Information processing device, information processing method, and program

Abstract

To provide an information processing device, information processing method, and program, which can be used to evaluate an antigenicity of a target peptide.SOLUTION: An information processing device disclosed herein is configured to perform steps including a first evaluation step of evaluating antigenicity of a candidate peptide based on contribution of each amino acid of the candidate peptide to antigenicity, where the contribution to antigenicity represents contribution computed from three-dimensional structure data of an antigen-antibody complex based on amino acid residues of epitope residues on the antigen interacting with the antibody.SELECTED DRAWING: Figure 7

Description

[Technical field]

[0001] The present disclosure relates to an information processing device, an information processing method, and a program. [Background technology]

[0002] In order to obtain antibodies against a specific amino acid sequence in a protein, it is common to administer a peptide having the amino acid sequence to a recipient such as an animal, thereby inducing the production of antibodies against a polypeptide consisting of the specific amino acid sequence (Non-Patent Document 1). [Prior art documents] [Non-patent literature]

[0003] [Non-Patent Document 1] Takeo Tanaka et.al., “Efficient generation of antibodies to oncoproteins by using synthetic peptide antigens”, Proc.Nati.Acad.Sci.USA, Vol.82, pp.3400-3404 Summary of the Invention [Problem to be solved by the invention]

[0004] However, in the subject of administration, antibody production against all peptides is not necessarily induced, and antibody production against the peptide of interest may not be induced. Furthermore, although the peptide used for immunization is designed taking into consideration the hydrophilicity, solubility in solvents, secondary structure, etc. of the peptide, this is not necessarily linked to the antigenicity of the peptide.

[0005] Therefore, an object of the present disclosure is to provide an information processing device, an information processing method, and a program that can be used to evaluate the antigenicity of a target peptide. [Means for solving the problem]

[0006] In order to achieve the object, the information processing device of the present disclosure includes a first evaluation step of evaluating antigenicity of a candidate peptide based on antigenicity of each amino acid of the candidate peptide, The contribution to antigenicity is calculated based on amino acid residues of epitope residues on the antigen that interact with the antibody, from data on the three-dimensional structure of an antigen-antibody complex.

[0007] The information processing method of the present disclosure includes a first evaluation step of evaluating the antigenicity of a candidate peptide based on the contribution of each amino acid to the antigenicity of the candidate peptide, The contribution to antigenicity is calculated based on amino acid residues of epitope residues on the antigen that interact with the antibody, from data on the three-dimensional structure of an antigen-antibody complex.

[0008] The program of the present disclosure is provided to a computer. executing a first evaluation process for evaluating the antigenicity of a candidate peptide based on the contribution of each amino acid to the antigenicity; The contribution to antigenicity is calculated based on amino acid residues of epitope residues on the antigen that interact with the antibody, from data on the three-dimensional structure of an antigen-antibody complex. Effect of the Invention

[0009] According to the present disclosure, the antigenicity of a peptide of interest can be assessed. [Brief description of the drawings]

[0010] [Figure 1] FIG. 1 is a block diagram showing an example of an information processing system including an information processing device according to the first embodiment. [Diagram 2] FIG. 2 is a block diagram showing an example of a hardware configuration of the information processing apparatus according to the first embodiment. [Diagram 3] FIG. 3 is a flowchart showing an example of the information processing method and program according to the first embodiment. [Figure 4] FIG. 4 is a block diagram showing an example of an information processing system including an information processing device according to the second embodiment. [Diagram 5] FIG. 5 is a flowchart showing an example of an information processing method and program according to the second embodiment. [Figure 6] FIG. 6 is a flowchart showing an example of an information processing method and program according to the second embodiment. [Figure 7] FIG. 7 is a graph showing the maximum antibody titer after the first immunization of the antisera obtained by immunization with each antigen peptide in Example 1. [Figure 8] FIG. 8 is a graph showing the antibody titers of antisera obtained by immunization with each antigen peptide in Example 2. [Figure 9] FIG. 9 is a graph showing the antibody titers of antisera obtained by immunization with each antigen peptide in Example 2. [Figure 10] FIG. 10 is a graph showing the cross-reactivity of each antisera in Example 2. [Figure 11] FIG. 11 is a graph showing the cross-reactivity of each antisera in Example 2. [Figure 12] FIG. 12 is a graph showing the antibody titers of antisera obtained by immunization with each antigen peptide in Example 3. [Figure 13] FIG. 13 is a graph showing the antibody titers of antisera obtained by immunization with each antigen peptide in Example 3. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0011] <Definition> In this disclosure, a "protein" refers to a polymer composed of unmodified amino acids (natural amino acids), modified amino acids, and / or artificial amino acids, for example, a peptide having a length of 10 amino acids or more. Also, in this disclosure, a "peptide" refers to a polymer composed of unmodified amino acids (natural amino acids), modified amino acids, and / or artificial amino acids.

[0012] In this disclosure, "antibody" refers to a protein comprising one or more polypeptides substantially or partially encoded by immunoglobulin genes or fragments of immunoglobulin genes. The antibody may be a full-length immunoglobulin or an antigen-binding fragment thereof.

[0013] In the present disclosure, "antigen" refers to a substance that can induce antibodies in vivo, either alone or in complex with other molecules.

[0014] In the present disclosure, "antigenicity" refers to the property of being able to elicit or induce a humoral immune response or antibody production when administered to a living body. The antigenicity is also referred to, for example, as immunogenicity.

[0015] In this disclosure, "epitope" means the site on an antigen to which an antibody binds.

[0016] In the present disclosure, the term "subject to be administered" refers to an animal or a cell, tissue or organ derived from an animal, and is used to mean a human being in particular. The animal refers to a human being and a non-human animal. The non-human animal includes, for example, a mammal such as a mouse, a rat, a rabbit, a dog, a cat, a cow, a horse, a pig, a monkey, a dolphin, a sea lion, a camel, etc.; an avian animal such as a chicken; a fish such as a shark, etc.

[0017] Hereinafter, the present disclosure will be described in detail with reference to the drawings, giving examples. However, the present disclosure is not limited by the following description. In addition, in the following Figs. 1 to 6, the same parts may be given the same reference numerals, and their description may be omitted. In addition, in the drawings, for convenience of description, the structure of each part may be appropriately simplified, and the dimensional ratio of each part may be shown schematically, different from the actual one. In addition, each embodiment and description can be mutually referred to unless otherwise specified. In addition, when the expression "~" is used in this specification, it is used to mean including the numerical value or physical value before and after it. In addition, in this specification, the expression "A and / or B" includes "A only", "B only", and "both A and B".

[0018] (Embodiment 1) This embodiment is an example of an information processing system including an information processing device of the present disclosure. As shown in FIG. 1, an information processing system 100 of this embodiment includes an information processing device 1. The information processing device 1 includes an acquisition unit 11, an analysis unit 12, a calculation unit 13, a first evaluation unit 14, and a first selection unit 15. As shown in FIG. 1, in the information processing system 100, the information processing device 1 can be connected (can communicate) with a three-dimensional structure database (DB) 2 in one or both directions via a communication line network 3 outside the system. The number of three-dimensional structure DBs 2 to which the information processing device 1 can be connected may be one, as shown in FIG. 1, or may be multiple. In the first embodiment, the information processing device 1 is configured as a server.

[0019] The information processing device 1 of the present embodiment may be incorporated in a personal computer (PC) in which the program of the present disclosure is installed, or in a server or the like as a system. The information processing device 1 of the present embodiment may also be a system consisting of one or more computers or servers capable of executing the program of the present disclosure, that is, a cloud computing system. The personal computer may constitute a computer cluster. Although not shown, the information processing device 1 may be configured to be connectable to an external terminal of a system administrator via a communication line network 3, so that the system administrator can manage the information processing device 1 from the external terminal. In the present embodiment, the information processing system 100 includes one information processing device 1, but each of them may be multiple.

[0020] The three-dimensional structure DB2 is a database server in which a plurality of data on the three-dimensional structure of an antigen-antibody complex is stored, as described later. The three-dimensional structure of the antigen-antibody complex is a three-dimensional structure in a state in which an antigen and an antibody are bound, and can be obtained, for example, by performing crystal structure analysis on a protein complex in a state in which an antigen and an antibody are bound. For example, a public database can be used as the three-dimensional structure DB2. For example, the public database includes the Protein Data Bank (PDB, https: / / www.rcsb.org / ), the Structural Antibody Database (SAbDab) (https: / / opig.stats.ox.ac.uk / webapps / sabdab-sabpred / sabdab / ), and the like. The hardware configuration of the three-dimensional structure DB2 can be described with reference to the hardware configuration of the information processing device 1. Note that the information processing device 1 of the first embodiment includes an analysis unit 12, a calculation unit 13, and a first selection unit 15, but the present disclosure is not limited thereto, and these configurations may or may not be present.

