JP6940752B2 - Probe molecule placement method and placement device, target molecule binding site search method, search device, and program - Google Patents

Description

In this case, a method of arranging a probe molecule around a target molecule in a coordinate space, an arranging device, a method of searching for a binding site of a target molecule using the arranging method, and a search device, and the arranging method or the search method are described. Regarding the program to be executed.

When a target molecule such as a protein has a functional site that adversely affects the body, it is necessary to design a ligand that stably binds to the functional site of the target molecule in drug discovery targeting the target molecule. .. When the ligand stably binds to the target molecule, the functional site of the target molecule is blocked. As a result, the adverse effects of the target molecule on the body are suppressed.

In order to increase the binding efficiency between the target molecule and the ligand or the probe molecule which is a fragment of the ligand when searching for the site where the ligand binds to the target molecule (hereinafter, may be referred to as “binding site”). Techniques for performing molecular dynamics (MD) calculations involving a target molecule and a large amount of ligand or probe molecule have been reported (see, for example, Patent Document 1). However, a large amount of ligand or probe molecule may be separated from the target molecule due to aggregation, and the desired bond may not be obtained.

Therefore, as a method for preventing aggregation between ligands or probe molecules, a technique for adding a repulsive potential between ligands or between probe molecules has been reported (see, for example, Non-Patent Document 1). However, when there is a wide pocket in the target molecule to which multiple ligands or probe molecules can be bound, the repulsion between the ligands or the probe molecules may prevent the desired plurality of ligand binding or probe binding from being obtained. be.

Japanese Unexamined Patent Publication No. 2006-209764

J. Chem. Inf. Model. , (2011) 51, 877

In order to solve the above problem, it is considered effective to arrange the probe molecules in an appropriate amount when performing MD calculation without adding a repulsive potential between the probe molecules.

In this case, a method and an arrangement device for probe molecules that enable appropriate arrangement of probe molecules when performing a molecular dynamics calculation including a target molecule and a large amount of probe molecules, and the above-mentioned arrangement method are used. It is an object of the present invention to provide a method for searching a binding site of a target molecule capable of appropriately searching for a binding site of a target molecule, a search device, and a program for executing the placement method or the search method.

The means for solving the above-mentioned problems are as follows. That is,
The disclosed probe molecule placement method is a method of placing a probe molecule around a target molecule using a computer.
A step of temporarily arranging a plurality of the probe molecules around the target molecule in the coordinate space, and
A step of performing molecular dynamics calculation under vacuum conditions using the target molecule and a plurality of temporarily arranged probe molecules, and
In the arrangement of the target molecule and the plurality of probe molecules obtained by the molecular dynamics calculation, at least one probe molecule separated from the surface of the target molecule by a predetermined distance or more is removed from the coordinate space. ,
including.

The disclosed method for searching for a binding site of a target molecule is a method for searching for a binding site for a target molecule using a computer.
It comprises a step of performing a molecular dynamics calculation in the presence of a water molecule using the arrangement of the target molecule and the plurality of probe molecules in the coordinate space determined by the method of arranging the probe molecule of the disclosure.

The disclosed probe molecule placement device
In the coordinate space, a temporary placement part that temporarily places a plurality of probe molecules around the target molecule,
A calculation unit that performs molecular dynamics calculations under vacuum conditions using the target molecule and a plurality of tentatively arranged probe molecules.
In the arrangement of the target molecule and the plurality of probe molecules obtained by the molecular dynamics calculation, at least one probe molecule separated from the surface of the target molecule by a predetermined distance or more is removed from the coordinate space. When,
To be equipped.

The disclosed device for searching the binding site of the target molecule is
The disclosed probe molecule placement device and
A calculation unit that performs molecular dynamics calculations in the presence of water molecules using the arrangement of the target molecule and the plurality of probe molecules in the coordinate space determined by the probe molecule arrangement device.
To be equipped.

The disclosed program is a program for arranging probe molecules.
On the computer
In the coordinate space, the process of temporarily arranging a plurality of probe molecules around the target molecule, and
A step of performing molecular dynamics calculation under vacuum conditions using the target molecule and a plurality of temporarily arranged probe molecules, and
In the arrangement of the target molecule and the plurality of probe molecules obtained by the molecular dynamics calculation, at least one probe molecule separated from the surface of the target molecule by a predetermined distance or more is removed from the coordinate space. ,
To execute.

The disclosed program is a program that searches for the binding site of the target molecule.
On the computer
A step of performing a molecular dynamics calculation in the presence of a water molecule using the arrangement of the target molecule and a plurality of the probe molecules in the coordinate space determined by the disclosed probe molecule arrangement method.
To execute.

