基于基因组和光谱特征的靶向和逻辑发现含有哒嗪酸基团的天然产物。
Targeted and Logical Discovery of Piperazic Acid-Bearing Natural Products Based on Genomic and Spectroscopic Signatures.
发表日期:2023 Aug 29
作者:
Daniel Shin, Woong Sub Byun, Sangwook Kang, Ilnam Kang, Eun Seo Bae, Joon Soo An, Ji Hyeon Im, Jiyoon Park, Eunji Kim, Keebeom Ko, Sunghoon Hwang, Honghui Lee, Yun Kwon, Yoon-Joo Ko, Suckchang Hong, Sang-Jip Nam, Seung Bum Kim, William Fenical, Yeo Joon Yoon, Jang-Cheon Cho, Sang Kook Lee, Dong-Chan Oh
来源:
BIOMEDICINE & PHARMACOTHERAPY
摘要:
针对天然产物中含有Piz(piperazic acid)的新发现方法被设计出来,该酸是由l-ornithine N-hydroxylase(KtzI)和N-N键形成酶(KtzT)通过从鸟氨酸生物合成而来的。通过利用针对ktzT的PCR引物,对包含2020株细菌DNA文库进行基于基因组特征的筛选,鉴定出62株(3.1%)。对编码KtzT的PCR扩增子进行系统发育分析,将这23个类群分类为I和II两个单系群。在含有15NH4Cl的培养基中培养这些优先级较高的菌株,并应用1H-15N异核多键相关(HMBC)、1H-15N异核单量子相干(HSQC)和1H-15N HSQC-总相关(HSQC-TOCSY)核磁共振实验,检测到了Piz和改性Piz的光谱特征。通过对基因组和光谱特征优先级较高的菌株的化学研究,我们发现了一种新的azinothricin类似物,polyoxyperuin B seco acid(1),以及以前报道的chloptosin(2)(在I类中),含有两个dehydropiperazic酸(Dpz)的depsidomycin D(3),以及I类中的一种结构新颖的31环脱氨肽lenziamides A和B(4和5)。通过整合系统发育和化学分析,得到了19个23个类群的类群-结构关系的阐明。Lenziamide A(4)能抑制STAT3的激活,并在人结直肠癌细胞中诱导G2/M细胞周期阻滞、细胞凋亡和抑制肿瘤生长。此外,Lenziamide A(4)在体外细胞培养和体内5-FU耐药肿瘤移植小鼠模型中增强了5-氟尿嘧啶(5-FU)的活性。本研究表明,基于基因组和光谱特征的搜索为含有特定结构动机的新型生物活性天然产物提供了一种高效且通用的策略。
A targeted and logical discovery method was devised for natural products containing piperazic acid (Piz), which is biosynthesized from ornithine by l-ornithine N-hydroxylase (KtzI) and N-N bond formation enzyme (KtzT). Genomic signature-based screening of a bacterial DNA library (2020 strains) using polymerase chain reaction (PCR) primers targeting ktzT identified 62 strains (3.1%). The PCR amplicons of KtzT-encoding genes were phylogenetically analyzed to classify the 23 clades into two monophyletic groups, I and II. Cultivating hit strains in media supplemented with 15NH4Cl and applying 1H-15N heteronuclear multiple bond correlation (HMBC) along with 1H-15N heteronuclear single quantum coherence (HSQC) and 1H-15N HSQC-total correlation spectroscopy (HSQC-TOCSY) NMR experiments detected the spectroscopic signatures of Piz and modified Piz. Chemical investigation of the hit strains prioritized by genomic and spectroscopic signatures led to the identification of a new azinothricin congener, polyoxyperuin B seco acid (1), previously reported chloptosin (2) in group I, depsidomycin D (3) incorporating two dehydropiperazic acids (Dpz), and lenziamides A and B (4 and 5), structurally novel 31-membered cyclic decapeptides in group II. By consolidating the phylogenetic and chemical analyses, clade-structure relationships were elucidated for 19 of the 23 clades. Lenziamide A (4) inhibited STAT3 activation and induced G2/M cell cycle arrest, apoptotic cell death, and tumor growth suppression in human colorectal cancer cells. Moreover, lenziamide A (4) resensitized 5-fluorouracil (5-FU) activity in both in vitro cell cultures and the in vivo 5-FU-resistant tumor xenograft mouse model. This work demonstrates that the genomic and spectroscopic signature-based searches provide an efficient and general strategy for new bioactive natural products containing specific structural motifs.