毛细管电泳结合电喷雾质谱分析人类癌基因c-myb四链体核酸与活性天然产物的相互作用

药物与靶点间的作用关系直接影响到药理和药效。药物-靶点结合能力、结合计量关系等信息是药物研发过程中必需的表征数据。人类癌基因c-myb在结直肠癌等多种癌症组织中存在过度表达,目前已成为结直肠癌、白血病等癌症疾病潜在的治疗靶点。位于癌基因c-myb启动子区的一段富含鸟嘌呤（G）的DNA序列,通过阳离子的诱导可自发折叠形成分子内G-四链体,而小分子的特异性识别可以稳定该G-四链体,进而调节基因的转录和表达过程。该文采用压力辅助毛细管电泳前沿分析（PACE-FA）结合电喷雾质谱（ESI-MS）研究人类癌基因c-myb启动子G-四链体（G4）与天然产物分子间的相互作用。PACE-FA法在毛细管电泳前沿分析（CE-FA）过程中施加一个与分析物迁移同向的压力,在保证结果准确度的前提下,能够大大加快分析速度。同时结合ESI-MS,可快速解析结合分子与靶点的亲合力和化学计量关系。首先,利用ESI-MS快速筛选出3种有亲合力的天然产物,亲合力大小依次为：土荆皮乙酸>丁溴东莨菪碱>荷叶碱。考虑到溶液相中存在特异性与非特异性结合,接着用PACE-FA法准确分析溶液相中结合的特异性和结合常数。结果发现：丁溴东莨菪碱能够特异性结合靶点G4 DNA,结合比为1：1,结合常数为1.18×10⁵ L/mol;荷叶碱属于非特异性结合,而土荆皮乙酸并未与靶点G4 DNA形成复合物。该组合方法不仅分析速度快,而且能够提高亲和分析的准确度和特异性,有望应用于靶向药物先导结构的发现和作用机制评价。     

G4 Sensing Pyridyl-Thiazole Polyamide Represses c-KIT Expression in Leukemia Cells

Specific sensing and functional tuning of nucleic acid secondary structures remain less explored to date. Herein, we report a thiazole polyamide TPW that binds specifically to c-KIT1 G-quadruplex (G4) with sub-micromolar affinity and ∼1 : 1 stoichiometry and represses c-KIT proto-oncogene expression. TPW shows up to 10-fold increase in fluorescence upon binding with c-KIT1 G4, but shows weak or no quantifiable binding to other G4s and ds26 DNA. TPW can increase the number of G4-specific antibody (BG4) foci and mark G4 structures in cancer cells. Cell-based assays reveal that TPW can efficiently repress c-KIT expression in leukemia cells via a G4-dependent process. Thus, the polyamide can serve as a promising probe for G-quadruplex recognition with the ability to specifically alter c-KIT oncogene expression.     

Out-cage metal ion coordination by novel benzoazacrown bisamides with carboxyl,pyridyl and picolinate pendant arms

A new series of macrocyclic diamides with carboxyl, pyridyl and picolinate pendant arms have been synthesized and the stability constants of their complexes with Ni²⁺, Cu²⁺, Zn²⁺, Cd²⁺, Pb²⁺ in water were determined. Complexes with a stoichiometry of 1 : 1 (M: L) were found for all ligands with the exception of 15-membered crown ethers with one pendant carboxyl or pyridine group. The ligand containing two picolinate backbone groups exhibits the highest values of the stability constants for all studied cations (logβ_ML?=?12.5–15.7). X-ray study of free ligands showed that the introduction of benzene and amide fragments into the macrocyclic moiety provides a flatten open structure of the ligand. The crystallographic analysis of Cu²⁺ and Zn²⁺ complexes revealed the external coordination of the metal atom by amine N atoms of the macrocycle and heteroatoms of the pendant groups.     

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.     

Design and development of bioactive α-hydroxy carboxylate group modified MnFe2O4 nanoparticle: Comparative fluorescence study,magnetism and DNA nuclease activity