According to the disclosed probe molecule placement method, the above-mentioned problems in the past can be solved, the above-mentioned object can be achieved, and the probe molecule in performing a molecular dynamics calculation including a target molecule and a large amount of probe molecules can be used. A method of placing probe molecules that allows proper placement can be provided.
According to the disclosed probe molecule placement device, the above-mentioned problems in the past can be solved, the above-mentioned object can be achieved, and the probe molecule in performing a molecular dynamics calculation including a target molecule and a large amount of probe molecules can be used. A device for placing probe molecules that enables proper placement can be provided.
According to the disclosure program for arranging probe molecules, the above-mentioned problems in the past can be solved, the above-mentioned objectives can be achieved, and the probe molecules for performing molecular dynamics calculations including a target molecule and a large amount of probe molecules. Can provide a program that enables proper placement of.
According to the disclosed method for searching for a binding site of a target molecule, a method for searching for a binding site for a target molecule that can solve the above-mentioned problems in the past, achieve the above-mentioned object, and appropriately search for a binding site for a target molecule. Can be provided.
According to the disclosed device for searching for binding sites of target molecules, a device for searching for binding sites of target molecules that can solve the above-mentioned problems in the past, achieve the above-mentioned objectives, and appropriately search for binding sites of target molecules. Can be provided.
According to the disclosure program for searching the binding site of the target molecule, it is possible to provide a program capable of solving the above-mentioned problems in the past, achieving the above-mentioned object, and appropriately searching for the binding site of the target molecule.

FIG. 1 is a flowchart for explaining an example of a method of arranging the disclosed probe molecules. FIG. 2 is a flowchart for explaining an example of a removal step in the disclosed probe molecule placement method. FIG. 3 is a flowchart for explaining an example of a method for searching for a binding site of the disclosed target molecule. FIG. 4 is a configuration example of the disclosed probe molecule placement device. FIG. 5 is another configuration example of the disclosed probe molecule placement device. FIG. 6 is another configuration example of the disclosed probe molecule placement device.

Drug discovery refers to the process of designing a drug. The drug discovery is performed in the following order, for example.
(1) Determination of target molecule (2) Search for lead compounds, etc. (3) Test of physiological action (4) Safety / toxicity test In search of lead compounds, etc. (lead compounds and compounds derived from them), a large number of drugs It is important to accurately evaluate the interaction between each of the candidate molecules and the target molecule.

The process of designing a drug using a computer is sometimes called IT drug discovery. IT drug discovery technology is available in drug discovery in general. Among them, the use of IT drug discovery technology for the search for lead compounds and the like is useful for increasing the period and probability of new drug development.

The disclosed technology can be used, for example, to search for lead compounds that are expected to have high pharmacological activity.

(Placement method of probe molecule)
The disclosed probe molecule placement method is a probe molecule placement method in which a probe molecule is placed around a target molecule using a computer.
The method for arranging the probe molecule includes a temporary arrangement step, an MD calculation step, and a removal step, and further includes other steps if necessary.

The method of arranging the probe molecules is performed using a computer. The number of the computers used in the method of arranging the probe molecules may be one or a plurality. For example, a plurality of computers may be allowed to disperse and execute the method of arranging the probe molecules.

In order to solve the problems of the prior art such as aggregation of probe molecules and failure to obtain a plurality of target ligand bonds, the probe molecules are used without adding a repulsive potential between the probe molecules and when performing MD calculation. The present inventor considered that it is effective to arrange it in an appropriate amount.

Therefore, as a result of diligent studies, the present inventor has made a probe that is separated from the surface of the target molecule by a predetermined distance or more when setting the initial arrangement of the probe molecule when performing the molecular dynamics calculation between the target molecule and the probe molecule. We have found that the elimination of molecules allows for the proper placement of probe molecules, leading to the completion of the disclosed technology.

Aggregation between probe molecules can be suppressed by eliminating excess probe molecules when setting the initial arrangement of the probe molecules when performing molecular dynamics calculations between the target molecule and the probe molecule. However, when the probe molecule is randomly excluded, the probe molecule that greatly contributes to the search for the binding site of the target molecule is also excluded, and as a result, the validity of the search for the binding site of the target molecule is reduced. Therefore, by excluding probe molecules that are separated from the surface of the target molecule by a predetermined distance or more, probe molecules that contribute less to the search for the binding site of the target molecule are excluded as excess probe molecules. Eliminating such probe molecules does not reduce the validity of the search for the binding site of the target molecule, and can suppress the aggregation of the probe molecules. Therefore, an appropriate arrangement can be obtained.

