DETAILED ACTION
The amendment filed on 04/24/2025 has been entered and fully considered. Claims 83, 85-96 and 99-105 are pending, of which claim 83, 85-89, 91-94 are amended, and Claims 96-105 are newly added.
Response to Amendment
In response to amendment, the examiner maintains objection to claim 90, and modifies rejection over the prior art established in the previous Office action.
Claim Objections
Claim 90 and 102 are objected to because of the following informalities: the pictures in the claims are not correct. Appropriate correction is required.
Claim 90 and 102 recites that “one or more cholesterol ester species represented by the general formula Ill”.
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However, the correct cholesterol ester structure should have two C(R4)3, instead of three C(R4)3.
Claim Rejections - 35 USC § 102
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim(s) 99 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Watkins (WO 2016/019140, IDS).
Regarding claim 99, Watkins discloses a universal lipid quantitative standard (ULQS) comprising a plurality of isotopically labeled lipid standards (par [0007]), wherein the plurality of isotopically labeled lipid standards includes at least one lipid species from one or more lipid classes selected from the group consisting of: a phospholipid class, a lysophospholipid class, a cholesterol ester class, a triacylglycerol class, a diacylglycerol class, a ceramide class, and a sphingomyelin class (par [0037][00105]).
Walkins teaches that “a method is provided for synthesizing one or more mixtures of lipid molecules representative of the composition of lipid molecular species present in one or more corresponding lipid classes in a sample of interest” (par [0007]). Claim 40 of Walkins further teaches that “composition for use as an internal standard comprising one or more mixtures of lipid molecules representative of the composition of lipid molecular species present in one or more corresponding lipid classes in a sample of interest, each mixture of lipid molecules comprising: a lipid backbone having an isotopically-labeled fatty acid at a first position on the lipid backbone, wherein the lipid backbone is for a lipid class having at least two acyl groups; and a mixture of at least two different fatty acids present at a separate position on the lipid backbone, wherein the mixture of fatty acids is representative of the fatty acids that occur in the corresponding lipid class in the sample of interest, and wherein each of the fatty acids in the mixture is present at a ratio representative of the ratio of occurrence of the fatty acid in the lipid molecular species present in the corresponding lipid class in the sample of interest.”. Here, Walkins teaches that the number of isotopically labeled lipid standards are the number of the potential corresponding lipid classes in a sample of interest.
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim(s) 83, 85-96 and 100-105 is/are rejected under 35 U.S.C. 103 as being unpatentable over Watkins (WO 2016/019140, IDS).
Regarding claim 83, Watkins discloses a universal lipid quantitative standard (ULQS) comprising a plurality of isotopically labeled lipid standards (par [0007]), wherein the plurality of isotopically labeled lipid standards includes at least one lipid species from one or more lipid classes selected from the group consisting of: a phospholipid class, a lysophospholipid class, a cholesterol ester class, a triacylglycerol class, a diacylglycerol class, a ceramide class, and a sphingomyelin class (par [0037][00105]).
Walkins teaches that “a method is provided for synthesizing one or more mixtures of lipid molecules representative of the composition of lipid molecular species present in one or more corresponding lipid classes in a sample of interest” (par [0007]). Claim 40 of Walkins further teaches that “composition for use as an internal standard comprising one or more mixtures of lipid molecules representative of the composition of lipid molecular species present in one or more corresponding lipid classes in a sample of interest, each mixture of lipid molecules comprising: a lipid backbone having an isotopically-labeled fatty acid at a first position on the lipid backbone, wherein the lipid backbone is for a lipid class having at least two acyl groups; and a mixture of at least two different fatty acids present at a separate position on the lipid backbone, wherein the mixture of fatty acids is representative of the fatty acids that occur in the corresponding lipid class in the sample of interest, and wherein each of the fatty acids in the mixture is present at a ratio representative of the ratio of occurrence of the fatty acid in the lipid molecular species present in the corresponding lipid class in the sample of interest.”. Here, Walkins teaches that the number of isotopically labeled lipid standards are the number of the potential corresponding lipid classes in a sample of interest.
