Olaparib, Rucaparib, and Niraparib - ACS Publications - American

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Patent Review of Manufacturing Routes to Recently Approved PARP Inhibitors: Olaparib, Rucaparib, and Niraparib David L Hughes Org. Process Res. Dev., Just Accepted Manuscript • DOI: 10.1021/acs.oprd.7b00235 • Publication Date (Web): 09 Aug 2017 Downloaded from http://pubs.acs.org on August 9, 2017

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Organic Process Research & Development

Patent Review of Manufacturing Routes to Recently Approved PARP Inhibitors: Olaparib, Rucaparib, and Niraparib

David L. Hughes Cidara Therapeutics, Inc., 6310 Nancy Ridge Dr., Suite 101, San Diego, California 92121, United States

ABSTRACT: Olaparib, rucaparib, and niraparib are three inhibitors of poly(ADP-ribose) polymerase (PARP) enzymes that have been recently approved for the treatment of ovarian cancer.

The current

article reviews the patent and journal literature regarding synthetic routes and final forms of these PARP inhibitors.

GRAPHICAL ABSTRACT:

1 ACS Paragon Plus Environment


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Lynparza (olaparib), Rubraca (rucaparib), and Zejula (niraparib) are recently approved inhibitors of poly(ADP-ribose) polymerase (PARP) enzymes for the treatment of ovarian cancer. Two other PARP inhibitors, talazoparib and veliparib, are in Phase 3 development. The structures of these five PARP inhibitors are provided in Figure 1 along with iniparib, an early drug candidate that was incorrectly designated as a covalent PARP inhibitor.

Nicotinamide adenine dinucleotide (NAD+) (Figure 1) is the natural substrate of PARP1 and PARP2 enzymes. The PARP enzymes cleave NAD+ at the nicotinamide-sugar bond to build oligomers of the resulting adenosine phosphate ribose (ADP-ribose) fragment. PARP inhibitors have been designed to competitively bind to the NAD+ active site of the enzyme. In addition to competitive inhibition, recent work has shown that a second mechanism of action of some PARP inhibitors is to facilitate formation of a PARP-DNA complex that also interferes with DNA repair in tumor cells.1

This article reviews the patent literature of synthetic routes and final forms of the three recently approved PARP inhibitors, olaparib, niraparib, and rucaparib.

Figure 1. PARP Inhibitors


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O NH N

O O

NO2

H N

N

I

N

F

NHMe

O

CONH2

F

iniparib Sanofi Discontinued

rucaparib Clovis Oncology Approved US

olaparib AstraZeneca Approved US, EU

N N CO2NH2

H

N

H N

O CONH2

N

N

N

N

N H

N H

N

F

N H

F niraparib Tesaro Approved US

talazoparib Pfizer Phase 3

N H

veliparib AbbVie Phase 3

CONH2 N OH

HO

O

HO

HO O P HO

O

O O P OH O

N

NH2

N O

N

N

Nicotinamide adenine dinucleotide (NAD+) Natural substrate of PARP enzymes

1. Brief History of PARP Inhibitors

Poly (ADP-ribose) polymerases (PARP) are a family of enzymes involved in DNA repair. While all cells require damaged DNA strands to be repaired to maintain genomic integrity and cell



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viability, it has been known since the early 1990s that certain tumor cells have a greater dependence on PARP enzymes for DNA repair than healthy cells, leading to the hypothesis that PARP inhibition could be a viable target for cancer therapy.2 In 2005, two independent research groups published papers with compelling evidence that inhibition of PARP enzymes in mutant cell lines of BRCA1 and BRCA2 tumors could be a highly effective way to treat breast, ovarian, and other cancers.3,4 These papers served to focus research on specific BRCA-mutant cancers as the most sensitive targets and stimulated renewed interest in PARP inhibitors. Shortly thereafter, several PARP inhibitors advanced through pre-clinical development and into clinical proof-ofconcept studies for the treatment of ovarian and breast cancers.

Iniparib was the first declared PARP inhibitor to progress into clinical studies in 2008 for the treatment of breast cancer. Iniparib was discovered by BiPar Sciences, which was acquired by Sanofi-Aventis in 2009. The active drug was believed to be the in vivo reduction product of inaparib, 4-iodo-3-nitrosobenzamide, which was reported to be a covalent inhibitor of the PARP1 enzyme.5 Early results were promising. In a Phase 2 study reported in late 2009, triplenegative breast cancer patients treated with iniparib in addition to chemotherapy had a median survival of 12.2 months vs. 7.7 months for patients treated only with chemotherapy, with a similar level of side effects.6 Follow up studies, however, were disappointing. In Jan 2011, Sanofi reported that iniparib failed to show statistical improvement in a Phase 3 study involving 519 breast cancer patients.7 In early 2012, researchers at Abbott discovered that iniparib was not a PARP inhibitor and that its effectiveness in some cancer trials must be due to a mechanism other than PARP inhibition.8 Finally, in June 2013, Sanofi disclosed that iniparib also failed in a


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study of lung cancer patients, resulting in the termination of this compound for the treatment of cancer.9 During this same period, Merck, Pfizer, and AstraZeneca were studying their small molecule PARP inhibitors in early oncology clinical trials. At the 2011 ASCO meeting, AstraZeneca reported encouraging results of their PARP inhibitor, olaparib, in an interim analysis of a Phase 2 study in ovarian cancer patients.10 However, analysis of the full Phase 2 study suggested the previously observed progression free survival was not likely to translate into overall survival, leading AstraZeneca to discontinue development in Dec 2011.11 When the study was reanalyzed, patients with mutant BRCA cell lines were shown to have a favorable response versus placebo.12 The company reversed course and decided to re-initiate development.13 A subsequent Phase 2 study in 137 ovarian cancer patients with deleterious or suspected deleterious gBRCAm, previously treated with three or more prior lines of chemotherapy, gave an overall response rate of 34%, providing the basis for FDA and EMA approval of olaparib in Dec 2014.14

Given the uncertainty surrounding the PARP inhibitors, Pfizer made the decision to out license its PARP inhibitor, now known as rucaparib, to Clovis Oncology in June 2011. Clovis completed clinical development and received FDA approval for rucaparib in Dec2016. Likewise, Merck out licensed its PARP inhibitor, now known as niraparib, to Tesaro in June 2012. Tesaro continued clinical development, culminating in FDA approval for niraparib in Mar2017.

