Office Action 1: Non-Final Rejection (2024-09-27)
Rejection types: 102 - Lack of Novelty, 101 - Patent-Eligible Subject Matter, 112 - Written Description/Enablement

CLAIMS:
AMENDMENTS TO THE CLAIMS

This Listing of claims will replace all prior versions and listings of claims in the application. No new matter is added.

Listing of Claims:

1\. (Original) An in vitro method of detecting phosphorylation of a Rubicon protein comprising:
isolating proteins from a sample;
contacting the isolated proteins with an antibody that hybridises to a phosphorylated Threonine at 166 of a Rubicon protein to form a complex;
detecting the complex wherein detection of the complex that varies from a predetermined value indicates that the sample comes from a subject having a disease associated with Leucine-rich repeat kinase 2 (LRRK2).

2\. (Original) The in vitro method according to claim 1, wherein the disease associated with Leucine-rich repeat kinase 2 (LRRK2) is Parkinson's disease.

3\. (Currently Amended) The in vitro method according to claim :., wherein the antibody is a chimeric humanised antibody.

4\. (Currently Amended) The in vitro method according to claim , wherein the antibody is a monoclonal antibody.

5\. (Currently Amended) The in vitro method according to y claims, wherein the complex is detected with an enzyme linked immunosorbent assay.

6\. (Currently Amended) The in vitro method according to a=?
claims', wherein the subject having a disease associated with Leucine-rich repeat kinase 2 (LRRK2) is treated with a compound able to block interaction of LRRK2 with Threonine 166 and/or Serine 189 of the Rubicon protein.
7\. (Currently Amended) The in vitro method according to w taibo dy. sttnwtcj wherein the compound comprises a treatment antibody.

8\. (Original) The in vitro method according to claim 7, wherein the treatment antibody is a chimeric humanised antibody.

9\. (Original) The in vitro method according to claim 7, wherein the treatment antibody is a monoclonal antibody.

10\. (Cancelled).

11\. (Cancelled).

12\. (Original) An antibody which is capable of binding to Rubicon phosphorylated at Threonine 166 and/or phosphorylated at Serine 189.

13\. (Original) The antibody according to claim 12, comprising at least one variable region incorporating a CDR selected from amino acid sequences i) to vi):
i) LC-CDR1: RSSQSLVHSNGNTYLH (SEQ ID NO. 4);
ii) LC-CDR2: KLSNRFS (SEQ ID NO. 5);
iii) LC-CDR3: SQSTHVPLT (SEQ ID NO. 6);
iv) HC-CDR1: NYGVS (SEQ ID NO. 7);
v) HC-CDR2: TINSNGGSKYYPDSVKG (SEQ ID NO. 8);
vi) HC-CDR3: DVWLRRQWYFDV (SEQ ID NO. 9); and
a functional variant with 99% amino acid sequence identity to any one of amino acid sequences i) to vi).

14\. (Original) The antibody according to claim 12, comprising amino acid sequences:
i) LC-CDR1: RSSQSLVHSNGNTYLH (SEQ ID NO. 4);
ii) LC-CDR2: KLSNRFS (SEQ ID NO. 5);
iii) LC-CDR3: SQSTHVPLT (SEQ ID NO. 6);
iv) HC-CDR1: NYGVS (SEQ ID NO. 7);
v) HC-CDR2: TINSNGGSKYYPDSVKG (SEQ ID NO. 8);
vi) HC-CDR3: DVWLRRQWYFDV (SEQ ID NO. 9); or
a functional variant with 99% amino acid sequence identity to any one of amino acid sequences i) to vi).

15\. (Currently Amended) The antibody according to a e 4fclaim 12 wherein the antibody is a chimeric humanised antibody.

16\. (Currently Amended) The antibody according to a m>-.claim; 12- wherein the antibody is a monoclonal antibody.

17\. (Cancelled).

18\. (Cancelled).

19\. (Original) An inhibitor of Rubicon interaction with Leucine-rich repeat kinase 2 (LRRK2) comprising a compound able to block interaction of LRRK2 with Threonine 166 and/or Serine 189 of the Rubicon protein.

20\. (Original) The inhibitor according to claim 19, wherein the compound comprises an antibody.

21\. - 26 (Cancelled). 2225

27\. (Original) A method of treating a subject in need having a disease associated with Leucine-rich repeat kinase 2 (LRRK2) comprising:
administering a compound able to block interaction of LRRK2 with Threonine 166 and/or Serine 189 of the Rubicon protein.
28\. (Currently Amended) The method according to claim 27, wherein the compound comprises an antibody bted

29\. (Original) The method according to claim 28, wherein the antibody is a chimeric humanised antibody.

30\. (Original) The method according to claim 28, wherein the antibody is a monoclonal antibody.

31\. (Cancelled).

