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 (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.
Response to Amendment
The amendment filed September 19, 2025 has been entered. Claims 1, 12-13, 19-20, 34 have been amended, claims 10, 18, 35, and 37-63 are cancelled, and claims 64-66 have been added. Applicant’s amendments to the claims have overcome the 112(b) and 112(d) rejections and objections to the specification previously set forth in the Non-Final Office Action mailed March 19, 2025. Applicants cancellation of claims 10, 18, 35, and 37 have rendered the corresponding rejections moot. As such, these rejections and objections are hereby withdrawn.
Applicant’s arguments filed September 19, 2025 were fully considered but they were not persuasive. Modified/New rejections necessitated by Applicant’s amendment are addressed below.
Claims 1-9, 11,-17, 19-34, 36, 64-66 are pending in this application.
Priority
This application is a 371 of PCT/US2020/039462 filed June 24, 2020 and claims benefit of provisional application 62/866,515 filed June 25, 2019.
New Claim Rejections - 35 USC § 112 (b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 66 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being incomplete for omitting essential elements, such omission amounting to a gap between the elements. See MPEP § 2172.01. The omitted elements are: how the ion exchange capacities are measured/determined.
According to the instant specification, ion exchange capacities of various matrices can be measured according to methods known to those of skill in the art and cites reference Kazarian et al (Anal Chim Acta, 2013, cited on PTO-892) as a possible method to be used (pg. 27, para. 0061), but provides no specific method. According to the instant specification, strong ion exchange groups show no variation in ion exchange capacity with changes in pH (pg. 26, para. 0058). Huang (Journal of Chromatography, 2018) teaches that manufacturers can use two different methods to measure ion exchange capacities: while the first determines capacity mostly by acid-base titration (convert all cation exchange groups to acid form, wash, determine how much standard strong base needs to be passed through the column before un-neutralized base is detected), the second manufacturer passes KCl solution through an H+-form column and after washing to remove excess, deter-mines the amount of potassium actually held by the column (pg. 75, col. 1, para. 1). Huang states that the two determinations will produce essentially the same value for a strong acid type cation exchange material (pg. 75, col. 2, para. 1). While Huang teaches that the method of determination capacities may not vary with strong cation exchange ligands, Kazarian (Anal Chim Acta, 2013, cited on PTO-892, the cited reference by the specification) teaches a separate method for determination of mixed-mode capacities in mixed-mode matrices using separate approaches for both anion-exchange capacity and cation exchange capacities (pg. 146, col. 1, section 2.4.2). Additionally, Kazarian teaches the capacity determined by Kazarian differed significantly compared to the capacity reported by the manufacturer (pg. 152, col. 2, last para.). Given that the measured capacities differ depending on the method utilized to measure them, the scope of the claim is unclear, thus, claim 66 is rendered indefinite.
Modified/New 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.
Claims 1-9, 11, 13-17, 20-24, 32-34, and 36 are rejected under 35 U.S.C. 103 as being unpatentable over Zhu (Bioconjug. Chem., 2010, IDS filed December 17, 2021) in view of Biba (J. Chromatography A., 2013, IDS filed December 17, 2021), IMTAKT (Scherzo C18 Family, 2016, cited in previous action), and McLaughlin (Chem. Rev., 1989, cited in previous action).
Regarding claim 1, 8-9, 11, 13-17, 20-24: Zhu teaches the conjugation of carbohydrates to siRNA for targeted delivery of siRNAs for therapeutic purposes (pg. 2, paras. 2-4). Zhu teaches a method of purification of M6P-PEG-siRNA conjugate (i.e. carbohydrate-oligonucleotide conjugate), the method comprising contacting a reaction mixture (i.e. conjugate and impurities in solution) with a Resource Q ion exchange column, passing a gradient mobile phase through the matrix, the mobile phase comprising A: 20 mM Tris-HCl buffer, B: 0.1 M sodium chloride buffer at 25 °C where the concentration of B changes from 0% to 80% over time (i.e. elution salt wherein concentration of salt changes over time), and collecting elution fractions from the anion exchange matrix (pg. 4, para. 1). Zhu teaches that the conjugate elutes first before the siRNA (i.e. first set has the conjugate, second set has the impurities, pg. 5, para. 3, pg. 14, figure 4). A similar separation was performed with Gal-PEG-siRNA (i.e. galactose unit, pg. 5, para. 3).
