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 .
Acknowledgement of Receipt
Applicant’s Response, filed 7/13/2026, in reply to the Office Action mailed 1/12/2026, is acknowledged and has been entered. Claim 1 has been amended. Claims 21 and 22 are newly added. Claims 1, 5, 7, 9, 10, 13 and 17-22 and are examined herein on the merits for patentability.
Response to Arguments
Any rejection not reiterated herein has been withdrawn as being overcome by claim amendment. The Examiner’s response to Applicant’s arguments is incorporated below.
Claim Rejections - 35 USC § 103
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.
Claim(s) 1, 5, 7, 9, 10, 13 and 17-20 are rejected under 35 U.S.C. 103 as being unpatentable over Cui et al. (J. Photochemistry and Photobiology A: Chem., 2007, 186, p. 85-92) in view of Taniguchi et al. (Med. Chem. Commun., 2019, 10, 1121), in further view of RU 2680090 and Kanazawa et al. (EP 3531132).
Cui teaches the synthesis and spectral properties and photostability of novel boron–dipyrromethene dyes. Generally, the BODIPY fluorophores present advantageous photo-spectral properties, such as high extinction coefficients and high fluorescence quantum yields, which facilitate their applications in DNA sequencing and bio-analysis. However, various substituents at BODIPY framework may lead to large difference on their spectral properties, especially on the quantum yields.
Two series of novel boron–dipyrromethene (BODIPY) dyes containing 8-phenyl groups have been synthesized and their spectral properties have been studied (page 85).
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The terminal COOH in 2e may be activated in the form of succinimide ester and used to label bio-molecules directly.
In summary, we have synthesized two series of BODIPY dyes (1 and 2) and researched their spectral properties. Dyes 2 with four methyl groups show much higher fluorescence quantum yields and extinction coefficients than dyes 1. The X-ray structure analysis of the crystals of 1c and 2c is used to reveal that blocking the rotation of 8-phenyl moiety by 1- and 7-methyl groups will suppress the intramolecular vibronic relaxation and internal conversion. The “push–pull” electronic effect caused by methyl groups at 3- and 5-position of BODIPY is another positive factor for the high quantum yields of 2. The photostability of dyes 1 are higher than that of dyes 2, and the electron withdrawing p-substituents at phenyl moiety of the dyes are beneficial to increasing the photostability. The BODIPY dyes with better photostability present comparatively lower quantum yields in our research (page 91).
Compound 1b is within the scope of the instant claims such that R1-R6, R21, R22, R24 and R25 are hydrogen, R23 is a carboxy group and Q1 is a halogen.
Compound 2b is within the scope of the instant claims such that R1, R2, R5 and R6 are Formula A (bond-alkyl), R3 and R4 are hydrogen, R21, R22, R24 and R25 are hydrogen, i.e. a substituent, R23 is a carboxy group and Q1 is a halogen.
Cui does not specifically teach wherein Q2 is an alkyl group and R3, R4 as sulfo group.
Taniguchi teaches the photophysical properties and application in live cell imaging of B,B-fluoro-perfluoroalkyl BODIPYs. The photophysical properties of newly identified B,B-fluoro-perfluoroalkyl BODIPYs (2 and 3), which possess a fluoro group and a trifluoromethyl or pentafluoroethyl group at the boron center, were investigated. B,B-Fluoro-perfluoroalkyl BODIPYs 2 and 3 exhibited better photophysical/chemical properties than B,Bdifluoro-BODIPY 1, as follows: (1) higher photostability both in methanol solvent and in a live cell environment, (2) higher stability against acid degradation, and (3) improved fluorescence signal-to-noise ratios in a cell system. These favorable properties of B,B-fluoro-perfluoroalkyl BODIPYs are likely due to the highly electron-withdrawing nature of the perfluoroalkyl groups on the boron atom, which reduces the reactivity to 1 O2 and strengthens the complexation of the dipyrromethene ligands to the boron atom. Thus, B,Bfluoro perfluoroalkyl BODIPYs may be useful functional molecules for various applications.
