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Article

Synthetic Routes to 2-aryl-1H-pyrrolo[2,3-b]pyridin-4-amines: Cross-Coupling and Challenges in SEM-Deprotection

by
Srinivas Reddy Merugu
1,
Sigrid Selmer-Olsen
1,
Camilla Johansen Kaada
1,
Eirik Sundby
2 and
Bård Helge Hoff
1,*
1
Department of Chemistry, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
2
Department of Materials Science and Engineering, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
*
Author to whom correspondence should be addressed.
Molecules 2024, 29(19), 4743; https://doi.org/10.3390/molecules29194743
Submission received: 11 September 2024 / Revised: 1 October 2024 / Accepted: 4 October 2024 / Published: 7 October 2024
(This article belongs to the Special Issue Exploring Heterocyclic Compounds: Design, Synthesis, and Their Role in Cancer, Antimicrobial Activity, and COVID-19 Treatment)
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Abstract

:
7-Azaindoles are compounds of considerable medicinal interest. During development of the structure–activity relationship for inhibitors of the colony stimulated factor 1 receptor tyrosine kinase (CSF1R), a specific 2-aryl-1H-pyrrolo[2,3-b]pyridin-4-amine was needed. Two different synthetic strategies were evaluated, in which the order of the key C-C and C-N cross-coupling steps differed. The best route relied on a chemoselective Suzuki–Miyaura cross-coupling at C-2 on a 2-iodo-4-chloropyrrolopyridine intermediate, and subsequently a Buchwald–Hartwig amination with a secondary amine at C-4. Masking of hydroxyl and pyrroles proved essential to succeed with the latter transformation. The final trimethylsilylethoxymethyl (SEM) deprotection step was challenging, as release of formaldehyde gave rise to different side products, most interestingly a tricyclic eight-membered 7-azaindole. The target 2-aryl-1H-pyrrolo[2,3-b]pyridin-4-amine (compound 3c) proved to be 20-fold less potent than the reference inhibitor, confirming the importance of the N-3 in the pyrrolopyrimidine parent compound for efficient CSF1R inhibition.

Graphical Abstract

1. Introduction

Azaindoles (pyrrolopyridines) are an important class of heterocycles. Derivatives have been used as probes in biological imaging [1,2], and have a rich coordination chemistry [3]. Most importantly, azaindoles are used as core scaffolds in medicinal chemistry to discovery new bioactivity, and since they are bioisosteres of indoles and pyrrolopyrimidines they are useful probe compounds in structure–activity relationship studies (SAR). The most prominent use of 7-azaindoles is as kinase inhibitors. Depending on their detailed structure, inhibitory activity towards different kinases has been discovered. FDA approved drugs include pexidartinib (PLX3397) [4], a colony stimulating factor 1 receptor kinase (CSF1R) inhibitor for treatment of tenosynovial giant cell tumours, and vemurafenib (PLX4032) [5], a serine/threonine-protein kinase B-Raf (B-Raf) inhibitor for late-stage melanoma (Figure 1). Other interesting kinase targets for 7-azaindoles include Janus kinase 3 (JAK3) [6], ataxia telangiectasia and Rad3-related protein kinase (ATR) [7]; epidermal growth factor receptor kinase (EGFR) [8]; proto-oncogene serine/threonine-protein kinase (PIM) kinase [9], activin-like kinase (Alk5) [10] and calcium/calmodulin dependent protein kinase 2 (CAMKK2) [11]. Methodology for functionalisation of the 7-azaindole scaffold has been provided by Barl et al. [12] and Scheider et al. [13].
By proper planning, intramolecular cyclization can be performed, giving rise to different polycyclic 7-azaindoles. Compound I is obtained by a Buchwald–Hartwig amination and a C-H arylation in sequence or tandem [14], while II, a fused 7-membered azaindole, is made starting with a Sonogashira coupling and finalising with a palladium catalysed Heck [15]. In contrast, compound III and the 8-membered IV are obtained after Suzuki–Miyaura cross-coupling followed by Pictet–Spengler condensation with aldehydes [16]. Of relevance to our work is also the tendency of 4-azaindoles to react with formaldehyde giving dimers like V [17]. During SAR studies for pyrrolopyrimidine-based CSF1R inhibitors [18,19,20], we needed the corresponding 7-azaindole. Despite a high synthetic activity in this field, routes to similar 2-aryl-1H-pyrrolo[2,3-b]pyridin-4-amines have not been published. Thus, here we report our investigation into synthetic routes involving protection group selection and implementation of cross-coupling methodology. Moreover, we also identified a new class of tricyclic azaindoles incorporating an 8-membered ring.

2. Results

The pyrrolopyrimidine 1 (Scheme 1) is a potent CSF1R inhibitor in enzymatic studies [18], while the corresponding thienopyrimidine 2 was far less active, indicating the NH to be important in inhibitor binding to the kinase. To investigate SAR further, the corresponding 7-azaindole analogue 3c was targeted. We assumed that a similar synthetic plan as that used for the corresponding pyrrolopyrimidines could be viable, involving a thermal SNAr nucleophilic aromatic substitution and a Suzuki–Miyaura cross-coupling; see Scheme 1.

2.1. Route A: Amination Followed by Suzuki–Miyaura Cross-Coupling

In the first synthetic approach, we evaluated the possibility of starting with an amination reaction at C-4, to give a 2-iodo derivative suitable for Suzuki–Miyaura cross-coupling; see Scheme 2. First, the SEM-protected building block 7 was attempted aminated in refluxing n-butanol under thermal SNAr conditions. However, after 48 h, no conversion was observed by 1H NMR spectroscopy. Noting that previous studies reported rather forcing conditions [21], we instead decided for palladium catalysed amination.
The RuPhos ligand has been found to be useful in similar aminations [22,23]. However, treatment of the 2-iodo derivative 7 under these conditions was unsuccessful and instead led to reduction at C-2 giving 6 and an unstable molecule assumed by 1H NMR to be structure 8 (Scheme 2). The above results strongly indicated that the oxidative addition of palladium preferably occurred at C-2 instead of at C-4. Therefore, we decided to introduce the 4-amino group prior to iodination. Palladium catalysed amination of 4-chloro-7-azaindole (4) with N-benzylmethylamine has previously been reported by Henderson et al. with a 96% yield [22], but their 1H NMR spectra were not in accordance with the proposed structure. We performed this reaction using the RuPhos ligand and the RuPhos Pd G2 pre-catalyst and achieved a 33% yield of the aminated structure 9. Loss in mass was seen in the extraction, indicating that water soluble side products were formed. Inferior result and incomplete conversion were noted when performing the same transformation with sodium tert-butoxide as base. (Under similar conditions the benzenesulfonyl derivative 5 gave after purification, 20% of the aminated structure 9 and 48% of 4-chloro-7-azaindole (4). Due to the low yield and the inconvenient deprotection occurring, we instead evaluated the use of the SEM-protected analogue 6 in conversion to the aminated derivative 10. The reaction was tested with XPhos Pd G2/XPhos, RuPhos Pd G2/RuPhos and Pd(OAc)2/RuPhos in n-butanol and tert-butanol. Dried solvents are needed for the reaction to proceed with ease. The highest conversion and yield were seen for the use of Pd(OAc)2/RuPhos in tert-butanol, giving 94% conversion in 5 min and 68% isolated yield. Reduction at C-4 leading to 11 (6%) was observed as a side reaction. This transformation can very likely be improved by further tuning of conditions. Unfortunately, the iodination of 10 attempted with 1.5 equiv. of lithium diisopropylamide (LDA) only resulted in 8% conversion to product and 6% isolated yield. The same reaction ran with 3 equiv. of LDA, terminated at 12% conversion. The use of n-butyl lithium could have led to better results. This was however not tested. Suzuki–Miyaura cross-coupling on 12 with XPhos Pd G2/XPhos provided the 2-phenyl derivative 13a with 77%. While 13a could be deprotected (see Section 2.3), the route proved inefficient due to a difficult iodination.

