What is the best coronavirus vaccine or therapeutic to Eternalize?

Yes the E-protein is expressed in the cytoplasm and is available for antigen generation.

Link to their viral informatics site.
https://www.sib.swiss/about-sib/news/10643-sib-experts-and-resources-in-the-fight-against-coronaviru…

SARS coronavirus 2 (SARS-CoV-2) proteome via Swiss Institute of Bioinformatics.https://viralzone.expasy.org/8996

This might be useful…
Multivariate Analyses of Codon Usage of SARS-CoV-2 and other betacoronaviruses.
https://www.biorxiv.org/content/10.1101/2020.02.15.950568v3.full.pdf

Nucleoprotein - the protein Swiss army knife

Nucleoproteins are not just hiding inside of the virus capsule. They can have multiple functions and are an active player throughout the virus production. 

According to this review paper, the nucleoprotein can: 

  • forms complexes with genomic RNA 

  • interacts with the viral membrane protein during virion assembly

  • enhancing the efficiency of virus transcription 

  • enhancing the efficiency of virus assembly

And these are just some of the mentioned functions from the paper. 

The Coronavirus Nucleocapsid Is a Multifunctional Protein

 

I found this preprint really interesting too. Excerpt from the abstract: 

“An analysis of virus-specific CD8+ T-cell immunity in 30 survivors showed that 26 of those individuals had a CD8+ response to at least one EBOV protein. The dominant response (25/26 subjects) was specific to the EBOV nucleocapsid protein (NP). It has been suggested that epitopes on the EBOV NP could form an important part of an effective T-cell vaccine for Ebola Zaire. We show that a 9-amino-acid peptide NP44-52 (YQVNNLEEI) located in a conserved region of EBOV NP provides protection against morbidity and mortality after mouse adapted EBOV challenge.” 

An Effective CTL Peptide Vaccine for Ebola Zaire Based on Survivors’ CD8+ Targeting of a Particular Nucleocapsid Protein Epitope with Potential Implications for COVID-19 Vaccine Design

Can short RNA (5-10 nucleotides) be used to inhibit the binding of the nucleoprotein to viral RNA?
If short RNA could bind to the nucleoprotein, the nucleoprotein might be prevented from binding and winding the viral RNA into the nucleocapsid.
There would be problems with such an approach that would have to be overcome, such off target binding, degradation and getting RNA through the cell membrane. Also, short RNA may not readily bind to nucleoprotein monomers.
Has this approach been tried?
If not, what sort of modifications could be done to short RNA to get around the potential problems?

This is a great idea, and it has been proposed for SARS and again recently. It would be very interesting to set these up as lab puzzles  in Eterna, and I hope you can work with others to set up player puzzles that can pilot the concept. Oligonucleotide binding can be simulated in Eterna, bu tsetting up the puzzle requires some special access at the moment. Please float in chat, and also post links here if you get things set up.

PTVYVY peptide C-terminus of E-protein. Good antigen hit.
http://www.swisstargetprediction.ch/result.php?job=859501568&organism=Homo_sapiens

LLV occurs in C-terminus & Transmembrane regions while the reverse VLL is also in Transmembrane region. LLV peptide hits DPP4 protease as top hit & is involved in viral propagation.

“…Hocke et al. (2013) undertake highly focused research on coronavirus disease. They bring out that MERS-CoV continues to cause lethal lower respiratory tract disease, raising urgent fundamental questions as to its cellular tropism and receptor usage in alveolar lung tissue, as well as to its pathogenic mechanism(s). As stated by these authors, then, in the absence of autopsy data from human victims, they succeed in modeling MERS-CoV propagation in human lung tissue and demonstrate an almost pantropic infection, as well as ubiquitous DPP4 receptor expression in bronchiole, alveoli, or vessels. Thus, Hocke et al. (2013) emphasize that antiviral approaches that block DPP4 usage are expected to reduce virus propagation in the distal parts of the respiratory tract.”

http://www.swisstargetprediction.ch/result.php?job=1699439445&organism=Homo_sapiens

![](https://d2r1vs3d9006ap.cloudfront.net/s3_images/1830735/RackMultipart20200404-98239-11gwxub-LLV_peptide segments T_C__of_E-protein_SARS-CoV2_inline.png?1585979268 “Image httpsd2r1vs3d9006apcloudfrontnets3_images1830735RackMultipart20200404-98239-11gwxub-LLV_peptide__segments__T_C__of_E-protein_SARS-CoV2_inlinepng1585979268”)

ACE2 work and Spike protein insert work, different format:
All run through SwissTargetPrediction website.

