Fast and Efficient Fragment-Based Lead Generation by Fully Automated Processing and Analysis of Ligand-Observed NMR Binding Data

Abstract

NMR binding assays are routinely applied in hit finding and validation during early stages of drug discovery, particularly for fragment-based lead generation. To this end, compound libraries are screened by ligand-observed NMR experiments such as STD, T1ρ, and CPMG to identify molecules interacting with a target. The analysis of a high number of complex spectra is performed largely manually and therefore represents a limiting step in hit generation campaigns. Here we report a novel integrated computational procedure that processes and analyzes ligand-observed proton and fluorine NMR binding data in a fully automated fashion. A performance evaluation comparing automated and manual analysis results on (19)F- and (1)H-detected data sets shows that the program delivers robust, high-confidence hit lists in a fraction of the time needed for manual analysis and greatly facilitates visual inspection of the associated NMR spectra. These features enable considerably higher throughput, the assessment of larger libraries, and shorter turn-around times.

19F NMR transverse and longitudinal relaxation filter experiments for screening: a theoretical and experimental analysis

“…There are already several examples reported in the literature where this methodology has been applied with success in different drug discovery projects . In the first step of this approach, large mixtures of fluorinated molecules are screened and the validated binders are then used as spy molecules for performing secondary screening and for measuring the binding constants of the hits. The possibility of screening large fluorinated molecule mixtures (e.g.…”

Fragment-based screening identifies molecules targeting the substrate-binding ankyrin repeat domains of tankyrase

“…We screened 1100 compounds in pools of four structurally dissimilar molecules with non-overlapping proton resonances (Fig. 3A,B) 60 . We split the top 100 hits into two groups for individual re-testing: those with a signal change >39% (3σ, 35 compounds), and those with a signal change of 26–39% reduction (2–3σ, 65 compounds) (Fig.…”

Process of Fragment-Based Lead Discovery—A Perspective from NMR

“…The NMR spectra are then acquired one-by-one with automatic shimming for each sample tube. The screening datasets are automatically stored in a shared network drive and processed/analyzed using third-party software (Figure 1a), such as ACD/Labs or Mnova [44,71]. In many cases, the buffer conditions are optimized to be compatible with proteins, which might differ from those used for the reference spectra.…”