Estimation Of Binding Constants Research Articles

Pyrene Based Schiff Base for Cascade Fluorescent "On-Off" Detection of Aluminium(III) and Fluoride Ions and its Applications in Live Cells Imaging.

An easy-to-prepare pyrene-based Schiff base PNZ was synthesized by condensing equimolar amount of 1-pyrenebutyric hydrazide with 2-hydroxy-naphthaldehyde, and employed as a fluorescent chemosensor for in-situ cascade detection of aluminium (Al3+) and fluoride (F-) ions. In DMSO:H2O (1 : 1, v/v), the weakly emissive PNZ showed a significant fluorescence enhancement at 455 nm selectively upon the addition of Al3+ due to the complexation-induced formation of a pyrene excimer. Schiff base PNZ and Al3+ formed a complex in 2 : 1 binding ratio with the estimated binding constants of K1:1=9826.01 M-1 and K2:1=3188.49 M-1. The sensing mechanism was explored by performing quantum mechanical calculations and 1H-NMR titration of PNZ with Al3+. The in-situ formed PNZ-Al3+ complex species enabled the fluorescent turn-off detection of F-. Using PNZ and PNZ-Al3+, the concentrations of Al3+ and F- ions can be detected down to 2.89×10-7 M and 1.88×10-7 M, respectively. The cytotoxicity of the PNZ and its ability to bioimage Al3+ and F- ions was examined in the human cervical cancer cell line. Finally, the receptor PNZ was applied for the quantification of Al3+ and F- ions in various real samples, such as tap water, river water, rainwater, mouthwash, and toothpaste.

A thiourea-based fluorescent turn-on chemosensor for detecting Hg2+, Ag+ and Au3+ in aqueous medium

A thiourea based fluorescence chemosensor (L) was synthesized and applied for the selective detection of Hg2+, Ag+ and Au3+ions in DMSO-H2O (10:90, v/v). The receptor L showed a weak fluorescence emission in DMSO-H2O due to the photo-induced electron transfer (PET) process. The fluorescence intensity of L was enhanced upon addition of Hg2+, Ag+ and Au3+ ions because of the complexation-induced inhibition of PET process. The 1:1 binding stoichiometry between L and the metal ions (Hg2+, Ag+ and Au3+) was found from the Benesi-Hildebrand plot. The density functional theory (DFT) calculations were performed to explain the binding modes. The estimated binding constants and detection limits of L are found to be 5.87 × 106 M−1 and 5.01 × 10-7 M for Hg2+, 8.78 × 106 M−1 and 2.14 × 10-8 M for Ag+, and 7.93 × 106 M−1 and 34 × 10-7 M for Au3+, respectively. The sensor L was applied to detect Hg2+, Ag+ and Au3+ ions in living Drosophila cell lines. Also, sensor L was employed to detect Hg2+ in soil samples.

Comparison of mobility shift affinity capillary electrophoresis and capillary electrophoresis frontal analysis for binding constant determination between human serum albumin and small drugs.

In this study, two capillary electrophoresis-based ligand binding assays, namely, mobility shift affinity capillary electrophoresis (ms-ACE) and capillary electrophoresis-frontal analysis (CE-FA), were applied to determine binding parameters of human serum albumin toward small drugs under similar experimental conditions. The substances S-amlodipine (S-AML), lidocaine (LDC), l-tryptophan (l-TRP), carbamazepine (CBZ), ibuprofen (IBU), and R-verapamil (R-VPM) were used as the main binding partners. The scope of this comparative study was to estimate and compare both the assays in terms of their primary measure's precision and the reproducibility of the derived binding parameters. The effective mobility could be measured with pooled CV values between 0.55% and 7.6%. The precision of the r values was found in the range between 1.5% and 10%. Both assays were not universally applicable. The CE-FA assay could successfully be applied to measure the drugs IBU, CBZ, and LDC, and the interaction toward CBZ, S-AML, l-TRP, and R-VPM could be determined using ms-ACE. The average variabilities of the estimated binding constants were 64% and 67% for CE-FA and ms-ACE, respectively.

Chiral analysis of β-alanyl-d,l-tyrosine and its derivatives and estimation of binding constants of their complexes with 2-hydroxypropyl-β-cyclodextrin by capillary electrophoresis.