<Temporary placement process>
The temporary placement step is not particularly limited as long as it is a step of temporarily placing a plurality of probe molecules around the target molecule in the coordinate space, and can be appropriately selected depending on the intended purpose.
The method for temporarily arranging the target molecule and the probe molecule in the coordinate space is not particularly limited and may be appropriately selected depending on the intended purpose. For example, the three-dimensional structure data of the target molecule and the three-dimensional structure of the probe molecule. Using the data, the three-dimensional structure of the target molecule and the three-dimensional structure of the probe molecule can be constructed in the three-dimensional coordinate space.
The three-dimensional structure data includes, for example, atomic information data, coordinate information data, and coupling information data.
The format of these data is not particularly limited and may be appropriately selected depending on the intended purpose. For example, it may be text data, SDF (Structure Data File) format, or MOL file. It may be in the form.

The method for constructing the three-dimensional structure of the target molecule and the three-dimensional structure of the probe molecule in the three-dimensional coordinate space is not particularly limited and may be appropriately selected depending on the intended purpose. Examples thereof include the following methods.
First, the three-dimensional structure of the target molecule is constructed in the three-dimensional coordinate space using the three-dimensional structure data of the target molecule. Subsequently, the three-dimensional structure of the probe molecule is constructed in the same three-dimensional coordinate space by using the three-dimensional structure data of the probe molecule. Here, in order to reproduce the real space, usually, the three-dimensional structure of the probe molecule does not overlap with the three-dimensional structure of the target molecule in the three-dimensional coordinate space.
The three-dimensional structure of the probe molecule may be constructed one molecule at a time, or a plurality of molecules may be collectively constructed.

The target molecule is not particularly limited and may be appropriately selected depending on the intended purpose. Examples thereof include proteins, RNA (ribonucleic acid, ribonic acid), DNA (deoxyribonucleic acid, deoxyribonucleic acid) and the like.

The probe molecule is a small molecule used when searching for a binding site and can be a fragment of a drug candidate molecule.
The search for the binding site using the probe molecule is performed, for example, as follows.
Molecular dynamics calculations are performed using the target molecule and multiple probe molecules. Then, by superimposing the snapshots in the molecular dynamics calculation, the location where the existence probability of the probe molecule is high is obtained in the vicinity of the target molecule. Although the existence probability of the probe molecule is high, it is presumed to be the binding site of the target molecule.

The number of the probe molecules temporarily arranged in the temporary arrangement step is not particularly limited, and for example, the size and type of the target molecule and the probe around the target molecule when temporarily arranged It is appropriately selected in consideration of the concentration of molecules and the like.

<MD calculation process>
The MD calculation step is not particularly limited as long as it is a step of performing molecular dynamics calculation under vacuum conditions using the target molecule and a plurality of temporarily arranged probe molecules, depending on the purpose. It can be selected as appropriate.
In the MD calculation step, the interaction of the probe molecules with each other is considered in the normal MD calculation. Such interactions include, for example, hydrogen bonds, van der Waals interactions, hydrophobic interactions and the like.
On the other hand, in the MD calculation step, it is preferable not to add an unnatural repulsive force to the probe molecules. By doing so, when searching for the binding site of the target molecule, it is possible to prevent the case where the probe molecule constitutes a multimer in the binding site is excluded.
The unnatural repulsive force means a repulsive force other than the interaction normally occurring between probe molecules in reality.

By performing the molecular dynamics calculation under vacuum conditions, the probe molecule can be appropriately aggregated on the surface of the target molecule.

When performing the molecular dynamics calculation, it is preferable that the heavy atom of the target molecule is constrained. Here, the heavy atom refers to an atom other than a hydrogen atom.
By constraining the heavy atom, it is possible to prevent the target molecule from moving or deforming more than necessary.
The method of restraint is not particularly limited and may be appropriately selected depending on the intended purpose. Examples thereof include restraint by a spring.

The molecular dynamics calculation can be performed using a molecular dynamics calculation program. Examples of the molecular dynamics calculation program include AMBER, CHARMMm, GROMACS, GROMOS, NAMD, and myPreso.

The time for the molecular dynamics calculation is not particularly limited and may be appropriately selected depending on the intended purpose. For example, about 200 ps can be mentioned.

<Removal process>
The removal step is a step of removing at least one probe molecule separated from the surface of the target molecule by a predetermined distance or more from the coordinate space in the arrangement of the target molecule and the plurality of probe molecules. There is no particular limitation, and it can be appropriately selected according to the purpose.
The arrangement of the target molecule and the plurality of probe molecules is an arrangement obtained by the molecular dynamics calculation.