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The fluoro-perfluoroalkyl BODIPYs 2 and 3 exhibited higher photostability and chemical stability than the corresponding BF2-BODIPY 1. Interestingly, when 2 and 3 were applied to a live cell system, the fluorescence signal-to-noise ratios were markedly improved compared with 1. In addition, the higher photostability of 2 and 3 compared with that of 1 was retained in the live cell environment. Mechanistic studies suggest that the strongly electron-withdrawing perfluoroalkyl groups render BODIPYs 2 and 3 more electron-deficient, which reduces the reactivity to 1 O2 and stabilizes the B–N bonds. The B,B-fluoroperfluoroalkyl BODIPYs complement previous BODIPYs whose photostability is improved by other structural modifications. In addition, the B-perfluoroalkyl modification was accessible to the dipyrromethene containing an alkyne functionality at the meso position,11 demonstrating potential applicability of the new BODIPY for the bioconjugation (page 1123).
With regard to claim 13, alkyl is not taught at positions R21 and R25.
RU 2680090 teaches salts of the compound of formula I with alkali metals, replacing hydrogen atoms in both sulfo groups, where R means the N-oxysuccinimidyl group. Also proposed a method of obtaining salts and their use. Salts of the compounds of formula I are fluorescent dyes with better characteristics than their analogues – water solubility, quantum yield, and extinction coefficient – and can be used as fluorescent labels of protein molecules (abstract).
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General formula I is taught, page 3:
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Including where R is H, Hal, alkyl, aryl, cycloalkyl, alkylaryl, acyl and sulfo group.
See compound IIIa, page 5.
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Alkali metal salts of the compounds of formula III are proposed for sulfo groups, alkali metals preferably Na and K.
The objective of the invention is to obtain 2- (4,4-difluoro-1,3,5,7-tetramethyl-2,6-disulfo-4-boro-3a, 4a-diaza-s-indacen-8-yl)-benzoic acid (compound IIIa), as well as its derivatives with N-oxysuccimidyl groups, characterized by the possibility of using for fluorescent labeling of proteins (fluorescein channel, 490-520 nm), characterized by solubility in water, higher quantum yield, higher extinction coefficient, compared to fluorescein and with known dyes of the formula (I), for example BODIPY FL, used for the fluorescein channel.
Kanazawa teaches compounds represented by Formula (1) that can be used by being bound to the first binding substance such as an antibody as a fluorescent label, and the compound represented by Formula (1) is useful as a fluorescent labeling agent (pages 2-3). A fluorescently labeled antibody bound through an amide bond is taught (page 4).
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Compounds in Example 1 include:
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It would have been obvious to one of ordinary skill in the art at the time of the invention to modify a compound 1b or 2b taught by Cui to have at least one alkyl or substituted alkyl group according to one of variables Q1 or Q2 of the instant claims when the teaching of Cui is taken in view of Tanaguchi. Each of Cui and Tanaguchi are directed to fluorescent BODIPY dyes, including for conjugation to a biomolecule. While Cui teaches halide at the stated position, one would have been motivated to provide a halide and alkyl halide according to B,B-fluoro perfluoroalkyl BODIPYs, with a reasonable expectation of success, because Tanaguchi teaches that doing so allows for high photostability which was retained in the live cell environment and that the strongly electron-withdrawing perfluoroalkyl groups render BODIPYs more electron-deficient, which reduces the reactivity to oxygen and stabilizes the B–N bonds. Regarding claim 18, it would have been further obvious to provide links between the dye and a biomolecule because Cui teaches that a dye having a terminal COOH may be activated in the form of succinimide ester and used to label bio-molecules directly.
It would have been further obvious to one of ordinary skill in the art to provide a sulfonated variable including a sulfo group or Formula A at position R3 and R4 of a bodipy derivative corresponding to the instant claims when the teaching of Cui and Taniguchi are taken in view of RU 2680090 and Kanazawa. Each of Cui, Tanaguchi, RU 2680090 and Kanazawa are directed to fluorescent BODIPY dyes, including for conjugation to a biomolecule. One would have been motivated to do so, with a reasonable expectation of success because RU 2680090 teaches that doing a sulfo group allows for solubilization of the dye. One would have had a reasonable expectation of success in doing so because RU 2680090 teaches a sulfonation method by sulfonation with chlorosulfonic acid (see methods) and teaches a carboxyl group as one of the active groups capable of forming a chemical bond with the ligand (claim 2).
