Molecular details of quinolone–DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it

Quinolones are antibacterial drugs that are thought to bind preferentially to disturbed regions of DNA. They do not fall into the classical categories of intercalators, groove binders or electrostatic binders to the backbone. We solved the 3D structure of the DNA duplex (ACGCGU-NA)(2), where NA denotes a nalidixic acid residue covalently linked to the 2′-position of 2′-amino-2′-deoxyuridine, by NMR and restrained torsion angle molecular dynamics (MD). In the complex, the quinolones stack on G:C base pairs of the core tetramer and disrupt the terminal A:U base pair. The displaced dA residues can stack on the quinolones, while the uracil rings bind in the minor groove. The duplex-bridging interactions of the drugs and the contacts of the displaced nucleotides explain the high UV-melting temperature for d(ACGCGU-NA)(2) of up to 53°C. Further, non-covalently linked complexes between quinolones and DNA of the sequence ACGCGT can be generated via MD using constraints obtained for d(ACGCGU-NA)(2). This is demonstrated for unconjugated nalidixic acid and its 6-fluoro derivative. The well-ordered and tightly packed structures thus obtained are compatible with a published model for the quinolone–DNA complex in the active site of gyrases

Red light-controlled polymerase chain reaction

A 23-mer DNA “caged” at its 3′-terminus with a 9-anthracenyl moiety was prepared. It can be uncaged in the presence of photosensitizer (In(pyropheophorbide-a)chloride)-containing DNAs (9–12 mers) and upon irradiation with red light. This mixture of DNAs was used to design red-light controlled polymerase chain reaction

Triggering RNA Interference by Photoreduction under Red Light Irradiation

RNA interference (RNAi) using small interfering RNAs (siRNAs) is a powerful tool to target any protein of interest and is becoming more suitable for in vivo applications due to recent developments in RNA delivery systems. To exploit RNAi for cancer treatment, it is desirable to increase its selectivity, e.g., by a prodrug approach to activate the siRNAs upon external triggering, e.g., by using light. Red light is especially well suited for in vivo applications due to its low toxicity and higher tissue penetration. Known molecular (not nanoparticle-based) red-light-activatable siRNA prodrugs rely on singlet oxygen (1O2)-mediated chemistry. 1O2 is highly cytotoxic. Additionally, one of the side products in the activation of the known siRNA prodrugs is anthraquinone, which is also toxic. We herein report on an improved redlight-activatable siRNA prodrug, which does not require 1O2 for its activation. In fact, the 5′ terminus of the antisense strand is protected with an electron-rich azobenzene promoiety. It is reduced and cleaved upon red light exposure in the presence of Sn(IV)(pyropheophorbide a)dichloride acting as a catalyst and ascorbate as a bulk reducing agent. We confirmed the prodrug activation upon red light irradiation both in cell-free settings and in human ovarian cancer A2780 cells

2,2′-Dihydroxybiphenyl-3,3′-di­carb­aldehyde dioxime

The mol­ecule of the title compound, C14H12N2O4, lies across a crystallographic inversion centre situated at the mid-point of the C—C intra-annular bond. The mol­ecule is not planar, the dihedral angle between the aromatic rings being 50.1 (1)°. The oxime group is in an E position with respect to the –OH group and forms an intra­molecular O—H⋯N hydrogen bond. In the crystal structure, inter­molecular O—H⋯O hydrogen bonds link mol­ecules into chains propagating along [001]. The crystal structure is further stabilized by inter­molecular stacking inter­actions between the rings [centroid-to-centroid distance = 3.93 (1) Å], resulting in layers parallel to the bc plane

Red light activated “caged” reagents for microRNA research

“Caged” reagents for miRNA research (siRNA targeting EGFR, involved in miRNA maturation, and mimics of miR-20a, playing a key role in tumor formation and metastasis) were prepared. It was demonstrated that these reagents can be activated by non-toxic to cells red light both in cells and in cell free settings

μ-Peroxido-bis­[acetonitrile­bis­(ethyl­enediamine)­cobalt(III)] tetrakis(per­chlorate)

The title compound, [Co2(O2)(CH3CN)2(C2H8N2)4](ClO4)4, consists of centrosymmetric binuclear cations and perchlorate anions. Two CoIII atoms, which have a slightly distorted octa­hedral coordination, are connected through a peroxido bridge; the O—O distance is 1.476 (3) Å. Both acetonitrile ligands are situated in a trans position with respect to the O—O bridge. In the crystal, the complex cations are connected by N—H⋯O hydrogen bonds between ethyl­endiamine NH groups and O atoms from the perchlorate anions and peroxide O atoms

Diaquabis­[3-(hydroxy­imino)­butanoato]nickel(II)

In the neutral, mononuclear title complex, [Ni(C4H6NO3)2(H2O)2], the Ni atom lies on a crystallographic inversion centre within a distorted octa­hedral N2O4 environment. Two trans-disposed anions of 3-hydroxy­imino­butanoic acid occupy four equatorial sites, coordinated by the deprotonated carboxyl­ate and protonated oxime groups and forming six-membered chelate rings, while the two axial positions are occupied by the water O atoms. The O atom of the oxime group forms an intra­molecular hydrogen bond with the coordinated carboxyl­ate O atom. The complex mol­ecules are linked into chains along b by hydrogen bonds between the water O atom and the carboxyl­ate O of a neighbouring mol­ecule. The chains are linked by further hydrogen bonds into a layer structure

Red Fluorescent Aminoferrocene (Pro)Drugs for in Cellulo and in Vivo Imaging

Red fluorescent dyes are usually charged, lipophilic molecules with relatively high molecular weight, which tend to localize in specific intracellular locations, e. g., a cyanine dye Cy5 is biased towards mitochondria. They are often used as markers of biomolecules including nucleic acids and proteins. Since the molecular weight of the dyes is much smaller than that of the biomolecules, the labelling has a negligible effect on the properties of the biomolecules. In contrast, conjugation of the dyes to low molecular weight (pro)drugs can dramatically alter their properties. For example, conjugates of Cy5 with lysosome‐targeting aminoferrocenes accumulate in mitochondria and exhibit no intracellular effects characteristic for the parent (pro)drugs. Herein we tested several neutral and negatively charged dyes for labelling lysosome‐targeting aminoferrocenes 7 and 8 as well as a non‐targeted control 3 . We found that a BODIPY derivative BDP‐TR exhibits the desired unbiased properties: the conjugation does not disturb the intracellular localization of the (pro)drugs, their mode of action, and cancer cell specificity. We used the conjugates to clarify the mechanism of action of the aminoferrocenes. In particular, we identified new intermediates, explained why lysosome‐targeting aminoferrocenes are more potent than their non‐targeted counterparts, and evaluated their distribution in vivo .A BODIPY derivative BDP‐TR was identified as a non‐biased red‐fluorescent dye for labelling of low molecular weight (pro)drugs. The labelling does not affect intracellular localization and mode of action of the (pro)drugs. The BDP‐TR‐conjugates were used to clarify the mechanism of activation and in vivo distribution of the representative (pro)drugs. imageDeutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659H2020 Future and Emerging Technologies http://dx.doi.org/10.13039/100010664HORIZON EUROPE Marie Sklodowska-Curie Actions http://dx.doi.org/10.13039/10001869

2-Hydroxy­amino-2-oxoacetohydrazide

In the title compound, C2H5N3O3, the hydroxamic group adopts an anti orientation with respect to the hydrazide group. In the crystal, mol­ecules are connected by N—H⋯O and O—H⋯N hydrogen bonds into zigzag chains along the c axis