The binding of Tb 3+ to chicken apoovotransferrin was studied by monitoring the fluorescent intensity of Tb 3+ at 549 nm. The conditional equilibrium constants for the complexation of Tb 3+ by chicken apoovotransferri...The binding of Tb 3+ to chicken apoovotransferrin was studied by monitoring the fluorescent intensity of Tb 3+ at 549 nm. The conditional equilibrium constants for the complexation of Tb 3+ by chicken apoovotransferrin in 0 1 mol/L hepes, at pH 7 4 and room temperature were measured. The successive macroscopic binding constants are lg K 1=9 08±0 12 and lg K 2=7 36±0 22. The molar fluorescence enhancement of Tb 3+ apoovotransferrin complex is (2 06±0 14)×10 4 mol -1 ·L. The fluorescence quenching experiment and the titration of N terminal monoferric ovotransferrin showed that Tb 3+ has a preference for being bound to the N terminal binding site of apoovotransferrin.展开更多
Sevelamer Carbonate is a crossolinked polymeric amine, it is the active ingredient in Renvela Tablets. Sevelamer Carbonate is indicated for the control of hyperphosphatamiea in patients with end-stage renal disease. T...Sevelamer Carbonate is a crossolinked polymeric amine, it is the active ingredient in Renvela Tablets. Sevelamer Carbonate is indicated for the control of hyperphosphatamiea in patients with end-stage renal disease. The binding parameter constants of Sevelamer Carbonate were determined using the Langmuir approximation for the dosage form at pH 4.0 and 7.0 by Ion Chromatography. An Ion Chromatogrpahy method has been developed to estimate free phosphate in in-vitro phosphate binding study of Sevelamer Carbonate Tablets. The method is selective and capable of detecting phosphate in the presence of placebo matrix. The method has been validated with a lower limit of quantitation of 0.2 mM for Phosphate. A linear response function was established in the range of concentrations 0.2 - 30.0 mM (r > 0.99) for Phosphate. The intra and inter day precision values for Phosphate met the acceptance as per Food and Drug Administrations guidelines. Phosphate was stable in the set of stability studies viz. bench-top and autosampler. The developed method was applied to in-vitro phosphate binding studies of Sevelamer Carbonate Tablets.展开更多
Sevelamer Hydrochloride is a crossolinked polymeric amine;it is the active ingredient in Renagel Tablets. Sevelamer Hydrochloride is indicated for the control of hyperphosphatamiea in patients with end-stage renal dis...Sevelamer Hydrochloride is a crossolinked polymeric amine;it is the active ingredient in Renagel Tablets. Sevelamer Hydrochloride is indicated for the control of hyperphosphatamiea in patients with end-stage renal disease. The binding parameter constants of Sevelamer Hydrochloride were determined using the Langmuir approximation for the dosage form at pH 4.0 and 7.0 by Inductively Coupled Plasma-Optical Emission Spectrometry. An ICP-OES method has been developed to estimate free phosphate in In-Vitro phosphate binding study of Sevelamer HCl Tablets. The method is selective and capable of detecting phosphate in the presence of placebo matrix. The method has been validated with a lower limit of quantitation of 0.2 mM for Phosphate. A linear response function was established for the range of concentrations 0.2 - 25.0 mM (r > 0.99) for Phosphate. The intra and inter day precision values for Phosphate met the acceptance as per Food and Drug Administrations guidelines. Phosphate was stable in the set of stability studies viz. bench-top and autosampler. The developed method was applied to in-vitro phosphate binding studies of Sevelamer HCl Tablets.展开更多
Binding kinetic properties of protein–ligand complexes are crucial factors affecting the drug potency.Nevertheless,the current in silico techniques are insufficient in providing accurate and robust predictions for bi...Binding kinetic properties of protein–ligand complexes are crucial factors affecting the drug potency.Nevertheless,the current in silico techniques are insufficient in providing accurate and robust predictions for binding kinetic properties.To this end,this work develops a variety of binding kinetic models for predicting a critical binding kinetic property,dissociation rate constant,using eight machine learning(ML)methods(Bayesian Neural Network(BNN),partial least squares regression,Bayesian ridge,Gaussian process regression,principal component regression,random forest,support vector machine,extreme gradient boosting)and the descriptors of the van der Waals/electrostatic interaction energies.These eight models are applied to two case studies involving the HSP90 and RIP1 kinase inhibitors.Both regression results of two case studies indicate that the BNN model has the state-of-the-art prediction accuracy(HSP90:R^(2)_(test)=0:947,MAE_(test)=0.184,rtest=0.976,RMSE_(test)=0.220;RIP1 kinase:R^(2)_(test)=0:745,MAE_(test)=0.188,rtest=0.961,RMSE_(test)=0.290)in comparison with other seven ML models.展开更多
