Chemistry:Depsipeptide

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A depsipeptide is a peptide in which one or more of its amide, -C(O)NHR-, groups are replaced by the corresponding ester, -C(O)OR-.[1] Many depsipeptides have both peptide and ester linkages.[2] Elimination of the N–H group in a peptide structure results in a decrease of H-bonding capability, which is responsible for secondary structure and folding patterns of peptides, thus inducing structural deformation of the helix and β-sheet structures.[2][3] Because of decreased resonance delocalization in esters relative to amides, depsipeptides have lower rotational barriers for cis-trans isomerization and therefore they have more flexible structures than their native analogs.[2][3] They are mainly found in marine and microbial natural products.[4]

Example of a depsipeptide with 3 amide groups (highlighted blue) and one ester group (highlighted green). R1 and R3 are organic groups (e. g. methyl) or a hydrogen atom found in α-hydroxycarboxylic acids. R2, R4 and R5 are organic groups or a hydrogen atom found in common amino acids.

Depsipeptide natural products

thumb|right|222px|[[Enterochelin is a depsipeptide that is an iron-transporter.[5]]] Several depsipeptides have been found to exhibit anti-cancer properties.[6]

A depsipeptide enzyme inhibitor includes romidepsin, a member of the bicyclic peptide class, a known histone deacetylase inhibitors (HDACi). It was first isolated as a fermentation product from Chromobacterium violaceum by the Fujisawa Pharmaceutical Company.[7]

Etamycin was shown in preliminary data in 2010 to have potent activity against MRSA in a mouse model.[8] Several depsipeptides from Streptomyces exhibit antimicrobial activity.[9][10] These form a new, potential class of antibiotics known as acyldepsipeptides (ADEPs). ADEPs target and activate the casein lytic protease (ClpP) to initiate uncontrolled peptide and unfolded protein degradation, killing many Gram-positive bacteria.[11][12][13]

Depsipeptides can be formed through a Passerini reaction.[14]

