Patent Grant
12024539
Key words/phrases: US and foreign patent search on peptide inhibitors for amyloid beta (google.com); Peptide inhibitors for amyloid beta (Google.com and PubMed.gov (NCBI) search); Peptide inhibitors and amyloid beta; peptide inhibitors and amyloid beta precursor protein; peptide inhibitor and gamma secretase; peptide inhibitor and presenilin1; peptide inhibitor and nicastrin (NCBI PubMed.gov).
Dementia is a dreadful outcome of neurodegeneration caused due to deposition of aggregated amyloid beta in various parts of brain of elderly people (24, 25, 26). Alzheimer's dementia is one of the forms which warrants medical care and treatment for cure. The FDA approved marketed Alzheimer's drugs are the modifiers of neurotransmitters and facilitate learning and memory function of brain (4, 23). But these drugs, though helpful, cannot prevent or minimize deposition and aggregation of amyloid beta (AB) in extracellular areas of brain thus, cannot block progressive neurodegeneration.
We took mission to construct peptide(s) as new therapeutic interventions to prevent or reduce generation, aggregation, and deposition of amyloid beta (1-42) responsible for Alzheimer's and related dementia. We performed extensive literature survey to find primarily any patented compound or drug either same or similar to the proposed invention we claim herewith.
We chose two search engines: www.google.com and www.pubmed.gov to find patented and peer reviewed published articles which could possibly demonstrate any peptides same or similar to the invented ones in this claim. Accordingly, we found 438000 scholarly articles using the key words mentioned above in this section. The US National Library of Medicine (NCBI) search engine www.pubmed.gov exhibited 8595 articles in the form of abstracts and/or full text formats. Amongst all these cross references, we found a reference: Findeis M A et al. 2001 Amyloid, 8 (4): 231-241; (PMID: 11791615) [page 5, Cross Reference Number 6] and related a few references claimed a pentapeptide inhibitor protein for amyloid beta. The published inhibitor peptide sequence is: Cholyl-LVFFA-OH [SEQ ID 20]. This sequence has similarity with one of the amyloid beta peptide sequences: HHQKLVFFAE [SEQ ID 9] we constructed for our project (Aβ chain L, 10-20). Except this one, none of our constructed peptides shows any similarity with any published or patented documents. Another PubMed.gov article (PMID 30886570) showed potential role of sequence GGVVIA [SEQ ID 21] of amyloid beta peptide in aggregation and inhibitor targeted to this sequence is beneficial in treatment of Alzheimer's disease. The sequence GGVVIA [SEQ ID 21] is a partial amyloid beta sequence we are using: GLMVGGVVIA [SEQ ID 7]. However, the non-homologous peptide construct which we propose as invention, is completely different than any of the published article. We propose the sequence GLRVEDAVIA [SEQ ID 2] as invented peptide construct [I-A β1 (32-42)].
We found eighty cross references separately when took the pentapeptide sequence: KLVFF [SEQ ID 22] as key word. All these references cited in PubMed search engine are directed towards inhibition of aggregation and deposition of amyloid beta.
We claim on one of the invented peptide sequences: QHDCLCFSGE [SEQ ID 4] is constructed and evaluated as interactive, form dimer complex with amyloid beta peptide sequence fragment: HHQKLVFFAE (ANN47479.1; 2MXU_L) [Seq ID 9] in overlay computer modeling. We define the physical parameters (hydrophobicity, dipole moments, number of atoms, number of bonds) to confirm that the overlay chemical structures are indeed interactive dimer forms of two non-homologous peptides obtained by computer modeling only.
We propose here five non-homologous peptide sequences with different physical parameters (hydrophobicity, dipole moment, number of atoms, number of bonds) constructed to interact with amyloid beta protein fragments (Table1) and three non-homologous sequences are constructed to interact with fragmented APP sequences (Table3).
We selected the most relevant cross references (numbers 1-3; 5-22: presented separately. References 4, 23-26 are general references) depicting short amino acid sequence of amyloid beta peptide and use it in different forms to establish effect of inhibitors targeted those sequences to reduce amyloid beta aggregation and deposition. The screened publications from different laboratories since 1990 till November 2019 exhibit very few references on constructing peptide-drug for Alzheimer's dementia. None of the published articles show equivalence or similarity with the invented peptides proposed in the application. However, the cross references raise importance to the proposed peptide constructs as contemporary evidence.
