Exploring the binding mechanism of dihydropyrimidinones to human serum albumin: spectroscopic and molecular modeling techniques

The binding mechanism of molecular interaction between 5-(ethoxycarbonyl)-6-methyl-4-phenyl-3,4-dihydropyrimidin-2(1H)-one (a dihydropyrimidinones derivative, EMPD) and human serum albumin (HSA) was studied using spectroscopic methods and modeling technique. The quenching mechanism was investigated in terms of the binding constants and the basic thermodynamic parameters. The results of spectroscopic measurements suggested that EMPD have a strong ability to quench the intrinsic fluorescence of HSA through static quenching procedure. The drug-protein complex was stabilized by hydrophobic forces and hydrogen bonding as indicated from the thermodynamic parameters and synchronous fluorescence spectra, which was consistent with the results of molecular docking and accessible surface area calculation. Competitive experiments indicated that a displacement of warfarin by EMPD, which revealed that the binding site of EMPD to HSA was located at the subdomains IIA. The distance between the donor and the acceptor was 4.85nm as estimated according to F?rster's theory of non-radiation energy transfer. The effect of metal ions on the binding constants was also investigated. The results indicated that the binding constants between EMPD and HSA increased in the presence of common metal ions.     

Characterization of the interaction between a platinum(II) complex and human serum albumin: spectroscopic analysis and molecular docking

In this study, the interaction between (2,2?-bipyridine)(pyrrolidinedithiocarbamato) platinum(II) nitrate, [Pt(bpy)(pyr-dtc]NO₃, and human serum albumin (HSA) was investigated by various spectroscopic methods (UV–vis, fluorescence, CD and FT-IR) and molecular docking technique at three temperatures. UV–vis absorption spectroscopy showed that Pt(II) complex can denature the protein at moderate concentrations. The results of emission quenching at two temperatures has revealed that the quenching mechanism of Pt(II) complex with HSA was static quenching mechanism. Binding constants (K), binding site number (n) and corresponding thermodynamic parameters ?G?, ?H? and ?S? were calculated and revealed that hydrophobic forces played a major role when Pt(II) complex interacted with HSA. The binding distance (r) between above complex and HSA based on Förster?s theory of non-radiation energy transfer was calculated as 3.22 nm. Alterations of HSA secondary structure induced by complex were confirmed by FT-IR and CD measurements. Also, a molecular docking study was performed for identification of key structural features of binding of the Pt complex into the receptor and predicting bioactive conformers. Our results may provide valuable information to understand the mechanistic pathway of drug delivery and to pharmacological behavior of drug.     

Fluorometric and molecular modeling deciphering the non-covalent interaction between cyromazine and human serum albumin

Cyromazine (CMZ) had been believed to be one of the safest pesticides and widely used for many years until its carcinogenesis was revealed recently. In this work, the interaction between cyromazine and human serum albumin (HSA) was systematically investigated by multiple spectroscopic methods and molecular docking techniques using warfarin and flufenamic acid as probes. The results demonstrated the fluorescence of HSA had been quenched by CMZ through static mechanism, with new non-covalent complexes formed at ground state. Fluorescence probe experiments indicated CMZ bound to Sudlow’s site I in subdomain IIA of HSA, having no competition with site marker in site II. The number of binding sites, equilibrium constants and thermodynamic parameters were calculated by monitoring the binding equilibriums at different temperatures. The positive enthalpy change (ΔH ^θ) and entropy change (ΔS ^θ) implied the binding was mainly conducted by hydrophobic interactions. The binding was an endothermic, spontaneous (ΔG ^θ?<?0) and entropy-driven process which made the energy distribution of the system more evenly. The force of interaction and the conformation of binding pocket were displayed by molecular simulation and discussed at molecular level. Circular dichroism (CD) spectra indicated distorted α-helix content of HSA decreased while other fine secondary structure increased when CMZ was added.     

