Manifestations of toxicity are frequently mediated by regulatory macromolecules such as
enzymes, receptors, ion channels or DNA. These targets represent complex and flexible three-dimensional entities that attempt to optimize their interaction with a small molecule (e.g., a xenobiotic) by adapting their 3D conformation, a mechanism referred to as “induced fit”. Protein-bound solvent molecules are frequently involved in stabilizing small-molecule ligands or, upon release to the “bulk solvent” contribute favorably to the binding entropy. Accounting and quantifying selleck antibody these effects belongs to the most challenging tasks in the computational sciences. In this account, we present the more recent developments of the VirtualToxLab—most noticeably, the change
from multi-dimensional QSAR (mQSAR) to 4D Boltzmann scoring for computing binding affinities based on the three-dimensional structure of protein–ligand complexes. By avoiding the training of a model against a set of compounds with known effects (such as in QSARs) but using an “ab initio” approach instead, the bias of a prediction from any training set is removed as the changes in free energy of ligand binding, ΔG, are computed by direct comparison of a compound’s “behavior” in aqueous solution (mimicking the this website cytoplasm) with those at the target protein employing the same directional force field. Moreover, the risk of extrapolation—occurring when attempting to predict properties of compounds not truly represented TNF-alpha inhibitor in a QSAR’s training set—is purged. The new protocol has been validated with a total of 1288 test compounds and employed to estimate the toxic potential of more than 2500 drugs, chemicals and natural products. All results are posted on http://www.virtualtoxlab.org. We explicitly invite all interested non-profit organizations to freely access/utilize the technology, and share their results with the scientific community
at http://www.biograf.ch/data/projects/OpenVirtualToxLab.php. The technology underlying the VirtualToxLab has recently been described in great detail ( Vedani et al., 2012). In this account, we therefore focus on the most recent extensions and the freely accessible platform—the OpenVirtualToxLab. The flow chart of the VirtualToxLab is shown in Fig. 1. The technology consists of two distinct modules: the user interface (light green) and the server backend (light blue) which communicate through an SSH protocol. The user interface features an embedded 3D viewer for inspecting both input (compounds to be uploaded) and output structures (resulting protein–ligand complexes) and a 3D model builder to readily generate the three-dimensional structure of any small molecule of interest. In a first step (blue borders) the compound’s behavior in aqueous solution is simulated.