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The untranslated regions (UTRs) of viral genomes contain a variety of conserved yet dynamic structures crucial for viral replication, providing drug targets for the development of broad spectrum anti-virals. We combine in vitro RNA analysis with molecular dynamics simulations to build the first 3D models of the structure and dynamics of key regions of the 5' UTR of the SARS-CoV-2 genome. Furthermore, we determine the binding of metallo-supramolecular helicates (cylinders) to this RNA structure. These nano-size agents are uniquely able to thread through RNA junctions and we identify their binding to a 3-base bulge and the central cross 4-way junction located in stem loop 5. Finally, we show these RNA-binding cylinders suppress SARS-CoV-2 replication, highlighting their potential as novel anti-viral agents., (© 2021 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

The dinuclear iron(II) supramolecular helicates [Fe2 L3 ]Cl4 (L=C25 H20 N4 ) bind to DNA through noncovalent (i.e., hydrogen-bonding, electrostatic) interactions and exhibit antimicrobial and anticancer effects. In this study, we show that the helicates condense plasmid DNA with a much higher potency than conventional DNA-condensing agents. Notably, molecules of DNA in the presence of the M enantiomer of [Fe2 L3 ]Cl4 do not form intermolecular aggregates typically formed by other condensing agents, such as spermidine or spermine. The helicates inhibit the activity of several DNA-processing enzymes, such as RNA polymerase, DNA topoisomerase I, deoxyribonuclease I, and site-specific restriction endonucleases. However, the results also indicate that the DNA condensation induced by the helicates does not play a crucial role in these inhibition reactions. The mechanisms for the inhibitory effects of [Fe2 L3 ]Cl4 helicates on DNA-related enzymatic activities have been proposed., (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Getting to the heart of it: Co-crystallization of an RNA three-way junction with a cylindrical di-iron(II)-based anti-cancer drug (green) results in π-stacking interactions between the cylinder and the central base pairs of the RNA structure. The shape, size, and cationic nature of the cylinder were found to be responsible for this perfect fit. Native gel electrophoresis studies confirmed stabilization of the RNA three-way junction by the iron(II) cylinder., (Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The interaction with native DNA of a 2,7-diazapyrenium-based ligand 1 and its Pt(II) rectangular metallacycle 2 is explored through circular and linear dichroism and fluorescence spectroscopies. The metal-free ligand 1 binds through intercalation, with a binding constant of approximately 5×10(5) M(-1), whereas the metallacycle 2 binds and bends the DNA with a binding constant of 7×10(6) M(-1). PCR assays show that metallo-supramolecular box 2 interferes with DNA transactions in vitro whereas the intercalator 1 does not. The metallacycle is active against four human cancer cell lines, with IC(50) values ranging between 3.1 and 19.2 μM and shows similar levels of efficacy, but a different spectrum of activity, to cisplatin., (Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Metallosupramolecular chemistry was used to design a new class of synthetic agents, namely, tetracationic supramolecular cylinders, that bind strongly and noncovalently in the major groove of DNA. To gain additional information on interactions of the cylinders with DNA we explored DNA unwinding and sequence-specific binding properties, as well as DNA photonuclease activity of ruthenium(II) metallosupramolecular cylinder [Ru(2)L(3)](4+), where L is a bis-pyridylimine ligand. We found that [Ru(2)L(3)](4+) unwinds negatively supercoiled plasmid DNA and exhibits binding preference to regular alternating purine-pyrimidine sequences in a similar way to the [Fe(2)L(3)](4+) analogue. Photocleavage studies showed that, unlike [Fe(2)L(3)](4+), [Ru(2)L(3)](4+) induces single-strand breaks on irradiation by visible and UVA light and cleaves DNA mainly at guanine residues contained preferentially in regularly alternating purine-pyrimidine nucleotides. As [Ru(2)L(3)](4+) binds and cleaves DNA in a sequence-dependent manner, it may provide a useful tool for basic and applied biology, such as for controlled manipulation of the genome.

