Enhancing Hoogsteen interactions: a pyrrole-containing purine nucleoside that competes with guanosine self-assembly

A pyrrole-appended purine nucleoside 1 is described that can form an "extended" three-point Hoogsteen-type interaction due to the stabilization of the donor-acceptor-acceptor (DAA) motif. Nucleoside 1 is shown to bind guanosine 10 (a classic ADD motif) to form ensemble I. This interaction competes effectively with guanosine self-assembly and, as such, is capable of disrupting guanosine quadruplex formation.     

Dynamic combinatorial development of a neutral synthetic receptor that binds sulfate with nanomolar affinity in aqueous solution

Using dynamic combinatorial disulfide chemistry we have developed a new generation of neutral synthetic receptors for anions, based on a macrobicyclic peptide structure. These receptors show an exceptional affinity and selectivity for sulfate ions in aqueous solution [log K(a) = 8.67 in 41 mol% (67 volume%) acetonitrile in water]. The high affinity depends on a delicate balance between rigidity and flexibility in the structure of the receptor.     

Simulations of DNA coiling around a synthetic supramolecular cylinder that binds in the DNA major groove

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.     

Dynamic combinatorial optimization of a neutral receptor that binds inorganic anions in aqueous solution

A dynamic combinatorial library of potential anion receptors was generated from a cyclic peptide disulfide dimer and a series of dithiol spacers. Exposing the library to KI or K2SO4 led to the amplification of two new neutral receptors that bind anions through hydrogen bonding with up to micromolar affinity in aqueous solution. Thermodynamic studies suggest that these second-generation receptors outclass the previously described first-generation receptor, largely as a result of a more favorable enthalpy of binding. These results demonstrate that dynamic combinatorial optimization of designed hosts can be a powerful strategy, bringing synthetic receptors that approach the efficiencies of proteins one step closer.     

A synthetic miniprotein that binds specific DNA sequences by contacting both the major and the minor groove

Attachment of a slightly modified basic region of a bZIP protein (GCN4) to a distamycin-related tripyrrole provides a bivalent system capable of binding with high affinity to specific DNA sequences. Appropriate adjustment of the linker between the two units has led to a hybrid that binds a 9 base-pair-long DNA site (TTTTATGAC) with low nanomolar affinity at 4 degrees C. Circular dichroism and gel retardation studies indicate that the binding occurs by simultaneous insertion of the bZIP basic region into the DNA major groove and the tripyrrole moiety into the minor groove of the flanking sequence. Analysis of hybrids bearing alternative linkers revealed that tight, specific binding is strongly dependent on the length and nature of the connecting unit.     

A membrane-bound synthetic receptor that promotes growth of a polymeric coating at the bilayer-water interface

Primed for action: Atom-transfer radical polymerization (ATRP) can be promoted at a bilayer-water interface by anchoring initiator molecules (see scheme; red) in a membrane-bound synthetic receptor (yellow). The bilayer is formed on a calcinated nanofilm (gray) on a gold surface.     

Small molecule microarray identifies inhibitors of tyrosyl-DNA phosphodiesterase 1 that simultaneously access the catalytic pocket and two substrate binding sites

Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a member of the phospholipase D family of enzymes, which catalyzes the removal of both 3′- and 5′-DNA phosphodiester adducts. Importantly, it is capable of reducing the anticancer effects of type I topoisomerase (TOP1) inhibitors by repairing the stalled covalent complexes of TOP1 with DNA. It achieves this by promoting the hydrolysis of the phosphodiester bond between the Y723 residue of human TOP1 and the 3′-phosphate of its DNA substrate. Blocking TDP1 function is an attractive means of enhancing the efficacy of TOP1 inhibitors and overcoming drug resistance. Previously, we reported the use of an X-ray crystallographic screen of more than 600 fragments to identify small molecule variations on phthalic acid and hydroxyquinoline motifs that bind within the TDP1 catalytic pocket. Yet, the majority of these compounds showed limited (millimolar) TDP1 inhibitory potencies. We now report examining a 21 000-member library of drug-like Small Molecules in Microarray (SMM) format for their ability to bind Alexa Fluor 647 (AF647)-labeled TDP1. The screen identified structurally similar N,2-diphenylimidazo[1,2-a]pyrazin-3-amines as TDP1 binders and catalytic inhibitors. We then explored the core heterocycle skeleton using one-pot Groebke–Blackburn–Bienayme multicomponent reactions and arrived at analogs having higher inhibitory potencies. Solving TDP1 co-crystal structures of a subset of compounds showed their binding at the TDP1 catalytic site, while mimicking substrate interactions. Although our original fragment screen differed significantly from the current microarray protocol, both methods identified ligand–protein interactions containing highly similar elements. Importantly inhibitors identified through the SMM approach show competitive inhibition against TDP1 and access the catalytic phosphate-binding pocket, while simultaneously providing extensions into both the substrate DNA and peptide-binding channels. As such, they represent a platform for further elaboration of trivalent ligands, that could serve as a new genre of potent TDP1 inhibitors.

Using small molecule microarray TDP1 inhibitors have been identified that bind in a trivalent mode.     

NMR studies on natural and synthetic Amavadin

The stereochemistry of isolated natural product Amavadin, which contains a 1:2 complex of V(IV) with N-hydroxyimino-2,2'-dipropionic acid (HIDPAH(3)), and some synthetic complexes have been investigated. Amavadin was isolated from Amanita muscaria and oxidized with [NH(4)](2)[Ce(NO(3))(6)]. H(2)[Delta-V(S,S-HIDPA)(2)].3H(2)O, H(2)[Delta,Lambda-V(S,S-HIDPA)(2)].3H(2)O and their equivalent oxidized species have been synthesized and characterized spectroscopically. A combination of COSY, NOE, (1)H, (13)C-NMR and CD spectroscopy have been used to prove that the isolated natural product Amavadin consists of an almost equal mixture of the Delta- and Lambda-isomers of [V(S,S-HIDPA)(2)](2-).     

Mechanistic studies in the synthesis of a series of thieno-expanded xanthosine and guanosine nucleosides

During the synthetic pursuit of guanosine (tri-G) and xanthosine (tri-X) tricyclic nucleosides analogues, an interesting side product was discovered. In an effort to uncover the mechanistic factors leading to this result, a series of reaction conditions were investigated. It was found that by varying the conditions, the appearance of the side product could be controlled. In addition, the yield of the desired products could be manipulated to afford either a 50:50 mix of both tri-G and tri-X, or a majority of one or the other. To demonstrate the broad utility of the method, it was also adapted to the synthesis of guanosine and xanthosine from 5-amino-1-β-d-ribofuranosyl-4-imidazolecarboxyamide (AICAR). The mechanistic details surrounding the synthetic efforts are reported herein.     

Sensitive and selective fluorescence detection of guanosine nucleotides by nanoparticles conjugated with a naphthyridine receptor

Novel fluorescent nanosensors, based on a naphthyridine receptor, have been developed for the detection of guanosine nucleotides, and both their sensitivity and selectivity to various nucleotides were evaluated. The nanosensors were constructed from polystyrene nanoparticles functionalized by (N-(7-((3-aminophenyl)ethynyl)-1,8-naphthyridin-2-yl)acetamide) via carbodiimide ester activation. We show that this naphthyridine nanosensor binds guanosine nucleotides preferentially over adenine, cytosine, and thymidine nucleotides. Upon interaction with nucleotides, the fluorescence of the nanosensor is gradually quenched yielding Stern–Volmer constants in the range of 2.1 to 35.9 mM⁻¹. For all the studied quenchers, limits of detection (LOD) and tolerance levels for the nanosensors were also determined. The lowest (3σ) LOD was found for guanosine 3’,5’-cyclic monophosphate (cGMP) and it was as low as 150 ng/ml. In addition, we demonstrated that the spatial arrangement of bound analytes on the nanosensors’ surfaces is what is responsible for their selectivity to different guanosine nucleotides. We found a correlation between the changes of the fluorescence signal and the number of phosphate groups of a nucleotide. Results of molecular modeling and ζ-potential measurements confirm that the arrangement of analytes on the surface provides for the selectivity of the nanosensors. These fluorescent nanosensors have the potential to be applied in multi-analyte, array-based detection platforms, as well as in multiplexed microfluidic systems.     

