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.     

Study of caffeine binding to human serum albumin using optical spectroscopic methods

The binding of caffeine to human serum albumin (HSA) under physiological conditions has been studied by the methods of fluorescence, UV-vis absorbance and circular dichroism (CD) spectroscopy. The mechanism of quenching of HSA fluorescence by caffeine was shown to involve a dynamic quenching procedure. The number of binding sites n and apparent binding constant K _b were measured by the fluorescence quenching method and the thermodynamic parameters ΔH, ΔG, ΔS were calculated. The results indicate that the binding is mainly enthalpy-driven, with van der Waals interactions and hydrogen bonding playing major roles in the reaction. The distance r between donor (HSA) and acceptor (caffeine) was obtained according to the Förster theory of non-radiative energy transfer. Synchronous fluorescence, CD and three-dimensional fluorescence spectroscopy showed that the microenvironment and conformation of HSA were altered during the reaction.     

Sorption of adamantane phenylamide derivatives on hyper-cross-linked polystyrene from water–acetonitrile eluents

Study of the main physicochemical features of the sorption of phenylamide adamantane derivatives on hyper-cross-linked polystyrene from water–acetonitrile solutions shows that both hydrophobic and electronic interactions make a large contribution to retention, especially for a chlorine-containing derivative in which there are π–p and π–d interactions between the outer-shell electrons of the chlorine atom in addition to π–π interactions between aromatic fragments of the sorbate and sorbent.     

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.     

Structural characterization of the crystalline diastereomeric complexes of enantiopure dimethylacridino-18-crown-6 ether and the enantiomers of 1-(1-naphthyl)ethylamine hydrogen perchlorate

This paper describes the X-ray crystal structure of the diastereomeric complexes formed by enantiopure dimethyl-substituted acridino-18-crown-6 ether (R,R)-1 and the enantiomers of 1-(1-naphthyl)ethylammonium perchlorate. We found that the heterochiral complex (R,R)-1–(S)-1-NEA is more stable than the homochiral one (R,R)-1–(R)-1-NEA. In the case of the heterochiral complex, the X-ray studies revealed a strong intermolecular π–π interaction between the naphthyl unit and the acridine moiety. However, in the case of the homochiral complex, π–π interaction was not found. We suggest that the existence or absence of the π–π interaction and the difference in steric repulsions in the diastereomers is responsible for the enantiomeric discrimination.     

The mutual influence between <Emphasis Type="Italic">π</Emphasis>-hole pnicogen bonds and <Emphasis Type="Italic">σ</Emphasis>-hole halogen bonds in complexes of PO<Subscript>2</Subscript>Cl and XCN/C<Subscript>6</Subscript>H<Subscript>6</Subscript> (X = F,Cl, Br)

The bimolecular and termolecular complexes involving PO₂Cl and XCN/C₆H₆ (X = F, Cl, Br) were designed to form the π-hole pnicogen bonds and σ-hole halogen bonds, to compare the two types of interactions and investigate the mutual influences between them. PO₂Cl was used as simultaneous π-hole and σ-hole donor; it can interact with electron donor to form π-hole pnicogen bond and σ-hole halogen bond. The π-hole interactions are stronger than the σ-hole interactions, in both the bimolecular and the termolecular complexes. Comparing the mutual effects of the π-hole interactions and σ-hole interactions, the π-hole interaction has a greater influence on the σ-hole interaction than vice versa. With the addition of σ-hole halogen bond, the V _S,max value outside the π-hole region of PO₂Cl becomes decreasingly positive, resulting in a weaker π-hole interaction. With the addition of π-hole pnicogen bond, the V _S,max value outside the σ-hole region of PO₂Cl becomes small, also resulting in a weaker σ-hole interaction. The π-hole pnicogen bond and σ-hole halogen bond weaken each other, i.e., there is a negative cooperative effect in the termolecular complexes.     

