SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database

Abstract

The Small Molecule Pathway Database (SMPDB, http://www.smpdb.ca) is a comprehensive, colorful, fully searchable and highly interactive database for visualizing human metabolic, drug action, drug metabolism, physiological activity and metabolic disease pathways. SMPDB contains >600 pathways with nearly 75% of its pathways not found in any other database. All SMPDB pathway diagrams are extensively hyperlinked and include detailed information on the relevant tissues, organs, organelles, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Since its last release in 2010, SMPDB has undergone substantial upgrades and significant expansion. In particular, the total number of pathways in SMPDB has grown by >70%. Additionally, every previously entered pathway has been completely redrawn, standardized, corrected, updated and enhanced with additional molecular or cellular information. Many SMPDB pathways now include transporter proteins as well as much more physiological, tissue, target organ and reaction compartment data. Thanks to the development of a standardized pathway drawing tool (called PathWhiz) all SMPDB pathways are now much more easily drawn and far more rapidly updated. PathWhiz has also allowed all SMPDB pathways to be saved in a BioPAX format. Significant improvements to SMPDB’s visualization interface now make the browsing, selection, recoloring and zooming of pathways far easier and far more intuitive. Because of its utility and breadth of coverage, SMPDB is now integrated into several other databases including HMDB and DrugBank.

Identification of endogenous metabolites in human sperm cells using proton nuclear magnetic resonance (1H-NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS)

“…The total list of metabolites was also analysed using the bioinformatic tool Metabolites Biological Role (MBRole; http:// csbg.cnb.csic.es/mbrole/) in order to identify over-represented or enriched biological pathways that could be putatively active (p-values < 0.05 were considered significant) (Chagoyen & Pazos, 2011). These pathway results were based on the Small Molecule Pathway Database (SMPDB; http://smpdb.ca) (Frolkis et al, 2010;Jewison et al, 2014). Combined analyses of protein and metabolite data sets were also performed to integrate the human sperm metabolomics data described here with the recently compiled human sperm proteome , in order to investigate significantly represented pathways.…”

Tetrahydrobiopterin regulates monoamine neurotransmitter sulfonation

“…The SULT1A1 control template helps gauge the specificity of candidate SULT1A3 allosteres. Given the high catalytic efficiency of SULT1A3 toward monoamine neurotranmitters, the screen was limited to the 115 human small-molecule metabolites associated with neurotransmitter metabolism found in the Small Molecule Pathways Database (SMPDB) (28). Screening was performed with the Genetic Optimization for Ligand Docking (GOLD) program (Materials and Methods).…”

Integrative methods for analyzing big data in precision medicine

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