The predetermined distance is not particularly limited and may be appropriately selected depending on the size and type of the target molecule, the size and type of the probe molecule, and the like, but the water molecule on the surface of the target molecule. It is preferable that the larger one when comparing the thickness (W) of three layers and the length (P) set based on the polarizability of the probe molecule is the predetermined distance.
The thickness (W) of the three layers of water molecules means the thickness of the three water molecules when the three water molecules are arranged in a direction orthogonal to the plane containing the two HO bonds in the water molecules. It is about 6-8 Å.
Generally, it is said that up to three layers of water molecules on the surface of a target molecule affect the target molecule. Examples of the effect include an electrostatic shielding effect.
On the other hand, the polarization rate affects the aggregation of the probe molecules.
Here, if the predetermined distance is larger than the thickness (W) of three layers of water molecules, the number of probe molecules that remain without being eliminated tends to increase. On the other hand, if the thickness (W) of three layers of water molecules is set to the predetermined distance without considering the polarizability of the probe molecules, many probe molecules may be excluded.
Therefore, the predetermined distance is not particularly limited and may be appropriately selected depending on the size and type of the target molecule, the size and type of the probe molecule, and the like, but on the surface of the target molecule. It is preferable that the larger one when comparing the thickness (W) of three layers of water molecules and the length (P) set based on the polarizability of the probe molecules is the predetermined distance.
The P is a length set based on the length in the third spindle direction obtained by calculating the polarizability tensor of the probe molecule, in that aggregation of the probe molecule can be further considered. preferable. Examples of such a length include a length that is an integral multiple (for example, 2 to 5 times) of the length in the third spindle direction obtained by calculating the polarizability tensor of the probe molecule. ..
The polarizability tensor can be calculated by classical mechanics calculation, quantum chemistry calculation, or the like.

The method of arranging the probe molecules is, for example, a normal computer system (for example, various network servers, workstations, personal computers, etc.) equipped with a CPU (Central Processing Unit), a RAM (Random Access Memory), a hard disk, various peripheral devices, and the like. ) Can be used.

Subsequently, an example of the method of arranging the disclosed probe molecules will be described with reference to the flowchart.
FIG. 1 is a flowchart for explaining an example of a method for arranging the probe molecules.
[Temporary placement process]
First, the temporary placement step is performed. In this step, a plurality of probe molecules are temporarily placed around the target molecule in the coordinate space. For example, first, a target molecule is placed in the coordinate space. Subsequently, a plurality of probe molecules are repeatedly arranged around the target molecule. By doing so, a large number of probe molecules are tentatively placed around the target molecule.
The probe molecules are arranged randomly, for example. At that time, if it overlaps with the space occupied by the target molecule, the arrangement is not performed, and another random arrangement is performed. By repeating this, a large amount of probe molecules are tentatively placed around the target molecule.
The end point of the temporary arrangement is not particularly limited and may be appropriately selected depending on the intended purpose. For example, the end point may be when a predetermined number of probe molecules are arranged, or a predetermined number of random arrangements may be made. May be the end point when
The number of repetitions is not particularly limited and can be appropriately selected depending on the purpose.

[MD calculation process]
Next, the MD calculation step is performed. In this step, the molecular dynamics calculation is performed under vacuum conditions using the target molecule and the plurality of tentatively arranged probe molecules. The molecular dynamics calculation is performed using, for example, a known molecular dynamics calculation program such as GROMACS. In this example, when the molecular dynamics calculation is performed, an unnatural repulsive force is not applied to the probe molecules.
By performing the MD step, a state in which the probe molecule is appropriately aggregated around the target molecule can be obtained.

[Removal process]
Next, the removal step is performed. In this step, at least one probe molecule separated from the surface of the target molecule by a predetermined distance or more in the arrangement of the target molecule and the plurality of probe molecules obtained by the molecular dynamics calculation is placed in the coordinate space. Exclude from.
By performing the removal step, as excess probe molecules, probe molecules having a small contribution to the search for the binding site of the target molecule are excluded. As a result, for example, an arrangement suitable for searching for a binding site of a target molecule can be obtained.

Subsequently, an example of the removal step will be described with reference to the flowchart.
FIG. 2 is a flowchart for explaining an example of the removal step.
In the removal step of this example, the larger one when comparing the thickness (W) of three layers of water molecules on the surface of the target molecule and the length (P) set based on the polarizability of the probe molecule. Is set to the predetermined distance, and the removal step is performed.
After the MD calculation step, the thickness (W) of three layers of water molecules on the surface of the target molecule calculated in advance is compared with the length (P) set based on the polarizability of the probe molecule. Then, the larger one is set as the predetermined distance, and the probe molecule separated from the surface of the target molecule by the predetermined distance or more is excluded from the coordinate space.
The P is, for example, twice the length in the third spindle direction obtained by calculating the polarizability tensor of the probe molecule.
The length in the third spindle direction can be obtained by, for example, the following method.
First, the polarizability of the probe molecule is calculated. Subsequently, the three eigenvector directions of the polarizability tensor are normal, and the three sides of the rectangular parallelepiped covering the probe molecule are obtained. Then, the length of half of the side of the rectangular parallelepiped in the direction of the eigenvector having the smallest eigenvalue is defined as the length in the third main axis direction. The reason why the length is halved is that it is considered as the distance in contact with the probe molecule.

