Toward improved drug discovery against flexible protein targets: an exhaustive study of glutamate racemase conformational dynamics, ligand binding, and catalysis

Whalen, Katie

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https://hdl.handle.net/2142/46911 Copy

Description

Title

Toward improved drug discovery against flexible protein targets: an exhaustive study of glutamate racemase conformational dynamics, ligand binding, and catalysis

Author(s)

Whalen, Katie

Issue Date

2014-01-16T18:26:05Z

Director of Research (if dissertation) or Advisor (if thesis)

Spies, Michael A.

Doctoral Committee Chair(s)

Martinis, Susan A.

Committee Member(s)

• Spies, Michael A.
• Gennis, Robert B.
• Fratti, Rutilio A.

Department of Study

Biochemistry

Discipline

Biochemistry

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

• glutamate racemase
• computer-aided drug discovery
• protein dynamics
• ligand binding
• enzyme catalysis
• structure-based drug discovery

Abstract

It is generally agreed that many proteins are structurally dynamic; sampling many conformations while in solution and also adopting new conformations upon complexation with a ligand. Many of these flexible enzymes are of biological interest, and hindering their function via binding of competitive inhibitors would open up valuable therapeutic avenues. Unfortunately due to the conformation-dependent nature of ligand binding, the act of discovering a new small molecule that will bind these particular proteins is analogous to aiming at a moving target. The following work focuses on one particular enzyme, glutamate racemase. Glutamate racemase is an essential and non-redundant enzyme in all species of bacteria, and inhibition of this enzyme results in cell wall degradation, followed by imminent cell death. Inhibitors of glutamate racemase could act as novel antibiotics against a target to which there are no current antibiotics, and thus no known resistance. My studies focus on three interdependent phenomenon related to enzymes: protein dynamics, ligand binding, and catalysis. Three main thrusts of my research lay at the intersection of these physical phenomenon. First and foremost, the Spies lab is interested in structure-based computer-aided drug discovery, and the discovery of glutamate racemase inhibitors is a project located at the intersection of ligand binding and catalysis, where small molecules inhibit the catalytic process. My second project builds on this by adding a deeper understanding of noncompetitive GR inhibitors and allostery in general. This entails exploring the relationship between protein dynamics and catalysis. Finally, my third project involves more fundamental biochemistry in that we closely examine facets of molecular recognition such as conformational changes induced by ligand binding, and the role of interstitial water. The results of the second two projects then feed back into our in silico methods in order to improve our capacity to predict small molecule binders of glutamate racemase. Much of the knowledge detailed here can be applied to similar proteins of alternate classes, thus improving structure-based computer-aided drug discovery against many flexible proteins.

Graduation Semester

2013-12

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http://hdl.handle.net/2142/46911

Copyright and License Information

Copyright 2013 Katie Whalen. Chapter 1: Reprinted (adapted) with permission from Whalen, K. L.; Pankow, K. L.; Blanke, S. R.; Spies, M. A. Exploiting enzyme plasticity in virtual screening: high efficiency inhibitors of glutamate racemase. ACS Med. Chem. Lett. 2010, 8, 9-13. Copyright 2010 American Chemical Society. Chapter 2: Reprinted (adapted) with permission from Whalen, K. L.; Chang, K. M.; Spies, M. A. Hybrid steered molecular dynamics-docking: an efficient solution to the problem of ranking inhibitor affinities against a flexible drug target. Mol. Inf. 2011, 30, 459-471. Copyright 2011 John Wiley and Sons. Chapter 3: Reprinted (adapted) with permission from Whalen, K. L.; Chau, A. C.; Spies, M. A. In silico optimization of a fragment-based hit yields biologically active, high-efficiency inhibitors for glutamate racemase. ChemMedChem 2013, DOI: 10.1002/cmdc.201300271 Copyright 2013 John Wiley and Sons. Chapter 4: Reprinted (adapted) with permission from Whalen, K. L.; Spies, M. A. Flooding enzymes: quantifying the contributions of interstitial water and cavity shape to ligand binding using extended linear response free energy calculations. J. Chem. Inf. Mod. 2013 DOI: 10.1021/ci400244x Copyright 2013 American Chemical Society. Chapter 5: Reprinted (adapted) with permission from Whalen, K. L.; Tussey, K. B.; Blanke, S. R.; Spies, M. A. Nature of allosteric inhibition in glutamate racemase: discovery and characterization of a cryptic inhibitory pocket using atomistic MD simulations and pKa calculations. J. Phys. Chem. B 2011, 115, 3416-3424. Copyright 2011 American Chemical Society.

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