Quadruplex–Duplex Junction: A High-Affinity Binding Site for Indoloquinoline Ligands

A parallel quadruplex derived from the Myc promoter sequence was extended by a stem-loop duplex at either its 5′- or 3′-terminus to mimic a quadruplex–duplex (Q–D) junction as a potential genomic target. High-resolution structures of the hybrids demonstrate continuous stacking of the duplex on the quadruplex core without significant perturbations. An indoloquinoline ligand carrying an aminoalkyl side chain was shown to bind the Q–D hybrids with a very high affinity in the order K_a≈10⁷ m ⁻¹ irrespective of the duplex location at the quadruplex 3′- or 5′-end. NMR chemical shift perturbations identified the tetrad face of the Q–D junction as specific binding site for the ligand. However, calorimetric analyses revealed significant differences in the thermodynamic profiles upon binding to hybrids with either a duplex extension at the quadruplex 3′- or 5′-terminus. A large enthalpic gain and considerable hydrophobic effects are accompanied by the binding of one ligand to the 3′-Q–D junction, whereas non-hydrophobic entropic contributions favor binding with formation of a 2:1 ligand-quadruplex complex in case of the 5′-Q–D hybrid.     

Towards the Development of Structure‐Selective G‐Quadruplex‐Binding Indolo[3,2‐b]quinolines

The interaction of phenyl‐substituted indolo[3,2‐b]quinolines with DNA G‐quadruplexes of different topology were studied by using a combination of spectroscopic and calorimetric methodologies. N5‐Methylated indoloquinoline derivatives (^MePIQ) with an aminoalkyl side chain exhibit high affinities for the parallel‐stranded MYC quadruplex and a (3+1)‐hybrid structure combined with an excellent discrimination against the antiparallel thrombin‐binding aptamer (TBA) and the human telomeric (HT) quadruplexes. Dissociation constants for the binding of the ligand to the MYC quadruplex are in the submicromolar range, being below the corresponding dissociation constants for the antiparallel‐stranded quadruplexes by about one order of magnitude. Competition experiments with double‐helical DNA reveal the impact of indoloquinoline structural features on the selectivity for the parallel quadruplex relative to duplex DNA. Based on a calorimetric analysis binding to MYC is shown to be equally driven by favorable enthalpic and entropic contributions with no significant impact on the type of cation present.     

Supramolecular Tetrad Featuring Covalently Linked Bis(porphyrin)–Phthalocyanine Coordinated to Fullerene: Construction and Photochemical Studies

A multimodular donor–acceptor tetrad featuring a bis(zinc porphyrin)–(zinc phthalocyanine) ((ZnP–ZnP)–ZnPc) triad and bis‐pyridine‐functionalized fullerene was assembled by a “two‐point” binding strategy, and investigated as a charge‐separating photosynthetic antenna‐reaction center mimic. The spectral and computational studies suggested that the mode of binding of the bis‐pyridine‐functionalized fullerene involves either one of the zinc porphyrin and zinc phthalocyanine (Pc) entities of the triad or both zinc porphyrin entities leaving ZnPc unbound. The binding constant evaluated by constructing a Benesi–Hildebrand plot by using the optical data was found to be 1.17×10⁵ M ^?1, whereas a plot of “mole‐ratio” method revealed a 1:1 stoichiometry for the supramolecular tetrad. The mode of binding was further supported by differential pulse voltammetry studies, in which redox modulation of both zinc porphyrin and zinc phthalocyanine entities was observed. The geometry of the tetrad was deduced by B3LYP/6‐31G* optimization, whereas the energy levels for different photochemical events was established by using data from the optical absorption and emission, and electrochemical studies. Excitation of the zinc porphyrin entity of the triad and tetrad revealed ultrafast singlet–singlet energy transfer to the appended zinc phthalocyanine. The estimated rate of energy transfer (k_ENT) in the case of the triad was found to be 7.5×10¹¹ s^?1 in toluene and 6.3×10¹¹ s^?1 in o‐dichlorobenzene, respectively. As was predicted from the energy levels, photoinduced electron transfer from the energy‐transfer product, that is, singlet‐excited zinc phthalocyanine to fullerene was verified from the femtosecond‐transient spectral studies, both in o‐dichlorobenzene and toluene. Transient bands corresponding to ZnPc ^{? +} in the 850 nm range and C₆₀ ^{? ?} in the 1020 nm range were clearly observed. The rate of charge separation, k_CS, and rate of charge recombination, k_CR, for the (ZnP–ZnP)–ZnPc ^{? +}:Py₂C₆₀ ^{? ?} radical ion pair (from the time profile of 849 nm peak) were found to be 2.20×10¹¹ and 6.10×10⁸ s^?1 in toluene, and 6.82×10¹¹ and 1.20×10⁹ s^?1 in o‐dichlorobenzene, respectively. These results revealed efficient energy transfer followed by charge separation in the newly assembled supramolecular tetrad.     

