Discovery of Antibacterial Piperazic Acid-containing Pseudopeptides from a Saccharothrix Strain Using Targeted Genetic Screening and Molecular Networking Strategies

Piperazic acid (Piz)-containing compounds are a distinctive
class
of microbial metabolites characterized by a unique N–N bond
and diverse bioactivities, rendering them as promising scaffolds for
drug discovery. Herein, we utilized an integrated discovery strategy
combining PCR-based genetic screening, genome mining and MS/MS-based
molecular networking to target Piz-containing metabolites from an
actinomycetes library. This effort led to the isolation of nine new
Piz-containing linear pseudopeptides, saccharothriotides A–I
(1–9), along with the known compound
Sch 382583 (10), from a desert-derived actinomycete Saccharothrix sp. 275. Their planar structures and absolute
configurations were elucidated by spectroscopic analysis, advanced
Marfey’s method, phenylglycine methyl ester (PGME) derivatization,
and biosynthetic pathway deduction. Bioactivity assays revealed compounds 1–3, which feature a hydroxamic acid moiety,
exhibited significant activity against Gram-positive pathogens (MIC
= 0.5–16 μg/mL). Notably, antibacterial efficacy of 1–3 against vancomycin-resistant Enterococcus faecium (MIC = 2–4 μg/mL)
markedly outperformed the antibiotic levofloxacin (MIC = 64 μg/mL).
They also moderately inhibited Gram-negative bacteria such as Escherichia coli and Acinetobacter
baumannii (MIC = 16–64 μg/mL). As the
first Piz-containing metabolites reported from the genus Saccharothrix, this work underscores the effectiveness of combining genetic and
metabolomic strategies for discovering bioactive natural products
from underexplored microorganisms.