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 .
Claims 1, 4-5, 8-16, 18-20 are pending.
Claims 2-3, 6-7, 17 are cancelled.
Applicant’s remarks filed on 12/10/2025 in response to the Non-Final Rejection mailed on 9/11/2025 have been fully considered and are not deemed persuasive to overcome at least one of the rejections and/or objections as previously applied.
The text of those sections of Title 35 U.S. Code not included in the instant action can be found in the prior Office Action.
Maintained Claim Rejections - 35 USC § 103
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 (i.e., changing from AIA to pre-AIA ) 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.
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 rejection of claims 1, 4-5, 8-15 under 35 U.S.C. 103 as being unpatentable over Florencio et al. (Date Published: 15 July 2015, Molecular Therapy – Methods & Clinical Development, cited on PTO-892 dated 9/11/2025) {herein Florencio} in view of Konstantinov et al. (US Patent Application No: US 2006/0149042 A1, cited on PTO-892 dated 9/11/2025) {herein Konstantinov} and in further view of Lazarev et al. (Date of Patent: US 9,458,190 B2, previously cited in PTO892 dated 10/25/2023) {herein Lazarev} is maintained.
Claims 1, 4-5, 8-15 are drawn to a method for separating adeno-associated virus (AAV) capsid proteins from surfactants, the method comprising:(a) adding to a molecular weight cutoff filter an amount of a sample diluent buffer and a sample consisting essentially of at least one AAV capsid protein and a surfactant, and incubating the molecular weight cutoff filter at room temperature to form a mixture in the incubated molecular weight cutoff filter;(b) adding an amount of an AAV capsid protein denaturing buffer to the mixture in the incubated molecular weight cutoff filter thereby forming a denatured solution wherein the at least one AAV capsid protein is denatured at room temperature, wherein the surfactant is a polyoxyethylene- polyoxypropylene block copolymer; and (c) filtering the denatured solution with the incubated molecular weight cutoff filter, thereby separating the at least one AAV capsid protein from the surfactant and the denaturing buffer, wherein the molecular weight cutoff filter has a molecular weight cutoff ranging from 10 kDa to 50 kDa and/or the molecular weight cutoff filter has a molecular weight cutoff ranging from 5% to 80 % of a molecular weight of the at least one AAV capsid protein.
With respect to claims 1, 13-14, Florencio teaches a method wherein cells expressing AAV capsid proteins are treated with Triton X-100 (a surfactant) for the recovery of AAV capsid proteins (page 5, column 1, para 1 and column 2, para 1) via purification utilizing a molecular weight cutoff filter (page 5, column 2, para 2). Examiner is interpreting the recovery of AAV capsid proteins as AAV being separated from Triton X-100 (surfactant). The AAV capsid proteins are purified via centrifugation and molecular weight cutoff filtration (page 5, column 2, para 2). Florencio further teaches AAV viral particles are collected and diluted twice with 1X PBS buffer before diafiltration (page 5, column 2, para 3). It is known by those of ordinary skill in the art that PBS is a commonly used diluent. As such, Examiner is interpreting the 1X PBS buffer in an amount to be a diluent since Florencio teaches its use in diluting the AAV sample. (page 6, column 1, para 4). Following centrifugation, cell lysate is filtered through a filter (page 6, column 1, para 4). The resulting fraction is suspended in a buffer and subjected to an additional round of filtration (page 6, column 1, para 4). Examiner is interpreting said buffer to be 1X PBS. Furthermore, Examiner is interpreting said teaching to be the AAV capsid proteins undergoing 2 rounds of filtration and dilution with the diluent since Florencio teaches said method. Examiner is interpreting the AAV viral particles taught by Florencio as a sample consisting essentially of at least one AAV capsid protein as recited by claim 1 of the instant application since AAV viral particles are comprised of AAV capsid protein. Furthermore, Examiner is interpreting diafiltration as a MW cutoff filter since it is known by those of ordinary skill in the art to utilize a semi-permeable membrane with a defined molecular weight cutoff to separate molecules based on size. Since Florencio teaches an assortment of materials for the purification of AAV capsid proteins (Triton X-100, molecular weight cut-off filter). Florencio further teaches the AAV particles were incubated with Triton X-100 for 1 hour (page 5, column 1, para 1). Although the reference of Florencio does not explicitly teach the limitation of claim 1 (‘incubating the molecular weight cutoff filter at room temperature to form a mixture in the incubated molecular weight cutoff filter’), MPEP 2144.05 states"[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955) (MPEP 2144.05 IIA)." One of ordinary skill would desire to optimize the temperature of incubating the mixture in the molecular weight cutoff filer depending on the particular application. It would be routine for one to arrive at the temperature at which to incubate the mixture in cutoff weight filter.
With respect to claim 5, Florencio teaches AAV capsid proteins with molecular weights of 82, 67 and 60 kDa (figure 2).
