Son of sevenless homologue 1 (SOS1) is a guanine nucleotide exchange factor that catalyzes the exchange of GDP for GTP on RAS. In its active form, GTP-bound RAS is responsible for numerous critical cellular processes. Aberrant RAS activity is involved in ∼30% of all human cancers; hence, SOS1 is an attractive therapeutic target for its role in modulating RAS activation. Here, we describe a new series of benzimidazole-derived SOS1 agonists. Using structure-guided design, we discovered small molecules that increase nucleotide exchange on RAS in vitro at submicromolar concentrations, bind to SOS1 with low double-digit nanomolar affinity, rapidly enhance cellular RAS-GTP levels, and invoke biphasic signaling changes in phosphorylation of ERK 1/2. These compounds represent the most potent series of SOS1 agonists reported to date.

Deregulated RAS activity, often the result of mutation, is implicated in approximately 30% of all human cancers. Despite this statistic, no clinically successful treatment for RAS-driven tumors has yet been developed. One approach for modulating RAS activity is to target and affect the activity of proteins that interact with RAS, such as the guanine nucleotide exchange factor (GEF) son of sevenless homologue 1 (SOS1). Here, we report on structure-activity relationships (SAR) in an indole series of compounds. Using structure-based design, we systematically explored substitution patterns on the indole nucleus, the pendant amino acid moiety, and the linker unit that connects these two fragments. Best-in-class compounds activate the nucleotide exchange process at submicromolar concentrations in vitro, increase levels of active RAS-GTP in HeLa cells, and elicit signaling changes in the mitogen-activated protein kinase-extracellular regulated kinase (MAPK-ERK) pathway, resulting in a decrease in pERK1/2 protein levels at higher compound concentrations.

K-RAS is mutated in approximately 30% of human cancers, resulting in increased RAS signaling and tumor growth. Thus, RAS is a highly validated therapeutic target, especially in tumors of the pancreas, lung and colon. Although directly targeting RAS has proven to be challenging, it may be possible to target other proteins involved in RAS signaling, such as the guanine nucleotide exchange factor Son of Sevenless (SOS). We have previously reported on the discovery of small molecules that bind to SOS1, activate SOS-mediated nucleotide exchange on RAS, and paradoxically inhibit ERK phosphorylation (Burns et al., PNAS, 2014). Here, we describe the discovery of additional, structurally diverse small molecules that also bind to SOS1 in the same pocket and elicit similar biological effects. We tested >160,000 compounds in a fluorescence-based assay to assess their effects on SOS-mediated nucleotide exchange. X-Ray structures revealed that these small molecules bind to the CDC25 domain of SOS1. Compounds that elicited high levels of nucleotide exchange activity in vitro increased RAS-GTP levels in cells, and inhibited phospho ERK levels at higher treatment concentrations. The identification of structurally diverse SOS1 binding ligands may assist in the discovery of new molecules designed to target RAS-driven tumors.

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Proteins in the RAS family are important regulators of cellular signaling and, when mutated, can drive cancer pathogenesis. Despite considerable effort over the last 30 years, RAS proteins have proven to be recalcitrant therapeutic targets. One approach for modulating RAS signaling is to target proteins that interact with RAS, such as the guanine nucleotide exchange factor (GEF) son of sevenless homologue 1 (SOS1). Here, we report hit-to-lead studies on quinazoline-containing compounds that bind to SOS1 and activate nucleotide exchange on RAS. Using structure-based design, we refined the substituents attached to the quinazoline nucleus and built in additional interactions not present in the initial HTS hit. Optimized compounds activate nucleotide exchange at single-digit micromolar concentrations in vitro. In HeLa cells, these quinazolines increase the levels of RAS-GTP and cause signaling changes in the mitogen-activated protein kinase/extracellular regulated kinase (MAPK/ERK) pathway.