2.2. Route B: Suzuki–Miyaura Cross-Coupling Followed by Amination

In the alternative approach, we aimed to establish a chemoselective Suzuki–Miyaura cross-coupling at C-2 on the 4-chloro-2-iodo intermediate 7. A similar reaction has been performed on the corresponding methyl [9] and benzenesulfonyl N-1 protected analogues [8]. The initial experiments were based on our previous selectivity study on thienopyrimidines [24], that showed preference for mono arylation at C-6 (analogous to C-2 in pyrrolopyridines) when using Pd(OAc)2 or tris(dibenzylideneacetone)dipalladium (Pd2(dba)3). Both these systems were investigated in a model reaction with 4-methoxyphenyl boronic acid, of which Pd2(dba)3 showed excellent selectivity for C-2 arylation, giving the para-methoxy compound 14b 68–71% isolated yield at 0.5–1 g scale; see Scheme 3. A trace amount of the 2,4-diarylated product 15b was also observed. The corresponding phenyl derivative 14a was formed in similar yield (75%).
This catalyst system was then tested for preparation of the para-hydroxymethyl derivative 14c, see Table 1. The cross-coupling provided a 92/4 ratio of mono- to di-arylated product, no reduction product (6), but also gave 4% of an unknown side product difficult to remove by silica-gel column chromatography. Lowering the temperature only increased the amount of the problematic impurity (entries 1–3). The effect of varying the catalyst in this transformation was therefore investigated through screening reactions. Aminations catalysed by XPhos Pd G2, XPhos, Pd(OAc)2, PEPPSITM-SIPr and (Dppf)PdCl2 (entries 4–7) suffered from low chemoselectivity, or the formation of other side product. On the other hand, the use of Pd(PPh3)4 only led to 5–8% of the C-2 reduced derivative 6 (entry 8). A preparative 1 g reaction (entry 9) resulted in 83% isolated yield of the product 14c. As the cross-coupling appeared to slow down on scaling, the 2 g reaction (entry 10) was performed at 90 °C for 22 h. Under these conditions, 6% of the diarylated product 15c was seen, but the product 14c could anyhow be isolated with 83% yield. Similarly, we prepared the tert-butyldimethylsilane (TBMDS) analogue 14d by Suzuki–Miyaura cross-coupling using Pd(PPh3)4 with 90% isolated yield (Scheme 4). The corresponding SEM analogue 14e was made from the alcohol 14c by a substitution reaction in DMF in mediocre 51% isolated yield. The formyl ester 14f was also isolated as a side product, originating from a reaction between the formed alkoxide and DMF (Scheme 4).
The next step was a palladium mediated amination of the advanced intermediates 14. We first aminated the phenyl and methoxy derivatives 14a–b using Pd(OAc)2 and the RuPhos ligand. Encouragingly, both substrates were fully converted in 1 h, giving the aminated products 13a–b with 74% and 76% isolated yield, respectively (Table 2, entries 1–2). However, when attempting the same reaction with the unprotected 14c, less than 40% conversion was seen in 24 h (Table 2, entry 3) and the product 13c could not be isolated in sufficiently pure form. Four ligands/catalyst systems including Pd(OAc)2/XantPhos PEPPSITM-SIPr pre-catalyst, tri(o-tolyl)-phosphine and (Dppf)PdCl2 were tested without any improvement in reaction outcome. Clearly, the acidic hydroxyl proton was again causing side reactions to dominate. The palladium catalysed amination of the TBDMS derivative 14d proceeded with good conversion. Some deprotection of the hydroxymethyl group also giving 13c was observed if the reaction was left stirring for several h. However, quenching the reaction after only 0.5 h allowed for isolation of the TBDMS protected analogue 13d with an 89% yield. The double SEM-protected analogue 14e was smoothly aminated to 13e (entry 5).

2.3. SEM-Deprotection

Regarding synthesis of the corresponding 6-arylated pyrrolopyrimidines, most SEM-deprotections proceeded with ease [19,25] by a two-step procedure, involving first the trifluoroacetic acid (TFA) treatment followed by a basic step. It has been assumed that the acidic step leads to a mixture of the product 3 and the intermediate VI. Then, basic conditions release formaldehyde and give full conversion to 3 (Scheme 5).
As the precursor 13c was difficult to obtain using Buchwald–Hartwig amination, our main target, compound 3c, could hopefully be formed by deprotection of 13d or 13e. The double deprotection of the tert-butyldimethylsilyl protected 13d proceeded decently and the product 3c was isolated with 51% yield after one round of silica-gel column chromatography and a crystallisation. The crystallisation ensured high quality material for the biotesting. In contrast, for the reaction of the double SEM protected analogue 13e, the O-SEM group at the benzylic position was less reactive, and a high number of compounds were observed. Thus, a low 13% yield was obtained after column chromatography. Interestingly, the 8-membered azaindole 16c was also isolated. The compound is evidenced by its mass, and a characteristic methylene unit residing at ca 31 ppm, with HMBC NMR coupling both to the phenyl unit of the 4-amino group and the pyrrole ring. Obviously, during SEM-deprotection formaldehyde is released which under the given conditions undergoes a two-step electrophilic aromatic substitution. The use of BF3-OEt2 in the deprotection of 13d–e was also attempted, but this resulted in even more complex reaction mixtures. Tetrabutylammonium fluoride was not evaluated.
Triggered by the interest for this new tricyclic eight-membered azaindole, we also performed deprotection of the analogue 13a. Performing the acidic step at 22 °C (rt) gave the product 3a with a 45% yield, alongside multiple products which we did not manage to isolate. When the same reaction was repeated at 50 °C, 3a was isolated with a 31% yield alongside 12% of the tricyclic 8-membered azaindole 16a. To increase the amount of 16a, we stirred 3a with formaldehyde (1.2 equiv.) and TFA. The main product under these conditions, however, was the dimer 17a (32%). The most characteristic 13C NMR signal is from the central methylene unit having a carbon shift of 23.8 ppm, distinguishing this structure from 16a. Although similar azaindole dimers have been made [17,26], this dimer is much more sterically crowded than those reported. Then, the methoxy analogue 13b was deprotected. After 6 h at rt with TFA and an extended stirring time with aq. NaHCO3, the product 3b was isolated after two rounds of column chromatography with a low 14% yield (semi-pure). We assumed that one of the side products was the 8-membered azaindole 16b. To promote formation of this compound, we reasoned that longer reaction time in TFA could be beneficial. Thus, the TFA treatment step was performed for 18 h instead of 6 h at 50 °C. This gave 16b as the main product with 69% isolated yield. Similar yield was obtained when reacting at 22 °C, while the addition of more formaldehyde had a negative effect (more complex reaction mixture).

2.4. Enzymatic CSF1R Kinase Activity

The initial aim of these synthetic endeavours was to evaluate the azaindole 3c as a CSF1R inhibitor. The CSF1R kinase inhibitory activity of 3c was compared with that of the corresponding pyrrolopyrimidine 1 and the thienopyrimidine 2. IC50 titration at low ATP concentration indicated that the azaindole 3c was decently active (IC50 = 3.0 nM), see Figure 2.
However, when profiled in an alternative CSF1R assay with higher ATP concentration, the IC50 value was much higher (IC50 = 105 nM), and compared to the corresponding pyrrolopyrimidine 20-fold lower activity was seen (Table 3). Apparently, the inhibitory profile of 3c is very sensitive to the ATP concentration. Obviously, the N-3 nitrogen in the pyrrolopyrimidines is of importance. The loss in activity is also in line with the X-ray co-crystal of the pyrrolopyrimidine 1 with the kinase domain of CSF1R, where N-3 is involved in hydrogen binding via a deeply situated water molecule [19].

