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 .
Election/Restrictions
Applicant’s election without traverse of Group 1, claims 1-3, 6-8, 13, 19, and 50-51 in the reply filed on February 9, 2026 is acknowledged.
Claims 4-5, 9-12, 14-18, 20-21, 23, 27-29, 31, 33-49, 52-55, 58-63, 65-66, and 68-69 were previously canceled. Claims 22, 24-26, 30, 32, 56-57, 64 and 67 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected inventions, there being no allowable generic or linking claim.
Claims 1-3, 6-8. 13-19, and 50-51 are examined on the merits.
Priority
The instant application is a 35 U.S.C 371 national stage filing of the International Application No. PCT/EP2021/058302 filed on March 30, 2021. The instant application claims foreign priority under 35 U.S.C 119(a)-(d) to European Patent Application EP20166803.5, filed on March 30, 2020. Receipt is acknowledged of a certified copy of the foreign patent application in the original language as required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on December 20, 2022; April 25, 2023; and February 9, 2026 are in compliance with the provisions of 37 CFR 1.97 and are being considered by the examiner.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Objections to the Specification
The use of the terms NANOBODY (Pgs. 3, 41, 46-67), High Five (Pg. 61), MabSELECT SuRe (Pg. 65), FAST FLOW (Pg. 65), Amsphere A3 (Pg. 65), TOYOPEARL (Pg. 65), MPC (Pg. 81), Glow response (Pg. 88, 89), Bio-Glo (Pg. 89) which are trade names or a marks used in commerce, has been noted in this application. The terms should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Objections
Claim 1 is objected to for the use of claim language “comprising or consisting of at least three or at least four…” which does not appear to limit scope of the claim beyond the broadest reasonable interpretation of comprising at least three.
Claim 7 is objected to for the use of claim language “comprising or consisting of at least four…” which does not appear to limit scope of the claim beyond the broadest reasonable interpretation of comprising at least four.
Claim 8 is objected to because of the following informalities: claim 8 recites the acronym “SE-HPLC” in line 6 and the acronym “IEX-HPLC” in line 8 without first defining the acronyms. It is recommended that Applicant amend the claims to first recite the full term followed by the acronym in parentheses. Appropriate correction is required.
Claim Interpretation
It is noted that claims 1, 3, 6, 19, and 51 recite limitations which include the word “optionally”. Limitations following the term “optionally” are interpreted as not being required. For example, claim 51 recites method steps which are optional. Therefore the entirety of claim 51 is interpreted as not required for the method as instantly claimed.
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 51 recites the limitation "the secreted polypeptide" in line 7. There is insufficient antecedent basis for this limitation in the claim as the prior recitation is to “a polypeptide”, thus it is unclear whether this limitation is intended to refer to the same polypeptide or a different polypeptide which has been secreted. Appropriate correction is required.
Claim 51 recites the limitation "the medium" in line 7. There is insufficient antecedent basis for this limitation in the claim as there is no prior recitation of a medium. Appropriate correction is required.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 51 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Specifically, claim 51 draws to a method of producing a polypeptide comprising at least three or at least four ISVDs comprising optional steps of culturing host cells, which does NOT narrow the scope of claim 50 directed to the method of method of producing a polypeptide comprising at least three or at least four ISVDs. As instantly claimed, claim 51, which depends from claim 50, recites additional method steps which are optional. Applicant may cancel the claim, amend the claim to place the claim in proper dependent form, rewrite the claim in independent form, or present a sufficient showing that the dependent claim complies with the statutory requirements.
Claim Rejections - 35 USC § 112(a) – Written Description
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 1-3, 6-8, 13, 19, and 50-51 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.
Independent claims 1 and 50 encompass methods of isolating or purifying a genus of polypeptides which comprise at least three or at least four immunoglobulin single variable domains (ISVDs) and a genus of conformational variants which can be converted to the polypeptide via application of a genus of low pH treatments.
In regard to the scope of the genus of polypeptides comprising ISVDs, Applicant’s specification describes the genus of ISVD comprising polypeptides to include those having three or more ISVD building blocks (Pg. 37) which could be light chain variable sequence, a heavy chain variable sequence, a single domain antibody, or a Nanobody (Pg.41 also see section 5.3).
In regard to the scope of the conformational variant, Applicant’s specification describes the genus of conformational variants to include those which have the same molecular weight as the polypeptide but a “more compact form”, decreased hydrodynamic volume, and/or altered surface charge and/or surface hydrophobicity (Pgs. 4, 37-38) and which is characterized by weak intramolecular interactions between ISVDs in the polypeptide (Pgs. 5, 37-38). Further, Applicant’s specification describes the conformational variants to be distinguishable by chromatographic techniques, including SE-HPLC and/or IEX-HPLC (Pgs. 5, 38).
