Structural Basis and Kinetic Pathway of RBM39 Recruitment to DCAF15 by a Sulfonamide Molecular Glue E7820.

E7820 and indisulam are two examples of aryl sulfonamides that recruit RBM39 to Rbx-Cul4-DDA1-DDB1-DCAF15 E3 ligase complex, leading to its ubiquitination and degradation by the proteasome. To understand their mechanism of action, we performed kinetic analysis on the recruitment of RBM39 to DCAF15 and solved a crystal structure of DDA1-DDB1-DCAF15 in complex with E7820 and the RRM2 domain of RBM39. E7820 packs in a shallow pocket on the surface of DCAF15 and the resulting modified interface binds RBM39 through the α1 helix of the RRM2 domain. Our kinetic studies revealed that aryl sulfonamide and RBM39 bind to DCAF15 in a synergistic manner. The structural and kinetic studies confirm aryl sulfonamides as molecular glues in the recruitment of RBM39 and provide a framework for future efforts to utilize DCAF15 to degrade other proteins of interest.

3-[(1S,2S,3R)-2,3-Difluoro-1-hydroxy-7-methylsulfonylindan-4-yl]oxy-5-fluorobenzonitrile (PT2977), a Hypoxia-Inducible Factor 2α (HIF-2α) Inhibitor for the Treatment of Clear Cell Renal Cell Carcinoma.

The hypoxia-inducible factor 2α (HIF-2α) is a key oncogenic driver in clear cell renal cell carcinoma (ccRCC). Our first HIF-2α inhibitor PT2385 demonstrated promising proof of concept clinical activity in heavily pretreated advanced ccRCC patients. However, PT2385 was restricted by variable and dose-limited pharmacokinetics resulting from extensive metabolism of PT2385 to its glucuronide metabolite. Herein we describe the discovery of second-generation HIF-2α inhibitor PT2977 with increased potency and improved pharmacokinetic profile achieved by reduction of phase 2 metabolism. Structural modification by changing the geminal difluoro group in PT2385 to a vicinal difluoro group resulted in enhanced potency, decreased lipophilicity, and significantly improved pharmacokinetic properties. In a phase 1 dose-escalation study, the clinical pharmacokinetics for PT2977 supports the hypothesis that attenuating the rate of glucuronidation would improve exposure and reduce variability in patients. Early evidence of clinical activity shows promise for PT2977 in the treatment of ccRCC.

Design and Activity of Specific Hypoxia-Inducible Factor-2α (HIF-2α) Inhibitors for the Treatment of Clear Cell Renal Cell Carcinoma: Discovery of Clinical Candidate ( S)-3-((2,2-Difluoro-1-hydroxy-7-(methylsulfonyl)-2,3-dihydro-1 H-inden-4-yl)oxy)-5-fluorobenzonitrile (PT2385).

HIF-2α, a member of the HIF family of transcription factors, is a key oncogenic driver in cancers such as clear cell renal cell carcinoma (ccRCC). A signature feature of these cancers is the overaccumulation of HIF-2α protein, often by inactivation of the E3 ligase VHL (von Hippel-Lindau). Herein we disclose our structure based drug design (SBDD) approach that culminated in the identification of PT2385, the first HIF-2α antagonist to enter clinical trials. Highlights include the use of a putative n → π*Ar interaction to guide early analog design, the conformational restriction of an essential hydroxyl moiety, and the remarkable impact of fluorination near the hydroxyl group. Evaluation of select compounds from two structural classes in a sequence of PK/PD, efficacy, PK, and metabolite profiling identified 10i (PT2385, luciferase EC50 = 27 nM) as the clinical candidate. Finally, a retrospective crystallographic analysis describes the structural perturbations necessary for efficient antagonism.

A Small-Molecule Antagonist of HIF2α Is Efficacious in Preclinical Models of Renal Cell Carcinoma.

More than 90% of clear cell renal cell carcinomas (ccRCC) exhibit inactivation of the von Hippel-Lindau (pVHL) tumor suppressor, establishing it as the major underlying cause of this malignancy. pVHL inactivation results in stabilization of the hypoxia-inducible transcription factors, HIF1α and HIF2α, leading to expression of a genetic program essential for the initiation and progression of ccRCC. Herein, we describe the potent, selective, and orally active small-molecule inhibitor PT2385 as a specific antagonist of HIF2α that allosterically blocks its dimerization with the HIF1α/2α transcriptional dimerization partner ARNT/HIF1ß. PT2385 inhibited the expression of HIF2α-dependent genes, including VEGF-A, PAI-1, and cyclin D1 in ccRCC cell lines and tumor xenografts. Treatment of tumor-bearing mice with PT2385 caused dramatic tumor regressions, validating HIF2α as a pivotal oncogenic driver in ccRCC. Notably, unlike other anticancer agents that inhibit VEGF receptor signaling, PT2385 exhibited no adverse effect on cardiovascular performance. Thus, PT2385 represents a novel class of therapeutics for the treatment of RCC with potent preclincal efficacy as well as improved tolerability relative to current agents that target the VEGF pathway. Cancer Res; 76(18); 5491-500. ©2016 AACR.

