Dynamic combinatorial selection of molecules capable of inhibiting the (CUG) repeat RNA-MBNL1 interaction in vitro: discovery of lead compounds targeting myotonic dystrophy (DM1)

Myotonic dystrophy type 1 (DM1), the most common form of muscular dystrophy in adults, is an RNA-mediated disease. Dramatically expanded (CUG) repeats accumulate in nuclei and sequester RNA-binding proteins such as the splicing regulator MBNL1. We have employed resin-bound dynamic combinatorial chemistry (RBDCC) to identify the first examples of compounds able to inhibit MBNL1 binding to (CUG) repeat RNA. Screening an RBDCL with a theoretical diversity of 11 325 members yielded several molecules with significant selectivity for binding to (CUG) repeat RNA over other sequences. These compounds were also able to inhibit the interaction of GGG-(CUG)(109)-GGG RNA with MBNL1 in vitro, with K(i) values in the low micromolar range.     

The Dimeric Form of 1,3-Diaminoisoquinoline Derivative Rescued the Mis-splicing of Atp2a1 and Clcn1 Genes in Myotonic Dystrophy Type 1 Mouse Model

Expanded CUG repeat RNA in the dystrophia myotonia protein kinase (DMPK) gene causes myotonic dystrophy type 1 (DM1) and sequesters RNA processing proteins, such as the splicing factor muscleblind-like 1 protein (MBNL1). Sequestration of splicing factors results in the mis-splicing of some pre-mRNAs. Small molecules that rescue the mis-splicing in the DM1 cells have drawn attention as potential drugs to treat DM1. Herein we report a new molecule JM642 consisted of two 1,3-diaminoisoquinoline chromophores having an auxiliary aromatic unit at the C5 position. JM642 alternates the splicing pattern of the pre-mRNA of the Ldb3 gene in the DM1 cell model and Clcn1 and Atp2a1 genes in the DM1 mouse model. In vitro binding analysis by surface plasmon resonance (SPR) assay to the r(CUG) repeat and disruption of ribonuclear foci in the DM1 cell model suggested the binding of JM642 to the expanded r(CUG) repeat in vivo, eventually rescue the mis-splicing.     

Design of a bioactive small molecule that targets the myotonic dystrophy type 1 RNA via an RNA motif-ligand database and chemical similarity searching

Myotonic dystrophy type 1 (DM1) is a triplet repeating disorder caused by expanded CTG repeats in the 3'-untranslated region of the dystrophia myotonica protein kinase (DMPK) gene. The transcribed repeats fold into an RNA hairpin with multiple copies of a 5'CUG/3'GUC motif that binds the RNA splicing regulator muscleblind-like 1 protein (MBNL1). Sequestration of MBNL1 by expanded r(CUG) repeats causes splicing defects in a subset of pre-mRNAs including the insulin receptor, the muscle-specific chloride ion channel, sarco(endo)plasmic reticulum Ca(2+) ATPase 1, and cardiac troponin T. Based on these observations, the development of small-molecule ligands that target specifically expanded DM1 repeats could be of use as therapeutics. In the present study, chemical similarity searching was employed to improve the efficacy of pentamidine and Hoechst 33258 ligands that have been shown previously to target the DM1 triplet repeat. A series of in vitro inhibitors of the RNA-protein complex were identified with low micromolar IC(50)'s, which are >20-fold more potent than the query compounds. Importantly, a bis-benzimidazole identified from the Hoechst query improves DM1-associated pre-mRNA splicing defects in cell and mouse models of DM1 (when dosed with 1 mM and 100 mg/kg, respectively). Since Hoechst 33258 was identified as a DM1 binder through analysis of an RNA motif-ligand database, these studies suggest that lead ligands targeting RNA with improved biological activity can be identified by using a synergistic approach that combines analysis of known RNA-ligand interactions with chemical similarity searching.     

