Fragment-based lead discovery by fluorine-detected NMR has gained popularity owing to its high sensitivity, robustness, and ease of use. Recently, we introduced a novel broadband NMR experiment and demonstrated its application to efficient library generation, quality control and screening. Resulting fragment hits have a high degree of chemical diversity with many different fluorine motifs, suggesting that the method is generally applicable to successfully obtaining tractable binders for chemistry optimization and targeting a broad range of disease-relevant biomacromolecules.

The presentation will discuss the design, synthesis, and screening of the 3F library, which contains 115 fluorinated, Fsp³-rich fragments that are shape diverse and natural product-like. The library is perfectly suited for rapid and efficient screening by NMR spectroscopy in a two-stage workflow of ¹⁹F- followed by ¹H-NMR methods. Hits against four protein targets were widely distributed among the scaffolds and a 67% validation rate was achieved in secondary assays.

We've previously shown the importance of designing a fragment library around the techniques used to screen it (Siegal et al, DDT, 2007). Here we will discuss further elaboration of the concept based on learnings from multiple fragment hit to lead projects. The impact of a holistic view of fragment chemistry, orthogonal biophysical techniques and structural biology for deriving novel, tractable chemical series will be illustrated. 

I will present several case studies to illustrate how Astex has developed a streamlined pipeline to facilitate fragment-based drug discovery (FBDD) using single-particle cryo-EM.

With the aim of discovering novel allosteric MEK1 inhibitors, a fragment-based screening campaign, designed to specifically discover allosteric binders by screening with the ATP-binding site blocked, is reported. These efforts led to the identification of multiple novel allosteric MEK1 binder chemotypes, one of which, advanced in the absence of structural information, was elaborated to sub-µM affinity, with promising physicochemical and in vitro ADMET properties.

We used fragment-based lead discovery to identify ligands to LC3, a protein that binds and targets autophagy substrates for destruction. LC3 binding sites were determined using X-ray crystallography. Ligands were optimized using traditional SAR approaches. We used newer methods such as peptide mimetics and DNA-encoded library compounds with similar fragment-like building blocks. We aim to create a degrader-equivalent autophagy tool for targeted degradation of proteins too large for the proteosome.

The HitS business unit is an integral part of the WuXi AppTec Research Services Division (RSD). We deliver customized, integrated hit finding and structure-based drug discovery solutions. By screening our proprietary fragment library by various biophysical methodologies such MST, SPR or nanoDSF we support our clients already at the early stages of their drug development projects.

LpxC catalyzes the first committed step in the biosynthesis of Lipid A, an essential component of the cell envelope of Gram-negative bacteria. In collaboration with colleagues at Taisho Pharmaceuticals, we have identified two series of compounds derived from fragments with differing modes of zinc chelation. Structure-guided design led to a compound exhibiting low nanomolar inhibition of LpxC and a minimum inhibitory concentration (MIC) of 4 µg/mL against Pseudomonas aeruginosa.    

Inhibition of TNFα and other cytokine signaling pathways such as IL-17, IL-23, and IL-6 have been clinically validated via macromolecular biologic drugs; however, efforts to modulate these pathways with small molecules by directly inhibiting interaction with their cognate receptors have been impeded by the challenges associated with the requirements of a small molecule to disrupt high-affinity, protein-protein interactions.  Here, we will present a fragment-based approach and some lessons we have learned in the development of orally efficacious TNFα inhibitors that can be more broadly applied to identify starting points for other cytokines of interest.

Drug Discovery is a discipline of compromises to achieve efficacy and safety with drug molecules. The balancing of properties required to enable passage across biological membranes is considered in the context of debates over the mechanism of crossing membranes, be this via the bilayer or carrier proteins. In particular, the evolutionary consequences of the latter are explored, suggesting opportunities for better biomimetic designs in molecules large and small.

Being able to test newly synthesized molecules is a pivotal part of early-stage drug discovery, with the data from assays driving decisions on the next molecules to be developed. The waveRAPID technology enables testing of full kinetic parameters for up to 400 compound fragments unattended in a 24-hour period. We present how Domainex are using waveRAPID to accelerate the analogue expansion to support our fragment and virtual screening hit ID platforms.