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 .
Claims Status
Claims filed 07/19/2024 are entered. Claims 1, 2, 4, 10-14, 16-18, 21-23, 25-27, 55-59, 61-63, 70 are pending and under examination.
Claim Objections
Claim 1 is objected to because of the following informalities: Claim 1 recites “a targeting small molecule probe that is specificity acted on by a β-lactamase” (emphasis in italics added). However, this is grammatically incorrect and does not correspond to known art-specific terminology. The Examiner suggests amending “specificity” to “specifically”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim(s) 23, 26, 27, 70 is/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 “about” in claim 23 is a relative term which renders the claim indefinite. The term “about” 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 disclosure provides definitive boundaries for what values are encompassed by “about 405 nm”.
Additionally, claim 26 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being incomplete for omitting essential elements, such omission amounting to a gap between the elements. See MPEP § 2172.01. The omitted elements are: a second pad. Claim 26 depends on claim 1, which only recites at least a first pad. Claim 26 then recites a third pad. Is this “third pad” implying the addition of a second pad, with elements defined by the limitation of claim 1, and further adds a third pad as defined by claim 26? Note that claim 2 recites a second pad.
Additionally, regarding claim 27, the recitation of that the solid substrate further comprises a fourth pad that comprises “components including the chromophore-releasing small molecule indicator that is activated by the enzyme amplifier” makes it unclear whether the fourth pad contains the enzyme amplifier or only the indicator that has already been activated by the enzyme amplifier.
Additionally, claim 70 recites the limitation "compound" in line 2. There is insufficient antecedent basis for this limitation in the claim and its parent claims. Since a compound can be any combination of at least two elements, one cannot assume whether the compound is referring to entire structure or partial structure of the small molecule probe of its parent claim.
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, 2, 4, 10-14, 21-23, 26-27, 55, 57, 59, 61-63 is/are also rejected under 35 U.S.C. 103 as being unpatentable over Murthy (Murthy et al, WO 2018/152443 Al, published 03/28/2018) in view of Henry (Henry et al, US 2020/0131558 Al, published 2020). Regarding claim 1, Murthy teaches a solid substrate (e.g. a 96-well plate) (p. 4, para. 024) comprising reagents or components for measuring the presence of a β-lactamase produced by a Gram- negative, Gram-positive, or pathogenic beta-lactam resistant bacteria (p. 9, para. 043 and 045), comprising:
the solid substrate which comprises one, two or three components selected from the group consisting of
(i) a targeting small molecule probe that is specifically acted on by a β-lactamase (i.e. thiophenol-β-lac; p. 10, para. 048);
(ii) a caged enzyme amplifier (i.e. disulfide-protected cysteine protease papain; p. 10, para. 048); and
a chromophore-releasing small molecule indicator that is activated by an uncaged enzyme amplifier (i.e. BAPA releases colorimetric product p-nitroaniline; p. 10, para. 047) (overall system: p. 10-11, para. 049). Murthy further teaches this colorimetric signal is both visible by eye and measurable by absorption spectroscopy at an absorbance of 405 nm (p. 10-11, para. 049).
Murthy further teaches the ever growing and developing need for affordable and rapid point-of-care diagnostic tools for measuring antibiotic resistance, valuing assays that are portable, low cost, easy to use, and require no processing time, which are also advantages of their assay (p. 5, para. 031). Murthy also teaches the assay can occur all at room temperature (p. 5, para. 031).
Murthy does not explicitly teach the pad.
However, Henry teaches a paper-based analytical device (i.e. a paper-based solid substrate, also called PAD) for testing for the presence of beta-lactamase (Abstract). Henry further teaches that paper-based analytical devices have been developed for a variety of point-of-care diagnostics as they are rapid, disposable, portable, inexpensive, and do not require specialized instrumentation or trained personnel (p. 1, para. 0005-0007). Specifically, the imaging device comprises a smartphone camera and a container that is impenetrable to visible light (p. 4, para. 0053). Henry further teaches the PAD platform provides sensitivity that matches that of a microtiter plate (p. 5, para. 0078).
