Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
DETAILED ACTION
This Non-Final Office Action is responsive to the communication received 02/03/2026.
Election/Restrictions
Applicant’s election without traverse in the Reply filed on 02/03/2026 of Group I, Claim(s) 1-5, 9 and 31-32 is acknowledged.
Applicant has elected without traverse in the Reply filed on 02/03/2026 the following species:
A. wherein the second plurality of peptide constructs comprises variant peptides that differ from the second peptide by a single point mutation and each point mutation is a substitution with alanine (claims 1 and 3)
The Restriction/Election Requirements are deemed proper and are made FINAL.
Claims 1-5, 9, 11-13, 16, 20, 22, 24, 30-32, 35, 39, 44 and 48 are pending.
Claims 11-13, 16, 20, 22, 24, 30, 35, 39, 44 and 48 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the Reply filed on 02/03/2026.
Claims 1-5, 9 and 31-32 are under examination in this Office Action.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-5, 9 and 31-32 are rejected under 35 U.S.C. 101 because the claimed invention is directed to nonstatutory subject matter. The claim(s) does/do not fall within at least one of the four categories of patent eligible subject matter because the claimed invention is directed to a judicial exception, an abstract idea involving mathematical concepts and mental processes, without significantly more. Claims 2-5, 9 and 31-32 depend directly or indirectly from claim 1.
The claim 1-2 and 31-32 limitations directed to an abstract idea involving mathematical concepts and mental processes identifying a first peptide having specific binding to the target molecule, the first peptide having an identified threshold z-score; and identifying at least one variant peptide with increased binding to the target molecule compared to the first peptide, wherein the identified at least one variant peptide has a z-score higher than the identified threshold z-score of the first peptide; wherein a second peptide is identified as having a z-score higher than the threshold z-score of the first peptide; wherein the identified at least one variant peptide has a z-score higher than the z-score of the second peptide; wherein the z-score of identified peptides is calculated according to a method comprising: determining a relative abundance level of each peptide constructs in the library of peptide constructs and/or the second library of peptide constructs; grouping peptide constructs into bins based on similarity of relative abundance level, wherein each bin comprises at least 300 peptide constructs; normalizing the relative abundance level of each peptide construct against the average of the relative abundance level of the negative control peptide constructs in the library of peptide constructs and/or the second library of peptide constructs to produce a normalized relative abundance level; and determinizing a mean and a standard deviation of the normalized relative abundance levels in each bin; calculating the z-score of each peptide construct based on the mean and the standard deviation of the normalized relative abundance levels in each bin; wherein the step of determinizing the mean and the standard deviation of the normalized relative abundance levels in each bin excludes peptide constructs having outlier relative abundance levels.
This judicial exception is not integrated into a practical application because data gathering steps required to use the correlation do not add a meaningful limitation to the method as they are insignificant extra-solution activity.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claim recites additional elements that consist of well understood, routine, conventional activity already engaged in by the scientific community.
The claim 1 limitations directed to well understood, routine, conventional activity already engaged in by the scientific community are a method of maturing a peptide library to improve binding to a target molecule, the method comprising: identifying a first peptide having specific binding to the target molecule; generating a library of peptide constructs based on the first peptide, the library of peptide constructs comprising: a peptide construct comprising the first peptide, and a plurality of peptide constructs comprising variant peptides that differ from the first peptide by a single point mutation and each point mutation is a substitution with alanine; and variant peptides that differ from the first peptide by a single point mutation and each point mutation is a substitution with glycine; contacting the target molecule with the library of peptide constructs; and identifying at least one variant peptide with increased binding to the target molecule compared to the first peptide.
Watt et al. (04/03/2008) US Patent Application Publication 2008/0081768 A1 cited in the 11/16/2022 IDS (hereinafter referred to as Watt) teaches a method of maturing a peptide library to improve binding to a target molecule, the method comprising: identifying a first peptide having specific binding to the target molecule; generating a library of peptide constructs based on the first peptide, the library of peptide constructs comprising: a peptide construct comprising the first peptide, and a plurality of peptide constructs comprising variant peptides that differ from the first peptide by a single point mutation and each point mutation is a substitution with alanine; and variant peptides that differ from the first peptide by a single point mutation and each point mutation is a substitution with glycine; contacting the target molecule with the library of peptide constructs; and identifying at least one variant peptide with increased binding to the target molecule compared to the first peptide (see [0046] to [0099], [0158] to [0201] and [0279] to [0281]).
Claim Rejections - 35 USC § 103(a)
The following is a quotation of 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102 of this title, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived by the manner in which the invention was made.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under 35 U.S.C. § 103(a) are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
5. Secondary considerations (objective evidence of nonobviousness): a) commercial success; b) long felt need; c) evidence of unexpected results; d) skepticism of experts; and e) copying.
Common Ownership of Claimed Invention Presumed
This application currently names joint inventors. In considering patentability of the claims under 35 U.S.C. 103(a), the Examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the Examiner to consider the applicability of 35 U.S.C. 103(c) and potential 35 U.S.C. 102(e), (f) or (g) prior art under 35 U.S.C. 103(a).
Claims 1-5, 9 and 31-32 are rejected under 35 U.S.C. 103(a) as being unpatentable over Watt et al. (04/03/2008) US Patent Application Publication 2008/0081768 A1 cited in the 11/16/2022 IDS (hereinafter referred to as Watt) in view of Sampson et al. (03/24/2011) US Patent Application Publication 2011/0071043 A1 cited in the 11/16/2022 IDS (hereinafter referred to as Sampson).
