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, claims 1-4, 10, 13, and 19 in the reply filed on 02/23/2026 is acknowledged.
Status of Claims
The amendment filed on 02/23/2026 cancelled claims 27, 44, 50, 65, 79, 84, 91, 93, 95, 110 and added new claims 119-127. Claims 5-9, 11-12, 14-18, 20-26, 28-43, 45-49, 51-64, 66-78, 80-83, 85-90, 92, 94, 96-109, 111-118 were previously cancelled and claims 3-4, 10, 13, 19 were previously amended in the preliminary amendment filed on 02/09/2024. Claims 1-4, 10, 13, 19, 119-127 are pending and will be examined on the merits.
Priority
Provisional application 63/181,118 is acknowledged as disclosing the claimed invention and the effective filing date is 04/28/2021.
Information Disclosure Statement
The Information Disclosure Statements filed on 10/25/2023 and 12/31/2024 have been considered. Signed copies are enclosed.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claim Interpretation
The terms “periplasmic”, “extracellular”, and “luminal”, recited in claims 1, 2, and 13, are being interpreted as synonymous with each other depending on the specific type of cell expressing the ABC transporter. If this is incorrect, appropriate clarification is required.
Claim Rejections - 35 USC § 112
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 1-4, 10, 13, 19, and 119-127 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.
The term “equivalent region” in claims 1, 13, and 19 is a relative term which renders the claim indefinite. The term “equivalent region” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. The specification provides, in paragraph [0041], "[a]s used herein, the "equivalent regions" being inserted from the different ABC transporter are those that in the same location within the protein when folded as the residues being removed from the parental ABC transporter. In some cases, the regions in the ABC transporter to remove and replace with regions from the chimeric ABC transporter may be determined using sequence alignments and structural information for the two proteins.” This is not a proper definition for the term, and does not provide sufficient information regarding the “equivalent regions”. The phrase ‘determined using sequence alignments and structural information’ does not provide sufficient guidance on determining what is an equivalent region or not. For example, do the regions need to be the same number of amino acids? Do they need to be located a certain number of positions away from each other? What if a protein does not have any structural information to use to make this determination? Do the genes need to be homologous, or are any regions on any ABC transporter potentially ‘equivalent’? Given these questions, one of ordinary skill in the art would not be able to determine the metes and bounds of the instant claim. Claims 3, 4, 10, and 119-127 inherit this rejection, as they do not provide further clarification on what is considered an ‘equivalent region’. Examiner notes that claim 19 recites the regions of interest, but does not inform one on how to determine what, exactly, the equivalent region is in the other species.
The term “corresponding region” in claim 2 is a relative term which renders the claim indefinite. The term “corresponding” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Paragraph [0041] of the instant specification recites that "corresponding region" is synonymous with "equivalent region". Therefore, the same questions mentioned above apply to this term as well, and one of ordinary skill in the art would not understand the metes and bounds of the claim.
The term “periplasmic, extracellular, or luminal facing loop(s)” in claim 13 is a relative term which renders the claim indefinite. The term “periplasmic, extracellular, or luminal facing loop(s)” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. It is unclear what amino acids are meant to be included in the periplasmic, extracellular, or luminal facing loops of the ABC transporter of interest. For example, in Figure 1A, is loop 1 meant to incorporate the region from P-L or from L-V? Is loop 2 meant to incorporate the region from E-L or Y-S? Similarly, in figure 1B, is loop 2 meant to only comprise the “T” amino acid, or is it meant to include more? Can a single amino acid be termed a “loop”? These questions mean that one of ordinary skill in the art cannot determine the metes and bounds of the instant claim, and the claim is therefore indefinite.
Examiner notes that claim 19 does rectify the indefiniteness of claim 13 for the protein EcMsbA, in that it specifically states which amino acids are included in each loop.
Claim 19 is indefinite due to the recitation of position identifiers in a sequence without identification of the corresponding SEQ ID NO.