Zhu does not teach wherein the method comprises utilizing a mixed-mode matrix comprising a strong anion exchange ligand, a strong cation exchange ligand, and a hydrophobic ligand. Zhu does not teach wherein the mobile phase pH is between 7.0 and 8.5, comprises an organic solvent wherein the organic solvent increases over time.
However, Biba teaches a method of utilizing mixed-mode columns consisting of reversed phase and ion exchange separation modes for the analysis of short RNA oligonucleotides (abstract). Bibi teaches typically these analysis typically involve the use of two complementary methods: strong anion exchange liquid chromatography for separation based on charge and ion-pair reversed phase liquid chromatography for separation based on hydrophobicity (abstract). Conventionally, strong anion-exchange liquid chromatography has been the preferred method for analyzing oligonucleotide samples, however Bibi suggests the use of mixed-mode chromatography combining the benefits of both known separation methods into a single analysis (pg. 69, col. 2, para. 1, pg. 70, col. 2, para. 1). Biba demonstrates the SW-C18 mixed-mode column comprising strong cation exchange functional groups, strong anion-exchange functional groups, and C18 (octadecyl) ligands is capable of serving this purpose (pg. 74, col. 2, para. 2). Biba teaches that utilizing strong anion-exchange liquid chromatography conditions such as NaBr or NaCl salt gradient, with the mixed-mode columns show improved shape (pg. 75, col. 2, para. 2, pg. 77, col. 2, para. 1). Bibi teaches the use of a tris (i.e. trizma hydrochloride/tris HCL, pg. 71, col. 1, para. 1) buffer/NaCl linear gradient mobile phase at pH 7.4 with organic solvent acetonitrile, combined with gradient wherein the amount of acetonitrile increases over time (pg. 74, fig. 8).
Taken together, it would have been prima facie obvious to a person of ordinary skill in the art to modify the method of Zhu by purifying using the SW-C18 column and conditions of Bibi (tris-HCl, NaCl or NaBr, acetonitrile linear gradient) for purifying the carbohydrate oligonucleotide conjugate. A person of ordinary skill in the art would have had the motivation to do so with a reasonable expectation of success as the use of mixed-mode chromatography is a known improvement over strong anion exchange chromatography in the art of separating oligonucleotide compounds.
The claimed method further differs from Zhu in that, Zhu does not teach wherein the increase in concentration of the organic solvent in the mobile phase is a gradient from about 8% to about 20% or about 10% to about 18% (v/v). They do not teach wherein the salt concentration changes from about 0.5 M to about 1.0 M.
However, Biba teaches the use of mixed mode chromatography with Scherzo SW-C18 column with NaCl gradient wherein the mobile phrase comprises: mobile phase A water and mobile phase B water/acetonitrile (85/15 (v/v%)), wherein a linear gradient of 20%-50% B over 30 minutes (pg. 72, figure 6) or mobile phase A water and mobile phase B water/acetonitrile (85/15 (v/v%)), wherein a linear gradient of 40%-85% B over 30 minutes (pg. 73, figure 7), or mobile phase A water and mobile phase B water/acetonitrile (90/10 (v/v%)), wherein a linear gradient of 35%-65% B over 30 minutes (pg. 74, figure 8). Biba teaches the pH of the mobile phase of the tris buffer mobile phase can be 7.4 (i.e. about 7.5, pg. 74, fig. 8). Biba teaches that utilizing strong anion-exchange liquid chromatography conditions such as NaBr or NaCl salt gradient, with the mixed-mode columns show improved shape (pg. 75, col. 2, para. 2, pg. 77, col. 2, para. 1). IMTAKT teaches as with ion-exchange columns, that with mixed-mode Scherzo C18 columns ionic strength (concentration of salt can be optimized to affect retention times of compounds (pg. 2, first four bullet points). IMTAKT teaches that concentration of organic solvent can be as high at 70% of the mobile phase (pg. 4, gradient elution).