(Method of searching for binding site of target molecule)
The disclosed method for searching for a binding site of a target molecule is a method for searching for a binding site for a target molecule using a computer.
The method for searching for a binding site of a target molecule includes at least an MD calculation step, and further includes other steps such as a presence probability search step, if necessary.

<MD calculation process>
In the MD calculation step, molecular dynamics calculation is performed in the presence of water molecules using the arrangement of the target molecule and the plurality of probe molecules in the coordinate space determined by the disclosure method of the probe molecule. The process is not particularly limited and can be appropriately selected according to the purpose.

The molecular dynamics calculation can be performed using a molecular dynamics calculation program. Examples of the molecular dynamics calculation program include AMBER, CHARMMm, GROMACS, GROMOS, NAMD, and myPreso.

<Existence probability search process>
As the step of searching for the existence probability, if it is a step of finding a place where the existence probability of the probe molecule is high in the vicinity of the target molecule in the coordinate space from the result of the molecular dynamics calculation in the presence of the water molecule. There is no particular limitation, and it can be appropriately selected according to the purpose. For example, there is a method of finding a place where the existence probability of the probe molecule is high in the vicinity of the target molecule by superimposing snapshots in the molecular dynamics calculation. Can be mentioned. For example, as a result, the existence probability of the probe molecule is high, but it is presumed to be the binding site of the target molecule.

Subsequently, an example of the method for searching the binding site of the disclosed target molecule will be described with reference to the flowchart.
FIG. 3 is a flowchart for explaining an example of a method for searching for a binding site of the target molecule.
First, before performing the MD calculation, the arrangement of the target molecule and the plurality of probe molecules in the coordinate space is determined by the disclosed probe molecule arrangement method.
Then, using the arrangement of the target molecule and the plurality of probe molecules in the coordinate space determined by the arrangement method of the probe molecule, molecular dynamics calculation is performed in the presence of water molecules.

(program)
The disclosed program for arranging probe molecules is a program for causing a computer to execute the method for arranging the probe molecules in the disclosure.
The disclosure program for searching for the binding site of the target molecule is a program for causing a computer to execute the method for searching for the binding site for the target molecule in the disclosure.
In the program for arranging the probe molecules, the preferred embodiment of the method for arranging the probe molecules is the same as the preferred embodiment for the method for arranging the probe molecules disclosed.
In the program for searching for the binding site of the target molecule, a preferred embodiment in the execution of the method for searching for the binding site for the target molecule is the same as the preferred embodiment for the method for searching for the binding site for the target molecule disclosed.

The program can be created by using various known programming languages according to the configuration of the computer system to be used, the type and version of the operating system, and the like.

The program may be recorded on a recording medium such as an internal hard disk or an external hard disk, or may be recorded on a recording medium such as a CD-ROM (Compact Disc Read Only Memory), a DVD-ROM (Digital Versailles Disk Read Only Memory), or an MO disk (MO disk). It may be recorded on a recording medium such as a Magnet-Optical disc) or a USB memory [USB (Universal Serial Bus) flash drive]. When recording the program on a recording medium such as a CD-ROM, DVD-ROM, MO disk, or USB memory, the program may be recorded directly or on a hard disk through a recording medium reader of a computer system as needed. It can be installed and used. In addition, the program is recorded in an external storage area (another computer, etc.) accessible from the computer system through the information communication network, and the program is recorded directly from the external storage area through the information communication network or as needed. It can also be installed and used on a hard disk.
The program may be divided and recorded on a plurality of recording media for each arbitrary process.

(Computer readable recording medium)
The computer-readable recording medium of the disclosure comprises recording the program of the disclosure.
The recording medium that can be read by the computer is not particularly limited and may be appropriately selected depending on the intended purpose. For example, an internal hard disk, an external hard disk, a CD-ROM, a DVD-ROM, a MO disk, a USB memory, or the like. Can be mentioned.
The recording medium may be a plurality of recording media in which the program is divided and recorded for each arbitrary process.

(Probe molecule placement device)
The disclosed probe molecule placement device includes at least a temporary placement unit, a calculation unit, a removal unit, and, if necessary, other units.
The temporary placement unit temporarily places a plurality of probe molecules around the target molecule in the coordinate space.
The calculation unit performs molecular dynamics calculation under vacuum conditions using the target molecule and a plurality of the probe molecules that are tentatively arranged.
The removal unit obtains the coordinates of at least one probe molecule at a distance of a predetermined distance or more from the surface of the target molecule in the arrangement of the target molecule and the plurality of probe molecules, which is obtained by the molecular dynamics calculation. Exclude from space.

