P3‐320: Molecular docking analysis of mitochondrial pyruvate carrier (MPC) 1 and 2 with pyruvate and inhibitors: Thiazolidinediones currently in clinical trials to delay mild cognitive impairment and Alzheimer's disease
Clyde F. Phelix, George L. Perry, Stanton F. McHardy · Alzheimer s & Dementia · 2015
Inhibition of the mitochondrial pyruvate carrier (MPC) is a novel therapeutic target being tested currently at Phase 3 and Phase 2 clinical trials to delay onset of and progression from mild cognitive impairment to dementia of Alzheimer's disease. Two thiazolidinediones (TZDs), pioglitazone and MSDC-0160, are the drugs being tested, respectively. Other than hypothetical data from biochemical analyses during the 1970s-1990s, no evidence has yet appeared in the literature for studies of the pyruvate and inhibitor interactions with MPC1&2. Autodock/Vina and PyMOL were used for docking and binding site analysis. First a predicted 3D structure of MPC1&2 was performed using the Bax Group (NIH) PDB Utility Server to create a file extended structure from amino acid residue sequences listed on UniProt. Additionally, Protter was used to generate a 2D visualization of MPC1&2 embedded within the inner mitochondrial membrane. Pyruvate and inhibitor 3D data were downloaded from PubChem as SDF files and Babel was used to convert them to PDB format required by Autodock. The TZDs, pioglitazone and MSDC-0160 were tested as novel MPC inhibitors and compared with well-established inhibitors, UK-5099 and α-cyano-4-hydroxycinnamate. Autodock/Vina was used to screen the entire MPC1&2 molecules for potential binding sites; PyMOL was used to visualize and analyze these binding sites in 3D. MPC1 and MPC2 each were predicted to have two transmembrane spanning alpha helical segments containing cysteine residues (C60&61 in MPC1 and C54 in MPC2). Both N- and C-terminals projected to the same side of the membrane, intermembrane space for MPC2 and matrix for MPC1. (Fig. 1) Pyruvate had 8 binding sites on the entire MPC1/2 complex and both TZDs and known inhibitors bound only to 7 or less, including the critical ones at the cysteine residues of MPC1/2 within the inner mitochondrial membrane. (Fig. 2). The TZDs had higher affinities comparable to the known inhibitors. (Fig. 3). Pyruvate binds to eight sites on MPC-1/2 complex (A-H). Note cysteine residues near E & F within the inner mitochondrial membrane (IMM) where MPC2 is facing the intermembrane space (mIMS) and MPC1 is facing the matrix. A) MPC1 (green) has pyruvate bound near CYS60-61 and MPC2 (orange) near LYS 49. This is at the intramembranous domains. B) Pioglitazone binds MPC1 at CYS60-61 near pyruvate (left of image) and at other sites closer to the N-terminal (middle and right of image). Graph of affinities for pyruvate and inhibitors at binding sites shown by amino acid residue numbers. A convergence of pyruvate, characterized inhibitor, and TZD binding sites were localized at cysteine residues of the MPC1/2 transmembrane regions, consistent with biochemical predictions made in the 1970s and 90s by A.P. Halestrap and K.A. Nalecz laboratories, respectively. Supported by Alzheimer's Association and NIHG12-MD007591.