Additionally, McLaughlin teaches that optimization in mixed-mode chromatography depends on salt, organic solvent, and pH of the mobile phase (pg. 316, col. 2, para. 2). A gradient of organic solvent concentration, salt concentration, or some combination of the two can be anticipated to resolve nucleic acids differing in hydrophobic character (nucleobase sequence) or charge (length or number of phosphodiester residues) (pg. 314, col. 2, para. 2). Up to 30% acetonitrile in the mobile phase is known in the art (pg. 314, col. 1, para. 1). McLaughlin teaches that salt concentration can be as low as 0.1 M up to 1.0 M in columns composed of octyl residues and quaternary amines (pg. 315, col. 1, para. 2). Where 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 (See MPEP 2144.05 (II)).
Taken together it would have been prima facie obvious to a person of ordinary skill in the art to optimize the chromatographic method by varying pH, organic solvent and salt concentration in the mobile phase as taught by McLaughlin. A person of ordinary skill in the art would have had the motivation to do so as the art recognizes that in the art of mixed-mode chromatography varying both organic solvent and salt concentration can affect retention of organic molecules and are established result effecting variables.
Regarding claims 2-7: According to the instant specification, the Scherzo SS-C18 column comprises quaternary ammonium, sulfonyl groups, and C18 (i.e. octadecyl) ligands (pg. 50-51, para. 0100). According to IMTAK the difference between Scherzo SW-C18 and SS-C18 is the concentration of ionic ligands loaded onto the column, thus SW-C18 comprises quaternary ammonium and sulfonyl groups (pg. 7, bottom of page). According to Biba, the SW-C18 column has a 130A (i.e. 13 nm) average pore size (pgs. 74-75, bridging para.).
Regarding claims 32-33: Zhu further teaches the conjugation of antisense strands of siRNA to the carbohydrates, which have 19-23 base-pairs (abstract, pg. 1, para. 1). Zhu specifically teaches the following antisense strands:
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(pg. 3, para. 1).
Regarding claims 34 and 36: As discussed above, the prior art render obvious a method of claim 1.
They do not teach a method wherein the fractions are further subjected to anion-exchange chromatography, or the solution to be purified is previously subjected to anion-exchange chromatography.
However, Zhu establishes that anion exchange chromatography is a known method in the art capable of purifying oligonucleotide-carbohydrate conjugates.
Taken together, it would have been prima facie obvious to either preemptively purify the solution with anion exchange chromatography or after mixed-mode chromatography. A person of ordinary skill in the art would have had the motivation to do so in order to improve purity of the isolated compound. A person of ordinary skill would have had a reasonable expectation of success given that anion exchange chromatography is a known method for purifying these types of conjugates.
Claims 12 and 19 are rejected under 35 U.S.C. 103 as being unpatentable over Zhu (Bioconjug. Chem., 2010, IDS filed December 17, 2021), Biba (J. Chromatography A., 2013, IDS filed December 17, 2021), IMTAKT (Scherzo C18 Family, 2016, cited in previous action), and McLaughlin (Chem. Rev., 1989, cited in previous action) as applied to claims 1-9, 11, 13-17, 20-24, 32-34, and 36 above in view of GE Healthcare (Ion Exchange Chromatography & Chromatofocusing Principles and Methods, 2004, cited in previous action).
Regarding claims 12 and 19: As discussed above, the prior art render obvious the method of claims 10 and 18.
They do not teach wherein the gradient is a step gradient.
However, GE Healthcare teaches for certain separations, when conditions for a high resolution separation using a linear gradient have been established, it may be possible to reduce the total separation time by using a more complex elution profile (pg. 44, para. 3). Shallow gradients can be used where maximum resolution is required while steeper gradients can be used in areas where resolution is satisfactory (pg. 44, para. 3). Thus, the use of step gradients in the art of chromatography are utilized to reduce total separation time once an appropriate linear gradient has been established.
Taken together, it would have been prima facie obvious to further modify the method by implementing a step gradient protocol into the separation as taught by GE Healthcare. A person of ordinary skill in the art would have had the motivation to do so with a reasonable expectation of success in order to improve total separation time compared to the linear gradients taught in the art.
