Fluorescence signatures of SARS CoV-2 spike S1 proteins and an human ACE-2: excitation-emission maps and fluorescence lifetimes

Fast and reliable detection of infectious virus loads of the SARS CoV-2 virus is still an important issue even after more than one year of the pandemic's outbreak. The spike protein's S1 subunit (including its receptor-binding domain) and human angiotensin-converting enzyme 2 (hACE2) are known as key players in the reproduction mechanism of the SARS CoV-2 virus. Because of its high sensitivity and simple application, fluorescence spectroscopy is promising to meet the sensitivity requirements for a virus detection in a clean environment. In such highly complex protein systems, a comprehensive knowledge of fluorescence data is presumed in order to evaluate the specificity of the spectra with respect to a possible detection. This includes full featured information on the fluorescence process, i. e. wavelength and time-dependent data. In this work, fluorescence spectral excitation-emission maps of the involved proteins are presented, namely the S1 part of the spike protein and its receptor-binding domain as well as the hACE2 enzyme. In addition, measurements of fluorescence lifetimes of the proteins are presented and analyzed by a bi-exponential kinetic approach.

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Engineered ACE2 counteracts vaccine-evading SARS-CoV-2 Omicron variant

10.1101/2021.12.22.473804 ◽

2021 ◽

Author(s):

Nariko Ikemura ◽

Shunta Taminishi ◽

Tohru Inaba ◽

Takao Arimori ◽

Daisuke Motooka ◽

...

Keyword(s):

Receptor Binding ◽

Mutational Analysis ◽

High Sensitivity ◽

Binding Domain ◽

Spike Protein ◽

The Novel ◽

Receptor Binding Domain ◽

Therapeutic Drugs ◽

Viral Mutation ◽

Therapeutic Value

The novel SARS-CoV-2 variant, Omicron (B.1.1.529) contains an unusually high number of mutations (>30) in the spike protein, raising concerns of escape from vaccines, convalescent sera and therapeutic drugs. Here we analyze the alteration of neutralizing titer with Omicron pseudovirus. Sera of 3 months after double BNT162b2 vaccination exhibit approximately 18-fold lower neutralization titers against Omicron. Convalescent sera from Alpha and Delta patients allow similar levels of breakthrough by Omicron. However, some Delta patients have relatively preserved neutralization efficacy, comparable to 3-month double BNT162b2 vaccination. Domain-wise analysis using chimeric spike revealed that this efficient evasion was, at least in part, caused by multiple mutations in the N-terminal domain. Omicron escapes the therapeutic cocktail of imdevimab and casirivimab, whereas sotrovimab, which targets a conserved region to avoid viral mutation, remains effective against Omicron. The ACE2 decoy is another virus-neutralizing drug modality that is free, at least in theory, from mutational escape. Deep mutational analysis demonstrated that, indeed, the engineered ACE2 overcomes every single-residue mutation in the receptor-binding domain, similar to immunized sera. Like previous SARS-CoV-2 variants, Omicron and some other sarbecoviruses showed high sensitivity against engineered ACE2, confirming the therapeutic value against diverse variants, including those that are yet to emerge.

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An interactive COVID-19 virus Mutation Tracker (CovMT) with a particular focus on critical mutations in the Receptor Binding Domain (RBD) region of the Spike protein

10.1101/2021.01.22.21249716 ◽

2021 ◽

Author(s):

Intikhab Alam ◽

Aleksandar Radovanovic ◽

Roberto Incitti ◽

Allan Kamau ◽

Muhammad Alarawi ◽

...

Keyword(s):

United Kingdom ◽

Receptor Binding ◽

Treatment Strategies ◽

Binding Domain ◽

Spike Protein ◽

Receptor Binding Domain ◽

Link Type ◽

The United Kingdom ◽

Public Resources ◽

One Year

AbstractAlmost one year has passed since the appearance of SARS-CoV-2, causing the COVID-19 pandemic. The number of confirmed SARS-Cov-2 cases worldwide has now reached ∼92 million, with 2 million reported deaths (https://covid19.who.int). Nearly 400,000 SARS-Cov-2 genomes were sequenced from COVID-19 samples and added to public resources such as GISAID (https://gisaid.org). With the vaccines becoming available or entering trials (https://covid19.trackvaccines.org), it is vital to keep track of mutations in the genome of SARS-CoV-2, especially in the Spike protein’s Receptor Binding Domain (RBD) region, which could have a potential impact on disease severity and treatment strategies.1–3 In the wake of a recent increase in cases with a potentially more infective RBD mutation (N501Y) in the United Kingdom, countries worldwide are concerned about the spread of this or similar variants. Impressive sampling and timely increase in sequencing efforts related to COVID-19 in the United Kingdom (UK) helped detect and monitor the spread of the new N501Y variant. Similar sequencing efforts are needed in other countries for timely tracking of this or different variants. To track geographic sequencing efforts and mutations, with a particular focus on RBD region of the Spike protein, we present our daily updated COVID-19 virus Mutation Tracker system, see https://www.cbrc.kaust.edu.sa/covmt.

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Improved production of SARS-CoV-2 spike receptor-binding domain (RBD) for serology assays

10.1101/2020.11.18.388868 ◽

2020 ◽

Author(s):

Jennifer Mehalko ◽

Matthew Drew ◽

Kelly Snead ◽

John-Paul Denson ◽

Vanessa Wall ◽

...

