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Posts Tagged ‘ACE2 receptor’

Cryo-EM disclosed how the D614G mutation changes SARS-CoV-2 spike protein structure.

Reporter: Dr. Premalata Pati, Ph.D., Postdoc

SARS-CoV-2, the virus that causes COVID-19, has had a major impact on human health globally; infecting a massive quantity of people around 136,046,262 (John Hopkins University); causing severe disease and associated long-term health sequelae; resulting in death and excess mortality, especially among older and prone populations; altering routine healthcare services; disruptions to travel, trade, education, and many other societal functions; and more broadly having a negative impact on peoples physical and mental health.

It’s need of the hour to answer the questions like what allows the variants of SARS-CoV-2 first detected in the UK, South Africa, and Brazil to spread so quickly? How can current COVID-19 vaccines better protect against them?

Scientists from the Harvard Medical School and the Boston Children’s Hospital help answer these urgent questions. The team reports its findings in the journal “Science a paper entitled Structural impact on SARS-CoV-2 spike protein by D614G substitution. The mutation rate of the SARS-CoV-2 virus has rapidly evolved over the past few months, especially at the Spike (S) protein region of the virus, where the maximum number of mutations have been observed by the virologists.

Bing Chen, HMS professor of pediatrics at Boston Children’s, and colleagues analyzed the changes in the structure of the spike proteins with the genetic change by D614G mutation by all three variants. Hence they assessed the structure of the coronavirus spike protein down to the atomic level and revealed the reason for the quick spreading of these variants.


This model shows the structure of the spike protein in its closed configuration, in its original D614 form (left) and its mutant form (G614). In the mutant spike protein, the 630 loop (in red) stabilizes the spike, preventing it from flipping open prematurely and rendering SARS-CoV-2 more infectious.

Fig. 1. Cryo-EM structures of the full-length SARS-CoV-2 S protein carrying G614.

(A) Three structures of the G614 S trimer, representing a closed, three RBD-down conformation, an RBD-intermediate conformation and a one RBD-up conformation, were modeled based on corresponding cryo-EM density maps at 3.1-3.5Å resolution. Three protomers (a, b, c) are colored in red, blue and green, respectively. RBD locations are indicated. (B) Top views of superposition of three structures of the G614 S in (A) in ribbon representation with the structure of the prefusion trimer of the D614 S (PDB ID: 6XR8), shown in yellow. NTD and RBD of each protomer are indicated. Side views of the superposition are shown in fig. S8.

IMAGE SOURCE: Bing Chen, Ph.D., Boston Children’s Hospital, https://science.sciencemag.org/content/early/2021/03/16/science.abf2303

The work

The mutant spikes were imaged by Cryo-Electron microscopy (cryo-EM), which has resolution down to the atomic level. They found that the D614G mutation (substitution of in a single amino acid “letter” in the genetic code for the spike protein) makes the spike more stable as compared with the original SARS-CoV-2 virus. As a result, more functional spikes are available to bind to our cells’ ACE2 receptors, making the virus more contagious.


Fig. 2. Cryo-EM revealed how the D614G mutation changes SARS-CoV-2 spike protein structure.

IMAGE SOURCE:  Zhang J, et al., Science

Say the original virus has 100 spikes,” Chen explained. “Because of the shape instability, you may have just 50 percent of them functional. In the G614 variants, you may have 90 percent that is functional. So even though they don’t bind as well, the chances are greater and you will have an infection

Forthcoming directions by Bing Chen and Team

The findings suggest the current approved COVID-19 vaccines and any vaccines in the works should include the genetic code for this mutation. Chen has quoted:

Since most of the vaccines so far—including the Moderna, Pfizer–BioNTech, Johnson & Johnson, and AstraZeneca vaccines are based on the original spike protein, adding the D614G mutation could make the vaccines better able to elicit protective neutralizing antibodies against the viral variants

Chen proposes that redesigned vaccines incorporate the code for this mutant spike protein. He believes the more stable spike shape should make any vaccine based on the spike more likely to elicit protective antibodies. Chen also has his sights set on therapeutics. He and his colleagues are further applying structural biology to better understand how SARS-CoV-2 binds to the ACE2 receptor. That could point the way to drugs that would block the virus from gaining entry to our cells.

