Nucleobase Protection of Deoxyribo- and Ribonucleosides.

Oligonucleotides carrying a variety of chemical modifications including conjugates are finding increasing applications in therapeutics, diagnostics, functional genomics, proteomics, and as research tools in chemical and molecular biology. The successful synthesis of oligonucleotides primarily depends on the use of appropriately protected nucleoside building blocks including the exocyclic amino groups of the nucleobases, the hydroxyl groups at the 2'-, 3'-, and 5'-positions of the sugar moieties, and the internucleotide phospho-linkage. This unit is a thoroughly revised update of the previously published version and describes the recent development of various protecting groups that facilitate reliable oligonucleotide synthesis. In addition, various protecting groups for the imide/lactam function of thymine/uracil and guanine, respectively, are described to prevent irreversible nucleobase modifications that may occur in the presence of reagents used in oligonucleotide synthesis. © 2017 by John Wiley & Sons, Inc.

Chemical etiology of nucleic acid structure: the pentulofuranosyl oligonucleotide systems: the (1'→3')-ß-L-ribulo, (4'→3')-α-L-xylulo, and (1'→3')-α-L-xylulo nucleic acids.

Under potentially prebiotic scenarios, ribose (pentose), the component of RNA is formed in meager amounts, as opposed to ribulose and xylulose (pentuloses). Consequently, replacement of ribose in RNA, with pentulose sugars, gives rise to prospective oligonucleotide candidates that are potentially prebiotic structural variants of RNA that could be formed by the same type of chemical pathways that gave rise to RNA from ribose. The potentially natural alternative (1'→3')-ribulo oligonucleotides and (4'→3')- and (1'→3')-xylulo oligonucleotides consisting of adenine and thymine were synthesized and found to exhibit no self-pairing or cross-pairing with RNA. This signifies that even though pentulose sugars may have been abundant in a prebiotic scenario, the pentulose nucleic acids (NAs), if and when formed, would not have been competitors of RNA, or interfered with the emergence of RNA as a functional informational system. The reason for the lack of base pairing in pentulose NA highlights the contrasting and central role played by the furanosyl ring in RNA and pentulose NA, enabling and optimizing the base pairing in RNA, while impeding it in pentulose NA.

Exploratory experiments on the chemistry of the "glyoxylate scenario": formation of ketosugars from dihydroxyfumarate.

In the context of a "glyoxylate scenario" of primordial metabolism, the reactions of dihydroxyfumarate (DHF) with reactive small molecule aldehydes (e.g., glyoxylate, formaldehyde, glycolaldehyde, and glyceraldehyde) in water were investigated and shown to form dihydroxyacetone, tetrulose, and the two pentuloses, with almost quantitative conversion. The practically clean and selective formation of ketoses in these reactions, with no detectable admixture of aldoses, stands in stark contrast to the formose reaction, where a complex mixture of linear and branched aldoses and ketoses are produced. These results suggest that the reaction of DHF with aldehydes could constitute a reasonable pathway for the formation of carbohydrates and allow for alternative potential prebiotic scenarios to the formose reaction to be considered.

An expedient synthesis of L-ribulose and derivatives.

A significant improvement in the production of l-ribulose from inexpensive and commercially available starting materials, L-arabinose and sodium aluminate, is demonstrated. This has facilitated expeditious access to gram-scale quantities of L-ribulofuranoside derivatives.

Chemokine receptor CXCR3 promotes growth of glioma.

Human glioblastoma multiforme (GBM) is the most common primary brain tumor in adults. The poor prognosis and minimally successful treatments of GBM indicates a need to identify new therapeutic targets. In this study, we examined the role of CXCR3 in glioma progression using the GL261 murine model of malignant glioma. Intracranial GL261 tumors express CXCL9 and CXCL10 in vivo. Glioma-bearing CXCR3-deficient mice had significantly shorter median survival time and reduced numbers of tumor-infiltrated natural killer and natural killer T cells as compared with tumor-bearing wild-type (WT) mice. In contrast, pharmacological antagonism of CXCR3 with NBI-74330 prolonged median survival times of both tumor-bearing WT and CXCR3-deficient mice when compared with vehicle-treated groups. NBI-74330 treatment did not impact tumor infiltration of lymphocytes and microglia. A small percentage of GL261 cells were identified as CXCR3(+), which was similar to the expression of CXCR3 in several grade IV human glioma cell lines (A172, T98G, U87, U118 and U138). When cultured as gliomaspheres (GS), the human and murine lines increased CXCR3 expression; CXCR3 expression was also found in a primary human GBM-derived GS. Additionally, CXCR3 isoform A was expressed by all lines, whereas CXCR3-B was detected in T98G-, U118- and U138-GS cells. CXCL9 or CXCL10 induced in vitro glioma cell growth in GL261- and U87-GS as well as inhibited cell loss in U138-GS cells and this effect was antagonized by NBI-74330. The results suggest that CXCR3 antagonism exerts a direct anti-glioma effect and this receptor may be a potential therapeutic target for treating human GBM.

Efficient synthesis of peptides by extension at the N- and C-terminii of arginine.

L-N(omega)-nitroarginine and L-arginine were coupled with N-(Cbz-alpha-aminoacyl)benzotriazoles and N-Cbz-dipeptidoylbenzotriazoles to provide arginine LL-dipeptides 9a-e, 11a-d; LLL-tripeptides 18a-c, 20; and diastereomeric mixtures (9b+9b'), (9c+9c'), (11b+11b') and (18c+18c') [compound numbers written within parentheses represent a diastereomeric mixture or racemate; compound numbers without parentheses represent an achiral compound or a single enantiomer] by extension at the N-terminus of arginine, in isolated yields of 66-95% with complete retention of chirality as evidenced by NMR and HPLC analysis. Arginine LL-dipeptides 15a-d were synthesized by extension at the C-terminus of arginine in isolated yield of 66-80%, using benzotriazole activated arginine L-(omega)NO2-Arg-Bt, 13. Our methodology has also been used to synthesize the protected RGD peptide (Cbz(alpha)-L-(omega)NO2-Arg-Gly-L-Asp-(OH)2) 21.

Peptides by extension at the N- or C-terminii of lysine.

Dipeptides 3a-g, (3a + 3a'), (3d + 3d'), (3l + 3l')a and tripeptides 6a-e, (6b + 6b'), (6e + 6e') incorporating Z(epsilon)-Lys were prepared in high yields (70-95%) and enantiopurity (> or =97%) in partially aqueous acetonitrile solution by coupling using (i) Z(epsilon)-Lys with N-(Z- and Fmoc-aminoacyl)benzotriazoles 1a-g, (ii) Z(epsilon)-Lys with N-Z-dipeptidoylbenzotriazoles 5a-c, and (iii) N-Fmoc(alpha)-Z(epsilon)-l-Lys-Bt 1h and amino acids 2a,c-e. Unnatural dipeptides 3h-j, (3h + 3h') and tripeptides 6f were similarly prepared from Z(alpha)-Lys. Retention of chirality was demonstrated by parallel experiments involving l-Ala, dl-Ala, l-Met, and dl-Met by NMR and HPLC analysis.