[0021] The communication network 3 is not particularly limited and may be a known network, for example, a wired or wireless network. Examples of the communication network 3 include the Internet, WWW (World Wide Web), telephone lines, LAN (Local Area Network), and WiFi (Wireless Fidelity).

[0022] 2 illustrates a block diagram of a hardware configuration of the information processing device 1. The information processing device 1 includes, for example, a CPU (Central Processing Unit) 101, which is a computing element, a memory 102, a bus 103, a storage device 104, an input device 108, a display 109, and a communication device (communication unit) 110. Each unit of the information processing device 1 is connected via the bus 103 by its respective interface (I / F).

[0023] The CPU 101 cooperates with other components through a controller (such as a system controller or an I / O controller) and controls the entire information processing device 1. In the information processing device 1, the CPU 101 executes the program 105 of the present disclosure and other programs, and also reads and writes various information or data. Specifically, in this embodiment, the CPU 101 functions as an acquisition unit 11, an analysis unit 12, a calculation unit 13, a first evaluation unit 14, and a first selection unit 15. The information processing device 1 includes a CPU as a calculation device (calculation element), but may include other calculation devices such as a GPU (Graphics Processing Unit) and an APU (Accelerated Processing Unit), or may include a combination of the CPU and these. Note that the CPU 101 functions as each unit other than the storage unit in other embodiments, for example.

[0024] The memory 102 includes a main memory. The main memory is also called a primary storage device. When the CPU 101 performs processing, the memory 102 reads various operation programs, such as a program 105 of the present disclosure, stored in a storage device 104 (auxiliary storage device) described below. The CPU 101 then reads data from the memory 102, decodes it, and executes the program. The main memory is a RAM (random access memory). The memory 102 may further include a ROM (read only memory).

[0025] The bus 103 can also be connected to external devices. Examples of the external devices include an external storage device (external database, etc.) and a printer. The information processing device 1 can be connected to a communication network 3 by a communication device 110 connected to the bus, and can also be connected to external devices such as a terminal 2 via the communication network 3.

[0026] The storage device 104 is also called an auxiliary storage device, for example, in contrast to the main memory (primary storage device). As described above, the storage device 104 stores an operation program including the program 105 of the present disclosure, and data including the three-dimensional structure data 106 and the contribution data 107. The storage device 104 includes, for example, a storage medium and a drive for reading and writing data from and to the storage medium. The storage medium is not particularly limited, and may be, for example, an internal or external type, and may be, for example, a hard disk (HD), a floppy disk (FD), a CD-ROM, a CD-R, a CD-RW, an MO, a DVD, a flash memory, a memory card, etc., and the drive is not particularly limited. The storage device 104 may be, for example, a hard disk drive (HDD) or a solid state drive (SSD) in which the storage medium and the drive are integrated.

[0027] The information processing device 1 further includes an input device 108 and a display 109 which is an output device. Examples of the input device 108 include pointing devices such as a touch panel, a track pad, and a mouse; a keyboard; an imaging means such as a camera and a scanner; a card reader such as an IC card reader and a magnetic card reader; and a voice input means such as a microphone. Examples of the display 109 include display devices such as an LED (light emitting diode) display and a liquid crystal display. In this embodiment, the input device 108 and the display 109 are configured separately, but the input device 108 and the display 109 may be configured as an integrated device, such as a touch panel display. In addition, in the information processing device 1, the input device 108 and the display 109 are of any configuration, and may be omitted or may include one or more of them.

[0028] Next, an example of processing in the information processing system 100 of this embodiment will be described with reference to the flowchart in Fig. 3, taking as an example a case in which contribution to antigenicity is calculated using data from crystal structure analysis of an antigen-antibody complex, and a candidate antigen peptide is selected from among candidate peptides based on the contribution to antigenicity thus obtained. As shown in Fig. 3, the information processing method and program of embodiment 1 performs each of the processes of S1 (acquisition), S2 (analysis), S3 (calculation), S4 (evaluation), and S5 (first selection) in this order.

[0029] First, the information processing device 1 calculates the contribution to antigenicity used in evaluating the antibody induction ability of a candidate peptide using data on the three-dimensional structure of an antigen-antibody complex. Specifically, in step S1, the acquisition unit 11 accesses a database in which three-dimensional structure data such as PDB, which is the three-dimensional structure DB2, is stored via the communication line network 3, and acquires data on crystal structure analysis (three-dimensional structure data) of a plurality of antigen-antibody complexes stored in the three-dimensional structure DB2. The crystal structure analysis data can be acquired from the Antibody database (AbDb) database of the PDB (URL: http: / / www.abybank.org / abdb / ) (see Reference 1 below). The three-dimensional structure data is preferably three-dimensional structure data of a complex between a molecule composed of amino acids such as a peptide or protein and an antibody. The number of the three-dimensional structure data to be acquired is a plurality. The lower limit of the number of the three-dimensional structure data is preferably 100, 200, 300, 400, or 500 or more, for example, since the contribution to antigenicity can be more accurately evaluated. The upper limit of the number of the three-dimensional structure data is not particularly limited, and is, for example, 5000, 4000, or 3000 or less. The number of the three-dimensional structure data is, for example, 100 to 5000, 200 to 5000, 300 to 4000, or 500 to 3000. The resolution of the three-dimensional structure data is preferably 4 Å or less, since the contribution to the antigenicity can be evaluated more accurately. The number of pieces of three-dimensional structure data with a resolution of 4 Å or less is, for example, about 800 pieces in the AbDb database. Reference 1: Ferdous, Saba et.al., “AbDb: antibody structure database-a database of PDB-derived antibody structures.” Database 2018 (2018)

[0030] Next, in step S2, the analysis unit 12 analyzes epitope residues on the antigen that interact with the antibody from the three-dimensional structure data of the antigen-antibody complex. As described below, the information processing device 1 calculates the contribution to antigenicity using amino acid information of the epitope residues in the three-dimensional structure data. Therefore, in step S2, in order to identify the epitope residues to be used in the calculation, the epitope residues in the antigen-antibody complex are analyzed from the three-dimensional structure data acquired in step S1.

[0031] The antigen and the antibody bind to each other via intermolecular interactions such as hydrogen bonds, electrostatic interactions, van der Waals forces, and hydrophobic interactions. In step S2, the intermolecular interactions formed between the antigen and the antibody, more specifically, between the molecules constituting the antigen and the amino acids constituting the antibody, are estimated from the data on the three-dimensional structure of the antigen-antibody complex. In step S2, the epitope residues in the antigen bound (recognized) by the paratope of the antibody are analyzed from the information on the intermolecular interactions estimated to have formed between the antigen and the antibody.

[0032] In step S2, the antigen-antibody intermolecular interaction may be estimated based on one type of intermolecular interaction, or the antigen-antibody intermolecular interaction may be estimated based on multiple types of intermolecular interactions. When analyzing epitope residues on the antigen using hydrogen bonds as the intermolecular interaction, step S2 can be performed, for example, using a molecular structure analysis program, specifically, ChimeraX (manufactured by RBVI (Resource for Biocomputing, Visualization, and Informatics), University of California). When analyzing epitope residues on the antigen using electrostatic interactions, van der Waals forces, or hydrophobic interactions as the intermolecular interactions, step S2 can be performed, for example, with reference to Reference 2 below. The interaction used for estimation in step S2 is preferably hydrogen bonds, since it allows for more accurate evaluation of the antigenicity of the target peptide. Reference 2: Tsumoto, Kouhei, and Jose MM Caaveiro. "Antigen-Antibody Binding." eLS (2016): 1-8.

[0033] Next, in step S3, the calculation unit 13 calculates the contribution of each amino acid to the antigenicity based on each amino acid residue constituting the epitope residue. The present inventors have found that there is a bias in the amino acid residues constituting the epitope residues of the antigen peptide recognized by the antibody. That is, the present inventors have found that there are amino acid residues that are frequently recognized by the antibody and amino acid residues that are frequently recognized by the antibody. In addition, as shown in the examples described below, the present inventors have found that when a target peptide is evaluated based on the bias, the obtained evaluation result (antigenicity of the peptide described below) correlates with the antibody induction ability when immunized to a living body. Furthermore, the present inventors have found that by using the evaluation to change the amino acid sequence of the target peptide in accordance with the bias, it is possible to adjust the induction ability of antibodies that can bind to the target peptide when immunized (administered) to a living body. Therefore, in step S3, the bias of the amino acid residues in the epitope residues used in the evaluation is calculated as the contribution of each amino acid to the antigenicity.