2. Olaparib



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Olaparib, marketed under the tradename Lynparza, was discovered by KuDOS Pharmaceuticals, which was acquired by AstraZeneca in 2006. Lynparza was approved for the treatment of ovarian cancer in Dec2014.

2.1 Medicinal Chemistry Route to Olaparib The original route to olaparib, designed to facilitate analog synthesis, is presented in Scheme 1.15, 16

2-Formylbenzoic acid (1) was reacted with dimethylphosphite to afford phosphonate 2 in 95%

yield. Horner-Wadsworth-Emmons reaction of phosphonate 2 with aldehyde 3 furnished a 1:1 E:Z mixture of olefin 4 in 96% yield. Hydrolysis of the nitrile of intermediate 4 was carried out in aq. NaOH at 90 oC followed by reaction with hydrazine hydrate in the same vessel to afford the phthalazinone 5 in 77% yield. Amide coupling with N-Boc-piperazine mediated by 2-(1Hbenzotriazol-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate (HBTU) in N,Ndimethylacetamide afforded 6 in 78% yield. The Boc group was removed in aq. ethanolic HCl to afford free amine 7 followed by amide formation with cyclopropanecarbonyl chloride in dichloromethane to form olaparib in 83% yield.

Scheme 1. Medicinal Chemistry Route to Olaparib


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O 1) MeO P OMe CO2H H CHO 1

O

O Et3N

O

NaOMe, MeOH

OMe OHC P O OMe

2) MsOH

O CN

CN

F F

95%

4 1:1 E:Z

3 96%

2 O

O NH N

1) NaOH, H2O 90 oC

NH N

HBTU, DMA

CO2H

2) NH2NH2 H2O 77% 5

HN

O

N Boc

N

F

N

F

Boc

6 O

O NH N

Aq. HCl EtOH

COCl O

Et3N 85% (2-steps)

N F

N

NH N

O N F

H

7

N

O

olaparib

2.2 Process Chemistry Route to Olaparib

The Process Chemistry route to olaparib is a modification of the Medicinal Chemistry route.17,18 In this route, the base, reagent, and solvents were optimized to facilitate telescoping the first two reactions. In the first reaction, dimethylphosphite was replaced with diethylphosphite, the base changed from methoxide to t-amylate, and the reaction was carried out in 2-MeTHF instead of MeOH. After the reaction was quenched with aq. bicarbonate, the 2-MeTHF solution of phosphonate 2b was directly reacted with aldehyde 3 to afford olefin 4, which crystallized 7 ACS Paragon Plus Environment


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directly from the reaction mixture and was isolated in 64% yield over the two steps. The E/Z mixture of 4 was reacted with hydrazine hydrate and HOAc in THF at 60 oC, then water was added to quench the reaction and directly crystallize nitrile 8 in 89% yield. Nitrile 8 was hydrolyzed using aq. NaOH, then neutralized with HCl to directly crystallize carboxylic acid 5, which was isolated in 95% yield. The 3-step Medicinal Chemistry conversion of 5 to olaparib was reduced to two steps by employing amide 9 which incorporates the cyclopropyl group. Amide coupling was mediated by HBTU to afford olaparib, which crystallized directly from the reaction mixture and was isolated in 62% yield. Overall yield for the 5-step process was 34%.

Scheme 2. Process Chemistry Route to Olaparib


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2.3 Alternate Approaches to Olaparib 2.3.1 Aminocarbonylation Lescot and co-workers have described an aminocarbonylation of bromide 10 with cyclopropyl amide 9 using 10 mol % Pd(dba)2, 10% Xantphos, carbon monoxide, and i-Pr2NEt in dioxane at 100 oC (Scheme 3).20 The primary purpose of this work was to incorporate a 13C or 14C label into olaparib using labeled carbon monoxide. Preparation of bromide 10 was not provided but



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could be prepared in an analogous approach as in Schemes 1 and 2 except using 3-bromo-4fluorobenzaldehyde in the Horner-Wadsworth-Emmons reaction.

Scheme 3. Aminocarbonylation Route to Olaparib

2.3.2. Convergent Route with Elaborated Amide

Chinese Patent Application CN105085407 from Guangzhou Health Pharmaceutical Company describes two convergent routes to olaparib employing an elaborated aldehyde fragment.21

In the first route (Scheme 4), 2-fluoro-5-formylbenzoic acid is converted to its corresponding acid chloride using thionyl chloride and catalytic DMF, then directly coupled with cyclopropyl amide 9 in dichloromethane to afford aldehyde 11 as a crude material in 84% yield. HornerWadsworth-Emmons reaction with phosphonate 2b was conducted in 1,4-dioxane using Et3N as base. At the end of the reaction the solvent was removed and the product slurried in water to afford a mixture of olefins 12 in 76% yield after filtration. Conversion to olaparib was accomplished by reacting 12 with hydrazine hydrate in EtOH at room temperature. At the end of 10 ACS Paragon Plus Environment

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the reaction the solvent was removed and olaparib was recrystallized from EtOAc in an isolated yield of 77%. The overall step count of five, which includes one step to generate 9 and one for 2b, is one step less than the AstraZeneca Process Chemistry route. The overall yield for the longest linear sequence (3-steps) was 49%.

