Biological recognition patterns implicated by the formation and stability of ternary metal ion complexes of low-molecular-weight formed with amino acid/peptides and nucleobases/nucleosides

Aptamer-Protein Interactions: From Regulation to Biomolecular Detection

Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.

Coupling 6-chloro-3-methyluracil with copper: structural features, theoretical analysis, and biofunctional properties

As nucleobases in RNA and DNA, uracil and 5-methyluracil represent a recognized class of bioactive molecules and versatile ligands for coordination compounds with various biofunctional properties. In this study, 6-chloro-3-methyluracil (Hcmu) was used as an unexplored building block for the self-assembly generation of a new bioactive copper(II) complex, [Cu(cmu)₂(H₂O)₂]·4H₂O (1). This compound was isolated as a stable crystalline solid and fully characterized in solution and solid state by a variety of spectroscopic methods (UV-vis, EPR, fluorescence spectroscopy), cyclic voltammetry, X-ray diffraction, and DFT calculations. The structural, topological, H-bonding, and Hirshfeld surface features of 1 were also analyzed in detail. The compound 1 shows a distorted octahedral {CuN₂O₄} coordination environment with two trans cmu^- ligands adopting a bidentate N,O-coordination mode. The monocopper(II) molecular units participate in strong H-bonding interactions with water molecules of crystallization, leading to structural 0D → 3D extension into a 3D H-bonded network with a tfz-d topology. Molecular docking and ADME analysis as well as antibacterial and antioxidant activity studies were performed to assess the bioactivity of 1. In particular, this compound exhibits a prominent antibacterial effect against Gram negative (E. coli, P. aeruginosa) and positive (S. aureus, B. cereus) bacteria. The obtained copper(II) complex also represents the first structurally characterized coordination compound derived from 6-chloro-3-methyluracil, thus introducing this bioactive building block into a family of uracil metal complexes with notable biofunctional properties.

Synthesis, characterization and multiple targeting with selectivity: Anticancer property of ternary metal phenanthroline-maltol complexes

The cobalt(II), copper(II) and zinc(II) complexes of 1,10-phenanthroline (phen) and maltol (mal) (complexes 1, 2, 3 respectively) were prepared from their respective metal(II) chlorides and were characterized by FT-IR, elemental analysis, UV spectroscopy, molar conductivity, p-nitrosodimethylaniline assay and mass spectrometry. The X-ray structure of a single crystal of the zinc(II) analogue reveals a square pyramidal structure with distinctly shorter apical chloride bond. All complexes were evaluated for their anticancer property on breast cancer cell lines MCF-7 and MDA-MB-231, and normal cell line MCF-10A, using (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay and morphological studies. Complex 2 was most potent for 24, 48 and 72 h treatment of cancer cells but it was not selective towards cancer over normal cells. The mechanistic studies of the cobalt(II) complex 1 involved apoptosis assay, cell cycle analysis, dichloro-dihydro-fluorescein diacetate assay, intracellular reactive oxygen species assay and proteasome inhibition assay. Complex 1 induced low apoptosis, generated low level of ROS and did not inhibit proteasome in normal cells. The study of the DNA binding and nucleolytic properties of complexes 1-3 in the absence or presence of H₂O₂ or sodium ascorbate revealed that only complex 1 was not nucleolytic.

Anion–Cation Recognition Pattern, Thermal Stability and DFT-Calculations in the Crystal Structure of H2dap[Cd(HEDTA)(H2O)] Salt (H2dap = H2(N3,N7)-2,6-Diaminopurinium Cation)

The proton transfer between equimolar amounts of [Cd(H2EDTA)(H2O)] and 2,6-diaminopurine (Hdap) yielded crystals of the out-of-sphere metal complex H2(N3,N7)dap[Cd(HEDTA)(H2O)]·H2O (1) that was studied by single-crystal X-ray diffraction, thermogravimetry, FT-IR spectroscopy, density functional theory (DFT) and quantum theory of “atoms-in-molecules” (QTAIM) methods. The crystal was mainly dominated by H-bonds, favored by the observed tautomer of the 2,6-diaminopurinium(1+) cation. Each chelate anion was H-bonded to three neighboring cations; two of them were also connected by a symmetry-related anti-parallel π,π-staking interaction. Our results are in clear contrast with that previously reported for H2(N1,N9)ade [Cu(HEDTA)(H2O)]·2H2O (EGOWIG in Cambridge Structural Database (CSD), Hade = adenine), in which H-bonds and π,π-stacking played relevant roles in the anion–cation interaction and the recognition between two pairs of ions, respectively. Factors contributing in such remarkable differences are discussed on the basis of the additional presence of the exocyclic 2-amino group in 2,6-diaminopurinium(1+) ion.