[0034] The bias of the amino acid residues can be evaluated as the frequency of each amino acid residue constituting the obtained epitope residues, i.e., the ratio of each amino acid to the total number of amino acid residues of all epitope residues, the occurrence rate (ratio), the number of occurrences, the occurrence frequency, the occurrence ratio, the occurrence degree, etc. For this reason, in step S3, the total number of amino acid residues and the total number of residues of each amino acid are tallied for each epitope residue analyzed in step S2. Then, in step S3, the occurrence frequency of each amino acid residue is calculated as the contribution to the antigenicity from the total number of amino acid residues and the total number of residues of each amino acid.

[0035] Next, in step S4, the first evaluation unit 14 evaluates the antigenicity of the candidate peptide based on the contribution of each amino acid to the antigenicity of the candidate peptide. Specifically, in step S4, the antigenicity of the candidate peptide is evaluated using the contribution of the candidate peptide to the antigenicity (index value of antigenicity) as an index. In step S4, the contribution of the candidate peptide to the antigenicity is evaluated (calculated) based on the amino acid sequence of the candidate peptide using the contribution of each amino acid to the antigenicity calculated in step S3. Specifically, in step S4, the contribution of each amino acid to the antigenicity of each amino acid corresponding to each amino acid is integrated based on the amino acid sequence of the candidate peptide. As described above, the contribution of each amino acid to the antigenicity is calculated, for example, as the frequency of the amino acid in the epitope residue. Therefore, if the integrated value of the contribution of each amino acid to the antigenicity of the candidate peptide is relatively large, the candidate peptide contains an amino acid that is frequently recognized by the antibody, and therefore the antibody induction ability is relatively high. On the other hand, if the cumulative value of the contribution of each amino acid of the candidate peptide to the antigenicity is relatively small, the candidate peptide contains an amino acid that is rarely recognized by the antibody, and therefore has a relatively low antibody-inducing ability. For this reason, in step S4, the cumulative value is used as the contribution of the antigenicity of the candidate peptide (index value of antigenicity) to evaluate the antigenicity of the candidate peptide.

[0036] The antigenicity can be, for example, the antibody induction ability when immunized in a living body. The living body can be, for example, the subject of administration of the candidate antigen peptide, etc., and specific examples include animals including humans and non-human animals. The antibody induction ability can be, for example, the antibody titer, or the rapidity of antibody induction (for example, the period until the antibody titer starts to increase).

[0037] In step S4, the number of candidate peptides to be subjected to the evaluation is not particularly limited and can be any number, specifically, 100 to 50,000, 500 to 40,000, 1,000 to 30,000, or 5,000 to 20,000.

[0038] The length (amino acid length) of the candidate peptide may be, for example, a polypeptide of a length capable of inducing an antibody. The length of the candidate peptide is, for example, 7 to 50 amino acids, 8 to 40 amino acids, 9 to 35 amino acids, or 10 to 30 amino acids, and preferably 10 to 30 amino acids.

[0039] The candidate peptide can be a polypeptide consisting of any amino acid sequence. The candidate peptide can be, for example, a polypeptide designed from a protein intended to induce an antibody, or a polypeptide intended to induce an antibody, or a mutant polypeptide in which a mutation is introduced into a template polypeptide using these polypeptides as a template. The candidate peptide can be designed as a peptide of a specified length from the amino acid sequence of the protein of interest, for example, according to a sliding window algorithm.

[0040] The mutant polypeptide can be designed, for example, by introducing one or more mutations into the amino acid sequence of the target polypeptide. Examples of the type of mutation include insertion, addition, deletion, and substitution. When the type of mutation is the addition of one or more amino acids to the N-terminus or C-terminus, the added amino acid residues may be the same as one or more amino acids (one or more corresponding amino acids) located at the N-terminus or C-terminus of the amino acid sequence of the candidate peptide in the protein from which the candidate peptide is derived. In designing the mutant polypeptide, one type of mutation may be introduced, or a combination of multiple types of mutations may be introduced. The position at which the mutation is introduced can be determined, for example, based on the contribution of each amino acid of the candidate peptide to the antigenicity before the mutation. Specifically, when N mutations (N: positive integer) are introduced into the candidate peptide, the mutations can be set, for example, from the lowest-ranked amino acid (1st) in the order of contribution of each amino acid of the candidate peptide to the antigenicity, up to the Nth amino acid from the bottom.

[0041] In the mutant polypeptide, the number of mutations (N) can be determined, for example, according to the length of the target candidate peptide, and is specifically 1 to 10 amino acids, 1 to 5 amino acids, or 1 to 3 amino acids, and preferably 1 to 3 amino acids. The length of the mutant polypeptide is, for example, -3 to +3 amino acids, -2 to +2 amino acids, or -1 to +1 amino acids based on the length of the template polypeptide, and is preferably 0 amino acid.

[0042] Then, in step S5, the first selection unit 15 selects the candidate peptide as a candidate antigen peptide if the contribution of the candidate peptide to the antigenicity satisfies the condition of the previously specified contribution. The condition of the contribution can be appropriately set, for example, based on the antigenicity required for the candidate antigen peptide. As a specific example, the condition of the contribution can be, for example, a range of ranks of the contribution to the antigenicity in the candidate peptide group to be evaluated (for example, a specified number of ranks from 1st place), a numerical range of the contribution of the candidate peptide to the antigenicity, etc. The candidate peptide to be evaluated that is ranked 1st is the candidate peptide to be evaluated that has the highest contribution to the antigenicity. The specified rank can be, for example, 10th, 20th, 30th, 40th, 50th, 60th, 70th, 80th, 90th, 100th, 200th, 300th, 400th, 500th, etc. The first selection unit 15 may select based on conditions (other conditions) other than the contribution of the candidate peptide to the antigenicity. The other conditions include, for example, the length of the candidate peptide. The number of candidate antigen peptides to be selected is not particularly limited and can be any number.

[0043] Then, the processing of the information processing system 100 and the information processing device 1 ends.

[0044] In the information processing device 1 of the first embodiment, the contribution of each amino acid residue that is correlated with the antigenicity of the peptide is calculated from the epitope residue recognized by the antibody using the three-dimensional structure of the antigen-antibody complex. Therefore, according to the information processing device 1, the contribution of each amino acid residue to the antigenicity can be used to evaluate the contribution of a candidate peptide to the antigenicity or the antigenicity of the candidate peptide. Furthermore, the information processing device 1 can select a candidate antigen peptide from the candidate peptides based on the contribution of the candidate peptide to the antigenicity. Therefore, according to the information processing device 1 of the first embodiment, a candidate antigen peptide with an adjusted antibody inducing ability can be selected.

[0045] In the information processing device 1 of the first embodiment, the three-dimensional structure data is acquired from the three-dimensional structure DB2, but the present disclosure is not limited thereto, and for example, the three-dimensional structure of an antigen-antibody complex may be predicted from the amino acid sequences of the antigen and antibody, and the obtained predicted structure may be used as the three-dimensional structure data. In this case, instead of or in addition to step S1, the information processing device 1 includes a step of predicting the three-dimensional structure of an antigen-antibody complex from the amino acid sequences of the antigen and antibody by a prediction unit. The prediction of the three-dimensional structure can be performed, for example, by predicting the three-dimensional structure of the antigen and the three-dimensional structure of the antibody, and predicting the binding state of the obtained two three-dimensional structures.

[0046] The three-dimensional structure of the antigen and the three-dimensional structure of the antibody can be predicted, for example, using software capable of predicting a three-dimensional structure from an amino acid sequence. Specific examples of software that can be used include AlphaFold, Meta ESM or Meta ESM2, Rosetta modelling, Swiss-model, Modeller, etc.

[0047] The binding state of the two three-dimensional structures can be predicted, for example, using software capable of predicting a docking simulation of two molecules, specific examples of which include Rosetta-dock, Haddock, Patchdock, Zdock, LightDock, and Hexserver.

[0048] The number of conformations of the antigen-antibody complex predicted in the prediction step is, for example, a plurality of conformations. The lower limit of the number of conformations is, for example, preferably 100, 200, 300, 400, or 500 or more, since the contribution to the antigenicity can be evaluated more accurately. The upper limit of the number of conformations is not particularly limited, and is, for example, 5000, 4000, or 3000 or less. The number of conformations is, for example, 100 to 5000, 200 to 5000, 300 to 4000, or 500 to 3000.