Discovery of AMG 925, a FLT3 and CDK4 dual kinase inhibitor with preferential affinity for the activated state of FLT3.

We describe the structural optimization of a lead compound 1 that exhibits dual inhibitory activities against FLT3 and CDK4. A series of pyrido[4',3':4,5]pyrrolo[2,3-d]pyrimidine derivatives was synthesized, and SAR analysis, using cell-based assays, led to the discovery of 28 (AMG 925), a potent and orally bioavailable dual inhibitor of CDK4 and FLT3, including many FLT3 mutants reported to date. Compound 28 inhibits the proliferation of a panel of human tumor cell lines including Colo205 (Rb(+)) and U937 (FLT3(WT)) and induced cell death in MOLM13 (FLT3(ITD)) and even in MOLM13 (FLT3(ITD, D835Y)), which exhibits resistance to a number of FLT3 inhibitors currently under clinical development. At well-tolerated doses, compound 28 leads to significant growth inhibition of MOLM13 xenografts in nude mice, and the activity correlates with inhibition of STAT5 and Rb phosphorylation.

Metabolism-guided discovery of a potent and orally bioavailable urea-based calcimimetic for the treatment of secondary hyperparathyroidism.

A series of urea based calcimimetics was optimized for potency and oral bioavailability. Crucial to this process was overcoming the poor pharmacokinetic properties of lead thiazole 1. Metabolism-guided modifications, characterized by the use of metabolite identification (ID) and measurement of time dependent inhibition (TDI) of CYP3A4, were essential to finding a compound suitable for oral dosing. Calcimimetic 18 exhibited excellent in vivo potency in a 5/6 nephrectomized rat model and cross-species pharmacokinetics.

Facile synthesis of substituted 5-amino- and 3-amino-1,2,4-thiadiazoles from a common precursor.

A novel approach to the synthesis of substituted 5-amino- and 3-amino-1,2,4-thiadiazoles beginning from a common precursor has been achieved. Derivatization by palladium-catalyzed Suzuki-Miyaura coupling enables the rapid preparation of analogs around this pharmaceutically relevant core. FMO calculations rationalize the observed chemoselectivity for coupling at chlorine.

A stereoselective synthesis of the bromopyrrole natural product (-)-agelastatin A.

Weaving an intricate web: A stereoselective synthesis of (-)-agelastatin A has been developed, which requires 11 steps from commercially available starting material. The application of a Rh-catalyzed intramolecular olefin aziridination reaction and the subsequent manipulation of the resulting tricyclic intermediate (see scheme) punctuate this study.

Exploring new uses for C-H amination: Ni-catalyzed cross-coupling of cyclic sulfamates.

[reaction: see text] Benzene-fused cyclic sulfamates are prepared from ortho-substituted phenolic starting materials through selective C-H amination or olefin aziridination. These unique heterocycles will engage in Ni-catalyzed cross-coupling reactions with aryl- and alkyl-Grignard reagents. Application of modern tools for C-N and C-C bond formation thus makes readily available functional amine derivatives and augments the possible uses for C-H amination in synthesis.

Stereochemical models for rh-catalyzed amination reactions of chiral sulfamates.

Oxidative C-H amination of chiral sulfamate esters using achiral Rh-carboxylate catalysts, PhI(OAc)(2), and MgO occurs in high yield and with good to excellent diastereocontrol. A number of examples are included to support a proposed transition state model that accounts for the observed stereoinduction. In addition, stereoselective intramolecular aziridination with substituted homoallyl sulfamates is demonstrated and is rationalized through an analogous stereochemical construct. [reaction: see text]

Enantioselective synthesis of the bromopyrrole alkaloids manzacidin A and C by stereospecific C-h bond oxidation.

The manzacidins represent a small family of structurally unique secondary metabolites found only sparingly in nature. Efforts to probe the pharmacological profile of these intriguing bromopyrrole alkaloids have been precluded by a deficiency of available material. Access to substantive quantities of both manzacidins A and C is now made possible through a rapid, enantioselective, and highly efficient synthesis that is described herein. The path to these targets showcases for the first time the distinct power of our catalytic C-H bond amination methodology for simplifying problems in alkaloid total synthesis. Application of this chemistry enables the facile and enantiospecific installation of tetrasubstituted carbinolamine stereocenters, functionality common to all of the manzacidins. The requisite materials for implementing our plan are assembled using modern tools for catalytic asymmetric synthesis that include both carbonyl-ene and directed hydrogenation reactions. In addition, a new protocol for tetrahydropyrimidine synthesis is established. The synthesis of each manzacidin comprises a 10-step sequence that proceeds in an overall yield of approximately 30%.