Early Process Development of an Irreversible EGFR T790M Inhibitor

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Early Process Development of an Irreversible EGFR T790M Inhibitor Yong Tao, Nandell F Keene, Kristin E Wiglesworth, Barbara Sitter, and James Christopher McWilliams Org. Process Res. Dev., Just Accepted Manuscript • DOI: 10.1021/acs.oprd.8b00437 • Publication Date (Web): 31 Jan 2019 Downloaded from http://pubs.acs.org on January 31, 2019

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Organic Process Research & Development

Early Process Development of an Irreversible EGFR T790M Inhibitor Yong Tao,* Nandell F. Keene, Kristin E. Wiglesworth, Barbara Sitter, J. Christopher McWilliams

Chemical Research and Development, Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States

TOC Graphics: SEM Enabled SEM Protection Route (8 Steps)

N

N

N Cl

N

Cl

HN

6 HN

N

HN N

Cl

3 Cl New Protection-free Route (6 Steps with 34% Yield)

HN

O

HN 2HCl

N N

I

N

N

O

12

O

N N N

NH N

N

N

N

N Cl

HN

N

O

1

19 N

Boc

ACS Paragon Plus Environment

1

Organic Process Research & Development 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

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ABSTRACT: The original synthesis of the irreversible EGFR T790M inhibitor 1 was enabled by successful application of ammonium hydroxide to cleanly cleave Nhydroxymethyl group and development of a high yielding condition for the subsequent amidation reaction. Furthermore, a protection-free and regioselective new synthetic route was developed that shortened the synthesis from the original 8 steps to 6 steps and improved the overall yield from 5% to 34% on scale. Crystallizations of 1 and intermediates were correspondingly developed to control the quality en route.

KEYWORDS: EGFR T790M Inhibitor, SEM deprotection, regioselective SNAr reaction, Negishi coupling, Buchwald-Hartwig coupling, amidation

INTRODUCTION

Treatment of EGFR mutant NSCLC (nonsmall cell lung cancer) patients with the first generation EGFR TKIs (Gefitinib and Erlotinib) provides excellent response rates and disease control for about one year, until they invariably become resistant to these therapies and their disease progresses due a second-site mutation in the EGFR kinase domain (T790M).1 In response to this unmet medical need, the pharmaceutical industry has put tremendous efforts into developing a highly potent irreversible inhibitor (3rd generation) with a good selectivity between the drugresistant double mutants T790M and WT EGFR. Both 12a and 22 (Figure 1) were identified at


2

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Pfizer as lead candidates that demonstrated high potency and specificity to the T790Mcontaining double mutant EGFRs. To expedite the program, two teams were formed to quickly enable the chemistry that would meet all API demands for both compounds to support toxicity evaluation and early clinical trials. Herein, the corresponding exploratory process development for 1 is described. Figure 1. Structures of 1 and 2

HN

N

HN

N HN

Cl

N N

O

N N N

N

HN

O

O N

N N

O O

1

2 (PF-06459988)

DISCUSSION AND RESULTS

Enabling the Original Synthesis: The original 8-step synthesis (Scheme 1) started from a widely available dichloropyrrolopyrimidine 3. The first five steps, including SEM protection, iodination with NIS, Negishi coupling to introduce the pyridinyl moiety, SNAr reaction with cylcobutanol 7 to construct the ether link and Buchwald coupling to connect pyrrolzylamine, worked smoothly and offered >70% yield in each step for intermediates 4, 5, 6, 8 and 10, with applying several chromatographic purifications. However, problems


3


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were encountered in the removal of the N-7 [2-(trimethylsilyl)ethoxy]methyl (SEM) group3 in steps 6 and 7. Treatment of 10 with TFA in dichloromethane cleaved both the N-Boc and the trimethylsilylethylene fragment of the SEM group to give 11, which could not be isolated cleanly by silica gel chromatography. Attempting to cleave the N7-hydroxymethyl group of 11 under basic conditions with K2CO3 in MeOH and water was problematic, resulting in the formation of many impurities, and proceeding to no more than 80% conversion. Re-subjecting isolated crude 12 to the same basic conditions pushed the reaction to near completion, but additional impurities arising from side reactions were observed. Silica gel chromatography of 12 removed some of the impurities. However, some conversion back to 11 was observed (10-20%),4 implying residual formaldehyde was still present. Carrying the partially purified 12 into the final amidation step under Schotten-Baumann conditions,5 i.e. reaction with acryloyl chloride in the presence of Na2CO3 in dichloromethane and water, afforded 1 in low yield. The overall yield from steps 6 to 8 was also highly scale dependent, decreasing from 40% on 98.0% purity) used to supply mouse exploratory toxicity studies.

