Nanobodies Protecting From Lethal SARS-CoV-2 Infection Target Receptor Binding Epitopes Preserved in Virus Variants Other Than Omicron

Integrating immune library probing with structure-based computational design to develop potent neutralizing nanobodies against emerging SARS-CoV-2 variants

To generate antibodies (Abs) against SARS-CoV-2 emerging variants, we integrated multiple tools and engineered molecules with excellent neutralizing breadth and potency. Initially, the screening of an immune library identified a nanobody (Nb), termed Nb4, specific to the receptor-binding domain (RBD) of the Omicron BA.1 variant. A Nb4-derived heavy chain antibody (hcAb4) recognized the spike (S) of the Wuhan, Beta, Delta, Omicron BA.1, and BA.5 SARS-CoV-2 variants. A high-resolution crystal structure of the Nb4 variable (VHH) domain in complex with the SARS-CoV-2 RBD (Wuhan) defined the Nb4 binding mode and interface. The Nb4 VHH domain grasped the RBD and covered most of its outer face, including the core and the receptor-binding motif (RBM), which was consistent with hcAb4 blocking RBD binding to the SARS-CoV-2 receptor. In mouse models, a humanized hcAb4 showed therapeutic potential and prevented the replication of SARS-CoV-2 BA.1 virus in the lungs of the animals. In vitro, hcAb4 neutralized Wuhan, Beta, Delta, Omicron BA.1, and BA.5 viral variants, as well as the BQ.1.1 subvariant, but showed poor neutralization against the Omicron XBB.1.5. Structure-based computation of the RBD-Nb4 interface identified three Nb4 residues with a reduced contribution to the interaction with the XBB.1.5 RBD. Site-saturation mutagenesis of these residues resulted in two hcAb4 mutants with enhanced XBB.1.5 S binding and virus neutralization, further improved by mutant Nb4 trimers. This research highlights an approach that combines library screening, Nb engineering, and structure-based computational predictions for the generation of SARS-CoV-2 Omicron-specific Abs and their adaptation to emerging variants.

Screening and functional studies of Norrin-related nanobodies

Norrin is a crucial regulator of the Wnt/β-catenin signaling pathway, playing a key role in retinal vascular development, blood-brain barrier maintenance, and neuroprotection. In this study, a Norrin fusion protein (Norrin-Fc) was successfully expressed and purified using an insect cell expression system. Camels were immunized with purified Norrin-Fc to generate nanobodies, which consist solely of the heavy chain variable domains of heavy chain antibodies (VHH) with a molecular weight of approximately 15 kDa. Two nanobody strains, Nb 1C4 and Nb 2B10, were identified for their specific binding to Norrin-Fc, and their binding affinities were further characterized. Flow cytometry analysis confirmed that Nb 1C4 and Nb 2B10 specifically bound to the Norrin-FZD4 fusion protein. Luciferase reporter assay results demonstrated that both nanobodies effectively disrupted LGR4-induced Wnt/β-catenin signaling upon Norrin stimulation. This study represents the first successful development of nanobodies targeting Norrin, providing a strong foundation for the advancement of Norrin-related diagnostic tools and antibody therapeutics.

Alshehri M, M. S. Alqahtani A, F. Kadasah S, Harthi N, Ali Alyami R, Alqurashi A, A. Al Ruwaithi A. Identification of Significant Mutations in Spike Protein of SARS-CoV-2 Variants of Concern and the Discovery of Potent Inhibitors

