Depsipeptide

A depsipeptide is a peptide in which one or more amide, -C(O)NHR-, linkages 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 produced in nature by soil and marine sediment inhabiting bacteria.[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.
Romidepsin


An example of a depsipeptide drug is the anticancer agent romidepsin, a known histone deacetylase inhibitor (HDACi). It was first isolated as a fermentation product from the soil bacterium Chromobacterium violaceum by the Fujisawa Pharmaceutical Company.[5][6]

Streptogramins, specifically streptogramin B antibiotics, are depsipeptides that bind to the 50S subunit of bacterial ribosomes.[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, 5th ed. (the "Gold Book") (2025). Online version: (2006–) "depsipeptides". doi:10.1351/goldbook.D01604
  2. ^ a b c 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.
  3. ^ a b 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.
  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. ^ 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.
  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. S2CID 22071968.
  7. ^ Aronson, J.K., ed. (2016). "Streptogramins". Meyler's Side Effects of Drugs. p. 499. doi:10.1016/B978-0-444-53717-1.01472-4. ISBN 978-0-444-53716-4. Streptogramins [1] are a class of antibiotics of two types, streptogramin A and streptogramin B. Separately, group A and group B streptogramins are bacteriostatic, by reversible binding to the 50S subunit of 70S bacterial ribosomes. Together, however, streptogramins from each group are synergic and bactericidal.
  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. PMC 2889693. 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; Gloyd, Melanie; Seon Chung, Yu; Ortega, Joaquin (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. PMC 2955292. PMID 20851345.
  12. ^ Hinzen, Berthold; Labischinski, Harald; Brötz-Oesterhelt, Heike; Endermann, Rainer; Benet-Buchholz, Jordi; Hellwig, Veronica; Häbich, Dieter; Schumacher, Andreas; Lampe, Thomas; Paulsen, Holger; Raddatz, Siegfried (2006). "Medicinal Chemistry Optimization of Acyldepsipeptides of the Enopeptin Class Antibiotics". ChemMedChem. 1 (7): 689–693. doi:10.1002/cmdc.200600055. PMID 16902918. S2CID 36525372.
  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. PMC 4004210. PMID 24422534.
  14. ^ Li, Jie Jack (2021), "Passerini Reaction", Name Reactions, Cham: Springer International Publishing, pp. 424–426, doi:10.1007/978-3-030-50865-4_115, ISBN 978-3-030-50864-7, retrieved 2022-10-26{{citation}}: CS1 maint: work parameter with ISBN (link)

Further reading

  • papuamide Ford, PW; Gustafson, KR; McKee, TC; Shigematsu, N; Maurizi, LK; Pannell, LK; Williams, DE; de Silva, ED; Lassota, P; Allen, TM; Van Soest, R; Andersen, RJ; Boyd, MR (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; McMahon, JB (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. PMC 2630844. PMID 19172193.

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