The preferred embodiment of the treatment method of each part in the probe molecule placement device is the same as the preferred mode of each step in the probe molecule placement method.
The probe molecule arranging device may be a plurality of probe molecule arranging devices each including a plurality of recording media in which the program is divided and recorded for each arbitrary process.

(Search device for binding sites of target molecules)
The disclosed device for searching the binding site of the target molecule includes at least a device for arranging the probe molecule disclosed, a second calculation unit, and, if necessary, another unit such as an existence probability search unit.
The second calculation unit uses the arrangement of the target molecule and the plurality of probe molecules in the coordinate space determined by the probe molecule arrangement device to perform molecular dynamics calculation in the presence of water molecules. conduct.
From the result of the molecular dynamics calculation in the presence of the water molecule, the existence probability search unit finds a place where the existence probability of the probe molecule is high in the vicinity of the target molecule in the coordinate space.

The preferred embodiment of the treatment method of each part in the device for searching the binding site of the target molecule is the same as the preferred embodiment of each step in the method for searching the binding site of the target molecule.
The device for searching the binding site of the target molecule may be a device for searching the binding site of a plurality of target molecules, each of which includes a plurality of recording media in which the program is divided and recorded for each arbitrary process.

FIG. 4 shows a configuration example of the disclosed probe molecule placement device. The same applies to the configuration example of the disclosed device for searching the binding site of the target molecule.
The probe molecule placement device 10 is configured by connecting, for example, a CPU 11, a memory 12, a storage unit 13, a display unit 14, an input unit 15, an output unit 16, an I / O interface unit 17, and the like via a system bus 18. NS.

The CPU (Central Processing Unit) 11 performs operations (four arithmetic operations, comparison operations, etc.), hardware and software operation control, and the like.

The memory 12 is a memory such as a RAM (Random Access Memory) and a ROM (Read Only Memory). The RAM stores an OS (Operating System), an application program, and the like read from the ROM and the storage unit 13, and functions as a main memory and a work area of the CPU 11.

The storage unit 13 is a device that stores various programs and data, and is, for example, a hard disk. The storage unit 13 stores a program executed by the CPU 11, data necessary for program execution, an OS, and the like.
The program is stored in the storage unit 13, loaded into the RAM (main memory) of the memory 12, and executed by the CPU 11.

The display unit 14 is a display device, for example, a display device such as a CRT monitor or a liquid crystal panel.
The input unit 15 is an input device for various data, such as a keyboard and a pointing device (for example, a mouse).
The output unit 16 is an output device for various data, for example, a printer.
The I / O interface unit 17 is an interface for connecting various external devices. For example, it enables input / output of data such as a CD-ROM, a DVD-ROM, an MO disk, and a USB memory.

FIG. 5 shows another configuration example of the disclosed probe molecule placement device.
The configuration example of FIG. 5 is a cloud-type configuration example, in which the CPU 11 is independent of the storage unit 13 and the like. In this configuration example, the computer 30 that stores the storage unit 13 and the like and the computer 40 that stores the CPU 11 are connected via the network interface units 19 and 20.
The network interface units 19 and 20 are hardware that communicates using the Internet.

FIG. 6 shows another configuration example of the disclosed probe molecule placement device.
The configuration example of FIG. 6 is a cloud-type configuration example, and the storage unit 13 is independent of the CPU 11 and the like. In this configuration example, the computer 30 that stores the CPU 11 and the like and the computer 40 that stores the storage unit 13 are connected via the network interface units 19 and 20.

Hereinafter, the disclosed technology will be described, but the disclosed technology is not limited to the following examples.

(Example 1)
The disclosed probe molecule placement method was carried out according to the flow shown in FIGS. 1 and 2. Specifically, it was carried out as follows.
A protein, blood coagulation factor Xa, was used as the target molecule.
Chlorobenzothiophen-2-ol was used as the probe molecule.
Here, the thickness (W) of three layers of water molecules was set to 6 Å. The third major axial length (a) obtained by calculating the polarizability tensor of chlorobenzothiophen-2-ol is 2 Å. Then, the W and the doubled a [2a] were compared, and the larger one, 6 Å, was set as a predetermined distance.

In the coordinate space, 829 (4 mol / L) probe molecules were randomly placed around the target molecule.
Subsequently, molecular dynamics calculations were performed under vacuum conditions using GROMACS. The simulation time was 200 ps.
Subsequently, in the arrangement of the calculation results, probe molecules separated from the surface of the target molecule by 6 Å or more were removed.
As a result, 275 probe molecules remained around the target molecule.

