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Simplified immunosuppressive and neuroprotective agents based on gracilin A


The architecture and bioactivity of natural products frequently serve as embarkation points for the exploration of biologically relevant chemical space. Total synthesis followed by derivative synthesis has historically enabled a deeper understanding of structure–activity relationships. However, synthetic strategies towards a natural product are not always guided by hypotheses regarding the structural features required for bioactivity. Here, we report an approach to natural product total synthesis that we term ‘pharmacophore-directed retrosynthesis’. A hypothesized, pharmacophore of a natural product is selected as an early synthetic target and this dictates the retrosynthetic analysis. In an ideal application, sequential increases in the structural complexity of this minimal structure enable development of a structure–activity relationship profile throughout the course of the total synthesis effort. This approach enables the identification of simpler congeners retaining bioactivity at a much earlier stage of a synthetic effort, as demonstrated here for the spongiane diterpenoid, gracilin A, leading to simplified derivatives with potent neuroprotective and immunosuppressive activity.

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Data availability

Crystallographic data for the structure reported in this Article have been deposited at the Cambridge Crystallographic Data Centre under deposition number CCDC 1557733 ((–)-21b). A copy of the data can be obtained free of charge at All other data supporting the findings of this study are available within the Article and its Supplementary Information, or from the corresponding author upon reasonable request.

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  1. 1.

    Li, J., Kim, S. G. & Blenis, J. Rapamycin: one drug, many effects. Cell Metab. 19, 373–379 (2014).

  2. 2.

    Trauner, D. Finding function and form. Nat. Prod. Rep. 31, 411–413 (2014).

  3. 3.

    Wilson, R. M. & Danishefsky, S. J. Small molecule natural products in the discovery of therapeutic agents: the synthesis connection. J. Org. Chem. 71, 8329–8351 (2006).

  4. 4.

    Wender, P. A. Toward the ideal synthesis and molecular function through synthesis-informed design. Nat. Prod. Rep. 31, 433–440 (2014).

  5. 5.

    Schreiber, S. L. Target-oriented and diversity-oriented organic synthesis in drug discovery. Science 287, 1964–1969 (2000).

  6. 6.

    van Hattum, H. & Waldmann, H. Biology-oriented synthesis: harnessing the power of evolution. J. Am. Chem. Soc. 136, 11853–11859 (2014).

  7. 7.

    Seiple, I. B. et al. A platform for the discovery of new macrolide antibiotics. Nature 533, 338–345 (2016).

  8. 8.

    Könst, Z. A. et al. Synthesis facilitates an understanding of the structural basis for translation inhibition by the lissoclimides. Nat. Chem. 9, 1140–1149 (2017).

  9. 9.

    Bathula, S. R., Akondi, S. M., Mainkar, P. S. & Chandrasekhar, S. ‘Pruning of biomolecules and natural products (PBNP)’: an innovative paradigm in drug discovery. Org. Biomol. Chem. 13, 6432–6448 (2015).

  10. 10.

    Yu, M. J., Zheng, W. & Seletsky, B. M. From micrograms to grams: scale-up synthesis of eribulin mesylate. Nat. Prod. Rep. 30, 1158–1164 (2013).

  11. 11.

    Crane, E. A. & Gademann, K. Capturing biological activity in natural product fragments by chemical synthesis. Angew. Chem. Int. Ed. 55, 3882–3902 (2016).

  12. 12.

    Romo, D. et al. Evidence for separate binding and scaffolding domains in the immunosuppressive and antitumor marine natural product, pateamine A: design, synthesis and activity studies leading to a potent simplified derivative. J. Am. Chem. Soc. 126, 10582–10588 (2004).

  13. 13.

    Trost, B. The atom economy—a search for synthetic efficiency. Science 254, 1471–1477 (1991).

  14. 14.

    Newhouse, T., Baran, P. S. & Hoffmann, R. W. The economies of synthesis. Chem. Soc. Rev. 38, 3010–3021 (2009).

