Comprehensive and High‐Throughput Exploration of Chemical Space Using Broadband ¹⁹F NMR‐Based Screening

Abstract

Fragment‐based lead discovery has become a fundamental approach to identify ligands that efficiently interact with disease‐relevant targets. Among the numerous screening techniques, fluorine‐detected NMR has gained popularity owing to its high sensitivity, robustness, and ease of use. To effectively explore chemical space, a universal NMR experiment, a rationally designed fragment library, and a sample composition optimized for a maximal number of compounds and minimal measurement time are required. Here, we introduce a comprehensive method that enabled the efficient assembly of a high‐quality and diverse library containing nearly 4000 fragments and screening for target‐specific binders within days. At the core of the approach is a novel broadband relaxation‐edited NMR experiment that covers the entire chemical shift range of drug‐like 19F motifs in a single measurement. Our approach facilitates the identification of diverse binders and the fast ligandability assessment of new targets.

Application of Fragment-Based Drug Discovery to Versatile Targets

“…The wide dispersion of 19 F signals make it possible to use fragment mixtures in screening, which saves the data acquisition time. The availability of 19 F-labeled compound libraries makes 19 F-NMR more powerful in FBDD ( Kang, 2019b ; Lingel et al, 2020 ). 19 F-NMR is most attractive in fragment screening for the reason that a mixture of compounds can be screened and the correct hit can be readily picked out, making it become a high-throughput method.…”

19F NMR viewed through two different lenses: ligand-observed and protein-observed19F NMR applications for fragment-based drug discovery

“…5a ). 64 Experimentally, it was shown to achieve on average 82% signal integral over 120 kHz. As an initial test, 35 compounds that spanned a chemical shift range of 183 ppm were sampled in a single 1D 19 F CPMG experiment.…”

“…62 These experiments have been prominently used for FBDD, and as such are extensively reviewed. 4,[16][17][18] In recent years several enabling methodologies have been developed that further the field, including creation of unique fluorinated fragment libraries, 63 broadband protocols for expanded mixtures, 64 quantitative methodology for measuring dissociation constants, 65,66 multi-dimensional NMR experiments (e.g., COSY, 67 ILOE 62 ), and screening protocols with both cellular lysates and intact cells. 68,69 Many of these advances will be highlighted here.…”

“…One newly developed solution is to maximize the chemical shift range of detection to not only allow simultaneous screening of diverse fluorine motifs, but also to screen larger mixtures. 64 The span of 19 F drug-like motifs covers from À20 to À240 ppm. 40 As described previously, current CPMG pulse sequences, the most commonly used 19 F NMR experiment used in ligand-observed screening, consist of a hard 901 excitation pulse followed by 1801 refocusing pulses.…”

A Practical Perspective on the Roles of Solution NMR Spectroscopy in Drug Discovery

“…Ligand-observed NMR experiments such as STD-NMR and WaterLOGSY are frequently applied in these screenings [ 76 , 77 , 123 ]. 19 F-NMR experiments have proven to be very powerful in fragment screening, with the following advantages [ 124 ]. First, 19 F-containting fragment libraries are commercially available.…”