Processing multimode binding situations in simulation-based prediction of ligand-macromolecule affinities

The linear response (LR) approximation and similar approaches belong to practical methods for estimation of ligand-receptor binding affinities. The approaches correlate experimental binding affinities with the changes upon binding of the ligand electrostatic and van der Waals energies and of solvation characteristics. These attributes are expressed as ensemble averages that are obtained by conformational sampling of the protein-ligand complex and of the free ligand by molecular dynamics or Monte Carlo simulations. We observed that outliers in the LR correlations occasionally exhibit major conformational changes of the complex during sampling. We treated the situation as a multimode binding case, for which the observed association constant is the sum of the partial association constants of individual states/modes. The resulting nonlinear expression for the binding affinities contains all the LR variables for individual modes that are scaled by the same two to four adjustable parameters as in the one-mode LR equation. The multimode method was applied to inhibitors of a matrix metalloproteinase, where this treatment improved the explained variance in experimental activity from 75% for the unimode case to about 85%. The predictive ability scaled accordingly, as verified by extensive cross-validations.     

Synthesis,Characterization, Crystal Structure,and Biological Activities of Transition Metal Complexes with 1‐Phenyl‐3‐methyl‐5‐hydroxypyrazole‐4‐methylene‐8′‐quinolineimine

The Schiff base ligand, 1‐phenyl‐3‐methyl‐5‐hydroxypyrazole‐4‐methylene‐8′‐quinolineimine, and its Cu^II, Zn^II, and Ni^II complexes were synthesized and characterized. The crystal structure of the Zn^II complex was determined by single‐crystal X‐ray diffraction, indicating that the metal ions and Schiff base ligand can form mononuclear six‐coordination complexes with 1:1 metal‐to‐ligand stoichiometry at the metal ions as centers. The binding mechanism and affinity of the ligand and its metal complexes to calf thymus DNA (CT DNA) were investigated by UV/Vis spectroscopy, fluorescence titration spectroscopy, EB displacement experiments, and viscosity measurements, indicating that the free ligand and its metal complexes can bind to DNA via an intercalation mode with the binding constants at the order of magnitude of 105–106 M ^–1, and the metal complexes can bind to DNA more strongly than the free ligand alone. In addition, antioxidant activities of the ligand and its metal complexes were investigated through scavenging effects for hydroxyl radical in vitro, indicating that the compounds show stronger antioxidant activities than some standard antioxidants, such as mannitol. The ligand and its metal complexes were subjected to cytotoxic tests, and experimental results indicated that the metal complexes show significant cytotoxic activity against lung cancer A 549 cells.     

Determination of ligand to DNA binding parameters from two-dimensional DSC curves

The application of the theory of DNA denaturation linked to ligand binding to differential scanning calorimetry (DSC) is a useful tool to simultaneously characterize the energetics of denaturation and binding. Although the general theory is well known, the current DSC-based approaches to study the DNA–ligand interaction do not utilize the full potential of this method. In this paper, we propose the analytical approach for detailed analysis of DNA–ligand interaction from DSC data. The DNA macromolecule is represented as an assembly of cooperative units which melt by two-state model. The explicit account of ligand distribution on polymeric DNA and the temperature dependences of melting and binding constants, as well as of enthalpies, are considered. Such approach enables to extract the binding constant, stoichiometry, enthalpy, entropy, and heat capacity changes from multiple excess heat capacity profiles obtained at varying concentrations of the ligand (i.e. two-dimensional DSC curves). The applicability of the developed approach was demonstrated using an example salmon testes DNA–proflavine DSC experiment. The full set of DNA melting and proflavine binding thermodynamic parameters was obtained. Comparison of the proflavine binding parameters obtained from DSC with those determined from alternative experimental methods has proved the usefulness of the DSC method for evaluation of the binding thermodynamics in DNA–ligand system. In addition, the approach developed in the present study, allows to evaluate the concentration dependences of all species in solution as a function of temperature. Analysis of these dependences has enabled to interpret fine effects on the DSC curves of DNA–ligand complexes.     

