DETAILED ACTION
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 . In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 30 April, 2025 has been entered.
Election/Restrictions
Applicants elected group I (method of synthesis) without traverse in the reply filed on 17 May, 2023.
Claims Status
Claims 46, 47, 49, 50, and 66-70 are pending.
Claims 66-70 are new.
Maintained/Modified Rejections
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 46, 47, 49, 50, and 69 are rejected under 35 U.S.C. 103 as being unpatentable over Simon et al (ChemBioChem (March 2014) 15 p713-720, cited by applicants) in view of Boroomand (US 20150217254, cited by applicants) and Bacsa et al (J. Org. Chem. (2008) 73 p7532-7542, cited by applicants), with evidentiary support from the Stamixco GV static mixer product bulletin GV2.2 (2006).
Simon et al discusses rapid, flow based peptide synthesis (title). The system requires continuous flow of reagents through the reaction vessel, quickly exchanging reagents, and high flow rates (abstract). Standard peptide reagents were used, such as HATU for coupling and piperidine in DMF for deprotection (p713, 2nd column, 2nd paragraph). Temperature was elevated to improve the reaction rate (p713, 2nd column, 3d paragraph). A flow diagram of the system is given in fig 8A (p719, top of page). DIEA (base) is pumped into a mixer, while the amino acids mixed with the coupling agent (p714, 2nd column, 3d paragraph) are also pumped to the same mixer. This mixer, in a water bath, flows into a vessel holding the resin for peptide synthesis, which flows out into the waste. Fig 8b gives the timeframe of the synthesis; note that the coupling cycle is only 7 seconds. In the language of the claims, this has a first fluid stream comprising amino acids, and a second fluid stream comprising a base connecting in a mixer to form a mixed stream, which flows to a reactor. All tubing lengths were minimized, (supplemental information, pS5, 2nd paragraph) and the mixer is 6 static mixers by StaMixCo (supplemental information, pS38, 2nd paragraph).
The difference between this reference and the remaining claims is that this reference does not have the activating agent, the base, and the amino acid in separate reservoirs flowing to a common mixer, nor does it talk about chaotropic salt, cosolvent and/or a surfactant.
While Simon et al mixes the activating agent with the amino acid, Boroomand teaches that the two can be separate in the device, and mixed during use (note the order of adding reagents in paragraphs 22-27). This reference teaches separating the activating agent and the amino acids until needed.
Basca et al discuss the synthesis of difficult peptide sequences at elevated temperatures (title). Peptides can be difficult to synthesize due to aggregation and folding of the peptide chain (p7533, 1st column, 2nd paragraph). Methods to suppress these effects include changes in the solvent composition (i.e. cosolvents), chaotropic salts, and elevating the reaction temperature (p7533, 1st column, 3d paragraph, continues to 2nd column). The reference compared different heating methods, microwaves vs. direct heating (abstract). Note that in these experiments, reagents were added to the reaction vessel then heated (p7541, 2nd column, 4th and 5th paragraphs, continues to p7542). Side reactions, such as racemization and aspartamide formation would be expected to be more problematic at higher temperatures (p7540, 1st column, 1st paragraph), meaning that this would be a parameter to optimize. This reference discusses adding chaotropic salts and cosolvents to the system to reduce aggregation.
Therefore, it would be obvious to keep the activating agent and the amino acid in different reservoirs, as a simple substitution of one known element (the combination of amino acid and activating agent of Simon et al) for another (the separate reservoirs for the activating agent and the amino acid) yielding expected results (peptide synthesis).
Furthermore, it would be obvious to include a system to add chaotropic salts or cosolvents to the system as needed for difficult sequences, as discussed by Basca et al. As these solutions are known in the art to be helpful, an artisan in this field would attempt this process with a reasonable expectation of success.
Simon et al discloses using a system where HATU and an amino acid are flowed into a mixer with a second stream containing base. Boroomand renders obvious separating the HATU and the amino acid. This mixed stream flows into a reactor with peptides immobilized on a solid support. While the reference does not explicitly discuss the limitation that the leading edge of the mixed fluid stream have a ratio of amino acid to activating agent that is within 10% of the same value 25 ms later, this is a measure of mixing efficiency. Simon et al minimized tubing length, so diffusional mixing of the prior solvent with the leading edge is minimized, so this is merely how efficiently the mixer works. The mixer is 6 Stamixco mixers, which, as evidenced by the Stamixco product bulletin is more than sufficient for excellent mixing (table 1, 3d page, bottom of page). This strongly suggests that the mixing limitation has been met, rendering obvious claims 46 and 47.