A Ligand That Targets CUG Trinucleotide Repeats

The development of small molecules that can recognize specific RNA secondary and tertiary structures is currently an important research topic for developing tools to modulate gene expression and therapeutic drugs. Expanded CUG trinucleotide repeats, known as toxic RNA, capture the splicing factor MBNL1 and are causative of neurological disorder myotonic dystrophy type 1 (DM1). Herein, the rational molecular design, synthesis, and binding analysis of 2,9‐diaminoalkyl‐substituted 1,10‐phenanthroline (DAP), which bound to CUG trinucleotide repeats, is described. The results of melting temperature (T_m) analyses, surface plasmon resonance (SPR) assay, and electrospray spray ionization time‐of‐flight (ESI‐TOF) mass spectrometry showed that DAP bound to r(CUG)₉ but not to r(CAG)₉ and r(CGG)₉. The dual luciferase assay clearly indicated DAP bound to the r(CUG)_n repeat by affecting the translation in vitro.     

Copper(II) complexes of 2-carbamoylethyl derivatives of linear diamines. Crystallographic evidence for amido oxygen binding prior to deprotonation of amide nitrogens

There has been considerable interest in the coordination chemistry of linear and macrocyclic amides⁽¹⁾. Deprotonation of the amide nitrogen is known to occur with various metal ions and the sites of coordination are generally considered to be the carbonyl oxygen prior to deprotonation and the amide nitrogen after deprotonation. However, oxygen binding has generally been inferred from indirect evidence^(2,3). We now report the results of some studies on the interaction of copper(II) with a series of 2-carbamoylethyl derivatives of linear diamines, namelyN,N′-bis(2-carbamoylethyl)ethylenediamine (1),N,N,N′,N′-tetrakis(2-carbamoylethyl)ethylenediamine (2)N,N′-bis(2-carbamoylethyl)trimethylenediamine (3) andN,N,N′,N′-tetrakis(2-carbamoylethyl)trimethylenediamine (4) which confirm carbonyl oxygen binding prior to amide deprotonation.     

2′-O-Lysylaminohexyladenosine modified oligonucleotides

Abstract  

Development of therapeutically active oligonucleotides for sequence-specific gene knockdown relies on chemical modifications that confer high stability and target affinity and ideally enable cellular uptake. 2′-O-Lysylaminohexyluridine-containing antisense and siRNA oligonucleotides have been shown to be well suited for gene knockdown. They are highly resistant to enzymatic degradation while having good affinity for the targeted RNA strand and efficiently down-regulate their target in cell culture tumor models. The 2′-O-lysylaminohexyl modification was expanded to adenosine nucleosides. The corresponding phosphoramidite building block was prepared in a straightforward procedure comprising six steps starting from adenosine. After 2′-O-alkylation with N-(6-bromohexyl)phthalimide and removal of the N-protecting group, the protected lysine was specifically attached to the alkylamino group. Incorporation of 2′-O-lysylaminohexyladenosine nucleotides in a test sequence confirmed that the cationic chains lead only to minor duplex destabilization and do not disturb the duplex structure. Results further emphasize the advantageous properties of 2′-O-lysylaminohexyl modified oligonucleotides for therapeutic applications.     

Study of cis-trans equilibrium of oxacarbocyanine dyes in solution and in a complex with DNA

Cis-trans equilibrium for a number of meso-substituted oxacarbocyanine dyes, 3,3′-diethyloxacarbocyanine iodide (K1), 3,3′-diethyl-9-methyloxacarbocyanine iodide (K2), 3,3′-dimethyl-9-ethyloxacarbocyanine iodide (K3), 3,3′,9-triethyl-6,6′-dimethoxyoxacarbocyanine iodide (K4), and 3,3′,9-triethyl-5,5′-dimethyloxacarbocyanine iodide (K5), has been studied in solutions and in a complex with DNA by spectral and fluorescent methods. A shift of the cis-trans isomer equilibrium toward the formation of the trans-isomer was observed in the presence of DNA, which determined in many respects the spectral effects observed upon the complexation of the oxacarbocyanine dyes. A steep rise of fluorescence (due to binding of the trans-isomer) in a complex with DNA is favorable for using oxacarbocyanine dyes to determine DNA.     

