Download MendeleyExpanding automated multiconformer ligand modeling to macrocycles and fragments.
Flowers, J., Echols, N., Correy, G.J., Jaishankar, P., Togo, T., Renslo, A.R., van den Bedem, H., Fraser, J.S., Wankowicz, S.A.(2025) Elife 14
- PubMed: 40586518
- DOI: https://doi.org/10.7554/eLife.103797
- Primary Citation of Related Structures:
7HHS, 7HHT, 7HHU, 7HHV, 7HHW, 7HHX, 7HHY, 7HHZ, 7HI0, 7HI1, 7HI2, 7HI3, 7HI4, 7HI5, 7HI6, 7HI7 - PubMed Abstract:
Small molecule ligands exhibit a diverse range of conformations in solution. Upon binding to a target protein, this conformational diversity is reduced. However, ligands can retain some degree of conformational flexibility even when bound to a receptor. In the Protein Data Bank, a small number of ligands have been modeled with distinct alternative conformations that are supported by macromolecular X-ray crystallography density maps. However, the vast majority of structural models are fit to a single-ligand conformation, potentially ignoring the underlying conformational heterogeneity present in the sample. We previously developed qFit-ligand to sample diverse ligand conformations and to select a parsimonious ensemble consistent with the density. While this approach indicated that many ligands populate alternative conformations, limitations in our sampling procedures often resulted in non-physical conformations and could not model complex ligands like macrocycles. Here, we introduce several improvements to qFit-ligand, including integrating RDKit for stochastic conformational sampling. This new sampling method greatly enriches low-energy conformations of small molecules and macrocycles. We further extended qFit-ligand to identify alternative conformations in PanDDA-modified density maps from high-throughput X-ray fragment screening experiments, as well as single-particle cryo-electron microscopy density maps. The new version of qFit-ligand improves fit to electron density and reduces torsional strain relative to deposited single-conformer models and our prior version of qFit-ligand. These advances enhance the analysis of residual conformational heterogeneity present in ligand-bound structures, which can provide important insights for the rational design of therapeutic agents.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.
Organizational Affiliation:
