Dear Kristin,
Although this may give me some enemies to say this, I personally would not put docking into a patent.  The number of incorrect docking poses I have seen is far greater than the number of incorrect crystal structures I have seen.  If you do docking and confirm with a crystal structure, or start with a crystal structure and dock related compounds, you are on more solid ground.  If you dock a novel scaffold into a novel target, then the docking is highly suspicious and anyone would be skeptical about it.  

My personal view is a crystal structure does add value to a patent because it defines the binding mode of the compound.  However, the reality is that many small molecule drug discovery patents don't include these data and authors instead will often publish the crystal structure in a journal after the patent comes out.  You would have to consult your own IP group to see what their philosophy would be.  Every attorney has their own personal views on this.  In the world of biologics and antibodies, having a crystal structure is generally considered important because the IP is generally around the antibody-antigen interaction and having that epitope precisely defined and CDR sequences protected is important.  (You don't want "rip-off biotech Inc" busting your IP by changing one residue in the CDR loop from V to I).  

Good luck.
Nick


  

On Tue, Aug 23, 2016 at 4:21 AM, Kristin Lee <[log in to unmask]> wrote:

Dear all,

I am a PhD student working on a structure-based drug discovery project that began from molecular docking simulations and have some questions regarding the importance of including crystallographic structures in a patent. I would appreciate your comments on this.

1. Is it really relevant to a patent to include a crystal structure or can one get away with just a docking?
2. Does it add value to the patent to have experimental evidence of how the compound binds to its target protein?
3. Is the pool of docking, biochemical, cellular and mouse assays sufficient, so the crystal structure would only add redundant information that will not be really necessary in the patent?
4. When both of them identify the compound binding in a similar pose, could the information from docking provide the same value to the patent as the information from the crystal structure?
5. Is there any public documentation (or real cases) where I can read more about it?

Thanks in advance.
Best,
Kristin.


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