Fluorescence and NMR studies of intramolecular stacking of mRNA cap-analogues.

Intramolecular stacking of a series of new synthesized dinucleotide mRNA cap analogues has been investigated in aqueous buffers by means of fluorescence and 1H-NMR at various pH and temperatures, and compared with that for 7-methylguanosine(5')ppp(5')guanosine (m7GpppG), as well as its hypermethylated derivative m(3)2,2,7GpppG. Thermodynamic parameters for intramolecular self-association stabilized by stacking were established by temperature-dependent fluorescence quenching, taking into account collisional deactivation of the excited states. Relative orientations of the stacked bases in the cap analogues were determined with the aid of a program GEOSHIFT (Stolarski et al., Biochim. Biophys. Acta (1996) 1293, 97), based on ring-current anisotropy. 1D-soft-TOCSY experiments were applied to extract the exact values of vicinal coupling constants, and hence to resolve solution conformation of the cap molecules. Stacking interaction has been discussed in detail in terms of the cap structural features, e.g., types of bases and length of the 5',5'-phosphate bridges, and regarding the interactions stabilizing intramolecular stacking.

1H-NMR studies on association of mRNA cap-analogues with tryptophan-containing peptides.

1H-NMR spectroscopy was applied to a study of the mode of interaction, in aqueous medium in the pH range 5.2-8.5 and at low and high temperatures, between several mono- and dinucleotide analogues of the mRNA cap m7GpppG and a selected tripeptide Trp-Leu-Glu, and a tetrapeptide Trp-Glu-Asp-Glu, the sequence of which corresponds to one of the suspected binding sites in the mRNA cap-binding protein (CBP). A program, GEOSHIFT, was developed, based on ring-current anisotropy theory, for analysis of experimentally observed changes in chemical shifts accompanying interactions between aromatic heterocyclic rings. This permitted quantitative evaluation of stacking interactions between the m7G cap and the tryptophan indole ring, and the relative orientations of the planes of the two rings, spaced about 3.2 angstroms apart. The structures of the stacked complexes were determined. In particular, stacking between m(2,2,7)3G (which has no free amino group for hydrogen bonding) and the indole ring is weaker and quite different from that between m7G and m(2,7)2G and indole. With the dinucleotide cap-analogues, only the m7G component stacks with the indole ring, without disruption of intramolecular stacking. In contrast to numerous earlier reports, the calculated stacking interactions are quantitatively in accord with the values derived from fluorescence measurements. It also has been shown that the positively charged (cationic) form of m7G stacks much more efficiently with the indole ring than the zwitterionic form resulting from dissociation of the guanine ring N1H (pKa approximately 7.3).

Crystal structure and solid-state NMR analysis of methyl 2,3,6-tri-O-acetyl-2-deoxy-2-[3-(2-phenylethyl)-ureido]-beta-D- glucopyranoside.

The X-ray diffraction analysis of methyl 2,3,6-tri-O-acetyl-2-deoxy-2-[3-(2-phenylethyl)-ureido]-beta-D- glucopyranoside has been performed, establishing that molecules are associated by two types of NH...O hydrogen bonds, N-1-H with carbonyl-oxygen and N-3-H with anomeric oxygen, with N...O distances 2.902 and 2.904 A, respectively. The urea moiety of the molecule is in anti Z,Z conformation. The signals in the 13C CP MAS NMR spectrum are neither multiplied nor split, indicating that there is one molecule in the crystal asymmetric unit. The difference in chemical shifts between solid- and liquid-state spectra are significant for C-2 and C-3 of D-glucose moiety (2.3-2.5 ppm) and for NCH2, CH2Ph carbon atoms.

Crystal structure and solid state 13C NMR analysis of N-(methyl 3,4,6-tri-O-acetyl-alpha, and beta-D-glucopyranosid-2-yl)-oxamide derivative of p-chloroaniline, N,N-diethylamine, N-methylaniline and N-ethylaniline.