It would have been obvious to one skilled in the art, before the effective filing date of the instant application, to substitute the microtiter plate with a paper-based substrate as the solid substrate for the advantages of paper-based analytical devices over microtiter plates, such as further reduced cost. Further, the paper-based system taught by Henry does not require quantification by a plate reader and can be imaged by a smartphone camera.
One skilled in the art, before the effective filing date of the instant application, would be motivated to continue to simplify point-of-care assays and reduce cost, especially without sacrificing sensitivity.
One skilled in the art, before the effective filing date of the instant application, would have reasonable expectation of success because (1) all reagents are stable at room temperature so would be compatible with the paper-based system taught by Henry, in that regards, and (2) the colorimetric signal generated by the detection system of Murthy is visible by eye, so would be compatible (i.e. detectable) with the camera imaging detection system taught by Henry. Therefore, the detection reagents used in Murthy can be substituted into the paper-based solid substrate of Henry with an expected retention of stability and detection sensitivity.
The teachings of the references regarding claim 1 are incorporated in its entirety for the dependent claims and discussed further below, as is relevant for each claim. In summary, Murthy is used to teach the reagent system and Henry is used to teach the solid substrate structure.
Regarding claim 2, Murthy further teaches two sample wells with the BAPA and inactive papain, and the thiophenol-β-lac was added to one sample well but not another sample well, where the well without thiophenol-β-lac added is used as a control to evaluate non-specific background signal (p. 14, para. 062 and Figure 5A). Therefore, this second pad does not comprise the targeting small molecule probe that is acted upon by the bata-lactamase.
Additionally, Henry shows their paper-based solid substrate is also capable of having more than one pad isolated from others, showing the transferability of this limitation from isolated wells to isolated absorbent pad regions.
Regarding claim 4, Henry teaches the pad comprise of absorbent paper, and how the reagents are added to the paper (Figure 6, Abstract, and p. 1, para. 0019).
It would have been obvious to one skilled in the art, before the effective filing date of the instant application, to substitute the microtiter plate with a paper-based substrate as the pad in the solid substrate for the advantages of paper-based analytical devices over microtiter plates, as explained for claim 1; therefore the teachings of Henry regarding the substrate are relevant over the teachings of Murthy regarding the substrate.
The motivation and reasonable expectation of success of using a paper-based substrate is also provided in the discussion for claim 1.
Regarding claim 10, Murthy further teaches the targeting small molecule probe comprises a β-lactam group (e.g. Figure 3A, thiophenol-β-lac). Additionally, Henry also teaches the targeting small molecule probe comprises a β-lactam group (Figure 1).
Regarding claim 11, Murthy further teaches when the targeting small molecule probe (thiophenol-β-lac) is acted upon by a β-lactamase the targeting small molecule probe releases a thiophenol group that interacts with the caged enzyme amplifier to uncage and activate the enzyme amplifier (liberate the papain via a disulfide interchange reaction, producing active papain) (p. 4, para. 023 and Figure 2A).
Regarding claims 12, 13, and 14, Murthy further teaches the caged enzyme amplifier is the caged cysteine protease papain (p. 10, para. 048).
Regarding claim 21, Murthy further teaches a chromophore is released from the chromophore-releasing small molecule indicator when acted on by the enzyme amplifier (p. 5, para. 035-036).
Regarding claims 22 and 23, Murthy further teaches the chromophore absorbs light in a wavelength of 405 nm (p. 11, para. 049).
Regarding claims 26 and 27, Murthy further teaches multiple wells can contain the claimed reagents for multiplexing and processing multiple samples, replicates, and/or controls (e.g. Figure 5A). Henry also teaches the solid substrate has multiple pads for independent assays (e.g. Figure 6).
Regarding claim 55, Murthy further teaches the β-lactamase detection system in a method to measure the presence of a β-lactamase produced by a pathogen in a sample comprising of contacting the solid substrate of claim 1 with the sample and measuring the light absorbance at a wavelength of 400 nm to 600 nm, wherein the measured change in light absorbance of the solid substrate is indicative that there is β-lactamase produced by a pathogen in the sample (Figure 4A and Figure 5A-B).