光谱-分子模拟法分析杨梅素与人血清白蛋白的分子作用机制

在模拟生理条件下,用多种光谱法结合分子对接法测定了杨梅素(MY)与人血清白蛋白(HSA)的相互作用.研究结果表明,MY能够明显猝灭HSA的荧光,MY与HSA的相互作用为复合式静态结合过程,结合强度较强.热力学和分子对接结果表明,MY与HSA是自发结合的,维持MY与HSA的相互作用力主要是氢键和范德华力.能量转移结果表明...     

The investigation of the interaction between NCP-EDA and bovine serum albumin by spectroscopic approaches

The fluorescence and ultraviolet spectroscopies were explored to study the interaction between N-confused porphyrins-edaravone diad (NCP-EDA) and bovine serum albumin (BSA) under simulative physiological condition at different temperatures. The experimental results show that the fluorescence quenching mechanism between NCP-EDA and BSA is a combined quenching (dynamic and static quenching). The binding constants, binding sites and the corresponding thermodynamic parameters (ΔG, ΔH, and ΔS) of the interaction system were calculated at different temperatures. According to F?rster non-radiation energy transfer theory, the binding distance between NCP-EDA and BSA was calculated to be 3.63 nm. In addition, the effect of NCP-EDA on the conformation of BSA was analyzed using synchronous fluorescence spectroscopy.     

Understanding the interaction of multi-walled carbon nanotubes with mutagenic organic pollutants using computational modeling and biological experiments

Carbon nanotubes (CNTs) are very promising materials to remove pollutants from the environment. To develop safe, efficient technologies, it is necessary to understand the mechanisms of interaction between CNTs and pollutants. This requires innovative, interdisciplinary approaches. Detailed chemical analysis of the CNTs along with computational modeling can provide important information about the mechanisms of interaction. If biological experiments are included in these studies, useful complementary information is obtained. To exemplify the use of this approach, we present a case study in which detailed calculations and the Salmonella mutagenicity assay were applied to elucidate how multi-walled CNTs interact with 1-nitropyrene, an important mutagenic pollutant.     

Binding interaction and conformational changes of human serum albumin with ranitidine studied by spectroscopic and time-resolved fluorescence methods

This study was designed to examine the interaction of histamine H₂-receptor antagonist drug ranitidine (RTN) with human serum albumin by multi-spectroscopic methods. The experimental results showed the involvement of dynamic quenching mechanism which was further confirmed by lifetime spectral studies. The binding constants (K _a) at three temperatures (288, 298, and 308 K) were 2.058 ± 0.020, 4.160 ± 0.010 and 6.801 ± 0.011 × 10⁴ dm³ mol^?1, respectively, and the number of binding sites (m) were 1.169, respectively; thermodynamic parameters ΔH ⁰ (44.152 ± 0.047 kJ mol^?1), ΔG ⁰ (?26.214 ± 0.040 kJ mol^?1), and ΔS ⁰ (236.130 ± 0.025 J K^?1 mol^?1) were calculated. The distance r between donor and acceptor was obtained (r = 3.40 nm) according to the Förster theory of non-radiative energy transfer. Synchronous fluorescence, CD, AFM and 3D fluorescence spectral results revealed the changes in secondary structure of the protein upon interaction with RTN. A molecular modeling study further confirmed the binding mode obtained by the experimental studies.     

Selective host-guest interaction of single-walled carbon nanotubes with functionalised fullerenes

Exohedrally functionalised fullerenes have been inserted in single-walled carbon nanotubes (SWNTs) with the aid of supercritical carbon dioxide to form peapods; C(61)(COOEt)(2) are encapsulated in SWNTs in high yield, whereas C(61)(COOH)(2) aggregate via hydrogen bonding to form a supramolecular complex, which sterically hinders encapsulation and causes it to adhere to the exterior surface of the SWNTs.     