Although enantiomers of 2-phenylpropionic acids (2-PPAs), or profens are important group of nonsteroidal anti-inflammatory drugs (NSAIDs) and have been in clinical use for many years, there is no literature covering i...Although enantiomers of 2-phenylpropionic acids (2-PPAs), or profens are important group of nonsteroidal anti-inflammatory drugs (NSAIDs) and have been in clinical use for many years, there is no literature covering its binding interaction in particular with cyclodextrins. NSAIDs are marketed as racemates, chiral discrimination and knowledge of enantiomeric bioavailability is essential. Circular dichroism (CD) spectroscopy is the technique of choice for elucidating chirality and monitoring and characterizing molecular recognition phenomena in solution. Methods em-ploying the fundamentals of the simultaneous measurements of absorbance and CD and a novel efficient titration method have been developed to study the binding of β-Cyclodextrin (β-CyD) and the two enantiomers of 2-PPA as a function of pH. The effect on physicochemical properties and bioavailability was investigated. The binding constant, stoichiometry and pKa for both the free and the bound drugs were determined using a Levenburg-Marquadt non-linear equation. The exact nature of the enantiomer discriminating interactions by cyclodextrins (CyDs) is not well understood. In this work, the interactions and co-conformations of both enantiomers of 2-PPA with β-CyD were explained and es-timated using spectroscopic variations upon complexation. The results indicated a change in the physicochemical prop-erties of 2-PPAs upon complexation and highlighted the enantioselective binding of β-CyD as a function of pH. The charge on the vip molecule and its stereochemistry are of great importance in regulating the stability of the vip/β-CyD complexes;hence the bioavailability of drugs. This work elucidates 2-PPAs/β-CyD binding interactions and highlights the effect of β-CyD on drugs with an effective novel method for binding titration and the potential of the simultaneous measurements of absorbance and CD in future chiral drug interactions studies.展开更多
Structural characteristics and proton binding properties of sub-fractions（FA3–FA13） of fulvic acid（FA）, eluted stepwise by pyrophosphate buffer were examined by use of fluorescence titration combined with fluores...Structural characteristics and proton binding properties of sub-fractions（FA3–FA13） of fulvic acid（FA）, eluted stepwise by pyrophosphate buffer were examined by use of fluorescence titration combined with fluorescence regional integration（FRI） and differential fluorescence spectroscopy（DFS）. Humic-like（H-L） and fulvic-like（F-L） materials, which accounted for more than 80% of fluorescence response, were dominant in five sub-fractions of FA. Based on FRI analysis, except the response of F-L materials in FA9 and FA13, maximum changes in percent fluorescence response were less than 10% as pH was increased from 2.5 to 11.5.Contents of carboxylic and phenolic groups were compared for fluorescence peaks of FA sub-fractions based on pH-dependent fluorescence derived from DFS. Static quenching was the dominant mechanism for binding of protons by FA sub-fractions. Dissociation constants（p Ka） were calculated by use of results of DFS and the modified Stern-Volmer relationship. The p Kaof H-L, F-L, tryptophan-like and tyrosine-like materials of FA subfractions exhibited ranges of 3.17–4.06, 3.12–3.97, 4.14–4.45 and 4.25–4.76, respectively, for acidic pHs. At basic pHs, values of p Ka for corresponding materials were in ranges of 9.71–10.24, 9.62–10.99, 9.67–10.31 and 9.33–10.28, respectively. At acidic pH, protein-like（P-L）materials had greater affinities for protons than did either H-L or F-L materials. The dicarboxylic and phenolic groups were likely predominant sites of protonation for both H-L and F-L materials at both acidic and basic pHs. Amino acid groups were significant factors during proton binding to protein-like materials of FA sub-fractions at basic pH.展开更多
The binding constant（KDOM） of pyrene onto different molecular weight（Mw） fractions of a dissolved organic matter（DOM） extract from an estuarine sediment was measured via a fluorescence quenching method,and the p...The binding constant（KDOM） of pyrene onto different molecular weight（Mw） fractions of a dissolved organic matter（DOM） extract from an estuarine sediment was measured via a fluorescence quenching method,and the possible binding mechanisms were discussed.The influence of water chemical parameters on pyrene binding was studied to elucidate the effects of DOM steric conformation.DOM fraction with larger M w（14000） showed a greater KDOM（2.02×10 5） than that with smaller Mw did,and the KDOMs were 1.16×105 and 1.13×105 for the fractions with M w of 1000―14000 and 1000,respectively.The K DOM s of different M w DOM fractions were correlated positively with the atomic ratio of C/H and absorbance at 280 nm;while a negative correlation existed between K DOM and（O＋C）/N（atomic ratio）,and K DOM and O-containing groups.These correlations indicate the positive influence of aromatic structure and the negative effect of polarity on DOM binding capacity.Infrared spectroscopy revealed that specific interactions existed between pyrene and the DOM fraction with larger M W besides hydrophobic partition,i.e.,NH-π interaction in DOM moiety（1000―14000） and π-π electron donor acceptor（EDA） forces in DOM moiety（14000）.KDOM varied in a complex pattern with increasing cation concentration and pH,which could be explained by the change in DOM steric conformation.Formed aggregates favored the lipophilic partition of pyrene.However,the accessibility to some interior binding sites became low when the aggregate was too large,leading to a reduced KDOM.展开更多