References

  1. ↑ IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version:  (2006–) "depsipeptides". doi:10.1351/goldbook.D01604
  2. ↑ 2.0 2.1 2.2 Avan, Ilker; Tala, Srinivasa R.; Steel, Peter J.; Katritzky, Alan R. (17 June 2011). "Benzotriazole-Mediated Syntheses of Depsipeptides and Oligoesters". The Journal of Organic Chemistry 76 (12): 4884–4893. doi:10.1021/jo200174j. PMID 21452874. https://pubs.acs.org/doi/10.1021/jo200174j. 
  3. ↑ 3.0 3.1 Avan, Ilker; Hall, C. Dennis; Katritzky, Alan R. (2014). "Peptidomimetics via modifications of amino acids and peptide bonds". Chemical Society Reviews 43 (10): 3575–3594. doi:10.1039/C3CS60384A. PMID 24626261. https://pubs.rsc.org/en/content/articlelanding/2014/cs/c3cs60384a. 
  4. ↑ Yasumasa Hamada; Takayuki Shioiri (2005). "Recent Progress of the Synthetic Studies of Biologically Active Marine Cyclic Peptides and Depsipeptides". Chem. Rev. 105 (12): 4441–4482. doi:10.1021/cr0406312. PMID 16351050. 
  5. ↑ Walsh; Christopher T.; Jun Liu; Frank Rusnak; Masahiro Sakaitani (1990). "Molecular Studies on Enzymes in Chorismate Metabolism and the Enterobactin Biosynthetic Pathway". Chemical Reviews 90 (7): 1105–1129. doi:10.1021/cr00105a003. 
  6. ↑ Kitagaki, J.; Shi, G.; Miyauchi, S.; Murakami, S.; Yang, Y. (2015). "Cyclic depsipeptides as potential cancer therapeutics". Anticancer Drugs 26 (3): 259–71. doi:10.1097/CAD.0000000000000183. PMID 25419631. 
  7. ↑ Yurek-George, Alexander; Cecil, Alexander Richard Liam; Mo, Alex Hon Kit; Wen, Shijun; Rogers, Helen; Habens, Fay; Maeda, Satoko; Yoshida, Minoru et al. (2007). "The First Biologically Active Synthetic Analogues of FK228, the Depsipeptide Histone Deacetylase Inhibitor". Journal of Medicinal Chemistry 50 (23): 5720–5726. doi:10.1021/jm0703800. PMID 17958342. 
  8. ↑ Haste, Nina M; Perera, Varahenage R; Maloney, Katherine N; Tran, Dan N; Jensen, Paul; Fenical, William; Nizet, Victor; Hensler, Mary E (2010). "Activity of the streptogramin antibiotic etamycin against methicillin-resistant Staphylococcus aureus". Journal of Antibiotics 63 (5): 219–24. doi:10.1038/ja.2010.22. PMID 20339399. 
  9. ↑ K. H. Michel, R. E. Kastner (Eli Lilly and Company), US 4492650, 1985 [Chem. Abstr. 1985, 102, 130459]
  10. ↑ Osada, Hiroyuki; Yano, Tatsuya; Koshino, Hiroyuki; Isono, Kiyoshi (1991). "Enopeptin A, a novel depsipeptide antibiotic with anti-bacteriophage activity". The Journal of Antibiotics 44 (12): 1463–1466. doi:10.7164/antibiotics.44.1463. PMID 1778798. 
  11. ↑ Li; Him Shun, Dominic; Guarné, Alba; Maurizi, Michael R.; Cheng, Yi-Qiang; Wright, Gerard D.; Ghirlando, Rodolfo; Joseph, Ebenezer et al. (2010). "Acyldepsipeptide Antibiotics Induce The Formation Of A Structured Axial Channel In ClpP: A Model For The ClpX/ClpA-Bound State Of ClpP". Chemistry & Biology 17 (9): 959–969. doi:10.1016/j.chembiol.2010.07.008. PMID 20851345. 
  12. ↑ Hinzen, Berthold; Labischinski, Harald; Brötz-Oesterhelt, Heike; Endermann, Rainer; Benet-Buchholz, Jordi; Hellwig, Veronica; Häbich, Dieter; Schumacher, Andreas et al. (2006). "Medicinal Chemistry Optimization of Acyldepsipeptides of the Enopeptin Class Antibiotics". ChemMedChem 1 (7): 689–693. doi:10.1002/cmdc.200600055. PMID 16902918. 
  13. ↑ Carney, Daniel W.; Schmitz, Karl R.; Truong, Jonathan V.; Sauer, Robert T.; Sello, Jason K. (2014). "Restriction of the Conformational Dynamics of the Cyclic Acyldepsipeptide Antibiotics Improves Their Antibacterial Activity". Journal of the American Chemical Society 136 (5): 1922–1929. doi:10.1021/ja410385c. PMID 24422534. 
  14. ↑ Li, Jie Jack (2021), "Passerini Reaction" (in en), Name Reactions (Cham: Springer International Publishing): pp. 424–426, doi:10.1007/978-3-030-50865-4_115, ISBN 978-3-030-50864-7, http://link.springer.com/10.1007/978-3-030-50865-4_115, retrieved 2022-10-26 

Further reading

  • papuamide Ford, PW; Gustafson, KR; McKee, TC; Shigematsu, N; Maurizi, LK; Pannell, LK; Williams, DE; de Silva, ED et al. (1999). "Papuamides A-D, HIV-Inhibitory and Cytotoxic Depsipeptides from the Sponges Theonella mirabilis and Theonella swinhoei Collected in Papua New Guinea". J. Am. Chem. Soc. 121: 5899–5909. doi:10.1021/ja990582o. 
  • neamphamide A Oku, N; Gustafson, KR; Cartner, LK; Wilson, JA; Shigematsu, N; Hess, S; Pannell, LK; Boyd, MR et al. (2004). "Neamphamide A. A new HIV-inhibitory depsipeptide from the Papua New Guinea marine sponge Neamphius huxleyi". J. Nat. Prod. 67 (8): 1407–11. doi:10.1021/np040003f. PMID 15332865. 
  • callipeltin A Zampella, A; D'Auria, MV; Paloma, LG; Casapullo, A; Minale, L; Debitus, C; Henin, Y (1996). "Callipeltin A, an Anti-HIV Cyclic Depsipeptide from the New Caledonian Lithistida Sponge Callipelta sp.". J. Am. Chem. Soc. 118 (26): 6202–9. doi:10.1021/ja954287p. 
  • mirabamides A-D Plaza, A; Gustchina, E; Baker, HL; Kelly, M; Bewley, CA (2007). "Mirabamides A-D. Depsipeptides from the sponge Siliquariaspongia mirabilis that inhibit HIV-1 fusion". J. Nat. Prod. 70 (11): 1753–60. doi:10.1021/np070306k. PMID 17963357. ; Andjelic, CD; Planelles, V; Barrows, LR (2008). "Characterizing the Anti-HIV Activity of Papuamide A.". Mar Drugs 6 (4): 528–49. doi:10.3390/md20080027. PMID 19172193. 



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