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Diamond Light Source: contributions to SARS-CoV-2 biology and therapeutics.

ABSTRACT: The impact of COVID-19 on public health and the global economy has led to an unprecedented research response, with a major emphasis on the development of safe vaccines and drugs. However, effective, safe treatments typically take over a decade to develop and there are still no clinically approved therapies to treat highly pathogenic coronaviruses. Repurposing of known drugs can speed up development and this strategy, along with the use of biologicals (notably monoclonal antibody therapy) and vaccine development programmes remain the principal routes to dealing with the immediate impact of COVID-19. Nevertheless, the development of broadly-effective highly potent antivirals should be a major longer term goal. Structural biology has been applied with enormous effect, with key proteins structurally characterised only weeks after the SARS-CoV-2 sequence was released. Open-access to advanced infrastructure for structural biology techniques at synchrotrons and high-end cryo-EM and NMR centres has brought these technologies centre-stage in drug discovery. We summarise the role of Diamond Light Source in responses to the pandemic and note the impact of the immediate release of results in fuelling an open-science approach to early-stage drug discovery.

SUBMITTER: Walsh MA

PROVIDER: S-EPMC7676326 | biostudies-literature |

REPOSITORIES: biostudies-literature

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SARS-CoV-2: Structure, Biology, and Structure-Based Therapeutics Development.

Project description:The pandemic of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been posing great threats to the world in many aspects. Effective therapeutic and preventive approaches including drugs and vaccines are still unavailable although they are in development. Comprehensive understandings on the life logic of SARS-CoV-2 and the interaction of the virus with hosts are fundamentally important in the fight against SARS-CoV-2. In this review, we briefly summarized the current advances in SARS-CoV-2 research, including the epidemic situation and epidemiological characteristics of the caused disease COVID-19. We further discussed the biology of SARS-CoV-2, including the origin, evolution, and receptor recognition mechanism of SARS-CoV-2. And particularly, we introduced the protein structures of SARS-CoV-2 and structure-based therapeutics development including antibodies, antiviral compounds, and vaccines, and indicated the limitations and perspectives of SARS-CoV-2 research. We wish the information provided by this review may be helpful to the global battle against SARS-CoV-2 infection.

| S-EPMC7723891 | biostudies-literature

Structures from "Engineering Neutralizing SARS-CoV Antibodies to Bind SARS-CoV-2"

Project description: Not available

| S-BSST379 | biostudies-other

Sec-Eliminating the SARS-CoV-2 by AlGaN Based High Power Deep Ultraviolet Light Source.

Project description:The world-wide spreading of coronavirus disease (COVID-19) has greatly shaken human society, thus effective and fast-speed methods of non-daily-life-disturbance sterilization have become extremely significant. In this work, by fully benefitting from high-quality AlN template (with threading dislocation density as low as ≈6×108 cm-2) as well as outstanding deep ultraviolet (UVC-less than 280 nm) light-emitting diodes (LEDs) structure design and epitaxy optimization, high power UVC LEDs and ultra-high-power sterilization irradiation source are achieved. Moreover, for the first time, a result in which a fast and complete elimination of SARS-CoV-2 (the virus causes COVID-19) within only 1 s is achieved by the nearly whole industry-chain-covered product. These results advance the promising potential in UVC-LED disinfection particularly in the shadow of COVID-19.

| S-EPMC7744859 | biostudies-literature

I22: SAXS/WAXS beamline at Diamond Light Source - an overview of 10 years operation.

Project description:Beamline I22 at Diamond Light Source is dedicated to the study of soft-matter systems from both biological and materials science. The beamline can operate in the range 3.7 keV to 22 keV for transmission SAXS and 14 keV to 20 keV for microfocus SAXS with beam sizes of 240 µm × 60 µm [full width half-maximum (FWHM) horizontal (H) × vertical (V)] at the sample for the main beamline, and approximately 10 µm × 10 µm for the dedicated microfocusing platform. There is a versatile sample platform for accommodating a range of facilities and user-developed sample environments. The high brilliance of the insertion device source on I22 allows structural investigation of materials under extreme environments (for example, fluid flow at high pressures and temperatures). I22 provides reliable access to millisecond data acquisition timescales, essential to understanding kinetic processes such as protein folding or structural evolution in polymers and colloids.

| S-EPMC8127364 | biostudies-literature

Discovering small-molecule therapeutics against SARS-CoV-2.

Project description:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly become a global health pandemic. The lack of effective treatments, coupled with its etiology, has resulted in more than 400,000 deaths at the time of writing. The SARS-CoV-2 genome is highly homologous to that of SARS-CoV, the causative agent behind the 2003 SARS outbreak. Based on prior reports, clinicians have pursued the off-label use of several antiviral drugs, while the scientific community has responded by seeking agents against traditional targets, especially viral proteases. However, several avenues remain unexplored, including disrupting E and M protein oligomerization, outcompeting host glycan-virus interactions, interfering with the heparan sulfate proteoglycans-virus interaction, and others. In this review, we highlight some of these opportunities while summarizing the drugs currently in use against coronavirus 2019 (COVID-19).

| S-EPMC7305878 | biostudies-literature

Ambient-pressure endstation of the Versatile Soft X-ray (VerSoX) beamline at Diamond Light Source.

