Structure-activity relationship optimization for lassa virus fusion inhibitors targeting the transmembrane domain of GP2
Lassa virus (LASV) belongs to the Mammarenavirus genus, Arenaviridae family. Arenaviruses are classified into two main groups—Old World (OW) and New World (NW)—based on virus genetics, serology, antigenic properties and geographical relationships. The OW LASV and Lujo virus (LUJV), as well as NW Junín virus (JUNV), Machupo virus (MACV), Guanarito virus (GTOV), Sabiá virus (SABV) and Chapare virus (CHAPV), are known to cause severe hemorrhagic fever and are listed as biosafety level 4 (BSL-4) agents. The arenavirus glycoprotein complex (GPC) contains three subunits—the retained stable-signal peptide (SSP), the receptor-binding subunit GP1, and the membrane fusion subunit GP2 (Lenz et al., 2001). Notably, the proximate external membrane region and TM of GP2, together with the ectodomain loop and TMs of SSP, form an SSP-GP2 interface, playing essential roles in regulating membrane fusion, and providing targets for distinct fusion inhibitors (Larson et al., 2008; Lee et al., 2008; York et al., 2008; York and Nunberg, 2009; Thomas et al., 2011; Burgeson et al., 2013a; Shankar et al., 2016; Wang et al., 2016; Wang et al., 2018).
To identify the viral target of the compounds, we selected adaptive mutant viruses by serially passaging the replication-competent recombinant virus of LASV (LASVrv, VSV backbone with a genome containing LASV GPC) in the presence of 1 μmol/L of any of the compounds 21, 29, and 72, or 10 nmol/L of compound 57, respectively, which approximately corresponded to the IC90 values of each compound. Parallel passaging of LASVrv in dimethyl sulfoxide (DMSO) was used as a control. As a result, two non-synonymous substitutions—L428S and F446L—were obtained in the compound 21 and the compound 29, 57 and 72 treatment groups, respectively (Fig. 1C). We next investigated the sensitivity of the two single nonsynonymous mutant viruses, as well as the double-mutant virus, to all the four hit compounds. Remarkably, the L428S mutant also conferred resistance to compounds 29, 57 and 72, in which L428S showed a stronger resistance to compound 57 compared with the F446L mutant. Moreover, the combined mutant virus was completely insensitive to any compound even at the highest tested concentration, suggesting these compounds might share the same viral target(s), and the adaptive mutants selected by similar compounds might show overlapping resistance effects (Fig. 1D).
Since the parent compound, ST-161, possessed specific antiviral activity against LASV, we investigated whether the four hit compounds extended their antiviral activities to other pathogenic arenaviruses. As shown in Figure S2, compounds 21, 29 and 72 largely maintained LASV specificity. In contrast, compound 57 showed promising inhibitory effects on the entry of NW pathogenic viruses, with a sharp blockage on the entry of GTOVpv and MACVpv in a picomolar range, as well as CHAPVpv, JUNVpv and SABVpv in a nanomolar range, suggesting that the tert-butyl (t-Bu) moiety in compound 57 might broaden the antiviral spectrum of the backbone (Fig. 1E). Notably, t-Bu was previously used to modify the acylhydrazone scaffold of ST-161 and led to a three- to twelvefold- decrease in IC50 value (Burgeson et al., 2013a), suggesting that this bulky, lipophilic moiety might raise the accessibility of the inhibitors to the viral target embedded in the TM domains. Meanwhile, the addition of the t-Bu motif might contribute to the specific contacts and result in a high binding affinity with the viral target. Notably, all four hit compounds had little effect on the entry of the OW pathogenic viruses, LCMVpv and LUJVpv. Further, none of the four hit compounds could inhibit the entry of EBOVpv and MARVpv (Fig. S2). Moreover, compound 57 blocked NW GPC-mediated membrane fusion. As shown in Figure 1F, when treated with a 15-min pulse of acidified (pH 5.0) medium, GPCs of GTOV, SABV, MACV, CHAPV and JUNV led to an extensive membrane fusion, resulting in the disappearance of the cell boundaries and the essentially black view which caused by the dilution of the green fluorescence. Since all the NW pathogenic arenaviruses utilize TfR1 as the cell receptor, we further investigated the impact of compound 57 on the virus-receptor interaction. We observed that compound 57 did not down-regulate the cell surface expression of TfR1, and it had no effect on binding of NW pathogenic viruses (Fig. S3). These results indicated that the extended antiviral activity of compound 57 acts intrinsically via targeting the membrane fusion process.
