Flavivirus: From Structure to Therapeutics Development

Abstract

Flaviviruses are still a hidden threat to global human safety, as we are reminded by recent reports of dengue virus infections in Singapore and African-lineage-like Zika virus infections in Brazil. Therapeutic drugs or vaccines for flavivirus infections are in urgent need but are not well developed. The Flaviviridae family comprises a large group of enveloped viruses with a single-strand RNA genome of positive polarity. The genome of flavivirus encodes ten proteins, and each of them plays a different and important role in viral infection. In this review, we briefly summarized the major information of flavivirus and further introduced some strategies for the design and development of vaccines and anti-flavivirus compound drugs based on the structure of the viral proteins. There is no doubt that in the past few years, studies of antiviral drugs have achieved solid progress based on better understanding of the flavivirus biology. However, currently, there are no fully effective antiviral drugs or vaccines for most flaviviruses. We hope that this review may provide useful information for future development of anti-flavivirus drugs and vaccines.

Keywords: drug target; epidemics; flavivirus; immunology; protein structure; vaccine.

Figure 1

(a) The long open reading fame (ORF) of flavivirus genome which encodes a polyprotein. The polyprotein is cleaved into 10 proteins by proteases. Capsid protein (C protein), pre-membrane protein (prM protein), and envelope protein (E protein) are structural proteins, whereas the remaining seven are non-structural proteins. There are cleavage sites between proteins, among which the sites indicated by brown arrows can be cleaved by viral proteases, and the sites indicated by blue arrows are the cleavage sites of host proteases. In addition, there is a cap structure at the 5-terminal. (b) Association of the structural proteins of flavivirus. There is a furinase site between prM protein and C protein. In the process of virus transportation to the Golgi body or after virus entry into the Golgi body, the prM is cleaved by furin at this furinase site in the host cell, making the virus particles mature and infectious.

Figure 2

The structures of capsid protein (C protein) and envelope protein (E protein). (a) The structure of the dimer of C protein of dengue virus (DENV; Protein Data Bank [PDB]: 1R6R DENV). (b) C protein tetramer. C protein is arranged in a symmetrical form of 2:2:2, forming a hydrophobic channel in the middle of the tetramer (PDB: 1SKF West Nile virus [WNV]). (c) The three domains of E protein; the detail of DIII is shown in the enlargement of the framed area. There is a flexible short chain between DII and DIII; the arrow indicates the conformational change of DIII towards DII during maturation (PDB: 1TG8 DENV).

Figure 3

The structure of non-structural protein 1 (NS1). (a) The dimer structure of the NS1 protein of Zika virus (ZIKV). Two NS1 monomers are combined in the head-to-head form to produce dimers of NS1, and the β chain is extended and tiled into a larger plane (Protein Data Bank [PDB]: 5IY3 ZIKV). (b) The domains of the NS1 dimer protein of West Nile virus (WNV). NS1 protein contains three structural units, namely β-roll, β-ladder, and wing, which are, respectively indicated in blue, orange, and yellow; each monomer has three glycosylation sites (red): asn130, asn175, and asn207 (PDB: 4O6C WNV). (c) An octapeptide sequence in the C-terminal of NS1 plays an important role in cleavage; thus, it can be used as a target of antiviral therapy. Arrows indicate potential therapeutic targets (PDB: 4O6C WNV).

Figure 4

The structures of non-structural protein 3 (NS3) and NS5 of flaviviruses. (a) NS3 protein structure of dengue virus (DENV; Protein Data Bank [PDB]: 2JLV). The gap between the three domains (indicated by three different colors) is the RNA-binding site, and the adenosine triphosphate (ATP)-binding site is between domains I and II (see the enlargement of the framed area). (b) NS3 of Zika virus (ZIKV) and DENV. The root mean square (RMS) of the two viruses is 1.43, indicating that they are very similar. According to this reason, some proteins of other flaviviruses are also similar, which is very helpful for structural development and vaccine design (PDB: 2JLR DENV; PDB: 5JRZ ZIKV). (c) In the methyltransferase (MTase) core of NS5, there is a binding site of S-adenosylmethionine (SAM) (green in the framed area, indicated by an arrow). This site is also termed AdoMet, and plays an important role in the RNA capping process. This site is wrapped in the hydrophobic pocket of the central split (PDB: 2WA2 NKV).

Figure 5

Anti-flavivirus compounds. (a) 4-(guanidinomethyl)-phenylacetyl-Arg-Tle-Arg-4-aminoboenzylamide (MI-1148) is a furin protease inhibitor which blocks the cracking of furin and weakens the toxicity of viral protein. (b) Compound 3 is an allosteric inhibitor which blocks the interaction between non-structural protein 2B (NS2B) and NS3. (c) ST-610 prevents adenosine triphosphate (ATP) hydrolysis in the cell culture of dengue virus (DENV). (d) Sinefungin is a natural product that potently inhibits the activity of flavivirus; however, like S-adenosylmethionine (SAM), it can produce cytotoxicity. The amino acids of flavivirus that interact with sinefungin are shown in the structure (PDB: 5KQS). (e) NSC12155 inhibits SAM by binding to the SAM cofactor site of the methyltransferase (MTase) (PDB: 5CUQ). (f) Compound 21 is a 2,6-diaminopurine derivative which inhibits the NS5 RNA-dependent RNA polymerase (RdRp) of DENV. (g) Compound 27 binds to the allosteric site of RdRp and inhibits the replication of dengue virus type 2 (DENV2) (Protein Data Bank [PDB]: 5K5M).