3. Materials and Methods

3.1. Chemicals and Analysis

4-Chloro-7-azaindole was purchased from 1Click Chemistry. All other reagents, starting materials, palladium catalysts and solvents were purchased from Sigma-Aldrich and used as is. Dry solvents were collected from a Braun MB SPS-800 solvent purification system. Reactions were monitored by thin-layer chromatography (TLC) using silica-gel on aluminium plates, F254, Merck. Purification of compounds by flash column chromatography was performed with silica-gel (40–63 mesh, 60 Å) using standard glassware. NMR spectra were recorded on a Bruker Avance III HD 400 or 600 MHz instrument in either CDCl3 containing tetramethylsilane or DMSO-d6 as solvents. 1H and 13C chemical shifts are reported in part per million (ppm) using tetramethylsilane (0.00 ppm) or residual solvent (DMSO-d5, 2.50/39.52 ppm) as an internal reference standard. Infrared absorption spectra were recorded on a Thermo Nicolet Nexus FT-IR spectrometer using a Smart Endurance reflection cell. Absorption bands are reported as strong (s), medium (m) or weak (w). Accurate mass determination was performed on a Synapt G2-S Q-TOF instrument from Waters TM in either positive or negative mode. The samples were ionized with an ASAP (APCI) or ESI probe. Exact mass calculations and spectra processing were done using Waters TM Software Masslynx v4.1 SCN871.

3.2. Synthesis

3.2.1. 4-Chloro-2-phenyl-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridine (14a)

To a mixture of 4-chloro-2-iodo-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridine (7) (350 mg, 0.856 mmol), phenylboronic acid (125 mg, 1.02 mmol), Pd2(dba)3 (24 mg, 0.026 mmol) and K2CO3 (350 mg, 2.56 mmol) was added de-gassed 1,4-dioxane:water (1:1, 5 mL) under an N2 atmosphere. The reaction mixture was stirred at 100 °C for 30 min before being allowed to cool to rt. The solvent was removed in vacuo, and the residue was partitioned between EtOAc (20 mL) and water (20 mL). The layers were separated, and the aqueous layer was extracted with EtOAc (3 × 20 mL). The combined organic phases were washed with brine (20 mL), dried over anhydrous Na2SO4, filtered and concentrated in vacuo. The product was purified by silica-gel column chromatography (n-hexane/EtOAc, 9:1, Rf = 0.30) to give 230 mg (0.641 mmol, 75%) of a yellow oil. 1H NMR (600 MHz, CDCl3) δ: 8.22 (d, J = 5.1 Hz, 1H), 7.80–7.78 (m, 2H), 7.50–7.41 (m, 3H), 7.15 (d, J = 8.5 Hz, 1H), 6.69 (s, 1H), 5.66 (s, 2H), 3.72 (t, J = 8.5 Hz, 2H), 0.95 (t, J = 8.5 Hz, 2H), 0.04 (s, 9H); 13CNMR (151 MHz, CDCl3): 150.4, 143.3, 142.9, 135.4, 131.7, 129.5, 128.9 (2C), 128.8 (2C), 120.0, 117.1, 99.2, 71.1, 66.7, 18.1, −1.2 (3C); HRMS (ES+, m/z): found 359.1349, calcd. for C19H23ClN2OSi, [M+H]+, 359.1346.

3.2.2. 4-Chloro-2-(4-methoxyphenyl)-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridine (14b)

The compound was made as described for 14a, starting with 4-chloro-2-iodo-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridine (7) (1.00 g, 2.44 mmol) and 4-methoxyphenylboronic acid (440 mg, 2.93 mmol). The reaction time was 30 min at 100 °C. The product was purified by silica-gel column chromatography (n-hexane/EtOAc, 4:1, Rf = 0.40) to give a yellow oil, 650 mg (1.67 mmol, 68%); 1H NMR (400 MHz, CDCl3) δ 8.18 (d, J = 5.2 Hz, 1H), 7.72 (d, J = 8.8 Hz, 2H), 7.11 (d, J = 5.2 Hz, 1H), 7.00 (d, J = 8.8 Hz, 2H), 6.61 (s, 1H), 5.63 (s, 2H), 3.84 (s, 3H), 3.74 (t, J = 8.3 Hz, 2H), 0.97 (t, J = 8.3 Hz, 2H), −0.04 (s, 9H); 13C NMR (100 MHz, CDCl3) δ 160.1, 150.2, 142.8 (2C), 134.9, 130.7 (2C), 123.9, 119.9, 116.9, 114.2 (2C), 98.2, 70.9, 66.5, 55.3, 18.0, −1.4 (3C); IR (neat, cm−1): 2951 (w), 2837 (w), 1613 (w), 1498 (m), 1246 (s), 1075 (m), 832 (s), 695 (w); HRMS (APCI/ASAP, m/z): found 389.1445, calcd. for C20H26N2O2SiCl, [M+H]+, 389.1452.

3.2.3. (4-(4-Chloro-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridin-2-yl)phenyl)methanol (14c)

The synthesis was performed as described for 14a, starting with compound 7 (1.23 g, 3.02 mmol); (4-(hydroxymethyl)phenyl)boronic acid (539 mg, 3.55 mmol), but using Pd(PPh3)4 (180 mg, 0.156 mmol). The reaction was run at 80 °C for 9 h. The product was purified by silica-gel column chromatography (n-pentane/EtOAc, 4:1, Rf = 0.27) giving a light-yellow oil, 936 mg (2.50 mmol, 79%); 1H NMR (400 MHz, DMSO-d6) δ 8.27 (d, J = 5.2 Hz, 1H), 7.77 (d, J = 8.3 Hz, 2H), 7.47 (d, J = 8.3 Hz, 2H), 7.33 (d, J = 5.2 Hz, 1H), 6.75 (s, 1H), 5.63 (s, 2H), 5.31 (t, J = 5.7 Hz, 1H), 4.58 (d, J = 5.7 Hz, 2H), 3.61 (t, J = 8.0 Hz, 2H), 0.84 (t, J = 8.0 Hz, 2H), −0.11 (s, 9H); 13C NMR (100 MHz, DMSO-d6) δ 149.8, 143.6, 143.4, 142.5, 133.8, 129.2, 128.7 (2C), 126.7 (2C), 118.9, 116.9, 98.2, 70.8, 65.9, 62.5, 17.3, −1.4 (3C); IR (neat, cm−1): 3330 (w, br), 2950 (m), 2893 (m), 1558 (m), 1368 (m), 1286 (s), 1120 (s), 930 (s, br), 909 (m, br), 831 (s, br)); HRMS (APCI/ASAP, m/z): found 389.1445, calcd. for C20H26N2O2SiCl, [M+H]+, 389.1452.

3.2.4. 2-(4-(((tert-Butyldimethylsilyl)oxy)methyl)phenyl)-4-chloro-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridine (14d)

The synthesis was performed as described as for 14a, but starting with compound 7 (901 mg, 2.2 mmol), (4-(((tert-butyldimethylsilyl)oxy)methyl)phenyl)boronic acid (644 mg, 2.42 mmol), Pd(PPh3)4 (127 mg, 0.110 mmol). The mixture was stirred at 85 °C for 2 h. The product was purified by silica-gel column chromatography (n-pentane/EtOAc, 97:3, Rf = 0.11) to give 991 mg (1.97 mmol, 90%) of a white solid; mp. 48.5–50 °C; 1H NMR (400 MHz, DMSO-d6) δ 8.27 (d, J = 5.2 Hz, 1H), 7.79 (d, J = 8.3 Hz, 2H), 7.46 (d, J = 8.3 Hz, 2H), 7.33 (d, J = 5.2 Hz, 1H), 6.76 (s, 1H), 5.64 (s, 2H), 4.80 (s, 2H), 3.59 (t, J = 8.0 Hz, 2H), 0.93 (s, 9H), 0.82 (t, J = 8.0 Hz, 2H), 0.11 (s, 6H), −0.11 (s, 9H); 13C NMR (100 MHz, DMSO-d6) δ 149.8, 143.5, 142.4, 142.2, 133.9, 129.4, 128.8 (2C), 126.3 (2C), 118.9, 117.0, 98.3, 70.8, 65.9, 63.9, 25.8 (3C), 18.0, 17.3, −1.5 (3C), −5.3 (2C); IR (neat, cm−1): 2951 (m), 2926 (m), 2883 (w), 2853 (w), 1554 (m), 1471 (m), 1458 (m), 1375 (m), 1249 (s), 1074 (s), 918 (m), 829 (s, br), 767 (s, br); HRMS (APCI/ASAP, m/z): found 503.2315, calcd. for C26H40N2O2Si2Cl, [M+H]+, 503.2317.

