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Full Paper

A Practical Synthesis of a PI3K InhibitorQingping Tian, Zhigang Cheng, Herbert M Yajima, Scott J Savage, Keena L Green,

Theresa Humphries, Mark E Reynolds, Srinivasan Babu, Francis Gosselin, David Askin,Isao Kurimoto, Norihiko Hirata, Mitsuhiro Iwasaki, Yasuharu Shimasaki, and Takashi Miki

Org. Process Res. Dev., Just Accepted Manuscript • DOI: 10.1021/op3002992 • Publication Date (Web): 16 Dec 2012

Downloaded from http://pubs.acs.org on December 25, 2012

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A Practical Synthesis of a PI3K Inhibitor under Non-

cryogenic Conditions via Functionalization of a Lithium

Triarylmagnesiate Intermediate

Qingping Tian

*, Zhigang Cheng, Herbert M. Yajima, Scott J. Savage, Keena L. Green, Theresa

Humphries, Mark E. Reynolds, Srinivasan Babu, Francis Gosselin and David Askin

Small Molecule Process Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080

Isao Kurimoto, Norihiko Hirata, Mitsuhiro Iwasaki, Yasuharu Shimasaki and Takashi Miki

Health & Crop Sciences Research Laboratory, Sumitomo Chemical Co., Ltd., 3 Utajima,

Nishiyodogawa-ku, Osaka 555-0021, Japan

RECEIVED DATE (to be automatically inserted after your manuscript is accepted if required according

to the journal that you are submitting your paper to)

*Corresponding author: [email protected]

ABSTRACT

We report a practical synthesis of PI3K inhibitor GDC-0941. The synthesis was achieved using a

convergent approach starting from a thienopyrimidine intermediate through a sequence of formylation

and reductive amination followed by Suzuki-Miyaura cross-coupling. Metalation of the

thienopyrimidine intermediate involving the intermediacy of triarylmagnesiates allowed formylation

under non-cryogenic conditions to produce the corresponding aldehyde. We also investigated

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aminoalkylation via a benzotriazolyl-piperazine substrate as an alternative to the reductive amination

route. We evaluated both palladium and nickel catalyzed processes for the borylation and Suzuki-

Miyaura cross-coupling. Final deprotection and salt formation afforded the API.

Introduction

The phosphatidylinositol 3-kinase (PI3K) pathway plays a central role in cell proliferation, survival,

migration and metabolism. The lipid kinases of the PI3K family are responsible for the phosphorylation

of the 3'-hydroxyl group of phosphatidylinositols, leading to the activation of the serine / threonine

protein kinase Akt and further downstream oncogenes.1 The PI3K pathway is one of the most

frequently activated pathways in tumors, with mutations in one of its components detected in a notable

percentage of human cancers.2 Thus, the essential role of PI3K in human cancer has spurred the

development of PI3K inhibitors.3 GDC-0941 (Pictilisib) is a novel small molecule PI3K inhibitor

discovered at Genentech and is currently being evaluated as an anticancer agent (Figure 1).4 Substantial

amounts of GDC-0941 were required to support on-going development activities. Herein we wish to

report a robust and practical synthesis of GDC-0941 suitable for preparation of multi-kilogram

quantities of GDC-0941.

Figure 1. Structure of PI3K Inhibitor GDC-0941

The synthesis is outlined retrosynthetically in Scheme 1. We envisioned that GDC-0941 could be

prepared from chloropyrimidine 1 and indazole boronate 2 through a Suzuki-Miyaura cross-coupling.

Further disconnection of 1 would lead to piperazine 3 and thienopyrimidine 4.

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Scheme 1. Retrosynthetic Analysis

Results and Discussion

Synthesis of Thienopyrimidine 4. The medicinal chemistry synthesis of thienopyrimidine 4 relied on

condensation of commercially available methyl 3-aminothiophene 2-carboxylate (5) with urea at 190 ºC

(Scheme 2, Route A).4 We sought milder conditions for the condensation reaction and replaced urea

with potassium cyanate in aqueous AcOH and the reaction proceeded smoothly at rt to afford 6 in 77%

yield (Scheme 2, Route B).5 Pyrimidinone 6 was then chlorinated with POCl3 to afford the

dichloropyrimidine 7. Subsequent site-selective SNAr reaction6 with morpholine in MeOH proceeded

under mild conditions and gave thienopyrimidine 4 in 96% yield.

Scheme 2. Synthesis of the Thienopyrimidine Core 4

We envisioned that intermediate 1 could be assembled from compounds 3 and 4 via a sequence of

metalation, formylation and reductive amination. In an alternative approach, the synthesis of

intermediate 1 would be achieved by a direct aminoalkylation.7

Reductive Amination Approach. The metalation and formylation of thienopyrimidine 4 is illustrated

in Scheme 3. Thus, thienopyrimidine 4 was deprotonated with n-BuLi at –70 °C. Warming the reaction

mixture to –50 °C achieved complete deprotonation as ascertained by 1H NMR spectroscopic analysis

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of aliquots quenched into D2O. Formylation was performed by addition of DMF at –70 °C, followed by

quenching the reaction mixture into cold aqueous HCl to afford the desired aldehyde 8.

Scheme 3. Organolithium Formylation

Although metalation of the thiophene ring could be performed with n-BuLi under cryogenic

conditions, the instability of the resulting organolithium species precluded its use on large scale.8

Lithium trialkylmagnesiates, have been used successfully in halogen-magnesium exchange,9 and for

deprotonation of a variety of heterocycles including furans and thiophenes.10

Lithium

triarylmagnesiates are generally more stable than the corresponding organolithium species, and

reactions can thus be performed under non-cryogenic conditions. To our delight, we found that use of

n-Bu2i-PrMgLi allowed for deprotonation and formylation under non-cryogenic conditions (–10 °C) and

provided aldehyde 8 in 87% yield (Scheme 4). The resulting lithium triarylmagnesiate 9 and the

components of the reaction mixture (after addition of DMF) were stable at –5 °C for > 6 h.11

In an

optimized procedure, i-PrMgCl and n-BuLi were added sequentially to a solution of 4 in THF at –10 °C.

This operationally simple process proved easy to perform on 20 kg scale and obviated the need for a

separate vessel to prepare n-Bu3MgLi as reported previously.10

Scheme 4. Improved Formylation Reaction

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The reductive amination of aldehyde 8 with piperazine 312

was performed using trimethyl orthoformate

as the dehydrating agent (Scheme 5). We evaluated a variety of solvents (CH2Cl2, THF, toluene, EtOAc

and CH3CN) for the reaction and found that CH3CN was superior and afforded the desired product 8 in

85% isolated yield. It was critical to allow sufficient time for complete iminium ion formation (ca. 2 h

under the optimized conditions) before the addition of the reducing agent, NaBH(OAc)3. Otherwise,

the corresponding alcohol 10 was observed at a higher level (> 10A% by HPLC) when the reducing

agent was added after aging for < 2 h.

