I have the list of proteins which are either inhibited or induced by action of certain small molecule. I would like to know the downstream effects of this action so that I can hypothesise a mode of action of the small molecule
You should try out David (https://david.ncifcrf.gov/) and select KEGG_pathways and try to find overrepresented pathways in your data. Then examine the pathways in detail and look for downstream pathways or components.
You could also try SPIA (www.bioconductor.org/packages/release/bioc/html/SPIA.html). This will give you more detail than DAVID because the method takes pathway topology and log fold change information into account.
You could use mechanistic approaches (see book: An Introduction to Systems Biology: Design Principles of Biological Circuits; https://www.crcpress.com/An-Introduction-to-Systems-Biology-Design-Principles-of-Biological-Circuits/Alon/p/book/9781584886426). Then, you can reconstruct ODEs, where reactions between proteins are represented by Michaelis-Menten or Hill equations. Other methods can be used if you don't know exactly the parameters for such a mechanistic model. You can create Boolean models and it can give you qualitative results.