32\. (Cancelled).
4 5 6

OFFICE 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 .
Application Status
Claims 1-9, 12-16, 19-20, and 27-30 are pending.
Claims 1-9, 12-16, 19-20, and 27-30 are examined on the merits herein.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-2 and 4-5 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e. law of nature) without significantly more. The claims recite an “in vitro method of detecting phosphorylation of a rubicon protein comprising: isolating proteins from a sample; contacting the isolated proteins with an antibody that hybridizes to a phosphorylated threonine at 166 of a rubicon protein to form a complex; detecting the complex wherein detection of the complex that varies from a predetermined value indicates that the sample comes from a subject having a disease associated with leucine -rich repeat kinase 2 (LRKK2)”. The judicial exception is: a law of nature in that the phosphorylation of the rubicon protein is a naturally occurring phenomenon in Parkinson’s patients. This judicial exception is not integrated into a practical application. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because a phosphothreonine antibody is capable of binding rubicon phosphorylated at threonine 166. These antibodies are known in the art as taught by Grønborg (Mol Cell Proteomics. 2002 Jul;1(7):517-27; PTO-892) and routinely used for detection of phosphorylated threonine residues on proteins.  Grønborg teaches an in vitro method of detecting phosphorylated threonine on all proteins, including rubicon (figures 1 and 4).
The 2019 Patent Subject Matter Eligibility Guidance (“Guidance”) provides a means of determining whether a particular claim is patent eligible under 35 U.S.C. 101. See MPEP 2106. The Guidance requires an analysis of multiple steps, Steps 1, 2A, and 2B:
Step 1 - Following a determination of the broadest reasonable interpretation of a claim, is the claim drawn to a process, machine, manufacture, or composition of matter? If the answer to this inquiry is “Yes,” the analysis moves on to step 2A.
Step 2A - A two-prong analysis. For prong one, does the claim recite an abstract idea, law of nature, or natural phenomenon? If “Yes,” the analysis proceeds to prong two, which asks whether the claim recites additional elements that integrate the judicial exception into a practical application.
Step 2B - Does the claim recite additional elements that amount to significantly more than the judicial exception? If “No,” the claim is not eligible subject matter under 35 U.S.C. 101.
In the instant case, the claims are drawn to a process, so the answer to Step 1 is “yes.” Specifically, the claim is drawn to an assessment method where the detection of phosphorylation of rubicon at threonine 166 in a sample of a subject relative to a predetermined value indicates the subject has a disease associated with LRRK2.
With respect to prong one of Step 2A, the answer is “yes”.  The claims are directed to a judicial exception.  The judicial exception is:  correlating levels of ruibcon phosphorylation at threnonine 166 with a disease associated with LRRK2.
With respect to Step 2B, claims 1-2 and 4-5 do not recite additional elements that amount to significantly more than the judicial exception. The method can be accomplished with by immunoprecipitation of a total cell lysate, which would contain rubicon, with a phosphothreonine antibody (figure 3) as taught by Grønborg and detected with an anti-rubicon antibody as taught by Yue (WO 2010/030936 A2; IDS filed September 7,2021). Yue teaches an anti-rubicon antibody that regulates autophagy that can be used to treat neurological disease (abstract). Further, the required active method steps are conventional and routine in the art for the reasons stated above and the claims do not amount to significantly more than the judicial exception(s).
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception(s). A claim that focuses on judicial exception(s) can be shown to recite something “significantly more” than the judicial exception(s) by reciting a meaningful limitation beyond the judicial exceptions. However, in the instant case, the claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the additional elements (when considered both individually and as an ordered combination) are limited to well-understood, routine and conventional limitations of detecting phosphorylated threonine on Rubicon (“Step 2B”).  Therefore the methods are routine to one of ordinary skill in the art and do not amount to significantly more than the judicial exception.
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.
Claims 1-9 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA  35 U.S.C. 112, the applicant), regards as the invention.
Claim 1 recites “ an antibody that hybridizes.” Antibodies are known to bind to proteins through a combination of electrostatic, hydrogen bonds, van der Waals forces and hydrophobic interactions, while antibody hybridization refers to a method that uses DNA probes to detect RNA targets to localize DNA sequences. The instant specification teaches that “in various embodiments the antibody engages, hybridizes to or binds the Rubicon protein at Threonine 166” (paragraph 0064). This does not clarify the meaning of an “antibody that hybridizes,” therefore the claim is indefinite.
In the interest of compact prosecution the claim is being interpreted as reading “an antibody that binds to.”
Claims 2-9 depend from claim 1 and are therefore included in this rejection.
Claim 7 recites the limitation the compound in line 2.  There is insufficient antecedent basis for this limitation in the claim.
Claims 8-9 are included in this rejection as they depend from claim 7.
Claims 12-16 and 28-30 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA  35 U.S.C. 112, the applicant), regards as the invention.
Claims 12 and 28 recite “an antibody which is capable of binding.” This language indicates that the while antibody “is capable” of binding rubicon phosphorylated at threonine 166 and/ or serine 189 it is not a required limitation in the claim.
In the interest of compact prosecution “an antibody which is capable of binding” is being interpreted as reading “an antibody that binds to.”
Claims 13-16 depend from claim 12 and claims 29-30 depend from claim 28 and are therefore included in this rejection.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA  35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-9, 12, 15-16, 19-20, and 27-30 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. This is a written description rejection.
The teachings of the specification and the claimed invention:
Claims 1-5 are directed to detection method comprising a genus of antibodies that bind to phosphorylated threonine 166 of rubicon.
Claims 6-9 are directed to a genus of antibodies that bind to rubicon phosphorylated at threonine 166 and/ or serine 189.
Claims 12 and 15-16 are directed to a genus of antibodies that bind to rubicon phosphorylated at threonine 166 and/ or serine 189.
Claims 19-20 are directed to a genus of compounds, including antibodies, that can block the interaction of LRRK2 with rubicon at threonine 166 and/ or serine 189.
Claims 27-30 are directed to a method of treating a disease comprised of administering a genus of compounds, including antibodies, able to block the interaction of LRRK2 with rubicon at threonine 166 and/ or serine 189. The genus of antibodies that is administered need to bind to rubicon phosphorylated at threonine 166 and/ or serine 189 and have a therapeutic effect.
The instant specification does not define the structural features of the paratope-epitope binding and the residues therein that facilitate binding of an antibody to rubicon phosphorylated at threonine 166. Claims 1-9, 12, 15-16, 19-20, and 27-30, do not define the CDRs comprising the binding paratope of the antibody. The instant specification discloses polyclonal antibodies generated against a synthesized peptide phosphorylated at threonine 166 sequence of rubicon in Table 8 (paragraph 00130) and 5 primary monoclonal antibodies split into 2 cell lines each in Table 9 (paragraph 00132). Epitope mapping was not done for any of the clones.
There are no examples of antibodies that bind to rubicon phosphorylated at serine 189 or capable of binding at both phosphorylation threonine 166 and serine 189. As detailed below the state of the art does not recognize that a person of ordinary skill in the art could envision a genus of antibodies defined by epitope or function.
The disclosed antibody clones are not representative of the claimed genus of antibodies. This is because when antibodies are raised to an antigen each monoclonal antibody raised comes from one unique cell with unique CDRs which are responsible for antibody binding, such that the structure of CDRs for one antibody cannot be considered representative of other antibodies with different CDRs that bind the same antigen or even substantially the same epitope.  Notably, the epitope structure that one antibody binds on an antigen, do not inform the skilled artisan as to what other antibodies would bind the same or substantially the same structure.
Claim analysis:
As detailed below, one skilled in the art would be unable to envision the entire genus of antibodies that would bind the epitope of rubicon phosphorylated at threonine 166 and/ or serine 189 or block the interaction of LRRK2 and rubicon at these residues.
The state of the art as it applies to the claimed invention:
Antibody binding to the same antigen, or even the same epitope on that antigen, can be accomplished with an impressively wide variety of antibody structures, even when the antibodies are limited to those from a particular source (Gershoni et al., Biodrugs (2007), 21 (3): 145-156; page 146, section 1.1). The skilled artisan therefore understood that antibodies from a variety of different sources may bind the same antigen and even mediate the same functional effects, but differ widely in the details of the structure of their antigen-binding sites, particularly in the amino acid sequence.
Further, it is not possible to predict the amino acid sequence when an epitope is recited, because there are many different epitope arrangements, such as linear and discontinuous epitopes that is dictated by the unique interaction between an antibody and its cognate epitope (Blythe et al. Protein Science (2005), 14:246–248; page 246). 3D structural analyses of antibody-epitope binding highlights the deficiency in the ability to predict the structural features of an antibody when the epitope is disclosed (Schreiber et al. J Comput Chem (2005), 26(9):879-87; page 879).
Ladner (Biotechnology and Genetic Engineering Reviews (2007), 24(1): 1-30) teaches that competitive binding assays demonstrate that two antibodies bind to overlapping or non-overlapping epitopes but not the same epitope (page 3; paragraph 3), so for accurate epitope mapping techniques that can be used are large energy transfer between labeled antibody to an antigen, antigen fragment binding, competitive peptide and antigen binding to antibody, antigen or antibody mutation, antigen-antibody complex analysis by NMR, determination of the 3D crystal structure of the antigen-antibody complex or electron microscopy (pages 5-7).