Hydrophobic interactions of phenoxazine modulators with bovine serum albumin

The interaction of 10-(3′-N-morpholinopropyl)phenoxazine [MPP], 10-(4′-N-morpholinobutyl)phenoxazine [MBP], 10-(3′-N-morpholinopropyl)-2-chlorophenoxazine [MPCP], 10-(3′-N-piperidinopropyl)-2-chlorophenoxazine [PPCP] or 10-(3′-N-morpholinopropyl)-2-trifluoromethylphenoxazine [MPTP] with bovine serum albumin (BSA) has been studied by gel filtration and equilibrium dialysis methods. The binding of these modulators, based on dialysis experiments, has been characterized using the following parameters: percentage of bound drug (Β), the association constant (K ₁), the apparent binding constant (k) and the free energy change (δF‡). The binding of phenoxazine derivatives to serum transporter protein, BSA, is correlated with their octanol-water partition coefficient, log₁₀ P. In addition, effect of the displacing activities of hydroxyzine and acetylsalicylic acid on the binding of phenoxazine derivatives to albumin has been studied. Results of the displacement experiments show that phenoxazine benzene rings and tertiary amines attached to the side chain of the phenoxazine moiety are bound to a hydrophobic area on the albumin molecule.     

Chemical synthesis of oligonucleotides. 3: Synthesis and characterization of N,O-protected ribophosphoesters for applications in RNA synthesis

The chemical synthesis of RNA, in contrast to that of DNA, poses problems due to fi) additional requirement of 2′-hydroxyl protection of the ribose moieties, and (ii) high lability of inter-ribophosphate bonds. Herein we report the synthesis and characterisation of N, O-protected ribophosphoesters 1 which are key monomeric derivatives in phosphotriester methodology for RNA synthesis. Both the isomeric 2′ and 3′-O-phosphates have been obtained and characterised. The utility of the t-butyl dimethylsilyl group for 2′-hydroxyl protection in the phosphotriester method is demonstrated by the synthesis of r(AUAU),r (UAUA) andr (CACA). Part 2, Rajendrakumaret al (1987) NCL communication number 4682     

Oxidation of camphor ethylene dithioacetal

(1R,1′R,2S,4R)-1,7,7-Trimethylspiro[bicyclo[2.2.1]heptane-2,2′-[1,3]dithiolane] 1′-oxide, (1R,2S,3′R,4R)-1,7,7-trimethylspiro[bicyclo[2.2.1]heptane-2,2′-[1,3]dithiolane] 1′,1′,3′-trioxide, and (1R,4R)-1,7,7-trimethylspiro[bicyclo[2.2.1]heptane-2,2′-[1,3]dithiolane] 1′,1′,3′,3′-tetraoxide were synthesized by oxidation of camphor ethylene dithioacetal with m-chloroperoxybenzoic acid at different substrate-tooxidant ratios. The structure of the products was proved by IR and NMR spectroscopy and X-ray analysis.     

Studies of the interaction between daidzein and 3′-daidzein sulfonic sodium with bovine serum albumin by spectroscopic methods

The interaction between daidzein and 3′-daidzein sulfonic sodium with bovine serum albumin (BSA) in physiological buffer (pH = 7.4) is investigated by fluorescence quenching technique and UV/vis absorption spectra. The results reveal that both daidzein and 3′-daidzein sulfonic sodium could strongly quench the intrinsic fluorescence of BSA. The quenching mechanism of both the daidzein and 3′-daidzein sulfonic sodium for BSA is static quenching procedure. The apparent binding constants K _a and number of binding sites n of daidzein and 3′-daidzein sulfonic sodium with BSA are obtained by fluorescence quenching method. The thermodynamic parameters, enthalpy change (Δ_r H ^m ), and entropy change (Δ_r S ^m ), are calculated, respectively, which indicate that the interaction of daidzein with BSA is driven mainly by hydrogen bonding and van der Waals, and 3′-daidzein sulfonic sodium with BSA is driven mainly by hydrophobic forces. The distance r between BSA with daidzein and 3′-daidzein sulfonic sodium are calculated to be 4.02 nm and 3.08 nm, respectively, based on F?rster’s non-radiative energy transfer theory. The results of synchronous fluorescence spectra show that binding of daidzein and 3′-daidzein sulfonic sodium with BSA cannot induce conformational changes in BSA.     

