Guanghu Tong‡
*,
Long V. Nguyen and
Timothy F. Jamison
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, 77 Massachusetts 02139, USA
First published on 5th June 2025
Nagelamide C (1), a dimeric pyrrole–imidazole alkaloid, exhibits antimicrobial and antibacterial activities. We demonstrate herein the first total synthesis of nagelamide C. This concise work was enabled by a series of significant transformations featuring: an imidazole benzylic Wittig olefination, a site selective bromination, and a regioselective trans-hydrostannylation/Stille coupling to construct a unique trisubstituted olefin. In addition, we show the original 13C NMR data of nagelamide C to be in error and revise the data.
The fascinating and intriguing structure of nagelamide alkaloids, containing cyclic guanidines, halogenated heterocycles, polar properties and nitrogen-rich skeletons, have been attracting synthetic chemists for decades.3 To date, however, only a few nagelamide alkaloids have been synthesized. In 2006, Horne et al. completed the first synthesis of nagelamide A (5) and D (6) featuring a biomimetic oxidative dimerization.4 Baran and coworkers accomplished a collective total synthesis of nagelamide E (7), ageliferin (8), and sceptrin (9).5 In 2009, Lovely and coworkers developed an elegant synthesis of putative nagelamide D, in which they found the synthetic sample did not completely match to the originally isolated spectroscopic data, but it was in good consistency with Horne's synthetic data.6 Thus far, the correct structure of 6 still yet to be confirmed. Recently, Tepe achieved the synthesis of nagelamide W (10).7 Lindel reported the only synthetic study of nagelamide C in 2010.8
Our synthesis commenced with the key trans-hydrostannylation investigation. Known amide 18 was readily prepared through Sonogashira coupling from commercially available 13 and N-Boc propargylamine 14.13 A general hydrostannylation condition14 was initially performed (Table 1, entry 1). Exposure of 18 to Bu3SnH/Pd(PPh3)2Cl2 in DCM at ambient temperature afforded cis-hydrostannylation product 11a exclusively in excellent yield (92%). The ruthenium-catalyzed trans-hydrostannylation protocol developed by Fürstner et al.15 was next evaluated. Although the desired stannane 11b could be observed (12–23% yield), the outcome of the trans-hydrostannylation was confronted with poor regioselectivity. Catalysts such as tetrameric [Cp*RuCl]4 and oligomeric [Cp*RuCl2]n favored formation of proximal isomer 11c and 11d (entries 2 and 3). Presumably, the mono-protected amine (–NHBoc) could form a hydrogen bond with the ruthenium species,15d then drive trans-hydrostannylation in favor of proximal adduct 11c and 11d. Moreover, Cp*Ru(cod)Cl gave 11a and 11d as major products (entry 4), the cationic acetonitrile adduct [Cp*Ru(MeCN)3]PF6 and [CpRu(MeCN)3]PF6 provided cis-adduct 11a/11c in modest yields (entries 5 and 6). Accordingly, we devised that installing an additional Boc group on the propargyl amide might improve regioselectivity in two ways: (1) –NBoc2 lacks an H-bond donor, preventing intermolecular hydrogen bond formation, (2) increasing steric hindrance around C9 might favor the formation of distal adduct 11b′. Upon treatment of amide 18′ (prepared from 13 and 14′) with [Cp*RuCl]4 (entry 7), the desired product 11b′ was obtained as an inseparable mixture (50:
20
:
30) with 11a′ and 11d′ in excellent yield. To our delight, [Cp*RuCl2]n polymer further improved regioselectivity of the transformation, and 11b′ was isolated as a 2
:
1 mixture with 11d′ in 89% yield on gram scale (entry 8). [Cp*Ru(MeCN)3]PF6 (entry 9), showed similar selectivity compare to [Cp*RuCl]4, while it's triflate salt (entry 10) provided no product. Ru-complexes such as [CpRu(MeCN)3]PF6, Cp*Ru(cod)Cl, [Ru(benzene)Cl2]2 as well as [Ru(p-cymene)Cl2]2 all provided cis-adduct 11a′ as the major isomer in good yields (entries 11–14). Other literature approaches that could access trans-hydrostannylation product were also investigated. Both catalytic and stoichiometric Lewis acid dibutyl magnesium16a decomposed starting material (entry 15), while zirconium mediated hydrostannylation16b provided mono-Boc protected 18 (entry 16). Only cis-adduct 11a′ was obtained in 53% yield under radical conditions16c (AIBN, entry 17). Switching to Pd(PPh3)2Cl2, 11a′ was afforded in 93% isolated yield (entry 18).