Bacsa et al render obvious adding various additive components, rendering obvious claim 49.
It seems inefficient to have multiple mixers, when one will do, rendering obvious claim 50.
response to applicant’s arguments
Applicants argue that the rejection does not meet the mixing limitations of the claims. This is supported by a declaration under 37 CFR 1.132 by Dr. Mark Simon, applicant.
Applicant's arguments filed 13 Feb, 2026have been fully considered but they are not persuasive.
Dr. Simon models the fluid flow of the equipment of Simon et al (which is his own work) to show that it is fully developed laminar flow. What is done next is unclear because Dr. Simon is pulling equations from references that are not of record, but he appears to be modeling a slug of a second fluid traveling down a tube following a first fluid under fully developed laminar conditions. He appears to be calculating the total concentration of the second fluid in radial slices along the flow path, and shows that it changes with position. Then data is presented which appears to be concentration vs time for a slug of material traveling through the mixing system of Simon et al under different (undefined) conditions, showing that the concentration rises with time on a timescale greater than 25 ms. Finally, there is chromatography data purportedly relating how closely in time the pumps are turned on to the synthesis yield.
There are serious issues with the last experiment; the data is of such poor resolution that the individual chromatographic traces cannot be followed, the experiment is not described in enough detail for a person of skill in the art to replicate it, and there appears to be assumptions made that are not backed up with experimentation. However, this experiment describes limitations not found in the rejected claims, so need not be discussed further.
The remaining modeling and experimentation is a model of a first fluid followed by a second fluid under laminar flow conditions, showing that the absolute value of the concentration of the second fluid changes with time as it flows across a detector on a timescale longer than 25 (or 10) ms. This is described as proof that the apparatus of Simon et al does not meet the mixing efficiency claim limitation. But that is not what is claimed. The limitation is that if two different fluids are flowing after the first fluid, the ratio of their concentration varies by only a small amount over a given time period. Indeed, if there is mixing in the direction of flow (which would lead to a less steep concentration/time curve), it would tend to make the ratio more even, because diluted material at the front of the solvent wave would be mixed with more concentrated material afterwards, which would even out small differences in concentration radially. In essence, applicants have demonstrated that the system of Simon et al does not have plug flow, but that is not the limitation that is claimed.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
first rejection
Claims 46, 47, 49, and 50 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of US 11,878,996 in view of over Simon et al (ChemBioChem (March 2014) 15 p713-720, cited by applicants) and Bacsa et al (J. Org. Chem. (2008) 73 p7532-7542, cited by applicants).
Competing claim 1 describes a method of synthesizing peptides, comprising flowing a first stream comprising amino acids and a second stream comprising an amino acid activation agent into a mixer, then flowing that mixture into a reactor comprising a solid support to which peptides have been immobilized. Note that this anticipates instant claim 46.
The difference between the competing claims and the remaining instant claims is that the competing claims do not specify a third stream or chaotropic salts.
Simon et al discusses rapid, flow based peptide synthesis (title), similar to the competing claims. The system requires continuous flow of reagents through the reaction vessel, quickly exchanging reagents, and high flow rates (abstract). Standard peptide reagents were used, such as HATU for coupling and piperidine in DMF for deprotection (p713, 2nd column, 2nd paragraph). Temperature was elevated to improve the reaction rate (p713, 2nd column, 3d paragraph). A flow diagram of the system is given in fig 8A (p719, top of page). DIEA (base) is pumped into a mixer, while the amino acids mixed with the coupling agent (p714, 2nd column, 3d paragraph) are also pumped to the same mixer. This mixer, in a water bath, flows into a vessel holding the resin for peptide synthesis, which flows out into the waste. Fig 8b gives the timeframe of the synthesis; note that the coupling cycle is only 7 seconds. In the language of the claims, this has a first fluid stream comprising amino acids, and a second fluid stream comprising a base connecting in a mixer to form a mixed stream, which flows to a reactor. All tubing lengths were minimized, (supplemental information, pS5, 2nd paragraph) and the mixer is 6 static mixers by StaMixCo (supplemental information, pS38, 2nd paragraph).