Calorimetric and spectroscopic studies on the interaction of anticancer drug mitoxantrone with human serum albumin

Binding of the anticancer drug mitoxantrone with the protein human serum albumin (HSA) has been studied by using isothermal titration calorimetry (ITC), in combination with fluorescence, UV–visible, and circular dichroism spectroscopy. The thermodynamic parameters of binding have been evaluated from ITC and spectroscopic results and compared. The ITC results demonstrate that the binding of mitoxantrone with HSA occurs according to two sets of binding sites on the protein as opposed to the fluorescence and UV–visible spectroscopic results. Blockage of one binding site on HSA for mitoxantrone in the presence of NaCl indicates strong involvement of electrostatic interactions in the binding of the drug with the protein. An insignificant temperature dependence of the association constant observed in fluorescence measurements suggests a very low enthalpy of binding which is in close agreement with the results obtained from ITC measurements. Fluorescence life time measurements suggest formation of a static complex between mitoxantrone and HSA. The discrepancies in the ITC and fluorescence results suggest that one of the binding sites on the protein for mitoxantrone does not contain tryptophan residue in its immediate vicinity. The calorimetric and spectroscopic results have provided quantitative information on the binding of mitoxantrone with HSA and suggest that the binding is dominated by electrostatic interactions.     

Effect of pH on the interaction of vitamin B12 with bovine serum albumin by spectroscopic approaches

The interaction mechanism between vitamin B12 (B12, cyanocobalamin) and bovine serum albumin (BSA) has been investigated by fluorescence, synchronous fluorescence, ultraviolet-vis (UV) absorbance, and three-dimensional fluorescence. The intrinsic fluorescence of BSA was strongly quenched by the addition of B12 in different pH buffer solutions (pH 2.5, 3.5, 5.0, 7.4, and 9.0) and spectroscopic observations are mainly rationalized in terms of a static quenching process at lower concentration of B12 (C(B12)/C(BSA)<5) and a combined quenching process at higher concentration of B12 (C(B12)/C(BSA)>5). The structural characteristics of B12 and BSA were probed, and their binding affinities were determined under different pH conditions. The results indicated that the binding abilities of B12 to BSA in the acidic and basic pH regions (pH 2.5, 3.5, 5.0, and 9.0) were lower than that at simulating physiological condition (pH 7.4). In addition, the efficiency of energy transfer from tryptophan fluorescence to B12 was found to depend on the binding distance r between the donor and acceptor calculated using F?rster's theory. The effect of B12 on the conformation of BSA was analyzed using UV, synchronous fluorescence and three-dimensional fluorescence under different pH conditions. These results showed that the binding of B12 to BSA causes apparent change in the secondary and tertiary structures of BSA.     

The effects of single-walled carbon nanotubes (SWCNTs) on the structure and function of human serum albumin (HSA): Molecular docking and molecular dynamics simulation studies

Here, the interaction of single-walled carbon nanotubes (SWCNTs) and human serum albumin (HSA) as one of the most important proteins for carrying and binding of drugs was investigated and the impact of radius to volume ratio and chirality of the SWCNTs was evaluated using molecular docking method. Molecular docking results represented that zigzag SWCNT with radius to volume ratio equal to 6.77 × 10^?3 Å^?2 has the most negative binding energy (?17.16 kcal mol^?1) and binds to the HSA cleft by four π–cation interactions. To study the changes of HSA structure, the complex of HSA–SWCNT was subjected to 30 ns molecular dynamics simulation. The MD results showed that HSA was compressed about 2% after interaction with SWCNT. The equilibrated structure of HSA–SWCNT complex was used to compare the binding of warfarin to HSA in the absence and presence of SWCNT. The obtained results represent that warfarin-binding site was changed in the presence of SWCNT and its binding energy was increased. Really, warfarin was bound on the surface of SWCNT instead of its binding site on HSA. It means that HSA function as a carrier for warfarin is altered, the free concentration of warfarin is changed, and its release is decreased in the presence of SWCNT.     

