Solid-phase synthesis of a nucleopeptide from the linking site of adenovirus-2 nucleoprotein, -Ser(p5'CATCAT)-Gly-Asp-. Convergent versus stepwise strategy

Chemistry of Peptide-Oligonucleotide Conjugates: A Review

Peptide-oligonucleotide conjugates (POCs) represent one of the increasingly successful albeit costly approaches to increasing the cellular uptake, tissue delivery, bioavailability, and, thus, overall efficiency of therapeutic nucleic acids, such as, antisense oligonucleotides and small interfering RNAs. This review puts the subject of chemical synthesis of POCs into the wider context of therapeutic oligonucleotides and the problem of nucleic acid drug delivery, cell-penetrating peptide structural types, the mechanisms of their intracellular transport, and the ways of application, which include the formation of non-covalent complexes with oligonucleotides (peptide additives) or covalent conjugation. The main strategies for the synthesis of POCs are viewed in detail, which are conceptually divided into (a) the stepwise solid-phase synthesis approach and (b) post-synthetic conjugation either in solution or on the solid phase, especially by means of various click chemistries. The relative advantages and disadvantages of both strategies are discussed and compared.

Fully automated sequential solid phase approach towards viral RNA-nucleopeptides

The synthesis of two ribonucleoprotein fragments of unprecedented complexity is reported. These hybrid biomolecules are prepared combining the use of an automated solid phase peptide and oligonucleotide synthesizer on a single solid support.

Solid-phase synthesis of oligonucleotide conjugates useful for delivery and targeting of potential nucleic acid therapeutics

Olignucleotide-based drugs show promise as a novel form of chemotherapy. Among the hurdles that have to be overcome on the way of applicable nucleic acid therapeutics, inefficient cellular uptake and subsequent release from endosomes to cytoplasm appear to be the most severe ones. Covalent conjugation of oligonucleotides to molecules that expectedly facilitate the internalization, targets the conjugate to a specific cell-type or improves the parmacokinetics offers a possible way to combat against these shortcomings. Since workable chemistry is a prerequisite for biological studies, development of efficient and reproducible methods for preparation of various types of oligonucleotide conjugates has become a subject of considerable importance. The present review summarizes the advances made in the solid-supported synthesis of oligonucleotide conjugates aimed at facilitating the delivery and targeting of nucleic acid drugs.

Stepwise solid-phase synthesis of nucleopeptides

Phosphodiester-linked peptide-oligonucleotide conjugates (nucleopeptides) are obtained by stepwise solid-phase procedures. The peptide is first assembled on a suitably derivatized solid matrix and the oligonucleotide is subsequently elongated at the free hydroxyl group of the linking amino acid. Temporary acid-labile and permanent base-labile protecting groups are combined. Careful choice of the protection scheme is required to prevent and minimize side reactions that may degrade the target molecule.

Synthesis of peptide-oligonucleotide phosphorothioate conjugates by convergent or stepwise solid-phase strategies

A convergent strategy was employed to link eight 10-27-mer peptides to oligonucleotide phosphorothioates, resulting in twenty-six various conjugates. A stepwise synthesis strategy for the preparation of peptide-oligonucleotide phosphorothioate conjugates, employing Fmoc peptide chemistry, was developed and applied to the synthesis of four conjugates. Three of these conjugates contained either a 10 or 16-mer peptide, incorporating either 2 or 3 arginine residues, respectively.

A facile synthesis of 5'-end solid-anchored, 3'-end free oligodeoxyribonucleotides via the (5'-->3')-elongated phosphoramidite strategy

It is demonstrated that not only N2- but also O6-protection of the guanine base is necessary for obtaining the oligodeoxyribonucleotides in high yields and at a high purity in the solid-phase synthesis via the (5'--> 3')-chain elongated phosphoramidite approach.