A Click Chemistry Approach to Developing Molecularly Targeted DNA Scissors

Nucleic acid click chemistry was used to prepare a family of chemically modified triplex forming oligonucleotides (TFOs) for application as a new gene-targeted technology. Azide-bearing phenanthrene ligands—designed to promote triplex stability and copper binding—were ‘clicked’ to alkyne-modified parallel TFOs. Using this approach, a library of TFO hybrids was prepared and shown to effectively target purine-rich genetic elements in vitro. Several of the hybrids provide significant stabilisation toward melting in parallel triplexes (>20 °C) and DNA damage can be triggered upon copper binding in the presence of added reductant. Therefore, the TFO and ‘clicked’ ligands work synergistically to provide sequence-selectivity to the copper cutting unit which, in turn, confers high stabilisation to the DNA triplex. To extend the boundaries of this hybrid system further, a click chemistry-based di-copper binding ligand was developed to accommodate designer ancillary ligands such as DPQ and DPPZ. When this ligand was inserted into a TFO, a dramatic improvement in targeted oxidative cleavage is afforded.     

Copper‐Induced Topology Switching and Thrombin Inhibition with Telomeric DNA G‐Quadruplexes

The topological diversity of DNA G‐quadruplexes may play a crucial role in its biological function. Reversible control over a specific folding topology was achieved by the synthesis of a chiral, glycol‐based pyridine ligand and its fourfold incorporation into human telomeric DNA by solid‐phase synthesis. Square‐planar coordination to a Cu^II ion led to the formation of a highly stabilizing intramolecular metal–base tetrad, substituting one G‐tetrad in the parent unimolecular G‐quadruplex. For the Tetrahymena telomeric repeat, Cu^II‐triggered switching from a hybrid‐dominated conformer mixture to an antiparallel topology was observed. Cu^II‐dependent control over a protein–G‐quadruplex interaction was shown for the thrombin–tba pair (tba=thrombin‐binding aptamer).     

Molecular docking analysis and spectroscopic investigations of zinc(II), nickel(II) N-phthaloyl-β-alanine complexes for DNA binding: Evaluation of antibacterial and antitumor activities

Herein, computational molecular docking, UV/visible and fluorescence spectroscopic techniques have been used to explore the DNA binding interactions of N-phthaloyl-β-alanine (NPA) ligand and its Zn(II) and Ni(II) complexes (NPAZn, NPANi). The compounds were further tested for anti-bacterial and anti-tumor activities. Docking analysis depicted that ligand NPA interacted with DNA via intercalation, while its metal complexes showed mixed mode of interactions. Spectroscopic experiments for DNA binding studies were run under physiological conditions of pH (stomach; 4.7, blood; 7.4) and temperature (37 °C). Based on changes in spectral responses, binding parameters for all the compounds were obtained which showed comparatively greater binding constant values (K_b: UV; 1.16 × 10⁵ M⁻¹, Flu; 1.35 × 10⁵ M⁻¹) and more negative free energy changes (ΔG: UV; −30.00 kJ mol⁻¹, Flu; −30.44 kJ mol⁻¹) for NPAZn at pH 4.7. The overall, binding results were also found more significant at stomach pH. Dynamic “K_D” and bimolecular “K_B” constants were evaluated, and the values affirmed the participation of static process for each compound–DNA binding. The greater binding site size values (n > 1) of metal complexes NPAZn and NPANi indicated other sites availability of intercalative compounds. DNA viscosity variation by increasing compound’s concentration further verified the compound–DNA interaction. Antibacterial and tumor inhibitory activities were observed significant for both metal complexes, while ligand has shown no activity. The greater binding affinity of metal complexes, as evaluated both computationally and spectroscopically, further validated the lower IC50 values of complexes as compared to ligand.     