The interaction of baicalein with bovine serum albumin（BSA） was investigated with the help of spectroscopic and molecular docking studies.The binding affinity of baicalein towards BSA was estimated to be in order of...The interaction of baicalein with bovine serum albumin（BSA） was investigated with the help of spectroscopic and molecular docking studies.The binding affinity of baicalein towards BSA was estimated to be in order of 10~5 M^（-1） from fluorescence quenching studies.Negative ΔH°（-5.66 ＋ 0.14 kJ/mol） and positive（ΔS°）（＋ 79.96 ＋ 0.65J/mol K） indicate the presence of electrostatic interactions along with the hydrophobic forces that result in a positive ΔS°.The hydrophobic association of baicalein with BSA diminishes in the presence of sodium dodecyl sulfate（SDS） due to probable hydrophobic association of baicalein with SDS,resulting in a negative ΔS°（-40.65 ＋ 0.87 J/mol K）.Matrix-assisted laser desorption ionization/time of flight（MALDI-TOF） experiments indicate a 1：1 complexation between baicalein and BSA.The unfolding and refolding phenomena of BSA were investigated in the absence and presence of baicalein using steady-state and fluorescence lifetime measurements.It was observed that the presence of urea ruptured the non-covalent interaction between baicalein and BSA.The presence of metal ions（Ag~＋,Mg^（2＋）,Ni^（2＋）,Mn^（2＋）,Co^（2＋） and Zn^（2＋）） increased the binding affinity of ligand towards BSA.The changes in conformational aspects of BSA after ligand binding were also investigated using circular dichroism（CD） and Fourier transform infrared（FT-IR） spectroscopic techniques.Site selectivity studies following molecular docking analyses indicated the binding of baicalein to site 1（subdomain MA） of BSA.展开更多
The parasite Plasmodium falciparum is responsible for the major world scourge malaria, a disease that affects 3.3 billion people worldwide. The development of new drugs is critical because of the diminished effectiven...The parasite Plasmodium falciparum is responsible for the major world scourge malaria, a disease that affects 3.3 billion people worldwide. The development of new drugs is critical because of the diminished effectiveness of current antimalarial agents mainly due to parasitic resistance, side effects and cost. Molecular docking was used to explore structural motifs responsible for the interactions between triose phosphate isomerase (TPI), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and aldolase (ALD) from human and Plasmodium cells with 8 novel sufonylamide derivatives. All the ligands modeled, interact with all three enzymes in the micromolar range. The top ligand (sulfaE) shows a 70-fold increase in selective binding to pfTPI compared to hTPI (dissociation constant-KI of 7.83 μM and 0.177 μM for hTPI and pfTPI respectively), on par with antimalarial drug chloroquine.ALD and GAPDH form complexes with similar binding sites, comprising amino acids of similar chemical properties and polarities. Human TPI and pfTPI bind sulfonamide derivatives using two distinct binding sites and residues. Key residues at the dimer interface of pfTPI (VAL44, SER45, TYR48, GLN64, ASN65, VAL78) form a tight pocket with favorable polar contacts. The affinity with TPI is the most specific, stable, and selective suggesting pfTPI is a candidate for development of antimalarial drugs.展开更多
A new simple and reliable in-situ mercury film sensor coupled with affinity differential pulse stripping voltammetry (ADSPV) or affinity cyclic voltammetry (ACV) was investigated. The interaction of fenoprofen with bo...A new simple and reliable in-situ mercury film sensor coupled with affinity differential pulse stripping voltammetry (ADSPV) or affinity cyclic voltammetry (ACV) was investigated. The interaction of fenoprofen with bovine serum albumin (BSA) onto the proposed electrochemical sensor was studied. The nature of the electrochemical process of fenoprofen by cyclic voltammetry was depicted. Reproducibility of the proposed method was checked giving a precision of 0.073 standard deviation. The limit of detection and limit of quantification were 7.0 and 22.0 nmol/L, respectively. Fenoprofen was interacted with BSA by 1:1 stoichiometry to form electroinactive supramolecular complex. The binding constant was precisely estimated by non-linear regression analysis based on the shifting of analyte peak potentials. The proposed experiments and data analysis could be used to investigate the drug-protein binding constant within a short analysis time compared to other chromatographic techniques.展开更多
