Synthesis of a library of stereo- and regiochemically diverse aminoglycoside derivatives

A library of forty modified aminoglycosides was prepared in which the configuration and regiochemistry of two or three rings was widely varied. The library was based around three core ring systems: the 2-deoxystreptamine ring system found in the natural products, and both enantiomers of (1R*,2R*,4R*,5R*)-2,5-diamino-cyclohexane-1,4-diol and (1R*,3R*,4R*,6R*)-4,6-diaminocyclohexane-1,3-diol. In each case, the core was modified by glycosylation with one or two sugar rings. The absolute configuration of the sugar substituents (d or l), the configuration of the anomeric centres (alpha or beta), and the regiochemical arrangement of the amine(s) were varied.     

Fluorescence-based approach for detecting and characterizing antibiotic-induced conformational changes in ribosomal RNA: comparing aminoglycoside binding to prokaryotic and eukaryotic ribosomal RNA sequences

Aminoglycoside antibiotics bind specifically to a conserved sequence of the 16S ribosomal RNA (rRNA) A site and interfere with protein synthesis. One model for the mechanism underlying the deleterious effects of aminoglycosides on protein synthesis invokes a drug-induced conformational change in the rRNA that involves the destacking of two adenine residues (A1492 and A1493 in Escherichia coli) at the A site. We describe here a fluorescence-based approach for detecting and characterizing this drug-induced conformational change in the target rRNA. In this approach, we insert the fluorescent base analogue 2-aminopurine in place of A1492 in an E. coli 16S rRNA A-site model oligonucleotide (EcWT) as well as in a mutant form of this oligomer (A1408G) in which A1408 has been replaced with a guanine. The presence of guanine at 1408 instead of adenine represents one of the major sequence differences between prokaryotic and eukaryotic A sites, with the latter A sites being resistant to the deleterious effects of aminoglycosides. Binding of the aminoglycoside paromomycin to the 2AP-substituted forms of EcWT and A1408G induced changes in fluorescence quantum yield consistent with drug-induced base destacking in EcWT but not A1408G. Isothermal titration calorimetry studies reveal that paromomycin binds to the EcWT duplex with a 31-fold higher affinity than the A1408G duplex, with this differential affinity being enthalpic in origin. In the aggregate, these observations are consistent with both rRNA binding affinity and drug-induced base destacking being important determinants in the prokaryotic specificity of aminoglycosides. Combining fluorescence quantum yield and lifetime data allows for quantification of the extent of drug-induced base destacking, thereby providing a convenient tool for evaluating the relative impacts of both novel and existing A-site targeting ligands on rRNA conformation and potentially for predicting relative antibiotic activities and specificities.     

Decoding a PNA encoded peptide library by PCR: the discovery of new cell surface receptor ligands

The ability to screen and identify new ligands for cell surface receptors has been a long-standing goal as it might allow targeting of pharmaceutically relevant receptors, such as integrins or G protein coupled receptors. Here, we present a method to amplify hits from a library of PNA-tagged peptides. To this end, human cells, overexpressing either integrins or the CCR6 receptor, were treated with a 10,000 member PNA-encoded peptide library. Extraction of the PNA tags from the surface of the cells was followed by a PNA-tag to DNA translation and amplification enabling decoding of the tags via microarray hybridization. This approach to ligand discovery facilitates screening for differences in surface-receptor ligands and/or receptor expression between different cell types, and opens up a practical approach to PNA-tag amplification.     

Cross-referenced combinatorial libraries for the discovery of metal-complexing ligands: library deconvolution by LC-MS

N-Acylthioureas are excellent ligands for a variety of heavy metals, but their metal selectivity is highly dependent on the precise nature of the substituents present. In this paper we show how combinatorial chemistry techniques can be used to establish relative affinities for copper within a mixture of 100 such thioureas. Following a straightforward synthesis, and copper extraction using standard liquid-liquid extraction techniques, LC-MS was used to identify the ligands which bind most strongly to the copper ions. Among the 100 ligands XC(O)N(Z)C(S)NHY, the most important substituent is the Y group bound to the NH: only aromatic Y substituents give strong binding to copper. The acyl X substituents are invariably aromatic, and an electron-rich X group is best; the affinity for copper seems to be less dependent on the Z substituent, although a large group such as benzyl disfavours copper binding. The five ligands from the library which bind copper most strongly have been clearly identified by a series of experiments: they all have aromatic groups in the Y position, but the X and Z substituents can be more varied. This is a very convincing demonstration of the power of combinatorial methods: to have found the same information by conventional methods would have required a lengthy and repetitive series of syntheses and investigations. In addition, our results give some preliminary evidence for synergistic binding of two different ligands, but this requires further investigation.     