3.2.5. 4-Chloro-2-(4-(((2-(trimethylsilyl)ethoxy)methoxy)methyl)phenyl)-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridine (14e)

(4-(4-Chloro-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridin-2-yl)phenyl)-methanol (14c) (1.05 g, 2.70 mmol) was dissolved in dry DMF (11 mL). NaH (114 mg, 4.75 mmol) was added under an N2 atmosphere at 0 °C. After stirring for 30 min, 2-(trimethylsilyl)ethoxymethyl chloride (0.7 mL, 3.96 mmol) was added dropwise over 10 min. The mixture was further stirred at 0 °C for 4 h and 45 min, before being allowed to warm to 22 °C. The mixture was quenched with sat. aq. NH4Cl (100 mL) and extracted with EtOAc (3 × 100 mL). The combined organic phases were washed with brine (100 mL), dried over anhydrous Na2SO4, filtered and concentrated in vacuo. The product was purified by silica-gel column chromatography (n-pentane/EtOAc, 96:4, Rf = 0.19) giving 717 mg (1.38 mmol, 51%) of a clear oil. 1H NMR (400 MHz, DMSO-d6) δ: 8.28 (d, J = 5.2 Hz, 1H), 7.80 (d, J = 8.2 Hz, 2H), 7.48 (d, J = 8.2 Hz, 2H), 7.34 (d, J = 5.2 Hz, 1H), 6.77 (s, 1H), 5.65 (s, 2H), 4.73 (s, 2H), 4.62 (s, 2H), 3.62 (t, J = 8.2 Hz, 2H), 3.60 (t, J = 8.0 Hz, 2H), 0.90 (t, J = 8.2 Hz, 2H), 0.83 (t, J = 8.0 Hz, 2H), 0.01 (s, 9H), −0.11 (s, 9H); 13C NMR (100 MHz, DMSO-d6) δ 149.8, 143.6, 142.2, 139.3, 133.9, 129.9, 128.9 (2C), 127.9 (2C), 118.8, 117.0, 98.5, 93.9, 70.8, 68.2, 65.9, 64.4, 17.6, 17.3, −1.3 (3C), −1.5 (3C); IR (neat, cm−1): 2951 (w), 2892 (w, br), 1557 (w), 1369 (m), 1248 (s), 1157 (m), 1055 (s, br), 1023 (s, br), 910 (m), 855 (s), 830 (s), 756 (m); HRMS (APCI/ASAP, m/z): found 519.2262, calcd. for C26H40N2O3Si2Cl, [M+H]+, 519.2266.

3.2.6. N-Benzyl-N-methyl-2-phenyl-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridin-4-amine (13a) via 12

A mixture of N-benzyl-2-iodo-N-methyl-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]-pyridin-4-amine (12) (49 mg, 0.10 mmol), phenylboronic acid (16 mg, 0.13 mmol), XPhos (2.9 mg, 6.1 µmol), XPhos Pd G2 (4.1 mg, 5.2 µmol), K2CO3 (42 mg, 0.31 mmol) was added to degassed 1,4-dioxane (1 mL) and water (0.5 mL) under an N2 atmosphere. The mixture was stirred at 100 °C for 1 h before being allowed to cool to 22 °C. The solvent was removed in vacuo before EtOAc (20 mL) and water (15 mL) were added to the mixture, and the layers were separated. The aqueous layer was extracted with EtOAc (2 × 20 mL). The combined organic phases were washed with brine (20 mL), dried over anhydrous Na2SO4, filtered and concentrated in vacuo. The product was purified by silica-gel column chromatography (n-pentane/EtOAc, 9:1, Rf = 0.21) to give 34 mg (0.077 mmol, 77%) of a yellow oil.1H NMR (400 MHz, CDCl3) δ 8.07 (d, J = 5.6 Hz, 1H), 7.67 (ap.d, 2H), 7.43–7.39 (m, 2H), 7.36–7.24 (m, 6H), 6.58 (s, 1H), 6.34 (d, J = 5.6 Hz, 1H), 5.63 (s, 2H), 4.81 (s, 2H), 3.72 (t, J = 8.3 Hz, 2H), 3.19 (s, 3H), 0.95 (t, J = 8.3 Hz, 2H), −0.04 (s, 9H); 13C NMR (100 MHz, CDCl3) δ 151.4, 150.4, 144.4, 138.1, 137.8, 132.5, 129.1 (2C), 128.7 (2C), 128.5 (2C), 127.8, 127.2, 126.8 (2C), 108.4, 101.2, 100.8, 70.8, 66.1, 57.2, 39.2, 18.1, −1.4 (3C); IR (neat, cm−1): 3061 (w), 2950 (w), 2893 (w, br), 1577 (s), 1347 (w), 1071 (m), 1027 (w), 835 (m), 697 (m); HRMS (APCI/ASAP, m/z): found 444.2462, calcd. for C27H34N3OSi, [M+H]+, 444.2471.

3.2.7. N-Benzyl-N-methyl-2-phenyl-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridin-4-amine (13a) via 14a

A mixture of 4-chloro-2-phenyl-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]-pyridine (14a) (230 mg, 0.640 mmol), N-benzylmethylamine (0.085 mL, 0.704 mmol), NaOt-Bu (185 mg, 1.92 mmol), RuPhos (15 mg, 0.032 mmol), Pd(OAc)2 (7.2 mg, 0.032 mmol) and t-BuOH (3 mL) were added under an N2 atmosphere. The reaction mixture was stirred at 85 °C for 1 h before being allowed to cool to rt. The solvent was removed in vacuo, and the mixture was added to EtOAc (15 mL) and water (15 mL). The layers were separated, and the aqueous layer was extracted with more EtOAc (3 × 15 mL). The combined organic phases were washed with brine (20 mL), dried over anhydrous Na2SO4, filtered and concentrated in vacuo. The product was purified by silica-gel column chromatography (n-hexane/EtOAc, 7:3, Rf = 0.20) to give 210 mg (0.473 mmol, 74%) of a yellow oil. The 1H NMR corresponded with that reported above.

3.2.8. N-Benzyl-2-(4-methoxyphenyl)-N-methyl-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]-pyridin-4-amine (13b)

The synthesis was done as described for 13a starting with 14b. The reaction time was 1 h at 85 °C. Purification by silica-gel column chromatography (n-hexane/EtOAc, 7:3, Rf = 0.41) gave 600 mg (1.26 mmol, 76%) of a yellow oil, 1H NMR (400 MHz, CDCl3) δ 8.05 (d, J = 5.6 Hz, 1H), 7.61 (d, J = 8.8 Hz, 2H), 7.36–7.24 (m, 5H), 6.95 (d, J = 8.8 Hz, 2H), 6.51 (s, 1H), 6.33 (d, J = 5.6 Hz, 1H), 5.61 (s, 2H), 4.80 (s, 2H), 3.83 (s, 3H), 3.74 (t, J = 8.3 Hz, 2H), 3.18 (s, 3H), 0.96 (t, J = 8.3 Hz, 2H), −0.03 (s, 9H); 13C NMR (100 MHz, CDCl3) δ 159.5, 151.2, 150.3, 144.0, 138.1, 137.7, 130.5 (2C), 128.7 (2C), 127.2, 126.8 (2C), 124.9, 114.0 (2C), 108.5, 100.8, 100.4, 70.8, 66.1, 57.1, 55.3, 39.1, 18.1, −1.4 (3C); IR (neat, cm−1): 2950 (w), 2836 (w, br), 1576 (m), 1495 (m), 1345 (w), 1069 (m), 832 (s); HRMS (APCI/ASAP, m/z): found 474.2570, calcd. for C28H36N3O2Si, [M+H]+, 474.2577.