Claims 25-30 and 64 are rejected under 35 U.S.C. 103 as being unpatentable over Zhu (Bioconjug. Chem., 2010, IDS filed December 17, 2021), Biba (J. Chromatography A., 2013, IDS filed December 17, 2021), IMTAKT (Scherzo C18 Family, 2016, cited in previous action), and McLaughlin (Chem. Rev., 1989, cited in previous action) as applied to claims 1-9, 11, 13-17, 20-24, 32-34, and 36 above in view of Prakash (Nucleic Acids Research, 2014, cited in previous action) as evidenced by GE Healthcare (Ion Exchange Chromatography & Chromatofocusing Principles and Methods, 2004, cited in previous action).
Regarding claims 25-30 and: As discussed above the prior art renders obvious the method of claim 1.
They do not teach wherein the carbohydrate comprises a trivalent N-acetylgalactosamine moiety. They do not teach wherein the oligonucleotide has a 2’-O-methoxyethyl modified nucleotide or at least one phosphorthioate internucleotide linkage.
However, Prakash teaches the synthesis of triantennary N-acetyl galactosamine conjugated ASOs with 20 nucleotides in length (pg. 8797, fig. 1, col. 2, last para., pg. 8799, table 1). The N-acetylgalactosamine are triantennary (i.e. trivalent) and the oligonucleotides comprise 2’-O-methoxyethyl modified nucleotides (pg. 8797, fig. 1). The oligonucleotides comprise at least one PS linkage (i.e. phosphorthioate linkage, pg. 8798, col. 1, para. 1, pg. 8799, table 1). Prakash teaches the Oligonucleotides were purified by ion-exchange chromatography using a gradient of NaBr across a column packed with Source 30Q resin (pg. 8798, col. 1, para. 1). According to GE Healthcare, Source 30Q is a strong anion exchange column (pg. 75, table at bottom of page).
Taken together, it would have been prima facie obvious to a person of ordinary skill in the art to modify the method by purifying the modified oligonucleotide carbohydrate conjugates of Prakash. A person of ordinary skill in the art would have had the motivation to do so with a reasonable expectation of success as the use of mixed-mode chromatography is a known improvement over strong anion exchange chromatography in the art of separating oligonucleotide compounds.
Claim 31 is rejected under 35 U.S.C. 103 as being unpatentable over Zhu (Bioconjug. Chem., 2010, IDS filed December 17, 2021), Biba (J. Chromatography A., 2013, IDS filed December 17, 2021), IMTAKT (Scherzo C18 Family, 2016), McLaughlin (Chem. Rev., 1989, cited in previous action), Prakash (Nucleic Acids Research, 2014), GE Healthcare (Ion Exchange Chromatography & Chromatofocusing Principles and Methods, 2004, cited in previous action) as applied to claims 1-9, 11, 13-17, 20-30, 32-34, 36 and 64 above, in view of Iwamoto (Nature Biotechnology, 2017, cited in previous action). Supporting figure 8 of Iwamoto has been provided by the examiner.
Regarding claim 31: As discussed above, the prior art renders obvious claim 30. Prakash establishes that N-acetyl galactosamine conjugated ASOs can be purified by ion-exchange chromatography (pg. 8797, fig. 1, col. 2, last para., pg. 8798, col. 1, para. 1)
They do not teach wherein the conjugates comprise phosphorothioate diastereomers that can be separated.
However, Iwamoto teaches the preparation of PS oligonucleotides in which PS stereochemistry can be exploited to tune the lipophilicity and ionic character of oligonucleotides (abstract, pg. 847, col. 2, para. 1). Iwamoto demonstrates that diastereomers of GalNac-conjugated ASOs exhibit different retention times in ion exchange HPLC data (supporting figure 8).
Taken together, it would have been prima facie obvious to a person of ordinary skill in the art to modify the method by chromatographing conjugates comprising phosphorothioate diastereomers that can be separated as taught by Iwamoto. A person of ordinary skill in the art would have had the motivation to do so with a reasonable expectation of success as the use of mixed-mode chromatography is a known improvement over strong anion exchange chromatography in the art of separating oligonucleotide compounds.