[0049] The information processing device 1 includes the prediction unit, and thus can generate the three-dimensional structure data even when it is difficult to obtain the three-dimensional structure data from the three-dimensional structure DB 2. Therefore, the information processing device 1 including the prediction unit can evaluate the antigenicity of a candidate peptide even when the three-dimensional structure DB 2 is not available.

[0050] (Embodiment 2) This embodiment is another example of an information processing system including an information processing device of the present disclosure. FIG. 4 is a block diagram showing an information processing system 100A including an information processing device 1A of the second embodiment. As shown in FIG. 4, the information processing device 1A of this embodiment includes a determination unit 16, a second selection unit 17, a second evaluation unit 18, a third selection unit 19, a generation unit 20, a re-evaluation unit 21, and a fourth selection unit 22 in addition to the configuration of the information processing device 1 of the first embodiment. The hardware configuration of the information processing device 1A is the same as that of the information processing device 1 of FIG. 2, except that the CPU 101 includes the configuration of the information processing device 1A of FIG. 4 instead of the configuration of the information processing device 1 of FIG. 2. Except for these points, the configuration of the information processing device 1A of the second embodiment is the same as the configuration of the information processing device 1 of the first embodiment, and the description thereof can be used.

[0051] Next, an example of the processing of the information processing system 100A including the information processing device 1A of the present embodiment will be described with reference to the flowcharts of Figures 5 and 6. As shown in Figures 5 and 6, the information processing method of the second embodiment includes, in addition to the steps S1 to S5 of the information processing method of the first embodiment, a step S6 (position determination), a step S7 (selection by position: second selection), a step S8 (similarity evaluation: second evaluation), a step S9 (selection by similarity: third selection), a step S10 (generation of peptides), a step S11 (reevaluation), and a step S12 (reselection: fourth selection). Note that, in the information processing method of the second embodiment, the steps S8 to S12 are performed after the steps S6 to S7 are performed, but in no particular order.

[0052] First, the information processing system 100A of the second embodiment performs steps S1 to S5 in the same manner as the information processing system 100 of the first embodiment.

[0053] Next, in step S6, the determination unit 16 determines the position of the candidate antigen peptide in the protein from which the candidate antigen peptide is derived. In determining the position, it is determined whether the candidate antigen peptide is present on the molecular surface (external) of the protein, present inside the molecule (inner), or present both on the molecular surface and inner molecule of the protein. Specifically, the position is determined by aligning the amino acid sequence of the candidate antigen peptide with the amino acid sequence of the protein to identify the position of the candidate antigen peptide in the protein. Next, in step S6, the position can be determined by referring to the three-dimensional structure data of the antigen-antibody complex obtained in step S1 and identifying the position of the candidate antigen peptide in the protein. In step S6, for example, the number of amino acid residues located on the surface of the protein in the candidate antigen peptide and the number of amino acid residues located inside the protein may be determined as the position.

[0054] In step S7, the second selection unit 17 selects the candidate antigen peptide when the position of the candidate antigen peptide in the protein satisfies a pre-specified position condition. The antibody mainly recognizes the surface of the protein. Thus, in step S7, by selecting a candidate antigen peptide in which at least a portion of amino acid residues are present outside (on the surface) of the protein, it is possible to select a candidate antigen peptide capable of inducing an antibody having a high binding ability to a protein containing the candidate antigen peptide.

[0055] First, in step S7, it is evaluated whether the position of the candidate antigen peptide in the protein obtained in step S6 satisfies the position condition. Specifically, if the candidate antigen peptide is present in the protein molecule (inside), in step S7, it is evaluated that the candidate antigen peptide does not satisfy the position condition. Then, if the position of the candidate antigen peptide in the protein does not satisfy the position condition, that is, in the case of No, the second selection unit 17 does not select the candidate antigen peptide, and the information processing device 1A ends the process. On the other hand, if the candidate antigen peptide is present on the molecular surface (outside) of the protein, or if it is present both on the molecular surface and inside the protein, in step S7, it is evaluated that the candidate antigen peptide satisfies the position condition. Then, if the position of the candidate antigen peptide in the protein satisfies the position condition, that is, in the case of Yes, the second selection unit 17 selects the candidate antigen peptide and proceeds to step S8.

[0056] The position condition may be that all amino acid residues are present outside the protein, since it is possible to select a candidate antigen peptide capable of inducing an antibody having a higher binding ability to a protein containing the candidate antigen peptide. Furthermore, when the number of amino acid residues located on the surface of the protein in the candidate antigen peptide is counted in step S6, the position condition may be set based on, for example, the number of amino acid residues located on the surface of the protein in the candidate antigen peptide.

[0057] Next, in step S8, the second evaluation unit 18 compares the amino acid sequence of the candidate antigen peptide or the amino acid sequence of the protein from which the candidate antigen peptide is derived with the amino acid sequence of the corresponding protein in the subject of administration of the candidate antigen peptide to evaluate the similarity of the two amino acid sequences. When the candidate antigen peptide is identical to or very similar to the amino acid sequence of the corresponding protein in the subject of administration, it generally has low antibody induction ability, i.e., low antigenicity. Therefore, in step S8, the similarity of the candidate antigen peptide to the amino acid sequence of the corresponding protein in the subject of administration is evaluated as an index of the antigenicity. Examples of the similarity include the number of amino acid residues that differ between the two amino acid sequences, and the identity between the two amino acid sequences.

[0058] Specifically, in step S8, the amino acid sequence of the candidate antigen peptide is compared with the amino acid sequence of the corresponding protein in the subject to which the candidate antigen peptide is administered, and the similarity between the two amino acid sequences is calculated. The comparison and calculation of similarity can be performed using a sequence analysis program, and specific examples that can be used include ClustalW and Clustal Omega.

[0059] In step S9, the third selection unit 19 evaluates whether the obtained similarity satisfies a pre-specified similarity condition and selects the candidate antigen peptide. That is, in step S9, the candidate antigen peptide is selected using the similarity as an index if it is not similar to the corresponding protein in the administration subject, since it is presumed to have high antigenicity. On the other hand, if it is similar to the corresponding protein in the administration subject, it is presumed to have low antigenicity, and therefore selection is not performed.

[0060] Then, in step S9, if the similarity evaluation result obtained in step S8 satisfies the similarity condition, i.e., if Yes, the third selection unit 19 selects a candidate antigen peptide to be evaluated, and the information processing device 1A ends the process. On the other hand, in step S9, if the similarity evaluation result obtained in step S8 does not satisfy the similarity condition, i.e., if No, the third selection unit 19 does not select a candidate antigen peptide to be evaluated, and proceeds to step S10.

[0061] The condition for the similarity can be set according to the type of similarity. When the identity between two amino acid sequences is used as the similarity, the condition for the similarity can be set, for example, that the identity is not 70% or more, 80% or more, or 90% or more, or less than 90%, less than 80%, or less than 70%. When the number of different amino acid residues between two amino acid sequences is used as the similarity, the number of consecutively matching amino acid residues can be set to be not 5 amino acids or more, not 6 amino acids or more, not 7 amino acids or more, or less than 7 amino acids, less than 6 amino acids, or less than 5 amino acids.

[0062] Next, in step S10, the generation unit 20 generates another candidate peptide in which one or more amino acids of the candidate antigen peptide have been mutated. Specifically, in step S10, the other candidate peptide can be generated by introducing one or more mutations into the amino acid sequence of the candidate antigen peptide.

[0063] The type of mutation may be, for example, insertion, addition, deletion, substitution, etc. When the type of mutation is the addition of one or more amino acids to the N-terminus or C-terminus, the added amino acid residues may be the same as one or more amino acids (corresponding one or more amino acids) located at the N-terminus or C-terminus of the amino acid sequence of the candidate peptide in the protein from which the candidate peptide is derived. In designing the mutant polypeptide, one type of mutation may be introduced, or multiple types of mutations may be introduced in combination.

[0064] The number of mutations can be determined depending on the length of the target peptide, for example, and is specifically 1 to 10 amino acids, 1 to 5 amino acids, or 1 to 3 amino acids, and preferably 1 to 3. The length of the mutant polypeptide is, for example, −3 to +3 amino acids, −2 to +2 amino acids, or −1 to +1 amino acids based on the length of the template polypeptide, and preferably 0 amino acid.

[0065] The number of different candidate peptides to be generated can be any number, and specific examples are 100 to 50,000, 500 to 40,000, 1,000 to 30,000, or 5,000 to 20,000.

