Chitinase 3-Like-1 (CHI3L1) Inhibitors Stops Replication Of SARS-CoV-2 Including Omicron In Human Host


Scientists from Brown University-Rhode Island have found that that Chitinase 3-Like-1 (CHI3L1) inhibitors stops replication of the SARS-CoV-2 coronavirus including the Omicron and Delta variants in the human host.
Chitinase-3-like protein 1 (CHI3L1), also known as YKL-40, is a secreted glycoprotein that is approximately 40kDa in size that in humans is encoded by the CHI3L1 gene.

The name YKL-40 is derived from the three N-terminal amino acids present on the secreted form and its molecular mass. YKL-40 is expressed and secreted by various cell-types including macrophages, chondrocytes, fibroblast-like synovial cells, vascular smooth muscle cells, and hepatic stellate cells.

The biological function of YKL-40 is unclear. It is not known to have a specific receptor. Its pattern of expression is associated with pathogenic processes related to inflammation, extracellular tissue remodeling, fibrosis and solid carcinomas and asthma.

The study team demonstrated that CHI3L1 augments epithelial cell infection by pseudoviruses that express the alpha, beta, gamma, delta or omicron S proteins and that the CHI3L1 inhibitors: anti-CHI3L1 and kasugamycin inhibit epithelial cell infection by these VOC pseudovirus moieties. Hence, CHI3L1 is a universal, VOC-independent therapeutic target in COVID 19.
The study findings were published on a preprint server and are currently being peer reviewed.

Typically, SARS-CoV-2 infection is caused by the spike (S) protein binding to cellular angiotensin-converting enzyme 2 (ACE2) receptors, which is subsequently processed by the S protein protease (SPP).
One recent study has found that chitinase 3-like-1 (CHI3L1) promotes ACE2 and SPPs. The researchers from that study have recently published new researchers, wherein they determining whether CHI3L1-targeted therapies are efficient inhibitors of SC2 viral variant infection.

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Coronaviruses are large enveloped single stranded viruses (8). Generally, the rates of nucleotide substitution of RNA viruses are fast and mainly the result of natural selection (29). This high error rate and the subsequent rapidly evolving virus populations can lead to the accumulation of amino acid mutations that affect the transmissibility, cell tropism, pathogenicity and or the responsiveness to vaccinations and or therapies (8, 29).

The SC2 VOC are known to manifest enhanced transmissibility and diminished vaccine effectiveness when compared to ancestral controls (30, 31). Their mutations are important causes of viral infection, the cause of new waves of illness and death and drivers of pandemic persistence (30).

This can be readily appreciated in the rapid spread of the delta and omicron variants with the latter now accounting for 99.5% of SC2 infections in the USA (, as of Jan 15, 2021). It can also be seen in delta’s enhanced ability to replicate which drives the viral load up beyond what many other variants can do and outpaces the body’s initial antiviral response (32).

The fact that the spectrum of mutations in and characteristics of these variants differs from one another has complicated approaches to vaccination and therapy. In light of the importance of the variants, especially delta and omicron, in COVID 19 studies were undertaken to determine if therapies could be developed by targeting host moieties that help to control many of the major VOC of SC2.

In keeping with the importance of ACE2 and SPP in SC2 infection and the impressive ability of CHI3L1 to stimulate these moieties, these studies focused on the relationships between CHI3L1, ACE2 in infections caused by the α, β, γ δ and o variants. They demonstrate that CHI3L1 stimulates the infection caused by these VOC by stimulating the expression and accumulation of ACE2 and SPP.

They also demonstrate that antibody-based and small molecule inhibitors of CHI3L1 inhibit the infection of human epithelial cells by these major SC2 VOC including delta and omicron. In combination, they suggest that CHI3L1 is a potential therapeutic target that can be manipulated to prevent or alter the natural history of SC2 infection caused by the current and possible future viral variants that utilize ACE2 and SPP.

The S glycoprotein of SC2 is located on the outer surface of the virion and undergoes cleavage into S1 and S2 subunits. The S1 subunit is further divided into a receptor binding domain (RBD) and an N-terminal domain (NTD) which serve as potential targets for neutralization in response to antisera and or antibodies induced by vaccines (8, 33).