In January, the team showed that a structurally engineered “decoy” ACE2 protein binds to SARS-CoV-2 200 times more strongly than the body’s own ACE2. The decoy potently inhibited the virus in cell culture, suggesting it could be an anti-COVID-19 treatment. Chen is now working to advance this research into animal models.

Main Source:

Abstract

Substitution for aspartic acid by glycine at position 614 in the spike (S) protein of severe acute respiratory syndrome coronavirus 2 appears to facilitate rapid viral spread. The G614 strain and its recent variants are now the dominant circulating forms. We report here cryo-EM structures of a full-length G614 S trimer, which adopts three distinct prefusion conformations differing primarily by the position of one receptor-binding domain. A loop disordered in the D614 S trimer wedges between domains within a protomer in the G614 spike. This added interaction appears to prevent premature dissociation of the G614 trimer, effectively increasing the number of functional spikes and enhancing infectivity, and to modulate structural rearrangements for membrane fusion. These findings extend our understanding of viral entry and suggest an improved immunogen for vaccine development.

https://science.sciencemag.org/content/early/2021/03/16/science.abf2303?rss=1

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Reporter : Irina Robu, PhD

https://pharmaceuticalintelligence.com/2021/02/17/covid-19-vaccine-rollout-risks-and-challenges/

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Reporter: Aviva Lev-Ari, PhD, RN

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Tiny biologic drug to fight COVID-19 show promise in animal models

Reporter : Irina Robu, PhD

https://pharmaceuticalintelligence.com/2020/10/11/tiny-biologic-drug-to-fight-covid-19-show-promise-in-animal-models/

Miniproteins against the COVID-19 Spike protein may be therapeutic

Reporter: Stephen J. Williams, PhD

https://pharmaceuticalintelligence.com/2020/09/30/miniproteins-against-the-covid-19-spike-protein-may-be-therapeutic/

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Llama inspired “AeroNabs” to strangle COVID-19 with an inhaler 

Reporter : Irina Robu, PhD

Llama and other camelids fight off pathogens like viruses with tiny antibodies called nanobodies. A USCF team used protein engineering to make a synthetic nanobody that prevents the spike protein on the surface of SARS-CoV-2 from binding to healthy cells and infecting them. The team indicates promising preclinical results for aerosol formulation and can be used as a self-administered form of protein against the virus.

According to the UCSF team, an aerosolized form of nanobody exhibit SARS-CoV-2 incapable of binding to the ACE2 receptor on healthy cells that line airways. The synthetic nanobody stays functional after it was freeze-dried, exposed to heat and aerosolized.

The researchers ongoing screening a library of synthetic nanobodies, ultimately landing on 21 that banned the spike-ACE2 interaction. The scientists decided that in order to be truly efficient, a nanobody based treatment with interact with all three of the receptor binding domains on the spike protein that attaches to ACE2.  Their solution was to engineer a molecular chain that connects three nanobodies together, which would ensure that when one of the nanobodies attached to RBD, the others would link to the two remaining RBD. This molecular chain resulted in a drug candidate proved to be 200,000 times more potent than a single antibody.

At the same time, ExeVir Bio is also developing an aerosolized COVID-19 treatment inspired by llamas and is currently trying to advance its candidate into clinical trials by the end of the year. Their main candidate, VHH-72Fc was considered to bind to an epitope that is found both in SARS-CoV-2 and SARS-CoV. Yet, the llama inspired treatments are still behind antibody efforts like that of Regeneron.

