Fluorimetric study of interaction of benzidine with trypsin

The interaction of benzidine (BEN) with trypsin was studied by fluorescence spectrum. It was shown that BEN has quenched the fluorescence launching from trypsin by reacting with it and forming a certain kind of new complex. The quenching and energy transfer mechanisms were discussed. The binding constants and thermodynamic parameters at three different temperatures, the binding locality, and the binding power were obtained. The conformation of trypsin was discussed by synchronous and three-dimensional fluorescence techniques.     

抑制剂Benzamidine与胰岛素作用机制的分子动力学和结合自由能计算研究

氢键和极性相互作用在抑制剂-蛋白结合专一性识别过程中起到重要作用. 抑制剂Benzamidine(BEN)与胰岛素trypsin相互作用机制的阐明有助于胰岛素高效抑制剂的研发.本文采用分子动力学模拟和MM-PBSA(molecular mechanics-Poisson Boltzmann surface area)从原子层次上研究BEN与胰岛素的结合模式.结果表明抑制剂BEN的脒基不仅与Asp189的羰基产生静电相互作用,而且与残基Ser190和Gly214形成氢键相互作用.基于残基能量分解的计算表明抑制剂的苯基与残基His58, Cys191, Gln192, Trp211, Gly212和Cys215形成有利于抑制剂结合的疏水性相互作用.期望当前的研究能为胰岛素有效抑制剂的研发提供重要的理论指导.     

抑制剂Benzamidine与胰岛素作用机制的分子动力学和结合自由能计算研究

氢键和极性相互作用在抑制剂-蛋白结合专一性识别过程中起到重要作用.抑制剂Benzamidine(BEN)与胰岛素trypsin相互作用机制的阐明有助于胰岛素高效抑制剂的研发.本文采用分子动力学模拟和MM-PBSA(molecular mechanics-Poisson Boltzmann surface area)从原子层次上研究BEN与胰岛素的结合模式.结果表明抑制剂BEN的脒基不仅与Asp189的羰基产生静电相互作用,而且与残基Ser190和Gly214形成氢键相互作用.基于残基能量分解的计算表明抑制剂的苯基与残基His58,Cys191,Gln192,Trp211,Gly212和Cys215形成有利于抑制剂结合的疏水性相互作用.期望当前的研究能为胰岛素有效抑制剂的研发提供重要的理论指导.     

美洛昔康与溶菌酶作用机制的光谱分析及理论模建研究

为了探究美洛昔康与溶菌酶的作用机制,在pH=7.40的实验条件下,采用荧光光谱、同步荧光光谱和理论模建分析技术研究了类风湿性关节炎药物美洛昔康与溶菌酶分子之间的相互作用。结果表明,美洛昔康能够以静态猝灭形式有效地猝灭溶菌酶的内源荧光,形成1∶1的复合物,并使溶菌酶的构象发生改变。热力学结果表明,美洛昔康-溶菌酶体系的主要作用力类型为疏水作用力。理论模建结果表明,该体系除疏水作用外还存在氢键作用,且美洛昔康被溶菌酶的活性氨基酸残基Glu35和Asp52包围,结合作用改变了溶菌酶催化活性中心处氨基酸残基的微环境。当患者服用15 mg美洛昔康时,美洛昔康与溶菌酶的蛋白结合率W(B)为3.71%~8.79%,说明美洛昔康与溶菌酶的结合对溶菌酶自身抗炎、抗菌功能的影响不大,体系药物结合率W(Q)为1.08%~1.14%,说明溶菌酶与美洛昔康结合不会影响美洛昔康的药效。该研究从理论上证明了溶菌酶在血浆环境中与药物美洛昔康结合后,对溶菌酶本身功能和美洛昔康的药效不会产生严重影响。     

Molecular interaction of silybin with hyaluronidase: A spectroscopic and molecular docking study

In this study, the molecular interaction of silybin with hyaluronidase was investigated by spectroscopic methods and molecular docking. It was found that silybin had strong ability to quench the intrinsic fluorescence of hyaluronidase by a static quenching procedure. The binding constants were obtained at three temperatures (293, 298, and 310 K). The results of synchronous fluorescence and three-dimensional fluorescence and molecular docking showed that silybin bound into the hyaluronidase cavity site and the binding of silybin to hyaluronidase could induce micro-environmental and conformational changes in hyaluronidase, which resulted in the reduced hyaluronidase activity. The thermodynamic parameter analysis and molecular docking experiments revealed that all types of non-covalent interaction, including hydrogen bonding interaction, van der Waals forces, hydrophobic interaction, and electrostatic interaction were present in the binding process of silybin with hyaluronidase. The results obtained here will provide direct evidence at a molecular level to understand the mechanism of the inhibitory effect of silybin against hyaluronidase.     

