July 29, 2020
As a result of a joint research effort involving Koichi Tanaka Mass Spectrometry Research Laboratory at Shimadzu Corporation and Professor Onaka and Professor Abe at The University of Tokyo, a novel class of hybrid compounds comprising lipids and peptides was identified. Moreover, the detailed molecular structures of these compounds were demonstrated using a mass spectrometry technique developed in Koichi Tanaka’s laboratory, “HiRID-MS/MS,” wherein radical species irradiation was used to promote analyte fragmentation within tandem mass spectrometers.
The newly discovered compounds, polyketide (PK)/ribosomally-synthesized and post-translationally modified peptides (RiPP) hybrid lipopeptides, were named “goadvionin.” Owing to their ability to inhibit the growth of Gram-positive bacteria, these hybrid lipopeptides are expected to be a new class of medicinal lead compounds.
The study was published online in Nature Chemistry on 27 July, 2020 (London time). [ref. 1]
Mass spectrometry methods for the structural analysis of compounds of interest usually involve two steps: the molecules are initially fragmented via collisions with inert gases (e.g., argon) as they travel in the mass spectrometer. This widely implemented step is usually called collision-induced dissociation (CID). Subsequently, the generated fragments undergo analysis aimed at measuring their masses. The resultant mass values are then examined and combined to identify plausible parent molecule candidates.
However, such an approach sometimes fails because certain types of bonds tend to resist cleavage, rendering structural analysis impossible.
To overcome this issue, we recently developed a novel fragmentation technique called highly-integrated radical induced dissociation (HiRID), wherein chemically active radical species are used as collision bullets. Furthermore, hydrogen radical [H·] or hydroxyl radical [OH·] species are used as the reaction reagent. The relevant hardware was developed in the context of an academic–industrial collaboration [ref. 2–7], and a theoretical study on the fragmentation process is still ongoing through cooperation with academia and government institutes [ref. 8–12].
The results of various studies revealed wide range application of HiRID technique, which afforded information on
- Lipids with high C–C bond contents [ref. 13,14]
- Post-translational modifications in peptides [ref. 10–12]
- Polyether molecular structure [ref. 15]
- Unknown biologically active substances [ref. 16]
In this study, the challenging analyses of several compounds comprising long and complicated carbon chains were efficiently conducted. The targets were PK/RiPP hybrid lipopeptides, which have characteristic lipid–peptide hybrid backbones. HiRID-based analysis was applied to these species, and it exhibited a crucial role in unveiling their detailed structures, which comprised six hydroxyl groups and one double bond. This success encouraged us to publish the results reported herein.
Shimadzu will continue to promote research in this field with the goal, including connecting HiRID to triple or quadrupole LC-MS and Q-TOF LC-MS instruments and conducting experiments aimed at the practical use of HiRID-MS/MS and the employment of this technique in commercial products.
PCT/JP2015/054214, JP application No. 2014-041206 including all parents, re-examinations, divisionals, continuations, continuations-in-part, reissued patents that claim a priority date based upon the said application, and any foreign counterparts.