Regarding claim 57, Murthy further teaches the method using E. coli as an example (p. 4, para. 025). Henry also teaches the method using E. coli as an example (p. 8, para. 0094).
Regarding claim 59, Murthy further teaches the method using urine samples as an example (p. 4, para. 026).
Regarding claims 61, 62, and 63, Murthy teaches the targeting small molecule probe for β-lactamase, is the β-lactam, thiophenol-β-lac (e.g. Figure 2B and 3A), of the structure below.
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T1 is a benzenethiol containing group, specifically
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86
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.
Z1 is a carboxylate, a carbonyl, or an ester, specifically an ester
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.
R1, R2, and R3 are H.
X1 comprises of R4, R5, and R6, which are all H, and R7 is an optionally substituted benzyl
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.
Y1 is
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.
Claim(s) 16-17 is/are rejected under 35 U.S.C. 103 as being unpatentable over Murthy (published 2018) in view of Henry (published 2020), as applied to claim 1 above, and further in view of Sueiro (Sueiro et al, A Comparison of the ISO and AACC Methods for Determining the Activity of Trypsin Inhibitors in Soybean Meal, published 2015).
The teachings of the references regarding parent claims are incorporated in its entirety for the dependent claims and discussed further below, as is relevant for each claim.
Regarding claim 16, Murthy further teaches the chromophore-releasing small molecule indicator is benzoyl-L-arginine-p-nitroanilide (L-BAPA) (p. 10, para. 0047), generating 4-nitroaniline (p. 3, para. 019), or a derivative thereof.
Murthy does not specifically teach benzoyl-DL-arginine-p-nitroanilide (underline emphasis added) (i.e. DL-BAPA).
However, Sueiro teaches benzoyl-DL-arginine-p-nitroanilide is a racemic mixture of benzoyl-D-arginine-p-nitroanilide and benzoyl-L-arginine-p-nitroanilide (p. 1391, Abstract and Introduction, para. 2). Sueiro also teaches that in standardized enzyme (i.e. trypsin) activity assay, one standard uses L-BAPA and one uses DL-BAPA, and although the activity measurements obtained using L-BAPA are likely more accurate than those obtained using DL-BAPA, since the substrate is L-BAPA, in most context, the increase in accuracy likely does not justify the approximately tenfold greater expense of using L-BAPA (p. 1396, column 1, para. 1).
It would have been obvious to one skilled in the art, before the effective filing date of the instant application, in practice, to use benzoyl-DL-arginine-p-nitroanilide (DL-BAPA) when the enzyme’s substrate is L-BAPA, since that is the more affordable alternative to pure L-BAPA, especially since the exact levels of activity are not required, but rather only a relative difference between a control sample.
One skilled in the art, before the effective filing date of the instant application, would be motivated to reduce costs by using more affordable reagents of racemic mixtures that can provide the same results as more pure reagents.
One skilled in the art, before the effective filing date of the instant application, would have reasonable expectation of success since benzoyl-DL-arginine-p-nitroanilide (DL-BAPA) can be used to assay the activity of enzymes with L-BAPA as their substrates.
The teachings of the references regarding claim 16 are incorporated in its entirety for the dependent claims and discussed further below, as is relevant for each claim.
Regarding claim 17, Murthy further teaches a derivative of BAPA comprising a different chromophore group replacing the p-nitroaniline group (p. 7, para. 036-037).
Claim(s) 18 is/are rejected under 35 U.S.C. 103 as being unpatentable over Murthy (published 2018) in view of Henry (published 2020) and Sueiro (published 2015), as applied to claim 16 above, and further in view of Zimmerlein (Zimmerlein et al, The M Protein Is Dispensable for Maturation of Streptococcal Cysteine Protease SpeB, published 2005) and Lecaille (Lecaille et al, Revisiting the S2 specificity of papain by structural analogs of Phe, published 1999).
The teachings of the references regarding claim 16 are incorporated in its entirety for the dependent claims and discussed further below, as is relevant for each claim.