There are antibodies that bind to rubicon known in the art. Hartlova (the EMBO Journal, 2018, 37(12): e98694; IDS filed September 7, 2021) teaches an anti-rubicon mAb clone D9F7 produced by immunizing an animal with a synthetic peptide as well as a sheep anti-rubicon antibody that was used for western blot (figure 5). Yue (WO 2010/030936 A2; IDS filed September 7,2021) teaches an anti-rubicon antibody that regulates autophagy that can be used to treat neurological disease (abstract). It is not disclosed whether these antibodies are capable of binding rubicon phosphorylated at threonine 166 and/ or serine 189, even though they were not raised to specifically target the phosphorylation sites it is entirely possible that they are still capable of binding the protein that has been phosphorylated. Gillardon (J Neurosci Methods, 2013, 214(1):62-8; PTO-892) teaches highly selective ATP competitive LRRK2 inhibitor LRRK2-IN1 (section 2.1, page 63) and that kinase inhibitors prevent autophosphorylation and refolding of the activation segment of LRRK2 and could potentially be used to prevent neurodegeneration in patients (abstract). These kinase inhibitors could also prevent the interaction between LRRK2 and rubicon and therefore the phosphorylation of rubicon at threonine 166 and/ or serine 189. Gillardon further teaches antibody clone 1E11 that preferentially binds to the active conformation of the activation segment of the LRRK2 kinase domain and could potentially therefore be used to inhibit LRRK2 mediated phosphorylation (introduction).
Accordingly, one skilled in the art would be unable to predict or envision a genus of antibodies that bind to rubicon phosphorylated at threonine 166 and/ or serine 189 or blocking the interaction between LRRK2 and rubicon at these sites. Since the disclosure fails to describe a sufficient number of species to describe the claimed genus, it is submitted that the written description requirement of 35 U.S.C. 112(a) has not been met.
Claims 13 and 14 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 pre-AIA  the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a written description rejection.
The teachings of the specification and the claimed invention:
Regarding claim 13: The nature and scope of the claimed invention at issue is a subgenus of antibodies that bind to rubicon phosphorylated at threonine 166 defined by a partial structure, a single CDR comprising one of SEQ ID NO: 4-9.
The instant specification discloses that the antibodies that bind to rubicon phosphorylated at threonine 166 is comprised of a heavy chain and light chain with 99% amino acid sequence identity between the 5 clones generated. The light chain and heavy chain are each comprised of 3 CDRs and therefore the antibody requires all 6 CDRs to generate a binding domain capable of binding rubicon phosphorylated at threonine 166 (paragraph 00134). The instant specification has not disclosed the structural features or amino acid sequences of a representative subgenus of antibodies comprising a single CDR comprising one of SEQ ID NO: 4-9 that have the ability to bind to rubicon phosphorylated at threonine 166.
Regarding claims 13-14: The nature and scope of the claimed invention at issue is a subgenus of antibodies that bind to rubicon phosphorylated at threonine 166 defined by a partial structure, CDRs comprising SEQ ID NO: 4-9 with 99% amino acid identity.
The instant specification discloses 5 monoclonal antibodies that bind rubicon phosphorylated at threonine 166 comprised of a heavy chain and light chain with 99% amino acid sequence identity between the 5 clones generated, but a single set of 6 CDRs is disclosed. The specification does not disclose the structural features or amino acid sequences of a representative subgenus of antibodies with CDRs comprising SEQ ID NOs: 4-9 with at least 99% sequence identity that have the ability to bind to rubicon phosphorylated at threonine 166.
Claim Analysis:
Regarding claim 13: The instant claim is directed to a subgenus of antibodies defined by partial structure (i.e. a single CDR) and function (i.e. bind to rubicon phosphorylated at threonine 166 and/ or serine 189). The invention relates to a subgenus of antibodies that bind to rubicon phosphorylated at threonine 166 and/ or serine 189 comprising at least one of the CDRs comprising SEQ ID NOs: 4-9.
A skilled artisan in the art would recognize that the specificity of an antibody is dependent upon six specific CDR sequences and different combinations of CDR sequences greatly alter antigen binding. The instant specification discloses that the antibodies that bind to rubicon phosphorylated at threonine 166 are comprised of a heavy chain and light chain with 99% amino acid sequence identity between the 5 clones generated. The light chain and heavy chain are each comprised of 3 CDRs each and therefore the antibody requires all 6 CDRs to generate a binding domain capable of binding rubicon phosphorylated at threonine 166 (paragraph 00134). The instant specification has not disclosed the structural features or amino acid sequences of a representative subgenus of antibodies comprising a single CDR comprising at least one of SEQ ID NO: 4-9 that have the ability to bind to rubicon phosphorylated at threonine 166. Therefore, a claim directed to at least one CDR sequence, would not permit a skilled artisan to envision the subgenus of antibodies comprising such sequences and have the ability to bind rubicon phosphorylated at threonine 166 as claimed.
Regarding claims 13-14: As detailed below, absent empirical determination, one skilled in the art would be unable to predict or envision which residues of the heavy and light chain CDRs of claims 13-14 may be changed to maintain 99% amino acid sequence identity, such that the resultant variant CDR residues form an antigen-binding site capable of binding rubicon phosphorylated at threonine 166. While the instant application does disclose an antibody with CDRs comprised of SEQ ID NOs: 4-9 from a murine hybridoma, this single species of antibody is not sufficient to claim the entire genus of antibodies described by the claims.
State of the Art
It is well established in the art that the formation of an intact antigen-binding site in an antibody usually requires the association of the complete heavy and light chain variable regions of a given antibody, each of which consists of three CDRs (or hypervariable regions), which provide structure of the antigen binding site and the majority of the contact residues for the binding of the antibody to its target epitope (Almagro & Fransson, Frontiers in Bioscience 2008; 13:1619-33; entire document, specifically note Section 3 “Antibody Structure and the Antigen Binding Site” and Figure 1). Through analysis of different methods for humanizing antibodies, Almagro et al. shows that all of the CDRs of the heavy and light chain, in their proper order of CDR1, then 2, then 3, and in the context of framework sequences which maintain their required conformation are generally required to produce a humanized antibody in which the heavy and light chains associate to form an antigen-binding region that binds the same antigen as the parental rodent antibody (entire document, specifically note “Section 4”).
Examples of antigen binding domains comprising only a VH (or less commonly, a VL) that in turn comprise only three CDRs certainly do exist in the literature, but those antibodies generally comprise unique structures such as CDR1 and CDR3’s that are elongated in length and that are often disulfide linked such as in heavy chain antibodies (De Genst et al., Developmental and Comparative Immunology, 2006, 30:187-98; entire document, specifically note “1. Introduction” and figure 1 in particular). Further, specific autonomous VH domains that can bind to antigens have also been described in the arts. Ward et al. (Nature, 1989, 341:544-546) teaches that the complete VH domains of several antibodies maintained the ability, although with reduced affinity than the VH-VL, to bind to lysozyme even when they are not paired with the corresponding VL domains (page 545, left column, 2nd complete paragraph; Table 1). Ward et al. also teaches that the autonomous VH domain lacks the binding cavity which is formed when paired with the VL domain (page 546, left column, lines 4-6). Ward et al. further teaches that the VH domain alone is very sticky and contributes to non-specific binding (page 546, left column, last paragraph). Barthelemy et al. (Journal of Biological Chemistry, 2008, 283:3639-3654) analyzed numerus autonomous VH domains that are isolated from a phage display screen that are conducive for producing single domain VH antibodies. Barthelemy et al. showed that several changes in the key residues in the VH framework region that mediates binding with the VL domain are required for stabilization of the autonomous VH domain antibodies (abstract; figure 1A and table 1). These findings further illustrates that residues in the VH framework region are required to stabilize a VH domain to form a functional antigen binding pocket and only some VH domains can function alone to bind to antigens. Furthermore, due to their increase in nonspecific binding, autonomous VH domains have not been shown to be functional in vivo to treat diseases.
Crystallization analysis of different antibody structures when unbound and bound to an antigen shows that the antigen binding domain adapts different confirmations when bound to an antigen (Choi et al., 2011, Molecular BioSystems, 2011, 7:3327-334; specifically page 3327, 1st and 2nd paragraphs in particular). Furthermore, the HV-CDR3 domain is highly variable (Choi et al., page 3327, right column, 1st full paragraph). Although greatly improved, a definitive computational method to accurately predict the structure of the antigen binding site when only analyzing just the CDR3 sequence or an “equivalent therefore” remains to be established (Choi et al., see “abstract”). Thus, a disclosure of a single CDR sequence is not sufficient to determine the antigen binding domain of an antibody because the other CDR sequences provide structure to the antigen binding domain.
Screening phage display libraries comprising human scFv have been used to isolate human antibodies that bind to a specific antigen. Griffiths et al. (The EMBO Journal, 1993, 12:725-734) teaches screening a phage display library with 2.9X107 clones of human scFv to identify the scFv for binding to different antigens (entire document, specifically page 732, see “Selection of phage library” and “screening and sequencing of clones”). One scFv is isolated to bind to MUC1, one scFv is isolated to bind to CEA, and seven different scFVs are isolated from the library to bind to TNFα (entire document, specifically note Table on page 726). This highlights one cannot simply predict which of the scFv out of the 2.9X107 scFv clones would bind to the specific antigen. Also, the phage library that is used for the screen can generate different antibodies.
Guide phage display screening of phages expressing 1.8X108 human scFv clones has been used to identity the five human CDR sequences that function with a heavy chain CDR3 sequence (Klimka et al., British Journal of Cancer, 2000, 83:252-260; page 252, left column). By performing multiple rounds of phage display using complex random pairing of human heavy variable domain with CDR1 and CDR2 sequences with the mouse HV-CDR3 and the light variable region (which has 3 CDR sequences, thus 4 CDR sequences are used in the screen), Klimka et al. identify the human heavy chain CDR1 and CDR2 sequences that can function with the mouse HV-CDR3 and light chain sequences. The identified heavy chain is then used to screen for a human light variable regions (entire document, page 259, left column, 1st full paragraph in particular). Only through a complex screen as taught by Klimka et al. is a skilled artisan able to randomly identify the remaining CDR sequences. Furthermore, similar to the phage display screening for antibodies described above, the CDR sequences that are identified to function with a particular HV-CDR3 sequence is dependent on the particular human antibody library that is used.
