骨细胞体外增殖过程中核酸(789、1094、1576 cm~(-1))含量降低、Ⅱ型胶原(特异组分为羟脯氨酸,1207 cm~(-1))和蛋白聚糖(特异组分为糖胺聚糖,1042、1063、1126、1160 cm~(-1))合成下降、脂质(1304 cm~(-1))及磷酸盐(957 cm~(-1))含量增加等分子水平变化,从而在活体单细胞层次初步揭示了去分化引起软骨细胞增殖变缓、分泌减弱、形态纤维化等现象的分子机制。     

以腐植酸为对象开展稳态和时间分辨荧光实验教学

腐植酸是天然有机质的重要组成部分,其结构复杂且具有多种荧光发射特征。我们结合目前环境科学领域腐植酸或其他天然有机质的研究重点,利用腐植酸开展稳态和时间分辨荧光综合实验教学。本实验可以使学生全面掌握分子荧光分析中拉曼散射、激发光能量对荧光发射影响、荧光寿命和内滤效应等知识。     

计算化学在分子轨道教学中的应用

分子轨道理论是理解分子电子结构与微观性质的重要理论之一,也是本科生与研究生结构化学教学中的重点与难点。学生对原子轨道组合形成分子轨道、分子轨道能级交叉混合等知识的理解缺乏形象直观、定量的认识。本文通过基于量子化学或密度泛函理论的Gaussian 03计算软件,计算、绘制并分析了F_2、O_2、N_2、HF、CO等的分子轨道能级图,将学生较难理解的内容定量、直观地呈现出来,形象地解释了分子轨道成键原则与电子填充原则等分子轨道理论中的重难点,加深了学生对分子轨道理论的理解,特别是sp轨道混杂导致的σ_(2p_z)与π_(2p)轨道能级交叉这一难点,激发了学生学习的主动性和积极性,提高了教学质量。在此基础上,利用分子轨道理论分析了CO_2的电子结构,使学生学会应用分子轨道理论解决实际问题,巩固了相关课堂理论知识。     

Metal ion-induced H-aggregation of a water-soluble anionic dye Congo red (CR) in Langmuir–Blodgett (LB) film

Present communication reports the preparation of Langmuir monolayer of water-soluble anionic dye Congo red (CR) by allowing it to adsorb from the aqueous subphase onto the preformed Langmuir monolayer of anionic stearic acid using divalent metal cations Mg²⁺ as mediator. Isotherm and compressibility studies of SA-Mg-CR hybrid monolayer gave valuable information about the molecular organisation in the Langmuir monolayer. Absorption spectroscopic studies revealed the formation of H-aggregates in the hybrid Langmuir–Blodgett (LB) films fabricated at lower salt concentration in the subphase. Atomic Force Microscopic image gave visual evidence of distinct nanocrystalline domains in the LB monolayer film.     

Virtual screening of B-Raf kinase inhibitors: A combination of pharmacophore modelling,molecular docking, 3D-QSAR model and binding free energy calculation studies

B-Raf kinase has been identified as an important target in recent cancer treatment. In order to discover structurally diverse and novel B-Raf inhibitors (BRIs), a virtual screening of BRIs against ZINC database was performed by using a combination of pharmacophore modelling, molecular docking, 3D-QSAR model and binding free energy (ΔG_bind) calculation studies in this work. After the virtual screening, six promising hit compounds were obtained, which were then tested for inhibitory activities of A375 cell lines. In the result, five hit compounds show good biological activities (IC₅₀ < 50 μM). The present method of virtual screening can be applied to find structurally diverse inhibitors, and the obtained five structurally diverse compounds are expected to develop novel BRIs.     

Disruption of redox catalytic functions of peroxiredoxin-thioredoxin complex in Mycobacterium tuberculosis H37Rv using small interface binding molecules

Mycobacterium tuberculosis has distinctive ability to detoxify various microbicidal superoxides and hydroperoxides via a redox catalytic cycle involving thiol reductants of peroxiredoxin (Prx) and thioredoxin (Trx) systems which has conferred on it resistance against oxidative killing and survivability within host. We have used computational approach to disrupt catalytic functions of Prx-Trx complex which can possibly render the pathogen vulnerable to oxidative killing in the host. Using protein–protein docking method, we have successfully constructed the Prx-Trx complex. Statistics of interface region revealed contact area of each monomer less than 1500 Å² and enriched in polar amino acids indicating transient interaction between Prx and Trx. We have identified ZINC40139449 as a potent interface binding molecule through virtual screening of drug-like compounds from ZINC database. Molecular dynamics (MD) simulation studies showed differences in structural properties of Prx-Trx complex both in apo and ligand bound states with regard to root mean square deviation (RMSD), radius of gyration (Rg), root mean square fluctuations (RMSF), solvent accessible surface area (SASA) and number of hydrogen bonds (NHBs). Interestingly, we found stability of two conserved catalytic residues Cys61 and Cys174 of Prx and conserved catalytic motif, WCXXC of Trx upon binding of ZINC40139449. The time dependent displacement study reveals that the compound is quite stable in the interface binding region till 30 ns of MD simulation. The structural properties were further validated by principal component analysis (PCA). We report ZINC40139449 as promising lead which can be further evaluated by in vitro or in vivo enzyme inhibition assays.     

Discovery of potential inhibitor against human acetylcholinesterase: a molecular docking and molecular dynamics investigation

Alzheimer’s disease (AD) is a progressive neurodegenerative disease of central nervous system among elderly people. Human acetylcholinesterase (hAChE), an important enzyme in neuronal signaling, is responsible for the degradation of acetylcholine which in turn prevents the post synaptic signal transmissions. hAChE has been an attractive target of drug discovery for the search of therapeutics against AD. In the recent past hAChE has become hot target for the investigation of new potential therapeutics. We performed virtual screening of entire database against hAChE. Further, the extra precision molecular docking was carried out to refine the docking results and the best complex was passed for molecular dynamics simulations in order of understanding the hAChE dynamics and its behavior in complex with the ligand which corroborate the outcomes of virtual screening. This also provides binding free energy data that establishes the ligands efficiency for inhibiting hAChE. The computational findings discussed in this paper provide initial information of inhibitory effects of ligand, (drugbank entry DB00983), over hAChE.     

Tetracyclines as a potential antiviral therapy against Crimean Congo hemorrhagic fever virus: Docking and molecular dynamic studies

Crimean-Congo Hemorrhagic Fever Virus (CCHFV) is one of the deadliest human diseases with mortality rate near 50%. Special attention should be paid to this virus since there is no approved treatment for it. On the other hand, the recent outbreak of Ebola virus which is a member of hemorrhagic fever viruses shows this group of viruses can be extremely dangerous. Previous studies have indicated that nucleoprotein of CCHFV, a pivotal protein in virus replication, is an appropriate target for antiviral drug development. The aim of this study is finding inhibitor(s) of this protein. Herein, a virtual screening procedure employing docking followed by molecular dynamic was used to identify small molecule inhibitors of the nucleoprotein from FDA-approved drugs. Regarding CCHFV, using in-silico method is a safe way to achieve its inhibitor(s) since this virus is categorized as a World Health Organization (WHO) biosafety level 4 pathogen and therefore investigation in general laboratories is restricted. In conclusion, considering docking and molecular dynamic results alongside with bioavailability of FDA-approved drugs, doxycycline and minocycline are proposed as potential inhibitors of CCHFV nucleoprotein. There is hope, this study encourage other research groups for in-vitro and in-vivo studies about the efficacy of those two medicines in CCHFV treatment.