RAS oncogenes are among the most frequently mutated genes in cancer, with common driver mutations occurring at codons 12, 13, and 61. Here, we describe RMC-7977, a potent, oral, non-covalent, tri-complex RASMULTI(ON) small molecule inhibitor with broad spectrum activity for the active state of both mutant and wild-type (WT) KRAS, NRAS, and HRAS variants (a RASMULTI(ON) inhibitor). Within cells, RMC-7977 forms a tri-complex along with RAS(ON) and cyclophilin A (CypA), driving a near-immediate disruption of RAS effector binding and extinction of RAS(ON) signaling through steric occlusion. 

The methylthioadenosine phosphorylase (MTAP)-encoding gene is co-deleted with p16/CDKN2a in ~10-15% of all human cancers, leading to elevated levels of the MTAP substrate methylthioadenosine (MTA) in these cancers. MTA binds Protein Arginine N-Methyl Transferase (PRMT5) to form the PRMT5/MTA complex. We describe biophysics-aided discovery of a 4-(aminomethyl)phthalazin-1(2H)-one fragment and its evolution into MRTX1719, a clinical-stage, selective inhibitor of the PRMT5/MTA complex as a potential precision medicine for treating MTAP-deleted tumors.

Many biomolecular interactions form very long-lived complexes. These can be extremely challenging to measure leading to unfavorably long incubation times in biochemical/biophysical assays and inaccurate measurements. SPR has the advantage of measuring kinetics with high accuracy, the “chaser” method extends the range of measurable half-lives with high accuracy but are low throughput. We present adjustments to the chaser assay to improve throughput and its application to measuring protein interactions.

Targeted protein degradation is based on bifunctional ligands to recruit the ubiquitin-proteasome system. As an alternative strategy, we explored here the idea to design protein degraders based on the section of ligands that cause protein destabilization, and that in turn induce target degradation in cell. In an application of this approach, we found that agents can act as molecular crowbars that, destabilizing critical intramolecular interactions, cause protein degradation in cell.

Protein complexes and many non-protein targets are degraded in the lysosome via autophagy. This is in contrast to the ubiquitin proteosome system which is the 'final' destination of proteins. I describe our targeted protein degradation platform for lysosome: the AUTOphagy-TArgeting Chimera (AUTOTAC) TPD platform was used to selectively degrade pathological aggregates, and combat neurodegeneration-associated pathophysiology.

Affinity Selection-Mass Spectrometry (ASMS) identifies novel small molecule ligands for soluble and membrane proteins via a mass-encoded readout. We have recently applied ASMS to several challenging targets across different protein classes. These target proteins generally lack recognized druggable clefts and include PPI moieties. This presentation will review the process and status of hit ID comprising distinct externalized library HTS as well as reaching into of Sanofi’s internal collection via an intermediate virtual screening step.

Most human proteins lack chemical probes, and while several large-scale and generalizable small-molecule binding assays have been introduced, how compounds discovered in "binding-first" assays affect protein function often remains unclear. Here, we describe a "function-first" proteomic strategy that uses size exclusion chromatography (SEC) in conjunction with cysteine-directed activity-based protein profiling to identify changes in protein-protein interactions, including stereoselective engagement of SF3B1, stabilizing a dynamic state of the spliceosome.

Peptidomimetic design to mimic protein-protein interaction hotspot is a logical approach to PPI inhibitor discovery. We had done so for the BCL-XL -BH3 binding groove by mimicking important BH3 protein binding residues. Unexpectedly, more optimized ligands induced an entirely unexpected conformation of BCL-XL. In light of the current AI debate, we revisit this observation as a challenging benchmark to which AI-enabled PPI discovery should aspire.

We present the application of FBDD to the oncology target SHP2 phosphatase. Hits at an allosteric site were evolved using structure-based design to a low-nanomolar lead which inhibits tumour growth in xenografts. Phosphatases have been deemed undruggable due to their polar and conserved active sites, and we highlight the ability of fragment-based screening to detect hits in novel pockets which can be exploited to identify differentiated modulators for challenging targets.

MALT1 is a key regulator of antigen-receptor signaling, wherein it partners with BCL10 and CARMA1 to form the CBM complex in which protease activity of MALT1 cleaves the negative regulators leading to activation of NF-kB. Constitutive activation of NF-kB is a key driver in B cell lymphomas. We have identified a development candidate that inhibits MALT1 with the “best-in-class” profile including potent activity in whole blood and selectivity over off-targets.

Ligand efficiency metrics have made a major impact in medicinal chemistry, from the prioritization of early hits through lead optimization. With the ascendancy of covalent inhibitors in drug discovery, it is important to consider how to translate efficiency metrics to covalent modalities. Herein, we introduce ligand reactivity efficiency (LRE) as a means of correcting potency for intrinsic electrophilic reactivity, and explore kinetic regimes in which this analysis is appropriate.

The protein-protein interaction (PPI) between HEG1 (Heart of glass 1) and KRIT1 (Krev interaction trapped 1) plays an important role in controlling vascular development and permeability. Small-molecule modulators of this PPI may be useful as candidate therapeutics and/or pharmacological tools. Here we report the identification/characterization of hydroxy-naphthaldehyde (HNA) fragments that act as targeted covalent reversible ligands of a noncatalytic Lys of KRIT1 with high specificity and long residence time (>8h) resulting in inhibition of the PPI in cell-free and cell-based assays.