Asymmetric Synthesis of N-Alkyl Amino Acids through a Biocatalytic Dynamic Kinetic Resolution of PEGylated N-Alkyl Amino Esters

The first examples of a practical procedure for a lipase-catalyzed dynamic kinetic resolution of PEGylated N-alkyl amino esters is reported. This method allows for the preparation of a broad range of aromatic and aliphatic enantiomerically enriched N-alkyl unnatural amino acids in up to 98% yield and 99% ee. We have found that PEGylated esters have a significant solubility advantage and improved reactivity over traditional hydrophobic lipase substrates, thereby allowing for efficient and scalable dynamic kinetic resolution (DKR) under aqueous conditions.

Abstract 1628: A small-molecule inhibitor of WRN selectively kills MSI-H cancer cells and phenocopies WRN genetic defects

Werner syndrome protein (WRN) is a RecQ-family helicase involved in the maintenance of genome integrity. Germline mutations in WRN cause premature aging and cancer predisposition. Analysis of systematic RNAi and CRISPR screening data has previously revealed that WRN is essential for the survival of cancer cell lines with high microsatellite instability (MSI-H). We have developed potent and selective small-molecule inhibitors of WRN helicase (WRNi) and showed that pharmacological inhibition of WRN causes lethality and induction of DNA damage markers selectively in MSI-H cancer cell lines compared to microsatellite-stable (MSS) cell lines. Screening of WRNi across a large panel of pooled, barcoded cell lines in the PRISM format revealed selective sensitivity in MSI-H cell lines and showed that pharmacological inhibition of WRN is highly correlated with genetic ablation of WRN across this panel, confirming selectivity for WRN. In vivo evaluation demonstrated robust and MSI-selective tumor regressions. These data provide pharmacological proof-of-concept for the WRN/MSI-H synthetic lethal relationship and support WRN inhibition as a novel therapeutic approach for the treatment of MSI-H cancers.

Citation Format: Yanhua Rao, Anjana Srivatsan, Marya Liimatta, Diana Munoz, Jeanne Quirit, Jianxia Shi, An Nguyen, Xin Linghu, Federowicz Federowicz, Brian Jones, Melissa Fleury, Zach Newby, Michael P. Dillon, Paul A. Barsanti, Mark R. Lackner, Michael A. White, Yang Lee, Phil Landis, Yang Peng, Michelle Cicchini, Josh Cottom, Leng Nickels, Ed Brnardic, Michael DeMartino, Josh Taygerly. A small-molecule inhibitor of WRN selectively kills MSI-H cancer cells and phenocopies WRN genetic defects [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1628.

Abstract 2043: Synthetic lethality of PARG inhibition in tumors with homologous recombination deficiencies

Background:The enzyme Poly(ADP-ribose) glycohydrolase (PARG) plays an important role during the DNA damage repair process through hydrolysis of poly(ADP-ribose)(PAR) chains and accounts for approximately 90% of dePARylation activity within the cell. PAR chain synthesis is achieved by poly(ADP-ribose) polymerases (PARPs), which use donor NAD+ molecules to link repeating ADP-ribose units. The resulting PAR chains serve as a platform to recruit DNA repair proteins that are critical for single-strand break (SSB) repair. Following DNA repair PARG hydrolyzes the linkages to break down PAR chains, completing the cycle. Recent studies also found that dePARylation is necessary for the translocation of DNA repair proteins such as XRCC1 to SSB suggesting a more direct role for PARG in DNA damage repair. PARP inhibitors (PARPi), demonstrate synthetic lethality in cells with impaired homologous recombination (HR)-mediated DNA repair. Clinical studies have shown that responses to PARPi are often accompanied by high rates of resistance, generating a need for additional therapies for patients with HR-deficient tumors. The ability of PARG inhibition (PARGi) to exacerbate replication deficiencies makes it a promising therapeutic target for a broad range of cancer types with genomic instability. We therefore sought out to evaluate the effects of PARGi in HR-deficient ovarian and breast cancer models.

Methods: To understand the effects of PARGi in cell growth and survival, a panel of HR-deficient cell lines and cell line derived xenografts (CDX) were exposed to PARGi alone or in combination with DNA damage response inhibitors (DDRi). In these studies, PAR chain accumulation was assessed as a marker of target engagement and PARPi was used to assess on target effects in vitro.