Regarding claim 18, Murthy further teaches the functions of the amplification enzyme substrate, such as BAPA, specifically their interaction with papain and release of active functional components (p. 3, para. 019).
Murthy and Henry do not explicitly teach using derivatives of BAPA comprising of a dipeptide or tripeptide in place of the arginine group of BAPA.
However, Lecaille teaches papain characteristically has a strong preference for L-aromatic amino acids, particularly phenylalanine (Phe) at one of its substrate binding sites. Therefore, the binding of Phe on a substrate improves the affinity and kinetics of papain (Abstract).
Further, Zimmerlein teaches that the catalytic domain of the cysteine protease SpeB is structurally similar to the papain superfamily of cysteine proteases (p. 859, col. 2, para. 1). Zimmerlein teaches measuring the activity of SpeB using the substrate n-benzoyl-Pro-Phe-Arg-p-nitroanilide hydrochloride (Abstract), which is like BAPA but with a tripeptide of proline, phenylalanine, and arginine, replacing the arginine in BAPA.
It would have been obvious to one skilled in the art, before the effective filing date of the instant application, in light of the knowledge that papain has a strong preference for phenylalanine, to choose a substrate that contains phenylalanine, such as n-benzoyl-Pro-Phe-Arg-p-nitroanilide hydrochloride that has been shown to be a substrate for a cysteine protease that shares the same structure in its active site as papain.
One skilled in the art, before the effective filing date of the instant application, would be motivated to improve substrate affinity to make the assay more efficient.
One skilled in the art, before the effective filing date of the instant application, would have reasonable expectation of success since n-benzoyl-Pro-Phe-Arg-p-nitroanilide hydrochloride is a known substrate for cysteine proteases that have the same active site structure as papain.
Claim(s) 25 is/are rejected under 35 U.S.C. 103 as being unpatentable over Murthy (published 2018) in view of Henry (published 2020), as applied to claim 22 above, and further in view of Greenhalgh (Greenhalgh et al, A Microfluidic Device for Nucleic Acid-Based Analysis of Helicobacter pylori and Antibiotic Susceptibility Testing, published 2020).
Regarding claim 25, Murthy teaches BAPA releases pale yellow chromophore p-nitroaniline, which is suboptimal for measuring urine samples, and teaches alternative papain probes capable of visually signaling the presence of beta-lactamase, such as one (BNThio) that releases a purple chromophore (p. 5, para. 035-036).
Murthy and Henry do not explicitly teach the chromophore is resorufin.
However, Greenhalgh teaches resorufin, a pink chromophore, used in bacterial antibiotic susceptibility testing (Abstract and p. 369, col. 2, para. 3), can be measured by colorimetric or fluorescence assays (p. 370, col. 1, para. 1).
It would have been obvious to one skilled in the art, before the effective filing date of the instant application, to choose a chromophore that is a substantially different color than the biological sample, such as urine, to distinguish it from the background sample, as Murthy teaches. It would be obvious to choose resorufin, as it is a pink chromophore, already used in antibiotic susceptibility testing assays.
One skilled in the art, before the effective filing date of the instant application, would be motivated to choose a chromophore that is easily distinguishable from the biological sample.
One skilled in the art, before the effective filing date of the instant application, would have reasonable expectation of success as resorufin has already been used in other antibiotic susceptibility testing assays using biological samples and its signal be measured by colorimetric or fluorescence assays, which are necessary for the assays of Murthy in view of Henry.
Claim(s) 56 is/are rejected under 35 U.S.C. 103 as being unpatentable over Murthy (published 2018) in view of Henry (published 2020), as applied to claim 55 above, and further in view of Tarlton (Tarlton et al, Genotypic and antimicrobial resistance gene analysis, and the development of rapid diagnostic tests, for ß-lactam-resistant Gram-negative bacteria, Thesis, published 2018).
The teachings of the references regarding parent claims are incorporated in its entirety for the dependent claim and discussed further below, as is relevant.
Murthy and Henry teach the detection of β-lactamase produced by bacteria in biological samples but do not explicitly teach a specific β-lactamase.