[0066] Next, in step S11, the reevaluation unit 21 reevaluates the antigenicity of the other candidate peptide based on the contribution of each amino acid to the antigenicity of the other candidate peptide. Step S11 can be performed in the same manner as step S4, except that the candidate peptide generated in step S10 is used instead of the other candidate peptide.

[0067] Next, in step S12, if the contribution degree to the antigenicity of the other candidate peptide satisfies the condition of the previously specified contribution degree, the fourth selection unit 22 selects the candidate peptide as a candidate antigen peptide. Step S12 can be performed in the same manner as step S5, except that the contribution degree to the antigenicity of the other candidate peptide reevaluated in step S10 is used instead of the contribution degree to the antigenicity of the candidate peptide.

[0068] Then, the information processing device 1A similarly performs the steps from S6 onwards, and ends the process.

[0069] In the information processing device 1A of the second embodiment, a candidate peptide is selected using the position in the protein from which the candidate peptide is derived as an index. Therefore, the information processing device 1A of the second embodiment can select a candidate antigen peptide capable of inducing an antibody having a higher binding ability to a protein containing the candidate antigen peptide. Furthermore, in the information processing device 1 of the second embodiment, the candidate antigen peptide is selected based on the similarity between the amino acid sequence of the candidate antigen peptide and the amino acid sequence of the corresponding protein in the subject to which the candidate antigen peptide is administered. Therefore, the information processing device 1A of the second embodiment can select a candidate antigen peptide with high antigenicity.

[0070] In the information processing device 1A of embodiment 2, in the case where the candidate antigen peptide does not satisfy the similarity condition, the introduction of amino acid mutations (S10), reevaluation of another candidate peptide (S11), and selection (S12) are performed. However, the present disclosure is not limited to this, and for example, in step S5, the same may be performed for a candidate peptide that does not satisfy the contribution condition, and in step S7, for a candidate antigen peptide that does not satisfy the position condition.

[0071] (Embodiment 3) The program of this embodiment is a program that causes a computer to execute the information processing method of the present disclosure. In the program of this embodiment, the "processing" can also be referred to as, for example, a "procedure" or an "instruction." The program of this embodiment may be recorded, for example, in a computer-readable recording medium. The recording medium is, for example, a non-transitory computer-readable storage medium. The recording medium is not particularly limited, and examples thereof include a random access memory (RAM), a read-only memory (ROM), a hard disk (HD), a solid state drive (SSD), an optical disk, and a floppy disk (FD). EXAMPLES

[0072] The present disclosure will be described in detail below using examples, but the present invention is not limited to the aspects described in the examples. Furthermore, unless otherwise specified, commercially available reagents and kits were used according to the attached protocols.

[0073] [Example 1] It was confirmed that the antigenic contribution of a peptide (antigenicity index, antigenicity score), calculated based on the amino acid sequence of the peptide and the contribution of each amino acid residue to antigenicity, correlates with the antibody induction ability.

[0074] (1) Calculation of antigenicity score Crystal structure information of 870 data of antigen-antibody complexes was collected from the AbDb database of the Protein Data Bank (PDB). Next, from the obtained crystal structure information, crystal structures with a resolution of 4 Å or less were selected (800 data). For the selected crystal structures, hydrogen bonds formed between the antibody and antigen were analyzed using ChimeraX (manufactured by RBVI (Resource for Biocomputing, Visualization, and Informatics) at the University of California), and amino acid residues of the epitope of the antigen that interacts with the antibody were extracted. The number of occurrences of each of the extracted amino acids was counted, and the frequency of occurrence (%) of each amino acid relative to the total number of amino acids in all epitopes was determined as the contribution to antigenicity.

[0075] (2) Preparation of antigen For each antigen, a peptide modified with KLH (Cosmo Bio, Eurofins Genomics) was used. The KLH-modified antigen was adjusted to an antigen concentration of 0.33 mg / 0.5 ml / bird with phosphate buffer solution (D-PBS) (Fujifilm Wako Pure Chemical Industries, Ltd.), and the resulting PBS containing the antigen was mixed with complete Freud's adjuvant (FCA, Fujifilm Wako Pure Chemical Industries, Ltd.) at a volume ratio of 1:1 to obtain 1.0 ml of emulsion. The emulsion was used as the antigen for primary immunization. The antigens used were: Porphyromonas gingivalisFour types of peptides derived from Lys-gingipain (NCBI accession number: WP_099896865.1, SEQ ID NO: 9) produced by Porphyromonas gingivalis Three peptides derived from Arg-gingipain (NCBI accession number: WP_271912163.1, SEQ ID NO: 10) produced by Porphyromonas gingivalis Two peptides derived from peptidylarginine deiminase PPAD (NCBI accession number: WP_005873463.1, sequence number 11) produced by P. cerevisiae, two peptides derived from human peptidylarginine deiminase 4 (NCBI accession number: NP_036519.21, sequence number 12), and one peptide derived from COVID-19 Spike glycoprotein (Uniprot accession number: P0DTC2.1, sequence number 13) were designed from the amino acid sequence of each protein and used. In addition, the antigenicity score of each antigen was calculated by integrating the frequency of occurrence of each amino acid based on the amino acid sequence of each antigen.

[0076] The KLH-modified antigen was adjusted with PBS to an antigen concentration of 0.33 mg / 0.5 ml / bird, and the resulting PBS containing the antigen was mixed with incomplete Freud's adjuvant (FIA, manufactured by Wako) at a volume ratio of 1:1 to obtain 1.0 ml of emulsion, which was used as an antigen for secondary immunization.

[0077] (3) Immunity Two to three chickens were used for each antigen. First, as a primary immunization, the antigen prepared for primary immunization was administered intraperitoneally to the chicken (week 0 of administration). Four weeks after the administration, as a secondary immunization, the antigen prepared for secondary immunization was administered intraperitoneally to the chicken. In addition, blood was collected from each chicken at week 0 of administration (before immunization), week 2 of administration, week 4 of administration, week 5 of administration, and week 6 of administration. The collected blood was centrifuged (14,000×g) to collect antiserum. The antiserum was stored at −20° C.

[0078] (4) Confirmation of antibody titer The antibody titer against the antigen of each antiserum was measured by ELISA. Antigen-specific antibodies were detected using bovine serum albumin (BSA) modified with each antigen (hereinafter the same). Specifically, 5 μg / ml of antigen-BSA (Cosmo Bio, Eurofins Genomics, solid-phase solution) was added to an immunoplate (Maxisorp, Nunc) as each antigen, and the antigen-BSA was solidified by treating at 4°C overnight. After the solidification, the solid-phase solution was discarded, and a blocking solution (25% Block Ace / PBS, KAC) was added to block at 37°C for 1 hour. Next, after washing with PBS-T (137 mmol / l NaCl, 8.9 mmol / l Na2HPO4·12H2O, 2.7 mmol / l KCl, 1.5 mmol / l KH2PO4, 0.05% Tween-20), a sample solution was added and reacted at 37°C for 1 hour. The sample solution was a solution in which the antiserum was serially diluted 1000-fold, 2000-fold, and 4000-fold using the blocking solution. After the reaction, the plate was washed with PBS-T, and a secondary antibody (HRP-anti-chicken-IgG, KPL) diluted 1000-fold with the blocking solution was added and reacted at 37°C for 1 hour. After the reaction, the plate was washed with PBS-T, and a coloring reagent (3,3',5,5'-tetramethylbenzidine:TMB, KPL) was added and coloring was performed for 10 to 30 minutes. After the color development, TMB stop solution (KPL) was added to stop the color development, and the absorbance (450 nm) of each well was measured using a plate reader (Cytation, BioTek). From the measurement results obtained, the number of days until the antibody titer reached its highest level after the first immunization was calculated for each antigen. These results are shown in FIG.

[0079] FIG. 7 is a graph showing the relationship between the antigenicity score and the number of days until the antibody titer reaches the maximum after the first immunization. In FIG. 7, the horizontal axis shows the number of days until the antibody titer reaches the highest after the first immunization, and the vertical axis shows the antigenicity score. The straight line in the figure shows an approximation curve, and R 2indicates the coefficient of determination. As shown in FIG. 7, a high negative correlation was confirmed between the antigenicity score and the number of days until the maximum antibody titer is reached after the first immunization. That is, it was confirmed that the higher the antigenicity score of the antigen, the shorter the number of days until the antibody titer increases, and conversely, the lower the antigenicity score of the antigen, the longer the number of days until the antibody titer increases. Therefore, it was found that the antigenicity score correlates with the antigenicity of the antigen.

