In the search for
fundamentally new, active, stable, and readily
synthetically accessible cycloalkynes as strain-promoted azide–alkyne
cycloaddition (SPAAC) reagents for bioorthogonal bioconjugation, we
integrated two common approaches: the reagent destabilization by the
increase of a ring strain and the transition state stabilization through
electronic effects. As a result new SPAAC reagents, heterocyclononynes
fused to a heterocyclic core, were created. These compounds can be
obtained through a general synthetic route based on four crucial steps:
the electrophile-promoted cyclization, Sonogashira coupling, Nicholas
reaction, and final deprotection of Co-complexes of cycloalkynes from
cobalt. Varying the natures of the heterocycle and heteroatom allows
for reaching the optimal stability-reactivity balance for new strained
systems. Computational and experimental studies revealed similar SPAAC
reactivities for stable 9-membered isocoumarin- and benzothiophene-fused
heterocycloalkynes and their unstable 8-membered homologues. We discovered
that close reactivity is a result of the interplay of two electronic
effects, which stabilize SPAAC transition states (πin* → σ* and π* → πin*)
with structural effects such as conformational changes from eclipsed
to staggered conformations in the cycloalkyne scaffold, that noticeably
impact alkyne bending and reactivity. The concerted influence of a
heterocycle and a heteroatom on the polarization of a triple bond
in highly strained cycles along with a low HOMO–LUMO gap was
assumed to be the reason for the unpredictable kinetic instability
of all the cyclooctynes and the benzothiophene-fused oxacyclononyne.
The applicability of stable isocoumarin-fused azacyclononyne IC9N-BDP-FL for in vitro bioconjugation was exemplified by
labeling and visualization of HEK293 cells carrying azido-DNA and
azido-glycans.