Regarding claim 56, Tarlton further teaches the β-lactamase CTX-M-15 is likely one of the best enzymes for triggering the β-lactamase dual-enzyme detection system taught by Murthy, followed by CTX-M-14 and CMY-2, and that these β-lactamases are produced by different isolates (p. 46, para. 4) and teaches these β-lactamases in the detection assay (p. 40, para. 5).
It would have been obvious to one skilled in the art, before the effective filing date of the instant application, that the β-lactamases used in the detection system are ones that are naturally produced by bacteria and can be detected by the system.
One skilled in the art, before the effective filing date of the instant application, would be motivated to develop a system that can detect β-lactamases commonly produced by many bacteria isolates.
One skilled in the art, before the effective filing date of the instant application, would have reasonable expectation of success since these β-lactamases are already validated in the same dual-enzyme detection system taught by Murthy.
Claim(s) 70 is/are rejected under 35 U.S.C. 103 as being unpatentable over Murthy (published 2018) in view of Henry (published 2020), as applied to claim 61 above, and further in view of Deboer (Deboer et al, WO 2021/041583, filed 08/26/2020) and Rageh (Rageh et al, Spectrophotometric method for determination of certain cephalosporins using 4-chloro-7-nitrobenzo-2-oxa-1,3-diazole (NBD-Cl), published 2010).
The applied reference has a common assignee and joint inventor with the instant application. Based upon the earlier effectively filed date of the reference, it constitutes prior art under 35 U.S.C. 102(a)(2).
This rejection under 35 U.S.C. 103 might be overcome by: (1) a showing under 37 CFR 1.130(a) that the subject matter disclosed in the reference was obtained directly or indirectly from the inventor or a joint inventor of this application and is thus not prior art in accordance with 35 U.S.C.102(b)(2)(A); (2) a showing under 37 CFR 1.130(b) of a prior public disclosure under 35 U.S.C. 102(b)(2)(B); or (3) a statement pursuant to 35 U.S.C. 102(b)(2)(C) establishing that, not later than the effective filing date of the claimed invention, the subject matter disclosed and the claimed invention were either owned by the same person or subject to an obligation of assignment to the same person or subject to a joint research agreement. See generally MPEP § 717.02.
The teachings of the references regarding parent claims are incorporated in its entirety for the dependent claims and discussed further below, as is relevant for each claim.
Murthy in view of Henry discloses the use of cephalosporin-like promiscuous β-lactams (p.18, para. 075) sharing a common structure with the claimed β-lactams (below) but does not explicitly disclose the specifically claimed β-lactam species of claim 70.
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However, Deboer teaches the β-lactam species below as a β-lactamase probe:
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(p. 12). Deboer further teaches specifically testing the resistance to antibiotic Cefazolin (p. 82, para. 107), a commonly used IV antibiotic. The difference between the β-lactam species taught by Murthy and the β-lactam species taught by Deboer is what the instant application calls the R7 group.
Additionally, Rageh teaches that the R7 group taught by Deboer is the same as that in the first-generation cephalosporin antibiotic Cefazolin (Table 1).
It would have been obvious to one skilled in the art, before the effective filing date of the instant application, to select a β-lactamase probe that closely mimics a known first-generation cephalosporin antibiotic, as it likely determines resistance to this antibiotic and others related to it, such as other broad spectrum first-generation cephalosporin antibiotics.
One skilled in the art, before the effective filing date of the instant application, would be motivated to determine the antibiotic resistance to commonly used broad spectrum first-generation cephalosporin antibiotics.
One skilled in the art, before the effective filing date of the instant application, would have reasonable expectation of success because these structures disclosed by Deboer are determined to be β-lactamase probes.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BONIRATH CHHAY whose telephone number is (571)272-0682. The examiner can normally be reached Mon-Thu 8AM-5PM EST.
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/BONIRATH CHHAY/Examiner, Art Unit 1645 Friday, October 9, 2026
/BAO-THUY L NGUYEN/Supervisory Patent Examiner, Art Unit 1677 October 14, 2026
