Total Synthesis of Keramaphidin B and Ingenamine

Abstract

The full details of the total synthesis of keramaphidin B and ingenamine are reported herein. The most conspicuous transformation in our total synthesis is the base-catalyzed Diels–Alder reaction using dynamic regioselective crystallization (alternatively referred to as crystallization-induced transformation). The tertiary alcohol, which is used for the base-catalyzed activation in the Diels–Alder reaction, is removed as its p-fluorobenzoate using SmI₂ (HMPA)₄. Double macrocyclic alkylation enables the regioselective construction of two macrocycles in a single step. The developed sequence is highly efficient, achieving the unified total synthesis of keramaphidin B and ingenamine within 13 steps from commercially available compounds. Our biological study elucidated the significant role of the two macrocycles in their antiproliferative effects against human cancer cell lines.

Keywords

Diels–Alder reaction - Dynamic crystallization - Macrocycle - Manzamine alkaloids - Total synthesis - Crystallization-induced transformation

Publication History

Received: 21 November 2025

Accepted after revision: 10 December 2025

Accepted Manuscript online:
11 December 2025

Article published online:
31 December 2025

• References


For recent reviews on Manzamine alkaloids:
• 1a Hu J-F, Hamann MT, Hill R, Kelly M. The Manzamine alkaloids. In: The Alkaloids: Chemistry and Biology. Cordell GA. ed. San Diego: Academic Press; 2003: 207-285
• 1b Berlinck RGS. In: Topics in Heterocyclic Chemistry. Gupta RR, Kahn MTH. eds. Vol. 10. Berlin Heidelberg: Springer-Verlag; 2007: 211-238
• 1c Peng J, Rao KV, Choo Y-M, Hamann MT. In: Modern Alkaloids, Structure, Isolation, Synthesis and Biology. Fattorusso E, Taglialatela-Scafati O. eds. Weinheim: Wiley-VCH; 2008: 189-232
• 1d Duval R, Poupon E. Poupon E, Nay B. eds. Biomimetic Organic Synthesis. Weinheim: Wiley-VCH; 2011: 181-224
• 1e Kubota T, Kurimoto S, Kobayashi J. In: The Alkaloids, Chemistry and Biology. Knölker H-J. ed. Vol. 84. San Diego: Academic Press; 2020: 1-124
• 1f Tang Y, Zhu L, Hong R. Tetrahedron Chem 2022; 3: 100025
• 1g Piwko AT, Miller BG, Smith JM. Nat Prod Rep 2023; 40: 964
• 2a Kobayashi J, Tsuda M, Kawasaki N, Matsumoto K, Adachi T. Tetrahedron Lett 1994; 35: 4383
• 2b Tsuda M, Inaba K, Kawasaki N, Honma K, Kobayashi J. Tetrahedron 1996; 52: 2319
• 2c Kobayashi J, Kawasaki N, Tsuda M. Tetrahedron Lett 1996; 37: 8203
• 3 Ohtani I, Kusumi T, Kashman Y, Kakisawa H. J Am Chem Soc 1991; 113: 4092
• 4a Kong F, Andersen RJ, Allen TM. Tetrahedron Lett 1994; 35: 1643
• 4b Kong F, Andersen RJ. Tetrahedron 1995; 51: 2895
• 5a Rodríguez J, Peters BM, Kurz L. et al. J Am Chem Soc 1993; 115: 10436
• 5b Rodríguez J, Crews P. Tetrahedron Lett 1994; 35: 4719
• 6a Meng Z, Fürstner A. J Am Chem Soc 2020; 142: 11703
• 6b Meng Z, Spohr SM, Tobegen S, Farès C, Fürstner A. J Am Chem Soc 2021; 143: 14402
• 6c Varlet T, Portmann S, Fürstner A. J Am Chem Soc 2023; 145: 21197
• 7a Baldwin JE, Whitehead RC. Tetrahedron Lett 1992; 33: 2059
• 7b Baldwin JE, Claridge TDW, Culshaw AJ. et al. Angew Chem Int Ed 1998; 37: 2661
• 7c Baldwin JE, Claridge TDW, Culshaw AJ. et al. Chem Eur J 1999; 5: 3154
• 8 Kondo K, Shigemori H, Kikuchi Y, Ishibashi M, Sasaki T, Kobayashi J. J Org Chem 1992; 57: 2480
• 9 Sakai R, Kohmoto S, Higa T, Jefford CW, Bernardinelli G. Tetrahedron Lett 1987; 28: 5493