As shown in Figure 2C, when treated with 1 µmol/L compound 29, those mutants caused a decrease in syncytium formation (that is, an increase of green puncta) were considered as the sensitive ones (green), while those unchanged mutants were judged as resistant ones (orange). Based on the distribution of those mutants, GP2 TM α-helix could be characterized as possessing distinct resistance (orange, sites d, a, b and e) and sensitive (green, sites f, c and g) sides (Fig. 2A). Of note, in the primary alanine scanning, L433A, L442A, I443A and S444A were found to act contrary to the resistance and sensitive side characteristics, in which L433A (site f) and S444A (site c) showed resistance to compound 29, while L442A (site a) and I443A (site b) were sensitive. To probe it, we individually mutated each residue into a similar residue. Remarkably, L433I and S444T rendered LASV GPC sensitive, while L442I conferred resistance to compound 29, which might be due to the effects of the similar side chains. I443L, however, maintained the sensitivity to compound 29. It has been reported that mutant A435I in JUNV GPC, the equivalent position to LASV I443, resulted in the resistance to fusion inhibitor ST-294 (York et al., 2008), suggesting that distinct fusion inhibitor might exclusively interact with special target(s) in the SSP-GP2 interface.
In this study, we conducted the SAR optimization of LASV specific fusion inhibitor ST-161, and found four hit compounds that retained the inhibitory effect against LASV GPC mediated membrane fusion, likely due to the effect on stabilization of the prefusion LASV GPC conformation (York et al., 2008; Thomas et al., 2011; Shankar et al., 2016). Especially, compound 57 could remarkably inhibit LASVpv infection at a picomolar range. Moreover, compound 57 extended its antiviral activities to NW pathogenic arenaviruses, in which the IC50 values of compound 57 against GTOVpv and MACVpv infection were three orders of magnitude less than those of ST-193 (Larson et al., 2008; Burgeson et al., 2013b; Dai et al., 2013), reaching a picomolar level. Selection and analysis of viruses resistant to the hit compounds revealed that the adaptive mutations were located in the transmembrane domain (TM) of GP2. Alanine substitution analysis indicated that one side of the GP2 TM helix regulates resistance to compound 29. Mutations in this side of the GPC made the virus resistant to compound 29, while mutations on the other side retained the sensitivity. Through our SAR study between the fusion inhibitor and GP2, we highlight the features involved in the regulation of sensitivity/resistance to fusion inhibitors and provide a platform for the design of entry inhibitors to combat arenavirus infections.
We thank the The Center for Instrumental Analysis and Metrology and the Core Facility and Technical Support, Wuhan Institute of Virology for providing technical assistance.
This work was supported by the National Key Research and Development Program of China (2018YFA0507204), the National Natural Sciences Foundation of China (Grant No. 31670165), the Open Research Fund Program of CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, and the Open Research Fund Program of Wuhan National Bio-Safety Level 4 Lab of CAS (NBL2017008), the Open Research Fund Program of the State Key Laboratory of Virology of China (2018IOV001).
Guangshun Zhang, Junyuan Cao, Yan Cai, Yang Liu, Yanli Li, Peilin Wang, Jiao Guo, Xiaoying Jia, Mengmeng Zhang, Gengfu Xiao, Yu Guo and Wei Wang declare that they have no conflict of interest.
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