Walkins does not specifically teach that wherein the plurality of isotopically labeled lipid standards includes
a. 15 phospholipid species, 10 lysophospholipid species, 3 cholesterol ester species, 5 triacylglycerol species, 3 diacylglycerol species, 3 ceramide species, and 3 sphingomyelin species;
b. 20 phospholipid species, 15 lysophospholipid species, 5 cholesterol ester species, 9 triacylglycerol species, 5 diacylglycerol species, 5 ceramide species, and 5 sphingomyelin species; or
C. 25 phospholipid species, 15 lysophospholipid species, 5 cholesterol ester species, 9 triacylglycerol species, 5 diacylglycerol species, 5 ceramide species, and 5 sphingomyelin species.
However, since Walkins teaches that the number of the isotopically labeled lipid standards are the number of the corresponding lipid classes in a sample of interest, it would have been obvious to one ordinary skill in the art to optimize the number of lipid species included in the standards based on the number of the potential corresponding lipid classes in the samples of interest, by routine experimentation. The result is predictable. No inventive step is required.
Regarding claim 85, Watkins discloses that wherein the phospholipid species, the lysophospholipid species, the cholesterol ester species, the triacylglycerol species, the diacylglycerol species, the ceramide species, and the sphingomyelin species lipid species for each lipid class are selected (par [0037][00105]).
“to correct for ionization efficiency, extraction efficiency, and differential fragmentation efficiency in a mass spectrometry analysis”, a stable isotope-labeled analog of the analyte is typically used as an internal standard; this means a molecule with the same chemical structure as the analyte but with a different isotopic mass (like deuterium substitution) that allows the mass spectrometer to distinguish between the analyte and the internal standard while still behaving similarly throughout the analytical process.
Besides, the phrase “to correct for at least one of the following: ionization efficiency, extraction efficiency, and differential fragmentation efficiency of the lipid species in a sample” merely describes an intended result and does not further limit the structure of the ULQS, therefore caried no weight in the patentability determination.
Regarding claim 86, Watkins discloses that wherein the phospholipid includes one or more phospholipid species selected from the group consisting of: phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), phosphatidylglycerol (PG), and phosphatidylinositol (Pl) (par [00105]).
Regarding claim 87, Watkins discloses that wherein the phospholipid species are represented by the general formula I, except the location of the deuterium substitution (Fig. 2, par [0057]):
wherein:
R1 is -(CH2)n-N(CH3)3, -(CH2)n-NH3, -(CH2)n-C(H)(NH3)-C(O)-O-, -(CH2)n-CH(OH)-CH(OH),
inositol, and H;
n is 1 to 6;
R2 is a C3 to C30 saturated or unsaturated acyl chain;
R3 is a C3 to C30 saturated or unsaturated acyl chain; and
R4 is independently H.
In a MALDI (Matrix-Assisted Laser Desorption/Ionization) mass spectrum, where the compound does not fragment, the location of isotopic labeling generally matters less compared to techniques where fragmentation occurs. However, there are still important considerations:
1. Mass Shift
The purpose of isotopic labeling in MALDI-MS is often to introduce a mass difference between the labeled and unlabeled compound for unambiguous identification or quantification.
As long as the isotope is incorporated into the molecule and does not get lost during ionization, its position typically does not affect the mass shift observed.
2. Ionization Efficiency
The position of the isotope can sometimes influence ionization efficiency due to subtle changes in the molecule's chemical properties. For example:
2H (deuterium) at exchangeable sites (e.g., hydroxyl or amine hydrogens) can undergo back-exchange with the solvent or matrix, potentially reducing the observed labeling.
3. Calibration and Quantification
In MALDI-MS quantitative analysis, isotopically labeled compounds are often used as internal standards. The label should be placed in a non-exchangeable position to ensure that the labeled standard behaves identically to the analyte during ionization and detection.
Since the difference of the location of deuterium substitution between Watkins and the instant claim does not affect the above considerations, the difference is merely a design of choices.
Indeed, in the instant claim 93, the deuterium substitution is on the backbone of sphingolipid.
Regarding claim 88, Watkins discloses that wherein the lysophospholipid includes one or more selected from the group consisting of: lysophosphatidylcholine (LPC), lysophosphatidylethanolamine (LPE), lysophosphatidylsphoserine (LPS), lysophosphatidylglycerol (LPG), and lysophosphatidylinositol (LPI) (par [00105]).