Designed, functionalized helix-loop-helix motifs that bind human carbonic anhydrase II: a new class of synthetic receptor molecules

Polypeptides designed to fold into helix-loop-helix motifs and to dimerize to form four-helix bundles were functionalized by the introduction of a sulfonamide derivative known to bind human carbonic anhydrase II (HCAII) and one or both of the dansyl- and methoxycoumarin fluorescent probes. The 42-residue sequence DC that carries all three substituents in solvent-exposed positions was found to bind HCAII with a dissociation constant of 5 nM in aqueous solution at pH 7. At 2 muM concentration, DC was mainly dimeric in aqueous solution but bound HCAII as a monomer. Upon addition of a large excess of a helix-loop-helix motif without a high-affinity ligand, KE2-Q, a ternary complex was formed between HCAII, DC, and KE2-Q. Hydrophobic interactions between DC and HCAII and coordination of the sulfonamide group to the zinc ion of HCAII contributed cooperatively to binding in a demonstration of the usefulness of folded polypeptide-small organic molecule chimera as novel protein receptors. The DC homodimer was found to be a very sensitive biosensor component due to intermolecular quenching of its fluorescence that was inhibited upon binding to HCAII.     

Thermodynamic studies on protonation constant of adenosine and guanosine at different temperatures and ionic strengths

Stepwise protonation constants of two purine nucleosides (adenosine and guanosine) were determined at different temperatures (293.15 to 308.15) and various ionic strengths (0.101 to 3.503 mol · kg⁻¹ NaClO₄) using a combination of potentiometric and spectrophotometric method. The thermodynamic parameters (i.e. enthalpy change, ΔH, and entropy change, ΔS) of the protonations were calculated at different temperatures using van’t Hoff and virial equations. The dependence of the protonation constant on ionic strength is modeled by a Debye–Hückel type equation and discussed. Finally, the protonation constants of the nucleosides and the enthalpy change of protonations were determined at zero ionic strength.     

Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor

We report the complete de novo design of a four-helix bundle protein that selectively binds the nonbiological DPP-Fe(III) metalloporphyrin cofactor (DPP-Fe(III) = 5, 15-Di[(4-carboxymethyleneoxy)phenyl]porphinato iron(III)). A tetrameric, D2-symmetric backbone scaffold was constructed to encapsulate two DPP-Fe(III) units through bis(His) coordination. The complete sequence was determined with the aid of the statistical computational design algorithm SCADS. The 34-residue peptide was chemically synthesized. UV-vis and CD spectroscopy, size-exclusion chromatography, and analytical ultracentrifugation indicated the peptide undergoes a transition from a predominantly random coil monomer to an alpha-helical tetramer upon binding DPP-Fe(III). EPR spectroscopy studies indicated the axial imidazole ligands were oriented in a perpendicular fashion, as defined by second-shell interactions that were included in the design. The 1-D 1H NMR spectrum of the assembled protein displayed features of a well-packed interior. The assembled protein possessed functional redox properties different from those of structurally similar systems containing the heme cofactor. The designed peptide demonstrated remarkable cofactor selectivity with a significantly weaker binding affinity for the natural heme cofactor. These findings open a path for the selective incorporation of more elaborate cofactors into designed scaffolds for constructing molecularly well-defined nanoscale materials.     

