Structural basis of mammalian respiratory complex I inhibition by medicinal biguanides

Abstract

The molecular mode of action of biguanides, including the drug metformin, which is widely used in the treatment of diabetes, is incompletely characterized. Here, we define the inhibitory drug-target interaction(s) of a model biguanide with mammalian respiratory complex I by combining cryo–electron microscopy and enzyme kinetics. We interpret these data to explain the selectivity of biguanide binding to different enzyme states. The primary inhibitory site is in an amphipathic region of the quinone-binding channel, and an additional binding site is in a pocket on the intermembrane-space side of the enzyme. An independent local chaotropic interaction, not previously described for any drug, displaces a portion of a key helix in the membrane domain. Our data provide a structural basis for biguanide action and enable the rational design of medicinal biguanides.

Mechanism of rotenone binding to respiratory complex I depends on ligand flexibility

“…These contacts, the binding mode and the ligand internal conformation match those observed for rotenone bound at ROT2 in the cryoEM model of complex I in open state (PDBs 6ZKL and 6ZKM) 8 . Moreover, this corresponds to the binding site closest to the Q-channel central region also observed for the substrate Q-headgroup 6,12 and other amphiphilic molecules 23,25,26 .…”

“…Compound IACS-2858, a derivative of IACS-010759 which is under clinical trials as an anticancer agent, binds with its oxadiazole and pyridone moieties in the hydrophilic central region and competitively inhibits complex I by a “cork-in-bottle” mechanism 23 . The biguanide IM1761092, a more hydrophobic and potent derivative of the widely used metformin antidiabetic drug, also binds in the Q-channel central region 25 . Even detergent molecules used for protein purification, such as n -dodecyl -D-maltoside (DDM), have been observed with their polar heads in the hydrophilic central region 26 .…”

“…A plethora of small molecules with diverse composition and physico-chemical properties inhibit the activity of complex I 20 . Recent structural data mainly from cryoEM have shown that many of these molecules bind into the amphipathic Q-channel 7,9,[21][22][23][24][25] . For instance, short-tail substrate analogs such as piericidin A, a piridinone with antibiotic activity, and 2-decyl-4-quinazolinylamine respectively bind to the Q-redox site with poses similar to the substrate 7,10,22 or slightly displaced towards NDUFS2 His59 21 .…”

Metformin: update on mechanisms of action and repurposing potential

“…Since the early 2000s, mitochondria have been considered the classic target organelles for the glucose-lowering actions of metformin, based on matrix enrichment and the specific, mild and reversible inhibition of the mitochondrial respiratory chain complex I 26 . Remarkably, a study published in 2023 combining cryo-electron microscopy and enzyme kinetics identified three possible independent binding or interaction sites for biguanides on various complex I protein subunits 62 . The major inhibitory site is located in the amphipathic region of the quinone-binding channel (Q-channel), adjacent to a mobile structural element in the NDUFS7 subunit; when a biguanide binds to this site, reactivation of the enzymatic deactivated state is prevented 62 , as previously reported 63 .…”

“…Remarkably, a study published in 2023 combining cryo-electron microscopy and enzyme kinetics identified three possible independent binding or interaction sites for biguanides on various complex I protein subunits 62 . The major inhibitory site is located in the amphipathic region of the quinone-binding channel (Q-channel), adjacent to a mobile structural element in the NDUFS7 subunit; when a biguanide binds to this site, reactivation of the enzymatic deactivated state is prevented 62 , as previously reported 63 . These structural data obtained using a synthetic biguanide-like molecule supports a specific effect on complex I.…”