From green innovations in oligopeptide to oligonucleotide sustainable synthesis: differences and synergies in TIDES chemistry

Ferrazzano, Lucia; Corbisiero, Dario; Tolomelli, Alessandra; Cabri, Walter

doi:10.1039/d2gc04547h

Cited by 12 publications

(6 citation statements)

References 84 publications

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“…26 In fact, in the widely used Fmoc/t-Bu variant 27 of Merrifield's SPPS, 28 DIC/Oxyma has been used for highly efficient synthesis of a wide range of peptides. 15,29 Furthermore, for SPPS in greener solvents, 30 needed due to risks related to the standard SPPS solvent DMF, 31 DIC/ Oxyma is used essentially exclusively, 32 with only a few suitable alternatives currently available. 33 With regards to DIC/Oxyma, it ought to be noted that McFarland these reagents as such or during amino acid (AA) activation leads to the formation of small amounts of the highly toxic prussic acid (H-CN), for which safety aspects of using DIC/ Oxyma should always be considered, in particular on industrial manufacturing scales.…”

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confidence: 99%

Assessment of Sulfur Impurities in GMP-Grade Diisopropylcarbodiimide and Their Impact on Coupling Reagent-Induced Side Reactions in Peptide Synthesis

Pawlas

Rasmussen

2023

Org. Process Res. Dev.

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Diisopropylcarbodiimide (DIC) constitutes one of the most widely used coupling reagents for amide bond formation in peptide synthesis. We have previously reported that DIC contains a varying amount of sulfur (61–2030 ppm), and that the main S-containing impurity in DIC is the thiourea DITU, which exhibits an excellent ability to suppress side reactions caused by N-oxyl radicals formed from common N-hydroxyl-coupling additives such as HOBt and Oxyma (Green Chem. 2019, 21, 5990). Aiming to understand how the quality of DIC impacts peptide synthesis, here, we report an evaluation of 14 batches of GMP-grade DIC from seven different vendors. With the evaluation by elemental analysis (S), gas chromatography–mass spectrometry, high-performance liquid chromatography, liquid chromatography-mass spectrometry, and nuclear magnetic resonance, we determined that the main S-containing impurity in DIC currently in use is not DITU, but rather the diazetidine-2-thione [1,3-diisopropyl-4-(isopropylimino)-1,3-diazetidine-2-thione, DIDT], formed by a 2 + 2 cycloaddition between DIC and iPr-NCS. The identity of DIDT was confirmed by a synthesis from DIC and iPr-NCS, followed by spiking a batch of DIC with the synthesized DIDT material. In a comparative evaluation of DITU and DIDT aimed at determining their ability to suppress breakdown of Fmoc-Cys(Trt)-OH caused by N-oxyl radicals formed from Oxyma, DITU completely prevented the Cys decomposition, whereas DIDT had no effect on the suppression of the breakdown of the amino acid. Finally, catalytic amounts of DITU as well as thiols DTT and NAC had a positive effect on minimization of the HOBt-induced breakdown of Fmoc-Trp(Boc)-OH, whereas the urea DIU, formed in every DIC-mediated peptide coupling reaction, accelerated the breakdown of the Trp substrate.

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confidence: 99%

Assessment of Sulfur Impurities in GMP-Grade Diisopropylcarbodiimide and Their Impact on Coupling Reagent-Induced Side Reactions in Peptide Synthesis

Pawlas

Rasmussen

2023

Org. Process Res. Dev.

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“…While both production methods of (modified) oligonucleotides are well-established, they suffer from shortcomings. Indeed, chemical synthesis based on the assembly of activated phosphoramidite building blocks is limited in terms of both scalability (<10 kg batches) and sustainability (over 4000 kg waste organic solvents and reagents per kg for a 20 nt long oligonucleotide [26][27][28] ). In addition, even though coupling yields of phosphoramidites are generally very high (≥99%), access to sequences larger than 150 nucleotides is difficult or impossible by this approach.…”

Section: Maëva Pichon and Marcel Hollensteinmentioning

confidence: 99%

Controlled enzymatic synthesis of oligonucleotides

Pichon,

Hollenstein

2024

Commun Chem

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Oligonucleotides are advancing as essential materials for the development of new therapeutics, artificial genes, or in storage of information applications. Hitherto, our capacity to write (i.e., synthesize) oligonucleotides is not as efficient as that to read (i.e., sequencing) DNA/RNA. Alternative, biocatalytic methods for the de novo synthesis of natural or modified oligonucleotides are in dire need to circumvent the limitations of traditional synthetic approaches. This Perspective article summarizes recent progress made in controlled enzymatic synthesis, where temporary blocked nucleotides are incorporated into immobilized primers by polymerases. While robust protocols have been established for DNA, RNA or XNA synthesis is more challenging. Nevertheless, using a suitable combination of protected nucleotides and polymerase has shown promises to produce RNA oligonucleotides even though the production of long DNA/RNA/XNA sequences (>1000 nt) remains challenging. We surmise that merging ligase- and polymerase-based synthesis would help to circumvent the current shortcomings of controlled enzymatic synthesis.

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“…Specifically, as employing the widely used HOBt has become untenable due to its explosive nature, Oxyma in combination with DIC has become the reagent of choice for SPPS . The reliance on DIC/Oxyma has been particularly pronounced in SPPS in greener solvents and investigated extensively in recent years due to health hazards associated with the standard SPPS solvent DMF . In fact, SPPS in greener solvents has relied on DIC/Oxyma practically exclusively, , with only a few coupling protocols not relying on aqueous SPPS, explosive , and allergenic reagents , being reported .…”

Section: Introductionmentioning

confidence: 99%

Elevating 1-tert-Butyl-3-ethylcarbodiimide (TBEC) as a Reagent for Sustainable Peptide Synthesis: Quality Assessment and Minimizing Racemization, Precipitation, and Radical-Induced Side Reactions by TBEC/Oxyma Couplings in an Environmentally Sensible Solvent

Pawlas

Choi

Bargen

et al. 2023

Org. Process Res. Dev.

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From green innovations in oligopeptide to oligonucleotide sustainable synthesis: differences and synergies in TIDES chemistry

Abstract: The growing market for therapeutic peptides and oligonucleotides (TIDES) draws attention to their manufacture, aiming at efficient and sustainable productive processes in view of the predicted massive application of these...

Cited by 12 publications

References 84 publications

Assessment of Sulfur Impurities in GMP-Grade Diisopropylcarbodiimide and Their Impact on Coupling Reagent-Induced Side Reactions in Peptide Synthesis

Assessment of Sulfur Impurities in GMP-Grade Diisopropylcarbodiimide and Their Impact on Coupling Reagent-Induced Side Reactions in Peptide Synthesis

Controlled enzymatic synthesis of oligonucleotides

Elevating 1-tert-Butyl-3-ethylcarbodiimide (TBEC) as a Reagent for Sustainable Peptide Synthesis: Quality Assessment and Minimizing Racemization, Precipitation, and Radical-Induced Side Reactions by TBEC/Oxyma Couplings in an Environmentally Sensible Solvent

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