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[Sequence listing text file: Sequencelisting_ST25 (size: 4734 bytes); Created Feb. 28, 2024].
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Dementia is a combinatorial outcome of different clinical manifestations developed due to degenerative conditions of neurons in various parts of human brain. The major causative agent is amyloid beta (AB) [24,25,26]. The amyloid beta Aβ (amino acids 1-42) is generated by specific cleavage of transmembrane (intramembrane) fragment of amyloid precursor protein by a protein degrading enzyme (protease), called gamma secretase (GSA). The Aβ (1-42) thus produced accumulate inside brain cells (neurons and astrocytes) and secrete out latter, form aggregate and deposit in different areas of brain. Chronic deposition of Aβ (1-42) is associated with abnormal function and neurodegeneration in different areas of human brain which regulate learning capability, retention of memory, language, and speech—as found in Alzheimer's and related diseases. Still today, there is no [effective] treatment to reduce Aβ aggregation and deposition.
Current Alzheimer's drugs improve learning and memory by modifying neurotransmitter acetylcholine and receptor recognition of N-methyl D-aspartate (NMDA), a small biomolecule without any alteration of Aβ aggregation and deposition. Thus, the currently available drugs improve clinical condition by delaying the severe outcome but there is no prevention of progression of Alzheimer's disease.
The current alarming context prompted to reconsider drug discovery program for dementia, define specifics of compounds, development of new or modified therapeutic interventions. The invention of non-homologous peptides interactive to fragmented amyloid beta and its precursor protein APP by computer modeling is the first stage or platform1 for the organization NeuroDrug Research LLC in the way of Alzheimer's drug discovery research.
There are multiple parameters need attention to develop preventive strategy for dementia and Alzheimer's neurodegeneration. These are, (i) to block aggregation and deposition of Aβ (1-42); (ii) to block amyloid beta precursor protein (APP) from specific cleavage; and (iii) to block catalytic site of transmembrane (intramembrane) protease enzyme gamma secretase (GSA). We strategically consider all three target points as mentioned in platform 1.
We choose first computer modeling and biophysical parameters (hydrophobicity, dipole moments) to synthesize new non-homologous peptide sequences. Here, our objective is to determine whether the invented non-homologous peptide [(inhibitor)] sequences demonstrate to form complex/dimer with fragmented sequences of either Aβ or APP and whether fragmented APP sequences can form dimer with selected GSA peptides.
We consider the change in physical parameters (hydrophobicity, dipole moments) in complex or dimerized chemical structure(s) generated by using fixed z-axis overlay computer modeling system. As, the alterations in physical parameters of two single peptides in dimerized/complex structure are indication of close interaction and bond formation between them in their new chemical structure.
The objective of the platform1 is to develop new non-homologous peptide [(inhibitor)] sequences and allow these to form complex/dimer structure with either amyloid beta (AB) or its precursor protein fragments (APP) by using computer modeling. The ball and stick three-dimensional structure configurations of each peptide are constructed individually by computer model system and taken to overlay on fixed z-axis with different protein fragments of Aβ and APP to generate a complex/dimer chemical structure. The physical parameters like hydrophobicity, dipole moments, number of atoms and bonds of each individual interacting peptide are recorded and compared with those in computer generated dimer chemical structures.
The attempt is also made to determine ability of defined fragmented APP sequences to form complex/dimer structure with peptide sequences derived from components of gamma secretase enzyme: presenilin1 (PSEN1) and nicastrin (Nicas). In the platform 1 stage, we invented peptide sequences (ID: Neursdg001 to 005): [(SEQ ID: 1-5)] and (I-APPa-Neursdg006; I-APPb-Neursdg007; I(2)-APPc Neursdg008): [(SEQ ID: 11-13)] interact with fragmented Aβ peptides [(SEQ ID: 6-9)] and APP sequences [(SEQ ID: 14-16)], respectively.
The invented peptide sequences with identifying numbers I-aβ (highlighted rows) and sequence IDs are presented in Table1-5 under detailed description of the invention. These peptide sequences are presented as covalently bonded amino acid sequences and by convention read from amino (NH2) terminal to carboxyl (COOH) terminal amino acids. The brief descriptions of invented peptides with drawings/figures are below:
The abovementioned invented peptide sequences presented in Table1 are tested by computer modeling for fixed z-axis overlay to determine dimer structure formed with fragmented amyloid beta peptides (amyloid beta chain A and L). The Table 2 shows the test results.
