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

Umer Bin Abdul Aziz; Ali Saoud; Marcel Bermudez; Maren Mieth; Amira Atef; Thomas Rudolf; Christoph Arkona; Timo Trenkner; Christoph Böttcher; Kai Ludwig; Angelique Hoelzemer; Andreas C Hocke; Gerhard Wolber; Jörg Rademann

doi:10.1038/s41467-024-47741-3

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

Nat Commun. 2024 Apr 26;15(1):3537. doi: 10.1038/s41467-024-47741-3.

Authors

Umer Bin Abdul Aziz^#¹, Ali Saoud^#¹, Marcel Bermudez^{1

2}, Maren Mieth³, Amira Atef^{1

4}, Thomas Rudolf¹, Christoph Arkona¹, Timo Trenkner⁵, Christoph Böttcher⁶, Kai Ludwig⁶, Angelique Hoelzemer^{5

7}, Andreas C Hocke³, Gerhard Wolber¹, Jörg Rademann⁸

Affiliations

¹ Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany.
² Institute for Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstr. 48, 48149, Münster, Germany.
³ Department of Infectious Diseases, Respiratory Medicine, and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
⁴ Department of Medicinal Chemistry, Faculty of Pharmacy, Assuit University, Assiut, 71526, Egypt.
⁵ Leibniz Institute of Virology, Hamburg, 20251, Germany.
⁶ Institute of Chemistry and Biochemistry, Research Center of Electron Microscopy (FZEM), Freie Universität Berlin, Fabeckstraße 36A, 14195, Berlin, Germany.
⁷ First Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), 20251, Hamburg, Germany.
⁸ Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany. joerg.rademann@fu-berlin.de.

^# Contributed equally.

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

A549 Cells
Bacterial Proteins* / antagonists & inhibitors
Bacterial Proteins* / chemistry
Bacterial Proteins* / metabolism
Bacterial Toxins* / antagonists & inhibitors
Bacterial Toxins* / chemistry
Bacterial Toxins* / metabolism
Cholesterol / metabolism
Cryoelectron Microscopy
Epithelial Cells / drug effects
Epithelial Cells / metabolism
Hemolysin Proteins* / chemistry
Hemolysin Proteins* / metabolism
Hemolysis* / drug effects
Humans
Small Molecule Libraries / chemistry
Small Molecule Libraries / pharmacology
Streptococcus pneumoniae* / drug effects
Streptolysins* / chemistry
Streptolysins* / metabolism
Virulence Factors / metabolism

Substances

Streptolysins
plY protein, Streptococcus pneumoniae
Bacterial Proteins
Bacterial Toxins
Hemolysin Proteins
Small Molecule Libraries
Cholesterol
Clostridium perfringens theta-toxin
Virulence Factors

Abstract

Publication types

MeSH terms

Substances

Grants and funding