Benchmarking in vitro covalent binding burden as a tool to assess potential toxicity caused by nonspecific covalent binding of covalent drugs

Chem Res Toxicol. 2013 Nov 18;26(11):1739-45. doi: 10.1021/tx400301q. Epub 2013 Oct 28.


Despite several advantages of covalent inhibitors (such as increased biochemical efficiency, longer duration of action on the target, and lower efficacious doses) over their reversible binding counterparts, there is a reluctance to use covalent inhibitors as a drug design strategy in pharmaceutical research. This reluctance is due to their anticipated reactions with nontargeted macromolecules. We hypothesized that there may be a threshold limit for nonspecific covalent binding, below which a covalent binding drug may be less likely to cause toxicity due to irreversible binding to off-target macromolecules. Estimation of in vivo covalent binding burden from in vitro data has previously been used as an approach to distinguish those agents more likely to cause toxicity (e.g., hepatotoxicity) via metabolic activation to reactive metabolites. We have extended this approach to nine covalent binding drugs to determine in vitro covalent binding burden. In vitro covalent binding burden was determined by incubating radiolabeled drugs with pooled human hepatocytes. These data were scaled to an estimate of in vivo covalent binding burden by combining the in vitro data with daily dose. Scaled in vivo daily covalent binding burden of marketed covalent drugs was found to be under 10 mg/day, which is in agreement with previously reported threshold value for metabolically activated reversible drugs. Covalent binding was also compared to the intrinsic reactivities of the covalent inhibitors assessed using nucleophiles glutathione and N-α-acetyl lysine. The intrinsic reactivity did not correlate with observed in vitro covalent binding, which demonstrated that the intrinsic reactivity of the electrophilic groups of covalent drugs does not exclusively account for the extent of covalent binding. The ramifications of these findings for consideration of using a covalent strategy in drug design are discussed.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adamantane / analogs & derivatives
  • Adamantane / chemistry
  • Adamantane / metabolism
  • Adamantane / toxicity
  • Aspirin / chemistry
  • Aspirin / metabolism
  • Aspirin / toxicity
  • Carbon Radioisotopes / chemistry
  • Cells, Cultured
  • Drug-Related Side Effects and Adverse Reactions*
  • Glutathione / chemistry
  • Glutathione / metabolism
  • Half-Life
  • Hepatocytes / drug effects*
  • Hepatocytes / metabolism
  • Humans
  • Lactones / chemistry
  • Lactones / metabolism
  • Lactones / toxicity
  • Lysine / chemistry
  • Lysine / metabolism
  • Nitriles / chemistry
  • Nitriles / metabolism
  • Nitriles / toxicity
  • Orlistat
  • Pharmaceutical Preparations / chemistry*
  • Pharmaceutical Preparations / metabolism
  • Pyrrolidines / chemistry
  • Pyrrolidines / metabolism
  • Pyrrolidines / toxicity
  • Tritium / chemistry
  • Vildagliptin


  • Carbon Radioisotopes
  • Lactones
  • Nitriles
  • Pharmaceutical Preparations
  • Pyrrolidines
  • Tritium
  • Orlistat
  • Glutathione
  • Vildagliptin
  • Lysine
  • Adamantane
  • Aspirin