羰基镍簇Ni(CO)n(n=1-4)的结构和Ni-CO键解离性质的密度泛函理论研究

在密度泛函理论框架下, 应用不同泛函计算了配合物Ni(CO)n(n=1~4)的平衡几何构型和振动频率. 考察了泛函和基组重叠误差对预测Ni—CO键解离能的影响. 计算结果表明, 用杂化泛函能得到与实验一致的优化几何构型和较合理的振动频率. 对Ni(CO)n(n=2~4)体系, 用“纯”泛函, 如BP86和BPW91, 可得到与CCSD(T)更符合、 并与实验值接近的解离能. 当解离产物出现单个金属原子或离子(如金属羰基配合物的完全解离)时, BSSE校正项的计算中应保持金属部分的电子结构一致. 只有考虑配体基组和不考虑配体基组两种情况下金属的电子构型与配合物中金属的构型一致时, 才能得到合理的BSSE校正, 从而预测合理的解离能.     

Oxovanadium complex as potential nucleic acid binder

DNA binding study of a vanadium(V) complex, Oxo-chloro-bis-N-phenylbenzohydroxamto-vanadium(V), derived from N-phenylbenzohydroxamic acid(PBHA) form a violet color complex with vanadium (V) in presence of hydrochloric acid is performed using absorption, fluorescence and viscometric techniques. The binding parameters of the PBHA-V(V) complex using calf thymus DNA (ct-DNA) and torula yeast RNA (t-RNA) have been determined. The complex shows the ability of cooperatively minor groove binding with ct-DNA as indicated by remarkable hyperchromicity and a blue shift of the absorption spectra. Quenching of metal complex calculation was carried out with Stern-Volmer equation and K_sv was found to be 2.32 ± 0.18 × 10⁴ M^?1, while in the case of t-RNA, enhancement is observed and that means the compound was not able to displace the Ethidium Bromide(EB)-t-RNA complex. Molecular docking was also applied to predict the mode of interaction of the hydroxamic acid with ct-DNA and t-RNA. DNA binding results of the complex are compared with those of the parent ligand.     

OFF-OFF-ON switching of fluorescence and electron transfer depending on stepwise complex formation of a host ligand with guest metal ions

Stepwise complex formation is observed between 2,3,5,6-tetrakis(2-pyridyl)pyrazine (TPPZ) and a series of metal ions (M(n+) = Sc3+, Y3+, Ho3+, Eu3+, Lu3+, Nd3+, Zn2+, Mg2+, Ca2+, Ba2+, Sr2+, Li+), where TPPZ forms a 2:1 complex [(TPPZ)2-M(n+)] and a 1:1 complex [TPPZ-M(n+)] with Mn+ at low and high concentrations of metal ions, respectively. The fluorescence intensity of TPPZ begins to increase at high concentrations of metal ions, when the 2:1 (TPPZ)2-M(n+) complex is converted to the fluorescent 1:1 TPPZ-M(n+) complex. This is regarded as an "OFF-OFF-ON" fluorescence sensor for metal ions depending on the stepwise complex formation between TPPZ and metal ions. The fluorescence quantum yields of the TPPZ-M(n+) complex vary depending on the metal valence state, in which the fluorescence quantum yields of the divalent metal complexes (TPPZ-M2+) are much larger than those of the trivalent metal complexes (TPPZ-M3+). On the other hand, the binding constants of (TPPZ)2-M(n+) (K1) and TPPZ-M(n+) (K2) vary depending on the Lewis acidity of metal ions (i.e., both K1 and K2 values increase with increasing Lewis acidity of metal ions). Sc3+, which acts as the strongest Lewis acid, forms the (TPPZ)2-Sc3+ and TPPZ-Sc3+ complexes stoichiometrically with TPPZ. In such a case, "OFF-OFF-ON" switching of electron transfer from cobalt(II) tetraphenylporphyrin (CoTPP) to O2 is observed in the presence of Sc3+ and TPPZ depending on the ratio of Sc3+ to TPPZ. Electron transfer from CoTPP to O2 occurs at Sc3+ concentrations above the 1:2 ratio ([Sc3+]/[TPPZ]0 > 0.5), when the (TPPZ)2-Sc3+ complex is converted to the TPPZ-Sc3+ complex and TPPZ-(Sc3+)2, which act as promoters of electron transfer (ON) by the strong binding of O2*- with Sc3+. In sharp contrast, no electron transfer occurs without metal ion (OFF) or in the presence at Sc3+ concentrations below the 1:2 ratio (OFF), when the (TPPZ)2-Sc3+ complex has no binding site available for O2*-.     

