Structural characterization and docking studies of acetylcholine binding proteins.

UNCG Author/Contributor (non-UNCG co-authors, if there are any, appear on document)
Leona Ravini Sirkisoon (Creator)
Institution
The University of North Carolina at Greensboro (UNCG )
Web Site: http://library.uncg.edu/
Advisor
Patricia Reggio

Abstract: Neuronal Nicotinic Receptors (NNRs) are ligand gated ion channels located both pre- and postsynaptically in the peripheral and central nervous systems. NNRs are important pharmaceutical targets for schizophrenia, pain, epilepsy, tobacco dependence, Tourette’s syndrome, Alzheimer’s disease, Parkinson’s disease, myasthenia gravis, and depression.1, 2 Rational drug design for NNRs has been hampered by the lack of crystallographic information about this important target. Currently, there exist two atomic level structures representing NNR subtypes. The first a cryoelectron micrograph of a muscle NNR3 at 4 Å resolution provided initial structural information about the complete receptor. A more recent crystal structure of the extracellular domain of the mouse nicotinic acetylcholine receptor (NNR) a1 subunit bound to a-bungarotoxin at 1.94 Å resolution is the first atomic-resolution view of a NNR subunit extracellular domain.2 Other receptor structural data has arisen from acetylcholine binding proteins (AChBPs) 4, 5 isolated from freshwater and marine snails. AChBPs are water-soluble proteins, which are homologues of the extracellular domain of the NNRs. Information collected during this project will be used to aid in the development of homology models for various NNR subtypes, based on a more complete understanding of AChBPs. To this end, available co-crystal structures were analyzed through measurement of distances and angles between residues that make up the ligand binding domain (LBD). Further, to evaluate the utility of various docking/scoring algorithms docking studies were performed on these AChBP co-crystal structures. Nineteen NNR ligands were docked into the AChBPs using Schrodinger’s Glide 5.0 software. A few of the key findings of this research are as follows. First, careful examination of the various geometric parameters shows that large changes occur to the AChBP LBD as a ligand binds. These changes include a 15 residue C-loop closing over the LBD with a concomitant movement of the two subunits that make up the LBD relative to each other to accommodate the ligand. The latter is illustrated by changes in the chi 1 and chi 2 of tyrosine (Y) 55 (from the complementary face) and changes in the chi 1 of tyrosine (Y) 93 in the lobeline AChBP to make room in the LBD for one of the phenyl rings on lobeline. Second, results from the docking studies on all available AChBP-cocrystal structure suggest that the AChBP lobeline structure is the best template for homology modeling based on the following: (1) Glide 5.0 was able to dock most of a diverse set of 19 NNR ligands into this structure, in contrast to more limited success for other AChBP starting points; (2) in cases where the crystal structure had been determined, poses similar to those found for the actual co-crystal structure could be reproduced; (3) the correlation between the Glide score (Gscore) for these expected poses and experimental pKd values was (while still modest) best for this structure (correlation, 0.30); (4) correlation between the best Gsore and the pKd was highest for the lobeline AChBP structure (R2 = 0.38). The lobeline AChBP structure is now under investigation as a template to generate homology models to aid in drug discovery at Targacept.

Additional Information

Publication
Thesis
Language: English
Date: 2009
Keywords
Acetylcholine Binding Proteins, AChBP, NNR, Nueronal Nicotinic Receptors, Structural Characterization
Subjects
Receptor-ligand complexes $x Structure.
Drugs $x Design $x Research.
Drug receptors $x Research.
Acetylcholine $x Receptors.
Neurotransmitter receptors.
Ion Channels $x Analysis.
Ligands (Biochemistry)
Neurons $x Physiology.