2ISE

Botulinum Neurotoxin A Light Chain WT Crystal Form A

Summary for 2ISE

• Entry DOI: 10.2210/pdb2ise/pdb
• Related: 2ISG 2ISH
• Descriptor: Neurotoxin BoNT/A, ZINC ION (3 entities in total)
• Functional Keywords: botulinum neurotoxin, toxin
• Biological source: Clostridium botulinum
• Total number of polymer chains: 2
• Total formula weight: 96457.49

Authors

Brunger, A.T.,Stegmann, C.M. (deposition date: 2006-10-17, release date: 2006-11-07, Last modification date: 2023-08-30)

Primary citation

Burnett, J.C.,Ruthel, G.,Stegmann, C.M.,Panchal, R.G.,Nguyen, T.L.,Hermone, A.R.,Stafford, R.G.,Lane, D.J.,Kenny, T.A.,McGrath, C.F.,Wipf, P.,Stahl, A.M.,Schmidt, J.J.,Gussio, R.,Brunger, A.T.,Bavari, S.
Inhibition of metalloprotease botulinum serotype A from a pseudo-peptide binding mode to a small molecule that is active in primary neurons.
J.Biol.Chem., 282:5004-5014, 2007

PubMed Abstract: 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.

PubMed: 17092934
DOI: 10.1074/jbc.M608166200

Experimental method

X-RAY DIFFRACTION (2.2 Å)