The interaction of metallosupramolecular cylinders with DNA three-way junctions has been studied by gel electrophoresis. A recent X-ray crystal structure of a palindromic oligonucleotide forming part of a complex with such a cylinder revealed binding at the heart of a three-way junction structure. The studies reported herein confirm that this is not solely an artefact of crystallisation and reveal that this is a potentially very powerful new mode of DNA recognition with wide scope. The cylinders are much more effective at stabilizing three-way junctions than simple magnesium di-cations or organic or metallo-organic tetra-cations, with the M cylinder enantiomer being more effective than P. The recognition is not restricted to three-way junctions formed from palindromic DNA with a central AT step at the junction; non-palindromic three-way junctions and those with GC steps are also stabilised. The cylinder is also revealed to stabilise other Y-shaped junctions, such as that formed at a fraying point in duplex DNA (for example, a replication fork), and other DNA three-way junction structures, such as those containing unpaired nucleotides, perhaps by opening up this structure to access the central cavity.

The effect of changes in the angles at the connection points of linear/circular helicates is explored as a route to control the nuclearity and architecture of metallo-supramolecular arrays. This effect is probed by changing the geometry of the metal centre used to assemble bis-pyridylimine ligands that contain a 1,3-bis(aminomethyl) benzene spacer group. Tetrahedral metal ions favour linear dimers, whereas octahedral nickel(II) predominantly gives a triangular circular helicate. Five-coordinate copper(II) falls in the middle of these extremes and results in the formation of solvent-dependent mixtures of dimer and trimer. The trinuclear, triangular, circular helicate structures, which result from coordination to copper(II) and nickel(II), are structurally characterised by X-ray crystallography and reveal that the units can aggregate into hexagonal arrays that contain anion-filled tube-like channels in the solid state.

A set of cyclic tetranuclear complexes of the metallacalix[4]arene type with formula [{Pt(en)(L)}(4)](4+) (en=ethylenediamine; 2: LH=5-chloro-2-hydroxypyrimidine (5-Cl-Hpymo); 3: LH=5-bromo-2-hydroxypyrimidine (5-Br-Hpymo); 4: LH=5-iodo-2-hydroxypyrimidine (5-I-Hpymo)) have been obtained from the reaction between cis-protected square-planar [Pt(en)(H(2)O)(2)](2+) metal entities and LH in aqueous media. Additionally, the binding properties of 2, 3, 4 and their congener [{Pt(en)(L)}(4)](4+) (1: LH=2-hydroxypyrimidine (Hpymo)) with calf thymus-DNA (ct-DNA) have been studied by using different techniques including circular and linear dichroism (CD and LD, respectively) and UV-visible absorbance spectroscopies, gel electrophoresis, fluorescence competitive-binding studies and atomic force microscopy (AFM). The results are consistent with significant non-covalent interactions taking place between the polynuclear cyclic species and ct-DNA. Moreover, gel electrophoresis, linear dichroism titrations and AFM images of ct-DNA with metallacalixarenes show ct-DNA coiling at low metallacalixarene concentrations and upon subsequent increments in metallacalixarene concentration ct-DNA can be seen to uncoil with concomitant formation of long and inflexible ct-DNA structures.

A new metallo-organic gelator formed from an admixture of a substituted nicotinic acid and its sodium salt is described. The nicotinic acid is substituted in the 6-position by an acetal functionality. The crystal structure of the 1:1 mixture revealed that the sodium atoms are aligned in infinite chains with the two organic units hydrogen bonded together to create potentially trinucleating ligands that encase the metal core, which leads to tube-like structures. These one-dimensional crystals were found to spontaneously gelify dichloromethane and provide pyridine gels with high thermal resistance. Gel formation was investigated by several analytical techniques, which included differential scanning calorimetry, TEM, freeze fracture electron microscopy (FFEM), IR spectroscopy and X-ray diffraction, and was found to be induced by the swelling of the one-dimensional material. FFEM and powder X-ray diffraction have revealed that the sodium chains are associated in a highly compacted state into a layered structure inside the gel. Doping these robust gels with dyes by diffusion, such as xylene cyanol, methyl yellow and bromo thymol blue, is feasible without destruction of the gels.

A platinum metal complex in which terpyridine joins estradiol (via an ethynyl link) to a platinum with a labile ligand (chloride) has been designed, synthesised and its X-ray crystal structure determined. The aim of this work was to link a targeting motif (in this case estrogen) to a metal-based biomolecule recognition unit (the platinum moiety). The target molecule: 17alpha-[4'-ethynyl-2,2':6',2'-terpyridine]-17beta-estradiol platinum(II) chloride (PtEEtpy) has been shown to bind to both human and bovine serum albumin (SA) and to DNA. FTICR mass spectrometry shows that the bimolecular units are in each case linked through coordination to the platinum with displacement of the chloride ligand. Circular dichroism indicates that a termolecular entity involving PtEEtpy, SA and DNA is formed. A range of electrospray mass spectrometry experiments showed that the PtEEtpy complex breaks and forms coordination bonds relatively easily. A whole cell estrogen receptor assay in an estrogen receptor positive cell (MCF-7) confirms binding of both EEtpy and PtEEtpy to the estrogen receptor in cells. The work demonstrates the concept of linking a targeting moiety (in this case estrogen) to a DNA binding agent.

