By Dr. Liji Thomas, MD May 12 2020
A new study published on the preprint server medRxiv * in May 2020 reports a multi-omics approach that could make it easier to develop drugs that are effective against COVID-19. Multi-omics is a biological analysis approach in which the data sets are multiple "omes", such as the genome, proteome, transcriptome, epigenome, metabolome, and microbiome (i.e., a meta-genome and/or meta-transcriptome, depending upon how it is sequenced). Three Data Sources for Prioritizing Drugs
Effective drug development must streamline the number of candidate drugs that enter the cycle, to bring down the cost and the time of the process. Recent studies recommend integrating a variety of techniques to develop pipelines for research and development (R&D) as well as using genetic data to identify the most likely successful new drugs. Proteomics and transcriptomics are among the most valuable fields towards this end.
At present, there are over 150 clinical trials testing drugs that are thought to be possibly effective in boosting the survival and improving the recovery of COVID-19 patients. These include hydroxychloroquine, chloroquine, and baricitinib.
Another route of gathering evidence on potentially useful drugs against COVID-19 is by finding the host proteins that facilitate viral entry and infection, and by examining the possibility of repurposing earlier drug targets in the SARS-CoV to combat the current virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Novel Coronavirus SARS-CoV-2 Colorized scanning electron micrograph of an apoptotic cell (green) heavily infected with SARS-COV-2 virus particles (yellow), isolated from a patient sample. Image captured at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland. Credit: NIAID Utility of this Approach
A recent study found over 330 human host proteins that are necessary for the virus to infect humans. These interact with 26 viral proteins. This could help advance R&D along the first route.
The second method has been used by a few studies, which have yielded 59 mouse genes that are linked to the earlier SARS-CoV infection. Among these, there are 44 that have equivalents in the human genome. By blocking viral-human protein interactions, it may be possible to target viral infection mechanisms more effectively with a lower chance of drug resistance, compared to directly targeting the virus.
A primary issue with this approach is the danger of inadvertently producing other effects that could worsen complex disease conditions– or even benefit them. The current study is aimed at evaluating how these drug targets could affect the human body’s functioning, based on an understanding of the underlying genetics. The Actual Study?
The researchers used the protocol for drug prioritization, which they successfully developed earlier, to test 353 drug targets that possibly interact with the virus. They wanted to observe how these drugs caused other outwardly discernible effects of the infection, as well as how they achieved both intended and unintended effects on complex diseases.
They first constructed a disease atlas displaying the human proteins and genes that take part in viral entry. This was via Mendelian randomization studies, providing over 372,000 unique predictions of how the drug affects a disease. This was based on plasma proteomics as well as tissue-specific transcriptomics.
As a result, they were able to evaluate how these 353 potential drugs might act in 49 phenotypes of viral infection, how they could affect over 500 complex diseases, and change 72 phenotypes of disease. These results were assessed with respect to data from drug trials, as well as the druggable genome, to identify the top drugs with the highest possibility for repurposing, and the least side effects.
They have created an online open-access platform that contains the results of all the tests, so as to allow anyone to examine the results for any of the drugs rapidly. What Did the Study Show?
The atlas of drug target-disease interactions provides over 370,000 target-disease associations in 11 tissues that are relevant in the COVID-19 scenario. Of them, 833 had strong evidence from MR imaging of the 11 tissues. 726 of these also showed robust colocalization, for a colocalization probability of over 70%. These were the study’s most robust findings.
The importance of detecting such associations is the ability to carry out analyses of how the expression of certain targets affects specific diseases, depending on the tissue. For instance, the effects of the drug targets on Crohn’s disease, hypertension, atopic disorders, and diabetes could be assessed. Anywhere from 11-17 of the target genes had associations with these four diseases, based on which tissue was studied.
Secondly, the drug targets were analyzed for association with 49 viral infection phenotypes. There were two strong associations, namely, the NEU1 gene with chronic hepatitis and the DPY19L1 gene with viral enteritis. There were also three less strong but suggestive associations, like the JAK2 gene with chronic hepatitis. Related Stories
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