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

• Published in: Cell & bioscience 2022-04, Vol.12 (1), p.44-44, Article 44
• Main Authors: Wang, De-Ping, Wang, Mei-Yue, Li, Yong-Mei, Shu, Wen, Cui, Wen, Jiang, Fang-Ying, Zhou, Xin, Wang, Wen-Ming, Cao, Ji-Min
• Format: Article
• Language: English
• Subjects: Adenosine triphosphatase; Analysis; ATP hydrolysis; Binding sites; Biopharmaceutics; Conformation; Crystal structure; Crystals; Dengue fever; DNA helicase; Double-stranded RNA; Drug development; Drug therapy; Encephalitis; Enzymatic activity; Genomes; Genomics; Health aspects; Hydrolysis; Ilheus virus; Infections; Molecular docking; Mutagenesis; NS3 helicase; Proteins; RNA; RNA helicase; Structure; Suramin; Suramin sodium; Triphosphatase; Unwinding; Vaccines; West Nile virus; Zika virus
• ISSN: 2045-3701; 2045-3701
• DOI: 10.1186/s13578-022-00777-8

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 5'-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. We determined the crystal structure of the ILHV helicase at 1.75-Å resolution. We then conducted molecular docking of ATP-Mn 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/Mn . 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. 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.