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Identifying Inhibitors of the HBx-DDB1 Interaction Using a Split Luciferase Assay System
Published on: December 21, 2019
Identification and optimization of first-in-class RNA helicase inhibitors of DDX1, LGP2, and MDA5
Xiaowen Wang1, Feijun Wang2, Deyu Kong2
1Department of Chemistry, University of Missouri, Columbia, MO, 65211, USA.
Abstract:
RNA helicases are essential, dynamic proteins that consume ATP to unwind and rearrange RNA. These activities place RNA helicases in roles as central mediators of signaling, especially those pathways dependent on RNA metabolism. Their binding of both ATP and RNA, as well as limited literature examples of small molecule ligands, support the tractability of RNA helicases. We employed structure-based virtual screening to rationally identify ligands that occupy the ATP-binding site of three human DExD/H-box RNA helicases: MDA5, LGP2, and DDX1. Following alignment of the well conserved nucleotide binding pocket for these RNA helicases, we docked and refined the list of potential ligands from the MolPort-2022-03 ligand library of ∼3.7 million members. A chemical lead with favorable solubility emerged from the 144 purchased compounds, which were evaluated in MDA5, LGP2, and DDX1 ATPase assays as well as corresponding SPR assays. It was found to be ATP un-competitive for MDA5 and to have similar affinity for the three RNA helicases. Analogs of the lead compound were designed to optimize the potency and selectivity of the scaffold, yielding both pan-helicase inhibitors and other analogs that are biased toward MDA5 inhibition.
Insights
Researchers identified novel small molecule inhibitors for RNA helicases, crucial proteins involved in RNA metabolism and signaling. These compounds target the ATP-binding site, offering potential for therapeutic development.
Area of Science:
- Biochemistry
- Molecular Biology
- Drug Discovery
Background:
- RNA helicases are vital ATP-dependent enzymes regulating RNA metabolism and cellular signaling pathways.
- Their role in RNA processing and their ATP-binding sites present opportunities for therapeutic intervention.
- Limited small molecule ligands for RNA helicases highlight the need for novel inhibitor discovery.
Purpose of the Study:
- To identify and characterize small molecule ligands targeting the ATP-binding sites of human DExD/H-box RNA helicases (MDA5, LGP2, DDX1).
- To rationally design and optimize potent and selective inhibitors for these enzymes.
Main Methods:
- Structure-based virtual screening of a large chemical library (MolPort-2022-03) against conserved nucleotide binding pockets.
- Docking and refinement of potential ligands.
- Biochemical evaluation of identified compounds using ATPase and Surface Plasmon Resonance (SPR) assays.
- Design and synthesis of analogs to optimize inhibitor properties.
Main Results:
- A chemical lead with favorable solubility was identified from 144 tested compounds.
- The lead compound exhibited ATP un-competitive inhibition for MDA5 and similar affinity across MDA5, LGP2, and DDX1.
- Analog development yielded pan-helicase inhibitors and analogs with MDA5-biased inhibition.
Conclusions:
- Structure-based virtual screening is an effective strategy for identifying RNA helicase inhibitors.
- The identified lead compound and its analogs represent promising scaffolds for developing targeted RNA helicase therapeutics.
- Further optimization could lead to selective inhibitors for specific RNA helicases involved in disease pathways.