The DNA binding of a dicationic pyridylimine-based dicopper(I) metallosupramolecular cylinder is reported together with its ability to act as an artificial nuclease. The cylinder binds strongly to DNA; more strongly than the spherical dication [Ru(phen)(3)](2+) (phen=1,10-phenanthroline), but more weakly than the corresponding tetracationic cylinders. DNA coiling effects are not observed with this dication, in contrast to the situation with the previously reported tetracationic cylinder involving a similar ligand. Linear dichroism (LD) data suggests that the dicopper cylinder binds in a different orientation from that of the tetracationic iron cylinder. Furthermore, the dicopper cylinder shows DNA-cleavage activity in the presence of peroxide. Of particular note is that the cylinder displays a marked and unusual ability to cleave both DNA strands at the same site, probably reflecting its dinuclear nature and possibly its mode of binding to the DNA.

In this work we present the results of a molecular simulation study of the interaction between a tetracationic bis iron(II) supramolecular cylinder, [Fe2(C25H20N4)3]4+, and DNA. This supramolecular cylinder has been shown to bind in the major groove of DNA and to induce dramatic coiling of the DNA. The simulations have been designed to elucidate the interactions that lead the cylinder to target the major groove and that drive the subsequent DNA conformational changes. Three sets of multi-nanosecond simulations have been performed: one of the uncomplexed d(CCCCCTTTTTCC) d(GGAAAAAGGGGG) dodecamer; one of this DNA complexed with the cylinder molecule; and one of this DNA complexed with a neutralised version of the cylinder. Coiling of the DNA was observed in the DNA-cylinder simulations, giving insight into the molecular level nature of the supramolecular coiling observed experimentally. The cylinder charge was found not to be essential for the DNA coiling, which implies that the DNA response is moderated by the short range interactions that define the molecular shape. Cylinder charge did, however, affect the integrity of the DNA duplex, to the extent that, under some circumstances, the tetracationic cylinder induced defects in the DNA base pairing at locations adjacent to the cylinder binding site.

A new tetracationic triple-stranded supramolecular cylinder is prepared from a bis(pyridylimine) ligand containing a diphenylmethane and two ketimine groups in the spacer. The cylinder is longer and slightly wider than the corresponding cylinder containing just diphenylmethane spacers. Inter-strand CH...pi interactions are not observed and this affects the relay of the chiral information within the cylinder; a mixture of rac and meso isomers results, with the meso isomer being the dominant solution species and characterised in the solid state by crystallography. This new cylinder does bind to DNA as confirmed by induced circular dichroism signals in both the metal-to-ligand charge transfer (MLCT) and in-ligand bands of the cylinder. Flow linear dichroism demonstrates that the cylinder binds to DNA in a specific orientation(s) and is consistent with (major) groove-binding as seen for the shorter cylinder. Some DNA bending/coiling is observed but the effect is much less dramatic than observed for the cylinder with diphenylmethane spacers confirming that coiling is not solely a consequence of the tetracationic charge, but rather is related to the precise size and shape of the cylinder.

New dinuclear supramolecular cylinders have been designed to exhibit spin-crossover behaviour, a form of molecular bistability. This has been achieved within the framework of our imine-based approach to supramolecular architecture by switching from pyridylimine systems to imidazolimines. Spin-crossover behaviour is achieved while retaining the simplicity and ease-of-synthesis of our molecular design. The imidazole groups used also introduce additional NH groups that engage in hydrogen-bonding to anions and solvents. In the case of the iron(II) tetrafluoroborate complex this hydrogen bonding links supramolecular cylinders into an extended two-dimensional array. Consistent with this, a sharper spin-crossover transition is observed for this compound than for the corresponding hexafluorophosphate salt. More subtle anion effects are indicated in the perchlorate salt which gives a two-step spin conversion, thereby displaying tristability.