Design and interaction mechanism of ligand targeted with folate receptor α and β

Four compounds 1 to 4 (folic acid, methotrexate and 2 dyes) were used to interact with folate receptor (FR)α and FRβ. The interaction structures and binding energies of the bound complexes were investigated. In order to analyze the differences between FRα and FRβ complexes, the details of the weak intermolecular interactions were analyzed, and the frontier orbital properties of the FR complexes were studied by a dispersion complemented density functional tight‐binding method. By comparing the different interaction properties of the 4 compounds with FRα and FRβ, the basic strategies for design of novel compound targeted with FR subtype were suggested. Further, a novel compound with high selectively with FRα based on compound 3 was designed to illustrate our conclusion. These data should be helpful for the design of novel molecules with extreme discerningly with FRα and FRβ.     

计算机模拟和光谱法研究头孢他美酯与胃蛋白酶的结合机理

采用多种光谱法及计算机模拟技术研究了298,303,310 K温度下,头孢他美酯（CFP）与胃蛋白酶（PEP）之间的结合机理。结果表明,CFP主要以非辐射能量转移的静态猝灭方式猝灭PEP的荧光,两者主要通过静电作用力结合,其结合率在310 K为74.73%~92.13%。采用同步荧光法和圆二色谱法研究CFP对PEP的反应,结果表明两者的结合诱导了PEP的构象变化,使PEP的内源荧光猝灭。采用计算机模拟CFP与PEP的对接,结果表明CFP结合在PEP的催化活性位点处,该结论与光谱法所得结果一致。利用CFP对PEP的荧光猝灭反应,可以实现对实际药品中CFP含量的快速测定。     

光谱法结合分子模拟技术研究左氧氟沙星与胃蛋白酶的相互作用机理

在模拟生理条件下,采用荧光光谱法结合分子对接技术研究了左氧氟沙星与胃蛋白酶的相互作用。不同温度下的Stern-Volmer曲线结果表明,左氧氟沙星主要以静态猝灭的方式使胃蛋白酶的荧光产生猝灭。由热力学数据确定了两者之间存在的作用力主要为静电作用力。三维荧光光谱实验结果表明,在左氧氟沙星与胃蛋白酶发生作用过程中引起了胃蛋白酶中酪氨酸和色氨酸残基构象的变化,从而导致胃蛋白酶发生了猝灭作用。为了进一步探讨左氧氟沙星与胃蛋白酶相互作用的分子机理,利用分子对接技术对两者的相互作用进行模拟。结果表明两者发生作用的区域位于胃蛋白酶的催化活性中心,左氧氟沙星的进入导致酶催化中心氨基酸残基的微环境发生改变,从而对胃蛋白酶的活性造成影响,这可能也是左氧氟沙星引起消化不良的主要原因。     

光谱法和分子对接模拟技术研究托拉塞米与胃蛋白酶和胰蛋白酶的相互作用

托拉塞米(TOR)属于吡啶磺酰脲类袢利尿剂,被广泛有效地用于高血压,心脏衰竭,慢性肾功能衰竭和肝脏疾病的治疗。TOR在治疗过程中易引起的不良反应之一为轻微肠胃不适。然而,TOR与消化蛋白酶(胰蛋白酶和胃蛋白酶)分子间的相互作用鲜有报道。在模拟生理条件下,采用荧光光谱、紫外-可见吸收光谱、圆二色谱和分子对接技术研究了不同温度下托拉塞米(Torasemide, TOR)与胃蛋白酶(Pepsin)和胰蛋白酶(Trypsin)间的相互作用。所有荧光数据均进行了内滤光校正以获得更准确的结合参数。结果表明,TOR-Pepsin和TOR-Trypsin体系的猝灭常数(K_SV)均与温度呈负相关,说明TOR与Pepsin及Trypsin之间的作用机制均为静态荧光猝灭。利用紫外-可见吸收光谱、同步荧光光谱、3D荧光光谱和圆二色光谱法考查了TOR对Trypsin和Pepsin构象的影响。结果发现胃蛋白酶或胰蛋白酶中酪氨酸残基的极性改变较色氨基更明显,TOR可改变色氨酸残基的微环境并降低Trypsin和Pepsin中β-折叠结构,进而可能影响其生理功能。分子对接结果表明,TOR与Pepsin的结合位点位于由Asp-32和Asp-215组成的活性中心周围,从而抑制Pepsin活性。而TOR通过疏水作用力结合在Trypsin的口袋型底物结合位点(S1口袋),促进底物进入酶活性中心,最终表现为Trypsin活性升高。该研究探讨了TOR与胃蛋白酶和胰蛋白酶的结合作用和毒性机制,为TOR的安全使用提供重要依据。     