Identification and analysis of stereoselective drug interactions with low-density lipoprotein by high-performance affinity chromatography

Columns containing immobilized low-density lipoprotein (LDL) were prepared for the analysis of drug interactions with this agent by high-performance affinity chromatography (HPAC). R/S-Propranolol was used as a model drug for this study. The LDL columns gave reproducible binding to propranolol over 60 h of continuous use in the presence of pH 7.4 0.067 M potassium phosphate buffer. Experiments conducted with this type of column through frontal analysis indicated that two types of interactions were occurring between R-propranolol and LDL, while only a single type of interaction was observed between S-propranolol and LDL. The first type of interaction, which was seen for both enantiomers, involved non-saturable binding; this interaction had an overall affinity (nK _a) of 1.9 (±0.1) × 10⁵ M⁻¹ for R-propranolol and 2.7 (±0.2) × 10⁵ M⁻¹ for S-propranolol at 37 °C. The second type of interaction was observed only for R-propranolol and involved saturable binding that had an association equilibrium constant (K _a) of 5.2 (±2.3) × 10⁵ M⁻¹ at 37 °C. Similar differences in binding behavior were found for the two enantiomers at 20 °C and 27 °C. This is the first known example of stereoselective binding of drugs by LDL or other lipoproteins. This work also illustrates the ability of HPAC to be used as a tool for characterizing mixed-mode interactions that involve LDL and related binding agents.     

Lanthanide complex of 1-phenyl-3-methyl-5-hydroxypyrazole-4-carbaldehyde-(isonicotinoyl) hydrazone: crystal structure and DNA-binding properties

A Schiff-base ligand derived from 1-phenyl-3-methyl-4-formyl-2-pyrazolin-5-one (PMFP) and isoniazid was prepared and its La(III) complex was characterized by X-ray single crystal diffraction. The La(III) is nine-coordinate in a space group P2₁/n. DNA-binding was investigated by UV-Vis, fluorescence titration, ethidium bromide displacement experiments, and viscosity measurements, which indicated that the ligand and La(III) complex strongly binds to calf thymus DNA presumably via groove binding and intercalation. The intrinsic binding constants of the ligand and La(III) complex were 0.86?×?10⁵ and 2.46?×?10^5?mol?L^?1, respectively. Antioxidant data from hydroxyl radical scavenging experiments in vitro suggest that the La(III) complex possesses higher scavenging ratio than the free ligand, metallic salt, and some standard antioxidants like mannitol.     

Ni(II) Ternary Complex Based on Antimicrobial Drug Enoxacin: Synthesis and Biological Properties

First Ni(II) ternary complex using the quinolone antibacterial agent enoxacin (HEn) as ligand and 1,10‐phenanthroline as co‐ligand has been synthesized and characterized. It is a mononuclear structure, in which enoxacin acts as a bidentate ligand bound to the metal through the ketone oxygen and a carboxylate oxygen atom. The complex exhibited good binding propensity to human and bovine serum albumin proteins having relatively high binding constants (6.40×10⁴ and 7.12×10⁴, respectively). The investigation of the interaction of the complex with calf‐thymus (CT) DNA has been performed with UV and circular dichroism (CD) spectroscopies, indicating that they bind to CT DNA probably by the intercalative binding mode. The binding constant (K_b) of the complex with CT DNA calculated with UV is 2.03×10⁵, which is higher than that of free enoxacin drug (2.09×10⁴) and even higher than that of typical intercalation indicator (1.23×10⁵) of ethidium bromide (EB). Fluorescence competitive studies with EB have revealed that the complex exhibited the ability to displace the DNA‐bound EB using the intercalative binding site. In addition, the antimicrobial activity showed that the complex exhibited a little bit good inhibition (MIC=1.843 (g·mL^?1) against B. subtilis than free HEn.     

