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 .
Response to Amendment
Claims 1-2, 5 and 7 have been amended as requested in the amendment filed on 22 May 2026.
Claims 10, 16, 22, 27-29, and 40-43 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected inventions, there being no allowable generic or linking claim.
Claims 1-5 and 7-9 are examined upon their merits.
Withdrawn Claim Objection:
As amended, the objection to Claim 2 is withdrawn because the punctuation has been fixe.
Withdrawn Specification Objection:
The disclosure has been amended to remove the embedded hyperlink and/or other form of browser-executable code.
Withdrawn Claim Rejection - 35 USC § 112(b)
Applicant’s arguments are persuasive to overcome the rejection. Upon further consideration, the term “satisfy” within Claims 1-2 is not subjective judgment without restriction because it is limited by the experimental structural NMR data or small angle X-ray scattering data of the protein (claim 1); or the experimental structural NMR data of the protein (claim 2). All other rejections under 112(b) have been remedied by amendment.
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 1-5 and 7-9 stand as rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more.
Applicants Arguments:
On pages 9-12 of Remarks, Applicant traverses the rejection on the following grounds. Applicant states that the claim when evaluated as an ordered combination amounts to significantly more than what was well-understood, routine and conventional activities before the effective filing date of the application. Applicant further discloses the current amendment reciting “accelerated molecular dynamic simulations” is not a generic recitation of a computer, but is a particular machine and computational methodology. Taken together the claim is unconventional technical solution to address the issues in the in silico field. Specifically, Applicant argues the claims provide a computational pipeline incorporating state-of-the-art enhanced MD method called accelerated MD (AMD) and in-silico peptide design algorithms. AMD, which uses energy rescaling, "capable of accessing timescales in the order of milliseconds, that are beyond the reach of conventional MD." "AMD is used to generate the initial conformational ensemble (e.g., having 50,000 [N-terminal domain (NTD)] conformations)." And "The NTD conformations are clustered by their structural similarity and for each cluster, the root mean square deviation (RMSD) from the experimental NMR CSDs are calculated. The clusters showing low CSD RMSD and a high number of NTD-CTD contacts (e.g., about 1300 conformations) are then selected for further processing." Paragraph [0217] explains that the computational pipeline "is unprecedented, since the NMR data alone only allowed the identification of the [C-terminal domain (CTD)] residues that interact with the NTD, but not the specific NTD structures that contribute to this interaction." Together, the Specification teaches an unconventional improvement in the technology of computational structural biology, namely the ability to generate and filter conformational ensembles of disordered protein domains to identify binding interfaces that were previously inaccessible. The claims, as here amended, cover that improvement by reciting the specific computational methodology (accelerated molecular dynamic simulations) combined with experimental data validation.
Answer to Arguments:
While all of these arguments have been reviewed in full, they are not persuasive to overcome the rejection because the newly added limitation “wherein the enhanced sampling comprises accelerated molecular dynamic simulations” does not provide an improvement in the technology. The following prior art teaches implementation of accelerated molecular dynamics is a widely used technique in the field of computational biology (Wang et al., Comput Sci Discov, 4(1), 2011). The prior art teaches this methodology uses reweighting equations to obtain the free energy profiles of peptides. Wang et al. state: “Achieving sufficient sampling of conformational space represents a challenge for most biologically relevant systems studied using MD simulations. The aMD method tackles this problem by modifying the system’s potential energy landscape and reducing barriers separating different states.” Thus, the prior art teaches this as solving the same issue, improving the specific computational methodology. Therefore, the prior art teaches this was not an “unconventional improvement in the technology” as asserted by Remarks.
For all of these reasons, the claimed steps/elements recited in addition to the judicial exception(s), alone or in combination, do not make an inventive contribution over the methods that were known in the art prior to filing, and they amount to nothing more than the judicial exception(s) itself.
For all of these reasons, the rejection is maintained.
Claim Rejections - 35 USC § 103 (New, Necessitated by Amendment)
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.
Claims 1-5 and 7-9 are rejected under 35 U.S.C. 103 as being unpatentable over Ippel et al., cited on the IDS filed 2 May 2023, in view of Bueren-Calabuig et al., PLoS Comput Biol 11(6): e1004282 (2015).
Applicant’s Arguments:
On the last paragraphs of page 12 of Remarks, Applicant traverses the rejections based upon Ippel and Lin prior art references on the grounds that neither Ippel nor Lin teach or suggest “accelerated molecular dynamic simulations” as now required by instant claim 1.
