Journal Article

Solution conformations of Zika NS2B-NS3pro and its inhibition by natural products from edible plants

Lu, Yimei, Lim, Liangzhong, Roy, Amrita, Srivastava, Shagun, Song, Jianxing

2017

Overview

The recent Zika viral (ZIKV) epidemic has been associated with severe neurological pathologies such as neonatal microcephaly and Guillain-Barre syndrome but unfortunately no vaccine or medication is effectively available yet. Zika NS2B-NS3pro is essential for the proteolysis of the viral polyprotein and thereby viral replication. Thus NS2B-NS3pro represents an attractive target for anti-Zika drug discovery/design. Here, we have characterized the solution conformations and catalytic parameters of both linked and unlinked Zika NS2B-NS3pro complexes and found that the unlinked complex manifested well-dispersed NMR spectra. Subsequently with selective isotope-labeling using NMR spectroscopy, we demonstrated that C-terminal residues (R73-K100) of NS2B is highly disordered without any stable tertiary and secondary structures in the Zika NS2B-NS3pro complex in the free state. Upon binding to the well-characterized serine protease inhibitor, bovine pancreatic trypsin inhibitor (BPTI), only the extreme C-terminal residues (L86-K100) remain disordered. Additionally, we have identified five flavonoids and one natural phenol rich in edible plants including fruits and vegetables, which inhibit Zika NS2B-NS3pro in a non-competitive mode, with Ki ranging from 770 nM for Myricetin to 34.02 μM for Apigenin. Molecular docking showed that they all bind to a pocket on the back of the active site and their structure-activity relationship was elucidated. Our study provides valuable insights into the solution conformation of Zika NS2B-NS3pro and further deciphers its susceptibility towards allosteric inhibition by natural products. As these natural product inhibitors fundamentally differ from the currently-known active site inhibitors in terms of both inhibitory mode and chemical scaffold, our finding might open a new avenue for development of better allosteric inhibitors to fight ZIKV infection.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Allosteric properties / Binding Sites / Biocatalysis - drug effects / Biological Products - chemistry / Biological Products - pharmacology / Biology and life sciences / Biophysical Phenomena - drug effects / Buffers / Catalysis / Cloning, Molecular / Conformation / Dengue fever / Drug development / Drug discovery / Drugs / E coli / Encephalitis / Enzymes / Epidemics / Flavonoids / Flowers & plants / Fruits / Genomes / Guillain-Barre syndrome / Hepatitis / Hydrogen Bonding / Immunoglobulins / Infections / Inhibitors / Kinetics / Magnetic resonance spectroscopy / Marking / Medicine and Health Sciences / Microencephaly / Models, Molecular / Molecular docking / Molecular structure / Mutation / Natural products / Neonates / NMR spectroscopy / Pancreas / Phenols / Physical Sciences / Physiological aspects / Plants (botany) / Plants, Edible - chemistry / Product inhibition / Protease / Protease inhibitors / Protein Conformation / Proteinase / Proteinase inhibitors / Proteins / Proteolysis / Public health / Replication / Research and analysis methods / Residues / RNA Helicases - antagonists & inhibitors / RNA Helicases - chemistry / RNA Helicases - isolation & purification / RNA Helicases - metabolism / Science / Serine / Serine Endopeptidases - chemistry / Serine Endopeptidases - isolation & purification / Serine Endopeptidases - metabolism / Serine proteinase / Solutions / Spectroscopy / Structure / Studies / Trypsin / Trypsin inhibitors / Vector-borne diseases / Vegetables / Viral Nonstructural Proteins - antagonists & inhibitors / Viral Nonstructural Proteins - chemistry / Viral Nonstructural Proteins - isolation & purification / Viral Nonstructural Proteins - metabolism / Zika virus / Zika Virus - chemistry / Zika Virus - drug effects