Guide phage display screening of phages expressing Fab was performed to isolate a human antibody that displayed similar binding properties as the parental antibody in Beiboer et al. (Journal of Molecular Biology, 2000, 296:833-849). In Beiboer et al, a disclosed variable heavy chain was mixed with a library of 108 light chain sequences and 2x107 light chain sequences to generate Fab libraries in, specifically page 834, see “Humanisation of the light chain”). Following 4 rounds of high stringent antigen selection, seven light chains were obtained (Table 2). The best binding light chain is then shuffled with a library of 1.2x107 human VH comprising the VH-CDR3 of the parent mouse antibody to obtain a Fab human antibody library (page 835, see “Humanisation of the heavy chain”). Following several rounds of screening, one high binding human antibody that maintains the VH-CDR3 sequence of the original parent mouse antibody is obtained that displayed similar binding properties as the parent antibody (abstract; page 835-837, bridging paragraph). Structural modeling of the parent mouse antibody with the selected human antibody showed that the selected human VL sequences are distinct from the parent mouse VL sequence and with each other demonstrating that the VH plays a dominant role in antigen binding (page 834-839, right column, bridging paragraph). Further, structural modeling further showed minimal structural conservation is observed in the CDRs of the human VH (which contains the same CDR3 sequence as the parent mouse antibody) with the parent mouse antibody (page 839, right column). Beiboer et al. highlighted that maintaining the VH-CDR3 sequence in a guide phage display is sufficient to screen for a human antibody with similar binding properties as the parent antibody (page 841, left column). The findings from Beiboer et al. highlighted that a skill artisan cannot predict the structural features of the antibody that will be obtained from a phage display screen when starting with a partial sequence. These findings showed that a skill artisan cannot predict the structural features of the antibody that will be obtained from a phage display screen when starting with a partial sequence, and cannot even predict the minimal structural feature of the antibody that will be obtained with a partial disclosed antibody CDR sequence that will have specific binding properties.
Regarding % sequence identity in the CDRs:
Applicant has not disclosed relevant, identifying characteristics of CDR region
amino acid sequences (or combinations thereof) that confer upon an antibody the ability
to bind rubicon phosphorylated at threonine 166, because the instant specification does not provide structural antibody features that correlate with a functional ability to bind rubicon phosphorylated at threonine 166. To elaborate on why the claimed antibodies, lack adequate written description, Dondelinger et al. (Frontiers in Immunology, 9: 2278, 2018) reviews the structural basis of antigen-antibody recognition and teaches that naturally occurring conventional antibodies comprise two polypeptides, the so-called light and heavy chains. The antigen-combining site of an antibody is a three-dimensional structure that fully comprises six CDRs, three each from the light and heavy chains. The amino acid sequences of the CDRs are hypervariable, as the amino acid residues contained within the CDRs determine much of the antibody’s binding specificity. While the prior art teaches some understanding of the structural basis of antigen-antibody recognition, it is noted that the art is characterized by a high level of unpredictability, since the skilled artisan still cannot accurately and reliably predict the consequences of amino acid substitutions, insertions, and deletions in the antigen binding domains. Lin et al. (African Journal of Biotechnology, 10(79):18294-18302, 2011) teaches that a single amino acid substitution in the VL CDR3 of an anti-avian infectious bronchitis virus (IBV) single-chain antibody (ZL.80) may abrogate binding. For example, at Figure 3, Lin et al. demonstrate that replacing either the Cys105 or Asp106 residue in the VL CDR3 of ZL.80 with an alanine residue reduces binding to near negative control levels. Lin et al. also teaches that some single amino acid substitutions in the VL CDR3 of ZL.80 may significantly improve binding. For example, replacing the Val108 residue in the VL CDR3 of ZL.80 with a tyrosine residue results in a 12.9-fold increase in affinity compared to parental ZL.80.
As discussed above, specific human antibodies can be isolated from phage display libraries. However, without performing the complex random screens to isolate the antibodies, a skilled artisan cannot predict the specific antibody structure or sequence of the claimed antibody. Because of the unpredictability of the art, the applicant has not shown they are in possession of the genus of antibodies that can function with the disclosed singular CDR sequence comprising at least one of SEQ ID NO: 4-9 that can bind to rubicon phosphorylated at threonine 166 as claimed. The variation encompassed by the present claims is large and the specification does not establish that the species described are representative of the claimed subgenus. Neither does the disclosure provide sufficient evidence of the structure function relationship to provide the claimed function(s).
It is noted that, “[r]egardless whether a compound is claimed per se or a method is claimed that entails the use of the compound, the inventor cannot lay claim to the subject matter unless he can provide a description of the compound sufficient to distinguish infringing compounds from non-infringing compounds, or infringing methods from non-infringing methods.” University of Rochester v. G.D. Searle Co., 69 USPQ2d 1886 1984 (CAFC 2004) (emphasis added). In this case, a skilled artisan cannot visualize the subgenus of antibodies that would bind to rubicon phosphorylated at threonine 166 by the disclosure of a partial antibody sequence as the instant claim broadly claimed.
Further, absent empirical determination, one skilled in the art would be
unable to predict or envision which CDR residues within the claimed rubicon phosphorylated at threonine 166 consensus sequences may be changed such that the resultant variant CDRs may be comprised of an antigen-binding site capable of binding rubicon phosphorylated at threonine 166. The general knowledge and level of skill in the art does not adequately supplement the omitted description, because specific, not general, guidance is needed. Since the disclosure fails to describe relevant, identifying structural characteristics, that correlate with the ability to bind rubicon phosphorylated at threonine 166, and because the disclosed species are not sufficient to describe the claimed genus, it is submitted that the written description requirement of 35 U.S.C. 112(a) has not been met.
The disclosure therefore does not show that applicant was in possession of the necessary common attributes or features possessed by the members of the claimed genus. Accordingly, the skilled artisan would not recognize that applicants were in possession of the invention as broadly claimed at the time the application was filed.
The rejection of claim 13 under 35 U.S.C. 112(a) may be overcome by removing “at least one” and “selected from” language.
The rejection of claims 13-14 under 35 U.S.C. 112(a) may be overcome by removing the percent sequence identity language.
Claims 6, 12-16, and 28-30 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 enablement requirement. The claims contain subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention. This is a scope of enablement rejection.
The factors to be considered in determining whether a disclosure would require undue experimentation include (1) the quantity of experimentation necessary, (2) the amount of 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. In re Wands, 8 USPQ2d, 1400 (CAFC 1988).
Nature of the invention/ Breadth of the claims: The claims are broadly drawn to a genus of antibodies that binding to rubicon phosphorylated at threonine 166 and/ or serine 189. The nature and scope of the claimed invention at issue is the claimed genus of antibodies that binds rubicon phosphorylated at threonine 166 and serine 189.
State/ predictability of the art: There are no examples in the prior art of antibodies that bind to rubicon phosphorylated at threonine 166 or serine 189 specifically, although other anti-rubicon antibodies may be capable of binding the protein that has been phosphorylated at these residues as detailed above.
Further Buus (Mol Cell Proteomics, 2012, 11(12):1790-800; PTO-892) teaches use of ultrahigh density peptide microarray technology to map 22 polyclonal anti-PrEST antibodies and found a maximum resolution of 2-20-mers (page 1792, column 2, paragraph 2). Buus teaches that the epitopes were 4-12 amino acids long (figure 5) but there are some important limitations to the ability of the current peptide microarray technology to address protein-specific antibody epitopes, as peptides do not readily represent more complex structures such as discontinuous and/or post-translationally modified epitopes (page 1798, column 2, paragraph 3). Therefore, without conformational analysis demonstrating that folding arranges these residues next to one another, it is unlikely that a single antibody would have the capability to bind both residues threonine 166 and serine 189 on rubicon as they are 21-mers apart.
Guidance in the specification: The instant specification teaches that “in various embodiment bispecific antibodies are monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens. In the present case, one of the binding specificities is for Rubicon protein phosphorylated at Threonine 166, the other one is for another compound having Rubicon protein phosphorylated at Serine 189. Methods for making bispecific antibodies are known in the art. Traditionally, the recombinant production of bispecific antibodies is based on the co-expression of two immunoglobulin heavy-chain/light-chain pairs, where the two heavy chains have different specificities” (paragraphs 0087-88).
Working examples: The instant specification provides no examples of an antibody that binds to rubicon phosphorylated at serine 189 or an antibody capable of binding rubicon phosphorylated at threonine 166 and serine 189. The instant specification does not disclose bispecific antibodies. Thus, there are no working examples commensurate in scope with the claims.
Amount of experimentation necessary: An extensive amount of additional research is required to determine that an antibody is capable of binding rubicon at both phosphorylation sites threonine 166 and serine 189 or to generate a bispecific antibody with these specific binding sites.
For the reasons discussed above, it would require undue experimentation for one skilled in the art to generate or determine an antibody capable of binding to rubicon phosphorylated at threonine 166 and serine 189.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 6, 19, and 27 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by (J Neurosci Methods, 2013, 214(1):62-8; PTO-892).
Regarding claims 6, 19, and 27, Gillardon teaches a highly selective ATP competitive LRRK2 inhibitor LRRK2-IN1 (section 2.1, page 63) and that kinase inhibitors prevent autophosphorylation and refolding of the activation segment of LRRK2 and could potentially be used to prevent neurodegeneration in patients (abstract). These kinase inhibitors could also prevent the interaction between LRRK2 and rubicon and therefore the phosphorylation of rubicon at threonine 166 and/ or serine 189.
Claims 12 and 16 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Grønborg (Mol Cell Proteomics. 2002 Jul;1(7):517-27; PTO-892).
Regarding claim 12, Grønborg teaches a phosphothreonine antibody that would bind rubicon phosphorylated at threonine 166. Grønborg teaches an in vitro method of detecting phosphorylated threonine on all proteins, including rubicon (figures 1 and 4).
Regarding claim 16, Grønborg teaches the phosphothreonine antibodies are monoclonal (cell culture and antibodies).
Conclusion
No claims are allowed.

