Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2025 Oct 15;147(41):37719-37731.
doi: 10.1021/jacs.5c13143. Epub 2025 Oct 7.

Logical Exploration of Cinnamoyl-Containing Nonribosomal Peptides via Metabologenomic Targeting and Regulator Overexpression

Sangwook Kang  1 , Thanh-Hau Huynh  1 , Jung Min Kim  2 , Bo Eun Heo  3 , Sung Chul Jang  2 , Chae Won Ock  2 , Jayho Lee  4 , Yejin Song  1 , Joon Soo An  2 , Ben Shen  5   6 , Seung Bum Kim  7 , Jichan Jang  3 , Sang Kook Lee  2 , Yeo Joon Yoon  2 , Dong-Chan Oh  1
Affiliations

Logical Exploration of Cinnamoyl-Containing Nonribosomal Peptides via Metabologenomic Targeting and Regulator Overexpression

Sangwook Kang et al. J Am Chem Soc. .

Abstract

A targeted method for discovering cinnamoyl-containing nonribosomal peptides (CCNPs), a unique class of bioactive compounds, was devised by using cinnamoyl isomerase, a key enzyme in the biosynthesis of the cinnamoyl moiety, as a genome mining probe. A total of 39 hit strains were obtained, including 35 from polymerase chain reaction-based screening of the in-house bacterial library (2.5% of 1400 strains) targeting the cinnamoyl isomerase-encoding gene and 4 from the genome mining of online databases. Sequence similarity networking and phylogenetic analyses of the isomerase amplicons (∼530 bp) classified the CCNPs into three major substructure-based groups (Z-, E-, and M-type CCNPs) and revealed distinct clade-structure relationships (13 clades). To overcome the challenge of silent biosynthetic gene clusters, we activated these clusters by overexpressing conserved cluster-situated LuxR regulators combined with extensive culture optimization. CCNP production was metabolomically detected in the bacterial extracts by using the characteristic UV absorption and MS/MS fragments of cinnamoyl moieties. CCNP production was observed in 20 of the 39 hit strains, resulting in the isolation of 6 new CCNPs, including oxy-skyllamycin B (2), gwanacinnamycin (3), and luxocinnamycins A-D (4-7), with high structural novelty. Their structures were elucidated using comprehensive spectroscopic analyses and multiple-step chemical derivatizations, and the putative biosynthetic pathways were bioinformatically proposed. Gwanacinnamycin (3) exhibited significant antimycobacterial activity, whereas luxocinnamycin A (4) displayed moderate antiproliferative activity against stomach cancer cells. Our findings highlight a targeted metabologenomic approach combined with transcriptional regulator overexpression as a logical and efficient platform for the discovery of bioactive compounds from nature.

PubMed Disclaimer

Figures

1
1
Biosynthesis of CCNPs. (A) Chemical structures of representative CCNPs. (B) Proposed biosynthetic pathway of the cinnamoyl moiety. (C) Organization of BGCs associated with CCNPs.
2
2
Classification of CCNPs. (A) SSN analysis of isomerase enzymes, with previously reported isomerases depicted as V-shaped nodes. (B) Overview of CCNP types and their corresponding substructures.
3
3
Metabologenomic targeting workflow for the discovery of novel CCNPs. (A) Phylogenetic tree of cinnamoyl isomerase amplicon sequences with bootstrap supporting values indicated on the branches. The reference sequences are shown in bold. (B) Activation of cryptic BGCs by the overexpression of cluster-situated LuxR regulators combined with the extensive culture optimization. (C) Metabolomic detection of CCNPs by LC-MS/MS analysis based on MS/MS fragmentation and the characteristic UV spectrum of the cinnamoyl moiety. (D) Structures of CCNPs isolated in this study.
4
4
(A) Structures and key 2D NMR correlations of oxy-skyllamycins A (1) and B (2). (B) Relative configurations of 10′,11′-epoxy cinnamoyl moieties.
5
5
Structure and key 2D NMR correlations of gwanacinnamycin (3).
6
6
Structures and key 2D NMR correlations of luxocinnamycins A–D (4–7).
See this image and copyright information in PMC

References

    1. Shi J., Liu C. L., Zhang B., Guo W. J., Zhu J., Chang C.-Y., Zhao E. J., Jiao R. H., Tan R. X., Ge H. M.. Genome Mining and Biosynthesis of Kitacinnamycins as a STING Activator. Chem. Sci. 2019;10(18):4839–4846. doi: 10.1039/C9SC00815B. - DOI - PMC - PubMed
    1. Hayashi K., Hashimoto M., Shigematsu N., Nishikawa M., Ezaki M., Yamashita M., Kiyoto S., Okuhara M., Kohsaka M., Imanaka H.. WS9326A, a Novel Tachykinin Antagonist Isolated from Streptomyces violaceusniger No. 9326. J. Antibiot. 1992;45(7):1055–1063. doi: 10.7164/antibiotics.45.1055. - DOI - PubMed
    1. Toki S., Agatsuma T., Ochiai K., Saitoh Y., Ando K., Nakanishi S., Lokker N. A., Giese N. A., Matsuda Y.. RP-1776, a Novel Cyclic Peptide Produced by Streptomyces sp., Inhibits the Binding of PDGF to the Extracellular Domain of Its Receptor. J. Antibiot. 2001;54(5):405–414. doi: 10.7164/antibiotics.54.405. - DOI - PubMed
    1. Sun C., Yang Z., Zhang C., Liu Z., He J., Liu Q., Zhang T., Ju J., Ma J.. Genome Mining of Streptomyces atratus SCSIO ZH16: Discovery of Atratumycin and Identification of Its Biosynthetic Gene Cluster. Org. Lett. 2019;21(5):1453–1457. doi: 10.1021/acs.orglett.9b00208. - DOI - PubMed
    1. Bae M., Kim H., Moon K., Nam S.-J., Shin J., Oh K.-B., Oh D.-C.. Mohangamides A and B, New Dilactone-Tethered Pseudo-Dimeric Peptides Inhibiting Candida albicans Isocitrate Lyase. Org. Lett. 2015;17(3):712–715. doi: 10.1021/ol5037248. - DOI - PubMed

LinkOut - more resources