Design and Synthesis of (3D) Cyclobutane Fragments for Use in Fragment-Based Drug Discovery
Authors:   , Hamilton David John 
Published: June 2023

Fragment-based drug discovery (FBDD) has grown into a well-established approach in the pursuit of new therapeutics, and has a growing need for unique screening libraries. Historically, fragment libraries have largely comprised planar compounds with a two-dimensional (2D) shape. It remains to be seen if three-dimensional (3D) fragments could also offer benefits e.g. improved solubility, selectivity, and fragment elaboration. Substantial interest has been placed on the design and synthesis of 3D fragments, and methodology which allows access to or diversification of such scaffolds. To this end, a review providing an overview of 25 synthetic (3D) fragments libraries from recent literature was conducted, providing a comprehensive summary of different collections according to their calculated physicochemical properties and 3D descriptors – fraction sp3 (Fsp3), plane of best fit (PBF) scores and principal moment of inertia (PMI) plots – allowing for fair comparison between different libraries.

Initially arising as an intermediate in fragment synthesis, the bromo-cyclobutenaminone scaffold was identified as a novel covalent warhead against a key antibacterial target: UDP-N-acetylglucosamine enolpyruvyl transferase (MurA). Screening a small library of cyclobutenone derivatives led to the identification of bromo-cyclobutenaminones as new covalent inhibitors or MurA. The electrophilic reactivity and cysteine specificity were determined in a glutathione (GSH) and an oligopeptide assay, respectively. Investigating the structure-activity relationship for MurA suggested a crucial role for the bromine atom. In addition, MS/MS experiments proved the covalent labelling of MurA at Cys115 and the observed loss of the bromine atom suggests a net nucleophilic substitution as the covalent reaction. This new set of compounds might be considered as a viable chemical starting point for the discovery of new MurA inhibitors.

To address the overpopulation of 2D moieties in fragment libraries, the cyclobutane ring was identified as an underrepresented yet attractive motif which could offer benefits in terms of generating 3D fragments. We report the design and synthesis of a focused set 33 cyclobutane fragments, via a key 3-azido-cyclobutanone building block, giving potential access to a range of functional groups with accessible growth vectors. In this work, the library was designed using Principal Component Analysis (PCA) within Molecular Operating Environment (MOE) and was guided by an expanded version of the rule of three (RO3), followed by Principal Moment of Inertia (PMI) analysis to achieve both chemical diversity and high 3D character. The synthesised cyclobutanol fragments comprised three functionalities at the 3-amino handle: secondary amines, amides, and sulfonamides. Both cis and trans ring isomers of library members were generated, as a means of maximising the shape diversity obtained, while limiting molecular complexity through abrogating enantiomers. Property analyses were conducted, with the cyclobutane library faring favourably against existing synthetic 3D fragment libraries in terms of shape and physicochemical properties. The utility of the cyclobutane fragment library, optimistically, remains to be seen in upcoming screening cascades. Indeed, a mixture of 2D and 3D fragment with a variety of molecular shapes and properties is likely necessary to maximise the chances of finding quality hits for screening cascades.