Intracellular flow cytometry complements RT-qPCR detection of circulating SARS-CoV-2 variants of concern

The chiral 5,6-cyclohexane-fused uracil ring-system: A molecular platform with promising activity against SARS-CoV-2

The recurrent global exposure to highly challenging viral epidemics, and the still limited spectrum of effective pharmacological options step on the accelerator towards the development of new antiviral medicines. In this work we explored the anti-SARS-CoV-2 potential of a recently launched chiral ring system based on the uracil scaffold fused to carbocycle rings. The asymmetric synthesis of two generations of chiral uracil-based compounds (overall 31 different products), and their in vitro cytotoxicity and antiviral screening against wild-type SARS-CoV-2 in U87.ACE cells allowed us to identify seven non-cytotoxic enantioenriched derivatives exhibiting in vitro EC50 in the 6-37 μM range. Among these compounds, bicyclic uracil 10 showed the best antiviral potency against SARS-CoV-2 (EC50 20A.EU2 = 7.41 μM and EC50 Omicron = 19.4 μM), combined with a favourable selectivity index. Additionally, it exhibited single-digit micromolar inhibition of the isolated SARS-CoV-2 RNA-dependent RNA polymerase (IC50 = 2.1 μM). Starting from a reported cryo-EM structure of RdRp, docking and molecular dynamics simulations were performed to rationalize possible binding modes of the active compounds. Interestingly, no inhibition of viral replication in cells was observed against a wide spectrum of human viruses, while some derivatives, and especially hit compound 10, exhibited specific low micromolar antiviral effect against β-coronavirus OC43. Collectively, these data indicate that this novel uracil-based ring system represents a valid starting point for further development of a new class of RdRp inhibitors to treat SARS-CoV-2 and, potentially, other β-coronavirus infections.

Activation of Antiviral Host Responses against Avian Influenza Virus and Remodeling of Gut Microbiota by rLAB Vector Expressing rIL-17A in Chickens

Low-pathogenic avian influenza virus (LPAIV) remains the most common subtype of type-A influenza virus that causes moderate to severe infection in poultry with significant zoonotic and pandemic potential. Due to high mutability, increasing drug resistance, and limited vaccine availability, the conventional means to prevent intra- or interspecies transmission of AIV is highly challenging. As an alternative to control AIV infections, cytokine-based approaches to augment antiviral host defense have gained significant attention. However, the selective application of cytokines is critical since unregulated expression of cytokines, particularly proinflammatory ones, can cause substantial tissue damage during acute phases of immune responses. Moreover, depending on the type of cytokine and its impact on intestinal microbiota, outcomes of cytokine-gut microflora interaction can have a critical effect on overall host defense against AIV infections. Our recent study demonstrated some prominent roles of chicken IL-17A (ChIL-17A) in regulating antiviral host responses against AIV infection, however, in an in vitro model. For more detailed insights into ChIL-17A function, in the present study, we investigated whether ChIL-17A-meditated elevated antiviral host responses can translate into effective immune protection against AIV infection in an in vivo system. Moreover, considering the role of gut health in fostering innate or local host responses, we further studied the contributory relationships between gut microbiota and host immunity against AIV infection in chickens. For this, we employed a recombinant lactic acid-producing bacterial (LAB) vector, Lactococcus lactis, expressing ChIL-17A and analyzed the in vivo functionality in chickens against an LPAIV (A/H9N2) infection. Our study delineates that mucosal delivery of rL. lactis expressing ChIL-17A triggers proinflammatory signaling cascades and can drive a positive shift in phylum Firmicutes, along with a marked decline in phylum Actinobacteriota and Proteobacteria, favoring effective antiviral host responses against AIV infection in chickens. We propose that ChIL-17A-mediated selective expansion of beneficial gut microbiota might form a healthy microbial community that augments the effective immune protection against AIV infections in chickens.

Novel Polymyxin-Inspired Peptidomimetics Targeting the SARS-CoV-2 Spike:hACE2 Interface

Though the bulk of the COVID-19 pandemic is behind, the search for effective and safe anti-SARS-CoV-2 drugs continues to be relevant. A highly pursued approach for antiviral drug development involves targeting the viral spike (S) protein of SARS-CoV-2 to prevent its attachment to the cellular receptor ACE2. Here, we exploited the core structure of polymyxin B, a naturally occurring antibiotic, to design and synthesize unprecedented peptidomimetics (PMs), intended to target contemporarily two defined, non-overlapping regions of the S receptor-binding domain (RBD). Monomers 1, 2, and 8, and heterodimers 7 and 10 bound to the S-RBD with micromolar affinity in cell-free surface plasmon resonance assays (KD ranging from 2.31 μM to 2.78 μM for dimers and 8.56 μM to 10.12 μM for monomers). Although the PMs were not able to fully protect cell cultures from infection with authentic live SARS-CoV-2, dimer 10 exerted a minimal but detectable inhibition of SARS-CoV-2 entry in U87.ACE2+ and A549.ACE2.TMPRSS2+ cells. These results validated a previous modeling study and provided the first proof-of-feasibility of using medium-sized heterodimeric PMs for targeting the S-RBD. Thus, heterodimers 7 and 10 may serve as a lead for the development of optimized compounds, which are structurally related to polymyxin, with improved S-RBD affinity and anti-SARS-CoV-2 potential.

