Structure–Activity Study of Bioisosteric Trifluoromethyl and Pentafluorosulfanyl Indole Inhibitors of the AAA ATPase p97

Abstract

Exploratory SAR studies of a new phenyl indole chemotype for p97 inhibition revealed C-5 indole substituent effects in the ADPGlo assay that did not fully correlate with either electronic or steric factors. A focused series of methoxy-, trifluoromethoxy-, methyl-, trifluoromethyl-, pentafluorosulfanyl-, and nitro-analogues was found to exhibit IC 50 s from low nanomolar to double-digit micromolar. Surprisingly, we found that the trifluoromethoxy-analogue was biochemically a better match of the trifluoromethyl-substituted lead structure than a pentafluorosulfanyl-analogue. Moreover, in spite of their almost equivalent strongly electron-depleting effect on the indole core, pentafluorosulfanyl-and nitro-derivatives were found to exhibit a 430-fold difference in p97 inhibitory activities. Conversely, the electronically divergent C-5 methyl-and nitro-analogues both showed low nanomolar activities.

Synthesis and Evaluation of Potent KCNQ2/3-Specific Channel Activators

“…2). Our guiding principle for this round of SAR studies was to modulate both steric and, in particular, electronic features in zone 1 by introducing fluoride, trifluoromethyl, and, importantly, a novel pentafluorosulfanyl group, which is considered a "super-trifluoromethyl" substituent (Wipf et al, 2009;Mo et al, 2010;Alverez et al, 2015). These modifications led to our class I analogs NR561_29, NR561_40, NR561_45, and NR561_50 (see Supplemental Data for full chemical names).…”

A threonine turnstile defines a dynamic amphiphilic binding motif in the AAA ATPase p97 allosteric binding site

“…11 Specifically, the analysis of substituent effects revealed a remarkably divergent electronic trend since both the 5-nitro and the 5-methyl substituent showed superior binding affinities versus the corresponding pentafluorosulfanyl-, methoxy-, trifluoromethoxy-, and trifluoromethyl-substituted analogs. 11 Even after the subsequent elucidation of a cryo-EM structure with a potent (IC 50 = 55 nM) 5-fluoro-substituted inhibitor of the same structural series bound to p97 (PDB entry 5FTJ), 3 the inhibitor binding data could not be fully explained by their steric, polar, or electronic properties. Therefore, in the present study, we computationally refined a model of this p97 allosteric site based on the SAR of additional 5-substituted indoles and select arene and heteroarene analogs, which together span a range of more than 3 orders of magnitude in a biochemical assay (Figure 1 and Table 1).…”

“…A solution of 2-(3-bromophenyl)-1 H -indole-5-carbonitrile ( 26 , 0.15 g, 0.50 mmol), LiHMDS (0.20 g, 1.2 mmol), Pd 2 (dba) 3 (9.2 mg, 0.010 mmol), and CyJohnPhos (14.0 mg, 0.040 mmol) in anhydrous THF was treated with tert -butyl (2-(4-isopropylpiperazin-1-yl)ethyl)(piperidin-4-yl)carbamate 3,11 ( A , 0.213 g, 0.600 mmol). The reaction mixture was heated at 75 °C overnight, cooled to room temperature, diluted with sat.…”

“…A suspension of 2-(3-bromophenyl)-1 H -indole 11 (0.40 g, 1.5 mmol), K 3 PO 4 (0.48 g, 2.2 mmol), Pd 2 (dba) 3 (32 mg, 0.034 mmol), CyJohnPhos (42 mg, 0.12 mmol) in dry, degassed dioxane (10 mL) was treated with 1,4-dioxa-8-azaspiro[4.5]decane (0.30 mL, 2.4 mmol). The flask was sealed and the reaction mixture was heated at 110 °C for 6 h under microwave irradiation.…”

“…A solution of tert -butyl (2-(4-isopropylpiperazin-1-yl)ethyl)(1-(3-(5-nitro-1 H -indol-2-yl)phenyl)piperidin-4-yl)carbamate 11 (0.102 g, 0.173 mmol) in MeOH (5 mL) was evacuated, flushed with argon (2x) and treated with 10% Pd/C (0.019 g, 0.17 mmol). The reaction mixture was evacuated and subjected to H 2 (1 atm - balloon).…”