Regarding claim 5, Kanazawa further teaches a sulfonated derivative corresponding to variables R3 and R4 as increasing solubility.
Regarding variables R21 and R25 of the instant claims, it would have been further obvious to provide an alkyl moiety because Kanazawa teaches formula Ar-1 having variables R121 and R122 equivalent to the stated positions which each independently represent a halogen atom, an alkyl group, or an alkoxy group, provided that R121 and R122 each may have a hydrophilic part or a capture part capable of forming a covalent bond with a biological molecule, n represents an integer of 0 to 4, and in a case where n is 2 or more, a plurality of R122's may be the same or different from each other (page 3-4).
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Accordingly, one of ordinary skill in the art would have found it obvious to select alkyl as a suitable substituent to represent R121 or R122 from among the limited number of variables set forth at position R21 and R22 of the instant claims.
Regarding claims 18-20, it would have been further obvious to provide links between the dye and a biomolecule because Kanazawa teaches that a NHS activated carboxylic acid is used to label an antibody via an amide bond.
Response to arguments
Applicant argues that Cui discloses a compound, wherein substituents corresponding to the claimed R³and R⁴ groups are represented by a hydrogen atom. Applicant asserts that Cui provides no structural indication that the substituents of Formula 1 can be a a carboxy group or a salt thereof, a sulfo group or a salt thereof, or a phosphono group or a salt thereof. Applicant further submits that Kanazawa discloses a compound… wherein Ar³ and Ar⁴ substituents are positioned orthogonal to the dipyrromethene skeleton and correspond to the claimed R³and R⁴ group. Applicant assrts that Kanazawa explicitly discloses the Ar³ and Ar⁴ substituents in the compound of Formula (1) are orthogonal to the dipyrromethene skeleton, to reduce molecular interaction and suppress aggregate quenching, thereby improving sensitivity; and argues that given that Kanazawa relies on this specific structural arrangement to achieve its objectives, a person of ordinary skill in the art would have no motivation to combine Kanazawa with Cui, Taniguchi (which utilize hydrogen atoms), Schimer (which requires a hydrophilic group), or RU2680090, to arrive at the invention as claimed.
Applicant’s arguments have been fully considered but are not found to be persuasive. In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). In the instant case, with regard to the argument that Cui and Kanagawa do not teach a sulfo group or a salt thereof directly bonded to a dipyrromethene ring structure, equivalent to position R3, R4 of the instant claims, it is noted that the rejection is based upon a combination of references. The RU 2680090 reference teaches sulfo groups equivalent to position R3, R4 for increasing solubility of the BODIPY compounds. See also MPEP 2144.09. A prima facie case of obviousness may be made when chemical compounds have very close structural similarities and similar utilities. "An obviousness rejection based on similarity in chemical structure and function entails the motivation of one skilled in the art to make a claimed compound, in the expectation that compounds similar in structure will have similar properties." In re Payne, 606 F.2d 303, 313, 203 USPQ 245, 254 (CCPA 1979). See In re Papesch, 315 F.2d 381, 137 USPQ 43 (CCPA 1963) and In re Dillon, 919 F.2d 688, 16 USPQ2d 1897 (Fed. Cir. 1990).
Claim(s) 1, 5, 7, 9, 13 and 17-22 are rejected under 35 U.S.C. 103 as being unpatentable over Cui et al. (J. Photochemistry and Photobiology A: Chem., 2007, 186, p. 85-92) in view of Wang et al. (J. Org. Chem., 2019, 84, 2732−274), in further view of RU 2680090 and Kanazawa et al. (EP 3531132).