Iridium(III) coordination of N(6) modified adenine derivatives with aminoacid chains

In this manuscript we report the preparation of three N⁶-aminoacid-adenine-derivatives: N-(7H-purin-6-yl)glycine·0.5H₂O (N⁶-GlyAde), N-(7H-purin-6-yl)-β-alanine·1.5H₂O (N⁶-β-AlaAde) and N-(7H-purin-6-yl)-γ-aminobutyric·2H₂O (N⁶-GabaAde) and the synthesis and X-ray characterization of three Ir(III) NAMI-A derivatives (NAMI-A is [imidazoleH][trans-Ru^IIICl₄(DMSO-κS)(imidazole)]) [trans-Ir^IIICl₄(DMSO-κS)(N³-H)-(7H-purin-6-yl)glycine-κN⁹] (1), [trans-Ir^IIICl₄(DMSO-κS)(N³-H)-(7H-purin-6-yl)-β-alanine-κN⁹] hydrate (2) and [trans-Ir^IIICl₄(DMSO-κS)(N³-H)-(7H-purin-6-yl)-γ-aminobutyryl-κN⁹] (3). In all complexes the metal center shows octahedral geometry with coordination to four chlorido ligands and one S coordinated dimethylsulfoxide (DMSO-κS). The coordination sphere of the metal is completed by the modified adenine molecule which is bound via N(9) and protonated at N(3). In two complexes the importance of lone pair (lp)-π interactions involving the adenine ring have been studied using density functional theory (DFT) calculations and the Bader's theory of atoms in molecules. Furthermore, the ability of complexes (1-3) to affect the cell viability was evaluated against three different cancer cell lines: human lung carcinoma cells (A549), human cervical carcinoma cells (HeLa) and human breast cancer cells (MCF7). We have also analyzed their ability to cleave the DNA experimentally and their affinity for two models of DNA has been studied using molecular docking simulations.

Regulation of Protein Activity and Cellular Functions Mediated by Molecularly Evolved Nucleic Acids

Regulation of protein activity is essential for revealing the molecular mechanisms of biological processes. DNA and RNA achieve many uniquely efficient functions, such as genetic expression and regulation. The chemical capability to synthesize artificial nucleotides can expand the chemical space of nucleic acid libraries and further increase the functional diversity of nucleic acids. Herein, a versatile method has been developed for modular expansion of the chemical space of nucleic acid libraries, thus enabling the generation of aptamers able to regulate protein activity. Specifically, an aptamer that targets integrin alpha3 was identified and this aptamer can inhibit cell adhesion and migration. Overall, this chemical-design-assisted in vitro selection approach enables the generation of functional nucleic acids for elucidating the molecular basis of biological activities and uncovering a novel basis for the rational design of new protein-inhibitor pharmaceuticals.

Crystal structures of N6-modified-amino acid related nucleobase analogs (II): hybrid adenine-β-alanine and adenine-GABA molecules

H-Bonding networks and anion–π interactions in the crystal structures of N⁶-modified-amino acid adenine analogs are investigated using X-ray crystallography and DFT calculations.

Ternary Zn(II) Complexes of FluoZin-3 and the Low Molecular Weight Component of the Exchangeable Cellular Zinc Pool

