The Development of a Versatile Trifunctional Scaffold for Biological Applications

Abstract

We describe the synthesis of a trifunctional scaffold constructed from a planar core of trimesic acid derivatized with three propargylamine moieties. The scaffold was attached to a solid‐phase resin through the carboxylic group of a fluorinated alkyl spacer arm. The orthogonal protection of two of the alkyne groups with triethylsilyl and triisopropylsilyl moieties enabled modular and efficient derivatization of the scaffold with three different azides by using solid‐phase synthesis on amphiphilic ChemMatrix resin. We showed that a fluorine label can be used to quantify the content of fluorine‐containing compounds by 19F NMR spectroscopic analysis after cleavage from the resin. We have thus designed a versatile and convenient tool that could be useful for simple and rapid solid‐phase syntheses of combinatorial libraries of the scaffold‐based compounds, for example as new protein binders.

A CuAAC–Hydrazone–CuAAC Trifunctional Scaffold for the Solid-Phase Synthesis of Trimodal Compounds: Possibilities and Limitations

“…We synthesized scaffold 2 in solution from diamide 3, which was prepared as previously described [4] (Scheme 2). During the amide coupling of diamide 3 and Fmoc-hydrazine [7], using conditions used for the synthesis of scaffold 1 (i.e., PyBrop, DMF, and TEA), we observed the partial deprotection of the Fmoc-hydrazide moiety.…”

“…Synthesis of scaffold 2. Reaction conditions: for the synthesis of 3 (steps (a,b)), refer to our previous report [4]; (c) Fmoc-hydrazine, DIPEA, PyBroP, ACN, 60 °C, 3 h, 57%-67%; (d) 50% TFA/DCM (v/v), r.t., 1 h, 87%-91%.…”

“…This allows for the construction of complex multimodal structures by simply "plugging in" different fragments (e.g., fluorescence tags, polymers, drugs) into the scaffold arms [1], which can be used to mimic discontinuous protein epitopes [3]. With this in mind, we developed a trifunctional scaffold specifically designed for the combinatorial solid-phase syntheses of protein binders [4]. We utilized solid-phase synthesis, which is a convenient and widely used method in combinatorial chemistry that generates simple mixtures of compounds by splitting and mixing the resin [5] and allows for clean post-reaction work-up.…”

“…Compound 1 is assembled on a central rigid core (trimesic acid) that directs the three arms in distinct positions. An additional fluorinated arm enables both the attachment of the scaffold onto the resin and quantitative analyses by 19 F-NMR [4]. Scheme 1.…”

“…First, only a limited number of azides are commercially available, which limits the size of the libraries and thus the chemical variants. Second, we reported [4] that TES groups are unstable in high copper concentrations, which is problematic when using bulky/hindered azides that often require higher copper loads for complete coupling. Thus, we developed a new scaffold by replacing the TES-protected alkyne arm with a hydrazide moiety (compound 2, Scheme 1).…”