PROTACs bearing piperazine-containing linkers: what effect on their protonation state?

Abstract

The pKa values of a dataset of PROTACs and PROTAC precursors have been analyzed in order to show how a fine modulation of piperazine-containing linkers can impact their protonation state.

Proteolysis Targeting Chimera Degraders of the METTL3–14 m6A-RNA Methyltransferase

“…Furthermore, we synthesized another set of 11 PROTACs that contained lipophilic and rigid handles such as piperidine (compounds 21 – 25 ), piperazine (compounds 29 – 32 ), and triazole (compounds 26 and 27 ) in combination with different alkyl linker lengths. After a round of protein degradation screening in cells and quantification by Western blot analysis (2 μM, 24 h MOLM-13) compounds 22 , 23 , 24 , 29 , 30 , and 31 , featuring piperidine or piperazine handle, showed a 50% or higher degradation of METTL3 and/or METTL14 (Table , Figure A,B). , The correlated degradation of the two proteins of the heterodimeric complex METTL3–14 provides evidence that a PROTAC binding at the SAM-pocket of METTL3 can degrade both proteins (Figure C, Figure S1). PROTAC 30 displayed the most significant degradation activity, achieving a reduction of both METTL3 and METTL14 by about 60%.…”

“…It is important to note that for SAM-competitive PROTACs the cellular activity at low micromolar concentration is in line with the low micromolar activity measured previously for UZH2 in cellular assays 25,29 3A,B). 55,56 The correlated degradation of the two proteins of the heterodimeric complex METTL3−14 provides evidence that a PROTAC binding at the SAM-pocket of METTL3 can degrade both proteins (Figure 3C, Figure S1). PROTAC 30 displayed the most significant degradation activity, achieving a reduction of both METTL3 and METTL14 by about 60%.…”

Use of ionic liquids in amidation reactions for proteolysis targeting chimera synthesis

“…We began our investigation on PROTACs synthesis by focusing on the amidation reaction between indomethacin (INM) (1) and the suitable E3 ligase ligand-linker intermediate (Von Hippel-Lindau (VHL) as the E3 ligase) (2) to prepare anti-SARS-CoV-2 INM-based PROTACs (3), previously synthesized and reported by us (Table 1). 21,22 In particular, by following common Approach A (Fig. 1), PROTACs 3a-3g were synthesized by an amidation reaction in the presence of HATU and DIPEA in anhydrous DMF at room temperature in poor isolated yields (17-32%) (Table 1).…”

“…To date, our group's interest in targeted protein degradation applied to different research fields [19][20][21][22] led us to synthesize a wide structurally heterogeneous library of more than 100 PROTACs. During the preparation of this library, we obtained consistently low yields, particularly in the last coupling synthetic amidation step, thus recognizing the need for exploring and identifying better reaction parameters/conditions.…”

Synthesis and DNA Cleavage Activity of Cationic Methylene-Blue-Backboned Polymers

“…As shown in Figure a, using the monomers DIA-r and DIA-f (Scheme S1), MBP-r and MBP-f were obtained in one pot via oxidative polymerization in the presence of FeCl 3 and H 2 S in 2 M HCl. MBP-r has a rigid piperazine ring spacer, − while MBP-f possesses a flexible alkyl chain spacer.…”