However, Florencio does not teach the method of claim 1, in that adding an amount of an AAV capsid protein denaturing buffer to the mixture in the incubated molecular weight cutoff filter… wherein the surfactant is a polyoxyethylene- polyoxypropylene block copolymer… filtering the denatured solution with the incubated molecular weight cutoff filter, thereby separating the at least one AAV capsid protein from the surfactant and the denaturing buffer, wherein the molecular weight cutoff filter has a molecular weight cutoff ranging from 10 kDa to 50 kDa and/or the molecular weight cutoff filter has a molecular weight cutoff ranging from 5% to 80 % of a molecular weight of the at least one AAV capsid protein (claim 1). The method of claim 4, wherein the surfactant in the mixture is in the form of micelles (claim 4). The method of clam 8, wherein the AAV capsid protein denaturing buffer has a pH ranging from 0 to 7 (claim 8). The method of claim 9, wherein the AAV capsid protein denaturing buffer comprises one or more organic solvents, water, and one or more acids (claim 9). The method of claim 10, wherein the one or more organic solvents comprise acetonitrile (claim 10). The method of claim 11, wherein the one or more acids comprise a halogenated organic acid and an alkyl organic acid (claim 11). The method of claim 12, wherein the one or more organic solvents comprise acetonitrile and isopropanol, and wherein the one or more acids comprise trifluoroacetic acid, formic acid and acetic acid (claim12). The method of claim 13, the method further comprises adding an additional amount of AAV capsid protein denaturing buffer to the separated at least one AAV capsid protein thereby forming a further denatured solution (claim 13). The method of claim 15, wherein the separated at least one AAV capsid protein is subsequently subjected to a liquid chromatographic separation step (claim 15).
With respect to claims 1, 4 Konstantinov teaches a method wherein polyoxypropylene (PPO) and polyethylene (PEO) are types of surfactant (para 0045) that form micelles in aqueous environments (para 0047) for the separation of macromolecules by filtration (para 0003 and para 0050). Examiner is interpreting AAV capsid proteins within the instant application as being macromolecules since they are comprised of genomic material and protein capsids of which are known to those of ordinary skill in the art to be macromolecules since the entire structure (genomic material and capsid proteins) has a diameter of 20-26nm, which classifies them as macromolecules. Afterward exposure to the surfactant, the macromolecules are concentrated by centrifugation utilizing a molecular weight cut-off membrane of 10kD (para 0054).
With respect to claim 15, Konstantinov teaches a method wherein the purified samples are subjected to chromatography (para 0055).
However, Konstantinov does not teach the method of claim 1, adding an amount of an AAV capsid protein denaturing buffer to the mixture in the incubated molecular weight cutoff filter (claim 1). The method of claim 8, wherein the AAV capsid protein denaturing buffer has a pH ranging from 0 to 7 (claim 8). The method of claim 9, wherein the AAV capsid protein denaturing buffer comprises one or more organic solvents, water, and one or more acids (claim 9). The method of claim 10, wherein the one or more organic solvents comprise acetonitrile (claim 10). The method of claim 11, wherein the one or more acids comprise a halogenated organic acid and an alkyl organic acid (claim 11). The method of claim 12, wherein the one or more organic solvents comprise acetonitrile and isopropanol, and wherein the one or more acids comprise trifluoroacetic acid, formic acid and acetic acid (claim12). The method of claim 13, further comprises adding an additional amount of AAV capsid protein denaturing buffer to the separated at least one AAV capsid protein thereby forming a further denatured solution… thereby separating the at least one AAV capsid protein from the surfactant and the additional amount of denaturing buffer (claim 13).
With respect to claims 1, 9-13, Lazarev teaches a method wherein a plurality of liquids comprised of: acetonitrile (organic solvent), isopropanol, water, acetonitrile, formic acid, trifluoroacetic acid, (column 6, lines 50-60), acetic acid (column 19, lines 50-51), halogenated acid and trifluoroacetic acid (column 1, lines 6-11) are used for the separation of viral particles (viruses) from solvent supernatant (column 5, line 10, column 14, lines 6-8 and lines 53-54). Absent evidence otherwise, it is the Examiner’s position that a plurality of liquids comprised of: acetonitrile (organic solvent), isopropanol, water, acetonitrile, formic acid, trifluoroacetic acid, (column 6, lines 50-60), acetic acid (column 19, lines 50-51), halogenated acid and trifluoroacetic acid (column 1, lines 6-11) taught by Lazarev would necessarily denature AAV capsid proteins. Since the Office does not have the facilities for examining and comparing Applicants’ AAV capsid protein denaturing buffer with the denaturing buffer of the prior art, the burden is on the Applicant to show a novel or unobvious difference between the claimed buffer and the buffer of the prior art (i.e., that the AAV capsid protein denaturing buffer of the prior art does not possess the same material structural and functional characteristics of the claimed AAV denaturing buffer). See In re Best, 562 F.2d 1252, 195 USPQ 430 (CCPA 1977) and In re Fitzgerald et al., 205 USPQ 594. ‘ As such, Examiner is interpreting a plurality of liquids comprised of: acetonitrile (organic solvent), isopropanol, water, acetonitrile, formic acid, trifluoroacetic acid, (column 6, lines 50-60), acetic acid (column 19, lines 50-51), halogenated acid and trifluoroacetic acid (column 1, lines 6-11) as the AAV denaturing buffer. Lazarev further teaches said denaturing buffer may be used an additional time, resulting in the production of another solvent (column 28, lines 12-13). Examiner is interpreting said teaching of the production of another solvent as an additional amount of an AAV capsid protein denaturing buffer being used as a solvent on the AAV capsid proteins. It is the Examiners interpretation that the MW cutoff filtering of the AAV particles taught by Florencio in combination with the additional AAV denaturing buffer taught by Lazarev would necessarily result in the separation of the at least one AAV capsid protein from the surfactant and the additional amount of denaturing buffer as Florencio teaches a method wherein AAV capsid proteins and surfactant are separated via purification utilizing a molecular weight cutoff filter (page 5, column 2, para 2) especially since Applicant recites ‘filtering the further denatured solution with the molecular weight cutoff filter, thereby separating the at least one AAV capsid protein from the surfactant and the additional amount of denaturing buffer’ in claim 13 of the instant application.