3.2.9. (4-(4-(Benzyl(methyl)amino)-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridin-2-yl)phenyl)methanol (13c)

Compound 13c was isolated as a minor product of the reaction described in preparation of 13d starting with 14d. Purification by silica-gel column chromatography (n-pentane/EtOAc, 9:1, Rf = 0.01) gave 45 mg (0.095 mmol, 6%) of a brownish wax. 1H NMR (400 MHz, DMSO-d6) δ 7.91 (d, J = 5.7 Hz, 1H), 7.64 (d, J = 8.2 Hz, 2H), 7.39 (d, J = 8.2 Hz, 2H), 7.35–7.31 (m, 2H), 7.27–7.24 (m, 3H), 6.68 (s, 1H), 6.34 (d, J = 5.7 Hz, 1H), 5.55 (s, 2H), 5.24 (t, J = 5.7 Hz, 1H), 4.85 (s, 2H), 4.54 (d, J = 5.7 Hz, 2H), 3.63 (t, J = 8.2 Hz, 2H), 3.25 (s, 3H), 0.85 (t, J = 8.2 Hz, 2H), −0.08 (s, 9H); 13C NMR (100 MHz, DMSO-d6) δ 151.1, 149.4, 143.9, 142.3, 138.4, 136.6, 130.3, 128.6 (2C), 128.2 (2C), 126.9, 126.6 (2C), 126.5 (2C), 107.4, 101.3, 100.5, 70.4, 65.5, 62.6, 56.1, 39.8, 17.4, −1.4 (3C); IR (neat, cm−1): 3400 (w, br), 2927 (w), 2853 (w), 1737 (w), 1578 (s), 1496 (m), 1354 (m), 1245 (s), 1205 (m), 1064 (s, br), 832 (s, sh), 695 (s); HRMS (APCI/ASAP, m/z): found 474.2571, calcd. for C28H36N3O2Si, [M+H]+, 474.2577.

3.2.10. N-Benzyl-2-(4-(((tert-butyldimethylsilyl)oxy)methyl)phenyl)-N-methyl-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridin-4-amine (13d)

A mixture of 2-(4-(((tert-butyldimethylsilyl)oxy)methyl)phenyl)-4-chloro-1-((2-(trimethylsilyl)ethoxy) methyl)1H-pyrrolo[2,3-b]pyridine (14d) (816 mg, 1.62 mmol), N-methyl-1-phenylmethylamine (1.5 mL, 11.6 mmol), NaOt-Bu (470 mg, 4.89 mmol), RuPhos (51 mg, 0.109 mmol) and Pd(OAc)2 (24 mg, 0.107 mmol) was added to degassed t-BuOH (28 mL), under an N2 atmosphere. The reaction mixture was stirred at 85 °C for 30 min before being cooled to rt. The pH was adjusted to 6 with (NH4)2SO4 (30% in H2O). The solvent was removed in vacuo. CH2Cl2 (50 mL) and water (50 mL) were added to the flask and the layers were separated. The water phase was extracted with more CH2Cl2 (3 × 50 mL). The combined organic phases were washed with brine (50 mL), dried over anhydrous Na2SO4, filtered and concentrated in vacuo. The product was purified by silica-gel column chromatography (n-pentane/EtOAc, 9:1, Rf = 0.27). This gave 847 mg (1.44 mmol, 89%) of a light-yellow oil. 1H NMR (400 MHz, DMSO-d6) δ 7.91 (d, J = 5.8 Hz, 1H), 7.65 (d, J = 8.3 Hz, 2H), 7.39–35 (m, 2H), 7.33–31 (m, 2H), 7.27–7.24 (m, 3H), 6.69 (s, 1H), 6.33 (d, J = 5.8 Hz, 1H), 5.55 (s, 2H), 4.85 (s, 2H), 4.75 (s, 2H), 3.60 (t, J = 8.1 Hz, 2H), 3.25 (s, 3H), 0.92 (s, 9H), 0.83 (t, J = 8.0 Hz, 2H), 0.09 (s, 6H), −0.09 (s, 9H); 13C NMR (100 MHz, DMSO-d6) δ 151.1, 149.4, 144.0, 140.9, 138.4, 136.4, 130.6, 128.6 (2C), 128.3 (2C), 126.9, 126.6 (2C), 126.1 (2C), 107.4, 101.5, 100.5, 70.4, 65.5, 63.9, 56.1, 39.9 25.8 (3C), 18.0, 17.4, −1.4 (3C), −5.3 (2C); IR (neat, cm−1): 2951 (m), 2928 (m), 2887 (w), 2855 (w), 1702 (w), 1577 (m), 1496 (m), 1248 (m), 1072 (s, br), 831 (s, br), 774 (s, br), 694 HRMS (APCI/ASAP, m/z): found 588.3446, calcd. for C34H50N3O2Si2, [M+H]+, 588.3442.

3.2.11. N-Benzyl-N-methyl-2-(4-(((2-(trimethylsilyl)ethoxy)methoxy)methyl)phenyl)-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridin-4-amine (13e)

A mixture of 4-chloro-2-(4-(((2-(trimethylsilyl) ethoxy)methoxy)methyl)phenyl)-1-((2-(trimethyl-silyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridine (14e) (111 mg, 0.213 mmol), N-methyl-1-phenylmethylamine (0.2 mL, 1.55 mmol), NaOt-Bu (71 mg, 0.739 mmol), RuPhos (6 mg, 0.013 mmol) and Pd(OAc)2 (4 mg, 0.018 mmol) was added to degassed t-BuOH (3 mL), under an N2 atmosphere. The reaction mixture was stirred at 85 °C for 5 h before being cooled to room temperature. The solvent was removed in vacuo. CH2Cl2 (15 mL) and water (15 mL) were added to the flask and the layers were separated. The water phase was then adjusted to pH 7 with sat. aq. NH4Cl and extracted with CH2Cl2 (3 × 15 mL). The combined organic phases were washed with brine (15 mL), dried over anhydrous Na2SO4, filtered and concentrated in vacuo. The product was purified by silica-gel column chromatography (n-pentane/EtOAc, 9:1, Rf = 0.19) to give 118 mg (0.196 mmol, 92%) of an oil. 1H NMR (400 MHz, DMSO-d6) δ 7.91 (d, J = 5.7 Hz, 1H), 7.66 (d, J = 8.2 Hz, 2H), 7.39 (d, J = 8.2 Hz, 2H), 7.35–7.31 (m, 2H), 7.27–7.24 (m, 3H), 6.70 (s, 1H), 6.35 (d, J = 5.8 Hz, 1H), 5.55 (s, 2H), 4.86 (s, 2H), 4.70 (s, 2H), 4.57 (s, 2H), 3.62 (t, J = 3.9 Hz, 2H), 3.59 (t, J = 4.4 Hz, 2H), 3.25 (s, 3H), 0.88 (t, J = 8.2 Hz, 2H), 0.84 (t, J = 7.9 Hz, 2H), 0.00 (s, 9H), −0.09 (s, 9H); 13C NMR (100 MHz, DMSO-d6) δ 151.1, 149.4, 144.1, 138.4, 137.9, 136.3, 131.1, 128.6 (2C), 128.3 (2C), 127.8 (2C), 126.9, 126.6 (2C), 107.3, 101.6, 100.5, 93.8, 70.4, 68.2, 65.5, 64.4, 56.1, 39.9, 17.5, 17.4, −1.3 (3C), −1.4 (3C); IR (neat, cm−1, neat) 2950 (w), 2883 (w, br), 1576 (s), 1495 (m), 1452 (m), 1245 (m), 1100 (s, br), 832 (s, br); HRMS (APCI/ASAP, m/z): found 604.3390, calcd. for C34H50N3O3Si2, [M+H]+, 604.3391.