Keyword(s):

Receptor Binding ◽

Protein Production ◽

High Sensitivity ◽

Magnetic Bead ◽

Binding Domain ◽

List Type ◽

Receptor Binding Domain ◽

Dna Elements ◽

Increased Sensitivity ◽

Higher Sensitivity

AbstractThe receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is a commonly used antigen for serology assays critical to determining the extent of SARS-CoV-2 exposure in the population. Different versions of the RBD protein have been developed and utilized in assays, with higher sensitivity attributed to particular forms of the protein. To improve the yield of these high-sensitivity forms of RBD and support the increased demand for this antigen in serology assays, we investigated several protein expression variables including DNA elements such as promoters and signal peptides, cell culture expression parameters, and purification processes. Through this investigation, we developed a simplified and robust purification strategy that consistently resulted in high levels of the high-sensitivity form of RBD and demonstrated that a carboxyterminal tag is responsible for the increased sensitivity in the ELISA. These improved reagents and processes produce high-quality proteins which are functional in serology assays and can be used to investigate seropositivity to SARS-CoV-2 infection.Highlights: Improved yields of SARS-CoV-2 spike RBD through modification of DNA constructs and purification parametersTwo versions of RBD show different sensitivity in serology assaysYields of greater than 50 mg/l obtained under optimal conditionsMagnetic bead purification technology improves throughput of protein production

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Destabilizing the Structural Integrity of SARS-CoV2 Receptor Proteins by Curcumin Along with Hydroxychloroquine: An Insilco Approach for a Combination Therapy

10.26434/chemrxiv.12090438.v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Akhileshwar Srivastava ◽

Divya Singh

Keyword(s):

Binding Energy ◽

Combination Therapy ◽

Receptor Binding ◽

Structural Integrity ◽

Binding Domain ◽

Receptor Binding Domain ◽

Receptor Proteins ◽

Main Protease ◽

The Stability ◽

Therapeutic Activities

Presently, an emerging disease (COVID-19) has been spreading across the world due to coronavirus (SARS-CoV2). For treatment of SARS-CoV2 infection, currently hydroxychloroquine has been suggested by researchers, but it has not been found enough effective against this virus. The present study based on in silico approaches was designed to enhance the therapeutic activities of hydroxychloroquine by using curcumin as an adjunct drug against SARS-CoV2 receptor proteins: main-protease and S1 receptor binding domain (RBD). The webserver (ANCHOR) showed the higher protein stability for both receptors with disordered score (<0.5). The molecular docking analysis revealed that the binding energy (-24.58 kcal/mol) of hydroxychloroquine was higher than curcumin (-20.47 kcal/mol) for receptor main-protease, whereas binding energy of curcumin (<a>-38.84</a> kcal/mol) had greater than hydroxychloroquine<a> (-35.87</a> kcal/mol) in case of S1 receptor binding domain. Therefore, this study suggested that the curcumin could be used as combination therapy along with hydroxychloroquine for disrupting the stability of SARS-CoV2 receptor proteins

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Amoxicillin Trihydrate-Clavulanate Potassium As Potential Inhibitor of 2019 Novel Coronavirus Main Protease with Strong Receptor-Binding Domain (RBD), Molecular Docking and SAR Study

SSRN Electronic Journal ◽

10.2139/ssrn.3580230 ◽

2020 ◽

Author(s):

Khedidja benarous ◽

Talia Serseg ◽

Mohamed Yousfi

Keyword(s):

Molecular Docking ◽

Receptor Binding ◽

Binding Domain ◽

Receptor Binding Domain ◽

Potential Inhibitor ◽

Main Protease ◽

Amoxicillin Trihydrate ◽

Novel Coronavirus ◽

Sar Study

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Amoxicillin and Clavulanate as Potential Multiple Effect Inhibitors of 2019 Novel Coronavirus Main Protease and RNA-Dependent RNA Polymerase with Strong Receptor-Binding Domain (RBD), Molecular Docking and SAR Study

SSRN Electronic Journal ◽

10.2139/ssrn.3618303 ◽

2020 ◽

Author(s):

Khedidja benarous ◽

Talia Serseg ◽

Mohamed Yousfi

Keyword(s):

Molecular Docking ◽

Rna Polymerase ◽

Receptor Binding ◽

Binding Domain ◽

Receptor Binding Domain ◽

Rna Dependent Rna Polymerase ◽

Multiple Effect ◽

Main Protease ◽

Novel Coronavirus ◽

Sar Study

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Role of key point Mutations in Receptor Binding Domain of SARS-CoV-2 Spike Glycoprotein

Infectious Disorders - Drug Targets ◽

10.2174/1871526520666200804161650 ◽

2020 ◽

Vol 20 ◽

Author(s):

Bipin Singh

Keyword(s):

Receptor Binding ◽

Point Mutations ◽

Binding Domain ◽

Receptor Binding Domain ◽

Spike Glycoprotein ◽

Angiotensin Converting Enzyme 2 ◽

Recent Outbreak ◽

Novel Coronavirus ◽

Genomic Similarity

: The recent outbreak of novel coronavirus (SARS-CoV-2 or 2019-nCoV) and its worldwide spread is posing one of the major threats to human health and the world economy. It has been suggested that SARS-CoV-2 is similar to SARSCoV based on the comparison of the genome sequence. Despite the genomic similarity between SARS-CoV-2 and SARSCoV, the spike glycoprotein and receptor binding domain in SARS-CoV-2 shows the considerable difference compared to SARS-CoV, due to the presence of several point mutations. The analysis of receptor binding domain (RBD) from recently published 3D structures of spike glycoprotein of SARS-CoV-2 (Yan, R., et al. (2020); Wrapp, D., et al. (2020); Walls, A. C., et al. (2020)) highlights the contribution of a few key point mutations in RBD of spike glycoprotein and molecular basis of its efficient binding with human angiotensin-converting enzyme 2 (ACE2).

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