This amendment warrants further search and consideration of the art, therefore the arguments are moot.
Regarding amended claim 1, the Ippel prior art teaches analysis of the binding between a disordered domain of galectin-3 and an ordered domain within galectin-3, and the ordered domain of ligand proteins and the computer simulations produced from this NMR data (equivalent to “in silico” methods of the claim). The authors obtaining an ensemble of conformations that are analyzed by NMR. The authors identify the amino acids within those conformations that affect binding between the disordered domains of galectin-3 and ordered domains within itself or within ligands. Specifically, Galectin-3 has a modular design comprising an N-terminal tail (NT, residues 1-111) and a conserved carbohydrate recognition domain (CRD, residues 112-250). The authors create chimera-type galectins that interacts with both glycan and peptide motifs. The authors perform complete 13C/15N-assignment of the human protein and perform NMR-based analysis of its structure beyond the CRD. Using two synthetic NT polypeptides covering residues 1-50 and 51-107, evidence for transient secondary structure (equivalent to “identifying a first set of structural conformations from the ensemble” of the instant claim) was found with helical conformation from residues 5 to 15 as well as proline-mediated (which reads on “identifying a first amino acid within the first set of structural conformations” of the instant claim), multi-turn structural conformation from residues 18 to 32 and around PGAYP repeats. Intramolecular interactions occur between the CRD F-face, which is the 5-stranded beta-sheet behind the canonical carbohydrate-binding 6-stranded beta-sheet of the S-face) and NT. This teaches binding analysis of domains within the protein itself. The authors identify the sequence P23GAW26 ... P37GASYPGAY45 as the region that defines the primary binding epitope within the NT. Further, the authors identify the PGAX motif is crucial for self-interactions between NT/CAD. Finally, galectin-3 molecules can interact weakly with each other via the F-faces of their CRDs, and this interaction appears to be assisted by their NTs. The authors conclude: “our results add insight to defining binding sites on galectin-3 beyond the canonical contact area for beta-galactosides” [ABSTRACT].
Regarding claim 3, Ippel Figure 2 demonstrates clustering the structural conformations by structural similarity to identify a template peptide (Fig. 2C).
Regarding claims 4 and 5, through 13C/15N-assignment over the entire protein, the Ippel prior art identifies the PGAX motif is crucial for galectin-3 self-interactions between NT/CAD. This teaches the method further comprising identifying at least a first amino acid within the first set of structural confirmations. The data demonstrate these residues are crucial for the interaction between domains of the same protein. The authors identify a proline-mediated (which reads on “identifying at least a first amino acid” of the instant claim) and PGAYP repeats within residues 18 to 32 mediate these confirmations. This fulfills the new limitation of Claim 5 “comprises the first amino acid” namely proline, “and a second amino acid”, namely the full PGAX motif, that is crucial for self-interactions between NT/CAD.
Regarding claim 8, the Ippel reference teaches methods comprising designing a plurality of template peptides that bind in silico to at least one amino acid in the ordered domain (see Figure 2C )based at least in part on the first set of structural conformations (see Figures 2 A and B). The authors use NOE(SY) or nuclear Overhauser effect spectroscopy to examine resonance assignments for NT peptide 1-50 made by using standard 1H homonuclear protocols, primarily based on DlPSI and NOESY data. This teaches in silico mutating each amino acid residue of each of the plurality of template peptides thereby producing a plurality of mutant peptides and selecting a set of candidate peptides from the plurality of mutant peptides based on in silico binding, as claimed. The authors then synthesize each of the set of candidate peptides thereby producing a set of synthesized candidate peptides; and experimentally measuring the effect of each of the synthesized candidate peptides on galectin-3 intramolecular binding.
Regarding claim 9, the authors specifically look at intramolecular binding of the domains within galectin-3 (see Figure 4, which demonstrates NMR spectra for the Gal-3 CRD [carbohydrate recognition domain], which is in the ordered C-terminal domain, in the absence and presence of NT peptide, which comprises the intrinsically disordered domain). Therefore, the effect that the prior art looks at is binding, as claimed.