Probing the binding of Azilsartan to DNA by molecular docking,steady-state/time-resolved fluorescence,viscosity, infrared,and circular dichroism spectra

Azilsartan, a new antihypertensive drug, has effects on the sympathetic nervous system and expression of genes. The interaction of Azilsartan with DNA was investigated using molecular docking and multi-spectral techniques. Molecular docking revealed that Azilsartan could interact with DNA via groove binding from a theoretical perspective. Time-resolved fluorescence measurements indicated that the quenching mechanism was static, and further analysis of quenching data demonstrated that the binding was spontaneous and mainly driven by hydrophobic forces. The results of interaction with denatured DNA, viscosity, infrared spectroscopy, and circular dichroism showed that Azilsartan could bind to DNA through groove binding, which was consistent with docking analyses.     

Deoxyribonucleic Acid and Bovine Serum Albumin Interaction with the Asymmetric Schiff Base Ligand and Its Molybdenum (VI) Complex: Multi Spectroscopic and Molecular Docking Studies

The interaction of an asymmetric Schiff base ligand derived from allylamine and 2,3-dihydroxybenzaldehyde and its molybdenum (VI) complex with deoxyribonucleic acid (DNA) and bovine serum albumin (BSA) were studied using spectroscopic and molecular docking methods. The spectroscopic results revealed that the DNA and BSA affinity for binding the Mo(VI) complex is greater than its ligand. Furthermore, the molecular docking calculations showed that H-bond, hydrophobic, π-π and π-cation interactions had the dominant roles in the stability of the compound-BSA complexes. The DNA interaction results suggested that the compounds interacted with DNA by the groove binding mechanism.     

Analysis of the binding mechanism between o-phenylenediamine and bovine hemoglobin by molecular spectroscopy and molecular modeling methods

Abstract

This study was aimed to reveal the binding mechanism between bovine hemoglobin and o-phenylenediamine by using molecular spectroscopy techniques and molecular modeling methods. The experimental results revealed that the fluorescence quenching mechanism was a combined dynamic and static quenching. The binding constant was (1.17?±?0.02)×10⁴ L/mol, and only a single binding site exists. The binding distance was 2.46?nm. The binding process was a spontaneous reaction, dominated by hydrophobic forces. The molecular docking simulations have also confirmed the results of the spectroscopic methods. The results reported here may significantly help understanding the interaction mechanism of o-phenylenediamine and hemoglobin.     

Study on the effect of protein on drug efficacy: cefonicid sodium–pepsin binding mechanism

The mechanism of interaction between cefonicid sodium and pepsin was investigated by various spectroscopic methods and molecular docking. Cefoncid sodium quenched the intrinsic fluorescence of pepsin at pH of 2.0 to form a new complex in a 1:1 binding mode driven by Van der Waals and hydrogen bonds. The mechanism of quenching was static. The results of molecular docking indicated that the cefonicid sodium-binding site was located in the active site of pepsin. The protein binding rates of cefonicid sodium in gastric juice was calculated and the binding model was established. It is concluded that cefonicid sodium is not suitable for oral administration.     

Investigation on the interaction of glipizide with bovine hemoglobin by spectroscopy and molecular docking

This study aims to investigate the interaction between glipizide and bovine hemoglobin using fluorescence quenching, circular dichroism spectroscopy in various temperatures (293, 303, and 310?K) and molecular docking methods. The results demonstrated that glipizide could cause strong fluorescence quenching of bovine hemoglobin by a dynamic quenching mechanism, during which the hydrophobic interaction played a dominant role in this system. The order of magnitude of binding constant is 10⁴, and the number of binding site in the system was close to 1. It also showed that tyrosine residues and tryptophan residues were both involved in the binding of glipizide with bovine hemoglobin, and was closer to the later. Circular dichroism spectra revealed that the conformation of bovine hemoglobin was changed during the binding reaction. The interaction of the system was studied by both spectroscopic method and molecular docking simulation, and the conclusions are consistent.     

Spectroscopic and Electrochemical Studies on the Interaction of Carmoisine Food Additive with Native Calf Thymus DNA

ABSTRACT

In this work, for the first time interaction between a carmoisine food additive and native calf thymus DNA was monitored using UV-Vis absorption, fluorescence, and circular dichroism (CD) spectroscopy, as well as cyclic voltammetry and viscosity measurements. It can be concluded that carmoisine could interact with DNA via a groove-binding mode as evidenced by a hyperchromic effect of absorption spectra, increases in the fluorescence quenching effect of DNA, certain induced CD spectral changes, and relatively small changes in the viscosity of DNA. The binding constants (K_b) for the carmoisine with DNA was estimated to be 6.2 × 10⁴ M^?1 through spectroscopic titrations. The cyclic voltammetry method showed that both anodic and cathodic peak currents of carmoisine decreased upon addition of the DNA. Circular dichroism spectra indicated that there are certain detectable conformational changes such as conversion from B-like to A-like in the DNA double helix when carmoisine was added.     