3.2.12. N-Benzyl-N-methyl-2-phenyl-1H-pyrrolo-[2,3-b]pyridin-4-amine (3a)

Compound 13a (140 mg, 0.316 mmol) was dissolved in dry CH2Cl2 (10 mL), and TFA (3 mL) was added dropwise over 5 min under N2 atmosphere. The reaction mixture was stirred at rt for 9.5 h. The solvent was removed in vacuo and the resulted crude was dissolved in THF (5 mL) and a saturated NaHCO3 solution (5 mL) was added dropwise over 10 min, and the mixture was stirred at rt for 18 h. Upon completion, the solvent was removed under reduced pressure and extracted with EtOAc (3 × 15 mL). The combined organic phases were washed with brine (10 mL), dried over anhydrous Na2SO4, filtered and concentrated in vacuo. The product was purified by silica-gel column chromatography (EtOAc, Rf = 0.30) giving 40 mg (0.128 mmol, 41%) of a pale-yellow solid; mp. 191–193 °C. 1H NMR (600 MHz, DMSO-d6) δ: 12.23 (s, 1H), 7.87 (d, J = 6.1 Hz, 1H), 7.83–7.81 (m, 2H), 7.43–7.40 (m, 2H), 7.37–7.34 (m, 2H), 7.30–7.25 (m, 2H), 7.08 (s, 1H), 6.35 (d, J = 6.2 Hz, 1H), 4.93 (s, 2H), 3.36 (s, 3H); 13C NMR (151 MHz, DMSO-d6) δ 150.5, 140.8, 137.8, 133.8, 131.4, 128.8 (2C), 128.6 (2C), 127.4, 127.0 (2C), 126.6 (2C), 124.8 (2C), 108.5, 99.6, 99.1, 56.2, 40.4; IR (neat, cm−1): 2923 (m), 1596 (s), 1453 (m), 1199 (w), 932 (m); HRMS (ES+, m/z): found 314.1661, calcd. for C21H19N3, [M+H]+, 314.1657.

3.2.13. N-Benzyl-N-methyl-2-(4-methoxyphenyl-1H-pyrrolo-[2,3-b]pyridin-4-amine (3b)

N-benzyl-2-(4-methoxyphenyl)-N-methyl-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo-[2,3-b]-pyridin-4-amine (16) (94 mg, 0.20 mmol) was dissolved in CH2Cl2 (6.6 mL) and added to TFA (1.3 mL, 17 mmol) under an N2 atmosphere. The mixture was stirred at 22 °C for 6 h before allowed to cool to rt. The solvent was removed in vacuo before THF (10 mL) and sat. aq. NaHCO3 (10 mL) was added to the residue. The mixture was stirred at 22 °C for 16 h. As analysis indicated incomplete conversion, more sat. aq. NaHCO3 (5 mL) was added, and the reaction was stirred for an additional 6 h, before the solvent was removed in vacuo. The residue was partitioned between sat. aq. NH4Cl (15 mL) and EtOAc (15 mL), and the layers were separated. The aqueous layer was extracted with more EtOAc (2 × 15 mL), and the combined organic phases were washed with brine (15 mL), dried over anhydrous Na2SO4, filtered and concentrated in vacuo. The product was purified twice by silica-gel column chromatography (CH2Cl2/MeOH, 97:3, Rf = 0.07) to give 9 mg (0.026 mmol, 14%) of a yellow oil being semi-pure. 1H NMR (400 MHz, CDCl3) δ 12.16 (s, br, 1H), 7.95 (d, J = 5.8 Hz, 1H), 7.63 (d, J = 8.7 Hz, 2H), 7.38–7.30 (m, 5H), 6.92 (d, J = 8.7 Hz, 2H), 6.63 (s, 1H), 6.26 (d, J = 5.8 Hz, 1H), 4.84 (s, 2H), 3.83 (s, 3H), 3.24 (s, 3H); 13C NMR (100 MHz, CDCl3) δ 159.2, 150.9 (2C), 142.9, 137.8, 135.0, 128.8 (2C), 127.3, 126.8 (2C), 126.6 (2C), 125.0, 114.4 (2C), 109.8, 99.9, 96.9, 57.1, 55.4, 39.3; IR (neat, cm−1): 3133 (w, br), 2926 (w), 2852 (w, br), 1600 (m), 1500 (s), 1249 (m), 833 (w), 697 (w); HRMS (APCI/ASAP, m/z): found 343.1685, calcd. for C22H21N3O, [M+H]+, 343.1685.

3.2.14. (4-(4-(Benzyl(methyl)amino)-1H-pyrrolo[2,3-b]pyridin-2-yl)phenyl)methanol (3c)

N-Benzyl-2-(4-(((tert-butyldimethylsilyl)oxy)methyl)phenyl)-N-methyl-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrrolo[2,3-b]pyridin-4-amine (13d) (430 mg, 0.731 mmol) was dissolved in dry CH2Cl2 (30 mL) and TFA (5 mL, 65.3 mmol) was added dropwise over a period of 5 min under an N2 atmosphere. The reaction mixture was stirred at room temperature for 4.5 h. The solvent was removed in vacuo. The mixture was dissolved in THF (30 mL) and NaHCO3 (sat. aq., 40 mL) was added dropwise over 10 min. The mixture was then stirred at room temperature for 19.5 h, before the solvent was removed in vacuo. The product was purified by silica-gel column chromatography (CH2Cl2/MeOH, 9:1, Rf = 0.15) to give an off-white powder, 186 mg (0.542 mmol, 74%). This material was dissolved in a mixture of MeOH and CHCl3 (1:1 by vol, 2 mL). Upon storage at 4 °C for 18 h, crystals formed. Slow evaporation of solvent gave after drying 128 mg (0.373 mmol 51%) of an off-white solid, mp. 200–201 °C; 1H NMR (600 MHz, DMSO-d6) δ 11.84 (s, 1H), 7.83 (d, J = 5.8 Hz, 1H), 7.77 (d, J = 8.2 Hz, 2H), 7.36–7.32 (m, 4H), 7.28–7.25 (m, 3H), 6.97 (s, 1H), 6.24 (d, J = 5.8 Hz, 1H), 5.17 (t, J = 5.7 Hz, 1H), 4.87 (s, 2H), 4.50 (d, J = 5.7 Hz, 2H), 3.27 (s, 3H); 13C NMR (150 MHz, DMSO-d6) δ 150.5, 149.6, 143.0, 141.5, 138.4, 133.5, 130.3, 128.6 (2C), 126.9, 126.8 (2C), 126.7 (2C), 124.4 (2C), 108.6, 99.5, 98.0, 62.6, 56.1, 40.1; IR (neat, cm−1): 3204 (m, br), 3063 (m, br), 3023 (m, br), 2919 (m), 2852 (m), 1574 (s), 1518 (s), 1499 (m), 1371 (m), 1294 (m), 1199 (s), 1027 (s), 1013 (s), 1013 (s, sh), 767 (s, br), 723 (s, sh); HRMS (APCI/ASAP, m/z): found 344.1757, calcd. for C22H22N3O, [M+H]+, 344.1763.

3.2.15. 6-Methyl-1-phenyl-2,6,7,12-tetrahydro-2,3,6-triazabenzo[6,7]cycloocta[1,2,3-cd]indene (16a)

Following the reaction to obtain compound 3a, purification with silica-gel column chromatography (EtOAc, Rf = 0.10) gave 12 mg (0.039 mmol, 12%) as a light-yellow solid, mp. 291–293 °C; 1H NMR (600 MHz, DMSO-d6) δ 11.51 (s, 1H), 7.80 (d, J = 5.7 Hz, 1H), 7.62–7.55 (m, 5H), 7.46–7.43 (m, 1H), 7.25–7.22 (m, 1H), 7.15–7.13 (m, 1H), 7.02 (dd, J = 7.6 Hz, 1.3 Hz, 1H), 6.16 (d, J = 5.8 Hz, 1H), 4.70 (s, 2H), 4.15 (s, 2H), 3.34 (s, 3H); 13C NMR (151 MHz, DMSO-d6) δ 149.3, 140.3, 137.1, 132.8 (2C), 131.4 (2C), 129.8 (2C), 128.5 (3C), 128.4, 127.7, 127.4, 127.0, 110.7, 106.3, 98.9, 53.9, 40.8, 31.6; HRMS (ES+, m/z): found 326.1661, calcd for C22H19N3, [M+H]+, 326.1657.