In regard to the scope of the genus of low pH treatments, Applicant’s specification describes the genus of low pH treatments to include decreasing the pH to about 3.2 or less, i.e., about 2.1 (Pgs. 5 and 68) for a “sufficient time” which is at least about 0.5 hours (Pg. 6) before, during, or after a purification step based on a chromatographic technique (Pg. 7).
Dependent claims 2-3 and 6 encompass a genus host cells capable of expressing the polypeptide and conformational variant. In regard to the scope of the host cells, Applicant’s specification describes the genus of host cells including an embodiment where the host is not a CHO cell (Pgs. 58, 60) and which is a lower eukaryotic host such as a yeast, for example Pichia (Komagataella), Hansenula, Saccharomyces, Kluyveromyces, Candida, Torulopsis, Torulaspora, Schizosaccharomyces, Citeromyces, Pachysolen, Debaromyces, Metschunikowia, Rhodosporidium, Leucosporidium, Botryoascus, Sporidiobolus, or Endomycopsis. (Pgs. 4, 60) and embodiments where the host cell comprises prokaryotic organisms (e.g., cornymform bacteria or enterobactericeae), insect cells, mammalian cells (e.g., CHO cells) (Pg. 61).
Dependent claim 7 encompasses a genus of polypeptides comprising at least four ISVDs the scope of which is detailed above.
Dependent claim 8 encompasses a genus of characterizations of the genus of conformational variants the scope of which is detailed above.
Dependent claim 13 and 19 encompass a genus of parameters of a low pH treatment the scope of which is detailed above.
Dependent claim 51 encompasses a genus of host cells which can express the polypeptide the scope of which is detailed above.
Under the written description guidelines (see MPEP 2163) the Examiner is directed to determine whether one skilled in the art would recognize that the Applicant was in possession of the claimed invention as a whole at the time of filing. The following considerations are critical to this determination.
To satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. See, e.g., Moba, B.V. v. Diamond Automation, Inc., 325 F.3d 1306, 1319, 66 USPQ2d 1429, 1438 (Fed. Cir. 2003); Vas-Cath, Inc. v. Mahurkar, 935 F.2d at 1563, 19 USPQ2d at 1116. An original claim may lack written description support when (1) the claim defines the invention in functional language specifying a desired result but the disclosure fails to sufficiently identify how the function is performed or the result is achieved or (2) a broad genus claim is presented but the disclosure only describes a narrow species with no evidence that the genus is contemplated. See Ariad Pharms., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1349-50 (Fed. Cir. 2010) (en banc). The written description requirement is not necessarily met when the claim language appears in ipsis verbis in the specification. "Even if a claim is supported by the specification, the language of the specification, to the extent possible, must describe the claimed invention so that one skilled in the art can recognize what is claimed. The appearance of mere indistinct words in a specification or a claim, even an original claim, does not necessarily satisfy that requirement." Enzo Biochem, Inc. v. Gen-Probe, Inc., 323 F.3d 956, 968, 63 USPQ2d 1609, 1616 (Fed. Cir. 2002).
Accordingly, to satisfy the written description requirement, the specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 1562-63, 19 USPQ2d 1111 (Fed. Cir. 1991). See also MPEP 2163.
ACTUAL REDUCTION TO PRACTICE
In regard to claims 1 and 50 encompassing a genus of methods of isolating or purifying polypeptides which comprise at least three or at least four immunoglobulin single variable domains (ISVDs) from a composition comprising the polypeptide and a genus of conformational variants which can be converted to the polypeptide via application of a genus of low pH treatments, the specification discloses a method of isolating/purifying five embodiments of the genus of polypeptides comprising ISVDs and related conformational variants of those polypeptides. Applicant discloses methods of isolating/purifying polypeptides of Compound A (SEQ ID NO:1, see Table 1 and Example 1) which comprises 5 total ISVDs (OX40L-binding ISVD - 9GS linker- OX40L binding ISVD - 9GS linker - TNFα-binding ISVD - 9GS linker - human serum albumin binding ISVD - 9GS linker - a TNFα-binding ISVD) linked by 9GS linkers; Compound B (SEQ ID NO: 2, see Table 13 and Example 7) which comprises four different ISVDs (TNFα-binding ISVD - 9GS linker - IL23p19 binding ISVD - 9GS linker - human serum albumin-binding ISVD - 9GS linker - IL23p19 binding ISVD) linked by 9GS linkers; Compound C (SEQ ID NO: 69, see Table 30 and Example 14) which comprises three ISVDs (TNFα-binding ISVD - 9GS linker- human serum albumin-binding ISVD - 9GS linker - TNFα-binding ISVD) linked by 9GS linkers; Compound D (SEQ ID NO: 70, see Table 32 and Example 16) which comprises four ISVDs (TNFα-binding ISVD - 9GS linker - IL-6-binding ISVD - 9GS linker - human serum albumin-binding ISVD - 9GS linker - IL-6-binding ISVD) linked by 9GS linkers; and Compound E (SEQ ID NO: 71, see Table 34 and Example 17) which comprises four ISVDs (TNFα-binding ISVD - 9GS linker - IL-6-binding ISVD - 9GS linker - human serum albumin-binding ISVD - 9GS linker - IL-6-binding ISVD) linked by 9GS linkers.