An open-framework cobalt molybdate possessing {Mo2O7} building block: hydrothermal synthesis and structural characterization of [CoMo2O7(4,4′-bipy)1.5]

The hydrothermal reaction of Co(COO)₂?·?4H₂O, MoO₃, H₃PO₄ and 4,4′-bipyridine yields bipyridine-ligated cobalt dimolybdate [CoMo₂O₇(4,4′-bipy)_1.5] (1) (4,4′-bipy?=?4,4′-bipyridine) in the triclinic system with space group of P 1 and cell parameters of a?=?7.1951(8)?Å, b?=?11.1708(17)?Å, c?=?11.4514(11)?Å, α?=?98.545(7)°, β?=?90.315(2)°, γ?=?105.777(5)°, V?=?874.88(19)?ų, and Z?=?2. Its structure consists of Co/Mo/O bimetal oxide layers with {Mo₂O₇} building blocks, linked by the coordination of 4,4′-bipy ligand with Co and Mo atoms, into a 3D porous hybrid framework.     

Metallderivate von Molekülverbindungen. VIII. catena-Poly[(2,5,8-trioxanonan-O2,O5) lithium-methylphosphanid] — eine Verbindung mit meso-Helix-Struktur

Metal Derivatives of Molecular Compounds. VIII. catena-Poly[(2,5,8-trioxanonane-O²,O⁵) lithium-methylphosphanide] — a Compound with a meso-Helix Structure Studies of Fritz et al. [10] showed methylphosphane to be lithiated at ?60°C in 1,2-dimethoxyethane or bis(2-methoxyethyl) ether solution by stoichiometric amounts of lithium n-butanide in n-hexane. After removing the hydrocarbons almost completely by distillation and cooling the solutions to ?60°C again, colourless square crystals of (1,2-dimethoxyethane-O,O′)lithium ( 1 ) and (2,5,8-trioxanonane-O²,O⁵)lithium methylphosphanide ( 2 ) precipitate. As shown by an X-ray structure determination (monoclinic, P2₁/n; a = 805.5(1); b = 1820.6(2); c = 851.5(1) pm; β = 116.76(1)° at ?100 ± 3°C; Z = 4 formula units; R = 0.034) complex 2 forms a polymer which has the shape of an up to now scarcely noted meso-helix. Four-coordinated lithium is bound to two phosphorus (P? Li 252.9 and 253.2 pm; P? Li? P 131.8°; Li? P? Li 132.1°) and to two oxygen atoms (Li? O 203.9 and 206.8; O …? O 270.7 pm; O? Li? O 82.5°) of the inherently tridentate 2,5,8-trioxanonane ligand. As compared to the standard value (185 pm) the P? C distance (187.4 pm) is slightly lengthened. Structure determinations of (2,5,8-trioxanonane-O²,O⁵,O⁸) lithium 1-(phenylsulfonyl)alkyl compounds published some years ago [26, 27], allow a comparison of molecular parameters characteristic for the twofold or threefold coordinating chelate ligand.     

Synthesis and crystal structures of new sodium phenolate compounds: coordination chemistry

Four new sodium complexes of phenolate and bisphenolate ligands have been synthesized and characterized by NMR spectroscopy and X-ray crystallography to study their coordination chemistry. The monoanionic tridentate [ONN] phenolate ligand gave a dimeric compound [Na₂L₂] (2), which crystallized in the orthorhombic crystal system, where the sodium ions have four coordination environments. The dianionic tridentate [ONO] phenolate ligand gave a dimeric [Na₂(L^IH)₂] (4) compound in the tetragonal crystal system. The sodium ions Na(1) and Na(1?) are four-coordinate both having a tetrahedral geometry with the O–Na–O angle being ca. 93°, the O^N^O ligand string comprising a tridentate ligand. Interestingly, despite the steric bulk of N(SiMe₃)₂, a mixture of compounds [NaL] (2) and NaN(SiMe₃)₂ was isolated as a dimeric structure [Na₂L(N(SiMe₃)₂)]₂ (5) crystallized in the monoclinic crystal system. Na(1) is four-coordinate bonding to the phenolic oxygen atom and two N atoms of the ligand L and the N of the N(SiMe₃)₂ ligand. The coordination around Na(1) is tetrahedrally distorted square planar with the ‘cis’ angles ranging from 75.11(4) to 117.40(5)° and the ‘trans’ angles being 140.87(4) and 154.82(5)°. Na(2) is three-coordinate, bonding to the two phenolate oxygen atoms and the N atom of the N(SiMe₃)₂ ligand. Na(2), however, is not coplanar with these atoms being displaced 0.42 Å from it. The coordination chemistry for 5 is very intriguing as the sodium ions have mixed four- and three-coordination numbers, probably due to the steric hindrance of the silylamide groups.     

