scholarly journals Binding Constants of Clinical Drugs and Other Organic Ligands with Human and Mammalian Serum Albumins

Biophysica ◽  
2021 ◽  
Vol 1 (3) ◽  
pp. 344-358
Author(s):  
Igor Sedov ◽  
Alena Nikiforova ◽  
Diliara Khaibrakhmanova
Keyword(s):  
Binding Constants ◽  
Organic Ligands ◽  
Third Party ◽  
Binding Studies ◽  
Serum Albumins ◽  
Experimental Conditions ◽  
Equilibrium Binding ◽  
Pharmacokinetic Properties ◽  
Clinical Drugs ◽  
Experimental Values

A dataset containing the experimental values of the equilibrium binding constants of clinical drugs, and some other organic ligands with human and mammalian (predominantly bovine) serum albumins, is assembled. The affinity of drugs to albumin governs their pharmacokinetic properties, related to permeability through physiological barriers and distribution within the organism. The dataset contains 1755 records gathered from 346 original literature sources describing the albumin affinity of 324 different substances. The data were extracted from both articles and existing protein-binding databases applied strict data selection rules in order to exclude the values influenced by the third-party compounds. The dataset provides the details on the experimental conditions of the measurements, such as temperature; protein and ligand concentrations; buffer pH, composition and concentration; and the method and model used for the binding constant calculations. Analysis of the data reveals discrepancies between the values from different studies, as well as the significant influence of the measurement method. Averaging the values from multiple independent measurements from the dataset may help to determine the reliable values of the binding constants. The dataset can be used as the reference dataset for the development of predictive models to calculate binding constants, and as the choice for the experimental setup in the future albumin-binding studies.

The physicochemical and DNA binding studies of some medicinal compounds in solutions

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Abbas Khan ◽  
Naila ◽  
Muhammad Humayun ◽  
Muhammad Sufaid Khan ◽  
Luqman Ali Shah ◽  
...  
Keyword(s):  
Flow Behavior ◽  
Aqueous Media ◽  
Research Work ◽  
Binding Constants ◽  
Physicochemical Study ◽  
Solution Temperature ◽  
Binding Studies ◽  
Experimental Conditions ◽  
Medicinal Compounds ◽  
Association Behavior

Abstract To understand the expected mode of action, the physicochemical study on the solution properties of medicinal compounds and their interaction with deoxyribonucleic acid (DNA), under varying experimental conditions, is of prime importance. The present research work illustrates the physicochemical study and interaction of certain medicinal compounds such as; Levofloxacin, Ciprofloxacin, and Ibuprofen with DNA. Density, viscosity and surface tension measurements have been performed in order to determine, in a systematic manner, the physicochemical, volumetric and thermodynamic properties of these compounds; and most of these parameters have shown different behavior with varying concentration of solution, temperature of the medium and chemical nature/structure of the compound. In addition, these drugs showed a spontaneous surface-active and association behavior in aqueous solutions. The flow behavior, surface properties, volumetric behavior and solute–solvent interaction of these drugs were prominently influenced by experimental variables and addition of DNA to their solutions. UV–Visible spectroscopy was also used to examine the interaction of these drugs with DNA in aqueous media in detail. Calculated values of binding constants (Kb) for all complexes of drug-DNA are positive, indicating a fruitful binding process. It is seen that a smaller Kb value reflects weaker binding of the drug with DNA and vise versa. Due to the difference in the chemical structure of drugs the values of binding constant are different for various drug-DNA complexes and follow the order Kb(Levofloxacin-DNA) > Kb(Ciprofloxacin-DNA) > Kb(Ibuprofen-DNA). On the basis of spectral changes and Kb it can be said that the binding of all these drugs with DNA may be of physicochemical nature and the dominating binding force be of hydrogen bonding between oxygen of drugs and hydrogen of DNA units and the drug having more oxygen atoms showed stronger binding ability. The data further suggest a limited possibility of chemical type attachment of these drugs with DNA.

scholarly journals Ultrafiltration Method for Plasma Protein Binding Studies and Its Limitations