Even though, there are multiple vaccines in development, researchers at UCSF believe that AeroNabs can be used as a sort of personal protective equipment until vaccines become available. The same researchers are planning human trials and are in discussion with partners who can provide manufacturing and distribution backing.

SOURCE

https://www.fiercebiotech.com/research/ucsf-engineers-develop-llama-inspired-aeronabs-to-strangle-covid-19-inhaler

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Blood Clots Tied to Coronavirus Problems

Reporter: Irina Robu, PhD

Frequent complications of COVID-19 include purple rashes, swollen legs, clogged catheters and sudden death. Anyone with a severe illness is at risk of developing clots, but hospitalized patients with COVID-19 appear to be more susceptible. Blood clots in the deep veins of the body can occur due to injury/damage, inactivity, surgery, chemotherapy for cancer. Injuries like bone fractures or muscle tears can cause damage to blood vessels, leading to clots. Yes, due to long periods of inactivity, gravity causes blood to stagnate in the lowest areas of your body.

Yet, blood clots can form a variety of reasons. One of the most known blood clots that form in veins is pulmonary embolism caused by deep vein thrombosis. In some cases, a pulmonary embolism can be difficult to diagnose when you have an underlying lung or heart condition. It is possible that anything that gets in the bloodstream and then lodges in the smaller pulmonary arteries can be a pulmonary embolism.

Research from Netherlands and France suggest that clots appear in 20% to 30% of critically ill COVID-19 patients. Researchers have a few credible hypotheses to explain the phenomenon and they are starting to launch studies aimed at gaining mechanistic visions. But with the death toll rising, they are also scrambling to test clot-curbing medications. Common anticoagulant blood thinners such as warfarin and enoxaparin don’t reliably avert clotting in people with COVID-19 and young people are dying of strokes caused by the blockages in the brain. It is indicated that patients in the hospital have extremely elevated levels of a protein fragment called D-dimer, which is generated when a clot breaks down. High levels of D-dimer appear to be a powerful predictor of mortality in hospitalized patients infected with coronavirus.

Jeffrey Laurence, a hematologist at Weill Cornell Medicine in New York City studied lung and skin samples from three people infected with COVID-19 and found that the capillaries were clogged with clots. Even with all the research, how clotting occurs is still a mystery. One probability is that SARS-CoV-2 is unswervingly attacking the endothelial cells that line the blood vessels, which harbor the same ACE2 receptor that the virus uses to enter lung cells. This is confirmed by researchers from University Hospital Zurich in Switzerland and Brigham and Women’s Hospital in Boston, Massachusetts, who observed SARS-Cov-2 in endothelial cells inside kidney tissue.

Clotting can also be affected by the virus effects, because in some people COVID-19 prompts immune cells to release a torrent of chemical signals that ramps up inflammation. As the virus appears to activate the complement system, it then sparks clotting which acts a defense mechanism. People with the COVID-19 disease who become hospitalized usually have a number of risk factors for clotting such as high blood pressure, diabetes and/or genetic predisposition to clotting.

While researchers initiate how clotting occurs in people with COVID-19, they’re hurrying to test new therapies meant at preventing and busting clots. Blood-thinning medications are usually the standard of care for patients in the intensive-care unit and patients with COVID-19 are no exception. Similar trials are planned for scientists at Beth Israel Deaconess Medical Center have started enrolment for a clinical trial to evaluate an even more powerful clot-busting medication, tissue plasminogen activator. TPK is a drug more potent that carries higher risks of serious bleeding than do blood thinners. Scientists anticipate that these trials and others will deliver the data required to help physicians to make difficult treatment decisions.

SOURCE

https://www.scientificamerican.com/article/blood-clots-are-mysteriously-tied-to-many-coronavirus-problems/?fbclid=IwAR2SsBh00fkPjSqgCYyFpwCu6FlZbmnsYtSDYHqZ7xW_Dw2yP7f9HaLUhTE

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