Three new α-hydroxy carboxylate group functionalized MnFe₂O₄ nanoparticles (NPs) have been developed to explore the microscopic origin of ligand modified fluorescence and magnetic properties of nearly monodispersed MnFe₂O₄ NPs. The surface functionalization has been carried out with three small organic ligands (tartrate, malate, and citrate) having different number of α-hydroxy carboxylate functional group along with steric effect. Detailed study unveils that α-hydroxy carboxylate moiety of the ligands plays key role to generate intrinsic fluorescence in functionalized MnFe₂O₄ NPs through the activation of ligand to metal charge transfer transitions, associated with ligand–Mn²⁺/Fe³⁺ interactions along with d–d transition corresponding to d–orbital energy level splitting of Fe³⁺ ions on NP surface. Further, MnFe₂O₄ NPs show a maximum 140.88% increase in coercivity and 97.95% decrease in magnetization compared to its bare one upon functionalization. The ligands that induce smallest crystal field splitting of d–orbital energy level of transition metal ions are found to result in strongest ferrimagnetic activation of the NPs. Finally, our developed tartrate functionalized MnFe₂O₄ (T-MnFe₂O₄) NPs have been utilized for studying DNA binding interaction and nuclease activity for stimulating their beneficial activities toward diverse biomedical applications. The spectroscopic measurements indicate that T-MnFe₂O₄ NPs bind calf thymus DNA by intercalative mode. The ability of T-MnFe₂O₄ NPs to induce DNA cleavage was studied by gel electrophoresis technique where the complex is found to promote the cleavage of pBR322 plasmid DNA from the super coiled form I to linear coiled form II and nicked coiled form III with good efficiency.     

DNA-binding properties and antioxidant activity of lanthanide complexes with the Schiff base derived from 3-carbaldehyde chromone and isonicotinyl hydrazine

Structural analyses indicate that the ligand and lanthanide ions form mononuclear 10-coordinate ([Ln L₂ · (NO₃)₂] · NO₃ [Ln(III) = La, Sm, Nd, and Yb; L is chromone-3-carbaldehyde-(isonicotinoyl) hydrazone) complexes with 1 : 2 metal-to-ligand stoichiometry. DNA-binding studies show that the ligand and its lanthanide complexes can bind to calf thymus DNA via an intercalation mode with binding constants of 10⁵ (mol L^?1)^?1, and the lanthanide complexes bind stronger than the free ligand alone. Antioxidant activities of the ligand and lanthanide complexes were determined by superoxide and hydroxyl radical scavenging methods in vitro. The ligand and complexes possess strong scavenging effects, and the lanthanide complexes show stronger antioxidant activities than the ligand and some standard antioxidants, such as vitamin C.     

β-Cyclodextrin and folic acid host–guest interaction binding parameters determined by Taylor dispersion analysis and affinity capillary electrophoresis

The thermodynamic properties of molecular recognition in host–guest inclusion complexes can be studied by Taylor dispersion analysis (TDA). Host–guest inclusion complexes have modest size, and it is possible to get convergent results fast, achieving greater certainty for the obtained thermodynamic properties. Cyclodextrins (CDs) and their derivatives can be used as drug carriers that can boost stability, solubility, and bioavailability of physiologically active substances. A simple and effective approach for assessing the binding properties of CD complexes that are critical in the early stages of drug and formulation development is needed to fully understand the process of CD and guest molecules’ complex formation. In this work, TDA was successfully used to rapidly determine interaction parameters, including binding constant and stoichiometry, between β-CD and folic acid (FA) along with the diffusivities of the free FA and its complex with β-CD. Additionally, the FA diffusion coefficient obtained by TDA was compared to the results previously obtained by nuclear magnetic resonance. Affinity capillary electrophoresis (ACE) was also used to compare the binding constants obtained by different methods. The results showed that the binding constants obtained by ACE were somewhat lower than those obtained by the two TDA procedures.     

Thermodynamic Parameters for the Association of Fluorinated Benzenesulfonamides with Bovine Carbonic Anhydrase II

This paper describes a calorimetric study of the association of a series of seven fluorinated benzenesulfonamide ligands (C₆H_nF_5?nSO₂NH₂) with bovine carbonic anhydrase II (BCA). Quantitative structure–activity relationships between the free energy, enthalpy, and entropy of binding and pK_a and log P of the ligands allowed the evaluation of the thermodynamic parameters in terms of the two independent effects of fluorination on the ligand: its electrostatic potential and its hydrophobicity. The parameters were partitioned to the three different structural interactions between the ligand and BCA: the Zn^II cofactor–sulfonamide bond (≈65 % of the free energy of binding), the hydrogen bonds between the ligand and BCA (≈10 %), and the contacts between the phenyl ring of the ligand and BCA (≈25 %). Calorimetry revealed that all of the ligands studied bind in a 1:1 stoichiometry with BCA; this result was confirmed by ¹⁹F NMR spectroscopy and X‐ray crystallography (for complexes with human carbonic anhydrase II).     

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.     