Synthesis,crystal structure,DNA interaction and anticancer evaluation of pyruvic acid derived hydrazone and its transition metal complexes

A novel tridentate chelating ligand, Ethyl 2‐(2‐(2‐chlorobenzoyl)hydrazono)propanoate and its late transition metal complexes were synthesized, characterized and evaluated for anticancer behavior. The structures were elucidated with the help of elemental analyses, spectral (vibrational, electronic, NMR and mass) and thermo‐gravimetric techniques. Single crystal X‐ray crystallographic studies of the ligand suggest an orthorhombic lattice structure with Pna21 space group. The interaction of ligand and complexes with DNA (CT‐DNA) has been extensively studied using absorption, emission, viscosity and thermal denaturation studies with E. coli DNA. The DNA cleavage ability of ligand and metal complexes was tested using plasmid pBR322 DNA by gel electrophoresis method. The ligand and its copper complex have been evaluated for their in vitro anticancer activity against human cancer cells of different origin such as KB (Oral), A431 (Skin), Mia‐Pa‐Ca (Pancreases), K‐549 (Lung), K‐562 (Leukemia), MCF‐7 (Breast) and VERO by MTT assay and the apoptosis assay was carried out with acridine orange/ethidium bromide (AO/EB) staining method. The studies suggest that ligand and copper complex exhibit significant cytotoxic activity on KB, MCF‐7, A‐431, Mia‐Pa‐Ca‐2 an d A‐549 cell lines compared to K‐562 and VERO cell lines.     

Modeling data from titration,amide H/D exchange,and mass spectrometry to obtain protein-ligand binding constants

We recently reported a new method for quantification of protein-ligand interaction by mass spectrometry, titration and H/D exchange (PLIMSTEX) for determining the binding stoichiometry and affinity of a wide range of protein-ligand interactions. Here we describe the method for analyzing the PLIMSTEX titration curves and evaluate the effect of various models on the precision and accuracy for determining binding constants using H/D exchange and a titration. The titration data were fitted using a 1:n protein:ligand sequential binding model, where n is the number of binding sites for the same ligand. An ordinary differential equation was used for the first time in calculating the free ligand concentration from the total ligand concentration. A nonlinear least squares regression method was applied to minimize the error between the calculated and the experimentally measured deuterium shift by varying the unknown parameters. A resampling method and second-order statistics were used to evaluate the uncertainties of the fitting parameters. The interaction of intestinal fatty-acid-binding protein (IFABP) with a fatty-acid carboxylate and that of calmodulin with Ca(2+) are used as two tests. The modeling process described here not only is a new tool for analyzing H/D exchange data acquired by ESI-MS, but also possesses novel aspects in modeling experimental titration data to determine the affinity of ligand binding.     

Mutual Influence of Ligands and Reactivity of Gd and Dy Acidophthalocyaninate Complexes

The results of the kinetic study of dissociation of Gd(III) and Dy(III) complexes with phthalocyanine of the composition (X)LnPc (X is single-charged acido ligand) with isolation of macrocyclic ligand depending on the temperature, composition of mixed ethanol–acetic acid solvent, and the nature of acido ligand are presented. The total kinetic equations, the rate constants, and activation parameters of dissociation reaction are determined. The stoichiomeric mechanism is suggested for the complex dissociation involving the limiting elementary reaction between acetic acid molecule and the complex that occurs as the chelate salt (X)LnPc or the outer-sphere complex [(HOAc)LnP]⁺X^–. The state of metal phthalocyaninate at the reaction slow stage is shown to be determined by the electronic structure of the metal cation, the strength of binding of the axial ligand, and by its cis-effect on the metal bonds with macrocycle.     

A comparative DFT study of some N-based aromatic ligand metal complexes as anticancer agents and analysis of their mode of interaction with DNA base pair

Metal complexed anticancer agents interact with DNA nucleobase pairs (AT and GC) through different types of binding mode such as intercalation, groove binding, covalent binding, etc. Minor and major groove binding mechanism of DNA base pair is the key factor for all kinds of anticancer agent; as metal complexes have a great affinity to bind with DNA nucleobase either through minor or major groove. Ligands in metal complexes also play a vital role during the interaction with DNA base pairs; these ligands directly interact with DNA through different interacting modes. Generally, anticancer agents with less sterically hindered N-based aromatic and planar ligands are the key component for DNA binding; as the structure of such ligands are quite compatible for following intercalation and groove binding mechanism. Since, the experimental investigation for drug-DNA nucleobase complexes are extremely complicated, therefore; quantum mechanical calculations might be very helpful for computing the actual interactions in drug-DNA complexes. Quantum mechanical approaches such as density functional theory (DFT) might be a very important and useful tool to investigate the actual mode of interaction of metal complexed antitumor agents with DNA nucleobase. Herein, we have taken some metal complexes with N-based aromatic ligands as antitumor agents to investigate the proper mode of interaction between drug-DNA complexes.     