  15. 15.

    Young, I. S. & Baran, P. S. Protecting-group-free synthesis as an opportunity for invention. Nat. Chem. 1, 193–205 (2009).

  16. 16.

    Corey, E. J. & Cheng, X.-M. The Logic of Chemical Synthesis (Wiley Interscience, New York, NY, 1995).

  17. 17.

    Czakó, B., Kürti, L., Mammoto, A., Ingber, D. E. & Corey, E. J. Discovery of potent and practical antiangiogenic agents inspired by cortistatin A. J. Am. Chem. Soc. 131, 9014–9019 (2009).

  18. 18.

    Mayol, L., Piccialli, V. & Sica, D. Gracilin A, an unique: nor-diterpene metabolite from the marine sponge Spongionella gracilis. Tetrahedron Lett. 26, 1357–1360 (1985).

  19. 19.

    Sanchez, J. A. et al. Identification of Spongionella compounds as cyclosporine A mimics. Pharmacol. Res. 107, 407–414 (2016).

  20. 20.

    Leiros, M. et al. Gracilins: Spongionella-derived promising compounds for Alzheimer disease. Neuropharmacology 93, 285–293 (2015).

  21. 21.

    Corey, E. J. & Letavic, M. A. Enantioselective total synthesis of gracilins B and C using catalytic asymmetric Diels–Alder methodology. J. Am. Chem. Soc. 117, 9616–9617 (1995).

  22. 22.

    Rateb, M. E. et al. Bioactive diterpene derivatives from the marine sponge Spongionella sp. J. Nat. Prod. 72, 1471–1476 (2009).

  23. 23.

    Rueda, A. L. A. et al. Cytotoxic bisnorditerpenes from Spongionella pulchella, and the anti-adhesive properties of gracilin B. Lett. Drug Des. Discov. 3, 753–760 (2006).

  24. 24.

    Puliti, R., Fontana, A., Cimino, G., Mattia, C. A. & Mazzarella, L. Structure of a keto derivative of 9,11-dihydrogracilin A. Acta Crystallogr. C 49, 1373–1376 (1993).

  25. 25.

    Potts, B. C., Faulkner, D. J. & Jacobs, R. S. Phospholipase A2 inhibitors from marine organisms. J. Nat. Prod. 55, 1701–1717 (1992).

  26. 26.

    Leiros, M. et al. Mitigation of ROS insults by Streptomyces secondary metabolites in primary cortical neurons. ACS Chem. Neurosci. 5, 71–80 (2014).

  27. 27.

    Leiros, M. et al. Spongionella secondary metabolites protect mitochondrial function in cortical neurons against oxidative stress. Mar. Drugs 12, 700–718 (2014).

  28. 28.

    Kofron, J. L., Kuzmic, P., Kishore, V., Colon-Bonilla, E. & Rich, D. H. Determination of kinetic constants for peptidyl prolyl cis-trans isomerases by an improved spectrophotometric assay. Biochem. 30, 6127–6134 (1991).

  29. 29.

    Walsh, C. T., Zydowsky, L. D. & McKeon, F. D. Cyclosporin A, the cyclophilin class of peptidylprolyl isomerases, and blockade of T cell signal transduction. J. Biol. Chem. 267, 13115–13118 (1992).

  30. 30.

    Ferreira, P. A. & Orry, A. From Drosophila to humans: reflections on the roles of the prolyl isomerases and chaperones, cyclophilins, in cell function and disease. J. Neurogenet. 26, 132–143 (2012).

  31. 31.

    Lee, J. & Kim, S. S. An overview of cyclophilins in human cancers. J. Int. Med. Res. 38, 1561–1574 (2010).

  32. 32.

    Hogan, P. G., Chen, L., Nardone, J. & Rao, A. Transcriptional regulation by calcium, calcineurin, and NFAT. Genes Dev. 17, 2205–2232 (2003).