Genetic variation in SC2 can have important implications for disease pathogenesis especially if the alterations involve the RBD. In keeping with this concept, the SC2 VOC have impressive mutations in the viral S proteins with alterations in RBD and NTD (34, 35). Three of the VOC have N501Y alterations which augment viral attachment to ACE2 and subsequent host cell infection (8). Omicron has 37 amino acid mutations in its S protein (23).

Fifteen of these mutations are in the RBD and nine are in the RBM which is the subdomain of the RBD that directly interacts with ACE2 (23). When viewed in combination, these studies highlight the importance of the viral S proteins and host ACE2 and SPP in the responses induced by SC2 variants. Because our data demonstrates that CHI3L1 is a potent stimulator of ACE2 and SPP they also provide a mechanism by which CHI3L1-based interventions can be effective therapies in all SC2 variants that utilize ACE2 and SPP to mediate viral infection.

Antibodies against the SC2 spike proteins are an evolving and important part of the immune response to SC2 and treatment tool kit against COVID 19. Because the S protein of omicron is heavily mutated, the therapeutic efficacy of vaccine-induced antibodies and commercial monoclonal anti-spike protein antibodies have been characterized.

These studies demonstrated that vaccine-induced antibodies can manifest diminished therapeutic efficacy compared to ancestral and other SC2 variants like delta (36, 37). In keeping with these findings, antibodies from Regeneron Inc and Eli Lilly Inc have been noted to manifest diminished potency against omicron while manifesting impressive efficacy against the delta and other variants (36, 37).

Our studies demonstrate that the anti-CHI3L1 antibody FRG and kasugamycin, an inhibitor of Chi3l1 decrease the expression of ACE2 and the ability of the ancestral and the alpha, beta, gamma, delta and omicron variants to infect epithelial cells.

This led us to hypothesize that FRG and kasugamycin could decrease the infection and spread of all SC2 variants that utilize ACE2 and SPP to elicit cell infection. In keeping with our findings, recent studies have demonstrated that omicron infection requires ACE2 and that omicron binds to ACE2 is more avidly than the binding of delta to ACE2 (38). This supports our contention that interventions that target CHI3L1 can be effective in the treatment of viruses that utilize ACE to infect epithelial cells.

Variants of interest (VOI) are defined as viral variants with specific genetic markers that may alter the transmissibility and or susceptibility of the virus to vaccination or therapeutic interventions when compared to ancestral strains (8). If the features of the variants are subsequently appreciated to exist, the variant is then reclassified as a VOC.

As of June 22, 2021, there were 7 VOI including epsilon, zeta, eta, theta, kappa, and lambda. More recently epsilon and Mu have been reclassified as a VOC (8). In all cases ACE2 is presumed to be needed for infection by these viral variants. In keeping with this presumption, we believe that CHI3L1 will also regulate VOI infection, replication and symptom generation by altering ACE2 and SPP. Additional experimentation, however, will be required to formally define the roles of CHI3L1 and effects of CHI3L1 blockade on the effects of these moieties.

Studies from our laboratory and others have demonstrated that CHI3L1 is a critical regulator of inflammation and innate immunity and a stimulator of type 2 immune responses, fibroproliferative repair and angiogenesis (39-46). These studies also demonstrated that CHI3L1 is increased in the circulation of patients that are older than 60 years of age and patients with a variety of comorbid diseases including obesity, cardiovascular disease, kidney disease, diabetes, chronic lung disease and cancer (41, 47-57).

In keeping with these findings, we focused recent efforts on the development of CHI3L1-based interventions for these disorders. One of the most effective was a monoclonal antibody raised against amino acid 223-234 of CHI3L1 which is now called FRG. There are a number of reasons to believe that FRG can be an effective therapy in COVID 19.

First, as noted by our laboratory (26) and in the studies noted above, it is a potent inhibitor of CHI3L1 stimulation of ACE2 and SPP which decreases the infection of epithelial cells by SC2. In addition, CHI3L1 is a potent stimulator of type 2 immune responses and type 2 and type 1 immune responses counter regulate each other.

