1. The residues predicting as coil or loop c tend to form a good basis for peptides chosen in the design of diagnostics and vaccines, irrespective of whether the prediction is correct and irrespective of rules for the water-liking character, exposure, or intrinsic immunogenicity, albeit that they naturally overlap
2. Give the peptide designer some ideas of the likely most populated conformations of residues as h, e, and c

Purpose for using peptides as a therapeutic agent

- avoid extensive stretches of strongly nonpolar amino acids
- some epitopes play dual B and T epitope role
- avoid N terminal asparagine N and glutamine Q and c-terminal proline P and glycine G

Potential Concerns:
- lack of biostability
- raising antibodies 
- implanting immune system memory in the case of vaccines
- specificity
- avoiding unwanted cross-reactions with other proteins with similar episodes to the target protein of interest

Suggestions and concerns for synthetic peptides

L peptide:
-B epitope synthesized with L amino acids that can attach to a carrier and raise antibodies as diagnostic of as a potential vaccine. 
-Concerns: L peptide is susceptible to proteolysis from human proteins. The B epitope antigenic determinants for antibody production are discontinuous section fo sequence and could deliver poor results

D peptide:
- synthesis from D amino acid to act as an antagonist to viral entry
- has a much longer half-life to work at binding to ACE2

Proposed design for synthetic peptides

- Has only be used in the veterinary environment but there is hope that it could be useful for humans
- Concern that the concentrations required for the synthetic peptide to work can cause issues with effects on blood pressure. Aerosol could be useful instead. 
- Using the combination of bioinformatics, human researchers, Q-UEL tools, that there will be rapid access to fighting against viruses and other pathogens

Future therapeutics for synthetic peptides

The probability of peptides being able to help with therapeutics and vaccines are becoming more relevant in clinical genomics that involved patient DNA sequences. The homologies that match viral protein sequences and uses of automated probabilistic reasoning are becoming more relevant.
The Q-UEL system has helped develop a preliminary set of predictive 3D protein structures of the virus.

Santa Clara University

Attempting to identify and isolate a short section of viral protein sequences that can be used as a preliminary design proposal for a peptide synthetic vaccine and a peptidomimetic therapeutic. Published 17 Februaray 2020
https://www.sciencedirect.com/science/article/abs/pii/S0010482520300627


Computers and viral diseases. Preliminary bioinformatics studies on the design of a synthetic vaccine and a preventative peptidomimetic antagonist against the SARS-COV-2 coronavirus

Q-UEL language helps to obtain literature to help identify sequences of amino acids that are well conserved across mnay coronaviuses including 2019-nCov. It was identified that this virus corresponded to the region aroudn one of the known cleaveage sites of the SARS virus that is required for virus activation for the cell entry

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