The effect of inter-strand and intra-strand interactions is explored in a metallo-supramolecular system in which the metal-ligand coordination requirements may be satisfied by more than one different supramolecular architecture. This is achieved by introducing alkyl substituents onto the spacers of readily prepared bis(pyridylimine) ligands. The alkyl substituents induce twisting within the ligand strand and this intra-strand effect favours formation of helical architectures. The alkyl substituents also introduce inter-strand CH.pi interactions into the system. For the smaller methyl group these are most effectively accommodated in a trinuclear circular helicate architecture. A solution mixture of dinuclear double-helicate and trinuclear circular helicate results from which, for copper(I), the trinuclear circular helicate crystallises. The CH.pi interactions endow the circular helicate with a bowl-shaped conformation and the triangular unit aggregates into a tetrahedral ball-shaped array. Low-temperature NMR studies indicate that the CH.pi interactions also confer a bowl-shaped conformation on the triangle in solution. The larger ethyl groups can sustain intra-strand CH.pi interactions in the lower nuclearity double-helical system and this is the unique architecture for that ligand system in both solution and the solid state. Crystal structures are described for both the copper(I) and silver(I) complexes. Thus we show that intra-strand interactions may be used to induce helicity within this system, while the nuclearity of the array can be prescribed by the inter-strand interactions.

A ligand in which two pyridylimine binding units are linked by a 1,5-naphthalene spacer is prepared and its silver(I) coordination chemistry investigated. In the solid state, a pair of C-H triplebond N interactions between pyridylimine units link the free ligands into chain structures, with further C-H triplebond N and some -stacking interactions linking these chains into a three-dimensional structure. The spacer constrains the ligand to dinucleate, and with silver(I) the metal coordinates to two pyridylimine units from two separate ligands and this leads to the formation of coordination polymers with a range of different anions. Different twisting motifs within the ligand control the tacticity of these coordination polymers and both isotactic, helical polymers and syndiotactic (achiral) polymers result. The core of the isotactic polymer strands contains two metallo-vectors and results in long-range ordering of the metal centres into a 2 x n grid arrangement. The solution behaviour indicates that exchange between the diastereomeric forms occurs. Since this must involve inversion at the metal centres, atactic species may also form a component of the solution library.

Multiple competing molecular interactions (metal-ligand, pi-stacking and hydrogen-bonding) in the silver(I) complexes of 4'-thiomethyl-2,2':6',2"-terpyridine give rise to a range of different molecular architectures, in which the metal-ligand coordination requirements are satisfied in quite different ways. Polynuclear supramolecular spirals, aggregated mononuclear and aggregated dinuclear units are all structurally characterised. The metallo-supramolecular architecture obtained displays a remarkable dependence both on the choice of non-coordinated anion and the type of solvent used (coordinating or non-coordinating). The anion dependence is particularly surprising, since the anions are not integrated into the centre of the supramolecular structure. The solution behaviour is also solvent and anion dependent, with aggregation of planar mononuclear cations observed in acetonitrile, but oligonuclear spiral species implicated in nitromethane. The extraordinarily variable geometries of these systems suggest that they provide a novel example of the "frustration" principle, in which opposing tendencies cannot simultaneously be satisfied and identify an alternative approach to the design of metallo-supramolecular systems whose structure is responsive to external agents.

Layer-by-layer deposition of π-assembled arrays of discrete metallo units with aryl tails and polystyrenesulfonate gives structurally well-defined thin films. The formation of these films, which is controlled by π-π interactions, metal-ion coordination, and electrostatic interactions, bridges the gap between supramolecular crystal engineering and design of layered materials., (© 2001 WILEY-VCH Verlag GmbH, Weinheim, Fed. Rep. of Germany.)

In the groove! A tetracationic supramolecular cylinder, [Fe 2 L 3 ] 4+ (L=C 25 H 20 N 4 ), with a triple-helical architecture is just the right size to fit into the major groove of DNA and too big to fit into the minor groove. NMR spectroscopic data confirm that the cylinder binds in the major groove. Linear dichroism shows that very low loadings of [Fe 2 L 3 ] 4+ have a dramatic bending effect on the DNA and atomic force microscopy images show that this is an intramolecular effect resulting in coils of DNA., (© 2001 WILEY-VCH Verlag GmbH, Weinheim, Fed. Rep. of Germany.)

Careful selection of the spacer group used to separate the metal-binding domains allows control of the directionality in a helix; self-assembly leads uniquely to a double-helical cation with a head-to-tail (HT) configuration (shown schematically) in both the solid state and solution., (© 1999 WILEY-VCH Verlag GmbH, Weinheim, Fed. Rep. of Germany.)