3.2.16. 1-(4-Methoxyphenyl)-6-methyl-2,6,7,12-tetrahydro-2,3,6-triazabenzo[6,7]cycloocta[1,2,3-cd]indene (16b)

Compound 13b (100 mg, 0.211 mmol) was dissolved in dry CH2Cl2 (5 mL) and TFA (1 mL) was added dropwise over 5 min under an N2 atmosphere. The reaction mixture was stirred at 50 °C for 18 h. The solvent was removed in vacuo. The mixture was dissolved in THF (5 mL) and saturated NaHCO3 solution (5 mL) was added dropwise over 10 min. The mixture was then stirred at rt for 4 h. The solvent was removed in vacuo, and water (15 mL) was added to the mixture followed by extraction with EtOAc (3 × 25 mL). The combined organic phases were washed with brine (10 mL), dried over anhydrous Na2SO4, filtered and concentrated in vacuo. The product was purified by silica-gel column chromatography (EtOAc/n-hexane, 9.5:0.5, Rf = 0.30), giving 52 mg (0.146 mmol, 69%) of an off-white solid; mp 287–289 °C (decomp.); 1H NMR (600 MHz, DMSO-d6) δ 11.38 (s, 1H), 7.75 (d, J = 5.7 Hz, 1H), 7.55 (d, J = 7.5 Hz, 1H), 7.50 (d, J = 8.1 Hz, 2H), 7.20 (t, J = 7.5 Hz, 1H), 7.10 (d, J = 8.3 Hz, 3H), 6.98 (d, J = 7.6 Hz, 1H), 6.11 (d, J = 5.8 Hz, 1H), 4.66 (s, 2H), 4.10 (s, 2H), 3.82 (s, 3H), 3.30 (s, 3H); 13C NMR (151 MHz, DMSO-d6) δ 158.6, 150.2, 149.0, 143.0, 140.4, 137.1, 131.3, 130.9 (2C), 128.5, 128.3, 127.7, 126.9, 125.1, 113.9 (2C), 109.9, 106.3, 98.8, 55.2, 53.9, 40.8, 31.7. HRMS (ES+, m/z): found 356.1763, calcd for C23H21N3O [M+H]+, 356.1763.

3.2.17. (4-(6-Methyl-2,6,7,12-tetrahydro-2,3,6-triazabenzo[6,7]cycloocta[1,2,3-cd]inden-1-yl)phenyl)methanol (16c)

Compound 13e (182 mg, 0.301 mmol) was dissolved in dry CH2Cl2 (40 mL) and added to TFA (2 mL, 26.2 mmol) under an N2 atmosphere. The reaction mixture was stirred at 50 °C for 2 h, before it was cooled to rt, and the solvent was removed in vacuo. The mixture was dissolved in THF (20 mL), before NaHCO3 (sat. aq., 20 mL) was added dropwise over 10 min. The mixture was then stirred at 22 °C for 22 h. The solvent was removed in vacuo, and the mixture was dissolved in CH2Cl2 (40 mL) and MeOH (20 mL) and stirred at rt for 1.5 h. The reaction mixture was then filtered, and solvent was removed in vacuo. The mixture was dissolved in MeOH (10 mL) before NH3 (12.5% in water, 20 mL, 133.6 mmol) was added dropwise over a period of 10 min. The mixture was stirred at rt for 22 h. The solvent was removed in vacuo, giving a yellow powder. The mixture was purified using silica-gel column chromatography (CH2Cl2, 9:1). This gave 12 mg (0.034 mmol, 11%) of 17c (Rf = 0.08) as a white solid. 1H NMR (600 MHz, DMSO-d6) δ 11.65 (s, 1H), 7.81 (m, 1H), 7.60–7.56 (m, 3H), 7.50 (d, J = 8.1 Hz, 2H), 7.24 (t, J = 7.4 Hz, 1H), 7.14 (t, J = 7.3 Hz, 1H), 7.00 (d, J = 7.3 Hz, 1H), 6.20 (d, J = 5.8 Hz, 1H), 5.30 (m, 1H), 4.71 (s, 2H), 4.61 (d, J = 4.2 Hz, 2H), 4.16 (s, 2H), 3.25 (s, 3H); 13C NMR (100 MHz, DMSO-d6) δ 150.3, 149.7, 142.1, 142.0, 140.4, 136.9, 131.6, 131.0, 129.5 (2C), 128.6, 128.4, 127.9, 127.1, 126.6 (2C), 110.8, 106.4, 99.0, 62.7, 48.6, 41.0, 31.7; IR (cm−1, neat): 3606 (w), 3460 (w, br), 3102 (w), 3024 (w), 3000 (w), 2947 (w), 2842 (m), 1596 (s), 1557 (s), 1540 (s), 1518 (s), 1460 (m), 1376 (m), 1342 (m), 1206 (m), 1097 (m), 1043 (s, br), 1015 (m), 917 (s, sh), 783 (s, sh), 756 (s, sh); HRMS (APCI/ASAP, m/z): found 356.1759, calcd. for C23H22N3O, [M+H]+, 356.1763. The material contains residual CH2Cl2 from purification. Also, isolated was 13 mg (0.038 mmol, 13%) of 3c (Rf = 0.21) as a white powder; mp. 199–201 °C. The spectral data were identical to that reported above.

3.2.18. 3,3-Methylenebis(N-benzyl-N-methyl-2-phenyl-1H-pyrrolo[2,3-b]pyridin-4-amine (17a)

Compound 3a (40 mg, 0.128 mmol) in dry CH2Cl2 (0.5 mL) was added to formaldehyde (5 mg,0.153 mmol) and TFA (0.012 mL, 0.153 mmol) under inert condition. The reaction mixture was stirred at rt for 6.5 h. Then the solvent was removed under reduced pressure, the mixture was neutralized with saturated NaHCO3 solution (5 mL) and extracted with EtOAc (3 × 10 mL). The layers were separated, and the combined organic phases were washed with brine (10 mL), dried over anhydrous Na2SO4, filtered and concentrated in vacuo. Purification by silica-gel column chromatography gave 13 mg (0.020 mmol, 32%) of a solid; mp. 276–278 °C; 1H NMR (600 MHz, DMSO-d6) δ 11.04 (s, 2H), 7.86 (d, J = 5.8 Hz, 2H), 7.24–7.16 (m, 10H), 7.03 (d, J = 12 Hz, 4H), 6.91–6.88 (m, 2H), 6.50 (m, J = 5.3 Hz, 2H), 5.08 (s, 2H), 4.70 (s, 2H), 4.18 (s, 2H), 2.58 (s, 3H) 13C NMR (151 MHz, DMSO-d6) δ 153.6 (2C), 149.2 (2C), 142.7 (2C), 137.7 (2C), 133.4 (2C), 132.0 (2C), 128.2 (4C), 127.8 (4C),127.4 (4C), 126.8 (2C), 126.5 (4C), 126.1 (2C), 114.2 (2C), 110.3 (2C), 104.7 (2C), 59.1 (2C), 40.3 (2C), 23.7. HRMS (ES+, m/z): found 639.3234, calcd for C43H38N6, [M+H]+, 639.3236.

4. Conclusions

Two different routes were investigated for the preparation of the 7-azaindole 3c, needed in SAR studies of CSF1R inhibition. The best strategy involved a regioselective Suzuki–Miyaura cross-coupling on C-2 catalysed by Pd(PPh3)4 and a Buchwald–Hartwig amination at C-4 employing RuPhos as a palladium ligand. The latter transformation only proceeds smoothly in the absence of acidic protons. Both inconveniently and interestingly the last SEM-deprotection proved most difficult, as the release of formaldehyde caused a side reaction. The major side product was a new type of 8-membered ring. By extending the reaction time in the TFA step, preparative useful reaction was seen for the methoxy derivative. Finally, CSF1R inhibition studies proved that the 7-azaindole 3c was less active than the corresponding pyrrolopyrimidine.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/molecules29194743/s1, Supplementary Materials contains synthesis and characterization of intermediates, description of the biochemical assays, NMR spectra and additional references related to synthesis of intermediates [8,9,22,27,28,29,30,31,32,33,34].