Protein:Ligand binding free energies: A stringent test for computational protein design

A computational protein design method is extended to allow Monte Carlo simulations where two ligands are titrated into a protein binding pocket, yielding binding free energy differences. These provide a stringent test of the physical model, including the energy surface and sidechain rotamer definition. As a test, we consider tyrosyl‐tRNA synthetase (TyrRS), which has been extensively redesigned experimentally. We consider its specificity for its substrate l ‐tyrosine (l ‐Tyr), compared to the analogs d ‐Tyr, p‐acetyl‐, and p‐azido‐phenylalanine (ac‐Phe, az‐Phe). We simulate l ‐ and d ‐Tyr binding to TyrRS and six mutants, and compare the structures and binding free energies to a more rigorous “MD/GBSA” procedure: molecular dynamics with explicit solvent for structures and a Generalized Born + Surface Area model for binding free energies. Next, we consider l ‐Tyr, ac‐ and az‐Phe binding to six other TyrRS variants. The titration results are sensitive to the precise rotamer definition, which involves a short energy minimization for each sidechain pair to help relax bad contacts induced by the discrete rotamer set. However, when designed mutant structures are rescored with a standard GBSA energy model, results agree well with the more rigorous MD/GBSA. As a third test, we redesign three amino acid positions in the substrate coordination sphere, with either l ‐Tyr or d ‐Tyr as the ligand. For two, we obtain good agreement with experiment, recovering the wildtype residue when l ‐Tyr is the ligand and a d ‐Tyr specific mutant when d ‐Tyr is the ligand. For the third, we recover His with either ligand, instead of wildtype Gln. © 2015 Wiley Periodicals, Inc.     

Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility

We present a series of molecular‐mechanics‐based protein refinement methods, including two novel ones, applied as part of an induced fit docking procedure. The methods used include minimization; protein and ligand sidechain prediction; a hierarchical ligand placement procedure similar to a‐priori protein loop predictions; and a minimized Monte Carlo approach using normal mode analysis as a move step. The results clearly indicate the importance of a proper opening of the active site backbone, which might not be accomplished when the ligand degrees of freedom are prioritized. The most accurate method consisted of the minimized Monte Carlo procedure designed to open the active site followed by a hierarchical optimization of the sidechain packing around a mobile flexible ligand. The methods have been used on a series of 88 protein‐ligand complexes including both cross‐docking and apo‐docking members resulting in complex conformations determined to within 2.0 Å heavy‐atom RMSD in 75% of cases where the protein backbone rearrangement upon binding is less than 1.0 Å α‐carbon RMSD. We also demonstrate that physics‐based all‐atom potentials can be more accurate than docking‐style potentials when complexes are sufficiently refined. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Quantifying the Thermodynamics of Ligand Binding to CsPbBr3 Quantum Dots

Cesium lead halide perovskites are an emerging class of quantum dots (QDs) that have shown promise in a variety of applications; however, their properties are highly dependent on their surface chemistry. To this point, the thermodynamics of ligand binding remain unstudied. Herein, ¹H NMR methods were used to quantify the thermodynamics of ligand exchange on CsPbBr₃ QDs. Both oleic acid and oleylamine native ligands dynamically interact with the CsPbBr₃ QD surface, having individual surface densities of 1.2–1.7 nm^?2. 10‐Undecenoic acid undergoes an exergonic exchange equilibrium with bound oleate (K_eq=1.97) at 25 °C while 10‐undecenylphosphonic acid undergoes irreversible ligand exchange. Undec‐10‐en‐1‐amine exergonically exchanges with oleylamine (K_eq=2.52) at 25 °C. Exchange occurs with carboxylic acids, phosphonic acids, and amines on CsPbBr₃ QDs without etching of the nanocrystal surface; increases in the steady‐state PL intensities correlate with more strongly bound conjugate base ligands.     