The reduction to practice of the disclosure of methods of converting the conformational variants of the polypeptides above by low pH treatment is limited to determining existence of the variant based on decreased hydrodynamic volume when using SE-HPLC and/or altered surface charge/hydrophobicity when using IEX-HPLC (Pg. 85, section 5.4.5 Analytical Methods). Further, Applicant discloses that the ability to identify the variant is dependent on the specific conditions used. (See Ex 1, Pg 93 and Fig 1; Ex. 2, Pg. 97). Specifically, it appears that conditions which use application of low pH (e.g., Protein A columns) interfere with the ability to detect conformational variants of at least Compound A due to low pH during purification causing conversion of any existing conformational variants.
In regard to dependent claims 2-3 and 6 encompassing a genus of methods comprising a genus of host cells capable of expressing the polypeptide and conformational variant. Applicant discloses a fixed number of host cells capable of expressing the polypeptides which is limited to Pichia for Compounds D and E (Examples 16 and 17) and specifically P. pastoris for Compounds A-C (Examples 1, 7, and 14).
In regard to dependent claim 7 encompassing a genus of methods comprising a genus of polypeptides comprising at least four ISVDs, as stated above, Applicant discloses a fixed number of polypeptides comprising at least four ISVDs: Compounds A, B, D, and E (SEQ ID NOs: 1-2 and 70-71 and Examples 1, 7, 16, and 17 respectively).
In regard to dependent claim 8 encompassing a genus of methods comprising characterizations by which the genus of conformational variants can be determined. As stated above, Applicant discloses a fixed number of conformational variants from a fixed number of polypeptides (Compounds A-E, SEQ ID NOs 1-2 and 69-71) which can be identified by a fixed number of characterizations.
In regard to dependent claim 13 and 19 encompass a genus methods comprising a genus of parameters of a low pH treatment including specific pH and duration and order of low pH treatment which can be used in order to convert the conformational variant, which appears to vary dependent upon the conformational variant derived from individual compounds (See Figs 16 B&C, 43B, 54, and 56-57). While a pH of 3.0 appears to be effective at reducing the amount of conformational variant of Compound A (SEQ ID NO: 1) at 0.5 hours (Fig 16B), it is unclear whether a pH of 3.0 has the same effect on Compounds C (Fig. 54), D (Fig. 56), and E (Fig 57) at 0.5 hours. For some of the instantly disclosed compounds, it appears that either a pH well below 3.0 or applied for a longer timeline is necessary for reduction of the conformational variant. Further, all low pH treatments in working examples were applied after a purification step based on a chromatographic technique (See Examples 4, 7, 14, 16, and 17).
In regard to dependent claim 51 encompasses a genus of methods comprising a genus of host cells which can express the polypeptide. As stated above, Applicant discloses a fixed number of host cells capable of expressing the polypeptides which is limited to Pichia, specific species undisclosed, for Compounds D and E (Examples 16 and 17) and specifically P. pastoris for Compounds A-C (Examples 1, 7, and 14).
However, as stated above, Applicant was only in possession of a limited number of polypeptides comprising ISVDs and a limited number of related conformational variants which are produced by a limited number of host cells where the conformational variant is able to be converted to the polypeptide via a limited number of low pH treatments performed at a limited number of timepoints.
DISCLOSURE OF STRUCTURE
The Applicant has provided no examples of a method of isolating or purifying a polypeptide comprising at least three or at least four ISVDs from a composition comprising the polypeptide and a conformational variant via application of a low pH treatment which converts the conformational variant to the polypeptide for ISVD polypeptides other than the disclosed sequence listings of SEQ ID NOs 1-2 and 69-71 (Compounds A-E) and related conformational variants of which can be produced by Pichia host cells. Applicant’s structural description of the conformational variants is limited to determination that the variants are detected by decreased hydrodynamic volume when using SE-HPLC and/or altered surface charge/hydrophobicity when using IEX-HPLC (Pg. 85, section 5.4.5 Analytical Methods) which Applicant discloses is indicative of a smaller/folded protein (Pgs. 54-55, Fig 52). Further, Applicant indicates that use of CHO cells as the host for production of Compound C results in no generation of conformational variants at all (Example 15, Fig. 55) indicating that conformational variants are not produced by all host cells. The prior art is silent as to the presence of conformational variants of ISVD polypeptides comprising at least three ISVD domains when produced by host cells, including Pichia.
