The Crystal Structure of Zika Virus Helicase: Insight for Antiviral Drug Design

Abstract

Background. Initially isolated in 1947 from the Zika forest in Uganda, the Zika virus (ZIKV) has recently caught global attention by causing unprecedented epidemics in South and Central America and the Caribbean. Neonatal microcephaly associated with ZIKV infection led to the announcement of a Public Health Emergency of International Concern by the World Health Organization (WHO). Unfortunately, no specific vaccine or medication is currently available to treat ZIKV infection or prevent devastating congenital abnormality. Methods. The ZIKV helicase, which plays a pivotal role in unwinding RNA genome and promoting viral replication, is an attractive target for therapy. We determined the crystal structure for ZIKV helicase at 1.8- resolution. We further characterized its enzymatic activity of unwinding RNA substrate. Results. The tertiary structure of ZIKV helicase is composed of three domains, of around 130-160 amino acid residues each. Structural analysis, consistent with biochemical results, revealed a triphosphate pocket for nonspecific hydrolysis of nucleoside triphosphate to support helicase activity. We also analyzed the structural diversity of the conformation of such triphosphate pocket among different flaviviruses. A positively charged tunnel was identified in the ZIKV helicase, potentially responsible for the accommodation of RNA. Superposition of ZIKV helicase to Dengue virus type 4 helicase bound with a 12-mer ssRNA generated an important atomic model to analyze the pattern of nucleic acid binding, which provided structural insight into the RNA unwinding activity of ZIKV helicase. A series of small molecule inhibitors were rationally designed based on the crystal structure. We are currently testing their efficacy in enzymatic inhibition. Conclusion. The recent outbreak of ZIKV and its association with fetal abnormalities including congenital microcephaly has caused global public health emergency. Here we present the high-resolution 3D structure of ZIKV helicase, which represents an important molecular target. The structure has revealed critical substrate-binding pockets for rational antiviral drug design. Pharmaceutical development of inhibitors targeting the RNA binding tunnel and the pivotal regulatory regions would be a plausible strategy for innovative anti-ZIKV therapies.