Basca et al discuss the synthesis of difficult peptide sequences at elevated temperatures (title). Peptides can be difficult to synthesize due to aggregation and folding of the peptide chain (p7533, 1st column, 2nd paragraph). Methods to suppress these effects include changes in the solvent composition (i.e. cosolvents), chaotropic salts, and elevating the reaction temperature (p7533, 1st column, 3d paragraph, continues to 2nd column). The reference compared different heating methods, microwaves vs. direct heating (abstract). Note that in these experiments, reagents were added to the reaction vessel then heated (p7541, 2nd column, 4th and 5th paragraphs, continues to p7542). Side reactions, such as racemization and aspartamide formation would be expected to be more problematic at higher temperatures (p7540, 1st column, 1st paragraph), meaning that this would be a parameter to optimize. This reference discusses adding chaotropic salts and cosolvents to the system to reduce aggregation.
Therefore, it would be obvious to add a third input with the base, as Simon et al does that successfully. This is a simple substitution of one element (the unknown location of the base in the competing claims) for another (placing the base in a separate reservoir, as Simon et al do it) yielding expected results (peptide synthesis).
Furthermore, it would be obvious to include a system to add chaotropic salts or cosolvents to the system as needed for difficult sequences. As these solutions are known in the art to be helpful, an artisan in this field would attempt this process with a reasonable expectation of success.
response to applicant’s arguments
Applicants repeated the arguments cited with respect to the rejection under 35 USC 103, above, which were discussed there.
second rejection
Claims 46, 47, 49, and 50 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 9,868,759 (previously cited) in view of over Simon et al (ChemBioChem (March 2014) 15 p713-720, cited by applicants) and Bacsa et al (J. Org. Chem. (2008) 73 p7532-7542, cited by applicants).
Competing claim 1 describes a method of synthesizing peptides, comprising flowing a first stream comprising amino acids and a second stream comprising an amino acid activation agent into a mixer, then flowing that mixture into a reactor comprising a solid support to which peptides have been immobilized.
The difference between the competing claims and the remaining instant claims is that the competing claims do not specify a third stream or chaotropic salts.
Simon et al discusses rapid, flow based peptide synthesis (title), similar to the competing claims. The system requires continuous flow of reagents through the reaction vessel, quickly exchanging reagents, and high flow rates (abstract). Standard peptide reagents were used, such as HATU for coupling and piperidine in DMF for deprotection (p713, 2nd column, 2nd paragraph). Temperature was elevated to improve the reaction rate (p713, 2nd column, 3d paragraph). A flow diagram of the system is given in fig 8A (p719, top of page). DIEA (base) is pumped into a mixer, while the amino acids mixed with the coupling agent (p714, 2nd column, 3d paragraph) are also pumped to the same mixer. This mixer, in a water bath, flows into a vessel holding the resin for peptide synthesis, which flows out into the waste. Fig 8b gives the timeframe of the synthesis; note that the coupling cycle is only 7 seconds. In the language of the claims, this has a first fluid stream comprising amino acids, and a second fluid stream comprising a base connecting in a mixer to form a mixed stream, which flows to a reactor. All tubing lengths were minimized, (supplemental information, pS5, 2nd paragraph) and the mixer is 6 static mixers by StaMixCo (supplemental information, pS38, 2nd paragraph).
Basca et al discuss the synthesis of difficult peptide sequences at elevated temperatures (title). Peptides can be difficult to synthesize due to aggregation and folding of the peptide chain (p7533, 1st column, 2nd paragraph). Methods to suppress these effects include changes in the solvent composition (i.e. cosolvents), chaotropic salts, and elevating the reaction temperature (p7533, 1st column, 3d paragraph, continues to 2nd column). The reference compared different heating methods, microwaves vs. direct heating (abstract). Note that in these experiments, reagents were added to the reaction vessel then heated (p7541, 2nd column, 4th and 5th paragraphs, continues to p7542). Side reactions, such as racemization and aspartamide formation would be expected to be more problematic at higher temperatures (p7540, 1st column, 1st paragraph), meaning that this would be a parameter to optimize. This reference discusses adding chaotropic salts and cosolvents to the system to reduce aggregation.
Therefore, it would be obvious to add a third input with the base, as Simon et al does that successfully. This is a simple substitution of one element (the unknown location of the base in the competing claims) for another (placing the base in a separate reservoir, as Simon et al do it) yielding expected results (peptide synthesis).
Furthermore, it would be obvious to include a system to add chaotropic salts or cosolvents to the system as needed for difficult sequences. As these solutions are known in the art to be helpful, an artisan in this field would attempt this process with a reasonable expectation of success.
response to applicant’s arguments
Applicants repeated the arguments cited with respect to the rejection under 35 USC 103, above, which were discussed there.
New Rejections
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 46, 47, 49, 50, and 66-70 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The MPEP lists factors that can be used to determine if sufficient evidence of possession has been furnished in the disclosure of the application. These include "level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention. Disclosure of any combination of such identifying characteristics that distinguish the claimed invention from other materials and would lead one of skill in the art to the conclusion that the applicant was in possession of the claimed species is sufficient" (MPEP 2163).