Thus, neither the specification nor the art indicate a relationship between the claimed genus of polypeptides comprising ISVDs and conformational variants produced by a host cell and the ability to successfully use the instantly claimed method to isolate/purify the polypeptide by applying low pH treatment to convert conformational variants to the polypeptide.
SUFFICIENT RELEVANT IDENTIFYING CHARACTERISTICS
Methods for purifying polypeptides comprising ISVDs and the effect of low pH treatment on protein unfolding is known in the art. However, in order to use the claimed method, a skilled artisan would need to recognize that a conformational variant was likely to be produced during production of a specific ISVD-comprising polypeptide and that the conformational variant was characterized by some structural alteration which could be adjusted by application of low pH.
As mentioned above, the specific SEQ ID NOs corresponding to Compounds A-E of which conformational variants are produced when said compounds are produced in specific host cells (Pichia) are provided as well as specific methods by which presence of existing conformational variants of those compounds can be detected and specific low pH treatment parameters which can be used to reduce the presence of the produced conformational variant. However, the breadth of the claims encompass a genus of compositions comprising polypeptides comprising at least three or at least four ISVDs and related conformational variants produced by a genus of host cells and which can be purified by application of low pH treatment, where the low pH treatment converts the conformational variant to the polypeptide and the present specification provides limited guidance and description of the particular polypeptides and conformational variants which can be purified via the instantly claimed method. Therefore, it is incumbent on the Applicant to provide the nexus between structure of polypeptides and outcome of the method in order to be given credit for the claimed genus of methods which can be used to isolate/purify the claimed genus of compositions comprising a polypeptide comprising ISVDs and a conformational variant.
Accordingly, if the skilled artisan sought to determine the claimed genus of compositions comprising polypeptides which comprise at least three or at least four ISVDs and a conformational variant that can be converted to the polypeptide using a low pH treatment, they would first need to know which ISVD-comprising polypeptides were likely to produce a conformational variant under which conditions as well as which conformational variants were likely to be converted to their related polypeptides via treatment using low pH. Hence, based on the written description guidelines, the Examiner should conclude that the applicant was not in possession of the claimed genus of methods which can be used to purify the claimed genus of polypeptides comprising ISVDs beyond the scope of sequences described in the specification which have been produced in Pichia cells.
STATE OF THE ART & QUANTITY OF EXPERIMENTATION
The method of practicing the claimed invention is not well established. Brown et al. (WO 2010056550, found in IDS dated 12/20/2022) teaches that the presence of impurities including variant and/or misfolded version of proteins (i.e., conformational variants) in antibody production by a host cell is known and that removal of impurities is typically performed by chromatography but is challenging due to the range of retention patterns exhibited by the impurities during the purification/chromatography process (Pg. 1, Background, 1st para.). Brown et al. teaches that antibody purification is performed based on size, charge, and/or solubility between impurities and the protein of interest including use of techniques including ion exchange chromatography, size exclusion chromatography, and hydrophobic interaction chromatography but that these techniques often present other issues which inhibit protein purification. For example, Brown et al. teaches that ion exchange an hydrophobic interaction chromatography induce the formation of protein aggregates based which can occur due to changes in pH during elution and that size exclusion chromatography is cumbersome and requires dilution of the end product, which is undesirable in antibody production (Pgs. 1-2, Background, 2nd para.). Further, Brown et al. teaches that Protein A based chromatography can be used to purify single domain antibody molecules (SDABs) (Pg. 2, 3rd para.) which can be fusion polypeptides comprising one or more single domain molecules and can be trivalent or tetravalent (i.e., ISVDs) (Pg. 12, 3rd para.). Further, Brown et al. teaches that SDABs which have been captured by a Protein A column can be eluted using a low pH elution buffer having a pH of 2.0, 2.5, 3.0, 3.5, or 4.0 (Pg. 6, 2nd para). However, Brown et al. provides no description or guidance for converting SDABs from a conformational variant to a functional purified SDAB peptide.
