Nucleobase-involved native chemical ligation: a novel reaction between an oxanine nucleobase and N-terminal cysteine for oligonucleotide-peptide conjugation

Aptamer-Guided, Hydrolysis-Resistant Deoxyoxanosine Enables Epitope- and Moiety-Selective Conjugation to Nonengineered Proteins Even in Complex Environments

In protein engineering, researchers have extensively explored the incorporation of nonprotein entities into proteins to extend their functionalities to various applications; however, achieving precise modifications of proteins is still challenging. This study demonstrates epitope- and moiety-selective conjugation of nonengineered proteins by integrating "slow-reactive and hydrolysis-resistant" deoxyoxanosine (dOxa) into a "target- and epitope-selective" aptamer. The amine-reactive dOxa-containing aptamers are dominantly single-lysine-selective at recognition sites, achieving significantly high conjugation yields with remarkably low off-target reactions in complex environments under near-physiological conditions through a catalyst-free, one-pot reaction. When stoichiometrically controlled protein-DNA conjugates are efficiently produced for various proteins, high conjugation selectivity enables semipermanent regulation of enzymatic functions, targeted labeling in a protein mixture, and even heterofunctionalization of a single protein. As our dOxa-containing aptamers selectively react with the recognition sites of target proteins among nontargets, we demonstrate bioorthogonal labeling of live-cell surface nucleolin and PTK7 in amine-rich cell media, displaying their distinct distributions. Aptamer-guided dOxa positioning offers a promising strategy for site-specific modification of native proteins in complex environments, opening new avenues for the synergistic collaboration between nucleic acids and proteins.

A unique reaction of diphenylcyclopropenone and 1,2-aminothiol with the release of thiol for multiple bioconjugation

Selective reaction of diphenylcyclopropenone (DPCP) and 1,2-aminothiol in water at pH 7.4 produces an amide conjugate with the release of thiol. In addition, structural modifications of DPCP enable the coupling rate to be tuned with a reaction constant of +3.68. Based on this chemistry, triple labelling was demonstrated by treating an N-terminal cysteine peptide with DPCP-Cl followed by thiol-maleimide and tyrosine-diazonium couplings in one pot. We anticipate that the DPCP motif will be a useful toolkit for multiple bioconjugation.

Oligodeoxynucleotides Modified with 2'-O-(Cysteinylaminobutyl)carbamoylethylribothymidine Residues for Native Chemical Ligation with Peptide at Internal Positions

We used native chemical ligation (NCL) to synthesize a 2'-O-{N-[N-(S-tert-butylthiocysteinyl)aminobutyl]carbamoylethyl} (CysBCE) ribothymidine-derived oligonucleotide to expand the variety of peptide conjugation sites, allowing the incorporation of peptides at the 2'-hydroxy group when the oligonucleotide forms a duplex with the complementary strand. The NCL reaction with a peptide thioester and the modified oligonucleotide proceeded smoothly even when the CysBCE modification was in the middle of the oligonucleotide sequence. In addition, we incorporated two CysBCEs into an oligonucleotide to conjugate two peptides to one oligonucleotide. The results indicated that the tandem NCL reactions proceeded efficiently when the oligonucleotide hybridized to the complementary strand to avoid intramolecular disulfide formation between the two CysBCE groups. This method could be useful for peptide conjugation on the 2'-position.

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.

Modular Synthesis of Trifunctional Peptide-oligonucleotide Conjugates via Native Chemical Ligation

Cell penetrating peptides (CPPs) are being increasingly used as efficient vectors for intracellular delivery of biologically active agents, such as therapeutic antisense oligonucleotides (ASOs). Unfortunately, ASOs have poor cell membrane permeability. The conjugation of ASOs to CPPs have been shown to significantly improve their cellular permeability and therapeutic efficacy. CPPs are often covalently conjugated to ASOs through a variety of chemical linkages. Most of the reported approaches for ligation of CPPs to ASOs relies on methodologies that forms non-native bond due to incompatibility with in-solution phase conjugation. These approaches have low efficiency and poor yields. Therefore, in this study, we have exploited native chemical ligation (NCL) as an efficient strategy for synthesizing CPP-ASO conjugates. A previously characterized CPP [ApoE(133-150)] was used to conjugate to a peptide nucleic acid (PNA) sequence targeting human survival motor neuron-2 (SMN2) mRNA which has been approved by the FDA for the treatment of spinal muscular atrophy. The synthesis of ApoE(133-150)-PNA conjugate using chemo-selective NCL was highly efficient and the conjugate was obtained in high yield. Toward synthesizing trifunctional CPP-ASO conjugates, we subsequently conjugated different functional moieties including a phosphorodiamidate morpholino oligonucleotide (PMO), an additional functional peptide or a fluorescent dye (Cy5) to the thiol that was generated after NCL. The in vitro analysis of the bifunctional CPP-PNA and trifunctional CPP-(PMO)-PNA, CPP-(peptide)-PNA and CPP-(Cy5)-PNA showed that all conjugates are cell-permeable and biologically active. Here we demonstrated chemo-selective NCL as a highly efficient and superior conjugation strategy to previously published methods for facile solution-phase synthesis of bi-/trifunctional CPP-ASO conjugates.

Exploring the Chemoselectivity towards Cysteine Arylation by Cyclometallated AuIII Compounds: New Mechanistic Insights

To gain more insight into the factors controlling efficient cysteine arylation by cyclometallated AuIII complexes, the reaction between selected gold compounds and different peptides was investigated by high-resolution liquid chromatography electrospray ionization mass spectrometry (HR-LC-ESI-MS). The deduced mechanisms of C-S cross-coupling, also supported by density functional theory (DFT) and quantum mechanics/molecular mechanics (QM/MM) calculations, evidenced the key role of secondary peptidic gold binding sites in favouring the process of reductive elimination.