Regarding claim 89 and 101, Watkins discloses that wherein the lysophospholipid species are represented by the general formula II, except the location of the deuterium substitution:
wherein:
R1 is -(CH2)n-N(CH3)3, -(CH2)n-NH3, -(CH2)n-C(H)(NH3)-C(O)-O-, -(CH2)n-CH(OH)-CH(OH), inositol, and H;
n is 1 to 6;
R2 is a C2 to C24 saturated or unsaturated acyl chain; and
R4 is independently H.
As has been discussed regarding claim 87 above, in a MALDI (Matrix-Assisted Laser Desorption/Ionization) mass spectrum, where the compound does not fragment, the location of isotopic labeling generally matters less compared to techniques where fragmentation occurs. However, there are still important considerations:
Since the difference of the location of deuterium substitution between Watkins and the instant claim does not affect the above considerations, the difference is merely a design of choices.
Regarding claim 89, Watkins discloses that wherein the lysophospholipid species are represented by the general formula II, except the location of the deuterium substitution:
wherein:
R1 is -(CH2)n-N(CH3)3, -(CH2)n-NH3, -(CH2)n-C(H)(NH3)-C(O)-O-, -(CH2)n-CH(OH)-CH(OH), inositol, and H;
n is 1 to 6;
R2 is a C2 to C24 saturated or unsaturated acyl chain; and
R4 is independently H.
As has been discussed regarding claim 87 above, in a MALDI (Matrix-Assisted Laser Desorption/Ionization) mass spectrum, where the compound does not fragment, the location of isotopic labeling generally matters less compared to techniques where fragmentation occurs. However, there are still important considerations:
Since the difference of the location of deuterium substitution between Watkins and the instant claim does not affect the above considerations, the difference is merely a design of choices.
Regarding claim 90 and 102, Watkins discloses that wherein the cholesterol ester species are represented by the general formula III, or a pharmaceutically acceptable salt thereof (Fig. 9, par [00144][0051]):
wherein:
R2 is a C9 to C29 saturated or unsaturated acyl chain; and
R4 is independently H or an isotope of H, provided that at least one of R4 is an isotope of H.
Regarding claim 91 and 103, Watkins discloses that wherein the triacylglycerol class includes one or more triacylglycerol species, and wherein the triacylglycerol species are represented by the general formula IV, except the location of the deuterium substitution (Fig. 7, par [0062]):
R2 is a C3 to C30 saturated or unsaturated acyl chain;
R3 are each independently a C3 to C25 saturated or unsaturated acyl chain; and
R4 is independently H.
As has been discussed regarding claim 87 above, in a MALDI (Matrix-Assisted Laser Desorption/Ionization) mass spectrum, where the compound does not fragment, the location of isotopic labeling generally matters less compared to techniques where fragmentation occurs. However, there are still important considerations:
Since the difference of the location of deuterium substitution between Watkins and the instant claim does not affect the above considerations, the difference is merely a design of choices.
Regarding claim 92 and 104, Watkins discloses that wherein the diacylglycerol class includes one or more diacylglycerol species, wherein the diacylglycerol species are represented by the general formula V, except the location of the deuterium substitution:
wherein:
R2 is a C3 to C30 saturated or unsaturated acyl chain;
R3 is a C3 to C25 saturated or unsaturated acyl chain; and
R4 is independently H.
As has been discussed regarding claim 87 above, in a MALDI (Matrix-Assisted Laser Desorption/Ionization) mass spectrum, where the compound does not fragment, the location of isotopic labeling generally matters less compared to techniques where fragmentation occurs. However, there are still important considerations:
Since the difference of the location of deuterium substitution between Watkins and the instant claim does not affect the above considerations, the difference is merely a design of choices.
Regarding claim 93 and 105, Watkins discloses that wherein the ceramide class includes one or more ceramide species, wherein the ceramide species are represented by the general formula VI, or a pharmaceutically acceptable salt thereof (with an isotopically-labeled sphingolipid backbone) (par [0051]):
wherein:
R2 is a C10 to C30 saturated or unsaturated acyl chain; and
R4 is independently H or an isotope of H, provided that at least one of R4 is an isotope of H.