Cui teaches the synthesis and spectral properties and photostability of novel boron–dipyrromethene dyes. Generally, the BODIPY fluorophores present advantageous photo-spectral properties, such as high extinction coefficients and high fluorescence quantum yields, which facilitate their applications in DNA sequencing and bio-analysis. However, various substituents at BODIPY framework may lead to large difference on their spectral properties, especially on the quantum yields.
Two series of novel boron–dipyrromethene (BODIPY) dyes containing 8-phenyl groups have been synthesized and their spectral properties have been studied (page 85).
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The terminal COOH in 2e may be activated in the form of succinimide ester and used to label bio-molecules directly.
In summary, we have synthesized two series of BODIPY dyes (1 and 2) and researched their spectral properties. Dyes 2 with four methyl groups show much higher fluorescence quantum yields and extinction coefficients than dyes 1. The X-ray structure analysis of the crystals of 1c and 2c is used to reveal that blocking the rotation of 8-phenyl moiety by 1- and 7-methyl groups will suppress the intramolecular vibronic relaxation and internal conversion. The “push–pull” electronic effect caused by methyl groups at 3- and 5-position of BODIPY is another positive factor for the high quantum yields of 2. The photostability of dyes 1 are higher than that of dyes 2, and the electron withdrawing p-substituents at phenyl moiety of the dyes are beneficial to increasing the photostability. The BODIPY dyes with better photostability present comparatively lower quantum yields in our research (page 91).
Compound 1b is within the scope of the instant claims such that R1-R6, R21, R22, R24 and R25 are hydrogen, R23 is a carboxy group and Q1 is a halogen.
Compound 2b is within the scope of the instant claims such that R1, R2, R5 and R6 are Formula A (bond-alkyl), R3 and R4 are hydrogen, R21, R22, R24 and R25 are hydrogen, i.e. a substituent, R23 is a carboxy group and Q1 is a halogen.
Cui does not specifically teach wherein Q2 is an alkyl group and R3, R4 as sulfo group.
Wang teaches a convenient procedure for the preparation of functionalized BODIPYs bearing both F and an organo substituent at the boron center, using one-pot reactions between in situ formed dipyrromethenes and organo trifluoroborate salts, has been reported. The complexation reaction utilizes stable and commercial accessible organotrifluoroborate potassium salts and provides a facile access to a variety of novel B-functionalized BODIPYs, which are hard to access through current synthetic methods.
Boron dipyrromethene (BODIPY) dyes have excellent photophysical properties and have found widely applications in diverse research fields. The key to their success is closely associated with their rich functionalization chemistry, and every position on the BODIPY core can be modified to tune the photophysical properties and to add tethering groups for further conjugation. Among them, substitutions on the boron center8 (4-position) open up elegant methods to modulate solubility, (photo)stability, Stokes shift, and optoelectronic properties of resultant dyes (page 2732).
See Table 1.
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For example, compound 2f is taught:
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High fluorescence quantum yields were also obtained for dyes 2a−g, 7, and 8 (page 2735).
In conclusion, we developed a general and facile one-pot synthesis of functionalized FC-BODIPYs bearing both Fand an organo substituent on boron from dipyrromethanes and organotrifluoroborate salts. The method utilizes stable and commercially accessible organotrifluoroborate potassium salts and thus provides a direct access to a variety of novel B functionalized BODIPYs, which were previously difficult to access. This method will thus stimulate the modulation of the boron position to generate novel dyes with desired properties including solubility, (photo)stability, Stokes shift, and optoelectronic properties for advance applications (page 2735).
RU 2680090 teaches salts of the compound of formula I with alkali metals, replacing hydrogen atoms in both sulfo groups, where R means the N-oxysuccinimidyl group. Also proposed a method of obtaining salts and their use. Salts of the compounds of formula I are fluorescent dyes with better characteristics than their analogues – water solubility, quantum yield, and extinction coefficient – and can be used as fluorescent labels of protein molecules (abstract).
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General formula I is taught, page 3:
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Including where R is H, Hal, alkyl, aryl, cycloalkyl, alkylaryl, acyl and sulfo group.
See compound IIIa, page 5.
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Alkali metal salts of the compounds of formula III are proposed for sulfo groups, alkali metals preferably Na and K.
