Identification of Novel Mitochondrial Pyruvate Carrier Inhibitors by Homology Modeling and Pharmacophore-Based Virtual Screening

Abstract

The mitochondrial pyruvate carrier (MPC) is an inner-mitochondrial membrane protein complex that has emerged as a drug target for treating a variety of human conditions. A heterodimer of two proteins, MPC1 and MPC2, comprises the functional MPC complex in higher organisms; however, the structure of this complex, including the critical residues that mediate binding of pyruvate and inhibitors, remain to be determined. Using homology modeling, we identified a putative substrate-binding cavity in the MPC dimer. Three amino acid residues (Phe66 (MPC1) and Asn100 and Lys49 (MPC2)) were validated by mutagenesis experiments to be important for substrate and inhibitor binding. Using this information, we developed a pharmacophore model and then performed a virtual screen of a chemical library. We identified five new non-indole MPC inhibitors, four with IC50 values in the nanomolar range that were up to 7-fold more potent than the canonical inhibitor UK-5099. These novel compounds possess drug-like properties and complied with Lipinski’s Rule of Five. They are predicted to have good aqueous solubility, oral bioavailability, and metabolic stability. Collectively, these studies provide important information about the structure-function relationships of the MPC complex and for future drug discovery efforts targeting the MPC.

Tubular Mitochondrial Pyruvate Carrier Disruption Elicits Redox Adaptations that Protect from Acute Kidney Injury

“…Understanding these processes could influence novel preemptive approaches to protectively modulate tubular metabolism during AKI. Given the continual discovery and development of MPC inhibitors like MSDC-0602 (57), zaprinast (58), new UK5099-like analogues (59), and non-indole inhibitors (60), modulating MPC activity pharmacologically as a preconditioning strategy or quickly after injury could be a potential approach to minimize AKI-dependent kidney damage. Next, Pax8-dependent Mpc1 knockout was not complete across all tubular segments.…”

Fifty years of the mitochondrial pyruvate carrier: New insights into its structure, function, and inhibition

“…65,66 Three different groups have presented structural models of MPC homo-or hetero-dimers based on structural alignment with the semiSWEETs 61,67 or de novo models using either trRosetta 67 or Alphafold. 60 Using semiSWEET transporters as a template, Lee and co-workers proposed a homology model for the hetero-dimer with inverted topology for the two protomers and identified highly conserved residues in human MPC1 and MPC2 in the proposed dimeric interface. Xu et al presented de novo models of the MPC1 and MPC2 using Rosetta and introducing an artificial linker between protomers.…”

“…Additionally, mutations Leu79His, Arg97Trp, Ala32Gly and Lys72Glu in MPC1 have been described as pathogenic and cause pyruvate deficiency 12,58,59 . Recently, Hegazy and co‐workers also described that MPC1 mutation Phe66Ala impairs substrate and inhibitor binding 60 . Most importantly, human MPC2 homomers did not bind the classic MPC inhibitors, such as (2E)‐2‐Cyano‐3‐(1‐phenyl‐1H‐indol‐3‐yl)acrylic acid (UK5099), with the expected affinities, implying that they do not form a functional binding pocket 55,61 …”

“…More recently, Hegazy and co‐workers have used a model based on the AlphaFold structural predictions of the protomers. The rational for the dimer assembly was not described, but a small number of residues with side chains facing into the dimer interface were mutated to alanine and inhibitor binding studies were performed 60 . The results suggested that Phe66 in MPC1 and Asn100 and Lys49 in MPC2 are important for inhibitor binding.…”

Metabolic Mechanisms Connecting Alzheimer’s and Parkinson’s Diseases: Potential Avenues for Novel Therapeutic Approaches

“…This has led to development of new TZDs for multiple indications ( Colca et al, 2013b ). More recently screening efforts are demonstrating the possibility of finding new molecular scaffolds that can interact with and attenuate the flux of pyruvate through the MPC ( Hegazy et al, 2022 ). It is not yet clear whether all of these new scaffolds will interact with the molecular target in a way that produces the same pleotropic pharmacology as the TZDs like pioglitazone ( Colca, 2015 ).…”