Category: Nature

IgA nephropathy is a typical intractable disease of chronic kidney disease in which IgA (one of the immunoglobulins) is deposited in the glomerulus (a urine filtration device) with aberrant glycan modification. It is also well known that abnormalities occur in the O-glycan modification in the IgA hinge region.
A group from Central South University, Changsha, China etc. has indicated that IgA, the glycan abnormality found in IgA nephropathy, might be controlled by microRNA (miR-630) derived from tonsil mononucleated cells.
https://www.frontiersin.org/articles/10.3389/fimmu.2020.563699/full

As for the mechanism of the onset of IgA nephropathy, it was suggested that miR-630 derived from the tonsils is produced excessively,  and targets Toll-like receptor 4 (TLR4)  as the target gene, and finally modulates the concentration of IgA and its glycosylation level through the NF-kB signaling pathway.

A group from Soka University etc. has reported on changes in glycan modification accompanied by change from ESC to epiblast-like cells (EpiLCs) and a control factor behind them.
https://www.nature.com/articles/s41598-020-79666-4

With the change from ESC to EpiLCs, the following changes in glycan modification occur:

1. For N-type glycans, the high mannose structure is the main structure in common, but in EpiLCs, fucose modification, bisecting, and Sia modification are increased, for Sia, α2-6 is the main linkage, and typeI LacNAc (Galβ1-3GlcNAc) is highly expressed with α1-2Fuc modified.
2. For O-type sugar chains, Tn antigen and O-GlcNAc are the main in common, but in EpiLCs, the expression of O-glycan is generally increasing, and elongated mucin type O-glycans also increase.
3. For Glycosaminoglycans (GAG), EpiLCs generally increase GAG expression, especially Heparan sulfate (HS), chondroitin sulfate (CS) and dermatan sulfate (DS).
4. For glycolipids, EpiLCs cause structural changes from globo (Gb) to ganglio (Gg).

Behind these glycan modification, polycomb repressive complex 2 (PRC2), a chromatin protein, was shown to be involved as a regulator. A number of glycosyltransferase genes involved in glycan modification of ESC is under the control of PRC2.

A group of Quilmes National University, Bernal, Buenos Aires Province, Argentina has reported characteristic glycan modification in gliomas.
https://www.oncotarget.com/article/27850/text/

In high-grade gliomas, its glycan modification is characterized by the progression of terminal sialic acid of N-glycans and multi-antennary N-glycans. The sialic acid modification is mainly α2-3 linkage along with the terminal fucosylation, suggesting that the terminal modification structure of N-glycans is SLex. To support this, glycosyltransferases (α1,3-fucosyltransperases (FuT3-7 and 9-11) and α2,3-sialyltransferases (ST3Gal3/4/6) ) are also highly expressed.

They concluded that changes in the glycan profile of tumor cell surfaces are the basis for the development of therapeutic drugs targeting such aberrant glycans and novel glycan markers.

A group from The University of Hong Kong etc. has reported on the effects of heparan sulfate and glycan modification of ACE2 in the infection of the new coronavirus (SARS-CoV-2).
https://www.nature.com/articles/s41467-020-20457-w

Calu3 (lung epithelial cells) and Caco2 (intestine epithelial cells) are used in SARS-CoV-2 infection experiments. Heparinase was used to investigate the effects of heparan sulfate, and Neuraminidase (NA) was used for the effects of ACE2 glycan modification, with a particular focus on sialic acid.

As shown in the figure below, heparinase suppresses viral infection and shows that heparan sulfate is involved in the capture of the virus as a co-receptor for ACE2. For the sialic acid modification of ACE2, it is shown that the infection of the virus is rather stronger by cleaving the sialic acid with NA.

A group from Yale University School of Medicine etc. has reported that the most dynamic unifying indicator of the pathophysiology of the new coronavirus (COVID-19) is the saliva viral load.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7805468/

Existing markers for COVID-19 include inflammatory cytokines and chemokines (CXCL10, IL-6, IL-10), inflammasome (IL-18, IL-1β), interferon (IFNα, IFNγ, IFNλ), etc.), however, they have found that the saliva virus load was very well correlated with the disease pathology. The nasopharyngeal viral load was also evaluated as a comparison. The amount of virus in saliva and nasopharyngeal (RNA copies/mL) was calculated from Ct values of RT-PCR extracting RNA from saliva. For the discrimination accuracy among non-hospitalization, moderate, severe, and deceased, strong predictive ability was obtained as follows, moderate disease (AUC = 0.96), severe disease (AUC = 0.89), and fatal (AUC = 0.91).

The upper figure of the below shows the correlation between the saliva viral load and the disease pathology, and the lower figure shows the nasopharyngeal viral load and the disease pathology.

