RNA oligomers at atomic resolution containing 1-methylpseudouridine, an essential building block of mRNA vaccines.

All widely used mRNA vaccines against COVID-19 contain in their sequence 1-methylpseudouridine (m1Ψ) instead of uridine. In this publication, we report two high resolution crystal structures (at up to 1.01 and 1.32 Å, respectively) of one such double-stranded 12-mer RNA sequence crystallized in two crystal forms. The structures are compared with similar structures which do not contain this modification. Additionally, the X-ray structure of 1-methyl-pseudouridine itself was determined.

Synthesis of eight stereoisomers of pochonicine: nanomolar inhibition of ß-N-acetylhexosaminidases.

Pochonicine, the first naturally occurring polyhydroxylated pyrrolizidine containing an acetamidomethyl group, which was isolated from Pochonia suchlasporia var. suchlasporia TAMA 87, together with its enantiomer and their C-1 and/or C-3 epimers, have been synthesized from the sugar-derived cyclic nitrones 9D and 9L, respectively. An in-depth NMR study showed that both the (1)H and (13)C NMR spectra of the synthetic pochonicines (1D and 1L) matched very well with those of natural pochonicine in D2O, which unequivocally determined the relative configuration of the natural product as 1D or 1L. In addition, comparison of the optical rotations of the synthetic pochonicines and that of the natural product, but more convincingly their glycosidase inhibition profiles, confirmed the absolute configuration of natural pochonicine as 1R,3S,5R,6R,7S,7aR. Thereby, the structure of natural pochonicine was unequivocally determined as (+)-(1R,3S,5R,6R,7S,7aR)-pochonicine (1D). Glycosidase inhibition experiments showed that natural pochonicine 1D and its epimers 2D, 3D, and 4D all are powerful inhibitors of hexosaminidases (five ß-N-acetylglucosaminidases and two ß-N-acetylgalactosaminidases) while their enantiomers 1L, 2L, 3L, and 4L are much weaker inhibitors of the same enzymes. (-)-3-epi-Pochonicine (2L) was found to be a potent and selective inhibitor of α-l-rhamnosidase. None of the compounds showed any inhibition of α-GalNAcase.

Steviamine, a new class of indolizidine alkaloid [(1R,2S,3R,5R,8aR)-3-hydroxy-meth-yl-5-methyl-octa-hydro-indolizine-1,2-diol hydro-bromide].

X-ray crystallographic analysis of the title hydro-bromide salt, C(10)H(20)N(+)·Br(-), of (1R,2S,3R,5R,8aR)-3-hydroxy-meth-yl-5-methyl-octa-hydro-indolizine-1,2-diol defines the absolute and relative stereochemistry at the five chiral centres in steviamine, a new class of polyhydroxy-lated indolizidine alkaloid isolated from Stevia rebaudiana (Asteraceae) leaves. In the crystal structure, mol-ecules are linked by inter-molecular O-H⋯Br and N-H⋯Br hydrogen bonds, forming double chains around the twofold screw axes along the b-axis direction. Intra-molecular O-H⋯O inter-actions occur.

Contrasting reactivity of thioglucoside and selenoglucoside donors towards promoters: implications for glycosylation stereocontrol.

The stereochemical outcome of glycosylation reactions with model thioglycosides and selenoglycosides proved to be dependent on the source of promoter iodonium ion, with iodine giving different results to N-iodosuccinimide (NIS) alone or N-iodosuccinimide/trimethylsilyltrifluoromethanesulfonate (NIS/TMSOTf). In contrast to armed thioglycosides, which anomerise, and disarmed thioglycosides, which do not react, both armed and disarmed selenoglycosides give rise to the corresponding glycosyl iodides when reacted with iodine. Further, whilst the single electron transfer agent DDQ alone is an ineffective promoter, in combination with iodine it produces better acetonitrile-assisted beta-stereoselectivity with both thioglycosides and selenoglycosides than does tris(4-bromophenyl)aminium hexachloroantimonate (BAHA).

Synthesis of fully substituted polyhydroxylated pyrrolizidines via Cope-House cyclization.

Total synthesis of the proposed structure of (-)-hyacinthacine C(5) and its epimers at C6 and C7 is described. A key step of the synthesis was the construction of the bicyclic pyrrolizidine system by means of a nucleophilic addition of a dithiane to a cyclic nitrone followed by a Cope-House cyclization.

Discovery of 2-arylbenzoxazoles as upregulators of utrophin production for the treatment of Duchenne muscular dystrophy.