The X<Superscript>−</Superscript>···benzohydrazide complexes: the interplay between anion-π and H-bond interactions

The compounds containing the benzohydrazide (BH) nucleus have a variety of biological activities because of various noncovalent intermolecular interactions. The interplay between anion-π and H-bond interactions, which can affect the activity of compounds, has been investigated in ten substituted BH exposed to the chloride ion using the quantum mechanical calculations. The total interaction energy is separated into the anion-π (ΔE _Aπ) and H-bond (ΔE _HB) contributions where both interactions are presented in the complexes. The electron-withdrawing substituents (EWSs) increase |ΔE _Aπ| and decrease |ΔE _HB|, while reversed changes are observed with the electron-donating substituents (EDSs). In addition, the total binding energy (ΔE) becomes more/less negative in the presence of EWSs/EDSs. The synergetic effects of mentioned interactions and substituent effects have also been investigated using the atoms in molecules (AIM), natural bond orbital (NBO) and molecular electrostatic potential (MEP) analyses. A good correlation is found between the energy data and the Hammett constants, the minimum of electrostatic potential (V _min) and the results of population analyses.     

Drug search for leishmaniasis: a virtual screening approach by grid computing

The trypanosomatid protozoa Leishmania is endemic in ~100 countries, with infections causing ~2 million new cases of leishmaniasis annually. Disease symptoms can include severe skin and mucosal ulcers, fever, anemia, splenomegaly, and death. Unfortunately, therapeutics approved to treat leishmaniasis are associated with potentially severe side effects, including death. Furthermore, drug-resistant Leishmania parasites have developed in most endemic countries. To address an urgent need for new, safe and inexpensive anti-leishmanial drugs, we utilized the IBM World Community Grid to complete computer-based drug discovery screens (Drug Search for Leishmaniasis) using unique leishmanial proteins and a database of 600,000 drug-like small molecules. Protein structures from different Leishmania species were selected for molecular dynamics (MD) simulations, and a series of conformational “snapshots” were chosen from each MD trajectory to simulate the protein’s flexibility. A Relaxed Complex Scheme methodology was used to screen ~2000 MD conformations against the small molecule database, producing >1 billion protein-ligand structures. For each protein target, a binding spectrum was calculated to identify compounds predicted to bind with highest average affinity to all protein conformations. Significantly, four different Leishmania protein targets were predicted to strongly bind small molecules, with the strongest binding interactions predicted to occur for dihydroorotate dehydrogenase (LmDHODH; PDB:3MJY). A number of predicted tight-binding LmDHODH inhibitors were tested in vitro and potent selective inhibitors of Leishmania panamensis were identified. These promising small molecules are suitable for further development using iterative structure-based optimization and in vitro/in vivo validation assays.     

Structural and Thermodynamic Investigation into the Protein-Binding Properties of a Natural Product Crytotanshinone

Crytotanshinone (CTSO) is a Chinese herbal medicine active ingredient isolated from Salvia miltiorrhiza. In this work, the interaction of CTSO and human serum albumin (HSA) was studied by fluorescence spectra, ultraviolet spectra, circular dichroism (CD) spectra, molecular probe and molecular modeling methods. The results showed that the endogenous fluorescence of HSA was quenched by CTSO through a static mechanism. The number of binding sites, equilibrium constants, and thermodynamic parameters of the reaction were calculated at three different temperatures. The positive enthalpy change (ΔH^θ) and entropy change (ΔS^θ) revealed that the interaction was an endothermic as well as an entropy-driven process, where hydrophobic power played the major role in stabilizing the structure of the new complex. Site-selective binding experiments were carried out using warfarin and ibuprofen as probes, which proved that CTSO binds to Sudlow’s site II in subdomain IIIA of the HSA molecule. Circular dichroism (CD) spectra was employed to detect the α-helix and β-strand contents in HSA before and after the binding of CTSO. Based on the experimental results, the structure of the CTSO–HSA complex was calculated by docking CTSO to the proven site using molecular modeling. The study obtained comprehensive information on structure and thermodynamics, which is essential for understanding the bioaffinity, delivery process and pharmacological mechanism.     

Interaction Between Plumbagin and Human Serum Albumin by Fluorescence Spectroscopy

The interaction of plumbagin (PLU) with human serum albumin (HSA) in physiological buffer (pH=7.4) was studied by fluorescence spectroscopy. Results obtained from analysis of the fluorescence spectra indicated that PLU has a strong ability to quench the intrinsic fluorescence of HSA through a static quenching procedure. Fluorescence quenching data revealed that the quenching constants (K) are 4.43×10⁴, 3.26×10⁴ and 1.69×10⁴ L?mol^?1 at 293, 303 and 313 K, respectively. The thermodynamic parameters ΔH° and ΔS° were calculated to be ?36.63 kJ?mol^?1, and ?35.702 J?mol^?1?K^?1 respectively, which suggested that van der Waals interactions and hydrogen bonds play a major role in the interaction of PLU with HSA. The distance between donor (HSA) and acceptor (PLU) was calculated to be 3.76 nm based on Förster’s non-radiative energy transfer theory. The results of synchronous fluorescence spectra showed that binding of PLU to HSA can induce conformational changes in HSA.     

