NMR quality control of fragment libraries for screening

Abstract

Fragment-based screening has evolved as a remarkable approach within the drug discovery process both in the industry and academia. Fragment screening has become a more structure-based approach to inhibitor development, but also towards development of pathway-specific clinical probes. However, it is often witnessed that the availability, immediate and longterm, of a high quality fragment-screening library is still beyond the reach of most academic laboratories. Within iNEXT (Infrastructure for NMR, EM and X-rays for Translational research), a EU-funded Horizon 2020 program, a collection of 782 fragments were assembled utilizing the concept of "poised fragments" with the aim to facilitate downstream synthesis of ligands with high affinity by fragment ligation. Herein, we describe the analytical procedure to assess the quality of this purchased and assembled fragment library by NMR spectroscopy. This quality assessment requires buffer solubility screening, comparison with LC/MS quality control and is supported by state-of-the-art software for high throughput data acquisition and on-the-fly data analysis. Results from the analysis of the library are presented as a prototype of fragment progression through the quality control process.

A COVID moonshot: assessment of ligand binding to the SARS-CoV-2 main protease by saturation transfer difference NMR spectroscopy

“…Ligand quality control is a recognised problem in screening campaigns stemming from a multitude of factors, including the exact amount of compounds provided by vendors, storage conditions, and ligand degradation and aggregation in aqueous buffers, among others (Lepre 2011 ). A recent study aiming to develop a robust fragment library for high-throughput screening reported that up to approximately 30% of fragments failed to pass one or more quality-control metrics, including ligand concentration (Sreeramulu et al 2020 ). Our own experience with bespoke M pro ligands was that ~ 20% of compounds had low or very low effective concentration in solution (Fig.…”

Applications of Solution NMR in Drug Discovery

“…Interestingly, there is generally no strict pooling strategy for fluorine-based fragments, and the number could be safely extended to more than 20 per group [ 76 , 77 ]. After fragment library construction, it is important to take the quality control into accounts for maintaining the quality of the compound library [ 78 ]. Normally, the compounds dissolved in DMSO- d 6 are suggested to be stored in a freezer (−20 °C), and the frequency for freeze-thaw cycles should better be controlled.…”

NMR-based Fragment Screening in a Minimum Sample but Maximum Automation Mode

“…At the BMRZ, optimized workflows to support technical assistance to fragment screening by NMR have been developed. These include quality control and solubility assessment of the fragment library 9 , buffer optimization for the chosen targets, 1…”