Biomedical subjects

Pasi Virta

Publications and source records attributed to Pasi Virta.

6 recordsLinked to original sources

PubMed2006

Orthogonally protected cyclo-beta-tetrapeptides as solid-supported scaffolds for the synthesis of glycoclusters.

Two novel peptide scaffolds, viz. cyclo[(N(alpha)-Alloc)Dpr-beta-Ala-(N(alpha)-Fmoc)Dpr-beta-Ala] (1) and cyclo[(N(alpha)-Alloc)Dpr-alpha-azido-beta-aminopropanoyl-(N(alpha)-Fmoc)Dpr-beta-Ala] (2), composed of orthogonally protected 2,3-diaminopropanoyl (Dpr) and beta-alanyl residues, have been described. Fmoc chemistry on a backbone amide linker derivatized resin has been used for the chain assembly. Selective removal of the 4-methyltrityl (Mtt) and 1-methyl-1-phenylethyl protections (PhiPr) exposes the beta-amino and carboxyl terminus, respectively, and on-resin cyclization then gives the desired orthogonally protected cyclo-beta-tetrapeptides (1 and 2). The alpha-amino groups, bearing the Fmoc and Alloc protections and the azide mask, allow stepwise orthogonal derivatization of these solid-supported cyclo-beta-tetrapeptide cores (1 and 2). This has been demonstrated by attachments of various sugar units [viz., acetyl- or toluoyl-protected carboxymethyl alpha-d-glycopyranosides (13-15) and methyl 6-O-(4-nitrophenoxycarbonyl)-alpha-d-glycopyranosides (22-24)] to obtain diverse di- and trivalent glycoclusters (33-42). Acidolytic release (TFA) from the support, followed by conventional NaOMe-catalyzed transesterification (33-40) or hydrazine-induced acyl substitution in DMF (41 and 42), gives the fully deprotected clusters (43-52) as final products.

Glycosides↗

PubMed2004

Pentaerythrityltetramine scaffolds for solid-phase combinatorial chemistry.

Straightforward synthesis for two pentaerythrityltetramine precursors, 2,2-bis(azidomethyl)propane-1,3-diamine (1) and 2-[N-(allyloxycarbonyl)aminomethyl]-2-azidomethylpropane-1,3-diamine (2), has been described. Both propane-1,3-diamines have been attached by reductive amination to a solid-supported backbone amide linker derived from 4-(4-formyl-3,5-dimethoxyphenoxy)butyric acid. The presence of the two methoxy substituents on the linker is essential to avoid cross-linking between two linkers. The remaining free primary amino group of the propane-1,3-diamine moiety may then be selectively acylated with an appropriately protected amino acid using conventional N,N-dicyclohexylcarbodiimide/1-hydroxybenzotriazole (DCC/HOBt) activation without any interference by the secondary amino function. The latter group may be subsequently acylated by an anhydride method. Sequential reduction of the azido group and removal of the allyloxycarbonyl protection from 2 allow further coupling of two different amino acids, and hence, this handle may be utilized in construction of branched structures containing four different amino acids or peptides. Solid-supported 1 may, in turn, be used for the synthesis of similar constructs containing two identical branches. It is worth noting that no acid-labile protecting groups are required in this approach, and hence, this dimension may be saved for the cleavage of the linker. The applicability of the scaffolds to library synthesis has been demonstrated by preparation of 11 pentaerythrityl-branched tetra- and octapeptides.

Amines↗

PubMed2003

Solid-supported synthesis of cryptand-like macrobicyclic peptides.

A straightforward method for the solid-supported synthesis of cryptand-like bicyclic peptides (1-5) on a backbone amide linker has been described. For the branching, two novel easily available building blocks, viz. N-(4-methoxytrityl)-N-(2-nitrobenzenesulfonyl)-protected N,N-bis(2-aminoethyl)-beta-alanine (6) and N-(9-fluorenylmethoxycarbonyl) protected iminodiacetic acid monoallyl ester (7), have been employed. The key steps of the synthesis are as follows: (i) stepwise coupling of one amino acid and 6 to the secondary amino group of the linker; (ii) removal of the 2-nitrobenzenesulfonyl group and SPPS by the Fmoc chemistry, using 7 as the penultimate and tert-butoxycarbonyl (Boc) protected glycine as the last amino acid; (iii) removal of the 4-methoxytrityl protection and subsequent SPPS by the Fmoc chemistry; (iv) removal of the allyl and Fmoc groups, followed by cyclization; and (v) removal of the Boc and tert-butyl groups, followed by cyclization. Final cleavage from the support and removal of benzyl-derived protecting groups gives the desired bicyclic products.

