Structure-Based Design and Evaluation of Reversible KRAS G13D Inhibitors.

Oncogenic KRAS mutations were identified decades ago, yet the selective inhibition of specific KRAS mutant proteins represents an ongoing challenge. Recent progress has been made in targeting certain P-loop mutant proteins, in particular KRAS G12C, for which the covalent inhibition of the GDP state via the Switch II pocket is now a clinically validated strategy. Inhibition of other KRAS mutant proteins such as KRAS G13D, on the other hand, still requires clinical validation. The remoteness of the D13 residue relative to the Switch II pocket in combination with the solvent exposure and conformational flexibility of the D13 side chain, as well as the difficulties of targeting carboxylate residues covalently, renders this specific protein particularly challenging to target selectively. In this report, we describe the design and evaluation of potent and KRAS G13D-selective reversible inhibitors. Subnanomolar binding to the GDP state Switch II pocket and biochemical selectivity over WT KRAS are achieved by leveraging a salt bridge with D13.

AzidoTMT Enables Direct Enrichment and Highly Multiplexed Quantitation of Proteome-Wide Functional Residues.

Recent advances in targeted covalent inhibitors have aroused significant interest for their potential in drug development for difficult therapeutic targets. Proteome-wide profiling of functional residues is an integral step of covalent drug discovery aimed at defining actionable sites and evaluating compound selectivity in cells. A classical workflow for this purpose is called IsoTOP-ABPP, which employs an activity-based probe and two isotopically labeled azide-TEV-biotin tags to mark, enrich, and quantify proteome from two samples. Here we report a novel isobaric 11plex-AzidoTMT reagent and a new workflow, named AT-MAPP, that significantly expands multiplexing power as compared to the original isoTOP-ABPP. We demonstrate its application in identifying cysteine on- and off-targets using a KRAS G12C covalent inhibitor ARS-1620. However, changes in some of these hits can be explained by modulation at the protein and post-translational levels. Thus, it would be crucial to interrogate site-level bona fide changes in concurrence to proteome-level changes for corroboration. In addition, we perform a multiplexed covalent fragment screening using four acrylamide-based compounds as a proof-of-concept. This study identifies a diverse set of liganded cysteine residues in a compound-dependent manner with an average hit rate of 0.07% in intact cell. Lastly, we screened 20 sulfonyl fluoride-based compounds to demonstrate that the AT-MAPP assay is flexible for noncysteine functional residues such as tyrosine and lysine. Overall, we envision that 11plex-AzidoTMT will be a useful addition to the current toolbox for activity-based protein profiling and covalent drug development.

Conformation-locking antibodies for the discovery and characterization of KRAS inhibitors.

Small molecules that stabilize inactive protein conformations are an underutilized strategy for drugging dynamic or otherwise intractable proteins. To facilitate the discovery and characterization of such inhibitors, we created a screening platform to identify conformation-locking antibodies for molecular probes (CLAMPs) that distinguish and induce rare protein conformational states. Applying the approach to KRAS, we discovered CLAMPs that recognize the open conformation of KRASG12C stabilized by covalent inhibitors. One CLAMP enables the visualization of KRASG12C covalent modification in vivo and can be used to investigate response heterogeneity to KRASG12C inhibitors in patient tumors. A second CLAMP enhances the affinity of weak ligands binding to the KRASG12C switch II region (SWII) by stabilizing a specific conformation of KRASG12C, thereby enabling the discovery of such ligands that could serve as leads for the development of drugs in a high-throughput screen. We show that combining the complementary properties of antibodies and small molecules facilitates the study and drugging of dynamic proteins.

Discovery of Spiro-azaindoline Inhibitors of Hematopoietic Progenitor Kinase 1 (HPK1).

Hematopoietic progenitor kinase 1 (HPK1) is implicated as a negative regulator of T-cell receptor-induced T-cell activation. Studies using HPK1 kinase-dead knock-in animals have demonstrated the loss of HPK1 kinase activity resulted in an increase in T-cell function and tumor growth inhibition in glioma models. Herein, we describe the discovery of a series of small molecule inhibitors of HPK1. Using a structure-based drug design approach, the kinase selectivity of the molecules was significantly improved by inducing and stabilizing an unusual P-loop folded binding mode. The metabolic liabilities of the initial 7-azaindole high-throughput screening hit were mitigated by addressing a key metabolic soft spot along with physicochemical property-based optimization. The resulting spiro-azaindoline HPK1 inhibitors demonstrated improved in vitro ADME properties and the ability to induce cytokine production in primary human T-cells.

Development of the Regiodivergent Asymmetric Prenylation of 3-Substituted Oxindoles.

This paper describes our efforts to design a Pd-catalyzed asymmetric prenylation of 3-substituted oxindoles that affords access to both the linear and reverse-prenylated products. Both 3-alkyl- and 3-aryloxindoles performed well under our optimized reaction conditions. The regiodivergent alkylation of monoterpene-derived electrophiles using this methodology was also investigated. The utility of this methodology in natural product synthesis was demonstrated through the efficient total syntheses of four Flustra alkaloids, which also allowed the absolute stereochemistry of the prenylated oxindole products to be assigned. Surprisingly, the same enantiomer of ligand produced linear and branched regioisomers of opposite chirality.