With respect to claim 8, although the reference of Lazarev does not explicitly teach the limitations of claim 8 (wherein the AAV capsid protein denaturing buffer has a pH ranging from 0 to 7), MPEP 2144.05 states"[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955) (MPEP 2144.05 IIA)." One of ordinary skill would desire to optimize the pH of the denaturing buffer depending on the particular application. It would be routine for one to arrive at the pH for the application they intend on using the denaturing buffer. Therefore, the above invention would have been prima facie obvious.
Before the effective filing date of the claimed invention, it would have been obvious to one of ordinary skill in the art to apply the teachings of Florencio et al of a method wherein cells expressing AAV capsid proteins are treated with Triton X-100 (a surfactant) for the recovery of AAV capsid proteins (page 5, column 1, para 1 and column 2, para 1) via purification utilizing a molecular weight cutoff filter (page 5, column 2, para 2) or combine the teaching of Konstantinov and Lazarev because Lazarev teaches a method wherein a plurality of liquids comprised of: acetonitrile (organic solvent), isopropanol, water, acetonitrile, formic acid, trifluoroacetic acid, (column 6, lines 50-60), acetic acid (column 19, lines 50-51), halogenated acid and trifluoroacetic acid (column 1, lines 6-11) are used for the separation of viral particles (viruses) from solvent supernatant (column 5, line 10, column 14, lines 6-8 and lines 53-54). Absent evidence otherwise, it is the Examiner’s position that a plurality of liquids comprised of: acetonitrile (organic solvent), isopropanol, water, acetonitrile, formic acid, trifluoroacetic acid, (column 6, lines 50-60), acetic acid (column 19, lines 50-51), halogenated acid and trifluoroacetic acid (column 1, lines 6-11) taught by Lazarev would necessarily denature AAV capsid proteins. Since the Office does not have the facilities for examining and comparing Applicants’ AAV capsid protein denaturing buffer with the denaturing buffer of the prior art, the burden is on the Applicant to show a novel or unobvious difference between the claimed buffer and the buffer of the prior art (i.e., that the AAV capsid protein denaturing buffer of the prior art does not possess the same material structural and functional characteristics of the claimed AAV denaturing buffer). See In re Best, 562 F.2d 1252, 195 USPQ 430 (CCPA 1977) and In re Fitzgerald et al., 205 USPQ 594. ‘ As such, Examiner is interpreting a plurality of liquids comprised of: acetonitrile (organic solvent), isopropanol, water, acetonitrile, formic acid, trifluoroacetic acid, (column 6, lines 50-60), acetic acid (column 19, lines 50-51), halogenated acid and trifluoroacetic acid (column 1, lines 6-11) as the AAV denaturing buffer. Whereas Konstantinov teaches a method wherein polyoxypropylene (PPO) and polyethylene (PEO) are types of surfactants (para 0045) that form micelles in aqueous environments (para 0047) for the separation of macromolecules by filtration (para 0003 and para 0050) of which Examiner is interpreting the AAV capsid proteins within the instant application as being macromolecules since they are comprised of genomic material and protein capsids of which are known to those of ordinary skill in the art to be macromolecules since the entire structure (genomic material and capsid proteins) has a diameter of 20-26nm, which classifies them as macromolecules.
One of ordinary skill in the art would be motivated to either use the teachings of Florencino et al. by itself or combine the teachings of Konstantinov and Lazarev because Lazarev provides the motivation for one of ordinary skill in the art to utilize a plurality of liquids comprised of: acetonitrile (organic solvent), isopropanol, water, acetonitrile, formic acid, trifluoroacetic acid, (column 6, lines 50-60), acetic acid (column 19, lines 50-51), halogenated acid and trifluoroacetic acid (column 1, lines 6-11) as Lazarev teaches said composition is used for the separation of viral particles (viruses) from solvent supernatant (column 5, line 10, column 14, lines 6-8 and lines 53-54). Konstantinov provides the motivation for Florencio to substitute F-68 (a polyoxyethylene- polyoxypropylene block copolymer) for Triton X-100 as the surfactant for the separation of AAV capsid proteins from surfactant as said surfactant induced a higher concentration factor than ordinary methods (para 0057). MPEP 2143.I.B states ‘The rationale to support a conclusion that the claim would have been obvious is that the substitution of one known element for another yields predictable results to one of ordinary skill in the art. If any of these findings cannot be made, then this rationale cannot be used to support a conclusion that the claim would have been obvious to one of ordinary skill in the art. One of ordinary skill in the art knowing the benefit of properly denaturing and precipitating AAV capsid protein for purification based on the teachings of Florencio, Konstantinov and Lazarev would have a reasonable expectation of success to combine prior art reference teachings to arrive at the claimed invention. MPEP 2143.I.G states, ‘The rationale to support a conclusion that the claim would have been obvious is that "a person of ordinary skill in the art would have been motivated to combine the prior art to achieve the claimed invention and whether there would have been a reasonable expectation of success in doing so." DyStar Textilfarben GmbH & Co. Deutschland KG v. C.H. Patrick Co., 464 F.3d 1356, 1360, 80 USPQ2d 1641, 1645 (Fed. Cir. 2006). If any of these findings cannot be made, then this rationale cannot be used to support a conclusion that the claim would have been obvious to one of ordinary skill in the art.
