Stereochemical Elucidation and Total Synthesis of Dihydropacidamycin D, a Semisynthetic Pacidamycin

Boojamra, Constantine G.; Lemoine, Rémy C.; Lee, Julie C.; Léger, Roger; Stein, Karin A.; Vernier, Nicole G.; Magon, Angela; Lomovskaya, Olga; Martin, Patrick K.; Chamberland, Suzanne; Lee, May D.; Hecker, Scott J.; Lee, Ving J.

doi:10.1021/ja003292c

Cited by 52 publications

(54 citation statements)

References 38 publications

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“…Consistent with DABA synthesis in friulimicin (19), PacS is proposed to catalyze the β-replacement of threonine hydroxyl by the α-amino of aspartate, and the intermediate then breaks down to give DABA with the release of fumarate promoted by argininosuccinate lyase PacQ or PacS. The configuration of DABA in pacidamycins was determined to be 2S,3S, different from the 2S,3R configuration of DABA in friulimicin and natural L-Thr (11). PacT, a PLP-dependent threonine aldolase homolog, not encoded in friulimicin gene cluster, is thus proposed to be responsible for the 3S configuration of DABA (Fig.…”

Section: Resultsmentioning

confidence: 85%

“…Similar to many other uridyl peptides and uridyl lipopeptides, including liposidomycins (3), tunicamycins (4), capuramycins (5,6), muraymycins (7), and more closely related mureidomycins (8) and napsamycins (9), pacidamycins exhibited antimicrobial activity targeting the translocase MraY to block formation of lipid I from UDP-N-acetylmuramoyl-pentapeptide and undecaprenyl phosphate during bacterial cell wall assembly ( Fig. S1) (10,11). The uracil-ribose moiety is a key determinant of binding to the MraY target (10).…”

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confidence: 91%

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Identification of the biosynthetic gene cluster for the pacidamycin group of peptidyl nucleoside antibiotics

Zhang

Ostash

Walsh³

2010

Proc. Natl. Acad. Sci. U.S.A.

102

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Pacidamycins are a family of uridyl tetra/pentapeptide antibiotics that act on the translocase MraY to block bacterial cell wall assembly. To elucidate the biosynthetic logic of pacidamcyins, a putative gene cluster was identified by 454 shotgun genome sequencing of the producer Streptomyces coeruleorubidus NRRL 18370. The 31-kb gene cluster encodes 22 proteins (PacA-V), including highly dissociated nonribosomal peptide synthetase (NRPS) modules and a variety of tailoring enzymes. Gene deletions confirmed that two NRPSs, PacP and PacO, are required for the biosynthesis of pacidamycins. Heterologous expression and in vitro assays of PacL, PacO, and PacP established reversible formation of m-Tyr-AMP, L-Ala-AMP, and diaminopropionyl-AMP, respectively, consistent with the amino acids found in pacidamycin scaffolds. The unusual Ala 4 -Phe 5 dipeptidyl ureido linkage was formed during in vitro assays containing purified PacL, PacJ, PacN, and PacO. Both the genetic and enzymatic studies validate identification of the biosynthetic genes for this subclass of uridyl peptide antibiotics and provide the basis for future mechanistic study of their biosynthesis.adenylation | ureido-bond | uridine P acidamycins are a family of uridyl tetra/pentapeptide antibiotics isolated from Streptomyces coeruleorubidus. Since their discovery in 1989, at least 10 related compounds have been reported (1, 2), which share a common structural skeleton with a 3′-deoxyuridine nucleoside attached to an N-methyl 2,3-diaminobutyric acid (DABA) residue via a 4′,5′-enamide linkage. Attached to the α-amino of DABA is L-Ala, which is linked to the C-terminal aromatic amino acid via a ureido linkage. An N-terminal amino acid or dipeptide is attached to the β-amino of DABA to give the tetra/pentapeptide framework (Fig. 1). Similar to many other uridyl peptides and uridyl lipopeptides, including liposidomycins (3), tunicamycins (4), capuramycins (5, 6), muraymycins (7), and more closely related mureidomycins (8) and napsamycins (9), pacidamycins exhibited antimicrobial activity targeting the translocase MraY to block formation of lipid I from UDP-N-acetylmuramoyl-pentapeptide and undecaprenyl phosphate during bacterial cell wall assembly (Fig. S1) (10, 11). The uracil-ribose moiety is a key determinant of binding to the MraY target (10).We have begun to focus on the biosynthesis of pacidamycin family uridyl peptide antibiotics due to their three unusual structural features (Fig. 1). The first one is the presence of the nonproteinogenic amino acids L-meta-tyrosine (L-m-Tyr) and DABA, which suggests that nonribosomal peptide synthetase (NRPS) modules might be involved in the tetra/pentapeptide framework formation. The second feature is that the peptide chain direction reverses twice during assembly. As exemplified in pacidamycin 1, the peptide bond between m-Tyr 2 and DABA 3 is a β-rather than an α-peptide linkage. Consequently, the DABA 3 -Ala 4 peptide bond uses the α-amino of DABA moiety and the chain is reversed at Ala 4 . Next, the attachment of that Al...