Scheme 1. Original Synthesis of 1

Si

SEM = Step 2

Step 1 HN

SEM

Si

O

N

Cl

SEM

NIS DMF

N

N N

Cl

LiHMDS, THF

Cl

Cl

75%

1. i-PrMgCl, THF, -78 °C N I

N N

94%

Cl

3

O

Step 3

Cl

4

N N

SEM

2. ZnBr2, THF, -78 °C to rt I

Cl

Cl 3. Pd(PPh3)4, THF, 65 °C

5

N

N

N N

Cl 6

88% yield OH

NH2

Step 4 SEM

N

1.

7

O

N

Cl

N

9

O

Cs2CO3, dioxane, 105 °C, 10 h 72% yield, 2 steps

N

HN N N

N

N HN

O

HN

N

N

O

11

Cl Aq. Na2CO3/DCM, rt

NH

NH

HN

N

N

O

N HN N N

N N

Boc

10

Step 7 K2CO3, MeOH, H2O

N

Step 6

O

N

Boc

Step 8 N

N

TFA, DCM , rt

8

HO

N

N

Pd2dba3, xantphos

2. Aq. workup N

SEM

N N

N

KHMDS, THF , rt

O

N

Step 5

HN

N

O

N N N

11-41% yield over 3 steps scale dependant

12

O

1

Figure 2. Proposed Side Products Formed in the Final Step


5


HN

O

N

N HN

HO

N N

N

N

O HN

N

O

N

O

N

O

N

N O

N

O

O

HN

N

N

O

NH

O N

N N HN

Cl 14 (Bis acylated)

NH N

N N

N N N

13 (Cl-adduct)

N N

N

N HN

N N N

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15

N N 16 (Dimer)

The presence of residual formaldehyde by-product from the SEM deprotection was considered a possible root-cause for low and scale-dependent yields. Once formed, formaldehyde was not easily removed from the reaction system and could reversibly undergo addition to active nitrogen positions, complicating the isolation of 11 and 12, confounding the subsequent amidation step, and resulting in a low yields and an irreproducible process. Based upon this hypothesis, both chemical and physical means were examined to remove the formaldehyde. To this end, either the addition of sodium borohydride to reduce formaldehyde, or benzylamine to form a Schiff base, to the N7hydroxymethyl cleavage reaction were found to moderately improve the reaction profile based on UPLC monitoring. Ultimately, using large excess ammonium hydroxide in a biphasic system (dichloromethane, t-amyl alcohol and water) provided clean conversion and yielded formaldehyde-free crude 12 with good purity (>90%) after removing


6

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hexamethylenetetramine,6 a highly water soluble side product from the reaction of formaldehyde and ammonia, to aqueous layer through phase separation. Treating crude 12 with excess HCl in isopropanol resulted in crystallization of the dihydrochloride salt 12•2HCl and purged most impurities. It was also discovered that exposing 10 to HCl in isopropanol cleanly removed the N-Boc group while leaving the N7-SEM group intact, and resulted in direct crystallization of the intermediate hydrochloride salt 17•HCl salt. Thus, a process converting 10 to 12 through isolation of intermediate 17•HCl (Scheme 2) for better process control was adopted for scale up. Reacting 10 with HCl in isopropanol afforded 17•HCl in 93% yield. SEM deprotection was achieved as a one-pot operation by treating 17•HCl with TFA in dichloromethane to generate 11, followed by slow addition of excess ammonium hydroxide in t-amyl alcohol to cleave the N7-hydroxymethyl group. After aqueous workup and concentration, exposing the residue to HCl in IPA resulted in crystallization of 12•2HCl with 96% purity in 91% yield.

With clean 12•2HCl in hand, we switched our attention to identify better amidation conditions for 1 using acryloyl chloride under biphasic Schotten-Baumann conditions. A