Syntheses,crystal structures and in vitro anticancer activities of oxovanadium(IV) complexes of amino acid Schiff base and 1,10-phenanthroline ligands

Four oxovanadium(IV) complexes, namely [VO(desa-met)(phen)]·MeOH·2H₂O (1) (desa-met = Schiff base derived from 4-(diethylamino)salicylaldehyde and dl-methionine, phen = 1,10-phenanthroline), [VO(o-van-met) (phen)]·MeOH·CH₂Cl₂·3H₂O (2) (o-van-met = Schiff base derived from o-vanillin and dl-methionine), [VO(dtbs-napa)(phen)]·2H₂O (3) (dtbs-napa = Schiff base derived from 3,5-di-tert-butyl salicylaldehyde and 3-(1-naphthyl)-l-alanine) and [VO(hyna-napa)(phen)]·1.5H₂O (4) (hyna-napa = Schiff base derived from 2-hydroxy-1-naphthaldehyde and 3-(1-naphthyl)-l-alanine), were synthesized and characterized by IR, HRMS, UV–vis spectra, molar conductance and single-crystal X-ray diffraction (XRD). X-ray structural analysis showed that the V(IV) atoms in all four complexes are six-coordinated in a distorted octahedral environment. In the crystals of complexes 1 and 2, π–π stacking interactions together with hydrogen bonds connect the molecular units into 2D networks. Meanwhile, CH–π stacking interactions are observed between the aromatic rings in the crystals of 1 and 4, while the π–π stacking interactions between aromatic rings in the crystals of 2 and 3 are arranged with a face-to-face mode. The in vitro anticancer activities of these complexes against A-549 and HeGp2 cells were tested by MTT assay.     

Investigation of the effect of <Emphasis Type="Italic">π</Emphasis>–<Emphasis Type="Italic">π</Emphasis> stacking interaction on the properties of –CONH<Subscript>2</Subscript> functional group of benzamide

The effect of π–π stacking between substituted benzene and benzamide on the properties of –CONH₂ functional group, as an important unit in the drugs activities, was studied at the M06-2X/6-311++G(d,p) level of theory. All substituents enhanced the π–π interaction energies, where a reasonably good correlation was found between the interaction energies and Hammett constants of substituents. A linear correlation is observed between the sum of electron charge density at the cage critical point ∑ρ _ccp obtained from the atoms in molecules (AIM) analysis and the interaction energies, where both values grow up with electron-withdrawing substituents (EWSs). The electrostatic potential around the O and N atoms, the natural charges, and the dipole moment of C=O bond have been calculated to predict the ability of functional group on the electrophilic and nucleophilic attacks. The charge transfer increases the electrostatic potential around the benzamide functional group in the presence of electron-donating substituents (EDSs). EWSs increase the acidity of the N atom of the –NH₂ group; a linear relationship is observed between the acidity calculated with the molecular electrostatic potential around the N atom and the natural valence orbital energies.     

Molecular interactions in binary mixtures of methyl formate with 1-butanol, 1-pentanol,and 1-hexanol by using ultrasonic data at 303 K

Density (ρ), viscosity (η), and ultrasonic velocity (U) have been measured for binary mixtures of methyl formate with 1-butanol, 1-pentanol and 1-hexanol at 303 K. From the experimental results, adiabatic compressibility (β), acoustic impedance (Z), viscous relaxation time (τ), free length (L_f), free volume (V_f), internal pressure (π_i), and Gibbs free energy (ΔG) have been determined. Excess values of various parameters have also been calculated and interoperated in terms of molecular interactions. The deviations in the parameters show that strength of intermolecular interactions between methyl formate with selected 1-alcohols have been observed in the order of 1-butanol < 1-pentanol < 1-hexanol.     