Regarding claim 94, Watkins discloses that wherein the sphingomyelin class includes one or more sphingomyelin species, wherein the sphingomyelin species are represented by the general formula VII, except the location of the deuterium substitution (par [0051]).
As has been discussed regarding claim 87 above, in a MALDI (Matrix-Assisted Laser Desorption/Ionization) mass spectrum, where the compound does not fragment, the location of isotopic labeling generally matters less compared to techniques where fragmentation occurs. However, there are still important considerations:
Since the difference of the location of deuterium substitution between Watkins and the instant claim does not affect the above considerations, the difference is merely a design of choices.
Regarding claim 95-96, Since the difference of the location of deuterium substitution between Watkins and the instant claims do not affect the above considerations, the difference is merely a design of choices.
Regarding claim 100, Walkins does not specifically teach that wherein the plurality of isotopically labeled lipid standards includes
a. 15 phospholipid species, 10 lysophospholipid species, 3 cholesterol ester species, 5 triacylglycerol species, 3 diacylglycerol species, 3 ceramide species, and 3 sphingomyelin species;
b. 20 phospholipid species, 15 lysophospholipid species, 5 cholesterol ester species, 9 triacylglycerol species, 5 diacylglycerol species, 5 ceramide species, and 5 sphingomyelin species; or
C. 25 phospholipid species, 15 lysophospholipid species, 5 cholesterol ester species, 9 triacylglycerol species, 5 diacylglycerol species, 5 ceramide species, and 5 sphingomyelin species.
However, Walkins teaches that “a method is provided for synthesizing one or more mixtures of lipid molecules representative of the composition of lipid molecular species present in one or more corresponding lipid classes in a sample of interest” (par [0007]). Claim 40 of Walkins further teaches that “composition for use as an internal standard comprising one or more mixtures of lipid molecules representative of the composition of lipid molecular species present in one or more corresponding lipid classes in a sample of interest, each mixture of lipid molecules comprising: a lipid backbone having an isotopically-labeled fatty acid at a first position on the lipid backbone, wherein the lipid backbone is for a lipid class having at least two acyl groups; and a mixture of at least two different fatty acids present at a separate position on the lipid backbone, wherein the mixture of fatty acids is representative of the fatty acids that occur in the corresponding lipid class in the sample of interest, and wherein each of the fatty acids in the mixture is present at a ratio representative of the ratio of occurrence of the fatty acid in the lipid molecular species present in the corresponding lipid class in the sample of interest.”. Here, Walkins teaches that the number of isotopically labeled lipid standards are the number of the potential corresponding lipid classes in a sample of interest.
Since Walkins teaches that the number of isotopically labeled lipid standards are the number of the corresponding lipid classes in a sample of interest, it would have been obvious to one ordinary skill in the art to optimize the number of lipid species included in the standards based on the number of the potential corresponding lipid classes in the samples of interest, by routine experimentation. The result is predictable. No inventive step is required.
Response to Arguments
Applicant's arguments filed 04/24/2025 have been fully considered but they are not persuasive.
Applicant argues that “Applicant respectfully disagrees with this rejection because the Examiner did not provide any reason as to why the depicted structures are incorrect and also because the structures are the same structures appearing in the claims of the PCT application. Withdrawal of this objection is requested.” (remark, page 10).
This argument is not persuasive. Claim 90 and 102 recites that “one or more cholesterol ester species represented by the general formula Ill”.
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However, the correct cholesterol ester structure should have two C(R4)3, instead of three C(R4)3.
Applicant argues that “In particular, Applicant points to claim 40 of Watkins in conjunction with claims 47 or 50 of Watkins. Claim 40 teaches an internal standard composition comprising one or more mixtures of lipid molecules representative of a lipid molecular species present in one or more corresponding lipid classes in a sample of interest. Such a claim relies on a person of ordinary skill in the art having analysed a sample of interest to understand which lipid classes are present in the sample and then reverse engineer the internal standard composition accordingly - this understanding is supported by the disclosure of Watkins at paragraph [0043] where the method of producing the mixture is described - this method relies upon the analysis of the sample of interest. As such, claim 40 does not explicitly teach or suggest to a person of ordinary skill in the art that any particular lipid or combination of species of lipids are necessarily present in the internal standard composition of Watkins - instead, given the complexity of the number and types of components, significant experimentation would be required to determine what class or classes of lipids are necessarily provided in the composition. This is not the case with the ULQS of claim 83, and in fact a chief objective of the ULQS of the present invention is that it can be used with no prior knowledge of the sample of interest- it conveniently and desirably provides a "drop in" standard alleviating the user's need to analyze the sample of interest to subsequently design a suitable internal standard and therefore speeds up the sample analysis process considerably.