Annulated heterocycles through a radical-cation cyclization: synthetic and mechanistic studies

The wide range of chemical transformations possible with furans and thiophenes, especially reactions leading to dearomatization of the nucleus, make them highly versatile synthons for complex molecule construction. As part of a program to exploit this intrinsic reactivity, we have developed a convenient method to prepare annulated versions of these heterocycles. The strategy is based on a two-step annulation involving the initial conjugate addition of a heteroaryl organometallic to an enone with trapping of the enolate as the silyl enolether. Anodic oxidation of this molecule leads to the initial formation of a radical-cation that is trapped in a heteroaryl-terminated cyclization to give the annulated products.     

Disruption of protein-protein interactions: design of a synthetic receptor that blocks the binding of cytochrome c to cytochrome c peroxidase

Synthetic receptor 1 has been found via fluorescence titration to compete effectively with cytochrome c peroxidase for binding cytochrome c (Cc), forming 1:1 Cc:1 complex with a binding constant of (3 +/- 1) x 10(8) M-1, and to disrupt Cc: Apaf-1 complex, a key adduct in apoptosis.     

Thermodynamic study on supramolecular complex formation of theophylline derivates with a synthetic receptor

Thermodynamic parameters for the supramolecular complex formation of macrobicyclophane with several theophylline dimers are reported. Solvation of guests plays an important role in the supramolecular complex formation. A good correlation between ΔG and guest solubility is obtained in different CHCl₃/CH₂Cl₂ proportions.     

Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation

Genetic selection provides the most powerful method to assay large libraries of biomolecules for function. However, harnessing the power of genetic selection for the detection of specific, nonendogenous small-molecule targets in vivo remains a significant challenge. The ability to genetically select for small molecules would provide a reaction-independent mechanism to clone biosynthesis genes from large DNA libraries and greatly facilitate the exploration of large libraries of mutant enzymes for improved synthetic capabilities including altered substrate specificities and enhanced regio- or stereoselectivities. While remarkable progress has been made in developing genetic methods to detect small molecules in vivo, many of these methods rely on engineering small-molecule-protein interactions which remains a difficult problem, and the potential for some of these systems to assay large libraries is limited by the low transformation efficiency and long doubling time of yeast relative to bacteria. Herein, we demonstrate that synthetic riboswitches that activate protein translation in response to a specific small molecule can be used to perform sensitive genetic screens and selections for the presence of small molecules in Escherichia coli. We further demonstrate that the exquisite molecular discrimination properties of aptamers selected in vitro translate directly into an in vivo genetic selection system. Finally, we demonstrate that a cell harboring a synthetic riboswitch with a particular ligand specificity can be selectively amplified from a million-fold larger pool of cells containing mutant riboswitches that respond to a closely related ligand, suggesting that it is possible to use genetic selection in E. coli to discover synthetic riboswitches with new ligand specificities from libraries of mutant riboswitches.     

Determination of inorganic phosphate in serum and saliva using a synthetic receptor

[structure: see text] A C(3)(v) symmetric synthetic receptor (1) was employed in an indicator-displacement assay to determine the phosphate concentrations in both horse serum and human saliva at biological pH. The determination of the phosphate concentrations in the serum and saliva using the colorimetric assay were 1.6 and 5.1 mM, respectively. These results further accentuate the usefulness of synthetic receptors in truly practical applications.     

Label-free molecular beacon system based on DNAs containing abasic sites and fluorescent ligands that bind abasic sites

A new class of label-free molecular beacon (MB) system based on DNA strands that contain abasic (AP) sites (AP-DNA) and adopt stem-loop structures, in combination with fluorescent ligands that bind these AP sites, has been developed. Unlike a conventional MB, which requires covalent labeling of the MB with a fluorophore and a quencher, the developed system (APMB) does not require covalent attachment of signal transduction units. Detailed sensing functions of a series of APMB systems were examined with the aid of the fluorescent ligand named ATMND to provide insight into the design strategy for APMB systems. The effects of the stem length and the position of the AP site in the stem moiety on the fluorescence response of the APMB system were examined. Genotyping of a G/C SNP of PCR amplification products was successfully demonstrated with the APMB system and blue-fluorescent ATMND as a ligand. The APMB system was further extended to a system that utilized green-fluorescent lumiflavin.