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 1-4, 10, 13, 19, and 119-127 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 instant claims are drawn to methods of determining whether a test molecule binds to the periplasmic, extracellular, and/or luminal face of a parental ABC transporter comprising providing a chimeric ABC transporter in which one or more regions of the periplasmic, extracellular, and/or luminal face of the parental ABC transporter are substituted with one or more equivalent regions of the periplasmic, extracellular, and/or luminal face of a different ABC transporter, and contacting the chimeric ABC transporter with a molecule that binds to the parental ABC transporter wherein the test molecule is determined to bind to the periplasmic, extracellular, and/or luminal face of the parental ABC transporter if the test molecule does not bind to the chimeric ABC transporter.
The specification teaches, in the Examples, chimeric MsbA transporter proteins, designed from E. coli MsbA (EcMsbA), wherein the three loop regions recited in claim 19 are replaced with regions from Pseudomonas psychrotolerans (PpMsbA), Candidatus Accumulibacter (CaMsbA), Janthinobacterium agaricidamnosum (JaMsbA), Thiomicrospira cyclica (TcMsbA), and Magnetospira strain-QH-2 (MqMsbA). The sequences of the 5 constructs themselves are shown in figure 10A.
The specification also defines type IV and type V ABC transporters, recited in claim 119, in paragraph [0038], and provides the reference Thomas et al. (594 FEBS Letters 3767-3775 (2020)) as a resource for identifying type IV and type V ABC transporters, and identifies MsbA as a type IV ABC transporter. Type V ABC transporters appear to have a substantially different structure than Type IV transporters. The diversity of ABC transporters reviewed in Thomas et al. indicates that not all ABC transporters will have the same mechanism of action, the same exposed regions on the periplasmic/extracellular/luminal face, or the same affinity for their substrates.
Finally, the specification demonstrates the method of using the EcMsbAChim5 chimeric ABC transporters identified above in the method of claims 1 and 2 in paragraph [00162], and also identifies molecules with inhibitory activity against EcMsbA, with similar levels of activity against Enterobacter cloacae and Klebsiella pneumoniae MsbA transporters and only modest activity on the Pseudomonas aeruginosa MsbA (see paragraph [00166]).
As the specification provides strong support for the claimed method executed with EcMsbAChim5, the method of claims 1 and 2 using this chimeric protein has written description support. However, the claims are drawn much more broadly than just this chimera, as they recite the method with any ABC transporter.
The specification only provides written description support for one ABC transporter – MsbA. EcMsbA was the first structure of an ABC transporter protein that was determined, and has been extensively studied (see Ford et al., Biochemical Society Transactions (2019) 47 23–36, page 24). However, many more ABC transporters have since been characterized, and Ford et al. clearly show that there are differences in the transport mechanisms between different ABC transporters. Moreover, Thomas et al. show that there are major structural differences between ABC transporters, even broadly categorizing them as seven different categories. Ford et al. disclose that ABC transporters stands for ATP-binding cassette (ABC) transporters (page 23), indicating that the most common features of these transporters is not the transmembrane or the extracellular/periplasmic/luminal face, but the ATP-binding cassette located on the cytoplasmic face. Ford et al. discuss that other bacterial ABC transporters include those incorporated into Type-1 Secretion Systems (T1SS) (see pages 26-27). This can include the MacB ABC transporter, which is shown in Figure 2(d) of Ford et al. to be connected on the periplasmic face to the MacA and TolC proteins, indicating that the periplasmic face of this particular ABC transporter would not be exposed to the periplasm in the same way as that of MsbA. Eukaryotic ABC transporters, reviewed by Ford et al. on pages 30-33, are also incredibly diverse in their function, structure, and affinity for their substrate. Therefore, one skilled in the art of ABC transporter proteins would know that these are diverse proteins that do not all function the same way or necessarily have the same structure. Therefore, there is no reasonable expectation that replacing the periplasmic/extracellular/luminal face of any ABC transporter would allow it to be successfully used in the claimed methods.