Applicant’s specification indicates that ISVD polypeptides which comprise more than three domains show a propensity for misfolding due to electrostatic interactions between ISVD domains which results in production of compositions comprising misfolded variant multivalent ISVD polypeptides (Pg. 37-38). However, based on Applicant’s disclosure, it appears that these conformational variants are only produced by certain host cells, specifically Pichia host cells. Applicant’s disclosure indicates that the instantly disclosed conformational variants are not produced when ISVDs are produced in other cells such as CHO cells – which is at least true for Compound C, the only compound for which Applicant investigated the presence of conformational variants produced by cells other than Pichia (see Example 15). Further, a skilled artisan would recognize that protein misfolding due to intermolecular interaction would be dependent upon many parameters including temperature, buffer components and concentrations, pH, length of the multivalent polypeptide, and length of the linkers between ISVD domains.
Although Brown et al. teaches that host cells used for production of SDABs can include bacterial cells such as E. coli, yeast cells such a Pichia pastoris, and mammalian cells such as CHO cells (Pg. 35, 1st para.), Brown et al.’s method of purification of SDABs appears to be drawn to exemplary embodiments where production of SDABs occurs in mammalian cells, specifically CHO cells (See claims 9 and 10). Based on Applicant’s disclosure and the state of the prior art, it is not clear that one of ordinary skill would have recognized, prior to the instant disclosure, the existence of the instantly disclosed conformational variants which are only produced in certain host cells (i.e., Pichia) but not CHO cells. Although a skilled artisan would be likely to apply the superior purification technique for SDABs which includes a Protein A column and elution of the SDAB using a low pH buffer as taught by Brown et al., one of ordinary skill would not have used application of a low pH buffer for the intended purpose as instantly disclosed based on what was known in the art at the time of filing. Further, as Applicant indicates that use of a Protein A column renders presence of conformational variants less detectable, likely due to the inherent conversion of variants due to the commonly used and well known low pH elution (See Example 1 and Fig 1), it is unclear that a skilled artisan would have recognized existence of the instantly disclosed conformational variants in the first place.
Applicant has claimed a genus of methods for purifying a genus of compositions comprising a genus of polypeptides comprising at least three ISVDs and a genus of related conformational variants which can converted to the polypeptide by a genus of low pH treatments and further that the compositions comprising ISVD polypeptides can be produced by a genus of host cells, yet the specification has not disclosed that this method can be used for compositions beyond those instantly disclosed (SEQ ID NOs 1-2 and 69-71) which have been produced by Pichia host cells. Additionally, the instant specification indicates that the parameters of the low pH treatment might need to be optimized based on the specific compound and conformational variant which is being converted. Further, the state of the art indicated that use of the claimed method is not well established in order to convert conformational variants to functional ISVD polypeptides which would require undue experimentation, and a skilled artisan would neither expect nor predict the claimed method would be successful for use according to the claimed genus of ISVD polypeptides and related variants which can be produced by the claimed genus of host cells and would be effective at the claimed genus of low pH treatments.
CONCLUSION
Therefore, the Examiner concludes that there is insufficient written description of the instantly claimed genus of methods of isolating or purifying a polypeptide comprising at least three or at least four ISVDs from a composition comprising the polypeptide and a conformational variant by application of a low pH treatment which converts the conformational variant into the polypeptide. Specifically, there is limited description of the structures of the claimed genus of polypeptides comprising at least three or at least four ISVDs and the structures of the claimed genus of related conformational variants capable of being produced by the claimed genus of host cells and which can be converted to the polypeptide by the claimed genus of low pH treatments. Thus, the Examiner concludes that a skilled artisan would find the specification inadequately describes the claimed genus of methods which could be used to convert the claimed genus of conformational variants of the claimed genus of polypeptides comprising at least three or at least four ISVDs produced by the claimed genus of host cells via the claimed genus of low pH treatments.
Claim Rejections - 35 USC § 112(a) – Scope of Enablement
Claims 1-3, 6-8, 13, 19, and 50-51 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for methods of purifying a composition comprising a polypeptide of SEQ ID NOs 1-2 and 69-71 and a conformational variant produced by Pichia host cells using a low pH treatment of about pH 3.0, does not reasonably provide enablement for methods of purifying any composition comprising a polypeptide which comprises at least three ISVDs and a conformational variant produced by any host cell. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
SCOPE OF THE INVENTION
The breadth of the claims encompasses a genus of methods which can be used to purify a genus of compositions comprising polypeptides which comprise at least three ISVDs and a conformational variant where a low pH treatment is used to convert the conformational variant to the polypeptide. As discussed supra, the specification fails to describe the genus of compositions comprising polypeptides which comprise at least three ISVDs and a conformational variant and would require undue experimentation to discover these compositions. The specification only discloses and provides guidance for limited species of compositions comprising polypeptides comprising SEQ ID NOs 1-2 and 69-71 and related conformational variant which have been produced by Pichia host cells and which the conformational variant can be converted by a limited species of low pH treatments.
