Glycoside hydrolase family 18 and 20 enzymes are novel targets of the traditional medicine berberine

J Biol Chem. 2018 Oct 5;293(40):15429-15438. doi: 10.1074/jbc.RA118.004351. Epub 2018 Aug 22.

Abstract

Berberine is a traditional medicine that has multiple medicinal and agricultural applications. However, little is known about whether berberine can be a bioactive molecule toward carbohydrate-active enzymes, which play numerous vital roles in the life process. In this study, berberine and its analogs were discovered to be competitive inhibitors of glycoside hydrolase family 20 β-N-acetyl-d-hexosaminidase (GH20 Hex) and GH18 chitinase from both humans and the insect pest Ostrinia furnacalis Berberine and its analog SYSU-1 inhibit insect GH20 Hex from O. furnacalis (OfHex1), with Ki values of 12 and 8.5 μm, respectively. Co-crystallization of berberine and its analog SYSU-1 in complex with OfHex1 revealed that the positively charged conjugate plane of berberine forms π-π stacking interactions with Trp490, which are vital to its inhibitory activity. Moreover, the 1,3-dioxole group of berberine binds an unexplored pocket formed by Trp322, Trp483, and Val484, which also contributes to its inhibitory activity. Berberine was also found to be an inhibitor of human GH20 Hex (HsHexB), human GH18 chitinase (HsCht and acidic mammalian chitinase), and insect GH18 chitinase (OfChtI). Besides GH18 and GH20 enzymes, berberine was shown to weakly inhibit human GH84 O-GlcNAcase (HsOGA) and Saccharomyces cerevisiae GH63 α-glucosidase I (ScGluI). By analyzing the published crystal structures, berberine was revealed to bind with its targets in an identical mechanism, namely via π-π stacking and electrostatic interactions with the aromatic and acidic residues in the binding pockets. This paper reports new molecular targets of berberine and may provide a berberine-based scaffold for developing multitarget drugs.

Keywords: berberine; chitinase; glycoside hydrolase; human; inhibitor; insect; protein crystallization; β-N-acetyl-D-hexosaminidase.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Berberine / chemistry*
  • Berberine / metabolism
  • Binding Sites
  • Chitinases / antagonists & inhibitors
  • Chitinases / chemistry*
  • Chitinases / genetics
  • Chitinases / metabolism
  • Cloning, Molecular
  • Crystallography, X-Ray
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Gene Expression
  • Genetic Vectors / chemistry
  • Genetic Vectors / metabolism
  • Glycoside Hydrolase Inhibitors / chemistry*
  • Humans
  • Isoenzymes / antagonists & inhibitors
  • Isoenzymes / chemistry
  • Isoenzymes / genetics
  • Isoenzymes / metabolism
  • Kinetics
  • Medicine, Chinese Traditional / methods
  • Models, Molecular
  • Moths / chemistry
  • Moths / enzymology
  • Protein Binding
  • Protein Conformation, alpha-Helical
  • Protein Conformation, beta-Strand
  • Protein Interaction Domains and Motifs
  • Quinazolinones / chemistry*
  • Quinazolinones / metabolism
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Saccharomyces cerevisiae / chemistry
  • Saccharomyces cerevisiae / enzymology
  • Static Electricity
  • Substrate Specificity
  • beta-N-Acetylhexosaminidases / antagonists & inhibitors
  • beta-N-Acetylhexosaminidases / chemistry*
  • beta-N-Acetylhexosaminidases / genetics
  • beta-N-Acetylhexosaminidases / metabolism

Substances

  • Glycoside Hydrolase Inhibitors
  • Isoenzymes
  • Quinazolinones
  • Recombinant Proteins
  • SYSU-ID-01
  • Berberine
  • Chitinases
  • beta-N-Acetylhexosaminidases

Associated data

  • PDB/5Y0V
  • PDB/5Y1B
  • PDB/3BTI
  • PDB/3D6Y
  • PDB/3VW2
  • PDB/3NSM
  • PDB/2PQR
  • PDB/1O7A
  • PDB/1HKK
  • PDB/3WQW
  • PDB/2YBT
  • PDB/5UN9
  • PDB/4J5T
  • PDB/1DHK