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[Sixes]

I'm trying to get confirmation on an issue in our lab.  Here's the short fact pattern:

-Protein X is a well known protein, published on thousands of times.  Its seuqence and domain structure are well established.
-We have expressed and purified a small region of this protein (a piece constituting ~5% of the total number of amino acids) using the published amino acid sequence and shown that it has biological activity.  It is not obvious that this small piece would possess biological activity.
-We believe that this and other peptides derived from this short amino acid sequence within the gene can be used to inhibit disease-related processes.  We would like to patent this method.

Can we do this?  Patent a method for using a peptide derived from a previously known amino acid sequence, when we are identifying a new and non-obvious function for peptides from that amino acid sequence?  Is this a 103 rejection?  101 even?

[bartmans]

Telomere,

to my opinion the peptide fragment is fully patentable (assuming that the sequence of the fragment has never been published as such, nor has been indicated as an important fragment or domain).
Further, again assuming that no novelty bar or lack of inventive step can be determined, the use of the fragment for inhibiting the disease-related processes can be patented (in the US presumably in a method claim).
The only problem is the peptides that are derived from the actual peptide sequences. Normally the USPTO only allows for peptides that are 95% identical, which means that on a sequence of 20 amino acids only one substitution is allowed (and for shorter peptides you will never reach the 95% identity). The only solution is to actually disclose the derivative peptides by their sequence. Further, to comply with the written description requirement you should be able to at least show activity for some of the derivatives and have arguments why the other derivatives should also work.

The above also applies for most countries outside the USA, except for the identity requirement, which is more lax in other countries (EPO generally accepts 70% identity).

[Sixes]

Normally the USPTO only allows for peptides that are 95% identical, which means that on a sequence of 20 amino acids only one substitution is allowed (and for shorter peptides you will never reach the 95% identity). The only solution is to actually disclose the derivative peptides by their sequence. Further, to comply with the written description requirement you should be able to at least show activity for some of the derivatives and have arguments why the other derivatives should also work.

Thank you for the reply Bartmans.  I have not read about the 95% requirement before...do you know where I can find the original source for that?  I can see now that many applications say something along the lines of "a peptide that is at least 95% identical to the original amino acid sequence".  So to assert this, we would need to show in our specification biological activity for some peptide that is at least 5% altered from the original sequence?  I think we may have, inadvertantly, already done this by adding a tagged sequence (FLAG tag) to the end of our peptide that isn't found in the original sequence.   

[bartmans]

Telomere,

The 95% limit can be found in the instruction material for assessing the written description requirement which is available on the website of the USPTO (http://www.uspto.gov/web/offices/pac/writtendesc.pdf)