Development of small-molecule viral inhibitors targeting various stages of the life cycle of emerging and re-emerging viruses

Abstract

In recent years, unexpected outbreaks of infectious diseases caused by emerging and re-emerging viruses have become more frequent, which is possibly due to environmental changes. These outbreaks result in the loss of life and economic hardship. Vaccines and therapeutics should be developed for the prevention and treatment of infectious diseases. In this review, we summarize and discuss the latest progress in the development of small-molecule viral inhibitors against highly pathogenic coronaviruses, including severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus, Ebola virus, and Zika virus. These viruses can interfere with the specific steps of viral life cycle by blocking the binding between virus and host cells, disrupting viral endocytosis, disturbing membrane fusion, and interrupting viral RNA replication and translation, thereby demonstrating potent therapeutic effect against various emerging and re-emerging viruses. We also discuss some general strategies for developing small-molecule viral inhibitors.

Keywords

emerging and re-emerging viruses / small-molecule inhibitor / coronavirus / Ebola virus / Zika virus / life cycle

1 Introduction

In recent years, increasing outbreaks of emerging and re-emerging virus diseases have threatened human public health and economic stability worldwide. These epidemics are possibly caused by anthropogenic, social, and behavioral changes [1].

In the late 2002 and early 2003, many patients with acute respiratory disease symptoms in Guangdong Province of China were infected with a new coronavirus called severe acute respiratory syndrome coronavirus (SARS-CoV) [2]. This virus spread rapidly in over 27 countries and causes over 8000 cases of SARS, which results in nearly 800 deaths (~10% case fatality rate). In 2012, another new coronavirus, named Middle East respiratory syndrome coronavirus (MERS-CoV), also spread throughout 27 countries, which results in 2029 confirmed cases and 704 deaths (~35% case fatality rate) [3–5]. In 2014–2016, the latest outbreak of Ebola virus (EBOV) disease (EVD) occurred in West Africa, with 28 646 EBOV-infected cases and 11 323 EVD-related deaths (case fatality rate of approximately 50%) [6]. Finally, starting from 2015, Zika virus (ZIKV) initially causes a local outbreak in Brazil and quickly spread to 84 countries and areas in Africa, the United States, Asia, and the Pacific Rim [7]. ZIKV infection can harm the human nervous system and male reproductive system [8–10], and it may cause the development of microcephaly in fetuses of ZIKV-infected pregnant women [11–13].

With increasing globalization, many emerging and re-emerging viral infectious diseases have been reported worldwide, thereby highlighting the importance of developing effective vaccines and therapeutics for the prevention and treatment of these infectious diseases.

Most antiviral drugs are small-molecule viral inhibitors targeting various stages of the viral life cycle [14]. For example, anti-HIV drugs inhibit viral infection by targeting viral proteins functioning at different stages of HIV replication, such as surface glycoprotein (GP), reverse transcriptase, integrase, and protease. Small-molecule viral inhibitors can be produced on a large scale and applied to considerable populations with lower cost than that of antibody-based drugs. Their high thermostability makes them easy to store and transport when used in tropical and subtropical areas. These inhibitors can also be taken orally, which is the most acceptable administration route for small-molecule viral inhibitors.

This review summarizes the advances in research and development of small-molecule viral inhibitors against emerging and re-emerging viruses, including SARS-CoV, MERS-CoV, EBOV, and ZIKV.

2 Research and development of small-molecule viral inhibitors against emerging and re-emerging viruses

2.1 Small-molecule viral inhibitors against SARS-CoV and MERS-CoV

Both SARS-CoV and MERS-CoV belong to coronaviruses, which are enveloped viruses consisting of single-stranded positive RNA that encodes nonstructural and structural proteins, including spike (S), envelope (E), membrane, and nucleocapsid proteins [15].

SARS-CoV attaches to the target cell through binding between the receptor-binding domain (RBD) in the S1 subunit of S protein and the cellular receptor angiotensin-converting enzyme 2 (ACE2) on the target cell [16]. This coronavirus enters the target cell mainly via the endosomal pathway [17]. After endocytosis, S protein changes conformation under acidic environment, which results in the formation of a six-helix bundle (6-HB) fusion core [18,19]. Afterward, the viral genome RNA is released through the fusion pore into the cytoplasm for replication [20]. Finally, the progeny virions are released by exocytosis. MERS-CoV binds to the target cell via interaction of its RBD with its cellular receptor, namely, dipeptidyl peptidase 4 (hDPP4) [21], and subsequently enters the cell mainly through plasma membrane fusion [22]. The life cycles of SARS-CoV and MERS-CoV are shown in Fig. 1.