The Table3 presents invented peptide sequences (I-APP a, b, and c) amyloid beta precursor peptide. The invented I-APP peptides are presented below:
Likewise, the other invented I-APP peptides are:
The invented I-APP peptide sequences [(SEQ ID: 11-13)] are also tested individually by using computer modeling and fixed z-axis overlay to determine whether they form dimer structures with APP fragments a, b and c [(SEQ ID: 14-16)] derived from protein database.
The Tables 2, 4 and
Descriptions of the dimeric structure figures are presented below:
A. Identification of Amyloid Beta (Aβ) Peptide Sequence from Protein Database
The invented five different peptides are designed by random shuffling of amino acid sequences by computer modeling technique (Table1). These peptide sequences are non-homologous to protein database derived amyloid beta sequences. The physical parameters like hydrophobicity, isoelectric point (pH) of the peptides is determined by using freely available software called, Pepdraw. The dipole moments, number of atoms and number of bonds of the same sequences are obtained by using another free software (Avogadro). The computer modeling is used to obtain three-dimensional overlay form of chemical structures of dimerized/complexed peptides. The dipole moment and hydrophobicity values with number of atoms and bonds in single peptides are obtained automatically from computer derived sequence analysis and documented in Table 1. The highlighted sequences are the invented peptides under proposition.
These invented peptides are tested for formation of dimer structure in fixed axis overlay modeling. Table2 and figures presented the constructed dimers formed by overlay of Z-axis aligned non-homologous peptide and amyloid beta peptide fragments.
9.A.1. Procedures for Constructing Invented Peptide Sequences.
Step 1. Selection of Appropriate Database in NCBI PubMed Site.
In NCBI PubMed, protein database has been selected for the purpose. The key word for feeding search engine is “HUMAN AMYLOID BETA” OR “HOMO SAPIENS AMYLOID BETA.” By clicking “enter” button, the search engine will lead to a page source which contains 2949 related and unrelated information on protein sequences.
We selected a Genebank resource title: amyloid beta A4 protein isoform a precursor [Homo sapiens].
The Accession number: ANN47479.1 and Gene Identity: 1040736956 are recorded.
Step II. Selection of Protein Sequence from Database.
We selected the 770 amino acid sequence (Coding Sequence: CDS 1-770) for screening out 42 amino acid amyloid beta sequence ranging from 661 amino acid position to 771.
Step III. Run Protein Blast.
The 770 amino acid sequence was fed into Blast engine for analysis and homology determination. The protein blast of this non redundant (nr) sequence (blastp) is run under specific job title.
The description section of the Blastp search engine provides one hundred related sequences.
Step IV. Selection of Protein Sequence ANA47479.1 and go for Alignment.
The Alignment search engine provides several sequence IDs with different matches in a wide range of related sequences found in mammalian system. The sequence ID ANN47479.1 is selected as desired sequence and saved separately.
In order to confirm the amyloid beta peptide sequence from the ANN47479.1 sequence, the protein data base PDB 2MXU_L is searched in addition. The search result in NCBI protein database will exhibit “Chain L, Amyloid beta A4 protein”.
This is the 42 amino acid amyloid beta peptide sequence used as template to design: unique non-homologous peptide and allowed to form dimer shown by computer modeling software.
Step V. The Design of Unique Peptides (Neursdg001-005) Corresponding to Randomized Fragmented 42 Amino Acid Amyloid Beta Sequences (I-A β-A Chain A and I-A β1, 2, 3, 4a Chain L).
The 42 amino acid amyloid beta (Aβ) peptide was fragmented into 10 amino acid containing sequences obtained from different protein data base sources (NCBI). The I-Aβ-A (Neursdg001) is obtained from PDB: 1QCM_A (chain A). The rest sequences are from chain L (2MXU_L) (Table 1).
The amino sequence of each I-A-β peptide (highlighted in Table 1) has been shuffled randomly and put in a software PepDraw (free software). The software provides length, mass, isoelectric point (pH at which net charge is neutral), net charge, hydrophobicity, and extinction coefficient.
