Traditionally, permeable macrocyclic peptides have been identified by discrete synthesis and careful side-chain variation of privileged, natural product scaffolds.  Recent advances in the principles governing passive permeability were applied to the prospective design of macrocyclic peptides with oral bioavailability.  Herein, we present an expanded set of permeability-biased scaffolds and a case study describing the design of a passively permeable, orally available scaffold from a 13-mer PCSK9 ligand.

Within this presentation I will discuss the barriers which exclude potential peptide therapeutics from peroral delivery and present some recent strategies in peptidomimetic design which have enabled just a handful of candidates to achieve regulatory approval by the oral route.

In addition to traditional high-throughput screening, the hit-identification toolbox now includes the screening of fragment and fragment-like libraries, affinity selection mass spectrometry, and selection against DNA-encoded libraries (DELs). I will discuss the unique advantages and limitations of these techniques that make them more, or less, suitable for different target classes or discovery objectives, with an emphasis on those that indicate when DEL makes a good fit for a program.

Recent advances in genome-wide screening have enabled the identification of numerous putative therapeutically relevant targets for hit identification programs, though pursuing all these targets is neither feasible nor reasonable. Encoded Library Technology (ELT) is a hit identification platform using large collections of chemically diverse DNA-encoded small molecules selected against therapeutically relevant protein targets. At GSK, we have integrated in silico and experimental methods to rapidly predict small molecule tractability of novel targets. These outcomes allow us to prioritize therapeutically relevant targets based on empirical data and focus small molecule hit identification efforts on those most likely to succeed.

We will present the development of a solid phase DNA encoded library-based screening platform to identify compounds that bind to RNA fold libraries.  Mining the emergent interactions across the human transcriptome identified a bioactive interaction between the DEL-derived ligand and an oncogenic microRNA precursor.  The compound affected cancer-associated phenotypes in cells.  DNA encoded library screening can therefore be used to inform design of bioactive ligands targeting RNA.

Encoded Library Technologies enable discovery chemists to identify thousands of hits from screening campaigns with billions of molecules. High-quality hit validation approaches are essential for fast hit follow-up, but they typically require extensive chemical syntheses and biophysical and biochemical assays. In this talk, we present an efficient hit validation method using switchSENSE, which is a DNA-based technology to determine the binding kinetics, to address these issues. We demonstrate the benefits of the method for both resynthesized on-DNA chemical matter and aptamers.

Cancer is the leading cause of death worldwide contributing to nearly 10 million fatalities as of 2020.  Over the past several years there has been considerable interest in the Hippo pathway and the part this pathway plays in tumorigenesis when dysregulated.  Many of the roles in the Hippo pathway are mediated by the co-activators YAP and TAZ which are required for the transcriptional activity of the TEAD family (Transcriptional Enhancer factor TEFs 1,4,5 and 3) of transcription factors.  Dysregulation of the YAP/TAZ-TEAD activity is associated with cancer thus making them attractive targets for cancer therapies.  However, small molecule approaches to the disordered proteins YAP and TAZ or to the protein-protein interaction (PPI) interface of YAP/TAZ-TEAD has remained challenging.  The recent discovery of a druggable central lipid pocket in TEADs opened the door to development of small molecule inhibitors.  However, due to the lipophilic nature of this allosteric pocket, developing a robust biochemical assay has been a barrier for drug discovery.  At Nimbus, we have overcome challenges of the central lipid pocket to develop a robust biochemical assay.  Further, we have used structural elucidation and computational chemistry, along with in-parallel orthogonal approaches to understand the mechanism of action (MOA) of small molecule inhibitors of TEADs.  Our work uncovers different MOAs of TEAD small molecule inhibitors and provides hypotheses for these MOAs which could help contribute to the discovery of more potent and selective inhibitors for this critical pathway leading to potential valuable therapies for cancer patients.

Human Arginase 1 (hArg1) is a metalloenzyme that modulates T cell-mediated immune response. All current hArg1 inhibitors are small molecules usually < 350 Da in size. Here we report the first cryo-electron microscopy structures of potent and inhibitory anti-hArg antibodies bound to hArg1 which form distinct macromolecular complexes > 650 kDa. We unambiguously mapped epitopes and paratopes and determined that the antibodies have different mechanisms of action. These complexes present an alternative mechanism to inhibit hArg1 activity and highlight the ability to utilize antibodies as probes in the discovery and development of peptide and small molecule inhibitors for enzymes in general.

Cryo-EM has increasingly been implemented in recent years by pharmaceutical companies for structure-based drug design. Highly druggable but challenging or intractable targets for crystallography, most notably integral membrane proteins such as GPCRs, ion channels, and solute carrier proteins (SLCs), which comprise a disproportionate fraction of drug targets, have become much more amenable to structural characterization by cryo-EM I will discuss recent instructive examples from the implementation of cryo-EM at Pfizer.

The methionine adenosyltransferase MAT2a is an emerging target for the treatment of MTAP-deleted cancers. Here, I present the design and in vivo evaluation of a series of potent inhibitors of this enzyme, starting from a weak fragment hit determined by X-ray crystallography to bind to an allosteric site. I will detail the biophysical screening cascade, selection of fragment hits, and structure- and computationally-supported design of key compounds through fragment merging.

At AbbVie we find that multipronged small molecule hit finding strategies yield the most diverse chemotypes, wherein multiple complementarity screening platforms are paired with multiple robust biophysical confirmation tools prior to execution on a hit.  Here we present several case studies which include hit-finding through in vivo POC for a series of cytokine targets within our exploratory portfolio.

A successful fragment screening campaign against KEAP1 provided key starting points and information to generate a highly potent series against this PPI. To develop a second potent series, the key pharmacophoric elements were used to search the GSK collection. An SBDD campaign on the resulting hits generated a second potent series suitable for lead optimisation.