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Title: Neutron structure of human carbonic anhydrase II in complex with methazolamide: mapping the solvent and hydrogen-bonding patterns of an effective clinical drug

Abstract

Carbonic anhydrases (CAs; EC 4.2.1.1) catalyze the interconversion of CO 2 and HCO 3 , and their inhibitors have long been used as diuretics and as a therapeutic treatment for many disorders such as glaucoma and epilepsy. Acetazolamide (AZM) and methazolamide (MZM, a methyl derivative of AZM) are two of the classical CA inhibitory drugs that have been used clinically for decades. The jointly refined X-ray/neutron structure of MZM in complex with human CA isoform II (hCA II) has been determined to a resolution of 2.2 Å with an R cryst of ∼16.0%. Presented in this article, along with only the second neutron structure of a clinical drug-bound hCA, is an in-depth structural comparison and analyses of differences in hydrogen-bonding network, water-molecule orientation and solvent displacement that take place upon the binding of AZM and MZM in the active site of hCA II. Even though MZM is slightly more hydrophobic and displaces more waters than AZM, the overall binding affinity ( K i ) for both of the drugs against hCA II is similar (∼10 n M ). The plausible reasons behind this finding have also been discussed using molecular dynamics and X-ray crystal structures of hCA II–MZM determined at cryotemperaturemore » and room temperature. This study not only allows a direct comparison of the hydrogen bonding, protonation states and solvent orientation/displacement of AZM and MZM, but also shows the significant effect that the methyl derivative has on the solvent organization in the hCA II active site.« less

Authors:
; ; ; ; ;
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1326115
Alternate Identifier(s):
OSTI ID: 1327752
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Published Article
Journal Name:
IUCrJ
Additional Journal Information:
Journal Name: IUCrJ Journal Volume: 3 Journal Issue: 5; Journal ID: ISSN 2052-2525
Publisher:
International Union of Crystallography (IUCr)
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; human carbonic anhydrase; acetazolamide; methazolamide; neutron structure; drug binding

Citation Formats

Aggarwal, Mayank, Kovalevsky, Andrey Y., Velazquez, Hector, Fisher, S. Zoë, Smith, Jeremy C., and McKenna, Robert. Neutron structure of human carbonic anhydrase II in complex with methazolamide: mapping the solvent and hydrogen-bonding patterns of an effective clinical drug. United Kingdom: N. p., 2016. Web. doi:10.1107/S2052252516010514.
Aggarwal, Mayank, Kovalevsky, Andrey Y., Velazquez, Hector, Fisher, S. Zoë, Smith, Jeremy C., & McKenna, Robert. Neutron structure of human carbonic anhydrase II in complex with methazolamide: mapping the solvent and hydrogen-bonding patterns of an effective clinical drug. United Kingdom. doi:10.1107/S2052252516010514.
Aggarwal, Mayank, Kovalevsky, Andrey Y., Velazquez, Hector, Fisher, S. Zoë, Smith, Jeremy C., and McKenna, Robert. Fri . "Neutron structure of human carbonic anhydrase II in complex with methazolamide: mapping the solvent and hydrogen-bonding patterns of an effective clinical drug". United Kingdom. doi:10.1107/S2052252516010514.
@article{osti_1326115,
title = {Neutron structure of human carbonic anhydrase II in complex with methazolamide: mapping the solvent and hydrogen-bonding patterns of an effective clinical drug},
author = {Aggarwal, Mayank and Kovalevsky, Andrey Y. and Velazquez, Hector and Fisher, S. Zoë and Smith, Jeremy C. and McKenna, Robert},
abstractNote = {Carbonic anhydrases (CAs; EC 4.2.1.1) catalyze the interconversion of CO 2 and HCO 3 − , and their inhibitors have long been used as diuretics and as a therapeutic treatment for many disorders such as glaucoma and epilepsy. Acetazolamide (AZM) and methazolamide (MZM, a methyl derivative of AZM) are two of the classical CA inhibitory drugs that have been used clinically for decades. The jointly refined X-ray/neutron structure of MZM in complex with human CA isoform II (hCA II) has been determined to a resolution of 2.2 Å with an R cryst of ∼16.0%. Presented in this article, along with only the second neutron structure of a clinical drug-bound hCA, is an in-depth structural comparison and analyses of differences in hydrogen-bonding network, water-molecule orientation and solvent displacement that take place upon the binding of AZM and MZM in the active site of hCA II. Even though MZM is slightly more hydrophobic and displaces more waters than AZM, the overall binding affinity ( K i ) for both of the drugs against hCA II is similar (∼10 n M ). The plausible reasons behind this finding have also been discussed using molecular dynamics and X-ray crystal structures of hCA II–MZM determined at cryotemperature and room temperature. This study not only allows a direct comparison of the hydrogen bonding, protonation states and solvent orientation/displacement of AZM and MZM, but also shows the significant effect that the methyl derivative has on the solvent organization in the hCA II active site.},
doi = {10.1107/S2052252516010514},
journal = {IUCrJ},
number = 5,
volume = 3,
place = {United Kingdom},
year = {2016},
month = {7}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1107/S2052252516010514

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Works referenced in this record:

A Short, Strong Hydrogen Bond in the Active Site of Human Carbonic Anhydrase II
journal, January 2010

