Structure-based design of small molecule inhibitors of the cagT4SS ATPase Cagα of Helicobacter pylori

Abstract

We here describe the structure-based design of small molecule inhibitors of the type IV secretion system of Helicobacter pylori. The secretion system is encoded by the cag pathogenicity island, and we chose Cagα, a hexameric ATPase and member of the family of VirB11-like proteins, as target for inhibitor design. We first solved the crystal structure of Cagα in a complex with the previously identified small molecule inhibitor 1G2. The molecule binds at the interface between two Cagα subunits and mutagenesis of the binding site identified Cagα residues F39 and R73 as critical for 1G2 binding. Based on the inhibitor binding site we synthesized 98 small molecule derivates of 1G2 to improve binding of the inhibitor. We used the production of interleukin-8 of gastric cancer cells during H. pylori infection to screen the potency of inhibitors and we identified five molecules (1G2_1313, 1G2_1338, 1G2_2886, 1G2_2889 and 1G2_2902) that have similar or higher potency than 1G2. Differential scanning fluorimetry suggested that these five molecules bind Cagα, and enzyme assays demonstrated that some are more potent ATPase inhibitors than 1G2. Finally, scanning electron microscopy revealed that 1G2 and its derivatives inhibit the assembly of T4SS-determined extracellular pili suggesting a mechanism for their anti-virulence effect.

Helicobacter pylori Infection in Patients with Gastric Cancer: A 2024 Update

“…The inhibition of T4SS-determined extracellular pili assembly by 1G2 and its derivatives provides a mechanism for their anti-virulence impact. [18] IL-6-driven autocrine and paracrine positive feedback loops between macrophages and stomach epithelial cells. [19] H. pylori changes the NKG2D pathway.…”

“…Consequently, in different studies, the efficacy of other inhibitors was evaluated by measuring the amount of IL-8 produced by GC cells infected with H. pylori . It has been determined that five molecules (1G2_1313, 1G2_1338, 1G2_2886, 1G2_2889, and 1G2_2902) exhibit potencies comparable to or greater than those of the small molecule inhibitor 1G2 [ 18 ]. In GC, IL-6 is significantly expressed and affects survival.…”