Open AccessQuantitative Structure–Activity Relationship (QSAR) Study Predicts Small-Molecule Binding to RNA Structure
Author(s) -
Zhengguo Cai,
Martina Zafferani,
Olanrewaju M. Akande,
Amanda E. Hargrove
Publication year - 2022
Publication title -
journal of medicinal chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.01
H-Index - 261
eISSN - 1520-4804
pISSN - 0022-2623
DOI - 10.1021/acs.jmedchem.2c00254
Subject(s) - quantitative structure–activity relationship , chemistry , rna , small molecule , biological system , computational biology , surface plasmon resonance , molecule , molecular descriptor , computational chemistry , stereochemistry , nanotechnology , biochemistry , nanoparticle , organic chemistry , biology , materials science , gene
The diversity of RNA structural elements and their documented role in human diseases make RNA an attractive therapeutic target. However, progress in drug discovery and development has been hindered by challenges in the determination of high-resolution RNA structures and a limited understanding of the parameters that drive RNA recognition by small molecules, including a lack of validated quantitative structure-activity relationships (QSARs). Herein, we develop QSAR models that quantitatively predict both thermodynamic- and kinetic-based binding parameters of small molecules and the HIV-1 transactivation response (TAR) RNA model system. Small molecules bearing diverse scaffolds were screened against TAR using surface plasmon resonance. Multiple linear regression (MLR) combined with feature selection afforded robust models that allowed direct interpretation of the properties critical for both binding strength and kinetic rate constants. These models were validated with new molecules, and their accurate performance was confirmed via comparison to ensemble tree methods, supporting the general applicability of this platform.