Using the obtained arrangement, molecular dynamics calculations were performed in the presence of water. The simulation time was 10 ns. Then, the average of the interaction energy between the target molecule and the probe molecule and the average of the interaction energy between the probe molecule and the probe molecule were calculated by the molecular dynamics calculation.
The results were as follows.
-Average interaction energy between target molecule and probe molecule: Approximately -46 kJ / mol
-Average of interaction energy between probe molecule and probe molecule: Approximately -15 kJ / mol
That is, the interaction between the target molecule and the probe molecule was more stable than the interaction between the probe molecule and the probe molecule.

(Comparative Example 1)
A protein, blood coagulation factor Xa, was used as the target molecule.
Chlorobenzothiophen-2-ol was used as the probe molecule.
In the coordinate space, 829 (4 mol / L) probe molecules were randomly placed around the target molecule in the same manner as in Example 1.
Using the obtained arrangement, molecular dynamics calculations in the presence of water were performed in the same manner as in Example 1. Then, the average of the interaction energy between the target molecule and the probe molecule and the average of the interaction energy between the probe molecule and the probe molecule were calculated by the molecular dynamics calculation.
The results were as follows.
-Average interaction energy between target molecule and probe molecule: Approximately -15 kJ / mol
-Average of interaction energy between probe molecule and probe molecule: Approximately -32 kJ / mol
That is, the interaction between the probe molecule and the probe molecule was more stable than the interaction between the target molecule and the probe molecule.

In Comparative Example 1 in which MD calculation was performed after placing the probe molecule around the target molecule by the conventional method, the interaction between the probe molecule and the probe molecule is more stable than the interaction between the target molecule and the probe molecule. Met. On the other hand, when the MD calculation is performed after arranging the probe molecule around the target molecule using the arrangement method disclosed, the interaction between the target molecule and the probe molecule is better than the interaction between the probe molecule and the probe molecule. It was more stable than the action. This indicates that the adsorption of the probe molecule to the target molecule is promoted when the disclosed arrangement method is used. Furthermore, this indicates that the arrangement method of the disclosure enables efficient binding site search.

Regarding the above embodiments, the following additional notes will be further disclosed.
(Appendix 1)
A method of arranging probe molecules around a target molecule using a computer.
A step of temporarily arranging a plurality of the probe molecules around the target molecule in the coordinate space, and
A step of performing molecular dynamics calculation under vacuum conditions using the target molecule and a plurality of temporarily arranged probe molecules, and
In the arrangement of the target molecule and the plurality of probe molecules obtained by the molecular dynamics calculation, at least one probe molecule separated from the surface of the target molecule by a predetermined distance or more is removed from the coordinate space. ,
A method for arranging probe molecules, which comprises.
(Appendix 2)
A note that the larger one when comparing the thickness (W) of three layers of water molecules on the surface of the target molecule and the length (P) set based on the polarizability of the probe molecule is the predetermined distance. The method for arranging probe molecules according to 1.
(Appendix 3)
The method for arranging a probe molecule according to any one of Supplementary note 1 to 2, wherein the heavy atom of the target molecule is constrained when the molecular dynamics calculation is performed.
(Appendix 4)
The method for arranging probe molecules according to any one of Supplementary note 1 to 3, wherein an unnatural repulsive force is not added to the probe molecules when the molecular dynamics calculation is performed.
(Appendix 5)
A method of searching for a binding site of a target molecule using a computer.
Molecular dynamics calculation in the presence of water molecules using the arrangement of the target molecule and the plurality of probe molecules in the coordinate space determined by the method of arranging the probe molecule according to any one of Appendix 1 to 4. A method for searching for a binding site of a target molecule, which comprises a step of performing the above.
(Appendix 6)
Further, the target molecule according to Appendix 5, further comprising a step of finding a location having a high probability of existence of the probe molecule in the vicinity of the target molecule in the coordinate space from the result of the molecular dynamics calculation in the presence of the water molecule. How to search for combined sites.
(Appendix 7)
In the coordinate space, a temporary placement part that temporarily places a plurality of probe molecules around the target molecule,
A calculation unit that performs molecular dynamics calculations under vacuum conditions using the target molecule and a plurality of tentatively arranged probe molecules.
In the arrangement of the target molecule and the plurality of probe molecules obtained by the molecular dynamics calculation, at least one probe molecule separated from the surface of the target molecule by a predetermined distance or more is removed from the coordinate space. When,
A device for arranging probe molecules, which comprises.
(Appendix 8)
The probe molecule placement device described in Appendix 7 and
A calculation unit that performs molecular dynamics calculations in the presence of water molecules using the arrangement of the target molecule and the plurality of probe molecules in the coordinate space determined by the probe molecule arrangement device.
A device for searching a binding site of a target molecule, which comprises.
(Appendix 9)
A program for placing probe molecules
On the computer
In the coordinate space, the process of temporarily arranging a plurality of probe molecules around the target molecule, and
A step of performing molecular dynamics calculation under vacuum conditions using the target molecule and a plurality of temporarily arranged probe molecules, and
In the arrangement of the target molecule and the plurality of probe molecules obtained by the molecular dynamics calculation, at least one probe molecule separated from the surface of the target molecule by a predetermined distance or more is removed from the coordinate space. ,
A program characterized by executing.
(Appendix 10)
A program that searches for binding sites of target molecules.
On the computer
Molecular dynamics calculation in the presence of water molecules using the arrangement of the target molecule and the plurality of probe molecules in the coordinate space determined by the method of arranging the probe molecule according to any one of Appendix 1 to 4. Process,
A program characterized by executing.

