Discovery of indole alkaloids crienamides A and B from penicillium citrinum by a simulated MS/MS-guided molecular network strategy

Peng, Yuanyang 1 ; Luo, Shang1 ; Li, Qin1; Li, Yongqi1; Zhang, Jiale1; Ding, Nanjin1; Sun, Weiguang1; Chen, Chunmei1; Liu, Junjun1; Ye, Ying1; Zhu, Hucheng1; Zhang, Yonghui1

Published May 12, 2025 on Dryad. https://doi.org/10.5061/dryad.1ns1rn951

Data files

May 12, 2025 version files 165.57 MB

Crienamide_A_NMR.jdx

337.43 KB
Crienamide_B_NMR.jdx

324.84 KB
Public_data.zip

164.91 MB
README.md

3.41 KB

Abstract

The Building blocks-based molecular network (BBMN) strategy is effective for targeted natural product identification but depends on existing MS/MS data. To address this, we propose the Simulated MS/MS-Guided Molecular Network (SMMN) strategy, which combines virtual molecule design and MS/MS simulation to identify novel compounds containing target building blocks. We developed the MZmol Analyzer, a user-friendly web tool, to automate the SMMN strategy. Using this approach and the target 6-methyl-L-pipecolate (6-MeP), we identified two new indole alkaloid hybrids, crienamides A and B. In vitro immunosuppressive assays showed that both compounds inhibited ConA-induced cell proliferation, with IC₅₀ values of 2.86 ± 1.33 μM and 0.96 ± 1.22 μM, respectively.

Dataset DOI: 10.5061/dryad.1ns1rn951

Description of the data and file structure

This dataset contains nuclear magnetic resonance (NMR) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) data supporting the discovery of two novel indole alkaloids, Crienamides A and B, from Penicillium citrinum using a Simulated MS/MS-Guided Molecular Network (SMMN) strategy.

The NMR dataset includes the 1H NMR, 13C NMR, HSQC, HMBC, H-H COSY, and NOESY spectra for both Crienamides A and B. Additionally, it contains the 1H NMR and H-H COSY spectra of the R-Mosher-ether and S-Mosher-ether derivatives of Crienamide A obtained through Mosher's reaction.

The LC-MS/MS dataset consists of mzML files converted from raw data acquired using an Agilent 6545 Q-TOF mass spectrometer coupled with an Agilent 1290 Infinity LC system. The data represent fractions Fr.1–Fr.6 from Penicillium citrinum extracts. The dataset also includes processed metabolomics data resulting from feature extraction with MZmine 3.72, which served as input data for the SMMN analysis.

All data were collected at the Analytical and Testing Center, Huazhong University of Science and Technology.

Files and variables

File: Public_data.zip

Description:
This file (Public_data.zip) contains experimental data supporting the identification of novel indole alkaloids, Crienamides A and B:

Crienamide A_NMR.mnova and Crienamide B_NMR.mnova: Original NMR data for compounds Crienamides A and B.
Fr1-6.mzml: LC-MS/MS data in mzML format corresponding to fractions Fr.1–Fr.6.
Penicillium_citrinum_metabolites.mgf and Penicillium_citrinum_metabolites.csv: Feature-Based Molecular Networking (FBMN) input data generated by MZmine 3.72 following parameters described in the supplementary information. These files serve as input data for the Simulated MS/MS-Guided Molecular Network (SMMN) strategy and MZmol Analyzer.

The JCAMP-DX format files (Crienamide_A_NMR.jdx and Crienamide_B_NMR.jdx) are open-access versions of the NMR data.

Code/software

NMR Data:

The NMR datasets (Crienamide A_NMR.mnova and Crienamide B_NMR.mnova) can be viewed and analyzed using MestReNova software (version ≥14.0, Mestrelab Research).
Link: https://mestrelab.com/software/mnova/

LC-MS/MS Data:

Raw LC-MS/MS data (Fr1-6.mzml) can be opened and analyzed using free mass spectrometry software such as:
- MZmine 3.72 for feature extraction and preprocessing.
  Link: https://mzmine.github.io
- GNPS platform (Feature-Based Molecular Networking) for molecular networking analyses.
  Link: https://gnps.ucsd.edu

FBMN and SMMN Analyses:

Penicillium_citrinum_metabolites.mgf and Penicillium_citrinum_metabolites.csv are intended as input files for FBMN and SMMN analysis workflows via:
- GNPS web platform (https://gnps.ucsd.edu)
- MZmol Analyzer (accessible at https://www.mzmol.com) for automated neutral loss and fragment ion mining, using parameters described in the manuscript supplementary materials.