title: InhibitingHelicobacter pyloriHtrA protease by addressing a computationally predicted allosteric ligand binding site.
abstract: Helicobacter pyloriis associated with inflammatory diseases and can cause gastric cancer and mucosa-associated lymphoma. One of the bacterium's key proteins is high temperature requirement A (HpHtrA) protein, an extracellular serine protease that cleaves E-cadherin of gastric epithelial cells, which leads to loss of cell-cell adhesion. Inhibition ofHpHtrA may constitute an intervention strategy againstH. pyloriinfection. Guided by the computational prediction of hypothetical ligand binding sites on the surface ofHpHtrA, we performed residue mutation experiments that confirmed the functional relevance of an allosteric region. We virtually screened for potential ligands addressing this surface cleft located between the catalytic and PDZ1 domains. Our receptor-based computational method represents protein surface pockets in terms of graph frameworks and retrieves small molecules that satisfy the constraints given by the pocket framework. A new chemical entity was identified that blocked E-cadherin cleavagein vitroby direct binding toHpHtrA, and efficiently blocked pathogen transmigration across the gastric epithelial barrier. A preliminary crystal structure ofHpHtrA confirms the validity of a comparative "homology" model of the enzyme, which we used for the computational study. The results of this study demonstrate that addressing orphan protein surface cavities of target macromolecules can lead to new bioactive ligands.
authors.affiliation: Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, 8093 Zurich, Switzerland.
authors.forename: Anna Maria
authors.initials: AM
authors.lastname: Perna
authors.affiliation: Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, 8093 Zurich, Switzerland.
authors.forename: Felix
authors.initials: F
authors.lastname: Reisen
authors.affiliation: University of Salzburg, Department of Molecular Biology, 5020 Salzburg, Austria.
authors.forename: Thomas P
authors.initials: TP
authors.lastname: Schmidt
authors.affiliation: Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, 8093 Zurich, Switzerland.
authors.forename: Tim
authors.initials: T
authors.lastname: Geppert
authors.affiliation: Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, 8093 Zurich, Switzerland.
authors.forename: Max
authors.initials: M
authors.lastname: Pillong
authors.affiliation: Goethe-University, Institute of Organic Chemistry and Chemical Biology, 60322 Frankfurt, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Weisel
authors.affiliation: University of Salzburg, Department of Molecular Biology, 5020 Salzburg, Austria.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Hoy
authors.affiliation: University of Oxford, Department of Oncology, Weatherall Institute of Molecular Medicine, OX3 9DS Oxford, UK.
authors.forename: Philip C
authors.initials: PC
authors.lastname: Simister
authors.affiliation: University of Oxford, Department of Oncology, Weatherall Institute of Molecular Medicine, OX3 9DS Oxford, UK ; Martin-Luther-University Halle-Wittenberg, Institute of Molecular Medicine, 06120 Halle, Germany.
authors.forename: Stephan M
authors.initials: SM
authors.lastname: Feller
authors.affiliation: University of Salzburg, Department of Molecular Biology, 5020 Salzburg, Austria.
authors.forename: Silja
authors.initials: S
authors.lastname: Wessler
authors.affiliation: Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, 8093 Zurich, Switzerland.
authors.forename: Gisbert
authors.initials: G
authors.lastname: Schneider
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