Scheme 5. Reductive Amination

1) NaOAc, CH3CNHC(OCH3)3, rt

2) NaBH(OAc)3N

NS

Cl

N

O

OHCN

S N

NS

Cl

N

O

N

N

S

85%

+

OO

OO

8 3 1

N

NS

Cl

N

O

HO

10

+

HN

HCl

Aminoalkylation Approach. The reductive amination reaction performed well; however, there were

concerns about the alcohol impurity 10 which was carried in the downstream chemistry resulting in

formation of additional impurities that were difficult to remove. We therefore explored an alternative

route involving aminoalkylation, as an effort to avoid the formation of the alcohol 10. We envisioned

that the aminoalkylation could be performed by direct addition of lithium triarylmagnesiate 9 to an

iminium equivalent of piperazine 3. As indicated in Scheme 6, the iminium salt 13 was generated from

the aminal 11 or aminol ether 12.13

The resulting iminium salt was then subjected to the lithium

triarylmagnesiate 9 to afford the desired product 1. However, a significant amount of the starting

material 4 was observed in the crude product possibly due to the impurities present in the iminium salt.14

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Scheme 6. Synthesis of Intermediate 1 via Iminium Salt

The iminium salt was also generated in situ by treating the aminol ether 12 with a Lewis acid (Scheme

7), followed by addition of the lithium triarylmagnesiate 9. We identified ZnCl2 as the preferred Lewis

acid with the desired product being obtained in ~ 80% yield.

Scheme 7. Synthesis of 1 from Iminium Salt Generated in situ from Aminol Ether

To further improve the aminoalkylation process, our efforts were then focused on the benzotriazole

substrates that have been widely used in the aminoalkylation reactions.15

Treatment of 3 with

benzotriazole, paraformadehyde and MeOH in the presence of KHCO3 afforded benzotriazolyl-

piperazine 14 in 90% yield after isolation by simple filtration (Scheme 8). Unlike the aminol ether 12,

compound 14 is not hygroscopic and can be isolated as a bench-stable solid. Treatment of compound 14

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with ZnCl2 followed by addition to a solution of lithium triarylmagnesiate 9 afforded the desired

product 1 in 93% yield (Scheme 8).

Scheme 8. Aminoalkylation via Benzotriazolyl-Piperazine 14

This route achieved a slightly higher yield than the reductive amination route and did not generate the

alcohol impurity 10. Although a large excess of ZnCl2 (4 equiv) was needed, this route offered a

complementary process to the reductive amination.

Synthesis of Indazole Boronate. Next, our attention was shifted to synthesis of indazole boronate 2

needed for the Suzuki-Miyaura cross-coupling reaction. The synthesis of the boronate is illustrated in

Scheme 9. We selected the THP protecting group to improve the solubility of the Suzuki-Miyaura

cross-coupling product and facilitate the removal of residual Pd and impurities. The synthesis began

with diazotization of 3-chloro-2-methylaniline (15) and subsequent cyclization under basic conditions,

producing 4-chloroindazole (16) in quantitative yield. Installation of the THP group was then

performed with 3,4-dihydro-2H-pyran (DHP) in the presence of pyridinium p-toluenesulfonate (PPTS),

leading to a mixture of indazole isomers 17a and 17b which were treated with bis(pinacolato)diboron in

the presence of PdCl2(PPh3)2 and PCy3 to afford boronates 2a and 2b, respectively (Scheme 9, Method

A).16

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Scheme 9. Synthesis of the Boronates 2a and 2b

We found that the THP group at the 2-position could easily be removed after the cross-coupling

reaction, but it proved difficult to deprotect the THP group at the 1-position. In general, the acid-

catalyzed THP protection of indazole at the 2-position is favored kinetically and the 1-THP regioisomer

is the thermodynamic product.16b

As such, installation of the THP group at the 2-position was achieved

under mildly acidic conditions.16b

We applied the similar conditions in our process, and obtained a

mixture of 2-THP and 1-THP products (Table 1, entry 1). We found that the site-selectivity of the

protection was solvent-dependent and could be improved to 94:6 17a/17b using toluene/heptane (3:4,

v/v) as solvent mixture (Table 1, entry 4). At higher temperature and with prolonged reaction time, the

site-selectivity was eroded as the kinetically favored product 17a would slowly be converted to the

thermodynamically favored product 17b. Under the optimized conditions, the reaction was performed at

40 ºC for 5 h. Palladium catalyzed borylation gave the desired 2-THP boronate ester 2a in 41% yield

over two steps, and chromatographic purification was required for removal of the undesired 1-THP

regioisomer 2b and residual Pd.

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Table 1. Regioselectivity of THP Protection of Indazole 16 in Various Solvents

entry solvents 17a : 17b

1 CH2Cl2 77 : 23

2 CH3CN 10 : 90

3 DMF 45 : 55

4 Toluene/heptane (3:4, v/v) 94 : 6

We next investigated the Ni-catalyzed borylation of indazoles 17a and 17b (Scheme 9, Method B).17

We found that in reactions using 4 mol% of Ni(NO3)2•6H2O/PPh3 as catalyst, the product could be

isolated in 53% yield over two steps and 99A% HPLC by a simple crystallization. Furthermore,

residual Ni was readily removed from the process stream by simple aqueous washes. Although a

relatively higher loading of the Ni catalyst (4 mol%) was employed, the process was still cost-effective

due to the significantly lower cost of the Ni catalyst, Ni(NO3)2•6H2O, compared to the expensive Pd

catalyst.

As a further improvement relative to metal-catalyzed borylation, we opted to replace the boronates

with the corresponding boronic acids 18a and 18b in the Suzuki-Miyaura cross-coupling reaction.

Indazoles 21a / 21b were prepared from 3-bromo-2-methylaniline (19) in two steps employing the

sequence used in Scheme 9. Halogen-metal exchange on indazoles 21a/21b and borylation with B(O-i-

Pr)3 gave the desired boronic acids in 60% yield (Scheme 10).18

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Scheme 10. Synthesis of Indazole Boronic Acid

Suzuki-Miyaura Cross-coupling. With intermediate 1 and the boronic acid 18a in hand, we turned to

the Suzuki-Miyaura cross-coupling reaction to provide the THP protected GDC-0941 22. We explored

the use of both Pd and Ni catalysts for the reaction and identified PdCl2(PPh3)2 in aqueous Na2CO3/1,4-

dioxane and Ni(NO3)2•6H2O/PPh3 in K3PO4/CH3CN as the catalyst systems of choice (Scheme 11). In

the Ni-catalyzed reaction, we found that boronic acid 18a performed better than the corresponding

boronate esters 2a and 2b and boronic acid 18b.19

The removal of the residual Pd contaminate required

the use of the expensive scavengers (Florisil®

and Thio-Silica ®

) and large volume of solvents. In

contrast, the residual Ni catalyst could be easily removed from the crude reaction mixture through an

aqueous ammonia wash and crystallization. This route afforded the THP protected GDC-0941 22 in

79% yield as the final key bond forming step.