Chiral CE methods were developed for the elucidation of l- or d-configuration of tyrosine residue in antimicrobial dipeptide β-alanyl-tyrosine (β-Ala-Tyr) isolated from the hemolymph of larvae of fleshfly Neobellieria bullata and for the evaluation of enantiopurity of its synthetic isomers (β-Ala-d-Tyr and β-Ala-l-Tyr), and enantiomers of their amidated and acetylated derivatives, β-Ala-d,l-Tyr-NH2 and N-Ac-β-Ala-d,l-Tyr, respectively. Baseline separations were achieved for all three pairs of enantiomers: (i) for β-Ala-d,l-Tyr in acidic background electrolyte composed of 32/50mM tris(hydroxymethyl)aminomethane/H3 PO4 , pH 2.5, and 20mg/mL 2-hydroxypropyl-β-cyclodextrin as chiral selector; (ii) for β-Ala-d,l-Tyr-NH2 enantiomers in acidic background electrolyte consisting of 48/50mM tris(hydroxymethyl)aminomethane/H3 PO4 , pH 3.5, and 30mg/mL 2-hydroxypropyl-β-cyclodextrin; and (iii) for enantiomers of N-Ac-β-Ala-d,l-Tyr in alkaline background electrolyte composed of 50/49mM Na2 B4 O7 /NaOH, pH 10.5, and 60mg/mL 2-hydroxypropyl-β-cyclodextrin. From CE analyses of mixed samples of isolated β-Ala-Tyr and synthetic standards β-Ala-l-Tyr and β-Ala-d-Tyr, it turned out that isolated β-Ala-Tyr was pure l-enantiomer. In addition, the average apparent binding constants, Kb , and average actual ionic mobilities of the complexes of β-Ala-d,l-Tyr and its above derivatives with 2-hydroxypropyl-β-cyclodextrin were determined. These complexes were weak, with Kb values ranging from 11.2 to 79.1 L/mol. Their cationic mobilities were equal to (5.6-9.2)×10-9 m2 /V/s, and anionic mobilities to (-1.3-1.6)×10-9 m2 /V/s.

Rapid Screening and Estimation of Binding Constants for Interactions of Fe3+ with Two Metalloproteins, Apotransferrin and Transferrin, Using Affinity Mode of Capillary Electrophoresis

The interaction behavior of Fe3+ with transferrin and apotransferrin (iron-free form) was investigated in this study using affinity capillary electrophoresis. Change in the mass and charge of protein upon binding to the metal ion in the capillary tube led to variation in its migration time and was used to measure the noncovalent binding interactions by fast screening method. Acetanilide was used as the electroosmotic flow (EOF) marker to avoid possible errors due to the change in EOF during the experiment. The binding results were calculated from the mobility ratios of protein (Ri) and EOF marker (Rf) using the formula (Ri − Rf)/Rf or ∆R/Rf. For more comprehensive understanding, the kinetics of the interaction was studied and binding constants were calculated. Results showed that the Fe3+ displayed insignificant interaction with both proteins at lower metal ion concentrations (5–25 μmol/mL). However, transferrin exhibited significant interactions with the metal ion at 50 and 100 μmol/mL (ΔR/Rf = 0.0114 and 0.0201, resp.) concentrations and apotransferrin showed strong binding interactions (ΔR/Rf = −0.0254 and 0.0205, resp.) at relatively higher Fe3+ concentrations of 100 and 250 μmol/mL. The binding constants of 18.968 mmol−1 and −13.603 mmol−1 were recorded for Fe3+ interaction with transferrin and apotransferrin, respectively, showing significant interactions. Different binding patterns of Fe3+ with both proteins might be attributed to the fact that the iron-binding sites in transferrin have already been occupied, which was not the case in apotransferrin. The present study may be used as a reference for the investigation of protein-metal ion, drug-protein, drug-metal ion, and enzyme-metal ion interactions and may be helpful to provide preliminary insight into the new metal-based drug development.

Comprehensive Characterisation of the Ketoprofen-β-Cyclodextrin Inclusion Complex Using X-ray Techniques and NMR Spectroscopy.

