Effect of donor atom identity on metal-binding pharmacophore coordination

  • Benjamin L. Dick
  • Ashay Patel
  • J. Andrew McCammon
  • Seth M. Cohen
Original Paper


The inhibition and binding of three metal-binding pharmacophores (MBPs), 2-hydroxycyclohepta-2,4,6-trien-1-one (tropolone), 2-mercaptopyridine-N-oxide (1,2-HOPTO), and 2-hydroxycyclohepta-2,4,6-triene-1-thione (thiotropolone) to human carbonic anhydrase II (hCAII) and a mutant protein hCAII L198G were investigated. These MBPs displayed bidentate coordination to the active site Zn(II) metal ion, but the MBPs respond to the mutation of L198G differently, as characterized by inhibition activity assays and X-ray crystallography. The L198G mutation increases the active site volume thereby decreasing the steric pressure exerted on MBPs upon binding, allowing changes in MBP coordination to be observed. When comparing the binding mode of tropolone to thiotropolone or 1,2-HOPTO (O,O versus O,S donor sets), structural modifications of the hCAII active site were shown to have a stronger effect on MBPs with an O,O versus O,S donor set. These findings were corroborated with density functional theory (DFT) calculations of model coordination complexes. These results suggest that the MBP binding geometry is a malleable interaction, particularly for certain ligands, and that the identity of the donor atoms influences the response of the ligand to changes in the protein active site environment. Understanding underlying interactions between a MBP and a metalloenzyme active site may aid in the design and development of potent metalloenzyme inhibitors.


Computational chemistry Density functional theory Ligand binding Metalloenzyme X-ray crystallography 



S.M.C. acknowledges support from the National Institutes of Health (R01 GM098435). B.L.D. is supported by the National Institute of Health Molecular Biophysics Training Grant (T32GM008326-26). Computational studies by A.P. and J.A.M. were supported by the National Science Foundation (MCB-1020765), National Institute of Health (R01 GM31749 and R01 GM095970), Howard Hughes Medical Institute, National Biomedical Computation Resource (NBCR), and NSF supercomputer centers. A.P. thanks M.D. Burkart for financial support through the National Institutes of Health (NIH GM095970). We thank J.P. Noel (Salk Instituted) for access and assistance with ITC experiments. We thank Prof. Arnold Rheingold and Dr. Curtis Moore (U.C. San Diego) for assistance with crystallographic data collection and structure determination. S.M.C. is a co-founder of and has an equity interest in Cleave Biosciences and Forge Therapeutics, companies that may potentially benefit from these research results. S.M.C. also serves on the Scientific Advisory Board for these companies. The terms of this arrangement have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies.

Supplementary material

775_2017_1454_MOESM1_ESM.pdf (1.7 mb)
Supplementary material 1 (PDF 1722 kb)


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Copyright information

© SBIC 2017

Authors and Affiliations

  • Benjamin L. Dick
    • 1
  • Ashay Patel
    • 1
  • J. Andrew McCammon
    • 1
    • 2
    • 3
    • 4
  • Seth M. Cohen
    • 1
  1. 1.Department of Chemistry and BiochemistryUniversity of California San DiegoLa JollaUSA
  2. 2.Department of PharmacologyUniversity of California San DiegoLa JollaUSA
  3. 3.Howard Hughes Medical InstituteUniversity of California San DiegoLa JollaUSA
  4. 4.National Biomedical Computation ResourceUniversity of California San DiegoLa JollaUSA

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