Scheme 11. Pd or Ni-catalyzed Suzuki-Miyaura Cross-coupling Reaction

S

N

N

N

O

Cl

NN

BOHHO

Method A:

1. PdCl2(PPh3)2, Na2CO3

1,4-dioxane, 88 oC

2. Florisil/Thio-Silica

60%

Method B:

Ni(NO3)2 6H2O, PPh3

K3PO4, CH3CN, 60oC

79%

+

S

N

N

N

O

N

N

S

OO

N

N

THP

THP

1 18a 22

N

N

S

OO

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End-Game Chemistry. The bis-methanesulfonate salt of GDC-0941 was identified as a suitable

crystal form for development. Deprotection of the THP group and salt formation was performed in one

operation by using methanesulfonic acid in aqueous MeOH (H2O/MeOH, 1:19 (v/v)) and the product

was isolated by simple filtration (Scheme 12). The crude product was then purified by recrystallization

from MeOH/H2O to afford GDC-0941 in 90% yield, HPLC: >99 A%, ICPMS analysis: <20 ppm Ni.

Because MeOH and methanesulfonic acid were used in the process, we had concerns about the

formation of methyl methanesulfonate, a known genotoxic impurity.20

Thus, water was employed as a

co-solvent to suppress the formation of methyl methanesulfonate.21

The amount of methyl

methanesulfonate in the final product was determined to be <1 ppm by GC/MS analysis. In addition, no

methyl methanesulfonate was detected in the mother liquor. These analyses demonstrated that no

methyl methanesulfonate was produced in the process.22

Scheme 12. Final Deprotection and API Salt Formation

Summary and Conclusion. We have developed a practical and convergent synthesis for GDC-0941

(Scheme 13). Non-cryogenic conditions were employed in the formylation of 4 via a triarylmagnesiate

intermediate. The synthesis of the key intermediate 1 was achieved through an aminoalkylation reaction

with preformed benzotriazolyl-piperazine 14, a complementary process to the reductive amination. We

investigated both metal-catalyzed borylation and halogen-metal exchange/borylation for the synthesis of

the boronate and boronic acid. Both palladium and nickel catalysts were evaluated for the Suzuki-

Miyaura cross-coupling reaction. The end-game featured THP deprotection and salt formation in one

operation to afford GDC-0941 in >99A% HPLC purity and 53% overall yield over four steps. This

preparation has been scaled up to a 55kg batch of API.

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Scheme 13. Multikilogram-scale Synthesis of GDC-0941

Experimental Section

General. All reactions were performed under a nitrogen atmosphere. Melting points were measured by

differential scanning calorimetry (DSC). HPLC methods for purity and assay analysis are listed below.

HPLC method for compounds 1, 4, 5, 6, 7 and 8: column, ACE C18 (150 × 4.6 mm, 5 µm); temperature, 30

oC; mobile phase A, 5% CH3CN in water; mobile phase B, CH3CN; gradient (25 min) 75:25 A/ B to 0:100 A/B

over 18 min, then hold at 0:100 A/B for 5 min, then change to 75:25 A/B in 0.1 min, 5 min equilibrium at 75:25

A/B; flow rate, 1.5 mL/min; detection, 210 nm; injection volume, 5 µL; tR of 1 = 6.76 min, tR of 4 = 4.67 min, tR

of 5 = 3.65 min, tR of 6 = 7.54 min, tR of 7 = 6.83 min, tR of 8 = 6.53 min.

HPLC method for compound 16: column, Shiseido Capcell Pak MG-II (250 × 4.6 mm, 5 µm); temperature, 40

oC; mobile phase A, 10 mM phosphate buffer and pH adjusted to 6.8 with KH2PO4; mobile phase B, CH3CN;

gradient (60 min) 75:25 A/B to 35/65 A/B over 13 min, hold for 8 min, then to 25:75 A/B over 2 min, hold for 27

min, then to 75:25 A/B over 0.01 min, 10 min equilibration at 75:25 A/B; flow rate, 1.0 mL/min; detection, 275

nm; injection volume, 1 µL; tR of 16 = 13.4 min.

HPLC method for compounds 17a and 17b: column, Shiseido Capcell Pak MG-II (250 × 4.6 mm, 5 µm);

temperature, 40 oC; mobile phase A, 10 mM phosphate buffer and pH adjusted to 6.8 with KH2PO4; mobile phase

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B, CH3CN; gradient (50 min) 75:25 A/B to 35/65 A/B over 40 min, then to 75:25 A/B over 0.01 min, 10 min

equilibration at 75:25 A/B; flow rate, 1.0 mL/min; detection, 275 nm; injection volume, 1 µL; tR of 16 = 19.1 min,

tR of 17a = 34.2 min, tR of 17b = 38.4 min.

HPLC method for compounds 2a and 2b: column, Shiseido Capcell Pak MG-II (250 × 4.6 mm, 5 µm),

temperature, 40 oC; mobile phase A, 10 mM phosphate buffer and pH adjusted to 6.8 with KH2PO4; mobile phase

B, CH3CN; gradient (60 min) 75:25 A/B to 35:65 A/B over 13 min, hold for 8 min, then to 25:75 A/B over 2 min,

hold for 27 min, then to 75:25 A/B over 0.01 min, 10 min equilibration at 75:25 A/B; flow rate, 1.0 mL/min;

detection, 220 nm; injection volume, 1 µL; tR of 17a = 19.6 min, tR of 17b = 21.7 min, tR of 2a = 24.0 min, tR

of 2b = 28.1 min.

HPLC method for compound 18a, 20, 21a and 21b: column, Phenomenex Luna C8 (250 × 4.6 mm, 5 µm);

temperature, 45 oC; mobile phase A, 0.02 M KH2PO4 and pH adjusted to 6.0 with KOH; mobile phase B, CH3CN;

gradient (30 min) 80:20 A/ B to 30:70 A/B over 20 min, then to 80:20 A/B over 5 min, then 5 min equilibration at

80:20 A/B; flow rate, 1.2 mL/min; detection, 210 nm; injection volume,10 µL; tR of 18a = 6.15 min, tR of 20 =

8.23 min, tR of 21a = 12.3 min, tR of 21b = 13.1 min.

HPLC method for compound 22, Shiseido Capcell Pak C18 MGII (250 × 3.0 mm, 5 µm); temperature, 40 oC;

mobile phase A, water; mobile phase B, CH3CN; gradient (40 min) 60:40 A/ B to 10:90 A/B over 20 min, then to

60:40 A/B over 10 min, then 10 min equilibration at 60:40 A/B; flow rate, 0.4 mL/min; detection, 210 nm;

injection volume, 3 µL; tR of 1 = 12.0 min, tR of 22 = 20.1 min.

HPLC method for GDC-0941: column, Zorbax Eclispe XDB-C18 (150 × 3.0 mm, 3.5 µm); temperature, 35 oC;

mobile phase A, 0.10% TFA in water; mobile phase B, 0.05% TFA in CH3CN; gradient (50 min) 95:5 A/ B for 2

min, then to 30:70 A/B over 33 min, hold for 10 min, then to 95:5 A/B over 0.1 min, 5 min equilibrium at 95:5

A/B; flow rate, 0.8 mL/min; detection, 230 nm; injection volume, 5 µL; tR of 22 = 16.3 min, tR of GDC-0941 =

12.5 min.