NF-κB plays a crucial role in regulating various biological processes including innate and adaptive immunity, inflammation, stress responses, B-cell development, and lymphoid organogenesis. Currently, several assays ...NF-κB plays a crucial role in regulating various biological processes including innate and adaptive immunity, inflammation, stress responses, B-cell development, and lymphoid organogenesis. Currently, several assays like electrophoretic mobility shift assay (EMSA), enzyme-linked immunosorbent assay (ELISA), fluorescence resonance energy transfer (FRET) and time-resolved fluorescence resonance energy transfer (TR-FRET) are widely used for studying the NFκB intraction with β-IFN-κB binding oligo. Each of these techniques has varying utility with distinct strengths and weaknesses. We describe a method AlphaLISA to identify NFκB p50 protein and β-IFN-κB binding oligo sequence and interaction is efficient at a given concentration (10 nM) in the EMSA and Biacore’s SPR assays. The method has many advantages such as use of small volume, high throughput (HTP), convenience of sample preparation and data analysis.展开更多
The binding pursuits of trans-resveratrol(t-RSV),an amazing health supplement are investigated with an antioxidant enzyme,superoxide dismutase(SOD1).The aim of the study is to dock t-RSV on the adrenaline binding site...The binding pursuits of trans-resveratrol(t-RSV),an amazing health supplement are investigated with an antioxidant enzyme,superoxide dismutase(SOD1).The aim of the study is to dock t-RSV on the adrenaline binding site on SOD1 in order to explore its potential to act as a safety net against amyotrophic lateral sclerosis(ALS),a fatal neurodegenerative disorder that affects motor neurons.In silico GLIDE docking methodology and in vitro microcalorimetry technique is utilized for the investigation of binding parameters of t-RSV with SOD1.The study provides useful and distinct information about the amino acids involved in the interactions at molecular level along with the nature of forces involved in binding of t-RSV with SOD1.The docking analysis using the scoring functions of Schrodinger’s Glide package depicts that GLU100,PRO28,LYS23,TRP32 residues of the peptide backbone on SOD1 interact with phenolic groups of t-RSV.The information on thermodynamic parameters,i.e.binding constant(Kb),free energy(△G)and enthalpy(△H)generated through calorimetric titrations suggests that the reaction between t-RSV and SOD1 is spontaneous and exothermic.Both the studies are found to be in close agreement with each other based as far as the magnitude of binding constant(Kb=9.9×10^4)is concerned.展开更多
Machine learning methodologies have been extensively leveraged across diverse domains of chemical research,yielding remarkable outcomes,and exhibit substantial potential for impactful future applications within the fi...Machine learning methodologies have been extensively leveraged across diverse domains of chemical research,yielding remarkable outcomes,and exhibit substantial potential for impactful future applications within the field of supramolecular chemistry.The recognition of alkali metal ions by crown ethers is one of the most classic and widely applied host-vip interactions in supramolecular chemistry.Due to the numerous factors affecting the host-vip interaction,it remains a great challenge to achieve fast and accurate prediction of the binding constants between crown ethers and alkali metal ions.Herein,we report a highly accurate machine learning model that can effectively predict the binding constants between crown ethers and alkali metal ions,i.e.,CrownBind-IA,with a low RMSE of 0.68 logK units.Moreover,this model proves robust extrapolative capabilities by accurately predicting out-of-sample data.The establishment of CrownBind-IA demonstrates the promising application potentials of data-driven machine learning methods in supramolecular chemistry,and it will substantially reduce the time and expense of experimental trials and characterizations,promote the exploration of the mechanism of host-vip interactions,as well as the rational design of novel functional supramolecular host molecules.展开更多
