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 I in the reply filed on May 7th, 2026 is acknowledged.
Applicant’s election without traverse of RumTrunkD9NTag, SEQ ID NO:47, and its encoding nucleotide SEQ ID NO:48 in the reply filed on May 7th, 2026 is acknowledged.
The elected species, SEQ ID NO: 47, was not found in the art, therefore the examination and search were extended to the non-elected species.
Claims 7-9 and 37-39 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on May 7th, 2026.
Priority
The instant application claims priority to 371 National Stage Application PCT/EP2021/062113, filed May 7th, 2021, and foreign application EP20173377.1 , filed May 7th, 2020 under 35 U.S.C. 119(a)-(d) and (f). The priority date of May 7th, 2020 is acknowledged.
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on July 15th, 2024, December 19th, 2023, and December 28th, 2022 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is considered by the examiner.
The second information disclosure statement (IDS) submitted on December 28th, 2022 is missing the attachments of three cited non-patent literature references. Accordingly, the three references are striked out and not considered by the examiner.
Claims Status
The claims listing filed on May 7th, 2026 is pending. Claims 13-33 are canceled. Claims 7-9 and 37-39 are withdrawn from further consideration for the reasons set forth in the restriction requirement, 37 CFR 1.142(b). Claims 1-6, 10-12, 34-36, and 40-41 are being examined on the merits in this office action.
Claim Rejections - 35 USC § 112
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.
Claims 1-2, 4-6, and 40-41 are 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.
In accordance with 35 U.S.C. 112(d), or pre-AIA 35 U.S.C. 112, fourth paragraph, a claim in dependent form shall contain:
(i) a reference to a claim previously set forth, and
(ii) 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.
Following the statute, the test as to whether a claim is a proper dependent claim is that it shall include every limitation of the claim from which it depends and specify a further limitation of the subject matter claimed. For example, if claim 1 recites the combination of elements A, B, C, and D, a claim reciting the structure of claim 1 in which D was omitted or replaced by E would not be a proper dependent claim, even though it placed further limitations on the remaining elements or added still other elements. A dependent claim does not lack compliance with 35 U.S.C. 112(d) simply because there is a question as to the significance of the further limitation added by the dependent claim [MPEP 608.01 (n)].
In the instant case, claim 1 fails to reference a claim previously set forth, as it is dependent on claim 3. Claims 2, 4-6, and 40-41 depend on claim 1. Therefore, claims 1-2, 4-6, and 40-41 are in improper dependent form.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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 1-6, 10-12, 34-36, and 40-41 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 3 recites “with the proviso that said fragments or homologues comprise the reactive residue involved in the formation of the isopeptide bond.” This limitation is indefinite because it is unclear which residues are necessary within the fragment to form the isopeptide bond and are therefore considered “reactive.” Thus, the claim limitation is indefinite because it is unclear which fragment or homologue the claim language embodies.
Claims 1-2, 4-6, 10-12, 34-36, and 40-41 are rejected under 35 U.S.C. 112(b) as they do not define what the reactive residue is and thus, do not overcome the indefiniteness of base claim 3
Where applicant acts as his or her own lexicographer to specifically define a term of a claim contrary to its ordinary meaning, the written description must clearly redefine the claim term and set forth the uncommon definition so as to put one reasonably skilled in the art on notice that the applicant intended to so redefine that claim term. Process Control Corp. v. HydReclaim Corp., 190 F.3d 1350, 1357, 52 USPQ2d 1029, 1033 (Fed. Cir. 1999). The term “homology” in claim 3 is used by the claim to mean “similarity or identity,” while the accepted meaning is “biological features including genes and their products that are descended from a feature present in a common ancestor.” [line 1] (National Library of Medicine. “Homology: Orthologs and Paralogs.” Www.nlm.nih.gov, www.nlm.nih.gov/ncbi/workshops/2023-08_BLAST_evol/ortho_para.html.)
The term is indefinite because the specification does not clearly redefine the term:
“Designing the modified binding partner, wherein the modified binding partner comprises or consists of i) the first reactive fragment, or a homologue thereof having at least 70% homology thereto, and the second residual fragment, or a homologue thereof having at least 70% homology thereto, wherein the first reactive fragment preferably is upstream of the second residual fragment, wherein the modified binding partner does not comprise both reactive residues involved in the formation of the isopeptide bond;” [0014].
If the applicant is using it to mean “identity” than the term is indefinite as it does not present any further limitations. If the applicant is using it in its accepted meaning, then the use of the term is not enabled as a homologous peptide has to a natural product and the claimed binding partners are not found in nature, and lacks written description support as the applicant does not show possession of homologous variants of the claimed binding partners and peptide tags that can form an isopeptide bond.
Claims 1-2, 4-6, 10-12, 34-36, and 40-41 are rejected under 35 U.S.C. 112(b) as they do not overcome the indefiniteness of base claim 3 because they do not use “homology” in its ordinary meaning.
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.
Claims 1-6, 10-12, 34-36, and 40-41 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. Claim 3 recites “or fragments or homologues thereof having at least 90% homology or identity thereto.” However, the specification does not support that all fragments or homologues with 90% identity or homology of the claimed binding partners comprising the reactive residue involved in the formation of the isopeptide bond, are still capable of binding to a peptide tag.