Knowledge of the nature of exchangeable (labile) intracellular Zn(II) is increasingly important for biomedical research. The detection and quantitative determination of Zn(II) ions is usually performed by using Zn(II)-specific fluorescent sensors, among which 2-[2-[2-[2-[bis(carboxylatomethyl)amino]-5-methoxyphenoxy]ethoxy]-4-(2,7-difluoro-3-oxido-6-oxo-4a,9a-dihydroxanthen-9-yl)anilino]acetate (FluoZin-3) has been used most widely. Selectivity of this sensor for Zn(II) over other divalent cations was demonstrated, but possible interference in its performance by other compounds has not been investigated. Many potential low molecular weight ligands for Zn(II) ions (LMWLs) are abundant in the cell. In this study we demonstrate that FluoZin-3 is susceptible to competition for Zn(II) from LMWLs and also forms strong ternary complexes with some of them. We determined the set of conditional stability constants ^C K_tern for ternary Zn(FluoZin-3)(LMWL) complexes using fluorescence titrations and applied it to model the response of exchangeable zinc to FluoZin-3. We found that competition and formation of ternary complexes with LMWLs together strongly affect (net reduce) the Zn(FluoZin-3) fluorescence. This effect may cause a significant underestimation of exchangeable Zn(II). We also demonstrated a strong pH dependence of this effect. Reduced glutathione (GSH) emerged as the most important Zn(II) partner among the LMWLs, characterized with K_tern = 2.8 ± 0.2 × 10⁶ M^-1. Our experiments and calculations suggest that Zn(LMWL) complexes contribute to the exchangeable cellular zinc pool.

Crystal structures of N6-modified-aminoacid/peptide nucleobase analogs: hybrid adenine–glycine and adenine–glycylglycine molecules

Anion–π interactions in crystal structures of N⁶-modified-aminoacid and dipeptide adenine analogs are investigated using X-ray crystallography and DFT calculations.

Nucleobases, nucleosides, and nucleotides: versatile biomolecules for generating functional nanomaterials

The incorporation of biomolecules into nanomaterials generates functional nanosystems with novel and advanced properties, presenting great potential for applications in various fields. Nucleobases, nucleosides and nucleotides, as building blocks of nucleic acids and biological coenzymes, constitute necessary components of the foundation of life. In recent years, as versatile biomolecules for the construction or regulation of functional nanomaterials, they have stimulated interest in researchers, due to their unique properties such as structural diversity, multiplex binding sites, self-assembly ability, stability, biocompatibility, and chirality. In this review, strategies for the synthesis of nanomaterials and the regulation of their morphologies and functions using nucleobases, nucleosides, and nucleotides as building blocks, templates or modulators are summarized alongside selected applications. The diverse applications range from sensing, bioimaging, and drug delivery to mimicking light-harvesting antenna, the construction of logic gates, and beyond. Furthermore, some perspectives and challenges in this emerging field are proposed. This review is directed toward the broader scientific community interested in biomolecule-based functional nanomaterials.

CH-π hydrogen bonds in biological macromolecules

This is a sequel to the previous Perspective "The CH-π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates", which featured in a PCCP themed issue on "Weak Hydrogen Bonds - Strong Effects?": Phys. Chem. Chem. Phys., 2011, 13, 13873-13900. Evidence that weak hydrogen bonds play an enormously important role in chemistry and biochemistry has now accumulated to an extent that the rigid classical concept of hydrogen bonds formulated by Pauling needs to be seriously revised and extended. The concept of a more generalized hydrogen bond definition is indispensable for understanding the folding mechanisms of proteins. The CH-π hydrogen bond, a weak molecular force occurring between a soft acid CH and a soft base π-electron system, among all is one of the most important and plays a functional role in defining the conformation and stability of 3D structures as well as in many molecular recognition events. This concept is also valuable in structure-based drug design efforts. Despite their frequent occurrence in organic molecules and bio-molecules, the importance of CH-π hydrogen bonds is still largely unknown to many chemists and biochemists. Here we present a review that deals with the evidence, nature, characteristics and consequences of the CH-π hydrogen bond in biological macromolecules (proteins, nucleic acids, lipids and polysaccharides). It is hoped that the present Perspective will show the importance of CH-π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Implication of this concept is enormous and valuable in the scientific community.

Lights and shadows in the challenge of binding acyclovir, a synthetic purine-like nucleoside with antiviral activity, at an apical-distal coordination site in copper(II)-polyamine chelates