Background: SARS-CoV-2 is a positive-sense single-stranded RNA virus that has a propensity for infecting epithelial cells and the respiratory system. The two important proteins, structural and nonstructural proteins, make the architecture of this virus. Aim: This research aimed at studying significant mutations in spike protein of SARS-CoV-2 variants of concern (VoCs) and finding shared mutations among omicron and other four variants (alpha, beta, gamma, and delta). The purpose of this study was to draw structural comparisons between wild type and mutant proteins, followed by identifying potent inhibitors (ligand) that could be used against SARS-CoV-2 spike protein and its latest omicron VoC. Methodology: In this research, we had studied 16 major mutations as well as shared mutations (6) present in spike region of SARS-CoV-2. Subsequently, we determined the structure of the wild-type SARS-CoV-2 protein from the Protein Data Bank (PDB) with the ID 7R4I. Furthermore, the structure of the mutant protein of SARS-CoV-2 omicron variant was modeled in SWISS-MODEL. The ligand dataset for spike protein of SARS-CoV-2 was also collected from literature and different databases. Both wild type and mutant proteins were docked with ligand database in Molecular Operating Environment (MOE). The docking analysis was performed, and two best ligand molecules, AZ_2 and AZ_13, were finalized based on their energy values, interactions, and docking scores to be used against our wild and mutant proteins. Results: AZ_2 demonstrated a docking score of -6.1753 in MOE, with energy values of -4.3889 and -6.1753. It formed key hydrogen bond interactions. AZ_13 showed a docking score of -5.9, with energy values of -9.3 and -5.9, forming hydrogen donor and acceptor interactions with Asp950 (3.06 Å), Ile312 (3.13 Å), and Glu309 (3.27 Å). These interactions suggest strong binding affinity and potential efficacy. Thus, present research work emphasized on identification of significant mutations and finding a potent target-based drug against SARS-CoV-2 and its omicron variant. Outcomes: Based on this computational analysis performed, it is suggested that proposed compound can be used as remedy against SARS-CoV-2 and its omicron variant.

Small but Mighty: Nanobodies in the Fight Against Infectious Diseases

Infectious diseases, caused by pathogenic microorganisms and capable of spreading, pose a significant threat to global public health. Developing efficient and cost-effective techniques for treating infectious diseases is crucial in curbing their progression and reducing patients' morbidity and mortality. Nanobodies (Nbs), a novel class of affinity reagents derived from unique heavy chain-only antibodies in camelids, represent the smallest intact and fully functional antigen-binding fragments. Compared with conventional antibodies and their antigen binding fragments, Nbs offer numerous advantages, including high affinity, exceptional target specificity, cost-effective production, easy accessibility, and robust stability, demonstrating immense potential in infectious disease treatment. This review introduces Nbs and focuses on discussing their mechanisms and intervention strategies in the treatment of viral and bacterial infections.

Synthetic heparan sulfate mimics based on chitosan derivatives show broad-spectrum antiviral activity

Enveloped viruses enter cells by binding to receptors present on host cell membranes, which trigger internalization and membrane fusion. For many viruses, this either directly or indirectly involves interaction with membrane-anchored carbohydrates, such as heparan sulfate, providing a potential target for a broad-spectrum antiviral approach. Based on this hypothesis, we screened a library of functionalized chitosan sulfates that mimic heparan sulfate in cellular membranes for inhibition of SARS-CoV-2 and respiratory syncytial virus (RSV) entry. An array of compounds blocking SARS-CoV-2 and RSV were identified, with the lead compound displaying broad-spectrum activity against multiple viral strains and clinical isolates. Mechanism of action studies showed the drug to block viral entry irreversibly, likely via a virucidal mechanism. Importantly, the drug was non-toxic in vivo and showed potent post-exposure therapeutic activity against both SARS-CoV-2 and RSV. Together, these results highlight the potential of functionalized carbohydrates as broad-spectrum antivirals targeting respiratory viruses.