Enhanced sampling molecular dynamics simulations correctly predict the diverse activities of a series of stiff-stilbene G-quadruplex DNA ligands

Ligands with the capability to bind G-quadruplexes (G4s) specifically, and to control G4 structure and behaviour, offer great potential in the development of novel therapies, technologies and functional materials. Most known ligands bind to a pre-formed topology, but G4s are highly dynamic and a small number of ligands have been discovered that influence these folding equilibria. Such ligands may be useful as probes to understand the dynamic nature of G4 in vivo, or to exploit the polymorphism of G4 in the development of molecular devices. To date, these fascinating molecules have been discovered serendipitously. There is a need for tools to predict such effects to drive ligand design and development, and for molecular-level understanding of ligand binding mechanisms and associated topological perturbation of G4 structures. Here we study the G4 binding mechanisms of a family of stiff-stilbene G4 ligands to human telomeric DNA using molecular dynamics (MD) and enhanced sampling (metadynamics) MD simulations. The simulations predict a variety of binding mechanisms and effects on G4 structure for the different ligands in the series. In parallel, we characterize the binding of the ligands to the G4 target experimentally using NMR and CD spectroscopy. The results show good agreement between the simulated and experimentally observed binding modes, binding affinities and ligand-induced perturbation of the G4 structure. The simulations correctly predict ligands that perturb G4 topology. Metadynamics simulations are shown to be a powerful tool to aid development of molecules to influence G4 structure, both in interpreting experiments and to help in the design of these chemotypes.

Enhanced sampling molecular dynamics simulations and solution-phase experiments come together to demonstrate the diverse effects of G4-interactive small molecules.     

Chemical and pharmacological aspects of novel hetero MLB complexes derived from NO2 type Schiff base and N2 type 1,10-phenanthroline ligands

A series of hetero ligand MLB complexes (1–5) were synthesised from tridentate NO₂ type Schiff base [H₂L: (E)-2-((2-hydroxy-4-methoxyphenyl)(phenyl)methyleneamino)benzoic acid; derived from 2-hydroxy-4-methoxybenzophenone and 2-aminobenzoic acid] and bidentate N₂ type 1,10-phenanthroline (B: phen) ligands. The structural characterization of the synthesised MLB complexes were carried out via analytical as well as various spectral studies. Additionally, the low molar conductance values (Λ_m = 14–22 Ω⁻¹ cm² mol⁻¹) imply that the complexes (1–5) are non-electrolytes. The obtained results reinforce that stoichiometry of the mononuclear hetero ligand complexes can be represented as [M(II)-Schiff base(L)-phen(B)·H₂O] and both H₂L and (B) ligands can act as tri and bidentates respectively. Moreover, both the ligands bind with metal(II) ions to build a stable six, six, five membered chelate rings with octahedral geometry. The existing solvent water molecule is confirmed from thermal as well as vibrational analysis. Their microcrystalline nature and uniform surface morphology were confirmed by both powder XRD and SEM studies. 3D molecular modeling and analysis of NiLB and CuLB complexes (3 and 4) were also studied. Mn(II), Ni(II) and Cu(II) complexes (1, 3 and 4) strongly interact with DNA through intercalation binding with strong binding constant values. The obtained K_app values were 5.23, 4.98, 6.36, 7.21 and 4.86 × 10⁵ mol⁻¹ for MLB complexes (1–5) respectively and the negative Δ³G values shown that all the complexes are strongly interact with DNA in a spontaneous manner. Further, remarkable biological, antioxidant and DNA activities were remarkably exhibited by MnLB, NiLB and CuLB complexes.     

Competition of Ligands and the 18-mer Binding Domain of the RHAU Helicase for G-Quadruplexes: Orthosteric or Allosteric Binding Mechanism?

Stabilizing the DNA and RNA structures known as G-quadruplexes (G4s) using specific ligands is a strategy that has been proposed to fight cancer. However, although G-quadruplex:ligand (G4:L) interactions have often been investigated, whether or not ligands are able to disrupt G-quadruplex:protein (G4:P) interactions remains poorly studied. In this study, using native mass spectrometry, we have investigated ternary G4:L:P complexes formed by G4s, some of the highest affinity ligands, and the binding domain of the RHAU helicase. Our results suggest that RHAU binds not only preferentially to parallel G4s, but also to free external G-quartets. We also found that, depending on the G4, ligands could prevent the binding of the peptide, either by direct competition for the binding sites (orthosteric inhibition) or by inducing conformational changes (allosteric inhibition). Notably, the ligand Cu–ttpy (ttpy=4′-tolyl-2,2′:6′,2′′-terpyridine) induced a conformational change that increased the binding of the peptide. This study illustrates that it is important to not only characterize drug–target interactions, but also how the binding to other partners is affected.     