The inventors provide direction by determining the kinetics and maximal binding of catcher and VLP-tag coupling, catcher and tag coupling, and catcher-VLP and tag coupling [instant pgs 83-86 Examples 2-4]. The results show the kinetics of the catchers: SdyCatcher, Mooncake, KATI, and SpyCatcher. While the catchers tested have at least 90% homology or identity with each other, the species are not representative of the entire genus of binding partners with 90% identity or homology with MoonCake, KatI, and QueenCatcher, especially since the binding partners are 113 residues long, embodying a large genus.
Satisfactory disclosure of a "representative number" depends on whether one of skill in the art would recognize that the inventor was in possession of the necessary common attributes or features possessed by the members of the genus in view of the species disclosed. For inventions in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus. See, e.g., Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406. Instead, the disclosure must adequately reflect the structural diversity of the claimed genus, either through the disclosure of sufficient species that are "representative of the full variety or scope of the genus," or by the establishment of "a reasonable structure-function correlation." Such correlations may be established "by the inventor as described in the specification," or they may be "known in the art at the time of the filing date." See AbbVie, 759 F.3d at 1300-01, 111 USPQ2d 1780, 1790-91 (Fed. Cir. 2014). [MPEP 2163]
The four species tested by the applicant are not representative of the entire genus of binding partners because the catchers are of an unpredictable art, with no state of the prior art to rely on for an understanding a skilled artisan could develop about the genus’s capability of binding to peptide tags. A peptide with 90% identity to SEQ ID NO: 39, 41, or 37 may possess residues or motifs that negatively impact the binding to the peptide tag. Thus, while there is support in the specification about SEQ ID NO:39 (MoonCake) and SEQ ID NO:41’s (KatI) ability to bind to peptide tags, there is not enough support for the complete genus fragments or homologues having at least 90% homology or identity, nor would one of ordinary skill in the art be able to attest to the complete genus’s ability to act as a binding partner.
The kinetics and binding of the RunTrunkD9NTag, SdyTag, and SpyTag were tested by the inventors [pg 83-85 Examples 2-4]. The peptide tags reduced to practice do not represent the entire genus of peptide tag “variants having at least 90% homology or identity thereto.” A sequence with 90% identity or homology to the listed peptide tags of claim 1 may not naturally form an intramolecular isopeptide bond, and thereby function as a peptide tag. Therefore, peptide tag variants with at least 90% homology or identity are not supported by the specifications nor by what one of ordinary skill in the art can deduce, to act as peptide tag.
Claims 1-2, 4-6, 10-12, 34-36, and 40-41 are also rejected under 35 U.S.C. 112(a) as failing to comply with the written description requirement because of their dependency to base claim 3 and recitation of “90% homology or identity,” referring to a binding partner or peptide tag.
Allowable Subject Matter
The following is a statement of reasons for the indication of allowable subject matter: The binding partners SEQ ID NO: 39 (MoonCake) and SEQ ID NO: 41 (KatI) are free of prior art and supported by the specifications.
The closest prior art is Tan et al. (Tan, L. L., Hoon, S. S., & Wong, F. T. (2016). Kinetic Controlled Tag-Catcher Interactions for Directed Covalent Protein Assembly. PloS one, 11(10), e0165074.)
Tan et al. engineered and characterized a new Tag-Catcher pair from a FbaB related fibronectin-binding protein in Streptococcus dysgalactiae [Abstract line 4]. The known SpyCatcher, derived from Streptococcus pyogenes fibronectin-binding protein, FbaB, was used by Tan et al. to arrive at the novel tag-catcher pair, SdyTag-Catcher. The S. pyogenes CnaB2 domain was used as a query to identify a homologous CnaB protein domain from S. dysgalactiae with 63% percent sequence identity [pg 4 pgh 2]. The comparison between the two sequences revealed sequence conservation restricted to the C-terminal region containing collagen binding protein domain B, CnaB, fibronectin binding repeats and anchor domains. Thus, this information and previous structure function studies were used to construct the SdyCatcher [pg 5 pgh 2 line 1].
The structural motifs taught by Tan et al would not be enough for one of ordinary skill in the art to reasonably arrive at the claimed sequences. Furthermore, the SdyCatcher and SpyCatcher sequences are less than 90% homologous or identical to instant SEQ ID NO: 37, 39 , and 41 and Tan et al. does not teach any modifications that would motivate one of ordinary skill to arrive at the instant sequences. Therefore, the binding partners SEQ ID NO: 39 and 41 are presently allowable subject matter over the prior art.
Summary
Claims 1-2, 4-6, and 40-41 are rejected under 35 U.S.C. 112(d). Claims 1-6, 10-12, 34-36, and 40-41 are rejected under 35 U.S.C. 112(a). Claims 1-6, 10-12, 34-36, and 40-41 are rejected under 35 U.S.C. 112(b).
Correspondence
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SACHI JAUHARI whose telephone number is (571)272-3769. The examiner can normally be reached Mon-Fri 9-4.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Lianko Garyu can be reached at (571) 270-7367. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/SACHI JAUHARI/Examiner, Art Unit 1654
/LIANKO G GARYU/Supervisory Patent Examiner, Art Unit 1654
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