Sandbox 20005

SARS-CoV-2 virus. The spikes, that adorn the virus surface, impart a corona like appearance (Fusion Animation).

A novel coronavirus SARS-CoV-2, detected in Wuhan, China in 2019, was found to cause severe respiratory illness named COVID-19^[1].

There’s a new NCBI site on COVID-19/SARS-CoV-2. It will help bench scientists, bioinformaticians, clinicians & others connect with information they need to study SARS-CoV-2 and end the pandemic.

A video (by Elara) shows how the virus interacts with its human (host) cells, via its spikes (3D structure determined in the McLellan Lab^[2]) and Wrobel, Benton & Gamblin labs PMID32647346</ref> (from the Crick Institute), thus permitting the viral genome to enter its host & begin infection.

Potential treatments for COVID-19

• Human trials begin on coronavirus vaccine developed by Univ of Queensland, Australia.

• US company trials coronavirus vaccine candidate in Australia

• COVID-19: What are our therapeutic options? - Slides courtesy of Prof. Mamta K. Jain, MD, MPH, UT Southwestern Medical Center.

• Oxygen administration could be more important than pressurised air when treating the illness induced by SARS-CoV-2. Homology modeling & molecular docking suggests that SARS-CoV-2 reduces hemoglobin's capacity to carry oxygen, resulting in the respiratory syndrome ^[3].

• Oxford Univ begins enrolling over 500 volunteers for a coronavirus vaccine trial, additional information at The Jenner Inst.

• An int'l group of scientists (UK, Israel & USA) are trying to combat COVID-19 via a massive crystal-based fragment screen. They determined 3D structures of over 90 fragments with 66 in the active site. Details are available at the Diamond Light Source. Contributions are welcome in many different forms PostEra.

• 31-Mar-2020 NY Times C.D.C. Weighs Advising Everyone to Wear a Mask.

• 27-Mar-2020 Science - Not wearing masks to protect against coronavirus is a big mistake, Dr. George Gao, Director General of the Chinese CDC says in Science.

• 23-Mar-2020 A USA, French & UK study identified 69 drugs to test against the coronavirus^[4]. As reported in the NY Times.

• 20-Mar-2020 - Analysis by Abby Olena in The Scientist on Remdesivir Works Against Coronaviruses in the Lab

Videos helping to explain COVID-19

The Czech Republic took the uncommon step of making wearing of masks mandatory in public spaces, prompting a grassroots effort to make masks, with wonderful results
.
Html5mediator: file extension not recognized
Scientists have turned the coronavirus spike protein structure into music(!!), as reported in Science by Soundcloud.


Japan researchers show how Coronavirus spreads through micro droplets. These tiny droplets containing the virus can stay in the air for extended periods.


Speaking face-to-face is exchanging saliva, so stop speaking face-to-face and stay healthy by stoptheviruscovid.


Modeling an epidemic (6-Mar-2020) We're not ready for the next epidemic by 3blue1brown.


Fighting Coronavirus with Soap by PDB-101.


Animation of 3D structure/function of Coronavirus-CoV-2 proteins by biolution GmBH.


COVID-19 outbreak shown via 3D animation (11-Feb 11-2020) by Sci Animations.


Bill Gates Ted Talk (3-Apr-2015) We're not ready for the next epidemic by Ted Talks.

George W. Bush urged us to prepare for future pandemics in 2005, at the NIH.


Jürgen Bosch Presentation (31-Mar-2020) Coronavirus: How it Ticks and What we are Doing to Stop it by Jürgen Bosch.

Useful sites on COVID-19

• What You Need to Know About the COVID-19 and HIV in English and Spanish from TheBody (The HIV/AIDS Resource).

• Coronavirus SARS-CoV-2: Filtering fact from fiction in the infodemic Q&A with virologist Prof. Urs Greber by Daniela Ruffell in FEBS Lett^[5].

• Computational predictions of 3D structures of COVID-19 proteins based on the AI AlphaFold system. Coordinates of the 3D structures can be download as a zip file.

• Up to date statistics on Coronavirus cases world-wide at worldometer

• A summary of key findings about COVID-19 can be found at the CDC.

• Coronavirus Evolved Naturally, and ‘Is Not a Laboratory Construct,’ in a study in Nature Med by Anderson and colleagues ^[6].

• Scientists are endeavoring to find antivirals specific to the virus. Several drugs such as chloroquine, arbidol, remdesivir & favipiravir are undergoing trials to test their efficacy & safety in the treatment of COVID-19 in China, with some promising results.^[7].