For selected examples on the biomimetic approach to keramaphidin B, see:
• 10a Gil L, Baucherel X, Martin M-T, Marazano C, Das BC. Tetrahedron Lett 1995; 36: 6231
• 10b Gomez J-M, Gil L, Ferroud C, Gateau-Olesker A, Martin M-T, Marazano C. J Org Chem 2001; 66: 4898

For recent biomimetic approach to halicyclamines, see:
• 10c Wayama T, Arai Y, Oguri H. J Org Chem 2022; 87: 5938
• 10d Wayama T, Oguri H. Org Lett 2023; 25: 3596

For synthetic studies on keramaphidin B, see:
• 11a Jakubec P, Farley AJM, Dixon DJ. Beilstein J Org Chem 2016; 12: 1096
• 11b Shimoda H, Shibata T, Sekine D, Nakada M. Heterocycles 2020; 100: 3

For an approach to keramaphidin B, see:
• 11c Ippoliti FM, Adamson NJ, Wonilowicz LG. et al. Science 2023; 379: 261
• 11d Mehta MM, Gonzalez JAM, Bachman JL, Garg NK. Org Lett 2023; 25: 5553

For base-catalyzed Diels-Alder reaction of 3-hydroxy-2-pyridones, see:
• 12a Okamura H, Nagaike H, Iwagawa T, Nakatani M. Tetrahedron Lett 2000; 41: 8317
• 12b Kipassa NT, Okamura H, Kina K, Hamada T, Iwagawa T. Org Lett 2008; 10: 815

For enantioselective Diels-Alder reaction of 3-hydroxy-2-pyridones, see:
• 12c Soh JY-T, Tan C-H. J Am Chem Soc 2009; 131: 6904
• 12d Chennapuram M, Reddy UVS, Seki C. et al. Eur J Org Chem 2017; 4633
• 12e Miskov-Pajic V, Willig F, Wanner DM, Frey W, Peters R. Angew Chem Int Ed 2020; 59: 19873

For selected reviews on dynamic crystallization, see:
• 13a Brands KMJ, Davies AJ. Chem Rev 2006; 106: 2711
• 13b Kolarovič A, Jakubec P. Adv Synth Catal 2021; 363: 4110
• 13c Putman JI, Armstrong DW. Chirality 2022; 34: 1338
• 13d Walsh MP, Barclay JA, Begg CS. et al. JACS Au 2022; 2: 2235
• 13e Sato T. Chem Lett 2025; 54: upae244
• 14 Part of this work was published as a preliminary communication, see: Kurihara Y, Yagi M, Noguchi T. et al. J Am Chem Soc 2024; 146: 11054
• 15 For a selected review on Negishi coupling, see: Negishi E, Hu Q, Huang Z, Qian M, Wang G. Aldrichim Acta 2005; 38: 71
• 16 Although the mechanistic role of lithium chloride is yet to be clarified, use of DMAP and LiCl might be related to the Roush-Masamune conditions (iPr2NEt and LiCl) in the Horner-Wadsworth-Emmons reaction, and might generate more reactive lithium alkoxides, see: Blanchette MA, Choy W, Davis JT. et al. Tetrahedron Lett 1984; 25: 2183

For selected examples on synthesis of natural products through dynamic crystallization, see:
• 17a Openshaw HT, Whittaker N. J Chem Soc 1963; 1461
• 17b Belanger F, Chase CE, Endo A. et al. Angew Chem Int Ed 2015; 54: 5108
• 17c Zanetti A, Chaumont-Olive P, Schwertz G. et al. Org Process Res Dev 2020; 24: 850
• 17d Grenet E, Géant P-Y, Salom-Roig XJ. Org Lett 2021; 23: 8539
• 17e Salom-Roig XJ. Eur J Org Chem 2022; e202101451
• 17f Hirasawa S, Kurashima T, Hasegawa T, Souma K, Kanomata N. Chem Lett 2022; 51: 985
• 17g Shieh W-C, Carlson JA. J Org Chem 1994; 59: 5463