Thieno[3,2-d]pyrimidine-2,4-dione (6).4, 23, 24

To a stirred mixture of methyl 3-amino-

thiophenecarboxylate (5) (125 kg, 795 mol) and acetic acid (1018 L) was added a solution of potassium

cyanate (155 kg, 1911 mol) in water (313 L) in two portions in 2 h. After aging at rt for 2 h, more water

(812 L) was added. The reaction mixture was cooled to 10 oC and stirred for 2 h. The resulting slurry

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was filtered and the filter cake was washed with water (344 L). The wet cake was then charged in two

portions in 1 h into a reactor containing a solution of NaOH (109 kg) in water (1875 L). The slurry was

stirred at rt for 12 h, the mixture was then cooled to 10 ºC and 35% aqueous HCl solution (~ 238 kg)

was added in one portion to adjust pH to 5−6. The resulting slurry was filtered and rinsed with water

(390 L), and the cake was dried under vacuum at 50 ºC for 24 h to afford 6 as an off-white solid (102.5

kg, 77% yield): mp 102.9 ºC; 1H NMR (300 MHz, DMSO−d6) δ 11.58 (s, 1H), 11.24 (s, 1H), 8.06 (d, J

= 5.2 Hz, 1H), 6.92 (d, J = 5.2 Hz, 1H); 13

C NMR (75 MHz, DMSO−d6) δ 159.0, 151.5, 146.4, 135.9,

117.2, 111.2; HRMS (ESI) calcd for C6H3N2O2S [M-H] 166.9921, found: 166.9922.

2,4-Dichlorothieno[3,2-d]pyrimidine (7).4, 23, 24

Phosphorus oxychloride (510 kg, 3326 mol) was

slowly added to a cold solution of thieno[3,2-d]pyrimidine-2,4-dione (6) (102 kg, 606 mol) and N,N-

dimethylaniline (50.7 kg, 418 mol) in CH3CN (604 L) in 2 h at ≤ 20 ºC. The mixture was then heated

to 80−85 ºC and was aged for 24 h. The reaction mixture was cooled to 40 ºC and then was quenched

into a reactor containing water (1425 L) in 2 h. The resulting slurry was filtered and the cake was rinsed

with water (100 L). The cake was dried under vacuum at 40 ºC for 24 h to afford 7 as an off-white solid

(111 kg, 89% yield): mp 137.7 ºC, lit. 138.8−139.3 oC;

23

1H NMR (300 MHz, DMSO−d6) δ 8.71 (d, J =

5.4 Hz, 1H), 7.74 (d, J = 5.4 Hz, 1H); 13

C NMR (75 MHz, DMSO−d6) δ 163.5, 154.71, 154.69, 142.3,

129.2, 124.0; HRMS (APCI) calcd for C6HCl2N2S [M-H] 202.9243, found: 202.9245.

4-(2-Chlorothieno[3,2-d]pyrimidin-4-yl)morpholine (4).4, 24

Morpholine (117 kg, 1343 mol) was

added to a solution of 2,4-dichloro-thieno[3,2-d]pyrimidine (7) (111 kg, 541 mol) in methanol (1110 L).

The reaction mixture was cooled to 0‒5 oC and filtered. The cake was then triturated in water (450 L)

at rt for 2 h and the resulting slurry was filtered, and the cake was rinsed with water (60 L) and dried

under vacuum at 45 ºC for 24 h to give an off-white solid 4 (133 kg, 96% yield): mp 197.5 ºC; 1H NMR

(300 MHz, DMSO‒d6) δ 8.32 (d, J = 5.4 Hz, 1H), 7.42 (d, J = 5.4 Hz, 1H), 3.93-3.89 (m, 4H), 3.79-

3.74 (m, 4H); 13

C NMR (75 MHz, DMSO-d6) δ 162.7, 158.2, 155.9, 135.4, 123.7, 112.5, 65.7, 45.9;

HRMS (ESI) calcd for C10H11ClN3OS [M+H] 256.0306, found: 256.0305.

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2-Chloro-4-morpholinothieno[3,2-d]pyrimidine-6-carbaldehyde (8).4, 24

A mixture of

2-chlorothieno[3,2-d]-pyrimidin-4-yl-)morpholine (4) (19.8 kg, 77.4 mol) and THF (197 L) was cooled

to below -10 ºC, and a 20% solution of i-PrMgCl in THF (20.1 kg, 39.1 mol) was added in 1.5 h,

followed by addition of a 15% solution of n-BuLi in hexanes (32.6 kg, 76.3 mol) in 1.5 h at ≤ -10 ºC.

The mixture was stirred at –10 ºC for 1 h and anhydrous DMF (8.8 kg, 120 mol) was then slowly added

while maintaining the internal temperature between -15 ºC and -5 ºC. The reaction mixture was stirred

for 4 h and then was transferred to a cold mixture of AcOH (58.7 kg), 35% aqueous HCl (21.3 kg) and

water (159 kg) in 1.5 h. After aging for 1 h, the slurry was heated to 55 ºC in 4 h and stirred for 3 h.

The mixture was then cooled to 20-30 ºC in 1 h and then was aged for 1 h. The product was isolated by

filtration and the filter cake was washed with water (4 × 25 kg), dried under vacuum at 50 ºC to afford a

brown-yellow solid 8 (19.2 kg, 87% yield): mp 239.4 ºC; 1H NMR (300 MHz, DMSO-d6) δ 10.21 (s,

1H), 8.29 (s, 1H), 4.01-3.87 (m, 4H), 3.83-3.67 (m, 4H); 13

C NMR (75 MHz, DMSO-d6) δ 186.5, 161.3,

158.6, 156.6, 147.0, 132.8, 116.3, 65.7, 46.1; HRMS (ESI) calcd for C11H11ClN3O2S [M+H] 284.0255,

found: 284.0260.

2-Chloro-6-(4-methylsulphonyl-piperazin-1-ylmethyl)-4-morpholin-4-yl-thieno[3,2-d]pyrimidine

(1) (Scheme 5, Reductive Amination).4, 24

To a suspension of 2-chloro-4-morpholin-4-yl-thieno[3,2-

d]pyrimidine-6-carbaldehyde (8) (36.2 kg, 128 mol), 1-(methylsulfonyl)piperazine hydrochloride (3)

(37.2 kg, 185 mol) and NaOAc (15.2 kg, 185 mol) in CH3CN (540 L) was added trimethyl orthoformate

(136.3 kg, 1284 mol) and the mixture was heated to 45 oC in 40 min. After aging for 2 h and 40 min,

sodium triacetoxyborohydride (43.9 kg, 207 mol) was added in 10 portions in 4 h and the reaction

mixture was stirred for 3 h. The reaction was then quenched with water (363 L) and the mixture was

heated to 70 ºC in 1 h and 25 min and stirred for 3 h. The mixture was cooled to 20−30 ºC in 4 h and 50

min and stirred for 1 h. The resulting slurry was filtered and rinsed successively with a mixture of

CH3CN (67 L) and water (45 L), water (3 × 72 L) and CH3CN (36 L), and the cake was dried under

vacuum at 50 ºC for 10 h to give 1 as an off-white solid (49.0 kg, 95.9wt%, 85% yield): mp 238.6 ºC;

1H NMR (300 MHz, CDCl3) δ 7.19 (s, 1H), 4.05−3.94 (m, 4H), 3.89−3.76 (m, 6H), 3.36−3.19 (m, 4H),

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2.81 (s, 3H), 2.73−2.57 (m, 4H); 13

C NMR (75 MHz, CDCl3) δ 163.2, 158.3, 156.9, 150.5, 122.8, 112.8,

66.7, 57.1, 52.4, 46.3, 45.7, 34.6; HRMS (ESI) calcd for C16H23ClN5O3S2 [M+H] 432.0925, found:

432.0916.