Author Contributions

Conceptualization, B.H.H.; methodology, S.R.M., S.S.-O. and C.J.K.; investigation, S.R.M., S.S.-O. and C.J.K.; writing—original draft preparation, B.H.H.; writing—review and editing, B.H.H.; visualization, B.H.H.; supervision, B.H.H. and E.S.; project administration, B.H.H. and E.S.; funding acquisition, E.S. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by Research Council of Norway, grant number NFR 284937 and the Norwegian NMR Platform (project number 226244/F50).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Data are available in the Supplementary Materials.

Acknowledgments

Authors appreciate for the assistance from the Mass Spectrometry Lab at the NV Faculty at NTNU by Susana Villa Gonzalez. Roger Aarvik is thanked for technical support.

Conflicts of Interest

The authors declare no conflicts of interest.

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Molecules 29 04743 g001
Figure 1. The FDA approved drugs PLX3397 and PLX4032; examples of polycyclic azaindoles I–IV and azaindole dimer V. The coloured bonds show the essential bond forming steps in preparation of I–V.
Figure 1. The FDA approved drugs PLX3397 and PLX4032; examples of polycyclic azaindoles I–IV and azaindole dimer V. The coloured bonds show the essential bond forming steps in preparation of I–V.
Molecules 29 04743 g001
Molecules 29 04743 sch001
Scheme 1. Structure of the CSF1R inhibitor 1, the less active thienopyrimidine 2 and 7-azaindole analogue 3c. The initial retrosynthetic plan (in the frame) is shown with red wavy bonds indicating disconnections. The numbering system of the different heterocycles is also shown.
Scheme 1. Structure of the CSF1R inhibitor 1, the less active thienopyrimidine 2 and 7-azaindole analogue 3c. The initial retrosynthetic plan (in the frame) is shown with red wavy bonds indicating disconnections. The numbering system of the different heterocycles is also shown.
Molecules 29 04743 sch001
Molecules 29 04743 sch002
Scheme 2. Initial route to 2-aryl-1H-pyrrolo[2,3-b]pyridine-4-amines, side products and structure of the RuPhos and XPhos Pd G2 catalyst.
Scheme 2. Initial route to 2-aryl-1H-pyrrolo[2,3-b]pyridine-4-amines, side products and structure of the RuPhos and XPhos Pd G2 catalyst.
Molecules 29 04743 sch002
Molecules 29 04743 sch003
Scheme 3. Synthesis of the model compound 14b by a chemoselective Suzuki–Miyaura cross-coupling. The 2,4-diarylated 15b is the major side product.
Scheme 3. Synthesis of the model compound 14b by a chemoselective Suzuki–Miyaura cross-coupling. The 2,4-diarylated 15b is the major side product.
Molecules 29 04743 sch003
Molecules 29 04743 sch004
Scheme 4. Synthesis of the protected analogues 14d and 14e.
Scheme 4. Synthesis of the protected analogues 14d and 14e.
Molecules 29 04743 sch004
Molecules 29 04743 sch005
Scheme 5. SEM-deprotection of compounds 13a–b and 13d–e to 3a–c and the side products 16 and 17.
Scheme 5. SEM-deprotection of compounds 13a–b and 13d–e to 3a–c and the side products 16 and 17.
Molecules 29 04743 sch005
Molecules 29 04743 g002
Figure 2. CSF1R inhibition (IC50 curves) for the 7-azaindole 3c (red squares), pyrrolopyrimidine 1 (blue circles) and thienopyrimidine 2 (green triangles). The solid lines are regression curves generated from 20 data points each. The assay was performed at ThermoFisher (Invitrogen, San Diego, CA, USA) using the Z-lyte technology; ATP level was equal to KM.
Figure 2. CSF1R inhibition (IC50 curves) for the 7-azaindole 3c (red squares), pyrrolopyrimidine 1 (blue circles) and thienopyrimidine 2 (green triangles). The solid lines are regression curves generated from 20 data points each. The assay was performed at ThermoFisher (Invitrogen, San Diego, CA, USA) using the Z-lyte technology; ATP level was equal to KM.
Molecules 29 04743 g002
Table 1. Effect of reaction conditions on product distribution in Suzuki–Miyaura cross-coupling of 7 using 1.3 equivalent of 4-hydroxymethylphenylboronic acid and 5–8 mol % of Pd catalyst.
Table 1. Effect of reaction conditions on product distribution in Suzuki–Miyaura cross-coupling of 7 using 1.3 equivalent of 4-hydroxymethylphenylboronic acid and 5–8 mol % of Pd catalyst.
Molecules 29 04743 i001
EntryCatalystPd
mol%		Temp.
[°C]		Scale
[mg]		Time
[h]		Product Distribution (mol %) 1
14c15c 2Unk. 36IX 4
1Pd2(dba)371001001.75924400
2Pd2(dba)37801001.75895500
3Pd2(dba)3760502.5876700
4XPhos/
XPhos Pd G2		780502.75152313049
5Pd(OAc)2580502.756871726
6PEPPSITM-SIPr 5580500.3441713918
7(Dppf)PdCl2 6580500.37931053
8Pd(PPh3)4880505920080
9Pd(PPh3)458012339950050
10Pd(PPh3)4590208722859060
1 Analysed by 1H NMR after extractive work-up. 2 Reference material 15c was synthesised using XPhos Pd G2/XPhos as catalyst. 3 Unidentified side product. 4 Products of oxidations of hydroxyl groups of compounds 14c and 15c. 5 (1,3-Bis(2,6-diisopropylphenyl)imidazolidene) (3-chloropyridyl) palladium(II) dichloride. 6 [1,1′-Bis(diphenylphosphino)ferrocene]dichloropalladium(II).
Table 2. Palladium catalysed aminations of the substrates 14a–e using Pd(OAc)2 and RuPhos ligand.
Table 2. Palladium catalysed aminations of the substrates 14a–e using Pd(OAc)2 and RuPhos ligand.
Molecules 29 04743 i002
EntrySubs.RScale (mg) 1Time (h)Conv. (%) 2Yield (%) 3Product
114aH2301>997413a
214bOCH36501>997613b
314cCH2OH10024ca 40-13c
414dCH2OTBDMS8160.5>998913d
514eCH2OSEM4550.33>998913e
1 Amount of starting material. 2 Conversion was measured by 1H NMR spectroscopy. 3 Isolated yield.
Table 3. IC50-values (nM) towards CSF1R of 3c compared with 1, 2 and PLX3397.
Table 3. IC50-values (nM) towards CSF1R of 3c compared with 1, 2 and PLX3397.
Molecules 29 04743 i003
InhibitorXYCSF1R IC50 1CSF1R IC50 2
3cCHN3.1105
1 3NN1.05
2 3NS707450
PLX3397 3 520
1 IC50 (nM) measured by Z’-LYTE® assay technology (ThermoFisher, Invitrogen, San Diego, CA, USA) [27]. ATP level equal to KM 10 μM. Unless otherwise noted, IC50 is based on two titration curves (20 data points). 2 IC50 (nM) measured LANCE Ultra assay (Perkin Elmer). ATP level (25 μM). 3 Previously reported data by Aarhus et al. [19].
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Merugu, S.R.; Selmer-Olsen, S.; Kaada, C.J.; Sundby, E.; Hoff, B.H. Synthetic Routes to 2-aryl-1H-pyrrolo[2,3-b]pyridin-4-amines: Cross-Coupling and Challenges in SEM-Deprotection. Molecules 2024, 29, 4743. https://doi.org/10.3390/molecules29194743

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Merugu SR, Selmer-Olsen S, Kaada CJ, Sundby E, Hoff BH. Synthetic Routes to 2-aryl-1H-pyrrolo[2,3-b]pyridin-4-amines: Cross-Coupling and Challenges in SEM-Deprotection. Molecules. 2024; 29(19):4743. https://doi.org/10.3390/molecules29194743

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Merugu, Srinivas Reddy, Sigrid Selmer-Olsen, Camilla Johansen Kaada, Eirik Sundby, and Bård Helge Hoff. 2024. "Synthetic Routes to 2-aryl-1H-pyrrolo[2,3-b]pyridin-4-amines: Cross-Coupling and Challenges in SEM-Deprotection" Molecules 29, no. 19: 4743. https://doi.org/10.3390/molecules29194743

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