Since the discovery that RNA can catalyze chemical reactions, the number and variety of noncoding RNAs and the important roles they play in biology have been growing steadily. Backbone-modified RNA may find broad application in the fundamental biology and biomedicine of noncoding RNAs, providing that the modifications mimic the structure of the phosphodiester linkage and do not alter the conformation of RNA. In particular, the potential of RNA interference to become a new therapeutic strategy has revitalized interest in chemical modifications that may optimize the pharmacological properties of short interfering RNAs (siRNAs).[1] We are interested in hydrophobic nonionic mimics of the phosphate backbone, such as formacetals [2] and amides, [3] that may confer high nuclease resistance to siRNAs along with reduced charge and increased hydrophobicity. Earlier studies showed that 3'-CH 2 -CO-NH-5' internucleoside amide linkages (abbreviated here as AM1) were well-tolerated in the DNA strand of an A-type DNA-RNA heteroduplex.[4] Subsequently, we found that AM1 modifications did not change the thermal stability of RNA-RNA duplexes.[3] Most importantly, Iwase et al. [5] recently showed that AM1 amides were well-tolerated in the 3' overhangs of siRNAs.Taken together, these data suggest that amides may be good mimics of phosphate linkages in RNA; however, beyond simple melting-temperature measurements, the structural and thermodynamic properties of amide-modified RNA have not been established. Herein we present the first comprehensive structural and thermodynamic study that clearly shows that AM1 linkages do not disturb the A-type structure, thermal stability, and hydration of RNA duplexes. Despite the different geometry, amide AM1 appears to be an excellent mimic of the phosphate linkage in RNA. Our study complements structural studies on amide-modified DNA [4,6] and provides the first detailed insight into how the AM1 amide is accommodated in an RNA duplex.We started by designing a new route for the synthesis of the r(U AM1 A) dimer phosphoramidite, which was used to prepare the amide-modified RNA sequences (Scheme 1). The tert-butyldimethylsilyl (TBS) groups in the known 3'-allyluridine 1 [3] were replaced with 5'-O-methoxytrityl (MMT) and 2'-O-acetyl protecting groups suitable for solid-phase RNA synthesis. Two-step oxidative degradation of the alkene gave the carboxylic acid part 6 of the r(U AM1 A) dimer. [4a,b] For the synthesis of the amine part, we designed a novel route involving selective protection of the 2'-OH group of 5'-aminoadenosine with the triisopropylsilyloxymethyl (TOM) group. Treatment of 5'-azido-N-benzoyladenosine (7) with dibutyltin chloride followed by TOM chloride gave a mixture of 2'-and 3'-O-TOM nucleosides, from which the desired compound 8 was isolated in 30 % yield. Reduction of the azide gave the amine 9, which was coupled with the carboxylic acid 6 to give the dimer 10 (Scheme 2). Although protection of the 2'-OH group of adenosine 7 was relatively low-yielding, this strategy was advant...

Activating mutations in KRAS are the most frequent oncogenic alterations in cancer. The oncogenic hotspot position 12, located at the lip of the switch II pocket, offers a covalent attachment point for KRAS G12C inhibitors. To date, KRAS G12C inhibitors have been discovered by first covalently binding to the cysteine at position 12 and then optimizing pocket binding. We report on the discovery of the in vivo active KRAS G12C inhibitor BI-0474 using a different approach, in which small molecules that bind reversibly to the switch II pocket were identified and then optimized for non-covalent binding using structure-based design. Finally, the Michael acceptor containing warhead was attached. Our approach offers not only an alternative approach to discovering KRAS G12C inhibitors but also provides a starting point for the discovery of inhibitors against other oncogenic KRAS mutants.

(Diisopinocampheyl)borane ((Ipc) 2 BH) is a useful chiral organoborane reagent for asymmetric synthesis. (Ipc) 2 BH has been widely used in hydroboration reactions with alkenes leading, after oxidation of the resulting B–C, bond to enantioenriched secondary alcohols. This article describes the significant enhancement of enantiomeric purity of (Ipc) 2 BH, to 97% ee, in comparison to the considerably lower enantiomeric purity of the commercially available, inexpensive (α)‐pinene starting materials.