Entry | R1, R2 | Conditions | Yield% | 11a/11b/11c/11d% |
---|---|---|---|---|
1 | H, Boc | Pd(PPh3)2Cl2 (10 mol%), DCM, rt | 92 | 100/0/0/0 |
2 | H, Boc | [Cp*RuCl]4 (10 mol%), DCM, rt | 91 | 5/23/22/50 |
3 | H, Boc | [Cp*RuCl2]n (10 mol%), DCM, rt | 84 | 6/17/21/56 |
4 | H, Boc | Cp*Ru(cod)Cl (10 mol%), DCM, rt | 88 | 39/12/18/31 |
5 | H, Boc | [Cp*Ru(MeCN)3]PF6 (10 mol%), DCM, rt | 65 | 64/0/36/0 |
6 | H, Boc | [CpRu(MeCN)3]PF6 (10 mol%), DCM, rt | 69 | 51/12/37/0 |
Entry | R1, R2 | Conditions | Yield% | 11a′/11b′/11c′/11d′% |
---|---|---|---|---|
a Reactions were carried out on 0.1 mmol scale (0.1 M), ratio in the crude reaction mixture was determined by 1H NMR spectroscopy, 1,3,5-trimethoxylbenzene as internal standard. 18 and 18′ were prepared from N-Boc-propargylamine and N,N-diBoc propargylamine, respectively.b The product was isolated in gram scale, 2.4 equiv. nBu3SnH was used.c 18 was isolated as the product.d Isolated yield. DCM: dichloromethane, THF: tetrahydrofuran. NR: no reaction.![]() |
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7 | Boc, Boc | [Cp*RuCl]4 (10 mol%), DCM, rt | 96 | 20/50/0/30 |
8 | Boc, Boc | [Cp*RuCl2]n (10 mol%), DCM, rt | 89b | 5/63/0/32 |
9 | Boc, Boc | [Cp*Ru(MeCN)3]PF6 (10 mol%), DCM, rt | 72 | 24/47/0/29 |
10 | Boc, Boc | [Cp*Ru(MeCN)3]OTf (10 mol%), DCM, rt | NR | — |
11 | Boc, Boc | [CpRu(MeCN)3]PF6 (10 mol%), DCM, rt | 87 | 71/19/0/10 |
12 | Boc, Boc | Cp*Ru(cod)Cl (10 mol%), DCM, rt | 82 | 55/34/0/11 |
13 | Boc, Boc | [Ru(benzene)Cl2]2 (10 mol%), DCM, rt | 69 | 100/0/0/0 |
14 | Boc, Boc | [Ru(p-cymene)Cl2]2 (10 mol%), DCM, rt | 80 | 100/0/0/0 |
15 | Boc, Boc | MgBu2 (1.0 equiv.), THF, 50 °C | Decom. | — |
16 | Boc, Boc | ZrCl4 (1.0 equiv.), THF, rt | 52c | — |
17 | Boc, Boc | AIBN (10 mol%), THF, 70 °C | 53 | 100/0/0/0 |
18 | Boc, Boc | Pd(PPh3)2Cl2 (10 mol%), DCM, rt | 93d | 100/0/0/0 |
With sufficient 11b′ in hand, we turned our attention to the construction of bromide 12. Condensation of 2-aminopyrimidine 15 with 1,3-dichloroacetone 16 under reflux in THF gave the corresponding HCl salt 19, which underwent water elimination upon treatment with triphenylphosphine (PPh3) in acetonitrile at 85 °C for 16 h. The resulting precipitates were easily collected and washed with acetone to furnish pure phosphonium salt 20 in 56% yield over two steps. Due to the instability of imidazo[1,2-a]pyrimidines towards strong bases, optimization of the benzylic Wittig olefination proved challenging. Inorganic base such as n-BuLi, LiHMDS, NaOMe, etc. all led to the decomposition of starting material. NaH, KOt-Bu gave variable and unscalable results. Unlike conventional Wittig reactions where an aldehyde was usually set on the imidazole ring, olefinations using imidazole benzylic phosphonium salt are far less documented.17 After exhaustive experimentation (Scheme 2B, see ESI† for details), an organic base, 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) was found to be optimal, furnishing the desired olefin 21 in 72% yield as a 3:
1 ratio of E/Z isomers which were easily separated on silica gel. In addition, when we subjected 3-bromoimidazole phosphonium salt to the same Wittig conditions, protodebromination was observed. Other attempted methods such as Julia–Kocienski olefination, Suzuki coupling/bromination, or cross-metathesis were fruitless (see ESI† for full details). It is noteworthy that a selective bromination on the imidazole ring of 21 was achieved utilizing N-bromosuccinimide (NBS) to provide 12 in excellent yield (92%) without any bromination observed on the E-olefin. This 4-step sequence could be executed on gram scale and required a single chromatographic purification.
![]() | ||
Scheme 2 (A) Construction of bromide 12, (B) Optimization of Wittig olefination. (C) Synthesis of nagelamide C and nagelamide C E-isomer. |
With straight-forward access to the desired building blocks, we pursued the total synthesis of 1. Pd-catalyzed coupling of 12 and a 2:
1 mixture of 11b′/11d′ was achieved in the presence of 10 mol% CuI and 2 equiv. of CsF,18 delivering 63% diene 22 and 26% 23 after chromatograph separation. Boc removal with TFA followed by acylation with 2,3-dibromo-5-trichloroacetylpyrrole (24) in the same flask produced the corresponding bis-pyrrole. Polar 2-aminoimidazoles were unveiled following exposure to an excess of hydrazine hydrate, delivering nagelamide C in 51% yield. The 1H NMR data for synthetic 1 was consistent with the reported 1H NMR data (Table 2). However, 13C NMR data of our synthetic sample was not in agreement with the reported spectroscopic data,2 where significant discrepancies were shown on multiple carbons: C8′, C9′, C10, C10′, C11, C11′, and C15 (Table 3). Interestingly, the original 13C chemical shift of both C8 and C8′ were reported as 37.40 ppm. We anticipated that since these two carbons are influenced by different chemical environment, their 13C chemical shifts are not likely the same. Besides the 1D & 2D NMR acquisition of synthetic 1, we also conducted two additional experimentations to further determine its structure. 1. Addition of trifluoroacetic acid directly to a solution of free base 1 in DMSO-d6 led to clear observation of in situ formation of nagelamide C TFA salt. 2. The 1H–15N HSQC and HMBC spectra assisted to characterize all nitrogen atoms and their correlation with related protons. Taken together, all these data supported our structural assignment.