A nanogold-quenched fluorescence duplex probe for homogeneous DNA detection based on strand displacement

A nanogold-quenched fluorescence duplex probe has been developed for lighting up homogenous hybridization assays. This novel probe is constructed from two strands of different lengths, and labeled by nanogold and a fluorophore at the long-strand 5′-end and the short-strand 3′-end, respectively. The two tags are in close contact, resulting in complete quenching of the probe fluorescence. If perfectly complemented to the nanogold-labeled strand, a long target oligonucleotide would displace the short fluorophore-labeled strand, and as a result, restore the fluorescence. By using nanogold in the probe, an extremely high quenching efficiency (99.1%) and removal of free fluorophore-labeled strand is achieved. The signal-to-noise ratio and the detection limit (50 pmol L⁻¹) of homogenous assays are therefore improved significantly, in comparison with similar probes using organic acceptors. Moreover, the probe has a great inhibition effect on hybridization to a mismatched oligonucleotide. This effect provides the assay with a high specificity, and particularly the assay has great potential in applications for discriminating variations in sequences. The assay sensitivity could be markedly enhanced by using fluorescent materials in the signal strand that are brighter and not quenched by nucleobases.     

Pyridoxal-5′-phosphate-dependent catalytic antibodies

Cofactors—i.e., metal ions and coenzymes—extend the catalytic scope of enzymes and might have been among the first biological catalysts. They may be expected to efficiently extend the catalytic potential of antibodies. Monoclonal antibodies (MAbs) against N^α-phosphopyridoxyl-l-lysine were screened for 1) binding of 5′-phosphopyridoxyl amino acids, 2) binding of the planar Schiff base of pyridoxal-5′-phosphate (PLP) and amino acids, the first intermediate of all PLP-dependent reactions, and 3), catalysis of the PLP-dependent α, β-elimination reaction with β-chloro-D/L-alanine. Antibody 15A9 fulfilled all criteria and was also found to catalyze the cofactor-dependent transamination reaction of hydrophobic D-amino acids and oxo acids (k′ _cat=0.42 min⁻¹ with D-alanine at 25°C). No other reactions with either D- or L-amino acids were detected. PLP markedly contributes to catalytic effecacy—it is a 10⁴ times more efficient acceptor of the amino group than pyruvate. The antibody ensures reaction specificity, stereospecificity, and substrate specificity, and further accelerates the transamination reaction (k′ _cat(Ab)/k′ _cat(PLP)=5×10³). The successive screening steps simulate the selection criteria that might have been operative in the evolution of protein-assisted psyridoxal catalysis.     

Suppression of MDR1 gene expression by chemically modified siRNAs

The ability of chemically modified siRNAs targeted to MDR1 mRNA to inhibit P-glycoprotein expression and to restore sensitivity of cancer cells to antibiotic vinblastine was investigated. The effects of chemical modifications on RNA stability in cell culture medium and inhibition of MDR1 gene expression were tested. We found that siRNAs containing 2′-O-methyl ribonucleotides within either sense or/and antisense strands display high stability in serum but exhibit a significant reduction in the biological activity. The protection of 3′-ends of siRNA by introduction of 3′-3′-inverted phosphodiester bonds and two 2′-O-methyl ribonucleotides in protruding 3′-ends considerably increase their biological activity, which allows a 30-fold decrease in the cytostatic agent concentration required for cancer cell death. The data obtained demonstrate that the chemically modified siRNAs can be considered as potential therapeutics, which enhances the efficiency of cancer chemotherapy. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1227–1235, July, 2006.     

