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Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem-loop RNAs and their implications for functional cellular assays.

Publication ,  Journal Article
Kelly, ML; Chu, C-C; Shi, H; Ganser, LR; Bogerd, HP; Huynh, K; Hou, Y; Cullen, BR; Al-Hashimi, HM
Published in: RNA
January 2021

Identifying small molecules that selectively bind an RNA target while discriminating against all other cellular RNAs is an important challenge in RNA-targeted drug discovery. Much effort has been directed toward identifying drug-like small molecules that minimize electrostatic and stacking interactions that lead to nonspecific binding of aminoglycosides and intercalators to many stem-loop RNAs. Many such compounds have been reported to bind RNAs and inhibit their cellular activities. However, target engagement and cellular selectivity assays are not routinely performed, and it is often unclear whether functional activity directly results from specific binding to the target RNA. Here, we examined the propensities of three drug-like compounds, previously shown to bind and inhibit the cellular activities of distinct stem-loop RNAs, to bind and inhibit the cellular activities of two unrelated HIV-1 stem-loop RNAs: the transactivation response element (TAR) and the rev response element stem IIB (RREIIB). All compounds bound TAR and RREIIB in vitro, and two inhibited TAR-dependent transactivation and RRE-dependent viral export in cell-based assays while also exhibiting off-target interactions consistent with nonspecific activity. A survey of X-ray and NMR structures of RNA-small molecule complexes revealed that aminoglycosides and drug-like molecules form hydrogen bonds with functional groups commonly accessible in canonical stem-loop RNA motifs, in contrast to ligands that specifically bind riboswitches. Our results demonstrate that drug-like molecules can nonspecifically bind stem-loop RNAs most likely through hydrogen bonding and electrostatic interactions and reinforce the importance of assaying for off-target interactions and RNA selectivity in vitro and in cells when assessing novel RNA-binders.

Duke Scholars

Published In

RNA

DOI

EISSN

1469-9001

Publication Date

January 2021

Volume

27

Issue

1

Start / End Page

12 / 26

Location

United States

Related Subject Headings

  • Yohimbine
  • Transcriptional Activation
  • Static Electricity
  • Small Molecule Libraries
  • RNA, Viral
  • Pentamidine
  • Nucleic Acid Conformation
  • Isoquinolines
  • Hydrogen Bonding
  • Humans
 

Citation

APA
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ICMJE
MLA
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Kelly, M. L., Chu, C.-C., Shi, H., Ganser, L. R., Bogerd, H. P., Huynh, K., … Al-Hashimi, H. M. (2021). Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem-loop RNAs and their implications for functional cellular assays. RNA, 27(1), 12–26. https://doi.org/10.1261/rna.076257.120
Kelly, Megan L., Chia-Chieh Chu, Honglue Shi, Laura R. Ganser, Hal P. Bogerd, Kelly Huynh, Yuze Hou, Bryan R. Cullen, and Hashim M. Al-Hashimi. “Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem-loop RNAs and their implications for functional cellular assays.RNA 27, no. 1 (January 2021): 12–26. https://doi.org/10.1261/rna.076257.120.
Kelly, Megan L., et al. “Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem-loop RNAs and their implications for functional cellular assays.RNA, vol. 27, no. 1, Jan. 2021, pp. 12–26. Pubmed, doi:10.1261/rna.076257.120.
Kelly ML, Chu C-C, Shi H, Ganser LR, Bogerd HP, Huynh K, Hou Y, Cullen BR, Al-Hashimi HM. Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem-loop RNAs and their implications for functional cellular assays. RNA. 2021 Jan;27(1):12–26.

Published In

RNA

DOI

EISSN

1469-9001

Publication Date

January 2021

Volume

27

Issue

1

Start / End Page

12 / 26

Location

United States

Related Subject Headings

  • Yohimbine
  • Transcriptional Activation
  • Static Electricity
  • Small Molecule Libraries
  • RNA, Viral
  • Pentamidine
  • Nucleic Acid Conformation
  • Isoquinolines
  • Hydrogen Bonding
  • Humans