  33. 33.

    Nigro, P., Pompilio, G. & Capogrossi, M. C. Cyclophilin A: a key player for human disease. Cell Death Dis. 4, e888 (2013).

  34. 34.

    Picone, P., Nuzzo, D., Caruana, L., Scafidi, V. & Di Carlo, M. Mitochondrial dysfunction: different routes to Alzheimer’s disease therapy. Oxid. Med. Cell Longev. 2014, 780179 (2014).

  35. 35.

    Schnermann, M. J. et al. Golgi-modifying properties of macfarlandin E and the synthesis and evaluation of its 2,7-dioxabicyclo[3.2.1]octan-3-one core. Proc. Natl Acad. Sci. USA 107, 6158–6163 (2010).

  36. 36.

    Kornienko, A. & La Clair, J. J. Covalent modification of biological targets with natural products through Paal–Knorr pyrrole formation. Nat. Prod. Rep. 34, 1051–1060 (2017).

  37. 37.

    Nirmal, N., Praba, G. O. & Velmurugan, D. Modeling studies on phospholipase A2–inhibitor complexes. Indian J. Biochem. Biophys. 45, 256–262 (2008).

  38. 38.

    Baker, B. J., Kopitzke, R. W., Yoshida, W. Y. & McClintock, J. B. Chemical and ecological studies of the antarctic sponge dendrilla membranosa. J. Nat. Prod. 58, 1459–1462 (1995).

  39. 39.

    Buckleton, J. S. et al. Structure of tetrahydroaplysulphurin-1. Acta Crystallogr. C 43, 2430–2432 (1987).

  40. 40.

    Abbasov, M. E., Hudson, B. M., Tantillo, D. J. & Romo, D. Stereodivergent, Diels–Alder-initiated organocascades employing α,β-unsaturated acylammonium salts: scope, mechanism, and application. Chem. Sci. 8, 1511–1524 (2017).

  41. 41.

    Harvey, N. L. et al. Synthesis of (±)-spongiolactone enabling discovery of a more potent derivative. Chem. Eur. J. 21, 1425–1428 (2015).

  42. 42.

    Burgess, E. M., Penton, H. R., Jr., Taylor, E. A. Synthetic applications of N-carboalkoxysulfamate esters. J. Am. Chem. Soc. 92, 5224–5226 (1970).

  43. 43.

    Alfonso, A. et al. Surface plasmon resonance biosensor method for palytoxin detection based on Na+,K+-ATPase affinity. Toxins 6, 96–107 (2014).

  44. 44.

    Sanchez, J. A. et al. Spongionella secondary metabolites regulate store operated calcium entry modulating mitochondrial functioning in SH-SY5Y neuroblastoma cells. Cell Physiol. Biochem. 37, 779–792 (2015).

  45. 45.

    Damsker, J. M., Bukrinsky, M. I. & Constant, S. L. Preferential chemotaxis of activated human CD4+ T cells by extracellular cyclophilin A. J. Leukoc. Biol. 82, 613–618 (2007).

  46. 46.

    Moreira, P. I. et al. Mitochondria: a therapeutic target in neurodegeneration. Biochim. Biophys. Acta 1802, 212–220 (2010).

  47. 47.

    Azzolin, L. et al. Antamanide, a derivative of Amanita phalloides, is a novel inhibitor of the mitochondrial permeability transition pore. PLoS One 6, e16280 (2011).

  48. 48.

    Guo, H. X. et al. Novel cyclophilin D inhibitors derived from quinoxaline exhibit highly inhibitory activity against rat mitochondrial swelling and Ca2 + uptake/release. Acta Pharmacol. Sin. 26, 1201–1211 (2005).

  49. 49.

    Rao, V. K., Carlson, E. A. & Yan, S. S. Mitochondrial permeability transition pore is a potential drug target for neurodegeneration. Biochim. Biophys. Acta 1842, 1267–1272 (2014).

