Insights into structure and activity of natural compound inhibitors of pneumolysin

Hongen Li,Liping Peng,Xuming Deng,Xiaoran Zhao,Jianfeng Wang,Meng Song,Xiaodi Niu

doi:10.1038/srep42015

Hongen Li, Liping Peng + Show 5 more

Open Access

https://doi.org/10.1038/srep42015

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Abstract

Pneumolysin is the one of the major virulence factor of the bacterium Streptococcus pneumoniae. In previous report, it is shown that β-sitosterol, a natural compound without antimicrobial activity, is a potent antagonist of pneumolysin. Here, two new pneumolysin natural compound inhibitors, with differential activity, were discovered via haemolysis assay. To explore the key factor of the conformation for the inhibition activity, the interactions between five natural compound inhibitors with differential activity and pneumolysin were reported using molecular modelling, the potential of mean force profiles. Interestingly, it is found that incorporation of the single bond (C22-C23-C24-C25) to replace the double bond (hydrocarbon sidechain) improved the anti-haemolytic activity. In view of the molecular modelling, binding of the five inhibitors to the conserved loop region (Val372, Leu460, and Tyr461) of the cholesterol binding sites led to stable complex systems, which was consistent with the result of β-sitosterol. Owing to the single bond (C22-C23-C24-C25), campesterol and brassicasterol could form strong interactions with Val372 and show higher anti-haemolytic activity, which indicated that the single bond (C22-C23-C24-C25) in inhibitors was required for the anti-haemolytic activity. Overall, the current molecular modelling work provides a starting point for the development of rational design and higher activity pneumolysin inhibitors.

Highlights

Streptococcus pneumoniae is an important bacterial pathogen that causes many infections, for example, otitis media pneumonia, meningitis and bacteraemia
Based on the methods of molecular dynamics (MD) simulations and free energy calculations, the binding of the five inhibitors to the conserved loop region of the cholesterol binding sites led to stable complex systems, which was consistent with the results of β-sitosterol binding
Fruthermore, the minimal inhibitory concentrations (MICs) of these five natural steroids for S. pneumoniae D39 were all greater than 1024 μg/ml, suggesting that no antibacterial acitivity was observed for these compounds

Summary

Introduction

Streptococcus pneumoniae is an important bacterial pathogen that causes many infections, for example, otitis media pneumonia, meningitis and bacteraemia. Such infections have led to approximately 2 million deaths, including 1 million children under 5 years old. Studies with PFO show that monomers can bind to the membrane (based on PFO’s interaction with cholesterol) and oligomerize on the surface to form a prepore ring, which leads to the cell rupture[4,5,6,7]. Based on the methods of molecular dynamics (MD) simulations and free energy calculations, the binding of the five inhibitors to the conserved loop region of the cholesterol binding sites led to stable complex systems, which was consistent with the results of β-sitosterol binding. The mechanism of the haemolytic activity of inhibitors and the structure-activity relationships of these inhibitors was investigated

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Conclusion