APPLICANT REBUTTAL: REMARKS
This is a reply to the Non-Final Office Action dated September 27, 2024. Applicant thanks the Examiner for carefully considering the application.
Status of Claims
Prior to the entry of the present Response, claims 1-9, 12-16, 19-20 and 27-30 were pending. In an interest to progress prosecution of the present application, Applicant is amending the claims as set forth herein, and following entry of these amendments, claims 1-6, 8-9, 12, 15-16, 19, 27, 29-30 and 33-37 are pending.
Claims 1-2 and 4-5 are rejected under 35 U.S.C. § 101 because the claimed invention is directed to a judicial exception without significantly more.
Claims 1-9, 12-16, and 28-30 are rejected under 35 U.S.C. § 112 as being
indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention. Claims 1-9, 12, 15- 16, 19-20 and 27-30 are rejected 35 U.S.C. § 112 as failing to comply with the written description requirement. Claims 13 and 14 are rejected under 35 U.S.C. § 112 as failing to complain with the written description requirement. Claims 6, 12-16, and 28-30 are rejected under 35 U.S.C. under § 112 for failing to comply with the enablement requirement.
Claims 6, 19, and 27 are rejected under 35 U.S.C. § 102 as being anticipated by (J Neurosci Methods, 2013, 214(1):62-8: PTO-892). Claims 12 and 16 are rejected under 35 U.S.C. § 102 as being anticipated by Gronborg (Mol Cell Proteomics. 2002 Jul; 1(7):517-27; PTO-892).
Claims 1, 6, 8-9, 12, 19, 27, 29-30 are amended. Claims 7, 10-11, 13-14, 17-18, 20-26, 28, 31-32 are cancelled. Claims 33-37 are new. No new subject matter is added to the amended claims or in the new claims.
Claims 1, 6, 12, 19 and 27 have been amended to include the limitation of an antibody comprising the CDR sequences as recited by previously pending Claim 14. Pursuant to this amendment, previously pending Claims 13, 14, 20 and 28 have been cancelled.
Claims 1 and 12 have been further amended to read "...an antibody that binds to...".Claims 6, 12, 19 and 27 have been amended to remove the feature of "Serine 189".
Claim 6 has been further amended to include the limitation of Claim 7
directed to a treatment antibody. Accordingly, claim 7 has been cancelled and the dependencies of Claims 8 and 9 have been amended to depend from Claim 6.
The dependencies of Claims 29 and 30 have been amended following the amendment to Claim 27 and cancellation of Claim 28.
New Claims 33 has been added and finds support from at least paragraph [00131] of the specification.
New Claims 34-37 have been added and find support from at least paragraphs [0059] and [00134], and [00139]-[00142] of the specification.
Applicant submits that the amendments and new claims are supported by the application as filed and do not introduce new matter. Applicant respectfully request reconsideration and allowance in view of these amendments and the following remarks.
Response to Rejections
35 U.S.C. 101
The Examiner has rejected Claims 1-2 and 4-5 under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e. law of nature) without significantly more.
In response, claim 1 has been amended to include the CDR sequences as
recited by previously pending Claim 14. Applicant submits that with the recitation of the CDR sequences in amended Claim 1, said claim includes additional elements that are sufficient to amount to significantly more than the judicial exception because neither Gronborg (Mol Cell Proteomics. 2002 Jul;1 (7):517-27; PTO-892) nor any other prior art references disclose an antibody that binds to phosphorylated Threonine at 166 of a Rubicon protein, the antibody comprising amino acid sequences:
i) LC-CDR1: RSSQSLVHSNGNTYLH (SEQ ID NO. 4);
ii) LC-CDR2: KLSNRFS (SEQ ID NO. 5);
iii) LC-CDR3: SQSTHVPLT (SEQ ID NO. 6);
iv) HC-CDR1: NYGVS (SEQ ID NO. 7);
v) HC-CDR2: TINSNGGSKYYPDSVKG (SEQ ID NO. 8); and
vi) HC-CDR3: DVWLRRQWYFDV (SEQ ID NO. 9).
The abovementioned specific CDR sequences are not well-understood, routine and/or conventional limitations of detecting phosphorylated threonine at 166 on the Rubicon protein.
In view of the above, Applicant submits that Claim 1 relates to patent eligible subject matter. Claims 2 and 4-5 which depend on Claim 1 and include the CDR sequences, would also include additional elements that are sufficient to amount to significantly more than the judicial exception and constitute patent eligible subject matter.
35 U.S.C. 112(b)
The Examiner has rejected Claims 1-9 under 35 U.S.C. 112(b) because Claim
1 recites "an antibody that hybridizes" and is indefinite.
In response, claim 1 has been amended to "...an antibody that binds to..." and Applicant submits that said claim is no longer indefinite. Claims 2-6 and 8-9 which depend from claim 1 are also no longer indefinite pursuant to this amendment to Claim 1.
The Examiner has rejected Claims 7-9 under 35 U.S.C. 112(b) because there is insufficient antecedent basis for the limitation "the compound" in line 2 of Claim
Claim 7 has been cancelled in the present Response and Applicant submits that the rejection to Claim 7 is now moot.
Claims 8-9 have been amended to depend on claim 6 which has been amended to recite "a treatment antibody" which provides antecedent basis for Claims 8-9. Applicant accordingly submits that there is sufficient antecedent basis for the limitations in Claim 8-9.
The Examiner has rejected Claims 12-16 and 28-30 under 35 U.S.C. 112(b) because Claims 12 and 28 recite "an antibody which is capable of binding" and are indefinite.
Claim 12 has been amended to "...an antibody that binds to..." and Applicant submits that said claim is no longer indefinite. Claims 15-16 which depend from Claim 12 are also no longer indefinite pursuant to this amendment to Claim 12.
Claim 28 has been cancelled and the rejection is now moot. Claims 29-30 are now dependent on Claim 27 which recites "...an antibody that binds to..." which Applicant submits is not indefinite, hence Claims 29-30 are no longer indefinite.
35 U.S.C. 112(a)
Claims 1-9, 12, 15-16, 19-20 and 27-30
The Examiner has rejected Claims 1-9, 12, 15-16, 19-20 and 27-30 under 35 U.S.C. 112(a) as failing to comply the written description requirement because "one skilled in the art would be unable to predict or envision a genus of antibodies that bind to rubicon phosphorylated at threonine 166 and/ or serine 189 or blocking the interaction between LRRK2 and rubicon at these sites".
In response, Claims 1, 6, 12, 19 and 27 have been amended to include the CDR sequences of previously pending Claim 14. Further, Claims 6, 12, 19 and 27 have been amended to remove the feature "Serine 189".
As acknowledged by the Examiner at least on pages 8 and 12 of the non-final Office Action, there is written description for an antibody that binds to phosphorylated Threonine at 166 of the Rubicon protein (paragraphs [00130] and [00132] of the PCT publication) and for an antibody comprising the 6 (six) CDR amino acid sequences disclosed at paragraphs [00139]-[00142] of the PCT publication. Accordingly, Applicant submits that with the amendments to Claims 1, 6, 12, 19 and 27, Claims 1-6, 8-9, 12, 15-16, 19, 27, 29-30 as pending in the present Response now comply with the written description requirement. New dependent Claims 33-37 also comply with the written description requirement for the same reasons.
Claims 13 and 14
The Examiner has rejected Claims 13 and 14 under 35 U.S.C. 112(a) as failing to comply the written description requirement because Claim 13 which is "directed to at least one CDR sequence, would not permit a skilled artisan to envision the subgenus of antibodies comprising such sequences and have the ability
to bind rubicon phosphorylated at threonine 166 as claimed" and with regards to Claims 13 and 14, "one skilled in the art would be unable to predict or envision which residues of the heavy and light chain CDRs of claims 13-14 may be changed to maintain 99% amino acid sequence identity, such that the resultant variant CDR residues form an antigen-binding site capable of binding rubicon phosphorylated at threonine 166".
Claims 13 and 14 have been cancelled in the present Response and Applicant submits that this rejection is now moot.
Applicant wishes to highlight that the "at least one" and "selected from" language of Claim 13 and the percentage sequence identity language of Claim 14 have been omitted in the amendments to Claims 1, 6, 12, 19 and 27 to include the CDR sequences. Accordingly, Applicant submits that these claims satisfy the written description requirement under 35 U.S.C. 112(a).
Claims 6, 12-16 and 28-30
The Examiner has rejected Claims 6, 12-16 and 28-30 under 35 U.S.C. 112(a) as failing to comply the enablement requirement because "it would require undue experimentation for one skilled in the art to generate or determine an antibody capable of binding to rubicon phosphorylated at threonine 166 and serine 189".
Claims 6 and 12 have been amended to remove the feature "Serine 189".
Claim 27 has also been amended in the same manner. Applicant accordingly submits that Claims 6, 12 and 27 now meet the enablement requirement under 35 U.S.C. 112(b) because the subject application discloses at paragraphs of [00131]-[00142] of the PCT publication, an antibody that is capable of binding to phosphorylated Threonine at 166 of the Rubicon protein. Claims dependent on Claims 6, 12 and 27 also meet the enablement requirement under 35 U.S.C. 112(a) for the same reasons.
Claims 13, 14 and 28 have been cancelled, hence this rejection is moot.
35 U.S.C. 102
The Examiner has rejected Claims 6, 19 and 27 under 35 U.S.C. 102(a)(1) as being anticipated by Gillardon (J Neurosci Methods, 2013, 214(1 ):62-8; PTO-892). The Examiner has rejected Claims 12 and 16 under 35 U.S.C. 102(a)(1) as being anticipated by Gronborg (Mal Cell Proteomics. 2002 Jul;1 (7):517-27; PTO-892).
In response, Claims 6, 12, 19 and 27 have been amended to an antibody that binds to phosphorylated Threonine at 166 of the Rubicon protein, the antibody comprising the CDR sequences of previously pending Claim 14 to which the Examiner has not found to be anticipated by Gillardon or Gronborg.
Applicant accordingly submits that Claims 6, 12, 19 and 27 are novel in view of Gillardon or Gronborg. Claim 16 is also novel in view of Gronborg because of its dependency on Claim 12.
In the present communication, any alteration to the application or claims and/or any characterization of claim scope or cited prior references are made to facilitate expeditious prosecution of this application and it is not conceded that any of the previously pending claims is not patentable. Applicant therefore reserves the right to pursue any previously pending or other broader or narrower claims and/or any subject matter therein that is supported by the present disclosure, including subject matter found to be specifically disclaimed herein or by any prior prosecution, at a later date. Accordingly, it shall not be reasonably inferred that Applicant has made any disclaimers or disavowals of any subject matter supported by the present application, in this application, or parent or child or related prosecution history.
CONCLUSION