Scheme 4. First Convergent Route to Olaparib

In a variation of this route, reaction of aldehyde 11 with phthalide in ethyl propanoate with NaOMe/MeOH afforded the diketone 13 in 57% yield (Scheme 5). The analogous reaction is described in the Medicinal Chemistry patents15 using 3-cyanobenzaldehyde to prepare the desfluoro analog of olaparib, but the authors noted that this approach was not viable with 3-cyano-4fluorobenzaldehyde (3) due to SNAr displacement of fluoride by NaOMe. In the current example, the more hindered aldehyde 11 may be less prone to fluoride displacement than 3, 11 ACS Paragon Plus Environment


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allowing for a modest yield of 57% for this conversion. In the final step of this route, reaction of 13 with hydrazine hydrate in EtOH at reflux afforded olaparib in 61% yield after recrystallization from EtOAc. Overall yield for the 3-step synthesis was 29%.

Scheme 5. Second Convergent Route to Olaparib

While both routes presented in Schemes 4 and 5 are short and efficient, use of hydrazine in the final step is a concern. Hydrazine has been shown to induce cancerous tumor growth in animal studies and has been classified as a probable human carcinogen by the US Environmental Protection Agency (EPA).22a Since olaparib is an anticancer drug, the ICH S9 guideline allows sponsors to justify higher limits for potential genotoxic impurities than the threshold of toxicological concern (TTC) or the staged TTC as outlined in the ICH M7 guideline.22b In alignment with the S9 guideline, the European Public Assessment Report (EPAR) notes that since olaparib is genotoxic and teratogenic, control of potential genotoxic impurities to the TTC 12 ACS Paragon Plus Environment

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or staged TTC was not necessary for approval in the EU.19 Nonetheless, in developing a second generation route to a marketed drug, the manufacturer may be required to control hydrazine to a level comparable to that in the currently approved API.

2.4 Olaparib Polymorphs

With a pKa of 12.5 (deprotonation of the phthalizinone N-H) olaparib is essentially neutral across relevant biological pHs. As such, olaparib exhibits low aq. solubility (approx. 0.1 mg/mL) across the pH range of 1 to 9. The highest solubility in biologically relevant fluid is 0.2 mg/mL in fed state simulated intestinal fluid (FeSSIF). Olaparib is classified by the Biopharmaceutical Classification System (BCS) as Class 4 at doses above 25 mg with low solubility and moderate permeability.19,23

2.4.1 Polymorph Selected for Commercialization The AstraZeneca and Kudos patents describe three forms of olaparib, including two anhydrous polymorphs (Form A and Form L) and a mono-hydrate polymorph (Form H). According to the EPAR, four polymorphic forms of olaparib have been identified, so one additional form is not disclosed in the patent literature.19

Form A is generated by crystallization from EtOH/water or MeOH/water mixtures and is the form which is generated from the manufacturing process. Based on DSC data, Form A has a melting point of 210 oC.17 Form L crystallizes from EtOH/water mixtures as well as from a variety of other solvents. Based on DSC data, Form L melts at 198.5 oC, then recrystallizes to



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Form A, which melts at 210 oC.18 Form H is a monohydrate described in a formulation patent and is present is some formulations.23 The DSC of Form H is complex. The water of hydration is slowly lost upon heating to 100 oC, then several shallow endotherms and exotherms indicate a number of phase transitions occur between 100 oC to 175 oC, followed by a sharper endotherm at 208 oC associated with Form A.

According to the EPAR, two polymorphic forms were under consideration as the final form for commercialization, presumably Forms A and L.19 The EPAR notes that the form selected for commercialization was the kinetic form that is produced during the manufacturing process although the other form was determined to be thermodynamically more stable below 60˚C. These data indicate that the two polymorphs are enantiotropic, meaning the most stable form is dependent on temperature.24a

A schematic of stability of two enantiotropic polymorphs as a function of temperature is shown in Fig 2. In this example, the two polymorphs have equivalent stability (solubility) at the transition temperature, which is 60 oC. Characterization of the transition temperature can be determined by Van’t Hoff plots of solubilities at different temperatures for each polymorph, which provide the heat of solution of each polymorph. Determining solubilities may not be possible if one polymorph rapidly converts to the other, so the transition temperature can also be determined by conducting competitive slurry experiments at different temperatures. In these studies a slurry of each individual polymorph is seeded with the other at a given temperature. The more stable polymorph will remain unchanged while the less stable polymorph will convert to the more stable form. Near the transition temperature, both polymorphs will likely persist.24b


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Figure 2. Schematic Showing Stability of Two Enantiotropic Polymorphs as a Function of Temperature

Form X Form Y ∆G

TTr = 60 oC Temperature

Based on the examples provided in the patent,18 Form L is the most stable form below 60 oC, since slurrying Form A in several solvents resulted in turnover to form L over a period of three days to three weeks at temperatures below 60 oC. Form A is the less stable form below 60 oC but was selected for commercialization for reasons that are not disclosed other than it readily forms under the process conditions used for manufacture, and that it turns over to Form L very slowly. That Form A is the commercial form is further corroborated by the melting point, which is noted as initiating at 206 oC in the FDA product monograph,25 consistent with the DSC provided in the Kudos patents for Form A.17



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According to the EPAR,19 the Committee for Medicinal Products for Human Use (CHMP) had significant concerns regarding the physical stability of the polymorph selected for commercialization. In response to questions from the reviewer, the applicant provided additional data that demonstrated a low risk for solid-to-solid polymorph conversion under the API storage conditions as well as demonstrating that polymorph interconversion does not occur in the formulation over the shelf life of the product under the recommended storage conditions.

Near IR was used to identify the desired polymorph and to quantify the level of the undesired polymorph. The CHMP requested that a second method, x-ray powder diffraction (XRPD), be used as an additional method for polymorph identification for ten commercial batches to provide additional validation of the near-IR method.