Some divalent metal(II) complexes of novel potentially tetradentate Schiff base N,N′‐bis(2‐carboxyphenylimine)‐2,5‐thiophenedicarboxaldhyde: Synthesis,spectroscopic characterization and bioactivities

A novel tetradentate dianionic Schiff base ligand, N ,N ′‐bis(2‐carboxyphenylimine)‐2,5‐thiophenedicarboxaldhyde (H₂L) and some first row d‐transition metal chelates (Co(II), Cu(II), Ni(II) and Zn(II)) were synthesized and characterized using various physicochemical and spectroscopic methods. The spectroscopic data suggested that the parent Schiff base ligand coordinates through both deprotonated carboxylic oxygen and imine nitrogen atoms. The free Schiff base and its metal chelates were screened for their antimicrobial activities for various pathogenic bacteria and fungi using the agar well diffusion method. The antibacterial and antifungal activities of all the newly synthesized compounds are significant compared to the standard drugs ciprofloxacin and nystatin. The antioxidant activities of the compounds were determined by reduction of 1,1‐diphenyl‐2‐picrylhydrazyl and compared with that of vitamin C as a standard. DNA binding ability of the novel Schiff base and its complexes was investigated using absorption spectroscopy, fluorescence spectroscopy, viscosity measurements and thermal denaturation. The obtained results clearly demonstrate that the binding affinity with calf thymus DNA follows the order: Cu(II) complex > Ni(II) complex > Zn(II) complex > Co(II) complex >H₂L. Furthermore, the DNA cleavage activity of the newly synthesized ligand and its metal complexes was investigated using supercoiled plasmid DNA (pUC18) gel electrophoresis.     

Induction of B- to Z-DNA transition by copper and zinc complexes with C(15) substituted macrocyclic pentaaza ligands

The new macrocyclic ligand 15-fluoro-15-methyl-1,4,7,10,13-pentaazacyclohexadecan-14,16-dione (2) was synthesised and its crystal structure determined together with the ones of the known analogues of 2, 15-fluoro-1,4,7,10,13-pentaazacyclohexadecan-14,16-dione (1) and 15,15-difluoro-1,4,7,10,13-pentaazacyclohexadecan-14,16-dione (3). The binding behaviour of all three ligands to copper and zinc was studied in the solid state. They can bind to the metal centre by either triple coordination (N3) with all secondary amines or after double deprotonation of the two amides with all five nitrogen atoms (N5). The N5 coordination mode is favoured by the presence of one or two fluorine substituents at the C(15) position and by a high pH in the case of aqueous solutions. Circular dichroism titrations of poly d(GC) with the metal complexes showed that only 4 and 5, that is the copper complexes of 1 and 2, induced a complete B- to Z-DNA transition. The degree of cooperativity of the transition was found to be 3.4 and 7.3 for 4 and 5 respectively. As a possible hypothesis to explain this difference, the additional methyl group in 5 compared with 4 may be involved in a hydrophobic interaction with the DNA. Ligand 2, the copper complex 6 of the bis fluoro substituted ligand 3, and the zinc complex 7 of ligand 1 did not induce any change in the direction of Z-DNA. In the case of 6, the CD spectrum of the DNA actually showed no change at all, indicating that the complex was even not interacting with the B form of DNA. Therefore it is assumed that the bis fluoro substitution is causing the complex to be in the neutral N5 coordination mode at the experimental conditions of pH 7. The electrostatic contribution together with the shielding effect of the ligand might explain the absence of any interaction with the DNA.     

DNA oligonucleotide-cis-platin binding: Ab initio interpretation of the vibrational spectra

The cis-platin binding to the d(CCTGGTCC)*d(GGACCAGG) model DNA octamer was monitored with infrared absorption (IR) and vibrational circular dichroism (VCD) spectroscopies. The spectra were modeled with the aid of density functional computations and a Cartesian coordinate-based transfer of molecular property tensors from smaller DNA fragments. Because of the fragmentation, the tensors could be calculated with a higher precision. Environmental effects, such as the presence of the solvent or the cis-platin ligand, could be included in the modeling. The solvent was modeled by an explicit inclusion of hydrogen-bound water molecules, positions of which were estimated from a molecular dynamics simulation, or by the polarized continuum COSMO model. The B3LYP and BPW91 functionals used for the calculations of the spectral parameters were combined with the relativistic LANL2DZ platinum pseudo-potentials. The simulations reproduced the main IR and VCD DNA spectral features and explained most of the changes observed experimentally upon metal binding. The results confirmed that the influence of the ligand on DNA vibrational properties is quite complex; it originates in the geometry deformation and normal mode coupling pattern changes of the platinated octamer, as well as in local perturbations of the electronic structure and force field of the GC base pairs to which the platinum is bound. Many of the local effects could be accounted for by a point charge used in place of the metal in the GC complex.     