Stereospecific analysis of flurbiprofen and its major metabolites in plasma and urine by chiral-phase liquid chromatography

Summary Direct chiral-phase HPLC methods have been developed for the determination of flurbiprofen and its major metabolites, namely 4′-hydroxyflurbiprofen and 3′-hydroxy-4′-methoxyflurbiprofen, in biological fluids using a derivatized amylose chiral stationary phase (CSP; Chiral-pak AD). Quantification of all three analytes, both free and conjugated, in urine was carried out following liquid-liquid extraction using tandem ultraviolet (UV) and fluorescence detection. Determination of flurbiprofen and the 4′-hydroxy-metabolite in plasma utilized the same CSP but required modification in the mobile phase composition and sole use of fluorescence detection. The urine assay was linear (r>0.998) between 0.05–10 μg mL⁻¹, 0.1–20 μg mL⁻¹ and 0.01–2 μg mL⁻¹ for the enantiomers of flurbiprofen, 4′-hydroxyflurbiprofen and 3′-hydroxy-4′-methoxyflurbiprofen respectively. The plasma assay was linear (r>0.997) between 0.1–6 μg mL⁻¹ and 0.01–0.6 μg mL⁻¹ for the enantiomers of flurbiprofen and 4′-hydroxyflurbiprofen respectively. Both assays, typically yielded within- and between-day imprecision and accuracy values less than 10% for the enantiomers of the different analytes. Initial volunteer studies suggest that the disposition of flurbiprofen displays modest enantioselectivity in humans.     

Reentrant behavior of poly(vinyl alcohol)–borax semidilute aqueous solutions

 The reentrant behavior of Poly(vinyl alcohol) (PVA)–borax aqueous semidilute solutions with a PVA concentration of 20 g/l and borax concentrations varies from 0.0 to 0.20 M was investigated using dynamic light scattering (DLS) and dynamic viscoelastic measurements. Two (fast and slow modes) and three (fast, middle, and slow) relaxation modes of PVA semidilute aqueous solutions without and with the presence of borax, respectively, were observed from DLS measurements. The fast and middle relaxation modes were q ²-dependent (q is the scattering vector) characteristic of diffusive behavior; however, the slow modes were q ³-dependent, characteristic of intraparticle dynamics. The experimental results showed that the slow relaxation mode dominates the DLS relaxation. The DLS slow mode relaxation time, τ_s, and the viscoelastic modulus G′(ω) and G′′(ω) data had a similar trend and demonstrated reentrant behavior as the borax concentration was increased from 0.0 to 0.20 M, i.e. τ_s, G′(ω), and G′′(ω) fluctuated with increasing borax concentration. The excluded-volume effect of polymers, charge repulsion among borate ions bound on PVA molecules, and intermolecular cross-linking didiol–borate complexation caused an expansion of the polymer chain; however, the screening effect of free Na⁺ ions on the negative charge of the borate ions bound on PVA and intramolecular cross-linking didiol–borate complexation led to a shrinkage of the polymer chain. The reentrant behavior was the consequence of the balance between expansion and shrinkage of the PVA–borate complex. Received: 26 March 1999/Accepted in revised form: 3 September 1999     

Five-membered 2,3-dioxo heterocycles: LXXVI. Reaction of methyl 1-aryl-3-benzoyl-4,5-dioxo-4,5-dihydro-1H-pyrrole-2-carboxylates with 6-amino-1,3-dimethylpyrimidine-2,4(1H,3H)-dione

Methyl 1-aryl-3-benzoyl-4,5-dioxo-4,5-dihydro-1H-pyrrole-2-carboxylates reacted with 6-amino-1,3-dimethylpyrimidine-2,4(1H,3H)-dione to give methyl 11-aryl-12-benzoyl-9-hydroxy-4,6-dimethyl-3,5,10-trioxo-4,6,8,11-tetraazatricyclo[7.2.1.0^2,7]dodec-2(7)-ene-1-carboxylates which underwent thermal recyclization to 1-aryl-3-benzoyl-4-hydroxy-1′,3′-dimethylspiro[pyrrole-2,5′-pyrrolo[2,3-d]pyrimidine]-2′,4′,5,6′(1H,1′H,3′H,7′H)-tetraones.     