A number of small-molecule viral inhibitors targeting different stages of the coronavirus life cycle, including both SARS-CoV and MERS-CoV, were reported [23]. The first group of inhibitors consists of those with the ability to block the attachment of the virus to host cells. The RBD in the S1 subunit of S protein plays critical roles in the viral entry stage based on its specific binding with host receptors. Peptides, which overlap with either the SARS-CoV RBD region (termed as S_471-503 peptide) [24] or its binding motifs of ACE2 (termed peptide P6), inhibit the entry of SARS-CoV into Vero cells and that of pseudotyped virus into ACE2-expressing HeLa cells [25]. The second group of inhibitors consists of those that can disrupt viral endocytosis. Chlorpromazine, an inhibitor of endocytosis, was identified as a suppressor of MERS-CoV infection at micromolar concentration through the screening of 348 approved compounds [26]. The third group of inhibitors consists of those with the capacity to interrupt membrane fusion. Tetra-O-galloyl-b-D-glucose blocks SARS-CoV infection by binding with the S2 domain of S protein, which suggests that it possibly hinders virus–cell fusion [27]. The peptides overlapping the heptad repeat 2 (HR2) domain in S2 domain of S protein inhibit coronavirus infection at a micromolar level through interrupting the formation of a 6-HB. For instance, CP-1 blocks SARS-CoV entry into Vero E6 cells [28], and HR2P inhibits MERS-CoV infection efficiently [18]. Intranasal application of HR2P-M2, the analog of HR2P, but with improved solubility and stability, could significantly reduce the titers of MERS-CoV in the lung of Ad5-hDPP4-transduced mice [29,30]. Peptide P9, which is derived from mouse b-defensin-4, could enter into cells, along with virions, to prevent endosomal acidification, thereby obstructing the membrane fusion of SARS-CoV and MERS-CoV [31]. ADS-J1 penetrates into the deep pocket of HR1 to interfere with interactions between HR1 and HR2 of coronavirus by hydrophobic force and consequently inhibit the entry of pseudotyped SARS-CoV and MERS-CoV [32,33]. Given that cathepsin L (CatL) facilitates the conformational changes of S protein in endosomes with low pH, CatL inhibitors, such as oxocarbazate and E-64-D, are effective in inhibiting coronavirus infection [34–36]. The fourth group of inhibitors includes those that can interrupt viral RNA replication and translation. Small interfering RNA (siRNA), which aims to silence the leader sequence of SARS-CoV, reduces the mRNA abundance and consequently suppresses viral replication in Vero E6 cells [37]. Furthermore, siSC2–5, which is siRNA duplexes directed against both S protein-coding and the ORF1b region of SARS-CoV, could reduce viral copies in the respiratory tract and relieve the symptoms of SARS-CoV-infected rhesus macaques [38]. Ribavirin, a nucleoside analog, can suppress MERS-CoV infection in vitro [39]. SSYA10-001, the helicase nsp13 inhibitor, blocks the replication of SARS-CoV and MERS-CoV [40]. Some coronavirus protease inhibitors, such as the compound 5c, can also suppress viral replication [41,42]. The fifth group of inhibitors includes those with undefined mechanism of action. According to high-throughput screening of FDA drug libraries, some clinically used drugs, including estrogen receptor inhibitors (tamoxifen citrate and toremifene citrate) and DNA metabolism inhibitor (gemcitabine hydrochloride), display significant antiviral effects with undefined mechanism [36]. Further studies on their mechanisms of action against SARS-CoV and MERS-CoV infection and potential repurposing using the described approaches are warranted. Inhibitors of SARS-CoV and MERS-CoV are shown in Table 1 and Fig. 1.

2.2 Small-molecule viral inhibitors against EBOV

EBOV is a negative-sense single-stranded enveloped RNA virus with approximately 19 kb genome, which encodes seven structural proteins, including two GPs, four virion proteins (VPs), one nucleoprotein (NP), and one nonstructural protein, namely, RNA-dependent RNA polymerase (RdRp) (L protein) [43]. Similar to other filoviruses, EBOV is a viral pathogen causing hemorrhagic fever and other EVDs with high mortality [44]. The recent epidemics of EVD in West Africa have claimed many lives, thereby highlighting the importance of developing anti-EBOV therapeutics.