  • Avvaru, Balendu Sankara; Kim, Chae Un; Sippel, Katherine H.
  • Biochemistry, Vol. 49, Issue 2
  • DOI: 10.1021/bi902007b

LAUEGEN version 6.0 and INTLDM
journal, June 1998

  • Campbell, J. W.; Hao, Q.; Harding, M. M.
  • Journal of Applied Crystallography, Vol. 31, Issue 3
  • DOI: 10.1107/S0021889897016683

Carbonic anhydrases: novel therapeutic applications for inhibitors and activators
journal, February 2008

  • Supuran, Claudiu T.
  • Nature Reviews Drug Discovery, Vol. 7, Issue 2
  • DOI: 10.1038/nrd2467

Neutron protein crystallography: beyond the folding structure of biological macromolecules
journal, December 2007

  • Niimura, Nobuo; Bau, Robert
  • Acta Crystallographica Section A Foundations of Crystallography, Vol. 64, Issue 1
  • DOI: 10.1107/S0108767307043498

Neutron diffraction studies of Escherichia coli dihydrofolate reductase complexed with methotrexate
journal, November 2006

  • Bennett, B.; Langan, P.; Coates, L.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 49
  • DOI: 10.1073/pnas.0604977103

HKL -3000: the integration of data reduction and structure solution – from diffraction images to an initial model in minutes
journal, July 2006

  • Minor, Wladek; Cymborowski, Marcin; Otwinowski, Zbyszek
  • Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 8
  • DOI: 10.1107/S0907444906019949

Insights towards sulfonamide drug specificity in α-carbonic anhydrases
journal, March 2013

  • Aggarwal, Mayank; Kondeti, Bhargav; McKenna, Robert
  • Bioorganic & Medicinal Chemistry, Vol. 21, Issue 6
  • DOI: 10.1016/j.bmc.2012.08.019

Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography
journal, April 2010

  • Gardberg, Anna S.; Del Castillo, Alexis Rae; Weiss, Kevin L.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 5
  • DOI: 10.1107/S0907444910005494

Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

Joint X-ray/Neutron Crystallographic Study of HIV-1 Protease with Clinical Inhibitor Amprenavir: Insights for Drug Design
journal, June 2013

  • Weber, Irene T.; Waltman, Mary Jo; Mustyakimov, Marat
  • Journal of Medicinal Chemistry, Vol. 56, Issue 13
  • DOI: 10.1021/jm400684f

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

PROCHECK: a program to check the stereochemical quality of protein structures
journal, April 1993

  • Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.
  • Journal of Applied Crystallography, Vol. 26, Issue 2
  • DOI: 10.1107/S0021889892009944

Neutron Diffraction of Acetazolamide-Bound Human Carbonic Anhydrase II Reveals Atomic Details of Drug Binding
journal, September 2012

  • Fisher, S. Zoë; Aggarwal, Mayank; Kovalevsky, Andrey Y.
  • Journal of the American Chemical Society, Vol. 134, Issue 36
  • DOI: 10.1021/ja3068098

Calculating Structures and Free Energies of Complex Molecules:  Combining Molecular Mechanics and Continuum Models
journal, December 2000

  • Kollman, Peter A.; Massova, Irina; Reyes, Carolina
  • Accounts of Chemical Research, Vol. 33, Issue 12
  • DOI: 10.1021/ar000033j

LAUEGEN , an X-windows-based program for the processing of Laue diffraction data
journal, April 1995


LSCALE – the new normalization, scaling and absorption correction program in the Daresbury Laue software suite
journal, June 1999

  • Arzt, Steffi; Campbell, John W.; Harding, Marjorie M.
  • Journal of Applied Crystallography, Vol. 32, Issue 3
  • DOI: 10.1107/S0021889898015350

Joint neutron crystallographic and NMR solution studies of Tyr residue ionization and hydrogen bonding: Implications for enzyme-mediated proton transfer
journal, April 2015

  • Michalczyk, Ryszard; Unkefer, Clifford J.; Bacik, John-Paul
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 18
  • DOI: 10.1073/pnas.1502255112

Free R value: a novel statistical quantity for assessing the accuracy of crystal structures
journal, January 1992


Neutron Structure of Human Carbonic Anhydrase II: A Hydrogen-Bonded Water Network “Switch” Is Observed between pH 7.8 and 10.0
journal, November 2011

  • Fisher, Zoë; Kovalevsky, Andrey Y.; Mustyakimov, Marat
  • Biochemistry, Vol. 50, Issue 44
  • DOI: 10.1021/bi201487b

Neutron Structure of Human Carbonic Anhydrase II: Implications for Proton Transfer
journal, January 2010

  • Fisher, S. Zoë; Kovalevsky, Andrey Y.; Domsic, John F.
  • Biochemistry, Vol. 49, Issue 3
  • DOI: 10.1021/bi901995n

Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules
journal, May 2009

  • Adams, Paul D.; Mustyakimov, Marat; Afonine, Pavel V.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 6
  • DOI: 10.1107/S0907444909011548

Global indicators of X-ray data quality
journal, April 2001


Crystal structure of the catalytic domain of the tumor-associated human carbonic anhydrase IX
journal, September 2009

  • Alterio, V.; Hilvo, M.; Di Fiore, A.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 38
  • DOI: 10.1073/pnas.0908301106