Results: Using cellular proliferation assays and xenograft models, we find that PARGi increases the cellular levels of PAR and significantly decreases the viability of HR-deficient cancer cell lines. Furthermore, inhibition of cell proliferation by PARGi is antagonized by PARPi, which is consistent with an on-target cellular mechanism of action (MOA). In conclusion, PARGi induces significant accumulation of PAR chains and decreases cell proliferation both in vitro and in vivo in HR-deficient tumor cells. Ongoing exploratory studies will further delineate the molecular underpinning of the relationship between HR-deficiency and PARGi.

Citation Format: Monah Abed, Diana Munoz, Firoz Jaipuri, Nandini Ravindran, Vidya Seshadri, Marya Liimatta, Claire Neilan, Xin Linghu, An Nguyen, Marie-Claire Wagle, Zineb Mounir. Synthetic lethality of PARG inhibition in tumors with homologous recombination deficiencies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2043.

Abstract 1956: In vitro and in vivo characterization of novel MAT2A allosteric inhibitors

Background: MAT2A (Methionine adenosyltransferase 2A) catalyzes the formation of S-adenosylmethionine (SAM) from methionine and ATP. PRMT5, a highly conserved protein arginine methyltransferase that is required for cell proliferation, uses SAM as its methyl donor. PRMT5 activity is inhibited by increased MTA levels in methylthioadenosine phosphorylase (MTAP)-deleted tumor cells. MTAP-deleted tumor cells are thus more vulnerable to MAT2A inhibition compared to MTAP-WT cells. This synthetic lethality between MTAP and MAT2A suggests that MAT2A inhibitors may be useful as anti-tumor agents in the MTAP-deleted cancers, which occurs in ~ 15% of all cancers.

Results: We have designed, synthesized and evaluated a novel series of small-molecule MAT2A inhibitors that are very potent in biochemical assays. Co-crystal structures of inhibitor-MAT2A complexes were solved and shed light on binding mode and key interactions. Biochemical mechanistic studies suggested that these compounds are allosteric inhibitors of MAT2A and are non-competitive inhibitors of MAT2A with respect to both ATP and methionine. These compounds displayed potent cellular anti-proliferation activity as well as cellular SAM modulation along with desired DMPK properties. Optimized compounds, upon oral dosing, demonstrated significant PD marker modulation and tumor growth inhibition in HCT116 MTAP-null and several endogenous MTAP-null xenograft mouse models. These agents demonstrated an acceptable safety profile in 7-day oral repeat dose tolerability studies in the rat.

Citation Format: Zhonghua Pei, Muzaffar Alam, Neil Bhola, Leah Cleary, Jake Drummond, Marcus Fisher, Melissa Fleury, Candy Garcia, Atieh Givmanesh, Xin Linghu, Ethan McSpadden, Zineb Mounir, Claire Neilan, Zach Newby, Senthil Perumal, Richard Steel, James Sutton, Kedar Vaidya, Marie-Claire Wagle, Jianhong Wang, Bing Yao, Mark Lackner, Michael P. Dillon. In vitro and in vivo characterization of novel MAT2A allosteric inhibitors [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1956.

Stereocontrolled Synthesis of Arylomycin-Based Gram-Negative Antibiotic GDC-5338

We report herein an efficient, stereocontrolled, and chromatography-free synthesis of the novel broad spectrum antibiotic GDC-5338. The route features the construction of a functionalized tripeptide backbone, a high-yielding macrocyclization via a Pd-catalyzed Suzuki-Miyaura reaction, and the late-stage elaboration of key amide bonds with minimal stereochemical erosion. Through extensive reaction development and analytical understanding, these key advancements allowed the preparation of GDC-5338 in 17 steps, 15% overall yield, >99 A % HPLC, and >99:1 dr.

Macrolactamization Approaches to Arylomycin Antibiotics Core

Two practical entries to arylomycin antibiotics core structures are investigated. In route A, the activation of l-Hpg for the key macrolactamization step is achieved in 89% yield in the presence of unprotected phenol and amine functionalities. Alternatively, a propanephosphonic acid anhydride (T3P)-promoted coupling between thel-Tyr and l-Ala moieties in route B led to a facile macrolactamization in 68% yield with a marked reduction in competing oligomerization.

