Crystal structure of the Ilheus virus helicase: implications for enzyme function and drug design

Abstract

Background The Ilheus virus (ILHV) is an encephalitis associated arthropod-borne flavivirus. It was first identified in Ilheus City in the northeast Brazil before spreading to a wider geographic range. No specific vaccines or drugs are currently available for the treatment of ILHV infections. The ILHV helicase, like other flavivirus helicases, possesses 5ʹ-triphosphatase activity. This allows it to perform ATP hydrolysis to generate energy as well as sustain double-stranded RNA’s unwinding during ILHV genome replication. Thus, ILHV helicase is an ideal target for inhibitor design. Results We determined the crystal structure of the ILHV helicase at 1.75-Å resolution. We then conducted molecular docking of ATP-Mn2+ to the ILHV helicase. Comparisons with related flavivirus helicases indicated that both the NTP and the RNA-ILHV helicase binding sites were conserved across intra-genus species. This suggested that ILHV helicase adopts an identical mode in recognizing ATP/Mn2+. However, the P-loop in the active site showed a distinctive conformation; reflecting a different local structural rearrangement. ILHV helicase enzymatic activity was also characterized. This was found to be relatively lower than that of the DENV, ZIKV, MVE, and ALSV helicases. Our structure-guided mutagenesis revealed that R26A, E110A, and Q280A greatly reduced the ATPase activities. Moreover, we docked two small molecule inhibitors of DENV helicase (ST-610 and suramin) to the ILHV helicase and found that these two molecules had the potential to inhibit the activity of ILHV helicase as well. Conclusion High-resolution ILHV helicase structural analysis demonstrates the key amino acids of ATPase activities and could be useful for the design of inhibitors targeting the helicase of ILHV.

Morphologic and Genetic Characterization of Ilheus Virus, a Potential Emergent Flavivirus in the Americas

“…The cysteines at ILHV C262 and C563 were found to be fully conserved amongst the nine considered flaviviruses and C375 was found to be conserved among all but YFV ( Supplementary Figure S2 ). However, the X-ray crystallography of the helicase portion of ILHV NS3, comprising residues 177–618, made no note of any disulfide bond formation [ 107 ].…”

Crystal structure of RNA helicase from Saint Louis encephalitis virus and discovery of its inhibitors

“… 3 Several structures have been reported for the flavivirus helicase previously, including those from Dengue Virus (DENV), Zika Virus (ZIKV), Japanese encephalitis virus (JEV), Kunjin virus (KUNV), and Ilheus virus (ILHV). 4 However, the structure of SLEV helicase has not been determined.…”