A virtual screen for diverse ligands: discovery of selective G protein-coupled receptor antagonists

Virtual screening has become a major focus of bioactive small molecule lead identification, and reports of agonists and antagonists discovered via virtual methods are becoming more frequent. G protein-coupled receptors (GPCRs) are the one class of protein targets for which success with this approach has been limited. This is likely due to the paucity of detailed experimental information describing GPCR structure and the intrinsic function-associated structural flexibility of GPCRs which present major challenges in the application of receptor-based virtual screening. Here we describe an in silico methodology that diminishes the effects of structural uncertainty, allowing for more inclusive representation of a potential docking interaction with exogenous ligands. Using this approach, we screened one million compounds from a virtual database, and a diverse subgroup of 100 compounds was selected, leading to experimental identification of five structurally diverse antagonists of the thyrotropin-releasing hormone receptors (TRH-R1 and TRH-R2). The chirality of the most potent chemotype was demonstrated to be important in its binding affinity to TRH receptors; the most potent stereoisomer was noted to have a 13-fold selectivity for TRH-R1 over TRH-R2. A comprehensive mutational analysis of key amino acid residues that form the putative binding pocket of TRH receptors further verified the binding modality of these small molecule antagonists. The described virtual screening approach may prove applicable in the search for novel small molecule agonists and antagonists of other GPCRs.     

Cationic corrole derivatives: a new family of G-quadruplex inducing and stabilizing ligands

Water-soluble cationic corrole derivatives were designed and synthesized, and the first observation of their interactions with the telomeric G-quadruplex was made.     

Selective photocleavage of DNA and RNA by anthraquinone derivatives: targeting the single-strand region of hairpin structures

A tetracationic anthraquinone derivative (27AQS2) binds to hairpin DNA and RNA. Ultraviolet irradiation of the bound quinone causes cleavage in the loop region of both oligonucleotides and at guanines in the stem region of the DNA hairpin. The absence of observable strand cleavage at guanines in the RNA hairpin suggests that either aniline treatment does not cause cleavage at damaged guanines in RNA or that radical cation migration does not occur readily in RNA duplexes. The ability to target the single-stranded regions of DNA and RNA structures is an important property of this photonuclease.     

Encoded peptide libraries and the discovery of new cell binding ligands

Cells over-expressing integrins or CCR6 were incubated on a DNA microarray, pre-hybridized with a 10,000 member PNA-encoded peptide library allowing novel cell specific ligands for integrins and CCR6 to be identified.     

Formation of pyranoanthocyanins in red wines: a new and diverse class of anthocyanin derivatives

Pyranoanthocyanins constitute one of the most important classes of anthocyanin-derived pigments occurring naturally in red wine. Nonetheless, correct assignment of their structures and pathways of formation in red wine has been relatively recent—less than two decades. Study of these newly discovered pigments is progressively unfolding the chemical pathways that drive the evolution of red wine colour during ageing. The objective of this paper is to review current knowledge regarding the pathway of formation in red wine of a great variety of pyranoanthocyanin structures, namely carboxypyranoanthocyanins, methylpyranoanthocyanins, pyranoanthocyanin-flavanols, pyranoanthocyanin-phenols, portisins, oxovitisins, and pyranoanthocyanin dimers. The chromatic features of some of the compounds, for example their colour expression and acid–base equilibria in aqueous media, are also discussed.     

Formation of pyranoanthocyanins in red wines: a new and diverse class of anthocyanin derivatives

Pyranoanthocyanins constitute one of the most important classes of anthocyanin-derived pigments occurring naturally in red wine. Nonetheless, correct assignment of their structures and pathways of formation in red wine has been relatively recent—less than two decades. Study of these newly discovered pigments is progressively unfolding the chemical pathways that drive the evolution of red wine colour during ageing. The objective of this paper is to review current knowledge regarding the pathway of formation in red wine of a great variety of pyranoanthocyanin structures, namely carboxypyranoanthocyanins, methylpyranoanthocyanins, pyranoanthocyanin-flavanols, pyranoanthocyanin-phenols, portisins, oxovitisins, and pyranoanthocyanin dimers. The chromatic features of some of the compounds, for example their colour expression and acid–base equilibria in aqueous media, are also discussed.     

Synthesis and characterization of new organocobaloxime derivatives with asymmetric dioxime ligands

New organocobaloxime derivatives of the types [Co(HL)₂(All)X], [CoL₂(All)XB₂F₄] and [CoL₂(All)X(Cu(phen))₂](ClO₄)₂ [H₂L¹ = 4-(4-chlorophenylamino)biphenylglyoxime and H₂L² = 4-(naphthyl-1-amino)biphenylglyoxime; phen = 1,10-phenanthroline; All = Allyl; X = H₂O, py (pyridine), APy (acetylpyridine)] were synthesized and characterized by elemental analysis, molar conductance, FT-IR, ¹H NMR and magnetic susceptibility measurements. Trinuclear complexes {CoL₂(All)X[Cu(phen)]₂}(ClO₄)₂ have planar N-donor heterocyclic base [1,10-phenanthroline (phen)]. The IR spectra indicated that the complexes coordinate through the N atom of the oxime group of each ligand. The magnetic susceptibilities of the complexes indicated that they are diamagnetic (low-spin d ⁶ octahedral) except trinuclear complex which show a subnormal magnetic moment.     

