O01_01
Unveiling the Potential of RNA-Targeted Small Molecule Therapies: Innovations in Computational and Biophysical Approaches
Ella MORISHITA* 1, Amiu SHINO 1, Maina OTSU 1, Koji IMAI 1, Kaori FUKUZAWA 2
1 Basic Research Division, Veritas In Silico Inc.
2 Graduate School of Pharmaceutical Sciences, Osaka University
( * E-mail: ecm@vi14si.com )
RNA molecules possess intricate structures that allow them to carry out a variety of roles in human biology and disease, making them attractive targets for small molecule therapies. The FDA-approval of risdiplam, an RNA splicing modulator to treat spinal muscular atrophy, exemplifies the potential of targeting RNA structures with small molecules. However, challenges persist, including the need for advanced computational and biophysical techniques essential for efficient drug discovery. To address these challenges, we are pioneering efforts to develop computational and biophysical technologies that would deepen our understanding of RNA structures and their interactions with small molecules [1].
Initially, we identify RNA structures suitable for targeting with small molecules using our proprietary RNA secondary structure prediction and structural analysis software. Subsequently, we employ quantitative fluorescence resonance energy transfer (qFRET) to screen small-molecule libraries against the target RNA. After primary screening with qFRET, we conduct orthogonal assays, including (1) biolayer interferometry (BLI) for determining binding kinetics; (2) 1D nuclear magnetic resonance (1D NMR) for identifying key residues on the RNA target that bind small molecules, and (3) isothermal titration calorimetry (ITC) for measuring the thermodynamic parameters of binding.
Upon identifying hit small molecules, we determine their 3D structures in complex with the target RNA using NMR or X-ray crystallography. Following successful 3D structure determination, we analyze the important interactions in the RNA–small molecule complex using the fragment molecular orbital (FMO) method. This information guides medicinal chemists in designing derivatives with enhanced pharmacological activity. Finally, we determine the correlation between the experimentally and computationally derived binding energies and exploit the correlation to rationally design derivatives of the hit molecules.
By integrating state-of-the-art computational analysis with rigorous biophysical characterization, our approach offers a comprehensive framework for the discovery and optimization of RNA-targeted small molecules, driving innovation in drug development especially for the treatment of diseases of unmet medical needs. In this presentation, I will illustrate our successful efforts in identifying fluoroquinolone compounds that bind to an RNA stem loop structure, A4G, and demonstrate the potential of FMO-guided design to develop more potent RNA-targeted small molecules [2].
[1] Morishita, E. C. Discovery of RNA-targeted small molecules through the merging of experimental and computational technologies, Expert Opin Drug Discov, 2023, 18, 207–226.
[2] Shino, A.; Otsu, M.; Imai, K.; Fukuzawa, K.; Morishita, E. C. Probing RNA–small molecule interactions using biophysical and computational approaches, ACS Chem Biol, 2023, 18, 2368–2376.