Selective and Cooperative Ligand Binding to Antiparallel Human Telomeric DNA G‐Quadruplexes

The quest for ligands that specifically bind to particular G‐quadruplex nucleic acid structures is particularly important to conceive molecules with specific effects on gene expression or telomere maintenance, or conceive structure‐specific molecular probes. Using electrospray mass spectrometry in native conditions, we reveal a highly cooperative and selective 2:1 binding of Cu^II‐tolylterpyridine complexes to human telomeric G‐quadruplexes. Circular dichroism and comparisons of affinities for different sequences reveal a marked preference for antiparallel structures with diagonal loops and/or wide‐medium–narrow‐medium groove‐width order. The cooperativity is attributed to conformational changes in the polymorphic telomeric G‐quadruplex sequences, which convert preferably into an antiparallel three‐quartet topology upon binding of two ligands.     

The Synthesis of 1,4,7,10-Tetraazacyclododecanes with Acetylsalicylic Side Arm as Potential Cobalt(II) Fluorophores

New derivatives of 1,4,7,10-tetraazacyclododecanes have been synthesized. The coordination properties toward Co²⁺ of these ligands have been studied by means of spectroscopic methods. The stability constants of cobalt complexes with ligand L-1 and L-2were determined. Unusual complexes with a 2:1 (L:Co²⁺) stoichiometry have been found.     

Synthesis, crystal structure, antioxidation and DNA binding properties of binuclear Ho(III) complexes of Schiff-base ligands derived from 8-hydroxyquinoline-2-carboxyaldehyde and four aroylhydrazines

X-ray crystal and other structural analyses indicate that Ho(III) and every newly synthesized ligand can form a binuclear Ho(III) complex with a 1:1 metal-to-ligand stoichiometry by nine-coordination at the Ho(III) center. Every ligand acts as a dibasic tetradentate ligand, binding to Ho(III) through the phenolate oxygen atom, nitrogen atom of quinolinato unit and the CN group, ⁻O-CN- group (enolized and deprotonated from OC-NH- group) of the aroylhydrazine side chain. One DMF molecule is binding orthogonally to the ligand-plane from one side to the metal ion, while another DMF and nitrate (bidentate) are binding from the other. Dimerization of this monomeric unit occurs through the phenolate oxygen atoms leading to a central planar four-membered (HoO)₂ ring. Investigations of DNA binding properties show that all the ligands and Ho(III) complexes can bind to Calf thymus DNA through intercalations with the binding constants at the order of magnitude 10⁵-10⁶ M⁻¹, but Ho(III) complexes present stronger affinities to DNA than ligands. All the ligands and Ho(III) complexes may be used as potential anticancer drugs. Investigations of antioxidation properties show that all the ligands and Ho(III) complexes have strong scavenging effects for hydroxyl radicals and superoxide radicals but Ho(III) complexes show stronger scavenging effects for hydroxyl radicals than ligands.     

Dissociation constants of some Schiff bases and stability constants of their copper,cobalt, nickel and zinc complexes

The stoichiometry and stability constant of metal complexes with 4-(3-methoxy-salicylideneamino)-5-hydroxynaphthalene-2,7-disulfonic acid monosodium salt (H₂L) and 4-(3-methoxysalicylideneamino)-5-hydroxy-6-(2,5-dichlorophenylazo)-2,7-naphthalene disulfonic acid monosodium salt (H₂L¹) were studied by potentiometric titration. The stability constants of H₂L and H₂L¹ Schiff bases have been investigated by potentiometric titration and u.v.–vis spectroscopy in aqueous media. The dissociation constants of the ligand and the stability constants of the metal complexes were calculated pH-metrically at 25 °C and 0.1 m KCl ionic strength. The dissociation constants for H₂L were obtained as 3.007, 7.620 and 9.564 and for H₂L¹, 4.000, 6.525, 9.473 and 10.423, respectively. The complexes were found to have the formulae [M(L)₂] for M = Co(II), Ni(II), Zn(II) and Cu(II). The stability of the complexes follows the sequence: Zn(II) < Co(II) < Cu(II) < Ni(II). The high stability of H₂L¹ towards Cu(II) and Ni(II) over the other ions is remarkable, in particular over Cu(II), and may be of technological interest. Concentration distribution diagram of various species formed in solution was evaluated for ligands and complexes. The formation of the hydrogen bonds may cause this increased stability of ligands. The pH-metric data were used to find the stoichiometry, deprotonation and stability constants via the SUPERQUAD computer program.     