• A computer game, developed at the Inst for Protein Design (Univ Washington), is being used to try to find new lead compounds that might become drugs to treat COVID-19.

SARS-CoV-2 virus proteins

The genome of the SARS-CoV-2 virus codes for 28 proteins: Out of those, 19 have already been characterized structurally.
Details of the 3D structure & function of the key proteins & RNA inside the virus can be seen in the NY Times Bad News Wrapped in Protein: Inside the Coronavirus Genome.

• Main protease: it is a cysteine protease that is essential for the viral life cycle.
• NSP1: Host translation inhibitor nsp1. Inhibits host translation by interacting with the 40S ribosomal subunit.
• NSP2: Non-structural protein 2.
• Papain-like proteinase
• NSP4: Non-structural protein 4.
• Proteinase 3CL-PRO
• NSP6: Non-structural protein 6.
• NSP7: Non-structural protein 7.
• NSP8: Non-structural protein 8.
• NSP9: Non-structural protein 9.
• NSP10: Non-structural protein 10.
• RNA-directed RNA polymerase (RdRp)
• Helicase (Hel): Multi-functional protein with a zinc-binding domain in N-terminus
• Guanine-N7 methyltransferase (ExoN)
• Uridylate-specific endoribonuclease (NendoU)
• 2'-O-methyltransferase (2'-O-MT): Methyltransferase that mediates mRNA cap 2'-O-ribose methylation to the 5'-cap structure of viral mRNAs.
• Surface glycoprotein (S)
• ORF3a: Forms homotetrameric potassium sensitive ion channels (viroporin) and may modulate virus release.
• Protein E: Plays a central role in virus morphogenesis and assembly.
• Protein M: Component of the viral envelope.
• ORF6: Could be a determinant of virus virulence.
• ORF7a: Non-structural protein which is dispensable for virus replication in cell culture.
• ORF8: Open Reading Frame 8.
• Protein N: Packages the positive strand viral genome RNA into a helical ribonucleocapsid (RNP).
• ORF10‎: It is currently unclear whether this region translates into a functional protein.

3D structural studies on SARS-CoV-2 virus

• A team of UK & Israeli scientists determined the 3D structures of over 90 fragments, 66 of which are in the active site. All the experimental details and results are available online at the Diamond Light Source'.

• A team of Chinese scientists determined, by Cryo-EM, the coronavirus spike receptor-binding domain complexed with its receptor ACE2 PDB-ID 6lzg (To be published).

• A team of US and Chinese scientists determined the crystal structure of 2019-nCoV spike receptor-binding domain bound with ACE2 6m0j

• A team of US scientists determined, by Cryo-EM, the structure of the SARS-CoV-2 spike glycoprotein (open & closed states) ^[8], PDB-ID 6vxx and 6vyb

• Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody CR3022 6w41

• Crystal Structure of the methyltransferase-stimulatory factor complex of NSP16 and NSP10 from SARS CoV-2 6w61 (To be published).

• Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 in complex with AMP 6w6y (To be published).

• Structure of NSP10 - NSP16 Complex from SARS-CoV-2 6w75 (To be published).

• Crystal structure of SARS-CoV-2 nucleocapsid protein N-terminal RNA binding domain 6m3m (To be published).

• Crystal structure of Nsp9 RNA binding protein of SARS CoV-2 6w4b (To be published).

• Crystal Structure of NSP16 - NSP10 Complex from SARS-CoV-2 6w4h (To be published).

• A Cryo-EM study by Zhou & colleagues on the structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2 gives insights to the molecular basis for coronavirus recognition and infection^[9] 6m17.

• Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from SARS coronavirus 2 6vyo (To be published).

• Crystal structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with a Citrate 6w01 (To be published).

• Crystal structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 in the complex with ADP ribose 6w02 (To be published).

• Crystal structure of 2019-nCoV chimeric receptor-binding domain complexed with its receptor human ACE2 6vw1

• Crystal structure of NSP15 Endoribonuclease from SARS CoV-2 6vww (To be published).

• Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 6vxs (To be published).

• Crystal structure of the 2019-nCoV HR2 Domain 6lvn (To be published).

• Crystal structure of post fusion core of 2019-nCoV S2 subunit 6lxt.

• Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors, from the Hilgenfeld lab^[10], Apo Struture: PDB-ID 6y2e, and complexes with inhibitors: PDB-ID 6y2f and 6y2g.