NEXT OFFICE ACTION: 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 .
Application Status
Claims 1-6, 8-9, 12, 15-16, 19, 27, 29-30, and 33-37 are pending.
Claims 1-6, 8-9, 12, 15-16, 19, 27, 29-30, and 33-37 are examined on the merits herein.
Grounds of Rejection Withdrawn
The previous rejection of claims 1-2 and 4-5 under 35 U.S.C. 101 are withdrawn in view of claim amendments.
The previous rejection of claims 1-9, 12-16, and 28-30 under 35 U.S.C. 112(b) are withdrawn in view of claim amendments and cancellations.
The previous rejection of claims 1-9, 12-16, 19-20, and 27-30 under 35 U.S.C. 112(a) are withdrawn in view of claim amendments and cancellations.
The previous rejection of claims 6, 19, and 27 under 35 U.S.C. 102 are withdrawn in view of claim amendments.
Allowable Subject Matter
Claims 1-6, 8-9, 12, 15-16, 19, 27, 29-30, and 33-37 are allowed.
The following is an examiner’s statement of reasons for allowance:
The CDRs comprising an antibody that binds to phosphorylated at 166 of the Rubicon protein comprising the amino acid sequences SEQ ID NOs: 4-9 have been found free of the prior art. Therefore independent claims 1, 12, 19, and 27 are allowable.
As claims 2-6, 8-9, 15-16, 29-30, and 33-37 are dependent from these independent claims and are therefore also allowable.
The state of the prior art teaches antibodies with specific binding to Rubicon as seen in Hartlova and Yue. Hartlova (the EMBO Journal, 2018, 37(12): e98694; IDS filed September 7, 2021) teaches an anti-rubicon mAb clone D9F7 produced by immunizing an animal with a synthetic peptide as well as a sheep anti-rubicon antibody that was used for western blot (figure 5). Yue (WO 2010/030936 A2; IDS filed September 7,2021) teaches an anti-rubicon antibody that regulates autophagy that can be used to treat neurological disease (abstract). It is not disclosed whether these antibodies are capable of binding rubicon phosphorylated at threonine 166 but they were not specifically generated to bind phosphorylated threonine 166 of Rubicon. There is no prior art that teaches antibodies that specifically bind to Rubicon protein phosphorylated at threonine 166.
Any comments considered necessary by applicant must be submitted no later than the payment of the issue fee and, to avoid processing delays, should preferably accompany the issue fee.  Such submissions should be clearly labeled “Comments on Statement of Reasons for Allowance.”
Conclusion

