GDC-0084 Chemical Properties

Density 

1.60±0.1 g/cm3(Predicted)

storage temp. 

Store at -20°C

solubility 

insoluble in H2O; insoluble in EtOH; ≥2.83 mg/mL in DMSO with ultrasonic

form 

Solid

pka

2.62±0.40(Predicted)

color 

White to off-white

InChI

InChI=1S/C18H22N8O2/c1-18(2)16-22-12-14(25-3-6-27-7-4-25)23-13(11-9-20-17(19)21-10-11)24-15(12)26(16)5-8-28-18/h9-10H,3-8H2,1-2H3,(H2,19,20,21)

InChIKey

LGWACEZVCMBSKW-UHFFFAOYSA-N

SMILES

C1(N)=NC=C(C2N=C(N3CCOCC3)C3=C(N=2)N2CCOC(C)(C)C2=N3)C=N1

GDC-0084 Usage And Synthesis

Uses

GDC-0084 is an inhibitor of phosphoinositide 3-kinase (PI3K) and mTOR (1,2). Inhibitors of PI3K are useful compounds for developing treatments for brain tumors.

Preparation

Stumpf et al. at Genentech Inc. (Roche group) developed an efficient multikilogram process to synthesize the brain penetrant PI3K inhibitor, GDC?\0084, a potential drug candidate for the treatment of several brain cancers. An efficient Suzuki coupling reaction between a chloropyrimidine and an arylboronic ester using a palladium catalyst at low loading was reported. The optimized conditions were demonstrated on 6.75 kg of a chloropyrimidine intermediate, providing 7.49 kg of crude GDC?\0084 (94% yield, 99.4% HPLC purity). Using the commercially available XPhos Pd G2 catalyst, instead of the usual PdCl2(dppf)·CH2Cl2 catalyst, it was possible to reduce the catalyst loading from 2 to 0.5 mol%. A final scavenging/recrystallization combination from Si?\Thiol (a solid?\supported resin) and acetic acid/water provided the crude GDC?\0084 with the required purity and polymorphic form (off?\white solid, 6.41 kg, 83% yield, 99.7% HPLC purity).

Genentech’s route to GDC?\0084 employing a pivotal Suzuki reaction.

Biological Activity

gdc-0084 is a potent and brain penetrant inhibitor of pi3k and mtor with ki values of 2 nm and 70 nm for pi3kα and mtor, respectively [1].glioblastoma (gbm) is the most common primary brain tumor in adults and aberrant pi3k signaling is associated with more than 80% of cases. the pi3k pathway represents a potential target for the treatment of this disease and the inhibitors would need to freely cross the blood-brain barrier (bbb) [1][2].gdc-0084 is a potent and brain penetrant inhibitor of pi3k and mtor. in vitro kinase assay, gdc-0084 exhibited ki values of 2 nm, 46 nm, 3 nm, 10 nm and 70 nm for pi3kα, pi3kβ, pi3kδ, pi3kγ and mtor, respectively. in five different gbm cell lines, gdc-0084 had antiproliferative activities with ec50 values ranging from 0.3 to 1.1 μm. gdc-0084 has excellent human metabolic stability in microsomal and hepatocyte incubations [1]. in transfected cell lines over-expressing human or mouse p-gp or bcrp, gdc-0084 was a poor substrate of these efflux transporters. in mice brain, gdc-0084 significantly lowered pakt and ps6 levels [2].in rats after a 15 mg/kg dose of gdc-0084, the total brain-to-plasma ratio was 1.9-3.3. in subcutaneous u87 glioblastoma tumor xenograft mice model, gdc-0084 significantly inhibited tumor growth in a dose-dependent way. gdc-0084 also concentration-dependently inhibited pakt [1].[1]. heffron tp1, ndubaku co1, salphati l1, et al. discovery of clinical development candidate gdc-0084, a brain penetrant inhibitor of pi3k and mtor. acs med chem lett. 2016 feb 16;7(4):351-6.[2]. salphati l, alicke b, heffron tp, et al. brain distribution and efficacy of the brain penetrant pi3k inhibitor gdc-0084 in orthotopic mouse models of human glioblastoma. drug metab dispos. 2016 dec;44(12):1881-1889. epub 2016 sep 16.

Synthesis

Step 3: 2-Chloro-6,6-dimethyl-4-morpholino-8,9-dihydro-6H-[1,4]oxazolo[3,4-e]purine (180 mg, 0.56 mmol) was dissolved with 2-aminopyrimidine-5-boronic acid pinacol ester (180 mg, 0.83 mmol) in 1,2-dimethoxyethane (5.1 mL) and 1.0 M cesium carbonate aqueous solution (1.7 mL). The reaction mixture was degassed for 5 min and circulated under nitrogen atmosphere. Subsequently, 1,1'-bis(diphenylphosphino)ferrocene palladium(II) chloride (54 mg, 0.067 mmol) was added, degassed again and circulated. The reaction vial was placed in a microwave reactor and radiated at 140 °C for 20 min. Upon completion of the reaction, the solid precipitate formed was collected by filtration and rinsed with excess water. The precipitate was dissolved in dichloromethane (DCM) and purified by fast column chromatography (FCC, 40 g silica gel, 0.5-4% methanol/DCM solution, slow gradient) to afford the target product, 5-(6,6-dimethyl-4-morpholino-8,9-dihydro-6H-[1,4]oxazino[4,3-e]purin-2-yl)pyrimidin-2-amine, as a tan powder (56 mg, 27% yield).MS (ESI+): m/z 383.1 (M + H+).1H NMR (400 MHz, DMSO) δ 9.09 (s, 2H), 7.00 (s, 2H), 4.23 (m, 4H), 4.13 (m, 4H), 3.79-3.68 (m, 4H), 2.50 (s, 6H).

in vivo

IC 50

PI3Kα: 2 nM (Ki); PI3Kδ: 3 nM (Ki); PI3Kγ: 10 nM (Ki); PI3Kβ: 46 nM (Ki); mTOR: 70 nM (Ki)

References

[1] Organic Process Research and Development, 2016, vol. 20, # 4, p. 751 - 759
[2] Patent: WO2012/82997, 2012, A1. Location in patent: Page/Page column 91
[3] ACS Medicinal Chemistry Letters, 2016, vol. 7, # 4, p. 351 - 356

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