2.4.2 Alternate Forms of Olaparib Crystal Pharmatech has disclosed a co-crystal of olaparib with urea that has 4- to 6-fold greater solubility than Form A in simulated gastric fluid (SGF) and fasted state simulated intestinal fluid (FaSSIF).26 The co-crystal has a melting point of 171 oC, below that of Form A (210 oC). The authors propose the higher solubility of the co-crystal could lead to improved bioavailability, but no data were provided.

2.5 Formulation of Olaparib Given the low solubility and moderate permeability of olaparib, development of a bioavailable oral formulation proved challenging. A number of prototype formulations were evaluated in fasted beagle dogs. A lipidic formulation of micronized olaparib as a solid dispersion in the


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water-disperiable surfactant lauroyl polyoxylglyceride27 at a 10% drug load provided a 2-fold increase in bioavailability versus a standard immediate release tablet. However, at higher drug loadings, such as 20% and 40%, bioavailability decreased significantly. 22 Therefore, the formulation taken into Phase 1 and 2 clinical studies was a 50 mg dose provided in a size 0 capsule (approx. 500 mg fill). Given that approval was granted based on a Phase 2 study, this was the formulation that was also commercialized.

Since the patient must swallow 16 capsules per day for the recommended dose of 400 mg twice daily, an improved formulation was developed. A second generation oral formulation is described in U.S. Patent 8,475,842 in which olaparib is formulated as a solid dispersion in copovidone, then compressed into 150 mg tablets.22,28 The solid dispersion is manufactured using a hot-melt extrusion process which involves mixing of olaparib with copovidone, increasing the temperature above the melting point of copovidone (140 oC) to produce a melt, then extrusion of the melt to form a solid dispersion. The cooled extrudate is milled and then mixed with other excipients, including silicon dioxide (glidant), mannitol (soluble filler), and sodium stearyl fumarate (lubricant) followed by compression into tablets. Tablets with 25% drug load and 30:70 drug:polymer load were shown in dog studies to have 2.5-fold greater bioavailability relative to the commercial lipidic capsule formulation.22

Since olaparib is a genotoxic drug, bioequivalence studies in healthy volunteers was not possible. Instead, clinical studies in cancer patients were undertaken with the 150 mg tablet formulation. Two daily doses of 300 mg (4 x 150 mg tablets daily) were shown to be effective for treatment of platinum-sensitive, relapsed ovarian cancer patients in the maintenance setting.29,30



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AstraZeneca announced in March 2017 that the FDA accepted the sNDA for olaparib tablets for this indication.30

2.6 Olaparib – Summary According to the EPAR,19 olaparib is synthesized in seven chemical steps followed by a purification step and micronization. In the original application, five steps were proposed for the GMP synthesis, suggesting that the sponsor had designated compounds 1, 3, and 9 (Scheme 2) as the regulatory starting materials. The CHMP required that two additional stages to one of the starting materials be included as a part of the GMP synthesis. While no specifics were provided, the two additional GMP stages are likely for the synthesis of the cyclopropyl amide 9 (one step reaction plus a purification) since this material is not commercially available and is used in the final step.

The convergent route (Scheme 5) reported by Guangzhou Health Pharmaceutical Company is two steps shorter than the AstraZeneca route. This route is attractive since it avoids phosphonate formation and is thus more atom economical. As noted above, in considering implementation as a second generation manufacturing route, control of hydrazine in the API would need to be demonstrated, as well as meeting all other specifications including control of the API polymorph.

The final form of olaparib presented a challenge due to the enantiotropic nature of two polymorphs. A thorough scientific understanding of the phase diagram combined with demonstrated control of the polymorph during API and drug product stability studies provided confidence in the choice of Form A for commercialization.


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3. Rucaparib camsylate Rucaparib camsylate (marketed under the tradename Rubraca) was discovered at as part of a collaboration among the Northern Institute of Cancer Research, Newcastle University, and Agouron Pharmaceuticals. After Agouron was acquired by Warner Lambert in 1999, and in turn acquired by Pfizer in 2000, Pfizer undertook early clinical development, then outlicensed the drug candidate to Clovis Oncology, which continued development and obtained accelerated U.S. approval in Dec 2016 for treatment of patients with advanced ovarian cancer.

3.1 Medicinal Chemistry Route to Rucaparib The Medicinal Chemistry route to rucaparib is outlined in a 2002 patent assigned to Agouron and Cancer Research Campaign Technology (Scheme 6).31,32 The experimental procedures and yields in the patent are provided primarily for the des-F compound with a note that the fluoro compound followed the same procedures. The route is 7 linear steps and has an overall yield of 22%, with key steps including indole formation via a Leimgruber-Batcho reaction and a Suzuki cross coupling for introduction of the side chain.

The route starts with synthesis of methyl 6-fluoro-indole-4-carboxylate 16 by condensation of DMF dimethylacetal (DMF-DMA)with methyl 5-fluoro-2-methyl-3-nitrobenzoate (14) in refluxing DMF to afford the enamine 15 in 97% yield followed by hydrogenation to furnish indole 16 in 81% yield. Reaction with 1-acetoxy-2-nitroethane in refluxing xylenes in the presence of catalytic t-butylcatechol afforded indole 17 in 89% yield. Zinc reduction of the nitro group followed by lactamization provided the 7-membered lactam 18 in 73% yield. Bromination



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occurred selectively in the 2-position of the indole to furnish 19, setting up the Suzuki reaction with 4-formylbenzene boronic acid which provided aldehyde 20 in 77% yield. Reductive amination with methylamine, mediated by sodium cyanoborohydride in MeOH, provided rucaparib in 68% yield.

Scheme 6. Medicinal Chemistry Route to Rucaparib

3.2 First Process Chemistry Route to Rucaparib


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The first Process Chemistry route to rucaparib is described in a 2008 patent assigned to Agouron (Scheme 7).33 The inventors do not provide details of why an alternate route was explored other than the original route was lengthy and linear. Further liabilities of the Medicinal Chemistry route are discussed in section 3.4 below.