AIM To study the interaction between ciprofloxacin and BSA in physiological condition by fluorescence spectroscopy. METHODS The affection of drug to the protein conformation was investigated. The binding constant betw...AIM To study the interaction between ciprofloxacin and BSA in physiological condition by fluorescence spectroscopy. METHODS The affection of drug to the protein conformation was investigated. The binding constant between drug and BSA from a double reciprocal Lineweaver Burk plot was determined and the main sort of binding force was found according to the thermodynamic parameters. RESULTS The binding constants between BSA and ciprofloxacin at 26℃and 45℃ are about 10 4. At 26℃, the thermodynamic parameters of reaction between BSA and ciprofloxacin are Δ H = -49 13 kJ·mol -1 , Δ G = -26 45 kJ·mol -1 , Δ S = -75 kJ·mol -1 . The maximum wavelength of the synchronous fluorescence spectra of BSA moved from 279 nm to 289nm with the incresing of the amount of ciprofloxacin. CONCLUSION There exists fluorescence energy transfer between BSA and ciprofloxacin. The main sort of binding force between BSA and ciprofloxacin is Van der Waals′ interaction. Ciprofloxacin can be deposited and be transported by serum protein in vivo . Ciprofloxacin affects the protein conformation.展开更多
文摘The binding of Tb 3+ to chicken apoovotransferrin was studied by monitoring the fluorescent intensity of Tb 3+ at 549 nm. The conditional equilibrium constants for the complexation of Tb 3+ by chicken apoovotransferrin in 0 1 mol/L hepes, at pH 7 4 and room temperature were measured. The successive macroscopic binding constants are lg K 1=9 08±0 12 and lg K 2=7 36±0 22. The molar fluorescence enhancement of Tb 3+ apoovotransferrin complex is (2 06±0 14)×10 4 mol -1 ·L. The fluorescence quenching experiment and the titration of N terminal monoferric ovotransferrin showed that Tb 3+ has a preference for being bound to the N terminal binding site of apoovotransferrin.
文摘Sevelamer Carbonate is a crossolinked polymeric amine, it is the active ingredient in Renvela Tablets. Sevelamer Carbonate is indicated for the control of hyperphosphatamiea in patients with end-stage renal disease. The binding parameter constants of Sevelamer Carbonate were determined using the Langmuir approximation for the dosage form at pH 4.0 and 7.0 by Ion Chromatography. An Ion Chromatogrpahy method has been developed to estimate free phosphate in in-vitro phosphate binding study of Sevelamer Carbonate Tablets. The method is selective and capable of detecting phosphate in the presence of placebo matrix. The method has been validated with a lower limit of quantitation of 0.2 mM for Phosphate. A linear response function was established in the range of concentrations 0.2 - 30.0 mM (r > 0.99) for Phosphate. The intra and inter day precision values for Phosphate met the acceptance as per Food and Drug Administrations guidelines. Phosphate was stable in the set of stability studies viz. bench-top and autosampler. The developed method was applied to in-vitro phosphate binding studies of Sevelamer Carbonate Tablets.
文摘Sevelamer Hydrochloride is a crossolinked polymeric amine;it is the active ingredient in Renagel Tablets. Sevelamer Hydrochloride is indicated for the control of hyperphosphatamiea in patients with end-stage renal disease. The binding parameter constants of Sevelamer Hydrochloride were determined using the Langmuir approximation for the dosage form at pH 4.0 and 7.0 by Inductively Coupled Plasma-Optical Emission Spectrometry. An ICP-OES method has been developed to estimate free phosphate in In-Vitro phosphate binding study of Sevelamer HCl Tablets. The method is selective and capable of detecting phosphate in the presence of placebo matrix. The method has been validated with a lower limit of quantitation of 0.2 mM for Phosphate. A linear response function was established for the range of concentrations 0.2 - 25.0 mM (r > 0.99) for Phosphate. The intra and inter day precision values for Phosphate met the acceptance as per Food and Drug Administrations guidelines. Phosphate was stable in the set of stability studies viz. bench-top and autosampler. The developed method was applied to in-vitro phosphate binding studies of Sevelamer HCl Tablets.
基金financial supports of“the Fundamental Research Funds for the Central Universities”(DUT22YG218),NSFC(22278053,22078041)China Postdoctoral Science Foundation(2022M710578)“the Dalian High-level Talents Innovation Support Program”(2021RQ105).
文摘Binding kinetic properties of protein–ligand complexes are crucial factors affecting the drug potency.Nevertheless,the current in silico techniques are insufficient in providing accurate and robust predictions for binding kinetic properties.To this end,this work develops a variety of binding kinetic models for predicting a critical binding kinetic property,dissociation rate constant,using eight machine learning(ML)methods(Bayesian Neural Network(BNN),partial least squares regression,Bayesian ridge,Gaussian process regression,principal component regression,random forest,support vector machine,extreme gradient boosting)and the descriptors of the van der Waals/electrostatic interaction energies.These eight models are applied to two case studies involving the HSP90 and RIP1 kinase inhibitors.Both regression results of two case studies indicate that the BNN model has the state-of-the-art prediction accuracy(HSP90:R^(2)_(test)=0:947,MAE_(test)=0.184,rtest=0.976,RMSE_(test)=0.220;RIP1 kinase:R^(2)_(test)=0:745,MAE_(test)=0.188,rtest=0.961,RMSE_(test)=0.290)in comparison with other seven ML models.
