How can I predict toxicity in drug discovery?
The importance of predicting toxicity early in drug development Highlighting safety and toxicity early in the drug development process is…
Abstract
We report a new method for X-ray density ligand fitting and refinement that is suitable for a wide variety of small-molecule ligands, including macrocycles. The approach (called “xGen”) augments a force field energy calculation with an electron density fitting restraint that yields an energy reward during the restrained conformational search. The resulting conformer pools balance goodness-of-fit with ligand strain. Real-space refinement from pre-existing ligand coordinates of 150 macrocycles resulted in occupancy-weighted conformational ensembles that exhibited low strain energy. The xGen ensembles improved upon electron density fit compared with the PDB reference coordinates without making use of atom-specific B-factors. Similarly, on nonmacrocycles, de novo fitting produced occupancy-weighted ensembles of many conformers that were generally better-quality density fits than the deposited primary/alternate conformational pairs. The results suggest ubiquitous low-energy ligand conformational ensembles in X-ray diffraction data and provide an alternative to using B-factors as model parameters.
More publications to browse
Why don’t my QSAR models work?
Why QSAR models matter in drug discovery Before we start troubleshooting, let’s remember why we build and run these models…
Leveraging structure-based and ligand-based techniques in drug discovery
In our recent article in Innovations in Pharmaceutical Technology, we explore the principles, techniques, and applications of structure-based and ligand-based…