Racemic ketoprofen (KP) and β-cyclodextrin (β-CD) powder samples from co-precipitation (1), evaporation (2), and heating-under-reflux (3) were analysed using X-ray techniques and nuclear magnetic resonance (NMR) spectroscopy. On the basis of NMR studies carried out in an aqueous solution, it was found that in the samples obtained by methods 1 and 2, there were large excesses of β-CD in relation to KP, 10 and 75 times, respectively, while the sample obtained by method 3 contained equimolar amounts of β-CD and KP. NMR results indicated that KP/β-CD inclusion complexes were formed and the estimated binding constants were approximately 2400 M−1, showing that KP is quite strongly associated with β-CD. On the other hand, the X-ray single-crystal technique in the solid state revealed that the (S)-KP/β-CD inclusion complex with a stoichiometry of 2:2 was obtained as a result of heating-under-reflux, for which the crystal and molecular structure were examined. Among the methods used for the preparation of the KP/β-CD complex, only method 3 is suitable.

Solvent Effects in Supramolecular Chemistry: Linear Free Energy Relationships for Common Intermolecular Interactions.

The proper choice of solvent is of major importance for all studies in supramolecular chemistry, including molecular recognition in host-guest systems, intramolecular folding, self-assembly, and supramolecular polymerization. In this Perspective, the usefulness of linear free energy relationships (LFERs) is highlighted to unravel the effect of solvents on coordinate bonding (e.g., cation-crown ether), hydrogen bonding, halogen bonding, dipolar aggregation, and π-π-stacking. For all of these intermolecular interactions widely applied in supramolecular systems, LFER relationships between the Gibbs binding energies and common solvent polarity scales including ET(30), π*, α or β based on solvatochromic dyes, scales derived from binding processes such as Gutmann donor and acceptor numbers or hydrogen bond donor and acceptor scales, or physical functions like the Kirkwood-Onsager or the Liptay-Onsager functions could be demonstrated. These relationships can now be applied toward a better understanding of the prevailing intermolecular forces for supramolecular interactions. They further enable a rational selection of the most suitable solvent for the preparation of self-assembled materials and the estimation of binding constants without the need for time-consuming comprehensive investigations of solvents.

Synthesis, physicochemical, thermal, and XRD/HSA interactions of mixed [Cu(Bipy)(Dipn)](X)2 complexes: DNA binding and molecular docking evaluation

Two water-soluble dicationic complexes, [Cu(bipy)(dipn)](BF4)2 (1) and [Cu(bipy)(dipn)](NO3)2 (2) (bipy = 2.2-bipyridine and dipn = dipropylenetriamine), were synthesized in high yields. The desired complexes were characterized by CHN-EA, UV–Vis, SEM, EDS, FT-IR, TGA, and XRD. The single-crystal XRD of [Cu(bipy)(dipn)](BF4)2 reflected that Cu(II) complex is formed in a distorted square pyramid configuration. The Hirshfeld surface analysis (HSA) confirmed more powerful atom–atom interaction, the hydrogen bonding in H…F, supporting the outcome of XRD. The influences of the CT-DNA/complexes were gathered by viscosity, CV, and electronic absorption measurements. The estimated binding constants (Kb) for 1 and 2 were 4.5 × 104 and 3.4 × 104 M−1, respectively. Complex 2 revealed slightly poorer DNA binding capability than 1. Eventually, the molecular docking of [Cu(bipy)(dipn)]+2 species was evaluated and demonstrated employing 1BNA-DNA segment.

The Free Hormone Hypothesis: When, Why, and How to Measure the Free Hormone Levels to Assess Vitamin D, Thyroid, Sex Hormone, and Cortisol Status.

