Hi,
Firstly this is very challenging task for synthesizing targeted molecule, Here I have some suggestions (not the stepwise strategy) for this work.
1. Firstly collect research articles on the crystal structure (or structural based) of the protein against which you want to synthesize your target molecule.
2. Look at the structural features of the protein for example what kind of domains are present (eg: HLH, HTH, Zinc Finger or any crucial domain) that specifically binds to that promoter region, but this is very challenging because there are many proteins (TFs) which have the common domain. You may be successful if your protein has unique domain that binds promoter.
3. You will be required a very precise work and understanding on the topology of the protein and detail understanding about it so you can specifically synthesize your target molecule. You will be needed the modeling and docking studies.
4. When you become ensure from all of your modeling and docking studies you can synthesize your molecule. Other than that here I am attaching one article regarding your protocol that may help you other way around.
5. Apart from all other above mentioned points if you just want to inhibit the protein then you can utilize siRNA or miRNA based strategy to target the transcript of your protein.
Thanks
Hi, your question is too broad and your should provide more information: e.g. at least which species you are working with, and why you want to design a molecule to inhibit the protein.
Naveen suggests very wisely that you could target the mRNA instead, which is much, much easier.
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