Claim 65 are rejected under 35 U.S.C. 103 as being unpatentable over Zhu (Bioconjug. Chem., 2010, IDS filed December 17, 2021), Biba (J. Chromatography A., 2013, IDS filed December 17, 2021), IMTAKT (Scherzo C18 Family, 2016, cited in previous action), McLaughlin (Chem. Rev., 1989, cited in previous action), Prakash (Nucleic Acids Research, 2014), GE Healthcare (Ion Exchange Chromatography & Chromatofocusing Principles and Methods, 2004, cited in previous action) as applied to claims 1-9, 11, 13-17, 20-30, 32-34, 36, and 64 in view of Prakash (WO 2015/168635, cited on PTO-892) and Prakash (J. Med. Chem., 2016, cited on PTO-892).
Regarding claims 65: As discussed above, the prior art renders obvious a method directed towards using the mixed-mode chromatographic method of claim 1 to the application of purification of triantennary N-acetyl galactosamine conjugated ASOs with 20 nucleotides in length as taught by Prakash.
They do not teach the purification of a oligonucleotide conjugate comprising the triantennary N-acetyl galactosamine group as recited by instant claim 65.
However, Prakash (WO 2015/168635) teaches the triantennary structure is contemplated to be conjugated to oligonucleotides
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(pg. 23, bottom structure), albeit without the claimed stereochemistry. Prakash (J. Med. Chem., 2016) discloses that these class of compounds conjugated to ASOs are recognized as Lys-Lys based GalNAc clusters that exhibit the claimed stereochemistry
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(pg. 2719, figure 2). Prakash (J. Med. Chem., 2016) further teaches that these are to be purified by strong anion exchange chromatography (pg. 2722, col. 1, para. 1). Thus, a person of ordinary skill in the art would recognize this stereochemistry to be implemented into the structure of Prakash (WO 2015/168635).
Taken together, it would have been prima facie obvious to a person of ordinary skill in the art to modify the method by purifying the modified oligonucleotide carbohydrate conjugate comprising the galactosamine group of claim 66 rendered obvious over Prakash (WO 2015/168635) and Prakash (J. Med. Chem., 2016). A person of ordinary skill in the art would have had the motivation to do so with a reasonable expectation of success as the use of mixed-mode chromatography is a known improvement over strong anion exchange chromatography in the art of separating oligonucleotide compounds.
Claim 66 is rejected under 35 U.S.C. 103 as being unpatentable over Zhu (Bioconjug. Chem., 2010, IDS filed December 17, 2021), Biba (J. Chromatography A., 2013, IDS filed December 17, 2021), IMTAKT (Scherzo C18 Family, 2016, cited in previous action), and McLaughlin (Chem. Rev., 1989, cited in previous action) as applied to claims 1-9, 11, 13-17, 20-24, 32-34, and 36 above in view of Huang (Journal of Chromatography A, 2018, cited on PTO-892)
Regarding claim 66: As discussed above the prior art render obvious the method of claim 1.
They do not teach wherein the mixed mode matrix has an anion-exchange capacity of about 7 µeq/mL to about 9 µeq/mL of matrix and a cation-exchange capacity of about 18 µeq/mL to about 22 µeq/mL of matrix as recited by instant claim 66.
However, Huang teaches that anion exchange capacities can range from 6 to 460 µeq/mL, 3 to 62 µeq/mL, or 12-19 µeq/mL and tend to be smaller than their cation exchange counterparts (pg. 65, col. 2, para. 2). Huang teaches CEX capacity can also vary depending on for porosity from between 6-180 µeq/mL to 17-500 µeq/mL (pg. 78, col. 1, para. 1). Huang teaches that the ion exchange capacity affects the retention factor for any given ion in a reasonably predictable way (abstract). Thus, the art establishes both anion and cation exchange capacities as result effecting variables as modification of the capacities has a predictable effect on the retention of ions.
Taken together it would have been prima facie obvious to further optimize the method and arrive at the claimed binding capacity ranges, absent a showing of a criticality of the range, as taught by Huang. A person of ordinary skill in the art would have the motivation to do so as a reasonable expectation of success as binding capacities are known in the art in broad ranges covering the claimed range, and have a known impact on retention factor. A person of ordinary skill in the art would do so in order to modify the retention of the ion to be purified.