[0080] [Example 2] Based on the antigenicity score, it was confirmed that antigenicity could be improved by modifying the amino acids of the VEGFA-derived antigen peptide.

[0081] (1) Preparation of antigen Using VEGFA (Vascular endothelial growth factor A) as a model antigen, it was confirmed that the antibody induction ability against the VEGFA-derived peptides could be improved based on the antigenicity score.

[0082] Amino acid sequence of VEGFA (SEQ ID NO:1) MNFLLSWVHW SLALLLYLHH AKWSQAAPMA EGGGQNHHEV VKFMDVYQRS YCHPIETLVD IFQEYPDEIE YIFKPSCVPLMRCGGCCNDE GLEC VPTEES NITMQIMRIK P[HQGQHIGEM SFLQHN]KCEC RPKKDRARQE KKSVRGKGKG QKRKRKKSRYKSWSVYVGAR CCLMPWSLPG PHPCGPCSER RKHLFVQDPQ TCKCSCKNTD SRCKARQLEL NERTCRCDKP RR

[0083] First, the underlined amino acid sequence in the amino acid sequence of VEGFA was used as the antigen peptide (antigen peptide 1 before modification, VPTEESNITMQIMRIK: SEQ ID NO: 2). After introducing a mutation into the amino acid sequence of the antigen peptide 1 before modification, the antigenic score of the antigen peptide 1 containing the mutation was recalculated. Then, a modified antigen peptide 1 having an antigenic score higher than that of the antigen peptide 1 before modification was obtained. Antigens for primary immunization and secondary immunization were prepared from the obtained antigen peptides 1 before and after modification in the same manner as in Example 1.

[0084] [Table 1]

[0085] In addition, in the amino acid sequence of VEGFA, the amino acid sequence enclosed in parentheses was designated as the antigen peptide (antigen peptide 2 before modification, HQGQHIGEMSFLQHN: SEQ ID NO: 4). The antigen peptide 2 was treated in the same manner as the antigen peptide 1 to obtain an antigen peptide 2 after modification, which has an antigenicity score higher than that of the antigen peptide 2 before modification. Antigens for primary immunization and secondary immunization were prepared in the same manner as in Example 1 using the obtained antigen peptides 2 before and after modification.

[0086] [Table 2]

[0087] (2) Immunity Immunization and blood sampling were performed in the same manner as in Example 1, except that two chickens were immunized with each of the antigen peptides 1 before and after modification, and the antigen peptides 2 before and after modification.

[0088] (3) Confirmation of antibody titer Antisera (mutation-1, 2 and original-1, 2) obtained by immunization with the pre- and post-modification antigen peptide 1 and the pre- and post-modification antigen peptide 2 were measured by ELISA for antibody titers against each antigen peptide used in immunization. The ELISA measurement method was the same as in Example 1. The pre- and post-modification antigen peptide 1, and the pre- and post-modification antigen peptide 2 were used as the immobilized antigen peptides. The measurement results obtained for antigen peptide 1 are shown in FIG. 8, and the measurement results obtained for antigen peptide 2 are shown in FIG. 9. The numbers in the figures indicate the individual numbers of the immunized chickens.

[0089] FIG. 8 is a graph showing the antibody titer of the antiserum obtained by immunization with each of the antigen peptides. In FIG. 8, (A) shows the results for antigen peptide 1 before modification, and (B) shows the results for antigen peptide 1 after modification. In FIG. 8(A) and (B), the horizontal axis shows the number of weeks from the day of primary immunization (week 0 of administration), and the vertical axis shows the absorbance value representing the antibody titer. As shown in FIG. 8(A), in the case of antigen peptide 1 before modification, the antibody titer only increased slightly at week 6. On the other hand, as shown in FIG. 8(B), in the case of antigen peptide 1 after modification, the antibody titer was confirmed to increase in all individuals at week 2. That is, it was found that the antigen peptide with a high antigenicity score has higher antigenicity, i.e., has higher antibody induction ability, compared to the antigen peptide with a low antigenicity score before modification.

[0090] FIG. 9 is a graph showing the antibody titer of the antiserum obtained by immunization with each of the antigen peptides. In FIG. 9, (A) shows the results for antigen peptide 2 before modification, and (B) shows the results for antigen peptide 2 after modification. In FIGS. 9(A) and (B), the horizontal axis shows the number of weeks from the day of primary immunization (week 0 of administration), and the vertical axis shows the absorbance value representing the antibody titer. As shown in FIG. 9(A), the antibody titer of the antigen peptide 2 before modification increased at 4 to 5 weeks. On the other hand, as shown in FIG. 9(B), it was confirmed that the antibody titer of the antigen peptide 2 after modification increased in all individuals at 2 weeks. That is, it was found that the antigen peptide with a high antigenicity score has higher antigenicity, i.e., has higher antibody induction ability, compared to the antigen peptide with a low antigenicity score before modification.

[0091] From the above, it was found that the antigenicity of a peptide can be adjusted by using the antigenicity score calculated based on the contribution of each amino acid residue to antigenicity as an index.

[0092] (4) Confirmation of cross-reactivity The cross-reactivity of the antiserum 6 weeks after immunization with the modified antigen peptides 1 and 2 was confirmed with the unmodified antigen peptides 1 and 2. The cross-reactivity was measured by ELISA. The N-terminus of the unmodified and modified antigen peptides 1 and the unmodified and modified antigen peptides 2 were modified with BSA, and the resulting BSA-modified peptides were immobilized on a plate. After the immobilization, the antiserum was serially diluted from 1000-fold to 2-fold to prepare a dilution solution and used as a sample solution. Except for these points, the ELISA was performed in the same manner as in Example 1. The measurement results obtained for the antigen peptide 1 are shown in FIG. 10, and the measurement results obtained for the antigen peptide 2 are shown in FIG. 11.

[0093] Figure 10 is a graph showing the cross-reactivity of each antiserum. In Figure 10, (A) shows the antibody titer of the antiserum obtained by immunization with the modified antigen peptide 1 against the unmodified antigen peptide 1, and (B) shows the antibody titer of the antiserum obtained by immunization with the modified antigen peptide 1 against the modified antigen peptide 1. In Figures 10(A) and (B), the horizontal axis shows the dilution rate of the antiserum, and the vertical axis shows the absorbance value. It was confirmed that the antiserum immunized with the modified antigen peptide 1 exhibited reactivity to each antigen peptide.

[0094] Figure 11 is a graph showing the cross-reactivity of each antiserum. In Figure 11, (A) shows the antibody titer of the antiserum obtained by immunization with the modified antigen peptide 2 against the unmodified antigen peptide 2, and (B) shows the antibody titer of the antiserum obtained by immunization with the modified antigen peptide 2 against the modified antigen peptide 2. In Figures 11(A) and (B), the horizontal axis shows the dilution rate of the antiserum, and the vertical axis shows the absorbance value. It was confirmed that the antiserum immunized with the modified antigen peptide 2 exhibited reactivity to each antigen peptide.

[0095] From the above, it was found that the antigenicity of a peptide can be adjusted by using the antigenicity score calculated based on the contribution of each amino acid residue to antigenicity. It was also found that when an antigenic peptide into which a mutation has been introduced based on the antigenicity score is immunized, an antibody that cross-reacts with the antigenic peptide before the mutation is introduced is induced.

[0096] [Example 3] Based on the antigenicity score, we confirmed that the antigenicity could be improved by modifying the amino acids of the antigenic peptide derived from calcitonin gene-related peptide type 1 receptor (CGRPR).

[0097] (1) Preparation of antigen Using CGRPR as a model antigen, we confirmed that the antibody induction ability against CGRPR can be improved based on the antigenicity score.

