Conjugation of Oligonucleotides to Peptide Aldehydes via a pH-Responsive <i>N</i>-Methoxyoxazolidine Linker

Aho, Aapo; Sulkanen, Mika; Korhonen, Heidi; Virta, Pasi

doi:10.1021/acs.orglett.0c01815

Cited by 9 publications

(11 citation statements)

References 44 publications

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“…The hydrolysis rate of the conjugates (i.e., reverse ligation) was studied at pH 4, 5, 6, and 7.4. The N-(methoxy)oxazolidine linker, bound to the β-Ala-H residue, clearly cleaved faster in acidic conditions (pH 4-6) than the previously studied Gly-H-based conjugates [37]. The cleavage was comparable to most hydrazone linkers, and the conjugates maintained their hydrolytic stability in physiological conditions (pH 7.4).…”

Section: Introductionmentioning

confidence: 75%

“…Four oligonucleotides elongated by U NOMe (AON-ISE-AR-V7-U NOMe (ON1), Nusinersen-U NOMe (ON2), IONIS-DGAT2 RX -U NOMe (ON3), and TfRA3-U NOMe (ON4) (Scheme 1a) were next synthesized using previously prepared solid support 2 [37], commercial phosphoramidite building blocks, and automated chain assembly. AON-ISE-AR-V7 suppresses prostate tumor cell survival by the inhibition of androgen receptor variant 7 mRNA synthesis [38], Nusinersen is an approved drug used for treating spinal muscular athropy [39], and IONIS-DGAT2 RX ASO reduces DGAT2 enzyme production and is a potential treatment for nonalcoholic steatohepatitis [40,41].…”

Section: Synthesis Of 2 -Deoxy -2 -(N-methoxyamino)uridine-modified Oligonucleotidesmentioning

confidence: 99%

“…Recently, the reversible formation of N-(methoxy)oxazolidine (Figure 1) was employed in conjugation between 2′-deoxy-2′-(N-methoxyamino)uridine (U NOMe , Scheme 1a)-modified ONs and Gly-H-modified peptide aldehydes [37]. The U NOMe -ONs and peptide aldehydes were both synthesized by automated assembly using appropriately modified solid supports.…”

Section: Introductionmentioning

confidence: 99%

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Expanding the Scope of the Cleavable N-(Methoxy)oxazolidine Linker for the Synthesis of Oligonucleotide Conjugates

et al. 2021

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Oligonucleotides modified by a 2′-deoxy-2′-(N-methoxyamino) ribonucleotide react readily with aldehydes in slightly acidic conditions to yield the corresponding N-(methoxy)oxazolidine-linked oligonucleotide-conjugates. The reaction is reversible and dynamic in slightly acidic conditions, while the products are virtually stable above pH 7, where the reaction is in a ‘‘switched off-state’’. Small molecular examinations have demonstrated that aldehyde constituents affect the cleavage rate of the N-(methoxy)oxazolidine-linkage. This can be utilized to adjust the stability of this pH-responsive cleavable linker for drug delivery applications. In the present study, Fmoc-β-Ala-H was immobilized to a serine-modified ChemMatrix resin and used for the automated assembly of two peptidealdehydes and one aldehyde-modified peptide nucleic acid (PNA). In addition, a triantennary N-acetyl-d-galactosamine-cluster with a β-Ala-H unit has been synthesized. These aldehydes were conjugated via N-(methoxy)oxazolidine-linkage to therapeutically relevant oligonucleotide phosphorothioates and one DNA-aptamer in 19–47% isolated yields. The cleavage rates of the conjugates were studied in slightly acidic conditions. In addition to the diverse set of conjugates synthesized, these experiments and a comparison to published data demonstrate that the simple conversion of Gly-H to β-Ala-H residue resulted in a faster cleavage of the N-(methoxy)oxazolidine-linker at pH 5, being comparable (T0.5 ca 7 h) to hydrazone-based structures.

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Section: Introductionmentioning

confidence: 75%

Section: Synthesis Of 2 -Deoxy -2 -(N-methoxyamino)uridine-modified Oligonucleotidesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Expanding the Scope of the Cleavable N-(Methoxy)oxazolidine Linker for the Synthesis of Oligonucleotide Conjugates

et al. 2021

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“…Over this narrow range, the reaction was nearly firstorder in hydronium ion, consistent with previous reports on Nmethoxyoxazolidines. [37][38][39] Modest upward curvature could, however, be seen at the higher end of the pH range, suggesting a minor contribution by a pH-independent pathway. Rate constants of these partial reactions were obtained by non-linear least-squares fitting of the experimental data to Equation 3.…”

Section: Kinetic Analysis Of Acid-catalyzed N-methoxy-13-oxazinane Hy...mentioning

confidence: 94%

Improved Synthesis Strategy for N‐Methoxy‐1,3‐oxazinane Nucleic Acids (MOANAs)

Wallin

Lönnberg

2022

Eur J Org Chem

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Dependence of the hydrolysis rate of a series of N-methoxy-2phenyl-1,3-oxazinanes on the Hammett substituent constant of the substituent of the phenyl ring was determined, yielding a reaction constant 1 = À 1.40 � 0.05. Based on this information, 4-(benzoyloxy)benzaldehyde was selected as a protecting group for a new (2R,3S)-4-(methoxyamino)butane-1,2,3-triol phosphoramidite building block. The yield of the preparation of this building block as well as its coupling in automated oligonucleotide synthesis were greatly improved compared to the method reported previously. The 2-[4-(benzoyloxy)phenyl]-1,3-oxazine protection persisted throughout the synthesis of short oligonucleotides but was rapidly removed when the oligonucleotides were released from solid support and dissolved in water.

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“…An elegant method of obtaining 2′-conjugates via N -methoxyoxazolidine formation was developed recently [ 290 ]. Unusually, this approach employed a peptide with an aldehyde group for conjugation to an oligonucleotide containing a 2′- N -methoxyamino group and a free 3′-OH.…”

Section: Post-synthetic Conjugation Approachesmentioning

confidence: 99%

Chemistry of Peptide-Oligonucleotide Conjugates: A Review

2021

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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.

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Conjugation of Oligonucleotides to Peptide Aldehydes via a pH-Responsive N-Methoxyoxazolidine Linker

Cited by 9 publications

References 44 publications

Expanding the Scope of the Cleavable N-(Methoxy)oxazolidine Linker for the Synthesis of Oligonucleotide Conjugates

Expanding the Scope of the Cleavable N-(Methoxy)oxazolidine Linker for the Synthesis of Oligonucleotide Conjugates

Improved Synthesis Strategy for N‐Methoxy‐1,3‐oxazinane Nucleic Acids (MOANAs)

Chemistry of Peptide-Oligonucleotide Conjugates: A Review

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