For selected examples on two-component reactions using dynamic crystallization, see:
• 18a Jakubec P, Cockfield DM, Helliwell M, Raftery J, Dixon DJ. Beilstein J Org Chem 2012; 8: 567
• 18b Uemura N, Toyoda S, Ishikawa H. et al. J Org Chem 2018; 83: 9300
• 18c Uemura N, Toyoda S, Shimizu W, Yoshida Y, Mino T, Sakamoto M. Symmetry 2020; 12: 910
• 18d Silverberg LJ, Kelly S, Vemishetti P. et al. Org Lett 2000; 2: 3281
• 18e Shimizu W, Uemura N, Yoshida Y, Mino T, Kasashima Y, Sakamoto M. Cryst Growth Des 2020; 20: 5676
• 18f De Jesús Cruz P, Cassels WR, Chen C-H, Johnson JS. Science 2022; 376: 1224
• 18g De Jesús Cruz P, Johnson JS. J Am Chem Soc 2022; 144: 15803
• 18h Cassels WR, Crawford ET, Johnson JS. ACS Catal 2023; 13: 6518
• 19 Deposition numbers 2331678 (for 11a), and 2331679 (for 18a) contain the supplementary crystallographic data for this paper. These data are provided free of charge by the joint Cambridge Crystallographic Data Centre (CCDC) and Fachinformationszentrum (FIZ) Karlsruhe Access Structures service.

For reviews on two-directional synthesis, see:
• 20a Poss CS, Schreiber SL. Acc Chem Res 1994; 27: 9
• 20b Magnuson SR. Tetrahedron 1995; 51: 2167
• 20c Hoffmann RW. Angew Chem Int Ed 2003; 42: 1096
• 21 For synthesis of phosphonium salt 20, see the Supporting Information.
• 22 For a review on Barton-McCombie deoxygenation, see: Crich D, Quintero L. Chem Rev 1989; 89: 1413
• 23 Lam K, Markó IE. Org Lett 2008; 10: 2773
• 24 Knowles H, Parsons AF, Pettifer RM. Synlett 1997; 271
• 25 Yoshida Y, Sakakura Y, Aso N, Okada S, Tanabe Y. Tetrahedron 1999; 55: 2183

For the alkyne metathesis and subsequent semihydrogenation in synthesis of manzamine alkaloids, see:
• 26a Jakubec P, Kyle AF, Calleja J, Dixon DJ. Tetrahedron Lett 2011; 52: 6094
• 26b Kyle AF, Jakubec P, Cockfield DM, Cleator E, Skidmore J, Dixon DJ. Chem Commun 2011; 47: 10037
• 26c Dalling AG, Späth G, Fürstner A. Angew Chem Int Ed 2022; 61: e202209651

For construction of madangamine-type macrocycles by alkylation, see:
• 27a Suto T, Yanagita Y, Nagashima Y. et al. J Am Chem Soc 2017; 139: 2952
• 27b Suto T, Yanagita Y, Nagashima Y. et al. Bull Chem Soc Jpn 2019; 92: 545
• 28 For formation of a macrocyclic amine by Z-selective ring-closing metathesis, see: Wang C, Yu M, Kyle AF. et al. Chem Eur J 2013; 19: 2726
• 29 The longest linear steps are counted based on the following paper, see: Johnson JS. Nat Synth 2023; 2: 6
• 30 Hashimoto H, Ueda Y, Takasu K, Kawabata T. Angew Chem Int Ed 2022; 61: e202114118
• 31 Dahlén A, Hilmersson G. Eur J Inorg Chem 2004; 3020
• 32 Frisch MJ, Trucks GW, Schlegel HB. et al. Gaussian 16, Revisions C.01 and C.02. Wallingford CT: Gaussian, Inc.; 2016
• 33 Schrödinger Release 2021-2 and 2025-1: MacroModel. New York, NY: Schrödinger, LLC; 2025
• 34a Neese F. WIREs Comput Mol Sci 2012; 2: 73
• 34b Neese F. WIREs Comput Mol Sci 2017; 8: e1327
• 34c Neese F, Wennmohs F, Becker U, Riplinger C. J Chem Phys 2020; 152: 224108
• 35a Grimme S, Bannwarth C, Shushkov P. J Chem Theory Comput 2017; 13: 1989
• 35b Bannwarth C, Ehlert S, Grimme S. J Chem Theory Comput 2019; 15: 1652
• 35c Bannwarth C, Caldeweyher E, Ehlert S. et al. WIREs Comput Mol Sci 2020; 11: e01493
• 36 Legault CY. CYLview20, Université de Sherbrooke, Sherbrooke, QC, Canada https://www.cylview.org/ (accessed June 23, 2025)
• 37 Fukaya K. ACCeL https://github.com/kfchem/accel/ (accessed June 23, 2025).