1-((4-(Methylsulfonyl)piperazin-1-yl)methyl)-1H-benzotriazole (14). 1-(Methylsulfonyl)piperazine

hydrochloride (3) (200 g, 1.00 mol), methanol (4.5 L) and water (0.5 L) were charged into a 12-L

reactor, followed by the addition of KHCO3 (120 g, 1.20 mol) and benzotriazole (119 g, 1.00 mol).

The resulting mixture was stirred at rt for 30 min and 37% aqueous formaldehyde solution (162 g, 2.00

mol) was added. After aging at rt for 15 h, the reaction mixture was filtered and the filter cake was

washed with water (4 L). The wet cake was re-slurried in water (4 L) for 3 h, filtered, washed with

water (500 mL), and dried under vacuum at 50 ºC for 16 h to afford 14 as a white solid (265 g, 90%

yield): mp 210.7 ºC; 1H NMR (300 MHz, DMSO−d6) δ 8.07 (d, J = 8.4 Hz, 1H), 8.02 (d, J = 8.4 Hz,

1H), 7.59 (t, J = 7.6 Hz, 1H), 7.42 (t, J = 7.6 Hz, 1H), 5.64 (s, 2H), 3.19−3.00 (m, 4H), 2.85 (s, 3H),

2.74−2.53 (m, 4H); 13

C NMR (75 MHz, DMSO−d6) δ 144.9, 133.8, 127.5, 124.0, 119.0, 111.1, 67.8,

49.0, 45.1, 34.0.

2-Chloro-6-(4-methylsulphonyl-piperazin-1-ylmethyl)-4-morpholin-4-yl-thieno[3,2-d]pyrimidine

(1) (Scheme 8, Aminoalkylation via Benzotriazolyl-piperazine 14).4, 24

A mixture of 4-(2-

chlorothieno[3,2-d]pyrimidin-4-yl-morpholine (4) (10.0 g, 39.1 mmol) and THF (anhydrous, 100 mL)

was cooled to −5 ºC and i-PrMgCl (9.8 mL, 19.6 mmol, 2 M in THF) was added at ≤ 0 ºC. The

resulting slurry was stirred for 30 min and was then cooled to −20 ºC. A solution of n-BuLi (15.6 mL,

39.0 mmol, 2.5 M in hexanes) was added at ≤ −10 ºC. At the same time, 1-((4-

(methylsulfonyl)piperazin-1-yl)methyl)-1H-benzotriazole (14) (13.9 g, 46.9 mmol) and THF (60 mL)

were charged into a 1-L flask. The solution was cooled to 10 ºC and a solution of ZnCl2 (313 mL, 156

mmol, 0.5 M in THF) was added. The mixture was stirred for 30 min and cooled to −20 ºC. The

resulting slurry was slowly added to the lithium triarylmagnesiate mixture formed in the 2-L flask via

cannula while maintaining the temperature below −10 ºC. Additional amounts of 14 (7.50 g, 25.4

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mmol) were added to the reaction mixture in two portions with a 2 h interval, and the reaction was then

stirred below −10 ºC for 12 h. Water was then added to the reaction mixture and the resulting slurry

was aged for 1 h and filtered. The filtrate was concentrated to remove THF and the resulting slurry was

filtered. The filter cakes from both filtrations were combined, stirred in CH2Cl2 (500 mL) at 30 ºC for

30 min, filtered and rinsed with CH2Cl2 (350 mL). The filtrate was concentrated to afford an off-white

solid (19.4 g) that was then triturated in MeOH (100 mL) at rt for 1 h. The product was collected by

filtration, rinsed with MeOH (10 mL), and dried under vacuum at 50 ºC for 12 h to afford an off-white

solid 1 (16.6 g, 93% yield).

4-Chloro-1H-indazole (16).25, 26

To a mixture of 2-methyl-3-chloroaniline (15) (53.1 kg, 375 mol) and

KOAc (44.2 kg, 450 mol) in 1,2-dimethoxyethane (458 L) was slowly added acetic anhydride (115 kg,

1126 mol) in 3 h. The mixture was stirred at rt for 3 h and isoamyl nitrite (87.2 kg, 744 mol) was added.

The reaction mixture was heated to 60 ºC and stirred for 15 h. The mixture was cooled to 0 ºC, water

(159 L) was added, followed by addition of a 28% NaOH aqueous solution (286 kg, 2000 mol). The

phases were separated and the aqueous phase was extracted with 1,2-dimethoxyethane (122 L). The

organic phases were combined, washed with brine (130 L) and concentrated to a volume of 280 L.

Water (398 L) was added and the mixture was concentrated to remove 1,2-dimethoxyethane, followed

by addition of water (319 L). The resulting slurry was filtered and the filter cake was rinsed with a

mixture of water (53 L) and methanol (17 L), dried under vacuum at 50 oC to yield an orange solid 16

(53.6 kg, 92wt%, 86% yield): mp 153.8 ºC; 1H NMR (300 MHz, DMSO−d6) δ 13.46 (s, 1H), 8.15 (s,

1H), 7.56 (d, J = 8.4 Hz, 1H), 7.36 (t, J = 7.9 Hz, 1H), 7.20 (d, J = 7.3 Hz, 1H); 13

C NMR (75 MHz,

DMSO−d6) δ 140.9, 131.6, 126.9, 124.6, 121.8, 119.8, 109.3; HRMS (ESI) calcd for C7H4ClN2 [M-H]

151.0068, found 151.0070.