The route outlined in Scheme 7 is 10 steps and provides rucaparib in 15% yield. While this process may be more convergent than the Medicinal Chemistry route by constructing the indole ring system at a later stage, the need to build the acetylene fragment and use of a carbamate as a nitrogen protecting group, adds additional steps versus the original route. As such, this route does not provide a meaningful improvement relative to the original route.

Scheme 7. First Process Route to Rucaparib



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The route began synthesis of alkyne 23 in four steps from 4-bromobenaldehyde via Pd-catalyzed cross coupling with TMS-acetylene to afford aldehyde 21 followed by reductive amination to introduce the methylamine side chain in intermediate 22. The resulting secondary amine 22 was protected with methyl chloroformate and the TMS group removed using carbonate to afford the alkyne 23 in 60% yield over the two steps.

The triflate of nitrophenol 24 required for the Sonagashira coupling was generated with triflic anhydride and triethylamine in MeCN. Alkyne 23 was added to the solution containing the triflate, then this solution was added to an MeCN solution of PdCl2(PPh3)2 in MeCN at 60 oC. This protocol minimized formation of the alkyne dimer 31. Copper co-catalysis, often required for Sonagashira couplings, was omitted in this protocol since probe studies indicated use of copper salts increased the amount of dimer formed. After work-up, crude 25 was reduced to amine 26 with iron powder activated with a catalytic amount of HCl. Cyclization to indole 27 was accomplished using catalytic CuI in DMF at 100 oC. Tituration with CH2Cl2/hexanes to remove dimer 31 afforded indole 27 in 52% yield over the 3 steps.

Construction of the requisite tricyclic structure of rucaparib began with reaction of indole 27 with 1-(dimethylamino)-2-nitroethylene in CH2Cl2 mediated by TFA to afford nitroalkene 28 in 95% yield, which was then reduced to nitroalkane 29 with NaBH4 in 20 vol of 9:1 EtOH:MeOH in 84% yield. A high volume of solvent was necessary for the reaction to complete due to the poor solubilities of 28 and 29.



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A number of conditions were tried for the reductive cyclization of 29 to the ε-lactam 30 before finding that Raney nickel in HOAc afforded clean reduction, which permitted clean cyclization under basic conditions in 96-98% yield. Using Pd/C or Pt/C, N-hydroxylactam 32 was the major byproduct under neutral conditions and C-N reduction product 33 formed under acidic conditions.

Figure 3. Byproducts Formed in the First Process Chemistry Route to Rucaparib

The carbamate group of 30 was deprotected using HBr/HOAc at ambient temperature to afford rucaparib in 88% yield. The MeBr generated during this reaction could be trapped using an aq. ethanolamine scrubber.34 Alkaline conditions were attempted for the deprotection, but led to unacceptable levels of lactam hydrolysis.


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3.3 Second Process Chemistry Route to Rucaparib A publication from the Pfizer process chemistry group describes the second Process Chemistry route to rucaparib, which involved modifications to the original Medicinal Chemistry route outlined in Scheme 6.35 Perhaps unable to reproduce the one-step conversion of 16 to nitroalkane 17, this chemistry was replaced with a two-step process using reaction with 1-(dimethylamino)2-nitroethylene followed by reduction with sodium borohydride, which only proceeded in 33% yield (Scheme 8).

Scheme 8. Second Process Chemistry Route, Conversion of 16 to 17

3.4 Third Process Chemistry Route to Rucaparib Although optimization of the original Medicinal Chemistry route (Schemes 6 and 8) was sufficient to prepare 2 kg of rucaparib, a number of issues remained before a scalable route could be defined, including: (1) Formation of enamine 15 resulted in an unacceptable exotherm at the intended reaction temperature of 120 oC;



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(2) Reduction of nitroalkene 34 to nitroalkane 17 performed poorly at scale, leading to a yield of only 33% and required purification by chromatography; (3) Suzuki coupling between bromide 19 and 4-formylbenzene boronic acid was sluggish at scale, requiring a higher catalyst load to complete; (4) Use of sodium cyanoborohydride for reduction amination of 20 was undesirable due to the release of HCN. Given these issues, further modifications of this route were undertaken to define a scalable route. The full route is outlined in Scheme 9.

To address the safety concern with the conversion of 14 to enamine 15, alternative reagents were screened. Bredereck’s reagent, (Me2N)2CHO-t-Bu, underwent reaction at an acceptable reaction temperature of 50 oC but provided 15 with a poor impurity profile that rendered it unreactive in the subsequent reduction. Tris(dimethylamino)methane also reacted at 50 oC but had a lower exothermic onset temperature of 75 oC and was not available in bulk quantities. Thus, development using the original reagent, DMF-DMA, was re-evaluated and found to be safe when carried out at a lower temperature (95 oC instead of 120 oC). At the end of the reaction, most of the solvent was removed under vacuum, then MeOH was added and the hydrogenation was carried out using Pd/C as catalyst. The resulting crude indole 16 was purified using silica gel chromatography, resulting in a 2-step yield of 32%.

To address the safety issues with use of 1-(dimethylamino)-2-nitroethylene and the poor yield in the reduction of 34 to 17, alternate reagents and conditions were probed for conversion of indole 16 to tricycle 18. Screening of 2-carbon electrophiles identified phthalimidoacetaldehyde diethyl


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acetal as the only promising alternative. After further development, the corresponding aldehyde 36 was found to be more reactive and gave a cleaner reaction. The optimized process involved dissolution of indole 16, aldehyde 36, and triethylsilane in dichloromethane, then TFA in dichloromethane was added over 30 min and the reaction stirred at 20 oC for 28 h. Product 37 crystallized from the reaction mixture and was isolated in 43% yield. Deprotection of the phthalimido group with concomitant cyclization to 18 was carried out in 40% aq. methylamine at ambient temperature. At the end of the reaction, an equal volume of water was added, directly providing crystalline tricylic indole 18 which was isolated in 82% yield. Bromination of indole 18 was carried out using pyridinium tribromide in 1:1 THF:CH2Cl2 to afford bromo-indole 19, which was crystallized in 83% isolated yield by adding a solution of 19 in THF to saturated aq. Na2CO3.