The objective of the invention is to obtain 2- (4,4-difluoro-1,3,5,7-tetramethyl-2,6-disulfo-4-boro-3a, 4a-diaza-s-indacen-8-yl)-benzoic acid (compound IIIa), as well as its derivatives with N-oxysuccimidyl groups, characterized by the possibility of using for fluorescent labeling of proteins (fluorescein channel, 490-520 nm), characterized by solubility in water, higher quantum yield, higher extinction coefficient, compared to fluorescein and with known dyes of the formula (I), for example BODIPY FL, used for the fluorescein channel.
Kanazawa teaches compounds represented by Formula (1) that can be used by being bound to the first binding substance such as an antibody as a fluorescent label, and the compound represented by Formula (1) is useful as a fluorescent labeling agent (pages 2-3). A fluorescently labeled antibody bound through an amide bond is taught (page 4).
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Compounds in Example 1 include:
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It would have been obvious to one of ordinary skill in the art at the time of the invention to modify a compound 1b or 2b taught by Cui to have at least one alkyl or substituted alkyl group according to one of variables Q1 or Q2 of the instant claims when the teaching of Cui is taken in view of Wang. Each of Cui and Wang are directed to fluorescent BODIPY dyes, including for conjugation to a biomolecule. While Cui teaches halide at the stated position, one would have been motivated to provide a halide and alkyl according to B,B-fluoro perfluoroalkyl BODIPYs, with a reasonable expectation of success, because Wang teaches that doing so allows for high fluorescence quantum yield, and that substitutions on the boron center8 (4-position) open up elegant methods to modulate solubility, (photo)stability, Stokes shift, and optoelectronic properties of resultant dyes. Regarding claim 18, it would have been further obvious to provide links between the dye and a biomolecule because Cui teaches that a dye having a terminal COOH may be activated in the form of succinimide ester and used to label bio-molecules directly.
It would have been further obvious to one of ordinary skill in the art to provide a sulfonated variable including a sulfo group or Formula A at position R3 and R4 of a bodipy derivative corresponding to the instant claims when the teaching of Cui and Wang are taken in view of RU 2680090 and Kanazawa. Each of Cui, Wang, RU 2680090 and Kanazawa are directed to fluorescent BODIPY dyes, including for conjugation to a biomolecule. One would have been motivated to do so, with a reasonable expectation of success because RU 2680090 teaches that a sulfo group allows for solubilization of the dye. One would have had a reasonable expectation of success in doing so because RU 2680090 teaches a sulfonation method by sulfonation with chlorosulfonic acid (see methods) and teaches a carboxyl group as one of the active groups capable of forming a chemical bond with the ligand (claim 2).
Regarding claim 5, Kanazawa further teaches a sulfonated derivative corresponding to variables R3 and R4 as increasing solubility.
Regarding variables R21 and R25 of the instant claims, it would have been further obvious to provide an alkyl moiety because Kanazawa teaches formula Ar-1 having variables R121 and R125 equivalent to the stated positions which each independently represent a halogen atom, an alkyl group, or an alkoxy group, provided that R121 and R122 each may have a hydrophilic part or a capture part capable of forming a covalent bond with a biological molecule, n represents an integer of 0 to 4, and in a case where n is 2 or more, a plurality of R122's may be the same or different from each other (page 3-4).
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Accordingly, one of ordinary skill in the art would have found it obvious to select alkyl as a suitable substituent to represent R121 or R125 from among the limited number of variables set forth at position R21 and R25 of the instant claims. Further, Wang teaches alkyl at the position equivalent to position R21 and R25.
Regarding claims 18-20, it would have been further obvious to provide links between the dye and a biomolecule because Kanazawa teaches that a NHS activated carboxylic acid is used to label an antibody via an amide bond.
Conclusion
No claims are allowed at this time.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to LEAH H SCHLIENTZ whose telephone number is (571)272-9928. The examiner can normally be reached Monday-Friday, 8:30am - 12:30pm EST.
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/LHS/
/Michael G. Hartley/Supervisory Patent Examiner, Art Unit 1618
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