4-Chloro-2-(tetrahydro-2H-pyran-2-yl)-2H-indazole (17a) and 1-THP isomer 17b.26, 27

4-Chloro-

1H-indazole (16) (53.6 kg, 92wt%, 323 mol), pyridinium p-toluenesulfonate (1.60 kg, 6.37 mol), 3,4-

dihydro-2H-pyran (59.5 kg, 707 mol), toluene (248 L) and heptane (318 L) were added to a reactor. The

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mixture was heated to 40 ºC and stirred for 11 h and then cooled to 25 ºC, followed by addition of 5%

aqueous NaHCO3 solution (164 kg). The phases were separated and the organic phase was washed with

5% aqueous NaHCO3 solution (2 × 164 kg). To the organic phase was added toluene (23 L) and

NaHCO3 (0.50 kg). The mixture was concentrated, flushed with MeOH (186 L), and concentrated to a

volume of ~ 100 L. The product was filtered and the filter cake was rinsed with MeOH (19 L) to afford

a filtrate as a 15:1 mixture of isomers 17a and 17b (121.2 kg, 63wt%, 100% yield). The filtrate was

used in the next step without further purification. Pure samples of 17a and 17b were isolated by

chromatography (silica, 5-10% EtOAc in hexanes) for the characterization. Major isomer 17a (oil): 1H

NMR (300 MHz, CDCl3) δ 8.25 (d, J = 1.0 Hz, 1H), 7.62 (dd, J = 8.4, 1.0 Hz, 1H), 7.20 (dd, J = 8.4, 7.5

Hz, 1H), 7.06 (dd, J = 7.5, 1.0 Hz, 1H), 5.69 (dd, J = 8.4, 3.8 Hz, 1H), 4.21−4.07 (m, 1H) 3.85−3.70 (m,

1H), 2.31−2.12 (m, 2H), 2.12−1.95 (m, 1H), 1.88−1.56 (m, 3H); 13

C NMR (75 MHz, CDCl3) δ 149.0,

126.6, 125.6, 121.8, 121.0, 120.8, 116.6, 89.1, 68.0, 31.4, 24.9, 22.0; HRMS (ESI) calcd for

C12H14ClN2O [M+H] 237.0789, found: 237.0786. Minor isomer 17b (solid): mp 65.2 ºC, 1H NMR (300

MHz, CDCl3) δ 8.10 (s, J = 1.0 Hz,1H), 7.49 (d, J = 8.4 Hz, 1H), 7.28 (dd, J = 8.4, 7.5 Hz, 1H), 7.13 (d,

J = 7.5 Hz, 1H), 5.70 (dd, J = 9.2, 2.9 Hz, 1H), 4.07−3.94 (m, 1H), 3.80−3.66 (m, 1H), 2.66−2.45 (m,

1H), 2.25−2.00 (m, 2H), 1.86−1.51 (m, 3H); 13

C NMR (75 MHz, CDCl3) δ 140.5, 132.4, 127.1, 126.5,

124.0, 120.8, 108.9, 85.7, 67.4, 29.4, 25.1, 22.4; HRMS (ESI) calcd for C12H14ClN2O [M+H] 237.0789,

found: 237.0784.

2-(Tetrahydro-2H-pyran-2-yl)-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-2H-indazole (2a)

(Scheme 9, Ni catalyst).24, 26

To a reactor was added bis(pinacolato)diboron (100 kg, 394 mol),

methanol (271 L), triethylamine (79.7 kg, 788 mol), and the product of the previous step, a 15:1 mixture

of 17a / 17b (113.8 kg, 63wt%, 303 mol). The mixture was cooled to 0 ºC, followed by addition of

Ni(NO3)2•6H2O (3.50 kg, 12.0 mol) and PPh3 (6.40 kg, 24.4 mol). The resulting slurry was warmed to

25 ºC and was aged for 3.5 h. tert-Butyl methyl ether (1064 L), water (72 L) and 5% aqueous HCl

solution (307 L) were added to adjust the pH to 7.5. The aqueous phase was separated and then

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extracted with tert-butyl methyl ether (871 L), and the combined organic phases were concentrated

under reduced pressure, flushed with toluene (331 L) and concentrated under reduced pressure. The

residue was dissolved in toluene (248 L) and the solution was washed with an aqueous MeOH solution

(MeOH/H2O, 1:3 v/v, 3 × 283 L). To the resulting organic phase was added activated carbon (3.6 kg)

and the slurry was aged for 1 h, and then filtered over a pad of Celite®

. The filtrate was concentrated

under reduced pressure and toluene (2 L) and heptane (163 L) were added. The mixture was heated to

45 ºC and seeded with 2a (140 g). The mixture was cooled to 0 ºC, filtered and rinsed successively with

a cold mixture of heptane (29 L) and toluene (10 L), and heptane (57 L). The cake was dried under

reduced pressure to afford an off-white solid 2a (56.7 kg, 93wt%, 53% yield): 1H NMR (300 MHz,

CDCl3) δ 8.47 (d, J = 0.8 Hz, 1H), 7.84 (dt, J = 8.8, 0.9 Hz, 1H), 7.63 (dd, J = 6.5, 0.8 Hz, 1H), 7.30

(dd, J = 8.8, 6.6 Hz, 1H), 5.69 (dd, J = 9.5, 2.9 Hz, 1H), 4.22−4.06 (m, 1H), 3.85−3.68 (m, 1H),

2.42−2.13 (m, 2H), 2.12−1.94 (m, 1H), 1.92−1.59 (m, 3H), 1.42−1.29 (s, 12H); 13

C NMR (75 MHz,

CDCl3) δ 147.9, 131.0, 125.8, 124.7, 123.4, 121.2, 89.1, 83.7, 68.1, 31.3, 24.99, 24.96, 22.4; HRMS

(ESI) m/z calcd for C18H26BN2O3+ (M+H)

+ 329.2031, found 329.2035.

4-Bromo-1H-indazole (20).4 To a mixture of 3-bromo-2-methylaniline (19) (14.0 kg, 75.2 mol) and

KOAc (8.90 kg, 90.7 mol) in chloroform (168 L) was slowly added acetic anhydride (9.20 kg, 90.1

mol). The reaction mixture was heated to 60 ºC and was stirred for 1 h; HPLC analysis confirmed

complete consumption of 19. Isoamyl nitrite (44.5 kg, 377 mol) was added and the reaction mixture

was stirred at 60 ºC for 22 h. Chloroform was removed under reduced pressure, water (70 L), THF (140

L) and LiOH•H2O (12.6 kg, 300 mol) were added, and the reaction mixture was stirred at ambient

temperature for 1 h. THF was then removed under reduced pressure, water (20 L) was added, and the

aqueous layer was extracted with EtOAc (3 × 84.0 L). The organic phases were combined, washed

sequentially with water (70 L) and brine (70 L). The organic phase was dried over anhydrous Na2SO4

(5.25 kg), filtered and concentrated under reduced pressure. To the residue was added water (70 L) and

hexanes (28 L), and the slurry was stirred at ambient temperature for 1 h, filtered and rinsed with

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hexanes (8.3 L). The cake was dried under reduced pressure to yield 20 (12.0 kg, 81% yield): mp 163.7

ºC; 1H NMR (300 MHz, DMSO-d6) δ 13.47 (br s, 1H), 8.06 (s, 1H), 7.60 (d, J = 8.0 Hz, 1H), 7.35 (d, J

= 7.4 Hz, 1H), 7.30 (t, J = 7.4 Hz, 1H); 13

C NMR (75 MHz DMSO−d6) δ 140.5, 133.0, 127.3, 123.6,

123.0, 113.0, 109.8. HRMS (APCI) m/z calcd for C7H6BrN2+ (M+H)

+ 196.9709, found 196.9707.