Spectroscopic studies on the interaction of serum albumins with plant derived natural molecules

Serum Albumins are the most abundant transport protein and they are important in the transport and delivery of small molecules and drugs to different parts of the body. Their binding with various ligand molecules has an important role in the pharmaco-kinetic behavior of these molecules. Plant derived natural molecules; flavonoids, alkaloids, stilbenes and coumarins, possess valuable pharmacological and therapeutic potentials. Their interaction with serum albumins is an area of interest for many researchers. This article reviews the interaction of flavonoids, alkaloids, stilbenes and coumarins with human and bovine serum albumins studied using various spectroscopic techniques such as uv-visible absorption, fluorescence, circular dichroism (CD), Fourier transform infrared (FTIR), nuclear magnetic resonance (NMR) spectroscopy and molecular modeling methods. The present review will throw light on selecting, designing and optimizing these molecules for biomedical applications which can selectively target their binding sites.     

光谱法结合分子对接模拟技术研究头孢他啶与胰蛋白酶的相互作用机理

本文主要通过荧光光谱法与分子对接技术研究了在298,303,310 K温度下头孢他啶(CFD)与胰蛋白酶(TRP)之间的作用机制。研究结果表明,CFD与TRP之间是通过1∶1的静态猝灭方式相互作用。依照双对数方程处理荧光猝灭数据得到了CFD与TRP作用的结合常数Ka和结合位点数n。通过热力学方程求得了不同温度下CFD与TRP作用的热力学参数。实验数据表明,它们之间的作用力主要是疏水作用和氢键作用,这与分子对接技术所得的结果是一致的。     

In-Silico Study on the Interaction of Saffron Ligands and Beta-Lactoglobulin by Molecular Dynamics and Molecular Docking Approach

Safranal, crocetin, and dimethylcrocetin are secondary metabolites found in saffron and have a wide range of biological activities. An investigation of their interaction with a transport protein, such as β-lactoglobulin (β-lg), at the atomic level could be a valuable factor in controlling their transport to biological sites. The interaction of these ligands and β-lg as a transport protein was investigated using molecular docking and molecular dynamics (MD) simulation methods. The molecular docking results showed that safranal and crocetin bind on the surface of β-lg. However, dimethylcrocetin binds in the internal cavity of β-lg. The β-lg affinity for binding saffron ligands decreases in the following order: crocetin > dimethylcrocetin > safranal. The analysis of MD simulation trajectories showed that the β-lg and β-lg–ligand complexes became stable at approximately 3000 ps and that there was little conformational change in the β-lg–safranal and β-lg–dimethylcrocetin complexes over a 10-ns timescale. In addition, the profiles of atomic fluctuations showed the rigidity of the ligand binding site during the simulation time.     

Molecular mechanism investigation on the interaction of Clothianidin with human serum albumin

Abstract

With the widespread application of neonicotinoid insecticides, Clothianidin has received much attention due to the potential harm to human health and ecological environment. However, the mechanism of Clothianidin's underlying toxicity to organisms remains unclear. In this work, the interaction between Clothianidin and human serum albumin was investigated and the intrinsic fluorescence of human serum albumin got quenched via static mechanisms upon the addition of Clothianidin. The binding constants between Clothianidin and human serum albumin at three different temperature were obtained to be 3.543?×?10⁴, 2.995?×?10⁴, and 2.490?×?10⁴ M^?1, respectively. Based on the van't Hoff equation, the thermodynamic parameters, ΔH⁰ and ΔS⁰ were estimated to be ?53.885?KJ mol^?1 and ?110.535?J mol^?1K^?1, respectively. A single binding site was predicted from the binding constants at different temperatures by multiple spectroscopic techniques and the negative values of ΔH⁰ and ΔS⁰ indicated the binding of human serum albumin with Clothianidin was driven by hydrogen bonds or van der Waals forces. Furthermore, the loose and unfolded secondary structure of human serum albumin along with the addition of clothianidin had been observed through ultraviolet-visible absorption and circular dichroism spectra. In addition, it was also found that Clothianidin had polar effects of structural microenviroment not only on Trp but also Tyr residues from synchronous fluorescence analysis. This study illuminates the molecular mechanism of the interaction between human serum albumin and clothianidin for the first time and helps to construct a specific pesticide biosensor system of human health.