Multiple binding modes for dicationic Hoechst 33258 to DNA

The binding of dicationic Hoechst 33258 (ligand) to DNA was characterized by means of the fluorescence spectra, fluorescence intensity titration, time-resolved fluorescence decay, light scattering, circular dichroism, and fluorescence thermal denaturation measurements, and two binding modes were distinguished by the experimental results. Type 1 binding has the stoichiometry of one ligand to more than 12 base pairs, and it is defined as quasi-minor groove binding which has the typical prolonged fluorescence lifetime of about 4.4 ns. In type 1 binding, planar conformation of the ligand is favorable. Type 2 binding with phosphate to ligand ratio (P/L) < 2.5 has the stoichiometry of one ligand to two phosphates. It is defined as a highly dense and orderly stacked binding with DNA backbone as the template. Electrostatic interactions between doubly protonated ligands and negatively charged DNA backbone play a predominant role in the type 2 binding mode. The characteristics of this type of binding result in a twisted conformation of the ligand that has a fluorescence lifetime of less than 1 ns. The results also indicate that the binding is in a cooperative manner primarily by stacking of the aromatic rings of the neighboring ligands. Type 1 binding is only observed for double-stranded DNA (dsDNA) with affinity constant of 1.83 x 10(7) M-1. In the type 2 binding mode, the binding affinity constants are 4.9 x 10(6) and 4.3 x 10(6) M-1 for dsDNA and single-stranded DNA (ssDNA), respectively. The type 2 binding is base pair independent while the type 1 binding is base pair related. The experiments described in this paper revealed that the dication bindings are different from the monocation bindings reported by previous study. The dication binding leads to stronger aggregation at low ligand concentration and results in orderly arrangements of the ligands along DNA chains. Furthermore the dication binding is demonstrated to be beneficial for enhancing the DNA's stability.     

Tryptophan receptors containing acridine-based thiourea

Four derivatives of acridine and acridinium compounds (L1, L2, L1H and L2H) comprised thiourea-binding sites were synthesised. The binding abilities of receptors L1, L2, L1H and L2H towards amino acids (l-Trp, l-Phe, l-Leu, l-Ala and l-Gly) were studied by ¹H NMR spectroscopy, UV–vis and fluorescence spectrophotometry. Hydrogen bonding interactions between thiourea-binding site of the ligand and the carboxylate groups in zwitterionic amino acids were found to be the main interactions driving complexation to take place. The stoichiometry of 1:1 ligand to amino acid was observed in all cases. Neutral ligands L1 and L2 showed weak binding towards all studied amino acids. The cyclic ligand L1 showed better binding ability towards tryptophan (Trp) than the acyclic ligand L2 did (K for Trp is 307 and 266 M^? 1 for L1 and L2, respectively). Interestingly, binding abilities of the protonated ligands, L1H and L2H, towards studied amino acids, especially Trp (K for Trp is 3157 and 2873 M^? 1 for L1H and L2H, respectively), were increased due to R–COO^? …H…N⁺–acridinium interactions. Calculated structures of L1H·Trp and L2H·Trp showed that the polyglycol moiety in L1H provided a hydrophobic cavity for binding Trp resulting in a stronger binding affinity of L1H over L2H.     

A Polarographic Study of Tl+, Pb2+ and Cd2+ Complexes with Aza-18-crown-6 and Dibenzopyridino-18-crown-6 in some Binary Mixed Non-aqueous Solvents

The complexation of Tl⁺, Pb²⁺and Cd²⁺ cations by macrocyclic ligands, aza-18-crown-6 (L1) and dibenzopyridino-18-crown-6 (L2) was studied in some binary mixtures of methanol (MeOH), n-propanol (n-PrOH), nitromethane (NM) and acetonitrile (AN) with dimethylformamide (DMF) at 22 °C using DC (direct current) and differential pulse polarographic techniques (DPP). The stoichiometry and stability constants of the complexes were determined by monitoring the shifts in half-waves or peak potentials of the polarographic waves of metal ions against the ligand concentration. In all of the solvent systems, the stability of the resulting 1:1 complexes was found to be L1 > L2. The selectivity order of the L2 ligand for the cations was found to be Pb²⁺ > Tl⁺ > Cd²⁺ and the selectivity of the L1 ligand for Pb²⁺ ion was greater than that of Tl⁺ ion. The results show that the stability of the complexes depends on the nature and composition of the mixed solvents. There is an inverse relationship between the stability constants of the complexes and the amount of dimethylformamide in the mixed solvent systems.