Rapid estimation of binding activity of influenza virus hemagglutinin to human and avian receptors

Avian influenza A H5N1 hemagglutinin protein models have distinct structural patterns re-occurring across the 1959-2023 strains

Influenza A H5N1 hemagglutinin (HA) plays a crucial role in viral pathogenesis and changes in the HA receptor binding domain (RBD) have been attributed to alterations in viral pathogenesis. Mutations often occur within the HA which in-turn results in HA structural changes that consequently contribute to protein evolution. However, the possible occurrence of mutations that results to reversion of the HA protein (going back to an ancestral protein conformation) which in-turn creates distinct HA structural patterns across the 1959-2023 H5N1 viral evolution has never been investigated. Here, we generated and verified the quality of the HA models, identified similar HA structural patterns, and elucidated the possible variations in HA RBD structural dynamics. Our results show that there are 7 distinct structural patterns occurring among the 1959-2023 H5N1 HA models which suggests that reversion of the HA protein putatively occurs during viral evolution. Similarly, we found that the HA RBD structural dynamics vary among the 7 distinct structural patterns possibly affecting viral pathogenesis.

Immunomodulatory effects of probiotic Lactobacillus casei on GM-CSF-adjuvanted influenza DNA vaccine

Aim: This study investigates the protective efficacy of influenza DNA vaccine combined with a granulocyte macrophage-colony stimulating factor (GM-CSF) adjuvant, and probiotic Lactobacillus casei, an oral immunomodulator, in a BALB/c mice. Materials & methods: The mice were immunized with HA1 DNA vaccine along with GM-CSF and probiotic twice within a one-week interval. Results: The results showed that both adjuvants exert a synergistic effect in enhancing the humoral and cellular immune responses of the DNA vaccine. This combination also deceased IL-6 and IL-17A levels in the lung homogenates. The protection patterns were closely associated with influenza virus-specific splenocyte proliferative and serum IgG antibody (Ab) responses. Conclusion: The Findings demonstrate L. casei modulate balanced Th1/Th2 immune responses toward HA1 DNA vaccine adjuvanted by GM-CSF.

Structural insights into the potential changes in receptor binding site found in the 1998-2018 influenza B/Yamagata hemagglutinin: A putative correlation between receptor binding site structural variability and seasonal infection

Influenza B virus has two distinct lineages (Victoria and Yamagata) and are associated with seasonal influenza epidemics that cause respiratory illness. Influenza B hemagglutinin (HA) is a major surface glycoprotein with the receptor-binding site (RBS) primarily involved in viral pathogenesis. Generally, influenza B exclusively infects the human population which would insinuate that the structural variability of the influenza B HA RBS rarely changes. However, to our knowledge, the potential impact of variations in the influenza B HA RBS structural variability was not fully elucidated. Throughout this study, we generated models from the transitioning (evolving viral lineage) 1998-2018 influenza B/Yamagata HA, verified the quality of each HA model, performed HA RBS structural variability measurements, superimposed varying HA models for comparison, and designed a phylogenetic tree network for further analyses. We found that measurements of the transitioning HA RBS structural variability were generally maintained and, similarly, measurements of the altered (years that differed from the evolving viral lineage, specifically 2003, 2007, 2017) HA RBS structural variability differed from the transitioning HA RBS. Moreover, we observed that the altered HA RBS structural variability favored the formation of a putative Y202-H191 hydrogen bond which we postulate may increase structural stability, thereby, allowing for a winter infection of the virus. Furthermore, we established that changes in HA RBS structural variability does not influence viral evolution, but putatively seasonal infection.

Targeting Hemagglutinin: Approaches for Broad Protection against the Influenza A Virus

Influenza A viruses are dynamically epidemic and genetically diverse. Due to the antigenic drift and shift of the virus, seasonal vaccines are required to be reformulated annually to match with current circulating strains. However, the mismatch between vaccinal strains and circulating strains occurs frequently, resulting in the low efficacy of seasonal vaccines. Therefore, several “universal” vaccine candidates based on the structure and function of the hemagglutinin (HA) protein have been developed to meet the requirement of a broad protection against homo-/heterosubtypic challenges. Here, we review recent novel constructs and discuss several important findings regarding the broad protective efficacy of HA-based universal vaccines.