Need compliment to these ACE2 binding pockets:

Baicalin site NRH, asn-arg-his, AAU_AGA_CAU -->
UUA_UCU_GUA —> compliment LSV

Scutellarin site E-(unk)-R glu-unk-arg (don’t know what to do here)

Hesperetin site YSRE, tyr-ser-arg-glu,
UAU_UCU_CGU_GAA–> AUA_AGA_GCA_CUU —>
compliment IRAL

Nicotianamine site RESQQ, arg-glu-ser-gln-gln,
AGA_GAA_UCA_CAA_CAG–>
UCU_CUU_AGU_GUU_GUC—> compliment SLSVV

Glycyrrhizin site RQRD, arg-gln-arg-asp,
AGA_CAA_AGG_GAU–> UCU_GUU_UCC_CUA—>
compliment SVSL

ACE2 receptor activity?
in C-terminus found: VSL (5’-3’)?, NVSL or VSLV, Glycyrrhizin
site (RQRD) compliment (SVSL). This is also reverse read of
Bailcalin site (NRH) compliment (LSV).

VSL:smiles:CC©C[C@H](NC(=O)C@HNC(=O)[C@@H]
(N)C©C)C(O)=O [PTGS2 & HLA-A3 hits]

NVSL:smiles:CC©C[C@H](NC(=O)C@HNC(=O)
C@@HC©C)C(O)=O

VSLV:smiles:CC©C[C@H](NC(=O)C@HNC(=O)
C@@HC©C)C(=O)NC@@HC(O)=O
 [antigen hit]

SVSL:smiles:CC©C[C@H](NC(=O)C@HNC(=O)
C@@HC©C)C(O)=O [PTSG2 &
antigen hit]

SLSVV:smiles:CC©CC@HC(=O)N
C@@HC(=O)NC@@HC(=O)NC@@H
C(O)=O [HLA-A3 top hit, DLG4, DPP4,etc]

SLSV:smiles:CC©CC@HC(=O)N
C@@HC(=O)NC@@HC(O)=O [much better hits]
LSVV:smiles:CC©CC@HC(=O)NC@@HC(=O)N
C@@HC(=O)NC@@HC(O)=O [not as good]

LSV:smiles:[H]NC@@HC(=O)NC@@HC(=O)
NC@@HC(O)=O [ok hits bit weak]


Spike Protein LRGAAPASHR (??my error??)

CCUCGGCGGGCA = PRRA insertion in Spike Protein
[hits NTSR1/2, FURIN, WDR5, F10, HGFAC, CFB, …, PLG]

PRRA compliment = GGA_GCC_GCC_CGU = GAAP
[strong hit ACE, DPP4, CAPN1, SLC5A, XIAP, HLA-A3, PTGS2]

cagacuaauucu = QTNS 12nts before PRRA insertion
[hits DLG4, BACE1, HLA-A3, MAPK8, ADAM8, FOS JUN,…HLA-DRB3]

QTNS compliment = gucugauuaaga = VstopLR
so, LRPRRA [much stronger NTSR1/2, Furin, PCSK6, CFB, TMPRSS6]

LRGAAP [very strong NTSR1,2, Furin, CFB]

cguaguguagcu = RSVA 12nts after PRRA insertion
[WDR5,PCSK6, F2RL1, CFB]

RSVA compliment = gcaucacaucga = ASHR
[hits CFB, GRK2, C3AR1, WDR5, HLA-DRB3, AGTR2, HLA-A3]

so, GAAPASHR [hits C3AR1, CFB, WDR5, AGTR2, HLA-A3,
HLA-DRB3, SIRT1/2, AGTR1]

cagacuaauucuccucggcgggcacguaguguagcu (12+insertion+12)
QTNSPRRARSVA (12+insertion+12) [bad stuff w/HLA-A3]

NSPRRARSVA compliment LRGAAPASHR [strong CFB w/
AGTR1/2, GRK2, WDR5, C3AR1, SIRT1/2, HLA-DRB3, HLA-A3]

Great news from Moderna this morning:

After two doses all participants evaluated to date across the 25 μg and 100 μg dose cohorts seroconverted with binding antibody levels at or above levels seen in convalescent sera

mRNA-1273 elicited neutralizing antibody titer levels in all eight initial participants across the 25 μg and 100 μg dose cohorts, reaching or exceeding neutralizing antibody titers generally seen in convalescent sera

mRNA-1273 was generally safe and well tolerated

mRNA-1273 provided full protection against viral replication in the lungs in a mouse challenge model

Anticipated dose for Phase 3 study between 25 μg and 100 μg; expected to start in July

https://investors.modernatx.com/news-releases/news-release-details/moderna-announces-positive-interim-phase-1-data-its-mrna-vaccine

Encouraging results from the BioNTech mRNA vaccine. 24 of the 24 volunteers injected at the two lower doses showed antibodies after 28 days at 1.8 to 2.8 times the level seen in recovered patients. The highest dosage was discontinued due to injection pain.

https://www.medrxiv.org/content/10.1101/2020.06.30.20142570v1.full.pdf

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Despite optimism with current mRNA vaccines, there’s a potential failure point that you may be hearing about.