One of skill in the art would have a reasonable expectation of success to make and use the claimed method for separating AAV capsid protein from surfactant because Lazarev teaches a method wherein a plurality of liquids comprised of: acetonitrile (organic solvent), isopropanol, water, acetonitrile, formic acid, trifluoroacetic acid, (column 6, lines 50-60), acetic acid (column 19, lines 50-51), halogenated acid and trifluoroacetic acid (column 1, lines 6-11) are used for the separation of viral particles (viruses) from solvent supernatant (column 5, line 10, column 14, lines 6-8 and lines 53-54). Konstantinov teaches a method wherein polyoxypropylene (PPO) and polyethylene (PEO) are types of surfactant (para 0045) that form micelles in aqueous environments (para 0047) for the separation of macromolecules by filtration (para 0003 and para 0050). Whereas Florencio teaches Florencio teaches a method wherein cells expressing AAV capsid proteins are treated with Triton X-100 (a surfactant) for the recovery of AAV capsid proteins (page 5, column 1, para 1 and column 2, para 1) via purification utilizing a molecular weight cutoff filter (page 5, column 2, para 2). Therefore there would be a reasonable expectation of success to arrive at the above invention. Therefore, the above invention would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
RESPONSE TO REMARKS: Beginning on p. 6 of Applicant’s remarks, Applicant contends that Florencio teaches denaturing/incubating the sample in a HYPERFlask® at 37 °C for 1 hour. Furthermore, contrary to Applicant's method which is performed in a molecular weight cutoff filter at room temperature, Florencio's methods include sample transfers from at least two flasks to multiple types of filtration systems. For example, prior to transferring the denatured AAV sample according to Florencio's method (i.e., denatured in a HYPERFlask® at 37 °C for 1 hour) to a MWCO filter, the AAV sample is at least clarified by filtration using a 0.45 pm pore membrane. The instant claims do not require this at least noted step.
This argument is found to be not persuasive. Examiner contends that Applicant has ‘comprising’ language within the instant application claim 1 which is by definition ‘open-ended.’ Said claim language does not limit the scope of the claim to only what is recited by Applicant. As such, Florencio’s teaching of clarification of the AAV sample prior to filtration via a MWCO filter (abstract) reads on the claimed limitation.
Applicant contends that as noted in the Abstract and the Discussion (page 6, column 2) of Florencio, Florencio's method requires an iodixanol-based isopycnic density gradient coupled with tangential filtration to purify the AAV particles. Applicant contends that the isopycnic ultracentrifugation step (120 minutes) in FIG. 1 is labeled as the purification step in the three different purification methods disclosed in Florencio. See, the figure legend for FIG. 1. Applicant's claims do not require an isopycnic ultracentrifugation step to successfully remove an AAV capsid protein from a sample consisting essentially of at least one AAV capsid protein and a surfactant, wherein the surfactant is a polyoxyethylene-polyoxypropylene block copolymer.
This argument is found to be not persuasive. Examiner contends that Applicant has ‘comprising’ language within the instant application claim 1 which is by definition ‘open-ended.’ Said claim language does not limit the scope of the claim to only what is recited by Applicant. Examiner contends that although Applicant argues that the recited claims within the instant application do not ‘require’ an isopycnic ultracentrifugation step, it does not preclude said step as Applicant’s method for separating adeno-associated virus (AAV) capsid proteins from surfactants is ‘open-ended’ due to the comprising language.
Applicant contends that the Examiner fails to provide any reason why one of ordinary skill would want to modify Florencio's disclosure, including by omitting a crucial purification step in Florencio's methods, to successfully arrive at Applicant's claims, without using Applicant's disclosure as a blueprint.
This argument is found to be not persuasive. Examiner contends that Applicant has not recited the criticality of the purification step within the instant application claims. Examiner is unclear which step Applicant is referencing as critical purification step. If Applicant is referencing the recited step of ‘filtering the denatured solution with the incubated molecular weight cutoff filter, thereby separating the at least one AAV capsid protein from the surfactant and the denaturing buffer’ (instant application claim 1), then Examiner contends that said step is well-known in the art and is routinely done to purify (protein) samples.
Applicant contends that this premises also applies to the Examiner's allegation that one of ordinary skill would optimize temperature depending on the particular application. Applicant contends that the Examiner fails to consider that Florencio's methods do not align with Applicant's claimed method and thus, it is unclear what rationale would drive temperature optimization under these circumstances. Applicant contends that it is unclear why and how one of ordinary skill in the art would optimize the temperature conditions, or why temperature would even need to be optimized at all.