Ventral striatal gamma oscillations are highly variable from trial to trial, and are dominated by behavioural state, and only weakly influenced by outcome value.

The human and rodent ventral striatal local field potentials show striking oscillations in the gamma band (~ 40-100 Hz), which have been linked to aspects of behaviour such as reward anticipation and delivery, movement initiation, learning from feedback, and decision-making. These oscillations show a rich temporal organization, whose relationship with behavioural variables is not well understood. Here, we show that, in rats performing a conditioned approach task, low-gamma and high-gamma oscillations during an immobile reward anticipation epoch were largely insensitive to outcome value, even though rats distinguished behaviourally between different outcomes, and single units encoded outcome value. Behaviour was highly stereotyped, yet we observed large variability from trial to trial in the occurrence and timing of these oscillations. Furthermore, higher-order features such as high-gamma power leading low-gamma power, and phase-amplitude coupling to lower-frequency bands, were only marginally modulated by outcome value. Moreover, these patterns closely resembled those found during off-task rest periods in which no rewards could be earned. These observations suggest a new interpretation of ventral striatal gamma oscillations as reflecting a default or resting state, with only minor and highly variable modulation by specific task-related variables.

Chemoselective chromium(II)-catalyzed cross-coupling reactions of dichlorinated heteroaromatics with functionalized aryl grignard reagents.

Chromium(II) chloride catalyzes the chemoselective cross-coupling reaction of dichloropyridines with a range of functionalized (hetero)aromatic Grignard reagents at room temperature. Functional groups, such as esters and acetals, are well tolerated in this transformation. Previously challenging substrates, quinolines and isoquinolines, participate in the selective Cr-catalyzed cross-coupling in cyclopentyl methyl ether (CPME) as the solvent. The effective purging of Cr salts is demonstrated by using various solid supports.

Palladium-catalyzed α-arylation of sultams with aryl and heteroaryl iodides.

Palladium(0)-catalyzed conditions for the α-arylation of sultams with aryl and heteroaryl iodides have been developed. Arylation of 3-substituted 1,3-propanesultams gave rise to high yields and high diastereomeric ratios, leading to the thermodynamically favored cis product. The arylation was broadly applicable to various electron-rich and electron-poor (hetero)aromatic iodides.

Asymmetric stereodivergent strategy towards aminocyclitols.

A concise asymmetric synthesis of aminocyclitols, such as diastereomeric 2-deoxystreptamine analogues and conduramine A, is described. The Pd-catalyzed asymmetric desymmetrization of meso 1,4-dibenzolate enables the synthesis of highly oxidized cyclohexane architectures. These scaffolds can potentially be used to access new aminoglycoside antibiotics and enantiomerically pure α-glucosidase inhibitors.

Chemoselective sp2-sp3 cross-couplings: iron-catalyzed alkyl transfer to dihaloaromatics.

The chemoselective functionalization of a range of dihaloaromatics with methyl, cyclopropyl, and higher alkyl Grignard reagents via iron-catalyzed cross-coupling is described. The site selectivity of C-X (X = halogen) activation is determined by factors such as the position of the halogen on the ring, the solvent, and the nucleophile. A one-pot protocol for the chemoselective synthesis of mixed dialkyl heterocycles is achieved solely employing iron catalysis.

Exploring the unique reactivity of diazoesters: an efficient approach to chiral ß-amino acids.

The development of a highly stereospecific process for the C-O to C-N exchange with retention of configuration is described. This transformation enables access to optically enriched ß-amido-α-diazoesters. These products are transformed to ß-amino acids not readily accessible using known methods.

Total synthesis of (-)-18-epi-peloruside A: an alkyne linchpin strategy.

A convergent synthetic route toward cytotoxic agent peloruside A that hinges on the use of an alkyne linchpin to assemble the natural product is described. Other highlights of this synthesis include an asymmetric desymmetrization reaction of a 1,3-diol, a one-pot conversion of a dibromoolefin to a stereodefined enone, and a diastereoselective aldol condensation. Misassignment of the absolute stereochemistry of the C18 stereocenter in our synthesis provided the natural product epimeric at the C18 ethyl stereocenter.

Theta phase precession beyond the hippocampus.