A series of novel 2-arylbenzoxazoles that upregulate the production of utrophin in murine H2K cells, as assessed using a luciferase reporter linked assay, have been identified. This compound class appears to hold considerable promise as a potential treatment for Duchenne muscular dystrophy. Following the delineation of structure-activity relationships in the series, a number of potent upregulators were identified, and preliminary ADME evaluation is described. These studies have resulted in the identification of 1, a compound that has been progressed to clinical trials.

Synthesis and glycosidase inhibition of the enantiomer of (-)-steviamine, the first example of a new class of indolizidine alkaloid.

(+)-Steviamine, the enantiomer of the natural (-)-steviamine, and its corresponding C5 epimer have been synthesized from the D-ribose-derived cyclic nitrone. (-)-Steviamine was found to be the first naturally occurring iminosugar that causes any inhibition of alpha-galactosaminidases.

From solution phase to "on-column" chemistry: trichloroacetimidate-based glycosylation promoted by perchloric acid-silica.

[reaction: see text] Activation of ester-protected glycosyl trichloroacetimidate donors by perchloric acid immobilized on silica afforded 1,2-trans disaccharides in 60-90% yields. Applying this approach to one-pot sequential glycosylation resulted in efficient syntheses of the N-linked glycan trimannoside and Le(X) and Le(A) trisaccharides in very good yield (76%, 62%, and 59% yields, respectively). Solution phase reactions were also translated to a solid phase format; priming the top of a standard silica chromatography column with perchloric acid immobilized on silica facilitated "on-column" glycosylation with subsequent "in situ" purification of products. Coupling yields from this approach were comparable to those obtained from the corresponding solution-phase disaccharide couplings. A series of glycosylated amino acids were also synthesized in high yield with use of the on-column approach.

Solid-phase synthesis of cyclic RGD-furanoid sugar amino acid peptides as integrin inhibitors.

The solid-phase synthesis of cyclic RGD peptides containing either one or two furanoid sugar amino acids (SAAs) is reported. Using a cyclization-cleavage approach five peptides were successfully assembled and consecutively tested on their ability to bind to the integrin receptors alpha(v)beta(3) and alpha(IIb)beta(3). The cyclic tetrapeptide c[RGD-SAA] (1) showed the most promising activity in an inhibition assay with an IC(50) of 1.49 microM for the alpha(v)beta(3) receptor and 384 nM for the alpha(IIb)beta(3) receptor.

Conformational analysis of furanoid epsilon-sugar amino acid containing cyclic peptides by NMR spectroscopy, molecular dynamics simulation, and X-ray crystallography: evidence for a novel turn structure.

Sugar amino acids (SAAs) are useful building blocks for the design of peptidomimetics and peptide scaffolds. The three-dimensional structures of cyclic hybrid molecules containing the furanoid epsilon-SAA III and several amino acids were elucidated to study the preferred conformation of such an epsilon-SAA and its conformational influence on the backbone of cyclic peptides. NMR-based molecular dynamics simulations and empirical calculations of the cyclic tetramer 1, consisting of two copies of the SAA residue and two amino acids, revealed that it is conformationally restrained. The two SAA residues adopt different conformations. One of them forms an unusual turn, stabilized by an intraresidue nine-member hydrogen bond. The methylene functionalities of the other SAA residue are positioned in such a way that an intraresidue H bond is not possible. The X-ray crystal structure of 1 strongly resembles the solution conformation. Molecular dynamics calculations in combination with NMR analysis were also performed for compounds 2 and 3, which contain the RGD (Arg-Gly-Asp) consensus sequence and were previously shown to inhibit alpha(IIb)beta(3)-receptor-mediated platelet aggregation. The biologically most active compound 2 adopts a preferred conformation with the single SAA residue folded into the nine-member H bond-containing turn. Compound 3, containing an additional valine residue, as compared with compound 2, is conformational flexible. Our studies demonstrate that the furanoid epsilon-SAA III is able to introduce an unusual intraresidue hydrogen bond-stabilized beta-turn-like conformation in two of the three cyclic structures.

A practical synthesis of gramicidin s and sugar amino Acid containing analogues.

A practical gram-scale and high-yielding synthesis of the antimicrobial peptide gramicidin S is presented. An Fmoc-based solid-phase peptide synthesis protocol is employed for the generation of the linear decapeptide precursor, which is cyclized in solution to afford the target compound. The versatility of our method is demonstrated by the construction of eight gramicidin S analogues (15a-h) having nonproteinogenic sugar amino acid residues (4-7) incorporated in the turn regions.