基于纳米金适配体传感器的激光诱导检测凝血酶

利用激光可使纳米金修饰的双链DNA(dsDNA)去杂化和适配体的特异性,设计了一种新颖、稳定、可控且高灵敏的凝血酶检测方法。将两端分别修饰金纳米粒子与荧光标记物的核酸适配体与其互补链杂化制成稳定的dsDNA传感器,当凝血酶存在时,通过激光触发传感器去杂化释放适配体并与凝血酶结合,拉近金纳米粒子与荧光标记物的距离,产生猝灭使荧光信号发生变化。对激光照射时间、激光输出功率、温育时间等条件进行优化。在最优条件下,荧光强度变化值(ΔI)与凝血酶浓度在0.55~33 nmol/L范围内呈现出良好的线性关系,其线性回归方程为y=0.0082x+0.2714,相关系数R^2为0.98,血清中加标回收率为95.5~102.7%,且溶菌酶等无明显干扰。该方法可作为凝血酶的检测方法。     

高灵敏选择性检测凝血酶的适体纳米银共振散射光谱探针

采用四氢硼钠制备了较稳定的纳米银,并用凝血酶(TB)适体修饰纳米银制各了识别凝血酶的适体纳米银探针.在pH 7.0的Tris-HCl缓冲溶液及KCl存在下,适体纳米银探针与凝血酶特异结合生成G-四分体和纳米银聚集体,导致体系在480 nm处的共振散射峰增强.随着凝血酶浓度的增大,生成的纳米银聚集体越多,共振散射强度线性...     

Structural and Binding Effects of Chemical Modifications on Thrombin Binding Aptamer (TBA)

The thrombin binding aptamer (TBA) is a promising nucleic acid-based anticoagulant. We studied the effects of chemical modifications, such as dendrimer Trebler and NHS carboxy group, on TBA with respect to its structures and thrombin binding affinity. The two dendrimer modifications were incorporated into the TBA at the 5′ end and the NHS carboxy group was added into the thymine residues in the thrombin binding site of the TBA G-quadruplex (at T4, T13 and both T4/T13) using solid phase oligonucleotide synthesis. Circular dichroism (CD) spectroscopy confirmed that all of these modified TBA variants fold into a stable G-quadruplex. The binding affinity of TBA variants with thrombin was measured by surface plasmon resonance (SPR). The binding patterns and equilibrium dissociation constants (K_D) of the modified TBAs are very similar to that of the native TBA. Molecular dynamics simulations studies indicate that the additional interactions or stability enhancement introduced by the modifications are minimized either by the disruption of TBA–thrombin interactions or destabilization elsewhere in the aptamer, providing a rational explanation for our experimental data. Overall, this study identifies potential positions on the TBA that can be modified without adversely affecting its structure and thrombin binding preference, which could be useful in the design and development of more functional TBA analogues.     

Practical synthesis of a peptidomimetic thrombin inhibitor

Compound 1 is a low molecular weight thrombin inhibitor developed for treatment of deep vein thrombosis and cardiovascular diseases. We herein report our efforts to develop a robust, efficient and reproducible process suitable for large-scale synthesis of compound 1.     

Flexible docking simulations: Scaled collective variable Monte Carlo minimization approach using Bezier splines,and comparison with a standard Monte Carlo algorithm

An algorithm for docking a flexible ligand onto a flexible or rigid receptor, using the scaled‐collective‐variables Monte Carlo with energy minimization approach, is presented. Energy minimization is shown to be one of the best techniques for distinguishing between native‐ and nonnative‐generated conformations. Incorporation of this technique into a Monte Carlo procedure enables one to distinguish the native conformation directly during the conformational search. It avoids the generation of a large number of ligand conformers for which more sophisticated energy evaluation tools would have had to be applied to identify the nativelike conformations. The efficiency of the Monte Carlo minimization was greatly improved by incorporating a new grid‐based energy evaluation technique using Bezier splines for which the energy function, as well as all of its derivatives, can be deduced from the values at the grid points. Comparison between our ECEPP/3‐based algorithm and the Monte Carlo algorithm presented elsewhere (Hart, T. N.; Read, R. J. Prot Struct Funct Genet 1992, 13, 206–222) has been made for docking NH₂ D Phe Pro Arg COOH, the noncovalent analog of NH₂ D Phe Pro Arg chloromethylketone (PPACK), onto the active site of human α‐thrombin. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 244–252, 1999     