10 Probe molecule placement device 11 CPU
12 Memory 13 Storage unit 14 Display unit 15 Input unit 16 Output unit 17 I / O interface unit 18 System bus 19 Network interface unit 20 Network interface unit 30 Computer 40 Computer

Claims (9)

A method of arranging probe molecules around a target molecule using a computer.
A step of temporarily arranging a plurality of the probe molecules around the target molecule in the coordinate space, and
A step of performing molecular dynamics calculation under vacuum conditions using the target molecule and a plurality of temporarily arranged probe molecules, and
The obtained by the molecular dynamics calculation, in the placement of the target molecule and a plurality of the probe molecule, at least one of said probe molecules apart a predetermined distance or more from the surface of the target molecule, in the step of excluding from the coordinate space Therefore, the predetermined distance is 2 of the thickness (W) of three layers of water molecules on the surface of the target molecule and the length in the third principal axis direction obtained by calculating the polarizability tensor of the probe molecule. The larger step when comparing the length (P) of an integral multiple of any of 2 to 5 times, and
A method for arranging probe molecules, which comprises. The method for arranging a probe molecule according to claim 1, wherein the heavy atom of the target molecule is constrained when performing the molecular dynamics calculation. The method for arranging probe molecules according to any one of claims 1 to 2, wherein a repulsive force other than the interaction normally occurring between probe molecules is not added to the probe molecules when the molecular dynamics calculation is performed. .. A method of searching for a binding site of a target molecule using a computer.
Molecular dynamics in the presence of water molecules using the arrangement of the target molecule and the plurality of probe molecules in the coordinate space determined by the method for arranging the probe molecule according to any one of claims 1 to 3. A method for searching for a binding site of a target molecule, which comprises a step of performing a calculation. Further, from the result of the molecular dynamics calculation in the presence of the water molecule, a step of estimating a portion having a high probability of existence of the probe molecule within the predetermined distance in the coordinate space as a binding site of the target molecule is performed. The method for searching for a binding site of a target molecule according to claim 4, which comprises. In the coordinate space, a temporary placement part that temporarily places a plurality of probe molecules around the target molecule,
A calculation unit that performs molecular dynamics calculations under vacuum conditions using the target molecule and a plurality of tentatively arranged probe molecules.
In the arrangement of the target molecule and the plurality of probe molecules obtained by the molecular dynamics calculation, at least one probe molecule separated from the surface of the target molecule by a predetermined distance or more is removed from the coordinate space. The predetermined distance is the thickness (W) of three layers of water molecules on the surface of the target molecule and the length in the third principal axis direction obtained by calculating the polarizability tensor of the probe molecule. The removal part, which is the larger one when comparing the length (P) of an integral multiple of 2 to 5 times, and
A device for arranging probe molecules, which comprises. The device for arranging the probe molecule according to claim 6 and
A calculation unit that performs molecular dynamics calculations in the presence of water molecules using the arrangement of the target molecule and the plurality of probe molecules in the coordinate space determined by the probe molecule arrangement device.
A device for searching a binding site of a target molecule, which comprises. A program for placing probe molecules
On the computer
In the coordinate space, the process of temporarily arranging a plurality of probe molecules around the target molecule, and
A step of performing molecular dynamics calculation under vacuum conditions using the target molecule and a plurality of temporarily arranged probe molecules, and
In the step of removing at least one probe molecule separated from the surface of the target molecule by a predetermined distance or more from the coordinate space in the arrangement of the target molecule and the plurality of probe molecules obtained by the molecular dynamics calculation. Therefore, the predetermined distance is 2 of the thickness (W) of three layers of water molecules on the surface of the target molecule and the length in the third principal axis direction obtained by calculating the polarizability tensor of the probe molecule. The larger step when comparing the length (P) of an integral multiple of any of 2 to 5 times, and
A program characterized by executing. A program that searches for binding sites of target molecules.
On the computer
Molecular dynamics in the presence of water molecules using the arrangement of the target molecule and the plurality of probe molecules in the coordinate space determined by the method for arranging the probe molecule according to any one of claims 1 to 3. The process of making calculations,
A program characterized by executing.

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