Identification of new highly selective inhibitors of the human ADP/ATP carriers by molecular docking and in vitro transport assays

Biochem Pharmacol. 2016 Jan 15:100:112-32. doi: 10.1016/j.bcp.2015.11.019. Epub 2015 Nov 23.


Mitochondrial carriers are proteins that shuttle a variety of metabolites, nucleotides and coenzymes across the inner mitochondrial membrane. The mitochondrial ADP/ATP carriers (AACs) specifically translocate the ATP synthesized within mitochondria to the cytosol in exchange for the cytosolic ADP, playing a key role in energy production, in promoting cell viability and regulating mitochondrial permeability transition pore opening. In Homo sapiens four genes code for AACs with different tissue distribution and expression patterns. Since AACs are dysregulated in several cancer types, the employment of known and new AAC inhibitors might be crucial for inducing mitochondrial-mediated apoptosis in cancer cells. Albeit carboxyatractyloside (CATR) and bongkrekic acid (BKA) are known to be powerful and highly selective AAC inhibitors, able to induce mitochondrial dysfunction at molecular level and poisoning at physiological level, we estimated here for the first time their affinity for the human recombinant AAC2 by in vitro transport assays. We found that the inhibition constants of CATR and BKA are 4 nM and 2.0 μM, respectively. For finding new AAC inhibitors we also performed a docking-based virtual screening of an in-house developed chemical library and we identified about 100 ligands showing high affinity for the AAC2 binding region. By testing 13 commercially available molecules, out of the 100 predicted candidates, we found that 2 of them, namely suramin and chebulinic acid, are competitive AAC2 inhibitors with inhibition constants 0.3 μM and 2.1 μM, respectively. We also demonstrated that chebulinic acid and suramin are "highly selective" AAC2 inhibitors, since they poorly inhibit other human mitochondrial carriers (namely ORC1, APC1 and AGC1).

Keywords: ADP/ATP carrier inhibitors; Apoptosis inducers; Bongkrekic acid; Bongkrekic acid (PubChem CID: 6433556); Carboxyatractyloside; Carboxyatractyloside (PubChem CID: 75069414); Chebulinic acid; Chebulinic acid (Pubchem CID: 72284); Docking-based virtual screening of chemical libraries; IC50; K(i); Mitochondrial carriers; Saikosaponin (Pubchem CID: 441945); Steviol (Pubchem CID: 9905087); Suramin; Suramin (Pubchem CID: 5361).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Atractyloside / analogs & derivatives
  • Atractyloside / chemistry
  • Atractyloside / metabolism
  • Atractyloside / pharmacology
  • B-Lymphocytes / drug effects
  • B-Lymphocytes / metabolism
  • Binding Sites / physiology
  • Bongkrekic Acid / chemistry
  • Bongkrekic Acid / metabolism
  • Bongkrekic Acid / pharmacology
  • Dose-Response Relationship, Drug
  • Humans
  • Mitochondrial ADP, ATP Translocases / antagonists & inhibitors*
  • Mitochondrial ADP, ATP Translocases / chemistry
  • Mitochondrial ADP, ATP Translocases / metabolism*
  • Molecular Docking Simulation / methods*
  • Molecular Sequence Data
  • Protein Transport / physiology


  • Bongkrekic Acid
  • Atractyloside
  • Mitochondrial ADP, ATP Translocases
  • carboxyatractyloside