Poster Presentation 8th Modern Solid Phase Peptide Synthesis & Its Applications Symposium 2022

A Concise Synthetic Strategy Towards the Novel Calcium-dependent Lipopeptide Antibiotic, Malacidin A and Analogues1 (#150)

Nadiia Kovalenko 1 , Georgina K Howard 1 , Jonathan A Swain 1 , Yann Hermant 1 , Alan J Cameron 1 2 3 , Gregory M Cook 3 4 , Scott A Ferguson 4 , Louise A Stubbing 1 3 , Paul WR Harris 1 2 3 , Margaret A Brimble 1 3
  1. School of Chemical Sciences, University of Auckland, Auckland, New Zealand
  2. School of Biological Sciences, University of Auckland, Auckland, New Zealand
  3. Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
  4. Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand

Malacidin A is a novel antimicrobial peptide isolated and reported by Brady et al during an extensive metagenomic mining study of bacterial DNA from soil samples.2 Malacidin A belongs to a family of calcium-dependent lipopeptide antibiotics (CDLAs), possessing potent antimicrobial activity against various Gram-positive strains, including MRSA and VRE (MIC 0.2-0.8, 0.8-2.0 µgmL-1, respectively).  Structurally, malacidin A differs from other members of the CDLA family in that the canonical calcium-binding motif Asp-AA-Asp-Gly (AA = Gly or D-amino acid) lacks the spacer AA residue, and an unusual 3-hydroxy aspartic acid replaces the first Asp residue of the motif. The structure also contains several other non-canonical amino acids: 3-MeAsp-1, 3-MeDap-2, D-Val-3, 3-HyAsp-5, D-3-MeAsp-8, and (4R)-4-MePro-10. At the time, the configuration of the β-carbon stereocentres in 3-MeAsp-1, 3-MeDap-2, 3-HyAsp-5, and D-3-MeAsp-8 were undetermined, giving rise to 16 possible diastereomers.

Herein we report a concise, robust synthetic route towards a diastereomer of malacidin A. Fmoc-SPPS of a linear precursor, followed by late-stage incorporation of the lipid tail and solution-phase cyclisation afforded the malacidin diastereomer. The utility of this approach was demonstrated through construction of six simplified analogues. Their antibacterial activity was then evaluated against S. aureus, however none were active. The stereochemistry of the (2S,3S)-3-MeAsp-1, (2S,3S)-3-MeDap-2, (2S,3S)-3-HyAsp-5, and (2R,3R)-D-3-MeAsp-8 building blocks used here were chosen based on structural and biosynthetic gene cluster similarities of malacidin A and friulimicin B;2,3 a later report of the total synthesis of malacidin A by Sun et al4 established the correct stereoconfiguration of residues (2S,3R)-3-MeDap-2, (2S,3R)-3-HyAsp-5, and (2R,3S)-D-3-MeAsp-8 in the natural product. 1H NMR spectra of the malacidin variant in the presence of CaCl2 indicated no interaction with Ca2+, suggesting the orientation of the β-hydroxy group in 3HyAsp-5 is highly important for coordination of Ca2+ and antibacterial activity.

  1. (1) Kovalenko, N.; Howard, G. K.; Swain, J. A.; Hermant, Y.; Cameron, A. J.; Cook, G. M.; Ferguson, S. A.; Stubbing, L. A.; Harris, P. W. R.; Brimble, M. A. A Concise Synthetic Strategy Towards the Novel Calcium-Dependent Lipopeptide Antibiotic, Malacidin A and Analogues. Front. Chem. 2021, 9, 421. https://doi.org/10.3389/fchem.2021.687875.
  2. (2) Hover, B. M.; Kim, S.-H.; Katz, M.; Charlop-Powers, Z.; Owen, J. G.; Ternei, M. A.; Maniko, J.; Estrela, A. B.; Molina, H.; Park, S.; Perlin, D. S.; Brady, S. F. Culture-Independent Discovery of the Malacidins as Calcium-Dependent Antibiotics with Activity against Multidrug-Resistant Gram-Positive Pathogens. Nat. Microbiol. 2018, 1. https://doi.org/10.1038/s41564-018-0110-1.
  3. (3) Müller, C.; Nolden, S.; Gebhardt, P.; Heinzelmann, E.; Lange, C.; Puk, O.; Welzel, K.; Wohlleben, W.; Schwartz, D. Sequencing and Analysis of the Biosynthetic Gene Cluster of the Lipopeptide Antibiotic Friulimicin in Actinoplanes Friuliensis. Antimicrob. Agents Chemother. 2007, 51 (3), 1028–1037. https://doi.org/10.1128/AAC.00942-06.
  4. (4) Sun, Z.; Shang, Z.; Forelli, N.; Po, K. H. L.; Chen, S.; Brady, S. F.; Li, X. Total Synthesis of Malacidin A by β-Hydroxyaspartic Acid Ligation-Mediated Cyclization and Absolute Structure Establishment. Angew. Chem. Int. Ed. 2020, 59 (45), 19868–19872. https://doi.org/10.1002/anie.202009092.