Copper Catalyzed ATRP of Methyl Methacrylate Using Aliphatic α-Bromo Ketone Initiator

The atom transfer radical polymerization (ATRP) of MMA was examined using 3-bromo-3-methyl-butanone-2 (MBB) as an initiator in the presence of CuBr as catalyst and 2,6-bis[1-(2,6-diisopropylphenylimino)ethyl]pyridine (BPIEP) as a tridentate N-donor ligand. The effect of various other N-donor ligands including a bisoxazoline ligand, namely, 2,6-bis(4,4-dimethyl-2-oxazolin-2-yl) pyridine (dmPYBOX) was studied in ATRP and reverse ATRP of MMA. The ATRP of MMA in toluene at 90 °C using MBB as initiator was relatively slow in the case of bidentate and faster in the case of tridentate N-donor ligands. The apparent rate constant, k_app, with MBB as initiator and BPIEP as ligand in toluene (50%, v/v) at 90 °C was found to be 7.15 × 10⁻⁵ s⁻¹. In addition, reverse ATRP of MMA in diphenylether at 70 °C using BPIEP/CuBr₂ as catalyst system was very effective in reducing the reaction time from several hours to 24 h for polymerization of MMA.     

Bis(η5‐isopropyltetramethylcyclo­pentadienyl)(tetrahydroborato‐κ3H,H′,H′′)(tetrahydrofuran‐O)‐samarium(III): a lanthanidocene complex with a tridentate tetrahydroborato ligand

The lanthanidocene complex [Sm(BH₄)(C₁₂H₁₉)₂(C₄H₈O)], (I), shows a distorted tetrahedral arrangement around the central Sm^III atom. It consists of two η⁵‐isopropyltetramethylcyclopentadienyl ligands, one tetrahydroborato (BH₄^?) ligand bridging via H atoms to the lanthanide atom and one coordinating tetrahydrofuran (thf) molecule. The BH₄^? unit of (I) coordinates as a tridentate ligand with three bridging H atoms and one terminal H atom [Sm—B—H4 176 (2)°]. The η⁵‐isopropyl­tetra­methylcyclopentadienyl ligands of this bent‐sandwich complex [Cp1—Sm—Cp2 133.53 (1)° where Cp denotes the centroid of the cyclopentadienyl ring] adopt staggered conformations.     

Nonlinear Optical Glass-Ceramic From a New Polar Phase-Transition Organic-Inorganic Hybrid Crystal

Melt-quenched glasses of organic–inorganic hybrid crystals, i.e., hybrid glasses, have attracted increasing attention as an emerging class of hybrid materials with beneficial processability and formability in the past years. Herein, we present a new hybrid crystal, (Ph₃PEt)₃[Ni(NCS)₅] ( 1 , Ph₃PEt⁺=ethyl(triphenyl)phosphonium), crystallizing in a polar space group P1 and exhibiting thermal-induced reversible crystal-liquid-glass-crystal transitions with relatively low melting temperature of 132 °C, glass-transition temperature of 40 °C, and recrystallization on-set temperature of 78 °C, respectively. Taking advantage of such mild conditions, we fabricated an unprecedented hybrid glass-ceramic thin film, i.e., a thin glass uniformly embedding inner polar micro-crystals, which exhibits a much enhanced intrinsic second-order nonlinear optical effect, being ca. 25.6 and 3.1 times those of poly-crystalline 1 and KH₂PO₄, respectively, without any poling treatments.     

Synthesis of highly dispersed super-refractory tantalum-zirconium carbide Ta<Subscript>4</Subscript>ZrC<Subscript>5</Subscript> and tantalum-hafnium carbide Ta<Subscript>4</Subscript>HfC<Subscript>5</Subscript> via sol-gel technology

Nanocrystalline powders of super-refractory complex carbides Ta₄HfC₅ and Ta₄ZrC₅ were synthesized using a hybrid method comprising sol-gel technology for preparing highly dispersed metal oxidescarbon starting mixtures and a relatively low-temperature (1300–1500°C) carbothermal synthesis under a dynamic vacuum (P = 1 × 10⁻³ to 1 × 10⁻⁵ MPa). The elemental and phase compositions of the products and average crystallite sizes were determined. TEM was used to study particle morphology and dispersion. Microstructures were observed by SEM. BET specific surface areas were determined for powders prepared at 1400°C.