Almost all the RNA vaccines are encoding for the coronavirus Spike (S) protein or subdomains of S.

There are now hints that antibodies against Spike protein vaccines may not last more than 3-6 months – the vaccines may not provide long-term protection. One paper:

We shouldn’t put all our eggs in the spike vaccine basket.

The other kind of vaccine displays peptide ‘epitopes’ that help boost not just antibodies but also cellular response. These are totally understudied at the moment, but may become increasingly important.

We have a multi-epitope vaccine candidate in our OpenVaccine challenges but should probably have more.

So I’d like to ask community to help scour the literature for potential additional epitopes and to prioritize them for Eterna’s OpenVaccine designs. Eternacac and others got the ball rolling earlier in 2020. Its time to revisit! Let’s put findings and ideas here.
@DigitalEmbrace if you or others have a sec, maybe setting up a Google sheet compiling our candidates so far and notes would be very useful!

Google sheet for compiling epitopes: Epitope Candidates

Fill in your top epitope ideas and I’ll work on compiling ideas from the forum as well.

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Another article explaining why we should look at epitope vaccines:

Paper that checks every SARS-CoV-2 peptide as a potential antigenic epitope:
https://www.nature.com/articles/s41392-020-00228-1
Which ones can we prioritize?

I found this link to an article on epitopes for CoVid-19. It mentions OC43,HKU1, 229E,
NL63. There is a table of 9 aa epitopes but the data is a bit over my head.
From the end of the Results paragraph: It is of note that the S protein, which is the prime candidate for inducing neutralizing antibodies (Cohen, 2020), is poorly suitable for inducing an MHC-I-restricted immune memory across the investigated viral species as between S protein of SARS-CoV-2 and S proteins of the common human coronaviruses there are no 9 aa matches, and, among the virus isolates compared in this study, only a single 8 aa match (DRLITGRL with HCoV-NL63 and -229E) (not shown).
The link is https://f1000research.com/articles/9-285 .

In the spirit of Rhiju’s request for epitopes in addition to targeting the Spike Protein, here is a short list of epitopes taken from this link: https://dx.doi.org/10.1016%2Fj.micpath.2020.104236.

HTL specific epitope in the Membrane glycoprotein “NRFLYIIKLIFLWLL”.

B-cell specific binding epitope in the Membrane glycoprotein “RSMWSFNPETNILLNV” OR “SFRLFARTRSMWSFNP”.

CTL specific epitope in the Membrane glycoprotein “LSYFIASFR”.

The study found that Spike and Membrane received received about equal responses from the CD8+ T cells.

It also found that the HTL, CTL and B-cells together received CD8+ T cell responses. I got the impression that the HTL, CTL, and B cell antibodies were not present in the worst cases where patients did not survive.

The article is very specific and details the amino acid links to connect the epitopes together.

Could these be incorporated into our lab puzzles?

Design of a Multiepitope-Based Peptide Vaccine against the E-Protein of Human COVID-19: An Immunoinformatics Approach

they find 10 useful epitopes in the E-protein all of which should be considered especially the cytoplasm expressing one.

Designing of a next generation multiepitope based vaccine (MEV) against SARS-COV-2: Immunoinformatics and in silico approaches

Table 4 all epitopes

as the CD8+ expression of Covid-19 patients is especially diminished emphasis on such epitopes may be preferred:
Mapping the T cell Response to Covid-19
https://www.nature.com/articles/s41392-020-00228-1.pdf

Covid T-cell response

I would also suggest the epitopes chosen pay attention to the known pathways illustrated in this paper:

Type I and Type III Interferons –Induction, Signaling, Evasion, and Applicationto Combat COVID-19

Identification of vaccine targets & design of vaccine against SARS-CoV-2 coronavirus using computational and deep learning-based approaches.

Tables 1-4

https://files.osf.io/v1/resources/f8zyw/providers/osfstorage/5e8d8c6f43016601aba05283?action=download&direct&version=3