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RNase P Inhibitors Identified as Aggregators.

Isabell Schencking1, Eva M Schäfer1, J H William Scanlan1,2

  • 1Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany.

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Many compounds identified as bacterial RNase P inhibitors actually cause aggregation of the RnpA protein cofactor. These findings suggest high-throughput screenings often yield false positives, known as pan-assay interference compounds (PAINS).

Keywords:
RNase P inhibitorsRnpA protein subunitbacterial RNase Pprotein aggregators

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Drug Discovery

Background:

  • RNase P is a crucial enzyme for tRNA 5'-end maturation in bacteria, typically composed of RNA and a protein cofactor (RnpA).
  • High-throughput screenings have identified potential small-molecule inhibitors for bacterial RNase P.

Purpose of the Study:

  • To investigate the mechanism of action of previously identified bacterial RNase P inhibitors.
  • To determine if reported inhibitors specifically target RNase P or exhibit off-target effects.

Main Methods:

  • Utilized bacterial RNase P from T. maritima, B. subtilis, and S. aureus.
  • Performed solubility analyses (microscopy, HPLC), co-pulldown assays, detergent addition, and enzyme activity titrations.
  • Conducted agar plate inhibition zone analyses using a B. subtilis RNase P depletion strain.

Main Results:

  • Identified compounds (e.g., RNPA2000, iriginol hexaacetate, purpurin) induced RnpA protein aggregation, not specific RNase P inhibition.
  • RNPA2000-induced aggregation was dependent on Mg2+ ions.
  • Cell-based assays did not support RNPA2000 as a specific bacterial RNase P inhibitor.

Conclusions:

  • Reported bacterial RNase P inhibitors may be false positives (PAINS) due to RnpA aggregation.
  • Re-evaluation of screening methodologies is necessary to avoid identifying PAINS.
  • This study highlights challenges in discovering specific inhibitors for ribonucleoprotein enzymes.