Antiviral Approaches against Influenza Virus

Abstract

Preventing and controlling influenza virus infection remains a global public health challenge, as it causes seasonal epidemics to unexpected pandemics. These infections are responsible for high morbidity, mortality, and substantial economic impact. Vaccines are the prophylaxis mainstay in the fight against influenza. However, vaccination fails to confer complete protection due to inadequate vaccination coverages, vaccine shortages, and mismatches with circulating strains. Antivirals represent an important prophylactic and therapeutic measure to reduce influenza-associated morbidity and mortality, particularly in high-risk populations. Here, we review current FDA-approved influenza antivirals with their mechanisms of action, and different viral- and host-directed influenza antiviral approaches, including immunomodulatory interventions in clinical development. Furthermore, we also illustrate the potential utility of machine learning in developing next-generation antivirals against influenza.

Keywords: antiviral agents; drug resistance mechanisms; influenza; machine learning; monoclonal antibodies.

FIG 1

Schematics showing the life cycle of the influenza virus and sites of action of anti-influenza drugs. Influenza virus enters the cell by attaching to the epithelial cell surface by binding the viral hemagglutinin (HA) to sialic acid receptors expressed on the surface of host cells. Once the virus is internalized through endocytosis and fusion, the viral M2 protein forms a channel facilitating the release of the viral genome in the cytoplasm. The viral RNPs are imported into the nucleus, where they undergo the process of cap snatching, as viral RNAP lacks capping abilities. Further, it is replicated and transcribed into mRNA to facilitate the viral protein expression and participate in synthesizing the genomic RNA for incorporation into new progeny viruses. The release of new virus particles to the extracellular milieu is promoted by the viral neuraminidase (NA). Steps at which different antiviral drugs target the virus life cycle are shown in blue boxes. RNA polymerase (RNAP) inhibitors either inhibit the RNA replication or cap-snatching properties of RNAP. The amantadine class of drugs blocks the internalization and uncoating of the virus. However, neuraminidase inhibitors prevent viruses from budding and dispersing. Similarly, as indicated in the figure, mAb and small-molecule inhibitors also potentially inhibit the entry of the virus. Drugs in clinical trials are denoted by asterisk.

FIG 2

Host innate immune sensing of the influenza virus by RIG-I-like receptors (RLRs) and Toll-like receptors (TLRs). The cytosolic and endosomal RNA sensors, RLRs and TLRs, can detect genomic RNA, dsRNA, and small RNA molecules produced during viral replication. An activated RLR, RIG-I, undergoes a conformational change that allows the RLRs to recruit other proteins and trigger the IFN-signaling pathway. On the other hand, TLR3 and TLR7/8 initiate the antiviral IFN program by recruiting the signal adaptor molecules that subsequently activate downstream kinases and transcription factors to elicit the production of the IFNs and proinflammatory cytokines. Agonists and inducers as potent stimulators of the innate antiviral response in pipeline as antiviral drugs are indicated.

FIG 3

Structures of FDA-approved antivirals for influenza. (A) Amantadine (IUPAC name, adamantan-1-amine). (B) Rimantadine (IUPAC name, 1-(1-adamantyl)ethanamine). (C) Oseltamivir (IUPAC name, ethyl (3R,4R,5S)-4-acetamido-5-amino-3-pentan-3-yloxycyclohexene-1-carboxylate). (D) Zanamivir (IUPAC name, (2R,3R,4S)-3-acetamido-4-(diaminomethylideneamino)-2-[(1R,2R)-1,2,3-trihydroxypropyl]-3,4-dihydro-2H-pyran-6-carboxylic acid). (E) Peramivir (IUPAC name, (1S,2S,3S,4R)-3-[(1S)-1-acetamido-2-ethylbutyl]-4-(diaminomethylideneamino)-2-hydroxycyclopentane-1-carboxylic acid). (F) Baloxavir marboxil (IUPAC name, [(3R)-2-[(11S)-7,8-difluoro-6,11-dihydrobenzo[c][1]benzothiepin-11-yl]-9,12-dioxo-5-oxa-1,2,8-triazatricyclo[8.4.0.03,8]tetradeca-10,13-dien-11-yl]oxymethyl methyl carbonate).

