APRIL 23, 2025
Computational strategies for discovering and optimizing RNA- and DNA-targeting molecules
Accurate nucleic acid-ligand binding prediction remains a significant challenge for current computational methods. This limitation has constrained the application of in silico approaches in developing small molecule drugs that modulate RNA and DNA activity, including those with anticancer, antiviral, and antibacterial potential.
In this webinar, we will showcase how Schrödinger’s advanced computational solutions are enabling accurate and efficient targeting of RNA and DNA systems by small molecules. We will demonstrate recent improvements made to in silico hit discovery workflows that can enable structure-based drug discovery into RNA receptors. Additionally, we will highlight a separate study leveraging relative binding free energy perturbation to reliably guide lead optimization in drug discovery programs targeting RNA and DNA. This study will illustrate the systematic retrospective assessment of diverse ligand and receptor classes as well as various ligand-nucleic acid binding modes.
Webinar Highlights
- Gain an understanding of methods and review recent results on docking small molecules to RNA and DNA with Glide, SiteMap, and absolute binding FEP+
- Explore strategies for optimizing RNA- and DNA-targeting molecules with relative binding FEP+
Our Speakers
Ara Abramyan
Principal Scientist I, Application Science, Schrödinger
Ara Abramyan is in the Application Science group, helping customers use Schrödinger’s drug discovery suite in their drug discovery endeavors. Outside of customer support, Ara leads external and internal collaborative projects involving nucleic acid- and membrane transporter-based systems using IFD-MD, Desmond, and FEP+ among other workflows. Prior to joining Schrödinger, Ara was a postdoc at the NIH where he led projects on compounds binding to neurotransmitter transporter systems using MD simulations and Markov state models. Before that he obtained his PhD at the University of the Sciences in Philadelphia working on foldamer- and foldamer-DNA-systems using MD and metadynamics simulations while parametrizing the force field for an accurate description of foldamers.
Gary Zhang
Director, Hit Discovery, Schrödinger
Gary Zhang, Ph.D. is the product manager of Schrödinger docking technologies. Gary leads the team improving the performance and expanding the domain of applicability of Schrödinger docking tools. He received his Ph.D. from Duke University working on engineering charge transfer pathways in biological systems and followed by postdoctoral training at Scripps Research working on improving peptide docking performance.