Production of Plant Virus-Derived Hybrid Nanoparticles Decorated with Different Nanobodies

Viral nanoparticles (VNPs) are self-assembled nanometric complexes whose size and shape are similar to those of the virus from which they are derived. VNPs are arousing great attention due to potential biotechnological applications in fields like nanomedicine and nanotechnology because they allow the presentation of polypeptides of choice linked to the virus structural proteins. Starting from tobacco etch virus (TEV), a plant plus-strand RNA virus that belongs to the genus Potyvirus (family Potyviridae), here we describe the development of recombinant hybrid VNPs in Nicotiana benthamiana plants able of exposing simultaneously different proteins on their surface. This system is based on the synergic coinfection of TEV and potato virus X (PVX; Potexvirus), in which PVX provides a second TEV CP in trans allowing a mixed assembly. We first generated genetically modified hybrid VNPs simultaneously displaying green and red fluorescent proteins on their surface. A population of decorated and nondecorated CPs resulting from the insertion of the picornavirus F2A ribosomal escape peptide was required for viral particle assembly. Correct assembly of the recombinant mosaic VNPs presenting the exogenous peptides was successfully observed by immunoelectron microscopy. We next achieved the production of hybrid VNPs expressing a nanobody against SARS-CoV-2 and a fluorescent reporter protein, whose functionality was demonstrated by ELISA and dot-blot assay. Finally, we engineered the production of hybrid multivalent VNPs carrying two different nanobodies against distinct epitopes of the same SARS-CoV-2 antigenic protein, emulating a nanobody cocktail. These plant-produced recombinant mosaic VNPs, which are filamentous and flexuous in shape, presenting two different fused proteins on the surface, represent a molecular tool with several potential applications in biotechnology.

Targeting plasmid-encoded proteins that contain immunoglobulin-like domains to combat antimicrobial resistance

Antimicrobial resistance (AMR) poses a significant threat to human health. Although vaccines have been developed to combat AMR, it has proven challenging to associate specific vaccine antigens with AMR. Bacterial plasmids play a crucial role in the transmission of AMR. Our recent research has identified a group of bacterial plasmids (specifically, IncHI plasmids) that encode large molecular mass proteins containing bacterial immunoglobulin-like domains. These proteins are found on the external surface of the bacterial cells, such as in the flagella or conjugative pili. In this study, we show that these proteins are antigenic and can protect mice from infection caused by an AMR Salmonella strain harboring one of these plasmids. Furthermore, we successfully generated nanobodies targeting these proteins, that were shown to interfere with the conjugative transfer of IncHI plasmids. Considering that these proteins are also encoded in other groups of plasmids, such as IncA/C and IncP2, targeting them could be a valuable strategy in combating AMR infections caused by bacteria harboring different groups of AMR plasmids. Since the selected antigens are directly linked to AMR itself, the protective effect extends beyond specific microorganisms to include all those carrying the corresponding resistance plasmids.

Susceptibility and transmissibility of SARS-CoV-2 variants in transgenic mice expressing the cat angiotensin-converting enzyme 2 (ACE-2) receptor

The emergence of SARS-CoV-2 in 2019 and its rapid spread throughout the world has caused the largest pandemic of our modern era. The zoonotic origin of this pathogen highlights the importance of the One Health concept and the need for a coordinated response to this kind of threats. Since its emergence, the virus has caused >7 million deaths worldwide. However, the animal source for human outbreaks remains unknown. The ability of the virus to jump between hosts is facilitated by the presence of the virus receptor, the highly conserved angiotensin-converting enzyme 2 (ACE2), found in various mammals. Positivity for SARS-CoV-2 has been reported in various species, including domestic animals and livestock, but their potential role in bridging viral transmission to humans is still unknown. Additionally, the virus has evolved over the pandemic, resulting in variants with different impacts on human health. Therefore, suitable animal models are crucial to evaluate the susceptibility of different mammalian species to this pathogen and the adaptability of different variants. In this work, we established a transgenic mouse model that expresses the feline ACE2 protein receptor (cACE2) under the human cytokeratin 18 (K18) gene promoter's control, enabling high expression in epithelial cells, which the virus targets. Using this model, we assessed the susceptibility, pathogenicity, and transmission of SARS-CoV-2 variants. Our results show that the sole expression of the cACE2 receptor in these mice makes them susceptible to SARS-CoV-2 variants from the initial pandemic wave but does not enhance susceptibility to omicron variants. Furthermore, we demonstrated efficient contact transmission of SARS-CoV-2 between transgenic mice that express either the feline or the human ACE2 receptor.