Independent claims 1 and 50 encompass methods of isolating or purifying a genus of polypeptides which comprise at least three or at least four immunoglobulin single variable domains (ISVDs) and a genus of conformational variants which can be converted to the polypeptide via application of a genus of low pH treatments.
Dependent claims 2-3 and 6 encompass a genus host cells capable of expressing the polypeptide and conformational variant.
Dependent claim 7 encompasses a genus of polypeptides comprising at least four ISVDs the scope of which is detailed above.
Dependent claim 8 encompasses a genus of characterizations of the genus of conformational variants the scope of which is detailed above.
Dependent claim 13 and 19 encompass a genus of parameters of a low pH treatment the scope of which is detailed above.
Dependent claim 51 encompasses a genus of host cells which can express the polypeptide the scope of which is detailed above.
The factors to be considered in determining whether undue experimentation is required are summarized In re Wands 858 F.2d 731, 8 USPQ2nd 1400 (Fed. Cir, 1988). The Court in Wands states: “Enablement is not precluded by the necessity for some 'experimentation.'” Clearly, enablement of a claimed invention cannot be predicated on the basis of quantity of experimentation required to make or use the invention. “Whether undue experimentation is needed is not a single simple factual determination, but rather is a conclusion reached by weighing many factual considerations.” (Wands, 8 USPQ2d 1404). The factors to be considered in determining whether undue experimentation is required include: (1) the quantity of experimentation necessary, (2) the amount or direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claims. While all of these factors are considered, a sufficient amount for a prima facie case is discussed below.
The office has analyzed the specification in direct accordance to the factors outlined in In re Wands. MPEP 2164.04 states: "[W]hile the analysis and conclusion of a lack of enablement are based on factors discussed in MPEP 2164.01(a) and the evidence as whole, it is not necessary to discuss each factor in written enablement rejection." These factors will be analyzed, in turn, to demonstrate that one of ordinary skill in the art would have had to perform "undue experimentation" to make and/or use the invention and therefore, Applicant's claims are not enabled commensurate with the scope of the invention.
ACTUAL REDUCTION TO PRACTICE
The specification does not provide guidance for or a working example for purification of any composition comprising any polypeptide comprising at least three ISVDs and a conformational variant produced by any host cell where the conformational variant is converted to the polypeptide via application of any low pH treatment. The absence of working examples directed to compositions comprising polypeptides other than SEQ ID NOs 1-2 and 69-72 produced by Pichia host cells. Additionally, the working examples indicate that the ability of the specific pH treatment to convert the variant to the polypeptide is dependent on the specific SEQ ID NO. Therefore, the specification does not provide sufficient guidance on how to make and use the invention commensurate in scope with the instant claims.
In regard to claims 1 and 50 encompassing a genus of methods of isolating or purifying polypeptides which comprise at least three or at least four immunoglobulin single variable domains (ISVDs) from a composition comprising the polypeptide and a genus of conformational variants which can be converted to the polypeptide via application of a genus of low pH treatments, the specification discloses a method of isolating/purifying five embodiments of the genus of polypeptides comprising ISVDs and related conformational variants of those polypeptides. Applicant discloses methods of isolating/purifying polypeptides of Compound A (SEQ ID NO:1, see Table 1 and Example 1) which comprises 5 total ISVDs (OX40L-binding ISVD - 9GS linker- OX40L binding ISVD - 9GS linker - TNFα-binding ISVD - 9GS linker - human serum albumin binding ISVD - 9GS linker - a TNFα-binding ISVD) linked by 9GS linkers; Compound B (SEQ ID NO: 2, see Table 13 and Example 7) which comprises four different ISVDs (TNFα-binding ISVD - 9GS linker - IL23p19 binding ISVD - 9GS linker - human serum albumin-binding ISVD - 9GS linker - IL23p19 binding ISVD) linked by 9GS linkers; Compound C (SEQ ID NO: 69, see Table 30 and Example 14) which comprises three ISVDs (TNFα-binding ISVD - 9GS linker- human serum albumin-binding ISVD - 9GS linker - TNFα-binding ISVD) linked by 9GS linkers; Compound D (SEQ ID NO: 70, see Table 32 and Example 16) which comprises four ISVDs (TNFα-binding ISVD - 9GS linker - IL-6-binding ISVD - 9GS linker - human serum albumin-binding ISVD - 9GS linker - IL-6-binding ISVD) linked by 9GS linkers; and Compound E (SEQ ID NO: 71, see Table 34 and Example 17) which comprises four ISVDs (TNFα-binding ISVD - 9GS linker - IL-6-binding ISVD - 9GS linker - human serum albumin-binding ISVD - 9GS linker - IL-6-binding ISVD) linked by 9GS linkers.