Amides↗

PubMedDate not supplied

Preparation of azacrown-functionalized 2'-O-methyl oligoribonucleotides, potential artificial RNases.

An improved synthesis for 3-(3-aminopropyl)- and 3-(3-mercaptopropyl)-1,5,9-triazacyclododecane has been developed and alternative methods for their conjugation to oligonucleotides have been described. Accordingly, the 3-aminopropyl azacrown and its N-(3-aminopropanoyl)-3-aminopropyl analogue have been tethered to the 3'-terminus of a 2'-O-methyloligoribonucleotide by aminolytic cleavage of the thioester linker utilized for the chain assembly. Studies on a monomeric model compound verify that the reaction proceeds solely by the attack of the primary amino group. 5'-Conjugation has been achieved by introducing a 2-benzylthio-2-oxoethyl group to the 5'-terminus as a phosphoramidite reagent and cleaving the thioester bond with the 3-aminopropyl azacrown. For intrachain conjugation, a phosphoramidite reagent derived from 1-deoxy-1-(2-benzylthio-2-oxoethyl)-beta-d-erythro-pentofuranose has been inserted in a desired position within the chain and subjected to on-support aminolysis with the 3-aminopropyl azacrown or its N-(3-aminopropanoyl)-3-aminopropyl and N-(6-aminohexanoyl)-3-aminopropyl analogues. The 3-mercaptopropyl-derivatized azacrown has been tetherd by a disulfide bond to a 3'-(3-mercaptoalkyl)phosphate-tailed oligonucleotide. The 3'- and intrachain-tethered conjugates have been shown to cleave as their Zn(II) chelate complementary oligoribonucleotide sequences.

Disulfides↗

PubMedDate not supplied

Solid-phase synthesis of multiantennary oligonucleotide glycoconjugates utilizing on-support oximation.

A novel method for preparation of multivalent oligonucleotide glycoconjugates on a solid support has been described. A pentaerythritol-based phosphoramidite (1) bearing two masked aminooxy groups has been used as the key building block. After conventional chain assembly, the aminooxy functions have been deblocked by a hydrazinium acetate treatment and subsequently oximated with fully acetylated 4-oxobutyl alpha-D-mannopyranoside. The conjugates obtained have been shown to withstand standard ammonolytic deprotection and cleavage from the support. Four different oligonucleotide glycoconjugates containing two, four, or six alpha-D-mannopyranosyl units (12-15) have been prepared to demonstrate the applicability of the procedure. The glycosyl residues only moderately retards hybridization of the oligonucleotide moiety.

Chromatography, High Pressure Liquid↗

PubMedDate not supplied

2,2-Bis(ethoxycarbonyl)- and 2-(alkylaminocarbonyl)-2-cyano-substituted 3-(pivaloyloxy)propyl groups as biodegradable phosphate protections of oligonucleotides.

Oligonucleotides bearing biodegradable phosphate protecting groups have been synthesized on a solid support. For this purpose, two dimeric building blocks, viz. 5'-O-(4,4'-dimethoxytrityl)-(R(P),S(P))-O(P)-[2,2-bis(ethoxycarbonyl)-3-(pivaloyloxy)propyl]-P-thiothymidylyl-(3',5')-thymidine 3'-[O-(2-cyanoethyl)-N,N-diisopropylphosphoramidite] (1) and 5'-O-(4,4'-dimethoxytrityl)-(R(P),S(P))-O(P)-[2-cyano-2-(2-phenylethylaminocarbonyl)-3-(pivaloyloxy)propyl]thymidylyl-(3',5')-thymidine 3'-(H-phosphonate) (2), were prepared. Phosphoramidite 1 was incorporated into an phosphorothioate oligothymidylate sequence on a base-labile hydroquinone-O,O'-diacetic acid linker (Q-linker) and on a photolabile 4-alkoxy-5-methoxy-2-nitrobenzyl carbonate linker (11). H-Phosphonate 2 was, in turn, incorporated into an oligothymidylate sequence only on the photolabile linker. Kinetics of the removal of the protecting groups by porcine liver esterase and subsequent retro aldol condensation/phosphate elimination were then studied. While the pro-oligonucleotide that contained only one phosphate protection gave the deprotected phosphorothioate oligonucleotide in a quantitative yield, the enzymatic step was markedly decelerated upon increasing the number of protection groups, and hence chain cleavage started to compete.

Biodegradation, Environmental↗