Commit 19d4a76b authored by Jeremy Zucker's avatar Jeremy Zucker

README and methods

parent 9c2b2fa6
......@@ -9,6 +9,34 @@ Originally developed to treat autoimmune disorders such as rheumatoid arthritis~
Tocilizumab is an antibody that targets the soluble IL6 receptor (SIL6R) and can effectively block the IL6 signal transduction pathway~\cite{zhang_2020}.
Tocilizumab has emerged as a promising drug repurposing candidate to reduce mortality in severely ill COVID-19 patients~\cite{coomes_2020,xaoling_2020}.
\medskip \noindent {\textbf{Methods}}
The IL6-AMP SBGN-AF model was developed manually using the Newt Editor.
The first draft of the IL6-AMP SBGN-PD model was developed using the Bob with Bioagents dialogue system:
\begin{itemize}
\item ACE2 inhibits Angiotensin II
\item Angiotensin II activates AGTR1
\item Angiotensin II activates AGTR1
\item AGTR1 activates ADAM17
\item Active AGTR1 activates ADAM17
\item Active ADAM17 activates EGF
\item Active ADAM17 activates TNF-alpha
\item Active ADAM17 activates soluble IL6R
\item Active IL6R activates STAT3
\item SARS-CoV-2 inactivates ACE2
\item STAT3 binds IL6
\item TNF activates NFkb1
\item NFKB1 activates IL6
\item Active NFKB1 activates IL6
\item EGF activates EGFR
\item EGFR activates NFKB1
\item SARS-CoV-2 binds ACE2
\item Active EGF activates EGFR
\end{itemize}
The IL6-AMP model that was generated was subsequently manually updated in Newt and exported to SBML and SBGN-PD.
Because the Newt to CellDesigner converter was unable to convert to CellDesigner format, the model was manually redrawn in the Cell Designer graphical user interface.
@article{ulhaq_2020,
title = {Interleukin-6 as a potential biomarker of {COVID}-19 progression.},
......@@ -73,3 +101,10 @@ volume={117},
pages={10970},
journal = {PNAS}
}
@article{gyori2017word,
title = {From word models to executable models of signaling networks using automated assembly},
author = {Gyori, B. M. and Bachman, J. A. and Subramanian, K. and Muhlich, J. L. and Galescu, L. and Sorger, P. K},
journal = {Molecular Systems Biology},
volume = {13},
year = {2017}
}
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