Targeting the Protein Tunnels of the Urease Accessory Complex: A Theoretical Investigation

• Published in: Molecules
• Main Authors: Matteo Masetti, Federico Falchi, Dario Gioia, Maurizio Recanatini, Stefano Ciurli, Francesco Musiani
• Format: Article
• Language: English
• Published: MDPI AG 2020-06-01
• Subjects: urease; <i>Helicobacter pylori</i>; virtual screening; protein tunnels; protein–protein interaction
• Online Access: https://www.mdpi.com/1420-3049/25/12/2911

Urease is a nickel-containing enzyme that is essential for the survival of several and often deadly pathogenic bacterial strains, including <i>Helicobacter pylori</i>. Notwithstanding several attempts, the development of direct urease inhibitors without side effects for the human host remains, to date, elusive. The recently solved X-ray structure of the <i>Hp</i>UreDFG accessory complex involved in the activation of urease opens new perspectives for structure-based drug discovery. In particular, the quaternary assembly and the presence of internal tunnels for nickel translocation offer an intriguing possibility to target the <i>Hp</i>UreDFG complex in the search of indirect urease inhibitors. In this work, we adopted a theoretical framework to investigate such a hypothesis. Specifically, we searched for putative binding sites located at the protein–protein interfaces on the <i>Hp</i>UreDFG complex, and we challenged their druggability through structure-based virtual screening. We show that, by virtue of the presence of tunnels, some protein–protein interfaces on the <i>Hp</i>UreDFG complex are intrinsically well suited for hosting small molecules, and, as such, they possess good potential for future drug design endeavors.