17 specific siRNA hitting 9 loci of SARS_CoV-2 - the cause of COVID-19

An RNAi pipeline is applied to the genome of the positive sense RNA, SARS-like corona virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; Wuhan-HU-1 NC_045512). This is the cause of COVID-19. I found 17 best candidate siRNA sequences potentially useful for nebulization therapy.

Methods

1. Generated all 21mers for the human genome transcriptome gencodev33 and the COVID-19 coronavirus (WH1; https://www.ncbi.nlm.nih.gov/nuccore/NC_045512)
2. Found all 21mers that were in the WH1 genome and not the human transcriptome
3. filtered the remaining 29,854 21mers into those that did not contain 5,4,3, or 2 stretches of bases (n=27951,22303,9351,123 resp.) These kmers should not be easy to inhibit with homo-polymer sequences at 5',3' or internal sites
4. Proceeded with the n=123 21mers to back compare against the entire NT database (all of life) for

4.1) circular top hits back to a coronavirus and

4.2) with a complete 21 bp alignment (see Wuhan_specific_21mers_nodimers.xlsx)

5. Of the 17 aligned candidates left, put the sequences through a thermodynamic nearest neighbor analysis for off -target binding

6. Inspected the distribution of target sites on the annotated Wuhan-Hu-1 genome for the targeting sites (see WH1.png). These 21mers hit 9 distinct locations all across the COVID-19 genome

7. Displaced the siRNA sequence allowing binding comparisons for neighboring kmers (ignoring G,U, and T) recorded lowest free energy of off-targets and the sequence to assess the genes that might be off-target hits in humans - see dataset (siRNA_df.xlsx)

7.1) no host off-target has a predicted free energy change of greater than -12 kcal/mol.

8. Release of the off-target gene stats

9. Report final selection for siRNA chemistry - Targets.seq

So these siRNA oligos are available for clinical research testing against cases that are not responding to vaccines or other therapy. The sequence plus the antisense RNA can be ordered (sources below) and annealed together in a suitable sterile physiological buffer to generate siRNA in a deliverable vapor form and taken into the lungs.

Sequence Sources:

sequences can be ordered here: https://www.thermofisher.com/order/custom-genomic-products/tools/sirna/

or here: https://horizondiscovery.com/en/products/tools/Custom-siRNA

or ... https://www.sigmaaldrich.com/life-science/custom-oligos/sirna-oligos.html

or ... choose your own

Simple Clinical Delivery Methods

https://www.jstage.jst.go.jp/article/cpb/64/1/64_c15-00615/_pdf/-char/en

https://www.future-science.com/doi/full/10.4155/tde-2019-0009

https://www.adwdiabetes.com/product/7537/omron-compair-lightweight-compressor-nebulizer?utm_source=google&utm_medium=cpc&utm_campaign=shopping&gclid=EAIaIQobChMIpNv7wrCY6AIV1Rx9Ch30fwAXEAQYAiABEgKAqvD_BwE

https://www.amazon.com/gp/product/B0832VKS79/ref=ppx_yo_dt_b_asin_title_o01_s00?ie=UTF8&psc=1

RNAi References

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC387140/pdf/pnas00328-0108.pdf https://www.frontiersin.org/articles/10.3389/fendo.2018.00402/full

miR-223 reference (promising miRNA that affects ARDS and ALI)

https://stm.sciencemag.org/content/9/408/eaah5360?utm_source=VancePak%20%28updated%206/30/2017%29&utm_campaign=2fa0418255-EMAIL_CAMPAIGN_2017_09_15&utm_medium=email&utm_term=0_56c46682ac-2fa0418255-126546449

For comments please open issues :-) best, Daniel J McGoldrick