Response to Arguments
Applicant’s arguments filed September 19, 2025 with respect to the 103 rejections have been fully considered but they are not persuasive.
On page 12 of Applicant’s response, Applicant argues a person of ordinary skill would lack the motivation to utilize the conditions as Biba as Biba discloses strong anion-exchange liquid chromatography is the preferred method for analyzing oligonucleotide samples (para. 3). Biba suggests that if one were trying to detect other impurities, one would turn to mixed-mode chromatography, but Zhu is not considered with these other types of impurities, rather separating an unconjugated oligonucleotide from a carbohydrate-oligonucleotide conjugate (para. 3). In short, Applicant argues that there is no reason one of ordinary skill upon reading the Zhu reference would be motivated to utilize mixed-mode chromatography as suggested by Zhu.
However, Biba teaches the benefit of mixed-mode chromatography is that allows a single column to replace two columns and methods typically used for complete oligonucleotide analysis (i.e. strong anion exchange, pg. 77, col. 2, para. 1). Biba also teaches that conditions of strong ion exchange can be comfortably used with mixed-mode Scherzo SW-C18 column and give satisfactory results (pg. 77, para. 1). Biba also teaches that interestingly, the resolution of a group of challenging isomeric oligonucleotides is surprisingly improved with the mixed-mode columns, affording separations that are better than either the ion-pair reversed-phase or the ion-exchange mode alone (pg. 77, para. 1). Thus, Biba suggests overall the implementation of mixed-mode is a general improvement in both efficacy and resolution over ion-exchange mode alone. The strongest rationale for combining references is a recognition, expressly or impliedly in the prior art or drawn from a convincing line of reasoning based on established scientific principles or legal precedent, that some advantage or expected beneficial result would have been produced by their combination (See MPEP 2144 (II)).
On page 13 of Applicant’s response, Applicant (para. 2). Applicant argues that the Scherzo SS-C18 column (a mixed mode matrix) was not suitable for oligonucleotide analysis Applicant argues that this column being incapable of eluting oligonucleotides would render the method of Zhu inoperable in that an oligonucleotide could not be successfully eluted from the column.
However, while the Examiner acknowledges this, the claims are not limited to SS-C18 columns, but rather to strong anion, strong cation, and hydrophobic ligand. Biba teaches that the Scherzo SW-C18, which is comparable to the SS-C18 column, is efficacious as a mixed-mode stationary phase and comprises a strong anion, strong cation, and hydrophobic ligand (pg. 71, figure 5, pg. 74, col. 2, para. 1). As discussed above the difference between SS-C18 and SW-C18 are the concentration of the ligands.
On page 14 of Applicant’s response, Applicant argues mixed-mode chromatography requires consideration of multiple factors such as ligands, functional groups of the oligonucleotides, type and strength of both mobile phase and ligands on the column (para. 1). Applicant argues that one of ordinary skill in the art could not reasonably predict or have an expectation of success in using a mixed-mode matrix to purify oligonucleotides given the amount of factors to be considered.
However, while optimization of parameters/variables may require a degree of experimentation, wherein the art establishes these variable of known result effecting variables, such parameters will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical (See MPEP 2144.05 (II)). Additionally the prior art relied upon provides ample guidance on parameters to be optimized, encompasses the concentrations and pHs utilized in the claimed invention, and recognize the impact the change in variable may have on a given separation. As discussed above, Biba teaches the pH of the mobile phase of the tris buffer mobile phase can be 7.4 (i.e. about 7.5, pg. 74, fig. 8). Biba teaches that utilizing strong anion-exchange liquid chromatography conditions such as NaBr or NaCl salt gradient, with the mixed-mode columns show improved shape (pg. 75, col. 2, para. 2, pg. 77, col. 2, para. 1). IMTAKT teaches as with ion-exchange columns, that with mixed-mode Scherzo C18 columns ionic strength (concentration of salt can be optimized to affect retention times of compounds (pg. 2, first four bullet points). IMTAKT teaches that concentration of organic solvent can be as high at 70% of the mobile phase (pg. 4, gradient elution). McLaughlin teaches that optimization in mixed-mode chromatography depends on salt, organic solvent, and pH of the mobile phase (pg. 316, col. 2, para. 2). A gradient of organic solvent concentration, salt concentration, or some combination of the two can be anticipated to resolve nucleic acids differing in hydrophobic character (nucleobase sequence) or charge (length or number of phosphodiester residues) (pg. 314, col. 2, para. 2). Up to 30% acetonitrile in the mobile phase is known in the art (pg. 314, col. 1, para. 1). McLaughlin teaches that salt concentration can be as low as 0.1 M up to 1.0 M in columns composed of octyl residues and quaternary amines (pg. 315, col. 1, para. 2).