Construction of Polycyclic β-Ketoesters Using a Homoconjugate Addition/Decarboxylative Dieckmann Annulation Strategy

The construction of arene-fused cyclic β-ketoesters from 2-iodoaryl esters and 1,1-cyclopropane diesters is detailed. The synthetic method takes advantage of a CuI·SMe₂-mediated homoconjugate addition followed by a decarboxylative Dieckmann cyclization to afford valuable polycyclic building blocks. Various iodoaryl esters and 1,1-cyclopropane diesters were evaluated, and the limitations of both reactions are discussed. Several mechanistic probes are detailed and synthetic applications are described.

Abstract DDT02-03: Discovery of GDC-0994, a potent and selective ERK1/2 inhibitor in early clinical development

The extracellular-signal-regulated kinases (ERK1 and ERK2) represent an essential node within the RAS/RAF/MEK/ERK signaling cascade that commonly is activated by oncogenic mutations in BRAF or RAS or by upstream oncogenic signaling, such as receptor tyrosine kinase (RTK) activation. While targeting upstream nodes with RAF and MEK inhibitors has proven effective clinically, resistance frequently develops through reactivation of the pathway. Simultaneous targeting of multiple nodes in the pathway, such as MEK and ERK, offers the prospect of enhanced efficacy as well as reduced potential for acquired resistance. Here, we present the discovery and characterization of GDC-0994, an orally bioavailable, small molecule inhibitor of ERK kinase activity. GDC-0994 is highly selective for ERK1 and ERK2, with biochemical potency of 1.1 nM and 0.3 nM, respectively. Daily, oral dosing of GDC-0994 results in significant single-agent activity in multiple in vivo cancer models, including KRAS-mutant and BRAF-mutant human xenograft tumors in mice. PD biomarker inhibition of phospho-p90RSK in these tumors correlates with potency in vitro and in vivo. In contrast to other published ERK inhibitors, GDC-0994 neither increases nor decreases phospho-ERK, suggesting that different ERK inhibitors have alternative mechanisms of action with respect to feedback signaling. Furthermore, we demonstrate a novel approach for targeting the oncogenic signaling through the RAS pathway by combining ERK and MEK inhibitors. GDC-0994 is currently in Phase I clinical development.

Citation Format: Kirk Robarge, Jacob Schwarz, Jim Blake, Michael Burkard, Jocelyn Chan, Huifen Chen, Kang-Jye Chou, Dolores Diaz, John Gaudino, Stephen Gould, Jonas Grina, Xin Linghu, Lichuan Liu, Matthew Martinson, David A. Moreno, Christine Orr, Patricia Pacheco, Ann Qin, Kevin Rasor, Li Ren, Sheerin Shahidi-Latham, Jeffrey Stults, Francis Sullivan, Weiru Wang, Peter Yin, Aihe Zhou, Marcia Belvin, Mark Merchant, John G. Moffat. Discovery of GDC-0994, a potent and selective ERK1/2 inhibitor in early clinical development. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr DDT02-03. doi:10.1158/1538-7445.AM2014-DDT02-03

Silyl glyoxylates. Conception and realization of flexible conjunctive reagents for multicomponent coupling

This Perspective describes the discovery and development of silyl glyoxylates, a new family of conjunctive reagents for use in multicomponent coupling reactions. The selection of the nucleophilic and electrophilic components determines whether the silyl glyoxylate reagent will function as a synthetic equivalent to the dipolar glycolic acid synthon, the glyoxylate anion synthon, or the α-keto ester homoenolate synthon. The ability to select for any of these reaction modes has translated to excellent structural diversity in the derived three- and four-component coupling adducts. Preliminary findings on the development of catalytic reactions using these reagents are detailed, as are the design and discovery of new reactions directed toward particular functional group arrays embedded within bioactive natural products.

