Hit clustering can improve virtual fragment screening: CDK2 and PARP1 case studies

Abstract

Virtual fragment screening could be a promising alternative to existing experimental screening techniques. However, reliable methods of in silico fragment screening are yet to be established and validated. In order to develop such an approach we first checked how successful the existing molecular docking methods can be in predicting fragment binding affinities and poses. Using our Lead Finder docking software the RMSD of the binding energy prediction was observed to be 1.35 kcal/mol(-1) on a set of 26 experimentally characterized fragment inhibitors, and the RMSD of the predicted binding pose from the experimental one was <1.5 Å. Then, we explored docking of 68 fragments obtained from 39 drug molecules for which co-crystal structures were available from the PDB. It appeared that fragments that participate in oriented non-covalent interactions, such as hydrogen bonds and metal coordination, could be correctly docked in 70-80% of cases suggesting the potential success of rediscovering of corresponding drugs by in silico fragment approach. Based on these findings we've developed a virtual fragment screening technique which involved structural filtration of protein-ligand complexes for specific interactions and subsequent clustering in order to minimize the number of preferable starting fragment candidates. Application of this method led to 2 millimolar-scale fragment PARP1 inhibitors with a new scaffold.

vsFilt: A Tool to Improve Virtual Screening by Structural Filtration of Docking Poses

“…Deficiencies of current scoring functions complicate ranking of docking poses and produce high “false positive” and “false negative” rates. However, the performance of virtual screening can be improved by postdocking structural filtration, allowing the selection of specifically bound ligands. − The main idea behind the structural filtration approach is that the presence of interactions characteristic for the substrate and/or known inhibitors could be taken as an effective criterion for the postdocking identification of new potent binders.…”

2,3‐Dihydroxy‐quinoxaline induces ATPase activity of Herpes Simplex Virus thymidine kinase

“…Initially we aimed at identification of novel fragment HSV-TK inhibitors using virtual fragment screening approach [8][9][10]. Model of the HSV-TK was constructed from PDB ID 1KI3…”

“…Initially we aimed at identification of novel fragment HSV-TK inhibitors using virtual fragment screening approach [8][9][10]. Model of the HSV-TK was constructed from PDB ID 1KI3 [11] (TK UL23 from type 1 HSV strain 17), while highly homologous recombinant TK UL23 from acyclovir-sensitive strain L2 of type 1 HSV was used in further experiments [12].…”