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Design of a small molecule that stimulates vascular endothelial growth factor A enabled by screening RNA fold–small molecule interactions

Nature Chemistry volume 12, pages 952–961 (2020)Cite this article

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Abstract

Vascular endothelial growth factor A (VEGFA) stimulates angiogenesis in human endothelial cells, and increasing its expression is a potential treatment for heart failure. Here, we report the design of a small molecule (TGP-377) that specifically and potently enhances VEGFA expression by the targeting of a non-coding microRNA that regulates its expression. A selection-based screen, named two-dimensional combinatorial screening, revealed preferences in small-molecule chemotypes that bind RNA and preferences in the RNA motifs that bind small molecules. The screening program increased the dataset of known RNA motif–small molecule binding partners by 20-fold. Analysis of this dataset against the RNA-mediated pathways that regulate VEGFA defined that the microRNA-377 precursor, which represses Vegfa messenger RNA translation, is druggable in a selective manner. We designed TGP-377 to potently and specifically upregulate VEGFA in human umbilical vein endothelial cells. These studies illustrate the power of two-dimensional combinatorial screening to define molecular recognition events between ‘undruggable’ biomolecules and small molecules, and the ability of sequence-based design to deliver efficacious structure-specific compounds.

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Fig. 1: Chemoinformatics and bioinformatics analysis of small molecules that bind RNA and the RNAs that bind small molecules.
Fig. 2: SMIRNA strategy and method validation in vitro and in HUVECs.
Fig. 3: Overview of Vegfa mRNA regulation, miR-377 pathway and targeting strategy.
Fig. 4: Activity of heterodimer TGP-377 in HUVECs.
Fig. 5: Proteomics analysis of HUVECs treated with TGP-377.
Fig. 6: TGP-377 stimulates angiogenesis.

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Data availability

All data supporting this manuscript are contained within the main text, source data and Supplementary figures. Specific data are freely available upon reasonable request from the corresponding author. The Inforna database9 can be accessed via the following URL https://disney.florida.scripps.edu/software/. Users wishing to obtain access must complete a software license agreement with TSRI, upon which login credentials will be provided after approval.

Code availability

No unique code was used in the described data analyses.

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Acknowledgements

This work was funded by the National Institutes of Health R01 GM097455 and R01 CA249180 (to M.D.D.) and AstraZeneca. We thank J. Childs-Disney and R. Rahaim, Jr. for editing the manuscript. We also thank U. Bauer for supporting the collaboration and K. Jennbacken for useful input on VEGFA biology. Correspondence and request for materials should be addressed to M.D.D.

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Authors and Affiliations

  1. Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA

    Hafeez S. Haniff, Xiaohui Liu, Daniel Abegg, Alexander Adibekian, Elizabeth Lekah & Matthew D. Disney

  2. Department of Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden

    Laurent Knerr, Jonas Boström & Malin Lemurell

  3. Informatic Core, The Scripps Research Institute, Jupiter, FL, USA

    Gogce Crynen

  4. Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, FL, USA

    Kye Won Wang & Ilyas Yildirim

  5. Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA

    Michael D. Cameron

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Contributions

M.D.D. conceived and directed the study. L.K., J.B. and M.L. conducted all physicochemical analyses and the library design for the AstraZeneca compound collection; H.S.H. conducted the screening and all in vitro and in cellulis experiments under the guidance of M.D.D.; D.A. and A.A. conducted proteomics analysis of HUVEC samples; E.L. conducted RAN translation analysis for binders to r(G4C2); K.W.W. and I.Y. conducted in silico modelling to assess the binding of the dimer to pre-miR-377; M.D.C. conducted cellular uptake analysis by LC-MS/MS; G.C. conducted all bioinformatic analyses for LOGOS analysis. All authors discussed the results and commented on the manuscript during preparation.

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Correspondence to Matthew D. Disney.

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Competing interests

M.D.D. is a founder of Expansion Therapeutics. M.L., J.B. and L.K. are employees of AstraZeneca.

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Supplementary Figs. 1–20, Discussion, Synthetic Methods and Characterization, and Supplementary Methods

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Haniff, H.S., Knerr, L., Liu, X. et al. Design of a small molecule that stimulates vascular endothelial growth factor A enabled by screening RNA fold–small molecule interactions. Nat. Chem. 12, 952–961 (2020). https://doi.org/10.1038/s41557-020-0514-4

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