First of all you should have a clear cut idea on the Pathway of the disease or the condition of your interest. Second you should know which parts you wanna target in that pathway(check in the latest articles for inhibitors of specific targets of the pathway of your interest). Third, now that you have selected the targets for action, you now have to go for designing part where you can use VIRTUAL SCREENING or just design like molecules from the publications or articles you have read..means just copy the structures of the molecules do slight modification and then try docking them individually to your targets. Before you could do docking you should know PHARMACOPHORE for inhibition ( basic chemical moieties which are to be present compulsorily for the inhibition to take place). Later if you have really performed all this steps further guidance wouldnt be necessary for you
By virtual screening of libraries, you will get inhibitors for each of your targets separately. Then go for docking of the best inhibitors of one target to the other target. This is called 'cross-docking'.
But as mentioned by Seshank, to have clear idea of the pathway is very important.
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