Several nucleic acid components and their metal complexes are known to be involved in crucial metabolic steps. Therefore the study of metal-nucleic acid interactions becomes essential to understand these biological processes. In this work, the synthetic purine-like nucleoside acyclovir (acv) has been used as a model of guanosine recognition with copper(II)-polyamine chelates. The chemical stability of the N9-acyclic arm in acv offers the possibility to use this antiviral drug to deepen the knowledge of metal-nucleoside interactions. Cu(II) chelates with cyclam, cyclen and trien were used as suitable receptors. All these copper(II) tetraamine chelates have in common the potential ability to yield a Cu-N7(apical) bond assisted by an appropriate (amine)N-H⋯O6(acv) intra-molecular interligand interaction. A series of synthesis afforded the following compounds: [Cu(cyclam)(ClO4)2] (1), {[Cu(cyclam)(μ2-NO3)](NO3)}n (2), {[Cu(cyclam)(μ2-SO4)]·MeOH}n (3), {[Cu(cyclam)(μ2-SO4)]·5H2O}n (4), [Cu(cyclen)(H2O)]SO4·2H2O (5), [Cu(cyclen)(H2O)]SO4·3H2O (6), [Cu(trien)(acv)](NO3)2·acv (7) and [Cu(trien)(acv)]SO4·0.71H2O (8). All these compounds have been characterized by X-ray crystallography and FT-IR spectroscopy. Our results reveal that the macrochelates Cu(cyclen)(2+) and Cu(cyclam)(2+) are unable to bind acv at an apical site. In contrast, the Cu(trien)(2+) complex has proved to be an efficient receptor for acv in compounds (7) and (8). In the ternary complex [Cu(trien)(acv)](2+), the metal binding pattern of acv consists of an apical Cu-N7 bond assisted by an intra-molecular (primary amino)N-H⋯O6(acv) interligand interaction. Structural comparisons reveal that this unprecedented apical role of acv is due to the acyclic nature of trien together with the ability of the Cu(trien)(2+) chelate to generate five-coordinated (type 4+1) copper(II) complexes.

A (3,6)-connected layer with an unprecedented adeninate nucleobase-derived heptanuclear disc

A (3,6)-connected layer with an adeninate nucleobase-derived Cu^II₇ disc was reported, in which six spin-parallel Cu^II ions in the exterior of the disc are antiferromagnetically coupled with the central one to give an S = 5/2 ground-state.

Simultaneous co-ordination of three cytosine ligands displaying different binding sites around the copper centres

The reaction of copper with 1,10-phenanthroline and cytosine forms a novel polymeric structure with two different cytosine binding modes coordinated to copper centers. Also the polymeric complex has mixed coordination geometry around the metal centers.

From 7-azaindole to adenine: molecular recognition aspects on mixed-ligand Cu(II) complexes with deaza-adenine ligands

For a better understanding of the versatile behaviour of adenine as a ligand, a series of 10 ternary copper(II) complexes with deaza-adenine ligands [7-azaindole (1,6,7-trideaza-adenine, H7azain), 4-azabenzimidazole (1,6-dideaza-adenine, H4abim), 5-azabenzimidazole (3,6-dideaza-adenine, H5abim), and 7-deaza-adenine (H7deaA)] have been synthesised and characterised by X-ray diffraction. Likewise, all the compounds studied have been analysed by spectral and thermal methods. The proton tautomers and donor capabilities of the above-mentioned deaza-adenine ligands have been calculated by DFT. We conclude that the increasing presence of N-donors in deaza-adenine ligands favours the proton tautomerism and their versatility as co-ligands. Notably, H7azain consistently uses the same tautomer, H4abim uses two different tautomers but is not protonated by the pentadentate H(2)EDTA(2-) ligand, and H(N1)5abim displays the μ(2)-N7,N9 mode, whereas H(N9)7deaA binds Cu(II) by N3 in cooperation with an intra-molecular N9-H···O interaction or using the unprecedented bidentate μ(2)-N1,N3 bridging mode.

Structural insights on the molecular recognition patterns between N(6)-substituted adenines and N-(aryl-methyl)iminodiacetate copper(II) chelates