The entry of EBOV into the host cell, which is the first critical step in its life cycle, is initiated by the interaction between viral surface protein (GP1) and receptors on the host cell, such as T cell immunoglobulin and mucin domain 1 (TIM-1). When this virus attaches to the cell surface, it will be internalized into endosome with enclosed acidic environment [45]. Within this acidic compartment, GP1 binds to Niemann–Pick C1 (NPC1), which is cleaved by the proteases CatL and CatB, and triggers membrane fusion. Afterward, the viral RNA genome is released into the cytoplasm of host cell for replication [46]. The host’s metabolic pathway is utilized for viral replication and transcription, where viral genome and NP, VP35, VP30, and L protein participate [47–49]. Final processing of assembly and budding allow newly infectious virions to invade the neighboring cell. These life cycle steps are attractive targets for the development of therapeutic agents against EBOV infection (Fig. 2).

A number of small-molecule viral inhibitor-based anti-EBOV drug candidates targeting different stages of the viral life cycle are under preclinical and clinical development [50,51]. First, inhibitors can disrupt viral endocytosis. Macropinocytosis is the primary endocytic pathway for internalizing EBOV, demanding equilibria of diverse ions both inside and outside the cell. Amiloride and its derivatives, such as 5-(N-ethyl-N-isopropyl) amiloride, can disturb such balance to inhibit the entry of EBOV into host cells [52,53]. Second, inhibitors can also disturb membrane fusion. LJ001, a broad-spectrum antiviral compound against enveloped viruses, restricts the entry of EBOV by intercalating into viral membranes to disrupt the critical step of membrane fusion [54]. Moreover, modified anti-EBOV peptides (e.g., Tat-Ebo), which consists of residues 610-633 of EBOV GP2 and the arginine-rich sequence from HIV-1 Tat spaced by a Gly-Ser-Gly linker, can accumulate in endosome and block 6-HB formation [55]. Oxocarbazate, the inhibitor of CatL, which is responsible for processing GP, blocks pseudotyped EBOV from infecting 293T cells [35]. Some viral inhibitors discovered through high-throughput screening, such as compound 7, can bind to a hydrophobic pocket in GP of EBOV [56]. Seventeen cationic amphiphilic drugs identified from FDA-approved drug libraries show considerably potent anti-EBOV activity by targeting NPC1 [57]. For example, bepridil and sertraline could block the membrane fusion step and protect C57BL/6 mice against EBOV infection [58]. Third, inhibitors can interrupt viral RNA replication and translation. Favipiravir (T-705), a broad-spectrum inhibitor of RNA polymerase, suppresses EBOV replication in Vero E6 cells and protects type I interferon receptor-deficient mice from EBOV infection [59,60]. The adenosine analog BCX4430 could suppress infections and confer protection in a rodent model against EBOV and other filoviruses [61]. Atovaquone and azacitidine, which disrupt the biosynthesis of pyrimidine, and mycophenolate mofetil, which deletes the guanosine triphosphate pool, could all inhibit EBOV infection [58,62–64]. In addition, siRNA acts as a kind of inhibitor that can hinder mRNA translation. AVI-6002, a mixture of phosphorodiamidate morpholino oligomers (PMOs), and TKM-Ebola interfere with VP24 and VP35 mRNA to suppress infection [65,66]. Fourth, some inhibitors exhibit undefined antiviral mechanisms. Strophanthin, which is typically used for heart diseases, displays anti-EBOV effect in drug screens [58]. These anti-EBOV drugs acting on different stages of viral life cycle are shown in Table 2 and Fig. 2.

2.3 Small-molecule viral inhibitors against ZIKV

ZIKV, a mosquito-borne flavivirus, is a single-stranded positive RNA virus with approximately 10 kb genome, which contains an open reading frame that encodes three structural proteins and seven nonstructural proteins [67]. After its isolation from a rhesus macaque, ZIKV is ignored for a long time, until intermittent outbreaks occur in the Pacific islands and the United States. The recent global pandemic that began in Brazil has attracted extensive attention from WHO due to its possible association with neurological complications [8–13]. Despite the progress in targeting the underlying molecular mechanisms of this pathogen, no anti-ZIKV drug has been approved for clinical use to date.