Computational and experimental study on the interaction of three novel rare earth complexes containing 2,9-dimethyl-1,10-phenanthroline with human serum albumin

In this paper, several rare earth [terbium(III), ytterbium(III) and yttrium(III)] complexes containing 2,9-dimethyl-1,10-phenanthroline (Me₂Phen) were successfully synthesized and characterized by means of elemental analysis (CHN), infrared spectroscopy (FT-IR), UV–vis absorption spectroscopy and ¹HNMR. To explore the potential medicinal value of these complexes (MMe₂Phen), their binding interactions with human serum albumin (HSA) were investigated through UV–vis and fluorescence spectroscopies and also molecular docking examinations. The thermodynamic parameters, binding forces and Förster resonance distance between these complexes and Trp-214 of HSA were estimated from the analysis of fluorescence measurements. The values of estimated binding constants (K_b) ranging for the formation of MMe₂Phen:HSA complex were in the order of 10⁵ M^?1. The thermodynamic parameters determined by van’t Hoff analysis of K_b (ΔH°?<?0 and ΔS°?<?0) clearly indicate the major rules of hydrogen bonds and van der Waals interactions in the formation process of MMe₂Phen:HSA. The values of Stern–Volmer constant and the evaluation of dynamic quenching constant at various temperatures provided good evidences for static quenching mechanism. Furthermore, the results of molecular docking calculation and competitive binding experiments represent the binding of these complexes to site 3 of HSA located in subdomain IB, containing both polar and apolar residues. The consistency of computational and experimental results, according to the binding sites and the order of binding affinities (TbMe₂Phen?>?YbMe₂Phen?>?YMe₂Phen), supports the accuracy of docking calculation.     

Alternative preparation and characterization of platinum(II) organometallic dinuclear complexes and oligomers with 3,8-diethynylphenanthroline derivatives

Novel platinum(II) organometallic dinuclear complexes and oligomers with two types of phenanthroline ligands, namely 3,8-diethynylphenanthroline (L1) and 3,8-bis-(4-ethynyl-phenylethynyl)-1,10-phenanthroline (L2), were synthesized from trans-Pt(PBu₃)₂(1-ethynyl-4-methyl-benzene)Cl and trans-Pt(PBu₃)₂Cl₂ by transmetalation of copper ion. The alternative procedure targeted platinum oligomer termination selection of either chloride or respective phenanthrolines and was successfully performed with different purifications by extraction and column chromatography. The structural formulae of these platinum complexes and oligomers were revealed with by analysis of both ³¹P{¹H}-NMR and ¹H-NMR spectral data. Alternative preparations of platinum oligomers with two types between chloride and respective phenanthroline termination are very useful for the selective synthesis for hybrid polymers with the coupling reaction with two different platinum oligomers with different diethynylaryl ligands. The platinum organometallic compounds showed similar absorption bands in the UV–Vis region. Those prepared with L1 had a strong absorption band at around 400 nm, assignable to the lowest energy metal-perturbed ¹[π–π*] transitions, while in compounds prepared with L2, the strong band appeared around 410 nm, because L2 has an extended π conjugation relative to L1. No distinct differences were observed in the absorption spectra of these platinum oligomers between the different terminal structures, chloride or various phenanthrolines. The luminescence spectra of the platinum compounds prepared with either L1 or L2, however, showed a distinct difference. Those with L1 showed only a phosphorescence assignable to a typical metal-perturbed ³[π–π*] transition with vibronic progressions centered at around 530 nm in deoxygenated CH₂Cl₂ at room temperature, while those with L2 showed weak dual emissions assignable to a mixture of typical metal-perturbed ¹[π–π*] and ³[π–π*] transitions in the visible region.     

Blinded predictions of standard binding free energies: lessons learned from the SAMPL6 challenge