Proton | Natural nagelamide Ca | Synthetic nagelamide Cb | Δδc/ppm | Synthetic E-isomer 26b | Δδc/ppm |
---|---|---|---|---|---|
a In DMSO-d6 in addition to 1% trifluoroacetic acid, see ref. 2.b In DMSO-d6 and the solvent was referenced at 2.50 ppm.c In comparison to the isolation data. | |||||
1-NH | 12.71 (s) | 12.72 (d, J = 2.9 Hz) | −0.01 | 12.74 (d, J = 2.8 Hz) | −0.03 |
1′-NH | 12.68 (s) | 12.69 (d, J = 2.8 Hz) | −0.01 | 12.64 (d, J = 2.8 Hz) | −0.04 |
4 | 6.93 (brs) | 6.93 (d, J = 2.7 Hz) | 0 | 6.94 (d, J = 2.8 Hz) | −0.01 |
4′ | 6.91 (brs) | 6.92 (d, J = 2.7 Hz) | −0.01 | 6.92 (d, J = 2.8 Hz) | −0.01 |
7-NH | 8.46 (t, J = 5.6 Hz) | 8.49 (t, J = 5.7 Hz) | −0.03 | 8.54 (t, J = 5.6 Hz) | −0.08 |
7′-NH | 8.45 (t, J = 5.8 Hz) | 8.46 (t, J = 5.8 Hz) | −0.01 | 8.41 (t, J = 5.8 Hz) | 0.04 |
8 | 3.96 (m) | 3.95 (t, J = 5.7 Hz) | 0.01 | 4.11 (t, J = 6.2 Hz) | −0.05 |
8′ | 3.86 (m) | 3.86 (t, J = 6.2 Hz) | 0 | 3.89 (t, J = 5.2 Hz) | −0.03 |
9 | 6.24 (t, J = 6.7 Hz) | 6.25 (t, J = 6.7 Hz) | −0.01 | 5.90 (t, J = 6.8 Hz) | 0.34 |
9′ | 6.16 (dt, J = 15.9, 5.9 Hz) | 6.17 (dt, J = 16.1, 5.9 Hz) | −0.01 | 6.17–6.05 (m) | |
10′ | 6.05 (d, J = 15.9 Hz) | 6.05 (d, J = 16.0 Hz) | 0 | 6.17–6.05 (m) | |
12-NH | 12.95 (brs) | 12.93 (s) | 0.02 | 12.47 (s) | 0.48 |
12′-NH | 13.12 (brs) | 13.10 (s) | 0.02 | 12.79 (s) | 0.33 |
13-NH2 | 7.87 (s) | 7.86 (s) | 0.01 | 7.66 (s) | 0.21 |
13′-NH2 | 7.73 (s) | 7.72 (s) | 0.01 | 7.60 (s) | 0.13 |
14-NH | 12.52 (brs) | 12.49 (brs) | 0.03 | 12.43 (s) | 0.09 |
14′-NH | 12.79 (brs) | 12.77 (brs) | 0.02 | 12.57 (s) | 0.22 |
15 | 6.79 (s) | 6.79 (s) | 0 | 7.20 (s) | −0.41 |
On the other hand, we suspected the reported structure of nagelamide C might be an E-isomer at the C9–C10 olefin. To this end, the nagelamide C E-isomer (26) was quickly synthesized following the established route to 1. Stannane 11a′ (Table 1, entry 18) was employed in the Stille coupling, and diene 25 was isolated in 79% yield. Lastly, a sequence of Boc-deprotection, acylation, and pyrimidine deprotection in one pot provided 26 in 56% yield. Both 1H and 13C NMR of 26 are inconsistent with natural nagelamide C's spectroscopic data. In the meantime, we communicated with the original isolation chemists in the Kobayashi group and copies of the 1H and 13C NMR spectra of natural nagelamide C were shared with us. Gratifyingly, the original 13C NMR spectra aligned well with our synthetic spectra (see ESI† for the comparison). Thus, the original 13C NMR data was revised and the structure of nagelamide C was confirmed.
Footnotes |
† Electronic supplementary information (ESI) available: Experimental procedures and copies of NMR spectra (PDF). See DOI: https://doi.org/10.1039/d5qo00721f |
‡ Current address: Medicinal Chemistry, Gilead Sciences, Foster City, California 94403, United States. E-mail: Guanghu.Tong1@gilead.com. |
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