[0098] Amino acid sequence of CGRPR (SEQ ID NO:6) MEKKCTLNFL VLLPFFMILV TAELEESPED SIQLGVTRNK IMTAQYECYQ KIMQDPIQQA EGVYCNRTWD GWLCWNDVAA GTESMQLCP D YFQDFDPSEK VTKI CDQDGN WFRHPASNRT WTNYTQCNVN THEKVKTALN LFYLTIIGHG LSIASLLISL GIFFYFKSLS CQRITLHKNL FFSFVCNSVV TIIHLTAVAN NQALVATNPV SCKVSQFIHL YLMGCNYFWM LCEGIYLHTL IVVAVFAEKQ HLMWYYFLGW GFPLIPACIH AIARSLYYND NCWISSDTHL LYIIHGPICA ALLVNLFFLL NIVRVLITKL KVTHQAESNL YMKAVRATLI LVPLLGIEFV LIPWRPEGKI AEEVYDYIMH ILMHFQGLLV STIFCFFNGE VQAILRRNWN QYKIQFGNSF SNSEALRSAS YTVSTISDGP GYSHDCPSEH LNGKSIHDIE NVLLKPENLY N

[0099] First, the underlined amino acid sequence in the amino acid sequence of CGRPR was used as an antigen peptide (antigen peptide 3 before modification, DYFQDFDPSEKVTKI: SEQ ID NO: 7). The antigen peptide 3 had a high antigenicity score of 5.82 before modification, but was highly homologous to the endogenous protein of the immunized animal. Therefore, it was predicted that the antibody titer of the antigen peptide 3 would increase slowly or would not increase easily, so the antigen peptide 3 was modified based on the antigenicity score. After introducing a mutation into the amino acid sequence of the antigen peptide 3 before modification, the antigenicity score was recalculated from that of the antigen peptide 1 containing the mutation. Then, the modified antigen peptide 3, which had a higher antigenicity score than the antigen peptide 3 before modification, was obtained. For the obtained antigen peptides 3 before and after modification, antigens for primary immunization and secondary immunization were prepared in the same manner as in Example 1.

[0100] [Table 3]

[0101] (2) Immunity Immunization and blood collection were performed in the same manner as in Example 1, except that three chickens were immunized with each of the antigen peptides 3 before and after modification (mutation-1, 2, 3 and original-1, 2, 3).

[0102] (3) Confirmation of antibody titer The antibody titers against each antigen of the antisera immunized with the pre- and post-modification antigen peptides 3 were measured by ELISA. The ELISA was performed in the same manner as in Example 2(3) above, except that the pre- and post-modification antigen peptides 3 were used instead of the pre- and post-modification antigen peptides 2. The measurement results obtained are shown in FIG.

[0103] FIG. 12 is a graph showing the antibody titer of the antiserum obtained by immunization with the antigen peptide 3. In FIG. 12, (A) shows the results for the antigen peptide 3 before modification, and (B) shows the results for the antigen peptide 3 after modification. In FIGS. 12(A) and (B), the horizontal axis shows the number of weeks from the day of primary immunization (week 0 after administration), and the vertical axis shows the absorbance value representing the antibody titer. As shown in FIG. 12(A), the antibody titer of the antigen peptide 3 before modification increased in weeks 2 to 5. On the other hand, as shown in FIG. 12(B), it was confirmed that the antibody titer of the antigen peptide 3 after modification increased in the second week in all individuals. That is, it was found that the antigen peptide with a high antigenicity score has higher antigenicity, i.e., has higher antibody induction ability, compared to the antigen peptide before modification with a low antigenicity score.

[0104] From the above, it was found that the antigenicity of peptides can also be adjusted for other proteins by using the antigenicity score calculated based on the contribution of each amino acid residue to antigenicity as an index.

[0105] (4) Confirmation of cross-reactivity The cross-reactivity of the antiserum immunized with the modified antigen peptide 3 to the unmodified antigen peptide 3 was confirmed. ELISA measurements were performed in the same manner as in Example 2(4) above, except that the antiserum against the unmodified and modified antigen peptides 3 were used and the unmodified and modified antigen peptides 3 were immobilized. The results are shown in FIG.

[0106] Figure 13 is a graph showing the cross-reactivity of each antisera. In Figure 13, (A) shows the antibody titer of the antisera obtained by immunization with the modified antigen peptide 3 against the unmodified antigen peptide 3, and (B) shows the antibody titer of the antisera obtained by immunization with the modified antigen peptide 3 against the modified antigen peptide 3. In Figures 13(A) and (B), the horizontal axis shows the dilution rate of the antisera, and the vertical axis shows the absorbance value. It was confirmed that the antisera immunized with the modified antigen peptide 3 exhibited reactivity to each antigen peptide.

[0107] From the above, it was found that the antigenicity of a peptide can be adjusted by using the antigenicity score calculated based on the contribution of each amino acid residue to antigenicity. It was also found that when an antigenic peptide into which a mutation has been introduced based on the antigenicity score is immunized, an antibody that cross-reacts with the antigenic peptide before the mutation is introduced is induced.

[0108] Although the present disclosure has been described above with reference to the embodiments and examples, the present disclosure is not limited to the above-mentioned embodiments and examples. Various modifications that can be understood by a person skilled in the art can be made to the configuration and details of the present disclosure within the scope of the present disclosure.