This argument is found to be not persuasive. Examiner contends that according to MPEP 2144.05.II.A. “Generally, differences in concentration or temperature will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical. "[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955) (Claimed process which was performed at a temperature between 40°C and 80°C and an acid concentration between 25% and 70% was held to be prima facie obvious over a reference process which differed from the claims only in that the reference process was performed at a temperature of 100°C and an acid concentration of 10%.); see also Peterson, 315 F.3d at 1330, 65 USPQ2d at 1382 ("The normal desire of scientists or artisans to improve upon what is already generally known provides the motivation to determine where in a disclosed set of percentage ranges is the optimum combination of percentages."); In re Hoeschele, 406 F.2d 1403, 160 USPQ 809 (CCPA 1969) (Claimed elastomeric polyurethanes which fell within the broad scope of the references were held to be unpatentable thereover because, among other reasons, there was no evidence of the criticality of the claimed ranges of molecular weight or molar proportions.). For more recent cases applying this principle, see Merck & Co. Inc. v. Biocraft Lab. Inc., 874 F.2d 804, 809, 10 USPQ2d 1843, 1848 (Fed. Cir. 1989), cert. denied, 493 U.S. 975 (1989)(Claimed ratios were obvious as being reached by routine procedures and producing predictable results); In re Kulling, 897 F.2d 1147, 1149, 14 USPQ2d 1056, 1058 (Fed. Cir. 1990)(Claimed amount of wash solution was found to be unpatentable as a matter of routine optimization in the pertinent art, further supported by the prior art disclosure of the need to avoid undue amounts of wash solution); and In re Geisler, 116 F.3d 1465, 1470, 43 USPQ2d 1362, 1366 (Fed. Cir. 1997)(Claims were unpatentable because appellants failed to submit evidence of criticality to demonstrate that that the wear resistance of the protective layer in the claimed thickness range of 50-100 Angstroms was "unexpectedly good"); Smith v. Nichols, 88 U.S. 112, 118-19 (1874) (a change in form, proportions, or degree "will not sustain a patent"); In re Williams, 36 F.2d 436, 438, 4 USPQ 237 (CCPA 1929) ("It is a settled principle of law that a mere carrying forward of an original patented conception involving only change of form, proportions, or degree, or the substitution of equivalents doing the same thing as the original invention, by substantially the same means, is not such an invention as will sustain a patent, even though the changes of the kind may produce better results than prior inventions."). See also KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 416, 82 USPQ2d 1385, 1395 (2007) (identifying "the need for caution in granting a patent based on the combination of elements found in the prior art.")” Examiner contends that Applicant has not submitted any evidence of the criticality of the temperature being ‘at room temperature.’ Examiner contends that Incubating MWCO with AAV particles at room temperature is a common, acceptable practice, as it is well-known in the art that AAV is relatively stable.
Applicant contends that Konstantinov is silent with respect to the purification of AAV proteins, which requires special treatments, as known in the art.
This argument is found to be not persuasive. Examiner contends that Konstantinov provides the motivation for Florencio to substitute F-68 (a polyoxyethylene- polyoxypropylene block copolymer) for Triton X-100 as the surfactant for the separation of AAV capsid proteins from surfactant as said surfactant induced a higher concentration factor than ordinary methods (para 0057). Absent evidence otherwise, Examiner contends that utilizing polyoxypropylene (PPO) and polyoxyethylene (PEO) for the separation of AAV particles is well-known in the art. Supporting the Examiner’s position is the reference of AlChe which recites, Adeno-associated virus (AAV) vectors have emerged as a leading delivery system for gene therapy. Poloxamer 188 (P188), a non-ionic surfactant, is increasingly utilized in viral vector purification and formulation to enhance AAV particle stability and prevent aggregation during the final tangential flow filtration (TFF) process (abstract). Examiner contends that it is unclear what Applicant means by ‘special treatment.’ Clarification is requested.
Applicant contends that although the molecular weight of the surfactant is much smaller compared to the AAV capsid proteins, the hydrodynamic radius is comparable. Therefore, it is difficult to remove the surfactant through traditional size-based methods, including dialysis, size exclusion chromatography, and molecular weight cut off filtration. Applicant contends that the concentration and quantity of the AAV particles are at very low levels, resulting in low recovery when removing the surfactant from the intact AAV capsids.
This argument is found to be not persuasive. Examiner contends that Applicant is claiming a method for separating adeno-associated virus (AAV) capsid proteins from surfactant. Examiner contends that since Florencio, in view of Konstantinov and Lazarev teach the instant application claims, it would inherently have the same concentration and quantity of the instant application. Examiner reminds Applicant that the product is not being claimed.
Applicant contends that Florencio, cited by the Office, also notes that "These last two decades offered large panel of upstream and downstream methods for rAAV, aimed at constantly improving the yields, the purity, but also the scale and the time of the processes." Therefore, Applicant disagrees with the Office's interpretation of AAV particles as macromolecules according to Konstantinov.
This argument is found to be not persuasive. Examiner contends that it is well-known in the art that AAV particles are macromolecules as they are macromolecular assemblies or protein-based nanoparticles. Additionally, they consist of a non-enveloped, icosahedral protein shell (capsid) that typically measures 20–26 nm in diameter and packages a small, single-stranded DNA genome.
Applicant contends that one of ordinary skill in the art would not consider Lazarev for teaching a "solvent including surfactant."
This argument is found to be not persuasive. Examiner contends that Lazarev teaches a plurality of liquids comprised of: acetonitrile (organic solvent), isopropanol, water, acetonitrile, formic acid, trifluoroacetic acid, (column 6, lines 50-60), acetic acid (column 19, lines 50-51), halogenated acid and trifluoroacetic acid (column 1, lines 6-11) that are used for the separation of viral particles (viruses) from solvent supernatant (column 5, line 10, column 14, lines 6-8 and lines 53-54). Examiner contends that Lazarev also teaches the utilization of surfactants (column 14, line 53) along with solvents for purification (column 14, line 55).
Applicant contends that Lazarev' s methods also require the use of "a device that allows for or facilitates liquid-liquid partitioning of samples (mixtures) can be employed. Applicant contends that Applicant's method claims do not require the use of a liquid-liquid partitioning device as described in Lazarev.
