Lead-oriented synthesis of epigenetic relevant scaffolds.

A simple and rational method to rank lead-likeness of molecules using continuous evaluation functions was hereby developed. This strategy proved to be competitive against known methods and finally helped in driving synthetic efforts towards candidates of interest for epigenetic applications against HDAC6, BRD4 and EZH2.

TAPBPR employs a ligand-independent docking mechanism to chaperone MR1 molecules.

Chaperones tapasin and transporter associated with antigen processing (TAP)-binding protein related (TAPBPR) associate with the major histocompatibility complex (MHC)-related protein 1 (MR1) to promote trafficking and cell surface expression. However, the binding mechanism and ligand dependency of MR1/chaperone interactions remain incompletely characterized. Here in vitro, biochemical and computational studies reveal that, unlike MHC-I, TAPBPR recognizes MR1 in a ligand-independent manner owing to the absence of major structural changes in the MR1 α2-1 helix between empty and ligand-loaded molecules. Structural characterization using paramagnetic nuclear magnetic resonance experiments combined with restrained molecular dynamics simulations reveals that TAPBPR engages conserved surfaces on MR1 to induce similar adaptations to those seen in MHC-I/TAPBPR co-crystal structures. Finally, nuclear magnetic resonance relaxation dispersion experiments using 19F-labeled diclofenac show that TAPBPR can affect the exchange kinetics of noncovalent metabolites with the MR1 groove, serving as a catalyst. Our results support a role of chaperones in stabilizing nascent MR1 molecules to enable loading of endogenous or exogenous cargo.

Degradation of NSD3: What to Myc of it all?

Preventing uncontrolled gene expression is a powerful therapeutic strategy for the treatment of cancers. In this issue of Cell Chemical Biology, Xu et al. (2022) describe a series of proteolysis targeting chimeras that induce the degradation of NSD3 and suppress cMyc-related oncogene transcription in a model of acute myeloid leukemia.

Photochemical synthesis of an epigenetic focused tetrahydroquinoline library.

Discovery of epigenetic chemical probes is an important area of research with potential to deliver drugs for a multitude of diseases. However, commercially available libraries frequently used in drug discovery campaigns contain molecules that are focused on a narrow range of chemical space primarily driven by ease of synthesis and previously targeted enzyme classes (e.g., kinases) resulting in low hit rates for epigenetic targets. Here we describe the design and synthesis of a compound collection that augments current screening collections by the inclusion of privileged isosteres for epigenetic targets.

Focused Libraries for Epigenetic Drug Discovery: The Importance of Isosteres.

Epigenetic drug discovery provides a wealth of opportunities for the discovery of new therapeutics but has been hampered by low hit rates, frequent identification of false-positives, and poor synthetic tractability. A key reason for this is that few screening collections consider the unique requirements of epigenetic targets despite significant medicinal chemistry interest. Here we analyze the suitability of some commercially available screening collections in the context of epigenetic drug discovery, with a particular focus on lysine post-translational modifications, and show that even privileged motifs found in U.S. Food and Drug Administration (FDA)-approved drugs are not present in these collections. We propose that the incorporation of epigenetic bioisosteres should become central in the design of new focused screening collections and highlight some opportunities for the development of synthetic methods which may improve the tractability of hit molecules.

Computational Mapping of Dirhodium(II) Catalysts.

The chemistry of dirhodium(II) catalysts is highly diverse, and can enable the synthesis of many different molecular classes. A tool to aid in catalyst selection, independent of mechanism and reactivity, would therefore be highly desirable. Here, we describe the development of a database for dirhodium(II) catalysts that is based on the principal component analysis of DFT-calculated parameters capturing their steric and electronic properties. This database maps the relevant catalyst space, and may facilitate exploration of the reactivity landscape for any process catalysed by dirhodium(II) complexes. We have shown that one of the principal components of these catalysts correlates with the outcome (e.g. yield, selectivity) of a transformation used in a molecular discovery project. Furthermore, we envisage that this approach will assist the selection of more effective catalyst screening sets, and, hence, the data-led optimisation of a wide range of rhodium-catalysed transformations.

Activity-Directed Synthesis of Inhibitors of the p53/hDM2 Protein-Protein Interaction.

Protein-protein interactions (PPIs) provide a rich source of potential targets for drug discovery and biomedical science research. However, the identification of structural-diverse starting points for discovery of PPI inhibitors remains a significant challenge. Activity-directed synthesis (ADS), a function-driven discovery approach, was harnessed in the discovery of the p53/hDM2 PPI. Over two rounds of ADS, 346 microscale reactions were performed, with prioritisation on the basis of the activity of the resulting product mixtures. Four distinct and novel series of PPI inhibitors were discovered that, through biophysical characterisation, were shown to have promising ligand efficiencies. It was thus shown that ADS can facilitate ligand discovery for a target that does not have a defined small-molecule binding site, and can provide distinctive starting points for the discovery of PPI inhibitors.

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A series of cyclometallated gold(iii) complexes supported by pyrazine-based (C^Npz^C)-type pincer ligands were synthesized via two different pathways. Nucleophilic attack on the isocyanide complex [(C^Npz^C)Au(C[triple bond, length as m-dash]NC6H3Me2-2,6)]SbF6 (2) gave [(C^Npz^C)Au(ACC)]SbF6 complexes with aniline (4·SbF6), adamantylamine (5), glycine ethyl ester (6), alanine methyl ester (7), valine methyl ester (8), phenylglycine methyl ester (9) and methionine methyl ester (10) substituents (ACC = acyclic carbene). The pathway via isocyanide insertion into gold-amide bonds was also investigated; e.g. the reaction of xylyl isocyanide with (C^Npz^C)AuNHPh followed by protonation with HBF4·OEt2 gave the acyclic carbene complex 4·BF4. To the best of our knowledge compounds 6-10 represent the first examples of gold(iii) acyclic carbene complexes bearing amino acid functions. The compounds provide a versatile platform for the study of the anti-proliferative properties of gold(iii) complexes. Tests against human adenoma-type lung cancer cells identified 5, 6, 7 and 10 as particularly promising and demonstrate the synthetic flexibility of acyclic carbene complexes and the potential of that class of compounds for anticancer applications. Compared to cisplatin, amino ester-containing ACC complexes showed improved selectivity for MCF-7 breast cancer cells over that for healthy fibroblasts.