Moreover, the instant specification shows that the E. cloacae and K. pneumoniae MsbA transporters respond to the compound G1365, determined in the specification to bind to the periplasmic face of MsbA, similarly to the EcMsbA. This indicates that, were the inventors to create a chimera comprising the ‘equivalent regions’ of the periplasmic face of either the E. cloacae or K. pneumoniae replacing those regions on EcMsbA, as recited in claims 120-124, the test molecule G1365 would still bind to the chimeric protein, which would, as per the ‘wherein’ clause of claim 1 located in lines 8-10, result in a determination that the test molecule does NOT bind to the periplasmic face of EcMsbA, which is incorrect, as shown in the instant specification. Therefore, substitution of the ’equivalent regions’ from any homologous protein from a different species to the ABC transporter of interest (as recited in claim 124) will not necessarily provide correct results.
Additionally, the inventors propose in the instant specification five chimeric proteins, using the ‘equivalent regions’ from PpMsbA, CaMsbA, JaMsbA, TcMsbA, and MqMsbA. Paragraph [00163] discloses that “Of the five chimeras constructed, chimera 2, chimera 4 and chimera 5 (MsbA-chim5) was stably expressed and purified from E. coli (Figures l lA-B)”. With no other mention of chimeras 1 and 3 elsewhere in the specification, one would be led to believe that these other two chimeras were not stably expressed or purified from E. coli, indicating that the chimeric protein was not necessarily viable. Therefore, the instant specification does not provide sufficient written description support for chimeras 1 and 3. Moreover, the fact that only three of the five proposed chimeras were viable for the most commonly studied ABC transporter indicates that Applicant has not clearly identified the critical structure needed to maintain the desired function of the chimeric proteins. Moreover, only chimera 5 was used in the experiments presented in the instant specification as it particularly retained comparable ATPase activity and displayed sensitivity to other inhibitors of EcMsbA. Therefore, only chimera 5 has written description support for use in the claimed method, as this disclosure indicates that chimeras 2 and 4 may not have had the same activity as EcMsbA and would not prove useful in these experiments.
Taken together, one can understand, from the instant specification, that the chimeric protein used in the method of claims 1 and 2 plays a significant role in whether it can be ‘determined’ if a test molecule binds to the extracellular/periplasmic/luminal face of an ABC transporter. There is not sufficient written description support in the specification for the method using any ABC transporter, nor even the narrowed claims of instant claim 19 or 119-124.
Therefore, instant claims 1-4, 10, 13, 19, and 119-127 are rejected under 35 USC 112(a).
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 1-4, 10, 13, 19, and 119-127 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claim(s) recite(s) a method of determining. This judicial exception is not integrated into a practical application because the claims are merely drawn to a yes/no determination. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the steps recited by the claims are routine in the art. The following analysis is laid out in accordance with MPEP §2106:
Applicant’s claims 1 and 2 recite methods of determining whether a test molecule binds to the periplasmic, extracellular, and/or luminal face of a parental ABC transporter. The claim recites a series of steps or acts. Thus the claim is directed to a process, which is one of the statutory categories of invention. (Step 1: Yes).
The claim is then analyzed to determine whether it is directed to any judicial exception. The claims are drawn to a method of determining the answer to a yes or no question, which is an abstract idea that can be performed by a human using mental steps or basic critical thinking. Thus, the claims are directed to the judicial exception of an abstract idea.
Next, the claim as a whole is analyzed to determine whether any element, or combination of elements, is sufficient to ensure that the claim amounts to significantly more than the exception.
Claim 1 recites the additional elements or steps of providing a chimeric ABC transporter in which one or more regions is substituted with an analogous region, and contacting said chimeric protein with a molecule known to bind to the parental transporter and determining that the test molecule binds to a specific region if the test molecule does not bind to the chimeric protein. This general methodology of screening for where a protein is bound by something is understood in the art (see Schumacher et al., 1993, where chimeric insulin receptors were generated to determine if IGF-R1 binds, or Lee et al., 1999, where a library of chimeric CCR5/CCR2 receptors were expressed in a cell in order to determine where antibodies to CCR5 bind). Similar methods are also very common in the art. For example, directed mutational analysis randomly mutates a protein’s predicted binding site and determines if the compound binds (See Mitamura et al., 1997, which used directed mutagenesis to determine diphtheria toxin binding). Another common method is forced resistance, or growing an organism in the presence of the inhibitor and sequencing resistant mutants to see where mutations have occurred to impart resistance (see, for example, Alexander et al., 2018 (Antimicrob Agents Chemother 62:e01142-18), page 13, “Frequency of resistance and sequencing of resistant mutants”).
