Covalent Inhibitor Library

Covalent modifiers are attractive molecules for drug discovery and HTS as they possess many desirable features, including increased biochemical efficiency of target disruption, lower sensitivity toward pharmacokinetic parameters and increased duration of action that outlasts pharmacokinetics of the compound. Safety concerns that must be mitigated include the lack of specificity and the potential immunogenicity of the protein-inhibitor adduct(s).

The Life Chemicals Covalent Inhibitor Library comprises 10,930 compounds for covalent screening selected from the Life Chemicals HTS Compound Collection by specific structural moieties (functional groups), sometimes referred to as “warheads”, that are known to form covalent bonds with amino acid residues in binding sites of target proteins: Lys, Cys, Ser, Asp, Glu, and Tyr.

The following chemical classes and structural features were used for selection of possible covalent binding irreversible inhibitors:

  • β-lactams
  • Alkyl halides
  • Epoxides, aziridines
  • Michael acceptors:
    • α,β-unsaturated ketones, -nitriles, -esters;
    • maleimide-like compounds;
    • activated vinyl derivatives, etc.    
  • Cyanoacrylamides
  • Sulfonate esters
  • Sulfonyl fluorides
  • Thioles
  • Rodanides
  • Thiourea and thioketones
  • o-quinones
  • p-quinones
  • Ketales
  • Acetales
  • Disulfides
  • Terminal acetylenes
  • Sulfoalkenes


The final set of small-molecule screening compounds  was obtained by applying the extended Rule of Five criteria:

  • MW 120 – 500
  • ClogP -0.4 – 5
  • Hb donor 0 – 5
  • Hb acceptor 0 – 10
  • Rotatable bonds ≤ 10
  • PSA ≤ 140 Å2

You can cherry-pick compounds or focus on a specific class of covalent modifiers. Separate focused sets of covalent binders targeting each of the indicated amino acid residues (Cysteine, Lysine, Serine, Histidine, Threonine) can be provided or request.


  1. K. Zhu, K. W. Borrelli, J. Greenwood, T. Day, R. Abel, R. Farid, E. Harder J. Chem. Inf. Model., June 2014. doi: 10.1021/ci500118s
  2. D. T. Warshaviak, G. Golan, K. W. Borrelli, K. Zhu, O. Kalid J. Chem. Inf. Model., March 2014. doi: 10.1021/ci500175r
  3. Q. Liu, Y. Sabnis, Z. Zhao, T. Zhang, S. J. Buhrlage, L. H. Jones, N. S. Gray Cell Press: Chem. Biol., Vol. 20 (2),
  4. 2013, pp. 146–159.
  5. R. Mah, J. R. Thomas, C. M. Shafer Bioorg. Med. Chem. Lett., Vol. 24, 2014, pp. 33–39.
  6. D. S. Johnson, E. Weerapana, B. F. Cravatt Future Med. Chem., Vol. 2 (6), 2010, pp. 949–964.
  7. E. Weerapana, G. M. Simon, B. F. Cravatt Nature Chemical Bioogyl., Vol. 4, 2008, pp. 405–407.
  8. S. G. Kathman, Z. Xu, A. V. Statsyuk J. Med Chem., Vol. 57 (11), 2014, pp. 4969–4974.