ABSTRACTThe free hormone hypothesis postulates that only the nonbound fraction (the free fraction) of hormones that otherwise circulate in blood bound to their carrier proteins is able to enter cells and exert biologic effects. In this review, I will examine four hormone groups—vitamin D metabolites (especially 25OHD), thyroid hormones (especially thyroxine [T4]), sex steroids (especially testosterone), and glucocorticoids (especially cortisol)—that are bound to various degrees to their respective binding proteins—vitamin D‐binding protein (DBP), thyroid‐binding globulin (TBG), sex hormone‐binding globulin (SHBG), and cortisol‐binding globulin (CBG)—for which a strong case can be made that measurement of the free hormone level provides a better assessment of hormonal status than the measurement of total hormonal levels under conditions in which the binding proteins are affected in levels or affinities for the hormones to which they bind. I will discuss the rationale for this argument based on the free hormone hypothesis, discuss potential exceptions to the free hormone hypothesis, and review functions of the binding proteins that may be independent of their transport role. I will then review the complications involved with measuring the free hormone levels and the efforts to calculate those levels based on estimates of binding constants and levels of both total hormone and total binding protein. In this review, the major focus will be on DBP and free 25OHD, but the parallels and differences with the other binding proteins and hormones will be highlighted. Vitamin D and its metabolites, thyroid hormones, sex steroids, and glucocorticoids are transported in blood bound to serum proteins. The tightness of binding varies depending on the hormone and the binding protein such that the percent free varies from 0.03% for T4 and 25OHD to 4% for cortisol with testosterone at 2%. Although the major function of the primary carrier proteins (DBP, TBG, SHBG, and CBG) may be to transport their respective lipophilic hormones within the aqueous media that is plasma, these proteins may have other functions independent of their transport function. For most tissues, these hormones enter the cell as the free hormone presumably by diffusion (the free hormone hypothesis), although a few tissues such as the kidney and reproductive tissues express megalin/cubilin enabling by endocytosis protein‐bound hormone to enter the cell. Measuring the free levels of these protein‐bound hormones is likely to provide a better measure of the true hormone status than measuring the total levels in situations where the levels and/or affinities of the binding proteins are altered. Methods to measure free hormone levels are problematic as the free levels can be quite low, the methods require separation of bound and free that could disturb the steady state, and the means of separating bound and free are prone to error. Calculation of free levels using existing data for association constants between the hormone and its binding protein are likewise prone to error because of assumptions of linear binding models and invariant association constants, both of which are invalid. © 2020 The Author. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.

Effect of ketoprofen-based ionic liquids on secondary structure and thermal stability of human serum albumin

This is the first study on the interactions of ionic liquids (ILs) composed of cations amino acid esters and anion ketoprofen (KETO) with human serum albumin (HSA). The effect of the ILs on the thermal unfolding of the HSA was negligible in comparison with that of the KETO. For the IL series, the denaturating transitions tend to shift to lower temperatures by 1–3 °C. The secondary structure analyses have shown that KETO, [L-LeuOEt][KETO] and [L-ValOBu][KETO] cause folding, and HSA molecule becomes more coiled. In the presence of [L-ValOPr][KETO] and [L-ValOiPr][KETO], HSA structure although partially unfolded seemed very close to that of the native protein. In contrast, [L-ValOEt][KETO] induces the same conformational changes of HSA as ketoprofen. For the latter, we performed binding assays and we found that the affinity of the HSA to bind the IL is comparable to that for the ketoprofen. The estimated binding constants were 3.1 × 104 and 1.4 × 104 L mol−1 for ketoprofen and [L-ValOEt][KETO], respectively. This study on KETO-ILs could be a basis to the development of a new drug formulation.

Correlations between functional porphyrin positions and accumulation in cancer cells

Porphyrin is accumulated in tumours due to its interaction with protein. Cancer therapy with porphyrin as a carrier molecule is attracting attention. Porphyrin displays two functional sites termed β- and meso-positions. A correlation between the functional position on the porphyrin molecule and the ability to accumulate in cancer cells is observed in the present study. The accumulation of porphyrin derivatives was determined by measuring fluorescence intensity after incubation for 2 and 24 h. The accumulation of cancer cells depended on the position and length of functional groups. Estimated binding constants between porphyrin and bovine serum albumin suggest that the position of functional groups leads to changes in binding affinity and influences the accumulation of porphyrin derivatives in cancer cells.

A Macrocycle Based on a Heptagon-Containing Hexa-peri-hexabenzocoronene.