SARS-CoV-2 membrane protein-specific antibodies from critically ill SARS-CoV-2-infected individuals interact with Fc receptor-expressing cells but do not neutralize the virus

The membrane (M) glycoprotein of SARS-CoV-2 is one of the key viral proteins regulating virion assembly and morphogenesis. Immunologically, the M protein is a major source of peptide antigens driving T cell responses, and most individuals who have been infected with SARS-CoV-2 make antibodies to the N-terminal, surface-exposed peptide of the M protein. We now report that although the M protein is abundant in the viral particle, antibodies to the surface-exposed N-terminal epitope of M do not appear to neutralize the virus. M protein-specific antibodies do, however, activate antibody-dependent cell-mediated cytotoxicity and cytokine secretion by primary human natural killer cells. Interestingly, while patients with severe or mild disease make comparable levels of M antigen-binding antibodies, M-specific antibodies from the serum of critically ill patients are significantly more potent activators of antibody-dependent cell-mediated cytotoxicity than antibodies found in individuals with mild or asymptomatic infection.

Aptamers and Nanobodies as New Bioprobes for SARS-CoV-2 Diagnostic and Therapeutic System Applications

The global challenges posed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have underscored the critical importance of innovative and efficient control systems for addressing future pandemics. The most effective way to control the pandemic is to rapidly suppress the spread of the virus through early detection using a rapid, accurate, and easy-to-use diagnostic platform. In biosensors that use bioprobes, the binding affinity of molecular recognition elements (MREs) is the primary factor determining the dynamic range of the sensing platform. Furthermore, the sensitivity relies mainly on bioprobe quality with sufficient functionality. This comprehensive review investigates aptamers and nanobodies recently developed as advanced MREs for SARS-CoV-2 diagnostic and therapeutic applications. These bioprobes might be integrated into organic bioelectronic materials and devices, with promising enhanced sensitivity and specificity. This review offers valuable insights into advancing biosensing technologies for infectious disease diagnosis and treatment using aptamers and nanobodies as new bioprobes.

Virus-Receptor Interactions and Receptor-Mediated Virus Entry into Host Cells

The virus particles described in the previous chapters of this book are vehicles that transmit the viral genome and the infection from cell to cell. To initiate the infective cycle, the viral genome must therefore translocate from the viral particle to the cell cytoplasm. Via distinct proteins or motifs in their outermost shell, the particles of animal viruses or bacteriophages attach initially to specific receptors on the host cell surface. These viral receptors thus mediate penetration of the viral genome inside the cell, where the intracellular infective cycle starts. The presence of these receptors on the cell surface is a principal determinant of virus-host tropism. Viruses can use diverse types of molecules to attach to and enter into cells. In addition, virus-receptor recognition can evolve over the course of an infection, and viral variants with distinct receptor-binding specificities and tropism can appear. The identification of viral receptors and the characterization of virus-receptor interactions have been major research goals in virology. In this chapter, we will describe, from a structural perspective, several virus-receptor interactions and the active role of receptor molecules in virus cell entry.

AG5 is a potent non-steroidal anti-inflammatory and immune regulator that preserves innate immunity

An archetypal anti-inflammatory compound against cytokine storm would inhibit it without suppressing the innate immune response. AG5, an anti-inflammatory compound, has been developed as synthetic derivative of andrographolide, which is highly absorbable and presents low toxicity. We found that the mechanism of action of AG5 is through the inhibition of caspase-1. Interestingly, we show with in vitro generated human monocyte derived dendritic cells that AG5 preserves innate immune response. AG5 minimizes inflammatory response in a mouse model of lipopolysaccharide (LPS)-induced lung injury and exhibits in vivo anti-inflammatory efficacy in the SARS-CoV-2-infected mouse model. AG5 opens up a new class of anti-inflammatories, since contrary to NSAIDs, AG5 is able to inhibit the cytokine storm, like dexamethasone, but, unlike corticosteroids, preserves adequately the innate immunity. This is critical at the early stages of any naïve infection, but particularly in SARS-CoV-2 infections. Furthermore, AG5 showed interesting antiviral activity against SARS-CoV-2 in humanized mice.

Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.

Single-domain antibody for binding the conserved epitope in the SARS-CoV-2 spike protein receptor-binding domain

Several COVID-19 vaccines have been developed in the last three years using various tecnhiques. Multiple virus-neutralizing antibodies against SARS-CoV-2 have been also obtained to combat the pandemic. However, the use of these medications for prevention and potential treatment faces significant challenges due to the emergence of new mutant virus variants, both more contagious and escaping neutralization by the immune system, that is why it is necessary to continuously renew the vaccines and develop new therapeutic antibodies. The study was aimed to use the technology of generating single-domain antibodies (nanobodies) to target the surface spike (S) protein RBD conserved epitope of the broad spectrum of SARS-CoV-2 variants. Recombinant proteins that corresponded to RBDs of three important SARS-СoV-2 strains and the full-length S protein (Wuhan) were used as antigens for immunization of a camel in order to induce production of appropriate antibodies and/or as immobilized proteins for further cross selection of the nanobody clones with pre-set specificity by the phage display. A nanobody capable of effectively recognizing the conservative region in the S protein RBDs of the broad spectrum of pandemic SARS-CoV-2 variants, including Omicron, was selected from the generated immune library. Along with conventional use in immunoassays and diagnosis, the generated nanobody can be potentially used as a module for target-specific binding used to trap coronavirus in human upper airways during the development of novel combination antiviral drugs.

Applications of nanobodies in the prevention, detection, and treatment of the evolving SARS-CoV-2

Global health and economy are deeply influenced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its newly emerging variants. Nanobodies with nanometer-scale size are promising for the detection and treatment of SARS-CoV-2 and its variants because they are superior to conventional antibodies in terms of cryptic epitope accessibility, tissue penetration, cost, formatting adaptability, and especially protein stability, which enables their aerosolized specific delivery to lung tissues. This review summarizes the progress in the prevention, detection, and treatment of SARS-CoV-2 using nanobodies, as well as strategies to combat the evolving SARS-CoV-2 variants. Generally, highly efficient generation of potent broad-spectrum nanobodies targeting conserved epitopes or further construction of multivalent formats targeting non-overlapping epitopes can promote neutralizing activity against SARS-CoV-2 variants and suppress immune escape.

Non-coding RNAs derived from the foot-and-mouth disease virus genome trigger broad antiviral activity against coronaviruses

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of a potentially severe respiratory disease, the coronavirus disease 2019 (COVID-19), an ongoing pandemic with limited therapeutic options. Here, we assessed the anti-coronavirus activity of synthetic RNAs mimicking specific domains in the non-coding regions of the foot-and-mouth disease virus (FMDV) genome (ncRNAs). These molecules are known to exert broad-spectrum antiviral activity in cell culture, mice and pigs effectively triggering the host innate immune response. The ncRNAs showed potent antiviral activity against SARS-CoV-2 after transfection in human intestinal Caco-2 and lung epithelium Calu-3 2B4 cells. When the in vivo efficacy of the FMDV ncRNAs was assessed in K18-hACE2 mice, administration of naked ncRNA before intranasal SARS-CoV-2 infection significantly decreased the viral load and the levels of pro-inflammatory cytokines in the lungs compared with untreated infected mice. The ncRNAs were also highly efficacious when assayed against common human HCoV-229E and porcine transmissible gastroenteritis virus (TGEV) in hepatocyte-derived Huh-7 and swine testis ST cells, respectively. These results are a proof of concept of the pan-coronavirus antiviral activity of the FMDV ncRNAs including human and animal divergent coronaviruses and potentially enhance our ability to fight future emerging variants.