For a better understanding of the metal binding pattern of N(6)-substituted adenines, six novel ternary Cu(II) complexes have been structurally characterized by single crystal X-ray diffraction: [Cu(NBzIDA)(HCy5ade)(H2O)]·H2O (1), [Cu(NBzIDA)(HCy6ade)(H2O)]·H2O (2), [Cu(FurIDA)(HCy6ade)(H2O)]·H2O (3), [Cu(MEBIDA)(HBAP)(H2O)]·H2O (4), [Cu(FurIDA)(HBAP)]n (5) and {[Cu(NBzIDA)(HdimAP)]·H2O}n (6). In these compounds NBzIDA, FurIDA and MEBIDA are N-substituted iminodiacetates with a non-coordinating aryl-methyl pendant arm (benzyl in NBzIDA, p-tolyl in MEBIDA and furfuryl in FurIDA) whereas HBAP, HCy5ade, HCy6ade and HdimAP are N(6)-substituted adenine derivatives with a N-benzyl, N-cyclopentyl, N-cyclohexyl or two N-methyl groups, respectively. Regardless of the molecular (1-4) or polymeric (5-6) nature of the studied compounds, the Cu(II) centre exhibits a type 4+1 coordination where the tridentate IDA-like chelators adopt a mer-conformation. In 1-5 the N(6)-R-adenines use their most stable tautomer H(N9)adenine-like, and molecular recognition consists of the cooperation of the CuN3(purine) bond and the intra-molecular interligand N9H···O(coordinated carboxy) interaction. In contrast, N(6),N(6)-dimethyl-adenine shows the rare tautomer H(N3)dimAP in 6, so that the molecular recognition with the Cu(NBzIDA) chelate consist of the CuN9 bond and the N3H···O intra-molecular interligand interaction. Contrastingly to the cytokinin activity found in the free ligands HBAP (natural cytokinin), HCy5ade and HCy6ade, the corresponding Cu(II) ternary complexes did not show any activity.

Synthesis, DNA recognition and cleavage studies of novel tetrapeptide complexes, Cu(II)/Zn(II)-Ala-Pro-Ala-Pro

New tetrapeptide complexes Cu(II)·Ala-Pro-Ala-Pro (1) and Zn(II)·Ala-Pro-Ala-Pro (2) were synthesized from the reaction of tetrapeptide, Ala-Pro-Ala-Pro and CuCl2/ZnCl2 and were thoroughly characterized by elemental analysis, IR,(1)H and (13)C NMR (in case of 2), ESI-MS, UV and molar conductance measurements. The solution stability study was carried out employing UV-vis absorption titrations over a broad range of pH which suggested the stability of the complexes in solution. In vitro interaction of complexes 1 and 2 with CT-DNA was studied employing UV-vis, fluorescence, circular dichroic and viscometry studies. To throw insight into molecular binding event at the target site, UV-vis titrations of 1 and 2 with mononucleotides of interest viz.; 5'-GMP and 5'-TMP were carried out. Cleavage activity of the complexes with pBR322 plasmid DNA was evaluated by agarose gel electrophoresis and, the electrophoresis pattern demonstrated that both the complexes 1 and 2 are efficient cleavage agents. Further, the Cu(II) complex displayed efficient oxidative cleavage of supercoiled DNA while various reactive oxygen species are responsible for the cleavage in Zn(II) complex.

Structural consequences of the N7 and C8 translocation on the metal binding behavior of adenine

7-Deaza-8-aza-adenine, namely 4-aminopyrazolo[3,4-d]pyrimidine (H4app), is a bioisoster of adenine (Hade) resulting from the translocation of N7 and C8 atoms on the purine moiety. With the aim of studying the influence of this translocation on the metal binding abilities of H4app, we have prepared and structurally characterized two ternary copper(II) complexes having H4app and one N-benzyl-iminodiacetate chelator (MEBIDA or FBIDA, with a methyl or fluoro group in para- of the benzyl aromatic ring): [Cu(2)(MEBIDA)(2)(μ(2)-N1,N8-H4app)(H(2)O)(2)]·4H(2)O (1) and [Cu(4)(FBIDA)(4)(μ(2)-N8,N9-H4app)(2)(H(2)O)]·3.5H(2)O (2). Furthermore, thermal, spectral, and magnetic properties have been also investigated. In 1, H(N9)4app is disordered over two equally pondered positions and the μ(2)-N1,N8 coordination mode is assisted by N6-H···O and N9-H···O intramolecular interactions, respectively. The acyclic nonlinear molecular topology of 2 is strongly influenced by two intramolecular H-bonding interactions (O-H···O-carboxylate) involving the apical aqua ligand of a terminal Cu(II) atom. Thus, both compounds have in common the Cu-N8 bond. In order to better understand our limited structural information, DFT calculations for the individual tautomers of H4app as well as mononuclear Cu(II) model systems have been carried out. According to previous results, we conclude that H(N9)4app is the most stable tautomer followed by H(N8)4app. When N9 and N8 are metalated, then the tautomer H(N1)4app can come into play as observed in compound 2. Likewise, the findings concerning compound 1 suggest that the formation of a Cu-N1 bond in H4app results was favored compared to neutral adenine, for which only one case has been reported with such coordination despite the large variety of related Cu(II)-Hade described in the literature.