[0109] <Additional Notes> Some or all of the above-described embodiments and examples may be described as follows, but are not limited to the following: <Information processing device> (Appendix 1) a first evaluation unit that evaluates the antigenicity of a candidate peptide based on the contribution of each amino acid to the antigenicity, The degree of contribution to antigenicity is calculated based on amino acid residues of epitope residues on the antigen that interact with the antibody from data on the three-dimensional structure of an antigen-antibody complex. (Appendix 2) an analysis unit that analyzes epitope residues on the antigen that interact with the antibody based on data on the three-dimensional structure of the antigen-antibody complex; and a calculation unit that calculates the contribution of each amino acid to antigenicity based on each amino acid residue constituting the epitope residue. (Appendix 3) 3. The information processing device according to claim 2, further comprising a first selection unit that selects the candidate peptide as a candidate antigen peptide when the contribution of the candidate peptide to antigenicity satisfies the prespecified condition of contribution. (Appendix 4) A determination unit that determines the position of the candidate antigen peptide in the protein from which the candidate antigen peptide is derived; 4. The information processing device according to claim 3, further comprising a second selection unit that selects the candidate antigen peptide when the position of the candidate antigen peptide in the protein satisfies a prespecified position condition. (Appendix 5) a second evaluation unit that compares the amino acid sequence of the candidate antigen peptide or the amino acid sequence of the protein from which the candidate antigen peptide is derived with the amino acid sequence of the corresponding protein in a subject to which the candidate antigen peptide is administered, to evaluate the similarity between the two amino acid sequences; The information processing device according to claim 3 or 4, further comprising a third selection unit that selects the candidate antigen peptide if the similarity of the amino acid sequences satisfies a prespecified similarity condition. (Appendix 6) a second evaluation unit that compares the amino acid sequence of the candidate antigen peptide or the amino acid sequence of the protein from which the candidate antigen peptide is derived with the amino acid sequence of the corresponding protein in a subject to which the candidate antigen peptide is administered, to evaluate the similarity between the two amino acid sequences; a generating unit that generates another candidate peptide in which one or more amino acids of the candidate antigen peptide are mutated when the similarity of the amino acid sequence does not satisfy the predetermined similarity condition; and a re-evaluation unit that re-evaluates the antigenicity of the other candidate peptide based on the contribution of each of the amino acids to the antigenicity of the other candidate peptide. (Appendix 7) The information processing device according to claim 6, further comprising a fourth selection unit that selects the other candidate peptide as a candidate antigenic peptide if the contribution of the other candidate peptide to antigenicity satisfies the pre-specified contribution condition. (Appendix 8) The information processing device according to any one of claims 1 to 7, wherein the analysis unit analyzes epitope residues on the antigen that interact with the antibody by analyzing at least hydrogen bonds between the antibody and the antigen. (Appendix 9) The information processing device according to any one of appendix 1 to 8, wherein the contribution of each amino acid to antigenicity is the occurrence frequency of each amino acid in the epitope residues. (Appendix 10) The information processing device according to any one of appendices 1 to 9, wherein the antigenicity is an antibody-inducing ability when immunized in a living body. <Information processing method> (Appendix 11) A first evaluation step of evaluating the antigenicity of a candidate peptide based on the contribution of each amino acid to the antigenicity of the candidate peptide, The information processing method, wherein the contribution to antigenicity is calculated based on amino acid residues of epitope residues on the antigen that interact with the antibody from data on the three-dimensional structure of an antigen-antibody complex. (Appendix 12) an analysis step of analyzing epitope residues on the antigen that interact with the antibody from data on the three-dimensional structure of the antigen-antibody complex; and calculating the contribution of each amino acid to antigenicity based on each amino acid residue constituting the epitope residue. (Appendix 13) An information processing method according to claim 12, comprising a first selection step of selecting the candidate peptide as a candidate antigen peptide if the contribution of the candidate peptide to antigenicity satisfies the pre-specified contribution condition. (Appendix 14) determining the location of the candidate antigenic peptide in the protein from which the candidate antigenic peptide is derived; The information processing method according to claim 13, further comprising a second selection step of selecting the candidate antigen peptide if the position of the candidate antigen peptide in the protein satisfies a pre-specified position condition. (Appendix 15) a second evaluation step of comparing the amino acid sequence of the candidate antigen peptide or the amino acid sequence of the protein from which the candidate antigen peptide is derived with the amino acid sequence of the corresponding protein in a subject to which the candidate antigen peptide is administered to evaluate the similarity between the two amino acid sequences; 15. The information processing method according to claim 13 or 14, further comprising a third selection step of selecting the candidate antigen peptide if the similarity of the amino acid sequences satisfies a pre-specified similarity condition. (Appendix 16) a second evaluation step of comparing the amino acid sequence of the candidate antigen peptide or the amino acid sequence of the protein from which the candidate antigen peptide is derived with the amino acid sequence of the corresponding protein in a subject to which the candidate antigen peptide is administered to evaluate the similarity between the two amino acid sequences; generating a candidate peptide in which one or more amino acids of the candidate antigen peptide have been mutated, if the similarity of the amino acid sequence does not satisfy the predetermined similarity condition; and a reevaluation step of reevaluating the antigenicity of the other candidate peptide based on the contribution of each of the amino acids to the antigenicity of the other candidate peptide. (Appendix 17) The information processing method according to claim 16, further comprising a fourth selection step of selecting the other candidate peptide as a candidate antigen peptide if the contribution of the other candidate peptide to antigenicity satisfies the pre-specified contribution condition. (Appendix 18) 18. An information processing method according to any one of appendices 11 to 17, wherein the analyzing step analyzes epitope residues on the antigen that interact with the antibody by analyzing at least hydrogen bonds between the antibody and the antigen. (Appendix 19) 19. The information processing method according to any one of Appendices 11 to 18, wherein the contribution of each amino acid to antigenicity is the occurrence frequency of each amino acid in the epitope residues. (Appendix 20) 20. The information processing method according to any one of appendix 11 to 19, wherein the antigenicity is the ability to induce antibodies when immunized in a living organism. <Program> (Appendix 21) On the computer, executing a first evaluation process for evaluating the antigenicity of a candidate peptide based on the contribution of each amino acid to the antigenicity; The contribution to antigenicity is calculated based on amino acid residues of epitope residues on the antigen that interact with the antibody from data on the three-dimensional structure of an antigen-antibody complex. (Appendix 22) an analysis process for analyzing epitope residues on the antigen that interact with the antibody from data on the three-dimensional structure of the antigen-antibody complex; and calculating the contribution of each amino acid to antigenicity based on each amino acid residue constituting the epitope residue. (Appendix 23) The program described in Appendix 22, comprising a first selection process for selecting the candidate peptide as a candidate antigen peptide if the contribution of the candidate peptide to antigenicity satisfies the pre-specified contribution condition. (Appendix 24) a determination process for determining the position of the candidate antigen peptide in the protein from which the candidate antigen peptide is derived; The program according to claim 23, further comprising a second selection process for selecting the candidate antigen peptide when the position of the candidate antigen peptide in the protein satisfies a pre-specified position condition. (Appendix 25) a second evaluation process for comparing the amino acid sequence of the candidate antigen peptide or the amino acid sequence of the protein from which the candidate antigen peptide is derived with the amino acid sequence of the corresponding protein in a subject to which the candidate antigen peptide is administered, to evaluate the similarity between the two amino acid sequences; The program according to claim 23 or 24, further comprising a third selection process for selecting the candidate antigen peptide if the similarity of the amino acid sequences satisfies a pre-specified similarity condition. (Appendix 26) a second evaluation process for comparing the amino acid sequence of the candidate antigen peptide or the amino acid sequence of the protein from which the candidate antigen peptide is derived with the amino acid sequence of the corresponding protein in a subject to which the candidate antigen peptide is administered, to evaluate the similarity between the two amino acid sequences; a generation process for generating another candidate peptide in which one or more amino acids of the candidate antigen peptide are mutated when the similarity of the amino acid sequence does not satisfy the predetermined similarity condition; and a re-evaluation process for re-evaluating the antigenicity of the other candidate peptide based on the contribution of each amino acid to the antigenicity of the other candidate peptide. (Appendix 27) The program described in Appendix 26, further comprising a fourth selection process for selecting the other candidate peptide as a candidate antigen peptide if the contribution of the other candidate peptide to antigenicity satisfies the pre-specified contribution condition. (Appendix 28) 28. The program according to any one of Appendices 21 to 27, wherein the analysis process analyzes epitope residues on the antigen that interact with the antibody by analyzing at least hydrogen bonds between the antibody and the antigen. (Appendix 29) 29. The program according to any one of Appendices 21 to 28, wherein the contribution of each amino acid to antigenicity is the occurrence frequency of each amino acid in the epitope residues. (Appendix 30) 30. The program according to any one of Appendices 21 to 29, wherein the antigenicity is the ability to induce antibodies when immunized in a living organism. [Industrial Applicability]

[0110] As described above, according to the present disclosure, the antigenicity of a target peptide can be evaluated. Therefore, the present disclosure is extremely useful, for example, in the field of drug discovery.

Claims

1. a first evaluation unit that evaluates the antigenicity of a candidate peptide based on the contribution of each amino acid to the antigenicity of the candidate peptide; The degree of contribution to antigenicity is calculated based on amino acid residues of epitope residues on the antigen that interact with the antibody from data on the three-dimensional structure of an antigen-antibody complex.

2. an analysis unit that analyzes epitope residues on the antigen that interact with the antibody based on data on the three-dimensional structure of the antigen-antibody complex; The information processing device according to claim 1 , further comprising: a calculation unit that calculates a contribution of each amino acid to antigenicity based on each amino acid residue constituting the epitope residue.

3. The information processing device according to claim 2 , further comprising a first selection unit that selects the candidate peptide as a candidate antigen peptide when the contribution degree of the candidate peptide to antigenicity satisfies the prespecified condition of the contribution degree.

4. A determination unit that determines the location of the candidate antigen peptide in the protein from which the candidate antigen peptide is derived; The information processing device according to claim 3 , further comprising a second selection unit that selects the candidate antigen peptide when the position of the candidate antigen peptide in the protein satisfies a prespecified position condition.

5. a second evaluation unit that compares the amino acid sequence of the candidate antigen peptide or the amino acid sequence of the protein from which the candidate antigen peptide is derived with the amino acid sequence of the corresponding protein in a subject to which the candidate antigen peptide is administered, to evaluate the similarity between the two amino acid sequences; The information processing device according to claim 3 , further comprising a third selection unit that selects the candidate antigen peptide when the similarity of the amino acid sequences satisfies a prespecified similarity condition.

6. a second evaluation unit that compares the amino acid sequence of the candidate antigen peptide or the amino acid sequence of the protein from which the candidate antigen peptide is derived with the amino acid sequence of the corresponding protein in a subject to which the candidate antigen peptide is administered, to evaluate the similarity between the two amino acid sequences; a generating unit that generates another candidate peptide in which one or more amino acids of the candidate antigen peptide are mutated when the similarity of the amino acid sequence does not satisfy the predetermined similarity condition; The information processing device according to claim 5 , further comprising a reevaluation unit that reevaluates the antigenicity of the other candidate peptide based on the contribution of each of the amino acids to the antigenicity of the other candidate peptide.

7. The information processing device according to claim 6 , further comprising a fourth selection unit that selects the other candidate peptide as a candidate antigenic peptide when the contribution of the other candidate peptide to antigenicity satisfies the prespecified condition for contribution.

8. The information processing device according to claim 2 , wherein the analysis unit analyzes epitope residues on the antigen that interact with the antibody by analyzing at least hydrogen bonds between the antibody and the antigen.

9. The information processing device according to claim 1 , wherein the contribution of each amino acid to antigenicity is a frequency of occurrence of each amino acid in the epitope residues.

10. The information processing device according to claim 1 , wherein the antigenicity is an antibody-inducing ability when immunized in a living body.

11. A first evaluation step of evaluating the contribution of antigenicity of a candidate peptide based on the contribution of each amino acid to antigenicity, The information processing method, wherein the contribution to antigenicity is calculated based on amino acid residues of epitope residues on the antigen that interact with the antibody from data on the three-dimensional structure of an antigen-antibody complex.

12. On the computer, executing a first evaluation process for evaluating the contribution of the candidate peptide to antigenicity based on the contribution of each amino acid to antigenicity; The contribution to antigenicity is calculated based on amino acid residues of epitope residues on the antigen that interact with the antibody from data on the three-dimensional structure of an antigen-antibody complex.

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