A claimed genus may be satisfied through sufficient description of a representative number of species or disclosure of relevant, identifying characteristics such as functional characteristics coupled with a known or disclosed correlation between function and structure(MPEP 2163(3)a(II)). The number of species that describe the genus must be adequate to describe the entire genus; if there is substantial variability, a large number of species must be described.
The analysis for adequate written description considers (a) actual reduction to practice, (b) disclosure of drawings or structural chemical formulas, (c) sufficient relevant identifying characteristics in the way of complete/partial structure or physical and/or chemical properties or functional characteristics when coupled with known or disclosed correlation with structure and (d) representative number of samples.
The issue is if applicants have possession of every way of mixing that meets the mixing limitations of the claims.
(a and b) actual reduction to practice and (b) disclosure of drawings or structural chemical formulas: Applicants describe two setups. Example 1 has multiple fluid streams merged together, with no mixer mentioned beyond the three tubes coming together at a point (p30, 1st paragraph). Example 5 mentions the streams merged together, followed by the tubing coiled 22 times around a 0.5 inch cylinder to facilitate mixing (p36, 1st paragraph). Applicants have provided no evidence that either of these configurations meet the claim limitation of the molar ratio of the amino acid to the activating agent at the leading edge is within 10% of the ratio 25 ms later (10 ms for claim 69), a measure of mixing efficiency.
:
(c) sufficient relevant identifying characteristics in the way of complete/partial structure or physical and/or chemical properties or functional characteristics when coupled with known or disclosed correlation with structure: Applicants have a limitation that the ratio of the amino acid to the activating agent at the leading edge is similar to the ratio either 10 or 25 ms later (depending on the claim). This is a functional limitation describing the evenness of mixing of two fluid streams in the synthesis apparatus. However, applicants have not described what structure(s) is/are required to meet this functional limitation. A person of skill in the art, given a potential embodiment of the claims, would not be able to verify it meets the claim limitations without testing it. In essence, applicants have defined an important part of their invention by function. That is not sufficient to meet the written description requirement.
The University of Bristol description of the work of Steve Wiggins and Rob Sturman (downloaded 25 June, 2026) states that reliable uniform mixing in microfluidics is notoriously difficult to attain (1st page, 1st paragraph) and that mixing systems are largely designed by trial and error (1st page, 3d paragraph).
Similarly, Tammaro et al (Chem. Eng. J. Adv. (2026) 27 (101287)) states that mixing is generally difficult due to laminar flow of the systems (abstract), well after applicant’s priority date. This is due to sub millimeter dimensions, which lead to low Reynolds numbers and high Peclet numbers (2nd page, 1st column, 2nd paragraph). By using multiple different mixing strategies, they were able to improve mixing efficiency from 35-40% to 50-55% (abstract).
While applicants are not using a microfluidic system, the dimensions of systems used for peptide synthesis are similar (note Tammaro et al, 2nd page, 2nd column, 6th paragraph, giving a flow dimension of 0.375x0.350 mm rectangular channel, compared to Simon et al (ChemBioChem (2014) 15 p713-720, previously cited) using a 0.76 mm ID tubing, p714, 2nd column, 4th paragraph) and applicant’s disclosure (0.020 inch ID (0.51 mm) and 0.03 inch (0.78 mm)(p36, 1st paragraph)), and the physics is the same.
Applicants have spent a great deal of time and effort trying to prove that the apparatus of Simon et al does not meet the claim limitations, note declarations of 13 Feb, 2026 and 30 April, 2025, for example. These involve a good deal of modeling and some experimental data. Yet they have not been able to conclusively show that the apparatus of Simon et al does nor does not meet the claim limitation.
(d) representative number of samples: Applicants have mentioned two mixing systems, but have not demonstrated that either meet the claim limitations. The University of Bristol document states that mixing in similar systems is notoriously difficult, and systems are designed by trial and error. This shows that there is no model that will predict the mixing. Tammaro et al, well after applicant’s priority date, discuss an advance that leads to mediocre mixing efficiencies, that are better than what had been tried before. As there is no art recognized device or structure that will reliably meet the claim limitations, and such systems require trial and error, applicants lack written description for systems that will provide the required mixing efficiency.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to FRED REYNOLDS whose telephone number is (571)270-7214. The examiner can normally be reached M-Th 9-3:30.
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/FRED H REYNOLDS/Primary Examiner, Art Unit 1658
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