For the Suzuki coupling of 19 with 4-formylbenzene boronic acid, screening experiments identified Pd(dffp)Cl2-CH2Cl2 as the optimum catalyst, but the reaction was capricious depending on the source of reagents used. The catalyst poison could not be identified, but a reproducible process was devised by combining bromide 19, 2.5 mol % of the Pd catalyst, and solvent MeCONMe2, then heating to 95 oC for 1 h. This procedure ensured activation of the catalyst (reduction of PdII to Pd0) and oxidative insertion of Pd with the aryl bromide. In a separate vessel the boronic acid was stirred in a solvent mixture of MeCONMe2 and aq. Na2CO3 for 3 h at 20 oC, then added to the hot solution of the aryl bromide. Upon completion of the reaction after 2 h at 95 oC, the mixture was cooled to room temperature, then addition of water resulted in crystallization of aldehyde 20. Further purification was accomplished by slurrying in MeOH, affording aldehyde 20 in 92% yield.



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Regarding the reductive amination of 20, the goal was to find an alternative to Na(CN)BH3 since the acidic conditions, required to avoid formation of the bis-amine byproduct 40, results in generation of HCN. Since H2 is also evolved in this reaction, scrubbing of HCN at scale would be challenging. Sodium borohydride was found to be a suitable replacement for Na(CN)BH3; however, alcohol by-product 39 was also generated and could not be completely purged from rucaparib when the reductive amination was carried out as a one-step process. Therefore, the imine 38 was prepared and crystallized from MeOH, removing all residual aldehyde 20, and then reduced with NaBH4 in MeOH/THF. The isolation consisted of addition of HCl, treatment with activated carbon to reduce the level of Pd carried in from the Suzuki coupling, then crystallization of the HCl salt of rucaparib. The (S)-camphorsulfonic acid salt final form, which is discussed in more detail in section 3.6, was prepared in two steps. First, the HCl salt was converted to the free base using aq. NaOH in MeOH followed by addition of water to crystallize the free base. The free base was further purified by slurrying the solids in THF to afford the THF solvate in 79% yield. The (S)-camphorsulfonate salt was then prepared by dissolution of the THF solvate of the free base and (S)-camphorsulfonic acid (1.2 equiv) in a 70 oC mixture of 2PrOH/water, cooling to ambient temperature, then completing crystallization by the addition of water.

Scheme 9. Pfizer Process Chemistry Route to Rucaparib


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Figure 4. Major Byproducts in Pfizer Route to Rucaparib 29 ACS Paragon Plus Environment


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3.5 Alternate route to Rucaparib Chinese patent application CN10600853036 filed by Shijiazhuang Biotechnology describes an alternate route to tricylic indole intermediate 18 based on a Bartoli-Dodd indole synthesis (Scheme 10).37 The 6-step sequence affords 18 in 16% yield. The synthesis started with chlorination of 3-fluoro-5-nitrobenzoic acid with NCS in DMF to afford 4-chloro-3-fluoro-5nitrobenzoic acid (41) in 88% yield. The chlorination blocks one ortho-position, thereby directing regioselectivity in the cyclization, a variant developed by Dodd.38 The indolization was carried out with four equiv of vinylmagnesium bromide at temperatures ranging from -10 to -45 o

C, affording indole product 42 in 41-52% yield after crystallization from EtOAc. After

formation of the methyl ester 43, Vilsmeier–Haack formylation furnished aldehyde 44 in 71% yield. Condensation of aldehyde 44 with neat nitromethane, mediated by ammonium acetate, afforded chain extended nitroalkene 45 in 63% yield. Hydrogenation using 10% Pt on carbon reduced the double bond, reductively cleaved the Cl group, and reduced the nitro group to an amino group to facilitate ring closure to afford tricylic indole 18 in 94% yield. 30 ACS Paragon Plus Environment

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Scheme 10. Alternate Route to Tricyclic Indole 18 CO2H

CO2H

CO2H MgBr THF

NCS F

NO2

DMF F 90%

Cl 41

o NO2 -45 C 49%

CHO

DMF

MeOH SOCl2 F 88%

POCl3

N H

Cl

N H

F

71%

Cl

43

44 NO2

MeNO2 NH4OAc 60 oC 63%

Cl 42

MeO2C

CO2Me

N H

F

MeO2C

F Cl

O

H2 10% Pt/C N H

MeOH 94%

H N

N H

F 18

45

3.6 Rucaparib Final Form The final form of rucaparib is an anhydrous (S)-camphorsulfonic acid salt, commonly referred to as the “camsylate salt.” Three polymorphs of the camsylate salts were discovered, denoted as Forms A, B, and C.39 Based on information in the patents39 and the Pfizer publication,35 Form A appears to be the most stable polymorph (highest melting) and is the form generated from the crystallization process using 2-PrOH/water.