Combinatorial chemistry: a tool for the discovery of new catalysts

The discovery of new reactions and catalysts has always presented an intriguing challenge to scientists. With the rise of combinatorial chemistry, a new method has emerged that holds considerable promise to facilitate the task since it allows for the simultaneous generation and testing of a large number of compounds. The crucial difficulty lies in establishing general technologies for rapid and reliable screening of libraries to determine the catalytic activity of their members. Several recent publications have addressed this question by using infrared thermography, colorimetric assays and fluorescence spectroscopy. These techniques have not only been applied successfully to the high-throughput screening of parallel compound arrays but also to the screening of one-bead-one-compound libraries. This demonstrates that combinatorial chemistry possesses indeed the potential to establish itself as a powerful tool for the discovery of new catalysts. This review describes the methodologies used so far for the detection of catalytic events and will place particular emphasis on the on-bead screening of one-bead-one-compound libraries.     

Expanding the chemical space: Discovery of new anticancer 3-arylbenzofuran derivatives

A new chemical space was generated via C₂-functionalization of 3-arylbenzofurans. Mannich reaction of 3-arylbenzofurans with secondary amines and formaldehyde allowed for installation of aminomethyl unit at C₂ position of benzofurans. A formyl group at C₂ site introduced as a result of Vilsmeier-Haack formylation of 3-arylbenzofurans was employed as a reacting partner for three-component Kabachnik-Fields reaction with various amines and triethyl phosphite to give a wide variety of aminomethylphosphonates. Furthermore, several benzo[d]oxazoles and pyrrolo[1,2-a]quinoxalines were prepared by using the formyl group. Biological screening of the synthesized compounds revealed that the benzofuran bearing a pyrrolo[1,2-a]quinoxaline moiety ( 5b ) most potently inhibited the viability of human blood cancer cells, but not solid tumor cells. Caspase activity assay, analysis of Annexin V-positive cells, and Western blot analysis indicated that 5b -induced death of human lymphoma U937 cells could result from its potential to induce the caspase-dependent apoptotic death of blood cancer cells with inhibition of ERK activation.     

Metal chelates with salicylidene-3-carboethoxy-4,5-dimethylthiophene derivatives as azomethine ligands of a new type

New azomethine derivatives of salicylidene-3-carboethoxy-4,5-dimethylthiophene and their metal chelates are synthesized. The enolimine tautomeric form of the azomethine system of the ligand is determined from the data of ¹H NMR and IR spectroscopy. According to the IR spectral data, the structures of the Co, Ni, Cu, and Zn complexes are octahedral (the structure of the nickel complex is proved by X-ray diffraction analysis), whereas the palladium chelate has a square structure.     

Disubstituted 2-phenyl-benzopyranopyrimidine derivatives as a new type of highly selective ligands for telomeric G-quadruplex DNA

A series of 2-phenyl-benzopyranopyrimidine (PBPP) derivatives with alkylamino side chains were synthesized and found to be a new type of highly selective ligand to bind with telomeric G-quadruplex DNA, and their biological properties were reported for the first time. Their interactions with telomeric G-quadruplex DNA were studied with FRET melting, surface plasmon resonance, CD spectroscopy, and molecular modeling. Our results showed that the disubstituted PBPP derivatives could strongly bind to and effectively stabilize the telomeric G-quadruplex structure, and had significant selectivity for G-quadruplex over duplex DNA. In comparison, the mono substituted derivatives had much less effect on the G-quadruplex, suggesting that the disubstitution of PBPP is essential for its interaction with the G-quadruplex. Furthermore, telomerase inhibition of the PBPP derivatives and their cellular effects were studied, and compound 11b was found to be the most promising compound as a telomerase inhibitor and telomeric G-quadruplex binding ligand for further development for cancer treatment.     

An efficient thermally induced RNA conformational switch as a framework for the functionalization of RNA nanostructures

RNA offers a variety of interactions and dynamic conformational switches not available with DNA that may be exploited for the construction of nanomolecular structures. Here, we show how the RNA loop-loop, or "kissing", interaction can be used to construct specific circular RNA arrangements that are capable of thermal isomerization to alternative structures. We also show how this thermally induced structural rearrangement can be used to unmask a functional RNA structure, in this case, a peptide-binding RNA structure, the Rev-response element (RRE) of HIV, thereby acting as a functional peptide-binding switch. The relative ease with which the RRE could be engineered into the RNA substrates suggested that a variety of functional RNA structures may be introduced. In addition, the structural rearrangement was extremely efficient, showing that the "kissing" complexes described in this study may provide a useful framework for the construction of functional RNA-based nanostructures, as well as aid in our understanding of the way RNA functions in biological systems.