Processes ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 382
Author(s):  
Camelia-Maria Toma ◽  
Silvia Imre ◽  
Camil-Eugen Vari ◽  
Daniela-Lucia Muntean ◽  
Amelia Tero-Vescan
Keyword(s):  
Protein Binding ◽  
Plasma Protein Binding ◽  
Plasma Protein ◽  
Specific Binding ◽  
Critical Role ◽  
Volume Ratio ◽  
Binding Studies ◽  
Experimental Conditions ◽  
Key Aspects

Plasma protein binding plays a critical role in drug therapy, being a key part in the characterization of any compound. Among other methods, this process is largely studied by ultrafiltration based on its advantages. However, the method also has some limitations that could negatively influence the experimental results. The aim of this study was to underline key aspects regarding the limitations of the ultrafiltration method, and the potential ways to overcome them. The main limitations are given by the non-specific binding of the substances, the effect of the volume ratio obtained, and the need of a rigorous control of the experimental conditions, especially pH and temperature. This review presents a variety of methods that can hypothetically reduce the limitations, and concludes that ultrafiltration remains a reliable method for the study of protein binding. However, the methodology of the study should be carefully chosen.

scholarly journals Kinetic mechanism of Na+-coupled aspartate transport catalyzed by GltTk

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Gianluca Trinco ◽  
Valentina Arkhipova ◽  
Alisa A. Garaeva ◽  
Cedric A. J. Hutter ◽  
Markus A. Seeger ◽  
...  
Keyword(s):  
Kinetic Mechanism ◽  
Protein Quantification ◽  
Detergent Solution ◽  
Sodium Ions ◽  
Binding Studies ◽  
Equilibrium Binding ◽  
Uptake Rates ◽  
Bona Fide ◽  
Inside Out

AbstractIt is well-established that the secondary active transporters GltTk and GltPh catalyze coupled uptake of aspartate and three sodium ions, but insight in the kinetic mechanism of transport is fragmentary. Here, we systematically measured aspartate uptake rates in proteoliposomes containing purified GltTk, and derived the rate equation for a mechanism in which two sodium ions bind before and another after aspartate. Re-analysis of existing data on GltPh using this equation allowed for determination of the turnover number (0.14 s−1), without the need for error-prone protein quantification. To overcome the complication that purified transporters may adopt right-side-out or inside-out membrane orientations upon reconstitution, thereby confounding the kinetic analysis, we employed a rapid method using synthetic nanobodies to inactivate one population. Oppositely oriented GltTk proteins showed the same transport kinetics, consistent with the use of an identical gating element on both sides of the membrane. Our work underlines the value of bona fide transport experiments to reveal mechanistic features of Na+-aspartate symport that cannot be observed in detergent solution. Combined with previous pre-equilibrium binding studies, a full kinetic mechanism of structurally characterized aspartate transporters of the SLC1A family is now emerging.

A Fluorescence Quenching Analysis of the Binding of Fluoroquinolones to Humic Acid

2017 ◽  
Vol 71 (11) ◽  
pp. 2512-2518 ◽  
Author(s):  
Ryan P. Ferrie ◽  
Gregory E. Hewitt ◽  
Bruce D. Anderson
Keyword(s):  
Humic Acid ◽  
Fluorescence Quenching ◽  
Water Solubility ◽  
Binding Constants ◽  
High Water ◽  
Static Quenching ◽  
Temperature Range ◽  
Equilibrium Binding ◽  
Quenching Analysis ◽  
High Water Solubility

Fluorescence quenching was used to investigate the interaction of six fluoroquinolones with humic acid. Static quenching was observed for the binding of ciprofloxacin, enoxacin, fleroxacin, levofloxacin, norfloxacin, and ofloxacin to humic acid. The equilibrium binding constants were found from Stern–Volmer plots of the data. The quenching experiments were repeated over a temperature range of 25–45 ℃ and van’t Hoff plots were generated. From these linear plots, thermodynamic values were calculated for Δ H, Δ G, and Δ S for each of the fluoroquinolones. The equilibrium binding constants were found to be <1 for all the antibiotics studied. The calculated ΔH values were all negative and ranged from −9.5 to −27.6 kJ/mol. The high water solubility of the antibiotics and low ΔH of binding suggests that the antibiotics will be transported easily through the environment. Finally, whether the fluoroquinolones are in a protonated, deprotonated, or partially protonated state is found to correlate to the strength of binding to humic acid.