Structural significance of residues 158-160 in the H3N2 hemagglutnin globular head: A computational study with implications in viral evolution and infection

Influenza A H3N2 has been linked to annual outbreaks within the human population attributable to continuous structural changes. H3N2 HA contains well identified antigenic sites and receptor-binding sites (RBS) that are possibly correlated to viral evolution and infection. However, the structural significance of amino acid residues associated with both viral evolution and infection were not fully demonstrated. Throughout this study, we generated and analyzed H3N2 HA models that represented the clade 3C.2 population (comprised of clades 3C.2, 3C.2a, and 3C.21 from the transitioning 2014-2018 H3N2 strains) and 3C.3a (from the 2016 H3N2 strain). Model quality estimation, structural analyses and superimposition, and network analytics of H3N2 HA1 evolution were performed. We found that the structural properties of residues 158-160 could influence the overall HA backbone. More specifically, amino acid substitutions at residues 159-160 affected the amino acid orientation at residue 158, thereby, causing the overall HA backbone structure to vary. Our results were consistent with 1968-2018 HA1 evolution. Taken together, we propose that our results would highlight the structural significance of residues 158-160 in HA1 for both antigenic drift and RBS.

Long-Term Culture of Distal Airway Epithelial Cells Allows Differentiation Towards Alveolar Epithelial Cells Suited for Influenza Virus Studies

As the target organ for numerous pathogens, the lung epithelium exerts critical functions in health and disease. However, research in this area has been hampered by the quiescence of the alveolar epithelium under standard culture conditions. Here, we used human distal airway epithelial cells (DAECs) to generate alveolar epithelial cells. Long-term, robust growth of human DAECs was achieved using co-culture with feeder cells and supplementation with epidermal growth factor (EGF), Rho-associated protein kinase inhibitor Y27632, and the Notch pathway inhibitor dibenzazepine (DBZ). Removal of feeders and priming with DBZ and a cocktail of lung maturation factors prevented the spontaneous differentiation into airway club cells and instead induced differentiation to alveolar epithelial cells. We successfully transferred this approach to chicken distal airway cells, thus generating a zoonotic infection model that enables studies on influenza A virus replication. These cells are also amenable for gene knockdown using RNAi technology, indicating the suitability of the model for mechanistic studies into lung function and disease.

Structural comparison among the 2013-2017 avian influenza A H5N6 hemagglutinin proteins: A computational study with epidemiological implications

Avian influenza viruses easily spread allowing viral re-assortment to simply occur which in-turn increases the potential for a pandemic. A novel 2013 H5N6 influenza strain was detected among the avian population and was reported to continuously evolve, however, this was never structurally demonstrated. Here, we elucidated the putative structural evolution of the novel H5N6 influenza strain. Throughout this study, we analyzed 2013-2017 H5N6 HA protein models. Model quality was first verified before further analyses and structural comparison was made using superimposition. We found that Leu was inserted at position 129₁ among the 2013-2015 models while Leu was not inserted among the 2016-2017 models. Moreover, presence of Leu at position 129₁ shifts residue E126₁ by 159.6° affecting nearby residues which may explain the difference between the 2013-2015 and 2016-2017 HA structural groups. Similarly, we believe that our results would support the hypothesis that the current H5N6 strain is still continuously evolving.

Effects of the cofactor binding sites on the activities of secondary alcohol dehydrogenase (SADH)

SADHs from Thermoanaerobacter ethanolicus are enzymes that, together with various cofactors, catalyze the reversible reduction of carbonyl compounds to their corresponding alcohols. To explore how cofactors bind to SADH, TeSADH was cloned in this study, and Ser(199) and Arg(200) were replaced by Tyr and Asp, respectively. Both sites were expected to be inside or adjacent to the cofactor-binding domain according to computational a prediction. Analysis of TeSADH activities revealed that the enzymatic efficiency (kcat/Km) of the S199Y mutant was noticeably enhanced using by NADH, NADPH as cofactors, and similar with that of wild-type using by NADP(+), NAD(+). Conversely, the activity of the R200D mutant significantly decreased with all cofactors. Furthermore, in yeast, the S199Y mutant substantially elevated the ethanol concentration compared with the wild type. Molecular dynamics simulation results indicated the H-bonding network between TeSADH and the cofactors was stronger for the S199Y mutant and the binding energy was simultaneously increased. Moreover, the fluorescence results indicated the S199Y mutant exhibited an increased preference for NAD(P)H, binding with NAD(P)H more compactly compared with wild type.