The only element that is missing from the Ippel et al. reference is the use of accelerated molecular dynamic (aMD) simulations during enhanced sampling, as required by the newly added limitation of Claim 1. However the Bueren-Calabuig et al. prior art reference remedies this deficiency. Bueren-Calabuig teach unstructured protein regions present challenges for enhancing the affinity of a lead molecule in the context of rational drug design. Bueren-Calabuig teach conformational ensembles for the disordered lid region of the N-terminal domain of the oncoprotein MDM2 in the presence of different ligands was performed by a novel combination of accelerated molecular dynamics, umbrella sampling, and variational free energy profile methodologies (Abstract). Specifically, Bueren-Calabuig state: “interactions between proteins involve very flexible protein regions. These disordered regions may undergo disorder/order transitions upon forming an interaction with another protein. Many successful approaches to medicinal chemistry are based on mimicking the interactions of biological molecules with man-made small molecules. However how drug-like small-molecules may modulate protein disorder is currently poorly understood, largely because it is difficult to measure in details this type of interaction with experimental methods. Here we have used computer simulations to resolve with great details the process by which different small-molecules modulate the flexibility of a disordered region of the protein MDM2. This protein is overexpressed in many cancers and small molecules that recognize MDM2 have been developed over the last decade as possible novel anti-cancer agents. We show that the flexible MDM2 “lid” region adopts different conformational states in the presence of different small-molecules. Our results suggest why some classes of small-molecules form favorable interactions with the lid region, whereas others do not. These findings may prove crucial to develop new and more effective MDM2 inhibitors, and more generally to help drug designers target disordered proteins regions with small-molecules” (Author Summary). The reference discloses sampling simulations (Figure 1) and observed “enhanced conformational fluctuations” with aMD (S1 Fig). The authors conclude, the simulations predict a higher population of open states than the NMR data, though the agreement is still reasonable (pg. 4/27, last paragraph). This specifically teaches the limitation “conformations that satisfy the experimental structural NMR data” of instant claims 1 and 2.
Regarding claim 7, the Bueren-Calabuig et al. methodology teaches the molecular dynamics of the instant claim.
It would have been obvious to a person having ordinary skill in the art, before the effective filing date of the application, to use the aMD sampling simulations as taught by Bueren-Calabuig et al., in the methods for determining conformation ensembles, as taught by Ippel et al. Motivation to use aMD is explicit within the Bueren-Calabuig reference wherein it teaches “enhanced conformational fluctuations” were observed using aMD and that the simulations confer the distinct advantage of predicting a higher population of open states than the NMR data alone, though the agreement with the NMR data is still reasonable. Given the guidance and direction in the prior art references, a skilled artisan would have been able to combine the two methodologies with predictable success in identifying in silico at least one amino acid that underlies binding within the disordered domains of galectin-3 and ordered domains within itself or within ligands.
Therefore the invention of Claims 1-5 and 7-9 fails to distinguish over the methods disclosed in the prior art.
As currently amended, Claims 1 and 7-9 is are rejected under 35 U.S.C. 103 as being unpatentable over Lin et al., cited on the ISR filed 2 May 2023, in view of Bueren-Calabuig et al. cited above.
Applicant’s Arguments:
On page 12 of Remarks, Applicant traverses the rejections based upon the Lin prior art reference on the grounds that Lin does not teach or suggest “accelerated molecular dynamic simulations” as now required by instant claim 1.
This amendment warrants further search and consideration of the art, therefore the arguments are moot.
Regarding claim 1, Lin et al teach methods comprising, in silico, performing an enhanced sampling of a disordered domain of a protein binding to an ordered domain of the same protein. Specifically, Lin et al. teach, “Ten thousand randomized NTD conformers attached to the CRD were generated using flexible -MECCANO” modelling (pg. 17854, second column, Modelling). The authors use this in silico modelling to select ensembles (pg. 17854, second column, Modelling) and then identifying a set of structural conformations from the ensemble of conformations that satisfy the known experimental structural NMR data (see pg. 17853, first column, NMR experiments and Figure 7). The authors further identifying the amino acids within the disordered domain of the protein (the N-terminal) that bind to the ordered domain the (CTD) of the same protein, Galectin-3 (see Figure 6).
Regarding claim 7, the Lin reference teaches the enhanced sampling simulation comprising Monte Carlo of the instant claims (pg. 17853, first column, NMR experiments, wherein it states “Peak intensities were fitted to exponential decays with a Monte Carlo procedure to estimate fitting error.”