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Section: Resultsmentioning

confidence: 85%

mentioning

confidence: 91%

Identification of the biosynthetic gene cluster for the pacidamycin group of peptidyl nucleoside antibiotics

Zhang

Ostash

Walsh³

2010

Proc. Natl. Acad. Sci. U.S.A.

102

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“…1). Pacidamycins were reported to exert antibiotic activities by virtue of functioning as a substrate analog of the UDP-MurNAc-pentapeptide of MraY in bacterial cell wall assembly of the pentapeptidyl-bactoprenol intermediate (3,4). Pacidamycins are of interest due to their unusual peptidyl-nucleoside structure features, and for the development of next generation antibacterial drugs inhibiting the clinically underexplored cell wall enzyme target MraY.…”

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confidence: 99%

tRNA-dependent peptide bond formation by the transferase PacB in biosynthesis of the pacidamycin group of pentapeptidyl nucleoside antibiotics

Zhang

Ntai

Kelleher

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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Pacidamycins are a family of uridyl tetra/pentapeptide antibiotics with antipseudomonal activities through inhibition of the translocase MraY in bacterial cell wall assembly. The biosynthetic gene cluster for pacidamycins has recently been identified through genome mining of the producer Streptomyces coeruleorubidus, and the highly dissociated nonribosomal peptide assembly line for the uridyl tetrapeptide scaffold of pacidamycin has been characterized. In this work a hypothetical protein PacB, conserved in known uridyl peptide antibiotics gene clusters, has been characterized by both genetic deletion and enzymatic analysis of the purified protein. PacB catalyzes the transfer of the alanyl residue from alanyl-tRNA to the N terminus of the tetrapeptide intermediate yielding a pentapeptide on the thio-templated nonribosomal peptide synthetase (NRPS) assembly line protein PacH. PacB thus represents a new group of tRNA-dependent peptide bond-forming enzymes in secondary metabolite biosynthesis in addition to the recently identified cyclodipeptide synthases. The characterization of PacB completes the assembly line reconstitution of pacidamycin pentapeptide antibiotic scaffolds, bridging the primary and secondary metabolic pathways by hijacking an aminoacyl-tRNA to the antibiotic biosynthetic pathway.aminoacyltransferase | uridyl pentapeptide | peptidyl carrier protein P acidamycins are a family of uridyl tetra/pentapeptide antibiotics produced by Streptomyces coeruleorubidus (1). More than 10 related family members have been reported (1, 2): Their common scaffold contains a central N β -methyl 2S,3S-diaminoburytic acid (DABA) moiety which is α-amino-capped by a ureido dipeptide (C-terminal), β-amino-capped by a single amino acid or a dipeptide (N-terminal), and carboxy-linked to a 3′-deoxy-4′,5′-enaminouridine ( Fig. 1). Pacidamycins were reported to exert antibiotic activities by virtue of functioning as a substrate analog of the UDP-MurNAc-pentapeptide of MraY in bacterial cell wall assembly of the pentapeptidyl-bactoprenol intermediate (3,4). Pacidamycins are of interest due to their unusual peptidyl-nucleoside structure features, and for the development of next generation antibacterial drugs inhibiting the clinically underexplored cell wall enzyme target MraY. The biosynthetic gene clusters for pacidamycins and closely related napsamycins were identified in parallel recently by three research groups via genome mining (5-7). Bioinformatic analysis revealed the building blocks in pacidamycins are assembled using a nonribosomal peptide synthetase (NRPS) thiotemplate logic, whereas the encoded NRPS modules and domains are highly dissociated and predicted to work with each other in trans. We further characterized the functions of the separate NRPS protein domains in vitro to delineate catalytic steps for activation and insertion of each building block in the pacidamycin scaffold (8, 9). We have shown that nine NRPS enzymes encoded by the producing organism S. coeruleorubidus, when heterologously expressed and purified ...

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“…These diverse series of compounds have wide series of applications ranging from plasticisers to pharmaceuticals. Importantly, ureas are also a key component of several bioactive natural products (Figure 1), [9] including mozamide A (1), oscillamide Y (2) and Figure 1. Urea-containing natural products.…”

Section: Introductionmentioning

confidence: 99%

A One‐Pot Synthesis of Symmetrical and Unsymmetrical Dipeptide Ureas

et al. 2015

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Stereochemical Elucidation and Total Synthesis of Dihydropacidamycin D, a Semisynthetic Pacidamycin

Cited by 52 publications

References 38 publications

Identification of the biosynthetic gene cluster for the pacidamycin group of peptidyl nucleoside antibiotics

Identification of the biosynthetic gene cluster for the pacidamycin group of peptidyl nucleoside antibiotics

tRNA-dependent peptide bond formation by the transferase PacB in biosynthesis of the pacidamycin group of pentapeptidyl nucleoside antibiotics

A One‐Pot Synthesis of Symmetrical and Unsymmetrical Dipeptide Ureas

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