Voltammetric measurements of the interaction of metal complexes with nucleic acids

Cyclic voltammetry and differential-pulse voltammetry at mm-sized electrodes were used to measure the decrease in the rate of diffusion of metal complexes upon binding to DNA and to extract the binding constants and effective binding site sizes. A linear correlation was observed between the site size determined electrochemically and the diameter of the complexes [site size: Cu(phen)2(2+) > Fe(phen)3(2+) > Co(bipy)3(3+) approximately Fe(bipy)3(2+) > Ru(NH3)6(3+)]. The binding constants were found to be influenced by the charge of the metal complex, the nature of ligand and the geometry about the metal centre. Competition experiments, in which differential pulse voltammetry was used to observe the release of bound metal complex on addition of a second DNA-binding molecule to the solution, were sensitive to the nature and location of the binding sites for the two species. Steady-state voltammetric experiments at microelectrodes are shown to have a number of advantages over cyclic voltammetry and differential pulse voltammetry at mm-sized electrodes for determination of binding constants. In particular, the steady-state diffusion limited current is directly proportional to the diffusion coefficient, rather than its square root, which improves the discrimination between DNA-bound and freely diffusing metal complex. Further, the kinetics of the binding process do not affect the steady state measurement, whereas for transient techniques, e.g., cyclic voltammetry, only a range of values can be extracted corresponding to the limits of fast and slow binding kinetics compared to the experimental timescale.     

Structural chemistry of a green fluorescent protein Zn biosensor

We designed a green fluorescent protein mutant (BFPms1) that preferentially binds Zn(II) (enhancing fluorescence intensity) and Cu(II) (quenching fluorescence) directly to a chromophore ligand that resembles a dipyrrole unit of a porphyrin. Crystallographic structure determination of apo, Zn(II)-bound, and Cu(II)-bound BFPms1 to better than 1.5 A resolution allowed us to refine metal centers without geometric restraints, to calculate experimental standard uncertainty errors for bond lengths and angles, and to model thermal displacement parameters anisotropically. The BFPms1 Zn(II) site (KD = 50 muM) displays distorted trigonal bipyrimidal geometry, with Zn(II) binding to Glu222, to a water molecule, and tridentate to the chromophore ligand. In contrast, the BFPms1 Cu(II) site (KD = 24 muM) exhibits square planar geometry similar to metalated porphyrins, with Cu(II) binding to the chromophore chelate and Glu222. The apo structure reveals a large electropositive region near the designed metal insertion channel, suggesting a basis for the measured metal cation binding kinetics. The preorganized tridentate ligand is accommodated in both coordination geometries by a 0.4 A difference between the Zn and Cu positions and by distinct rearrangements of Glu222. The highly accurate metal ligand bond lengths reveal different protonation states for the same oxygen bound to Zn vs Cu, with implications for the observed metal ion specificity. Crystallographic anisotropic thermal factor analysis validates metal ion rigidification of the chromophore in enhancement of fluorescence intensity upon Zn(II) binding. Thus, our high-resolution structures reveal how structure-based design has effectively linked selective metal binding to changes in fluorescent properties. Furthermore, this protein Zn(II) biosensor provides a prototype suitable for further optimization by directed evolution to generate metalloprotein variants with desirable physical or biochemical properties.     

Metalated Hexaphyrins: From Understanding to Rational Design

The heretofore unpredictable behavior of [26] and [28]hexaphyrins upon metalation has been elucidated through quantum chemical calculations. It is demonstrated that the molecular topology of Group 10 and Group 11 metal complexes of hexaphyrins depends on sensitive interplay between the intrinsic ligand strain and the metal–ligand interaction strength. As such, the aromaticity of the ligand and effective charge of the metal are revealed as key factors determining the binding mode and the preference for Möbius or Hückel structures. These findings offer a new perspective to rationalize experimental observations for metalated hexaphyrins. More importantly, the proposed guidelines could be useful for designing novel complexes of hexaphyrins, such as a hitherto unknown Möbius [26]hexaphyrin complex.