CITED REFERENCE SUMMARIES: Ref WO2010030936A2: Claims:
1. An isolated polypeptide that has an amino acid sequence up to 99% identical to SEQ ID NO: 1, comprising at least one sequence selected from the group consisting of amino acids 75 to 95 of SEQ ID NO: 1 and amino acids 148 to 178 of SEQ ID NO: 1.
2. The isolated polypeptide of claim 1, comprising a sequence of amino acids 99 to 492 of SEQ ID NO: 1.
3. An isolated polypeptide that has an amino acid sequence up to 99% identical to SEQ ID NO: 2, comprising at least a sequence of amino acids 488 to 508 of SEQ ID NO: 2.
4. The isolated polypeptide of claim 3, comprising a sequence of amino acids 208 to 836 of SEQ ID NO: 2.
5. The isolated polypeptide of claim 3, comprising a sequence of amino acids 1 to 836 of SEQ ID NO: 2.
6. The isolated polypeptide of claim 3, comprising a sequence of amino acids 208 to 941 of SEQ ID NO: 2.
7. An isolated polypeptide that has an amino acid sequence up to 99% identical to SEQ ID NO: 3, comprising at least one sequence selected from the group consisting of amino acids 75 to 95 of SEQ ID NO: 3 and amino acids 148 to 178 of SEQ ID NO: 3.
8. An isolated polypeptide that has an amino acid sequence up to 99% identical to SEQ ID NO: 4, comprising at least a sequence of amino acids 518 to 538 of SEQ ID NO: 4.
9. A nucleic acid encoding the polypeptide of any one of claims 1 -8.
10. The nucleic acid of claim 9 which is comprised in an expression vector.
11. A pharmaceutical composition comprising a therapeutically effective amount of the polypeptide of any one of claims 1-8 in a pharmaceutically acceptable carrier.
12. A pharmaceutical composition comprising a therapeutically effective amount of the expression vector of claim 10, and a pharmaceutically acceptable carrier.
13. An isolated oligonucleotide less than 50 base pairs in length that hybridizes under physiological conditions to an ATGl 4L nucleic acid coding sequence as set forth in SEQ ID NO: 5 or a complementary sequence thereof.
14. An isolated oligonucleotide less than 50 base pairs in length that hybridizes under physiological conditions to an ATGl 4L nucleic acid coding sequence as set forth in SEQ ID NO: 6 or a complementary sequence thereof.
15. The isolated oligonucleotide of claim 13 or 14, which is an RNAi oligonucleotide.
16. The RNAi of claim 15, which has a nucleotide sequence as set forth in SEQ ID NO: 11.
17. The isolated oligonucleotide of claim 13 or 14, which is an antisense oligonucleotide.
18. An isolated oligonucleotide less than 50 base pairs in length that hybridizes under physiological conditions to a Rubicon nucleic acid coding sequence as set forth in SEQ ID NO: 7 or a complementary sequence thereof.
19. An isolated oligonucleotide less than 50 base pairs in length that hybridizes under physiological conditions to a Rubicon nucleic acid coding sequence as set forth in SEQ ID NO: 8 or a complementary sequence thereof.
20. The isolated oligonucleotide of claim 18 or 19, which is an RNAi oligonucleotide.
21. The RNAi of claim 20, which has a nucleotide sequence as set forth in SEQ ID NO: 12.
22. The isolated oligonucleotide of claim 18 or 19, which is an antisense oligonucleotide.
23. An isolated antibody, or antigen binding portion thereof, which binds to an ATG 14L protein having an amino acid sequence as set forth in SEQ ID NO: 1.
24. An isolated antibody, or antigen binding portion thereof, which binds to an ATG 14L protein having an amino acid sequence as set forth in SEQ ID NO: 3.
25. An isolated antibody, or antigen binding portion thereof, which binds to a Rubicon protein having an amino acid sequence as set forth in SEQ ID NO: 2.
26. An isolated antibody, or antigen binding portion thereof, which binds to a Rubicon protein having an amino acid sequence as set forth in SEQ ID NO: 4.
27. A method of increasing autophagic activity in a cell, which comprises administering to the cell an effective amount of an agent which increases or enhances the biological activity of ATGl 4L.
28. The method of claim 27, wherein the agent is selected from the group consisting of an ATG 14L, a functional agonistic fragment thereof, an ATG 14L polypeptide equivalent, an ATG 14L mimetic compound, a therapeutic vector comprising a nucleic acid molecule encoding ATG 14L protein, a binding enhancer which enhances or prolongs the binding between ATG 14L and a class III PI3K/Vρs34-Beclin-l autophagic complex, and a binding enhancer which enhances or prolongs the binding between ATG 14L and Beclin 1.
29. A method of increasing autophagic activity in a cell, which comprises administering to the cell an effective amount of an agent which decreases or inhibits the biological activity of Rubicon.
30. The method of claim 29, wherein the agent is selected from the group consisting of a functional antagonistic fragment of Rubicon, an anti-Rubicon antibody, an anti-Rubicon antibody fragment, an antisense nucleic acid, a ribozyme, and an RNAi.
31. A method of decreasing autophagic activity in a cell, which comprises administering to the cell an effective amount of an agent which increases or enhances the biological activity of Rubicon.
32. The method of claim 31 , wherein the agent is selected from the group consisting of a Rubicon, a functional agonistic fragment thereof, a Rubicon polypeptide equivalent, a Rubicon mimetic compound, a therapeutic vector comprising a nucleic acid molecule encoding Rubicon protein, and a binding enhancer which enhances or prolongs the binding between Rubicon and a class III PI3K/Vps34-Beclin-1 autophagic complex.
33. A method of decreasing autophagic activity in a cell, which comprises administering to the cell an effective amount of an agent which decreases or inhibits the biological activity of ATGl 4L.
34. The method of claim 33, wherein the agent is selected from the group consisting of a functional antagonistic fragment of ATGl 4L, an anti-ATG14L antibody, an anti-ATG14L antibody fragment, an antisense nucleic acid, a ribozyme, and an RNAi.
35. A method of increasing class III PI3K/Vps34 kinase activity in a cell, which comprises administering to the cell an effective amount of an agent which increases or enhances the biological activity of ATGl 4L.
36. The method of claim 35, wherein the agent is selected from the group consisting of an ATGl 4L, a functional agonistic fragment thereof, an ATG 14L polypeptide equivalent, an ATG 14L mimetic compound, a therapeutic vector comprising a nucleic acid molecule encoding ATG 14L protein, a binding enhancer which enhances or prolongs the binding between ATGl 4L and a class III PI3K/Vps34-Beclin-1 autophagic complex, and a binding enhancer which enhances or prolongs the binding between ATG 14L and Beclin 1.
37. A method of increasing class III PI3K/Vps34 kinase activity in a cell, which comprises administering to the cell an effective amount of an agent which decreases or inhibits the biological activity of Rubicon.
38. The method of claim 37, wherein the agent is selected from the group consisting of a functional antagonistic fragment of Rubicon, an anti-Rubicon antibody, an anti-Rubicon antibody fragment, an antisense nucleic acid, a ribozyme, and an RNAi.
39. A method of decreasing class III PI3K/Vps34 kinase activity in a cell, which comprises administering to the cell an effective amount of an agent which increases or enhances the biological activity of Rubicon.
40. The method of claim 39, wherein the agent is selected from the group consisting of a Rubicon, a functional agonistic fragment thereof, a Rubicon polypeptide equivalent, a Rubicon mimetic compound, a therapeutic vector comprising a nucleic acid molecule encoding Rubicon protein, and a binding enhancer which enhances or prolongs the binding between Rubicon and a class III PI3K/Vps34-Beclin-1 autophagic complex.
41. A method of decreasing class III PI3K/Vps34 kinase activity in a cell, which comprises administering to the cell an effective amount of an agent which decreases or inhibits the biological activity of ATGl 4L.
42. The method of claim 41, wherein the agent is selected from the group consisting of a functional antagonistic fragment of ATGl 4L, an anti-ATG14L antibody, an anti-ATG14L antibody fragment, an antisense nucleic acid, a ribozyme, and an RNAi.
43. A method of screening for a compound that binds to an ATGl 4L polypeptide, which comprises (a) providing the ATG 14L polypeptide; (b) contacting a candidate compound with ATG 14; and (c) determining whether the candidate compound has bound to the ATG 14L polypeptide.
44. A method of screening for a compound that binds to a Rubicon polypeptide, which comprises (a) providing an Rubicon polypeptide; (b) contacting a candidate compound with the Rubicon polypeptide; and (c) determining whether the candidate compound has bound to the Rubicon polypeptide.
45. The method of claim 43, wherein the ATG14L polypeptide is selected from the group consisting of murine ATG 14L protein having an amino acid sequence of SEQ ID NO: 1, a polypeptide having an amino acid sequence that has at least 95% identity with SEQ ID NO: 1, human ATGl 4L protein having an amino acid sequence of SEQ ID NO: 3, and a polypeptide having an amino acid sequence that has at least 95% identity with SEQ ID NO: 3.
46. The method of claim 44, wherein the Rubicon polypeptide is selected from the group consisting of murine Rubicon protein having an amino acid sequence of SEQ ID NO: 2, a polypeptide having an amino acid sequence that has at least 95% identity with SEQ ID NO: 2, human Rubicon protein having an amino acid sequence of SEQ ID NO: 4, and a polypeptide having an amino acid sequence that has at least 95% identity with SEQ ID NO: 4.
47. A transgenic knock-out mouse comprising a disruption in the endogenous ATG 14L gene, wherein disruption of the ATG 14L gene results in decreased expression of ATGl 4L protein.
48. A transgenic knock-out mouse comprising a disruption in the endogenous
Rubicon gene, wherein disruption of the Rubicon gene results in decreased expression of Rubicon protein.