文摘Although enantiomers of 2-phenylpropionic acids (2-PPAs), or profens are important group of nonsteroidal anti-inflammatory drugs (NSAIDs) and have been in clinical use for many years, there is no literature covering its binding interaction in particular with cyclodextrins. NSAIDs are marketed as racemates, chiral discrimination and knowledge of enantiomeric bioavailability is essential. Circular dichroism (CD) spectroscopy is the technique of choice for elucidating chirality and monitoring and characterizing molecular recognition phenomena in solution. Methods em-ploying the fundamentals of the simultaneous measurements of absorbance and CD and a novel efficient titration method have been developed to study the binding of β-Cyclodextrin (β-CyD) and the two enantiomers of 2-PPA as a function of pH. The effect on physicochemical properties and bioavailability was investigated. The binding constant, stoichiometry and pKa for both the free and the bound drugs were determined using a Levenburg-Marquadt non-linear equation. The exact nature of the enantiomer discriminating interactions by cyclodextrins (CyDs) is not well understood. In this work, the interactions and co-conformations of both enantiomers of 2-PPA with β-CyD were explained and es-timated using spectroscopic variations upon complexation. The results indicated a change in the physicochemical prop-erties of 2-PPAs upon complexation and highlighted the enantioselective binding of β-CyD as a function of pH. The charge on the vip molecule and its stereochemistry are of great importance in regulating the stability of the vip/β-CyD complexes;hence the bioavailability of drugs. This work elucidates 2-PPAs/β-CyD binding interactions and highlights the effect of β-CyD on drugs with an effective novel method for binding titration and the potential of the simultaneous measurements of absorbance and CD in future chiral drug interactions studies.
基金supported by the National Natural Science Foundation of China(Nos.41173084,41521003,41573130,41630645,41703115 and 41503104)the Beijing Natural Science Foundation(No.8162044)the Canada Research Chair program,Einstein Professor Program of the Chinese Academy of Sciences,and the High Level Foreign Experts Program(#GDT20143200016)
文摘Structural characteristics and proton binding properties of sub-fractions（FA3–FA13） of fulvic acid（FA）, eluted stepwise by pyrophosphate buffer were examined by use of fluorescence titration combined with fluorescence regional integration（FRI） and differential fluorescence spectroscopy（DFS）. Humic-like（H-L） and fulvic-like（F-L） materials, which accounted for more than 80% of fluorescence response, were dominant in five sub-fractions of FA. Based on FRI analysis, except the response of F-L materials in FA9 and FA13, maximum changes in percent fluorescence response were less than 10% as pH was increased from 2.5 to 11.5.Contents of carboxylic and phenolic groups were compared for fluorescence peaks of FA sub-fractions based on pH-dependent fluorescence derived from DFS. Static quenching was the dominant mechanism for binding of protons by FA sub-fractions. Dissociation constants（p Ka） were calculated by use of results of DFS and the modified Stern-Volmer relationship. The p Kaof H-L, F-L, tryptophan-like and tyrosine-like materials of FA subfractions exhibited ranges of 3.17–4.06, 3.12–3.97, 4.14–4.45 and 4.25–4.76, respectively, for acidic pHs. At basic pHs, values of p Ka for corresponding materials were in ranges of 9.71–10.24, 9.62–10.99, 9.67–10.31 and 9.33–10.28, respectively. At acidic pH, protein-like（P-L）materials had greater affinities for protons than did either H-L or F-L materials. The dicarboxylic and phenolic groups were likely predominant sites of protonation for both H-L and F-L materials at both acidic and basic pHs. Amino acid groups were significant factors during proton binding to protein-like materials of FA sub-fractions at basic pH.