A cyclophane is reported incorporating two units of a heptagon-containing extended polycyclic aromatic hydrocarbon (PAH) analogue of the hexa-peri-hexabenzocoronene (HBC) moiety (hept-HBC). This cyclophane represents a new class of macrocyclic structures that incorporate for the first time seven-membered rings within extended PAH frameworks. The saddle curvature of the hept-HBC macrocycle units induced by the presence of the nonhexagonal ring along with the flexible alkyl linkers generate a cavity with shape complementarity and appropriate size to enable π interactions with fullerenes. Therefore, the cyclophane forms host-guest complexes with C60 and C70 with estimated binding constants of Ka =420±2 m-1 and Ka =(6.49±0.23)×103 m-1 , respectively. As a result, the macrocycle can selectively bind C70 in the presence of an excess of a mixture of C60 and C70 .

A Macrocycle Based on a Heptagon‐Containing Hexa‐peri‐hexabenzocoronene

AbstractA cyclophane is reported incorporating two units of a heptagon‐containing extended polycyclic aromatic hydrocarbon (PAH) analogue of the hexa‐peri‐hexabenzocoronene (HBC) moiety (hept‐HBC). This cyclophane represents a new class of macrocyclic structures that incorporate for the first time seven‐membered rings within extended PAH frameworks. The saddle curvature of the hept‐HBC macrocycle units induced by the presence of the nonhexagonal ring along with the flexible alkyl linkers generate a cavity with shape complementarity and appropriate size to enable π interactions with fullerenes. Therefore, the cyclophane forms host–guest complexes with C60 and C70 with estimated binding constants of Ka=420±2 m−1 and Ka=(6.49±0.23)×103 m−1, respectively. As a result, the macrocycle can selectively bind C70 in the presence of an excess of a mixture of C60 and C70.

Synthesis, structural identification, DNA interaction and biological studies of divalent Mn, Co and Ni chelates of 3‐amino‐5‐mercapto‐1,2,4‐triazole azo ligand

New Mn (II), Co (II) and Ni (II) azo chelates of 3‐amino‐5‐mercapto‐1,2,4‐triazole have been designed and obtained. The structures of these newly isolated complexes were assigned according to elemental, thermal analyses, spectral measurements, conductivity and magnetic moment. The metal complexes were predicted to be not electrolytic from the measured molar conductance values. The magnetic moment and UV–Vis spectral data denoted the formation of octahedral geometries for Mn (II), Co (II) and Ni (II) complexes. Thermal properties and decomposition kinetics of the metal chelates are investigated using Coats‐Redfern method. The kinetic parameters like activation energy (E*), pre‐exponential factor (A) and entropy of activation (ΔS*) were quantified. The geometry of the metal complexes is optimized with the help of molecular modeling. The interaction of metal chelates with calf thymus DNA (CT‐DNA) was evaluatedviaUV–Vis absorption and viscosity measurements. The obtained data elucidated that the Ni (II) chelate interact with DNA by groove binding while partial intercalative binding mode have been predicted for Mn (II) and Co (II) chelates. The estimated binding constants for the DNA‐complexes are 3.85 ± 0.03 × 104, 1.03 ± 0.2 × 105and 2.81 ± 0.02 × 105M−1, for Mn (II), Co (II) and Ni (II) azo chelates, successively. Also, the synthesized complexes were tested for their in‐vitro antimicrobial and anticancer efficacy.

Ketoprofen-Based Ionic Liquids: Synthesis and Interactions with Bovine Serum Albumin.

The development of ionic liquids based on active pharmaceutical ingredients (API-ILs) is a possible solution to some of the problems of solid and/or hydrophobic drugs such as low solubility and bioavailability, polymorphism and an alternative route of administration could be suggested as compared to the classical drug. Here, we report for the first time the synthesis and detailed characterization of a series of ILs containing a cation amino acid esters and anion ketoprofen (KETO-ILs). The affinity and the binding mode of the KETO-ILs to bovine serum albumin (BSA) were assessed using fluorescence spectroscopy. All compounds bind in a distance not longer than 6.14 nm to the BSA fluorophores. The estimated binding constants (KA) are in order of 105 L mol−1, which is indicative of strong drug or IL-BSA interactions. With respect to the ketoprofen-BSA system, a stronger affinity of the ILs containing l-LeuOEt, l-ValOBu, and l-ValOEt cation towards BSA is clearly seen. Fourier transformed infrared spectroscopy experiments have shown that all studied compounds induced a rearrangement of the protein molecule upon binding, which is consistent with the suggested static mechanism of BSA fluorescence quenching and formation of complexes between BSA and the drugs. All tested compounds were safe for macrophages.

