Conformational Sampling of the Botulinum Neurotoxin Serotype a Light Chain: Implications for Inhibitor Binding

Authors

James C. Burnett, Developmental Therapeutics Program, NCI Frederick, Frederick, MD 21702, USA
James J. Schmidt, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
Connor F. McGrath, Developmental Therapeutics Program, NCI Frederick, Frederick, MD 21702, USA
Tam L. Nguyen, Developmental Therapeutics Program, NCI Frederick, Frederick, MD 21702, USA
Ann R. Hermone, Developmental Therapeutics Program, NCI Frederick, Frederick, MD 21702, USA
Rekha G. Panchal, Developmental Therapeutics Program, NCI Frederick, Frederick, MD 21702, USA
Jonathan L. Vennerstrom, College of Pharmacy, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198, USA
Krishna Kodukula, Office of Technology and Strategy, Innovation and Acquisitions, Sarnoff Corporation, 201 Washington Road, Princeton, NJ 08543, USA
Daniel W. Zaharevitz, Developmental Therapeutics Program, NCI Frederick, Frederick, MD 21702, USA
Rick Gussio, Developmental Therapeutics Program, NCI Frederick, Frederick, MD 21702, USA
Sina Bavari, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA

Document Type

Article

Date of this Version

2005

Comments

Published in Bioorganic & Medicinal Chemistry 13 (2005) 333–341.

Abstract

Botulinum neurotoxins (BoNTs) are the most potent of the known biological toxins, and consequently are listed as category A biowarfare agents. Currently, the only treatments against BoNTs include preventative antitoxins and long-term supportive care. Consequently, there is an urgent need for therapeutics to counter these enzymes––post exposure. In a previous study, we identified a number of small, nonpeptidic lead inhibitors of BoNT serotype A light chain (BoNT/A LC) metalloprotease activity, and we identified a common pharmacophore for these molecules. In this study, we have focused on how the dynamic movement of amino acid residues in and surrounding the substrate binding cleft of the BoNT/A LC might affect inhibitor binding modes. The X-ray crystal structures of two BoNT/A LCs (PDB refcodes = 3BTA and 1E1H) were examined. Results from these analyses indicate that the core structural features of the examined BoNT/A LCs, including a-helices and b-sheets, remained relatively unchanged during 1ns dynamics trajectories. However, conformational flexibility was observed in surface loops bordering the substrate binding clefts in both examined structures. Our analyses indicate that these loops may possess the ability to decrease the solvent accessibility of the substrate binding cleft, while at the same time creating new residue contacts for the inhibitors. Loop movements and conformational/ positional analyses of residues within the substrate binding cleft are discussed with respect to BoNT/A LC inhibitor binding and our common pharmacophore for inhibition. The results from these studies may aid in the future identification/development of more potent small molecule inhibitors that take advantage of new binding contacts in the BoNT/A LC.