Scale-Up of a Heck Alkenylation Reaction: Application to the Synthesis of an Amino-Modifier Nucleoside ‘Ruth Linker’

Abstract

Ruth linker is a C5 pyrimidine modified nucleoside analogue widely utilized for the incorporation of a primary amine in a synthetic oligonucleotide. The increasing demand for non-radioactive labeling, detection of biomolecules, and assembly of COVID-19 test kits has triggered a need for scale-up of Ruth linker. Herein, an efficient protocol involving a palladium-catalyzed Heck alkenylation is described. The synthesis has been optimized with a goal of low catalyst concentration, column-free isolation, high product purity, reproducibility, and shorter reaction time. The scalability and utility of the process have been demonstrated successfully on a 100 g scale (starting material). Additionally, for scale-up of the Heck alkenylation protocol, 7-phospha-1,3,5-triaza-adamantanebutane sulfonate (PTABS) as the coordinating caged phosphine ligand was also synthesized on a multigram scale after careful optimization of the conditions.

Rapid plugged flow synthesis of nucleoside analogues via Suzuki-Miyaura coupling and heck Alkenylation of 5-Iodo-2’-deoxyuridine (or cytidine)

“…This problem was overcome by our group through the development of catalytic systems that were able to functionalize all 4 nucleosides efficiently (see Scheme 1). Performing the catalytic reactions in reaction vessels (Schlenck tubes or round bottom flasks) is a common practice but often fails at higher concentrations making the scale-up difficult [51]. The catalytic processes may require product isolation via column chromatographic purification involving large quantities of volatile organic solvents.…”

PTABS: A Unique Water-Soluble π-Acceptor Caged Phosphine

“…20% improvement of the overall yield compared with the existing company protocol (10 mol% Pd(OAc) 2 ) as well as those reported in literature, and HPLC purity of 97%. 52…”