scholarly journals Interaction of 2′R-ochratoxin A with Serum Albumins: Binding Site, Effects of Site Markers, Thermodynamics, Species Differences of Albumin-binding, and Influence of Albumin on Its Toxicity in MDCK Cells

Toxins ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 353 ◽  
Author(s):  
Zelma Faisal ◽  
Diána Derdák ◽  
Beáta Lemli ◽  
Sándor Kunsági-Máté ◽  
Mónika Bálint ◽  
...  
Keyword(s):  
Binding Site ◽  
Ochratoxin A ◽  
Mdck Cells ◽  
Binding Constants ◽  
Albumin Binding ◽  
Serum Albumins ◽  
Site Markers ◽  
Fetal Bovine ◽  
Toxic Concentrations ◽  
Insight Into

Ochratoxin A (OTA) is a nephrotoxic mycotoxin. Roasting of OTA-contaminated coffee results in the formation of 2′R-ochratoxin A (2′R-OTA), which appears in the blood of coffee drinkers. Human serum albumin (HSA) binds 2′R-OTA (and OTA) with high affinity; therefore, albumin may influence the tissue uptake and elimination of ochratoxins. We aimed to investigate the binding site of 2′R-OTA (verses OTA) in HSA and the displacing effects of site markers to explore which molecules can interfere with its albumin-binding. Affinity of 2′R-OTA toward albumins from various species (human, bovine, porcine and rat) was tested to evaluate the interspecies differences regarding 2′R-OTA-albumin interaction. Thermodynamic studies were performed to give a deeper insight into the molecular background of the complex formation. Besides fluorescence spectroscopic and modeling studies, effects of HSA, and fetal bovine serum on the cytotoxicity of 2′R-OTA and OTA were tested in MDCK kidney cell line in order to demonstrate the influence of albumin-binding on the cellular uptake of ochratoxins. Site markers displaced more effectively 2′R-OTA than OTA from HSA. Fluorescence and binding constants of 2′R-OTA-albumin and OTA-albumin complexes showed different tendencies. Albumin significantly decreased the cytotoxicity of ochratoxins. 2′R-OTA, even at sub-toxic concentrations, increased the toxic action of OTA.

scholarly journals Synthesis, Characterization, and BSA Binding Studies of Some New Benzamides Related to Schiff Base

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
M. K. Prashanth ◽  
M. Madaiah ◽  
H. D. Revanasiddappa ◽  
K. N. Amruthesh
Keyword(s):  
Schiff Base ◽  
Antioxidant Activities ◽  
Antioxidant Properties ◽  
Radical Scavenging ◽  
Binding Constants ◽  
Spectral Studies ◽  
Spectroscopic Techniques ◽  
Binding Studies ◽  
Mass Spectral ◽  
H Nmr

Condensation of amine 1 with aldehyde 2 gives Schiff base, N-(4-((benzofuran-2-ylmethylene) amino)phenyl)acetamide 3. Schiff base on N-acylation with different substituted acid chlorides in the presence of triethylamine gives the corresponding benzamides, N-acetyl-N-(4-((benzofuran-2-ylmethylene)amino)phenyl)substitutedbenzamide (NABP) 5a–j. The structures of newly synthesized compounds were characterized by elemental analysis, 1H NMR, 13C NMR FT-IR, and mass spectral studies. Compounds 3 and 5a–j have been screened for their antimicrobial activity using the disc diffusion and minimum inhibitory concentration (MIC) method against the selected bacterial and fungal strain. Compounds 5a, 5e, 5g, and 5h were found to be more active against all tested strains. The antioxidant properties were evaluated by 2,2-diphenyl-1-picrylhydrazyl (DPPH) and superoxide radical scavenging methods. Compounds 5i and 5j showed predominant antioxidant activities among the synthesized analogues. The interaction between NABP and bovine serum albumin (BSA) was investigated using fluorescence and ultraviolet spectroscopic techniques at 298 K under imitated physiological conditions. The results revealed that NABP caused the fluorescence quenching of BSA through a static quenching procedure. The binding constants and the number of binding sites were calculated. The binding distance between the donor (BSA) and acceptor (NABP) was determined based on Forster’s theory.