9.A.2. Experiment by Using Overlay Computer Modeling to Determine Interaction Between Non-Homologous Invented Peptides and Fragmented Amyloid Beta Peptides.
9.A.2.i. Test to Determine Overlay Pattern of Invented Non-Homologous Peptide and Amyloid Beta Peptide Fragment at Fixed Aligned Z-Axis to Form Dimer in Computer Model.
The constructed novel I-Aβ peptides and 10 amino acid Aβ peptide sequences are analyzed in Avogadro peptide analysis and drawing software (free software) individually. The ball and stick three-dimensional structure models are used to construct the single and overlay dimerized peptide structures. The number of atoms and bonds in the structure are calculated automatically by the software system. The estimated dipole moment (measure of net polarity of positive and negative charge in an inorganic or organic compound) for each peptide and overlaid dimer structure are calculated and presented by the software (Table 2). The figures of each dimer are presented after Table 2 for invented peptides interact with amyloid beta.
Outline of Avogadro software operation. The Avogadro software has provision to calculate bond length and number of atoms in the structure. The automatic calculations are found under “view” section within “property” sub section of the software. The “build” section and “peptide” sub section within it are used to construct peptide structure for analysis.
#Dipole moment (D) defines separation of charges or partial charges in an inorganic or organic compound.
9.A.2.ii. Test to Determine Overlay Pattern of Invented Peptide and Amyloid Beta Precursor Protein (APP) Fragment at Fixed Aligned Z-Axis to Form Dimer in Computer Model
In a similar procedure, the non-homologues peptide sequences are constructed for amyloid precursor protein (APP). The key word phrases “Amyloid precursor protein and Homo sapiens” are used to search contents in protein database (NCBI PubMed). The sequence ID AAB26265.2 Length 82; NP_000475.1 Length 770 are selected to screen efficacy of invented peptide sequences to form dimer. All these and invented non-homologous peptides (highlighted) are presented in Table3.
The computer modeling overlay of the non-homologous peptides with corresponding APP sequence template to form dimer construct structural formula is shown in the Table 4.
#Dipole moment defines separation of charges or partial charges in an inorganic or organic compound.
The amino acid sequence IDs are provided in the left column—Sequence (Table 3).
9.A.2.iii. Test to Determine Overlay Pattern of Amyloid Beta Precursor Protein (APP) Fragment and Peptide Sequences Selected from Presinilin1 (PSEN1) and Nicastrin Components of Enzyme Gamma Secretase at Fixed Aligned Z-Axis to Form Dimer in Computer Model
In addition, we analyze the physical parameters and use computer modeling to evaluate if the protein database derived fragmented APP sequences (APP a, b, and c) form any dimer/complex with components of protease enzyme gamma secretase (GSA): presinilin1 (PSEN1) and nicastrin (Nicas). The concept is, the substrate APP must bind with catalytic side of GSA to form an enzyme-substrate complex which lower the reaction energy level and catalyze the reaction to drive forward to form product. The experiment will determine the closest interaction and/or dimer formation between NCBI database derived APP sequences (a, b, c) and PSEN1 (b, c) or Nicas (a1) sequences.
Table5 presents the identified APP, PSEN1 and nicastrin sequences and their overlaid composite dimer structures constructed by computer modeling taking a fixed Z-axis.
The chemical structures of dimers found following overlay of two non-homologous peptide sequences in a fixed z-axis are mentioned in the Table5 check boxes.
This has been found; the identified APP sequences interact with selected PSEN1 and nicastrin sequences and exhibit formation of a dimer with alteration in their individual dipole moment, number of atoms and number of bonds. The sequence IDs for each amino acid sequences are mentioned in the parenthesis in the left-Gamma Secretase component-column (Table 5).
9.B. Analysis of Observations
The computer modeling is used to identify interaction of non-homologues invented peptides with parent amyloid beta or its precursor protein sequences. The two freely available educational software systems Pepdraw and Avogadro are used [initially] to determine peptide length, mass, hydrophobicity, isoelectric point, dipole moment, number of atoms and bonds formed in single as well as computer modeling derived dimer peptide constructs. As we see, the hydrophobicity and dipole moment are inversely related for a peptide or protein molecule.
| Number | Date | Country | |
|---|---|---|---|
| 62941021 | Nov 2019 | US |