This argument is found to be not persuasive. Examiner contends that Applicant has ‘comprising’ language within the instant application claim 1 which is by definition ‘open-ended.’ Said claim language does not limit the scope of the claim to only what is recited by Applicant. As such, Lazarev' s teaching of ‘a device’ is moot as Applicant’s claims do preclude the utilization of said device.
The rejection of claims 16, 18-20 are rejected under 35 U.S.C. 103 as being unpatentable over Florencio et al. (Date Published: 15 July 2015, Molecular Therapy – Methods & Clinical Development, cited on PTO-892 sated 12/10/2025) {herein Florencio} in view of Konstantinov et al. (US Patent Application No: US 2006/0149042 A1, cited on PTO-892 sated 12/10/2025) {herein Konstantinov} and in further view of Lazarev et al. (Date of Patent: US 9,458,190 B2, previously cited in PTO892 (filed on 10/25/2023) {herein Lazarev} is maintained.
Previously presented claims 16, 18-20 are drawn to a kit for the separation of at least one AAV capsid protein from at least one surfactant according to claim 1, which comprises: a molecular weight cutoff filter and an AAV capsid protein denaturing buffer, wherein the surfactant is a polyoxyethylene- polyoxypropylene block copolymer and the molecular weight cutoff filter has a molecular weight cutoff ranging from 10 kDa to 50 kDa and/or the molecular weight cutoff filter has a molecular weight cutoff ranging from 5% to 80 % of a molecular weight of the at least one AAV capsid protein.
With respect to claims 16, 18, Florencio teaches cells expressing AAV capsid proteins are treated with Triton X-100 (a surfactant) for the recovery of AAV capsid proteins (page 5, column 1, para 1 and column 2, para 1) via purification utilizing a molecular weight cutoff filter (page 5, column 2, para 2). Examiner is interpreting the recovery of AAV capsid proteins as AAV being separated from Triton X-100 (surfactant). The AAV capsid proteins are purified via centrifugation and molecular weight cutoff filtration (page 5, column 2, para 2). Florencio further teaches AAV viral particles are collected and diluted twice with 1X PBS buffer before diafiltration (page 5, column 2, para 3). It is known by those of ordinary skill in the art that PBS is a commonly used diluent. As such, Examiner is interpreting the 1X PBS buffer in an amount to be a diluent since Florencio teaches its use in diluting the AAV sample. (page 6, column 1, para 4). Following centrifugation, cell lysate is filtered through a filter (page 6, column 1, para 4). The resulting fraction is suspended in a buffer and subjected to an additional round of filtration (page 6, column 1, para 4). Examiner is interpreting diafiltration as a MW cutoff filter since it is known by those of ordinary skill in the art to utilize a semi-permeable membrane with a defined molecular weight cutoff to separate molecules based on size. Since Florencio teaches an assortment of materials for the purification of AAV capsid proteins (Triton X-100, molecular weight cut-off filter) Examiner is interpreting said method to encompass a kit for the purification of AAV capsid proteins. Florencio further teaches the AAV particles were incubated with Triton X-100 for 1 hour (page 5, column 1, para 1). Although the reference of Florencio does not explicitly teach the limitation of claim 1 (‘incubating the molecular weight cutoff filter at room temperature to form a mixture in the incubated molecular weight cutoff filter’), MPEP 2144.05 states"[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955) (MPEP 2144.05 IIA)." One of ordinary skill would desire to optimize the temperature of incubating the mixture in the molecular weight cutoff filter depending on the particular application. It would be routine for one to arrive at the temperature at which to incubate the mixture in the cutoff weight filter.
However, Florencio does not teach the method of claim 16, of an AAV capsid protein denaturing buffer, wherein the surfactant is a polyoxyethylene- polyoxypropylene block copolymer and the molecular weight cutoff filter has a molecular weight cutoff ranging from 10 kDa to 50 kDa (claim 16). The method of claim 19, wherein the AAV capsid protein denaturing buffer has a pH ranging from 0 to 7 (claim 19). The method of claim 20, wherein the AAV capsid protein denaturing buffer comprises one or more organic solvents, water, and one or more acids (claim 20).
With respect to claim 16 Konstantinov teaches polyoxypropylene (PPO) and polyethylene (PEO) are types of surfactants (para 0045) that form micelles in aqueous environments (para 0047) for the separation of macromolecules by filtration (para 0003 and para 0050). Examiner is interpreting AAV capsid proteins as being macromolecules since they are comprised of genomic material and protein capsids of which are known to those of ordinary skill in the art to be macromolecules since the entire structure (genomic material and capsid proteins) has a diameter of 20-26nm, which classifies them as macromolecules. Konstantinov further teaches after exposure to the surfactant, the macromolecules are concentrated by centrifugation utilizing a molecular weight cut-off membrane of 10kD (para 0054). Since Konstantinov teaches an assortment of materials for the purification of AAV capsid proteins (Triton X-100, molecular weight cut-off filter) Examiner is interpreting said method to encompass a kit for the separation of macromolecules (AAV capsid proteins) from surfactant (PPO and PEO).
However, Konstantinov does not teach the method of claim 16, a AAV denaturing buffer (claim 16). The method of claim 19, wherein the AAV capsid protein denaturing buffer has a pH ranging from 0 to 7 (claim 19). The method of claim 20, wherein the AAV capsid protein denaturing buffer comprises one or more organic solvents, water, and one or more acids (claim 20).