Project description:The ambient-pressure endstation and branchline of the Versatile Soft X-ray (VerSoX) beamline B07 at Diamond Light Source serves a very diverse user community studying heterogeneous catalysts, pharmaceuticals and biomaterials under realistic conditions, liquids and ices, and novel electronic, photonic and battery materials. The instrument facilitates studies of the near-surface chemical composition, electronic and geometric structure of a variety of samples using X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine-structure (NEXAFS) spectroscopy in the photon energy range from 170 eV to 2800 eV. The beamline provides a resolving power hν/Δ(hν) > 5000 at a photon flux > 1010 photons s-1 over most of its energy range. By operating the optical elements in a low-pressure oxygen atmosphere, carbon contamination can be almost completely eliminated, which makes the beamline particularly suitable for carbon K-edge NEXAFS. The endstation can be operated at pressures up to 100 mbar, whereby XPS can be routinely performed up to 30 mbar. A selection of typical data demonstrates the capability of the instrument to analyse details of the surface composition of solid samples under ambient-pressure conditions using XPS and NEXAFS. In addition, it offers a convenient way of analysing the gas phase through X-ray absorption spectroscopy. Short XPS spectra can be measured at a time scale of tens of seconds. The shortest data acquisition times for NEXAFS are around 0.5 s per data point.

| S-EPMC7467337 | biostudies-literature

Biology of the SARS-CoV-2 Coronavirus.

Project description:New coronavirus infection causing COVID-19, which was first reported in late 2019 in China, initiated severe social and economic crisis that affected the whole world. High frequency of the errors in replication of RNA viruses, zoonotic nature of transmission, and high transmissibility allowed betacoronaviruses to cause the third pandemic in the world since the beginning of 2003: SARS-CoV in 2003, MERS-CoV in 2012, and SARS-CoV-2 in 2019. The latest pandemic united scientific community and served as a powerful impetus in the study of biology of coronaviruses: new routes of virus penetration into the human cells were identified, features of the replication cycle were studied, and new functions of coronavirus proteins were elucidated. It should be recognized that the pandemic was accompanied by the need to obtain and publish results within a short time, which led to the emergence of an array of conflicting data and low reproducibility of research results. We systematized and analyzed scientific literature, filtered the results according to reliability of the methods of analysis used, and prepared a review describing molecular mechanisms of functioning of the SARS-CoV-2 coronavirus. This review considers organization of the genome of the SARS-CoV-2 virus, mechanisms of its gene expression and entry of the virus into the cell, provides information on key mutations that characterize different variants of the virus, and their contribution to pathogenesis of the disease.

| S-EPMC9839213 | biostudies-literature

Chemistry and Biology of SARS-CoV-2.

Project description:SARS-CoV-2 (previously 2019-nCoV or Wuhan coronavirus) caused an unprecedented fast-spreading worldwide pandemic. Although currently with a rather low mortality rate, the virus spread rapidly over the world using the modern world's traffic highways. The coronavirus (CoV) family members were responsible for several deadly outbreaks and epidemics during the last decade. Not only governments but also the scientific community reacted promptly to the outbreak, and information is shared quickly. For example, the genetic fingerprint was shared, and the 3D structure of key proteins was rapidly solved, which can be used for the discovery of potential treatments. An overview is given on the current knowledge of the spread, disease course, and molecular biology of SARS-CoV-2. We discuss potential treatment developments in the context of recent outbreaks, drug repurposing, and development timelines.

| S-EPMC7243793 | biostudies-literature

Angiotensin receptor blockers as tentative SARS-CoV-2 therapeutics.

Project description:At the time of writing this commentary (February 2020), the coronavirus COVID-19 epidemic has already resulted in more fatalities compared with the SARS and MERS coronavirus epidemics combined. Therapeutics that may assist to contain its rapid spread and reduce its high mortality rates are urgently needed. Developing vaccines against the SARS-CoV-2 virus may take many months. Moreover, vaccines based on viral-encoded peptides may not be effective against future coronavirus epidemics, as virus mutations could make them futile. Indeed, new Influenza virus strains emerge every year, requiring new immunizations. A tentative suggestion based on existing therapeutics, which would likely be resistant to new coronavirus mutations, is to use available angiotensin receptor 1 (AT1R) blockers, such as losartan, as therapeutics for reducing the aggressiveness and mortality from SARS-CoV-2 virus infections. This idea is based on observations that the angiotensin-converting enzyme 2 (ACE2) very likely serves as the binding site for SARS-CoV-2, the strain implicated in the current COVID-19 epidemic, similarly to strain SARS-CoV implicated in the 2002-2003 SARS epidemic. This commentary elaborates on the idea of considering AT1R blockers as tentative treatment for SARS-CoV-2 infections, and proposes a research direction based on datamining of clinical patient records for assessing its feasibility.

| S-EPMC7228359 | biostudies-literature

Antiviral Peptides as Promising Therapeutics against SARS-CoV-2.

Project description:Over 50 peptides, which were known to inhibit SARS-CoV-1, were computationally screened against the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2. Based on the binding affinity and interaction, 15 peptides were selected, which showed higher affinity compared to the α-helix of the human ACE2 receptor. Molecular dynamics simulation demonstrated that two peptides, S2P25 and S2P26, were the most promising candidates, which could potentially block the entry of SARS-CoV-2. Tyr489 and Tyr505 residues present in the "finger-like" projections of the RBD were found to be critical for peptide interaction. Hydrogen bonding and hydrophobic interactions played important roles in prompting peptide-protein binding and interaction. Structure-activity relationship indicated that peptides containing aromatic (Tyr and Phe), nonpolar (Pro, Gly, Leu, and Ala), and polar (Asn, Gln, and Cys) residues were the most significant contributors. These findings can facilitate the rational design of selective peptide inhibitors targeting the spike protein of SARS-CoV-2.

| S-EPMC7605242 | biostudies-literature

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