1) Ryosuke Kozakai, Takuto Ono, Shotaro Hoshino, Hidenori Takahashi, Yohei Katsuyama, Yoshinori Sugai, Taro Ozaki, Kazuya Teramoto, Kanae Teramoto, Koichi Tanaka, Ikuro Abe, Shumpei Asamizu and Hiroyasu Onaka
"Acyltransferase that catalyses the condensation of polyketide and peptide moieties of goadvionin hybrid lipopeptides"
Nat. Chem., published online, 2020
2) Hidenori Takahashi, Sadanori Sekiya, Takashi Nishikaze, Kei Kodera, Shinichi Iwamoto, Motoi Wada, Koichi Tanaka
"Hydrogen Attachment/Abstraction Dissociation (HAD) of Gas-Phase Peptide Ions for Tandem Mass Spectrometry"
Anal. Chem., 88, 7, 3810-3816, 2016
3) Hidenori Takahashi
"Fragmentation of Organic Compounds Using Gas-Phase Radical Species"
J. Mass Spectrom. Soc. Jpn., 65, 6, 268-273, 2017
4) Yuji Shimabukuro, Hidenori Takahashi, Shinichi Iwamoto, Koichi Tanaka, Motoi Wada
"Tandem Mass Spectrometry of Peptide Ions by Microwave Excited Hydrogen and Water Plasmas"
Anal. Chem., 90, 12, 7239-7245, 2018
5) Hidenori Takahashi
"Development of Novel Tandem Mass Spectrometer (HAD-MS/MS) Using Gas-Phase Radicals"
SHIMADZU REVIEW, 75, No.3・4, 2018
6) (Ref. 5 in Japanese journal SHIMADZU HYORON)
7) Yuji Shimabukuro, Hidenori Takahashi, Shinichi Iwamoto, Koichi Tanaka and Motoi Wada
"Microwave excitation of a low-energy atomic hydrogen"
Plasma Sources Sci. Technol., 29, 015005, 2020
8) Daiki Asakawa, Hidenori Takahashi, Shinichi Iwamoto, Koichi Tanaka
"Fundamental study of hydrogen-attachment-induced peptide fragmentation occurring in the gas phase and during the matrix-assisted laser desorption/ionization process"
Phys. Chem. Chem. Phys., 20, 13057-13067, 2018
9) Daiki Asakawa, Hidenori Takahashi, Shinichi Iwamoto and Koichi Tanaka
"Hydrogen atom attachment to histidine and tryptophan containing peptides in the gas phase"
Phys. Chem. Chem. Phys., 21, 11633-11641, 2019
10) Daiki Asakawa, Hidenori Takahashi, Shinichi Iwamoto, Koichi Tanaka
"De Novo Sequencing of Tryptic Phosphopeptides Using Matrix-Assisted Laser Desorption/Ionization Based Tandem Mass Spectrometry with Hydrogen Atom Attachment"
Anal. Chem., 90, 4, 2701-2707, 2018
11) Daiki Asakawa, Hidenori Takahashi, Sadanori Sekiya, Shinichi Iwamoto and Koichi Tanaka
"Sequencing of Sulfopeptides Using Negative-Ion Tandem Mass Spectrometry with Hydrogen Attachment/Abstraction Dissociation"
Anal. Chem., 91, 16, 10549-10556, 2019
12) Daiki Asakawa, Hidenori Takahashi, Shinichi Iwamoto and Koichi Tanaka
"Hydrogen attachment dissociation of peptides containing disulfide bonds"
Phys. Chem. Chem. Phys., 21, 26049-26057, 2019
13) Hidenori Takahashi, Yuji Shimabukuro, Daiki Asakawa, Shosei Yamauchi, Sadanori Sekiya, Shinichi Iwamoto, Motoi Wada, Koichi Tanaka
"Structural Analysis of Phospholipid Using Hydrogen Abstraction Dissociation and Oxygen Attachment Dissociation in Tandem Mass Spectrometry"
Anal. Chem., 90, 12, 7230-7238, 2018
14) Hidenori Takahashi, Yuji Shimabukuro, Daiki Asakawa, Akihito Korenaga, Masaki Yamada, Shinichi Iwamoto, Motoi Wada, Koichi Tanaka
"Identifying Double Bond Positions in Phospholipids Using Liquid Chromatography-Triple Quadrupole Tandem Mass Spectrometry Based on Oxygen Attachment Dissociation"
Mass Spectrom (Tokyo), 8(2), S0080, 2019
15) Daiki Asakawa, Hidenori Takahashi, Shinichi Iwamoto and Koichi Tanaka
"Characterization of Polyethers Using Tandem Mass Spectrometry with Hydrogen Abstraction Dissociation and Thermal Activation"
J. Am. Soc. Mass Spectrom., 31, 2, 450-457, 2020
16) Masamitsu Maekawa, Isamu Jinnoh, Yotaro Matsumoto, Aya Narita, Ryuichi Mashima, Hidenori Takahashi, Anna Iwahori, Daisuke Saigusa, Kumiko Fujii, Ai Abe, Katsumi Higaki, Shosei Yamauchi, Yuji Ozeki, Kazutaka Shimoda, Yoshihisa Tomioka, Torayuki Okuyama, Yoshikatsu Eto, Kousaku Ohno, Peter T Clayton, Hiroaki Yamaguchi and Nariyasu Mano
"Structural Determination of Lysosphingomyelin-509 and Discovery of Novel Class Lipids from Patients with Niemann-Pick Disease Type C"
Int. J. Mol. Sci., 20, 5018, 2019
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