With respect to claims 16, 20, Lazarev teaches a method wherein surfactant (column 14, lines 53-54) is separated from viral particles (viruses) (column 5, line 10, column 14, lines 6-8). The viral particles are exposed to a plurality of liquids comprised of: acetonitrile (organic solvent), isopropanol, water, acetonitrile, formic acid, trifluoroacetic acid, (column 6, lines 50-60), acetic acid (column 19, lines 50-51), halogenated acid and trifluoroacetic acid (column 1, lines 6-11) doe the separation of viral particles from surfactant (column 5, line 10, column 14, lines 6-8, 53-54). Absent evidence otherwise, it is the Examiner’s position that a plurality of liquids comprised of: acetonitrile (organic solvent), isopropanol, water, acetonitrile, formic acid, trifluoroacetic acid, (column 6, lines 50-60), acetic acid (column 19, lines 50-51), halogenated acid and trifluoroacetic acid (column 1, lines 6-11), as taught by Lazarev, would necessarily denature AAV capsid proteins. Since the Office does not have the facilities for examining and comparing Applicants’ AAV capsid protein denaturing buffer with the denaturing buffer of the prior art, the burden is on the Applicant to show a novel or unobvious difference between the claimed buffer and the buffer of the prior art (i.e., that the AAV capsid protein denaturing buffer of the prior art does not possess the same material structural and functional characteristics of the claimed AAV denaturing buffer). See In re Best, 562 F.2d 1252, 195 USPQ 430 (CCPA 1977) and In re Fitzgerald et al., 205 USPQ 594. ‘ As such, Examiner is interpreting a plurality of liquids comprised of: acetonitrile (organic solvent), isopropanol, water, acetonitrile, formic acid, trifluoroacetic acid, (column 6, lines 50-60), acetic acid (column 19, lines 50-51), halogenated acid and trifluoroacetic acid (column 1, lines 6-11) as the AAV denaturing buffer. Furthermore, since Lazarev teaches an assortment of materials for the separation of AAV capsid particles from surfactant, Examiner is also interpreting said method to encompass a kit for the separation of AAV capsid particles from surfactant.
With respect to claim 19, although the reference of Lazarev does not explicitly teach the limitations of claim 19 (wherein the AAV capsid protein denaturing buffer has a pH ranging from 0 to 7), MPEP 2144.05 states"[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955) (MPEP 2144.05 IIA)." One of ordinary skill would desire to optimize the pH of the denaturing buffer depending on the particular application. It would be routine for one to arrive at the pH for the application they intend on using the denaturing buffer. Therefore, the above invention would have been prima facie obvious.
Before the effective filing date of the claimed invention, it would have been obvious to one of ordinary skill in the art to apply the teachings of Florencio et al of cells expressing AAV capsid proteins are treated with Triton X-100 (a surfactant) for the recovery of AAV capsid proteins (page 5, column 1, para 1 and column 2, para 1) via purification utilizing a molecular weight cutoff filter (page 5, column 2, para 2) or combine the teaching of Konstantinov and Lazarev because Lazarev teaches a plurality of liquids comprised of: acetonitrile (organic solvent), isopropanol, water, acetonitrile, formic acid, trifluoroacetic acid, (column 6, lines 50-60), acetic acid (column 19, lines 50-51), halogenated acid and trifluoroacetic acid (column 1, lines 6-11) are used for the separation of viral particles (viruses) from solvent supernatant (column 5, line 10, column 14, lines 6-8 and lines 53-54). Absent evidence otherwise, it is the Examiner’s position that a plurality of liquids comprised of: acetonitrile (organic solvent), isopropanol, water, acetonitrile, formic acid, trifluoroacetic acid, (column 6, lines 50-60), acetic acid (column 19, lines 50-51), halogenated acid and trifluoroacetic acid (column 1, lines 6-11) taught by Lazarev would necessarily denature AAV capsid proteins. Since the Office does not have the facilities for examining and comparing Applicants’ AAV capsid protein denaturing buffer with the denaturing buffer of the prior art, the burden is on the Applicant to show a novel or unobvious difference between the claimed buffer and the buffer of the prior art (i.e., that the AAV capsid protein denaturing buffer of the prior art does not possess the same material structural and functional characteristics of the claimed AAV denaturing buffer). See In re Best, 562 F.2d 1252, 195 USPQ 430 (CCPA 1977) and In re Fitzgerald et al., 205 USPQ 594. ‘ As such, Examiner is interpreting a plurality of liquids comprised of: acetonitrile (organic solvent), isopropanol, water, acetonitrile, formic acid, trifluoroacetic acid, (column 6, lines 50-60), acetic acid (column 19, lines 50-51), halogenated acid and trifluoroacetic acid (column 1, lines 6-11) as the AAV denaturing buffer. Whereas Konstantinov teaches a method wherein polyoxypropylene (PPO) and polyethylene (PEO) are types of surfactants (para 0045) that form micelles in aqueous environments (para 0047) for the separation of macromolecules by filtration (para 0003 and para 0050) of which Examiner is interpreting the AAV capsid proteins within the instant application as being macromolecules since they are comprised of genomic material and protein capsids of which are known to those of ordinary skill in the art to be macromolecules since the entire structure (genomic material and capsid proteins) has a diameter of 20-26nm, which classifies them as macromolecules.
