Targeted small molecule inhibitors blocking the cytolytic effects of pneumolysin and homologous toxins

• Published in: Nature communications 2024-04, Vol.15 (1), p.3537-3537, Article 3537
• Main Authors: Aziz, Umer Bin Abdul, Saoud, Ali, Bermudez, Marcel, Mieth, Maren, Atef, Amira, Rudolf, Thomas, Arkona, Christoph, Trenkner, Timo, Böttcher, Christoph, Ludwig, Kai, Hoelzemer, Angelique, Hocke, Andreas C., Wolber, Gerhard, Rademann, Jörg
• Format: Article
• Language: English
• Subjects: 119/118; 13/2; 13/31; 14/28; 140/131; 49; 631/114/2248; 631/154/309/2144; 631/154/556; 631/535/1258/1260; 82/16; 82/58; 9/10; A549 Cells; Antibiotics; Bacteria; Bacterial Proteins - antagonists & inhibitors; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Bacterial Toxins - antagonists & inhibitors; Bacterial Toxins - chemistry; Bacterial Toxins - metabolism; Cell death; Cholesterol; Cholesterol - metabolism; Cryoelectron Microscopy; Cytolysis; Epithelial cells; Epithelial Cells - drug effects; Epithelial Cells - metabolism; Epithelium; Hemolysin Proteins - chemistry; Hemolysin Proteins - metabolism; Hemolysis - drug effects; Homology; Humanities and Social Sciences; Humans; Immune system; Inhibitors; multidisciplinary; Pneumolysin; Pneumonia; Pore formation; Science; Science (multidisciplinary); Small Molecule Libraries - chemistry; Small Molecule Libraries - pharmacology; Streptococcus infections; Streptococcus pneumoniae; Streptococcus pneumoniae - drug effects; Streptolysins - chemistry; Streptolysins - metabolism; Toxins; Virulence; Virulence factors; Virulence Factors - metabolism
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-47741-3

Pneumolysin (PLY) is a cholesterol-dependent cytolysin (CDC) from Streptococcus pneumoniae , the main cause for bacterial pneumonia. Liberation of PLY during infection leads to compromised immune system and cytolytic cell death. Here, we report discovery, development, and validation of targeted small molecule inhibitors of PLY (pore-blockers, PB). PB-1 is a virtual screening hit inhibiting PLY-mediated hemolysis. Structural optimization provides PB-2 with improved efficacy. Cryo-electron tomography reveals that PB-2 blocks PLY-binding to cholesterol-containing membranes and subsequent pore formation. Scaffold-hopping delivers PB-3 with superior chemical stability and solubility. PB-3 , formed in a protein-templated reaction, binds to Cys428 adjacent to the cholesterol recognition domain of PLY with a K D of 256 nM and a residence time of 2000 s. It acts as anti-virulence factor preventing human lung epithelial cells from PLY-mediated cytolysis and cell death during infection with Streptococcus pneumoniae and is active against the homologous Cys-containing CDC perfringolysin (PFO) as well. The pore-forming toxin pneumolysin is responsible for the high mortality seen in pneumococcal infections unresponsive to antibiotics. In this work, authors report a small molecule inhibitor targeting pneumolysin and related ones as an anti-virulence strategy protecting human cells during infection.