49. A host cell comprising an expression vector coding for an ATG 14L protein or a functional fragment thereof, wherein the host cell expresses ATG 14L protein.
50. A host cell comprising an expression vector coding for a Rubicon protein or a functional fragment thereof, wherein the host cell expresses Rubicon protein.
51. A functional Beclin 1 fusion protein, comprising a tag for detecting the fusion protein, and a mature Beclin 1 having an amino acid sequence set forth in SEQ ID NO: 9 or SEQ ID NO: 10, or an amino acid sequence that has at least 95% sequence identify with SEQ ID NO: 9 or SEQ ID NO: 10, and which retains Beclin 1 biological activity.
52. The functional Beclin 1 fusion protein of claim 51 , wherein the biological activity of the Beclin 1 fusion protein is reduced by no more than 10% compared to the mature Beclin 1.
53. The fusion Beclin 1 fusion protein of claim 51, wherein the tag is green fluorescent protein (GFP).
54. An isolated nucleic acid molecule encoding the functional Beclin 1 fusion protein of claim 51.
55. An expression vector comprising the nucleic acid molecule of claim 54.
56. A transgenic non-human animal comprising the vector of claim 55.
57. A host cell comprising the vector of claim 55.
58. A method of screening for a compound that modulates biological activity of ATG 14L, which comprises (a) contacting ATG 14L with a candidate compound in a manner wherein the candidate compound interacts with ATG 14L; (b) evaluating the biological activity of ATGl 4L; and (c) identifying a candidate compound as a modulator of biological activity of ATGl 4L based upon observing increased or decreased biological activity of ATGl 4L in the presence of the candidate compound compared to a control sample.
59. A method of screening for a compound that modulates biological activity of Rubicon, which comprises (a) contacting Rubicon with a candidate compound in a manner wherein the candidate compound interacts with Rubicon; (b) evaluating the biological activity of Rubicon; and (c) identifying a candidate compound as a modulator of biological activity of Rubicon based upon observing increased or decreased biological activity of Rubicon in the presence of the candidate compound compared to a control sample.
60. A method of treating cancer in a subject, the method comprising administering to said subject a therapeutically effective amount of an agent which increases or enhances the biological activity of ATGl 4L.
61. The method of claim 60, wherein the agent is selected from the group consisting of an ATGl 4L, a functional agonistic fragment thereof, an ATG 14L polypeptide equivalent, an ATG 14L mimetic compound, a therapeutic vector comprising a nucleic acid molecule encoding ATG 14L protein, a binding enhancer which enhances or prolongs the binding between ATG 14L and a class III
PI3K/Vps34-Beclin-1 autophagic complex, and a binding enhancer which enhances or prolongs the binding between ATG 14L and Beclin 1.
62. A method of treating cancer in a subject, the method comprising administering to the subject a therapeutically effective amount of an agent which decreases or inhibits the biological activity of Rubicon.
63. The method of claim 62, wherein the agent is selected from the group consisting of a functional antagonistic fragment of Rubicon, an anti-Rubicon antibody, an anti-Rubicon antibody fragment, an antisense nucleic acid, a ribozyme, and an RNAi.
64. A method of treating neurodegenerative disease in a subject, the method comprising: administering to the subject a therapeutically effective amount of an agent which increases or enhances the biological activity of ATGl 4L.
65. The method of claim 64, wherein the agent is selected from the group consisting of an ATGl 4L, a functional agonistic fragment thereof, an ATG 14L polypeptide equivalent, an ATG 14L mimetic compound, a therapeutic vector comprising a nucleic acid molecule encoding ATG 14L protein, a binding enhancer which enhances or prolongs the binding between ATGl 4L and a class III
PI3K/Vps34-Beclin-1 autophagic complex, and a binding enhancer which enhances or prolongs the binding between ATG 14L and Beclin 1.
66. A method of treating neurodegenerative disease in a subject, the method comprising: administering to the subject a therapeutically effective amount of an agent which decreases or inhibits the biological activity of Rubicon.
67. The method of claim 66, wherein the agent is selected from the group consisting of a functional antagonistic fragment of Rubicon, an anti-Rubicon antibody, an anti-Rubicon antibody fragment, an antisense nucleic acid, a ribozyme, and an RNAi.
68. A method of treating inflammatory diseases in a subject, the method comprising: administering to the subject a therapeutically effective amount of an agent which increases the biological activity of ATGl 4L.
69. The method of claim 68, wherein the agent is selected from the group consisting of an ATG 14L, a functional agonistic fragment thereof, an ATG 14L  polypeptide equivalent, an ATG 14L mimetic compound, a therapeutic vector comprising a nucleic acid molecule encoding ATG 14L protein, a binding enhancer which enhances or prolongs the binding between ATG 14L and a class III PI3K/Vps34-Beclin-1 autophagic complex, and a binding enhancer which enhances or prolongs the binding between ATG 14L and Beclin 1.
70. A method of treating inflammatory diseases in a subject, the method comprising: administering to the subject a therapeutically effective amount of an agent which decreases the biological activity of Rubicon.
71. The method of claim 70, wherein the agent is selected from the group consisting of a functional antagonistic fragment of Rubicon, an anti-Rubicon antibody, an anti-Rubicon antibody fragment, an antisense nucleic acid, a ribozyme, and an RNAi.
72. A method of treating age-related diseases in a subject, the method comprising: administering to the subject a therapeutically effective amount of an agent which increases the biological activity of ATG 14L .
73. The method of claim 72, wherein the agent is selected from the group consisting of an ATGl 4L, a functional agonistic fragment thereof, an ATG 14L polypeptide equivalent, an ATG 14L mimetic compound, a therapeutic vector comprising a nucleic acid molecule encoding ATG 14L protein, a binding enhancer which enhances or prolongs the binding between ATG 14L and a class III
PI3K/Vps34— Beclin- 1 autophagic complex, and a binding enhancer which enhances or prolongs the binding between ATG 14L and Beclin 1.
74. A method of treating age-related diseases in a subject, the method comprising: administering to the subject a therapeutically effective amount of an agent which decreases the biological activity of Rubicon.
75. The method of claim 74, wherein the agent is selected from the group consisting of a functional antagonistic fragment of Rubicon, an anti-Rubicon antibody, an anti-Rubicon antibody fragment, an antisense nucleic acid, a ribozyme, and an RNAi.
76. A method of treating heart diseases in a subject, the method comprising: administering to the subject a therapeutically effective amount of an agent which modulates the biological activity of ATGl 4L.
77. The method of claim 76, wherein the agent increases the biological activity of ATG 14L during ischemia.
78. The method of claim 76, wherein the agent decreases the biological activity of ATG 14L during reperfusion.
79. A method of treating heart diseases in a subject, the method comprising: administering to the subject a therapeutically effective amount of an agent which modulates the biological activity of Rubicon.
80. The method of claim 79, wherein the agent decreases the biological activity of Rubicon during ischemia.
81. The method of claim 79 wherein the agent increases the biological activity of Rubicon during reperfusion.
82. The method of claim 77, wherein the agent is selected from the group consisting of an ATG 14L, a functional agonistic fragment thereof, an ATG 14L polypeptide equivalent, an ATG 14L mimetic compound, a therapeutic vector comprising a nucleic acid molecule encoding ATG 14L protein, a binding enhancer which enhances or prolongs the binding between ATG 14L and a class III PI3K/Vps34-Beclin-1 autophagic complex, and a binding enhancer which enhances or prolongs the binding between ATG 14L and Beclin 1.
83. The method of claim 78, wherein the agent is selected from the group consisting of a functional antagonistic fragment of ATGl 4L, an anti-ATG14L antibody, an anti-ATG14L antibody fragment, an antisense nucleic acid, a ribozyme, and an RNAi.
84. The method of claim 80, wherein the agent is selected from the group consisting of a functional antagonistic fragment of Rubicon, an anti-Rubicon antibody, an anti-Rubicon antibody fragment, an antisense nucleic acid, a ribozyme, and an RNAi.
85. The method of claim 81 , wherein the agent is selected from the group consisting of an Rubicon, a functional agonistic fragment thereof, a Rubicon polypeptide equivalent, a Rubicon mimetic compound, a therapeutic vector comprising a nucleic acid molecule encoding Rubicon protein, and a binding enhancer which enhances or prolongs the binding between Rubicon and a class III PI3K/Vps34- Beclin 1 autophagic complex.
86. A method for evaluating expression of ATG 14L in a cell in a biological sample, which comprises detecting an ATG14L polypeptide in the biological sample.
87. A method for evaluating expression of ATG14L in cells in a biological sample which comprises detecting ATG 14L mRNA in the biological sample.
88. The method of claim 86 or 87, wherein the expression of ATGl 4L correlates to autophagic activity in a manner that increased expression of ATGl 4L indicates increased autophagic activity, and decreased expression of ATGl 4L indicates decreased autophagic activity.
89. The method of claim 86 or 87, wherein the expression of ATGl 4L correlates to class III PI3K/Vps34 kinase acti
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