Divergent Two-Step Total Synthesis of Sclerotioloid A and B

Abstract

A two-step divergent total synthesis of the structurally unique N-propargylated alkaloids sclerotioloid A and B has been achieved. The synthesis relies on a robust aldol-propargylation domino reaction yielding the key divergent intermediate. Single-crystal X-ray structure studies of the natural product sclerotioloid A show that it exists as a helically chiral racemate in the solid state.

 

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Key words

alkaloids - natural products - total synthesis - domino reaction

2,5-Diketopiperazines are an abundant class of alkaloids with a broad range of biological activities.[1] Recently, an unusual 2,5-diketopiperazine substitution pattern was observed in sclerotioloid A (1) and its seco-form sclerotioloid B (2), both alkaloids having been isolated from the marine fungus Aspergillus sclerotiorum ST0501 in 2023 (Scheme [1]A).[2] Namely, sclerotioloids A (1) and B (2) represent the first natural isolates to contain an N-propargyl motif. This is in stark contrast to other known terminal acetylide natural products, which are common motifs in fungal secondary metabolites.[3] Furthermore, we expected the highly congested benzylidene motif of sclerotioloid A (1) to be significantly folded, rendering sclerotioloid A helically chiral. While helically chiral molecules are well-established in catalysis and nanoscience, they are rare in the realm of alkaloids and in particular alkaloids of such low molecular weight as sclerotioloids.[4] [5] Intrigued by these structural features, we targeted the total synthesis of sclerotioloid A (1) and B (2).

Scheme 1 (A) Structure of sclerotioloid A (1) and B (2). (B) Divergent retrosynthesis of sclerotioloid A (1) and B (2).

To gain synthetic access to these natural products, we considered the diketopiperazine imide 3 as a potential point of divergence (Scheme [1]B) with N-deacetylation of the imide 3 giving sclerotioloid A (1) and methanolysis of ring A giving sclerotioloid B (2). The side chains of the divergent intermediate 3 were envisioned to be disconnected by N-alkylation and aldol condensation to reveal N,N′-diacetyl glycine anhydride (4), propargyl bromide (5), and benzaldehyde (6) as the starting materials (Scheme [1]B).

The synthesis plan requires differentiation of the ketopiperazine 3 nitrogens N4 and N1. In particular, the alkylation must be achieved on the sterically more congested N4 amide flanking the Z-benzylidene motif. Such proximal differentiation can be achieved by an aldol–acyl migration–E1cB domino reaction, which has precedence in diacetylated ketopiperazines.[6] In 2016, the groups of Li and Liu developed a one-pot method using this chemistry to access 1,3,6-trisubstituted 3,6-di-unsaturated (3Z,6Z)-2,5-diketopiperazine derivatives (of type 10, Scheme [2]).[7] The method involved heating (95 °C) aryl aldehydes, diacetyl glycine anhydride, and allyl bromide in the presence of Cs₂CO₃ and 3 Å molecular sieves in DMF. This method provided a highly promising starting point for our synthesis, as the Li–Liu sequence could potentially be interrupted at mono-aldol stage and deployed using propargyl bromide instead of allyl bromide to achieve a one-step synthesis of the divergent intermediate 3.

Scheme 2 Total synthesis of sclerotioloid A (1) and sclerotioloid B (2) and hypothetical mechanism of the domino reaction. (a) 4 (1.0 equiv) PhCHO (6, 1.1 equiv), Cs₂CO₃ (2.5 equiv), propargyl bromide (5, 5.0 equiv), 3 Å MS (425 wt%), DMF, r.t., 2 h, 58%; (b) hydrazine hydrate (80% aq. solution, 20 equiv), MeOH, r.t., 5 min, 84%; (c) MeOH (anhydrous), 50 °C, 2 days, 33%.

In the synthetic direction, we attempted to employ the Li–Liu conditions to our system but opted to run the reaction at room temperature and with only 1.1 equiv of benzaldehyde (6) to favor the mono-aldol product. Exposing N,N′-diacetyl glycine anhydride (4, 1.0 equiv) to benzaldehyde (6, 1.1 equiv), Cs₂CO₃ (2.5 equiv), propargyl bromide (5, 5.0 equiv) and 3 Å molecular sieves in anhydrous DMF at room temperature gratifyingly led to the desired aldol–acetyl–migration–E1cB–N-alkylation domino reaction (via 7 → 8 → 9 → 3) delivering 3 as a highly crystalline solid in 58% yield over 2 hours (Table [1], entry 1).[8] [9] Using alternative bases, such as Na₂CO₃ and K₂CO₃ resulted in lower yields and longer reaction times (30%, 23 h and 51%, 24 h respectively; Table [1], entries 2 and 3). We also noted that when the molecular sieves were not freshly activated, the yield dropped significantly to 28%, although full conversion into the aldol condensation product 9 was observed by TLC. Attempts at improving the yield by heating the reaction mixture to 60 °C led to complex mixtures based on TLC – presumably starting to favor the double-aldol product 10.