The first step of ZIKV’s life cycle is its attachment to the host cell mediated by interaction between the virus and specific receptor on the host cell, such as AXL and its ligand Gas6 [68]. After internalization through clathrin-dependent endocytosis, the virus undergoes uncoating, which is induced by the special acidic environment of the endosome, where the fusion between viral envelope and the endosomal membrane is facilitated by the transformation of viral envelope proteins into a fusion-active state [69]. Subsequently, the viral RNA genome is released into the cytoplasm for replication. The replication complex is formed by viral nonstructural proteins (NS3 and NS5) and probably some host proteins; this complex also assists with the synthesis of the viral genomic RNA [70,71]. The capsid protein, a viral structural protein, combines with the RNA genome to form the nucleocapsid core. Viral assembly occurs in the endoplasmic reticulum where the budding obtains a lipid envelope; the progeny virus is finally released through the exocytotic pathway [69,72]. The life cycle of ZIKV is shown in Fig. 3.

Following the outbreak of ZIKV epidemic, a wide variety of small-molecule viral inhibitors were reported. The first category of inhibitors blocks the binding between virus and host cells. We found that a peptide-based anti-ZIKV inhibitor (Z2), derived from the stem region of E protein, is highly effective in inhibiting ZIKV infection in type I or type I/II interferon receptor-deficient mice; this inhibitor also prevents the vertical transmission of ZIKV from pregnant C57BL/6 mice to their fetuses through its interaction with viral surface envelope (E) proteins to form a membrane pore and disrupt the integrity of the viral membrane [73]. ZINC33683341, a small-molecule inhibitor with preferential binding affinity to ZIKV E protein, can reduce virus titer at the noncytotoxic concentration of 100 μmol/L using an in vitro assay [74]. Curcumin inhibits the infection of ZIKV and other enveloped viruses by blocking interactions between virus and host cells [75]. The second category of inhibitors can disrupt the viral endocytosis process. Nanchangmycin, a natural bacterial product, inhibits ZIKV infection in vitro through blocking clathrin-mediated endocytosis [76]. The third category of inhibitors can disturb membrane fusion. Chloroquine and niclosamide, anthelmintic medications that are effective against cestodes, inhibit the acidification of endosome and the low pH-dependent conformational changes of E protein that is necessary for membrane fusion. Both chloroquine and niclosamide can block ZIKV infection through in vitro experiments [77,78]. Moreover, 25-hydroxycholesterol can inhibit ZIKV infection in both in vitro and in vivo assays, especially protecting rhesus monkeys against infection by reducing viremia duration and shortening viral shedding [79]. The fourth category of inhibitors can interrupt viral RNA replication and translation. NS2B and NS3 form a viral protease complex that is essential for ZIKV replication. Ten inhibitors of HCV NS3/NS4A can inhibit ZIKV replication based on the structural similarity between ZIKV NS2B/NS3 and HCV NS3/NS4A [80]. Furthermore, NS3 shows an NTP-dependent RNA helicase domain at the C terminus for unwinding RNA, and NS5 contains domains of methyltransferase and RdRp to assist the replication process, thereby providing attractive targets for designing ZIKV therapies [81,82]. Sofosbuvir and DMB213, inhibitors of ZIKV RdRp, suppress viral replication in Huh7 cells [83]. Recently, temoporfin was demonstrated to inhibit ZIKV infection both in vitro and in vivo by disturbing polyprotein processing through blocking the interactions between NS2B and NS3 [84]. Additionally, the polymerase inhibitor 7-deaza-2´-C-methyladenosine inhibits in vitro ZIKV replication efficiently and relieves the viremia of infected AG129 mice [85]. Another class of antiviral agents consists of nucleoside analogs that can terminate viral RNA synthesis. The 2´-C-methylated nucleosides and derivatives can inhibit ZIKV replication in cellular assays in a dose-dependent manner [86]. NITD008, an adenosine analog, also protects mice from ZIKV infection [87]. To differentiate between viral translation and RNA synthesis, ZIKV replicon systems were established for the screening and characterization of viral replication inhibitors [88]. The fifth category of inhibitors consists of those without defined mechanism of action. To control ZIKV epidemics, researchers carried out high-throughput screening of many compounds for ZIKV therapies in multidimension, including inhibitors of ZIKV infection in placental trophoblast cells and neuroprotective agents [76]. Emricasan, an inhibitor of caspase-3 that is essential in the pathogenicity of ZIKV, relieves the neural damage caused by ZIKV [78]. A new mouse model recapitulates the adulthood sequelae of congenital ZIKV infection, which enables the screening and evaluation of small-molecule drugs that repair the impaired nervous system of fetuses or directly suppress viral replication to improve prognosis [89,90]. Potential therapies according to life cycle are shown in Table 3 and Fig. 3.

