Characterization of natural peptides in Pheretima by integrating proteogenomics and label-free peptidomics

peer-reviewed · Journal of Pharmaceutical Analysis · 2023

peer-reviewed · Journal of Pharmaceutical Analysis · 2023. Xiaoxiao Luo et al. Pheretima, also called “earthworms”, is a well-known animal-derived traditional Chinese medicine that is…
Date 2023-09-01
Type peer-reviewed
Venue Journal of Pharmaceutical Analysis
Publisher Elsevier BV
Contribution downstream-application
DOI 10.1016/j.jpha.2023.06.006
Citations (OpenAlex) 14

Abstract

Pheretima, also called “earthworms”, is a well-known animal-derived traditional Chinese medicine that is extensively used in over 50 Chinese patent medicines (CPMs) in Chinese Pharmacopoeia (2020 edition). However, its zoological origin is unclear, both in the herbal market and CPMs. In this study, a strategy for integrating in-house annotated protein databases constructed from close evolutionary relationship-sourced RNA sequencing data from public archival resources and various sequencing algorithms (restricted search, open search, and de novo) was developed to characterize the phenotype of natural peptides of three major commercial species of Pheretima, including Pheretima aspergillum (PA), Pheretima vulgaris (PV), and Metaphire magna (MM). We identified 10,477 natural peptides in the PA, 7,451 in PV, and 5,896 in MM samples. Five specific signature peptides were screened and then validated using synthetic peptides; these demonstrated robust specificity for the authentication of PA, PV, and MM. Finally, all marker peptides were successfully applied to identify the zoological origins of Brain Heart capsules and Xiaohuoluo pills, revealing the inconsistent Pheretima species used in these CPMs. In conclusion, our integrated strategy could be used for the in-depth characterization of natural peptides of other animal-derived traditional Chinese medicines, especially non-model species with poorly annotated protein databases.

Authors

  1. Xiaoxiao Luo · China Pharmaceutical University, Chinese Academy of Sciences, Shanghai Institute of Materia Medica
  2. Qirui Bi · Chinese Academy of Sciences, Shanghai Institute of Materia Medica
  3. Dongdong Huang · Chinese Academy of Sciences, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences
  4. Yun Li · Chinese Academy of Sciences, Shanghai Institute of Materia Medica
  5. Changliang Yao · Chinese Academy of Sciences, Shanghai Institute of Materia Medica
  6. Jianqing Zhang · Chinese Academy of Sciences, Shanghai Institute of Materia Medica
  7. Wenlong Wei · Chinese Academy of Sciences, Shanghai Institute of Materia Medica
  8. Jiayuan Li · Chinese Academy of Sciences, Shanghai Institute of Materia Medica
  9. Zhenwei Li · Chinese Academy of Sciences, Shanghai Institute of Materia Medica
  10. Jingxian Zhang · Chinese Academy of Sciences, Shanghai Institute of Materia Medica
  11. Shen Ji · Chinese Academy of Sciences, Shanghai Institute of Materia Medica
  12. Yurong Wang · China Pharmaceutical University
  13. De-an Guo · China Pharmaceutical University, Chinese Academy of Sciences, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences

Methods and tools

  • Pheretima natural peptide authentication: Combines proteogenomic databases with open and de novo search to characterise earthworm natural peptides and derive species marker peptides for traditional medicines.

Methods it uses

  • PEAKS: Commercial DP-based de novo

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