Table 1 Optimization of Synthesis of 3

Entry	Base	Notes	Time (h)	Yield (%)b
1	Cs2CO3	–	2	58
2	Na2CO3	–	23	30
3	K2CO3	–	24	51
4	Cs2CO3	MS not freshly activated	2	28

^a Reaction carried out on a 1.0 mmol scale, base (2.5 equiv), 4 (1.0 equiv), 5 (5.0 equiv), 6 (1.1 equiv), DMF, r.t..

^b Isolated yield after flash column chromatography.

The key divergent intermediate 3 was now accessible in a single step from commercially available starting materials, which set the stage for completing the total syntheses. First focusing on sclerotioloid A (1), the N1 acetyl group of imide 3 was removed using hydrazine hydrate to give sclerotioloid A (1) in 84% yield after flash purification (Scheme [1]).[10] [11] The spectroscopic data for the thus obtained synthetic sclerotioloid A (1) were identical to those reported for the isolated material.[2]

We then approached the synthesis of sclerotioloid B (2) from the divergent intermediate 3. This would require the ring A C2 carbonyl of the imide 3 to react with methanol as opposed to the N–Ac group. Attempted methanolysis of the ring A of 3 with refluxing MeOH and 0.1 equiv of p-toluenesulfonic acid as a catalyst resulted simply in the deacetylation of the material, giving 1 in 57% yield in 2 hours. Under milder conditions – simply heating at 50 °C with methanol – a similar deacetylation to 1 occurred, albeit more slowly, with the reaction taking several days to complete. Re-evaluating our stance, we recognized that trace amounts of water could function as a competing nucleophile to methanol and attack the undesired N–Ac carbonyl of 3. Following this line of thought, we used anhydrous methanol as the reaction solvent. With this change the desired methanolysis of the diketopiperazine ring A took place, yielding sclerotioloid B (2) in 33% yield in conjunction with 1 in 36% yield over 2 days at 50 °C (Scheme [1]).[12] The spectroscopic data for the thus obtained synthetic sclerotioloid B (2) were identical to those reported for the isolated material.[2]

As hypothesized at the outset of the study, the single-crystal X-ray structure of sclerotioloid A (1) (Scheme [2], inset) showcased significant folding of the benzylidene system, with the θ_{C7–N4–C3–C10} dihedral angle being 39.3°. Furthermore, the diketopiperazine ring of 1 was observed to be in a boat conformation.[13] The highly folded arrangement of the benzylidene and propargyl motifs in 1 results in the crystal lattice comprising of a packing unit of two helical enantiomers M-1 and P-1, rendering crystalline 1 racemic.[14]

Finally, we attempted a telescoped one-pot synthesis of sclerotioloid A (1) by first carrying out the domino reaction followed by quenching with hydrazine hydrate (Scheme [3]). This approach yielded sclerotioloid A (1) in 66% yield in one pot. The method was also amenable to facile synthesis of sclerotioloid A derivatives, as demonstrated by the synthesis of 11 in 57% yield using p-bromobenzaldehyde as the starting material.

Scheme 3 One-pot synthesis of sclerotioloid A (1) and sclerotioloid A analogue 11

In conclusion, we have achieved a divergent two-step total synthesis of the first reported N-propargylated alkaloids sclerotioloid A (1) and sclerotioloid B (2) using a domino reaction to construct the divergent intermediate 3. Considering that sclerotioloid A (1) is an entirely unique structure in both the 2,5-diketopiperazine and alkyne alkaloid space, the possible biogenetic origins of this alkaloid warrant further studies.

 

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Conflict of Interest

The authors declare no conflict of interest.

Acknowledgment

We thank M.Sc. Anton Bannykh and Prof. Petri Pihko for their assistance with the scXRD characterization of 1 and 3.

