Inhibition of metalloprotease botulinum serotype A from a pseudo-peptide binding mode to a small molecule that is active in primary neurons.
An efficient research strategy integrating empirically guided, structure-based modeling and chemoinformatics was used to discover potent small molecule inhibitors of the botulinum neurotoxin serotype A light chain. First, a modeled binding mode for inhibitor 2-mercapto-3-phenylpropionyl-RATKML (K(i) = 330 nM) was generated, and required the use of a molecular dynamic conformer of the enzyme displaying the reorientation of surface loops bordering the substrate binding cleft. These flexible loops are conformationally variable in x-ray crystal structures, and the model predicted that they were pivotal for providing complementary binding surfaces and solvent shielding for the pseudo-peptide. The docked conformation of 2-mercapto-3-phenylpropionyl-RATKML was then used to refine our pharmacophore for botulinum serotype A light chain inhibition. Data base search queries derived from the pharmacophore were employed to mine small molecule (non-peptidic) inhibitors from the National Cancer Institute's Open Repository. Four of the inhibitors possess K(i) values ranging from 3.0 to 10.0 microM. Of these, NSC 240898 is a promising lead for therapeutic development, as it readily enters neurons, exhibits no neuronal toxicity, and elicits dose-dependent protection of synaptosomal-associated protein (of 25 kDa) in a primary culture of embryonic chicken neurons. Isothermal titration calorimetry showed that the interaction between NSC 240898 and the botulinum A light chain is largely entropy-driven, and occurs with a 1:1 stoichiometry and a dissociation constant of 4.6 microM.
Burnett
James C
JC
Target Structure-based Drug Discovery Group, SAIC-Frederick, Inc., and the National Cancer Institute-Frederick, Frederick, Maryland 21702.
Ruthel
Gordon
G
United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702.
Stegmann
Christian M
CM
Howard Hughes Medical Institute (HHMI) and Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, and the Stanford Synchrotron Radiation Laboratory, Stanford University, School of Medicine, Stanford, California 94305, and the.
Panchal
Rekha G
RG
Target Structure-based Drug Discovery Group, SAIC-Frederick, Inc., and the National Cancer Institute-Frederick, Frederick, Maryland 21702.
Nguyen
Tam L
TL
Target Structure-based Drug Discovery Group, SAIC-Frederick, Inc., and the National Cancer Institute-Frederick, Frederick, Maryland 21702.
Hermone
Ann R
AR
Target Structure-based Drug Discovery Group, SAIC-Frederick, Inc., and the National Cancer Institute-Frederick, Frederick, Maryland 21702.
Stafford
Robert G
RG
United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702.
Lane
Douglas J
DJ
Target Structure-based Drug Discovery Group, SAIC-Frederick, Inc., and the National Cancer Institute-Frederick, Frederick, Maryland 21702.
Kenny
Tara A
TA
Target Structure-based Drug Discovery Group, SAIC-Frederick, Inc., and the National Cancer Institute-Frederick, Frederick, Maryland 21702.
McGrath
Connor F
CF
Target Structure-based Drug Discovery Group, SAIC-Frederick, Inc., and the National Cancer Institute-Frederick, Frederick, Maryland 21702.
Wipf
Peter
P
Combinatorial Chemistry Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260.
Stahl
Andrea M
AM
United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702.
Schmidt
James J
JJ
United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702.
Gussio
Rick
R
Information Technology Branch, Developmental Therapeutics Program, National Cancer Institute-Frederick, Frederick, Maryland 21702.
Brunger
Axel T
AT
Howard Hughes Medical Institute (HHMI) and Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, and the Stanford Synchrotron Radiation Laboratory, Stanford University, School of Medicine, Stanford, California 94305, and the. Electronic address: brunger@stanford.edu.
Bavari
Sina
S
United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702. Electronic address: sina.bavari@us.army.mil.
D000818:Animals; D019274:Botulinum Toxins, Type A / Q000737:chemistry* / Q000378:metabolism; D001906:Botulism / Q000188:drug therapy / Q000201:enzymology; D002478:Cells, Cultured; D002642:Chick Embryo; D045726:Metalloproteases / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D009474:Neurons / Q000737:chemistry* / Q000201:enzymology; D011480:Protease Inhibitors / Q000737:chemistry* / Q000378:metabolism / Q000627:therapeutic use
D011480:Protease Inhibitors; D045726:Metalloproteases; D019274:Botulinum Toxins, Type A