In Silico Analysis of HA2/Mx Chimera Peptide for Developing an Adjuvanted Vaccine to Induce Immune Responses Against Influenza Viruses

PURPOSE

The direct transmission of avian influenza viruses to human and increasing drug resisted strains posing new threats for public health. Therefore, development of efficient vaccines is needed to generate protective and persistent immunity to the viruses.

METHODS

Three motifs of Mx protein sequence in human, mouse and poultry located in interferon induced (GTP ase) domain were candidate as biologic adjuvant for enhancing the immune responses against influenza virus. Chimera proteins composed with the conserved HA2 subunit of influenza virus and the Mx motifs named HA2/Mx were modeled and evaluated by in silico analysis includes bioinformatics algorithms in order to explore biological characteristics of these peptides.

RESULTS

Amongst the predicted models, HA2/Mx1 peptide showed the better results following protein structures prediction, antigenic epitopes determination and model quality evaluation. Comparative homology modeling was performed with Swiss Model and the model was validated using ProSA. Epitope predictions revealed the construct could induce both B and T cell epitopes that expect a high immune response.

CONCLUSION

Taken together, these data indicate that the HA2/Mx1 chimera peptide can be potentiated for developing an adjuvant-fused influenza vaccine capable of stimulating effective immune response.

Structural differences between the avian and human H7N9 hemagglutinin proteins are attributable to modifications in salt bridge formation: a computational study with implications in viral evolution

Influenza A hemagglutinin (HA) is a homotrimeric glycoprotein composed of a fibrous globular stem supporting a globular head containing three sialic acid binding sites responsible for infection. The H7N9 strain has consistently infected an avian host, however, the novel 2013 strain is now capable of infecting a human host which would imply that the HA in both strains structurally differ. A better understanding of the structural differences between the avian and human H7N9 strains may shed light into viral evolution and transmissibility. In this study, we elucidated the structural differences between the avian and human H7N9 strains. Throughout the study, we generated HA homology models, verified the quality of each model, superimposed HA homology models to determine structural differences, and, likewise, elucidated the probable cause for these structural differences. We detected two different types of structural differences between the novel H7N9 human and representative avian strains, wherein, one type (Pattern-1) showed three non-overlapping regions while the other type (Pattern-2) showed only one non-overlapping region. In addition, we found that superimposed HA homology models exhibiting Pattern-1 contain three non-overlapping regions designated as: Region-1 (S157₁-A160₁); Region-3 (R262₁-S265₁); and Region-4 (S270₁-D281₁), whereas, superimposed HA homology models showing Pattern-2 only contain one non-overlapping region designated as Region-2 (S137₁-S145₁). We attributed the two patterns we observed to either the presence of salt bridges involving the E114₁ residue or absence of the R141₁:D77₁ salt bridge. Interestingly, comparison between the human H7N7 and H7N9 HA homology models showed high structural similarity. We propose that the putative absence of the R141₁:D77₁ salt bridge coupled with the putative presence of the E114₁:R262₁ and E114₁:K264₁ salt bridges found in the 2013 H7N9 HA homology model is associated to human-type receptor binding. This highlights the possible significance of HA salt bridge formation modifications in viral infectivity, immune escape, transmissibility and evolution.

Homology modeling study toward identifying structural properties in the HA2 B-loop that would influence the HA1 receptor-binding site

Influenza hemagglutinin (HA) consists of a fibrous globular stem (HA2) inserted into the viral membrane supporting a globular head (HA1). HA1 receptor-binding has been hypothesized to be structurally correlated to the HA2 B-loop, however, this was never fully understood. Here, we elucidated the structural relationship between the HA2 B-loop and the HA1 receptor-binding site (RBS). Throughout this study, we analyzed 2486 H1N1 HA homology models obtained from human, swine and avian strains during 1976-2012. Quality of all homology models were verified before further analyses. We established that amino acid residue 882 is putatively strain-conserved and differs in the human (K882), swine (H882) and avian (N882) strains. Moreover, we observed that the amino acid at residue 882 and, similarly, its orientation has the potential to influence the HA1 RBS diameter measurements which we hypothesize may consequentially affect influenza H1N1 viral infectivity, immune escape, transmissibility, and evolution.