A ruthenium nitrosyl cyclam complex with appended anthracenyl fluorophore

The complex trans-[Ru(NO)(H2O)(L)](ClO4)3 (L = (1-anthracen-9-ylmethyl)-1,4,8,11-tetraazacyclotetradecane) (RuNOL) was synthesized and characterized, and its photophysics and reactivity were investigated. The FTIR spectrum displays a νNO band at 1840 cm−1, indicating a nitrosonium character. 1H and 13C signals in 1D and 2D NMR spectra were assigned and are consistent with the trans configuration. The UV–Vis spectrum displays maximal absorption bands at 341 nm (log ε 3.74), 363 nm (log ε 3.91), 378 nm (log ε 3.97) and 397 nm (log ε 3.91). Coordination of the [RuNO] moiety to the L ligand strongly quenches the anthracenyl fluorescence, and thus RuNOL exhibits only very weak emission at 390, 418, 440 and 472 nm. Electrochemical studies indicate that cathodic peak potentials at +1.10 V(Ic), −0.1 V(IIc) and −0.4 V(IIIc) (vs Ag/AgCl) are related to An+/An, {RuNO}6/7 and {RuNO}7/8 reduction processes, respectively. The pKa of coordinated water was estimated as 2.8 ± 0.2 by DPV. The emission of the pendant fluorophore increases upon electrochemical or chemical reduction of RuNOL, and the resulting switch-ON fluorescence is possibly due to NO release from the target complex. Spectroscopic titrations with DNA resulted in hypochromism and red shifts and allowed estimation of binding constants of 1.9 × 103 (L) and 1.8 × 103 (RuNOL). Molecular docking showed that RuNOL complex has a great affinity with DNA. The RuNOL complex showed low cytotoxicity toward MCF-7 and NIH-3T3 and was ineffective in healthy HUVEC and A7r5 cell lines in the range of concentration of 1 × 10−7–1 × 10−4 mol L−1.

Nuclear magnetic resonance spectroscopic study of the inclusion complex of (R)-tedizolid with HDAS-β-CD, β-CD, and γ-cyclodextrin in aqueous solution

NMR spectroscopy is used to investigate the host–guest complexation of (R)-tedizolid, such as tedizolid with the hydroxymethyl substituent at the C5 position of the oxazolidinone ring ((R)-TED) or tedizolid with 5-methyl dihydrogen phosphate ((R)-TED-PO4) with heptakis-(2,3-diacetyl-6-sulfo)-β-cyclodextrin (HDAS-β-CD), β-CD and γ-CD, in particular to obtain information about the mode and strength of the guest complexation into the hydrophobic cavity of the host. The complex stoichiometries of 1:1 (host:guest) and 1:2 were detected in millimolar concentrations for HDAS-β-CD and γ-CD with TED-PO4 complexes, respectively. In the meantime, the mixed of complexes with stoichiometries of 1:1 and 2:1 were found for β-CD with both TED and TED-PO4, however the 1:1 complex had a significant advantage.The binding mode was proposed. The estimated binding constants Ka of the complexes of TED or TED-PO4 with CDs differ significantly in the order HDAS-β-CD<<β-CD<<γ-CD.

Separation of rotamers of 5-nitrosopyrimidines and estimation of binding constants of their complexes with β-cyclodextrin by capillary electrophoresis