On page 14 of Applicant’s response, Applicant argues that the prior art does not teach the mobile phase concentrations of the organic solvent or elution salt gradient (para. 2).
However, as discussed above, the art establishes that these variables are known result-effecting variables in the prior art when developing a mixed-mode chromatographic method.
On page 14 of Applicant’s response, Applicant argues that the instant application demonstrates the unexpected results of applying the SS-C18 column for the separation of oligonucleotide conjugates (para. 3). On page 15 of Applicant’s response, Applicant argues the instant specification demonstrates the claimed method results in faster separation and sharper peaks compared to anion-exchange chromatography method (para. 1).
However, the instant claims are not limited to this specific mixed-mode stationary phase. As discussed above, Biba teaches that the Scherzo SW-C18, which is comparable to the SS-C18 column, is efficacious as a mixed-mode stationary phase and comprises a strong anion, strong cation, and hydrophobic ligand (pg. 71, figure 5, pg. 74, col. 2, para. 1). As discussed above the difference between SS-C18 and SW-C18 are the concentration of the ligands.
On pages 15-16 of Applicant’s response (bridging para.), Applicant summarizes the above arguments as it being unpredictable whether any given oligonucleotide could be purified on a mixed-mode matrix because there are a lot of factors to consider in developing the method. Biba teaches away from using mixed-mode matrix with high ion exchange capacity, such as the Scherzo SS-C18 column, for purification of any oligonucleotide. Thus, a person of ordinary skill in the art would not look to modify the method of Zhu by implementing such a method. On pages 16-17 of Applicants’ response (bridging para.), Applicant argues that McLaughlin does not cure the deficiency of these references as Mclaughlin only teaches that conditions of mobile phase can be manipulated to resolve nucleic acids differing in nucleobase length or sequence (bridging para.). Applicant argues McLaughlin does not teach how mobile phase conditions should be adjusted to purify such conjugate compounds.
However, with respect to the SS-C18 argument, as discussed above, Biba teaches that the Scherzo SW-C18, which is comparable to the SS-C18 column, is efficacious as a mixed-mode stationary phase and comprises a strong anion, strong cation, and hydrophobic ligand (pg. 71, figure 5, pg. 74, col. 2, para. 1). Additionally, as discussed above, while optimization of parameters/variables may require a degree of experimentation, wherein the art establishes these variable of known result effecting variables, such parameters will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical (See MPEP 2144.05 (II)). Additionally the prior art relied upon provides ample guidance on parameters to be optimized, encompasses the concentrations and pHs utilized in the claimed invention, and recognize the impact the change in variable may have on a given separation. While McLaughlin does not specifically teach adjusting conditions to purify oligonucleotide-conjugates, the teachings of Mclaughlin directed towards optimizing a given separation would be understood by one in the art to be applied in any situation wherein mixed-mode purification or ion chromatography could be used. McLaughlin teaches that optimization in mixed-mode chromatography depends on salt, organic solvent, and pH of the mobile phase (pg. 316, col. 2, para. 2). A gradient of organic solvent concentration, salt concentration, or some combination of the two can be anticipated to resolve nucleic acids differing in hydrophobic character (nucleobase sequence) or charge (length or number of phosphodiester residues) (pg. 314, col. 2, para. 2). Up to 30% acetonitrile in the mobile phase is known in the art (pg. 314, col. 1, para. 1). McLaughlin teaches that salt concentration can be as low as 0.1 M up to 1.0 M in columns composed of octyl residues and quaternary amines (pg. 315, col. 1, para. 2).