With regards to claims 1-5 and 9, Watt teaches:
a) as in claims 1-5 and 9, a method of maturing a peptide library to improve binding to a target molecule, the method comprising: identifying a first peptide having specific binding to the target molecule; generating a library of peptide constructs based on the first peptide, the library of peptide constructs comprising: a peptide construct comprising the first peptide, and a plurality of peptide constructs comprising variant peptides that differ from the first peptide by a single point mutation and each point mutation is a substitution with alanine; and variant peptides that differ from the first peptide by a single point mutation and each point mutation is a substitution with glycine; contacting the target molecule with the library of peptide constructs; and identifying at least one variant peptide with increased binding to the target molecule compared to the first peptide; the method further comprising: generating a second library of peptide constructs comprising: a peptide construct comprising the second peptide, and a second plurality of peptide constructs comprising variant peptides; contacting the target molecule with the second library of peptide constructs; and identifying at least one variant peptide from the second library of peptide constructs with increased binding to the target molecule compared to that of the second peptide; wherein the second plurality of peptide constructs comprises variant peptides that differ from the second peptide by a single point mutation and each point mutation is a substitution with alanine; wherein at least two variant peptides are identified from the library of peptide constructs with increased binding to the target molecule compared to that of the first peptide, the method further comprising generating a library of peptide constructs that comprise multimers of the at least two variant peptides; wherein the library of peptide constructs based on the first peptide comprises at least 10,000 peptide constructs; the library of peptide constructs based on the first and/or second peptide comprise a plurality of negative control peptide constructs; wherein the first peptide comprises a consensus sequence generated from bound peptides, the plurality of peptide constructs comprise variant constructs comprising a core sequence having at least 5 consecutive amino acids from the consensus sequence (see [0046] to [0099], [0158] to [0201] and [0279] to [0281]).
Watt does not explicitly teach:
a) as in claims 1-2 and 31-32, a method comprising: identifying a first peptide having specific binding to the target molecule, the first peptide having an identified threshold z-score; and identifying at least one variant peptide with increased binding to the target molecule compared to the first peptide, wherein the identified at least one variant peptide has a z-score higher than the identified threshold z-score of the first peptide; wherein a second peptide is identified as having a z-score higher than the threshold z-score of the first peptide; wherein the identified at least one variant peptide has a z-score higher than the z-score of the second peptide; wherein the z-score of identified peptides is calculated according to a method comprising: determining a relative abundance level of each peptide constructs in the library of peptide constructs and/or the second library of peptide constructs; grouping peptide constructs into bins based on similarity of relative abundance level, wherein each bin comprises at least 300 peptide constructs; normalizing the relative abundance level of each peptide construct against the average of the relative abundance level of the negative control peptide constructs in the library of peptide constructs and/or the second library of peptide constructs to produce a normalized relative abundance level; and determinizing a mean and a standard deviation of the normalized relative abundance levels in each bin; calculating the z-score of each peptide construct based on the mean and the standard deviation of the normalized relative abundance levels in each bin; wherein the step of determinizing the mean and the standard deviation of the normalized relative abundance levels in each bin excludes peptide constructs having outlier relative abundance levels.
With regards to claims 1-2 and 31-32, Sampson teaches:
a) as in claims 1-2 and 31-32, a method comprising: identifying a first peptide having specific binding to the target molecule, the first peptide having an identified threshold z-score; and identifying at least one variant peptide with increased binding to the target molecule compared to the first peptide, wherein the identified at least one variant peptide has a z-score higher than the identified threshold z-score of the first peptide; wherein a second peptide is identified as having a z-score higher than the threshold z-score of the first peptide; wherein the identified at least one variant peptide has a z-score higher than the z-score of the second peptide; wherein the z-score of identified peptides is calculated according to a method comprising: determining a relative abundance level of each peptide constructs in the library of peptide constructs and/or the second library of peptide constructs; grouping peptide constructs into bins based on similarity of relative abundance level, wherein each bin comprises at least 300 peptide constructs; normalizing the relative abundance level of each peptide construct against the average of the relative abundance level of the negative control peptide constructs in the library of peptide constructs and/or the second library of peptide constructs to produce a normalized relative abundance level; and determinizing a mean and a standard deviation of the normalized relative abundance levels in each bin; calculating the z-score of each peptide construct based on the mean and the standard deviation of the normalized relative abundance levels in each bin; wherein the step of determinizing the mean and the standard deviation of the normalized relative abundance levels in each bin excludes peptide constructs having outlier relative abundance levels (see [0042] to [0134] and [0167] to [0172]).
One of ordinary skill in the art before the time of the effective filing date of the claimed invention would have had a reasonable expectation of success in arriving at the Applicant's invention as claimed with the above cited references before them. Sampson teaches that z-scores are useful in identifying library variants with specific binding to a target molecule from non-specific background noise (see [0042] to [0134] and [0167] to [0172]). One of ordinary skill in the art before the time of the effective filing date of the claimed invention would have recognized the advantages of combining Sampson's z-score analysis with Watt's library screening identifying library variants with specific binding to a target molecule from non-specific background noise. Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art before the time of the effective filing date of the claimed invention.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Christian Boesen whose telephone number is 571-270-1321. The Examiner can normally be reached on Monday-Friday 9:00 AM to 5:00 PM.
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/CHRISTIAN C BOESEN/Primary Examiner, Art Unit 1684
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