For the first time, capillary electrophoresis has been successfully employed for the fast and highly efficient separations of a novel type of stereoisomers – planar rotamers (planamers) of four newly synthesized 5-nitrosopyrimidine derivatives. These derivatives can form two rotamers differing in the orientation of nitroso group due to strong intramolecular hydrogen bonds. Partial separation of rotamers of two 5-nitrosopyrimidines was achieved in alkaline 50 mM sodium tetraborate, pH 9.3, and in acidic 18.5/42 mM Tris/phosphate, pH 2.3, background electrolytes (BGEs) free of stereoselectors. To improve the separation of these rotamers and to attain the baseline or better separation of rotamers of other two 5-nitrosopyrimidines, various BGEs and different cyclodextrins-based stereoselectors were tested. The most effective, i.e. the fastest and baseline or better separations of rotamers of all analyzed 5-nitrosopyrimidines were achieved within a short time, 3.7–9.3 min, in the above alkaline or acidic BGEs using β-cyclodextrin (β-CD) or carboxymethyl-β-CD as stereoselectors. Moreover, since the experiments with β-CD resulted in good separations of rotamers of all the investigated 5-nitrosopyrimidines, the apparent binding constants of their complexes with this selector were determined from the dependence of their effective mobilities on the β-CD concentration in the BGEs. The examined complexes were found to be relatively weak, with the apparent binding constants in the range 11.3–153.0 L/mol.

Tuning the chain length of new pyrene derivatives for site-selective photocleavage of avidin

Rational design of photoreagents with systematic modifications of their structures can provide valuable information for a better understanding of the protein photocleavage mechanism by these reagents. Variation of the length of the linker connecting the photoactive moiety with the protein anchoring-group allowed us to investigate the control of the protein photocleavage site. A series of new photochemical reagents (PMA-1A, PMA-2A and PMA-3A) with increasing chain lengths is examined in the current study. Using avidin as a model system, we examined the interaction of these probes by UV–Vis, fluorescence spectroscopic methods, photocleavage and computational docking studies. Hypochromism of the absorption spectrum was observed for the binding of these new photochemical reagents with estimated binding constants (Kb) of 6.2 × 105, 6.7 × 105 and 4.6 × 105 M−1, respectively. No significant changes of Stern-Volmer quenching constant (Ksv) with Co(NH3)6Cl3 has been noted and the data indicated that the probes bind near the surface of the protein with sufficient exposure to the solvent. Photoexcitation of the probe-avidin complex, in the presence of Co(NH3)6Cl3, resulted in protein fragmentation, and the cleavage yield decreased with the increase in the linker length, and paralleled with the observed Ksv values. Amino acid sequencing of the photofragments indicated that avidin is cleaved between Thr77 and Val78, as a major cleavage site for all the three photoreagents. This site is proximate to the biotin binding site on avidin, and molecular docking studies indicated that the H-bonding interactions between the polar end-group of the photoreagents and hydrophilic amino acids of avidin were important in positioning the reagent on the protein. The major cleavage site, at residues 77–78, was within 5 Å of the pyrenyl moiety of the probe, and hence, molecular tuning of the linker provided a simple approach to position the photoreagent along the potential photocleavage site.

Multi experimental and computational studies for DNA and HSA interaction of new nano-scale ultrasound-assisted synthesized Pd(II) complex as a potent anticancer drug

As for daily increasing mortality rate in world due to the growth of cancer causing agents, design and synthesis of new compounds with anticancer potential benefits is one of the most important challenges for researchers. In the present work, we synthesized a new Schiff base Pd(II) complex in bulk-scale and also in nano-scales by Sonochemical method. The structure of synthesized complex was determined by single crystal X-ray diffraction technique. Then the cell viability percent of HeLa cancer cells was studied by MTT assay. The results confirmed that reducing the size has salient effect in annihilation of cancer cells. Also, nano-scale complex reached to IC50 in 10 μM of concentration. Binding ability of the nano- and bulk-scale Pd(II) Schiff base complex with calf thymus DNA and human serum albumin was investigated using combination of experimental (fluorescence, circular dichroism (CD) and viscosity) and computational (molecular docking, molecular dynamics simulation and QM/MM) methods. The estimated binding constants for the complex in both of bulk- and nano-scales showed that the nano-scale complex binds more tightly to DNA than its bulk-scale form. This finding is in good agreement with MTT assay results. Molecular docking studies revealed that Pd(II) complex binds to the minor groove and IB binding site of DNA and HSA, respectively. Also, MD simulation studies showed that complexation with the Pd(II) complex changes the structure of HSA with compared to free protein. Finally, the ONIOM results indicated that the structural parameters of the compound changed along with binding to DNA and HSA, indicating the strong interaction between the compound and these biomacromolecules. The values of binding constants depend on the extent of the resultant changes.