Comment on the validation of continuum electrostatics models

A validation based on solvation energies (vacuum to water transfer) is not sufficient to justify the use of approximated models of electrostatics to rank ligand/protein complexes. A full validation should be based on energies in solution, i.e., solvation plus vacuum Coulomb energies, because of the anticorrelation between solvation and vacuum energies. The energy in solution is the relevant quantity in simulations of biological macromolecules and complexes. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1533–1536, 1999     

Chemistry and biology of glycosaminoglycans in blood coagulation

Glycosaminoglycans (GAGs) are widely distributed in animal tissues where they are usually associated with proteins. Six types are commonly recognized: heparin (Hep), heparan sulfate (HS), dermatan sulfate (DS), chondroitin sulfate (Ch-S), keratan sulfate (KS) and hyaluronic acid (Hyal). They are structurally related with a carbohydrate backbone consisting of alternating hexuronic acid (L-iduronic acid and/or D-glucuronic acid) or galactose units and hexosamine (D-glucosamine or D-galactosamine) residues. All GAGs, except Hyal, show sulfate groups along their chains. Certain sulfate glycoaminoglycans have the ability to interfere with blood coagulation, as demonstrated by the extensive clinical use of Hep as an anticoagulant agent. HS and DS show a good anticoagulant activity, although weaker than that of Hep. In contrast, Ch-S has a low ability to inhibit plasma serine proteases, and KS and Hyal are devoid of any effect on coagulation cascade. The interaction between blood coagulation serine proteases and GAGs can be found to have two principle mechanisms: the specific “lock and key” binding and the nonspecific cooperative electrostatic association. This different ability of GAGs to interact with coagulation cascade proteins depends on the molecular weight, the ratio of iduronic/glucoronic acid and the sulfation degree. Many attempts have been made to improve or induce anticoagulant activity of natural GAGs-by chemical modification. Increasing sulfation degree of DS and Ch-S is followed by their biological activity increasing. Hyal, which is devoid of any anticoagulant effect, acquires a good ability to inactivate plasma serine proteases, i.e. thrombin and Factor Xa, when it is sulfated. This ability increases by increasing the number of sulfate groups per disaccharide unit, although the mechanism of action is different from that of Hep, but seems to be independent of its molecular weight.     

适配体传感器检测凝血酶的研究进展

适配体是通过指数富集配体系统进化技术(SELEX)筛选得到的,能与多种目标物质高特异性、高选择性结合的寡核苷酸序列.适配体因合成简单、稳定性高、设计多样化、修饰方便、成本低等优点被用作为识别探针,并与不同的转导技术相结合,构建了多种类型的适配体传感器,并借助纳米材料独特的光、电特性,提高适配体传感器的性能.凝血酶是一种...     

De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks

An evolutionary algorithm was developed for fragment-based de novo design of molecules (TOPAS, TOPology-Assigning System). This stochastic method aims at generating a novel molecular structure mimicking a template structure. A set of 25,000 fragment structures serves as the building block supply, which were obtained by a straightforward fragmentation procedure applied to 36,000 known drugs. Eleven reaction schemes were implemented for both fragmentation and building block assembly. This combination of drug-derived building blocks and a restricted set of reaction schemes proved to be a key for the automatic development of novel, synthetically tractable structures. In a cyclic optimization process, molecular architectures were generated from a parent structure by virtual synthesis, and the best structure of a generation was selected as the parent for the subsequent TOPAS cycle. Similarity measures were used to define `fitness', based on 2D-structural similarity or topological pharmacophore distance between the template molecule and the variants. The concept of varying library `diversity' during a design process was consequently implemented by using adaptive variant distributions. The efficiency of the design algorithm was demonstrated for the de novo construction of potential thrombin inhibitors mimicking peptide and non-peptide template structures.