The disclosure of methods of converting the conformational variants of the polypeptides above by low pH treatment is limited to determining existence of the variant based on decreased hydrodynamic volume when using SE-HPLC and/or altered surface charge/hydrophobicity when using IEX-HPLC (Pg. 85, section 5.4.5 Analytical Methods) which Applicant discloses is dependent on the specific conditions used. (See Ex 1, Pg 93 and Fig 1; Ex. 2, Pg. 97). Specifically, it appears that conditions which use application of low pH (e.g., Protein A columns) interfere with the ability to detect conformational variants of Compound A due to the conditions inherently causing conversion of any existing conformational variants.
In regard to dependent claims 2-3 and 6 encompassing a genus of methods comprising a genus of host cells capable of expressing the polypeptide and conformational variant. Applicant discloses a fixed number of host cells capable of expressing the polypeptides which is limited to Pichia for Compounds D and E (Examples 16 and 17) and specifically P. pastoris for Compounds A-C (Examples 1, 7, and 14).
In regard to dependent claim 7 encompassing a genus of methods comprising a genus of polypeptides comprising at least four ISVDs, as stated above, Applicant discloses a fixed number of polypeptides comprising at least four ISVDs: Compounds A, B, D, and E (SEQ ID NOs: 1-2 and 70-71 and Examples 1, 7, 16, and 17 respectively).
In regard to dependent claim 8 encompasses a genus of methods comprising characterizations by which the genus of conformational variants can be determined. As stated above, Applicant discloses a fixed number of conformational variants from a fixed number of polypeptides (Compounds A-E, SEQ ID NOs 1-2 and 69-71) which can be identified by a fixed number of characterizations.
In regard to dependent claim 13 and 19 encompass a genus methods comprising a genus of parameters of a low pH treatment including specific pH and duration and order of low pH treatment which can be used in order to convert the conformational variant, which appears to vary dependent upon the conformational variant derived from individual compounds (See Figs 16 B&C, 43B, 54, and 56-57). While a pH of 3.0 appears to be effective at reducing the amount of conformational variant of Compound A (SEQ ID NO: 1) at 0.5 hours (Fig 16B), it is unclear whether a pH of 3.0 for 0.5 hours has the same effect on Compounds C (Fig. 54), D (Fig. 56), and E (Fig. 57). For some of the instantly disclosed compounds, it appears that either a pH well below 3.0 or applied for a longer timeline is necessary for reduction of the conformational variant. Further, all low pH treatments in working examples were applied after a purification step based on a chromatographic technique (See Examples 4, 7, 14, 16, and 17).
In regard to dependent claim 51 encompasses a genus of methods comprising a genus of host cells which can express the polypeptide. As stated above, Applicant discloses a fixed number of host cells capable of expressing the polypeptides which is limited to Pichia, specific species undisclosed, for Compounds D and E (Examples 16 and 17) and specifically P. pastoris for Compounds A-C (Examples 1, 7, and 14).
STATE OF THE ART & QUANTITY OF EXPERIMENTATION
The state of the art teaches that purification of antibodies is not always a highly successful technique and has highly variable results. Consequently, there is ample reason to conclude that there would be a high degree of unpredictability in the ISVD embodiment of the instant invention.
As detailed above, Brown et al. teaches that removal of impurities including conformational variants from an antibody composition (Pg. 1, Background, 1st para.) is typically done by chromatography which can be used to identify and separate impurities based on size, charge, and/or solubility. However, Brown et al. teaches that use of chromatography leads to undesired outcomes such as protein aggregation due to pH changes and or excessive dilution of the end product (Pgs. 1-2, Background, 2nd para.). Brown et al. teaches a superior purification method which can be used to purify multivalent ISVDs comprising use of a Protein A column (Pg. 2, 3rd para.) followed by elution of the ISVD using a low pH buffer (Pg. 6, 2nd para).
Since the prior art at the effective filing date of the present application did not provide guidance for purification of compositions comprising multivalent ISVD polypeptides and related conformational variants produced by a host cell using low pH treatment to convert the variant to the ISVD polypeptide, it is incumbent upon the instant specification to do so.
Although Brown et al. teaches that host cells used for production of SDABs can include bacterial cells such as E. coli, yeast cells such a Pichia pastoris, and mammalian cells such as CHO cells (Pg. 35, 1st para.), Brown et al.’s method of purification of SDABs appears to be drawn to exemplary embodiments where production of SDABs occurs in mammalian cells, specifically CHO cells (See claims 9 and 10). Based on Applicant’s disclosure and the state of the prior art, it is not clear that one of ordinary skill would have recognized, prior to the instant disclosure, the existence of the instantly disclosed conformational variants which are only produced in certain host cells (i.e., Pichia) but not CHO cells. Although a skilled artisan would be likely to apply the superior purification technique for SDABs which includes a Protein A column and elution of the SDAB using a low pH buffer as taught by Brown et al. and Brown et al.’s purification process would inherently convert conformational variants as instantly disclosed to the functional polypeptide, it is not clear that one of ordinary skill would use application of a low pH buffer for the intended purpose as instantly disclosed based on what was known in the art at the time of filing. Further, as Applicant indicates that use of a Protein A column renders presence of conformational variants less detectable, likely due to the inherent conversion of variants due to the commonly used and well known low pH elution (See Example 1 and Fig 1), it is unclear that a skilled artisan would have recognized existence of the instantly disclosed conformational variants in the first place.