Thermodynamic and structural changes associated with the interaction of a dirhamnolipid biosurfactant with bovine serum albumin

The interaction of a dirhamnolipid biosurfactant secreted by Pseudomonas aeruginosa with bovine serum albumin was studied by means of various physical techniques. Binding of the biosurfactant to bovine serum albumin was first characterized by isothermal titration calorimetry, showing that one or two molecules of dirhamnolipid, in the monomer state, bound to one molecule of the protein with high affinity. These results were confirmed by surface tension measurements in the absence and presence of bovine serum albumin. As seen by differential scanning calorimetry, dirhamnolipid shifted the temperature of the thermal unfolding of bovine serum albumin toward higher values, thus increasing the stability of the protein on heating. The impact of dirhamnolipid on the structure of the native protein was low, since most of the secondary structure remained unaffected upon interaction with the biosurfactant, as shown by FTIR spectroscopy. However, 2D correlation infrared spectroscopy indicated that the sequence of temperature-induced structural changes in native bovine serum albumin was modified by the presence of the biosurfactant. The consequences of these results in relation to possible applications of these dirhamnolipid biosurfactants for protein studies are discussed.     

Formation and structural observation of cesium encapsulated single-walled carbon nanotubes

Cesium encapsulation inside single-walled carbon nanotubes (SWNTs) is for the first time realized by ion irradiation of SWNTs immersed in a magnetized alkali-metal plasma, the configuration of which is confirmed to comprise three varieties by field emission type transmission electron microscopy (FE-TEM) and scanning TEM (STEM) observation.     

Interaction of coumarin derivatives with human serum albumin: investigation by fluorescence spectroscopic technique and modeling studies

Interactions of several 7-aminocoumarins with human serum albumin (HSA) were studied by using fluorescence spectroscopic technique and modeling studies. There is a large change in fluorescence spectral parameters like intensity, emission maxima and anisotropy for all aminocoumarins. There were two binding sites for cou-1, 311 and a single binding site for other coumarins. The binding constant(s) are large for all coumarins reflective of a strong binding. These spectral studies show that structural variants at the third, fourth and seventh position affects binding. The probable location of these coumarins in domain II has been predicted based on modeling. The effect of structural modification on the efficiency of binding was obtained for various other coumarins, using modeling.     

多壁碳纳米管对质谱分析中的血清蛋白富集作用研究

通过多壁碳纳米管(MWCNTs)对临床血清蛋白提取物进行富集处理,经表面增强激光解析离子化飞行时间质谱(SELDI-TOF-MS)检测,发现MWCNTs对血清中小分子量蛋白(<20 kDa)具有很好的富集效果。同时还考察了内径、长度等参数对血清蛋白富集效果的影响。该方法可用于临床血清样本中低丰度的小分子量蛋白的检测。     

Infrared spectroscopic study of O2 interaction with carbon nanotubes

Infrared reflection-absorption spectroscopic measurements have been performed on single-wall carbon nanotubes (SWNTs), cleaned by heating to approximately 500 degrees C in vacuo, during exposure to pure 16O2 or 18O2 at room temperature and at pressures of up to approximately 630 Torr. No vibrational signature of any form of adsorbed O is detected. However, structure is seen which is very similar to that observed for the adsorption of atomic H or D and which indicates changes in the SWNT vibrational spectrum. The close similarity between the spectra for atomic H and D, on one hand, and O2 on the other is an unexpected result. Changes are also noted in the broad background extending throughout the mid-IR which arises from the Drude contribution to the reflectance. All these effects increase with O2 exposure and are essentially irreversible upon evacuation of the gas. The results are consistent with other data indicating that O2 interacts only weakly with, and does not chemisorb on, pristine regions of the SWNT under these conditions. The small and irreversible effects seen upon O2 exposure are interpreted in terms of enhanced chemisorption, at or near defective regions of the SWNT wall, which saturates at a low O coverage.     

Interaction between phillygenin and human serum albumin based on spectroscopic and molecular docking