scholarly journals Structural basis of nucleoside and nucleoside drug selectivity by concentrative nucleoside transporters

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Zachary Lee Johnson ◽  
Jun-Ho Lee ◽  
Kiyoun Lee ◽  
Minhee Lee ◽  
Do-Yeon Kwon ◽  
...  
Keyword(s):  
Antiviral Agents ◽  
Nucleoside Transporters ◽  
Structural Basis ◽  
Biological Processes ◽  
Functional Information ◽  
Binding Studies ◽  
X Ray ◽  
Equilibrium Binding ◽  
Drug Selectivity ◽  
Proof Of Principle

Concentrative nucleoside transporters (CNTs) are responsible for cellular entry of nucleosides, which serve as precursors to nucleic acids and act as signaling molecules. CNTs also play a crucial role in the uptake of nucleoside-derived drugs, including anticancer and antiviral agents. Understanding how CNTs recognize and import their substrates could not only lead to a better understanding of nucleoside-related biological processes but also the design of nucleoside-derived drugs that can better reach their targets. Here, we present a combination of X-ray crystallographic and equilibrium-binding studies probing the molecular origins of nucleoside and nucleoside drug selectivity of a CNT from Vibrio cholerae. We then used this information in chemically modifying an anticancer drug so that it is better transported by and selective for a single human CNT subtype. This work provides proof of principle for utilizing transporter structural and functional information for the design of compounds that enter cells more efficiently and selectively.

scholarly journals NAD(P)H-dependent aldose reductase from the xylose-assimilating yeast Candida tenuis: Isolation, characterization and biochemical properties of the enzyme

1997 ◽  
Vol 326 (3) ◽  
pp. 683-692 ◽  
Author(s):  
Wilfried NEUHAUSER ◽  
Dietmar HALTRICH ◽  
Klaus D. KULBE ◽  
Bernd NIDETZKY
Keyword(s):  
Aldose Reductase ◽  
Binding Constants ◽  
Catalytic Efficiency ◽  
Anion Exchange Chromatography ◽  
Competitive Inhibitor ◽  
Biochemical Properties ◽  
Product Inhibition ◽  
Exchange Chromatography ◽  
Binding Studies ◽  
Coenzyme Binding

During growth on D-xylose the yeast Candida tenuis produces one aldose reductase that is active with both NADPH and NADH as coenzyme. This enzyme has been isolated by dye ligand and anion-exchange chromatography in yields of 76%. Aldose reductase consists of a single 43 kDa polypeptide with an isoelectric point of 4.70. Initial velocity, product inhibition and binding studies are consistent with a compulsory-ordered, ternary-complex mechanism with coenzyme binding first and leaving last. The catalytic efficiency (kcat/Km) in D-xylose reduction at pH 7 is more than 60-fold higher than that in xylitol oxidation and reflects significant differences in the corresponding catalytic centre activities as well as apparent substrate-binding constants. The enzyme prefers NADP(H) approx. 2-fold to NAD(H), which is largely due to better apparent binding of the phosphorylated form of the coenzyme. NADP+ is a potent competitive inhibitor of the NADH-linked aldehyde reduction (Ki 1.5 μM), whereas NAD+ is not. Unlike mammalian aldose reductase, the enzyme from C. tenuisis not subject to oxidation-induced activation. Evidence of an essential lysine residue located in or near the coenzyme binding site has been obtained from chemical modification of aldose reductase with pyridoxal 5′-phosphate. The results are discussed in the context of a comparison of the enzymic properties of yeast and mammalian aldose reductase.

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