The phosphate salt was used for early clinical trials in which the drug was administered intravenously. However, due to its propensity to hydrate, an alternate salt was required for a



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tablet formulation.39 A number of crystalline salt forms were prepared, including the three anhydrous (S)-camphorsulfonate salt polymorphs noted above, one anhydrous (R)camphorsulfonate salt form, mixtures of (R)- and (S)-camphorsulfonate salts, two anhydrous maleate salt polymorphs, and an HCl trihydrate.39

Since the maleate and (S)-camphorsulfonic acid salts could be readily prepared and were less hygroscopic than the other salts, they were further evaluated for tablet formulation.40 The (S)camphorsulfonic acid was found to be highly compressible, permitting tablet drug loading >45% and a small image size. Therefore, the (S)-camphorsulfonate salt was selected as the final form for the commercial 200 mg and 300 mg dose strength tablets. 40

3.7 Summary –Rucaparib Camsylate The Pfizer route outlined in Scheme 9 is ten linear chemical steps followed by a complex purification via the HCl salt, free base THF solvate, and (S)-CSA salt. This route achieved the initial goal of providing a process that is safe and scalable. However, the route is long, many steps are low yielding, and the overall yield is only 3%. No other process patents or publications from Pfizer or Clovis Oncology have published since the Pfizer journal article, so it remains unclear if this route has been further developed into a manufacturing process.

The alternate route to tricyclic indole 18 described by Shijiazhuang Biotechnology (Scheme 10) proceeds in six steps, the same number as the Pfizer route, but has a reported yield of 16% versus 6% for the Pfizer route. While the patent application provides few details, it appears this route could be developed into a viable manufacturing process for this intermediate.


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The (S)-camphorsulfonic acid salt provided an excellent final form for rucaparib. The most stable polymorph of the salt can be readily prepared and has physical properties (nonhygroscopic and compressible) that allow for formulation as a high-dose tablet.

Lonza manufactured rucaparib camsylate during late stage clinical development and is continuing to manufacture API for commercial launch.41 In Oct 2016, Lonza and Clovis Oncology announced plans to construct a dedicated production train at Lonza for future manufacture of the final steps of rucaparib. The new suite, which is targeted to be operationally qualified by 2019, will consolidate processes that are currently run in shared facilities. Due to the genotoxicity and teratogenicity of rucaparib,42 the final steps of the rucaparib process must be conducted in high containment equipment. Of note, the new process train will include extensive process analytical technology (PAT) that will allow for on-line analytical monitoring and for real time release of API.

4. Niraparib Tosylate Monohydrate FDA approved niraparib (tradename ZEJULA) in Mar 2017 for the maintenance treatment of adult patients with recurrent epithelial ovarian, fallopian tube, or primary peritoneal cancer who are in a complete or partial response to platinum-based chemotherapy.

4.1 Medicinal Chemistry Route The Medicinal Chemistry route to niraparib is presented in Scheme 11.43,44 The route involves ten chemical steps with a longest linear sequence of 7 steps, a low yielding resolution, and a final 33 ACS Paragon Plus Environment


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preparative SFC purification to upgrade the enantiomeric purity, with an overall yield of 3-4%. Since the first process chemistry route was a modification of this route, individual reactions and isolations are discussed in the following section.

Scheme 11. Medicinal Chemistry Route to Niraparib


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CO2H NO2 CH3 46

1) AcCl, MeOH

CHO

47

48

N Me O 74% NH2

H2/PtO2

4-IC6H4NO2 THF 60%

MeOH HCl 90%

1) L-tartaric acid resolution 20%

N

NH

N

Boc (S)-52 80-90% ee

51

CO2Me NaN3, DMF

Boc N

N N

90 oC 46%

N

EtOH

NH2

2) Boc2O

50

CO2Me NO2

CO2Me NO2

CH2Br

B(OH)2 Pd(PPh3)4 Na2CO3

49

4A Sieves CH3CN O

2) NBS (PhCH2O)2 (6%) CCl4, reflux 34%

NO2

N

o

CO2Me NO2

NH3 MeOH 60 oC 82%

55 N Boc

53

CO2NH2

CO2NH2

Boc N

N

HCl

N

N

EtOAc 93%

56 CO2NH2

niraparib H

HCl N

N Chiral SFC separation

H N

N

N niraparib HCl

4.2 First Process Chemistry Route



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In order to make material to support early development, process chemists at Merck focused on development of the Medicinal Chemistry route.45 A number of issues needed to be addressed for scale up, including: 1) A low yielding resolution (20%) that provided product with 80-90% ee after several recrystallizations, requiring an ee upgrade by preparative chiral SFC chromatography at the end of the synthesis; 2) Safety concerns carrying out the azide chemistry at 90 oC; 3) Isolation of the final product via lyophilization as an amorphous, hygroscopic HCl salt; 4) General process improvement including reaction efficiency, replacing undesirable solvents, reducing catalysis loadings, and purification of intermediates by crystallization instead of chromatography.

Synthesis of Aniline 52. To improve robustness of the Suzuki cross coupling of 49, the catalyst was changed from (PPh3)4Pd to the more robust PdCl2(dppf) with a reduced loading of 2%. 4Bromo-1-nitrobenzene was used as the coupling partner instead of 1-iodo-4-nitrobenzene.

The resolution of racemic 51 remained problematic. A 1:2 bis salt with dibenzoyl-L-tartraric acid (L-DBT) showed some difference in solubility of the two diastereomeric salts and was selected for further development. A crystallization and re-slurry at 40 oC in MeOH afforded the bis-DBT salt in 25% yield and 95% de.

Synthesis of Aldehyde 48. An alternate route to the aldehyde 48 was designed to avoid the problematic low yielding bromination step that required chromatographic purification. Reaction


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of methyl 2-nitro-m-toluate with DMA-DMF in DMF at 130 oC afforded enamine 57, which was precipitated from the reaction mixture by addition of water and isolated in 70% yield. The enamine 57 was oxidized with sodium periodate in water/DMF to afford aldehyde 48 in 80% yield after crystallization from EtOAc.