7


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brief screen of bases (K3PO4, Na2CO3, triethylamine, Hunig’s base and DBU) and organic solvents (t-amyl alcohol, MTBE, THF, 2-MeTHF and acetonitrile) indicated that K3PO4 in either t-amyl alcohol or THF offered clean and fast conversion with minimal formation of side products. t-Amyl alcohol was chosen for the final API-forming step reaction as it is an ICH Class 3 solvent.7 Accordingly, on 110 g scale, acryloyl chloride (1.2 equiv.) was added to a biphasic mixture of 12•2HCl and K3PO4 (5.0 equiv.) in a 1:1 water/t-amyl alcohol. The reaction was complete within 5 min at 20 °C to form a mixture that contained 90% 1 with 3.4% dimer 16 and 2.5% Cl-adduct 13. These two major side products were partially purged by passing through a silica gel pad with 3:1 isopropanol and methanol as eluent to enhance the purity of 1 to ~95%. Isopropanol was identified as the crystallization solvent based upon a solubility screen of 1 in 24 common solvents.8 Recrystallization of 1 twice in hot isopropanol (65 °C) improved the purity of 1 to 98.38% and afforded the desired polymorph. The modified amidation reaction and crystallization process produced 160 g of 1 in 65% yield to supply the dog exploratory toxicity studies.

Scheme 2. Improved Process to Remove SEM


8

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SEM

SEM N

N HCl, i-PrOH

N HN

N

O

93%

N

N

N HN

N

N N

N N N 10

Boc

NH

HCl

17 (mono HCl Salt)

N

N HN

O

N

HO TFA, DCM

N

O

HN

1. NH4OH (aq) t-AmOH 2. HCl, i-PrOH 91%

N

N HN

N

O

2 HCl

N N

N N

NH 11

NH 12 (di-HCl salt)

New Synthesis Development: Although a practical process was developed to address the problematic SEM cleavage, the overall synthesis of intermediate 10 by the 1st generation route remained expensive due to using costly SEM chloride. In the design of a new synthetic route, more common N7 protecting groups, such as Tosyl, Boc, Cbz or PMB, were considered. However, a protection-free route would be an ideal solution to save cost and reduce the steps in the synthesis. With this as a goal, our development efforts focused on a more efficient protection-free route (Scheme 3).

Scheme 3. New Synthetic Route to 1


9


OH

STEP C

STEP B 7

N

STEP A HN N Cl

N N

Cl

97%

N

Cl

N

Cl

18

NH2 .HCl

STEP D

HN

9

N N

4% t-BuXPhos Palladacycle DBU, t-AmOH, 75 °C

19

N

HN

N HN

STEP E N

N N

O

N

81% 21

OH

Boc

HCl, i-PrOH 70 °C 93%

N

N Cl

O

N

68% N

3

HN

0.5% Pd(t-Bu3P)2 THF, 67 °C

O

90%

Cl

Zn Br

I

N

t-BuOK, MeTHF, rt

I

N

HN

O O

HN

NIS, DMF

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20

N

K3PO4 t-AmOH/H2O, rt

O 2HCl

N N NH 12

N

N

Cl N

Boc

HN

STEP F

O

N HN

N

Boc

N

HN

O

N N N

75%

O

1

The iodination at C-5 (Step A) was straightforward by treating 3 with 1 equiv. of Niodosuccinimide in DMF. The reaction reached to completion at ambient temperature within 1 h. Adding water to the reaction mixture induced recrystallization of 18 in near quantitative yield. The SNAr reaction to construct the ether bond at C-4 position was selected as the second step in the sequence based upon calculations from Pfizer’s internal Molecular Reactivity Indices Tool,9 which predicted that the C-4 position was substantially more electrophilic relative to the C-2 and C-5 positions (Figure 3). Indeed, the reaction between 18 and alcohol 7 in the presence of a strong base cleanly provided 19 with little evidence of regioisomer or bis-alkoxylated side products. Thus, reaction between 7 and 18 at 1:1 molar ratio with 2.5 equiv. of KOt-Bu in 2-MeTHF at 20 °C for 5 h,


10

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followed by aqueous workup and crystallization from a 2-MeTHF/EtOAc/heptane mixed solvent system, provided 19 in 90% yield. Figure 3. Calculated Electrophilicity of 18

To introduce the 2-pyridinyl moiety to the C-5 position at step C, a Negishi crosscoupling reaction10 was selected because iodide substitution is superior to achieve good regioselectivity.11 In addition, the reagent 2-pyridylzinc bromide (0.5 M in THF) is a readily available commodity.12 Pd(t-Bu3P)2 was identified as a very effective catalyst for this coupling, with only 0.5 mole% required to achieve reaction completion within 2 h in


11


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refluxing THF. 2.5 equiv. of 2-pyridylzinc bromide was required for full conversion because ~1.0 equiv. of the reagent was sacrificed to neutralize the free proton at N7 position.13 The reaction profile was relatively clean with >75% of the desired 20 and 96.0% (with

Early Process Development of an Irreversible EGFR T790M Inhibitor

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