A kinetic investigation into the rate of chloride substitution from chloro terpyridine platinum(II) and analogous complexes by a series of azole nucleophiles

The substitution kinetics of the complexes [Pt(terpy)Cl]Cl·2H₂O (PtL1), [Pt(^tBu₃terpy)Cl]ClO₄ (PtL2), [Pt{4′-(2′′′-CH₃-Ph)terpy}Cl]BF₄ (PtL3), [Pt{4′-(2′′′-CF₃-Ph)terpy}Cl]CF₃SO₃ (PtL4), [Pt{4′-(2′′′-CF₃-Ph)-6-Ph-bipy}Cl] (PtL5) and [Pt{4′-(2′′′-CH₃-Ph)-6-2′′-pyrazinyl-2,2′-bipy}Cl]CF₃SO₃ (PtL6) with the nucleophiles imidazole (Im), 1-methylimidazole (MIm), 1,2-dimethylimidazole (DIm), pyrazole (Pyz) and 1,2,4-triazole (Trz) were investigated in a methanolic solution of constant ionic strength. Substitution of the chloride ligand from the metal complexes by the nucleophiles was investigated as a function of nucleophile concentration and temperature under pseudo first-order conditions using UV/Visible and stopped-flow spectrophotometric techniques. The reactions follow the rate law k_\textobs = k₂ [ \textNu ] + k _{- 2} k_{\text{obs}} = k_{2} \left[ {\text{Nu}} \right] + k_{ - 2} . The results indicate that changing the nature or distance of influence of the substituents on the terpy moiety affects the π-back-donation ability of the chelate. This in turn controls the electrophilicity of the metal centre and hence its reactivity. Electron-donating groups decrease the reactivity of the metal centre, while electron-withdrawing groups increase the reactivity. Placing a strong σ-donor cis to the leaving group greatly decreases the reactivity of the complex, while the addition of a good π-acceptor group significantly enhances the reactivity. The results indicate that the metal is activated differently by changing the surrounding atoms even though they are part of a conjugated system. It is also evident that substituents in the cis position activate the metal centre differently to those in the trans position. The kinetic results are supported by DFT calculations, which show that the metal centre is less electrophilic when a strong σ-donor is cis to the leaving group and more electrophilic when a good π-acceptor group is part of the ring moiety. The temperature dependence studies support an associative mode of activation. An X-ray crystal structure of Pyz bound to PtL3 was obtained and confirmed the results of the DFT calculations as to the preferred N-atom as a binding site.     

Studies on the Synthesis and Thermodynamic Stability of Two Multidentate Ligands 2,9-disubstituted 1,10-phenanthroline

Two multidentate ligands: N,N′-di-(propionic acid-2′-yl-)-2,9-di-aminomethylphenanthroline (L₁) and N,N′-di-(3′-methylbutyric acid-2′-yl-)-2,9-di-amino-methylphenanthroline (L₂) were synthesized and fully characterized by ¹H NMR and elemental analysis. The binding ability of L₁ and L₂ to metal ions such as M(II) (M = Cu, Zn, Co and Ni) and Ln(III) (Ln = La, Nd, Sm, Eu, and Gd) has been investigated by potentiometric titration in aqueous solution and 0.1 mol dm⁻³KNO₃ at 25.0 ± °C. In view of the structure of L₁ and L₂, mononuclear metal complexes can be formed in solution. The stability constants of binary complexes of ligands L1 and L2 with metal ions M(II) and Ln(III) have been determined respectively and further discussed.     

Reaction of methyl 1-bromocyclopentane- and 1-bromocyclohexanecarboxylates with zinc and 2-arylmethylidene-2,3-dihydro-1<Emphasis Type="Italic">H</Emphasis>-inden-1-ones or 2-arylmethylidene-3,4-dihydronaphthalen-1(2<Emphasis Type="Italic">H</Emphasis>)-ones

Methyl 1-bromocyclopentanecarboxylate and methyl 1-bromocyclohexanecarboxylate reacted with zinc and 2-arylmethylidene-2,3-dihydro-1H-inden-1-ones or 2-arylmethylidene-3,4-dihydronaphthalen-1(2H)-ones to give 4′-aryl-4′,5′-dihydro-2′H-spiro[cyclopentane(cyclohexane)-1,3′-indeno[1,2-b]pyran]-2′-ones or 4-aryl-5,6-dihydrospiro[benzo[h]chromene-3,1′-cyclopentane(cyclohexane)]-2(4H)-ones, respectively.