Scheme 12. First Process Chemistry Rou to Niraparib via Resolution



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CO2Me NO2 CH3

CO2Me NO2

DMF-DMA DMF, 130 oC 70%

57

Na2CO3

N 49

1) Boc2O

25%

69%

2 DBT

NH

N

Rac-51

(S)-51

N 50

2) EtOH

NH2

MeOH HCl 79%

4-BrC6H4NO2 THF 79%

CHO 48

L-DBT resolution

H2/PtO2

Pd(dppf)Cl2

DMF H2O 80%

NH2

NO2 B(OH)2

CO2Me NO2

NaIO4 NMe2

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H

95% de CO2Me NO2

CO2Me N3

1) NaN3, DMF 2,6-lutidine 110 oC

-N2

Boc N

N N

2) NaOH THF

N

CO2H

69%

N

58

53

NH4HCO3 Boc2O Pyr, THF 52%

N Boc

54

CO2NH2

N Boc

Boc 1) p-TsOH N

N N

CO2NH2

THF

p-TsOH

H N

N N

2) CH3CN/H2O

56

74%

niraparib p-TsOH H2O

Conversion to Niraparib. After salt break, (S)-51 free base was protected using Boc2O in EtOH, then condensed with aldehyde 48. Upon cooling, the imine 53 crystallized from the reaction mixture and was isolated in 69% yield.


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An in-depth study of the reaction of imine 53 with NaN3 to form indazole 55 was conducted in order to develop a reaction that could be safely run at scale. Mass spectroscopy indicated the reaction proceeded via azide 54, which was shown to be non-shock sensitive. The reaction was carried out under basic conditions using 2,6-lutidine and a nitrogen sweep to avoid formation of hydrazoic acid, which can form explosive gas mixtures at a concentration above 10%.46 Thermal analysis indicated the reaction could be safely carried out at 110 oC, instead of the original 90 oC, allowing for a reduction in azide to 1.0 equiv. Although exothermic at this temperature, a runaway reaction could be avoided since refluxing of the solvent (DMF) would dissipate any excess energy that might be generated. During the reaction, the ester was partially hydrolyzed, so it was decided to fully hydrolyze the product using aq. NaOH in THF, affording indazole 58 in 69% yield as a solution in THF.

Conversion to the primary amide 56 was accomplished by activation with Boc2O, mediated by pyridine, followed by reaction with ammonium bicarbonate. The product was crystallized from iPrOAc then re-slurried in MTBE to afford 56 in 52% yield.

A survey of final forms of the API identified the p-tosylate salt as a stable and non-hygroscopic salt. Therefore, a Boc-deprotection process was developed using p-TsOH in water/THF at 60 oC. On cooling the p-TsOH salt of niraparib crystallized from the reaction mixture and was isolated in 86% yield. The ee of the salt was 95%, essentially unchanged from the aniline intermediate (S)-51. Due to the much lower solubility of the racemic product than (S)-niraparib, ee upgrade was carried out by crystallization in CH3CN/water to afford material having 30% ee in about 5%



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yield, then concentration of the filtrate to remove CH3CN, resulting in crystallization of niraparib with >99.5% ee in 85% yield. The overall yield for this route was 3%.

4.3 Second Process Chemistry Route to Niraparib via Chiral Chromatography Further development of the resolution proved unfruitful, so a chromatographic separation of enantiomers was investigated. Racemic amine 52 was identified as the best candidate for separation using a Chiralpak AD column with ethanol/heptane as eluent. With a productivity of 0.27 kg product separated per kg of stationary phase per day, separation of 8.5 kg of racemate was achieved on a 30 cm column to provide (S)-52 in 46% yield and 99.3% ee.

Optimization of the downstream processing led to an improvement in yield for imine 53 to 93% by conducting the reaction in MTBE instead of EtOH. The purity of amide 56 was upgraded by filtration through silica, which improved the crystallization yield and afforded a 3-step yield of 52% for the 3-steps from imine 53. The overall yield to niraparib was improved to 11% via this route.

Scheme 13. Second Process Chemistry Route to Niraparib via Chiral Chromatography


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CO2Me NO2

NH2

NH2

CO2Me NO2

CHO

ChiralPak AD

48

Heptane-EtOH 46% N Boc

N

MTBE N

Boc

93% N Boc

53

(S)-52

rac-52

99.3% ee

1) NaN3, DMF 2,6-lutidine 110 oC

CO2H

Boc N

N N

2) NaOH THF

Pyr, THF 52% (3-steps)

58

CO2NH2

Boc N

N N

NH4HCO3 Boc2O

p-TsOH THF

CO2NH2

p-TsOH

H N

N N

86% 56

niraparib p-TsOH H2O

4.4 Third Process Chemistry Route to Niraparib via Tranaminase Chemistry While the optimization of the Medicinal Chemistry route provided kilogram quantities of niraparib for early development activities, a number of opportunities remained for an improved route, including: 1. An asymmetric route to avoid the inefficient resolution or preparative scale chiral chromatography; 2. Alternative disconnections to avoid use of azide chemistry; 3. Minimization of unit operations involving late stage, high potency intermediates that require use of dedicated facilities and equipment for handling highly potent compounds;



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4. Diminish environmental impact through use of less toxic solvents, avoiding platinum metals, and improving overall process mass intensity. An alternate route employing an asymmetric transaminase and a late stage C-N bond coupling was designed and developed by Merck process chemists.47 The final steps, including C-N cross coupling, deprotection, and salt formation (Scheme 14) are discussed first, followed by two asymmetric approaches to piperidine 61.

The t-Bu protected amide indazole 60 was prepared from indazole-7- carboxylic acid by activating the acid with CDI in DMF at room temperature then coupling with t-butylamine at 40 o

C. The product was isolated in 86% yield by addition of water to directly crystallize 60 from the

reaction mixture. Catalyst, ligand, solvent and base for the coupling of indazole 60 with aryl bromide 61 were optimized through high throughput screening. The final conditions included use 5% CuBr, 10% 8-hydroxyquinoline, and K2CO3 in CH3CONMe2 at 110 oC, affording product 62 in 94% yield. The reaction was selective for the desired N-2 nitrogen with 100 mg/mL) and the tosylate salt (

Olaparib, Rucaparib, and Niraparib - ACS Publications - American

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