"To Be or Not to Be" Protonated: Atomic Details of Human Carbonic Anhydrase-Clinical Drug Complexes by Neutron Crystallography and Simulation

Andrey Kovalevsky, Mayank Aggarwal, Hector Velazquez, Matthew J. Cuneo, Matthew P. Blakeley, Kevin L. Weiss, Jeremy C. Smith, S. Zoë Fisher, Robert McKenna

Research output: Contribution to journalArticlepeer-review

20 Citations (SciVal)

Abstract

Human carbonic anhydrases (hCAs) play various roles in cells, and have been drug targets for decades. Sequence similarities of hCA isoforms necessitate designing specific inhibitors, which requires detailed structural information for hCA-inhibitor complexes. We present room temperature neutron structures of hCA II in complex with three clinical drugs that provide in-depth analysis of drug binding, including protonation states of the inhibitors, hydration water structure, and direct visualization of hydrogen-bonding networks in the enzyme's active site. All sulfonamide inhibitors studied bind to the Zn metal center in the deprotonated, anionic, form. Other chemical groups of the drugs can remain neutral or be protonated when bound to hCA II. MD simulations have shown that flexible functional groups of the inhibitors may alter their conformations at room temperature and occupy different sub-sites. This study offers insights into the design of specific drugs to target cancer-related hCA isoform IX. Kovalevsky et al. used macromolecular neutron crystallography and molecular dynamics simulations to obtain a detailed picture of clinical inhibitors binding to human carbonic anhydrase II. The study visualized hydrogen atom positions, revealing protonation/deprotonation events and intricate hydrogen-bonding networks, providing insights for drug design.

Original languageEnglish
Pages (from-to)383-390.e3
JournalStructure
Volume26
Issue number3
Early online date2018 Feb 8
DOIs
Publication statusPublished - 2018 Mar

Subject classification (UKÄ)

  • Pharmaceutical Sciences
  • Cell and Molecular Biology

Keywords

  • Brinzolamide
  • Dorzolamide
  • Drug binding
  • Ethoxzolamide
  • Human carbonic anhydrase
  • Hydrogen bonding
  • MD simulations
  • Neutron crystallography
  • Perdeuteration

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