Claim 2 recites similar steps to claim 1, but adds the initial step of trapping the parental ABC transporter in an outward-facing conformation and selecting a test molecule that binds to the parental ABC transporter while it is in the outward facing conformation. Again, the step of trapping the ABC transporter in an outward facing conformation is well-understood, routine, and conventional in the art, as seen in Ward et al. (2007) and as stated in Alexander et al. (see page 10, lines 54-46). Moreover, selecting a test molecule based on if it binds to the protein while in that particular state is, again, an abstract idea, as it is a yes or no question determined through methods routine in the art, as explained above.
Therefore, claims 1 and 2 are directed to answering a yes or no question, an abstract idea performed with basic mental steps, without significantly more, as they use techniques that are well understood, routine, and conventional in the art. Thus, claims 1 and 2 are not patent eligible.
Dependent claims 3-4, 10, 13, 19, and 119-127 do not add any meaningful limitations that would overcome this rejection, and therefore inherit it. In other words, the dependent claims do not provide limitations that amount to significantly more than instant claims 1 and 2. Claims 3 and 4 recite trapping the chimeric transporter in an outward facing conformation, again, a concept routine in the art as seen in Ward et al. and Alexander et al. Claims 10, 13, 19, and 119-124 define the ABC transporter more specifically, claim 125 recites where the target molecule binds more specifically, and claims 126 and 127 recite assays used in additional steps of the method of claim 1, which are also well understood, routine, and conventional assays (see, for example, Alexander et al., which uses growth assays with homologous proteins and MsbA inhibitors (pages 2-6 and 12), and Glavinas et al., which discloses use of ATPase assays detect the interaction of compounds with different ATP-binding cassette transporters (abstract)). None of these limitations add significantly more to the judicial exception, and thus they are included in the rejection under 35 USC 101.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 1-4, 10, 13, 119-122, 124-125, and 127 is/are rejected under 35 U.S.C. 103 as being unpatentable over Alexander et al., Antimicrob Agents Chemother 62:e01142-18 (2018), in view of Sachs et al., J Membrane Biol 212, 71–82 (2006).
The instant claims are drawn to a method of determining if a test molecule binds to the periplasmic/extracellular/luminal face of an ABC transporter (hereinafter referred to as the periplasmic face) by providing a chimeric ABC transporter, which has the periplasmic regions of the transporter swapped for homologous regions from another ABC transporter, and contacting it with a test molecule.
Alexander et al. teach a method of determining if a test molecule binds to an ABC transporter by using protein modeling, variation in protein levels, and microscopy. Additionally, Alexander et al. use a homolog of E. coli MsbA, from the species Acinetobacter baumannii, known to be significantly different from E. coli MsbA due to protein structural studies, to confirm the test molecule specifically targets E. coli MsbA. Importantly, the structural studies of E. coli and A. baumannii were able to implicate the periplasmic face of the protein as the target of the test molecule. The A. baumannii MsbA was selected as a replacement due to steric clash at the test molecule’s binding site observed in the structural modeling (see page 5-6). Alexander et al. does not replace only the periplasmic face of the E. coli MsbA transporter with only the periplasmic face of the A. baumannii MsbA transporter.
Sachs et al. disclose a method of determining if the periplasmic domains are important for pH gating urea transport by exchanging the periplasmic region of the ABC transporter UreI from Helicobacter pylori with the periplasmic domain of the UreI homologue found in Streptococcus salivarius, known to allow non-pH dependent urea transport (see page 78, right column). Sachs et al. do not disclose testing if an inhibitor binds to this periplasmic region specifically.