The X-ray diffraction analysis of N-(methyl 3,4,6-tri-O-acetyl-alpha-D-glucopyranosid-2-yl)-N'-p-chlorophenyloxamide (1), N-(methyl 3,4,6-tri-O-acetyl-alpha-D-glucopyranosid-2-yl)-N',N'-diethyloxamide (2), N-acetyl, N-(methyl 3,4,6-tri-O-acetyl-beta-D-glucopyranosid-2-yl), N'-methyl, N'-phenyloxamide (3), N-acetyl, N-(methyl 3,4,6-tri-O-acetyl-beta-D-glucopyranosid-2-yl), N'-ethyl, N'-phenyloxamide (4) was performed. It was found that the oxamide group in compounds 1-4 can be characterized as two structurally independent amides because there is no pi conjugation across the oxalyl OC-CO bond. Only the oxamide group of 1 is planar and adopts trans conformation stabilized as two intramolecular N-H...O hydrogen bonds.

13C CP MAS NMR study of ureido sugars, derivatives of 2-amino-2-deoxy-beta-D-glucopyranose and dipeptides.

3C CP MAS NMR spectra of solid methyl 3,4,6-tri-O-acetyl-2-deoxy-2-ureido-beta-D-glucopyranosides with dipeptide residues (protected by OMe, OEt or OBz group) were recorded. Broader resonances enabled assignment of carbons linked to nitrogen. Chemical shifts of sugar carbons varied within 2-6 ppm although the acetylated glucose moiety is the same in all compounds. From the six carbonyl groups in the molecule only the resonances of N6-C5=O are shifted by 2.9-8.3 ppm downfield in the spectra of solid compounds, comparing to the solution, indicating that the molecules are linked by NH...O=C5 hydrogen bonds. The C2=O group of ureido bridge is not involved in H-bonding, ester group probably forms intramolecular H-bonds.

Use of hydrophilic diamines for bridging of two opioid peptide pharmacophores. Synthesis and receptor binding of two new analogues.

The bivalent ligand approach, which assumes that two pharmacophores are connected by a spacer, was used to design receptor type-selective ligands for opioid receptors. The first two opioid peptide bivalent ligands with different spacer lengths containing different numbers of hydroxyl groups, (Tyr-D-Ala-Gly-Phe-NH-CH2-CHOH-)2 (Tyr-D-Ala-Gly-Phe-NH-CH2-CHOH-CHOH-)2, were synthesized and their binding to mu, delta, and kappa opioid receptors was characterized. Both analogues were found to possess high opioid in vitro activities. The length of the hydrophilic spacer does not affect the affinity for delta receptors, whereas shorter spacer length increases affinity for mu and even more so for kappa receptors. Thus receptor type-selective peptides for opioid receptors can be designed using the bivalent approach.

Inhibition of eukaryotic translation by nucleoside 5'-monophosphate analogues of mRNA 5'-cap: changes in N7 substituent affect analogue activity.

Nucleotide cap analogues of 7-methylguanosine 5'-monophosphate (m7GMP) were synthesized in which the 7-methyl moiety was replaced with 7-ethyl (e7), 7-propyl (p7), 7-isopropyl (ip7), 7-butyl (b7), 7-isobutyl (ib7), 7-cyclopentyl (cp7), 7-(carboxymethyl) (cm7), 7-benzyl (bn7), 7-(2-phenylethyl) [7-(2-PhEt)], and 7-(1-phenylethyl) [7-(1-PhEt)]. These derivatives were assayed as competitive inhibitors of capped mRNA translation in reticulocyte lysate. We observed that N7 alkyl and alicyclic substituents larger than ethyl significantly decreased the inhibitory activity of these cap analogues presumably by decreasing their affinity for cap binding proteins, which participate in the initiation of translation. This result defined a maximum size for this class of N7 substituents in the nucleotide binding domain of cap binding proteins. Like m7GMP, the N7-substituted GMP derivatives synthesized in this study were found to be predominantly in the anti conformation as determined by proton NMR analyses. However, bn7GMP and 7-(2-PhEt)GMP, which have aromatic N7 substituents, were more effective than m7GMP as competitive inhibitors of translation. The increased affinity of bn7GMP for cap binding proteins was further examined by synthesis of beta-globin mRNA containing 5'-bn7G, 5'-m7G, or 5'-e7G cap structures. These modified mRNAs were tested as translation templates. Messenger RNA capped with bn7G was observed to increase the translation activity of the template 1.8-fold relative to that of its m7G-capped mRNA counterpart. By contrast, e7G-capped mRNA was 25% less active than m7G-capped mRNA.2+V photo-cross-linking of m7G-capped mRNA to cap binding proteins