A group from School of Medicine, Keio Univ. has reported a cohort study on antibody responses in asymptomatic to mild new coronavirus (COVID-19) patients who were positive for PCR testing in Japan.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7787511/

Many overseas cohort studies have targeted patients with more symptomatic and severe cases, and antibody responses have appeared in 80% to 100% of patients three weeks after infection. Numerous studies have also shown that these antibodies correlate with age, severity, lymphopenia, and serum CRP levels.

This cohort study was conducted in asymptomatic to milder patients than in known cohort studies, and 87.5% of asymptomatic patients and 23.5% of mild patients did not have antibody responses.

A group of Fondazione IRCCS Estituto Neurologico Carlo Besta, Via Padova, Milan, Italy etc. believes that the low efficacy of antiviral drugs such as cytokine inhibitors is (1) probably due to delays in administration in which the virus causes an inflammatory response and is no longer the main protagonist, (2) the relatively low efficacy of cytokine inhibitors is explained because they only act on one or a few of the dozens of cytokines, and (3) other inflammatory mediators (reactive oxygen and nitrogen species) are not targeted.

When inflammatory mediators are over-generated, reactive species cause extensive cell and tissue damages. The only drug known to inhibit the over production of active species and cytokines is methylene blue, a low-cost dye with antiseptic properties that is effectively used in the treatment of malaria, urinary tract infections, septic shock, and methaemoglobinaemia. They suggest testing methylene blue to treat COVID-19 acute respiratory distress syndrome.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7728423/

The virus envelope of the new coronavirus (SARS-CoV-2) contains S proteins, E proteins, and M proteins. Because S proteins are so deeply involved in the infection, so much research has been done targeting S proteins. However, very little information is available on the structure and function of M proteins. In general, the function of the M protein is understood as the protection of the viral particle structure, and it is thought that the RNA-N protein complex and the S-protein bind to the M protein, bud out as infectious particles in the small cavity, and are released out of the cell by exocytosis.

A group of King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia focused on M proteins and its differences between SARS-CoV-2, SARS-CoV, and MERS-CoV.
https://www.sciencedirect.com/science/article/pii/S1018364720304493?via%3Dihub

The following points are pointed out:

The M protein is a transmembrane protein, and there are N-terminal domain and C-terminal domain on either side of the three transmembrane domains.
From the viewpoint of the amino acid sequence, SARS-CoV-2 has an S4 residue (221-224) inserted, and it would be an unique feature of SARS-CoV-2.
As intrinsically disordered regions, there are two regions (1-7, 205-222) in SRAS-CoV-2, three regions (1-6, 207-210, 216-221) in SARS-CoV, and two regions (1-6, 216-219) in MERS-CoV, and these differences would reflect viral particles protection capability in different environments of the virus and might be related to viral transmission mode.
Domains that could be potential B-cell epitopes would be:
SARS-CoV2    183-189 ASQRVAG, 200-217 RIGNYKLNTDHSSSSDNI
SARS-CoV     183-188 SQRVGT, 199-215 RIGNYKLNTDHAGSNDN
MERS-CoV     180-188 MVKRQSYGT, 200-211 AGNYRSPPITAD

Similar to the last blog, a group of Ladake Akintola Unyv. of Technology, Ogbomoso, Oyo State Nigeria has evaluated the inhibitory effects of saponins and tannins by molecular docking and molecular dynamics simulations, targeting SARS-CoV-2 precursor protein main protease (M^pro).
https://link.springer.com/article/10.1007/s40203-020-00071-w

Saponins are found in plant roots, leaves, stems, etc., but are especially found in beans and are known to have antioxidant properties. On the other hand, tannins are astringent components contained in many seeds, and astringency of persimmons is a good example of tannin. Tannins strongly bind to proteins and have the effect of causing denaturation, and the effect of tannins on their properties is called “Astringent.”

The results are as follows, but may show potential antiviral effects that are no less so than remdesivir. Evaluation in vivo is expected.

When the new coronavirus (SARS-CoV-2) infects host cells, a huge precursor protein is synthesized from RNA derived from the virus. The precursor protein is cleaved by various proteases and becomes functional proteins necessary for the growth of viruses. The main protease (M^pro) is one of the such precursor proteases and is an essential one for the growth of viruses.

A group of Univ. of Medical Sciences and Technology, Khartoum, Sudan has used this main protease to evaluate the inhibitory effects of plant-derived components used as traditional Sudanese medicines by molecular docking and molecular dynamic simulations.
https://link.springer.com/article/10.1007/s40203-020-00073-8

As a result, the following plant-_derived ingredients are expected as inhibitors of the novel coronavirus. Expect in vivo ratings.