FIG 4

Solved structures of IAV M2 wild type (PDB accession no. 6BKK) with Amantadine bound (left) and the Ser31Asn mutant (PDB accession no. 6MJH), which blocks Amantadine binding (right). The top left structure depicts the IAV M2 wild type (orange) from a top-down perspective, i.e., looking through the transmembrane channel. The Ser31 residues from all four chains in the quaternary structure interact with the bound Amantadine (green). The bottom left vignette depicts a 90°rotation of the structure to show the overall structural geometry of the wild-type IAV M2. The top right structure represents the Ser31Asn mutant IAV M2, which blocks Amantadine binding. The asparagines from each chain interact with one another to cause a structural change to the protein, which prevents the Amantadine to bind yet maintains protein function. The Ser31Asn mutation in the IAV M2 protein renders the antiviral Amantadine ineffective.

FIG 5

N1 neuraminidase (NA) wild type (PDB accession no. 2HU0) with bound Oseltamivir (left) and NA H274Y mutant (PDB accession no. 3CL0) with bound Oseltamivir (right). The left structure shows Oseltamivir (green) firmly bound to the NA wild-type protein (orange) through interactions with numerous residues, including Arg224, Glu276, Asn294, Tyr406, Arg371, and Arg292. The right structure shows the H274Y mutant, which results in a modified binding pocket. While the residue at 274 does not directly interact with the bound antiviral molecule, the mutation from histidine to tyrosine negatively affects the binding affinity of the drug through changes in the overall binding pocket, as seen by the reduced number of interactions on the right. The H274Y mutation in the NA protein renders the antiviral Oseltamivir less effective.

FIG 6

Polymerase acidic (PA) protein wild type (PDB accession no. 6FS6) bound with Baloxavir (left) and PA Ile38Thr mutant (PDB accession no. 6FS7) bound with Baloxavir (right). The left structure depicts the binding mode of Baloxavir (green) in the binding pocket of the wild-type PA protein (orange). The right structure shows Baloxavir bound to the mutant PA protein, where the Threonine does not interact with the Baloxavir, reducing the binding affinity of the antiviral to the mutated binding pocket. In addition, the I38T mutation in the PA protein renders the antiviral Baloxavir less effective.

FIG 7

Structures of influenza antivirals in clinical trials. (A) Laninamivir (IUPAC name, (2R,3R,4S)-3-acetamido-4-(diaminomethylideneamino)-2-[(1R,2R)-2,3-dihydroxy-1-methoxypropyl]-3,4-dihydro-2H-pyran-6-carboxylic acid) and its prodrug (CS-8958). (B) Favipiravir (IUPAC name, 5-fluoro-2-oxo-1H-pyrazine-3-carboxamide). (C) Pimodivir (IUPAC name, (2S,3S)-3-[[5-fluoro-2-(5-fluoro-1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl]amino]bicyclo[2.2.2]octane-2-carboxylic acid). (D) Polymerase basic protein 2 (PB2) wild type (PDB accession no. 7AS0) bound with pimodivir (JNJ-63623872). This structure depicts the strong binding mode of the antiviral pimodivir (green) in the binding pocket of PB2 (orange). Studying mutant variations of the residues in direct contact with pimodivir could be informative as to possible escape mutants for this investigational therapeutic. (E) Enisamium (IUPAC name, N-benzyl-1-methylpyridin-1-ium-4-carboxamide) and its active metabolite. (F) Arbidol (IUPAC name, ethyl 6-bromo-4-[(dimethylamino)methyl]-5-hydroxy-1-methyl-2-(phenylsulfanylmethyl)indole-3-carboxylate. (G) Flufirvitide 3 (IUPAC name, (2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-4-amino-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S,3S)-2-[[(2S)-6-amino-2-[[(2S,3R)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-amino-3-methylbutanoyl]amino]-4-carboxybutanoyl]amino]-3-carboxypropanoyl]amino]-3-hydroxybutanoyl]amino]hexanoyl]amino]-3-methylpentanoyl]amino]-3-carboxypropanoyl]amino]-4-methylpentanoyl]amino]-3-(1H-indol-3-yl)propanoyl]amino]-3-hydroxypropanoyl]amino]-3-(4-hydroxyphenyl)propanoyl]amino]-4-oxobutanoyl]amino]propanoyl]amino]-4-carboxybutanoyl]amino]-4-methylpentanoyl]amino]-4-methylpentanoic acid).