Cellular electrical impedance to profile SARS-CoV-2 fusion inhibitors and to assess the fusogenic potential of spike mutants

Despite the vaccination campaigns for COVID-19, we still cannot control the spread of SARS-CoV-2, as evidenced by the ongoing circulation of the Omicron variants of concern. This highlights the need for broad-spectrum antivirals to further combat COVID-19 and to be prepared for a new pandemic with a (re-)emerging coronavirus. An interesting target for antiviral drug development is the fusion of the viral envelope with host cell membranes, a crucial early step in the replication cycle of coronaviruses. In this study, we explored the use of cellular electrical impedance (CEI) to quantitatively monitor morphological changes in real time, resulting from cell-cell fusion elicited by SARS-CoV-2 spike. The impedance signal in CEI-quantified cell-cell fusion correlated with the expression level of SARS-CoV-2 spike in transfected HEK293T cells. For antiviral assessment, we validated the CEI assay with the fusion inhibitor EK1 and measured a concentration-dependent inhibition of SARS-CoV-2 spike mediated cell-cell fusion (IC₅₀ value of 0.13 μM). In addition, CEI was used to confirm the fusion inhibitory activity of the carbohydrate-binding plant lectin UDA against SARS-CoV-2 (IC₅₀ value of 0.55 μM), which complements prior in-house profiling activities. Finally, we explored the utility of CEI in quantifying the fusogenic potential of mutant spike proteins and in comparing the fusion efficiency of SARS-CoV-2 variants of concern. In summary, we demonstrate that CEI is a powerful and sensitive technology that can be applied to studying the fusion process of SARS-CoV-2 and to screening and characterizing fusion inhibitors in a label-free and non-invasive manner.

The emergence of SARS-CoV-2 Omicron subvariants: current situation and future trends

The SARS-CoV-2 Omicron variant (B.1.1.529) has been the most recent variant of concern (VOC) established by the World Health Organization (WHO). Because of its greater infectivity and immune evasion, this variant quickly became the dominant type of circulating SARS-CoV-2 worldwide. Our literature review thoroughly explains the current state of Omicron emergence, particularly by comparing different omicron subvariants, including BA.2, BA.1, and BA.3. Such elaboration would be based on structural variations, mutations, clinical manifestation, transmissibility, pathogenicity, and vaccination effectiveness. The most notable difference between the three subvariants is the insufficiency of deletion (Δ69-70) in the spike protein, which results in a lower detection rate of the spike (S) gene target known as (S) gene target failure (SGTF). Furthermore, BA.2 had a stronger affinity to the human Angiotensin-converting Enzyme (hACE2) receptor than other Omicron sub-lineages. Regarding the number of mutations, BA.1.1 has the most (40), followed by BA.1, BA.3, and BA.3 with 39, 34, and 31 mutations, respectively. In addition, BA.2 and BA.3 have greater transmissibility than other sub-lineages (BA.1 and BA.1.1). These characteristics are primarily responsible for Omicron's vast geographical spread and high contagiousness rates, particularly BA.2 sub-lineages.

Carbohydrate-binding protein from stinging nettle as fusion inhibitor for SARS-CoV-2 variants of concern

Urtica dioica agglutinin (UDA) is a carbohydrate-binding small monomeric protein isolated from stinging nettle rhizomes. It inhibits replication of a broad range of viruses, including coronaviruses, in multiple cell types, with appealing selectivity. In this work, we investigated the potential of UDA as a broad-spectrum antiviral agent against SARS-CoV-2. UDA potently blocks transduction of pseudotyped SARS-CoV-2 in A549.ACE2⁺-TMPRSS2 cells, with IC₅₀ values ranging from 0.32 to 1.22 µM. Furthermore, UDA prevents viral replication of the early Wuhan-Hu-1 strain in Vero E6 cells (IC₅₀ = 225 nM), but also the replication of SARS-CoV-2 variants of concern, including Alpha, Beta and Gamma (IC₅₀ ranging from 115 to 171 nM). In addition, UDA exerts antiviral activity against the latest circulating Delta and Omicron variant in U87.ACE2⁺ cells (IC₅₀ values are 1.6 and 0.9 µM, respectively). Importantly, when tested in Air-Liquid Interface (ALI) primary lung epithelial cell cultures, UDA preserves antiviral activity against SARS-CoV-2 (20A.EU2 variant) in the nanomolar range. Surface plasmon resonance (SPR) studies demonstrated a concentration-dependent binding of UDA to the viral spike protein of SARS-CoV-2, suggesting interference of UDA with cell attachment or subsequent virus entry. Moreover, in additional mechanistic studies with cell-cell fusion assays, UDA inhibited SARS-CoV-2 spike protein-mediated membrane fusion. Finally, pseudotyped SARS-CoV-2 mutants with N-glycosylation deletions in the S2 subunit of the spike protein remained sensitive to the antiviral activity of UDA. In conclusion, our data establish UDA as a potent fusion inhibitor for the current variants of SARS-CoV-2.