It is noted that claim 41 of Watkins (which depends from claim 40) makes reference to the possibility of the inclusion (from among a list of many options) of phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), phosphatidylglycerol (PG), or phosphatidylinositol (Pl), but there is no requirement that either of these necessarily be selected, nor is there a requirement that they are selected in combination with a lipid of a different class, and more especially not in combination with at least one lipid species from one or more lipid classes selected from the group consisting of a lysophospholipid class, a cholesterol ester class, a triacylglycerol class, a diacylglycerol class, a ceramide class, and a sphingomyelin class, even less the specific combinations of specific numbers of species represented by these classes of lipids as recited in amended claim 83. It is also noted that claim 47 of Watkins makes reference to inclusion of phosphatidylcholines, but again this is not in combination with any other particular lipid class in accordance with amended claim 83 of the present invention, especially with the recited numbers of species of each of the lipid classes in combination with each other. Applicant submits that the Examiner' position on page 4 of the Office Action that it would have been obvious to one or ordinary skill in the art to optimize the number of the lipid species by routine experimentation is based on improper hindsight and would also require undue experimentation to achieve the specific combinations of components within each of a, b and c as recited in amended claim 83. Withdrawal of this rejection is requested.” (remark, page 11-12).
This argument is not persuasive. Walkins does not specifically teach that wherein the plurality of isotopically labeled lipid standards includes
a. 15 phospholipid species, 10 lysophospholipid species, 3 cholesterol ester species, 5 triacylglycerol species, 3 diacylglycerol species, 3 ceramide species, and 3 sphingomyelin species;
b. 20 phospholipid species, 15 lysophospholipid species, 5 cholesterol ester species, 9 triacylglycerol species, 5 diacylglycerol species, 5 ceramide species, and 5 sphingomyelin species; or
C. 25 phospholipid species, 15 lysophospholipid species, 5 cholesterol ester species, 9 triacylglycerol species, 5 diacylglycerol species, 5 ceramide species, and 5 sphingomyelin species.
However, Walkins teaches that “a method is provided for synthesizing one or more mixtures of lipid molecules representative of the composition of lipid molecular species present in one or more corresponding lipid classes in a sample of interest” (par [0007]). Claim 40 of Walkins further teaches that “composition for use as an internal standard comprising one or more mixtures of lipid molecules representative of the composition of lipid molecular species present in one or more corresponding lipid classes in a sample of interest, each mixture of lipid molecules comprising: a lipid backbone having an isotopically-labeled fatty acid at a first position on the lipid backbone, wherein the lipid backbone is for a lipid class having at least two acyl groups; and a mixture of at least two different fatty acids present at a separate position on the lipid backbone, wherein the mixture of fatty acids is representative of the fatty acids that occur in the corresponding lipid class in the sample of interest, and wherein each of the fatty acids in the mixture is present at a ratio representative of the ratio of occurrence of the fatty acid in the lipid molecular species present in the corresponding lipid class in the sample of interest.”. Here, Walkins teaches that the number of isotopically labeled lipid standards are the number of the potential corresponding lipid classes in a sample of interest.
Since Walkins teaches that the number of isotopically labeled lipid standards are the number of the corresponding lipid classes in a sample of interest, it would have been obvious to one ordinary skill in the art to optimize the number of lipid species included in the standards based on the number of the potential corresponding lipid classes in the samples of interest, by routine experimentation. The Reverse Engineering would have been one obvious way of the routine experimentations. The result is predictable.
Conclusion
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 XIAOYUN R XU, Ph. D. whose telephone number is (571)270-5560. The examiner can normally be reached M-F 8am-5pm.
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/XIAOYUN R XU, Ph.D./ Primary Examiner, Art Unit 1797