Proteomic quantitative pathway analysis aided potential target mining of alkaloids from herbal medicine

Abstract

Alkaloids are chemical compounds that are naturally occurred in many plants, bacteria, fungi and animals. Some alkaloids and/or their derivatives had been thoroughly studied about their pharmaceutical properties and underlining mechanisms, were being used as FDA approved anti-cancer drug. For example, topotecan and irinotecan the two derivatives of camptothecin found in Camptotheca (Camptotheca acuminate) are being used for cancer chemotherapy. Some of the alkaloids found in traditional Chinese herbal medicine had drawn enough attention from researchers around the world, for example, berberine found in coptis rhizome (huang lian) while some of them are less thoroughly explored. Those less explored alkaloids can be potential anti-cancer drugs in the future if the drug efficacies and mechanisms of drug action are known. Herein, we demonstrated the ability to use mass spectrometry based proteomics expression data for quantitative pathway analysis to aid finding potential drug targets of alkaloids from herbal medicine. Three types of cancer cell lines (HepG2, SKOV-3, AGS) were treated with each of the three selected alkaloids (camptothecin, corydaline and capsaicin) for 1hour, 6 hours and 48 hours. Treated and control cells were lysed, digested and subjected to LC-MS/MS analysis using LTQ Orbitrap Velos mass spectrometer (Thermo Scientific, USA). The subsequent proteomics data was processed and analyzed with MaxQuant (Max-Planck Institute of Biochemistry). The quantitative proteomics data was then uploaded to ExPlainTM 3.1 (BioBase) for signaling pathway analysis and searching of potential drug targets. The method was first validated using a known system, camptothecin treated system. The validated procedures were then applied to other alkaloids.