In this paper, the interaction of human serum albumin (HSA) with phillygenin was investigated by fluorescence, circular dichroism (CD), UV-vis spectroscopic and molecular docking methods under physiological conditions. The Stern-Volmer analysis indicated that the fluorescence quenching of HSA by phillygenin resulted from static mechanism, and the binding constants were 1.71×10(5), 1.61×10(5) and 1.47×10(4) at 300, 305 and 310K, respectively. The results of UV-vis spectra show that the secondary structure of the protein has been changed in the presence of phillygenin. The CD spectra showed that HSA conformation was altered by phillygenin with a major reduction of α-helix and an increase in β-sheet and random coil structures, indicating a partial protein unfolding. The distance between donor (HSA) and acceptor (phillygenin) was calculated to be 3.52nm and the results of synchronous fluorescence spectra showed that binding of phillygenin to HSA can induce conformational changes in HSA. Molecular docking experiments found that phillygenin binds with HSA at IIIA domain of hydrophobic pocket with hydrogen bond interactions. The ionic bonds were formed with the O (4), O (5) and O (6) of phillygenin with nitrogen of ASN109, ARG186 and LEU115, respectively. The hydrogen bonds are formed between O (2) of phillygenin and SER419. In the presence of copper (II), iron (III) and alcohol, the apparent association constant K(A) and the number of binding sites of phillygenin on HSA were both decreased in the range of 88.84-91.97% and 16.09-18.85%, respectively. In view of the evidence presented, it is expected to enrich our knowledge of the interaction dynamics of phillygenin to the important plasma protein HSA, and it is also expected to provide important information of designs of new inspired drugs.     

A spectroscopic study on the interaction between the anticancer drug erlotinib and human serum albumin

The interaction between erlotinib and human serum albumin (HSA) in simulated physiological conditions was investigated by spectroscopic methods. The results revealed that erlotinib caused the fluorescence quenching of HSA through a static quenching procedure. The binding constants at 293, 298, 303 and 308 K were obtained as 2.53 × 10⁵, 8.13 × 10⁴, 3.59 × 10⁴ and 1.93 × 10⁴ M^?1, respectively. There may be one binding site of erlotinib on HSA at 298 K. The thermodynamic parameters indicated that the interaction between erlotinib and HSA was driven mainly by hydrogen bonding or van der Waals forces. Synchronous fluorescence spectra, UV–Vis spectra, circular dichroism and Fourier Transform infrared spectroscopy results showed erlotinib binding slightly changed the conformation of HSA with secondary structural content changes. Förster resonance energy transfer study revealed high possibility of energy transfer with erlotinib-Trp-214 distance of 3.48 nm. The results of the present study may provide valuable information for studying the distribution, toxicological and pharmacological mechanisms of erlotinib in vivo.     

Study of the interaction of aglycon of daunorubicin with human serum albumin by spectroscopy and modeling

The interaction between aglycon of daunorubicin (DNR-A) and human serum albumin (HSA) was investigated using fluorescence quenching and modeling. Results shown that fluorescence quenching of HSA by DNR-A resulted from the formation of DNR-A-HSA complex. The quenching constants were determined via measurement of the binding affinity between DNR-A and HSA using the Stern-Volmer equation. The thermodynamic parameters DeltaG, DeltaH, DeltaS and the binding distance r were calculated. Furthermore, SFS and UV spectra suggested that the complex changed the conformation of HSA and that hydrophobic interactions played a major role in DNR-A-HSA association, which was in good agreement with the results of the modeling study. Moreover, the SFS technique was successfully applied to determine the total proteins in biology samples with satisfactory results.     

Characterization of the interaction between 8-bromoadenosine with human serum albumin and its analytical application

This study was designed to examine the interaction of 8-bromoadenosine with human serum albumin (HSA) by fluorescence spectroscopy in combination with molecular modeling under simulative physiological conditions. The results of fluorescence measurements indicate that 8-bromoadenosine has a strong ability to quench the intrinsic fluorescence of HSA through static quenching procedure. The binding constants (K) at different temperatures and thermodynamic parameters, enthalpy changes (ΔH) and entropy changes (ΔS) were calculated according to the fluorescence data. The results showed that the hydrophobic force played the major role in the binding of 8-bromoadenosine to HSA. The fluorescence experimental results were in agreement with the results obtained by molecular modeling study. The effects of some normal positive and negative ions on the binding constants were also discussed. Moreover, the synchronous fluorescence technique was used to characterize the interaction of 8-bromoadenosine to HSA and successfully applied to determine the total proteins in human serum, urine and saliva samples at room temperature under the optimum conditions with a wide linear range and satisfactory results.