3 General strategies for developing small-molecule viral inhibitors

We have reviewed relevant inhibitors against representative viruses in the context of viral life cycle. On the basis of this summary, we can extrapolate some general strategies that may guide further research and development of small-molecule viral inhibitors.

Viral entry into host cell is the first stage for viral infections. Hence, this stage is the most attractive target for designing and developing inhibitors against various viruses [90]. For all of the enveloped viruses with class I fusion protein, such as HIV, SARS-CoV, MERS-CoV, and EBOV, 6-HB formation is required to facilitate the fusion between virus and cell membrane. Small molecules that can block the formation of 6-HB are generally effective in inhibiting the infection of such viruses [91]. Since the first discovery of the potent HIV fusion inhibitory peptide SJ-2176 and clinical application of T20 for treatment of HIV infection [92,93], many viral fusion inhibitory peptides that can block the formation of 6-HB, such as HR2P and HR2P-M2 peptides against MERS-CoV and Tat-Ebo peptide against EBOV [18,30,55], have been reported. Recently, we developed a new tripartite model for designing viral fusion inhibitory peptides with improved efficacy to disturb the formation of 6-HB [94]. This model can be adapted for designing viral inhibitors against other enveloped viruses, including those that may emerge in the future. Another general strategy is to suppress the viral endocytosis pathway utilized by many enveloped viruses. For example, we have reviewed small molecules that can interfere with clathrin-mediated endocytosis and/or caveolin-mediated endocytosis (e.g., chlorpromazine). We have also reviewed the compounds that can prevent the acidification of endosome and consequently inhibit the activities of host proteases in endosome critical for proteolysis and conformational change of viral envelope proteins during fusion between virus and endosome membrane. For example, chloroquine and CatL/CatB inhibitors fall into this category; these inhibitors generally suppress the infection of viruses internalized through endocytosis. The inhibitors against common cellular pathways utilized by different viruses can suppress virus infections with broad spectrum. However, they target host proteins, instead of specific viral proteins, which may raise the concern about side effects because of their nonspecificity. Therefore, further extensive in vitro experiments and in vivo animal studies should be conducted to evaluate the potential toxicity of drug candidates targeting host proteins. In addition, small molecules, such as nucleoside analogs (e.g., BCX4430, favipiravir, 2´-C-methylated nucleoside, and NITD008), siRNAs (e.g., TKM-Ebola), and PMOs (e.g., AVI-6002), can inhibit the activity of viral RdRp or target viral RNA and interfere with viral RNA replication, transcription, and translation. Consequently, the RNA virus infection is suppressed. Finally, timely, effective therapies are available for emerging and re-emerging viruses through repurposing clinical small-molecule drugs. Taking the recent ZIKV epidemic as an example, both emricasan, a pan-caspase inhibitor, and niclosamide, an anthelmintic drug, can protect against ZIKV infection. These general strategies (Fig. 4) can be adapted for the development of small-molecule viral inhibitors against emerging and re-emerging viruses that may cause future pandemics.

4 Conclusions

Most viruses utilize host cellular components to satisfy various physiological processes, including viral entry, genomic replication, and the assembly and budding of virions, thereby resulting in pathological damage to the host. Therefore, any key stage through the life cycle could be a potential target for developing small-molecule viral inhibitors. Upon the emergence or re-emergence of viral outbreak, researchers use high-throughput screening approaches to determine rapidly effective small-molecule viral inhibitors and pharmacological compounds for clinical treatment. The research and development stages of small molecules are relatively inexpensive. Small-molecule viral inhibitors are also convenient for oral administration. Generally, therapeutic small molecules are superior to other antiviral therapies, such as antibodies. Hence, their use is widespread in both developing and developed countries. The antiviral activities of small-molecule viral inhibitors are typically not as potent as those of antibodies, and small molecules exhibit shorter half-life in vivo than those of antibodies. Their relatively high toxicity also restricts their use, especially in pregnant women and neonates infected with ZIKV. To overcome this problem, repurposing of approved clinically safe drugs in pregnant women is an advisable alternative solution.

We have observed a consistent lag time between the emergence or re-emergence of outbreaks and the development of effective antiviral drugs. In addition, many large pharmaceutical companies are reluctant to develop antiviral drugs against viruses with potential to cause short-term epidemic because of their unpredictable market values. This challenge may be addressed with the development of broad-spectrum, cross-reactive drugs, which may represent an important future trend.

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