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A cryptic pocket in Ebola VP35 allosterically controls RNA binding.

Matthew A Cruz1, Thomas E Frederick1, Upasana L Mallimadugula1

  • 1Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA.

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|April 28, 2022
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This summary is machine-generated.

Researchers identified a cryptic pocket in Ebola virus protein 35 (VP35) using computational methods. This discovery enables allosteric disruption of viral dsRNA binding, offering a new strategy for antiviral drug development.

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Area of Science:

  • Virology
  • Structural Biology
  • Drug Discovery

Background:

  • Protein-protein and protein-nucleic acid interactions are challenging drug targets due to the absence of apparent druggable pockets.
  • Cryptic pockets offer potential for targeting these interactions, but their identification and exploitation are difficult.

Purpose of the Study:

  • To develop and apply a general pipeline for identifying cryptic pockets.
  • To investigate the interferon inhibitory domain (IID) of Ebola virus VP35 as a case study for this pipeline.
  • To explore the potential of targeting VP35 for antiviral drug design.

Main Methods:

  • Adaptive sampling simulations and machine learning algorithms were employed to predict cryptic pockets.
  • Thiol labeling experiments were used to validate the predicted pocket.
  • Mutagenesis studies were performed to investigate the allosteric network and its role in dsRNA binding.

Main Results:

  • A cryptic pocket was identified in the IID of Ebola virus VP35, allosterically coupled to its dsRNA-binding interface.
  • Experimental validation confirmed the existence of the predicted pocket.
  • Targeting this cryptic pocket through covalent modifications disrupted the essential dsRNA binding of VP35, inhibiting immune evasion.

Conclusions:

  • The developed pipeline is effective for identifying cryptic pockets in proteins.
  • The identified cryptic pocket in VP35 presents a viable allosteric target for antiviral drug development against Ebola virus.
  • This approach holds promise for targeting other challenging protein-protein and protein-nucleic acid interactions.