4-Bromo-2-(tetrahydro-2H-pyran-2-yl)-2H-indazole (21a) and 1-THP isomer 21b.27, 28

A mixture of

4-bromo-1H-indazole (20) (11.2 kg, 56.8 mol), pyridinium p-toluenesulfonate (285 g, 1.13 mol), 3,4-

dihydro-2H-pyran (15.3 kg, 182 mol) in toluene (45.9 L) and heptane (45.9 L) was heated to 40 ºC and

stirred for 9 h. The reaction mixture was cooled to 25 ºC and toluene (56 L) was added. The solution

was sequentially washed with 5% of aqueous NaHCO3 solution (3 × 56 L) and water (56 L). The

organic phase was dried over anhydrous MgSO4 (5.6 kg), filtered and concentrated to yield a brown

solid as a 92:8 mixture of 21a and 21b (15.2 kg, 95% yield). The product was used in the next step

without further purification. Pure samples of 21a and 21b were isolated by chromatography (silica, 5-

10% EtOAc in hexanes) for the characterization. 21a: mp 52.6 ºC; 1H NMR (300 MHz, CDCl3) δ 8.19

(s, 1H), 7.66 (d, J = 8.6 Hz, 1H), 7.23 (d, J = 7.1 Hz, 1H), 7.13 (dd, J = 8.6, 7.2 Hz, 1H), 5.66 (dd, J =

8.4, 3.8 Hz, 1H), 4.18−4.08 (m, 1H), 3.83−3.71 (m, 1H), 2.30−2.10 (m, 2H), 2.10−1.93 (m, 1H),

1.85−1.56 (m, 3H); 13

C NMR (75 MHz, CDCl3) δ 148.4, 127.0, 124.4, 123.6, 122.2, 117.1, 113.4, 89.1,

68.0, 31.4, 24.9, 22.0; HRMS (APCI) m/z calcd for C12H14BrN2O+ (M+H)

+ 281.0284, found 281.0280.

21b: mp 73.9 ºC; 1H NMR (300 MHz, CDCl3) δ 8.03 (s, 1H), 7.55 (d, J = 8.3 Hz, 1H), 7.32 (d, J = 7.4

Hz, 1H), 7.23 (t, J = 7.9 Hz, 1H), 5.71 (dd, J = 9.1, 2.8 Hz, 1H), 4.08−3.91 (m, 1H), 3.81−3.65 (m, 1H),

2.64−2.42 (m, 1H), 2.24−2.00 (m, 2H), 1.90−1.57 (m, 3H); 13

C NMR (300 MHz, CDCl3) δ 140.1,

133.9, 127.4, 125.8, 124.1, 114.6, 109.4, 85.7, 67.4, 29.4, 25.1, 22.4; HRMS (APCI) m/z calcd for

C12H14BrN2O+ (M+H)

+ 281.0284, found 281.0285.

2-(Tetrahydro-2H-pyran-2-yl)-2H-indazol-4-ylboronic acid (18a). A mixture of 4-bromo-2-

(tetrahydro-2H-pyran-2-yl)-2H-indazole (21a) (5.25 kg, a 92:8 mixture of 21a:21b, 18.7 mol) and

triisopropylborate (14.1 kg, 75.0 mol) in THF (105 L) was cooled to −70 °C and 2.5 M solution of n-

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BuLi in THF (22.4 L, 56.0 mol) was slowly added at ≤ −60 °C. The reaction mixture was stirred at −60

oC to −50 °C for 1 h and cooled to −70 °C, and triisopropylborate (7.1 kg, 37.8 mol) and 2.5 M solution

of n-BuLi in THF (15 L, 37.5 mol) were slowly added sequentially at ≤ −60 °C. The reaction mixture

was stirred at −50 °C for 1 h and was slowly quenched with water (53.0 L) at ≤ −50 °C. The mixture

was allowed to slowly warm to ambient temperature; water (53.0 L) was added and the mixture was

aged for 4 h. After being concentrated under reduced pressure to remove THF, the residue was

extracted with tert-butyl methyl ether (1 × 53.0 L), and the organic phase was back-extracted with 0.50

M aqueous NaOH solution (53.0 L). The aqueous phases were combined and ammonium acetate (5.7

kg, 73.9 mol) was added, and the mixture was stirred for 30 min. After the mixture was cooled to 0−10

°C, 10% sodium dihydrogen phosphate buffer solution (1155 L) was added to adjust the pH to 5.8. The

slurry was stirred for 4 h, cooled to 0−10 °C, filtered and rinsed with cold water (5.3 L). The cake was

dried under reduced pressure at 45 °C to afford light brown solid 18a (2.92 kg, 60% yield): mp 121.2

ºC; 1H NMR (300 MHz, DMSO−d6) δ 8.52 (s, 1H), 8.17 (s, 2H), 7.67 (d, J = 8.4 Hz, 1H), δ 7.57 (d, J =

6.6 Hz, 1H), 7.25 (dd, J = 8.4, 6.6 Hz, 1H), 5.76 (dd, J = 9.3, 2.7 Hz, 1H), 4.06−3.94 (m, 1H), 3.81−3.66

(m, 1H), 2.27−1.45 (m, 6H); 13

C NMR (75 MHz, DMSO-d6) δ 147.1, 129.1, 125.3, 124.4, 124.0, 119.5,

87.9, 67.0, 30.7, 24.6, 21.7; HRMS calcd for C12H16BN2O3 [M+H] 247.1248, found 247.1246.

4-(6-((4-(Methylsulfonyl)piperazin-1-yl)methyl)-2-(2-(tetrahydro-2H-pyran-2-yl)-2H-indazol-4-

yl)thieno[3,2-d]pyrimidin-4-yl)morpholine (22) (Scheme 11, Pd catalyst). To a solution of 2-chloro-

6-(4-methylsulphonyl-piperazin-1-yl methyl)-4-morpholin-4-yl-thieno[3,2-d]pyrimidine (1) (96.5 g, 223

mmol) in 1,4-dioxane (1.75 L) was added water (772 mL), sodium carbonate (47.4 g, 447 mmol) and 2-

(tetrahydro-2H-pyran-2-yl)-2H-indazol-4-ylboronic acid (18a) (68.6 g, 279 mmol). The mixture was

degassed for 30 min with subsurface nitrogen sparge. Bis(triphenylphosphine)palladium (II) chloride

(6.28 g, 9.94 mmol) was added and the resulting slurry was degassed for 30 min with subsurface

nitrogen sparge. The mixture was heated to 88 oC and stirred for 16 h. The reaction mixture was cooled

to 50 ºC, concentrated under reduced pressure to one half of the original volume, cooled to 15 ºC and

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CH3CN (900 mL) was added. After aging for 2 h, the resulting slurry was cooled to −5 ºC, filtered and

rinsed sequentially with CH3CN (40 mL), water (90 mL), and CH3CN (40 mL). The cake was dissolved

in CH2Cl2 (1.93 L) and Florisil®

(60−100 mesh, 193 g) was then added. After aging at ambient

temperature for 5 h, Thio-Silica®

(68.0 g) was added and the slurry was aged for at least 10 h, then was

filtered and rinsed successively with CH2Cl2 (2 L), and a mixture of CH2Cl2 and EtOAc (4 L, 1:1 (v/v)).