Symbiotic reagent activation: Oppenauer oxidation of magnesium alkoxides by silylglyoxylates triggers second-stage aldolization

The treatment of silylglyoxylates with magnesium alkoxides at ambient temperature results in symbiotic Oppenauer oxidation of the alkoxide and Meerwein-Ponndorf-Verley reduction of the silylglyoxylate. The reduced silylglyoxylate undergoes subsequent [1,2]-Brook rearrangement and aldol reaction with the carbonyl oxidation product. The magnesium alkoxide may be accessed via deprotonation of primary or secondary alcohols with EtMgBr, via addition of Grignard reagents to aldehydes, or via CuI-catalyzed alkylation of epoxides. For aliphatic primary alkoxides, moderate levels of anti diastereoselection are observed. A crossover experiment reveals that dissociation of the nascent aldehyde from the magnesium center is faster than [1,2]-Brook rearrangement and aldolization.

Enantioselective Synthesis of γ-Hydroxyenones by Chiral Base-Catalyzed Kornblum DeLaMare Rearrangement

A cinchona-alkaloid catalyzed asymmetric Kornblum DeLaMare rearrangement has been developed. Thus, enantioenriched 4-hydroxyenones are prepared from dienes by a two-step sequence involving photochemical dioxygenation and chiral base-catalyzed desymmetrization of the resulting endoperoxides.

Symbiotic reagent activation: Oppenauer oxidation of magnesium alkoxides by silylglyoxylates triggers second-stage aldolization

The treatment of silylglyoxylates with magnesium alkoxides at ambient temperature results in symbiotic Oppenauer oxidation of the alkoxide and Meerwein-Ponndorf-Verley reduction of the silylglyoxylate. The reduced silylglyoxylate undergoes subsequent [1,2]-Brook rearrangement and aldol reaction with the carbonyl oxidation product. The magnesium alkoxide may be accessed via deprotonation of primary or secondary alcohols with EtMgBr, via addition of Grignard reagents to aldehydes, or via CuI-catalyzed alkylation of epoxides. For aliphatic primary alkoxides, moderate levels of anti diastereoselection are observed. A crossover experiment reveals that dissociation of the nascent aldehyde from the magnesium center is faster than [1,2]-Brook rearrangement and aldolization.

Mechanism and Scope of the Cyanide-Catalyzed Cross Silyl Benzoin Reaction

In this work, cross silyl benzoin addition reactions between acylsilanes (1) and aldehydes (2) catalyzed by metal cyanides are described. Unsymmetrical aryl-, heteroaryl-, and alkyl-substituted benzoin adducts can be generated in moderate to excellent yields with complete regiocontrol using potassium cyanide and a phase transfer catalyst. From a screen of transition metal cyanide complexes, lanthanum tricyanide was identified as an improved second-generation catalyst for the cross silyl benzoin reaction. A study of the influence of water on the KCN-catalyzed cross silyl benzoin addition revealed more practical reaction conditions using unpurified solvent under ambient conditions. A sequential silyl benzoin addition/cyanation/O-acylation reaction that resulted in two new C-C bonds was achieved in excellent yield. The mechanism of cross silyl benzoin addition is proposed in detail and is supported by crossover studies and a number of unambiguous experiments designed to ascertain the reversibility of key steps. No productive chemistry arises from cyanation of the more electrophilic aldehyde component. Formation of the carbon-carbon bond is shown to be the last irreversible step in the reaction.

Metallophosphites as umpolung catalysts: the enantioselective cross silyl benzoin reaction

Carbonyl polarity reversal (umpolung) has been realized employing metallophosphites as catalysts. As a result, nonenzymatic asymmetric cross silyl benzoin reactions have been achieved, giving optically active silyl ether-protected benzoin adducts. The reaction is general with respect to aryl, alkyl, and heterocyclic substrates with good to excellent yields and good to excellent enantioselectivities.

Tandem carbon-carbon bond constructions via catalyzed cyanation/Brook rearrangement/C-acylation reactions of acylsilanes

[reaction: see text] A tandem nucleophile-catalyzed cyanation/Brook rearrangement/C-acylation has been developed. Phase transfer cocatalysts facilitate cyanide-catalyzed reactions between acylsilanes and cyanoformates to afford protected tertiary carbinol products. A catalytic cycle is proposed involving cyanation of an acylsilane, [1,2]-Brook rearrangement, and C-acylation of the derived carbanion by a cyanoformate ester. The reaction offers an efficient method for the preparation of functionalized, unsymmetrical malonic acid derivatives.