One of ordinary skill in the art of bacterial ABC transporters would reasonably be appraised of both Alexander et al. and Sachs et al., as they both investigate ABC transporter function in Gram-negative bacteria through mechanisms of genetic manipulation. Before the effective filing date of the claimed invention, one of ordinary skill in the art would be motivated to modify the methods of Alexander et al. with the methods of Sachs et al. in order to demonstrate that the periplasmic face of MsbA is specifically targeted by G592. Alexander et al. use the substitution of the entire MsbA protein from A. baumanii (hereinafter AbMsbA) for the MsbA protein of E. coli (hereinafter EcMsbA) (see Alexander et al., pages 5-6). Alexander et al. performed this substitution because protein structural models indicated that 1) G592 likely bound to the periplasmic face of EcMsbA trapped in an outward facing configuration by vanadate, 2) AbMsbA would not allow for binding in the same location due to steric clash between the protein and the test molecule at the binding site, and 3) both EcMsbA and AbMsbA can perform the functional duties of the MsbA transporter in vivo, allowing for testing of the compound on live bacteria cells. Sachs et al. teach that interchanging of the periplasmic regions of two homologous ABC transporters can allow for elucidation of the role of said periplasmic region in protein biology. Sachs et al. also teach that chimeric proteins containing an alternate periplasmic region can be successfully expressed in a host strain and allow for elucidation of periplasmic region-dependent characteristics (see page 78, right column). As Alexander et al. implicate the periplasmic face as the target of the test molecule, and show that AbMsbA does not bind the inhibitor, it would be obvious to one of ordinary skill in the art to substitute the periplasmic face of AbMsbA for that of EcMsbA in order to test the hypothesis that the test molecule binds the periplasmic face of EcMsbA. One would be motivated to do so in order to confirm that the test molecule binds to the periplasmic face of Enterobacteriaceae MsbA specifically. One would have a reasonable expectation of success as Sachs et al. demonstrate that these chimeric proteins can be functional in a live cell and can be used to measure protein function. Therefore, the method of claim 1 is obvious over Alexander et al. in view of Sachs et al.
Moreover, Alexander et al. teach that it is known in the art to use vanadate to trap the protein in an outward facing configuration, exposing the periplasmic cleft, and Alexander et al. further teach that a test molecule that binds to the periplasmic cleft would allow for more optimal use as an antibiotic (see page 10), it would be obvious to add vanadate to the method of Alexander et al. and Sachs et al. in order to determine targets that bind the periplasmic cleft on the periplasmic face of the chimeric transporter, rendering claims 2-4 and 125 obvious. Alexander et al. teach MsbA, a Type IV transporter, wherein the parental and the different ABC transporters are from two different species of Gram-negative bacteria, teaching instant claims 10, 119-122, and 124. Sachs et al. teach ABC transporter functional assays on page 78, right column, in that they test for the ABC transporter function of urea transport. Therefore, it would be obvious to use a similar functional assay to test chimeric MsbA function, rendering claim 127 obvious.
Claim(s) 1-4, 10, 13, 119-122, and 124-127 is/are rejected under 35 U.S.C. 103 as being unpatentable over Alexander et al. in view of Sachs et al. as applied to claims 1-4, 10, 13, 119-122, 124-125, and 127 above, and further in view of Glavinas et al., Drug Metabolism and Disposition, 35(9), 1533-1542 (2007).
The teachings of Alexander et al. and Sachs et al. regarding claims 1-4, 10, 119-122, 124-125, and 127 are recited above. Alexander et al. and Sachs et al. do not teach conducting an ATPase assay on the parental ABC transporter in the presence of the molecule. However, Glavinas et al. disclose that ATPase assays are commonly used to detect the interaction of test molecules with ABC transporters (see abstract). Therefore, it would be obvious to one of ordinary skill in the art of ABC transporters to use an ATPase assay on the parental ABC transporter in the presence of the test molecule, as recited in claim 126, in order to detect interactions between the parent ABC transporter and the test molecules. Therefore, claims 1-4, 10, 119-22, and 124-127 are obvious in view of Alexander et al. and Sachs et al., and further in view of Glavinas et al.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Amelia Stephens whose telephone number is (571)272-1006. The examiner can normally be reached M-F 8-5 EST.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Anne Gussow can be reached at (571) 272-6047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/AMELIA STEPHENS/ Examiner, Art Unit 1645
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683
Prosecution Insights