基金Supported by the National Natural Science Foundation of China(Nos.20737002,41073087)
文摘The binding constant（KDOM） of pyrene onto different molecular weight（Mw） fractions of a dissolved organic matter（DOM） extract from an estuarine sediment was measured via a fluorescence quenching method,and the possible binding mechanisms were discussed.The influence of water chemical parameters on pyrene binding was studied to elucidate the effects of DOM steric conformation.DOM fraction with larger M w（14000） showed a greater KDOM（2.02×10 5） than that with smaller Mw did,and the KDOMs were 1.16×105 and 1.13×105 for the fractions with M w of 1000―14000 and 1000,respectively.The K DOM s of different M w DOM fractions were correlated positively with the atomic ratio of C/H and absorbance at 280 nm;while a negative correlation existed between K DOM and（O＋C）/N（atomic ratio）,and K DOM and O-containing groups.These correlations indicate the positive influence of aromatic structure and the negative effect of polarity on DOM binding capacity.Infrared spectroscopy revealed that specific interactions existed between pyrene and the DOM fraction with larger M W besides hydrophobic partition,i.e.,NH-π interaction in DOM moiety（1000―14000） and π-π electron donor acceptor（EDA） forces in DOM moiety（14000）.KDOM varied in a complex pattern with increasing cation concentration and pH,which could be explained by the change in DOM steric conformation.Formed aggregates favored the lipophilic partition of pyrene.However,the accessibility to some interior binding sites became low when the aggregate was too large,leading to a reduced KDOM.
基金Department of Science and Technology(DST,Project no.SR/SO/BB-54/2007),Government of India for financial support
文摘The interaction of baicalein with bovine serum albumin（BSA） was investigated with the help of spectroscopic and molecular docking studies.The binding affinity of baicalein towards BSA was estimated to be in order of 10~5 M^（-1） from fluorescence quenching studies.Negative ΔH°（-5.66 ＋ 0.14 kJ/mol） and positive（ΔS°）（＋ 79.96 ＋ 0.65J/mol K） indicate the presence of electrostatic interactions along with the hydrophobic forces that result in a positive ΔS°.The hydrophobic association of baicalein with BSA diminishes in the presence of sodium dodecyl sulfate（SDS） due to probable hydrophobic association of baicalein with SDS,resulting in a negative ΔS°（-40.65 ＋ 0.87 J/mol K）.Matrix-assisted laser desorption ionization/time of flight（MALDI-TOF） experiments indicate a 1：1 complexation between baicalein and BSA.The unfolding and refolding phenomena of BSA were investigated in the absence and presence of baicalein using steady-state and fluorescence lifetime measurements.It was observed that the presence of urea ruptured the non-covalent interaction between baicalein and BSA.The presence of metal ions（Ag~＋,Mg^（2＋）,Ni^（2＋）,Mn^（2＋）,Co^（2＋） and Zn^（2＋）） increased the binding affinity of ligand towards BSA.The changes in conformational aspects of BSA after ligand binding were also investigated using circular dichroism（CD） and Fourier transform infrared（FT-IR） spectroscopic techniques.Site selectivity studies following molecular docking analyses indicated the binding of baicalein to site 1（subdomain MA） of BSA.
文摘The parasite Plasmodium falciparum is responsible for the major world scourge malaria, a disease that affects 3.3 billion people worldwide. The development of new drugs is critical because of the diminished effectiveness of current antimalarial agents mainly due to parasitic resistance, side effects and cost. Molecular docking was used to explore structural motifs responsible for the interactions between triose phosphate isomerase (TPI), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and aldolase (ALD) from human and Plasmodium cells with 8 novel sufonylamide derivatives. All the ligands modeled, interact with all three enzymes in the micromolar range. The top ligand (sulfaE) shows a 70-fold increase in selective binding to pfTPI compared to hTPI (dissociation constant-KI of 7.83 μM and 0.177 μM for hTPI and pfTPI respectively), on par with antimalarial drug chloroquine.ALD and GAPDH form complexes with similar binding sites, comprising amino acids of similar chemical properties and polarities. Human TPI and pfTPI bind sulfonamide derivatives using two distinct binding sites and residues. Key residues at the dimer interface of pfTPI (VAL44, SER45, TYR48, GLN64, ASN65, VAL78) form a tight pocket with favorable polar contacts. The affinity with TPI is the most specific, stable, and selective suggesting pfTPI is a candidate for development of antimalarial drugs.
文摘A new simple and reliable in-situ mercury film sensor coupled with affinity differential pulse stripping voltammetry (ADSPV) or affinity cyclic voltammetry (ACV) was investigated. The interaction of fenoprofen with bovine serum albumin (BSA) onto the proposed electrochemical sensor was studied. The nature of the electrochemical process of fenoprofen by cyclic voltammetry was depicted. Reproducibility of the proposed method was checked giving a precision of 0.073 standard deviation. The limit of detection and limit of quantification were 7.0 and 22.0 nmol/L, respectively. Fenoprofen was interacted with BSA by 1:1 stoichiometry to form electroinactive supramolecular complex. The binding constant was precisely estimated by non-linear regression analysis based on the shifting of analyte peak potentials. The proposed experiments and data analysis could be used to investigate the drug-protein binding constant within a short analysis time compared to other chromatographic techniques.