One of ordinary skill in the art would be motivated to either use the teachings of Florencino et al. by itself or combine the teachings of Konstantinov and Lazarev because Lazarev provides the motivation for one of ordinary skill in the art to utilize a plurality of liquids comprised of: acetonitrile (organic solvent), isopropanol, water, acetonitrile, formic acid, trifluoroacetic acid, (column 6, lines 50-60), acetic acid (column 19, lines 50-51), halogenated acid and trifluoroacetic acid (column 1, lines 6-11) as Lazarev teaches said composition is used for the separation of viral particles (viruses) from solvent supernatant (column 5, line 10, column 14, lines 6-8 and lines 53-54). Konstantinov provides the motivation for Florencio to substitute F-68 (a polyoxyethylene- polyoxypropylene block copolymer) for Triton X-100 as the surfactant for the separation of AAV capsid proteins from surfactant as said surfactant induced a higher concentration factor (para 0057). MPEP 2143.I.B states ‘The rationale to support a conclusion that the claim would have been obvious is that the substitution of one known element for another yields predictable results to one of ordinary skill in the art. If any of these findings cannot be made, then this rationale cannot be used to support a conclusion that the claim would have been obvious to one of ordinary skill in the art. One of ordinary skill in the art knowing the benefit of properly denaturing and precipitating AAV capsid protein for purification based on the teachings of Florencio, Konstantinov and Lazarev would have a reasonable expectation of success to combine prior art reference teachings to arrive at the claimed invention. MPEP 2143.I.G states, ‘The rationale to support a conclusion that the claim would have been obvious is that "a person of ordinary skill in the art would have been motivated to combine the prior art to achieve the claimed invention and whether there would have been a reasonable expectation of success in doing so." DyStar Textilfarben GmbH & Co. Deutschland KG v. C.H. Patrick Co., 464 F.3d 1356, 1360, 80 USPQ2d 1641, 1645 (Fed. Cir. 2006). If any of these findings cannot be made, then this rationale cannot be used to support a conclusion that the claim would have been obvious to one of ordinary skill in the art.
One of skill in the art would have a reasonable expectation of success to make and use the claimed method for separating AAV capsid protein from surfactant because Lazarev teaches a method wherein a plurality of liquids comprised of: acetonitrile (organic solvent), isopropanol, water, acetonitrile, formic acid, trifluoroacetic acid, (column 6, lines 50-60), acetic acid (column 19, lines 50-51), halogenated acid and trifluoroacetic acid (column 1, lines 6-11) are used for the separation of viral particles (viruses) from solvent supernatant (column 5, line 10, column 14, lines 6-8 and lines 53-54). Konstantinov teaches a method wherein polyoxypropylene (PPO) and polyethylene (PEO) are types of surfactant (para 0045) that form micelles in aqueous environments (para 0047) for the separation of macromolecules by filtration (para 0003 and para 0050). Whereas Florencio teaches Florencio teaches a method wherein cells expressing AAV capsid proteins are treated with Triton X-100 (a surfactant) for the recovery of AAV capsid proteins (page 5, column 1, para 1 and column 2, para 1) via purification utilizing a molecular weight cutoff filter (page 5, column 2, para 2). Therefore there would be a reasonable expectation of success to arrive at the above invention. Therefore, the above invention would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
RESPONSE TO REMARKS: Beginning on p. 6 of Applicant’s remarks, Applicant contends that the collective disclosure of Florencio, Konstantinov, and Lazarev fails to teach, suggest, or make obvious Applicant's instant method and kit claims.
This argument is found to be not persuasive. Examiner contends that Examiner contends that Florencio, Konstantinov, and Lazarev teaches the instant application of ‘a method for separating adeno-associated virus (AAV) capsid proteins from surfactants, the method comprising:(a) adding to a molecular weight cutoff filter an amount of a sample diluent buffer and a sample consisting essentially of at least one AAV capsid protein and a surfactant, and incubating the molecular weight cutoff filter at room temperature to form a mixture in the incubated molecular weight cutoff filter;(b) adding an amount of an AAV capsid protein denaturing buffer to the mixture in the incubated molecular weight cutoff filter thereby forming a denatured solution wherein the at least one AAV capsid protein is denatured at room temperature, wherein the surfactant is a polyoxyethylene- polyoxypropylene block copolymer; and (c) filtering the denatured solution with the incubated molecular weight cutoff filter, thereby separating the at least one AAV capsid protein from the surfactant and the denaturing buffer, wherein the molecular weight cutoff filter has a molecular weight cutoff ranging from 10 kDa to 50 kDa and/or the molecular weight cutoff filter has a molecular weight cutoff ranging from 5% to 80 % of a molecular weight of the at least one AAV capsid protein’ (claim 1) and ‘a kit for the separation of at least one AAV capsid protein from at least one surfactant according to claim 1, which comprises: a molecular weight cutoff filter and an AAV capsid protein denaturing buffer, wherein the surfactant is a polyoxyethylene- polyoxypropylene block copolymer and the molecular weight cutoff filter has a molecular weight cutoff ranging from 10 kDa to 50 kDa and/or the molecular weight cutoff filter has a molecular weight cutoff ranging from 5% to 80 % of a molecular weight of the at least one AAV capsid protein’ as set forth in the modified 103 rejection.
Conclusion
Status of the claims:
Claims 1, 4-5, 8-16, 18-20 are pending.
Claims 2-3, 6-7, 17 are cancelled.
Claims 1, 4-5, 8-16, 18-20 are rejected.
No claims are in condition for allowance.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/ERICA NICOLE JONES-FOSTER/ Examiner, Art Unit 1656
/MANJUNATH N RAO/ Supervisory Patent Examiner, Art Unit 1656