On page 17-18 of Applicant’s response, Applicant argues GE Healthcare does not make up for the deficiencies described above (bridging para.). Applicant argues that GE Healthcare is focused on ion-exchange chromatography and says nothing about mixed-mode chromatography, thus there is nothing to suggest step gradients can be established to reduce separation time in mixed-mode chromatography where linear gradients have been established.
However, GE Healthcare is directed to general teachings of routine practice in the art of ion-exchange chromatography. Mixed-mode chromatography is a type of ion-exchange chromatography. A person of ordinary skill in the art would recognize the applicability of stepwise/linear gradients in mixed-mode chromatography as it a general/routine practice in the art of chromatography as a whole, absent a teaching that step gradients are not applicable to mixed-mode chromatography.
On page 19 of Applicant’s response, Applicant argues the conjugates of Prakash represent more complicated molecules having different functional groups that can interact and create unpredictable or undesirable results using mixed-mode chromatography (para. 2). Biba teaches it is unknown ether mixed-mode columns will provide general improvements for other complex oligonucleotide separations.
However, as discussed above, wherein Biba makes the general suggestion of using mixed-mode chromatography to separate oligonucleotides as an improvement/alternative to ion chromatography, it is prima facie obvious to do so, absent a showing of unexpected results that are commensurate with the claims. Given that Prakash utilizes ion chromatography for purification, and these conjugates are in need of purification as demonstrated by the art, a person of ordinary skill in the art would have the requisite motivation to utilized mixed-mode chromatography with a reasonable expectation of success. It is prima facie obvious to apply a known technique (mixed-mode chromatography) to a known method (ion chromatographic purification of oligonucleotide-carbohydrate conjugates) ready for improvement to yield predictable results (See MPEP 2143 (I)(D)).
On page 20 of Applicant’s response, Applicant argues Iwamoto teaches ion exchange chromatographs of a diastereomer and a stereorandom control. Iwamoto does not teach that ion-exchange can separate mixtures of diastereomers, but rather a chromatogram showing a single diastereomer.
However, Iwamoto demonstrates that a stereorandom control (diastereomer 1), and a pure diastereomer (diastereomer) have different elution times with ion-exchange chromatography. A person of ordinary skill in the art would recognize the ability of ion-exchange chromatographic methods to separate diastereomers given that they have different retention times. The rationale to modify or combine the prior art does not have to be expressly stated in the prior art; the rationale may be expressly or impliedly contained in the prior art or it may be reasoned from knowledge generally available to one of ordinary skill in the art (See MPEP 2144 (I)). Additionally, diastereomeric purity affects the pharmacological properties of antisense oligonucleotides (abstract, pg. 846, col. 1, para. 1) Thus a person of ordinary skill would have the requisite motivation to utilize chromatographic methods, such as mixed mode ion chromatography, a recognized improvement of ion chromatography to separate them.
In summation Applicant argues that the instant invention is not one of routine optimization, but rather the development of a specific method which would have been unpredictable to a person of ordinary skill in the art. Applicant points to the use of a specific stationary phase (Scherzo SS-C18 column) and cites its unexpected ability to separate specific oligonucleotide-carbohydrate conjugates.
However, the Examiner argues that mixed-mode chromatography is a recognized improvement or at the very least an alternative known method for purifying oligonucleotides. The art similarly recognizes the variables to be optimized when developing a chromatographic method (i.e. gradient, concentration, salt, solvent). Taken together, it would have been prima facie obvious to utilize a mixed-mode stationary phase to purify oligonucleotide conjugates. Applicant has demonstrated a specific stationary phase separation of specific conjugates that are not commensurate with the scope of the claims, thus a showing of unexpected results is not persuasive.
Applicant’s reply is considered to be a bona fide attempt at a response and is being accepted as a complete response. The 35 USC § 103 rejections are maintained for reason of record and foregoing discussion.
Conclusion
No claims are allowed in this action.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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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/S.L.G./Examiner, Art Unit 1693
/ERIC OLSON/Primary Examiner, Art Unit 1693