Discovery of a Cryptic Pocket in <i>Ec</i> DsbA Opens New Opportunities for Antibacterial Discovery
Abstract
Abstract We have used nuclear magnetic resonance (NMR) spectroscopy to characterize dynamics in the bacterial oxidoreductase enzyme Escherichia coli disulfide bond protein A ( Ec DsbA). Through this process we identified a cryptic pocket in the structure. We demonstrate that we can identify small molecule “fragments” that bind entirely within this cryptic site. The fragments bind to the cryptic pocket with unusually slow kinetics and a preference for interacting with the oxidized state of Ec DsbA where the two cysteine residues at the active site form a disulfide bond. We characterize the mechanism of binding, involving conformational changes in the active‐site helix of Ec DsbA, which are observed preferentially in the oxidized state. This dynamics‐driven binding mechanism explains both the slow kinetics and the redox‐dependent binding of the ligands. Furthermore, we demonstrate that compounds binding to the cryptic pocket inhibit Ec DsbA activity. These findings highlight the value of dynamics data in identification of the cryptic pocket and identify a new target site for developing more potent inhibitors of Ec DsbA.
Article Details
Authors (14)
Biswaranjan Mohanty
Sydney Analytical Core Research Facility
Wesam S. Alwan
Medicinal Chemistry Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville 3052 Australia
Menachem J. Gunzburg
Medicinal Chemistry Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville 3052 Australia
Olga Ilyichova
Medicinal Chemistry Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville 3052 Australia
Martin L. Williams
Medicinal Chemistry Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville 3052 Australia
Gaurav Sharma
Geqing Wang
Department of Biochemistry and Chemistry La Trobe Institute for Molecular Science School of Agriculture Biomedicine and Environment La Trobe University Bundoora Bundoora 3083 Australia
Begoña Heras
Department of Biochemistry and Chemistry La Trobe Institute for Molecular Science School of Agriculture Biomedicine and Environment La Trobe University Bundoora Bundoora 3083 Australia
Robert B. Fenwick
Department of Integrative Structural and Computational Biology The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
Peter E. Wright
Pramodh Vallurapalli
36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District Hyderabad 500046 India
Bradley C. Doak
Medicinal Chemistry Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville 3052 Australia
Ben Capuano
Medicinal Chemistry Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville 3052 Australia
Martin J. Scanlon
Medicinal Chemistry Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville 3052 Australia