In the context of the SAMPL6 challenges, series of blinded predictions of standard binding free energies were made with the SOMD software for a dataset of 27 host–guest systems featuring two octa-acids hosts (OA and TEMOA) and a cucurbituril ring (CB8) host. Three different models were used, ModelA computes the free energy of binding based on a double annihilation technique; ModelB additionally takes into account long-range dispersion and standard state corrections; ModelC additionally introduces an empirical correction term derived from a regression analysis of SAMPL5 predictions previously made with SOMD. The performance of each model was evaluated with two different setups; buffer explicitly matches the ionic strength from the binding assays, whereas no-buffer merely neutralizes the host–guest net charge with counter-ions. ModelC/no-buffer shows the lowest mean-unsigned error for the overall dataset (MUE 1.29?<?1.39?<?1.50 kcal mol^?1, 95% CI), while explicit modelling of the buffer improves significantly results for the CB8 host only. Correlation with experimental data ranges from excellent for the host TEMOA (R² 0.91?<?0.94?<?0.96), to poor for CB8 (R² 0.04?<?0.12?<?0.23). Further investigations indicate a pronounced dependence of the binding free energies on the modelled ionic strength, and variable reproducibility of the binding free energies between different simulation packages.     

Investigating the interaction of juglone (5-hydroxy-1, 4-naphthoquinone) with serum albumins using spectroscopic and in silico methods

The interaction between juglone at the concentration range of 10–110 µM and bovine serum albumin (BSA) or human serum albumin (HSA) at the constant concentration of 11 µM was investigated by fluorescence and UV absorption spectroscopy under physiological-like condition. Performing the experiments at different temperatures showed that the fluorescence intensity of BSA/HSA was decreased in the presence of juglone by a static quenching mechanism due to the formation of the juglone–protein complex. The binding constant for the interaction was in the order of 10³ M^?1, and the number of binding sites for juglone on serum albumins was determined to be equal to one. The thermodynamic parameters including enthalpy (ΔH), entropy (ΔS) and Gibb’s free energy (ΔG) changes were obtained by using the van’t Hoff equation. These results indicated that van der Waals force and hydrogen bonding were the main intermolecular forces stabilizing the complex in a spontaneous association reaction. Moreover, the interaction of BSA/HSA with juglone was verified by UV absorption spectra and molecular docking. The results of synchronous fluorescence, UV–visible and CD spectra demonstrated that the binding of juglone with BSA/HSA induces minimum conformational changes in the structure of albumins. The increased binding affinity of juglone to albumin observed in the presence of site markers (digoxin and ibuprofen) excludes IIA and IIIA sites as the binding site of juglone. This is partially in agreement with the results of molecular docking studies which suggests sub-domain IA of albumin as the binding site.     

Water-soluble palladacycles containing hydroxymethyl groups: synthesis,crystal structures and use as catalysts for amination and Suzuki coupling of reactions

Two water-soluble monophosphine [PPh₃ and 2-dicyclohexylphosphino-2′,6′-dimethoxybiphenyl(Sphos)]-palladacycles containing hydroxymethyl groups 2–3 were prepared by cyclopalladation and chloride bridge-splitting reactions. The complexes were characterized by elemental analysis, ESI–MS and NMR. In addition, single-crystal X-ray analysis reveals that they have one-dimensional lamellar structures involving intermolecular hydrogen bonds and π–π interactions. The use of these palladacycles as catalysts for amination and Suzuki coupling of aryl chlorides in water was investigated. Complex 3 was found to be very efficient for these coupling reactions. Additionally, it was also successfully used in Suzuki coupling of (hydroxymethyl)phenylboronic acid for the synthesis of substituted 2-N-heterocyclic biarylmethanols.     

In Vitro Binding of Furadan to Bovine Serum Albumin

Under physiological conditions, the interaction between furadan (FRD) and bovine serum albumin (BSA) was investigated by spectroscopy including fluorescence emission, UV-visible absorption, scattering, circular dichroism (CD) spectra, synchronous and three-dimensional fluorescence spectra. The observed binding constant K _b and the number of binding sites n were determined by the fluorescence quenching method. The distance r between donor (BSA) and acceptor (FRD) was obtained according to the Förster theory of non-radiation energy transfer. The enthalpy change (ΔH ^θ ), Gibbs energy change (ΔG ^θ ) and entropy change (ΔS ^θ ) at four different temperatures were calculated. The process of binding was proposed to be a spontaneous process since the ΔG ^θ values were negative. The positive ΔS ^θ and ΔH ^θ values indicated that the interaction of FRD and BSA was driven mainly by hydrophobic interactions. The addition of FRD to BSA solutions leads to enhancement in scattering intensity, exhibiting the formation of an aggregate in solution. CD spectra, synchronous and three-dimensional fluorescence spectra were used to measure the structural change of BSA molecules with FRD present.