文摘NF-κB plays a crucial role in regulating various biological processes including innate and adaptive immunity, inflammation, stress responses, B-cell development, and lymphoid organogenesis. Currently, several assays like electrophoretic mobility shift assay (EMSA), enzyme-linked immunosorbent assay (ELISA), fluorescence resonance energy transfer (FRET) and time-resolved fluorescence resonance energy transfer (TR-FRET) are widely used for studying the NFκB intraction with β-IFN-κB binding oligo. Each of these techniques has varying utility with distinct strengths and weaknesses. We describe a method AlphaLISA to identify NFκB p50 protein and β-IFN-κB binding oligo sequence and interaction is efficient at a given concentration (10 nM) in the EMSA and Biacore’s SPR assays. The method has many advantages such as use of small volume, high throughput (HTP), convenience of sample preparation and data analysis.
文摘The binding pursuits of trans-resveratrol(t-RSV),an amazing health supplement are investigated with an antioxidant enzyme,superoxide dismutase(SOD1).The aim of the study is to dock t-RSV on the adrenaline binding site on SOD1 in order to explore its potential to act as a safety net against amyotrophic lateral sclerosis(ALS),a fatal neurodegenerative disorder that affects motor neurons.In silico GLIDE docking methodology and in vitro microcalorimetry technique is utilized for the investigation of binding parameters of t-RSV with SOD1.The study provides useful and distinct information about the amino acids involved in the interactions at molecular level along with the nature of forces involved in binding of t-RSV with SOD1.The docking analysis using the scoring functions of Schrodinger’s Glide package depicts that GLU100,PRO28,LYS23,TRP32 residues of the peptide backbone on SOD1 interact with phenolic groups of t-RSV.The information on thermodynamic parameters,i.e.binding constant(Kb),free energy(△G)and enthalpy(△H)generated through calorimetric titrations suggests that the reaction between t-RSV and SOD1 is spontaneous and exothermic.Both the studies are found to be in close agreement with each other based as far as the magnitude of binding constant(Kb=9.9×10^4)is concerned.
基金the financial support of the National Natural Science Foundation of China(Nos.22193020 and 22193022)the financial support of the National Natural Science Foundation of China(No.32301691)+4 种基金Tsinghua University Initiative Scientific Research Programthe financial support of the Science and Technology Innovation Program of Hunan Province(No.2023RC3188)the financial support of the Science and Technology Innovation Program of Hunan Province(No.2022RC1112)the Elite Youth Program by the Department of Education of Hunan Province(No.21B0666)the financial support of the Scientific Research Foundation of Hunan Provincial Education Department(No.24C0380)。
文摘Machine learning methodologies have been extensively leveraged across diverse domains of chemical research,yielding remarkable outcomes,and exhibit substantial potential for impactful future applications within the field of supramolecular chemistry.The recognition of alkali metal ions by crown ethers is one of the most classic and widely applied host-vip interactions in supramolecular chemistry.Due to the numerous factors affecting the host-vip interaction,it remains a great challenge to achieve fast and accurate prediction of the binding constants between crown ethers and alkali metal ions.Herein,we report a highly accurate machine learning model that can effectively predict the binding constants between crown ethers and alkali metal ions,i.e.,CrownBind-IA,with a low RMSE of 0.68 logK units.Moreover,this model proves robust extrapolative capabilities by accurately predicting out-of-sample data.The establishment of CrownBind-IA demonstrates the promising application potentials of data-driven machine learning methods in supramolecular chemistry,and it will substantially reduce the time and expense of experimental trials and characterizations,promote the exploration of the mechanism of host-vip interactions,as well as the rational design of novel functional supramolecular host molecules.
文摘AIM To study the interaction between ciprofloxacin and BSA in physiological condition by fluorescence spectroscopy. METHODS The affection of drug to the protein conformation was investigated. The binding constant between drug and BSA from a double reciprocal Lineweaver Burk plot was determined and the main sort of binding force was found according to the thermodynamic parameters. RESULTS The binding constants between BSA and ciprofloxacin at 26℃and 45℃ are about 10 4. At 26℃, the thermodynamic parameters of reaction between BSA and ciprofloxacin are Δ H = -49 13 kJ·mol -1 , Δ G = -26 45 kJ·mol -1 , Δ S = -75 kJ·mol -1 . The maximum wavelength of the synchronous fluorescence spectra of BSA moved from 279 nm to 289nm with the incresing of the amount of ciprofloxacin. CONCLUSION There exists fluorescence energy transfer between BSA and ciprofloxacin. The main sort of binding force between BSA and ciprofloxacin is Van der Waals′ interaction. Ciprofloxacin can be deposited and be transported by serum protein in vivo . Ciprofloxacin affects the protein conformation.