Applicant’s specification indicates that ISVD polypeptides which comprise more than three domains show a propensity for misfolding due to electrostatic interactions between ISVD domains which results in production of compositions comprising misfolded variant multivalent ISVD polypeptides (Pg. 37-38). Since the instantly claimed conformational variants were not known in the art, it is unclear whether production of all multivalent ISVD polypeptides would also produce the instantly claimed variants. In fact, based on Applicant’s disclosure, it appears that these conformational variants are only produced by certain host cells, specifically Pichia host cells. Applicant’s disclosure indicates that conformational variants are not produced when ISVDs are produced in other cells such as CHO cells – which is at least true for Compound C, the only compound for which Applicant investigated the presence of conformational variants produced by cells other than Pichia (see Example 15). Thus, there is reason to believe that conformational variants might not be produced for all multivalent ISVD polypeptides in all host cells. Additionally, it appears that there is a level of unpredictability regarding the specific pH and/or length of low pH treatment which is effective for conversion of variants based on the specific compound (See Figs 16 B&C, 43B, 54, and 56-57) and that a pH treatment of 3.0 for 0.5 hours might be effective for use in the instantly claimed method for Compound A (SEQ ID NO:1, Fig 16B) but not for Compound C (SEQ ID NO: 69, Fig. 54).
Further, a skilled artisan would recognize that protein misfolding due to intermolecular interaction would be dependent upon many additional parameters including temperature, buffer components/concentrations, pH, length of the multivalent ISVD polypeptide, and length of the linkers between ISVD domains. For example, it is not clear that the instantly claimed low pH treatment method would be effective at converting conformational variants to polypeptides at increased temperatures, which would be likely to denature proteins. Similarly, it is unclear whether the method would be effective for multivalent ISVD polypeptides comprising shorter or longer linkers or increased numbers of domains, both of which would be expected to influence the intramolecular interactions responsible for formation of the instantly disclose conformational variants.
The physiological art is recognized as unpredictable (MPEP 2164.03). As set forth in In re Fisher, 166 USPQ 18 (CCPA 1970), compliance with 35 USC 112(a) requires: “That scope of claims must bear a reasonable correlation to scope of enablement provided by specification to persons of ordinary skill in the art; in cases involving predictable factors, such as mechanical or electrical elements, a single embodiment provides broad enablement in the sense that, once imagined, other embodiments can be made without difficulty and their performance characteristics predicted by resort to known scientific laws; in cases involving unpredictable factors, such as most chemical reactions and physiological activity, scope of enablement varies inversely with degree of unpredictability of factors involved.” Moreover, the courts have also stated that reasonable correlation must exist between scope of exclusive right to patent application and scope of enablement set forth in the patent application (27 USPQ2d 1662 Ex parte Maize!.). In view of the foregoing, due to the lack of sufficient guidance provided by the specification regarding the issues set forth above, the state of the relevant art, and the breadth of the claims, it would have required undue experimentation for one skilled in the art to use the instant broadly claimed invention.
CONCLUSION
In conclusion, since the prior art and instant disclosure teaches that success of said method is prone to influence by multiple factors, and is highly unpredictable with respect to the specific multivalent ISVD polypeptide and related conformational variant, the production of conformational variants by any given host cell, and specific low pH treatment which can be effective and the specification does not provide ample guidance with respect to achieving the results which are commensurate in scope with the instantly claimed method, one would be burdened with undue experimentation to use the claimed method in order to purify any composition comprising multivalent ISVDs produced by any host cell using any low pH treatment. In conclusion, given the breadth of the claims and the limited scope of the specification, an undue quantity of experimentation is required to use the invention beyond the scope of the instantly disclosed polypeptides comprising at least three ISVDs (SEQ ID NOs: 1-2 and 69-71) and related conformational variants which are produced by Pichia host cells and which can be converted to functional multivalent ISVD polypeptides via application of a low pH treatment of about pH 3.0.
Conclusion
No claims are allowed.
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/ERIN V PAULUS/Examiner, Art Unit 1631
/ARTHUR S LEONARD/Examiner, Art Unit 1631