DOI: 10.5061/dryad.1ns1rn951
title: Discovery of indole alkaloids crienamides A and B from penicillium citrinum by a simulated MS/MS-guided molecular network strategy

description: 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.
description: # Discovery of indole alkaloids crienamides A and B from *Penicillium
 citrinum* by a simulated MS/MS-guided molecular network strategy Dataset
 DOI: [10.5061/dryad.1ns1rn951](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/](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](https://mzmine.github.io) * **GNPS platform (Feature-Based Molecular Networking)** for molecular networking analyses. Link: [https://gnps.ucsd.edu](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](https://gnps.ucsd.edu)) * **MZmol Analyzer** (accessible at [https://www.mzmol.com](https://www.mzmol.com)) for automated neutral loss and fragment ion mining, using parameters described in the manuscript supplementary materials. ## Access information NA