Regarding claim 8, the Lin et al. prior art teaches designing a plurality of template peptides that bind in silico to at least one amino acid in the ordered domain based at least in part on the first set of structural conformations, wherein it teaches “Ten thousand randomized [N-terminal domain] NTD conformers attached to the CRD were generated using flexible -MECCANO” modelling (pg. 17854, second column, Modelling). The prior art produces a plurality of N-terminal and CRD truncations (equivalent to a “a plurality of mutant peptides” of the instant claim; See Figure 3 for a summary of truncation mutants). The authors actually synthesizing each of the set of candidate peptides (see pgs. 17852-53 sections titled DNA constructs and Protein expression and purification) thereby producing a set of synthesized candidate peptides (see Figure 3 for these mutant peptides). The Lin prior art experimentally measuring the effect of each of these synthesized candidate peptides on intramolecular Galectin-3 binding (see Figure 3, Figure 5 – NMR paramagnetic relaxation studies, and Figure 6 – Hydrophobicity drives self-association of galectin-3).
Regarding claim 9, Lin et al. specifically look at intramolecular binding of the domains within galectin-3, wherein it states: “Here we used NMR spectroscopy, mutagenesis, small-angle X-ray scattering, and computational modeling to study the self-association-related multivalency of galectin-3 at the residue-specific level. We show that the disordered N-terminal domain (residues ~20-100) interacts with itself and with a part of the [carbohydrate recognition domain] CRD not involved in carbohydrate recognition (beta-strands 7-9; residues ~200-220)” [ABSTRACT]. Therefore, the effect that the prior art looks at is binding, as claimed.
The only element that is missing from the Lin et al. reference is the use of accelerated molecular dynamic (aMD) simulations during enhanced sampling, as required by the newly added limitation of Claim 1. However, the Bueren-Calabuig et al. prior art reference remedies this deficiency. Bueren-Calabuig teach unstructured protein regions present challenges for enhancing the affinity of a lead molecule in the context of rational drug design. Bueren-Calabuig teach conformational ensembles for the disordered lid region of the N-terminal domain of the oncoprotein MDM2 in the presence of different ligands was performed by a novel combination of accelerated molecular dynamics, umbrella sampling, and variational free energy profile methodologies (Abstract). Specifically, Bueren-Calabuig state: “interactions between proteins involve very flexible protein regions. These disordered regions may undergo disorder/order transitions upon forming an interaction with another protein. Many successful approaches to medicinal chemistry are based on mimicking the interactions of biological molecules with man-made small molecules. However how drug-like small-molecules may modulate protein disorder is currently poorly understood, largely because it is difficult to measure in details this type of interaction with experimental methods. Here we have used computer simulations to resolve with great details the process by which different small-molecules modulate the flexibility of a disordered region of the protein MDM2. This protein is overexpressed in many cancers and small molecules that recognize MDM2 have been developed over the last decade as possible novel anti-cancer agents. We show that the flexible MDM2 “lid” region adopts different conformational states in the presence of different small-molecules. Our results suggest why some classes of small-molecules form favorable interactions with the lid region, whereas others do not. These findings may prove crucial to develop new and more effective MDM2 inhibitors, and more generally to help drug designers target disordered proteins regions with small-molecules” (Author Summary). The reference discloses sampling simulations (Figure 1) and observed “enhanced conformational fluctuations” with aMD (S1 Fig). The authors conclude, the simulations predict a higher population of open states than the NMR data, though the agreement is still reasonable (pg. 4/27, last paragraph). This specifically teaches the limitation “conformations that satisfy the experimental structural NMR data” of instant claims 1 and 2.
It would have been obvious to a person having ordinary skill in the art, before the effective filing date of the application, to use the aMD sampling simulations as taught by Bueren-Calabuig et al., in the methods for determining conformation ensembles, as taught by Lin et al. Motivation to use aMD is explicit within the Bueren-Calabuig reference wherein it teaches “enhanced conformational fluctuations” were observed using aMD and that the simulations confer the distinct advantage of predicting a higher population of open states than the NMR data alone, though the agreement with the NMR data is still reasonable. Given the guidance and direction in the prior art references, a skilled artisan would have been able to combine the two methodologies with predictable success in identifying in silico at least one amino acid that underlies binding within the disordered domains of galectin-3 and ordered domains within itself or within ligands, as claimed.
Therefore, the method of the instant claims fails to distinguish over the methods disclosed in the prior art, and Claims 1 and 7-9 are rejected.
Conclusion
No claim is allowed.
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.
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/STACEY N MACFARLANE/Examiner, Art Unit 1675
/KIMBERLY BALLARD/Primary Examiner, Art Unit 1675
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