Synthesis and properties of aminoacylamido-AMP: chemical optimization for the construction of an N-acyl phosphoramidate linkage

This paper describes the design and synthesis of a new type of aminoacyl-adenylate analogue (aa-AMPN) having an N-acyl phosphoramidate linkage where the oxygen atom of the mixed anhydride bond of aminoacyl-adenylate (aa-AMP) is replaced by an amino group. This new type of aa-AMP analogue is expected to be useful as material for studies on the recognition mechanism of the aminoacylation of tRNA and other biochemical reactions. The condensation of phosphoramidite derivatives of carboxamides with nucleoside derivatives failed, because the activated phosphoramidite derivatives reacted with not only the hydroxyl groups but also another reactive species. An alternative approach was examined by the reaction of 5'-O-phosphoramidite adenosine derivatives with carboxamide derivatives. The TBTr and TSE groups were chosen for protection of the amino group of amino acid amides and the phosphate group, respectively. Detailed studies revealed that the use of 5-(3,5-dinitrophenyl)-1H-tetrazole as an activating catalyst of phosphoramidites resulted in rapid condensation within 10 min to give fully protected aa-AMPN derivatives. No side reaction occurred. Deprotection of these products via a two-step procedure gave aa-AMPN derivatives in good yields. It also turned out that aa-AMPNs thus obtained are stable under both acidic and basic conditions, such as 0.1 M HCl (pH 1.0) and 0.1 M NaOH (pH 13.0).

Solid-phase synthesis of cyclic peptide-DNA hybrids

[reaction: see text] A methodology for preparing cyclic peptide-DNA hybrids on controlled pore glass in high yield is reported. This methodology employs Fmoc/Alloc-protected amino acid and nucleoside phosphoramidites on an omega-hydroxylauric acid-derivatized support and is suitable for library synthesis. A cyclic hybrid of the sequence Glu-Leu-TT-DP-Lys, where Glu and Lys are linked and T denotes a 5'-amino-5'-deoxynucleotide, exhibited high resistance to exo- and endonucleases.

Synthesis of 3',5'-Dipeptidyl Oligonucleotides

Peptide-DNA hybrids are richly functionalized analogues of biomolecules that may have applications as hybridization probes and antisense agents with tunable binding and targeting properties. So far, synthetic efforts have mainly focused on hybrids bearing a single peptide chain, either at the 5'- or the 3'-terminus. Such singly modified analogues are vulnerable to nuclease attack at the unmodified terminus. Here we report a convenient and high-yielding solid-phase synthesis of 3'- and 5'-modified analogues of DNA with aminoacyl and peptidyl appendages at both termini. Using MALDI-TOF mass spectra of crude products as the criterion, serine, glycolic acid, hydroxylauric acid, and dimethyl hydroxypropionic acid were tested as 3'-linker residues. The latter, together with a direct amide link at the 5'-terminus, gave the highest yields of hybrids. The optimized procedure assembles hybrids on a controlled pore glass support bearing three consecutive omega-hydroxy lauric acid linkers. This support greatly reduces side reactions observed with conventional supports, probably due to its ability to increase steric accessibility during coupling ("swelling") and its rapid hydrolysis during deprotection with ammonium hydroxide. Dihybrids with aromatic, basic, and acidic amino acid residues were prepared, including H-Phe-Gly-TGCGCA-DP-Phe-OH, where DP denotes the dimethyl hydroxypropionic acid linker, whose structure was confirmed via mass spectrometry and one- and two-dimensional NMR. Further, a mixed coupling with seven Fmoc-protected amino acids was shown to produce a combinatorial library of dipeptidyl DNA hybrids.

5'-Peptidyl substituents allow a tuning of the affinity of oligodeoxyribonucleotides for RNA

The affinity of amide-linked 5'-aminoacyl and 5'-dipeptidyl DNA octamers for two RNA undecamers with 3'-overhangs was measured via UV melting analysis. A sequence-dependent increase in melting points was observed. At low ionic strength, two appended lysine residues elevate melting points more than two additional A:U base pairs.