• 3D Structure of RNA-dependent RNA polymerase from COVID-19, a major antiviral drug target from the Rao lab in Beijing^[11].

• Crystal structure of the Mpro from COVID-19 and discovery of inhibitors in a study by scientists from Shanghai & Beijing^[12], PDB-ID 6lu7.

• Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2 in a study by scientists from USA^[13], PDB-ID 6w01.

• The CoV spike (S) glycoprotein is a key target for vaccines, therapeutic antibodies, and diagnostics. A study by McLellan and colleagues in "Science" on the Cryo-EM structure of the COVID-19 spike protein. This structure should greatly aid in the rapid development and evaluation of medical countermeasures to address the ongoing public health crisis^[2], PDB-ID 6vsb.

• Public resource for the structures from beta-coronavirus with a focus on SARS-CoV and SARS-CoV-2

References

1. ↑ Naming the coronavirus disease (COVID-19) and the virus that causes it
2. ↑ ^{2.0 2.1} Wrapp D, Wang N, Corbett KS, Goldsmith JA, Hsieh CL, Abiona O, Graham BS, McLellan JS. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science. 2020 Feb 19. pii: science.abb2507. doi: 10.1126/science.abb2507. PMID:32075877 doi:http://dx.doi.org/10.1126/science.abb2507
3. ↑ COVID-19 Disease ORF8 and Surface Glycoprotein Inhibit Heme Metabolism by Binding to Porphyrin [1]
4. ↑ Gordon, et al. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing: bioRxiv (online) 2020 http://doi.org/10.1101/2020.03.22.002386
5. ↑ Ruffell D. Coronavirus SARS-CoV-2: filtering fact from fiction in the infodemic: Q&A with virologist Professor Urs Greber. FEBS Lett. 2020 Apr 4. doi: 10.1002/1873-3468.13784. PMID:32246722 doi:http://dx.doi.org/10.1002/1873-3468.13784
6. ↑ Andersen, et al. The proximal origin of SARS-CoV-2: Nature Med (in press) 2020 http://dx.doi.org/10.1038/s41591-020-0820-9]
7. ↑ Dong L, Hu S, Gao J. Discovering drugs to treat coronavirus disease 2019 (COVID-19). Drug Discov Ther. 2020;14(1):58-60. doi: 10.5582/ddt.2020.01012. PMID:32147628 doi:http://dx.doi.org/10.5582/ddt.2020.01012
8. ↑ Walls AC, Park YJ, Tortorici MA, Wall A, McGuire AT, Veesler D. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell. 2020 Mar 6. pii: S0092-8674(20)30262-2. doi: 10.1016/j.cell.2020.02.058. PMID:32155444 doi:http://dx.doi.org/10.1016/j.cell.2020.02.058
9. ↑ Yan R, Zhang Y, Li Y, Xia L, Guo Y, Zhou Q. Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2. Science. 2020 Mar 4. pii: science.abb2762. doi: 10.1126/science.abb2762. PMID:32132184 doi:http://dx.doi.org/10.1126/science.abb2762
10. ↑ Zhang L, Lin D, Sun X, Curth U, Drosten C, Sauerhering L, Becker S, Rox K, Hilgenfeld R. Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors. Science. 2020 Mar 20. pii: science.abb3405. doi: 10.1126/science.abb3405. PMID:32198291 doi:http://dx.doi.org/10.1126/science.abb3405
11. ↑ Gao, et al. Structure of RNA-dependent RNA polymerase from 2019-nCoV, a major antiviral drug target: bioRxiv (online) 2020 http://doi.org/10.1101/2020.03.16.993386
12. ↑ Jin Z, Du X, Xu Y, Deng Y, Liu M, Zhao Y, Zhang B, Li X, Zhang L, Peng C, Duan Y, Yu J, Wang L, Yang K, Liu F, Jiang R, Yang X, You T, Liu X, Yang X, Bai F, Liu H, Liu X, Guddat LW, Xu W, Xiao G, Qin C, Shi Z, Jiang H, Rao Z, Yang H. Structure of M(pro) from COVID-19 virus and discovery of its inhibitors. Nature. 2020 Apr 9. pii: 10.1038/s41586-020-2223-y. doi:, 10.1038/s41586-020-2223-y. PMID:32272481 doi:http://dx.doi.org/10.1038/s41586-020-2223-y
13. ↑ Kim, et al. Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2: bioRxiv (online) 2020 http://doi.org/10.1101/2020.03.02.968388