  50. 50.

    Dawar, F. U., Tu, J., Khattak, M. N., Mei, J. & Lin, L. Cyclophilin A: a key factor in virus replication and potential target for anti-viral therapy. Curr. Issues Mol. Biol. 21, 1–20 (2016).

  51. 51.

    Satoh, K. Cyclophilin A in cardiovascular homeostasis and diseases. Tohoku J. Exp. Med. 235, 1–15 (2015).

  52. 52.

    Abbasov, M. E., Hudson, B. M., Tantillo, D. J. & Romo, D. Acylammonium salts as dienophiles in Diels–Alder/lactonization organocascades. J. Am. Chem. Soc. 136, 4492–4495 (2014).

  53. 53.

    Halliwell, B. & Whiteman, M. Measuring reactive species and oxidative damage in vivo and in cell culture: how should you do it and what do the results mean? Br. J. Pharmacol. 142, 231–255 (2004).

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The authors acknowledge support from the NIH (R37 GM052964 to D.R.), NSF (CHE-1800411, to D.R.) the Robert A. Welch Foundation (AA-1280 to D.R.), FEDER co-funded grants from CONSELLERIA DE Cultura, EDUCACION e ordenación Universitaria Xunta de Galicia (2017 GRC GI-1682, ED431C 2017/01), CDTI and Technological Funds, supported by Ministerio de Economía, Industria y Competitividad (AGL2014-58210-R, AGL2016-78728-R, AEI/FEDER, UE) (to L.M.B.), ISCIII/PI1/01830 (to A.A.) and RTC-2016-5507-2 and ITC-20161072, from EU POCTEP 0161-Nanoeaters-1-E-1, Interreg AlertoxNet EAPA-317-2016 and H2020 778069-EMERTOX (to L.M.B.) and from the European Union’s Seventh Framework Programme managed by the Research Executive Agency (FP7/2007-2013 under grant agreement 312184 PHARMASEA to L.M.B. and M.J.). N. Bhuvanesh and J. Reibenspies (Center for X-ray Analysis, TAMU) secured X-ray data and W. Russell (Laboratory for Biological Mass Spectrometry, TAMU) provided mass data. Correspondence and requests for materials should be directed to D. Romo (chemistry) and L. Botana (biology).

Author information

M.E.A., C.M.C. and M.C. synthesized and characterized all gracilin A derivatives described herein. R.A. and J.A.S. performed the neuroprotection and immunosuppression assays and compiled and wrote the assay data, respectively. L.M.B., E.A. and A.A. designed, analysed and wrote the neuroprotection and immunosuppression assay results and data. D.R. and M.E.A. analysed SARs and wrote the manuscript with input from all authors. M.J. provided samples of the initial lead compound, gracilin A.

Competing interests

The authors declare no competing interests.

Correspondence to Luis M. Botana or Daniel Romo.

Supplementary Information

  1. Supplementary Information

    Synthetic procedures and characterization data for all new compounds, assay descriptions.

  2. Reporting Summary

  3. Crystallographic data

    CIF for compound (–)-21b; CCDC reference: 1557733.

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Fig. 1: Pharmacophore-directed retrosynthesis (PDR) applied to gracilin A and comparison to other synthetic strategies harvesting the rich information content of natural products.
Fig. 2: Select members of the gracilin A family and application of PDR to gracilin A.
Fig. 3: Pharmacophore-directed retrosynthesis applied to gracilin A.
Fig. 4: Synthesis of gracilin A derivatives toward SAR profile gap filling.
Fig. 5: Immunosuppressive activity of gracilin A derivatives.
Fig. 6: Activity of gracilin A derivatives as neuroprotective agents.
Fig. 7: SAR profile of gracilin A for both immunosuppressive and neuroprotective activity enabled through application of PDR.