• References and Notes

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• 8 ( Z)-1-Acetyl-3-benzylidene-4-(prop-2-yn-1-yl)piperazine-2,5-dione (3): A mixture of 4 (200 mg, 1.01 mmol, 1.00 equiv), Cs₂CO₃ (822 mg, 2.52 mmol, 2.50 equiv), benzaldehyde (6, 0.11 mL, 1.11 mmol, 1.10 equiv, vacuum distilled), propargyl bromide (5, 0.38 mL, 5.05 mmol, 5.00 equiv) and flame-dried 4 Å MS (840 mg, 425 wt-%) in anhydrous DMF (8 mL) was stirred at room temperature for 2 h under argon. The resulting brown suspension was concentrated under reduced pressure followed by addition of DI water (50 mL) and EtOAc (25 mL). The layers were separated, and the aqueous layer was extracted with EtOAc (3 × 20 mL). The combined organic layers were washed with brine (10 mL), dried with Na₂SO₄, and concentrated in vacuo. The thus obtained crude product was purified using flash column chromatography (SiO₂, 30% EtOAc/Hexane) to yield 3 as a yellow crystalline solid (166 mg, 58%). R_f 0.29 (25% EtOAc/Hex; UV, KMnO₄); mp 173.1–174.0 °C. ¹H NMR (400 MHz, CDCl₃): δ = 7.45 (s, 1 H), 7.43–7.36 (m, 5 H), 4.56 (s, 2 H), 4.27 (d, J = 2.5 Hz, 2 H), 2.65 (s, 3 H), 2.14 (t, J = 2.5 Hz, 1 H). {¹H}¹³C NMR (101 MHz, CDCl₃): δ = 171.6, 164.7, 164.1, 132.5, 130.0, 129.6, 129.05, 128.95, 127.8, 77.0, 73.1, 45.3, 33.8, 26.8. FTIR (ATR): 2921, 2851, 1698, 1628, 1354, 1192, 936, 743 cm^–1. HRMS (ESI⁺): m/z [M+Na⁺] calcd. for C₁₆H₁₄N₂O₃: 305.0897; found: 305.0899.
• 9 CCDC 2338001 contains the supplementary crystallographic data for 3. The data can be obtained free of charge from The Cambridge Crystallographic Data Centre via www.ccdc.cam.ac.uk/structures
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• 10b Dawson IM, Pappin AJ, Peck CJ, Sammes PG. J. Chem. Soc., Perkin Trans 1 1989; 453
• 11 Sclerotioloid A (1): To a stirred suspension of 3 (20 mg, 1.0 equiv) in MeOH (1 mL), hydrazine hydrate (60 μL, 62 mmol, 80% v/v solution in water, 22 equiv) was added. The resulting suspension was stirred at room temperature for 5 min. TLC showed full conversion and all material had dissolved. The reaction mixture was concentrated in vacuo and purified using flash column chromatography (SiO₂, 75% EtOAc/Hexane) to yield sclerotioloid A (1) as a white solid (14.3 mg, 84%). Spectroscopic data matched those reported previously.² R_f 0.29 (25% EtOAc/Hex; UV, KMnO₄). ¹H NMR (400 MHz, CDCl₃): δ = 8.42 (s, 1 H), 7.46–7.35 (m, 5 H), 4.56 (s, 2 H), 4.27 (d, J = 2.5 Hz, 2 H), 2.65 (s, 3 H), 2.14 (t, J = 2.5 Hz, 1 H). {¹H}¹³C NMR (101 MHz, CDCl₃): δ = 171.6, 164.7, 164.1, 132.5, 130.0, 129.6, 129.05, 128.95, 127.8, 77.0, 73.1, 45.3, 33.8, 26.8.
• 12 Sclerotioloid B (2): A solution of 3 (32 mg, 0.113 mmol, 1.00 equiv) in anhydrous MeOH (2 mL) was stirred at 50 °C for 2 days. The reaction mixture was concentrated in vacuo and purified using flash column chromatography (SiO₂, EtOAc) to yield sclerotioloid B (2) as a white crystalline solid (11.7 mg, 33%). Spectroscopic data matched those reported previously.² R_f 0.16 (75% EtOAc/Hex; UV, KMnO₄). ¹H NMR (400 MHz, DMSO-d ₆): δ = 8.06 (t, J = 5.58 Hz, 1 H), 7.85 (s, 1 H), 7.75 (d, J = 1.2 Hz, 1 H), 7.73 (d, J = 1.8 Hz, 1 H), 7.45–7.50 (m, 3 H), 4.38 (dd, J = 17.6 Hz, 2.6 Hz, 1 H), 4.25 (dd, J = 17.6 Hz, 2.6 Hz, 1 H), 3.81 (s, 3 H), 3.67 (dd, J = 17.0 Hz, 5.7 Hz, 1 H), 3.56 (dd, J = 17.0 Hz, 5.6 Hz, 1 H), 3.14 (t, J = 2.6 Hz, 1 H), 1.77 (s, 3 H). {¹H}¹³C NMR (101 MHz, DMSO-d₆): δ = 169.3, 168.7, 164.7, 139.7, 131.8, 131.3, 130.5, 129.1, 126.9, 77.8, 76.1, 52.8, 40.7, 35.8, 22.2.
• 13a Bettens FL, Bettens RP. A, Brown RD, Godfrey PD. J. Am. Chem. Soc. 2000; 122: 5856
• 13b Hirst JD, Persson BJ. J. Phys. Chem. A 1998; 102: 7519
• 14 CCDC 2338002 contains the supplementary crystallographic data for 1. The data can be obtained free of charge from The Cambridge Crystallographic Data Centre via www.ccdc.cam.ac.uk/structures

Publication History

Received: 15 July 2024

Accepted after revision: 27 January 2025

Accepted Manuscript online:
07 February 2025

Article published online:
12 May 2025