As a consequence, anti-CHI3L1 augments type 1 immune responses which have potent antiviral properties. Anti-CHI3L1 also inhibits the abnormal fibroproliferative repair responses that are seen in pathologic tissue fibrosis such as that seen in lungs from patients with COVID 19 who require prolonged mechanical ventilation.

The present studies add to these insights by highlighting the ability of FRG to inhibit the infection of epithelial cells by the alpha, beta, gamma, delta and omicron SC2 VOC. When viewed in combination, these studies suggest that FRG is a potent therapeutic that can be used to prevent or diminish SC2 infection and or the COVID 19 disease manifestations induced by SC2 and its major variants while augmenting type 1 antiviral responses and controlling tissue fibrosis.

REGEN-COV-2 is a combination of the monoclonal antibodies casirivimab and imdevimab that bind to non-competing epitopes of the RBD of the S protein of SC2 (58). When administered via a subcutaneous route iREGEN-COV2 markedly decreases the risk of hospitalization or death among high-risk persons with COVID 19 (58).

Subcutaneous REGEN-COV2 also prevents symptomatic infection in previously uninfected household contracts of infected persons and decreases the duration of the symptoms and the titers of the virus after SC2 infection (58). Because the SC2 VOC have S protein mutations that involve the RBD, one can appreciate the importance of combining two antibodies that target different RBD epitopes to allow these antibodies to neutralize the various VOC including alpha, beta, gamma, delta and epsilon (58-61).

Because FRG and casirivimab/imdevimab control SC2 via different mechanisms, it is tempting to speculate that additive or synergistic antiviral and or anti-disease effects including preexposure and postexposure prophylaxis will be seen when FRG and REGEN-COV2 are administered simultaneously. One can also see how the administration of FRG and REGEN-COV2 in combination could protect against the selection of resistant SC2 variants (58).

Kasugamycin was discovered in 1965 in Streptomyces kasugaensis and has proven to have antibacterial and antifungal properties (62, 63). Since the 1960s it has been employed as a pesticide to combat agricultural diseases like rice blast fungus and, as a result, has been extensively studied by the Environment Protection Agency (EPA) (64). Most recently Kasugamycin was shown to inhibit influenza and other viral infections (65).

Previous studies from our laboratory have added to our understanding of kasugamycin by demonstrating that it is a powerful inhibitor of CHI3l1 induction of ACE2 and SPP that also inhibits type 2 adaptive immune responses and pathologic fibrosis (26, 27). Importantly, the studies in this submission go further by demonstrating that these CHI3L1-based effects of kasugamycin can be seen in the ancestral and alpha, beta, gamma, delta and omicron SC2 VOC. When viewed in combination, these observations suggest that kasugamycin can be used as a prophylactic or therapeutic in COVID 19. This is an interesting concept because kasugamycin can be given via an intravenous or oral route and is known to have minimal toxicity in man (62, 66).

At the onset of the SC2 pandemic there was an urgency to mitigate this new viral illness. Since then significant progress has been made in the treatment of COVID 19 due to intense research efforts that resulted in novel therapeutics and vaccine development at an unprecedented rate (8).

The progress that was made, however was diminished by the appearance of SC2 viral variants, particularly delta and omicron. It is now known that SC2 infection results in a disease with two phases. The early phase is characterized by cell infection and viral replication and the latter phase is characterized by a robust host antiviral immune response (8).

Current, therapies that are used in the early phase of SC2 infection include antivirals like remdesivir and anti-SC2 monoclonal antibody pairings like bamlanivimab/etesvimab and casirivimab/imdevfimab. When inflammation and a robust immune response have been triggered anti-inflammatories like dexamethasone and immunomodulators are available.

The present studies add to our understanding of the therapies for the early phase of SC2 by demonstrating that the inhibition of ChI3L1 with FRG and or Kasugamycin ameliorates the infection induced by the alpha, beta, gamma, delta and omicron SC2 VOC. This raises the exciting possibility that FRG or Kasugamycin, alone or in combination with each other or other SC2 monoclonals can have powerful prophylactic effects and or inhibit viral infection in SC2-exposed individuals.

They also demonstrate that FRG and Kasugamycin can directly diminish viral replication and, by decreasing viral load, decrease disease pathology and severity. Additional studies of the importance of CHI3L1 and its roles in infections caused by SC2 variants is warranted.



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