The spike timing of spatially tuned cells throughout the rodent hippocampal formation displays a strikingly robust and precise organization. In individual place cells, spikes precess relative to the theta local field potential (6-10 Hz) as an animal traverses a place field. At the population level, theta cycles shape repeated, compressed place cell sequences that correspond to coherent paths. The theta phase precession phenomenon not only has afforded insights into how multiple processing elements in the hippocampal formation interact, but is also believed to facilitate hippocampal contributions to rapid learning, navigation, and lookahead. However, theta phase precession is not unique to the hippocampus, suggesting that insights derived from hippocampal phase precession could elucidate processing in other structures. In this review, we consider the implications of extrahippocampal phase precession in terms of mechanisms and functional relevance. We focus on phase precession in the ventral striatum (vStr), a prominent output structure of the hippocampus in which phase precession systematically appears in the firing of reward-anticipatory 'ramp' neurons. We outline how ventral striatal phase precession can advance our understanding of behaviors thought to depend on interactions between the hippocampus and the vStr, such as conditioned place preference and context-dependent reinstatement. More generally, we argue that phase precession can be a useful experimental tool in dissecting the functional connectivity between the hippocampus and its outputs.

Development of the enantioselective addition of ethyl diazoacetate to aldehydes: asymmetric synthesis of 1,2-diols.

A novel synthetic strategy toward the asymmetric synthesis of vicinal diols bearing a tertiary center is presented. The method encompasses the dinuclear Mg-catalyzed asymmetric addition of ethyl diazoacetate into several aldehydes, oxidation of the diazo functionality, and diastereoselective alkyl transfer of various organometallics into the resulting chiral ß-hydroxy-α-ketoesters to afford a diverse range of 1,2-diols in high yield, diastereoselectivity, and chirality transfer.

Synthesis and reactivity of unique heterocyclic structures en route to substituted diamines.

Rhodium-catalyzed oxidative cyclization of allylic hydroxylamine-derived sulfamate esters furnishes a novel family of bicyclic aziridines that serve as functional precursors to substituted diamines. Investigations with the N4-Troc form of these heterocycles have led to manifold improvements in reaction performance and scope and have revealed unique differences in the stability and reactivity of such compounds dictated by the choice of N4-protecting group.

Exercising regiocontrol in palladium-catalyzed asymmetric prenylations and geranylation: unifying strategy toward flustramines A and B.

Pd-catalyzed asymmetric prenylation of oxindoles to afford selectively either the prenyl or reverse-prenyl product has been demonstrated. Control of the regioselectivity in this transformation is governed by the choice of ligand, solvent, and halide additive. The resulting prenylated and reverse-prenylated products were transformed into ent-flustramides and ent-flustramines A and B. Additionally, control of the regio- and diastereoselectivity was obtained using π-geranylpalladium complexes.

Asymmetric synthesis of diamine derivatives via sequential palladium and rhodium catalysis.

The use of a bifunctional nitrogen nucleophile and an allyl carbonate starting material in successive enantioselective palladium- and diastereoselective rhodium-catalyzed reactions enables the rapid assembly of unique amino aziridine products. Further elaboration of these materials affords complex, stereodefined polyamine architectures, thus demonstrating the power of these combined methods for simplifying asymmetric C-N bond construction.

Magnesium-catalyzed asymmetric direct aldol addition of ethyl diazoacetate to aromatic, aliphatic, and alpha,beta-unsaturated aldehydes.

Magnesium-catalyzed enantioselective aldol between ethyl diazoacetate and aromatic, aliphatic, and alpha,beta-unsaturated aldehydes affords alpha-diazo-beta-hydroxy-esters in high enantioselectivities. Aldol adducts resulting from this asymmetric transformation are versatile intermediates toward the synthesis of several ester containing chiral building blocks.

Dinuclear zinc-catalyzed asymmetric desymmetrization of acyclic 2-substituted-1,3-propanediols: a powerful entry into chiral building blocks.

The asymmetric acylation of meso-2-substituted-1,3-propanediols by using an amphoteric chiral dinuclear zinc catalyst is described. It is has been demonstrated that both 2-alkyl- and 2-aryl-1,3-propanediols can be desymmetrized in high yields and enantioselectivities by using the same family of ligands. Given that both antipodes of the chiral catalyst are available, both enantiomers of the desymmetrized product can be obtained from the same starting material. The synthetic utility of the desymmetrized products has been demonstrated by the synthesis of several chiral building blocks with high enantiomeric purities.

The development of potent and selective bisarylmaleimide GSK3 inhibitors.

Many 3-aryl-4-(1,2,3,4-tetrahydro[1,4]diazepino[6,7,1-hi]indol-7-yl)maleimides exhibit potent GSK3 inhibitory activity (<100 nM IC(50)), although few show significant selectivity (>100x) versus CDK2, CDK4, or PKCbetaII. However, combining 3-(imidazo[1,2-a]pyridin-3-yl), 3-(pyrazolo[1,5-a]pyridin-3-yl) or aza-analogs with a 4-(2-acyl-(1,2,3,4-tetrahydro[1,4]diazepino[6,7,1-hi]indol-7-yl)) group on the maleimide resulted in very potent inhibitors of GSK3 (160 to >10,000-fold selectivity versus CDK2/4 and PKCbetaII. These compounds also inhibited tau phosphorylation in cells and were effective in lowering plasma glucose in a rat model of type 2 diabetes (ZDF rat).