N‐Phenylbenzamides as Potent Inhibitors of the Mitochondrial Permeability Transition Pore

Abstract

Persistent opening of the mitochondrial permeability transition pore (PTP), an inner membrane channel, leads to mitochondrial dysfunction and renders the PTP a therapeutic target for a host of life-threatening diseases. Herein, we report our effort toward identifying small-molecule inhibitors against this target through structure-activity-relationship optimization studies, which led to the identification of several potent analogs around the N-phenylbenzamide compound series identified by high-throughput screening. In particular, compound 4, (3-(benzyloxy)-5-chloro-N-(4-(piperidin-1-ylmethyl)phenyl)benzamide), displayed noteworthy inhibitory activity in the mitochondrial swelling assay (EC50 of 280 nM), poor to very good physicochemical as well as in vitro pharmacokinetic properties, and conferred very high calcium retention capacity to mitochondria. From the data, we believe compound 4 in this series represents a promising lead for the development of PTP inhibitors of pharmacological relevance.

Identification of ER-000444793, a Cyclophilin D-independent inhibitor of mitochondrial permeability transition, using a high-throughput screen in cryopreserved mitochondria

“…More recently, a number of groups have also undertaken large compound library screens aimed at identifying novel inhibitors of mPTP opening343653. Following structure-activity relationship studies around the N -phenyl-benzamide scaffold, Roy et al .…”

“…Following structure-activity relationship studies around the N -phenyl-benzamide scaffold, Roy et al . identified 3-(benzyloxy)-5-chloro- N -(4-(piperidin-1-ylmethyl)phenyl)benzamide as providing protection against both Ca 2+ and oxidative stress-induced mPTP opening53. Unfortunately, due to toxicity the therapeutic potential of N -phenyl-benzamides in disease models was not assessed.…”

Calcium and reactive oxygen species in regulation of the mitochondrial permeability transition and of programmed cell death in yeast

“…We have already found that genetic ablation of the e and/or g subunits, whose presence is important for F-ATP synthase dimerization [101], confers at least partial resistance to PTP opening [65]. Identification of the cysteine residues responsible for the sensitizing effects of oxidative stress and the availability of novel, CyP-independent PTP inhibitors [102-104] should soon allow a stringent test of this hypothesis.…”

Shutting down the pore: The search for small molecule inhibitors of the mitochondrial permeability transition

“…In addition to the IZ PTP inhibitors described above, the HTS of MLMSR library revealed several benzamide (BZ) compounds (e.g., 5 in Figure 3C) that were also chosen as starting points for the SAR studies 15 . When compared to the IZ compounds outlined above, biochemical characterization of one of the molecules in this class (i.e.…”

“…The restriction of cyclophilin inhibitors is that CyPD modulates the pore indirectly as shown by the fact that the PTP can still open when CyPD has been genetically ablated 12 . Therefore, a number of programs have been aimed at identifying novel PTP inhibitors through the unbiased high-throughput screening (HTS) of several small molecule libraries 131415 . Since our recognition of the molecular components forming the PTP is only beginning to be appreciated, each represents a “phenotypic screen”; a widely-used alternative to the target-centric approaches that have dominated since the molecular biology revolution in the 1980s 16 .…”