Structure-Based Design of Antivirals against Envelope Glycoprotein of Dengue Virus

Abstract

Dengue virus (DENV) presents a significant threat to global public health with more than 500,000 hospitalizations and 25,000 deaths annually. Currently, there is no clinically approved antiviral drug to treat DENV infection. The envelope (E) glycoprotein of DENV is a promising target for drug discovery as the E protein is important for viral attachment and fusion. Understanding the structure and function of DENV E protein has led to the exploration of structure-based drug discovery of antiviral compounds and peptides against DENV infections. This review summarizes the structural information of the DENV E protein with regards to DENV attachment and fusion. The information enables the development of antiviral agents through structure-based approaches. In addition, this review compares the potency of antivirals targeting the E protein with the antivirals targeting DENV multifunctional enzymes, repurposed drugs and clinically approved antiviral drugs. None of the current DENV antiviral candidates possess potency similar to the approved antiviral drugs which indicates that more efforts and resources must be invested before an effective DENV drug materializes.

Keywords: antiviral; dengue virus; envelope glycoprotein; structural biology.

Figure 1

Schematic representation of the DENV genome and the encoded proteins.

Figure 2

The envelope (E) glycoprotein. (A) The discontinuous domains of dengue E protein. Domain I (EDI) is in red, domain II (EDII) is in yellow and domain III (EDIII) is in blue. The stem region and the transmembrane (TM) domain spanning amino acids 394–495 are represented in black and white, respectively. (B) The E protein dimer in the mature DENV2 virion and in an environment with neutral pH (PDB ID: 1OAM). (C) The structure of trimeric DENV1 E protein in its postfusion conformation. The domains have rotated and shifted with EDIII undergoes the most significant rearrangement with 70° folding towards EDI and EDII (PDB ID: 4GSX). The fusion loop is buried at the dimer interface in mature virion. In contrast, the fusion loop is exposed at the tip of the E protein trimer in immature virion and during fusion.

Figure 3

DENV attachment and fusion (PDB IDs: 1OAM and 4GSX). (A) Endocytic entry pathway of DENV. B-E) Proposed mechanism for DENV-host cell membrane fusion. The stem region of E protein is in white while the transmembrane anchor is in grey. The EDI, EDII and EDIII are in red, yellow and blue, respectively. (B) The binding of E protein to the receptor leads to the internalization of the DENV into an endosome. Reduced pH in the endosome causes the rearrangement of the E protein from dimer to trimer. (C) During the rearrangement, the tip of the EDII hinges outwards from the virion surface, allowing the fusion loop to be inserted into the cellular membrane to bridge cellular and viral membranes. (D) The bending and hemifusion of the membranes are mediated by the contacts made between EDIII-EDI and EDII-stem region. (E) Finally, the fusion loop makes contact with the transmembrane domain, completing membrane fusion and formation of pores. Figure 3A was modified from Hidari et. al. (2013) and Figure 3B-E was modified from Klein et. al. (2013) [92,93].

Figure 4

Locations of the amino acids postulated to be important for DENV2 attachment to the cells. The amino acids are shown as spheres in light grey and labelled. The EDI, EDII and EDIII are shown in red, yellow and blue, respectively (PDB ID: 1OAM). The majority of the amino acids that were implicated in DENV attachment to the cellular receptors are located in the EDIII.

Figure 5

Stem region interactions with the groove formed by adjacent EDIIs in the trimeric DENV1 E protein (PDB ID: 4GSX). EDI, EDII and EDIII are represented in red, yellow and blue, respectively. The amino acids of the stem region are represented as sticks and labelled. The key hydrophobic amino acids of the stem region including I398, M401 and F402 interacted with the hydrophobic pocket formed by L216, P217, L218 and M260 of the EDII [93]. The figure was modified from Klein et. al. (2013) [93].

Figure 6

Structure-based dengue antiviral design. There are two approaches in structure-based antiviral design which are the structure-based ligand screening and the de novo ligand design. (A) In the structure-based ligand screening (virtual screening), molecular docking will be performed to identify compounds that can bind to the target binding site (circled). Thereafter, the compound hits will be assessed through in vitro assays such as antiviral assay. (B) In the de novo ligand design, compounds will be designed computationally to fit the target binding site (circled). Thereafter, in vitro assays will be performed to evaluate the antiviral activities of the compounds. Both approaches often require structure-based optimization to improve druggability and efficacy.

Figure 7

The superimposition of the structures of DENV2 E protein in the absence (ribbon) and presence (tube) of a detergent molecule. (A–C) The detergent molecules β-OG are shown in black. The domains of the E protein were labelled as EDI, EDII and EDIII, and colored as red, yellow and blue, respectively. The fusion loop is indicated by an arrow and labelled. The kl hairpin is labelled. The key difference between the two structures is the position of the kl hairpin. (B) In the presence of detergent, the kl hairpin will open up the hydrophobic pocket under the kl hairpin and the detergent can bind to the hydrophobic pocket (PDB ID: 1OAM). (C) In the absence of detergent, the kl hairpin is in the “closed position” and the hydrophobic amino acids are buried in the pocket (PDB ID: 1OAN). The figure was modified from Modis et. al. (2003) [85].