The filtrate and the rinses were combined and concentrated to give an off-white solid 22 (80.0 g, 60%

yield): mp 190.9 ºC; 1H NMR (300 MHz, DMSO−d6) δ 9.17 (s, 1H), 8.26 (d, J = 6.9 Hz, 1H), 7.78 (d, J

= 8.4 Hz, 1H), 7.54 (s, 1H), 7.41 (t, J = 7.7 Hz, 1H), 5.55 (d, J = 8.6 Hz, 1H), 4.14−3.62 (m, 12H),

3.23−3.01 (m, 4H), 2.90 (s, 3H), 2.72−2.55 (m, 4H), 2.34−1.88 (m, 3H,), 1.88−1.43 (m, 3H); 13

C NMR

(75 MHz, DMSO−d6) δ 162.1, 159.2, 157.4, 149.9, 148.4, 131.2, 125.7, 124.5, 123.6, 122.6, 120.0,

119.1, 112.3, 88.0, 67.0, 66.0, 56.1, 51.8, 46.0, 45.3, 33.8, 30.5, 24.6, 21.7; HRMS (ESI) m/z calcd for

C28H36N7O4S2 [M+H] 598.2265, found 598.2264.

4-(6-((4-(Methylsulfonyl)piperazin-1-yl)methyl)-2-(1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-4-

yl)thieno[3,2-d]pyrimidin-4-yl)morpholine (22) (Scheme 11, Ni catalyst). To a mixture of 2-chloro-

6-(4-methylsulphonyl-piperazin-1-ylmethyl)-4-morpholin-4-yl-thieno[3,2-d]pyrimidine (1) (47.6 kg,

110 mol) in acetonitrile (477 L) was added water (0.6 kg), potassium phosphate (70.1 kg, 330 mol) and

2-(tetrahydro-2H-pyran-2-yl)-2H-indazol-4-ylboronic acid (18a) (40.7 kg, 165 mol). The mixture was

degassed for 30 min with subsurface nitrogen sparge. Nickel(II) nitrate hexahydrate (9.05 g, 31.1

mmol) and triphenylphosphine (16.4 g, 62.5 mmol) were added, and the resulting slurry was degassed

for 60 min with subsurface nitrogen sparge. The mixture was heated to 60 oC in 1.5 h and stirred for 25

h. A mixture of water (390 L) and 28% aqueous ammonium hydroxide solution (85 kg) was slowly

added in 2 h and the slurry was aged for 2 h. The resulting solution was cooled to 10−20 ºC in 4 h and

the phases were separated. To the organic phase was added CH3CN (190 L), and the mixture was

heated to 40−50 ºC in 1.5 h and then aged for 1 h. The mixture was cooled to 20−30 ºC in 4 h and aged

for 1 h. The slurry was filtered and rinsed successively with CH3CN (237 L), water (238 L), and

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acetonitrile (237 L). The cake was dried under vacuum at 50 ºC for 16 h to afford an off-white solid 22

(54.4 kg, 95.9wt% by HPLC, 79% yield).

4-(2-(1H-indazol-4-yl)-6-((4-(methylsulfonyl)piperazin-1-yl)methyl)thieno[3,2-d]pyrimidin-4-

yl)morpholine (GDC-0941). A mixture of 4-(2-(1-(tetrahydro-2H-pyran-2-yl)-2H-indazol-4-yl)-6-((4-

(methylsulfonyl)piperazin-1-yl)methyl)thieno[3,2-d]pyrimidin-4-yl)morpholine (22) (53.7 kg, 95.9wt%,

86.2 mol) in MeOH (1920 L) and water (101 L) was cooled to 5 oC. Methanesulfonic acid (41.1 kg, 428

mol) was slowly added in 2 h (a mild exotherm was observed) and the resulting slurry was heated to 65

ºC in 5 h. After aging for 4 h, the reaction mixture was cooled to 0−5 ºC in 6.5 h and stirred for 4 h.

The slurry was filtered and rinsed sequentially with cold MeOH (154 L, 0−5 ºC), a mixture of EtOAc

(259 L) and tert-butyl methyl ether (513 L), and tert-butyl methyl ether (51 L). The filter cake was

dried under vacuum for 12 h and was then charged into a hot mixture of methanol (112 L) and water (67

L) at 55 oC. After aging for 1 h, the resulting solution was filtered through a 0.5 µm in-line filter and

rinsed with a hot mixture of water (6 L) and MeOH (23 L) at 55 oC. To the hot filtrate was slowly

added MeOH (233 L) in 1 h and 10 min, followed by addition of crystal seeds of GDC-0941 (50 g).

More MeOH (693 L) was slowly added in 6 h and methanesulfonic acid (15.3 kg, 159 mol) was then

added in 35 min. After aging for 3 h, the mixture was cooled to 5 oC in 7 h and stirred for 3 h and 40

min. The slurry was filtered and rinsed sequentially with cold MeOH (168 L, 0−5 ºC), a mixture of

EtOAc (282 L) and with tert-butyl methyl ether (559 L), and tert-butyl methyl ether (56 L). The filter

cake was dried under vacuum at 55 ºC for 12 h to afford GDC-0941 bis-methanesulfonate as an off-

white solid (54.9 kg, 99.4wt%, 90%yield): mp 288.6 ºC; 1H NMR (300 MHz, D2O) δ 8.18 (s, 1H), 7.58

(d, J = 7.1 Hz, 1H), 7.55 (d, J = 7.9 Hz, 1H), 7.47 (s, 1H), 7.31 (t, J = 8.0 Hz, 1H), 4.74 (s, 2H),

3.95−3.85 (m, 4H), 3.85−3.75 (m, 4H), 3.62−3.50 (m, 4H), 3.49−3.36 (m, 4H), 3.01 (s, 3H), 2.71 (s,

6H); 13

C NMR (125 MHz, D2O) δ 155.7, 154.6, 148.9, 140.1, 140.0, 133.3, 126.3, 123.8, 123.7, 122.4,

119.0, 114.9, 113.6, 65.5, 53.0, 51.3, 46.6, 42.8, 38.5, 35.5; HRMS (ESI) calcd for C23H28N7O3S2

[M+H] 514.1690, found 514.1684.

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Supporting Information. Copies of 1H and

13C spectra for all the compounds listed in the experimental

section. This material is available free of charge via the Internet at http://pubs.acs.org.

Acknowledgment. We thank Dr. Jane Li, Dr. Jackson Pellett, Mr. Hong Lin and Ms. Stefanie Gee for

analytical support, Dr. Alan Deese for help with NMR analysis, and Dr. Christine Gu for HRMS

analysis. We also thank Professor Scott E. Denmark (University of Illinois at Urbana-Champaign) for

his valuable suggestions during the preparation of this manuscript.

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triarylmagnesiate solution was aged at −5 oC for 6 h. The reaction mixture after addition of DMF was

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(19) For Ni-catalyzed Suzuki-Miyaura cross-coupling, see: (a) Haneda, S.; Sudo, K.; Hayasi, M.

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methanesulfonic acid which contained <1 ppm of methyl methanesulfonate.

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