Biophysical Analysis of Small Molecule Binding to Viral RNA Structures

Liang-Yuan Chiu; Jesse Davila-Calderon; Zhengguo Cai; Blanton S Tolbert

doi:10.1007/978-1-0716-2695-5_16

Biophysical Analysis of Small Molecule Binding to Viral RNA Structures

Methods Mol Biol. 2023:2570:205-222. doi: 10.1007/978-1-0716-2695-5_16.

Authors

Liang-Yuan Chiu¹, Jesse Davila-Calderon¹, Zhengguo Cai², Blanton S Tolbert³

Affiliations

¹ Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA.
² Department of Chemistry, Duke University, Durham, NC, USA.
³ Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA. bst18@case.edu.

PMID: 36156785
DOI: 10.1007/978-1-0716-2695-5_16

Abstract

RNA molecules are essential for carrying genetic information and regulating gene expression in most organisms including human pathogenic RNA and relate retro viruses. Targeting viral RNA (vRNA) structures provide broad opportunities to develop chemical tools to probe molecular virology and to discover novel targets for therapeutic intervention. An increasing number of RNA binding small molecules are being identified, stimulating increased interests in small molecule drug discovery for RNA targets. In this chapter, we describe protocols to characterize and robustly validate vRNA-small molecule (vRNA-sm) interactions starting from vRNA sample preparation, followed by small molecule screening against vRNA targets and finally to validating the vRNA-sm interactions via NMR spectroscopy and calorimetric titrations.

Keywords: Amilorides; In vitro transcription; Isotopically labeled rNTPs; NMR spectroscopy; RNA-small molecule screening; Residual dipolar couplings; Titration calorimetry.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Biophysics
Calorimetry
Humans
RNA, Viral* / chemistry

Substances

RNA, Viral

Grants and funding

R01 AI150830/AI/NIAID NIH HHS/United States